Document [original]

Unravelling the impacts of palaeoecology,

palaeoenvironment and lithofacies on sedimentary

organic NSO compounds

vorgelegt von

M. Sc. Geologin

Huiwen Yue

ORCID: 0000-0002-0624-2647

von der Fakultät VI - Planen Bauen Umwelt

der Technischen Universität Berlin

zur Erlangung des akademischen Grades

Doktorin der Naturwissenschaften

- Dr. rer. nat. -

genehmigte Dissertation

Promotionsausschuss:

Vorsitzender: Prof. Dr. Thomas Neumann

Gutachter: Prof. Dr. Brian Horsfield

Gutachter: Prof. Dr. Christian Hallmann

Tag der wissenschaftlichen Aussprache: 6. Juli 2023

Berlin 2023

Dedication

This document is dedicated to my family!

ACKNOWLEDGEMENTS

This dissertation was carried out in the framework of Huiwen Yue's PhD at the Technical

University of Berlin, which was sponsored by China Scholarship Council (CSC) and

Technische Universität Berlin Center for Junior Scholars (CJS).

First of all, I would like to express my gratitude towards Prof. Dr. Brian Horsfield for giving

me the opportunity to join his research group. I would also like to thank him for his support and

guidance with matter of a scientific, financial and logistical nature.

Dr. Andrea Vieth-Hillebrand is highly acknowledged for supervising me at the first four years

of the project, for supporting me to achieve my own ideas, and for her efficient corrections on

my manuscripts.

My sincere gratitude is extended to my supervisor Dr. Stefanie Pötz in the last two years. She

gave me constructive suggestions and unreserved support. Without her dedication, it would not

have been possible to present the work.

Special thanks go to Priv. Doz. Dr. Hans-Martin Schulz, Dr. Shengyu Yang, Dr. Yuanjia Han,

Dr. Mareike Noah, Dr. Nicolaj Mahlstedt, Dr. Kai Mangelsdorf and Prof. Dr. Christian

Hallmann for their inspiring discussion, professional advice and collaboration on publications.

Further thanks are directed to Cornelia Karger, Anke Kaminsky, Ferdinand Perssen, Kristin

Günther, Mirco Rahn, Andrea Gottsche and Dr. Anja Schleicher. My research cannot carry out

without their reliable technical supports. Besides, I would like to thank Claudia Engelhardt for

helping handle numerous obstacles.

All my friends are sincerely appreciated for sharing joy and sorrow, even though we might be

thousands of miles away.

My endless thanks go to my mother Aihua Jiang, father Meishu Yue and brother Changhao Yue

for their love and encouragement.

Words cannot express my love to my husband Dr. Wendong Liang. Only he can make the end

of the world sound like a good thing (quotes from Ice Age: Collision Course).

III

LIST OF PUBLICATIONS

Articles in peer-reviewed journals

(1) Huiwen Yue, Andrea Vieth-Hillebrand, Yuanjia Han, Brian Horsfield, Anja Maria

Schleicher, Stefanie Poetz, 2021. Unravelling the impact of lithofacies on the

composition of NSO compounds in residual and expelled fluids of the Barnett, Niobrara

and Posidonia formations. Organic Geochemistry, 155, 104225, (postprint),

https://doi.org/10.1016/j.orggeochem.2021.104225.

(2) Huiwen Yue, Andrea Vieth-Hillebrand, Shengyu Yang, Hans-Martin Schulz, Brian

Horsfield, Stefanie Poetz, 2022. The retention of precursor biotic signatures in the

organonitrogen and organooxygen compounds of immature fine-grained sedimentary

rocks. International Journal of Coal Geology, 259, 104039, (postprint),

https://doi.org/10.1016/j.coal.2022.104039.

(3) Huiwen Yue, Brian Horsfield, Hans-Martin Schulz, Shengyu Yang, Andrea Vieth-

Hillebrand, Stefanie Poetz, 2023. Preservation of biotic and palaeoenvironmental

signatures in organosulfur compounds of immature fine-grained sedimentary rocks.

International Journal of Coal Geology, 265, 104168, (postprint),

https://doi.org/10.1016/j.coal.2022.104168.

This cumulative thesis includes three manuscripts. Chapters 2, 3, 4 were already

published as the articles (2), (3), (1).

Presentations at international symposia

(1) Huiwen Yue, Stefanie Poetz, Yuanjia Han, Brian Horsfield, and Andrea Vieth-

Hillebrand. Unravelling the role of lithofacies in controlling organic matter composition

in unconventional systems using FT-ICR-MS. In 29th International Meeting on Organic

Geochemistry (IMOG), Gothenburg, Sweden, September 1–6, 2019 (Poster).

(2) Huiwen Yue, Yuanjia Han, Mareike Noah, Brian Horsfield, and Andrea Vieth-

Hillebrand. Unravelling the role of lithofacies in controlling organic matter composition

in unconventional systems using FT-ICR-MS. In 28th International Meeting on Organic

Geochemistry (IMOG), Florence, Italy, September 17–22, 2017 (Poster).

ABSTRACT

The organic matter in sedimentary rocks that is soluble in common organic solvents

comprises a complex mixture of hydrocarbons and NSO compounds (nitrogen, sulfur and

oxygen bearing). The N, S, O atoms can be derived from both biogenic sources and abiogenic

processes, thus organic NSO compounds are intrinsically well suited to record precursor biotic

and palaeoenvironmental signatures. In addition, their physical properties are such that they

possess the capacity to interact specifically with minerals of distinct surface chemistry, so they

can provide precise indications for elucidating lithofacies-influenced fractionation during

petroleum expulsion and migration. Until relatively recently, their molecular-level

characterization was limited to the low-molecular-weight fraction, but now this range has been

extended, thanks to ultra-high resolution mass spectrometry. This thesis utilises that technique

to provide information on biomass input, depositional conditions and lithofacies-influenced

fractionation using heavy NSO compounds, thus complementing and supplementing

information contained in lower molecular weight biomarkers.

The impact of biological sources (marine algae, terrestrial plants and lacustrine

Botryococcus braunii) on organooxygen and organonitrogen compounds was revealed through

the investigations on the solvent extracts of immature–early mature rock samples from the

marine Dynow, Schöneck, Posidonia formations, the lacustrine Wealden Formation, and the

terrestrial Waikato and Brunner coal measures. Coals, being the in-situ deposits of terrestrial

plant remains, primarily consist of aromatic polyoxygenated Ox and N1Ox compounds,

representing degradation products of lignin and tannin such as phenolic ketones and phenolic

carboxylic acids as well as their condensation products with the proteinaceous degradation

intermediates. Aliphatic Ox moieties derived from the plant protective substances (mainly

waxes and cutan) show a pronounced even or odd carbon number predominance among the

C23–C33 range with C26, 28, 30 or C27, 29, 31 as the major homologs. In contrast, marine and lake

microbial communities contribute abundant middle-chain C22, C24 or C23, C25 Ox compounds.

The marine rock extracts are furthermore characterized by abundant organonitrogen

compounds, especially the N2 and N2Ox classes, interpreted as signatures of protein-rich marine

algae. The highly aliphatic algaenan of Botryococcus braunii sterically protects its oxygen-

bearing groups leading to a great abundance of Ox compounds, furthermore, it characterizes the

Botryococcus braunii source by substantial heteroatomic compounds containing more than 40

carbon atoms.

Organosulfur compounds, as inorganic-organic incorporation products during early

diagenesis, were characterized in extracts of the aforementioned lacustrine and marine samples

to obtain both palaeoecological and palaeoenvironmental information. The iron-deficient

sulfidic depositional settings of the Posidonia and Schöneck formations are reflected by

abundant organosulfur compounds bearing up to three sulfur atoms. The high ratios of reduced

relative to oxidized forms (Sz versus SzOx) further illustrate the restricted presence of oxidants

at the oxic-anoxic interfaces. The observed prominent enrichment of organosulfur compounds

containing 40, 35, 30, 25 carbon atoms are associated with the selective preservation of

polyfunctionalized biomolecules via sulfurization, such as C40 carotenoids, C35

bacteriohopanepolyols, C30 unsaturated tetracyclic polyprenoid alcohols, C30 or C25 highly

branched isoprenoid (HBI) polyenes. The strong enrichment of sulfurized C35

bacteriohopanepolyols can be developed as an indicator of the low levels of oxygen exposure

prior to sulfurization, which occur only in the Dynow and Schöneck formations. The prominent

enrichment of sulfurized carotenoids is typically associated with high primary productivity.

While the strongly enriched sulfurized HBI polyenes are indicative for diatom blooms, the

precursors of C30 pentacyclic polyprenoid organosulfur compounds are more abundant in

fresh/brackish water algae.

For petroleum systems having undergone expulsion and migration, the composition of

NSO compounds retained in rocks is determined not only by their origin but also by their

interactions with different mineral surfaces. The controls of lithofacies on NSO inventories

were investigated using examples of unconventional systems with the three globally most

significant lithofacies, namely the biogenic carbonate-rich Niobrara Shale, the biogenic quartz-

rich Barnett Shale and the detrital clay-rich Posidonia Shale. Extracts of the siliciclastic Barnett

and Posidonia samples reveal high fractions of NSO compounds confirming their generally

higher retention capacities for the polar compounds. While biogenic quartz preferentially

preserves and retains organonitrogen compounds, the more polar acidic organooxygen

compounds are preferably retained by clay minerals. Within the Niobrara and the Barnett

systems, lithofacies variations respectively in carbonate and biogenic quartz content lead to

intra-formation migration. The low-polarity organonitrogen compounds are preferentially

retained in both Niobrara (to a less extent) and Barnett source rock units. While the highly

alkylated small acidic NSO molecules preferably migrate out of the Niobrara carbonate source

rock units, acidic NSO compounds irrespective of molecule size and alkylation degree are all

strongly retained in the biogenic quartz-rich Barnett source showing no fractionation.

VII

KURZFASSUNG

Organisches Material in Sedimentgestein, das in organischen Lösungsmitteln löslich ist,

ist ein komplexes Gemisch, das eine Vielzahl organischer Stickstoff-, Schwefel- und

Sauerstoffhaltiger (NSO) Verbindungen enthält. Stickstoff-, Schwefel- und Sauerstoffatome

können sowohl aus biogenen als auch aus abiogenen Quellen stammen, so dass organische

Stickstoff-, Schwefel- und Sauerstoffhaltige Verbindungen exzellent dafür geeignet sind,

paläoökologische und Signaturen sowie die Art des abgelagerten organischen Materials zu

erfassen. Darüber hinaus führen ihre physikalischen Eigenschaften zu einer erhöhten Fähigkeit,

mit Mineralen unterschiedlicher Oberflächenchemie in Wechselwirkung zu treten, so dass sie

spezifische Hinweise zur Aufklärung der lithofazies-beeinflussten Fraktionierung während der

Erdölexpulsion und -migration liefern können. Ihre Charakterisierung auf molekularer Ebene

war jedoch lange analytisch auf die niedermolekulare Fraktion beschränkt, bevor sie hier mit

Hilfe der ultrahochauflösenden Massenspektrometrie ein Quantensprung erzielt wurde. Diese

Arbeit untersucht mittels hochauflösender Massenspektrometrie den Biomasseeintrag, die

Ablagerungsbedingungen und die lithofaziesbeeinflusste Fraktionierung, die durch die

höhermolekularen Stickstoff-, Schwefel- und Sauerstoffhaltigen Verbindungen dokumentiert

wurden, anhand von ausgewählten repräsentativen Erdölsystemen.

Der Einfluss biologischer Quellen (Meeresalgen, Landpflanzen und lakustrische Algen

wie Botryococcus braunii) auf sdie Zusammensetzung auerstoff- und stickstofforganischer

Verbindungen wurde anhand von Lösungsmittelextrakten aus unreifen bis früh reifen

Gesteinsproben aus den marinen Dynow-, Schöneck- und Posidonia-Formationen, der

lakustrischen Wealden-Formation und den terrestrischen Waikato- und Brunner-Kohleflözen

untersucht. Kohlen als In-situ-Ablagerungen von Landpflanzen bestehen in erster Linie aus

aromatischen polyoxygenierten Ox- und N1Ox-Verbindungen, die Abbauprodukte von Lignin

und Tannin wie phenolische Ketone und phenolische Carbonsäuren sowie deren

Kondensationsprodukte mit den proteinhaltigen Abbauprodukten sind. Aliphatische Ox Anteile

aus Pflanzenmembranen und –strukturstoffen (hauptsächlich Wachse und Cutan) weisen eine

ausgeprägte Dominanz gerader oder ungerader Kohlenstoffzahlen im Bereich C23–C33 auf,

wobei C26, 28, 30 oder C27, 29, 31 die wichtigsten Homologe sind. Im Gegensatz dazu tragen die

mikrobiellen Gemeinschaften aus Meer und Seen reichlich mittelkettige C22, C24 oder C23, C25

Ox-Verbindungen bei. Die marinen Gesteinsextrakte zeichnen sich darüber hinaus durch einen

höheren Anteil an organischen Stickstoffverbindungen aus, insbesondere die N2- und N2Ox-

VIII

Klassen, die als Signaturen proteinreicher mariner Algen interpretiert werden. Das

hochaliphatische Algaenan von Botryococcus braunii schützt sterisch seine sauerstoffhaltigen

Funktionsgruppen, was zu einer großen Fülle von Ox-Verbindungen führt. Darüber hinaus

zeichnet sich organisches Material von Botryococcus braunii durch umfangreiche

heteroatomare Verbindungen mit mehr als 40 Kohlenstoffatomen aus.

Schwefelorganische Verbindungen als anorganische-organische Inkorporationsprodukte

während der frühen Diagenese wurden in Extrakten der oben genannten marinen und

lakustrischen Proben charakterisiert, um Hinweise auf sowohl Ablagerungsbedingungen als

auch das organische Ursprungsmaterial zu erhalten. Die eisenarmen sulfidischen

Ablagerungsbedingungen der Posidonia- und Schöneck-Formationen führen zu reichlich

vorhandenen schwefelorganischen Verbindungen mit bis zu drei Schwefelatomen. Das hohe

Verhältnis von reduzierten zu oxidierten Formen (Sz versus SzOx) verdeutlicht die begrenzte

Präsenz von Oxidationsmitteln an den oxisch-anoxischen Grenzflächen. Die beobachtete starke

Anreicherung von schwefelorganischen Verbindungen mit 40, 35, 30 und 25

Kohlenstoffatomen steht im Zusammenhang mit der selektiven Erhaltung

polyfunktionalisierter Biomoleküle durch Sulfurisierung, wie z. B. C40-Carotinoide, C35-

Bakteriohopanepolyole, C30-ungesättigte tetrazyklische polyprenoide Alkohole oder C30- oder

C25-stark verzweigte Isoprenoide Alkene. Die starke Anreicherung von geschwefelten C35-

Bakteriohopanepolyolen kann als Indikator für die geringe Sauerstoffbelastung vor der

Schwefelung angesehen werden, die nur in den Dynow- und Schöneck-Formationen auftritt.

Die starke Anreicherung von geschwefelten Carotinoiden ist typischerweise mit einer hohen

Primärproduktivität verbunden. Während die starke Anreicherung von sulfurisierten stark

verzweigten isoprenoiden Alkenen auf Kieselalgenblüten hinweisen, stammen die Vorläufer

der C30-pentacyclischen polyprenoiden schwefelorganischen Verbindungen aus Süß- und

Brackwasseralgen.

Bei Erdölsystemen, in denen das Erdöl bereits aus dem Muttergestein gewandert ist, wird

die Zusammensetzung der in den Gesteinen zurückgehaltenen NSO Verbindungen nicht nur

durch ihren Ursprung, sondern auch durch ihre Wechselwirkungen mit den verschiedenen

Mineraloberflächen bestimmt. Die Auswirkungen der Lithofazies auf das Inventar an NSO

Verbindungen wurden anhand von drei Beispielen unkonventioneller Erdölsysteme mit den

weltweit bedeutendsten Lithofazies, nämlich dem biogenen karbonatreichen Niobrara-Schiefer,

dem biogenen quarzreichen Barnett-Schiefer und dem detritischen tonreichen Posidonia-

Schiefer. Die Extrakte der siliklastischen Barnett- und Posidonia-Proben weisen hohe Anteile

an NSO Verbindungen auf, was ihr generell höheres Adsorbtionsvermögen für die polaren

Verbindungen bestätigt. Während biogener Quarz bevorzugt organische

Stickstoffverbindungen zurückhält, werden die polareren sauren organischen

Sauerstoffverbindungen vorzugsweise von Tonmineralen zurückgehalten. Innerhalb des

Niobrara- und des Barnett-Systems führen lithofaziale Unterschiede im Karbonat- bzw.

biogenen Quarzgehalt zu einer Migration innerhalb der Formation. Die niederpolaren

organischen Stickstoffverbindungen werden vorzugsweise sowohl in den Niobrara- als auch

in den Barnett-Quellgesteinseinheiten zurückgehalten. Während die stark alkylierten kleinen

sauren NSO Moleküle vorzugsweise aus den Niobrara-Quellgesteinseinheiten abwandern,

werden saure NSO Verbindungen unabhängig von der Molekülgröße und dem

Alkylierungsgrad alle stark in der Barnett-Quelle zurückgehalten und zeigen keine

Fraktionierung.

CONTENTS

ACKNOWLEDGEMENTS ................................................................................................................... I

LIST OF PUBLICATIONS ................................................................................................................ III

ABSTRACT .......................................................................................................................................... V

KURZFASSUNG ............................................................................................................................... VII

CONTENTS ......................................................................................................................................... XI

LIST OF FIGURES............................................................................................................................ XV

LIST OF TABLES ........................................................................................................................ XXIII

LIST OF ABBREVIATIONS ......................................................................................................... XXV

1 INTRODUCTION ........................................................................................................................ 1

1.1 Origin of NSO compounds in sedimentary systems ............................................................ 1

1.1.1 Organic origin—Preservation potential of biomolecules ................................................. 3

1.1.2 Inorganic origin—Abiotic incorporation of inorganic small NSO compounds into organic

matter ........................................................................................................................................ 7

1.2 Palaeoecological and palaeoenvironmental signatures documented by sedimentary NSO

compounds ................................................................................................................................... 10

1.2.1 NSO bearing moieties in kerogen .................................................................................. 10

1.2.2 Low-molecular-weight NSO biomarkers in rock bitumen ............................................. 14

1.3 Controls of lithofacies on fractionation of NSO compounds during petroleum expulsion

and migration .............................................................................................................................. 21

1.3.1 Fractionation mechanisms .............................................................................................. 21

1.3.2 Fractionation of NSO compounds .................................................................................. 22

1.3.3 Controls of lithofacies on fractionation ......................................................................... 23

1.4 Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS) .............. 25

1.4.1 Fundamentals of FT-ICR-MS ........................................................................................ 25

1.4.2 Fundamentals of electrospray ionization ....................................................................... 26

1.4.3 Fundamentals of atmospheric pressure photoionization ................................................ 28

1.5 Applications of FT-ICR-MS in petroleum systems ........................................................... 30

1.5.1 Precursor biotic and palaeoenvironmental signatures .................................................... 32

1.5.2 Expulsion- and migration-related fractionation ............................................................. 33

1.5.3 Fractionation on distinct mineral surfaces ..................................................................... 33

1.6 Research objectives and outline .......................................................................................... 34

XII

2 PRECURSOR BIOTIC SIGNATURES IN ORGANONITROGEN AND

ORGANOOXYGEN COMPOUNDS OF IMMATURE ROCKS ................................................... 41

2.1 Abstract ................................................................................................................................. 41

2.2 Introduction .......................................................................................................................... 42

2.3 Sample Description ............................................................................................................... 45

2.3.1 Marine Schöneck and Dynow formations in the Molasse Basin ................................... 45

2.3.2 Marine Posidonia Formation in the Lower Saxony Basin ............................................. 46

2.3.3 Lacustrine Wealden Formation in the Lower Saxony Basin .......................................... 47

2.3.4 Terrestrial Waikato and Brunner coal measures in the Waikato and West Coast basins 48

2.4 Analytical Methods ............................................................................................................... 49

2.4.1 Open system pyrolysis-gas chromatography (Py-GC) ................................................... 49

2.4.2 Organic solvent extraction ............................................................................................. 49

2.4.3 Gas chromatography-mass spectrometry (GC-MS) and gas chromatography-flame

ionization detector (GC-FID) .................................................................................................. 50

2.4.4 (+)-APPI FT-ICR-MS analysis ...................................................................................... 50

2.4.5 (–)-ESI FT-ICR-MS analysis ......................................................................................... 50

2.4.6 (+)-ESI FT-ICR-MS analysis ......................................................................................... 51

2.4.7 Mass calibration and data analysis of FT-ICR-MS results ............................................ 51

2.5 Results .................................................................................................................................... 52

2.5.1 Rock Eval pyrolysis and open system Py-GC ................................................................ 52

2.5.2 Biomarker characterization by GC-MS and GC-FID .................................................... 53

2.5.3 Organooxygen and organonitrogen compounds detected with FT-ICR-MS ................. 55

2.6 Discussion .............................................................................................................................. 65

2.6.1 Terrestrial plant input ..................................................................................................... 65

2.6.2 Lacustrine algal input ..................................................................................................... 70

2.6.3 Marine algal input .......................................................................................................... 74

2.7 Summary and Conclusions .................................................................................................. 76

2.8 Acknowledgments ................................................................................................................. 77

2.9 Supplementary material ....................................................................................................... 78

3 BIOTIC AND PALAEOENVIRONMENTAL SIGNATURES IN ORGANOSULFUR

COMPOUNDS OF IMMATURE ROCKS ....................................................................................... 89

3.1 Abstract ................................................................................................................................. 89

3.2 Introduction .......................................................................................................................... 90

3.3 Sample Description ............................................................................................................... 93

3.3.1 Marine Lower Toarcian Posidonia Shale in the Lower Saxony Basin .......................... 93

3.3.2 Marine Eocene–Oligocene Schöneck and Dynow formations in the Molasse Basin .... 95

XIII

3.3.3 Lacustrine Berriasian Wealden Formation in the Lower Saxony Basin ........................ 95

3.4 Analytical Methods ............................................................................................................... 96

3.4.1 Open system pyrolysis-gas chromatography (Py-GC) ................................................... 96

3.4.2 Organic solvent extraction ............................................................................................. 97

3.4.3 Gas chromatography-mass spectrometry (GC-MS) ....................................................... 97

3.4.4 FT-ICR-MS .................................................................................................................... 97

3.5 Results .................................................................................................................................... 97

3.5.1 Low-molecular-weight organosulfur compounds in rock pyrolyzates and extracts ...... 97

3.5.2 High-molecular-weight organosulfur compounds in rock extracts ................................ 98

3.5.3 Hydrocarbons with polyfunctionalized biomolecule precursors prone to sulfurization

.............................................................................................................................................. 107

3.6 Discussions ........................................................................................................................... 108

3.6.1 Indicators of iron-deficient sulfidic depositional condition ......................................... 108

3.6.2 Marine versus lacustrine biomass input ....................................................................... 110

3.6.3 Preservation through sulfurization: Biogenetic polyfunctionalized molecules ............ 110

3.7 Summary and Conclusions ................................................................................................ 117

3.8 Acknowledgments ............................................................................................................... 119

3.9 Supplementary material ..................................................................................................... 120

4 IMPACT OF LITHOFACIES ON COMPOSITION OF HETEROATOMIC COMPOUNDS

IN RESIDUAL AND EXPELLED FLUIDS OF MATURE ROCKS ........................................... 131

4.1 Abstract ............................................................................................................................... 131

4.2 Introduction ........................................................................................................................ 132

4.3 Sample description ............................................................................................................. 135

4.3.1 Geological background and sample selection .............................................................. 135

4.3.2 Mineralogical composition .......................................................................................... 137

4.3.3 Bulk organic geochemical data .................................................................................... 137

4.4 Analytical methods ............................................................................................................. 139

4.4.1 Organic solvent extraction ........................................................................................... 139

4.4.2 FT-ICR-MS .................................................................................................................. 139

4.5 Results .................................................................................................................................. 139

4.5.1 Aromatic hydrocarbons and low-polarity NSO compounds detected by (+)-APPI FT-

ICR-MS ................................................................................................................................. 139

4.5.2 High-polarity acidic NSO compounds detected by (-)-ESI FT-ICR-MS ..................... 145

4.6 Discussion ............................................................................................................................ 148

4.6.1 Influence of lithofacies on generation and expulsion of NSO compounds .................. 148

4.6.2 Influence of lithofacies on petroleum migration within unconventional systems ........ 152

4.7 Summary and Conclusions ................................................................................................ 154

XIV

4.8 Acknowledgements ............................................................................................................. 155

4.9 Supplementary material ..................................................................................................... 156

5 SUMMARY AND PERSPECTIVES ...................................................................................... 165

5.1 Summary ............................................................................................................................. 165

5.1.1 Precursor biotic information recorded by organooxygen and organonitrogen compounds

.............................................................................................................................................. 166

5.1.2 Palaeoecological and palaeoenvironmental signatures in organosulfur compounds ... 169

5.1.3 Controls of lithofacies on fractionation of NSO compounds during petroleum expulsion

and migration ........................................................................................................................ 170

5.2 Perspectives ......................................................................................................................... 171

REFERENCES .................................................................................................................................. 175

LIST OF FIGURES

Figure 1.1. Atomic N/C and O/C ratios of some living organisms and biomolecules (Baxby et al., 1994;

Vandenbroucke and Largeau, 2007)........................................................................................................ 4

Figure 1.2. Some important NSO compounds in rock bitumen. .......................................................... 21

Figure 1.3. Schematic diagram of an ICR cell with induced ion motions, modified after

https://commons.wikimedia.org/wiki/File:FTICR_cell.png.................................................................. 26

Figure 1.4. (A and B) Simplified structures of ESI and APPI sources, modified from the Bruker Daltonik

User Manual; (C) droplet production in ESI operated under positive mode (Gaskell, 1997); (D)

ionization mechanism of APPI operated under positive mode, modified after https://uwaterloo.ca/mass-

spectrometry-facility/appi-supplementary-information; (E) major theories describing the creation of the

fully desolvated gas-phase ions in positive ESI mode. ......................................................................... 29

Figure 2.1. Regional maps displaying the study areas for the (A) Wealden Formation (well EX-A), (B)

Posidonia Shale (boreholes Wenzen and Wickensen), (C) Schöneck and Dynow formations (borehole

Oberschauersberg 1) and (D) Waikato and Brunner coal measures (Reefton and Rotowaro coalfields),

modified after Blumenberg et al. (2019), Klaver et al. (2012), Jochum et al. (1995), Yang and Schulz

(2019) and Vu (2008). The black lines mark the borders between different countries in (A) and (C). 46

Figure 2.2. Ternary diagrams for molecular kerogen structure typing developed by (A) Larter (1984)

and (B) Horsfield (1989) based on open system Py-GC results. (C) Diagram of hydrogen index versus

Tmax for the classification of kerogen types (Espitalié et al., 1984b) based on Rock Eval pyrolysis

results summarized from Vu (2008), Rippen et al. (2013), Ziegs et al. (2018) and Yang and Schulz

(2019). (D) CPI (carbon preference index), Ster/Hop (regular steranes/homohopanes), and 4-MSI (4-

methylsteranes/C29 regular steranes) ratios based on GC-MS measurements for OM input assessment.

............................................................................................................................................................... 53

Figure 2.3. Absolute abundances of the peaks assigned as Ox, Ny and NyOx compounds in negative ESI

(A), positive ESI (B) and positive APPI (C) modes. Summed numbers of these peaks are marked out by

yellow dots. ........................................................................................................................................... 56

Figure 2.4. Ternary plots showing the relative proportions of Ny, NyOx and Ox classes (in terms of

abundances) detected with (A) negative ESI, (B) positive ESI and (C) positive APPI. ....................... 57

Figure 2.5. (A, B) Compound class distributions of the positive APPI ionizable Ox, Ny and NyOx

compounds. (C) Diagram plotting average oxygen number against average nitrogen number of the

positive APPI accessible NyOx compounds, displaying proportions of multi-nitrogen and multi-oxygen

bearing compounds. TMIA: total abundances of the assigned monoisotopic peaks. ............................ 58

XVI

Figure 2.6. (A) DBE distributions of the negative ESI detectable Ox classes (x=2–4), which are

normalized by the most abundant DBE species (DBEmax_abund) in each specific compound class. (B)

Average DBE values of the negative ESI ionizable ≥ 5 DBE Ox compounds are plotted over oxygen

numbers for all the studied extracts. ...................................................................................................... 59

Figure 2.7. Carbon number distributions of the negative ESI accessible O3, 1 DBE O2, 1 DBE O3, the

positive ESI ionizable N1, and the positive APPI detectable 3 DBE O1, 1 DBE O2 species, which are

normalized by the most abundant species in specific compound class or DBE class in certain sample.

The dot size represents the relative abundance of variable compounds within a certain DBE class in a

specific sample. ..................................................................................................................................... 61

Figure 2.8. (A) Crossplot of the NyOx/(Ox + NyOx) ratio and the Ster/Hop. (B) Crossplot of the

NyOx/(NyOx + Ny) ratio and the pyrolysis derived oct-1-ene amount (% n-C8:1). (C) Crossplot of the

DBE1-4/DBEAll O1 ratio versus average DBE of the ≥ 5 DBE O1 species detected in positive APPI mode.

(D) The % n-C8:1 index plots against the slope extracted from the linear correlation between average

DBE values of the positive APPI accessible ≥ 5 DBE Ox species and their respective oxygen numbers

(see Figure 2.6B, S2.8). (E) The pyrolysis derived C6+ n-alkenes and n-alkanes amount (% n-C6+) plots

against average carbon number of the positive ESI accessible N1 class. .............................................. 68

Figure S2.1. Comparison of the ionization ranges of positive APPI, negative ESI and positive ESI

modes, after Gross (2017) and Huba et al. (2016). “V” stands for successful ionization, while “-” marks

nonionizable species. ............................................................................................................................. 78

Figure S2.2. (A–D) Parameters developed based on GC-MS and GC-FID results providing organic

matter input (TAR and Pr/Ph) and thermal maturity (C29 βα/αβ hopanes and C29 ααα 20S/(20R + 20S)

steranes) information. TAR: terrigenous/aquatic ratios. Pr/Ph: pristane/phytane. (E) Ternary diagram of

C27–C29 regular sterane isomers (ααα (20S + 20R) and αββ (20S + 20R)) for typing organic matter input,

modified after Rippen et al. (2013) and Grantham and Wakefield (1988). ........................................... 79

Figure S2.3. Hopane traces. Peaks in blue, green and red colour mark out αβ, ββ and βα hopanes,

respectively. The red dot and the red diamond respectively mark out C29 30-norneohop-13(18)-ene and

C30 neohop-13(18)-ene. Ts: 18α-trisnorneohopane. Tm: 17α-trisnorhopane. ....................................... 80

Figure S2.4. Compound class distributions of Ox, Ny and NyOx elemental classes detected with distinct

modes. ................................................................................................................................................... 81

Figure S2.5. Average oxygen or nitrogen numbers for NyOx, Ox and Ny classes detected in distinct

modes. ................................................................................................................................................... 82

Figure S2.6. DBE distributions of the negative ESI accessible N1Ox (x=2–5), the positive ESI ionisable

Ox (x=2, 3), N1, N1O1 as well as the positive APPI detectable Ox (x=1–4), N1, N1Ox (x=1–3) classes,

which are normalized by the most abundant species (DBEmax_abund) in each specific compound class.

DBE distributions of those classes whose abundances lower than 1% TMIA are not displayed here. . 83

XVII

Figure S2.7. (A–I) Some representative parameters describing DBE and carbon number distributions of

Ox and N1 compounds under distinct modes, including DBE1-4/DBEAll ratio, average DBE value and

EOPI. (J–R) Slope extracted from the linear correlations between average DBE or carbon numbers of

N1Ox or ≥ 5 DBE Ox classes and the respective oxygen numbers (See Figure 6B, S8). ....................... 84

Figure S2.8. Average DBE or carbon number of N1Ox or ≥ 5 DBE Ox species detected in distinct modes

are plotted over the respective oxygen numbers. Average DBE or carbon numbers of those species

whose abundances lower than 1% TMIA are not displayed here. ......................................................... 85

Figure S2.9. (A–D) Crossplot of the NyOx/(NyOx + Ny) ratio and the pyrolysis derived oct-1-ene amount

(% n-C8:1) or the Pr/Ph ratio. (E, F) The % n-C8:1 index plots against average DBE value of the positive

APPI ionizable N1O1 class or the negative ESI accessible ≥ 5 DBE O3 species. (G, H) The % n-C8:1 ratio

plots against the slope extracted from the linear correlation between average DBE values of the positive

APPI or the negative ESI ionizable ≥ 5 DBE Ox species and the respective oxygen numbers (see Figure

6A, S8). ................................................................................................................................................. 86

Figure S2.10. (A–C) The pyrolysis derived C6+ n-alkenes and n-alkanes amount (% n-C6+) plots against

average carbon number of the positive APPI ionizable N1O1, the positive ESI accessible N1 or the

negative ESI detectable ≥ 5 DBE O3 species. (D, E) 4-MSI value plots against average carbon number

of the positive APPI ionizable N1O1 or the positive ESI accessible N1 compounds. (F) Crossplot of the

4-MSI value and the % n-C6+ ratio. (G–I) Crossplot of the NyOx/(Ox + NyOx) ratio and the Ster/Hop. 87

Figure 3.1. (A, B) Ternary diagrams for typing molecular kerogen structure especially its organic sulfur

content, developed by Eglinton et al. (1990) and di Primio and Horsfield (1996) based on open system

Py-GC results. (C, D) DBT/Phen and MDBT/MPhen ratios, neither DBT nor Phen homologues can be

assigned in spectrum of the Wealden extract W2 due to its poor data quality. (E, F, H, I) Concentrations

of C25 HBI alkane, C30 tetracyclic polyprenoid hydrocarbons, aryl isoprenoids and C19 2,3,5ˊ-6-

tetramethyl-2-alkylbiphenyl. (G) C35/C34 homohopanes ratio, neither C35 or C34 homohopanes can be

detected in the Wealden extracts W1 and W2. ...................................................................................... 98

Figure 3.2. Peak number and absolute abundance of organosulfur compounds detectable in distinct

modes. ................................................................................................................................................... 99

Figure 3.3. Elemental class distributions of the positive APPI or the positive ESI ionizable organosulfur

compounds. ......................................................................................................................................... 100

Figure 3.4. Compound class distributions of the positive APPI accessible organosulfur compounds.

............................................................................................................................................................. 101

Figure 3.5. (A, B) Average sulfur number of the positive APPI or the positive ESI accessible SzOx class.

(C, D) Average oxygen number of the positive APPI or the negative ESI ionizable S1Ox class. (E–G)

DBE1–4/DBEAll ratio of the positive APPI or the positive ESI accessible S1Ox class. (H, I) DBE0–3/DBEAll

ratio of the negative ESI ionizable S1O3 or S1O4 class. (J, K) DBE0–4/DBEAll ratio of the negative ESI

XVIII

ionizable S1O5 or S1O6 class. Values for elemental or compound classes in extracts with abundances <

1% TMIA are not included here. ......................................................................................................... 101

Figure 3.6. DBE distributions of the positive APPI accessible S1, S1O1, the positive ESI accessible S1O1,

and the negative ESI ionizable S1O3, S1O5 classes, which are normalized by the most abundant species

(DBEmax_abund) in specific compound class. DBE distributions of the compound classes whose

abundances lower than 1% TMIA in extracts are not displayed here. ................................................ 102

Figure 3.7. Carbon number distributions of the positive APPI accessible (A) S1O1 compound class, (B)

hydrocarbons, (C) 1, 3, 5, 6 DBE S1O1 compounds and (D) 3 DBE hydrocarbons, which are normalized

to the most abundant species (Cmax_abund) in specific compound class or DBE class. The dot size in (C)

and (D) represents the relative abundance of variable compounds within a certain DBE class in a specific

sample. ................................................................................................................................................. 104

Figure 3.8. Some possible organosulfur compounds. ......................................................................... 111

Figure S3.1. Partial mass spectra showing only monoisotopic assigned peaks in distinct ionization

modes. Peaks assigned as different elemental classes are respectively colored. Pie charts showing

elemental class distributions are also displayed here. “HC” refers to hydrocarbons, whereas “V + Ni”

refers to vanadyl and nickel porphyrins. ............................................................................................. 120

Figure S3.2. Peak number and relative abundance of organosulfur compounds detectable in distinct

modes. ................................................................................................................................................. 121

Figure S3.3. Compound class distributions of the positive or negative ESI accessible organosulfur

compounds. ......................................................................................................................................... 121

Figure S3.4. DBE versus carbon number distributions of the positive APPI ionizable S1, S1Ox (x=1, 2),

hydrocarbons and the positive ESI accessible S1O1 compound classes. ............................................. 122

Figure S3.5. DBE versus carbon number distributions of the positive APPI accessible S2, S2Ox (x=1–

4), S3, S3O2, S1Ox (x=3–5), N1S1 and the positive ESI ionizable N1S1 compound classes. ................. 123

Figure S3.6. Carbon number distributions of the positive APPI ionizable Sz (z=1–3), S1Ox (x=1–5),

S2Ox (x=1–4), S3O2, hydrocarbons as well as the positive ESI accessible S1O1 classes, which are

normalized to the most abundant species (Cmax_abund) in specific compound class. ............................. 124

Figure S3.7. Carbon number distributions of individual 1–9 DBE S1 or S1Ox (x=1, 2) classes accessible

by positive APPI or positive ESI, which are normalized to the most abundant species in specific DBE

class. The dot size represents the relative abundance of variable compounds within a certain DBE class

in a specific sample. ............................................................................................................................ 126

Figure S3.8. Carbon number distributions of the positive APPI ionizable individual 0–9 DBE S1O3 and

S2Ox (x=1, 2) classes as well as the negative ESI accessible 1, 6, 7 DBE S1Ox (x=3, 4) classes, which

XIX

are normalized to the most abundant species in specific DBE class. The dot size represents the relative

abundance of variable compounds within a certain DBE class in a specific sample. ......................... 127

Figure S3.9. Aryl isoprenoid traces and their concentrations in the studied extracts (m/z 133). ....... 128

Figure S3.10. C35/(C31–C35) homohopanes and pristane/phytane ratios. ............................................ 129

Figure 4.1. Comparison of the ionization ranges of positive APPI and negative ESI modes, after Huba

et al. (2016) and Gross (2017). ‘‘V” stands for successful ionization, while ‘‘–” marks nonionizable

species. ................................................................................................................................................ 134

Figure 4.2. (A) Location of the study areas and (B) geochemical depth profiles of samples, which are

partly published elsewhere (Han et al., 2019b, 2017, 2015; Klaver et al., 2012; Littke et al., 1991). Map

of the Barnett and Niobrara unconventional plays (as of May 2011) was published by the U.S. Energy

Information Administration. Mineralogical compositions of the Niobrara and Barnett samples were

detected by X-ray powder diffraction (XRD), while the Posidonia samples were analyzed by attenuated

total reflection Fourier transform infrared spectroscopy (ATR-FTIR). Comparability of results from

both methods has been shown by Müller et al. (2014). ....................................................................... 136

Figure 4.3. (A) Classification of kerogen types by hydrogen index versus Tmax (Espitalié et al., 1984b)

based on Rock Eval pyrolysis measurements. (B) Open system Py-GC results typing molecular kerogen

structures using the ternary diagram of Horsfield (1989). (C) Bulk compositions of the solvent extracts:

relative percentages of saturate, aromatic, resin, and asphaltene fractions by weight. (D) DBT/Phen and

MDBT/MPhen ratios. Data for the Barnett and Niobrara samples have been partly published elsewhere

(Han et al., 2019b, 2015). .................................................................................................................... 139

Figure 4.4. Radar plots showing elemental class distributions of the compounds in extracts from the

Niobrara (left), the Barnett (middle) and the Posidonia Shale (right) in positive APPI and negative ESI

modes. ................................................................................................................................................. 140

Figure 4.5. (A, C, E, G) Atomic N/C and O/C ratios of the positive APPI and negative ESI accessible

inventories. (B, D, F, H) Average nitrogen and oxygen numbers (NNO. and ONO.) of Ox, NyOx and Ny

classes in positive APPI and negative ESI modes. Abundance of the negative ESI ionizable Ox class in

the Niobrara extracts NB1, NB2, NB4 and the Barnett extracts BN1, BN3, BN4 is less than or

approximately equal to 1% TMIA, whose average oxygen numbers are not included here. .............. 141

Figure 4.6. (A) Atomic S/C ratio of the positive APPI and negative ESI ionizable compounds, (B, C)

Ternary diagrams displaying compound class distributions of OSCs characterized with positive APPI

(Sz, SzOx and SzNy classes) and negative ESI modes (SzOx, SzNyOx and SzNy classes). ..................... 142

Figure 4.7. (A) DBE distributions of the positive APPI ionizable O1, O2, N1O1 and S1O1 classes, which

are normalized to the most abundant DBE class (DBEmax_abund) in each compound class. (B) Average

DBE values of the positive APPI detected O1, O2, S1O1, N1O1, HC, N1 and S1 classes. (C) Average DBE

values of the negative ESI detected N1, N2, N1O1, N1O2, N2O1 and S1N1 classes. .............................. 143

Figure 4.8. (A, B) Carbon number distributions of 15 and 18 DBE N1 compounds in both positive APPI

and negative ESI modes, which are normalized to the most abundant species (Cmax_abund) in each DBE

class. (C) Average carbon numbers of 15 and 18 DBE N1, N1O1, HC, S1O1, S1 species as well as 13 and

16 DBE O1, O2 species in positive APPI mode. (D) Average carbon numbers of the negative ESI

accessible DBE15,18 N1 and N1O1, DBE15,17 N2 and N2O1, DBE17,20 S1N1 and DBE13,16 N1O2 species. 145

Figure S4.1. Compounds used by Huba et al. (2016) to test the ionization ranges of positive APPI and

negative ESI modes. ............................................................................................................................ 156

Figure S4.2. Handling of contamination peaks. The most “suspicious” peaks are those with very high

abundance but with few or no other assigned peaks in the same compound class, for example as the

peaks assigned as C14H27O4 and C22H43O4 in positive APPI spectra of the investigated Barnett extracts.

They are of very high abundance, but no other peaks can be assigned as O4 compounds. They have been

excluded from further assessment. They are possibly from drilling additives and they are striking only

in the Barnett extracts but not in the Niobrara and Posidonia extracts when detected by positive APPI.

Peaks marked by blue triangles can also be contaminations, which are common in positive APPI spectra

of all the Barnett extracts. However, they do not influence the subsequent evaluation since they cannot

be assigned as a formula (a maximum value per assignment of C100H202S4N2O5) within the allowed mass

error of 0.5 ppm. Here, in positive APPI spectrum of the representative Barnett extract BN4, the

monoisotopic assigned peaks used for further evaluation are marked out using green color. In negative

ESI mode, striking contamination peaks are only present in some Barnett and Niobrara extracts like

BN4, similar rules are followed. ......................................................................................................... 157

Figure S4.3. Partial mass spectra showing only monoisotopic assigned peaks in positive APPI and

negative ESI modes. Peaks assigned as different elemental classes are coloured, respectively. Peak

number and absolute abundance of the monoisotopic assigned peaks (Peak No. and TMIA) are also

recorded here. ...................................................................................................................................... 158

Figure S4.4. Compound class distributions of the positive APPI and negative ESI accessible inventories

in different extracts. Compound classes whose abundances lower than 1% TMIA for every sample are

not shown. ........................................................................................................................................... 159

Figure S4.5. DBE distributions of the positive APPI ionizable hydrocarbons, N1 and S1 classes as well

as the negative ESI accessible N1, N2, N1O1, N1O2, N2O1 and S1N1 classes, which are normalized to the

most abundant DBE class (DBEmax_abund) in each compound class. .................................................... 160

Figure S4.6. DBE versus carbon number distributions of the positive APPI ionizable hydrocarbons, N1,

N1O1, O1, O2, S1O1 and S1 classes in the representative Niobrara, Barnett and Posidonia extracts NB1,

BN1 and PS1. ...................................................................................................................................... 161

XXI

Figure S4.7. DBE versus carbon number distributions of the negative ESI ionizable N1, N2, N1O1, S1N1,

N1O2 and N2O1 classes in the representative Niobrara, Barnett and Posidonia extracts NB1, BN1 and

PS1. ..................................................................................................................................................... 162

Figure S4.8. Carbon number distributions of the positive APPI accessible 5, 8, 9, 15 DBE S1O1 and 6,

9, 10, 15 DBE N1O1 classes, which are normalized to the most abundant species (Cmax_abund) in each DBE

class. .................................................................................................................................................... 163

XXII

XXIII

LIST OF TABLES

Table 1.1. Comparison of the ionization ranges of ESI and APPI, after Huba et al. (2016). “V” stands

for successful ionization, while “-” marks non-ionizable species. ........................................................ 30

Table 1.2. Important ionization processes occurred for the analyte [M], solvent [S] and dopant [D] when

APPI is operated in positive mode (Hanold et al., 2004; Kauppila et al., 2002; Klee et al., 2013). ..... 30

Table 2.1. Geological background information, huminite/vitrinite reflectance (Ro), and total organic

carbon content (TOC), summarized from Vu (2008), Rippen et al. (2013) and Yang and Schulz (2019).

“/”: no available data. ............................................................................................................................ 47

Table 3.1. Geological background information, huminite/vitrinite reflectance (Ro), total organic carbon

content (TOC), total sulfur content (TS), and kerogen type of the studied rock samples, summarized

from Littke et al. (1991), Rippen et al. (2013), Song et al. (2017), and Yang and Schulz (2019). “/”: no

available data. ........................................................................................................................................ 94

Table S4.1. Mineralogical compositions. ........................................................................................... 163

Table S4.2. Average DBE values of some organosulfur classes in positive APPI and negative ESI modes.

............................................................................................................................................................. 164

XXIV

XXV

LIST OF ABBREVIATIONS

% n-C

amount of pyrolyzed C

n-alkenes and n-alkanes (n-C

/(C

1–5

+ n-C

))

% n-C

8:1

amount of pyrolyzed oct-1-ene (n-C

8:1

/(n-C

8:1

+ m,p-xylene + phenol))

°C

degree Celsius

4-MSI

4-methylsteranes/C

regular steranes

AIR

aryl isoprenoid ratio

APPI

atmospheric pressure photoionization

ATR-FTIR

attenuated total reflection Fourier transform infrared spectroscopy

max_abund

the most abundant species in each DBE class

dalton

DBE

double-bond equivalents

DBE

max_abund

the most abundant DBE species in each compound class

DBT

dibenzothiophene

DMT

dimethylthiophene

EOPI

even-over-odd preference indexes

ESI

electrospray ionization

electronvolt

FT-ICR-MS

Fourier transform ion cyclotron resonance mass spectrometer

GC-FID

gas chromatography-flame ionization detector

GC-MS

gas chromatography mass spectrometry

HBI

highly branched isoprenoid

hydrocarbons

hydrogen index

a photon of energy

I/S

illite/smectite mixed-layer minerals

ionization energy

XXVI

liter

LSB

Lower Saxony Basin

meter

m/z

mass-to-charge-ratio

mDa

millidalton

MDBT

methyldibenzothiophenes

milligram

min

minute

milliliter

millimeter

MPhen

methylphenanthrenes

NSO compounds

nitrogen, sulfur and oxygen bearing compounds

oxygen index

organic matter

OSCs

organosulfur compounds

PAHs

polycyclic aromatic hydrocarbons

Phen

phenanthrene

Pr/Ph

pristane/phytane

Py-GC

pyrolysis-gas chromatography

calculated vitrinite reflectance (%)

huminite/vitrinite reflectance (%)

Ster/Hop

regular steranes/homohopanes

TAR

terrigenous/aquatic ratio

max

the temperature at which the maximum release of hydrocarbons from kerogen

via cracking occurs during Rock Eval pyrolysis

TOC

total organic carbon content

total sulfur content

XXVII

microliter

ultraviolet

v/v

volume by volume

vol.%

volume percentage

wt.%

weight percentage

microgram

micrometer

cyclotron frequency

magnetron motion

axial oscillation

XRD

X-ray powder diffraction

XXVIII

1 INTRODUCTION

1.1 Origin of NSO compounds in sedimentary systems

The portion of organic matter (OM) in sedimentary rocks that is soluble and insoluble in

common organic solvents is referred to as bitumen and kerogen, respectively (Forsman and

Hunt, 1958). Kerogen is formed under mild temperature and pressure conditions of young

sediments and represents from 80 to 99% of the OM in sedimentary rocks. It is a mixture of

various macromolecular structures made of condensed cyclic nuclei linked by heteroatomic

bonds or aliphatic chains (Tissot and Welte, 1984); small amounts of metals are contained as

organo-metal complexes (e.g., Filby, 1994; Hirner, 1987). A shallow immature kerogen

consists of not only preserved resistant biomacromolecules (de Leeuw and Largeau, 1993;

Eglinton and Logan, 1991; Tegelaar et al., 1989) but also geomacromolecules formed from

polymerization of bacterial degradation and non-degradation products (Damsté et al., 1998;

Eglinton and Logan, 1991; Gupta et al., 2007b; Huc, 1980; Kohnen et al., 1990; Koopmans et

al., 1996a; Mycke et al., 1987; Riboulleau et al., 2001). Bitumen is only to a minor extent

inherited directly from the biomass; the main portion is generated during the thermodynamic

conversion of metastable kerogen over time due to a progressive elimination of functional

groups and of linkages between nuclei (including carbon chains) with increasing overburden

(Tissot and Welte, 1984). Subsurface inorganic materials in particular water and minerals may

participate as reactants or catalysts during OM maturation (e.g., Berthonneau et al., 2016;

Pomerantz et al., 2014; Seewald, 2003, 2001; Tannenbaum et al., 1986; Wu et al., 2012).

Bitumen is an extremely complex mixture of macromolecular and molecular organic

compounds, consisting of hydrocarbons and NSO (nitrogen, sulfur and oxygen bearing)

compounds, a small percentage of the latter being organo-metal complexes such as nickel or

vanadyl porphyrins. The high-molecular-weight constituents of the rock bitumen (typically

over 500 Da) usually contain N, S, O atoms and occasionally metals, amounting to around 50%

of the rock bitumen by weight on average (Tissot and Welte, 1984).

Depositional and ecological conditions that result in enhanced primary productivity

and/or preservation by stagnation are the prerequisites for the formation of organic-rich

sediments. Primary sources include phytoplankton and bacteria, with land plants being

important later than the Devonian period (Tissot and Welte, 1984). Upon burial, they undergo

progressive compositional changes that are initially determined by microbial agencies and

thermodynamic instability, and later mainly by thermal stress (Horsfield and Rullkötter, 1994).

The continuum of processes is divided into three consecutive stages, diagenesis, catagenesis

and metagenesis. Diagenesis comprises the biological, physical and chemical alterations of

organic debris in sediments up to about 50°C (vitrinite reflectance Ro < 0.5%), while the

succeeding zone of catagenesis is one of changes induced by thermal cracking occurring at

temperatures up to about 150°C and is the principle zone of oil and wet gas generation (0.5% <

Ro < 2.0%; Tissot and Welte, 1984). Finally, the zone of metagenesis (2.0% < Ro < 4.0%)

refers to the reorganization of the aromatic network in the residual kerogen and the generation

of methane (dry gas) and non-hydrocarbon gases such as carbon dioxide, hydrogen sulfide and

nitrogen (Vandenbroucke and Largeau, 2007 and the references therein).

Generally, less than 1% of the whole living biomass enter the sedimentary carbon cycle

(Tissot and Welte, 1984). Distinct types of biomolecules exhibit large differences in their

intrinsic resistance to degradation during sedimentation and diagenesis (de Leeuw and Largeau,

1993; Eglinton and Logan, 1991; Tegelaar et al., 1989). The resistant biomolecules such as

cutan in the protective layers of some higher plants can be selectively preserved (e.g., Tegelaar

et al., 1991). In contrast, the labile biomolecules have the chance to survive only when their

reactive sites for microbial utilization are blocked or altered, such as via adsorption (e.g., on

clay minerals; Salmon et al., 2000, 1997), steric encapsulation (e.g., by algaenan; Knicker and

Hatcher, 1997), or transformation into more stable geo(macro)molecules during early

diagenesis through polymerization (e.g., Gupta et al., 2007b; Huc, 1980; Mycke et al., 1987;

Tissot and Welte, 1984) or abiotic introduction of inorganic sulfur, oxygen or metals (Hebting

et al., 2006; Piotrowicz et al., 1984; Riboulleau et al., 2001; Schouten et al., 1994; van Dongen

et al., 2006).

Thus, the N, S, O atoms in sedimentary OM might originate from both biogenic and

abiogenic sources, but in different relative proportions. The nitrogen in sedimentary OM is

believed to almost exclusively originate from biological precursors such as proteins

(Vandenbroucke and Largeau, 2007). In contrast, it has been widely accepted that organosulfur

compounds are primarily formed from the abiotic incorporation of inorganic sulfur into reactive

OM sites during early diagenesis (e.g., Damsté and de Leeuw, 1990b; Tissot and Welte, 1984).

Abiotic sulfurization has been estimated to account for at least 75% of total sedimentary organic

sulfur (Anderson and Pratt, 1995; Werne et al., 2004, 2003). Oxygen-bearing moieties in

sedimentary OM can be preserved from precursor biomolecules or partly from the introduction

of molecular oxygen in air and/or dissolved in meteoric water during or after diagenesis

(Riboulleau et al., 2001; Vandenbroucke and Largeau, 2007; Volkman, 2006).

1.1.1 Organic origin—Preservation potential of biomolecules

1.1.1.1 Nitrogen bearing biomolecules

Amino acids in forms of proteins are the principal nitrogen-bearing structures in living

organisms. Others, including amino sugars, nucleic acid bases (purines and pyrimidines),

porphyrins (chlorophylls, bacteriochlorophylls, hemes, etc) and alkaloids, account for only a

small proportion of the nitrogen in living organisms (Baxby et al., 1994). Proteins dominate

bacteria (around 50 wt.%) and marine plankton (up to 50 wt.% or more), whereas in higher

plants they typically account for only 3 wt.% or less (Baxby et al., 1994). High atomic N/C

ratios have been reported for bacteria and benthic organisms, followed by zooplankton,

phytoplankton and higher plants (Figure 1.1; Baxby et al., 1994).

The tertiary structure of proteins seems to play a major part in determining their resistance

to diagenetic modification (Eglinton and Logan, 1991). While most proteins are very rapidly

depolymerized into amino acid monomers that are then used in microbial metabolism, the

water-insoluble structural proteins could survive the early diagenetic biodegradation to some

extent (de Leeuw and Largeau, 1993). In addition, some proteins can be mechanically protected

quite well when they serve as the matrix molecules for the formation of skeletons in the shells

and bones (Lowenstein, 1981; Muyzer et al., 1984; Poinar and Stankiewicz, 1999; Robbins and

Brew, 1990; Weiner et al., 1976). Resistant organic matrix (e.g., algaenan; Knicker and Hatcher,

1997) also offers an efficient protection for the proteinaceous moieties through steric

encapsulation. Moreover, adsorption on clay minerals can significantly lower the loss of

proteinaceous materials during early diagenesis (e.g., Henrichs, 1992; Lynch and Cotnoir Jr,

1956; Vandenbroucke and Largeau, 2007). Furthermore, via the classical neogenesis pathway,

a small part of the decomposition intermediates of protein can undergo condensation reactions

with the degradation products of the other biomolecules, thereby progressively forming

randomized stable macromolecules like melanoidin-like moieties that can escape

mineralization in the water column and sediments (Huc, 1980; Tissot and Welte, 1984).

Chlorophylls, bacteriochlorophylls, or hemes, starts to transform during sedimentation or

early diagenesis, in which the loss of magnesium or iron as well as a re-chelation with vanadyl

or nickel ion stabilize the tetrapyrrolic molecules and insure their preservation (Tissot and

Welte, 1984). Their preservation efficiency can be enhanced when they are bound to kerogen

matrix via ester bonds (Huseby and Ocampo, 1997; Huseby et al., 1996) or entrapped into

kerogen network (Barakat and Yen, 1989), in which etioporphyrins are evidenced to be

selectively and/or more readily preserved by this route relative to cycloalkanoporphyrins. In

addition, the preservation efficiency of bicycloalkanoporphyrins can be enhanced through

incorporation into macromolecular entities via (poly)sulfide linkages (Schaeffer et al., 1994,

1993). However, porphyrins, nucleic acids, and alkaloids still just make a neglectable

contribution to the sedimentary organic nitrogen (each < 1%, Baxby et al., 1994).

Figure 1.1. Atomic N/C and O/C ratios of some living organisms and biomolecules (Baxby et al.,

1994; Vandenbroucke and Largeau, 2007).

1.1.1.2 Oxygen bearing biomolecules

Distinct types of biomolecules contain variable oxygen contents (see Figure 1.1): atomic

O/C ratios reported for the carbohydrates (e.g., cellulose) and lignin are higher than those of

the proteins or lipids. Since higher land plants are largely composed of cellulose (30–50%) and

lignin (15–25%), they have high oxygen contents (Figure 1.1; Baxby et al., 1994; Tissot and

Welte, 1984). In contrast, proteins only account for less than 3% on average in high plants

(Baxby et al., 1994), and the relatively low content of lipids is chiefly concentrated in fruiting

bodies and leaf cuticles. Bacterial biomass is composed of ca. 50% proteins, ca. 10% lipids,

and 20% cell-wall materials (including membranes mainly composed of polysaccharides, lipids

and some proteins) (Baxby et al., 1994). Phytoplankton, such as diatoms and dinoflagellates,

are dominated by proteins (up to 50% or more), with variable amounts of lipids (5–25%) and

carbohydrates (< 40%) (Baxby et al., 1994; Parsons et al., 1961; Raymont, 1980). It has been

observed that the chemical composition of eukaryotic algae is species-specific and usually

regulated by hydrogeochemical factors like salinity, nitrate concentration and various other

nutrients (e.g., Ben-Amotz et al., 1985; Lewin, 1974; Pohl and Zurheide, 1979; Wood, 1974).

Carbohydrates are polyhydroxy-substituted carbonyl compounds serving for energy

storage (such as starch and glycogen) and structural support (such as cellulose in plants and

chitin in arthropods). The storage materials make up a very important part of the biomass,

nevertheless, they are seldomly preserved in sediments either as such or altered, because the

enzymes that can decompose or mineralize them are omnipresent (de Leeuw and Largeau,

1993). Most structural carbohydrates have low preservation potentials during early diagenesis;

they can survive better when they are mechanically protected (e.g., mucilages in seeds) or

naturally complexed with other biomolecules (e.g., lignin-cellulose complex in vascular plants)

(de Leeuw and Largeau, 1993; Eglinton and Logan, 1991). In addition, via the classical

neogenesis pathway (i.e., degradation-recondensation), a small fraction of the decomposition

products of carbohydrates can be recondensed and preserved as randomized insoluble

macromolecules, e.g., melanoidin-like moieties (Huc, 1980; Tissot and Welte, 1984), which are

precursors of kerogen.

Biolipids have a wide variety of carbon skeletons made up of linear, branched, and cyclic

structures. In general, these carbon skeletons are fully saturated, apart from the occasional

double bonds and oxygen-bearing substituents (Eglinton and Logan, 1991). Simple compounds

such as aliphatic carboxylic acids or alcohols can be found, but most lipids exist as

combinations of these simple molecules with one another (e.g., wax esters, triglycerides, steryl

esters, and phospholipids) or with the other compound classes such as carbohydrates

(glycolipids) and proteins (lipoproteins). The stability of lipids depends on multiple factors,

including their structure, stereochemistry, head-group, degree of saturation, and ether or ester

linkages (Cranwell, 1981; Eglinton and Logan, 1991; Middelburg, 2019; Volkman, 2006;

Wakeham and Canuel, 2006), for instance, an order of stability of free lipids has been reported

as n-alkanes > alkan-2-ones > sterols > n-alkanoic acids > n-alkanols > n-alkenoic acids

(Cranwell, 1981). In addition, appropriate functionalized lipids, such as bacteriohopanepolyols,

plant waxes, steroids, could bound more or less intact via their functional groups into

macromolecules to escape mineralization (Eglinton and Logan, 1991; Gupta et al., 2009, 2007b;

Koopmans et al., 1996a; Lee et al., 2019; Michaelis et al., 1989; Mycke et al., 1987). Moreover,

clay minerals can provide an efficient physical protection for lipids via adsorption (Salmon et

al., 2000, 1997). It has been widely recognized that most lipids are less degradable during early

diagenesis in comparison with proteins and carbohydrates (e.g., Arndt et al., 2013; Eglinton and

Logan, 1991; Liu et al., 2020). Although some alterations may occur (e.g., hydrogenation of

double bonds or loss of functional groups), structure of the original precursor biolipids can often

be inferred from structure of the resulting geolipids, leading to the concept of lipid biomarkers

(e.g., Mackenzie et al., 1982). The lipid compositions of organisms vary dramatically across

the three domains of life, for instance, bacteriohopanepolyols, sterols, and isoprenoid glycerol

dialkyl glycerol tetraethers are diagnostic compounds respectively for the Bacteria, Eukarya,

and Archaea domains (e.g., Briggs and Summons, 2014; Brocks and Pearson, 2005 and

references therein). Moreover, some biolipids have distinct taxonomic associations and can be

assigned to a specific group or groups of organisms with high taxonomic precision (e.g., Brocks

and Grice, 2011; Volkman, 2006), for example, okenone is a carotenoid specific for purple

sulfur bacteria (Brocks and Schaeffer, 2008; van Gemerden and Mas, 1995).

Algaenan, lignin, sporopollenin, cutan, suberan, tannin, cutin and suberin are

biomolecules that are strongly resistant to biodegradation and major chemical transformations

(e.g., hydrolysis or oxidation) during diagenesis. Therefore, they survive and become

quantitatively important in kerogen even when they constitute a minor part of their source

organisms (summarized by de Leeuw and Largeau, 1993; Eglinton and Logan, 1991; Tegelaar

et al., 1989). Lignin is a wood-derived biopolymer based on phenylpropanoid units, originating

from the dehydrogenative condensation of three primary building blocks: p-coumaryl alcohol,

coniferyl alcohol, and sinapyl alcohol (Goodwin and Mercer, 1972). It is part of the plant cell

wall and represents the most abundant polyphenol in nature. Tannin biopolymer is the second

most abundant polyphenol after lignin. It can be found in various plant parts (seeds, fruits,

leaves, wood, bark) and in some algae (de Leeuw and Largeau, 1993; Tegelaar et al., 1989).

Sporopollenin is a lipid- and phenolic-based polymer in outer walls (exines) of the lower plant

spores and the higher plant pollen (reviewed by Brooks and Shaw, 1978). Cutan and suberan

are insoluble, non-hydrolyzable polymethylenic biopolymers respectively in the leaf and bark

materials. While cutan is crystalline composed of C7–C33 long-chain polymethlyenic chains

with alcohol, aryl, and acid groups (Boom et al., 2005; Deshmukh et al., 2005; McKinney et al.,

1996; Schouten et al., 1998), suberan is crystalline with C18, C20, and C22 (the most abundant)

alkyl chains bearing alcohol, acid, and a small amount of epoxide (Turner et al., 2013). Cutin

and suberin are insoluble, hydrolyzable polyesters in vascular plants. Cutin is a characteristic

component of plant leaf and fruit cuticular membranes; it consists mainly of C16 and C18 fatty

acid, (poly)hydroxy fatty acid, and epoxy fatty acid monomers (Deshmukh et al., 2003;

Kolattukudy, 1980; Pollard et al., 2008). Suberin is primarily present as a wall component of

cork cells that comprise the periderm layers of woody plant bark and roots. It is rich in C16, C18,

C20, C22 and C24 monomers (hydroxy fatty acid, dicarboxylic acid, and to a less extent, fatty

acid, alcohol); the relative abundance of monomer constituents varies considerably between

biological species (del Rio and Hatcher, 1998; Graça and Pereira, 2000; Pollard et al., 2008;

Ranathunge and Schreiber, 2011; Schreiber et al., 1999). To date, biopolymer algaenan has

been identified in a large array of genera belonging mainly to the Chlorophyceaee (Berkaloff

et al., 1983; de Leeuw et al., 2006; Derenne et al., 1992; Gelin et al., 1999; Vandenbroucke and

Largeau, 2007). These genera are not ubiquitous in the marine environment and would rarely

become a major constituent of marine phytoplankton (Vandenbroucke and Largeau, 2007). In

most cases, algaenan amounts to only 1–2% of the total biomass by weight, but in Botryococcus

braunii, up to 30 wt.% of the total biomass is algaenan (Derenne and Largeau, 2001; Derenne

et al., 1992). The chemical structures of algaenan in distinct genera have been extensively

studied (reviewed in de Leeuw et al., 2006; Metzger and Largeau, 1999; Petersen et al., 2008).

They are typically highly aliphatic, containing functional groups like ether, ester linkages,

unsaturations, and aldehydes. For instance, algaenan in Botryococcus braunii race A has been

reported as unsaturated aldehydes and hydrocarbons with on average 40 carbon atoms that are

cross-linked by acetal and ester bonds (Simpson et al., 2003). However, studies on the Chlorella

marina (Derenne et al., 1996) and dinoflagellate Lingulodinium polyedrum resting cyst

(Kokinos et al., 1998) suggest that aromatic moieties might also exist.

1.1.1.3 Sulfur bearing biomolecules

Sulfur participates in many biochemical processes such as protein biosynthesis, and as an

electron donor/acceptor for respiration (e.g., Gibbs and Schiff, 1960; Schiff and Hodson, 1973;

Sievert et al., 2007), but only a small fraction is bound in the living biomass. It constitutes only

about 1% on average of the dry weight of living organisms, residing principally as the amino

acids cysteine, cystine, and methionine (Goldhaber and Kaplan, 1974; Shen and Buick, 2004;

Sievert et al., 2007). Since proteinaceous substances are labile, the amount of bio-sulfur that

can survive diagenesis is generally very small (de Leeuw and Largeau, 1993).

1.1.2 Inorganic origin—Abiotic incorporation of inorganic small NSO

compounds into organic matter

During early diagenesis small inorganic molecules in the depositional environment, such

as hydrogen sulfide and molecular oxygen, can be incorporated abiotically into appropriate

functionalized biomolecules or even act as cross-linking reagents to facilitate the formation of

geomacromolecules (Damsté et al., 1998; Kohnen et al., 1990; Lee et al., 2019; Riboulleau et

al., 2001; Schouten et al., 1994; van Dongen et al., 2003b). This is not only a major abiogenic

source of heteroatoms in the sedimentary OM, but also an important preservation pathway for

the carbon skeletons of these labile biomolecules, as it blocks or alters their reactive sites for

microbial utilization. In general, the natural sulfurization of lipids and carbohydrates takes place

via substitution of the oxo-groups or via addition at the double bonds (e.g., Kohnen et al., 1990;

Schouten et al., 1994; van Dongen et al., 2003a, 2003b), whereas the oxidative polymerization

of lipids occurs through cross-linking by ether bridges at the double bonds (Riboulleau et al.,

2001). At or near the oxic/anoxic interface, oxygen and sulfur might compete for reaction with

double bonds (Riboulleau et al., 2001).

It is worth mentioning that abiotic incorporation of inorganic molecules can occur (but

not always) at later stages of the subsurface organic carbon cycle, potentially further altering

the heteroatomic characteristics of sedimentary OM (e.g., Ho et al., 1974; Petsch et al., 2000;

Vandenbroucke and Largeau, 2007).

1.1.2.1 Incorporation of inorganic sulfur during early diagenesis

Sulfate SO42- sourced from weathering and leaching of rocks and sediments is the most

stable form of sulfur in the ocean (a major reservoir of sulfur on Earth) (Vairavamurthy et al.,

1995). In oxygen-poor environments, it can be utilized by bacteria and archaea to produce

energy as a terminal electron acceptor for OM oxidation (such as below the water-sediment

interface of aquatic systems; see Widdel and Hansen, 1992 for a detailed review on sulfate

reducing bacteria). Its end products, reduced sulfur species typically as H2S, are released back

into the environment (le Gall and Postgate, 1973; Postgate, 1959). This process, known as

dissimilatory sulfate reduction, is common in geologic settings with temperatures ranging from

0 to about 60–80°C (reviewed by Machel, 2001). Above this temperature range, almost all

sulfate-reducing bacteria cease to metabolize (e.g., Jørgensen et al., 1992; Machel, 2001;

Machel and Foght, 2000).

During early diagenesis, H2S can be consumed by oxidation or through formation of iron

sulfides or organosulfur compounds (Vairavamurthy et al., 1994). Oxidation is prominent at the

oxic-anoxic interface (e.g., at or near the sediment-water interface), where sulfide encounters

molecular oxygen or metal (Fe, Mn) oxides (Vairavamurthy et al., 1997, 1995, 1994; Werne et

al., 2004). Several partial oxidation products are formed, including elemental sulfur (S0),

polysulfides (HSx-, Sx2-), sulfite (SO32-), thiosulfate (S2O32-), polythionates (e.g., S4O62-), and

eventually, sulfate. Since most of the partial oxidation products, particularly polysulfides,

thiosulfate, and sulfite, are strong sulfur nucleophiles, together with H2S they form the pool of

reactive sulfur species in sediments. Pyrite is usually the major sink for the reduced inorganic

sulfur species in the geological record (Berner, 1984; Berner and Raiswell, 1983; Werne et al.,

2004). Extensive OM sulfurization typically occurs only under specific conditions where metal

ions are present in low concentrations (e.g., carbonate depositional settings), since reactive iron

is generally considered outcompeting OM for sulfur incorporation (Berner, 1985, 1984; Damsté

et al., 1989a; Hartgers et al., 1997). However, in some settings, abiotic sulfurization of OM may

compete with pyrite formation despite the presence of Fe (Filley et al., 2002; Shawar et al.,

2018; Urban et al., 1999).

The abiotic sulfurization of organic compounds occurs rapidly within the sediment

column on a timescale of 60–10,000 years (summarized by Kutuzov et al., 2020), and in

extreme cases it starts within the anoxic or euxinic water column on a timescale of days

(Kutuzov et al., 2020; Raven et al., 2016; Wakeham et al., 2007). The preferred sulfurization

pathway is the reaction of OM with polysulfides, but other mechanisms such as reactions with

H2S, S0 or S2O32- cannot be eliminated (Werne et al., 2004). The potential and rate of a given

biomolecule undergoing sulfurization strongly depends on its reactivity (Adams, 2014; Amrani

and Aizenshtat, 2004b; Kok et al., 2000; Schouten et al., 1994), since sulfurization typically

occurs at the reactive sites within the molecules (Kohnen et al., 1990). Carbonyl and conjugated

double bonds are the most reactive groups (Schouten et al., 1994; van Dongen et al., 2003b),

whereas the less reactive sites like isolated double bonds, hydroxy or carboxyl groups could be

transformed to labile moieties via low-temperature biological and chemical diagenetic

alterations such as dehydration, oxidation and double bond migration (Amrani, 2014;

Blumenberg et al., 2010; Grossi et al., 1998; Rontani et al., 1999; Schaeffer et al., 2006).

Two principal mechanisms have been proposed for sulfurization (Damsté et al., 1989c):

the first is intramolecular addition, in which sulfur is incorporated into organic molecules and

principally rearranged to form a ring, such as thiolane, thiane, thiophene, dithiane, trithiepane,

and organic sulfonate (e.g., Damsté and de Leeuw, 1990b; Kohnen et al., 1991c; Vairavamurthy

et al., 1994); the second is intermolecular addition, which forms macromolecules via sulfide or

polysulfide bridges and contributes to the formation of kerogen (e.g., Adam et al., 1993;

Kohnen et al., 1991b). The compounds created by the intramolecular sulfurization pathway, if

not further bound into macromolecules, can be found in the free fraction of bitumen.

1.1.2.2 Incorporation of inorganic sulfur during catagenesis

In relatively high temperature regimes (ca. 100–140°C, sometimes 160–180°C), OM can

be abiotically oxidized by sulfate (almost invariably from the dissolution of gypsum and/or

anhydrite), producing hydrogen sulfide and carbon dioxide (Krouse et al., 1988; Machel, 2001;

Orr, 1974). This high-temperature reduction, known as thermochemical sulfate reduction,

becomes important only in the catagenesis zone and is considered to be responsible for the

elevated H2S concentrations (> 10%) in many deep carbonate gas reservoirs around the world

(e.g., Cai et al., 2003; Krouse et al., 1988; Worden and Smalley, 1996). A variety of

organosulfur compounds can be newly formed through the back reaction of OM with the H2S/S0

system, such as thioadamantanes (Cai et al., 2016; Gvirtzman et al., 2015; Hanin et al., 2002;

Wei et al., 2012, 2007), thiols (Cai et al., 2003; Ho et al., 1974), thiolanes (Cai et al., 2009),

benzothiophenes, dibenzothiophenes (Amrani et al., 2012; Cai et al., 2016; Zhang et al., 2015),

but the competitive decomposition of organosulfur compounds due to high temperatures keeps

the level of organic sulfur low (Vairavamurthy et al., 1995).

1.1.2.3 Incorporation of inorganic oxygen

Post-sedimentary oxidation of OM might (but not always) occur at any stage of kerogen

evolution (Vandenbroucke and Largeau, 2007). Early diagenetic oxidation has been

documented to be accompanied by a decrease in amount of OM (partial degradation of

immature OM) and an increase in atomic O/C ratio (oxygen cross-linking via ether bridges at

the unsaturated sites of the residual organic fraction) (Riboulleau et al., 2001). In addition,

kerogen in uplifted sedimentary rocks, especially at outcrops, has also been observed to be

altered by oxygen in air and/or dissolved in meteoric water (e.g., Petsch et al., 2000).

1.1.2.4 Incorporation of inorganic nitrogen

Inorganic nitrogen from the complete decomposition of protein, mainly in forms of

ammonia or ammonium, were supposed to aid in the formation of kerogen as nitrogen cross-

linking at low temperatures during early diagenesis, although the importance of this route in

natural systems has not been solidly evidenced (Amrani et al., 2007; McKee and Hatcher, 2010).

In contrast, Schimmelmann et al. (1997) suggested that ammonia reacts more readily with

sedimentary OM at elevated temperatures.

1.2 Palaeoecological and palaeoenvironmental signatures

documented by sedimentary NSO compounds

1.2.1 NSO bearing moieties in kerogen

A shallow immature kerogen comprises not only resistant biomacromolecules (de Leeuw

and Largeau, 1993; Eglinton and Logan, 1991; Tegelaar et al., 1989), but also

geomacromolecules formed from biodegraded or non-biodegraded biomolecules (such as the

decomposed proteinaceous materials or the approximately intact lipids) by direct condensation

or by crosslinking reagents such as hydrogen sulfide and molecular oxygen (Damsté et al., 1998;

Eglinton and Logan, 1991; Gupta et al., 2007b; Huc, 1980; Kohnen et al., 1990; Koopmans et

al., 1996a; Mycke et al., 1987; Riboulleau et al., 2001). The respective contributions of these

different units are controlled by the depositional milieu and the natures of the starting biological

materials. Therefore, chemical structures of immature kerogen, such as the relative importance

of different nuclei, bonds and functions, vary with the original organism assemblages and the

physical, chemical and biochemical depositional conditions.

The N, S, O in kerogen are present not only as atomic constituents of heterocyclic

(condensed) structures like thiane, thiophene, and pyridine, but also as bridges such as sulfide,

disulfide, and ether bonds (Tissot and Welte, 1984). Although a detailed molecular

configuration of macromolecular kerogen cannot be obtained, several approaches have been

applied to chemically describe its NSO-bearing moieties, and the information obtained was

visualized as conceptual averaged molecular models (e.g., Behar and Vandenbroucke, 1987).

For example, heteroatomic content and heteroatomic functional group composition can be

provided by elemental analysis and various spectroscopic techniques such as infrared, nuclear

magnetic resonance, X-ray photoelectron, and X-ray absorption near-edge structure (e.g.,

Durand and Monin, 1980; Fester and Robinson, 1966; Kelemen et al., 2007, 2002, 1999, 1990;

Mitra-Kirtley et al., 1993; Olivella et al., 2002; Sarret et al., 2002; Wiltfong et al., 2005). Further

details can be offered by thermal or chemical degradation of kerogen followed by analysis of

the resulting fragments (e.g., Larter and Horsfield, 1993; Rullkötter and Michaelis, 1990;

Schaeffer-Reiss et al., 1998; Schaeffer et al., 1995). Rock-Eval pyrolysis and open system

pyrolysis-gas chromatography are two of these powerful tools that allow a rapid

structure screening of kerogen inside whole rock without the need to isolate it from minerals

(e.g., Eglinton et al., 1990; Espitalié et al., 1977; Larter and Horsfield, 1993), but they must be

used with care due to the so called ‘‘matrix effect’’, especially for samples with low organic

carbon content (e.g., Horsfield and Douglas, 1980; Larter, 1984). Hydrogen index and oxygen

index are two important parameters obtained by Rock-Eval pyrolysis (Espitalié et al., 1977). A

good correlation is observed between hydrogen index and atomic H/C ratio on the one hand,

and between oxygen index and atomic O/C ratio on the other hand. Open system pyrolysis-gas

chromatography can produce fingerprint pyrogram of kerogen (reviewed by Larter and

Horsfield, 1993), in which the main quantified components include normal and branched/cyclic

hydrocarbons, alkyl aromatic hydrocarbons, sulfur-bearing alkylated aromatic compounds,

alkylphenols, etc. The phenolic and thiophenic compounds have been found to be proportional

to the gross structural parameters of kerogen, i.e., the absolute concentrations of aryl-oxygen

bonds and organic sulfur, respectively (Eglinton et al., 1990; Horsfield, 1989; Larter and

Horsfield, 1993).

1.2.1.1 Oxygen in kerogen

Oxygen is a quantitatively significant component of immature kerogen (10–25 wt.%),

especially those associated with significant terrestrial plant input (Tissot and Welte, 1984).

Three main kerogen types I–III have been defined based on the atomic composition of three

major elements C, H, O.

Type I refers to kerogen with a low initial atomic O/C ratio (generally smaller than 0.1)

and a high initial atomic H/C ratio (ca. 1.5 or more). Such kerogen comprises many lipid

materials particularly aliphatic chains (Tissot and Welte, 1984), which was related to either “a

selective accumulation of algal materials” such as Botryococcus braunii remains, or “a severe

biodegradation of OM other than lipids and microbial waxes” (Tissot and Welte, 1984). Oxygen

in the type I kerogen is principally present as ether and ester groups (Behar and Vandenbroucke,

1987; Glombitza et al., 2009; Petersen et al., 2008; Robin and Rouxhet, 1978; Tissot and Welte,

1984).

Type II kerogen is particularly common in petroleum source rocks, such as the Lower

Toarcian black shales in the Paris Basin of France and its equivalent Posidonia Shale in

Germany. It has a relatively low O/C ratio (ca. 0.15) and a high H/C ratio (ca. 1.3)

(Vandenbroucke and Largeau, 2007). It is usually associated with marine reducing

environments where autochthonous OM is derived from a mixture of phytoplankton,

zooplankton and bacteria (Tissot and Welte, 1984). Esters are also abundant in type II kerogen;

ketone and carboxylic acid groups are more important than in type I kerogen, but less important

than in type III kerogen.

Type III is commonly taken to be synonymous with kerogen sourced from continental

plants (Horsfield, 1984), with a high initial atomic O/C ratio (as high as 0.2 or 0.3) and a

relatively low H/C ratio (usually less than 1.0). The immature type III kerogen is a condensed

polyaromatic network containing varying amounts of quinone, ketone, hydroxyl, carboxyl,

ether, and ester groups, among which phenols, quinones and aromatic acids are more important

(Behar and Vandenbroucke, 1987; Glombitza et al., 2009; Petersen et al., 2008; Robin and

Rouxhet, 1978; Tissot and Welte, 1984). In the case of type III kerogen, if OM accounts for

greater than 50% of the deposit, the material is commonly referred to as coal.

1.2.1.2 Sulfur in kerogen

The organic sulfur content of kerogen is generally low (S/C= ca. 0.01–0.035; Tissot and

Welte, 1984), but in some cases it can even exceed 14% by weight (S/C as high as 0.08–0.09;

Orr and Damsté, 1990). Type I-S, II-S, III-S kerogen (S/C > 0.04) are designated to distinguish

the organic sulfur-rich kerogen formed in sulfur-rich and iron-deficient depositional settings

from the classical type I, II, III kerogen (Damsté et al., 1993a, 1992; di Primio and Horsfield,

1996; Orr, 1986).

Sulfur in kerogen can be present as building blocks or bond linking. Aliphatic reduced

forms like acyclic or cyclic (poly)sulfides or thiols, aromatic reduced forms such as thiophenes,

and oxidized forms like sulfoxides, have been found to exist in different amounts in distinct

kerogen (Kelemen et al., 2007; Kohnen et al., 1991b; Krein, 1993; Olivella et al., 2002; Sarret

et al., 2002; Wang et al., 2015; Wiltfong et al., 2005). For instance, the ratio of aliphatic to

aromatic sulfur forms in the type I kerogen was found to be higher than the type II kerogen

(Wang et al., 2017; Wiltfong et al., 2005). In addition, Wiltfong et al. (2005) noted that the

content of sulfoxides is low in type I-S and II-S kerogen (e.g., Olivella et al., 2002; Riboulleau

et al., 2000; Sarret et al., 2002).

1.2.1.3 Nitrogen in kerogen

The nitrogen content in kerogen is usually low (atomic N/C= ca. 0.005–0.03; Tissot and

Welte, 1984) and varies considerably in each kerogen type I, II, III. A correlation between

nitrogen content and organic facies was proposed but not adequately tested (Durand and Monin,

1980; Kelemen et al., 2007).

Neutral pyrroles and basic pyridines are the two major nitrogen-bearing structures in

kerogen; the non-basic nitrogen typically predominates (Bartle et al., 1987; Burchill and Welch,

1989; Mitra-Kirtley et al., 1993). Other forms, including amides/amines, porphyrins, pyridone,

and protonated pyridines are also present, but principally in kerogen at low thermal maturity

(Derenne et al., 1998; Gorbaty and Kelemen, 2001; Huseby et al., 1996; Kelemen et al., 2006b,

1994; Mitra-Kirtley et al., 1993; Mullins et al., 1993; Sundararaman et al., 1988; Wang et al.,

2017). To date, the influence of thermal maturation on nitrogen speciation in kerogen has been

recognized, but little is known about the impact of biomass input or depositional environment.

1.2.2 Low-molecular-weight NSO biomarkers in rock bitumen

An extremely complex mixture of macromolecular and molecular NSO compounds is

present in the bitumen of sedimentary rocks. Only the low-molecular-weight NSO compounds

are sufficiently volatile and thermally stable to be amenable to gas chromatography (one of the

most fundamental techniques to separate petroleum compounds enabling their further

identification, e.g., by mass spectrometry). There are also a number of specific techniques for

selectively degrading and identifying NSO compounds (Damsté and de Leeuw, 1990b; Damsté

et al., 1989b). A useful method is the Raney Ni desulfurization, in which organosulfur

compounds can be transformed into hydrocarbons that possess the same carbon skeleton(s) but

are amenable to gas chromatography. However, these preparation procedures are time-

consuming, labor-intensive, and might even introduce errors affecting significantly the

accuracy of the final results. High performance liquid chromatography-mass spectrometry

obviates some problems associated with gas chromatography-mass spectrometry, such as the

separation of organonitrogen and organooxygen compounds from the polynuclear aromatic

hydrocarbons, and the separation of polar compounds bearing distinct functional groups

(Matsunaga, 1983). Unfortunately, even when resolved, the peak identification is difficult

because the authentic reference compounds might not be available, the fragmentation patterns

are not unique, or the mass resolution might be insufficient to yield unambiguous molecular

formula. Even the conventional double-focusing sector mass spectrometers lack the resolving

power and mass accuracy necessary to distinguish the very narrow mass doublets commonly

found in petroleum samples, such as the C3/SH4 doublet with a mass difference of 3.4 mDa

across a broad mass range of 200–1200 Da (Hughey et al., 2004). Therefore, characterization

at the molecular level mainly concerns the small NSO compounds (< 500 Da) in rock bitumen

that are relatively readily amenable to gas- or liquid- chromatographic analysis.

Various types of heteroatomic compounds have been identified in rock bitumen, such as

porphyrins, pyrroles, pyridines, fatty acids, sterols, dibenzofurans, xanthones, hopanoid thianes,

HBI thiophenes. Some of them might result from the thermodynamic conversion of metastable

kerogen by elimination of functional groups (e.g., carbonyl, carboxyl) or cleavage of bonds

such as (poly)sulfides with increasing overburden (e.g., Orr, 1986; Tissot and Welte, 1984).

There are also compounds inherited directly from biomass that were already present in rock

bitumen during early diagenesis, which are structurally intact or rearranged by early diagenetic

reduction, intramolecular sulfurization, etc. (e.g., Damsté and de Leeuw, 1990b; Damsté et al.,

1989c; Mackenzie et al., 1982; Treibs, 1936).

A portion of these NSO compounds can be trace back to biochemicals such as lipids,

pigments (e.g., chlorophylls, bacteriochlorophylls, carotenoids), lignin, cutin, suberin, and

algaenan in once-living organisms (e.g., Mackenzie et al., 1982; Treibs, 1936; Volkman, 2006).

Some of them have distinct taxonomic associations and can be assigned to a specific group or

groups of organisms, thus they can be used as diagnostic biomarkers to obtain information on

the composition of past (microbial) ecosystems (e.g., Brocks and Schaeffer, 2008; Brocks and

Grice, 2011; Cranwell, 1982; Hsu et al., 2003; Meyers and Ishiwatari, 1995; Treibs, 1936;

Volkman, 2006, 1988, 1986; Volkman et al., 1998), for example as 24-isopropylcholesterol

produced primarily by certain genera of the Demospongiae (Bergquist et al., 1980; Love et al.,

2009; McCaffrey et al., 1994). Besides, there are also some of them can be considered as

biomarkers only under specific conditions, because their relationship to specific biological

precursor(s) is ambiguous and supplemental information such as relative distribution is required.

For instance, the straight-chain monocarboxylic fatty acids have so many potential precursors

and therefore they could be biomarkers only if their distribution corresponds to specific biota,

for example, an enrichment of the C22–C32 long-chain fatty acids showing a strong even-over-

odd predominance is usually considered to be characteristic of vascular plants (e.g., Cranwell,

1982; Volkman, 2006, 1988). Therefore, the biological information gleaned from biomarkers

arise not only from the occurrence but also from their relative distribution.

Many organisms prefer specific habitats, and the lipid composition of individual

organisms frequently adjusts to the changing physical and chemical conditions, thus, the

biomarkers can serve as palaeoenvironmental proxies for salinity, temperature, oxygen

availability, etc. (reviewed by Brocks and Grice, 2011; Luo et al., 2019). Moreover, diagenetic

processes transform biomolecules to geomolecules through complex pathways that include

oxidation, reduction, sulfurization, etc. Such processes are strongly milieu-dependent, and thus

if the transformation pathways can be reconstructed, the insights into ambient environmental

conditions in deep-time systems can be gained (reviewed by Luo et al., 2019). For instance, the

diagenetic pathways of the phytol side chain of chlorophyll a are observed to vary with the

oxic/anoxic depositional conditions (Didyk et al., 1978); the euxinic environment generally

promotes the preservation of appropriate functionalized biochemicals through early diagenetic

intra- or inter-molecular sulfur incorporation (e.g., Damsté and de Leeuw, 1990b; Grice et al.,

1998; Hebting et al., 2006).

Furthermore, there are some heteroatomic compounds whose exact biological origins are

still not known, but their occurrence and distribution in rock bitumen were empirically observed

to respond to changes in source facies and deposition conditions. For instance, the methylated

isoprenoid chromans were proposed as useful biomarkers for palaeosalinity based on abundant

empirical evidences (Damsté et al., 1993b, 1987a).

These mentioned NSO biomarkers bearing diverse palaeoecological and

palaeoenvironmental signatures are particularly abundant in immature rock bitumen. Under

thermal conditions mostly associated with oil generation, the defunctionalized hydrocarbon

biomarkers prevail due to the diagenetic alterations such as decarboxylation or dehydration (e.g.,

Mackenzie et al., 1982).

1.2.2.1 Organonitrogen compounds

Pyrrolic compounds and pyridinic compounds are the two major nitrogen-bearing

fractions in rock bitumen (e.g., Mitra-Kirtley et al., 1993). Several potential pathways have

been proposed for their generation (e.g., Bakel and Philp, 1990; Bennett et al., 2004b; Cordell,

1981; Dorbon et al., 1984; Falk, 1964), including the consolidation of the protected labile amino

groups, and the degradation of natural products already containing pyridine or pyrrolic rings,

such as alkaloids, porphyrins, and tryptophan. The commonly occurring C0–C6 carbazoles and

C0–C2 benzocarbazoles are the most investigated pyrroles on the molecular scale (see Dias et

al., 2020, and references therein). The compositional variations such as the relative abundances

of benzocarbazole or alkylcarbazole isomers have been found to respond to changes in source

facies and depositional conditions (Bakr, 2009; Bakr and Wilkes, 2002; Bennett and Olsen,

2007; Bennett et al., 2004b; Clegg et al., 1997), but the underlying causes for these changes

remain poorly understood. Data on pyridinic compounds, such as quinoline, benzoquinolines,

and their alkylated homologues, are rather rare due to the challenging chemical isolation (Li

and Larter, 2001; Yamamoto et al., 1991). The ratio of alkylquinolines to alkylbenzoquinolines

has been proposed to differentiate between marine and non-marine sediments (Yamamoto et

al., 1991).

Porphyrins in rock bitumen are tetrapyrrolic compounds that occur as metal complexes

(e.g., nickel, vanadium) or free-base species with varying alkyl substitution patterns. They are

the first compounds of definitive biological origin that can be traced from biological precursors

through water column and into sediment column (Filby and van Berkel, 1987; Treibs, 1936).

Cycloalkanoporphyrins (such as deoxophylloerythroetioporphyrin) and etioporphyrins (like

etioporphyrin III) are the most common tetrapyrroles (Figure 1.2), which have been associated

with precursors chlorophylls, bacteriochlorophylls, and heme-like pigments (Baker and Louda,

1986; Bauder et al., 1990; Boreham et al., 1989; Callot and Ocampo, 2000; Killops and Killops,

2005; Ocampo et al., 1989, 1987, 1985; Peters et al., 2005a; Pomerantz et al., 2016; Treibs,

1936). Some of them do possess unique structural features that can identify origins from

specific biota (e.g., reviewed by Keely, 2006), for instance, the cycloalkanoporphyrins (> C32)

with extended (> C2) alkyl substitution are characterized for the bacteriochlorophyll d in green

photosynthetic bacteria Chlorobiaceae, and thus indicative for photic zone anoxia (Gibbison et

al., 1995; Hayes et al., 1987; Keely and Maxwell, 1993; Ocampo et al., 1985). In addition, the

abundance of porphyrins and the ratio of nickel to vanadyl components are also able to

document the changes in both productivity and depositional conditions such as hydrogen ion

activity, redox potential, and sulfide activity (Didyk et al., 1978; Ekardt et al., 1991; Lewan,

1984; Sundararaman et al., 1993).

1.2.2.2 Organooxygen compounds

Aliphatic or monoaromatic oxygen-bearing biomarkers have been the subjects of multiple

research and reviews over several decades. Various types have been identified particularly in

immature rock bitumen, such as fatty acids (mono-, or di-carboxylic acids, mono- or poly-

hydroxy monocarboxylic acids, etc.), alicyclic alcohols (n-alkanols, long-chain alkyl diols, etc.),

ketones (e.g., n-alkan-2-ones), long-chain n-aldehydes, intact esterified lipid classes (e.g., wax

alkyl esters), ether lipids (e.g., glyceryl dialkyl glyceryl tetraethers), terpenoids (phytol, steroids,

hopanoids, carotenoids, etc.), phenols, and methylated isoprenoid chromans (Figure 1.2; e.g.,

Cranwell, 1982; Damsté et al., 1993b; Derrien et al., 2017; Hedges and Parker, 1976; Hedges

et al., 1997; Huang and Meinschein, 1979; Ioppolo-Armanios, 1996; Luo et al., 2019; Meyers

and Ishiwatari, 1995, 1993; Schouten et al., 2013; Stephanou, 1989; Volkman, 2006, 1988).

Most of them are structurally intact or rearranged biomolecules that can be traced back to

biochemicals like lipids, pigments, cutin, suberin, or algaenan in once-living organisms. Their

occurrence and relative distribution have been recognized to bear diverse palaeoecological and

palaeoenvironmental information, even though some of them might (at least partially) originate

from the chemical or biochemical transformations, such as oxidation. In general, it is a

relatively straightforward task to identify organooxygen compounds derived from vascular

plants in immature sediments, such as high concentrations of C22–C32 long-chain n-alkanoic

acids and n-alkanols with a strong predominance of even chain lengths, certain hydroxy acids

and dicarboxylic acids from plant cutin and suberin, diterpenoid resin acids, C40–C64 long-chain

saturated wax alkyl esters, C29 sterols like 24-ethylcholest-5-en-3β-ol, and pentacyclic

triterpenoids such as oleanoid, ursanoid and lupanoid series that commonly occur as plant resin

constituents (reviewed by Cranwell, 1982; Huang and Meinschein, 1979; Meyers and Ishiwatari,

1995; Volkman, 1988). Microalgae synthesize many unusual compounds such as long-chain

alkenones, alkenoates, alkyl diols, as well as, distinctive sterols and unsaturated fatty acids, thus

their input can also be easily recognized (reviewed by Brocks and Grice, 2011; Volkman, 2006).

4-methyl sterols such as dinosterol, C37–C39 n-alkenones, and fucoxanthin have been viewed as

the respective indicators for dinoflagellates, prymnesiophytes, and diatoms (Boon et al., 1979;

Hedges and Prahl, 1993; Marlowe et al., 1984; Stauber and Jeffrey, 1988). A diverse range of

compounds can be synthesized by bacteria, such as branched fatty acids, hopanoids and the

other terpenoids (reviewed by Brocks and Grice, 2011; Volkman, 2006). In immature rock

bitumen, the distributions of fatty acids and steroids are the most common and useful biomarker

records to differentiate OM sources (e.g., Huang and Meinschein, 1979; Volkman, 1986, 1980).

Moreover, various organooxygen biomarkers have been applied to reconstruct

palaeoenvironments such as sea-surface temperature, redox state and palaeosalinity (Luo et al.,

2019). For instance, the distributions of isoprenoid glycerol dialkyl glycerol tetraethers, C37

alkenones, and C28 and C30 alkyl 1,13- or 1,15-diols have been used for palaeotemperature

analysis.

Among the polyaromatic organooxygen compounds in rock bitumen, only the C0–C5 non-

or lowly-alkylated species containing up to four rings have been characterized at the molecular

level, such as dibenzofurans, phenyldibenzofurans, benzo[b]naphthofurans, dibenzo-p-dioxins,

xanthones, fluoren-9-ones, naphthylketones, phenylketones, naphthaldehydes, benzaldehydes,

1-indanones, 1-tetralones, as well as, naphthalene, anthracene or phenanthrene carboxylic acids

(Armstroff et al., 2007; Asif, 2010; Bakr, 2009; Bennett and Larter, 2000; Born et al., 1989;

Cesar and Grice, 2017; Fan et al., 1991, 1990; Fenton et al., 2007; Li and Ellis, 2015;

Ogbesejana and Bello, 2020; Oldenburg et al., 2002; Pastorova et al., 1994; Peres et al., 2000;

Radke et al., 2000; Sephton et al., 2015, 1999; Wilkes et al., 1998a, 1998b; Yang et al., 2017).

In contrast to the present sediments where wildfires are an important natural source for these

polyaromatic organooxygen compounds (Born et al., 1989; Fine et al., 2001; Hoekstra et al.,

1999; Martınez et al., 2000; Meharg and Killham, 2003; Sephton et al., 2015), in ancient

sedimentary rocks significant contributions via pyro-synthesis due to vegetation burning or

intrusive magmatism only occurred under specific geological backgrounds such as the

ubiquitous wildfires at the end of the Permian (Sephton et al., 2015). These polyaromatic

organooxygen compounds in ancient sedimentary rocks are supposed to be primarily formed

from non-specific precursors via abiotic or biotic transformation without direct biological

precursors; exceptions are, for example, dibenzofurans, benzo[b]naphthofurans, and xanthones,

whose signatures in rock bitumen show great promise as terrestrial plant markers. However,

although the major components of terrestrial plants such as lignin comprise oxygen-bearing

aromatic structures, their breakdown into smaller moieties is unspecific and thus direct

precursor-product relationships are still difficult to infer (Armstroff et al., 2007).

1.2.2.3 Organosulfur compounds

Various types of organosulfur compounds (some with biomarker carbon skeletons) have

been identified in rock bitumen and classified according to their functional groups (thiane,

thiolane, thiophene, benzothiophene, dibenzothiophene, dithiane, bithiophene, trithiepane,

sulfoxide, etc.) and carbon skeletons (linear, mid-chain methylalkane, mid-chain

dimethylalkane, phytane, linearly extended phytane, HBIs, steroids, hopanoids, carotenoids,

etc.) (e.g., Damsté and de Leeuw, 1990b; Pomerantz et al., 2014; Schouten et al., 1995;

Vairavamurthy et al., 1994).

Since organosulfur compounds are formed by incorporation of sulfur into appropriate

functionalized biomolecules, they potentially preserve the carbon skeletons and the information

concerning the original sites of functionalities, and are therefore considered to be molecular

indicators with great potential in palaeoecological and palaeoenvironmental assessment

(reviewed by Damsté and de Leeuw, 1990b). For instance, C25 HBI thiophenes could be traced

back to sulfurization of C25 HBI polyenes biosynthesized by diatoms (Kohnen et al., 1990). C37

and C38 2,5-dialkylthiolanes and -thiophenes and 2,6-dialkylthianes could be a reminiscence of

the C37 and C38 alkenones, alkadienes and alkatrienes from prymnesiophytes (e.g., Damsté et

al., 1988). C40 lycopadiene and C34 (bi)cyclobotryococcene derived cyclic sulfides were

respectively associated with the Botryococcus braunii algae races L and B (Grice et al., 1998).

C30 isoprenoid thiophenes and C35 hopanoid thiophene could be related to the sulfurization of

squalenes and bacteriohopanepolyols in bacteria (e.g., Damsté et al., 1987b). Moreover,

structural isomers of C20 isoprenoid thiophenes can be traced back to sulfurization of different

biochemicals (phytadienols and geranylgeraniol as moieties of certain bacteriochlorophylls in

photosynthetic sulfur bacteria and Archaea that restrictedly occur in hypersaline environments

on the one hand, phytol widespread in photoautotrophs as moieties of chlorophylls or certain

bacteriochlorophylls on the other hand), whose distribution patterns respond to changes in

palaeosalinity (Damsté and de Leeuw, 1990a). Furthermore, DBT/Phen

(dibenzothiophene/phenanthrene) and MDBT/mPhen (methyl DBT/methyl Phen) ratios were

proposed to assess the availability of sulfur in depositional environment for incorporation into

OM, based on empirical observations (Hughes et al., 1995).

Often, the information preserved by organosulfur compounds is not contained anymore,

or has not been contained at all, in the hydrocarbon or oxygenated biomarkers of very immature

rock bitumen (Damsté and de Leeuw, 1990b; Grice et al., 1998; Kohnen et al., 1991a), for

instance, the C34 (bi)cyclobotryococcene has only been reported as the intra- or inter-molecular

sulfur incorporation products in an ancient hypersaline euxinic ecosystem (Grice et al., 1998).

Thus, the sulfur-bound biomarkers should be taken into account for a complete and thus more

correct characterization of the palaeoecology and palaeoenvironment especially for the very

immature rocks containing a high content of organic-sulfur (e.g., Kohnen et al., 1991a). These

labile functionalized structures selectively protected by sulfur quenching during early

diagenesis could only be released during late diagenetic degradation via chemical cleavage of

C-S or S-S bonds, resulting in increased concentrations of the corresponding saturated

hydrocarbon biomarkers such as C25 HBI alkane (Kohnen et al., 1991a; Werne et al., 2000) or

C35 homohopane (Köster et al., 1997; Schaeffer et al., 2006).

The oxidized organosulfur compounds like sulfoxides and sulfones have attracted far less

research attention relative to the reduced species such as thiophene, thiolane, thiane (e.g.,

Damsté and de Leeuw, 1990b), because they have been widely regarded as the oxidation

products of reduced organosulfur compounds during long-time storage or outcrop weathering

(Schouten et al., 1995). In contrast, Pomerantz et al. (2014) argued that sulfoxides could be

formed by oxidation during oil generation. Alternatively, sulfoxides and sulfonates have been

speculated to be formed during early diagenesis, and their abundance might be sensitive to

depositional environment even though the correlations have not been well established (Bolin et

al., 2016; Vairavamurthy et al., 1995, 1994). Overall, there are still gaps in understanding the

geochemical significance of the oxidized sulfur forms.

Figure 1.2. Some important NSO compounds in rock bitumen.

1.3 Controls of lithofacies on fractionation of NSO

compounds during petroleum expulsion and migration

Under appropriate geochemical conditions, petroleum molecules would release from

kerogen and transport within and through the capillaries and narrow pores of fine-grain source

rocks, which is termed as expulsion or primary migration (Tissot and Welte, 1984). Secondary

migration occurs when petroleum is expelled from a source bed through wider pores of more

permeable porous rock units, i.e., carrier beds and reservoirs. Fractures offer extra conduits for

the secondary and especially the primary migration (Leythaeuser et al., 1988b; Littke et al.,

1988; Mann, 1990; Mann et al., 1991; Meissner, 1978; Talukdar, 1987); additional primary

migration pathway can be provided by pressure solution seams and stylolites (Hofmann and

Leythaeuser, 1995; Leythaeuser et al., 1995; Mann, 1994).

1.3.1 Fractionation mechanisms

A petroleum system is a natural geo-chromatographic system consisting of two or more

immiscible phases, one or more of which are stationary phases such as minerals, kerogen,

sorbed films of pore water or bitumen, and at least one of which is a mobile phase for example

as petroleum fluids, natural gases, and water. Numerous works have been published discussing

the fractionation mechanisms with respect to petroleum expulsion and migration (e.g., Kelemen

et al., 2006a; Krooss et al., 1991; Lafargue et al., 1994; Larter et al., 2000; Leythaeuser et al.,

1988b; Mann et al., 1997; Tannenbaum et al., 1986).

Petroleum compounds might be involved into distinct geo-chromatographic processes

(mobile–stationary phase interactions) such as adsorption, partitioning, size exclusion, and ion

exchange (e.g., Krooss et al., 1991). Adsorption is generally considered as the predominant

geo-chromatographic fractionation process (e.g., Krooss et al., 1991). The more polar the

petroleum molecules, the greater their ability to interact with mineral surfaces (e.g., Barker,

1989; Brother et al., 1991; Carlson and Chamberlain, 1986; Tannenbaum et al., 1986) or

kerogen (e.g., Lamberson and Bustin, 1993; Ritter and Grøver, 2005). Partitioning due to

differences in solubilities of compounds in two phases could occur between kerogen-retained

bitumen and expelled petroleum from kerogen during petroleum expulsion (Kelemen et al.,

2006a), between petroleum and water during petroleum migration, reservoiring or water

washing (Bennett and Larter, 1997; Bennett et al., 2003; Lafargue and Barker, 1988; Larter and

Aplin, 1995; Thomas, 1989), or between petroleum fluids and gas phase during gas washing

(Meulbroek et al., 1998; Thompson, 1987). Size exclusion refers to the size and molecular

weight of organic compounds, which is important especially during primary migration in fine-

grained clastic source rocks, which can act as semipermeable membranes to filter petroleum

(e.g., Krooss et al., 1991). Ion exchange involves chemical interactions between organic

carboxylic acids and mineral matrix (Barth et al., 1988; Krooss et al., 1991).

Monophasic fractionation processes of petroleum can only occur over short distances (up

to kilometer) under external field gradients, such as chemical diffusion of petroleum through

kerogen or in water (Krooss and Leythaeuser, 1988; Krooss et al., 1991; Stainforth and Reinders,

1990; Thomas and Clouse, 1990a, 1990b, 1990c), and thermal diffusion and gravity segregation

of petroleum in reservoir unit (Costesèque et al., 1987; Schulte, 1980).

1.3.2 Fractionation of NSO compounds

Our present understanding of petroleum’s compositional changes during expulsion and

migration has been gained through case history studies in well-defined geological situations

and experimental simulations of natural systems (e.g., Lafargue et al., 1994; Larter et al., 2000;

Leythaeuser et al., 1988b), in addition to theoretical considerations and numerical modelling

(e.g., Kelemen et al., 2006a). Chemical analysis of the residual soluble OM in source rocks (e.g.,

Leythaeuser et al., 1988b) and the comparison with the reservoired or produced crude oils (e.g.,

Bennett et al., 2002; Lafargue et al., 1994; Li et al., 1995), as well as, the comparison of oils in

different reservoirs along migration routes (e.g., Larter et al., 1996) are of fundamental

importance to elucidate the type and extent of fractionation process(es) that have occurred

during expulsion and migration. Comparison was performed in terms of the concentrations of

petroleum compound groups, homologous series, isomers and individual molecules with

distinctive chemical and physical properties.

NSO molecules are surface-active compounds that interact relatively strongly with solid

organic/mineral phases (via sorption), water (via partitioning), and each other (e.g., Bennett et

al., 2004a, 2007; Larter and Aplin, 1995), in which the embedded heteroatoms act as active

sites. It has been observed that the ratio of NSO compounds to hydrocarbons is higher in the

source rock bitumen compared to the migrated oils in conventional reservoirs (Brenneman and

Smith Jr, 1958; Pelet and Tissot, 1971; Safronova et al., 1972). Later, this preferential retention

of NSO compounds (Leythaeuser et al., 1988b) was experimentally reproduced (Lafargue et al.,

1990; Sandvik et al., 1992) and theoretically modelled (Kelemen et al., 2006a; Ritter, 2003).

The concentration and distribution of distinct low-molecular-weight NSO molecules have

been widely developed as geochemical expulsion and migration tracers to assess the magnitude

of fractionation, such as C0–C6 carbazoles, C0–C2 benzocarbazoles, C0–C1 dibenzocarbazoles

(e.g., Bennett et al., 2002; Larter et al., 1996; Li et al., 1997, 1995, 1994, 1992), C1–C4

benquinolines (Yamamoto, 1992), C0–C5 phenols (Bennett and Larter, 1997; Bennett et al.,

2007; Galimberti et al., 2000; Taylor et al., 1997), C0–C2 dibenzofurans (Li et al., 2018),

benzo[b]naphthofurans (Li and Ellis, 2015), C0–C2 xanthones (Oldenburg et al., 2002),

carboxylic acids (Jaffé et al., 1988a, 1988b), C0–C3 dibenzothiophenes, and benzo [b]

naphthothiophenes (Li et al., 2014). Taking pyrrolic compounds as examples (summarized by

Li et al., 1997), compared with the corresponding source rock extracts, the migrated petroleum

fluids have (1) a greater proportion of carbazoles to benzocarbazoles and dibenzocarbazoles;

(2) a greater proportion of alkylcarbazoles with methyl groups adjacent to the pyrrolic-nitrogen

versus those alkylated elsewhere; (3) a higher relative abundance of the highly-alkylated versus

the low-alkylated carbazoles (Li et al., 1995); (4) a higher relative abundances of the sub-

spherical benzo[c]carbazole versus the more rod-shaped benzo[a]carbazole (Larter et al., 1997,

1996). These fractionations appear to resemble a “normal phase chromatographic” process

involving irreversible adsorption (Larter et al., 2000, 1997, 1996; Li et al., 1997, 1994). The

interfacially active petroleum compounds are more prevalent in the high-molecular-weight

fractions as compounds containing N, S, O atoms (Anderson, 1986), however, their molecular-

level investigations are still relatively restricted.

1.3.3 Controls of lithofacies on fractionation

The magnitude of fractionation during petroleum expulsion and migration varies from

case to case. Simple chromatographic theory suggests that this depends critically on the

properties of expulsion or migration conduits, specifically, mineralogical assemblages, pore

size distribution, permeability, fracture network, development of pressure solution seams and

stylolites, physicochemical properties of kerogen, volume of conduits accessed by petroleum,

etc. (e.g., Bennett et al., 2002; Hofmann and Leythaeuser, 1995; Kelemen et al., 2006a;

Leythaeuser et al., 1988b; Mann et al., 1997; Sandvik et al., 1992; Tannenbaum et al., 1986).

The host rock’s petrophysical attributes appear to have an important role to play. It has

been documented that oils sourced from claystones experience stronger fractionation when

compared to oils from carbonate source rocks (Bennett et al., 2002; Huizinga et al., 1987; Jones,

1984). Empirically, heavy oils comprising a high proportion of NSO compounds are frequently

associated with organic-rich carbonate sequences, whereas light oils are often associated with

clastic sequences containing argillaceous source rocks (summarized by Huizinga et al., 1987).

In addition, within a single source rock unit, the concentration of NSO compounds in the

residual soluble OM were found to vary considerably at the meter or even centimeter scale, and

more or less correlated with the changes in petrophysical attributes that influence expulsion

efficiency, such as mineral composition, porosity, permeability, fracture network, and pressure

solution seams and stylolites (Han et al., 2018d, 2015; Hofmann and Leythaeuser, 1995;

Leythaeuser et al., 1988a, 1988b). Moreover, within a single reservoir unit, heterogeneity in the

concentration and distribution of NSO molecules in reservoired crude oils were also observed

at the meter or even centimeter scale and commonly associated with mineral composition,

porosity, permeability, etc. (Bennett et al., 2007; Horstad et al., 1990; Larter et al., 1997;

Leythaeuser and Rückheim, 1989; Stoddart et al., 1995; Wilhelms and Larter, 1994).

Different minerals have distinct surface chemistry and thus distinct adsorption properties

(Adams, 2014; González and Moreira, 1994). Clay minerals are hydrous aluminium

phyllosilicates with negatively charged surfaces (Uddin, 2008; Wu et al., 2012). OM can

interact via surface complexes with the Si-OH and Al-OH groups on clay edges and

hydrophobic surfaces or with the hydrated exchangeable cations, e.g., Na+ or K+ (Cornejo et

al., 2008; Wu et al., 2012). The negatively charged (or neutral) and weakly acidic Si-OH groups

are recognized as the active sites at the quartz surface (González and Moreira, 1994; Parida et

al., 2006), while the weakly basic Ca-OH group and Ca+ cation predominate at the surface of

calcite. The more active sites per volume or area of a mineral, the greater its adsorption capacity

to retain higher proportions of NSO compounds, such as clay minerals (Tannenbaum et al.,

1986). In addition, minerals tend to adsorb compounds of the opposite polarity (acidity) through

acid-base reactions (Anderson, 1986). Thus, in contrast with the preferential interaction

between calcite surfaces and acidic organic groups (Ataman et al., 2016a, 2016b), silanol

groups on quartz surfaces preferably interact with weakly basic groups (González and Moreira,

1994).

The other petrophysical attributes such as porosity, permeability, fracture networks and

pressure solution features might to some extent vary with lithofacies (Gamero-Diaz et al., 2013;

Mann, 1994; Mann et al., 1997). For instance, pressure solution seams, stylolites and their

accompanied process zone fractures were found to have a much greater potential to develop in

carbonate, evaporite and siliceous source rocks and thus enable a more efficient expulsion of

NSO compounds, in contrast to the siliciclastic source rocks (Hofmann and Leythaeuser, 1995;

Leythaeuser et al., 1995; Mann, 1994; Raynaud and Carrio-Schaffhauser, 1992; Sassen et al.,

1987).

1.4 Fourier transform ion cyclotron resonance mass

spectrometer (FT-ICR-MS)

1.4.1 Fundamentals of FT-ICR-MS

The first Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS) was

built in the early 1970s (Comisarow and Marshall, 1974a, 1974b). Since then, FT-ICR-MS has

grown to become a very powerful analytical tool, due to its capability to achieve an unparalleled

high resolution power coupled with a high mass accuracy over a broad mass range (typically

between 200 and 1200 Da), extending the analytical window to non-volatile polar compounds

(Hughey et al., 2001; Rodgers and Marshall, 2007). The precise mass provided by FT-ICR-MS

allows for an accurate molecular formula assignment via a statistical combination of the

monoisotopic masses of various elements (Hsu, 2012). Thousands of peaks can be

unequivocally assigned in one single mass spectrum. Thereby, compositions of complex

composites like petroleum fluids can be deconvoluted (Marshall and Rodgers, 2004).

The ICR cell as the core of FT-ICR-MS is placed in a strong magnetic field provided by

a superconducting magnet. A typical ICR cell consists of two excitation plates and two

detection plates that are parallel to the direction of the magnetic field, as well as, of two trapping

plates that are perpendicular to the magnetic field (Figure 1.3).

After passing through the ion focusing and mass filtering devices, ions are accumulated

in the ion trap prior to ICR analysis. In the ICR cell, the ions are forced to move in a circular

cyclotron motion by the Lorentz force under the perpendicular magnetic field. The cyclotron

frequency (ωc) is proportional to the strength of the magnetic field and inversely related to the

mass-to-charge-ratio (m/z) of the ions, thus, m/z of the ions can be determined based on their

orbital motion (Marshall et al., 1998). However, the initial cyclotron radii are too small to be

measured. Thus, an oscillating electric field is supplied to excite the ions, which accelerates the

ions into larger orbital radii that can be easily measured by the detector plates.

The frequency information of the ions is recorded by the detector as a time-domain signal

that is transformed via Fourier Transformation to a frequency spectrum (Figure 1.3). This is

further converted to a mass spectrum based on the relationship between frequency and m/z

(Marshall et al., 1998).

The cyclotroning ions are influenced by axial electrical trapping, resulting in axial

oscillations (ωz), which further introduce additional radial motions at the magnetron frequency

(magnetron motion, ωm). Thus, superimposed ion motions are present (Figure 1.3). The axial

quadrupolar electric field shifts the ion cyclotron frequency, but the excitation and detection

remain essentially linear with only a reduction in the proportionality constant. A simple mass

calibration follows as a treatment.

Strong magnetic fields lead to an improvement in the critical performance parameters

such as mass accuracy (Marshall et al., 1998). Magnetic field strengths of 9.4–15 Tesla are

frequently used to study petroleum samples (Kim and Kim, 2010; Shi et al., 2010a). In the

framework of this thesis, FT-ICR-MS (Bruker Daltonics GmbH) equipped with a 12 Tesla

refrigerated superconducting magnet was used.

Figure 1.3. Schematic diagram of an ICR cell with induced ion motions, modified after

https://commons.wikimedia.org/wiki/File:FTICR_cell.png.

1.4.2 Fundamentals of electrospray ionization

Compounds in complex mixtures can be detected and analyzed by a mass spectrometer

only if the molecules can be effectively ionized into molecular ions or quasi-molecular ions.

An external source ionizes the analyte before it enters the ion trap, which is particularly useful

for the non-volatile compounds in petroleum fluids (Hauschild, 2012). Soft ionization does not

cause extensive fragmentation of the analyte molecules and thus produces mainly molecular

ions (Wollschläger, 2019). The most common soft ionization methods are electrospray

ionization (ESI) and atmospheric pressure photoionization (APPI). Both have advantages in

targeting at different specific chemical structures or functionalities (Panda et al., 2009). There

is no universal ionization technique that can simultaneously ionize all compounds in crude oils,

hence, a comprehensive characterization requires a combination of various sources.

ESI targets large, low-volatile polar compounds that are readily protonated or

deprotonated in an electric field (Kujawinski, 2002). The interface between ESI source and

mass spectrometry was pioneered simultaneously by Fenn and Alexandrov (Alexandrov et al.,

1984; Yamashita and Fenn, 1984a, 1984b). Nowadays, ESI has become one of the most widely

used ionization techniques. Its work mechanism has been discussed in great details elsewhere

(Gaskell, 1997).

Briefly, ESI is achieved by applying a high voltage to an analyte dissolved in a polar

solvent, such as a mixture of toluene and methanol. The high voltage source establishes an

electric field between the needle and the plate with an inlet into FT-ICR-MS (Figure 1.4A). The

dissolved analyte is pumped through the needle forming a “Taylor cone” at the end of capillary

nozzle (Figure 1.4C). This cone is drawn to a filament, and produces charged droplets via a

budding process when the applied electrostatic force exceeds the surface tension (Figure 1.4C).

The droplets shrink rapidly due to the solvent evaporation, which is assisted by a heated

nebulizer gas, molecular nitrogen (Kogej and Schalley, 2006). Once the droplet reaches the

Rayleigh limit (the magnitude of charge outweighs the surface tension holding the droplet

together), it undergoes a Coulombic explosion or fission, producing smaller charged droplets

that subsequently undergo further evaporation.

Two major theories describe the creation of the fully desolvated gas-phase ions (Figure

1.4E): the charged residue model postulates that the repeated events of evaporation and

Coulombic fission ultimately lead to the creation (Dole et al., 1968); the ion evaporation model

assumes that the droplet breaks apart before complete desolvation due to the repulsion between

analyte ions and the other charges within the droplet (Iribarne and Thomson, 1976).

ESI can be operated in either negative or positive mode. In negative mode, ion is formed

through the loss of single or multiple labile hydrogen(s), thus, acidic compounds like carboxylic

acids are preferentially ionized (Table 1.1). Positive mode involves the formation of adducts

such as [M+H]+, enabling the ionization of basic compounds like pyridines or ketones (Table

1.1).

1.4.3 Fundamentals of atmospheric pressure photoionization

The APPI source was developed with the motivation to broaden the range towards less

polar molecules (Table 1.1) that are ordinarily not ionized by ESI (Hayen and Karst, 2003;

Robb et al., 2000; Syage et al., 2000). The original concept of APPI refers to the generation of

analyte ions directly from a vaporized liquid sample stream utilizing single photon ionization.

A molecule can absorb a photon of energy (hv) when this is above its ionization energy (IE)

(e.g., Eq. 1 in Table 1.2; Robb et al., 2000; Syage et al., 2000). Ultraviolet (UV) lamp is used

to emit photons that are high enough to ionize the target molecules (Figure 1.4B). The krypton

lamp is the most suitable source (Robb and Blades, 2008), since it delivers photons of 10.0 and

10.6 eV, well-above the IE of most organic molecules but below that of surrounding gases

(components of air: molecular nitrogen, water, molecular oxygen) and common solvents (such

as water, methanol and acetonitrile). Aromatic group is a good chromophore for absorbing UV,

hence, APPI is sensitive to aromatic compounds (Table 1.1). Non-polar compounds that do not

readily accept or donate a proton could be photon ionized, thus, dependency of APPI on the

acid-base chemistry is reduced (Robb and Blades, 2008). Ionization efficiency of the analyte

could be significantly enhanced if the bulk components of a vaporized sample stream besides

the analyte is photo-ionizable (Robb and Blades, 2008). Therefore, a de facto standard method

of APPI always includes the addition of a photoionizable reagent, i.e., a component of solvent

or a dopant species with IE lower than 10.0 or 10.6 eV such as toluene or acetone.

Operated in positive mode, the initial ionization reaction is the direct atmospheric

pressure photoionization of the analyte with IEs lower than 10.0 or 10.6 eV (Equation 1 in Table

1.2; Figure 1.4D). A component of solvent or a dopant species with IEs lower than 10.0 or 10.6

eV could also be photoionized forming protonated ions (e.g., Equation 2 in Table 1.2), which

subsequently serve as the reagents for the indirect ionization of analyte through proton transfer

or charge exchange. Proton could transfer from a reagent ion to a neutral analyte molecule with

higher proton affinity, forming protonated analyte ion (e.g., Equation 3 in Table 1.2). Besides,

if IE of the analyte molecule is less than that of the reagent, an electron can be transferred from

the analyte to a reagent radical cation generating a radical analyte ion (e.g., Equation 4 in Table

1.2). This charge exchange ionization is an efficient alternative for non-polar compounds poorly

ionized by proton transfer, which is a key feature that distinguishes APPI from ESI and

ultimately makes APPI the most universal ionization source (Robb and Blades, 2008).

Preliminary results of the negative APPI mode indicate that negative ions can be formed by

electron capture, charge exchange, proton transfer, or substitution (Kauppila et al., 2002). More

details on its ionization mechanism have been shown elsewhere (Kauppila et al., 2004b).

Within the framework of this thesis, APPI is equipped with 10.6 eV Krypton lamp. A

solvent mixture of methanol and n-hexane (9:1, v/v) was used to dilute the analyte, leading to

a dominance of protonated analyte ions when operated in positive mode (Kauppila et al., 2004a,

2002). Herein, n-hexane (IE: 10.13 eV) works as the photoionizable reagent to enhance the

ionization efficiency of the analyte.

Figure 1.4. (A and B) Simplified structures of ESI and APPI sources, modified from the Bruker

Daltonik User Manual; (C) droplet production in ESI operated under positive mode (Gaskell, 1997); (D)

ionization mechanism of APPI operated under positive mode, modified after https://uwaterloo.ca/mass-

spectrometry-facility/appi-supplementary-information; (E) major theories describing the creation of the

fully desolvated gas-phase ions in positive ESI mode.

Table 1.1. Comparison of the ionization ranges of ESI and APPI, after Huba et al. (2016). “V”

stands for successful ionization, while “-” marks non-ionizable species.

Compound Type

Elemental

Class

Response in

(-)-ESI

(+)-ESI

(+)-APPI

Nonpolar

Saturated Hydrocarbons

–

Polycyclic Aromatic Hydrocarbons (PAHs)

–

Sulfur PAHs: Dibenzothiophene

–

Polar

Nitrogen

PAHs

Pyridinic Nitrogen: Dibenzoacridine

–

Pyrrolic Nitrogen: Dibenzocarbazole

Oxygen PAHs: Dibenzofuran

–

Aliphatic Alcohols and Aldehydes

–

Aromatic Alcohols and Aldehydes

–

Aliphatic and Aromatic Ketones

–

Aliphatic Carboxylic Acids

–

Aromatic Carboxylic Acids

–

Phenol

–

Table 1.2. Important ionization processes occurred for the analyte [M], solvent [S] and dopant

[D] when APPI is operated in positive mode (Hanold et al., 2004; Kauppila et al., 2002; Klee et al.,

2013).

Process

Equation

Photoionization

M + hv → M

˙+

+ e

Equation 1

(D or S) + hv → (D˙+ + S˙+) + e- Equation 2

Proton Transfer M + ([D + H]+ or [S + H]+) → [M + H]˙+ + (D or S) Equation 3

Charge Transfer M + (D˙+ or S˙+) → M˙+ + (D or S) Equation 4

1.5 Applications of FT-ICR-MS in petroleum systems

Direct infusion FT-ICR-MS has been attempted to characterize a wide variety of

petroleum liquids. The precise mass provided by FT-ICR-MS allows for an accurate molecular

formula assignment via a statistical combination of the exact masses of various elements C, H,

O, N, S, V, Ni commonly found in petroleum fluids. These assigned compounds are generally

classified into different classes based on numbers of their contained heteroatoms, carbon atoms,

and double-bond equivalents (DBE, number of rings and double bonds), to facilitate exploration

and analysis of extensive information obtained. Functional groups that heteroatoms are bound

into can be further inferred based on the selectivity of ionization modes. ESI operated in

negative mode is the most widely used ionization source, and thus, the acidic and neutral

petroleum compounds have received extensive studies. The positive APPI mode can provide a

more comprehensive characterization, but its application has only recently attracted attention

(Huba et al., 2016). Moreover, chromatographic separation and/or chemical derivatization

followed by FT-ICR-MS have also been developed to allows the analysis of specific petroleum

compound class such as thiols, sulfoxides and ketones, although they have not been widely

promoted (Ren et al., 2019; Wang et al., 2018, 2016).

FT-ICR-MS enables the first-time molecular-level characterization of various high-

molecular-weight NSO compounds such as the highly alkylated, cyclized or aromatized

analogues, especially those comprising multiple heteroatoms. For instance, new

metalloporphyrins bearing extra and peripheral carbonyl, carboxyl, amino, thiophene, aryl,

cyclic, and alkyl substituents around the porphyrin nucleus were discovered (Liu et al., 2015a;

Putman et al., 2014; Qian et al., 2008; Zhao et al., 2013; Zheng et al., 2018). Different origins

have been proposed for these oxygen, nitrogen and sulfur heteroatoms: carbonyl and carboxyl

groups might be parts of the original tetrapyrrole pigments; amino group could be protein

fragments; thiophene structure possibly derives from pyrolytic release of kerogen (e.g., Liu et

al., 2015a; Zhao et al., 2015). In addition, studies on the naphthenic acids were extended from

the classical type like acyclic and cycloaliphatic monocarboxylic acids to the compounds

containing aromatic rings and extra N, S, O substituents (Ajaero et al., 2016; Barrow et al.,

2009; Headley et al., 2009; Tomczyk et al., 2001).

NSO compounds characterized by FT-ICR-MS have been proven valuable in

reconstructing palaeoecology and palaeoenvironment (Cui et al., 2014; dos Santos Rocha et al.,

2018a; Li et al., 2011; Melendez-Perez et al., 2020; Orrego-Ruiz et al., 2020; Wan et al., 2017),

understanding the geological processes happened after diagenesis such as thermal maturation

(e.g., Noah et al., 2020; Oldenburg et al., 2014; Poetz et al., 2014), petroleum expulsion,

migration (Han et al., 2018b, c; Hosseini et al., 2017; Liu et al., 2015b; Pan et al., 2019; Ziegs

et al., 2018), biodegradation (e.g., Kim et al., 2005; Liao et al., 2012; Oldenburg et al., 2017;

Pan et al., 2017, 2013), thermal sulfate reduction (Walters et al., 2011; Walters et al., 2015),

and characterizing the chemical/physical properties of petroleum liquids like nitrogen, sulfur,

vanadium, nickel contents, acidity or American Petroleum Institute gravity (Corilo et al., 2016;

Hur et al., 2010; Kim et al., 2016; Muller et al., 2012; Terra et al., 2017; Vaz et al., 2013).

Herein, studies that utilize FT-ICR MS to investigate the impact of biomass input,

depositional environment, and lithofacies (by controlling the expulsion- and migration-related

fractionation) on the heavy NSO inventories in rock bitumen and crude oils were introduced in

detail.

1.5.1 Precursor biotic and palaeoenvironmental signatures

Many attempts have been made to unravel the palaeocological and palaeoenvironmental

information documented by sedimentary heavy NSO compounds utilizing FT-ICR-MS.

Some NSO features have been associated with the varying kerogen types. In conventional

crude oils and mature rock extracts associated with kerogen of type I to III, Wan et al. (2017)

observed an increasing abundance and aromaticity of acidic organooxygen compounds as well

as a narrower carbon number range of neutral N1 class. In addition, Ziegs et al. (2018)

documented a stronger even-over-odd carbon number preference of the negative ESI accessible

C20–C30 monocarboxylic acids in the immature-mature rock bitumen associated with type II/III

kerogen, in comparison with those related to type II kerogen.

Some NSO characteristics were found to be sensitive to specific depositional settings and

OM input. For instance, the marine crude oils were observed to be distinguished from the

lacustrine ones by their more abundant neutral S1N1 class (Orrego-Ruiz et al., 2020), lower

S1O1/S1 index, higher S2/S1 ratio (Li et al., 2011), as well as, narrower carbon number range

and higher aromatization degree of organosulfur classes (Wu et al., 2019). Besides, substantial

neutral Ny compounds were primarily detected in the crude oils and mature rock bitumen

associated with lacustrine settings, whereas acidic Ox compounds were found to be more

abundant in those related to marine settings (Cui et al., 2014; dos Santos Rocha et al., 2019,

2018a; Ke et al., 2018; Melendez-Perez et al., 2020). In addition, in oils associated with

brackish lacustrine, neutral organonitrogen compounds were found to be more enriched when

compared to those related to alkaline lacustrine (Zhang et al., 2020). Moreover, the ratio of the

negative ESI accessible C27 and C29 DBE4 O1 compounds with assumed structures as sterols

could differentiate marine and terrestrial OM input (Orrego-Ruiz et al., 2020). Furthermore,

redox depositional environment was considered to impose a further impact on abundances of

the negative ESI ionizable O1 and O2 compounds (Orrego-Ruiz et al., 2020).

However, the associations between NSO composition and palaeoecology or

palaeoenvironment were sometimes proposed based only on observations of a series of

geological samples (always limited in number), no further explanations in terms of the structure,

habitat, and preservation pathways of biomass were given to rationalize these correlations. In

addition, these involved samples are primarily conventional crude oils and mature rock extracts,

whose initial hetero-compound composition determined by origin (i.e., palaeoecology and

palaeoenvironment) has already been altered by maturation, expulsion, migration and in-

reservoir alterations. On the one hand, a deconvolution in terms of biological and

paleoenvironmental features might be impeded. On the other hand, the influence of these

geological factors on NSO compounds might be misinterpreted as precursor biological and

paleoenvironmental signatures.

1.5.2 Expulsion- and migration-related fractionation

The compositional changes of acidic and neutral high-molecular-weight NSO compounds

during expulsion and migration has only been investigated in a few nature petroleum systems

or simulation experiments utilizing (–)-ESI FT-ICR-MS (Han et al., 2018b, c; Hosseini et al.,

2017; Liu et al., 2015b; Mahlstedt et al., 2016; Pan et al., 2019; Zhang et al., 2019, 2018). The

fractionation was elucidated by the molecular-level analysis of the residual soluble OM in

source rock (Ziegs et al., 2018) and its comparison with the reservoired or produced crude oils

(Han et al., 2018b, c; Mahlstedt et al., 2016; Pan et al., 2019; Zhang et al., 2019), as well as, the

comparison of crude oils in different reservoirs along migration routes (Liu et al., 2015b). Han

et al. (2018c) recorded that Ny compounds were preferentially retained in the biogenic quartz-

rich Barnett source rocks, whereas NyOx compounds were preferably expelled out. Mahlstedt

et al. (2016) observed a preferential expulsion of N1O1 and N1 compounds with lower DBE

values and higher carbon numbers from the clay-rich Posidonia Shale. These observed changes

regarding the compound class, carbon number and DBE distributions were associated with

fractionation based on the type and accessibility (steric hindrance induced by alkylation) of

molecular active sites (i.e., heteroatomic functional groups), as well as, the size of molecular

aromatic core structure (e.g., Han et al., 2018c; Mahlstedt et al., 2016).

1.5.3 Fractionation on distinct mineral surfaces

Present knowledge concerning the fractionation of the high-molecular-weight NSO

compounds during expulsion and migration in nature petroleum systems is still limited. The

fractionation of petroleum compounds on a variety of rock surfaces or mineral surfaces (such

as silica, calcite, bentonite and kaolinite) has been properly documented in laboratory step-wise

sequential extraction experiments utilizing FT-ICR-MS in distinct ionization modes, recorded

as the compositional changes in compound class, DBE, and carbon number distributions (e.g.,

Chacón-Patiño et al., 2015; Nascimento et al., 2016; Pinto et al., 2017; Villabona-Estupiñan et

al., 2020; Wicking et al., 2020; Zeng et al., 2020). These laboratory simulations show

differences in fractionation on distinct surfaces, for instance, fractionation on bentonite and

kaolinite surfaces was found to differ from that occurring on silica and alumina surfaces by a

preferential adsorption of basic organonitrogen compounds (Villabona-Estupiñan et al., 2020).

1.6 Research objectives and outline

The OM in sedimentary rocks that is soluble in common organic solvents, widely referred

to as bitumen, comprises a complex mixture of NSO compounds and hydrocarbons.

Organonitrogen compounds are believed to almost exclusively originate from biological

precursors (Vandenbroucke and Largeau, 2007). In contrast, organosulfur compounds are

widely accepted to be primarily formed from the abiotic incorporation of inorganic sulfur into

appropriately functionalized biomolecules during early diagenesis (e.g., Anderson and Pratt,

1995; Damsté and de Leeuw, 1990b; Schouten et al., 1994; Tissot and Welte, 1984).

Organooxygen compounds are thought to be preserved from precursor biomolecules or partly

from the oxidation during or after diagenesis (e.g., reviewed by Volkman, 2006). Therefore,

organic NSO compounds are intrinsically well suited to record the inherent biomass signal, to

document the physicochemical and biochemical conditions of deposition, and to track the

processes that have been active since deposition. Moreover, the physical properties of organic

NSO compounds lead to their enhanced capabilities for interactions with mineral surfaces (e.g.,

Barker, 1989; Brother et al., 1991; Carlson and Chamberlain, 1986; Tannenbaum et al., 1986).

Since distinct minerals have different surface chemistry, the compositional changes of organic

NSO compounds associated with petroleum formation such as during expulsion and migration

might be linked to the lithofacies of petroleum systems (Adams, 2014; González and Moreira,

1994).

The molecular-level characterization of organic NSO compounds has long been restricted

to the low-molecular-weight fractions < 500 Da largely because of mass resolution limitations

for the common organic geochemistry workhorse, GC-MS. Ultrahigh resolution FT-ICR-MS,

while less commonly utilized, enables a much broader molecular-weight range of NSO

compounds (200–1200 Da) to be analyzed. The precise mass provided by FT-ICR-MS allows

for an accurate molecular formula assignment via a statistical combination of the exact masses

of various elements C, H, O, N, S, V, Ni commonly found in rock bitumen. The composition

of complex composite rock bitumen can be deconvoluted. Thousands of peaks can be

unequivocally assigned in one single mass spectrum. These assigned compounds are generally

classified into different classes based on numbers of their contained heteroatoms, carbon atoms,

and DBE, to facilitate the exploration and analysis of extensive information and to glean

meaningful patterns and trends. Further structural discussions of the detected species are only

speculative based on the unambiguous molecular formulas and the selectivity of ionization

modes, since FT-ICR-MS data cannot distinguish isomers.

The composition of NSO compounds obtained by FT-ICR-MS has provided new insights

into the processes that take place after diagenesis, namely thermal maturation (e.g., Noah et al.,

2020; Poetz et al., 2014), petroleum expulsion, migration (e.g., Han et al., 2018b; Mahlstedt et

al., 2016; Pan et al., 2019), and in-reservoir alteration (e.g., Liao et al., 2012; Oldenburg et al.,

2017; Walters et al., 2015). Yet, there are still major gaps in our understanding as to how these

compounds originated in the first place, because most FT-ICR-MS studies to date have been

conducted principally on conventional crude oils or source rock bitumen (e.g., dos Santos

Rocha et al., 2018a; Orrego-Ruiz et al., 2020; Wan et al., 2017), whose organic NSO inventories

have been affected by the aforementioned processes.

Moreover, even though the geo-chromatographic fractionations of organic heavy NSO

compounds during expulsion and migration have been elucidated in several nature petroleum

systems using FT-ICR-MS, the potential impacts of lithofacies were not identified. Systematic

studies on the partition behavior of high-molecular-weight NSO compounds between oil and

mineral phases, i.e., the extent of retention on distinct rock surfaces or mineral surfaces such as

silica, calcite, bentonite and kaolinite, are still lacking and have only been documented in

laboratory experiments (Chacón-Patiño et al., 2015; Nascimento et al., 2016; Pan et al., 2019;

Pinto et al., 2017; Villabona-Estupiñan et al., 2020; Wicking et al., 2020; Zeng et al., 2020).

Additionally, most FT-ICR-MS studies on the sedimentary NSO compounds have been

conducted exclusively on the acidic compounds using ESI in negative ion mode. A

comprehensive characterization requires a combination of different ionization techniques such

as ESI and APPI. The negative ESI, positive ESI, and positive APPI modes preferentially ionize

the acidic, basic, and low-polarity compounds, respectively.

To better understand how biological precursors, palaeoenvironment and lithofacies have

strongly influenced the high-molecular-weight NSO compounds in sedimentary rocks, the main

questions addressed within the scope of this thesis are:

(1) How does marine algae, terrestrial higher plants, and lacustrine algae like

Botryococcus braunii control the composition of organooxygen and

organonitrogen compounds in immature sedimentary rocks?

(2) Which type of information about palaeoecology and palaeoenvironment is

recorded by organosulfur compounds in immature sedimentary rocks?

(3) How does the mineral phase of the source/host rocks, e.g., biogenic carbonate,

biogenic quartz or detrital clay, influence the fractionation of NSO compounds

during petroleum expulsion and migration?

This cumulative thesis addresses the above-mentioned objectives in chapters 2, 3 and 4.

In Chapter 2–Precursor biotic signatures in organonitrogen and organooxygen compounds

of immature rocks–high-molecular-weight organooxygen and organonitrogen compounds Ox,

Ny, NyOx in solvent extracts of rocks with different geological histories were characterized by

FT-ICR-MS using a combination of ESI (negative ion mode) and APPI (negative and positive

ion modes). The analyzed natural laboratories are the Paleogene marine Dynow and Schöneck

formations (the Molasse Basin, Austria), the Lower Jurassic marine Posidonia Formation (the

Lower Saxony Basin, Germany), the Lowermost Cretaceous lacustrine Wealden Formation (the

Lower Saxony Basin, Germany), the Paleogene terrestrial Waikato and Brunner coal measures

(the Waikato and West Coast basins, New Zealand), which are in the late diagenetic or early

catagenetic stages.

The obtained characteristics of Ox, Ny, NyOx compounds were correlated with the

biological source indicators based on hydrocarbons (like regular steranes/homohopanes,

Ster/Hop) and low-molecular-weight heteroatomic compounds (such as phenol) in rock extracts

or pyrolyzates. Thereafter, these features were associated with the preservation potentials and

pathways of oxygen- and/or nitrogen-bearing biomolecules that are contained in distinct

biomass in variable proportions.

The coals as the in-situ deposits of terrestrial plants consist predominantly of aromatic

polyoxygenated Ox and N1Ox compounds, representing the degradation products of lignin and

tannin (such as phenolic ketones and phenolic carboxylic acids) as well as their condensation

products with the protein degradation intermediates. Aliphatic Ox moieties originated from the

plant protective substances principally the waxes and cutan show a pronounced even or odd

carbon number predominance in the long-chain C23–C33 range, whereas marine and lacustrine

microbial communities contribute abundant middle-chain C22, C24 or C23, C25 homologs. The

marine rock extracts are furthermore characterized by high amounts of organonitrogen

compounds especially the N2 and N2Ox classes, interpreted as signatures of protein-rich marine

biomass that are preserved via a degradation-recondensation pathway. The selectively

preserved highly aliphatic algaenan characterizes the lacustrine Botryococcus braunii input by

substantial organooxygen and organonitrogen compounds containing more than 40 carbon

atoms.

In Chapter 3–Biotic and palaeoenvironmental signatures in organosulfur compounds of

immature rocks–elemental and molecular composition of high-molecular-weight organosulfur

classes (Sz, SzOx, SzNy, SzNyOx) in solvent extracts of the aforementioned immature to early-

mature marine and lacustrine rock samples were analyzed by FT-ICR-MS measurements

combined with ESI and APPI. Their characteristics were correlated with the palaeoecological

and palaeoenvironmental indicators based on hydrocarbons and small heteroatomic compounds

such as dibenzothiophene or dimethylthiophenes in rock extracts or pyrolysates. Noticeably,

OSCs containing a specific number of carbon atoms and DBE show up as a strong enrichment,

which was associated with the selective preservation of the carbon skeletons of some

appropriate labile biomolecules via sulfurization. Their preserved information was

deconvoluted to achieve palaeoecological and palaeoenvironmental details that might not be

documented by the other biomarkers.

The prevailing iron-deficient sulfidic depositional settings of the Schöneck and Posidonia

formations are characterized by abundant organosulfur compounds bearing up to two sulfur

atoms. Moreover, the high ratios of reduced versus oxidized forms (Sz versus SzOx) further

illustrate that small amounts of oxidants were present at the oxic-anoxic interfaces. In addition

to abiotic source, some oxygen atoms in the organosulfur compounds are of biogenic origin.

Terrestrial plants contain the highest proportions of multi-oxygen bearing compounds that can

be sulfurized such as the polyoxygenated aromatic breakdown products of plant lignin and

tannin, followed by marine organisms, and finally lacustrine organisms, as illustrated by the

decreasing average oxygen number of S1Ox compounds. In contrast, the lacustrine organisms

comprise the most abundant sulfurizable aliphatic moieties, followed by marine organisms and

higher plants, as documented by the decreasing ratios of aliphatic versus aromatic organosulfur

compounds. Nitrogen-containing organosulfur compounds SzNy and SzNyOx solely found in the

marine rock extracts might be specific for the marine biomass which contain significantly high

amounts of sulfurizable proteinaceous moieties, since organosulfur compounds related to the

lacustrine and terrestrial settings contain exclusively SzOx and/or Sz classes.

The observed prominent enrichment of Sz and SzOx compounds containing 25, 30, 35 and

40 carbon atoms were associated with the selective and efficient preservation of C25, C30 HBI

polyenes, C30 unsaturated tetracyclic polyprenoid alcohols, C35 bacteriohopanepolyols, and C40

carotenoids via sulfurization. The strong enrichment of sulfurized C35 bacteriohopanepolyols

can be developed as an indicator of the low levels of oxygen exposure prior to sulfurization,

which occur only in the Dynow and Schöneck formations. The prominent enrichment of

sulfurized carotenoids is generally associated with high primary productivity. While the

strongly enriched sulfurized HBI polyenes in the Upper Schöneck Formation is indicative for

diatom blooms, the precursors of C30 pentacyclic polyprenoid organosulfur compounds are

more abundant in fresh/brackish water algae.

In Chapter 4–Impact of lithofacies on composition of heteroatomic compounds in residual

and expelled fluids of mature rocks–acidic and low-polarity heavy NSO compounds in solvent

extracts of source rocks from unconventional petroleum systems with the three globally most

significant lithofacies, namely the biogenic carbonate-rich Niobrara Shale, the biogenic quartz-

rich Barnett Shale and the detrital clay-rich Posidonia Shale, were characterized by FT-ICR-

MS measurements. These chosen sample sets all contain abundant marine type II kerogen in

the peak–late oil window, having experienced intensive petroleum expulsion, thus, variations

in the retained NSO compounds among these three source rock series were primarily linked to

the distinct retention behavior of compounds on different mineral phases during petroleum

expulsion. Solvent extracts of the siliciclastic Barnett and Posidonia shales reveal higher

proportions of NSO compounds versus hydrocarbons in comparison with the carbonate

Niobrara extracts, confirming their generally higher retention capacities for the polar organic

compounds. However, different retention specificities of biogenic quartz- and clay-rich rocks

are shown: in the Barnett extracts the enrichment of organonitrogen compounds might be the

consequence of a preferential preservation and retention through steric encapsulation and

adsorption by biogenic quartz, whereas high abundances of more polar acidic organooxygen

compounds in the Posidonia extracts might be related to their high adsorption affinities towards

clay mineral surfaces.

Within the Barnett and the Niobrara unconventional systems, there are variations

respectively in content of porous siliceous and calcareous fossil skeletons that can provide

petroleum storage space, thus, intra-formation migration occurred. While the three Posidonia

samples all come from the source rock units, the Barnett and Niobrara sample sets also each

include one sample from the intra-reservoir units enabling the investigation of lithofacies’

impact on migration (biogenic quartz- versus carbonate-rich). The compositional differences

between solvent extracts of the reservoir and the source could to some extent record the

migration-induced fractionations occurred within a petroleum system. Between the Barnett and

the Niobrara systems, the migration-induced fractionations of the low-polarity or acidic NSO

compounds display distinctions. For instance, while the highly alkylated small acidic NSO

molecules preferably migrate out of the Niobrara source rock units, the acidic NSO compounds

irrespective of their molecule size and alkylation degree are all strongly retained in the Barnett

source showing no fractionation. Besides, the low-polarity organonitrogen compounds are also

found to be retained to a greater extent in the Barnett source rock units when compared to the

Niobrara source rock units.

2 PRECURSOR BIOTIC SIGNATURES IN

ORGANONITROGEN AND ORGANOOXYGEN

COMPOUNDS OF IMMATURE ROCKS1

2.1 Abstract

To reveal the impact of biomass input (marine algae, terrestrial plants and lacustrine

Botryococcus braunii) on the composition of high-molecular-weight organooxygen and

organonitrogen compounds (Ox, Ny and NyOx), solvent extracts of immature–early mature rock

samples were systematically characterized by Fourier transform ion cyclotron resonance mass

spectrometry (FT-ICR-MS) in different ionization modes. In total, 16 samples from the marine

Dynow, Schöneck, Posidonia formations, the lacustrine Wealden Formation and the terrestrial

Waikato and Brunner coal measures were investigated.

Coals as the in-situ deposits of terrestrial plants consist to a great degree of aromatic

polyoxygenated Ox and N1Ox compounds, representing the degradation products of lignin and

tannin like phenolic ketones and phenolic carboxylic acids as well as their condensation

products with the degradation intermediates of labile organonitrogen biomolecules (mainly

proteins). Aliphatic Ox moieties derived from the plant protective substances principally the

waxes and cutan show a pronounced even or odd carbon number predominance of the C23–C33

compounds with C26, 28, 30 or C27, 29, 31 as the major homologs. In contrast, marine and lacustrine

microbial communities contribute plentiful middle-chain C22, C24 or C23, C25 compounds. The

marine rock extracts are furthermore characterized by abundant organonitrogen compounds,

especially N2 and N2Ox classes, interpreted as signatures of protein-rich marine algae that were

successfully preserved via a degradation-recondensation pathway, whereas the low protein

content of the lacustrine Botryococcus braunii is reflected by a low amount of N1Ox and N1

classes. The highly aliphatic algaenan of Botryococcus braunii sterically protected its oxygen-

bearing groups from degradation, leading to a great abundance of Ox compounds, moreover, it

1This chapter has been published as: Huiwen Yue, Andrea Vieth-Hillebrand, Shengyu Yang, Hans-Martin Schulz,

Brian Horsfield, Stefanie Poetz, 2022. The retention of precursor biotic signatures in the organonitrogen and

organooxygen compounds of immature fine-grained sedimentary rocks. International Journal of Coal Geology,

259, 104039, (postprint), https://doi.org/10.1016/j.coal.2022.104039.

characterizes the Botryococcus braunii source by substantial heteroatomic compounds

containing more than 40 carbon atoms.

2.2 Introduction

The organic matter (OM) in sedimentary rocks comprises a complex physicochemical

mixture of components, including a wide variety of organonitrogen, organosulfur and

organooxygen compounds. While organonitrogen compounds are believed to almost

exclusively originate from biological precursors (Vandenbroucke and Largeau, 2007), it has

been widely accepted that organosulfur compounds are commonly formed from the abiotic

incorporation of inorganic sulfur like H2S into OM during diagenesis (e.g., Damsté and de

Leeuw, 1990b; Tissot and Welte, 1984). The organooxygen compounds can be preserved from

precursor biomolecules or partly from the introduction of oxygen during or after diagenesis

(e.g., Behar and Albrecht, 1984; Eglinton and Hamilton, 1967; Ioppolo-Armanios, 1996). In

this paper, biomass sourced organooxygen and organonitrogen compounds are targeted.

Depositional and ecological conditions that bring about enhanced primary productivity

and/or preservation by stagnation are the prerequisites for the formation of organic-rich

sediments (Tissot and Welte, 1984). Through the classical neogenesis pathway, products of the

readily decomposed biomolecules such as carbohydrates and proteins undergo condensation

reactions, thereby progressively forming randomized stable organo-chemical structures that

escape mineralization in the water column and in sediments (del Rıo et al., 2004; Huc, 1980;

Tissot and Welte, 1984). Besides, selective preservation occurs for the insoluble and protected

biomacromolecules such as algaenan in the cell walls of some algae or cutan in the protective

layers of some higher plants, which exhibit a high resistance to chemical or bacterial

degradation (de Leeuw and Largeau, 1993; Goth et al., 1988; Gupta, 2015; Tegelaar et al., 1989).

Moreover, in-situ polymerization of labile aliphatic organic compounds in the case of fossil

insects and plants, e.g., plant waxes, was invoked as an alternative process (Gupta, 2015, 2007a,

2007b; Mösle et al., 1998; Stankiewicz et al., 2000). Less than 1% of these biomass entered the

sedimentary carbon cycle (Tissot and Welte, 1984), and over 90% of sedimentary OM are

present as non-hydrolyzable macropolymers kerogen (de Leeuw and Largeau, 1993) that are

insoluble in conventional organic solvents and produce petroleum upon catagenesis (Tissot and

Welte, 1984).

Amino acids as building blocks of proteins are the principal nitrogen-bearing structures

in living organisms, and thus protein-rich organisms usually have relatively high atomic N/C

ratios (Baxby et al., 1994). Proteins dominate bacteria (around 50 wt.%) and marine plankton

(up to 50 wt.% or more), whereas they account for only 3 wt.% or less (sometimes up to 10

wt.%) in higher plants (Baxby et al., 1994). The nitrogen-containing biomolecules other than

proteins, e.g., porphyrins, nucleic acids, and alkaloids, found in distinct organisms like higher

plants, plankton and bacteria just make a neglectable contribution to the sedimentary organic

nitrogen (each < 1%, Baxby et al., 1994). Nitrogen atoms (atomic N/C = ca. 0.005–0.03) are

usually in low abundance in kerogen (Tissot and Welte, 1984). Their amount appears to be

highly dependent on organic facies, but the correlations have not been well established (Durand

and Monin, 1980; Kelemen et al., 2007). Pyrrolic and pyridinic nitrogen represent the major

organonitrogen structures in sedimentary rocks. They are either consolidation products of the

protected labile and hydrolyzable nitrogen species, or source from degradation of porphyrins,

alkaloids, and tryptophan (e.g., Bakel and Philp, 1990; Bennett et al., 2004b; Simoneit et al.,

1971; Snyder, 1965; Vandenbroucke and Largeau, 2007). On a molecular scale, the commonly

occurring C0–C6 carbazoles and C0–C2 benzocarbazoles are the most investigated sedimentary

neutral organonitrogen compounds. Their abundances and distributions (e.g., compositional

variations in benzocarbazole or alkylcarbazole isomers) have been shown to respond to the

changes in source organic input and depositional conditions (Bakr, 2009; Bakr and Wilkes,

2002; Bennett and Olsen, 2007; Clegg et al., 1997), knowing that substantial controls can also

be imposed by maturity, migration, and biodegradation (e.g., Clegg et al., 1998; Fedorak and

Westlake, 1984; Li et al., 1995). Data about pyridinic compounds are rather rare due to their

challenging chemical isolation (Li and Larter, 2001). A ratio of 2-ring to 3-ring azaarenes was

proposed to differentiate between marine and non-marine sediments (Yamamoto et al., 1991).

Higher land plants are largely composed of cellulose (30–50%) and lignin (15–25%) and

thus have high oxygen contents (Baxby et al., 1994; Tissot and Welte, 1984). Cellulose is

preferentially degraded and lost during early diagenesis, while lignin, an aromatic wood

biopolymer, is selectively preserved (Hatcher and Clifford, 1997; Hatcher et al., 1982; Stout et

al., 1988; Tegelaar et al., 1989). Besides, plant biomacromolecules like tannin, sporopollenin,

cutan, suberan, cutin and suberin can also partly escape degradation (de Leeuw and Largeau,

1993; Tegelaar et al., 1989). Highly aliphatic algaenan also exhibits a high resistance to

degradation and thus provides a steric protection for its oxygen-bearing groups (Metzger and

Largeau, 1999). The algaenan-producing organisms would rarely be a major constituent of

marine phytoplankton; most of them belong to the Chlorophyceae like lacustrine Botryococcus

braunii (Derenne et al., 1992; Gelin et al., 1999; Vandenbroucke and Largeau, 2007). Oxygen

in the type I kerogen is present mainly as ester and ether group. In contrast, ketone and

carboxylic acid groups are more important in the type II kerogen than in the type I kerogen and

ester bonds are also abundant (Fester and Robinson, 1966; Siskin et al., 1995; Tissot and Welte,

1984). Phenols, quinones and aromatic acids are the main oxygen-bearing functional groups in

the classical type III kerogen derived essentially from terrestrial plants (Behar and

Vandenbroucke, 1987; Petersen et al., 2008; Robin and Rouxhet, 1978; Tissot and Welte, 1984).

Organic oxygen has been recorded to be less abundant in the type II kerogen than in the type

III kerogen (with initial atomic O/C ratio as high as 0.2 or 0.3), but more abundant than in the

type I (< 0.1) (Gupta, 2014; Tissot and Welte, 1984). On a molecular level, saturated or

monoaromatic organooxygen compounds such as carboxylic acids, ketones, aldehydes or

phenols have been studied, which could directly originate from biological precursors, or (at

least partly) from abiotic or biotic transformations (e.g., Bastow et al., 2005; Behar and Albrecht,

1984; Eglinton and Hamilton, 1967; Ioppolo-Armanios, 1996). Among polyaromatic

compounds, only the non- or lowly- alkylated species containing four or less rings like C0–C2

dibenzofurans have been analyzed at the molecular level. Most of them are formed from non-

specific precursors via abiotic or biotic transformation without direct biological precursors

(exceptions are, for example, xanthone and dibenzofuran; Bennett and Larter, 2000; Oldenburg

et al., 2002; Peres et al., 2000; Radke et al., 2000; Wilkes et al., 1998b). Even though the major

components of terrestrial plants such as lignin comprise oxygen-bearing aromatic structures,

they breakdown into smaller moieties unspecifically and thus direct precursor-product

relationships are difficult to infer (Armstroff et al., 2007).

Sedimentary high-molecular-weight heteroatomic compounds such as the highly

alkylated, cyclized or aromatized analogues can be successfully characterized on the molecular

level using FT-ICR-MS. In crude oils and rock extracts associated with kerogen of type I to III,

Wan et al. (2017) observed an increasing abundance and aromaticity of acidic organooxygen

compounds as well as a narrower carbon number range of neutral N1 class. While a substantial

fraction of neutral Ny compounds was found in lacustrine oils, acidic Ox compounds were more

abundant in marine oils (Cui et al., 2014; dos Santos Rocha et al., 2019, 2018a; Melendez-Perez

et al., 2020); similar trends have also been reported for rock extracts (Ke et al., 2018). However,

these studies are restricted to the acidic and neutral compounds accessible by electrospray

ionization (ESI) in negative ion mode (Figure S2.1). Besides, these samples were conventional

crude oils or mature rock extracts, and thus, maturation, expulsion, migration and in-reservoir

alterations may have already altered the hetero-compound composition (e.g., Han et al., 2018b,

2018c; Hosseini et al., 2017; Liao et al., 2012; Liu et al., 2015b; Poetz et al., 2014; Yue et al.,

2021) impeding a deconvolution in terms of their origin, i.e., the biomass input.

In the current study, we elucidate the contrasting compositions of organooxygen and

organonitrogen compounds in 16 solvent extracts of immature to early-mature source rocks

with different kerogen types (I–III) deposited in broadly different depositional settings (marine,

lacustrine and terrestrial) of variable geological ages from Jurassic to late Eocene. A

combination of negative ESI, positive ESI as well as positive APPI (atmospheric pressure

photoionization) was applied to achieve a more holistic portrait of heteroatomic compounds.

Positive ESI preferentially ionizes basic compounds (e.g., pyridines) and ketones, whereas

APPI extends the range towards less polar compounds (Figure S2.1).

2.3 Sample Description

2.3.1 Marine Schöneck and Dynow formations in the Molasse Basin

The Molasse Basin is an asymmetric foreland basin, extending along the northern margin

of the Alps from France to the eastern border of Austria (Figure 2.1C; Roeder and Bachmann,

1996; Sissingh, 1997). The Schöneck and Dynow formations of the Eocene–Oligocene age

were deposited in marine to brackish settings: an increased continental run-off since the

deposition of the Upper Schöneck Formation finally led to the brackish depositional condition

of the Dynow Marlstone (Schulz et al., 2004, 2002). Both formations are consistently immature

(huminite/vitrinite reflectance Ro < 0.35%; Figure 2.1C, Table 2.1; Schulz et al., 2002) and

bituminite-rich (Schulz et al., 2004, 2002) in the well Oberschauersberg 1. A very minor

proportion of detrohuminite and inertodetrinite is observed in the Lower Schöneck Formation

(about 1 vol.% of total visible OM), whereas fairly constant amounts of lamalginite (about 2–4

vol.%) are present in most black shales of the Upper Schöneck Formation (Schulz et al., 2002).

Within the Dynow Marlstone, a slight but progressive input of terrestrial organic material is

recorded: alginate and detrohuminite represent over 5 vol.% of total visible OM in the upper

part (Schulz et al., 2004). The marlstones M3 and M1 are respectively from the Lower Schöneck

Formation and the upper part of the Dynow Marlstone, while the carbonate-free claystone M2

belongs to the Upper Schöneck Formation (Table 2.1; Yang and Schulz, 2019).

Figure 2.1. Regional maps displaying the study areas for the (A) Wealden Formation (well EX-

A), (B) Posidonia Shale (boreholes Wenzen and Wickensen), (C) Schöneck and Dynow formations

(borehole Oberschauersberg 1) and (D) Waikato and Brunner coal measures (Reefton and Rotowaro

coalfields), modified after Blumenberg et al. (2019), Klaver et al. (2012), Jochum et al. (1995), Yang

and Schulz (2019) and Vu (2008). The black lines mark the borders between different countries in (A)

and (C).

2.3.2 Marine Posidonia Formation in the Lower Saxony Basin

During the Early Jurassic, present-day western and central Europe was located on the

Laurussian continental shelf (Ziegler, 1988). This shallow shelf area comprised multiple islands

of variable size, submarine sills and deeper subbasins (Ziegler, 1988). Deposition of the Lower

Toarcian Posidonia Shale in the Hils syncline area of the Lower Saxony Basin (LSB) in

northwest Germany (Figure 2.1B) was initiated after a widespread transgression (Littke et al.,

1991). It displays a threefold stratigraphic subdivision: lower marlstone, middle calcareous

shale with bivalve shells, and upper calcareous shale. Alginite B (with liptodetrinite) derived

from small phytoplankton is the most abundant maceral in all Posidonia units of wells Wenzen

(0.48% Ro) and Wickensen (0.53% Ro). Less abundant are bituminite, large alginitic

phytoplankton (alginite A) of Tasmanales and Leiosphaeridales types, and terrestrially derived

vitrinite, inertinite and sporinite (Littke et al., 1991, 1988). The sample P1 is selected from the

well Wenzen belonging to the lower unit of the Posidonia Shale, whereas the samples P2 and

P3 are collected from the well Wickensen belonging to the middle and lower units, respectively

(Table 2.1, Figure 2.1B).

Table 2.1. Geological background information, huminite/vitrinite reflectance (Ro), and total

organic carbon content (TOC), summarized from Vu (2008), Rippen et al. (2013) and Yang and Schulz

(2019). “/”: no available data.

Sample

G-number

Formation/

Coal Measures

Age Basin Settings

Depth

(m)

TOC

(wt.%)

Ro (%)

G010272

Wealden Berriasian

Lower Saxony

Lacustrine

833.3

1.7

0.50–0.60

G010299

917.0

3.8

G010302

919.3

4.7

G010317

972.8

9.3

G010319

974.6

8.1

G010322

994.9

4.5

G010324

997.3

3.6

G000420

Posidonia Lower

Toarcian

Marine

0.48

G007144

46.5

10.1

0.53

G007156

58.2

9.9

G015912

Dynow

Eocene-

Oligocene Molasse

1378.6

1.5

< 0.35

G015917

Upper Schöneck

1385.8

7.3

G015918

Lower Schöneck

1389.4

2.6

NZ1

G001981

Waikato

Eocene

Waikato

Terrestrial

61.2

0.45

NZ2

G001996

Brunner West Coast

65.5

0.52

NZ3

G001997

67.4

0.52

2.3.3 Lacustrine Wealden Formation in the Lower Saxony Basin

The Berriasian Wealden Formation in the LSB can be lithostratigraphically subdivided

into six zones, Wealden 1–6 (Elstner and Mutterlose, 1996). In the central basin of the LSB,

there was a shift from a freshwater-dominated lacustrine system (Wealden 1) towards more

brackish condition (Wealden 2–4) (Figure 2.1A; Schneider et al., 2019), in the latest Berriasian

(Wealden 5–6), marine influence intensified. Well EX-A targeted the Wealden facies with Ro

values between 0.50 and 0.60% (Figure 2.1A, Table 2.1; Rippen et al., 2013). Four depth

intervals are characterized by varying depositional environments (1029–1058m, deep lacustrine;

966–998m, deep lacustrine; 910–928m, sublittoral lake; 831–850m, deep marine; Ziegs, 2013).

The middle two depth intervals represents the unit Wealden 3, and the intervals which are

stratigraphically higher or lower are respectively from younger and older units (Rippen et al.,

2013). Homogeneous kerogen of lacustrine origin are contained in the middle–lower depth

intervals (910–1058 m); OM in the uppermost interval is more heterogeneous and less stable,

but still of lacustrine origin (Ziegs et al., 2015). OM in all depth intervals consist predominantly

of telalginite derived from lacustrine Botryococcus braunii and lamalginite (Rippen et al., 2013).

Other macerals in particular vitrinite and inertinite are rare, but fossil shells and fish remains

are sometimes abundant (Rippen et al., 2013). Seven samples (W1–W7) collected from the

upper–middle non-calcareous shale/marlstone intervals (Table 2.1) were deposited in

freshwater/brackish lacustrine setting with intercalations of only short-lived marine

transgressions (e.g., at the transition between Wealden 3 and 4 units; Elstner and Mutterlose,

1996; Mutterlose and Bornemann, 2000; Strauss et al., 1993). Mineral compositions of the

samples W4, W6 and W7 have been confirmed by X-ray powder diffraction (XRD) as non-

calcareous shales.

2.3.4 Terrestrial Waikato and Brunner coal measures in the Waikato and

West Coast basins

Te Kuiti Group sediments in the Waikato region of New Zealand (Figure 2.1D) were

deposited between the late Eocene (Kaiatan) and the earliest Miocene (Waitakian) age as a

predominantly transgressive sequence (Nelson, 1978; Pocknall, 1991). The Waikato Coal

Measures are the basal sequence (Kear and Schofield, 1959). In the Rotowaro area (Figure

2.1D), they were deposited in a small, localised, fault-angle depression in a fluvial–lacustrine

system, including several phases of prolonged peat development (Pocknall, 1991, 1989). Their

thickness are up to 200 m, including sub-bituminous coal seams up to 20 m thick (Edbrooke,

2005). The vegetation at Rotowaro during the late Kaiatan age was dominated by Casuarina but

also included several gymnosperms (including Podocarpaceae), Myrtaceae, and pteridophytes

(Pocknall, 1989). Araceae/Palmae are sometimes dominant, reflecting a local presence on peat

swamp (Pocknall, 1989). OM in the coal seams consists mostly of land plant material of

gymnosperm and angiosperm origin (Pocknall, 1989; Vu et al., 2009). Vitrinite is the most

abundant maceral, with minor amounts of liptinite and subordinate inertinite (Beamish et al.,

1998). One coal sample (NZ1, 0.45% Ro) belonging to the Waikato Coal Measures was selected

from the Rotowaro coalfield (Figure 2.1D, Table 2.1).

The Eocene Brunner Coal Measures constitute the typical basal Cenozoic unit over much

of the west coast region of the South Island, New Zealand (Figure 2.1D; Nathan et al., 2002;

Rattenbury et al., 1998). They have been described as the lowest member of a regional

transgressive sequence from the Eocene to the Oligocene (Lever, 1999; Nunweek, 2001). They

are generally composed of coarse sandstones, interbedded carbonaceous siltstones and

mudstones, and coal seams (Nathan et al., 2002; Rattenbury et al., 1998; Titheridge, 1988). The

majority was deposited by low-sinuosity meandering rivers, with coals and fine-grained

sediments accumulating on floodplains and mire complexes (Flores and Sykes, 1996).

Casuarina was recorded as the dominant vegetation species over most of the west coast region

during the Eocene Kaiatan age (Pocknall, 1989). OM in the coal seams are mostly originated

from gymnosperms and angiosperms (Vu et al., 2009). They are consistently vitrinite rich, with

subordinate proportions of liptinite and inertinite (Vu et al., 2009). In the Reefton area (Figure

2.1D), the Eocene Brunner Coal Measures are around 300 m thick (Suggate, 1957). Two high

volatile bituminous coal samples (NZ2 and NZ3, 0.52% Ro) were collected from the Reefton

Coalfields (Figure 2.1D, Table 2.1).

2.4 Analytical Methods

2.4.1 Open system pyrolysis-gas chromatography (Py-GC)

Open system Py-GC was used to characterize the kerogen in source rock. Up to 35 mg

finely ground sample was placed into the glass capillaries (open on both sides) and sealed by

thermally cleaned quartz wool at both ends. Non-isothermal heating at 300°C for 4 min was

used to thermovaporize and vent volatile products prior to pyrolysis. Pyrolysis products were

released over the range 300–600°C (at a heating rate of 50°C/min, and thereafter held for 2

minutes) and collected in a liquid nitrogen-cooled trap. By heating the trap to 300°C, the

products were released and measured on line with an Agilent GC 6890A gas chromatograph

equipped with a flame ionization detector (Keym et al., 2006). Identification of peaks based on

reference chromatograms was done manually with the Agilent ChemStation© software.

2.4.2 Organic solvent extraction

Soxhlet extraction was carried out on the powdered whole rock samples for 48 hours at

60 °C using the ternary azeotropic solvent mixture of methanol, acetone and chloroform

(30:38:32, v/v/v). This high-polarity solvent was chosen for extraction because of its particular

capacity to extract polar compounds. After asphaltene precipitation (Theuerkorn et al., 2008),

maltenes were separated into aliphatic hydrocarbons, aromatic hydrocarbons and resin fractions

by medium pressure liquid chromatography (Radke et al., 1980).

2.4.3 Gas chromatography-mass spectrometry (GC-MS) and gas

chromatography-flame ionization detector (GC-FID)

The aliphatic hydrocarbon fraction was characterized by both GC-MS and GC-FID. An

Agilent 6890 GC equipped with an HP Ultra 1 capillary column (50 m × 0.2 mm × 0.33 µm)

was used in combination with FID, whereas GC-MS was performed using an Agilent 6890 GC

equipped with a BPX5 fused silica capillary column (50 m × 0.22 mm × 0.25 µm). Qualification

was done using 5α-androstane as the internal standard in both measurements.

2.4.4 (+)-APPI FT-ICR-MS analysis

After concentrating the total extracts from Soxhlet extraction under a weak nitrogen

stream, they were re-dissolved in a small volume of dichloromethane and diluted with methanol

and n-hexane (9:1, v/v) to a final concentration of 20 μg/ml. Mass analysis was performed with

a 12 Tesla FT-ICR-MS equipped with APPI source (both from Bruker Daltonik GmbH,

Germany) using a krypton UV-lamp at 10.6 eV operated in positive-ion mode. Molecular

nitrogen was used as the drying gas at a flow rate of 3.0 L/min and a temperature of 210 °C and

as the nebulizing gas at 2.3 bar. Spectra were recorded in broadband mode using 4 megaword

data sets. For each mass spectrum, 300 scans were accumulated in a mass range from m/z 147

to m/z 1200. Positive APPI mode allows the generation and detection of analyte components as

protonated and/or radical ion species. The ionization mechanism and the type of detectable ions

depend mainly on the analytes and solvents used (Kauppila et al., 2004a, 2002). The solvent

mixture used in our experiments leads to a dominance of protonated ions (Kauppila et al., 2004a,

2002).

2.4.5 (–)-ESI FT-ICR-MS analysis

Dried sample extracts were re-dissolved in a small amount of dichloromethane and

diluted with methanol and toluene (1:1, v/v) to a final concentration of 100 ug/mL. 10 uL of a

concentrated aqueous ammonia solution were added to facilitate the deprotonation of the

sample constituents. An Apollo II ESI source from Bruker Daltonik GmbH (Germany) operated

in negative-ion mode was used with molecular nitrogen as the drying gas at a flow rate of 4.0

L/min and a temperature of 220 °C and as the nebulizing gas with 1.4 bar. For each mass

spectrum, 200 scans have been accumulated in a mass range from m/z 147 to m/z 750. ESI

targets large, low-volatile polar compounds that are readily protonated or deprotonated in an

electric field (Kujawinski, 2002). In negative ESI mode, ion is formed through the loss of single

or multiple labile hydrogen(s), whereas positive ESI mode involves the formation of adducts

such as [M+H]+.

2.4.6 (+)-ESI FT-ICR-MS analysis

Methanol was used to dilute the analytes to a final concentration of 2 μg/ml. An Apollo

II ESI source from Bruker Daltonik GmbH (Germany) operated in positive-ion mode was

employed with molecular nitrogen as the drying gas (4.0 L/min, 220 °C) and as the nebulizing

gas with 1.3 bar. For each mass spectrum, 200 scans have been accumulated in a mass range

from m/z 147 to m/z 1000.

2.4.7 Mass calibration and data analysis of FT-ICR-MS results

In positive APPI mode, a mixture of polyaromatic hydrocarbons and polyethylene glycols

was used for external calibration, whereas a mixture of fatty acids and polyethylene glycol

sulfates was used for the negative ion ESI mode. Subsequently, internal recalibration was

performed under quadratic calibration mode with a standard deviation error below 0.008 ppm.

Signals with signal-to-noise ratio ≥ 12 were included in further data assessment.

The precise mass provided by FT-ICR-MS allows for an accurate molecular formula

assignment via a statistical combination of the exact masses of various elements. In terms of

the positive APPI measurements of rock extracts, elemental isotopes 1H, 12C, 13C, 14N, 16O, 32S,

23V and 28Ni were used to do formula assignment, with a maximum value per assignment of

C100H202O20N5S4V1Ni1. 23Na was included to assign sodium adducts formed during electrospray

ionization. If no chemical formula within the allowed mass error of 0.5 ppm was found, the

peak was not included in the mass formula list. Data evaluation was done with the help of Data

Analysis 4.0 SP5 (Bruker Daltonik GmbH, Germany) and Excel 2010 (Microsoft Corp.,

Redmond, WA).

Thousands of peaks were unequivocally assigned in one single mass spectrum. In

subsequent data evaluation and discussion, only the monoisotopic assigned peaks were included.

They were classified into different classes based on numbers of heteroatoms, carbon atoms, and

double-bond equivalents (DBE, number of rings and double bonds) in their assigned molecular

formulas, to facilitate the exploration and analysis of extensive information about their intensity

and elemental composition, and to glean meaningful patterns and trends. The DBE was

calculated for each molecule containing carbon, hydrogen, oxygen, sulfur, nitrogen, vanadium,

nickel and sodium atoms CcHhOxNySzVvNinNaa using the formula DBE= c − 0.5h − 0.5a + 0.5y

+ 1 (e.g., Koch and Dittmar, 2006). Further structural discussions of the detected species are

only speculative based on the unambiguous molecular formulas and the selectivity of ionization

modes, since FT-ICR-MS data cannot distinguish isomers.

2.5 Results

2.5.1 Rock Eval pyrolysis and open system Py-GC

Tmax values (the temperature at which the maximum release of hydrocarbons from

kerogen via cracking occurs during Rock Eval pyrolysis) in the range of 412–440°C point

towards an immature to early-mature stage of the samples with variable organic facies (Figure

2.2C, Yang and Horsfield, 2020), in agreement with the measured huminite/vitrinite reflectance

values (see Table 2.1).

According to the diagram proposed by Larter (1984), pyrolysis products of the Wealden

sample W2 are highly paraffinic (Figure 2.2A). They are rich in long chain n-alkenes and n-

alkanes (Figure 2.2B), falling in the Paraffinic High Wax field defined by Horsfield (1989),

typical of Botryococcus-derived type I kerogen (Rippen et al., 2013) and consistent with

hydrogen index (HI, calculated after S2/TOC×100, S2: amount of petroleum generated by Rock

Eval pyrolysis) of 800 mg HC/g TOC (Figure 2.2C).

The coal samples NZ1–NZ3 and the Wealden sample W1 have low HI (154–230 mg

HC/g TOC) and Tmax values, and therefore fall in the type III field (Figure 2.2C). Their

pyrolysis products comprise a large fraction of gaseous hydrocarbons (Figure 2.2B) and display

a predominance of m- and p-xylene (Figure 2.2A). However, while the sample W1 contains

phenol-poor type III kerogen, the coal samples are phenol-rich (Figure 2.2A).

As compared to the classical type II organic-rich Posidonia samples P1–P3 which

generate Paraffinic-Naphthenic-Aromatic Low Wax pyrolysates (Figure 2.2B; di Primio and

Horsfield, 2006; Muscio et al., 1991), pyrolysis products of the Wealden samples W3–W7 and

the Upper Schöneck sample M2 are more paraffinic (Figure 2.2A) and richer in C6+ n-alkenes

and n-alkanes (Figure 2.2B) indicating a mixed type I/II kerogen. In contrast, the Dynow and

the Lower Schöneck samples M1 and M3 have lower HI values (Figure 2.2C) and their

pyrolysates are richer in aromatic compounds (Figure 2.2A) pointing towards a mixed type

II/III kerogen.

A good consistency is present using HI value and pyrolysate composition in kerogen

categorization (Figure 2.2A–C). The HI value and the ternary Figure 2.2A clearly display the

distinction between the (phenol rich) type III kerogen and the others, while the ternary given as

Figure 2.2B is more efficient to distinguish type I kerogen.

Figure 2.2. Ternary diagrams for molecular kerogen structure typing developed by (A) Larter

(1984) and (B) Horsfield (1989) based on open system Py-GC results. (C) Diagram of hydrogen index

versus Tmax for the classification of kerogen types (Espitalié et al., 1984b) based on Rock Eval pyrolysis

results summarized from Vu (2008), Rippen et al. (2013), Ziegs et al. (2018) and Yang and Schulz

(2019). (D) CPI (carbon preference index), Ster/Hop (regular steranes/homohopanes), and 4-MSI (4-

methylsteranes/C29 regular steranes) ratios based on GC-MS measurements for OM input assessment.

2.5.2 Biomarker characterization by GC-MS and GC-FID

n-Alkanes in the coal extracts NZ1–NZ3 comprise substantial C27+ long-chain

homologues, strongly exceeding the short-chain homologues as expressed by a high

terrigenous/aquatic ratio (TAR, 11.2–20.1, Figure S2.2A; calculated after Bourbonniere and

Meyers (1996) as (C27 + C29 + C31)/(C15 + C17 + C19)), and with a high carbon preference index

(CPI, 2.6–3.6, Figure 2.2D; calculated after Bray and Evans (1961) as [(C25 + C27 + C29 + C31

+ C33)/(C24 + C26 + C28 + C30 + C32) + (C25 + C27 + C29 + C31 + C33)/(C26 + C28 + C30 + C32 +

C34)]/2). A lower fraction of C27–C31 n-alkanes is found in the Wealden extracts W1–W7 (TAR,

2.5–9.3) displaying a reduced or no carbon number preference (CPI, 1.0–1.5), among these, the

extract W1 has the highest CPI value (Figure 2.2D). Small amounts of long-chain n-alkanes

(TAR, 0.7–1.4) are present in the Posidonia extracts P1–P3 showing an even carbon number

predominance (CPI of 0.3–0.8). The Schöneck extracts M2 and M3 contain the smallest

fractions of long-chain n-alkanes (TAR, 0.4 and 0.2) with the CPI values as 1.4 and 0.9, while

the TAR and CPI values for the Dynow extract M1 are 5.2 and 2.0.

The largest pristane/phytane ratios (Pr/Ph, 8.4–9.0) occur in the coal extracts NZ1–NZ3,

whereas the Wealden extracts W2–W7 and the Dynow extract M1 display the smallest values

(< 0.3, Figure S2.2B). For the other extracts, ratios are in the range of 1.1–2.3.

Regular steranes are more abundant than 17α-hopanes in the Posidonia extracts P1–P3,

the Dynow extract M1, and the Lower Schöneck extracts M3 (Ster/Hop, 1.8–2.6, Figure 2.2D).

In the Wealden extracts W3–W7 and the Upper Schöneck extract M2, they are of approximately

equal amounts (0.7–1.2). In contrast, hopanes are more plentiful in the Wealden extracts W1

and W2 (Ster/Hop, 0.3 and 0.5) and even strongly dominate over steranes in the coal extracts

NZ1–NZ3 (≤ 0.1). In terms of absolute concentrations, regular steranes are more plentiful in

the Dynow and Schöneck extracts M1–M3 when compared to the other extracts (4.2–4.8 versus

0.02–1.9 mg/g extract).

C29 steranes are the dominant regular steranes (C27–C29) in the coal extracts NZ1–NZ3,

whereas the Dynow extract M1 is characterized by a high proportion of C28 steranes (Figure

S2.2E). In the other extracts, all these three sterane homologues are present in comparable

amounts (Figure S2.2E).

C31 αβ 22R homohopane is markedly predominant among the 17α-hopane series of the

coal extracts NZ1–NZ3 (Figure S2.3). While the C31 αβ 22R homohopane is of similar

abundance as the C30 αβ homohopane in the Wealden extract W1, C30 αβ homohopane

predominates the hopane series in the other extracts (Figure S2.3).

C28–C30 analogues of steranes substituted at C-4 and C-24 (e.g., the C30 compounds are

4α- and 4β-methyl-24-ethylcholestanes) are only observed in the lacustrine and marine rock

extracts. Their abundances are strongly variable in the Wealden extracts W1–W7 as illustrated

by the 4-MSI values (4-methylsteranes/C29 regular steranes) ranging over 0.03–0.85 (Figure

2.2D); the lowest and the highest values are respectively present in the extracts W2 and W7. In

contrast, 4-MSI value is constantly low in the marine rock extracts (0.03–0.05).

Configurational isomerization of hopanes and steranes expressed by ratios such as C29

βα/αβ hopanes (0.28–1.09) and C29 ααα 20S/(20R + 20S) steranes (Figure S2.2C, D) indicates

an immature to early-mature stage of all the studied samples (Espitalié et al., 1984a; Peters et

al., 2005b; Seifert and Moldowan, 1981, 1980). The unstable biological C27–C31 ββ hopanes

(Peters et al., 2005b) are only abundant in the Wealden extract W1, the Dynow extract M1, and

the coal extracts NZ1 and NZ3 (Figure S2.3). Unsaturated C29 30-norneohop-13(18)-ene and

C30 neohop-13(18)-ene occurring primarily in the immature settings (Damsté et al., 2014)

represent high abundances in the Wealden extract W1, the Dynow extract M1, the Posidonia

extract P1, and the coal extract NZ1 (Figure S2.3). The samples W1 and M1 are on the

uppermost part of their respective sampling intervals (Table 2.1).

2.5.3 Organooxygen and organonitrogen compounds detected with FT-ICR-

Ox compounds in the studied extracts were detected as both protonated ions and sodiated

species [M + Na]+ in positive ESI mode. NaOx ions are found to be more abundant than the

protonated Ox species, illustrating that many organooxygen compounds like carboxylic acids

produce sodium adducts rather than protonated molecules in positive ESI mode (Habicht et al.,

2008; Sugimura et al., 2015), thus, in the following, the positive ESI accessible Ox compounds

represent both protonated and sodiated species. In negative ESI mode, dimer adducts are formed

between two deprotonated Ox analyte ions and sodium ([2M − 2H + Na]−) (e.g., Schug and

McNair, 2002). Since information about the monomer analyte ions cannot be extracted, the

sodiated Ox dimer adducts are excluded from the data interpretation.

Negative ESI measurements of the Wealden extracts W5–W7 and the Upper Schöneck

extract M2 were not considered for data evaluation and discussion (Figure 2.3) since the organic

analyte signals in these spectra were completely overprinted by the sodium chloride cluster

signals.

High numbers of monoisotopic peaks are assigned as Ox, NyOx and Ny compounds in

positive ESI spectra of the Posidonia extracts P1–P3 and the coal extract NZ1 (1981–3031)

representing the highest absolute abundances (2.3 × 1010–3.1 × 1010) among the sample set

(Figure 2.3B). In negative ESI or positive APPI mode, the coal extracts NZ1–NZ3 contain the

most abundant organooxygen and organonitrogen compounds (Figure 2.3A, C).

Figure 2.3. Absolute abundances of the peaks assigned as Ox, Ny and NyOx compounds in

negative ESI (A), positive ESI (B) and positive APPI (C) modes. Summed numbers of these peaks are

marked out by yellow dots.

2.5.3.1 Ox compounds

The coal extracts NZ1–NZ3 have the greatest absolute abundances of Ox compounds

independently of ionization mode, followed by the Wealden extract W2 and the Dynow extract

M1 (Figure 2.3). The other extracts differ from them by up to one order of magnitude with

regard to Ox compounds’ absolute abundances.

The relative proportion of Ox compounds among the classes containing only oxygen or

nitrogen or both heteroatoms (Ox, NyOx and Ny) is displayed by the ternary diagram Figure 2.4.

A strong dominance of Ox class is observed in the coal extracts NZ1–NZ3 and the lacustrine

type I kerogen related rock extract W2 (90–98% with negative ESI, 82–87% with positive APPI,

49–82% with positive ESI, Figure 2.4), whereas in the Posidonia extracts P1–P3, Ox class

represents the smallest relative proportions. The remaining Wealden extracts W1 and W3–W7

contain a larger fraction of Ox compounds relative to the Dynow and Schöneck extracts M1–

M3 when detected by negative ESI (Figure 2.4A), but not in terms of the basic or low-polarity

Ox compounds (Figure 2.4B, C).

Figure 2.4. Ternary plots showing the relative proportions of Ny, NyOx and Ox classes (in terms

of abundances) detected with (A) negative ESI, (B) positive ESI and (C) positive APPI.

Ox compounds in the coal extracts NZ1–NZ3 mainly comprise O1 to O11 classes in

positive APPI mode, showing a gaussian-like compound class distribution that maximizes at

O4 class (Figure 2.5A). The gaussian-like compound class distributions are also observed for

the Ox compounds in the coal extracts in negative ESI (O2–O14 classes maximizing at O7, Figure

S2.4A) or positive ESI (O1–O10 classes maximizing at O3, Figure S2.4C) modes. In the marine

and lacustrine rock extracts, Ox compounds contain 1–6, 1–8, and 1–5 oxygen atoms

respectively in positive APPI, negative ESI, and positive ESI modes. Gaussian-like distribution

patterns are observed for the acidic O1–O8 classes in all the marine and lacustrine rock extracts

(maximizing at O3 or O4 class, Figure S2.4A) as well as for the basic O1–O4 classes in the

marine rock extracts and the lacustrine Wealden extracts W1, W2, W7 (maximizing at O2 class,

Figure S2.4C). In contrast, O1 is the predominant class among the basic O1–O5 compounds in

the lacustrine Wealden extracts W3–W6 (Figure S2.4C) or among the low-polarity O1–O6

compounds in all the marine and lacustrine rock extracts (Figure 2.5A); abundances of these Ox

classes significantly decrease with increasing oxygen numbers. Overall, average oxygen

numbers (calculated after ∑Ii(ONo.)ii ∑Iii

⁄, the (ONo.)i is the numbers of oxygen atoms

assigned for a specific signal i, whereas Ii represents its intensity) of Ox compounds for the coal

extracts NZ1–NZ3 are significantly larger than values for the marine and lacustrine rock

extracts (3.35–7.08 versus 1.31–4.33, Figure 2.5, S2.5D, E).

Figure 2.5. (A, B) Compound class distributions of the positive APPI ionizable Ox, Ny and NyOx

compounds. (C) Diagram plotting average oxygen number against average nitrogen number of the

positive APPI accessible NyOx compounds, displaying proportions of multi-nitrogen and multi-oxygen

bearing compounds. TMIA: total abundances of the assigned monoisotopic peaks.

Bimodal DBE distributions (1–4 and ≥ 5 DBE) are observed for the acidic O2–O5 classes

and the low-polarity O1–O4 classes in all the studied extracts (Figure 2.6A, S2.6C). The highly

oxygenated compounds like the acidic O6–O14 and the low-polarity O5–O11 classes contain no

or few 1–4 DBE compounds, showing a unimodal DBE distribution principally in the higher

DBE range. With regard to the basic inventories, 1–4 DBE species are solely observed for the

O2–O5 classes in the coal extracts NZ1–NZ3 and the Wealden extracts W2, W4, W5, W7

(Figure S2.6B).

The 1–4 DBE Ox compounds accessible by positive APPI or positive ESI might be acyclic

or non-aromatic cyclic compounds containing at least one ketone group (Huba et al., 2016),

whereas the negative ESI ionizable 1–4 DBE Ox compounds could be aliphatic compounds

containing at least one carboxylic group, with small contribution from phenols (Huba et al.,

2016). In contrast, the compounds with more than 4 DBE are to a large degree aromatic species

(e.g., aromatic acids, Shi et al., 2010a) with possible contributions from nonaromatic polycyclic

structures like hopanoic, secohopanoic or steroidal acids (e.g., Liao et al., 2012; Shi et al.,

2010b). The ratio DBE1–4/DBEAll Ox is here used to quantitatively describe the fraction of 1–4

DBE compounds within each individual Ox class. The values for this ratio are generally larger

in the type I–I/II kerogen related extracts, i.e., the Wealden extracts W2–W7 and the Upper

Schöneck extract M2 (up to 89%; Figure 2.8C, S2.7B–D), with the exception of the ratio for

the acidic O2 class (Figure 2.6A, S2.7A).

Figure 2.6. (A) DBE distributions of the negative ESI detectable Ox classes (x=2–4), which are

normalized by the most abundant DBE species (DBEmax_abund) in each specific compound class. (B)

Average DBE values of the negative ESI ionizable ≥ 5 DBE Ox compounds are plotted over oxygen

numbers for all the studied extracts.

The high DBE Ox compounds like the acidic 10–21 DBE O3 species are more abundant

or exclusively present in the coal extracts especially the NZ2 and NZ3 (e.g., Figure 2.6A, S2.6B,

C). Therefore, average DBE values (calculated after ∑Ii(DBE)ii ∑Iii

⁄, the (DBE)i is the

numbers of DBE for a specific signal i) for the aromatic ≥ 5 DBE Ox compounds are greater in

the coal extracts relative to the marine and lacustrine rock extracts (Figure 2.6B, 2.8C, S2.8B,

C). Among the marine and lacustrine rock extracts, relatively larger average DBE values are

observed for the extracts associated with type II–III kerogen, i.e., the Wealden extract W1, the

Dynow extract M1, the Lower Schöneck extract M3, and the Posidonia extracts P1–P3.

DBE ranges of Ox classes in the coal extracts NZ1–NZ3 extend to higher values with

increasing oxygen numbers independently of ionization mode (Figure 2.6A, S2.6B, C), leading

to a strong linear increase of the average DBE values for the aromatic (≥ 5 DBE) Ox classes

(R2=0.93–1.00, Figure 2.6B, S2.8B, C). The slopes of the regression lines in Figure 2.6B and

S2.8B, C are in the range of 0.94–1.22 (Figure S2.7J–L), indicating that the addition of one

oxygen atom to an aromatic compound class results in a mean increase between 0.94 and 1.22

in its average DBE. A linear growth, but with a reduced slope (0.04–1.12), is found for the

acidic or low-polarity aromatic Ox classes in all the marine and lacustrine rock extracts as well

as for the basic Ox compounds in the lacustrine Wealden extracts W3, W6 and W7 (Figure 2.6B,

S2.7J–L, S2.8B, C). Among these marine and lacustrine rock extracts, the largest slopes are

observed in the Wealden extract W1 and the Lower Schöneck extract M3, whereas the smallest

ones are present in the Wealden extracts W5–W7.

The acidic or the basic Ox classes display a unimodal carbon number distribution over a

range of 10–59 in the studied extracts (e.g., Figure 2.7A), while the low-polarity compounds

range over 14–76. Compounds containing > 40 or even > 30 carbon atoms are more abundant

or only present in the Wealden extract W2 independently of ionization mode (e.g., Figure 2.7A).

In the coal extracts NZ1–NZ3, a strong even or odd carbon number predominance is observed

mainly in the range of C23–C33 among individual aliphatic 1–4 DBE Ox species in all three

ionization modes (e.g., Figure 2.7C–F). A prominent even-over-odd preference is observed for

both positive and negative ESI accessible aliphatic O2–O5 species in the coal extracts NZ1–

NZ3, with C26, C28 and C30 as the most abundant compounds (e.g., Figure 2.7C, D). While an

even-numbered predominance is also observed for the positive APPI ionizable individual 2–4

DBE O1, 2–4 DBE O2 and 2 DBE O4 species in the coal extracts NZ1–NZ3 (e.g., Figure 2.7E),

an odd-numbered predominance is observed for the 1 DBE O1, 1 DBE O2 and 2–4 DBE O3

species in positive APPI mode with C27, C29 and C31 as the main homologues (e.g., Figure 2.7F).

In the marine and lacustrine rock extracts, the carbon number preference for the aliphatic C23–

C33 Ox species is generally weak (e.g., Figure 2.7C–F) as expressed by their even-over-odd

preference indexes (EOPI) closer to 1 (calculated after 0.5 × [(C24 + C26 + C28 + C30 + C32)/(C23

+ C25 + C27 + C29 + C31) + (C24 + C26 + C28 + C30 + C32)/(C25 + C27 + C29 + C31 + C33)], Figure

S2.7G–I); an exception is the strong dominance of the C28 compounds among the low-polarity

4 DBE O1 species in the Dynow and Schöneck extracts M1–M3. The middle-chained species

are more important for the marine and lacustrine rock extracts when compared to the coal

extracts, quantified by the higher ratios of the middle-chain (C23, C25 or C22, C24) versus the

long-chain (C27, C29, C31 or C26, C28, C30) species (Figure 2.7C–F). These middle-chain species

even dominate the aliphatic Ox compounds in certain rock extracts, for example as the C22 and

C24 homologues in the Wealden extract W1, the Dynow extract M1, the Lower Schöneck extract

M3, and the Posidonia extracts P1 and P2 shown in Figure 2.7D and E.

Figure 2.7. Carbon number distributions of the negative ESI accessible O3, 1 DBE O2, 1 DBE

O3, the positive ESI ionizable N1, and the positive APPI detectable 3 DBE O1, 1 DBE O2 species, which

are normalized by the most abundant species in specific compound class or DBE class in certain sample.

The dot size represents the relative abundance of variable compounds within a certain DBE class in a

specific sample.

Average carbon numbers (calculated after ∑𝐼𝐼𝑖𝑖𝑖𝑖 (𝐶𝐶𝑁𝑁𝑁𝑁.)∑𝐼𝐼𝑖𝑖𝑖𝑖

⁄, the (CNo.)i is the numbers of

carbon atoms assigned for a specific signal i) of the acidic aromatic Ox classes increase linearly

with the increasing oxygen numbers (Figure S2.7P, S2.8D) in the coal extracts NZ1–NZ3

(R2=0.98; slope: 1.26–1.41), the Wealden extract W4 (slope: 1.03) and the Posidonia extracts

P1–P3 (slope: 0.66–0.74). For the basic aromatic Ox classes (Figure S2.8E), higher slopes are

also observed for the coal extracts NZ1–NZ3 (0.40–0.45) than for the Wealden extract W6

(0.13) and the Dynow extract M1 (0.30). In positive APPI mode, a linear increase of average

carbon numbers is not observed in any extracts (Figure S2.8F).

2.5.3.2 NyOx compounds

The Wealden extracts W1–W7 contain the smallest absolute abundances of NyOx

compounds in distinct ionization modes, whereas the largest abundances are generally present

in the Dynow extract M1 and the Posidonia extracts P1–P3 (Figure 2.3).

The Wealden extract W2 displays the smallest fraction of NyOx compounds among the

Ox, NyOx and Ny classes independently of ionization mode (1–6%, Figure 2.4). A large

proportion of acidic or low-polarity NyOx is present in the marine rock extracts (Figure 2.4A,

C), whereas the basic NyOx compounds account for greater proportions not only in the marine

rock extracts but also in the coal extract NZ3 and the lacustrine Wealden extract W4 (Figure

2.4B). The fraction of basic NyOx compounds varies to a large extent in the coal extracts NZ1–

NZ3 (16–42%, Figure 2.4B), while that of the acidic or low-polarity NyOx compounds is rather

constant (Figure 2.4A, C).

N1Ox class dominate the NyOx compounds in all the analyzed extracts (Figure 2.5B, S2.4B,

D). N2Ox class is abundant or only present in the marine rock extracts, represented by their

larger average nitrogen numbers (calculated after ∑Ii(NNo.)ii ∑Iii

⁄), the (NNo.)i is the numbers

of nitrogen atoms assigned for a specific signal i) of NyOx (1.08–1.37 versus 1.00–1.02, Figure

2.5C, S2.5A, B). Among the marine rock extracts, the Upper Schöneck extract M2 has the

smallest average nitrogen numbers of NyOx.

N1Ox compounds in the coal extracts NZ1–NZ3 comprise of N1O3–N1O11 (negative ESI),

N1O1–N1O6 (positive ESI) and N1O1–N1O8 (positive APPI) classes (Figure 2.5B, S2.4B, D),

which display a gaussian-like compound class distribution with a maximum respectively at

N1O6, N1O2 and N1O4 class. In the marine and lacustrine rock extracts, N1Ox compounds

contain 1–6, 1–3 and 1–7 oxygen atoms respectively in negative ESI, positive ESI and positive

APPI modes. A gaussian-like pattern is observed for the acidic N1O1–N1O6 compounds with

N1O2 or N1O3 as the dominant class (Figure S2.4B), while abundances of the basic and the low-

polarity N1Ox classes maximize at the N1O1 and significantly decrease with increasing oxygen

numbers (Figure 2.5B, S2.4D). N2Ox compounds being mainly present in the marine rock

extracts contain no more than 6, 3 and 5 oxygen atoms in negative ESI, positive ESI and positive

APPI modes, respectively (Figure 2.5B, S2.4B, D). Their abundances generally maximize at

the N2O1 class, with the exception of a gaussian-like distribution of the acidic N2O1–N2O5

classes (maximizing at N2O3) in the Dynow extract M1 and the Lower Schöneck extract M3.

The largest average oxygen numbers of NyOx are found in the coal extracts NZ1–NZ3 in all

three ionization modes (2.06–6.84, Figure 2.5C, S2.5A, B).

N1Ox compounds in the studied extracts principally display a monomodal DBE

distribution in the ≥ 4 DBE range (Figure S2.6). Aliphatic 0–3 DBE species are exclusively

found in the marine and lacustrine rock extracts among their N1O1–N1O3 classes. The DBE

ranges of N1Ox compounds in the Wealden extract W2 are restricted to lower values when

compared to the other extracts (Figure S2.6B, C), illustrated by its smallest average DBE values

of N1Ox classes (Figure S2.8H, I). In contrast, the high DBE compounds like the acidic 15–23

DBE N1O5 species are only abundant in the coal extracts especially the NZ2 and NZ3 (Figure

S2.6).

The DBE ranges of N1Ox classes become enlarged with increasing oxygen numbers

especially in the coal extracts NZ1–NZ3 independently of ionization mode (Figure S2.6A, C).

Average DBE values of N1Ox classes in the coal extracts NZ1–NZ3 increase linearly with the

enhanced oxygen numbers in all three ionization modes (R2=0.97–1.00, Figure S2.8G–I). The

slopes from equations of these linear correlations are larger for the basic N1Ox classes (1.13–

1.37) than for the low-polarity (1.07–1.13) and the acidic (0.96–1.02) compounds (Figure

S2.7M–O). This kind of linear correlation is also observed in nearly all the marine and

lacustrine rock extracts for the basic or the low polarity N1Ox classes, but it is only present in

the Dynow extract M1, the Lower Schöneck extract M3 and the Posidonia extract P1 for the

acidic N1Ox classes (Figure S2.7M–O, S2.8G–I). The slopes calculated for these marine and

lacustrine rock extracts (0.19–1.17) are generally smaller than or equal to those for the coal

extracts; exceptions are found for the Wealden extract W2 (2.03) and the Lower Schöneck

extract M3 (1.50) in positive APPI mode.

Unimodal carbon number distributions are observed for the N1Ox compounds over a range

of 13–43 (negative ESI), 11–55 (positive ESI) and 16–65 (positive APPI). Compounds

containing more than 40 carbon atoms are exclusively abundant in the Wealden extract W2,

represented by the largest average carbon numbers of the basic and the low-polarity N1Ox

classes among the sample set (Figure S2.8K, L).

Average carbon numbers of the acidic N1Ox classes increase linearly with the increasing

oxygen numbers (Figure S2.7Q, S2.8J) in the coal extracts NZ1–NZ3 (R2=0.98–1.00; slope:

1.29–1.50), the Posidonia extract P1 (slope: 0.65), and the Wealden extracts W1, W3 and W4

(slope: 0.63–1.09). This type of linear correlation is also observed for the basic N1Ox classes in

the coal extract NZ3, the Wealden extracts W6 and W7, and the Posidonia extracts P2 and P3

(Figure S2.7R, S2.8K), in which a larger slope is present in the coal extract NZ3 relative to

these marine and lacustrine rock extracts (1.36 versus 0.16–0.96). In positive APPI mode, a

linearity is only traced in the coal extract NZ3 with a slope of 0.92 (Figure S2.8L).

2.5.3.3 Ny compounds

Ny compounds are only detected in the studied extracts in positive ESI and positive APPI

modes (Figure 2.3). The Posidonia extracts P1–P3 have the greatest absolute abundances of Ny

compounds, whereas the smallest abundances are found in the coal extracts NZ1–NZ3 in

absolute and relative terms (Figure 2.3, 2.4).

N1 class consistently dominates the Ny compounds in the studied extracts (Figure 2.5A,

S2.4D). N2 class is totally absent in the coal extracts NZ1–NZ3 and the lacustrine Wealden

extract W2, whereas the marine Upper Schöneck extract M2 has the greatest average nitrogen

numbers of Ny compounds among the studied extracts (Figure S2.5G, H), representing a large

proportion of N2 class.

N1 compounds display unimodal DBE distributions mainly in the range of 4–25 (Figure

S2.6B, C), potentially as aromatic compounds like pyridines or pyrroles. The 0–3 DBE species

possibly as aliphatic amines are only found in the marine and lacustrine rock extracts in very

low amounts. The DBE ranges of N1 compounds are found to be restricted to low values (≤ 14)

in the lacustrine Wealden extract W2, resulting in the smallest average DBE values of N1

compounds among the sample set (Figure S2.7E, F).

Unimodal carbon number distributions are observed for the N1 compounds over a range

of 13–59 (positive ESI, Figure 2.7B) or 17–75 (positive APPI). Compounds containing more

than 40 carbon atoms are exclusively abundant in the lacustrine Wealden extract W2 (e.g.,

Figure 2.7B).

2.6 Discussion

2.6.1 Terrestrial plant input

2.6.1.1 High oxygen content—in-situ deposition of oxygen-rich higher plant biomass

Ox compounds occur in large absolute and relative abundances in the coal extracts NZ1–

NZ3 in all three ionization modes (Figure 2.3, 2.4), in accordance with the high oxygen content

of terrestrial plants as source (Baxby et al., 1994; Tissot and Welte, 1984).

Organonitrogen compounds in the coal extracts NZ1–NZ3 are mainly present as N1Ox

class (Figure 2.3–2.5, S2.4). The ratio describing oxygenated versus reduced forms NyOx/(NyOx

+ Ny) decreases with the increasing percentage of pyrolyzed oct-1-ene that represents an

enhanced paraffinicity of pyrolyzates (n-C8:1/(n-C8:1 + m,p-xylene + phenol), R2=0.79 and 0.78,

Figure 2.8B, S2.9B). Thus, this decrease accompanies a gradual switch from kerogen type III

to I using HI values and open system pyrolysates as references (Figure 2.2A–C). Labile

organonitrogen compounds like amino acids from proteins are assumed to be largely

mineralized during diagenesis, with only a small proportion retained in sediments through

‘‘degradation-recondensation’’ reactions with degradation products of other biomolecules (del

Rıo et al., 2004; Huc, 1980; Vandenbroucke and Largeau, 2007). They might have been

condensed to a large extent together with the substantial oxygen-bearing structures degraded

from terrestrial plants such as phenolic groups from lignin (Ertel and Hedges, 1984; Haider and

Martin, 1967; Martin and Haider, 1971; Stevenson and Butler, 1969; Vandenbroucke and

Largeau, 2007; Zaccone et al., 2008).

The Dynow sample M1 receives more terrigenous input relative to the Schöneck samples

M2 and M3, as demonstrated by a higher CPI (Figure 2.2D), a greater TAR (Figure S2.2A;

Bourbonniere and Meyers, 1996; Peters et al., 2005b), a larger amount of detrohuminite (Schulz

et al., 2004, 2002) and a minimally higher pyrolyzed phenol content (Figure 2.2A; Larter, 1984).

Correspondingly, in its extract the absolute abundance of Ox compounds is greater (Figure 2.3),

which seems able to record the relative amount of the preserved terrestrial material in aquatic

environment, even though the organooxygen compounds like phenolic molecules derived from

the degradation of lignin could have been extensively diluted by autochthonous materials, or

highly degraded or reworked during the long-distance aquatic transport before sedimentation

(Bergamaschi et al., 1997; da Cunha et al., 2001; Thompson et al., 1985). However, a special

case occurs when plentiful Ox compounds can also originate from aquatic autochthonous

material (e.g., Botryococcus braunii, see chapter 2.6.2.2). Even though the Wealden sample W1

possibly received more terrestrial input relative to the Wealden samples W2–W7 as illustrated

by a slightly higher CPI value (Figure 2.2D; Bourbonniere and Meyers, 1996; Peters et al.,

2005b), a larger amount of C31 αβ 22R homohopane (Figure S2.3; Killops et al., 1998; Quirk

et al., 1984; Ries-Kautt and Albrecht, 1989; Thiel et al., 2003), a minimally higher pyrolyzed

phenol fraction (Figure 2.2A; Larter, 1984) and a lower TOC content (Table 2.1; Froidl et al.,

2021b), its extract only show a higher fraction of Ox compounds relative to the extracts W3–

W7 but not relative to the extract W2 (see chapter 2.6.2.2; Figure 2.3, 2.4).

Besides a successful preservation of the oxygen that is originally present in the terrestrial

organic material by the in-situ coal deposits NZ1–NZ3, an extensive inorganic oxygen

incorporation might have happened during early diagenesis (Riboulleau et al., 2001;

Vandenbroucke and Largeau, 2007) due to the oxic conditions indicated by high Pr/Ph ratios

(8.4–9.0, Figure S2.2B; Didyk et al., 1978). A logarithmic growth of NyOx/(NyOx + Ny) ratio is

observed with the Pr/Ph ratio in the sample set (R2=0.70 and 0.76, Figure S2.9C, D), and in

addition, a positive correlation between abundance of acidic Ox compounds and Pr/Ph ratio was

reported in crude oils (Orrego-Ruiz et al., 2020).

2.6.1.2 Phenolic ketones and phenolic carboxylic acids in the low–medium rank

coals—breakdown products of lignin and tannin

Plentiful polyoxygenated Ox and N1Ox compounds are exclusively found in the coal

extracts NZ1–NZ3 in distinct ionization modes (expressed by the largest average oxygen

numbers of Ox and N1Ox among the sample set, Figure 2.5, S2.4, S2.5), in accordance with the

earlier studies on lignite (Rathsack et al., 2014; Zhang et al., 2016) and immature marine or

lacustrine rocks (dos Santos Rocha et al., 2018b; Pan et al., 2019; Wan et al., 2017; Ziegs et al.,

2018). These compounds are considered as unspecific breakdown products of plant

macromolecules such as lignin and tannin, the most and the second most abundant polyphenols

in nature (Armstroff et al., 2007), as well as their condensation products with the degradation

intermediates of labile organonitrogen compounds. We do not exclude the possibilities that

some organooxygen compounds might derive from non-specific precursors (e.g., alkylated

aromatic hydrocarbons, Wilkes et al., 1998a) via abiotic or biotic transformation, or have other

direct biological precursors such as alkyldibenzofurans originating from lichens whose fossils

were found in coal measures (Radke et al., 2000).

High DBE organooxygen compounds like acidic 10–21 DBE O3 or 15–23 DBE N1O5

species are abundant or only present in the coal extracts NZ1–NZ3, which are possibly sourced

from lignin and tannin (Figure 2.6A, S2.6). The average DBE values of N1Ox and ≥ 5 DBE Ox

compounds characterizing their aromaticity roughly decrease with the changes from kerogen

type III to I (Figure 2.6B, 2.8C, S2.8), as illustrated by their negative linear correlations with

the % n-C8:1 ratio of open system pyrolysates (e.g., R2=0.63–0.86, Figure S2.9E, F). These are

in accordance with the lower content of aromatic nuclei in kerogen from type III to I (Tissot

and Welte, 1984; Vandenbroucke and Largeau, 2007). Similar trends have been reported for

the acidic organic compounds in crude oils (Melendez-Perez et al., 2020; Wan et al., 2017).

The addition of one oxygen atom to an aromatic compound class N1Ox and ≥ 5 DBE Ox

generally results in a mean increase of its average DBE between 0.94 and 1.37 in the coal

extracts NZ1–NZ3 in distinct ionization modes (Figure 2.6B, S2.7J–O, S2.8). A mean increase

of 1 DBE shows that every new oxygen atom is bound via a double bond to carbon assuming

that no additional carbon contributes to the increase of DBE (e.g., Bae et al., 2011; Qin et al.,

2019; Zhu et al., 2019). An increase higher than 1 DBE demonstrates an increased amount of

aromatic carbon while adding carbonyl-oxygen, which is furthermore illustrated by a mean

increase of average carbon number by greater than 1 (e.g., 1.26–1.50 in negative ESI mode,

Figure S2.7P–R, S2.8). As oxygen might also be bound in structures like hydroxyl or carboxyl

groups, aromatic carbon must significantly contribute to the increasing DBE values. These

aromatic organooxygen classes in the coal extracts NZ1–NZ3 appear homologous but differing

by an oxygen-bearing unit, like -C3H2O2- for acidic N1Ox classes in the extract NZ3.

Degradation products of lignin such as phenolic ketones and phenolic carboxylic acids might

be their potential structures (Ertel and Hedges, 1984; Hatcher, 1990; Hatcher et al., 1992;

Hedges and Parker, 1976; Zaccone et al., 2008), correspondingly, ketone, carboxyl and phenolic

groups have been reported to represent an important fraction of oxygen in the vitrinite of sub-

bituminous coals and high-volatile bituminous coals (Hatcher, 1990; Petersen et al., 2008). The

mean increase of average DBE and average carbon number values is generally lower in the

marine and lacustrine rock extracts relative to the coal extracts (Figure 2.6B, S2.7J–R, S2.8),

here again dependent on the changes of kerogen from type I to III (Figure 2.8D, S2.9H). As

known, ketone and carboxylic acid groups in the type II kerogen are less important than that in

the type III kerogen, but more important than that in the type I kerogen, besides, a low content

of aromatic nuclei has been recorded in the kerogen type II and I (Tissot and Welte, 1984;

Vandenbroucke and Largeau, 2007).

Figure 2.8. (A) Crossplot of the NyOx/(Ox + NyOx) ratio and the Ster/Hop. (B) Crossplot of the

NyOx/(NyOx + Ny) ratio and the pyrolysis derived oct-1-ene amount (% n-C8:1). (C) Crossplot of the

DBE1-4/DBEAll O1 ratio versus average DBE of the ≥ 5 DBE O1 species detected in positive APPI mode.

(D) The % n-C8:1 index plots against the slope extracted from the linear correlation between average

DBE values of the positive APPI accessible ≥ 5 DBE Ox species and their respective oxygen numbers

(see Figure 2.6B, S2.8). (E) The pyrolysis derived C6+ n-alkenes and n-alkanes amount (% n-C6+) plots

against average carbon number of the positive ESI accessible N1 class.

2.6.1.3 Strong carbon number preference of the long-chain aliphatic Ox species—

signals of plant waxes and cutan

In addition to the predominant high DBE Ox compounds derived from lignin and tannin,

coal extracts NZ1–NZ3 contain a minor fraction of aliphatic Ox moieties (1–4 DBE O1–O5,

Figure 2.6A, S2.6) as indicated by their low DBE1–4/DBEAll Ox ratios (e.g., Figure 2.8C, S2.7B–

D), with the exception of abundant acidic 1 DBE O2 species possibly as fatty acids (Figure 2.6A,

S2.7A).

Plant protective substances including waxy materials, cutan, suberan, cutin and suberin

were evidenced as the major contributors to these aliphatic constituents, which have a great

potential to be preserved during sedimentation and diagenesis because of their very high

resistance to chemical and microbial degradation or the in-situ polymerization of waxes (de

Leeuw and Largeau, 1993; Gupta, 2015, 2007a, 2007b; Hayes and Swift, 2018). The

pronounced even or odd carbon number preferences of aliphatic O1–O5 compounds and n-

alkanes in the coal extracts NZ1–NZ3 with C26, 28, 30 or C27, 29, 31 as the major homologs (e.g.,

Figure 2.2D, 2.7C–F) possibly point towards a main origin from plant waxes and cutan that are

predominately composed of long-chain units (Boom et al., 2005; Eglinton and Hamilton, 1967;

Kunst and Samuels, 2003; Leide et al., 2020; McKinney et al., 1996; Samuels et al., 2008;

Schouten et al., 1998). In contrast, cutin primarily comprises C16 and C18 fatty acid,

(poly)hydroxy- and epoxy-fatty acid monomers (Deshmukh et al., 2003; Kolattukudy, 1980).

Suberin is rich in C16, C18, C20, C22 and C24 hydroxy fatty acid, dicarboxylic acid, fatty acid and

alcohol monomers (del Rio and Hatcher, 1998; Graça and Pereira, 2000; Pollard et al., 2008;

Ranathunge and Schreiber, 2011; Schreiber et al., 1999). Suberan’s structure is crystalline with

alkyl chain lengths C18, C20, and C22 bearing alcohol, acid, and a small amount of epoxide

functional groups (Turner et al., 2013).

The positive APPI accessible 1 DBE O1 (Figure S2.7G), 1 DBE O2 (Figure 2.7F) and 2–

4 DBE O3 species in the coal extracts NZ1–NZ3 with C27, C29, C31 as the major homologues

perhaps mainly consist of ketones (Holloway, 1994; Lehtonen and Ketola, 1993; Ortiz et al.,

2011), hydroxyketones (Niklas and Gensel, 1976) and hydroxy-β-diketones (Holloway, 1994;

Schmid and Bandi, 1971) from plant waxes. The 2–4 DBE O1 species maximizing at C26, C28,

C30 homologues (e.g., Figure 2.7E, S2.7H, I) might be primarily linked to the unsaturated

aldehydes in plant waxes (Perera et al., 2010). The 2–4 DBE O2 species with C26, C28, C30 as

the major homologues might chiefly comprise ketoaldehydes sourced from plant waxes (Jetter

and Riederer, 1999). In terms of the predominantly even-numbered 2 DBE O4 species,

dicarboxylic acids derived from cutan maximizing at C26, C28, C30 homologues might be the

principal structures (Schouten et al., 1998).

The negative ESI accessible aliphatic O2 compounds in the coal extracts NZ1–NZ3

principally with 1 DBE (Figure 2.6A, 2.7C) might primarily contain fatty acids derived from

plants waxes and cutan maximizing at C26, C28, C30 homologues (Eglinton and Hamilton, 1967;

Gülz et al., 1989; Gülz et al., 1992; Leide et al., 2020; Prasad and Gülz, 1990; Schouten et al.,

1998). The acidic O3–O5 compounds with C26, C28, C30 as the major homologues (e.g., Figure

2.7D) seem to be predominately composed of (poly)hydroxy-fatty acids, dicarboxylic acids,

and hydroxy dicarboxylic acids from waxes and cutan (e.g., Leide et al., 2020; Mingrone and

Castagneto, 2006; Racovita et al., 2015; Schouten et al., 1998).

The positive ESI ionizable aliphatic sodiated O2–O4 compounds in the coal extracts NZ1–

NZ3 might primarily constitute of fatty acids, hydroxyketones, ketoaldehydes, (poly)hydroxy-

fatty acids, and dicarboxylic acids sourced from plant waxes and cutan with C26, C28, C30 as

major homologues. It is worth mentioning that adducts with sodium cations allow for successful

positive ESI analysis of various organooxygen compounds (Ackloo et al., 2000; Cech and Enke,

2001; Habicht et al., 2008; Saf et al., 1994; Sugimura et al., 2015).

2.6.2 Lacustrine algal input

2.6.2.1 Selectively preserved algaenan containing very long chain n-alkyl units

The lacustrine Wealden sample W2 is characterized by the most abundant pyrolyzed C6+

n-alkenes and n-alkanes (Figure 2.2B), which has been related to the selective preservation of

highly aliphatic algaenan in the thick outer cell walls of Botryococcus braunii pointing towards

a typical Botryococcus-derived type I kerogen (Metzger and Largeau, 1999; Rippen et al., 2013;

Vandenbroucke and Largeau, 2007; Ziegs et al., 2015). In its solvent extract W2, Ox, N1 and

N1Ox compounds containing > 40 carbon atoms are abundant or even exclusively occur (Figure

2.7A, B). Algaenan of the Botryococcus braunii (at least race A) has been evidenced to be an

aliphatic biopolymer composed of unsaturated aldehyde and hydrocarbon monomers (on

average 40 carbon atoms) crosslinked by acetal and ester bonds (de Leeuw et al., 2006; Simpson

et al., 2003), and thus, it might be the precursor of these very long chain C>40 Ox compounds

and hydrocarbons. Proteinaceous moieties can be efficiently protected through encapsulation

in the highly aliphatic hydrophobic algaenan during early diagenesis (Knicker and Hatcher,

2001, 1997; Knicker et al., 1996; Nguyen and Harvey, 2003; Nguyen et al., 2003; Zang et al.,

2001, 2000). They might incorporate with the algaenan-derived C>40 hydrocarbons or Ox

compounds during the subsequent diagenesis, forming very long chain organonitrogen

compounds (e.g., Figure 2.7B). A positive linear relationship is observed between the average

carbon number of these soluble heteroatomic classes and the amount of pyrolyzed C6+ n-alkenes

and n-alkanes (n-C6+/(C1–5 + n-C6+), R2=0.59–0.74, Figure 2.8E, S2.10A, C). This is in

accordance with the decreased aliphatic chain length in the kerogen from type I to III

(Vandenbroucke and Largeau, 2007). In addition, selective preservation of the highly aliphatic

algaenan leads to a high ratio of aliphatic over aromatic compounds in solvent extract or

pyrolysis products of the sample W2, illustrated by high DBE1–4/DBEAll Ox ratios (Figure 2.8C,

S2.7A–D) and a predominance of oct-1-ene over m- and p-xylene (Figure 2.2A).

The lacustrine Wealden samples W3–W7 are also characterized by high DBE1–4/DBEAll

Ox ratios (Figure 2.8C, S2.7A–D) and a predominance of pyrolyzed oct-1-ene over m-, p-xylene

(Figure 2.2A), but their contained hydrocarbons (Figure 2.2B) and heteroatomic classes (e.g.,

Figure 2.7A, B, 2.8E, S2.10A, C) are of strongly decreased waxiness in comparison with the

sample W2. It is thus the conclusion that organisms prevailed during their deposition might

consist mainly of aliphatic medium–long chain moieties but rarely of very long-chains with

more than 40 carbon atoms. Botryococcus braunii and the other algaenan-producing organisms

mainly belonging to the Chlorophyceae featured by very long chain n-alkyl units (reviewed in

Allard et al., 2002; de Leeuw et al., 2006; Metzger and Largeau, 1999; Petersen et al., 2008)

might not be the dominant constituent of the prevailing organisms. Dinoflagellates were

documented by fossils as an important algal material in the Wealden facies in the central LSB,

in addition to the Botryococcus (Schneider et al., 2019). Relative species abundance of

dinoflagellates and Botryococcus directly reflected the fluctuation in waterbody salinity, and

the dinoflagellates were abundant only when salinity increased and short-lived marine flooding

events occurred (Schneider et al., 2019, 2018). 4-methylsteranes probably originating from 4α-

methylsterols in living dinoflagellates (Wolff et al., 1986) are more abundant in the samples

W3–W7 relative to the sample W2 (Figure 2.2D). The prymnesiophyte microalgae of the genus

Pavlova might be an additional source for the 4α-methylsterols (Volkman et al., 1990), but the

bacteria source (notably Methylococcus capsulatus; Bird et al., 1971) is excluded here because

high 4-MSI values are accompanied by high Ster/Hop ratios (Figure 2.2D). Extended n-

hydrocarbon chains have been reported to be generally absent in dinoflagellates and the other

organisms (e.g., prasinophytes, acritarchs, Celyphus rallus and benthic foraminifera; Schneider

et al., 2019) that were adapted to the freshwater–brackish transitional environments of the

Wealden Formation (Arouri et al., 1999; Gelin et al., 1999; Kodner et al., 2009; Kokinos et al.,

1998; Vandenbroucke and Largeau, 2007; Versteegh and Blokker, 2004). The waxiness of

hydrocarbons and heteroatomic classes is observed to decrease logarithmically with the 4-MSI

values among the samples W2–W7 (e.g., R2=0.65–0.87, Figure S2.10D–F).

In addition to the changeable autochthonous microbial communities, the highly variable

OM within the lacustrine Wealden sample set W1–W7 might also be attributed to the distinct

allochthonous terrestrial plant input. The sample W1 that received more terrigenous input

relative to the samples W2–W7 is featured by a lower fraction of aliphatic moieties in its solvent

extract and pyrolysis products (Figure 2.2A, 2.8C, S2.7B–D), with the exception of abundant

soluble aliphatic C14–C36 fatty acids (Figure S2.7A).

In summary, the data support the fact that a lacustrine depositional environment is

characterized by varying kerogen types (Horsfield et al., 1994; Sachsenhofer et al., 1995; Talbot,

1988; Vandenbroucke and Largeau, 2007). Herein, the variability might be mainly related to

the great variations in autochthonous microbial communities (potentially controlled by salinity)

and allochthonous terrestrial plant input.

2.6.2.2 Plentiful Ox but few N1Ox and N1 compounds

The lacustrine Wealden extract W2 displays low relative and absolute abundances of

organonitrogen compounds N1Ox and N1 (Figure 2.3–2.5, S2.4), in accordance with the low

nitrogen content reported for the Botryococcus braunii derived kerogen (Kelemen et al., 1999).

Even though algaenan can provide efficient protection for the proteinaceous moieties through

encapsulation (e.g., Knicker and Hatcher, 2001), a very small amount of nitrogen is originally

contained in Botryococcus braunii (15–22 wt.% protein; Ben-Amotz et al., 1985).

Oxygen has been reported to be less important in the type I kerogen relative to the type II

or III kerogen (Tissot and Welte, 1984) possibly due to the small amount of oxygen originally

in Botryococcus braunii, however, absolute abundance of Ox compounds is high in the

lacustrine Wealden extract W2 (Figure 2.3). The plentiful Ox but few N1Ox compounds in the

extract W2 (Figure 2.3, 2.4) illustrate that oxygen might be bound to a large extent in those

molecules containing no other heteroatoms, partially because algaenan provides an efficient

steric protection for its oxygen-bearing groups from chemical and microbial degradation

(Metzger and Largeau, 1999; Vandenbroucke and Largeau, 2007).

The lacustrine Wealden extracts W3–W7 and W1 contain more organonitrogen

compounds but less abundant Ox class in comparison with the extract W2 (Figure 2.3, 2.4),

which might be attributed to the changes of environmental conditions (e.g., enhanced salinity)

and autochthonous microbial communities. Chemical composition of eukaryotic algae is

generally regarded as species-specific and usually regulated by hydrogeochemical factors like

salinity, nitrate concentration and various other nutrients (e.g., Ben-Amotz et al., 1985; Lewin,

1974; Pohl and Zurheide, 1979; Wood, 1974). However, as reported, protein content of

Botryococcus braunii decreases during haloadaptation while carbohydrates and lipids remain

unchanged (Ben-Amotz et al., 1985; Vazquez-Duhalt and Arredondo-Vega, 1991). Thus, the

organisms adapted to the freshwater–brackish transitional environment of the samples W3–W7

and W1 like dinoflagellates, prasinophytes, acritarchs, Celyphus rallus and benthic foraminifera

are supposed to contain more proteins but less carbohydrates and lipids (Baxby et al., 1994;

Parsons et al., 1961; Raymont, 1980).

The lacustrine Wealden extract W1 generally displays a slightly greater abundance of Ox

compounds and a slightly larger ratio of oxygenated versus reduced organonitrogen compounds

when compared with the extracts W3–W7 (Figure 2.3, 2.4, 2.8B), which might be associated

with its plentiful terrestrial plant input.

2.6.2.3 Weak carbon number preference of the middle–long chain aliphatic Ox

species sourced from lacustrine organisms

n-Alkanes and aliphatic Ox species in the lacustrine rock extracts lack a pronounced

carbon number preference when compared to the coal extracts (Figure 2.2D, 2.7C–F, S2.7G–

I), even though they are partly sourced from higher land plants (e.g., Albaiges et al., 1984;

Matsuda and Koyama, 1977; Rippen et al., 2013). This might to some extent be related to the

advanced degradation of plants during the riverine or eolian transport (e.g., Matsuda and

Koyama, 1977). Besides, carbon number preference of n-alkanes and aliphatic Ox species

originated from autochthonous microbial communities might be less pronounced (e.g.,

Volkman et al., 1998), or even opposite to the allochthonous plants-derived compounds

constituting a specific DBE species. For instance, while the positive APPI accessible 2 DBE O2

species in the lacustrine rock extracts exhibits C23, C25, C27, C29 as the major homologues, an

even number predominance occurs in the coal extracts, thus, the odd number dominated

diketones sourced from lacustrine autochthonous communities like Botryococcus braunii

(Gatellier et al., 1993) might predominate over the allochthonous C22–C30 even number

dominated ketoaldehydes from plant protective substances constituting this DBE species. Take

the lacustrine Wealden extract W2 as an example, carbon number preference of its positive

APPI accessible 1 DBE O1 (even), 2–4 DBE O3 (even), 3, 4 DBE O2 (odd) species and its

negative ESI ionizable 4 DBE O2 (odd), 1, 2 DBE O3 (odd) species in the range of 22–30 are

also opposite to that of the coal extracts (e.g., Figure 2.7D, S2.7G), thus, these species might

predominantly derive from lacustrine autochthonous microbial communities as even number

dominated aldehydes (Metzger et al., 1989), unsaturated hydroxy fatty acids (Volkman et al.,

1999), and odd number dominated unsaturated diketones (Gatellier et al., 1993), keto-diols

(Bauersachs et al., 2015). In contrast, the other aliphatic Ox species in the Wealden extracts

might be plants-derived compounds admixture in variable proportions with the lacustrine

autochthonous materials showing similar but less pronounced carbon number preference for

example as the even-number dominated saturated and unsaturated fatty acids (Douglas et al.,

1969; Řezanka, 1989), (poly)hydroxy-fatty acids, dicarboxylic acids (Dunstan et al., 1992;

Gelin et al., 1997; Volkman, 2006; Volkman et al., 1999, 1998, 1980) and the odd number

dominated methyl-branched fatty acids (Metzger et al., 1991); the sample W1 that received

plentiful allochthonous terrigenous input displays a stronger carbon number preference of these

species relative to the samples W2–W7 (e.g., Figure 2.7C–F, S2.7H, I).

The ratio of middle-chain (C23, C25 or C22, C24) versus long-chain (C27, C29, C31 or C26,

C28, C30) aliphatic Ox species (Figure 2.7C–F) are higher in the lacustrine Wealden extracts

W1–W7 relative to the coals extracts NZ1–NZ3, in accordance with the observations that

middle-chain homologs generally predominate in lacustrine autochthonous microbial

communities (Douglas et al., 1969; Dunstan et al., 1992; Gatellier et al., 1993; Řezanka, 1989;

Volkman et al., 1999, 1998, 1980).

2.6.3 Marine algal input

2.6.3.1 Organonitrogen compounds as the preserved proteinaceous material

While NyOx compounds are detected in all three ionization modes in the studied extracts,

Ny compounds are only detectable by positive APPI and positive ESI (Figure 2.3), mainly as a

result of the large differences in ionization efficiencies between acidic organooxygen

compounds and neutral Ny compounds in especially negative ESI mode (Figure S2.1, Huba et

al., 2016; Hughey et al., 2004).

The marine Posidonia samples P1–P3 received substantial protein-rich marine algae input

as illustrated by their high Ster/Hop ratios, followed by the marine Dynow sample M1 and the

marine Lower Schöneck sample M3 (Figure 2.2D). High abundances of organonitrogen

compounds in their extracts in absolute and relative terms (Figure 2.3, 2.4) represent the

molecular signatures of protein-rich marine algae that have been preserved via a ‘‘degradation-

recondensation’’ route (del Rıo et al., 2004; Huc, 1980; Kelemen et al., 1999; Vandenbroucke

and Largeau, 2007). The superimposing impact of thermal maturity on the relative abundance

of organonitrogen compounds ((Ny + NyOx)/Ox) is observed at the example as the similar values

for the early-mature lacustrine Wealden samples W1 and W3–W7 and for the immature marine

Dynow and Schöneck samples M1–M3 (Figure 2.4B, C): even though nitrogen content of

kerogen will not change much after early diagenesis until the end of oil window

(Vandenbroucke and Largeau, 2007), the temperature-sensitive organooxygen compounds are

reduced via decarboxylation and dehydration (Covas et al., 2019; Poetz et al., 2014). Hence,

NyOx/(NyOx + Ox) ratio is proposed. It is less affected by thermal stress because both Ox and

NyOx decrease in abundance with the increased thermal stress. It positively correlates with the

Ster/Hop ratio independently of ionization modes (R2=0.60–0.78, Figure 2,8A, S2.10H, I).

2.6.3.2 Abundant multi-nitrogen containing compounds formed via random

recondensation

Large amounts of N2 and N2Ox compounds are present in the marine rock extracts as

expressed by their high average nitrogen numbers of Ny and NyOx classes (Figure 2.5, S2.4,

S2.5). Substantial amino acids degraded from protein-rich marine organisms are the basic

building blocks for the formation of considerable N2Ox and N2 compounds during the

subsequent random recondensation (Vandenbroucke and Largeau, 2007). The marine rock

extracts consistently have higher average nitrogen numbers of NyOx than the lacustrine rock

extracts (Figure 2.5C, S2.5A–C), but solvent extracts of some lacustrine non-calcareous shales

such as W6 and W7 even have higher average nitrogen numbers of Ny relative to solvent

extracts of the marine calcareous shales or marls like the Posidonia sample P3 (Figure S2.5G,

H). Besides, the marine carbonate-free claystone M2 of the Upper Schöneck Formation that

received a smaller contribution from protein-rich marine algae relative to the other marine

calcareous shale or marl samples (Figure 2.2D) displays a lower average nitrogen number of

NyOx compounds (Figure 2.5C, S2.5B) but a higher average nitrogen number of Ny (Figure

S2.5G, H). These situations both illustrate that sorptive protection provided by clay minerals

during early diagenesis (Vandenbroucke and Largeau, 2007; Yue et al., 2021) is supposed to

be more important for the N2 rather than the N2Ox compounds whose nitrogen functional groups’

reactivity might be affected by stereo-electronic effects such as steric shielding of oxygen atoms.

The crossplot of average oxygen number versus average nitrogen number for NyOx class in

distinct modes work efficiently in differentiating samples associated with various OM types

(terrestrial, lacustrine and marine, Figure 2.5C, S2.5A, B).

2.6.3.3 Weak carbon number preference of the middle–long chain aliphatic Ox

species originated from marine organisms

Carbon number preference of long chain n-alkanes and aliphatic Ox species in the marine

rock extracts is less pronounced, or even opposite to the coal extracts (e.g., Figure 2.2D, 2.7C–

F, S2.7G–I), partly because n-alkanes and aliphatic Ox species originating from marine

autochthonous communities display a less pronounced (e.g., Volkman et al., 1998, 1980), or

even opposite carbon number preference when compared with the allochthonous plants-derived

compounds constituting a specific DBE species.

The positive APPI ionizable 2 DBE O1 species in the marine Posidonia extracts P1–P3

exhibits C23, C25, C27, C29, C31 as the major homologues, while an even number predominance

prevails in the coal extracts and the marine Dynow and Schöneck extracts M1–M3 (Figure

S2.7H), thus, abundant odd number dominated unsaturated ketones might originate from

autochthonous microbial communities prevailing during sedimentation of the Posidonia

samples but not of the Dynow and Schöneck samples (summarized by Zhang et al., 2016). In

contrast, the positive APPI accessible 2 and 3 DBE O2 (odd, C23–C31) and 3 DBE O3 (even,

C24–C28) species in the Dynow and Schöneck extracts especially the Upper Schöneck extract

M2 exhibits an opposite carbon number preference with the coal extracts and the Posidonia

extracts, thus, substantial odd number dominated saturated and unsaturated diketones and even

number dominated diunsaturated hydroxy fatty acids might source from autochthonous

communities prevailing during sedimentation of the Dynow and Schöneck samples but not of

the Posidonia samples (Volkman, 2006; Volkman et al., 1980). The dominance of C28 4 DBE

O1 compounds being present only in the Dynow and Schöneck extracts M1–M3 in positive

APPI mode correlates with their high concentrations of C28 steranes (mainly sourced from

diatoms, Grantham and Wakefield, 1988), possibly as C28 sterols.

Ratios of the middle-chain (C23, C25 or C22, C24) versus long-chain (C27, C29, C31 or C26,

C28, C30) aliphatic Ox species are higher in the marine rock extracts when compared with the

coal extracts (Figure 2.7C–F), in accordance with the observations that middle-chain species

commonly predominate in the marine autochthonous communities (e.g., Řezanka, 1989;

Volkman, 2006; Volkman et al., 1980). The middle-chain C22 and C24 homologues are strongly

enriched principally in the Dynow extract M1, the Lower Schöneck extract M3, the Posidonia

extracts P1and P2, and the lacustrine Wealden extract W1 (e.g., Figure 2.7D, E), possibly

reflecting variations in autochthonous organisms input within each sample set.

2.7 Summary and Conclusions

Direct infusion FT-ICR-MS measurements reveal how sedimentation and preservation of

marine algae, lacustrine Botryococcus braunii and terrestrial plants impact the high-molecular-

weight organooxygen and organonitrogen compound inventories in sedimentary rocks that are

soluble in common organic solvents.

The selectively preserved highly aliphatic algaenan characterizes the lacustrine

Botryococcus braunii input by substantial organooxygen and organonitrogen compounds

containing > 40 carbon atoms. Algaenan sterically protects its oxygen-bearing groups and

proteinaceous moieties from degradation, but Botryococcus braunii originally contains low

amounts of protein, thus featuring the preserved OM by abundant Ox but few N1Ox and N1

compounds. Plentiful organonitrogen compounds, especially substantial N2 and N2Ox classes,

represent signatures of protein-rich marine algae which were preserved via degradation-

recondensation pathway.

Coals as the in-situ deposits of terrestrial plants consist predominantly of the aromatic

derivatives sourced from lignin and tannin, and the aliphatic moieties derived from plant

protective substances like cutan, cutin, suberan, suberin and waxy materials, which are

selectively preserved during sedimentation and diagenesis because of their very high resistance

to chemical and microbial degradation or due to the in-situ polymerization of waxes. The former

part is indicative by substantial (poly) oxygen-bearing aromatic compounds in forms of both

Ox and N1Ox, with possible structures as phenolic ketones, phenolic carboxylic acids as well as

their condensation products with nitrogenous biodegradation products. The latter part is a minor

fraction of the total organic constituents; the pronounced even or odd carbon number

predominance of n-alkanes and aliphatic Ox compounds with the major homologs in the range

of 26–31 illustrates that cutan and waxes rich in long-chain homologues predominate over the

cutin, suberan and suberin comprising middle-chain C≤24 monomers. In contrast, a high number

of middle-chain homologs (C23, C25 or C22, C24) in the marine and lacustrine rock extracts

reflects the contributions from algal and bacterial communities.

2.8 Acknowledgments

This study is financially supported by the Chinese Scholarship Council (CSC) [Grants

No. 201606450015] and Technical University of Berlin Center for Junior Scholars (CJS).

Cornelia Karger, Anke Kaminsky, Kristin Günther and Ferdinand Perssen in GFZ are

acknowledged for their technical support. We are grateful to Deolinda Flores and two

anonymous reviewers for their careful and constructive reviews of this paper.

2.9 Supplementary material

Figure S2.1. Comparison of the ionization ranges of positive APPI, negative ESI and positive

ESI modes, after Gross (2017) and Huba et al. (2016). “V” stands for successful ionization, while “-”

marks nonionizable species.

Figure S2.2. (A–D) Parameters developed based on GC-MS and GC-FID results providing

organic matter input (TAR and Pr/Ph) and thermal maturity (C29 βα/αβ hopanes and C29 ααα 20S/(20R

+ 20S) steranes) information. TAR: terrigenous/aquatic ratios. Pr/Ph: pristane/phytane. (E) Ternary

diagram of C27–C29 regular sterane isomers (ααα (20S + 20R) and αββ (20S + 20R)) for typing organic

matter input, modified after Rippen et al. (2013) and Grantham and Wakefield (1988).

Figure S2.3. Hopane traces. Peaks in blue, green and red colour mark out αβ, ββ and βα hopanes,

respectively. The red dot and the red diamond respectively mark out C29 30-norneohop-13(18)-ene and

C30 neohop-13(18)-ene. Ts: 18α-trisnorneohopane. Tm: 17α-trisnorhopane.

Figure S2.4. Compound class distributions of Ox, Ny and NyOx elemental classes detected with

distinct modes.

Figure S2.5. Average oxygen or nitrogen numbers for NyOx, Ox and Ny classes detected in distinct

modes.

Figure S2.6. DBE distributions of the negative ESI accessible N1Ox (x=2–5), the positive ESI

ionisable Ox (x=2, 3), N1, N1O1 as well as the positive APPI detectable Ox (x=1–4), N1, N1Ox (x=1–3)

classes, which are normalized by the most abundant species (DBEmax_abund) in each specific

compound class. DBE distributions of those classes whose abundances lower than 1% TMIA are not

displayed here.

Figure S2.7. (A–I) Some representative parameters describing DBE and carbon number

distributions of Ox and N1 compounds under distinct modes, including DBE1-4/DBEAll ratio, average

DBE value and EOPI. (J–R) Slope extracted from the linear correlations between average DBE or carbon

numbers of N1Ox or ≥ 5 DBE Ox classes and the respective oxygen numbers (See Figure 6B, S8).

Figure S2.8. Average DBE or carbon number of N1Ox or ≥ 5 DBE Ox species detected in distinct

modes are plotted over the respective oxygen numbers. Average DBE or carbon numbers of those

species whose abundances lower than 1% TMIA are not displayed here.

Figure S2.9. (A–D) Crossplot of the NyOx/(NyOx + Ny) ratio and the pyrolysis derived oct-1-ene

amount (% n-C8:1) or the Pr/Ph ratio. (E, F) The % n-C8:1 index plots against average DBE value of the

positive APPI ionizable N1O1 class or the negative ESI accessible ≥ 5 DBE O3 species. (G, H) The % n-

C8:1 ratio plots against the slope extracted from the linear correlation between average DBE values of

the positive APPI or the negative ESI ionizable ≥ 5 DBE Ox species and the respective oxygen numbers

(see Figure 6A, S8).

Figure S2.10. (A–C) The pyrolysis derived C6+ n-alkenes and n-alkanes amount (% n-C6+) plots

against average carbon number of the positive APPI ionizable N1O1, the positive ESI accessible N1 or

the negative ESI detectable ≥ 5 DBE O3 species. (D, E) 4-MSI value plots against average carbon

number of the positive APPI ionizable N1O1 or the positive ESI accessible N1 compounds. (F) Crossplot

of the 4-MSI value and the % n-C6+ ratio. (G–I) Crossplot of the NyOx/(Ox + NyOx) ratio and the

Ster/Hop.

3 BIOTIC AND PALAEOENVIRONMENTAL

SIGNATURES IN ORGANOSULFUR COMPOUNDS

OF IMMATURE ROCKS2

3.1 Abstract

Organosulfur compounds (OSCs) in sedimentary rocks are considered to have formed

primarily by abiotic incorporation of inorganic sulfur species into biogenetic functionalized

molecules during early diagenesis, thus preserving carbon skeletons of appropriate

biomolecules. OSCs could be characterized at a molecular level by Fourier transform ion

cyclotron resonance mass spectrometry (FT-ICR-MS) even when they are small in amounts and

large in molecular weights. Herein, to reveal the palaeoecological and palaeoenvironmental

information that OSCs have recorded but might not be contained in other biomarkers, OSCs’

composition in solvent extracts of rocks with different geological histories were determined

utilizing FT-ICR-MS. The analyzed natural laboratories are the marine Schöneck, Dynow and

Posidonia formations and the lacustrine Wealden Formation which are in the late diagenetic or

early catagenetic stages.

The prevailing iron-deficient sulfidic depositional settings of the marine Posidonia and

Schöneck formations are reflected by abundant OSCs bearing up to three sulfur atoms. The

high ratios of reduced relative to oxidized forms (Sz versus SzOx) further illustrate the restricted

presence of oxidants at the oxic-anoxic interfaces. The high average oxygen numbers of S1Ox

compounds and the exclusive presence of nitrogenous OSCs (SzNy and SzNyOx) found in the

marine rock extracts document the high abundances of polyoxygenated compounds and

proteinaceous moieties in marine organisms that can be sulfurized. In contrast, the lacustrine

organisms contain abundant sulfurizable aliphatic moieties.

The observed prominent enrichment of Sz and SzOx compounds containing 40, 35, 30, 25

carbon atoms are associated with the selective and efficient preservation of polyfunctionalized

2 This chapter has been published as: Huiwen Yue, Brian Horsfield, Hans-Martin Schulz, Shengyu Yang, Andrea

Vieth-Hillebrand, Stefanie Poetz, 2023. Preservation of biotic and palaeoenvironmental signatures in

organosulfur compounds of immature fine-grained sedimentary rocks. International Journal of Coal Geology, 265,

104168, (postprint), https://doi.org/10.1016/j.coal.2022.104168.

biomolecules via sulfurization, such as C40 carotenoids, C35 bacteriohopanepolyols, C30

unsaturated tetracyclic polyprenoid alcohols, or C25 or C30 highly branched isoprenoid (HBI)

polyenes. The strong enrichment of sulfurized C35 bacteriohopanepolyols can be developed as

an indicator of the low levels of oxygen exposure prior to sulfurization, which occur only in the

Dynow and Schöneck formations. The prominent enrichment of sulfurized carotenoids is

generally associated with high primary productivity. While the strongly enriched sulfurized

HBI polyenes in the Upper Schöneck Formation is indicative for diatom blooms, the precursors

of C30 pentacyclic polyprenoid organosulfur compounds are more abundant in fresh/brackish

water algae.

3.2 Introduction

The geochemical fate of organic matter (OM) and sulfur are intertwined through a

biogeochemical web of oxidation-reduction reactions (summarized by Pratt and Davis, 1992).

The high organic carbon content (> 0.5 wt%) in shales generally owe their presence to anoxia

during deposition as a result of enhanced primary productivity (e.g., Brumsack, 1986) and water

stratification (e.g., Leventhal, 1989). The depletion or exclusion of molecular oxygen forces

microbiota to utilize alternative electron acceptors to oxidize OM for energy production, such

as sulfate (see Widdel and Hansen, 1992 for a detailed review on sulfate reducing bacteria). Its

end products are reduced sulfur species (typically as H2S) and could be consumed during early

diagenesis via oxidation or through the formation of iron sulfides or OSCs (Vairavamurthy et

al., 1994).

Sulfur only constitutes about 1% on average of the dry weight of living organisms. It

resides principally as amino acids cysteine, cystine, and methionine (Goldhaber and Kaplan,

1974; Shen and Buick, 2004; Sievert et al., 2007) that are labile during diagenesis (de Leeuw

and Largeau, 1993). Thus, more often than not, OSCs in sedimentary rocks are formed from

the abiotic introduction of inorganic sulfur into OM after sedimentation rather than inherited

from organisms (de Graaf et al., 1992; Schouten et al., 1993; Vairavamurthy et al., 1994). It has

been estimated that at least 75–80% of the total sedimentary organic sulfur came from abiotic

sulfurization (Anderson and Pratt, 1995; Werne et al., 2004, 2003).

OSCs represent one of the three major sedimentary sulfur sinks, in addition to sulfate and

sulfide minerals particularly pyrite. Extensive OM sulfurization typically occurs in iron-poor

environments where terrestrial detrital input is low, because reactive iron is considered to

outcompete OM for sulfur incorporation (Berner, 1985, 1984; Damsté et al., 1989a; Hartgers et

al., 1997).

The reactive inorganic sulfur pools include H2S generated by microbial sulfate reduction

and its oxidation intermediates like HSx-, Sx2-, S2O32- and SO32- (Vairavamurthy et al., 1995;

Werne et al., 2004). Sulfurization of various organic compounds occurs rapidly within the

sediment column on a timescale of 60–10,000 years (summarized by Kutuzov et al., 2020), and

in extreme cases it starts within the anoxic or euxinic water column on a timescale of days

(Kutuzov et al., 2020; Raven et al., 2016; Wakeham et al., 2007).

The potential and rate of a given biomolecule undergoing sulfurization strongly depends

on its reactivity (Adams, 2014; Amrani and Aizenshtat, 2004b; Kok et al., 2000; Schouten et

al., 1994): carbonyl and conjugated double bonds are the most reactive groups (Schouten et al.,

1994), whereas the less reactive functionalities like isolated double bonds and alcohols could

be altered to labile moieties via low-temperature biological and chemical diagenetic alterations

such as dehydration, oxidation, double bond migration and thus increasing their sulfurization

potentials (Amrani, 2014; Blumenberg et al., 2010; Grossi et al., 1998; Rontani et al., 1999;

Schaeffer et al., 2006).

The natural sulfurization can take place via substitution of the oxo-groups or via addition

at the double bonds (e.g., Kohnen et al., 1990; Schouten et al., 1994; van Dongen et al., 2003a,

2003b). Two principal routes have been proposed (Damsté et al., 1989c): a. intramolecular

addition, in which sulfur is incorporated into organic molecules and principally rearranged to

form a ring, such as thiolane, thiane, thiophene, dithiane, trithiepane, and organic sulfonate (e.g.,

Amrani, 2014; Kohnen et al., 1991c; Schaeffer et al., 2006; Vairavamurthy et al., 1994; Werne

et al., 2003); b. intermolecular addition, which forms macromolecules via sulfide or polysulfide

bridges and contributes to the formation of kerogen (e.g., Adam et al., 1993; Kohnen et al.,

1991b; Riboulleau et al., 2000). The compounds created by intramolecular sulfurization may

also be further bound into macromolecules.

Since organosulfur compounds potentially preserve the carbon skeletons of appropriate

functionalized lipids and the information concerning the original sites of functionalities, they

have been considered as molecular indicators with an excellent potential for palaeoecology and

palaeoenvironment assessment (reviewed by Damsté and de Leeuw, 1990b), even though these

indicators’ research and applications are primarily restricted to the high organic-sulfur samples

partly due to the analytical limitations. For instance, C25 HBI thiophenes can be traced back to

the sulfurization of C25 HBI polyenes biosynthesized by diatoms (Kohnen et al., 1990). C37 and

C38 2,5-dialkylthiolanes and -thiophenes and 2,6-dialkylthianes could be a reminiscence of C37

and C38 unsaturated ketones and alkenes from prymnesiophytes (e.g., Damsté et al., 1988). C40

lycopadiene and C34 (bi)cyclobotryococcene derived cyclic sulfides were respectively

associated with the Botryococcus braunii algae races L and B (Grice et al., 1998). C30

isoprenoid thiophenes and C35 hopanoid thiophenes have been linked to the sulfurization of

squalenes and bacteriohopanepolyols in bacteria (e.g., Damsté et al., 1987b). Moreover,

structural isomers of C20 isoprenoid thiophenes can be traced back to sulfurization of different

biochemicals (phytadienol and geranylgeraniol as moieties of certain bacteriochlorophylls

restrictedly occurring in hypersaline environments on the one hand, phytol widespread in

photoautotrophs as moieties of chlorophylls or certain bacteriochlorophylls on the other hand),

whose distribution patterns respond to changes in palaeosalinity (Damsté and de Leeuw, 1990a,

1987; Scheer, 2006).

Often, the information preserved by OSCs is not contained anymore, or has not been

contained at all, in the hydrocarbon or oxygenated biomarkers of very immature rock bitumen

(Damsté and de Leeuw, 1990b; Grice et al., 1998; Kohnen et al., 1991a); for instance, the C34

(bi)cyclobotryococcene has only been observed as sulfur incorporation products in an ancient

euxinic ecosystem (Grice et al., 1998). Thus, the sulfur-bound biomarkers should be taken into

account for a complete and thus more correct characterization of the palaeoecology and

palaeoenvironment especially for the very immature rocks containing large amounts of organic-

sulfur (e.g., Kohnen et al., 1991a). These functionalized structures selectively protected by early

diagenetic sulfur quenching could only be released during late diagenesis via cleavage of C-S

or S-S bonds, resulting in increased concentrations of corresponding saturated hydrocarbon

biomarkers such as C25 HBI alkane (Kohnen et al., 1991a; Werne et al., 2000) or C35

homohopane (Köster et al., 1997; Schaeffer et al., 2006).

The oxidized organosulfur compounds like sulfoxides and sulfones have attracted far less

research attention relative to the reduced species such as thiophene, thiolane, or thiane (e.g.,

Damsté and de Leeuw, 1990b), because they are widely regarded as the oxidation products of

reduced organosulfur compounds during long-time storage or outcrop weathering (Schouten et

al., 1995), In contrast, Pomerantz et al. (2014) argued that sulfoxides could be formed by

oxidation during oil generation. Alternatively, the oxidized species like sulfoxides and

sulfonates have been speculated to be formed during early diagenesis, and their abundances

might be sensitive to depositional environment even though the correlations have not been well

established (Bolin et al., 2016; Vairavamurthy et al., 1995, 1994). Overall, there are still gaps

in understanding the geochemical significance of the oxidized sulfur forms.

FT-ICR-MS prompts studies on the high-molecular-weight OSCs, especially those

comprising multiple heteroatoms. Cooperated with electrospray ionization (ESI) in negative

and positive modes, acidic and basic OSCs such as sulfonic acids and sulfoxides can be

respectively accessible (Liu et al., 2018; Poetz et al., 2019, 2014), whereas atmospheric pressure

photoionization (APPI) in positive mode broadens the ionization range to the less polar species

such as thiophenes (Purcell et al., 2006; Robb and Blades, 2008). These achieved information

have shown great potential in distinguishing geological samples associated with different

depositional conditions and biomass input (Lu et al., 2014), for instance, marine crude oils were

reported to differ from the lacustrine ones by abundant neutral N1S1 class (Orrego-Ruiz et al.,

2020), low S1O1/S1 index and high S2/S1 ratio (Li et al., 2011). Up to now, FT-ICR-MS has

been mainly applied to conventional crude oils or mature rock extracts. Their contained OSCs

may have already altered by maturation, expulsion, migration and in-reservoir alternations (Han

et al., 2018b, c; Liao et al., 2012; Liu et al., 2015b; Oldenburg et al., 2017; Pan et al., 2019),

therefore impeding a deconvolution in terms of their origin.

To better understand how biomass input and depositional environment govern the

formation and occurrence of OSCs, rock samples from different depositional settings in the late

diagenetic or early catagenetic stages were investigated. They are the Paleogene marine

Schöneck and Dynow formations, the Lower Jurassic marine Posidonia Formation, and the

Lowermost Cretaceous Wealden Formation from a lacustrine deposystem. A combination of

negative ESI, positive ESI and positive APPI modes was used to achieve a holistic portrait of

the analytes.

3.3 Sample Description

3.3.1 Marine Lower Toarcian Posidonia Shale in the Lower Saxony Basin

Three samples of the Lower Toarcian Posidonia Shale holding type II kerogen were

selected from the wells Wenzen (P1, 0.45% Ro, huminite/vitrinite reflectance) and Wickensen

(P2 and P3, 0.52% Ro) in the Hils syncline area of the Lower Saxony Basin (LSB), northwest

Germany (Table 3.1, Figure 3.1A; Littke et al., 1988). During the Early Jurassic, present-day

western and central Europe was located between 20° and 40°N on the broad and extensive

Laurussian continental shelf, which opened towards the southeast into the deep Tethyan Ocean

and connected to the Arctic Sea by a narrow seaway (Ziegler, 1988). This shallow shelf area

was composed of multiple islands of variable sizes, submarine sills, and deeper subbasins

(Ziegler, 1988). The Lower Toarcian deposition in the Hils syncline area was initiated after sea-

level rise and widespread transgression over the Pliensbachian disconformity surface (Littke et

al., 1991). It displays a threefold stratigraphic subdivision (Littke and Rullkötter, 1987): the

lower marlstone (unit I), the middle calcareous shale with bivalve shells (unit II, absent at

Wenzen), and the upper calcareous shale (unit III). While the sample P2 is selected from the

unit II, the samples P1 and P3 are both chosen from the unit I. During deposition of the

Posidonia Shale, water depths persisted deeper than the wave base (Littke et al., 1991). Whether

or not bottom waters were completely anoxic or periodically oxygenated was intensely debated

(Littke and Rullkötter, 1987; Littke et al., 1991; Song et al., 2017; Sundararaman et al., 1993).

Song et al. (2017) suggested that anoxic conditions could extend to the photic zone episodically.

Throughout the Posidonia Shale in the wells Wenzen and Wickensen, the sulfur content is

around 3–5 wt.% on average (Littke et al., 1991; Song et al., 2017). A constantly high extent of

OM sulfurization potentially indicates an iron-deficient environment (Bernard et al., 2012;

Song et al., 2017).

Table 3.1. Geological background information, huminite/vitrinite reflectance (Ro), total organic

carbon content (TOC), total sulfur content (TS), and kerogen type of the studied rock samples,

summarized from Littke et al. (1991), Rippen et al. (2013), Song et al. (2017), and Yang and Schulz

(2019). “/”: no available data.

G-

number

Formation Age Basin Settings

Depth

(m)

TOC

(wt.%)

Kerogen type

(%)

G010272

Wealden Berriasian

Lower

Saxony

Lacustrine

833.3

1.7

3.02

III (phenol poor)

0.50–

0.60

W2 G010299 917.0 3.8 2.82 I

W3 G010302 919.3 4.7 /

I/II

W4 G010317 972.8 9.3 2.94

G010319

974.6

8.1

2.79

W6 G010322 994.9 4.5 3.85

W7 G010324 997.3 3.6 5.34

P1 G000420

Posidonia Lower

Toarcian

Marine

/ / 3–5

average

0.48

P2 G007144 46.5 10.1 0.53

P3 G007156 58.2 9.9

M1 G015912 Dynow

Eocene-

Oligocene Molasse

1378.6 1.5 0.79 II/III

0.35

M2 G015917 Upper Schöneck 1385.8 7.3 3.58 I/II

G015918

Lower Schöneck

1389.4

2.6

2.15

II/III

3.3.2 Marine Eocene–Oligocene Schöneck and Dynow formations in the

Molasse Basin

Three immature Eocene–Oligocene samples (< 0.35% Ro) from the Schöneck Fm.

(nannoplankton zone NP19–20 to NP22) and the overlying Dynow Fm. (NP23) are part of this

study (Schulz et al., 2005, 2004, 2002). The marlstones M1 and M3 respectively from the

Dynow and the Lower Schöneck formations are of type II/III kerogen, whereas the kerogen in

the carbonate-free claystone M2 chosen from the lower part of the Upper Schöneck Fm. is

classified as type I/II (Table 3.1, Figure 3.1A; Yang and Schulz, 2019; Yue et al., 2022). These

three samples are all from the borehole Oberschauersberg 1, which is located on the upper

palaeo-basin slope of the Eastern Alpine (Austrian) Molasse basin, representing the western

part of the Central Paratethys (Schulz et al., 2002). The separation of the Paratethys from the

Tethys as a marginal sea commenced at the Eocene/Oligocene boundary and reached a

maximum during the middle Kiscellian time (NP23) when the Paratethys lost its connection to

the World Ocean (Popov et al., 1993; Rögl, 1999, 1996). The Lower Schöneck marl deposition

was characterized by dysoxic/euxinic bottom waters (Schulz et al., 2005, 2002). High amounts

of OSCs rather than pyrite were formed from reactive sulfur because of the iron limitation

(Gratzer et al., 2011; Schulz et al., 2002; Yang and Schulz, 2019). The Upper Schöneck organic-

rich mud deposition was mainly associated with photic zone anoxia and high surface water

salinity (Schulz et al., 2002). Pyrite formation in this scenario was principally limited by the

lack of sulfate (Schulz et al., 2002). The environment changed significantly over the uppermost

Schöneck Fm. probably due to the increased continental run-off, including a decrease of both

surface water salinity and bottom water anoxia (Schulz et al., 2004, 2002). During NP 23,

estuarine circulation patterns established, photic zone anoxia again occurred, and massive

blooms of coccolithophorids happened (Schulz et al., 2005, 2004). The increasing fresh water

ingressions resulted in brackish surface water (Schulz et al., 2005, 2004). The total sulfur

content averages 1 wt.% throughout the Dynow marlstone, compared to an average of 3 wt.%

in the Lower Schöneck marlstones and the Upper Schöneck black shales (Table 3.1; Schulz et

al., 2005, 2004, 2002).

3.3.3 Lacustrine Berriasian Wealden Formation in the Lower Saxony Basin

Seven early-mature samples W1–W7 (0.50–0.60% Ro) belonging to the non-calcareous

shale/marlstone intervals of the Wealden Fm. (Berriasian) were collected from the well EX-A

in the central part of the LSB (Rippen et al., 2013). They contained type I–III kerogen (Table

3.1, Figure 3.1A); remains of Botryococcus braunii were commonly observed (Rippen et al.,

2013). The Wealden Fm. comprises six lithostratigraphic units, namely Wealden 1–6 (Elstner

and Mutterlose, 1996). While the samples W2–W7 in depth intervals of 910–998m represent

the unit Wealden 3, the sample W1 selected from a stratigraphically higher interval is younger

(Rippen et al., 2013). A shift from a freshwater-dominated lacustrine system (Wealden 1)

towards more brackish conditions (Wealden 2–4) with intercalations of short-lived marine

transgressions (e.g., at the transition between Wealden 3 and 4 units; Elstner and Mutterlose,

1996; Mutterlose and Bornemann, 2000; Schneider et al., 2019; Strauss et al., 1993) was

reported. In the latest Berriasian (Wealden 5–6), the marine influence intensified. Anoxic–

dysoxic bottom water conditions have been documented to exist over long periods in the central

basin during the Berriasian (Berner, 2011; Froidl et al., 2021a, 2021b; Rippen et al., 2013;

Schneider et al., 2019), which might temporarily reach the photic zone (Blumenberg et al.,

2019). Oxic bottom waters at least occasionally occurred, which can be evidenced by the

presence of benthic organisms (ostracods, bivalves; Rippen et al., 2013; Schneider et al., 2019).

Total sulfur content shows a strong variability through the Wealden Fm. in the well EX-A

(1.41–5.85 wt.%, 3.18 wt.% on average); in a large number of samples sulfur is exceptionally

enriched (Table 3.1; Rippen et al., 2013). Sulfur could be supplied by the dense seawater

invading from the Proto-North Sea, or by the underlying evaporitic Münder Fm. or the salt-

leaking Permian Zechstein diapirs during freshwater phases (Rippen et al., 2013; Schneider et

al., 2019). However, low amounts of sulfur were incorporated as OSCs (Rippen et al., 2013);

pyrite and sulfate minerals such as gypsum were observed (Mathia, 2015).

3.4 Analytical Methods

3.4.1 Open system pyrolysis-gas chromatography (Py-GC)

Open system Py-GC was used to provide rapid structural elucidation of the kerogen inside

whole rock. Up to 35 mg powdered rock sample was placed into glass capillaries and secured

by thermally cleaned quartz wool at both ends. Prior to pyrolysis, non-isothermal heating at

300°C for 4 min was used to thermovaporize and vent volatile products. Pyrolysis products

released over the range 300–600°C (at a heating rate of 50°C/min, and thereafter held for 2

minutes) were collected in a liquid nitrogen-cooled trap, then liberated by ballistic heating into

an Agilent GC 6890A gas chromatograph equipped with a flame ionization detector (Keym et

al., 2006). Identification of the major components was done manually with the ChemStation©

software from Agilent Technologies based on reference chromatograms.

3.4.2 Organic solvent extraction

Soxhlet extraction was performed on the ground samples for 48 hours at 60 °C using the

ternary azeotropic solvent mixture of methanol, acetone and chloroform (30:38:32, v/v/v). After

asphaltene precipitation (Theuerkorn et al., 2008), the maltenes were separated into aliphatic

hydrocarbons, aromatic hydrocarbons and resin fractions using medium pressure liquid

chromatography (Radke et al., 1980).

3.4.3 Gas chromatography-mass spectrometry (GC-MS)

The aliphatic and aromatic hydrocarbon fractions were individually analyzed by a DSQ

Thermo Finnigan Quadrupole MS coupled to a GC. The GC was equipped with a BPX5 (SGE)

fused silica capillary column (50 m × 0.22 mm × 0.25 µm). 5α-androstane and 1-ethylpyrene

were used as the internal standards for respective quantification of aliphatic and aromatic

biomarkers.

3.4.4 FT-ICR-MS

Total extracts were analyzed by 12 Tesla FT-ICR-MS in positive APPI, positive ESI and

negative ESI modes. Testing and data handling procedures have been described in chapters

2.4.4–2.4.7.

3.5 Results

3.5.1 Low-molecular-weight organosulfur compounds in rock pyrolyzates

and extracts

The open system pyrolysis products of the Posidonia samples P1–P3 and the Lower

Schöneck sample M3 contain large amounts of dimethylthiophenes (DMTs), as illustrated by

their high %2,3-DMT and %2,5-DMT ratios (calculated as 2,3-DMT/(2,3-DMT+o-xylene+n-

C9:1) and 2,5-DMT/(2,5-DMT+toluene+n-C9:1+n-C25:1); see Figure 3.1A and 3.1B), indicating

abundant organic sulfur in their hosted kerogen (di Primio and Horsfield, 1996; Eglinton et al.,

1990). The high values of DBT/Phen (dibenzothiophene/phenanthrene) and MDBT/MPhen

(methyl DBT/methyl Phen) indexes (Figure 3.1C, D) in their solvent extracts further suggest

that abundant sulfur is available for incorporation into OM during their deposition (Hughes et

al., 1995).

The sample M2 from the Upper Schöneck Fm. comprises a relatively smaller amount of

these low-molecular-weight OSCs when compared to the Posidonia samples P1–P3 and the

Lower Schöneck sample M3, as illustrated by its slightly lower DBT/Phen and MDBT/MPhen

indices, and significantly lower %2,3-DMT and %2,5-DMT ratios (Figure 3.1A–D). In contrast,

in pyrolyzates or solvent extracts of the other samples including the Wealden samples W1–W7

and the Dynow sample M1, these low-molecular-weight OSCs are consistently low in amount

or even absent (Figure 3.1A–D).

Figure 3.1. (A, B) Ternary diagrams for typing molecular kerogen structure especially its organic

sulfur content, developed by Eglinton et al. (1990) and di Primio and Horsfield (1996) based on open

system Py-GC results. (C, D) DBT/Phen and MDBT/MPhen ratios, neither DBT nor Phen homologues

can be assigned in spectrum of the Wealden extract W2 due to its poor data quality. (E, F, H, I)

Concentrations of C25 HBI alkane, C30 tetracyclic polyprenoid hydrocarbons, aryl isoprenoids and C19

2,3,5ˊ-6-tetramethyl-2-alkylbiphenyl. (G) C35/C34 homohopanes ratio, neither C35 or C34 homohopanes

can be detected in the Wealden extracts W1 and W2.

3.5.2 High-molecular-weight organosulfur compounds in rock extracts

FT-ICR-MS data on the high-molecular-weight OSCs (Sz, SzOx, SzNy and SzNyOx) in

three ionization modes, negative ESI, positive ESI and positive APPI, are present here in terms

of abundance, compound class, DBE, and carbon number distributions. Negative ESI

measurements of the Wealden extracts W5–W7 and the Upper Schöneck extract M2 are not

considered here for data evaluation and discussion since organic analyte signals in these spectra

are completely suppressed by sodium chloride cluster signals (Figure 3.2, S3.1).

It is observed that, independently of ionization mode, a large number of monoisotopic

peaks are assigned as OSCs in spectra of the Posidonia extracts P1–P3 and the Lower Schöneck

extract M3 representing the highest absolute abundances, generally followed by the Upper

Schöneck extract M2 (Figure 3.2).

Figure 3.2. Peak number and absolute abundance of organosulfur compounds detectable in

distinct modes.

Not only OSCs but also Ny, NyOx, Ox, NaOx, hydrocarbons, metalloporphyrins can be

assigned in the FT-ICR-MS measurements of the studied rock extracts (Figure S3.1). In positive

APPI mode, OSCs are found to account for 35.8–54.6 % of the total monoisotopic ion

abundance (TMIA) in the Posidonia extracts P1–P3 and the Schöneck extracts M2 and M3,

whereas in the other extracts they only constitute 0–26.7 %TMIA (Figure S3.1, S3.2A).

However, in the positive ESI mode, OSCs are observed to represent the highest relative

abundance in the Wealden extract W2 (Figure S3.1, S3.2B), whereas in the negative ESI mode,

the relative abundance of OSCs in the Wealden extract W4 is second only to that of the Lower

Schöneck extract M3 (Figure S3.1, S3.2C).

3.5.2.1 Abundance and compound class distribution of SzOx compounds

In negative ESI mode, OSCs in the both marine and lacustrine rock extracts consist

exclusively of SzOx compounds (Figure S3.3B). In contrast, in positive APPI or positive ESI

modes, SzOx represents a higher fraction of OSCs in the lacustrine rock extracts relative to the

marine rock extracts (86–100% versus 68–84%, Figure 3.3A; 100% versus 30–69%, Figure

3.3B).

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Figure 3.3. Elemental class distributions of the positive APPI or the positive ESI ionizable

organosulfur compounds.

The S1Ox compounds dominate the SzOx class in the studied extracts independently of

ionization mode (Figure 3.4, S3.3). High abundances of S2Ox compounds are solely present in

the Posidonia extracts P1–P3 and the Lower Schöneck extract M3 in positive APPI and positive

ESI modes, as reflected by their highest average sulfur numbers of SzOx compounds (calculated

after ∑𝐼𝐼𝑖𝑖(𝑆𝑆𝑁𝑁𝑁𝑁.)𝑖𝑖𝑖𝑖 ∑𝐼𝐼𝑖𝑖𝑖𝑖

⁄, the (SNo.)i is the numbers of sulfur atoms assigned for a specific signal

i, whereas Ii represents its intensity) among the studied rock extracts, followed by the Upper

Schöneck extract M2. In negative ESI mode, S2Ox compounds are only detected in the

Posidonia extracts P1 and P3, in very low amounts (Figure S3.3B).

S1Ox compounds in both marine and lacustrine rock extracts are dominated by S1O1 class

in positive APPI mode (Figure 3.4). While the low-polarity S1Ox compounds in the lacustrine

rock extracts contain exclusively S1O1 and S1O2 classes, S1O1–S1O5 classes are present in the

marine rock extracts (Figure 3.4) and thus show a larger average oxygen number of S1Ox

compounds (Figure 3.5C; calculated after ∑Ii(ONo.)ii ∑Iii

⁄, the (ONo.)i is the numbers of

oxygen atoms assigned for a specific signal i) among the studied extracts. In negative ESI mode,

the S1O3–S1O7 compounds in the Wealden extracts W3 and W4 are dominated by S1O3 class,

whereas in the other extracts S1O4 is the most abundant class among the S1O3–S1O8 compounds

(Figure S3.3B). Higher average oxygen numbers of acidic SzOx compounds are observed in the

marine rock extracts and the lacustrine type III kerogen related extract W1 (Figure 3.5D). In

positive ESI mode, S1Ox compounds primarily or even exclusively comprise S1O1 class, with

small amounts of S1O2 compounds being only found in the Wealden extract W2, the Posidonia

extracts P1 and P3, and the Lower Schöneck extract M3 (Figure S3.3A).

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Figure 3.4. Compound class distributions of the positive APPI accessible organosulfur

compounds.

Figure 3.5. (A, B) Average sulfur number of the positive APPI or the positive ESI accessible

SzOx class. (C, D) Average oxygen number of the positive APPI or the negative ESI ionizable S1Ox

class. (E–G) DBE1–4/DBEAll ratio of the positive APPI or the positive ESI accessible S1Ox class. (H, I)

DBE0–3/DBEAll ratio of the negative ESI ionizable S1O3 or S1O4 class. (J, K) DBE0–4/DBEAll ratio of the

negative ESI ionizable S1O5 or S1O6 class. Values for elemental or compound classes in extracts with

abundances < 1% TMIA are not included here.

3.5.2.2 DBE distribution of SzOx compounds

The S1Ox compounds in the lacustrine rock extracts in positive APPI, positive ESI and

negative ESI modes are distributed in the DBE ranges of 1–15, 1–10 and 0–10, respectively

(Figure 3.6B–E, S3.4). In contrast, broader DBE ranges (0–21) are generally observed for the

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marine rock extracts, with the only exception being the Dynow extract M1 detected by negative

ESI (0–7).

Figure 3.6. DBE distributions of the positive APPI accessible S1, S1O1, the positive ESI accessible

S1O1, and the negative ESI ionizable S1O3, S1O5 classes, which are normalized by the most abundant

species (DBEmax_abund) in specific compound class. DBE distributions of the compound classes whose

abundances lower than 1% TMIA in extracts are not displayed here.

In both lacustrine and marine rock extracts, the low-polarity S1O1 and S1O2 compounds

and the basic S1O1 compounds always display bimodal (1–4 and ≥ 5 DBE) or trimodal (two

local maxima in ≥ 5 DBE range) DBE distributions (Figure 3.6B, C). The 1–4 DBE species are

predominantly present as aliphatic sulfoxides or sulfones (Hur et al., 2010; Kim and Kim, 2010),

aromatic rings like thiophene, furan or benzene are supposed to be the common constituents for

the ≥5 DBE species. The latter seems also receive contributions from polycyclic non-aromatic

compounds for example as C35 hopanoid sulfoxides (Schouten et al., 1995), as demonstrated by

a strong enrichment of C35 6 DBE S1O1 species in the Dynow and Schöneck extracts M1–M3

(Figure 3.6B, 3.7C). Fraction of these 1–4 DBE compounds within an individual S1Ox class is

described here by DBE1–4/DBEAll ratio. The ratios are always higher in the lacustrine type I–

I/II kerogen related extracts W2–W7 when compared to the marine rock extracts and the

lacustrine type III kerogen related extract W1 (Figure 3.5E–G).

The acidic S1O3 and S1O4 classes here contain abundant 0 DBE species and also show

bimodal or trimodal DBE distributions, but with a pattern as 0–3 and ≥ 4 DBE (one or two local

maxima in the ≥ 4 DBE range; Figure 3.6D). These 0–3 DBE compounds could be aliphatic

organic sulfonic acids or sulfates in which oxygen atoms do not contribute to the DBE (Hughey

et al., 2004; Ren et al., 2019). The bimodal DBE pattern of the acidic S1O5 and S1O6 classes as

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0–4 and ≥ 5 DBE (e.g., Figure 3.6E) possibly illustrates that some oxygen atoms are bound as

carbonyl or carboxylic groups contributing to the DBE. Fraction of these acidic 0–3 or 0–4

DBE compounds within an individual Ox class is described by DBE0–3/DBEAll or DBE0–

4/DBEAll ratios, which are constantly low in the marine rock extracts and the lacustrine type III

kerogen related extract W1 (Figure 3.5H–K).

3.5.2.3 Carbon number distribution of SzOx compounds

The low-polarity S1O1 and S1O2 compounds and the basic S1O1 compounds in the studied

extracts contain up to 68 carbon atoms (Figure S3.4B–D). They generally display monomodal

carbon number distributions, with strong C25, C30, C35 and C40 enrichment being only observed

in some extracts (Figure 3.7A, S3.6). C25 compounds are strongly enriched in the Upper

Schöneck extract M2, chiefly among its 1–2(3) DBE S1Ox (x=1, 2) species (Figure 3.7A, C,

S3.6C, D, S3.7A–C). Among its 4 DBE S1Ox (x=1, 2) species, C26 rather than C25 compounds

are more abundant (Figure S3.7D). S1Ox (x=1, 2) compounds containing 30 carbon atoms are

of high abundance in all the studied extracts (Figure 3.7A, S3.6C, D), and among their 1–8 DBE

species, C30 enrichment occasionally occurs in varying degrees. Among individual 1–4 DBE

S1Ox (x=1, 2) species, C30 enrichment is always prominent in the Upper Schöneck extract M2

(Figure 3.7C, S3.7A–D) but generally in small degree in the other extracts. Among the 5 DBE

S1Ox (x=1, 2) species, strong C30 enrichment is commonly observed, but generally more

prominent in the lacustrine rock extracts relative to the marine rock extracts (Figure 3.7C,

S3.7E). Among the 6–8 DBE species, C30 enrichment is only present in certain extracts, like

the low-polarity 6 DBE S1O1 species in the Wealden extracts W4–W7 and the Posidonia

extracts P1–P3 (Figure 3.7C, S3.7F–H). C35 enrichment is found to be prominent in the Dynow

and Schöneck extracts M1–M3 among their individual 6–8 DBE S1Ox (x=1, 2) species (Figure

3.7A, C, S3.4B–D, S3.7F–H). In the Posidonia extract P1 the C35 6 or 7 DBE S1O1 compounds

are also observed to be strongly enriched, but in the other rock extracts C35 enrichment is rarely

found and consistently in very small degree. C40 enrichment among the 1–15 DBE S1Ox (x=1,

2) species occurs in nearly all the studied extracts excluding those only containing C<40

compounds like the Wealden extract W1 (Figure 3.7A, C, S3.4B–D, S3.6C, D, S3.7). It is found

to be relatively more prominent in the Posidonia extracts P1–P3, the Upper Schöneck extract

M2, and the Wealden extract W3. The other categories of enrichment are also identified. For

instance, while the C20 enrichment among the 1 DBE S1Ox (x=1, 2) species is observed in the

Posidonia extracts P1–P3 and the Lower Schöneck extract M3, the C33 compounds strongly

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dominate the low-polarity 1 DBE S1Ox (x=1, 2) species in the Dynow extract M1 (Figure 3.7C,

S3.7A).

Figure 3.7. Carbon number distributions of the positive APPI accessible (A) S1O1 compound

class, (B) hydrocarbons, (C) 1, 3, 5, 6 DBE S1O1 compounds and (D) 3 DBE hydrocarbons, which are

normalized to the most abundant species (Cmax_abund) in specific compound class or DBE class. The dot

size in (C) and (D) represents the relative abundance of variable compounds within a certain DBE class

in a specific sample.

Among the multi-sulfur bearing classes such as the low-polarity S2O1 and S2O2 classes

found only in the marine rock extracts and the lacustrine rock extract W2, the C40 enrichment

is prevalently prominent, but the C35 enrichment is barely observed (Figure S3.6G, H). In the

Upper Schöneck extract M2, both C30 and C25 enrichment are prominent among its 2–4 DBE

S2Ox (x=1, 2) species, in which the C30 compounds are found to be far more abundant relative

to the C25 compounds (Figure S3.5B, C, S3.8B, C). C30 enrichment can also be observed in the

Posidonia extracts P1–P3 among their (2)3–9 DBE S2O1 species but generally to a low extent,

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whereas in the Lower Schöneck extract M3 a low-level C29 enrichment is found among its 4–

10 DBE S2O1 species (Figure S3.8B).

The OSCs containing more oxygen atoms such as the low-polarity S1Ox (x=3–5) and S2Ox

(x=3, 4) compounds solely found in the marine rock extracts generally do not display

remarkable enrichment of specific species (Figure S3.6I, J, M–O). A relatively high-level

enrichment can only be found among the low-polarity S1O3 or S2O3 compounds, including the

C35 enrichment solely present in the Dynow and Schöneck extracts M1–M3 among their 6–9

DBE S1O3 species, the C30 and C29 enrichment respectively in the extracts P1–P3 and M1–M3

among their 5–9 DBE S1O3 compounds, as well as, the C40 enrichment found in the marine rock

extracts among their 2–13 DBE S2O3 species (Fig. S3.5D, H, S3.6I, M, S3.8A).

The acidic S1O3 and S1O4 compounds in the studied extracts generally contain ≤ 40

carbon atoms and they also show overall monomodal carbon number distributions without

remarkable enrichment of specific species. However, in the Lower Schöneck extract M3, the 1

DBE S1O3 and 6 DBE S1O4 species are observed to be strongly dominated by the C25 and C35

compounds, respectively (Fig. S3.8D, E). In addition, C35 enrichment is also recorded in the

extract M3 among its 6 and 7 DBE S1O3 and 7 DBE S1O4 species (Fig. S3.8D, E).

3.5.2.4 Characteristics of Sz compounds

Sz compounds in the studied rock extracts are only detectable in positive APPI mode

(Figure 3.3, S3.1). They account for 9–30% of the positive APPI accessible OSCs inventories

in most cases, excluding the very low proportions (< 1%) in the lacustrine rock extracts W2 and

W5–W7 (Figure 3.3A). These Sz compounds occur primarily or exclusively as S1 class, a few

S2 and S3 compounds are solely observed in the Posidonia extract P1 and the Schöneck extracts

M2 and M3 (Figure 3.4). Higher ratios of the reduced versus oxidized organosulfur forms Sz/(Sz

+ SzOx) are found in the Posidonia extracts P1–P3 and the Schöneck extracts M2 and M3 when

compared to the Dynow extract M1 and the Wealden extracts W1–W7 (15–31% versus 0–14%,

Figure 3.3A). A better distinction can be made using the S1/(S1 + S1O1) ratio (27–41% versus

0–15%, Figure 3.4).

The S1 compounds in the studied extracts are distributed over a DBE range of 1–22

(Figure 3.6A) and the sulfur atoms could be present as thiolane, thiane, or thiophene. In most

cases they show a monomodal DBE distribution; only in the Wealden extracts W3 and W7 and

the Upper Schöneck extract M2, the relatively high abundance of 1–3 DBE S1 species results

in a bimodal DBE distribution pattern (1–3 and ≥ 4 DBE, Figure 3.6A).

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The S1 compounds typically show a monomodal carbon number distribution in the range

of 17–69, with strong C25, C30, C35 and C40 enrichment being observed only in some extracts

(Figure S4A, S3.6A). C25 enrichment is prominent solely in the Upper Schöneck extract M2

among its 1–4 DBE S1 species (Figure S3.6, S3.7A–D). Even though C25 enrichment can also

be observed in the Lower Schöneck extract M3 among its 1–3 DBE S1 species, it is generally

in small degrees (Figure S3.7A–C). S1 compounds containing 30 carbon atoms are of high

abundance in all the studied extracts (Figure S3.6A), and among their 1–7 DBE S1 species C30

enrichment is commonly observed but to different extents (Figure S3.7). For instance, the C30

enrichment among individual 1–4 DBE S1 species is only constantly prominent in the Upper

Schöneck extract M2 (Figure S3.7A–D), besides, the C30 5 DBE S1 enrichment is found to be

generally stronger in the lacustrine rock extracts relative to the marine ones (Figure S3.7E). C35

enrichment is observed to be prominent in the Dynow and Schöneck extracts M1–M3 among

their 6–8 DBE S1 species (Figure S3.6A, S3.7F–H). C40 enrichment being found mainly among

the 1–15 DBE S1 species is more prominent in the Posidonia extracts P1–P3, the Wealden

extract W3 and the Upper Schöneck extract M2 (Figure S3.6A).

Among the S2 class being only present in the Posidonia extract P1 and the Schöneck

extracts M2 and M3, the C40 compounds are prominently enriched and dominant (Figure S3.5A,

S3.6F). The S2 class in the extract M2, for example, only comprise C40 4–14 DBE, C30 2–6

DBE, and C25 2–5 DBE species, in which the C40 and C30 compounds are far more abundant

relative to the C25 compounds (Figure S3.5A, S3.6F). The S3 compounds being solely observed

in the Posidonia extract P1 and the Lower Schöneck extract M3 only comprise C40 compounds

(Figure S3.5F).

3.5.2.5 Features of SzNy and SzNyOx compounds

Nitrogen-bearing organosulfur compounds SzNy and SzNyOx are only detectable in the

marine rock extracts in positive APPI and positive ESI modes (Figure 3.3A, B, S3.1),

representing 3–11% and 31–70% of the respectively achieved OSCs inventories. They occur

primarily or exclusively as S1N1 and S1N1O1 classes (Figure 3.4, S3.3A), which both exhibit

monomodal DBE (5–24) and carbon number (17–64) distributions showing no prominent

enrichment of specific species (Figure S3.5K, L). Their potential structures could be pyrroles

or pyridines fused with thiophenes or cyclic sulfides.

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3.5.3 Hydrocarbons with polyfunctionalized biomolecule precursors prone to

sulfurization

3.5.3.1 Hydrocarbons detected by GC-MS

Both C25 and C30 HBI alkanes (m/z 238 and m/z 308) are identified in the Upper Schöneck

extracts M2 respectively at concentrations of 130 and 66 ug/g extracts (Figure 3.1E). In the

Lower Schöneck extract M3, only the C25 HBI alkane is detected but in a relatively low

concentration (22 ug/g extract, Figure 3.1E).

C30 tetracyclic polyprenoid hydrocarbons (m/z 259; Holba et al., 2003, 2000; Poinsot et

al., 1998) are identified in all the studied extracts. They generally represent higher

concentrations in the type I–I/II kerogen related extracts, i.e., the lacustrine rock extracts W2–

W7 and the marine Upper Schöneck extract M2; in the extract W3 the highest value is present,

39ug/g extract (Figure 3.1F).

C35 homohopanes (m/z 191) are abundant in the marine Schöneck extracts M2 and M3

and the marine Posidonia extract P1 displaying the largest C35/C34 homohopane ratios among

the studied extracts (1.5–2.2), followed by the other marine rock extracts including M1, P2 and

P3 (0.9–1.1; Figure 3.1G). In the lacustrine rock extracts W3–W7, the ratio is only in the range

of 0.5–0.8, whereas neither C35 or C34 homohopanes can be detected in the other lacustrine rock

extracts W1 and W2 (Figure 3.1G).

A series of β-carotene or isorenieratene derivatives, C13–C22 aryl isoprenoids (m/z 133;

Koopmans et al., 1996b, 1996c; Summons and Powell, 1987, 1986), represents high but

variable concentrations in the Posidonia extracts P1–P3 (16.6–114.8 ug/g extracts); the highest

value is present in the extract P2 (Figure 3.1H, S3.9). The proportion of C13–17 versus C18–22

aryl isoprenoids (aryl isoprenoid ratio AIR; Schwark and Frimmel, 2004) is calculated, which

ranges over 0.4–0.6 (Figure S3.9). In the Upper Schöneck extract M2, only C16–C19 aryl

isoprenoids can be distinguished (12.5 ug/g extract), whereas solely C18 and/or C19 homologues

are identified in the Lower Schöneck extract M3 and the Dynow extract M1 (1.6 and 1.2 ug/g

extracts). In the Wealden extracts W1–W7, concentrations of the C18–C20 aryl isoprenoids are

constantly low (0.01–0.9 ug/g extracts); a relatively high value is present in the extract W3

(Figure 3.1H, S3.9).

A series of isorenieratene derivatives C19–C21 2,3,5ˊ-6-tetramethyl-2-alkylbiphenyls (m/z

237; Koopmans et al., 1996c; Pagès et al., 2016) is identified in the Posidonia extracts P1–P3,

whose distribution is strongly dominated by the C19 component (0.8–13.8 ug/g extracts; Figure

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3.1I). In the other extracts, only the C19 homolog can be distinguished. C19 biphenyl is found to

represent a higher concentration in the Upper Schöneck extract M2 (1.7 ug/g extract) relative

to the Dynow extract M1 and the Lower Schöneck extract M3 (0.5 and 0.4 ug/g extracts; Figure

3.1I). In the Wealden extracts W1–W3, C19 biphenyl occurs in very low concentrations (0.01–

0.1 ug/g extracts), whereas in the Wealden extracts W4–W7 it is totally absent (Figure 3.1I).

3.5.3.2 Hydrocarbons accessible by positive APPI mode

The positive APPI detectable hydrocarbons in the studied extracts are distributed in the ≥

3 DBE ranges and are dominated by the C29 compounds (Figure S3.4E). In the Upper Schöneck

extract M2, the C25 and C30 compounds are strongly enriched among its 3 DBE hydrocarbons

(Figure 3.7D). A slight C35 hydrocarbon enrichment is observed in the Wealden extracts W1–

W3 and the Dynow and Schöneck extracts M1–M3 (Figure 3.7B). The C40 hydrocarbon

enrichment is common in the studied rock extracts principally among the ≥ 6 DBE species

(Figure 3.7B, S3.4E). It is more prominent in the Posidonia extracts P1–P3, the Upper Schöneck

extract M2 and the Wealden extract W3.

3.6 Discussions

3.6.1 Indicators of iron-deficient sulfidic depositional condition

Substantial low-molecular-weight OSCs in solvent extracts and pyrolysis products,

shown as high DBT/Phen, MDBT/MPhen, %2,3-DMT, %2,5-DMT indexes (Figure 3.1A–D),

indicate that the Posidonia samples P1–P3, the Lower Schöneck sample M3 and to a lesser

extent the Upper Schöneck sample M2 were deposited under iron-deficient sulfidic conditions

(Littke et al., 1991; Schulz et al., 2002; Song et al., 2017). Large amounts of the high-molecular-

weight OSCs in terms of both peak number and absolute abundance independently of ionization

mode further confirm this (Figure 3.2). However, higher relative abundances of OSCs are

present in these mentioned extracts in positive APPI mode (Figure S3.2A), but not in positive

ESI or negative ESI mode (Figure S3.2B, C), which is in accordance with the previous

observations that relative abundance of the positive APPI ionizable OSCs could provide a semi-

quantitative proxy of crude oils’ sulfur content (Corilo et al., 2016; Han et al., 2018a; Hur et al.,

2010; Kim et al., 2016; Muller et al., 2012) in contrast to the ESI approaches (Ren et al., 2019).

This is possibly related to the distinct ionization efficiencies of individual OSC classes in

different ionization modes. For instance, in positive ESI mode, the S1O1 class seems to be

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overestimated (up to 34.7%TMIA, Figure S3.1), since sulfoxides have been reported to account

only for very low proportions of the sulfur in petroleum fluids (Ren et al., 2019).

Abundant multi-sulfur bearing compounds S2Ox, S2 and S3 exclusively in the Posidonia

extracts P1–P3, the Lower Schöneck extract M3 and to a lesser extent the Upper Schöneck

extract M2 (Figure 3.4, 3.5A, B, S3.3) potentially reflect that sulfurization could have occurred

at multiple functional sites of appropriate polyfunctionalized biomolecules (for example

carotenoids or HBI polyenes; see chapters 3.6.3.1 and 3.6.3.4) when abundant sulfur was

available for incorporation into OM (e.g., Liu et al., 2018; Silva et al., 2020). Even though these

functional sites are also susceptible to other chemical reactions like oxidation (Riboulleau et al.,

2001), sulfurization seems to outcompete them under iron-deficient sulfidic conditions.

The high ratios of reduced versus oxidized organosulfur forms in the Posidonia extracts

P1–P3 and the Schöneck extracts M2 and M3 represented by large Sz/(Sz + OxSz) and S1/(S1 +

S1O1) indexes (Figure 3.3A, 3.4) are in accordance with the low amounts of oxidized

organosulfur forms having been reported in the sulfur-rich kerogen (Wiltfong et al., 2005).

While the reduced organosulfur compounds are primarily related to the incorporation of H2S

and polysulfides (HSx-, Sx2-) into OM during early diagenesis, the oxidized species are

speculated to be partly derived from the incorporation of sulfite (SO32-) or thiosulfate (S2O32-)

(Vairavamurthy et al., 1997, 1995, 1994) although the exact functional group types of sulfur

and oxygen in the compounds cannot be obtained by FT-ICR-MS alone. The polysulfides,

sulfite, and thiosulfate are all partial oxidation products formed when H2S encounters oxygen

or metal (Fe, Mn) oxides at oxic-anoxic interfaces (Vairavamurthy et al., 1995; Werne et al.,

2004), with sulfite and thiosulfate being more highly oxidized. Thus, the high ratios of reduced

versus oxidized organosulfur forms might be to some extent associated with the small amounts

of oxidants at the oxic-anoxic interfaces. However, unexpectedly, the largest ratio is observed

in the Upper Schöneck sample M2 rather than the Posidonia samples P1–P3 and the Lower

Schöneck sample M3 (Figure 3.3A, 3.4) whose depositional conditions are the iron-poorest and

the sulfite-richest (Schulz et al., 2002). This is possibly because some of the oxygen atoms in

OSCs are of biogenic source. The organic materials that can be sulfurized during deposition of

the sample M2 might contain a lower proportion of oxygen relative to the Posidonia and the

Lower Schöneck samples. This might be attributed to the changes in marine autochthonous

microbial communities or the transport of substantial amounts of allochthonous lacustrine algal

OM into the depositional environment of sample M2 (see chapter 3.6.3.3 illustrated by abundant

C30 tetracyclic polyprenoid hydrocarbons), since further evidences suggest that lacustrine

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organisms contain relatively lower amounts of the sulfurizable multi-oxygen bearing

compounds in comparison with marine organisms (see chapters 3.6.2).

3.6.2 Marine versus lacustrine biomass input

The nitrogen containing OSCs in forms of SzNy and SzNyOx being found solely in the

marine rock extracts (Figure 3.3A, B) possibly represent the nitrogen-rich marine organism

residues that have been preserved via sulfur incorporation (Yue et al., 2022). Amino acids in

forms of proteins are the principal nitrogen-bearing structures in living organisms. The

composition of marine plankton and bacteria is found to be dominated by proteins (around 50%;

Baxby et al., 1994) and the marine kerogen precursors have been reported to contain substantial

amounts of nitrogen (Vandenbroucke and Largeau, 2007).

The higher average oxygen numbers of both low-polarity and acidic S1Ox compounds in

the marine rock extracts (Figure 3.5C, D) relative to the lacustrine rock extracts (especially the

samples W2–W7 that have received low terrigenous plant input; Yue et al., 2022) possibly

illustrates that marine organisms and terrestrial plants contain higher amounts of multi-oxygen

bearing compounds that can be sulfurized in comparison with lacustrine organisms.

The highest proportions of aliphatic versus aromatic oxygenated OSCs in the lacustrine

rock extracts W2–W7 (Figure 3.5E–K) indicates that lacustrine organisms such as

Botryococcus braunii comprise more abundant aliphatic moieties that could be sulfurized than

marine organisms and terrestrial plants (Rippen et al., 2013; Schneider et al., 2019;

Vandenbroucke and Largeau, 2007; Yue et al., 2022).

3.6.3 Preservation through sulfurization: Biogenetic polyfunctionalized

molecules

3.6.3.1 Enrichment of C40 1–15 DBE organosulfur compounds: Carotenoids

The commonly observed enrichment of Sz and SzOx (z=1–3) compounds containing 40

carbon atoms in the DBE range of 1–15 in the studied rock extracts (Figure 3.7A, S3.4, S3.5,

S3.6) points towards inorganic sulfur incorporation into multiple double bond sites of

carotenoids shortly after deposition (Figure 3.8; Liu et al., 2018; Silva et al., 2020). Carotenoids

are a class of photosynthetic tetraterpenoid pigments widespread in both oxygenic (such as

plants, algae, and cyanobacteria) and anoxygenic (like purple and green sulfur bacteria)

photoautotrophs (Britton, 1995; Ma and Cui, 2022; Takaichi, 1999). They are featured by a

long series of conjugated double bonds and could be quickly degraded in oxic environments.

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Once in anoxic conditions where reactive inorganic sulfur species are actively generated,

carotenoids could be rapidly and selectively sulfurized at the sites of double bonds and thus

being preserved (Grice et al., 1998; Hebting et al., 2006; Kohnen et al., 1992, 1991a). The

presence of sulfur-bound carotenoids may imply either a rapid transfer of carotenoids from the

upper oxic photic zone (where oxygenic photoautotrophs develops) into a lower anoxic zone,

or their production by anoxygenic photoautotrophs living directly in the anoxic layer that

reaches into photic zone, or a combination of both processes (Liaaen-Jensen, 1979, 1978;

Repeta, 1989; Schaeffer et al., 1995). In general, carotenoids could be naturally acyclic, or

cyclized/aromatized at one or both ends thus displaying various hydrogenation levels (Britton,

1995). This is likely the explanation for the wide DBE range of the enriched C40 OSCs (1–15;

Figure S3.4, S3.5), in addition to the thermally-induced cyclization and aromatization due to

thermal stress (Liu et al., 2018; Poetz et al., 2014; Silva et al., 2020).

Figure 3.8. Some possible organosulfur compounds.

The constantly prominent enrichment of sulfurized carotenoids in the Posidonia extracts

P1–P3 might be associated with the high productivities of primary producers including both

anoxygenic and oxygenic photoautotrophs in their depositional milieu. The evidences exist as

follows. On the one hand, these enrichments go along with high concentrations of C13–C22 aryl

isoprenoids (Figure 3.1H) multi-sourced from isorenieratene in green sulfur bacteria

Chlorobiaceae (Koopmans et al., 1996c; Summons and Powell, 1987, 1986) and β-carotene

universally in oxygenic photoautotrophs (Koopmans et al., 1996b). On the other hand, these

enrichments are accompanied by abundant isorenieratene derivatives C19–C21 biphenyls

specific for Chlorobiaceae (Figure 3.1I; Koopmans et al., 1996c; Pagès et al., 2016) and

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consistently low AIR values indicative of persistent photic zone anoxia (PZA) or euxinia (PZE)

phase (0.4–0.6, Figure S3.9; Schwark and Frimmel, 2004). A much higher primary productivity

is expected for the sample P2 derived from the Posidonia calcareous shale unit II interval

possibly due to a higher level of land-derived nutrients (Littke et al., 1991; Sundararaman et al.,

1993), because the extract P2 is observed to have a similar AIR value (Figure S3.9) but a much

higher concentration of biphenyls and aryl isoprenoids (Figure 3.1H, I) relative to the extracts

P1 and P3.

Relative to the Lower Schöneck extract M3 and the Dynow extract M1, the Upper

Schöneck extract M2 shows a more prominent enrichment of sulfurized carotenoids (Figure

3.7A, S3.6), as well as, a higher concentration of both biphenyl and aryl isoprenoids (Figure

3.1H, I). These likely reflect its higher productivity of primary producers including both

anoxygenic and oxygenic photoautotrophs, which might be caused by a higher availability of

nutrients brought from bottom water by upwelling (Schulz et al., 2002; Schwark and Frimmel,

2004; Wagner, 1996; Yang and Schulz, 2019), or an intensified PZA or PZE condition (Schulz

et al., 2004, 2002).

The Wealden extract W3 displays a more prominent C40 organosulfur enrichment (Figure

3.7A, S3.6) and a relatively higher abundance of aryl isoprenoids (0.9 ug/g extract, Figure 3.1H)

when compared to the other Wealden extracts, yet the very low concentration of isorenieratene

derivative C19 biphenyl in the extract W3 (0.01 ug/g extract, Figure 3.1I) reflects that an anoxic

bottom water might not have reached the photic zone. Therefore, the oxygenated

photoautotrophs prevailing during deposition of sample W3 were supposed to be of the highest

productivity. Consistent with this, the C30 tetracyclic polyprenoid hydrocarbons probably

originating from fresh/brackish water algae (Holba et al., 2003, 2000) represent the highest

concentration in the extract W3 among the studied Wealden extracts (Figure 3.1F).

The enrichment of C40 organosulfur compounds and C40 hydrocarbons are always linked,

both occurring more prominently in the Posidonia extracts P1–P3, the Upper Schöneck extract

M2, and the Wealden extract W3 (Figure 3.7A, B, S3.6), accompanied with enhanced

concentrations of short-chain carotenoid diagenetic derivatives like aryl isoprenoids or

biphenyls (Figure 3.1H, I). These observations support the view that the early diagenetic

sulfurization of carotenoids and the subsequent late diagenetic desulfurization due to the

thermal cleavage of C-S or S-S bonds act as the principal formation pathway for the saturated

carotenoid hydrocarbons during early stage of thermal maturation. In accordance, abiotic

sulfurization has been speculated to outcompete hydrogenation for the preservation of

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polyunsaturated carotenoids during early diagenesis (Hebting et al., 2006; Kutuzov et al., 2020),

besides, it has been recoded that nearly 100% of the carotenoids are present in sulfur bound

forms in rocks of early diagenetic stage (Kohnen et al., 1991a; Wakeham et al., 1995).

3.6.3.2 Enrichment of C35 6–8 DBE organosulfur compounds:

Bacteriohopanepolyols

The C35 enrichment among the 6–8 DBE S1 and S1Ox (x=1–4) species is prominent in the

Dynow and Schöneck extracts M1–M3, followed by the Posidonia extract P1 (Figure 3.7A, C,

S3.6, S3.7F–H, S3.8). The C35 6 DBE organosulfur compounds might represent C35 hopanoid

sulfides (Figure 3.8; Damsté et al., 1995), sulfoxides (Schouten et al., 1995), sulfones (Charrié-

Duhaut et al., 2000), sulfonic acids and sulfates, whereas the 7 and 8 DBE species are possibly

their thiophene counterparts (Damsté et al., 1995). The barely observed C35 enrichment among

the multi-sulfur bearing Sz and SzOx classes (z=2, 3; Fig. S3.6, S3.8B, C) documents the small

numbers of functional sites in the C35 bacteriohopanepolyol derivatives that are available for

intramolecular sulfurization.

C35 bacteriohopanepolyol derivatives like bacteriohopanetetrol are generally

biosynthesized by bacteria as membrane rigidifiers (Damsté et al., 1995; Rohmer et al., 1992,

1984). During early diagenesis, they could be abiotically sulfurized, or undergo oxidative

cleavage forming short-chain derivatives like C32–C34 hopanediols and triols (Damsté et al.,

1995; Innes et al., 1997; Rodier et al., 1999; Watson and Farrimond, 2000). If C35

bacteriohopanepolyols are not altered by significant oxidation prior to sulfurization, their intact

carbon skeleton could be preserved, leading to a prominent domination of C35 homologues

among the sulfurized homohopanoids (Damsté et al., 1995; Köster et al., 1997), for examples

as shown in the Dynow and Schöneck samples M1–M3. In contrast, in the Posidonia sample

P1, C35 bacteriohopanepolyols might have been intensively degraded due to severe oxygen

exposure (dependent on duration, oxygen level, etc.) prior to sulfurization. More intense

oxidative degradation in the Posidonia samples P2 and P3 and the Wealden samples W1–W7

is recorded by a very low or no C35 organosulfur enrichment (Figure 3.7A, C, S3.6, S3.7F–H,

S3.8A).

Enrichment of C35 homohopanes (high C35/C34 homohopanes indexes and large C35/(C31–

C35) homohopanes ratios) occur solely in the Schöneck extracts M2 and M3 and the Posidonia

extract P1, but not in the Dynow extract M1 (Figure 3.1G, S3.10A). This possibly indicates that

the early diagenetic sulfurization and later diagenetic desulfurization of C35

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bacteriohopanepolyols and their short-chain C31–C34 functionalized derivatives is not the only

diagenetic pathway for the formation of C31–C35 homohopanes. It has been proposed that

hopanoids could be bound into kerogen during early diagenesis by a mixture of di-/polysulfide

linkages and ether bonds, or even mainly by ether linkages (Farrimond et al., 2003; Richnow et

al., 1993, 1992). In addition, oxygen-linked hopanoids have been evidenced to show a great

proportion of side-chain shortened homologues (Richnow et al., 1992). Thus, considering that

the Dynow sample M1 was deposited in a lower-sulfur environment relative to the Schöneck

samples M2 and M3 and the Posidonia sample P1, a lower fraction of hopanoids might have

been preserved in the Dynow sample M1 via sulfurization/desulfurization.

3.6.3.3 Enrichment of C30 5 DBE organosulfur compounds: C30 unsaturated

tetracyclic polyprenoid alcohols

The enriched C30 compounds of the 5 DBE S1 and S1Ox (x=1, 2) species in the studied

extracts (Figure 3.7C, S3.7E) could be C30 pentacyclic polyprenoid organosulfur compounds

(Figure 3.8). They are formed from the abiotic sulfurization of C30 unsaturated tetracyclic

polyprenoid alcohols that initially source from the incomplete cyclization of precursors C30

regular unsaturated polyprenoid alcohols during very early diagenesis (Poinsot et al., 1998,

1997). These precursors were suggested to principally originate from organisms living in the

oxic part of water column (Poinsot et al., 1998). The more prominent enrichment in the

lacustrine rock extracts (Figure 3.7C, S3.7E) supports the assumptions that these precursors are

more abundant in fresh/brackish water algae (Holba et al., 2003, 2000).

C30 tetracyclic polyprenoid hydrocarbons were documented to be typically more abundant

in the lacustrine deposits relative to the marine deposits and coals, and their precursors were

also supposed to be C30 regular unsaturated polyprenoid alcohols (Holba et al., 2003, 2000).

Herein, these hydrocarbons are found to represent high concentrations in the lacustrine rock

extracts W2–W7 and the marine Upper Schöneck extract M2, but not in the lacustrine rock

extract W1 (Figure 3.1F). The low concentration in the extract W1 is assumed to be related to

the dilution by terrigenous plant input (Holba et al., 2003; Yue et al., 2022); a high concentration

in the extract M2 is potentially due to the fluvial transport of substantial fresh/brackish water

algal OM from non-marine to marine environments (Holba et al., 2003).

Sulfurization/desulfurization of the C30 unsaturated tetracyclic polyprenoid alcohols (Poinsot et

al., 1998) is still suggested as an important early diagenetic pathway for the formation of C30

tetracyclic polyprenoid hydrocarbons. Here, the discrepancy between the C30 5 DBE

organosulfur enrichment (Figure 3.7C, S3.7E) and the concentration of C30 tetracyclic

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polyprenoid hydrocarbons (Figure 3.1F) is possibly because C30 unsaturated tetracyclic

polyprenoid alcohols of the fresh/brackish water algal input might have already suffered strong

alteration upon transportation into the marine depositional milieu of sample M2 and were not

prone to further sulfur incorporation during settling and sedimentation (Vandenbroucke and

Largeau, 2007).

3.6.3.4 Enrichment of C25 and C30 1–4 DBE organosulfur compounds: Highly

branched isoprenoid polyenes

The enriched C25 and C30 compounds among the 1–4 DBE S1, 1–3 DBE S1Ox (x=1, 2),

2–6 DBE S2 and 2–4 DBE S2Ox (x=1, 2) species in the Upper Schöneck extract M2 (Figure

3.7A, C, S3.6, S3.7A–D, S3.8B, C) represent the inorganic sulfur incorporation into the C25 and

C30 HBI polyenes during very early diagenesis (Figure 3.8; Damsté et al., 1989b; Kohnen et al.,

1990). The far more abundant C30 relative to C25 compounds among the multi-sulfur bearing S2

and S2Ox (x=1, 2) classes (Figure S3.6F–H, S3.8B, C) documents the higher numbers of double

bond sites in the C30 HBI polyenes that are available for sulfurization.

HBI polyenes are widely accepted as common biomarkers derived from diatoms in

upwelling systems (e.g., Volkman et al., 1994). Indeed, upwelling models were proposed for

the Upper Schöneck Fm. in the Molasse Basin by Wagner (1996) and Yang and Schulz (2019),

even though diatomites were absent (Schulz et al., 2002). In addition, successions in this Eastern

Alpine Molasse foreland basin were speculated to accumulate in continuous depositional

conditions with the Western Carpathians (Picha et al., 2006; Pupp et al., 2018). In the lateral

equivalent of this formation (biozone NP22), diatomites and abundant C25 HBI thiophenes were

reported in the Carpathians area (Picha et al., 2006; Pupp et al., 2018; Rospondek et al., 1997).

C26 rather than C25 compounds are more abundant among the 4 DBE S1Ox species in the

Upper Schöneck extract M2 (Figure S3.7D), potentially indicating the abiotic sulfurization of

C26 HBI polyenes. C26 HBI thiophenes were documented in its contemporaneous deposits in

the Carpathians area (Rospondek et al., 1997), and the C26 and C25 HBI polyenes were

speculated to originate from the same diatom species (Rospondek et al., 1997).

In the Lower Schöneck extract M3 a relatively small degree of C25 enrichment is observed

among its 1–3 DBE S1 species potentially illustrating a relatively low abundance of diatoms,

whereas in the Dynow extract M1 the enrichment is totally absent (Figure S3.7A–C). In

accordance, smaller amounts of C25 thiophenes were reported in the contemporaneous

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successions of the Lower Schöneck Fm. in the Carpathians, but not in the counterparts of the

Dynow Fm. (Picha et al., 2006; Pupp et al., 2018).

The association between the saturated HBI hydrocarbons and the sulfur-bound HBI

derivatives in terms of enrichment or concentration supports the view that the abiotic

sulfurization of HBI polyenes and subsequent desulfurization act as the principal generation

pathway of the saturated HBI hydrocarbons rather than hydrogenation (Kohnen et al., 1990;

Requejo and Quinn, 1983). For instance, while the Upper Schöneck extract M2 is featured by

a high concentration of C25 and C30 HBI alkanes (Figure 3.1E, Yang and Schulz, 2019) and a

strong enrichment of C25 and C30 3 DBE hydrocarbons (Figure 3.7D), the Lower Schöneck

extract M3 contains a relatively small amount of C25 HBI alkane (Figure 3.1E). In addition, C26

HBI alkane is below the detection limit in the Upper Schöneck extract M2. In accordance, C26

HBI alkane was recorded to be much less abundant relative to the C25 HBI alkane in its

contemporaneous deposits in the Carpathians area (Rospondek et al., 1997). These possibly

illustrate a very small amount of C26 HBI polyenes from indigenous diatoms.

3.6.3.5 Enrichment of C20 1 DBE organosulfur compounds: C20 isoprenoid alcohols

as a constituent of chlorophylls and some bacteriochlorophylls

C20 enrichment among the 1 DBE S1 and S1Ox (x=1, 2) species is only present in the

extracts associated with iron-deficient sulfidic conditions, i.e., the Posidonia extracts P1–P3

and the Lower Schöneck extract M3 (Figure 3.7C, S3.7A). Phytol is ubiquitous as a constituent

of chlorophylls and some bacteriochlorophylls (Scheer, 2006). It has been reported to be readily

sulfurized under euxinic conditions (e.g., Kohnen et al., 1991a; Wakeham et al., 1995). The

enriched C20 1 DBE organosulfur compounds are speculated to be sulfurized phytane (Figure

3.8) formed from inorganic sulfur incorporation into the early diagenetic products of phytol,

e.g., phytenal or to a lesser extent phytadiene (Adam et al., 2000; Amrani and Aizenshtat, 2004a;

Fukushima et al., 1992; Krein and Aizenshtat, 1994; Rontani and Giusti, 1988; Rowland and

Maxwell, 1990). In addition, the di- or poly-unsaturated isoprenoid alcohols of direct biological

sources, such as phytadienol and geranylgeraniol as moieties of certain bacteriochlorophylls

biosynthesized by green and purple sulfur bacteria and Archaea, are potential alternative

sources of the C20 1 DBE organosulfur compounds especially for the Posidonia samples P1–P3

(see chapter 3.6.3.1; Caple et al., 1978; Damsté and de Leeuw, 1987; Gloe and Pfennig, 1974;

Katz et al., 1972; Kushwaha and Kates, 1978; Scheer, 2006; Steiner et al., 1981).

Pristane is the diagenetic product of phytol under oxic conditions as a result of

decarboxylation (Didyk et al., 1978). The low pristane/phytane ratio is not specific for the

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Posidonia samples P1–P3 and the Lower Schöneck sample M3 (Figure S10B), possibly because

phytane can also derive from catalytic dehydration/hydrogenation of phytol in reducing

environment besides the sulfurization/desulfurization under euxinic conditions (Powell and

McKirdy, 1973; Prahl et al., 1996). This alternative preservation process even contributes to

most or possibly all of the phytane in some young sediments (Prahl et al., 1996), and classically,

this is the major pathway (Ikan et al., 1975; ten Haven et al., 1987). Moreover, pristane and

phytane could also respectively derive from pristenes (zooplankton) and archaeol (archaea

species) (Kuypers et al., 2001).

3.7 Summary and Conclusions

In this study, elemental and molecular composition of the high-molecular-weight OSCs

in organic solvent extracts of marine and lacustrine rocks were characterized utilizing FT-ICR-

MS. Their contained palaeoecological signatures and palaeoenvironmental information such as

levels of dissolved sulfide, iron and oxygen were unravelled, since they are primarily formed

from the abiotic introduction of inorganic sulfur into appropriate functionalized biomolecules

after sedimentation. Noticeably, carbon skeletons of some labile biomolecules can be

selectively preserved from biodegradation via sulfurization, which have been evidenced to even

act as their principal preservation pathway during early diagenesis such as for carotenoids and

HBI polyenes. They show up as strong enrichment of specific OSCs. Herein, the prominent

enrichment of Sz and SzOx compounds containing 40, 35, 30, 25, 20 carbon atoms was linked

to the selective preservation of C40 carotenoids, C35 bacteriohopanepolyols, C30 unsaturated

tetracyclic polyprenoid alcohols, C25 or C30 HBI polyenes, and C20 isoprenoid alcohols via

sulfurization. Their contained information was deconvoluted to support or even extend the

established palaeoecological and palaeoenvironmental theories of the studied sample set based

on hydrocarbon biomarkers. Most importantly, thanks to the fact that OSCs can be

characterized at a molecular level by FT-ICR-MS even when they are in small amounts, the

application of these potential molecular indicators is not limited to the high organic-sulfur

samples any more.

Here, the iron-deficient sulfidic depositional settings of the Posidonia samples are

characterized by high abundances of OSCs and especially the multi-sulfur bearing S2Ox and S2

classes. The constantly high proportions of reduced relative to oxidized organosulfur forms (Sz

versus SzOx) furthermore argue for the small amounts of oxidants at the oxic-anoxic interfaces.

High productivities are expected for the primary producers in all the Posidonia samples

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including both anoxygenic and oxygenic autotrophs, because the observed prominent

enrichment of sulfurized carotenoids is accompanied with hydrocarbon biomarker distributions

characteristic for PZA or even PZE such as the low ratios of C13–17 versus C18–22 aryl isoprenoids

and the abundant isorenieratene derivatives like biphenyls. Variations in productivities are also

present. A much higher primary productivity possibly due to a higher land-derived nutrient

level is expected for the Posidonia calcareous shale unit II interval relative to the marlstone unit

I interval, as shown by the high amounts of the diagenetic derivatives of carotenoid

photosynthetic pigments like biphenyls and aryl isoprenoids.

Marine depositional conditions of the Schöneck and the overlying Dynow formations

show highly variable ratios of sulfide to iron, as reflected by the changes in abundances and

compound class distributions of OSCs. Only the Lower Schöneck sample is characterized by

sulfide-rich and iron-deficient environment, whereas the Upper Schöneck and especially the

Dynow samples have low ratios. Levels of oxygen exposure prior to sulfurization were

consistently low during deposition of the Dynow and Schöneck samples, which are indicated

by the persistently strong enrichment of sulfurized C35 bacteriohopanepolyols. The higher

productivity of primary producers in the Upper Schöneck sample, including both anoxygenic

(such as green sulfur bacteria) and oxygenic (like diatoms) autotrophs, might be associated with

a higher availability of essential nutrients carried up by strong upwelling or an intensified PZA

or PZE, as evidenced by the stronger enrichment of sulfurized carotenoids, sulfurized HBI

polyenes, and higher abundance of biphenyls.

The ratios of sulfide to iron were consistently low during deposition of the lacustrine

Wealden samples, as reflected by the persistently low concentrations of OSCs. Lacustrine

organisms synthesized low amounts of proteinaceous moieties that could have been sulfurized,

since OSCs in the Wealden extracts are found to contain exclusively SzOx and/or Sz compounds,

and the nitrogen containing OSCs are solely observed in the marine rock extracts in forms of

SzNy and SzNyOx. Besides, lacustrine organisms might have produced lower proportions of

multi-oxygen bearing compounds that were sensitive for sulfurization, as illustrated by the

lower average oxygen numbers of S1Ox compounds. In contrast, the Wealden extracts are not

only more abundant in sulfur-bound aliphatic moieties but also more prominently enriched in

C30 pentacyclic polyprenoid organosulfur compounds whose precursors are more abundant in

fresh/brackish water algae. The variable productivities of these oxygenic photoautotrophs in the

Wealden samples are documented by the different enrichment of sulfurized carotenoids, with

the most prominent enrichment accompanied by the highest concentration of C30 tetracyclic

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polyprenoid hydrocarbons originated from fresh/brackish water algae. Moreover, a very low

concentration of isorenieratene derivatives C19 biphenyl point against PZA.

3.8 Acknowledgments

This study is financially supported by the Chinese Scholarship Council (CSC) [Grants

No. 201606450015] and Technical University of Berlin Center for Junior Scholars (CJS).

Cornelia Karger, Anke Kaminsky, Kristin Günther and Ferdinand Perssen in GFZ are

acknowledged for their technical support. We are grateful to Deolinda Flores and two

anonymous reviewers for their careful and constructive reviews of this paper.

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3.9 Supplementary material

Figure S3.1. Partial mass spectra showing only monoisotopic assigned peaks in distinct ionization

modes. Peaks assigned as different elemental classes are respectively colored. Pie charts showing

elemental class distributions are also displayed here. “HC” refers to hydrocarbons, whereas “V + Ni”

refers to vanadyl and nickel porphyrins.

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Figure S3.2. Peak number and relative abundance of organosulfur compounds detectable in

distinct modes.

Figure S3.3. Compound class distributions of the positive or negative ESI accessible organosulfur

compounds.

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Figure S3.4. DBE versus carbon number distributions of the positive APPI ionizable S1, S1Ox

(x=1, 2), hydrocarbons and the positive ESI accessible S1O1 compound classes.

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Figure S3.5. DBE versus carbon number distributions of the positive APPI accessible S2, S2Ox

(x=1–4), S3, S3O2, S1Ox (x=3–5), N1S1 and the positive ESI ionizable N1S1 compound classes.

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Figure S3.6. Carbon number distributions of the positive APPI ionizable Sz (z=1–3), S1Ox (x=1–

5), S2Ox (x=1–4), S3O2, hydrocarbons as well as the positive ESI accessible S1O1 classes, which are

normalized to the most abundant species (Cmax_abund) in specific compound class.

125

126

Figure S3.7. Carbon number distributions of individual 1–9 DBE S1 or S1Ox (x=1, 2) classes

accessible by positive APPI or positive ESI, which are normalized to the most abundant species in

specific DBE class. The dot size represents the relative abundance of variable compounds within a

certain DBE class in a specific sample.

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Figure S3.8. Carbon number distributions of the positive APPI ionizable individual 0–9 DBE

S1O3 and S2Ox (x=1, 2) classes as well as the negative ESI accessible 1, 6, 7 DBE S1Ox (x=3, 4) classes,

which are normalized to the most abundant species in specific DBE class. The dot size represents the

relative abundance of variable compounds within a certain DBE class in a specific sample.

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Figure S3.9. Aryl isoprenoid traces and their concentrations in the studied extracts (m/z 133).

129

Figure S3.10. C35/(C31–C35) homohopanes and pristane/phytane ratios.

130

131

4 IMPACT OF LITHOFACIES ON COMPOSITION OF

HETEROATOMIC COMPOUNDS IN RESIDUAL

AND EXPELLED FLUIDS OF MATURE ROCKS3

4.1 Abstract

The influence of lithofacies on the composition of NSO compounds in unconventional

petroleum systems has been investigated using examples of the biogenic carbonate-rich

Niobrara Shale, the biogenic quartz-rich Barnett Shale and the detrital clay-rich Posidonia Shale.

The chosen samples all contain marine type II kerogen in the peak–late oil window. Their

solvent extracts were analyzed using Fourier transform ion cyclotron resonance mass

spectrometry (FT-ICR-MS), combined with atmospheric pressure photoionization (APPI) in

positive ion mode and electrospray ionization (ESI) in negative ion mode. Covering both source

and reservoir units, our study furthermore enables tracing the impact of lithofacies on petroleum

migration within the Niobrara and Barnett shales.

Solvent extracts of the siliciclastic Barnett and Posidonia shales reveal higher proportions

of NSO compounds confirming the generally higher retention capacities of siliciclastic rocks

for polar organic compounds. However, different retention specificities of biogenic quartz- and

clay-rich rocks are indicated by varying NSO compound compositions in their bitumen fraction:

biogenic quartz preferentially preserves and retains organonitrogen compounds, while the more

polar acidic organooxygen compounds are preferably retained by clay minerals. Extracts of the

carbonate rocks contain a larger fraction of nonaromatic cyclic sulfoxides and amides that are

likely formed by oxidation processes during maturation of organic matter.

Fractionations induced by the intra-formation migration differ between the Barnett and

Niobrara sample sets. While the low-polarity organonitrogen compounds are retained in both

Barnett (to a greater extent) and Niobrara source units, a preferential migration of highly

3 This chapter has been published as: Huiwen Yue, Andrea Vieth-Hillebrand, Yuanjia Han, Brian Horsfield, Anja

Maria Schleicher, Stefanie Poetz, 2021. Unravelling the impact of lithofacies on the composition of NSO

compounds in residual and expelled fluids of the Barnett, Niobrara and Posidonia formations. Organic

Geochemistry, 155, 104225, (postprint), https://doi.org/10.1016/j.orggeochem.2021.104225.

132

alkylated and small acidic NSO compounds out of the source is only observed in the Niobrara

samples.

4.2 Introduction

Sedimentary facies of petroleum source rocks can be described according to the organic

(organofacies) and mineralogical compositions (lithofacies). Reflecting the input of organic

versus inorganic matter, both are primarily the results of depositional conditions during

sedimentation. Progressive maturation, as well as, petroleum generation, expulsion and

migration all further impact the organic chemical signatures. Mineral matrix could participate

in these processes via interactions with the organic phase at interfaces for example as mineral

catalysts in petroleum generation (Berthonneau et al., 2016; Jones, 1984; Seewald, 2001;

Tannenbaum et al., 1986; Wu et al., 2012).

Expulsion and migration processes cause chemical fractionation of those organic fluids

in petroleum systems. The extent of fractionation depends on various attributes of inorganic

components like lithofacies type or pore size distribution on the one hand and the

physicochemical properties of organic compounds on the other. The most important processes

occurring during geo-chromatographic fractionation are adsorption, ion exchange and size

exclusion (Krooss et al., 1991), while partitioning is thought to take place mainly during

diffusion-based fractionation (Thomas, 1989). Size exclusion is especially important during the

primary migration in fine-grained clastic sediments (Mileshina and Safonova, 1963). For

migration of the ionizable organic compounds like carboxylic acids, ion exchange is of

increased significance (Barth et al., 1988).

While size exclusion refers to compounds’ size and shape, adsorption and ion exchange

mainly depend on compounds’ polarity. Source rock bitumen is strongly enriched in polar

compounds as compared to the migrated oils in conventional reservoirs (Brenneman and Smith

Jr, 1958; Pelet and Tissot, 1971; Safronova et al., 1972). Later, this preferential retention of

polar compounds (Leythaeuser et al., 1988b) was experimentally reproduced (Lafargue et al.,

1990; Sandvik et al., 1992) and theoretically modelled (Kelemen et al., 2006a; Ritter, 2003).

Heteroatoms like nitrogen, sulfur and oxygen embedded in compounds function as active sites

and can result in strong interactions with mineral matrices (Bennett et al., 2002; Brother et al.,

1991; Charlesworth, 1986; Li et al., 1995; Stoddart et al., 1995). Diverse groups have been

shown to behave differently while interacting with individual minerals, for example, carboxylic

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acid groups interact most strongly with calcite surfaces, followed by alcohol, pyridine, pyrrole,

furan and thiophene structures (Ataman et al., 2016a, 2016b).

From the mineral perspective, the type of active sites on their surface impacts the

inorganic-organic interactions (Adams, 2014; González and Moreira, 1994). Clay minerals are

hydrous aluminium phyllosilicates with a negatively charged surface (Uddin, 2008; Wu et al.,

2012). Organic matter (OM) can interact via surface complexes with the Si-OH and Al-OH

groups at clay edges and hydrophobic surfaces or with the hydrated exchangeable cations (e.g.,

Na+ or K+) (Cornejo et al., 2008; Wu et al., 2012). Negatively charged (or neutral) and weakly

acidic Si-OH groups at the quartz (SiO2) surface are recognized as active sites (González and

Moreira, 1994; Parida et al., 2006). Weakly basic Ca-OH group and Ca+ predominate at the

surface of calcite (CaCO3). In contrast to the preferential interaction between calcite surface

and acidic organic groups (Ataman et al., 2016a, 2016b), the quartz surface silanol groups might

interact preferably with those weakly basic groups (González and Moreira, 1994).

The number of active sites on minerals per volume or area (which is proportional to the

specific surface area) influences their adsorption capacity. Minerals with a higher adsorption

capacity (e.g., clay minerals) retain higher proportions of NSO compounds (Tannenbaum et al.,

1986). Retention of NSO compounds also depends on the existing migration pathways enabling

petroleum to leave the rocks (Bennett et al., 2002; Mann, 1994). For instance, pressure solution

seams and stylolites (Hofmann and Leythaeuser, 1995; Leythaeuser et al., 1995; Mann, 1994;

Sassen et al., 1987) as well as their accompanied process zone fractures (Raynaud and Carrio-

Schaffhauser, 1992) are far more common in carbonate rocks, enabling efficient expulsion of

NSO compounds (Hofmann and Leythaeuser, 1995). On the molecular level, oils expelled from

carbonate rocks have been shown to experience lower levels of benzocarbazole fractionation

when compared to the oils sourced from claystones, represented by small differences in

concentration of benzo [a] plus [c] carbazoles between reservoired petroleum and source

petroleum (Bennett et al., 2002).

The effects of lithofacies on geo-chromatographic fractionation have been mainly

investigated in terms of petroleum compositions as well as small NSO compounds. Studies on

the high-molecular-weight NSO compounds that are expected to be mostly affected by these

fractionation processes are rare, largely because their characterization is still an analytical

challenge. Ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry

FT-ICR-MS coupled with distinct soft ionization techniques overcomes these difficulties and

enables their detections on a molecular level. Electrospray ionization in negative ion mode (–)-

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ESI preferentially ionizes acidic polar organic compounds, e.g., carboxylic acids (Figure 4.1,

S4.1). An atmospheric pressure photoionization (APPI) source was developed with the

motivation to broaden the range towards less polar molecules such as polycyclic aromatic

hydrocarbons or nonpolar thiophene species that are ordinarily not ionized by ESI (Hayen and

Karst, 2003; Robb et al., 2000; Syage et al., 2000) (Figure 4.1). APPI is sensitive towards

aromatic components having either basic (e.g., pyridines, ketones) or acidic features (Figure

4.1). Several studies on geo-chromatographic fractionation have applied FT-ICR-MS combined

with negative ESI mode (Han et al., 2018b, c; Hosseini et al., 2017; Liu et al., 2015b; Mahlstedt

et al., 2016; Pan et al., 2019). Up to now, positive APPI has been used for documenting the

fractionation of petroleum fluids on mineral surfaces (e.g., SiO2) in laboratory experiments

(Chacón-Patiño et al., 2015; Nascimento et al., 2016). However, no studies about the influence

of lithofacies on geochromatographic fractionation in petroleum systems have been done with

negative ESI or positive APPI.

Figure 4.1. Comparison of the ionization ranges of positive APPI and negative ESI modes, after

Huba et al. (2016) and Gross (2017). ‘‘V” stands for successful ionization, while ‘‘–” marks

nonionizable species.

Here we elucidate the contrasting compositions of NSO compounds in examples of the

three globally most significant lithofacies seen in unconventional shale plays (e.g., Chermak

and Schreiber, 2014), namely carbonate-dominated Niobrara Shale, biogenic quartz-rich

Barnett Shale and clay-rich Posidonia Shale. Solvent extracts of 12 rock samples were

investigated. The chosen sample sets all contain marine type II kerogen in the peak to late oil

window. While the three Posidonia samples all come from source rock units, the Barnett and

Niobrara sample sets also include one sample from an intra-reservoir unit within their

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unconventional petroleum systems enabling the additional investigation of lithofacies’ impacts

on the intraformational migration induced fractionation of NSO compounds.

4.3 Sample description

4.3.1 Geological background and sample selection

The Upper Cretaceous Niobrara Formation in the Denver Basin was deposited under

pelagic and hemipelagic conditions in well-oxygenated to progressively dysoxic (possibly

anoxic) bottom waters (Da Gama et al., 2014). The well 3, drilled in Weld County, Colorado,

USA, was investigated in the current study (Figure 4.2A). Characterized as an alternating

sequence of organic-poor chalk and organic-rich marl beds (Locklair and Sageman, 2008), the

Niobrara Formation is recognized as a typical hybrid shale oil play (Figure 4.2B; Han et al.,

2019b, 2018d; Jarvie, 2012), where oils generated from marl intervals (total organic carbon

content TOC > 2.5 wt.%) rich in type II kerogen migrate into the juxtaposed chalks (carbonates >

70 wt.%). This migration-induced fractionation results in a higher concentration of saturated

hydrocarbons in the chalk units, equating to higher quality (more economic) producible liquids

(Han et al., 2018d, 2019a). Here, four marl samples NB1–NB4 from the Smoky Hill Member

and one chalk sample NB5 from the Fort Hays Member at the late oil window maturity (~0.9%

Rc, calculated vitrinite reflectance based on Tmax value, phenanthrene derivatives, or

dibenzothiophene derivatives; Han et al., 2019a) were chosen (Figure 4.2B).

The Mississippian Barnett Shale was deposited in a deep foreland marine basin under

dysoxic, strongly upwelling conditions (Loucks and Ruppel, 2007). The Marathon 1 Mesquite

exploration well was drilled in Hamilton County, Texas (Figure 4.2A), targeting the Barnett

Shale at the late oil window maturity (~1.0% Rc; Han et al., 2017, 2015). A vertical intra-

formation migration pathway in the Barnett Shale (Figure 4.2B) from the organic rich 3rd

interval (TOC averaging 6 wt.%) to the overlying 2nd interval (TOC around 3 wt.%) was

suggested by Han et al. (2015). Three samples BN1–BN3 from the main source rock interval

and one sample BN4 from the juxtaposed reservoir unit were selected (Figure 4.2B).

The Lower Toarcian Posidonia Shale of northern Germany was deposited in a restricted

epi-continental sea of moderate depth under prevailing anoxic conditions (Littke et al., 1991;

Röhl et al., 2001). In the Hils syncline area, the type II OM rich Posidonia Shale has undergone

widely variable levels of maturation over short distances due to its proximity to the deep-seated

Vlotho Massiv (Rullkötter et al., 1988) and the labile nature of its OM (Schaefer et al., 1990).

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The three samples PS1–PS3 are from the Harderode borehole, this being one of the six research

wells drilled in the Hils Syncline in the 1980s (Figure 4.2). The Posidonia Shale in the

Harderode borehole (0.88% Ro, vitrinite reflectance) has experienced intense petroleum

generation and expulsion (Rullkötter et al., 1988). Lithologic variability among the selected

Posidonia calcareous shale unit II and III intervals is not appreciable (Figure 4.2B; Bernard et

al., 2012; Littke et al., 1991).

Figure 4.2. (A) Location of the study areas and (B) geochemical depth profiles of samples, which

are partly published elsewhere (Han et al., 2019b, 2017, 2015; Klaver et al., 2012; Littke et al., 1991).

Map of the Barnett and Niobrara unconventional plays (as of May 2011) was published by the U.S.

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Energy Information Administration. Mineralogical compositions of the Niobrara and Barnett samples

were detected by X-ray powder diffraction (XRD), while the Posidonia samples were analyzed by

attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). Comparability of

results from both methods has been shown by Müller et al. (2014).

4.3.2 Mineralogical composition

Detailed mineralogy-based descriptions of the investigated samples can in part be found

in Han et al. (2017) and Han et al. (2019b). The Niobrara samples NB1–NB5 are dominated by

carbonates (principally calcites, 51–80 wt.%) related to coccolith and foraminifera (Han et al.,

2019b), while the Posidonia and Barnett samples mainly consist of silicates (75–91 wt.%)

(Table S4.1). Silicates are mostly composed of clay minerals in the Posidonia samples PS1–

PS3, among which illite/smectite mixed-layer minerals (I/S) dominate. In our Barnett samples

BN1– BN4, quartz, clay minerals, and mica are in equal abundance. The quartz in these Barnett

samples is mainly biogenic (sponge spicules or agglutinated foraminifera), as shown by thin-

section identification and scanning electron microscopy (Han et al., 2015; Loucks and Ruppel,

2007; Milliken et al., 2007). Figure 4.2B displays variations in mineralogical composition

among these three sample sets by the relative percentages of clays, quartz and carbonates.

Our Niobrara and Barnett sample sets cover a large variability in mineralogy, allowing us

to study the influence of intra-formation lithofacial changes on their retained NSO composition.

The Niobrara samples show a decrease in clay and quartz contents and an increase in carbonate

content from NB1 to NB5 (Figure 4.2B, Table S4.1), while decreasing contents of clays and

increasing contents of quartz and carbonates are found from BN1 to BN4. In both samples sets,

the sample with the highest carbonate content represents a reservoir-type unit within the

unconventional shale system (Han et al., 2019b, 2017).

4.3.3 Bulk organic geochemical data

According to the Rock Eval pyrolysis and open system pyrolysis–gas chromatography

(Py-GC) results (Han et al., 2019b, 2015), the three sample sets are all classified as type II

kerogen (Figure 4.3A, B). The Niobrara and Barnett samples have lower hydrogen index values

(HI, calculated after S2/TOC×100, S2: amount of petroleum generated by Rock Eval pyrolysis)

than the Posidonia samples, probably because their initial HI was at the low end of the type II

spectrum, but maturity may also have played a role. The samples are all in the peak to late oil

generation stage. Slightly higher Tmax values (the temperature at which the maximum release

of hydrocarbons from kerogen via cracking occurs during Rock Eval pyrolysis) are found for

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the Barnett (455–458 °C) and Niobrara (446–455 °C) source rock samples when compared to

the Posidonia (447–449 °C; Figure 4.3A). All generated pyrolysates are rich in n-alkenes and

n-alkanes, but the chain lengths are shorter in the Niobrara and Barnett pyrolysates (Figure

4.3B).

Looking at the relative fractions of saturates, aromatics, resins and asphaltenes derived

by medium pressure liquid chromatography (Radke et al., 1980), the Posidonia extracts have

lower proportions of saturates and higher proportions of resins and asphaltenes when compared

to the Barnett and Niobrara extracts (Figure 4.3C). The Niobrara and Barnett reservoir unit

extracts NB5 and BN4 have slightly higher proportions of saturates than their corresponding

source rock extracts (Figure 4.3C).

Based on gas chromatography-mass spectrometry analysis of the aromatic fraction, the

Niobrara and Posidonia extracts have elevated values of DBT/Phen

(dibenzothiophene/phenanthrene) and MDBT/MPhen (methyl DBT/methyl Phen) indexes than

the Barnett extracts (Figure 4.4D).

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Figure 4.3. (A) Classification of kerogen types by hydrogen index versus Tmax (Espitalié et al.,

1984b) based on Rock Eval pyrolysis measurements. (B) Open system Py-GC results typing molecular

kerogen structures using the ternary diagram of Horsfield (1989). (C) Bulk compositions of the solvent

extracts: relative percentages of saturate, aromatic, resin, and asphaltene fractions by weight. (D)

DBT/Phen and MDBT/MPhen ratios. Data for the Barnett and Niobrara samples have been partly

published elsewhere (Han et al., 2019b, 2015).

4.4 Analytical methods

4.4.1 Organic solvent extraction

After being crushed and finely ground, core samples (4 g) were extracted for 48 h at 60 °C

in a Soxhlet extractor using the ternary azeotropic solvent mixture of methanol, acetone and

chloroform (30:38:32, v/v/v).

4.4.2 FT-ICR-MS

Total extracts were analyzed by 12 Tesla FT-ICR-MS under positive APPI and negative

ESI modes. Testing and data handling procedures have been described in chapters 2.4.4–2.4.6.

The handling process for potential contamination peaks is displayed in Figure S4.2.

4.5 Results

In the following, we describe the composition of NSO compounds in rock extracts

separately according to the ionization modes, positive APPI and negative ESI. Each subsection

starts with the characterization of general differences between the three lithofacies types

(carbonate-, clay- and quartz-rich) followed by a description of variations observed between

the source rock and intra-reservoir units within the Barnett and Niobrara sample sets.

4.5.1 Aromatic hydrocarbons and low-polarity NSO compounds detected by

(+)-APPI FT-ICR-MS

4.5.1.1 Broad band spectra

Higher numbers of monoisotopic peaks (6869–7105) are assigned in positive APPI

spectra of the Posidonia extracts than in the Barnett (5647–6110) and Niobrara (4629–5617)

spectra (Figure S4.3). Total absolute abundances of these assigned monoisotopic peaks (TMIA)

accessible by positive APPI for the studied extracts are all in the range of 6.8 × 1010–1.3 × 1011.

Reservoir rock extracts BN4 and NB5 have lower TMIA than their corresponding source rock

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extracts (Figure S4.3). For Barnett, a constant decrease in TMIA can be observed from sample

BN1 to BN4.

4.5.1.2 Elemental and compound class distributions

Hydrocarbons (HC), nitrogen (Ny), oxygen (Ox), nitrogen and oxygen (NyOx), and sulfur

(OSCs, including Sz, SzOx, SzNy, and SzNyOx) containing organic compounds were detected in

all the studied extracts in positive APPI mode (Figure 4.4A–C).

Figure 4.4. Radar plots showing elemental class distributions of the compounds in extracts from

the Niobrara (left), the Barnett (middle) and the Posidonia Shale (right) in positive APPI and negative

ESI modes.

The Niobrara extracts contain larger fractions of hydrocarbons (43.0–46.1 %TMIA) but

lower fractions of Ox (8.9–12.9 %TMIA) and NyOx (7.8–10.2 %TMIA) classes relative to the

Barnett and Posidonia extracts in positive APPI mode, whereas the Barnett extracts are

characterized by the largest fractions of NyOx compounds among the studied extracts (Figure

4.4A–C). The positive APPI accessible inventories in the Niobrara extracts reveal the lowest

N/C and O/C ratios, whereas both ratios are high for the Barnett (Figure 4.5A, E). O/C and N/C

ratios are calculated after [∑Ii(ONo.)i/(CNo.)ii ]∑Iii

⁄ and [∑Ii(NNo.)i/(CNo.)ii ]∑Iii

⁄,

respectively; the (ONo.)i, (CNo.)i and (NNo.)i are the numbers of oxygen, carbon and nitrogen

atoms assigned for a specific signal i, whereas Ii represents its intensity.

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Ny, NyOx and Ox classes mainly consist of N1, N1O1 and O1 compounds in all the studied

extracts in positive APPI mode (Figure S4.4A). Compounds containing two and more nitrogen

or oxygen atoms are relatively more abundant in the Posidonia and Barnett extracts than in the

Niobrara (Figure 4.5B, F, S4.4A; average oxygen and nitrogen numbers respectively calculated

after ∑Ii(ONo.)ii ∑Iii

⁄ and ∑Ii(NNo.)ii ∑Iii

⁄). While the Barnett extracts (especially the

Barnett source rock extracts) are mostly enriched in components containing more than one

nitrogen atom, i.e., N2 and N2Ox, the Posidonia extracts have the highest average oxygen

numbers of Ox class.

The Posidonia and Niobrara extracts show increased fractions of OSCs (Figure 4.4A–C)

and thus increased S/C ratios (Figure 4.6A; S/C ratio calculated after

[∑Ii(SNo.)i/(CNo.)ii ]∑Iii

⁄, the (SNo.)i is the number of sulfur atoms assigned for a specific

signal i) in comparison with the Barnett extracts in positive APPI mode. OSCs in the Barnett

source rock extracts have higher contribution from SzNy class when compared to OSCs in the

other extracts (Figure 4.6B, S4.4A).

Figure 4.5. (A, C, E, G) Atomic N/C and O/C ratios of the positive APPI and negative ESI

accessible inventories. (B, D, F, H) Average nitrogen and oxygen numbers (NNO. and ONO.) of Ox, NyOx

and Ny classes in positive APPI and negative ESI modes. Abundance of the negative ESI ionizable Ox

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class in the Niobrara extracts NB1, NB2, NB4 and the Barnett extracts BN1, BN3, BN4 is less than or

approximately equal to 1% TMIA, whose average oxygen numbers are not included here.

Figure 4.6. (A) Atomic S/C ratio of the positive APPI and negative ESI ionizable compounds,

(B, C) Ternary diagrams displaying compound class distributions of OSCs characterized with positive

APPI (Sz, SzOx and SzNy classes) and negative ESI modes (SzOx, SzNyOx and SzNy classes).

Both reservoir rock extracts BN4 and NB5 are slightly richer in hydrocarbons when

compared to their corresponding source rock extracts in positive APPI mode (Figure 4.4A, B).

Reservoir rock extract BN4 contains significantly lower abundances of Ny and NyOx classes but

a higher abundance of Ox class than the Barnett source rock extracts (Figure 4.4B). The same

trends are found, albeit less pronounced within the Niobrara extracts (Figure 4.4A). As

compared to the extracts derived from source rock units, both reservoir extracts show smaller

N/C ratios (Figure 4.5A), lower average nitrogen numbers of Ny and NyOx classes (Figure 4.5B)

as well as slightly higher average oxygen numbers of Ox class (Figure 4.5F), while a slightly

larger O/C ratio can only be found for the Niobrara reservoir rock extract NB5 (Figure 4.5E).

Within the Barnett extracts from BN1 to BN4 in positive APPI mode, decreasing

abundances of OSCs and declining atomic S/C ratios are observed, while both parameters are

similar for the Niobrara reservoir and source rock extracts (Figure 4.4A, B, 4.6A). OSCs in both

Barnett and Niobrara reservoir rock extracts have lower fractions of SzNy and Sz classes as well

as larger proportions of SzOx compounds than that was documented for source rock extracts

(Figure 4.6B, S4.4A).

4.5.1.3 DBE distributions

DBE distributions of several chosen abundant positive APPI accessible compound classes

in the studied extracts are given in Figure 4.7A and S4.5A. DBE distributions of HC, N1 and S1

classes have comparable patterns in all the studied extracts (Figure S4.5A), while those of O1,

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O2, N1O1 and S1O1 classes reveal differences between the Niobrara extracts on the one hand

and the Posidonia and Barnett extracts on the other (Figure 4.7A). O1 and O2 classes in the

Niobrara extracts are dominated respectively by DBE13–21 O1 and DBE16–21 O2 compounds,

while in the Barnett and Posidonia extracts O1 and O2 classes contain large fractions of the low

DBE species, i.e., DBE≤12 O1 and DBE≤11 O2 components (Figure 4.7A). Besides, the low DBE

N1O1 compounds (5–9 DBE) are observed to be more abundant in the Niobrara extracts than in

the Barnett and Posidonia extracts (Figure 4.7A). In addition, while S1O1 class in the Niobrara

extracts is dominated by 3–8 DBE species, the 9–20 DBE species account for a higher

proportion of S1O1 class in the Posidonia and Barnett extracts (Figure 4.7A). Average DBE

values of these classes further quantitatively display these described variations between the

three sample sets (Figure 4.7B; average DBE values calculated after ∑Ii(DBE)ii ∑Iii

⁄, the

(DBE)i is the numbers of DBE for a specific signal i), for example as the higher average DBE

values of O1 and O2 classes in the Niobrara extracts than in the Posidonia and Barnett extracts.

Figure 4.7. (A) DBE distributions of the positive APPI ionizable O1, O2, N1O1 and S1O1 classes,

which are normalized to the most abundant DBE class (DBEmax_abund) in each compound class. (B)

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Average DBE values of the positive APPI detected O1, O2, S1O1, N1O1, HC, N1 and S1 classes. (C)

Average DBE values of the negative ESI detected N1, N2, N1O1, N1O2, N2O1 and S1N1 classes.

Both reservoir rock extracts BN4 and NB5 have lower average DBE values of nearly all

the displayed compound classes (excluding the low-abundance S1O1 class in the Barnett

extracts) when compared to the source rock extracts (Figure 4.7B). A constant decrease in

average DBE values of O1, O2, N1O1, HC, and N1 classes is observed within the Niobrara

extracts from NB1 to NB4, while within the Barnett extracts from BN1 to BN4 decreasing

average DBE values of HC, N1 and S1 classes can be traced (Figure 4.7B).

4.5.1.4 Carbon number distributions

Carbon number distributions of the positive APPI accessible high DBE (> ~10) species

(Figure S4.6) as exemplified by 15 and 18 DBE N1 species in Figure 4.8A maximize within the

first five members of each distribution, i.e., components with low carbon numbers, in the

Barnett and Niobrara source rock extracts, while those of the Posidonia source rock extracts

have their maximum at higher carbon numbers. Thus, quantitatively, average carbon numbers

of several representative DBE classes (illustrated in Figure 4.8C and calculated after

∑𝐼𝐼𝑖𝑖𝑖𝑖 (𝐶𝐶𝑁𝑁𝑁𝑁.)∑𝐼𝐼𝑖𝑖𝑖𝑖

⁄, the (CNo.)i is the numbers of carbon atoms assigned for a specific signal i)

are lower in the Barnett and Niobrara source rock extracts when compared to the Posidonia

source rock extracts. Also, these DBE class-specific average carbon numbers are, in general,

higher in the Niobrara source rock extracts than in the Barnett source rock extracts, except the

similar values documented for the 13 or 16 DBE O1 and O2 species (Figure 4.8C).

An increased fraction of high carbon number compounds is observed in both reservoir

rock extracts NB5 and BN4 when compared to the source rock extracts in positive APPI mode,

as expressed by their larger average carbon numbers (Figure 4.8A, C). This difference in

average carbon numbers between the source and the reservoir is generally more prominent

within the Barnett than within the Niobrara, excluding that for 15 and 18 DBE N1 species

(Figure 4.8C). Within the Barnett extracts from BN1 to BN4, increasing average carbon

numbers of DBE15,18 N1 and DBE18 N1O1 species can be found, whereas average carbon

numbers of DBE15 N1 and DBE13 O2 species are observed to increase within the Niobrara

extracts from NB1 to NB5 (Figure 4.8C).

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Figure 4.8. (A, B) Carbon number distributions of 15 and 18 DBE N1 compounds in both positive

APPI and negative ESI modes, which are normalized to the most abundant species (Cmax_abund) in each

DBE class. (C) Average carbon numbers of 15 and 18 DBE N1, N1O1, HC, S1O1, S1 species as well as

13 and 16 DBE O1, O2 species in positive APPI mode. (D) Average carbon numbers of the negative ESI

accessible DBE15,18 N1 and N1O1, DBE15,17 N2 and N2O1, DBE17,20 S1N1 and DBE13,16 N1O2 species.

4.5.2 High-polarity acidic NSO compounds detected by (-)-ESI FT-ICR-MS

4.5.2.1 Broad band spectra

Higher numbers of monoisotopic peaks are assigned in negative ESI spectra of the Barnett

and Posidonia extracts (1453–2107) when compared to the Niobrara spectra (528–1184; Figure

S4.3). The TMIA is higher for the Barnett extracts (1.9 × 1010–3.5 × 1010) than for the Posidonia

and Niobrara extracts (5.4 × 109–1.8 × 1010). The reservoir rock extract BN4 reveals a lower

TMIA relative to the Barnett source rock extracts, while the TMIA for the Niobrara reservoir

and source rock extracts are similar (Figure S4.3).

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4.5.2.2 Elemental and compound class distributions

NyOx and Ny classes dominate the negative ESI accessible inventories of all the studied

extracts (Figure 4.4D–F). While Ny class makes up the major fraction of the Niobrara and

Barnett extracts, NyOx and Ox classes represent relatively higher fractions in the Posidonia

extracts. While the negative ESI accessible inventories of the Posidonia extracts have the

highest O/C ratios, the Barnett extracts are characterized by the highest N/C ratios (Figure 4.5C,

G).

N1, N1O1 and O2 are the most prominent compound classes among the Ny, NyOx and Ox

elemental classes in the Niobrara and Posidonia extracts in negative ESI mode (Figure S4.4B).

In the Barnett extracts, compounds containing two nitrogen atoms N2 and N2Ox show similar

or even higher abundances when compared to the N1 and N1Ox compounds (Figure S4.4B).

Thus, Ny and NyOx elemental classes in the Barnett extracts are characterized by their elevated

average nitrogen numbers (Figure 4.5D). In contrast, extracts from the Posidonia Shale have

the highest average oxygen numbers of Ox and NyOx classes (Figure 4.5H).

The negative ESI accessible inventories of extracts from the Niobrara and Posidonia

source rock units contain larger fractions of OSCs and have greater S/C ratios when compared

with the Barnett (Figure 4.4D–F, 4.6A). OSCs in the Posidonia extracts reveal an enrichment

of SzOx class over SzNy class when compared to the Niobrara and Barnett extracts (Figure 4.6C,

S4.4B).

In comparison with extracts from the Barnett and Niobrara source rock units, the

corresponding reservoir rock extracts BN4 and NB5 detected in negative ESI mode both display

reduced fractions of OSCs (Figure 4.4D, E), declined S/C ratios (Figure 4.6A), slight

enrichment of SzOx versus SzNy compounds (Figure 4.6C), elevated O/C ratios (Figure 4.5G),

slightly increased average oxygen numbers of NyOx class (Figure 4.5H) as well as decreased

average nitrogen numbers of NyOx class (Figure 4.5D), whereas an increased average nitrogen

number of Ny compounds is only found in extract BN4 from the Barnett reservoir unit relative

to the source unit (Figure 4.5D).

4.5.2.3 DBE distributions

Regardless of lithofacies, DBE values of compound classes with high abundances in the

studied extracts in negative ESI mode including N1, N2, N1O1, N1O2, N2O1 and S1N1 are all in

the same range, namely 9–30 (Figure S4.5B). The general shape and local maxima of individual

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DBE distributions are almost identical for all the studied extracts (e.g., local maxima at DBE

12, 15, 18, 20 and 23 commonly observed in the N1 class), except DBE distribution of N1O1

class that shows a local maximum at DBE 16 in the Posidonia extracts instead of 15 in the

Barnett and Niobrara extracts (Figure S4.5B).

The Niobrara reservoir rock extract NB5 has lower average DBE values of all these

negative ESI accessible compound classes relative to the Niobrara source rock extracts

especially the NB1 (Figure 4.7C). Within the Barnett extracts, differences in DBE distributions

are minimal for all these compound classes (Figure 4.7C). The Barnett reservoir rock extract

BN4 has higher average DBE values of N1, N2, N2O1 and S1N1 classes and similar average DBE

values of N1O1 and N1O2 classes compared to that documented for the Barnett source rock

extracts (Figure 4.7C).

4.5.2.4 Carbon number distributions

Differences in carbon number distributions of individual DBE classes of the negative ESI

accessible inventories between extracts from distinct lithofacies are minimal (Figure 4.8B,

S4.7). Average carbon numbers of several representative DBE classes shown in Figure 4.8D

(including DBE15,18 N1 and N1O1, DBE15,17 N2 and N2O1, DBE17,20 S1N1 and DBE13,16 N1O2) in

the Posidonia source rock extracts are similar to or slightly higher than that for the Niobrara

and Barnett source rock extracts (Figure 4.8D). Furthermore, these values for the Barnett source

rock extracts are similar to or slightly higher than that for the Niobrara (Figure 4.8D).

Within both Barnett and Niobrara sample sets, variations in average carbon numbers

between the source and the reservoir rock extracts are minimal as shown for the selected

negative ESI ionizable DBE classes in Figure 4.8D. While in the Niobrara these average carbon

numbers in the reservoir extract NB5 are higher than or similar to that in the source rock extracts,

the opposite is observed in the Barnett where the reservoir extract BN4 reveals slightly lower

or similar values than the source rock extracts (Figure 4.8D). The Niobrara sample set shows

increased average carbon numbers of DBE15,18 N1 compounds with the increasing carbonate

content from sample NB1 to NB5 (Figure 4.8D).

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4.6 Discussion

4.6.1 Influence of lithofacies on generation and expulsion of NSO compounds

In terms of bulk composition, extractable OM from the clay-rich Posidonia Shale contains

more resins and asphaltenes than those derived from the biogenic quartz-rich Barnett Formation

and the carbonate Niobrara Formation (Figure 4.3C). The positive APPI accessible inventories

in both Posidonia and Barnett extracts contain more NSO compounds and less hydrocarbons in

comparison with the Niobrara extracts (Figure 4.4A–C), in which the positive APPI ionizable

hydrocarbons and NSO compounds roughly correspond to the aromatic and resin fractions,

respectively.

These findings are in agreement with the previous observations that mineral composition

imposes impacts on petroleum expulsion process (Huizinga et al., 1987), suggesting that NSO

compounds are expelled as efficiently as hydrocarbons from the carbonate source rocks which

have a low adsorption capacity, whereas fluids in the clay-rich source rocks experience strong

fractionation, i.e., NSO compounds are not expelled as efficiently as hydrocarbons. For

biogenic quartz, the small inter-particle pores lead to their high adsorption capacity (Xi et al.,

2019), which explains the high proportions of polar compounds especially the resins fraction

retained in the Barnett samples. In addition, for carbonate rocks, their petrophysical properties

are also important in enhancing the expulsion of unfractionated petroleum (Hofmann and

Leythaeuser, 1995) for example as the pressure solution seams and stylolites reported in the

Niobrara Formation in this study area (Gary, 2016; Hefton, 2015; Rietman, 2015). Moreover,

the high retention capacity of the Posidonia and Barnett shales might also be related to their

high TOC (Figure 4.2B), especially the high Rock-Eval parameter S2 (Figure 4.3A)

representing abundant ‘‘live” or ‘‘labile” organic components (Han et al., 2015).

The following sections address how compositions of NSO compounds differ as a function

of lithofacies.

4.6.1.1 Strong retention of organooxygen compounds in the clay-dominated

Posidonia Shale

The negative ESI detectable organooxygen compounds account for a significant fraction

in the Posidonia extracts (Figure 4.4D–F, 4.5G), potentially illustrating their higher adsorption

affinities on clay mineral surfaces (Adams, 2014). Oxygen atoms in these compounds are

principally present as acidic functional groups like carboxyl group (Figure 4.1B, Gonsior et al.,

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2011; Huba et al., 2016; Poetz et al., 2019), which could interact with the surface hydroxyl

groups of clay minerals like silanol and aluminol groups through ligand exchange (Jada and

Debih, 2009; Jada et al., 2006; Wu et al., 2012). In contrast, the other compounds such as the

organonitrogen compounds interact weakly with the clay mineral surfaces, for example through

physical adsorption, e.g., hydrogen bonding (Charlesworth, 1986; Wang et al., 2013). Moreover,

the increased number of active sites in the acidic polyoxygenated compounds enables them to

be retained in the clay-rich Posidonia samples with a higher priority (Figure 4.5H, S4.4B).

Oxygen atoms in the compounds detected by positive APPI are chemically bound in a

broader variety of functional groups including the less polar structures such as oxo or ether

groups (Figure 4.1B). The Posidonia and the Barnett extracts contain similar high proportions

of the positive APPI accessible organooxygen compounds and polyoxygenated compounds

(Figure 4.5E, F), possibly indicating that both clay minerals and biogenic quartz have similar

high retention capacities for these compounds. Moreover, the clay- or biogenic quartz-rich

rocks might even enable the efficient retention of the DBE≤12 O1 and DBE≤11 O2 compounds

(i.e., the organooxygen compounds with small molecular size) that are readily expelled from

carbonate rocks (Figure 4.7A). However, these low DBE compounds could also be generated

from the subsurface oxidation or the other diagenetic processes of the kerogen derived activate

hydrocarbons, which are supposed to be more prominent for the kerogen hosted by siliciclastic

rocks (see chapter 4.6.1.4).

4.6.1.2 Preferential preservation and retention of organonitrogen compounds in the

biogenic quartz-dominated Barnett Shale

Irrespective of ionization mode, the Barnett extracts especially the Barnett source rock

extracts always contain the highest proportions of organonitrogen compounds and multi-

nitrogen bearing compounds among the studied extracts (Figure 4.5A–D, S4.4). This can partly

be explained by the higher affinity of organonitrogen compounds (especially the multi-nitrogen

bearing compounds with more active sites) to the silica surfaces (Curtis et al., 1989). In

accordance, a preferential retention of the positive APPI accessible organonitrogen compounds

on silica surfaces has been reported (Chacón-Patiño et al., 2015; Nascimento et al., 2016).

The early diagenesis is where the main loss of nitrogen from OM occurs. The elimination

rate strongly depends on the nature of the associated minerals (Vandenbroucke and Largeau,

2007). Siliceous sponge spicules and agglutinated foraminifera are the two main kind of

biogenic quartz in the Barnett Shale (Han et al., 2015; Loucks and Ruppel, 2007; Milliken et

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al., 2007). Their external skeletons might help preserve the indigenous nitrogen compounds

(originally proteinaceous) through sorption and steric encapsulation during early diagenesis.

Thus, the Barnett samples might have already been coated with more organonitrogen

compounds from the proteinaceous residues in comparison with the other samples before

expulsion process, even though abundant clay minerals in the Posidonia Shale and substantial

coccolith and foraminifera in the Niobrara Formation (Han et al., 2019b) might also be

beneficial for the preservation of labile nitrogen (Vandenbroucke and Largeau, 2007).

4.6.1.3 Sulfur in organosulfur compounds does not control the retention behaviour

Both Posidonia and Niobrara source rock extracts show higher abundances of OSCs when

compared to the Barnett (Figure 4.4, 4.6A). This is consistent with the elevated values of both

DBT/Phen and MDBT/MPhen ratios (Figure 4.3D), which are interpreted as indicating higher

abundances of reactive sulfur available for incorporation into OM during the deposition of

Niobrara and Posidonia formations (Hughes et al., 1995). Note that here a stronger adsorption

of OSCs has been reported on surfaces of clay minerals such as kaolinite and illite (Gaboriau

and Saada, 2001; Tu et al., 2006a, 2006b) than surfaces of SiO2 (Chacón-Patiño et al., 2015;

Xing et al., 2010) and carbonates (Taheri-Shakib et al., 2018).

Compositions of OSCs differ between these three sample sets. While acidic SzOx class is

more enriched in the Posidonia source rock extracts (Figure 4.6C, S4.4B), the positive APPI

ionizable OSCs in the Barnett source rock extracts show higher proportions of the SzNy class

(Figure 4.6B). We therefore assume that the retention behaviour of OSCs is mainly controlled

by their oxygen or nitrogen functional groups, due to the weak dipole moment of a sulfur-

carbon bond (Adams, 2014).

4.6.1.4 Enrichment of the low-polarity aliphatic S1O1 and N1O1 species in carbonate

rocks: results of oxidation process during maturation?

Enrichment of the positive APPI accessible low DBE S1O1 (≤ 8 DBE) and N1O1 (≤ 9

DBE) compounds is observed in solvent extracts of both marls and chalks in the Niobrara Shale

(Figure 4.7A), which is more likely generation-related rather than a retention feature.

While the DBE≤5 S1O1 compounds primarily represent aliphatic sulfoxides, the > 8 DBE

compounds are more likely hydroxo-thiophenic compounds (Kim and Kim, 2010). Different

carbon number distribution types, i.e., the unimodal Gaussian-type for the ≤ 8 DBE compounds

and the bimodal pattern with maxima at lower carbon numbers for the > 8 DBE compounds,

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can be interpreted as a further indication of their respective aliphatic versus aromatic character

(Figure S4.8A; Poetz et al., 2019). Pomerantz et al. (2014) found large quantities of sulfoxides

in carbonate source rock extracts. They proposed that sulfoxides were mainly formed via

subsurface oxidation of the active sulfur-bearing species cracked from kerogen during

maturation. By analogy, the low DBE N1O1 (≤ 9 DBE) compounds possibly as cyclic amides

might have been formed via similar pathways, i.e., subsurface oxidation of the kerogen derived

activated nitrogen-bearing species (Lewan, 1997; Seewald, 2001; Surdam et al., 1993).

Minerals have been reported to participate in the subsurface oxidation process, for

example a metastable thermodynamic equilibrium between carbonate minerals, oxygenated

compounds and water (Bernard et al., 2012; Helgeson et al., 1993; Seewald, 2003, 2001; Shebl

and Surdam, 1996; Surdam and Crossey, 1985). The basicity of carbonates as well as the acidity

of clay minerals and quartz differently influence the pH environment of a subsurface oxidation

milieu. Basic carbonates therefore seem to better support the oxidation of active sulfur- or

nitrogen-bearing species formed from kerogen. In addition, a higher abundance of reactive

sulfur- or nitrogen-bearing species cracked from the kerogen hosted by carbonate rocks might

also be the reason. In accordance, the low DBE S1O1 compounds identified as sulfoxides were

also found to represent large proportions in extracts of the carbonate-rich Eagle Ford Formation

at a similar thermal maturity using (+)-ESI FT-ICR-MS (Poetz et al., 2019).

By analogy, the low DBE O1 (≤ 12 DBE) and O2 (≤ 11 DBE) compounds observed in

higher abundances in the Posidonia and Barnett extracts might be formed via subsurface

oxidation of the active hydrocarbons cracked from kerogen that preferentially occurs in the

clays- or biogenic quartz-rich rocks (Figure S4.7A). Further investigations are needed to

understand the mechanism of the maturation-driven formation of organooxygen compounds in

rock bitumen.

4.6.1.5 Different alkylation degrees of the low-polarity NSO compounds

Within a selected NSO compound class at a given DBE value, members in the low carbon

number range represent molecules with few and/or short alkyl side chains. This concept was

originally developed for the pyrrolic nitrogen compounds detected by negative ESI (Poetz et

al., 2014) and used to assess shielding effects on the retention behaviour of NSO compounds

(Mahlstedt et al., 2016). It is also applicable for the positive APPI detected compounds, but in

a less strict manner, since one DBE class represents more than one possible (poly)cyclic

aromatic core structure.

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In our study, alkylation degrees of the negative ESI accessible acidic NSO compounds in

the three source rock types are very similar (Figure 4.8B, D). Higher alkylation degrees of the

positive APPI detected low-polarity NSO compounds observed in the Posidonia source rock

extracts (Figure 4.8A, C) are controlled more by their parent kerogen structure than by a

different retention behaviour. Indeed, the differences in carbon number distributions between

solvent extracts of the Posidonia and the other two sample sets reproduce variations in the chain

lengths as seen in the open system Py-GC results (Figure 4.3B), meaning that n-alkyl moieties

in kerogen are transferred to the daughter NSO compounds during catagenesis. In that regard,

Mahlstedt et al. (2016) have shown similarities in chain length distribution of the negative ESI

ionizable N1 class between solvent extracts and kerogen pyrolysates of the Posidonia samples.

These alkylation features inherited from kerogen might be further modified by the

expulsion induced fractionation, however, in different degrees depending on lithofacies.

Compounds with lower alkylation degrees are of higher polarity and lower solubility in an oil

phase (Mahlstedt et al., 2016; Poetz et al., 2014) and thus they interact more strongly with

surfaces of minerals like quartz or carbonates (Chacón-Patiño et al., 2015; Pinto et al., 2017)

resulting in a preferential retention. Therefore, alkylation degrees of the retained NSO

compounds in the Barnett and Posidonia source rocks with strong retention capacity are

expected to be lower than that in the Niobrara. Indeed, average carbon numbers of all the

organonitrogen and organosulfur compounds in the Barnett source rock extracts are lower than

that observed for the Niobrara, except values of the 13 and 16 DBE O1 and O2 compounds

(Figure 4.8A, C). Adsorption behaviour of oxygen-containing groups seems to be less

significantly influenced by side group effects in comparison with nitrogen- and sulfur-bearing

structures (Ataman et al., 2016a, 2016b).

4.6.2 Influence of lithofacies on petroleum migration within unconventional

systems

Lithofacies variations within unconventional petroleum systems such as the Niobrara and

Barnett shales impose impacts on the (vertical) intra-formational migration (Han et al., 2018d,

2015; Jarvie, 2012). For instance, oils generated by the Niobrara marls and the Barnett 3rd

interval could migrate into the Niobrara chalks and the Barnett 2nd interval that contain

abundant carbonates or biogenic quartz as petroleum storage space (Figure 4.2B). Fractionation

of NSO compounds occurring during intra-formational migration might vary for each system,

which is expected to be influenced by lithofacies of systems, herein, the biogenic quartz

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dominated versus the carbonate-rich. Differences in this fractionation observed between the

Barnett and Niobrara sample sets are described here in detail.

4.6.2.1 Reduced capacity of organonitrogen compounds to migrate in the biogenic

quartz-rich petroleum system relative to the carbonate petroleum system

Resins and asphaltenes are preferentially retained in both Barnett and Niobrara source

rock units when compared specifically to the aliphatic hydrocarbons (Figure 4.3C, 4.4A, B).

Preferential retention of the negative ESI detected high-polarity acidic inventories particularly

the acidic Ny and NyOx classes is only observed in the Barnett source as illustrated by their

lower absolute abundances in the reservoir extract BN4, but not in the Niobrara source (e.g.,

Figure S4.3). Both source rock units particularly the Barnett strongly retain the low-polarity Ny

and NyOx compounds (Figure 4.4A, B, 4.5A), especially the multi-nitrogen bearing compounds

with more active sites (Figure 4.5B). In contrast, organooxygen compounds especially the Ox

class of either high or low-polarity seem not show any significant depletion in both reservoir

rock extracts when compared to the source rock extracts (Figure 4.4A, B, D, E, 4.5E, G). In

terms of OSCs, the SzOx compounds preferentially migrate out of both Barnett and Niobrara

source units in comparison to the other organosulfur compounds like SzNy (Figure 4.6B, C),

which could be attributed to the presence of oxygen in their structures and/or their lower

molecular size as indicated by the lower range of DBE values (Table S4.2).

4.6.2.2 Highly alkylated small acidic NSO molecules migrate better in the carbonate

petroleum system: clues from carbon number and DBE distributions

Either high or low polarity NSO compounds with lower DBE values representing smaller

molecular size preferentially migrate out of the Niobrara source rock units, according to a

comparison of average DBE values between the reservoir and source rock extracts (especially

when comparing the extracts NB5 and NB1; Figure 4.7B, C). This molecular size-based

fractionation, i.e., size exclusion, is also observed in the Barnett sample set, but only for the

low-polarity NSO components (Figure 4.7B). In contrast, average DBE values of the high-

polarity acidic classes shown in Figure 4.7C are similar or even higher in the Barnett reservoir

extract BN4 when compared to the Barnett source rock extracts. Therefore, acidic NSO

compounds regardless of their molecular size might all be strongly retained in the Barnett

source, thus displaying no migration fractionation.

The low-polarity N1 compounds with low carbon numbers representing lower alkylation

degree are preferentially retained in both Barnett and Niobrara source rock units, whereas the

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highly alkylated homologues preferably migrate out of the source (Figure 4.8A, C) due to the

side chain shielding effects that reduce interactions with the mineral active sites. For the other

low-polarity NSO compounds like N1O1 and O2, fractionations due to side chain shielding

effects are found in the Barnett sample set (Figure 4.8C), whereas the Niobrara reveals this kind

of fractionation only for some classes and to a lesser extent (Figure 4.8C), which might be

attributed to the Niobrara’s generally lower retention capacity for these low-polarity NSO

molecules irrespective of their alkylation degree. Fractionations caused by side chain shielding

effects can be found for some acidic NSO compounds such as the DBE15 N1 species in the

Niobrara samples in low degree, whereas the acidic NSO compounds irrespective of alkylation

degree might all be strongly retained in the Barnett source rock units thus showing no

fractionation, in fact, an opposite trend is even observed (Figure 4.8D).

These molecular size- or alkylation degree-based fractionations of NSO compounds

within each sample set correlate with its changing mineral compositions, further indicating

these trends are controlled by lithofacies. In the Niobrara sample set, a constant decrease in

average DBE values of the low-polarity O1, O2, N1O1 and N1 classes is observed with the

increasing carbonate content from sample NB1 to NB5, whereas the decrease in average DBE

values of the low-polarity N1 and S1 classes in the Barnett from sample BN1 to BN4 correlates

with the increasing quartz content (Figure 4.2B, 4.7B). Porous calcareous and siliceous fossil

skeletons like coccolith, foraminifera and sponge spicules are the main carbonate and quartz

forms in the Niobrara and Barnett formations, which provide petroleum storage space and

migration avenues (Han et al., 2019b, 2015). Their contents seem to determine the molecular

size-based fractionation occurring within each unconventional petroleum system. Similar

trends are found for the fractionation of NSO components based on side chain shielding effects

(Figure 4.8C, D).

4.7 Summary and Conclusions

Direct infusion FT-ICR-MS measurements reveal different NSO compound inventories

in solvent extracts from source and reservoir facies in the lithologically/mineralogically diverse

shales (namely, the carbonate-rich Niobrara Formation, the biogenic quartz-rich Barnett Shale

and the clay-rich Posidonia Shale) containing similar marine type II kerogen in the peak to late

oil window, which seems to be largely controlled by the organo-lithological interactions

occurring during petroleum expulsion and migration. NSO compounds are retained to a greater

extent in the Barnett and Posidonia samples than in the Niobrara, indicating the generally higher

155

retention capacities of clay minerals and biogenic quartz for NSO compounds as compared to

carbonates. Enrichment of organonitrogen compounds in the Barnett extracts might be the

consequence of a preferential preservation and retention of organonitrogen compounds through

steric encapsulation and adsorption by biogenic quartz such as sponge spicules and agglutinated

foraminifera. Higher abundances of acidic organooxygen compounds in the Posidonia extracts

might be related to their higher adsorption affinities towards clay mineral surfaces, while the

comparable abundances of low-polarity organooxygen compounds in both Barnett and

Posidonia extracts seems to reflect their comparable adsorption affinities for clay minerals and

quartz. Retention behaviour of organosulfur compounds is mainly determined by the adsorption

affinity of their accompanying heteroatoms like nitrogen and oxygen. In contrast to the

siliciclastic rock extracts, the carbonate Niobrara extracts contain larger fractions of cyclic

aliphatic sulfoxides and amides. These compounds may be formed via subsurface oxidation or

the other diagenetic processes of the activate nitrogen- or sulfur-bearing species cracked from

kerogen, which might be more prominent for the kerogen hosted by carbonate rocks.

Lithofacies variations within the unconventional petroleum systems influence the intra-

formational migration. Different fractionation patterns found for the Barnett and Niobrara

sample sets might be lithofacies related (biogenic quartz- versus carbonate-rich). The low-

polarity organonitrogen compounds are preferentially retained in both Barnett (to a greater

extent) and Niobrara source rock units. The highly alkylated small acidic NSO molecules

preferably migrate out of the Niobrara source rock units, whereas these acidic NSO compounds

irrespective of their molecule size and alkylation degree are all strongly retained in the Barnett

source showing no fractionation.

4.8 Acknowledgements

This study is financially supported by the Chinese Scholarship Council. Cornelia Karger,

Anke Kaminsky, Ferdinand Perssen and Andrea Gottsche in GFZ are acknowledged for their

technical support. We are grateful to John K. Volkman, Joseph A. Curiale, Renzo Silva and an

anonymous reviewer for their careful and constructive reviews of this paper.

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4.9 Supplementary material

Figure S4.1. Compounds used by Huba et al. (2016) to test the ionization ranges of positive APPI

and negative ESI modes.

157

Figure S4.2. Handling of contamination peaks. The most “suspicious” peaks are those with very

high abundance but with few or no other assigned peaks in the same compound class, for example as

the peaks assigned as C14H27O4 and C22H43O4 in positive APPI spectra of the investigated Barnett

extracts. They are of very high abundance, but no other peaks can be assigned as O4 compounds. They

have been excluded from further assessment. They are possibly from drilling additives and they are

striking only in the Barnett extracts but not in the Niobrara and Posidonia extracts when detected by

positive APPI. Peaks marked by blue triangles can also be contaminations, which are common in

positive APPI spectra of all the Barnett extracts. However, they do not influence the subsequent

evaluation since they cannot be assigned as a formula (a maximum value per assignment of

C100H202S4N2O5) within the allowed mass error of 0.5 ppm. Here, in positive APPI spectrum of the

representative Barnett extract BN4, the monoisotopic assigned peaks used for further evaluation are

marked out using green color. In negative ESI mode, striking contamination peaks are only present in

some Barnett and Niobrara extracts like BN4, similar rules are followed.

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Figure S4.3. Partial mass spectra showing only monoisotopic assigned peaks in positive APPI

and negative ESI modes. Peaks assigned as different elemental classes are coloured, respectively. Peak

number and absolute abundance of the monoisotopic assigned peaks (Peak No. and TMIA) are also

recorded here.

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Figure S4.4. Compound class distributions of the positive APPI and negative ESI accessible

inventories in different extracts. Compound classes whose abundances lower than 1% TMIA for every

sample are not shown.

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Figure S4.5. DBE distributions of the positive APPI ionizable hydrocarbons, N1 and S1 classes

as well as the negative ESI accessible N1, N2, N1O1, N1O2, N2O1 and S1N1 classes, which are normalized

to the most abundant DBE class (DBEmax_abund) in each compound class.

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Figure S4.6. DBE versus carbon number distributions of the positive APPI ionizable

hydrocarbons, N1, N1O1, O1, O2, S1O1 and S1 classes in the representative Niobrara, Barnett and

Posidonia extracts NB1, BN1 and PS1.

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Figure S4.7. DBE versus carbon number distributions of the negative ESI ionizable N1, N2, N1O1,

S1N1, N1O2 and N2O1 classes in the representative Niobrara, Barnett and Posidonia extracts NB1, BN1

and PS1.

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Figure S4.8. Carbon number distributions of the positive APPI accessible 5, 8, 9, 15 DBE S1O1

and 6, 9, 10, 15 DBE N1O1 classes, which are normalized to the most abundant species (Cmax_abund) in

each DBE class.

Table S4.1. Mineralogical compositions.

Sample

G-

number

Calcite Dolomite Ankerite I/S Chlorite Kaolinite Quartz Mica Feldspar Rutile Apatite Pyrite

(wt.%)

NB1 G015836 51 1 0 23 0 0 17 4 0 0 0 4

NB2 G015825 53 5 0 20 0 0 14 4 0 0 0 4

NB3 G015824 69 2 0 11 0 0 10 2 0 0 0 6

NB4 G015832 73 2 0 11 0 0 9 3 2 0 0 2

NB5* G015839 79 1 0 9 0 0 9 2 0 0 0 1

BN1 G012618 0 1 0 26 4 0 25 26 10 1 1 6

BN2 G009621 0 1 0 25 4 0 26 25 10 1 5 4

BN3 G012617 0 3 0 15 4 0 33 16 8 1 19 2

BN4* G012616 11 1 4 10 0 0 40 13 14 0 4 2

PS1 G007041 20 3 0 50 3 14 12 / 3 / / /

PS2 G007035 20 3 0 49 4 14 12 / 3 / / /

PS3 G007060 17 2 0 56 4 13 11 / 3 / / /

I/S: illite/smectite mixed-layer minerals. “/” marks out the minerals that are not included in the

measurement. Results for the Barnett and Niobrara samples have been published by Han et al. (2017)

and Han et al. (2019b). “*” marks out the reservoir samples.

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Table S4.2. Average DBE values of some organosulfur classes in positive APPI and negative ESI

modes.

NB1 NB2 NB3 NB4 NB5* BN1 BN2 BN3 BN4*

Ave.

DBE

(+)-

APPI

SzOx 9 8 8 8 7 10 11 9 10

SzNy 16 21 13 21 21 21 21 21 19

Sz 17 17 16 16 15 18 18 17 15

(-)-ESI SzOx 14 3 2 / 7 12 4 7 13

SzNy 20 18 18 19 18 20 19 20 20

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5 SUMMARY AND PERSPECTIVES

5.1 Summary

The elemental and molecular composition of organic high-molecular-weight NSO

compounds in sedimentary rocks contains a wealth of valuable geological information, however,

acquisition and deconvolution of these information is still at a very preliminary stage.

The primary objective of this dissertation is to reveal how biomass input, depositional

condition, and lithofacies (via controlling fractionation during petroleum expulsion and

migration) influence the composition of heavy NSO compounds in sedimentary rocks that are

soluble in common organic solvents. A ternary azeotropic mixture of methanol, acetone and

chloroform (30:38:32, v/v/v) was chosen for rock extraction because its high polarity gives it a

particular capacity to extract polar NSO compounds. Direct infusion FT-ICR-MS in different

ionization modes including positive APPI, negative ESI and positive ESI were used to get a

holistic portrait of the high-molecular-weight NSO compounds in rocks extracts, including the

low-polarity, basic and acidic NSO inventories.

To properly and most accurately deconvolute the effects of each geological factor on the

NSO compound composition, appropriate sample series were selected that were almost

exclusively affected by the geological factors of interest (organic matter input, depositional

environment or lithofacies).

16 immature to early mature rocks with different geological histories having not

undergone significant thermal stress were used to reveal the impact of biomass input and/or

depositional conditions on NSO compound composition. The analyzed natural laboratories are

the marine Dynow and Schöneck formations in the Molasse Basin (Austria), the marine

Posidonia Shale and the lacustrine Wealden Formation in the Lower Saxony Basin (Germany),

as well as the terrestrial Waikato coal measures in the Waikato Basin and the terrestrial Brunner

coal measures in the West Coast Basin (New Zealand). NSO compositions from FT-ICR-MS

analyses were correlated with the palaeoecological and palaeoenvironment information

obtained from conventional/established geological and geochemical methods such as GC-MS,

GC-FID and open system Py-GC. The composition of heavy organonitrogen and organooxygen

compounds Ox, Ny, NyOx was primarily associated with the preservation potentials and

pathways of individual oxygen- and/or nitrogen-bearing biomolecules with distinct taxonomic

associations (herein, terrestrial plants, marine or lacustrine autochthonous microbial

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communities), such as algaenan, lignin, cutin, and protein that can be assigned to a specific

group or groups of organisms or contained in organisms in variable proportions. In contrast, the

composition of heavy OSCs (Sz, SzOx, SzNy, SzNyOx) was associated with both biomass input

and depositional conditions (such as levels of dissolved sulfide, oxygen and iron), since OSCs

are primarily formed through abiotic incorporation of inorganic sulfur into appropriate

functionalized biomolecules during early diagenesis.

10 thermally mature source rocks from unconventional petroleum systems with the three

globally most significant lithofacies, namely the biogenic carbonate-rich Niobrara Shale, the

biogenic quartz-rich Barnett Shale and the detrital clay-rich Posidonia Shale were investigated

to study the impact of lithofacies on NSO compound composition. All three source rock series

contain abundant marine type II kerogen in peak–late oil window, thus, the variations in their

retained NSO compounds were primarily linked to the distinct retention behavior of individual

compounds on different mineral phases during petroleum expulsion, i.e., the impact of

lithofacies on fractionation during expulsion. Within the Barnett and the Niobrara

unconventional systems, lithofacies variations are present in terms of the content of porous

siliceous and calcareous fossil skeletons that can provide petroleum storage space, respectively,

thus intra-formational migration occurred. The NSO compositional differences between the

reservoir and the source rock extracts could to some extent record the migration-induced

fractionation within a petroleum system. The Barnett and the Niobrara sample sets each include

one sample from the intra-reservoir units, allowing the investigation of lithofacies’ impact on

heavy NSO compounds via controlling the fractionation during migration (biogenic quartz-

versus carbonate-rich).

5.1.1 Precursor biotic information recorded by organooxygen and

organonitrogen compounds

5.1.1.1 In-situ deposits of terrestrial plants

Coals as the in-situ deposits of oxygen-rich terrestrial plants were found to contain

predominantly oxygen-bearing compounds in forms of both Ox and N1Ox.

The detected aromatic Ox and N1Ox compounds, particularly the highly aromatic

polyoxygenated species, are assumed to represent the breakdown products of the highly

resistant plant macromolecules lignin and tannin (the most and the second most abundant

polyphenols in nature) such as derivatives of phenolic ketones and phenolic carboxylic acids,

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as well as their condensation products with the degradation intermediates of other labile

proteinaceous biomolecules.

The observed carbon number preference (even or odd) of aliphatic Ox species with C26,

28, 30 or C27, 29, 31 as the most dominant homologues indicate their primary origin as the plant

protective substances (e.g., cutan, cutin, suberan, suberin and waxy materials) that have been

selectively preserved during early diagenesis due to their very high resistance to degradation or

the in-situ polymerization of waxes. The contribution of cutan and waxes rich in long-chain

homologs apparently exceeded that of the middle-chain C≤24 monomers dominated cutin,

suberan and suberin. The long-chain Ox molecules mainly comprise the even-number

dominated fatty acids, (poly)hydroxy fatty acids, dicarboxylic acids, hydroxy dicarboxylic

acids that are originated from waxes and cutan, as well as, the even-number dominated

ketoaldehydes, unsaturated aldehydes and odd-number dominated ketones, hydroxyketones,

hydroxy-β-diketones that are derived from plant waxes.

5.1.1.2 Marine autochthonous microbial communities

The high abundances of organonitrogen compounds in forms of both Ny and NyOx found

in the marine rock extracts (especially in those extracts associated with substantial marine algae

input) were interpreted as signatures of protein-rich marine organisms (particularly algae) that

have been preserved via degradation-recondensation reactions. The random recondensation of

substantial proteinaceous decomposition intermediates was found to lead to the formation of

significant amounts of N2Ox and N2 compounds. However, the biomass input information

preserved by N2 compounds is prone to be biased by lithofacies effects. Clay minerals (in

comparison with carbonates) provide increased sorption protection for organonitrogen

compounds, and this protection was found to be more important for the N2 rather than for the

N2Ox compounds. One explanation is the type and polarity differences of the nitrogen-bearing

functional groups in the N2 and N2Ox compounds, where the reactivity of nitrogen-bearing

groups in the N2Ox compounds is significantly lowered by stereoelectronic effects such as steric

shielding of oxygen atoms.

The weak carbon number preference of the middle–long chain aliphatic Ox compounds is

commonly observed in the marine rock extracts, in which the amounts of medium-chain species

(C23, C25 or C22, C24) are comparable to or even dominant over the long-chain species (C27, C29,

C31 or C26, C28, C30). These document the common features of marine microbial communities.

The individual patterns of aliphatic Ox compounds help to further distinguish between different

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marine depositional settings: the microbial communities that were present during the deposition

of the Posidonia samples are characterized by abundant odd-number dominated unsaturated

ketones, the communities related to the Dynow and Schöneck samples are found to be featured

by high amounts of C28 sterols (mainly sourced from diatoms), odd-number dominated

saturated and unsaturated diketones, and even-number dominated diunsaturated hydroxy fatty

acids.

5.1.1.3 Lacustrine autochthonous microbial communities at different salinities

Botryococcus braunii and dinoflagellates were two important algal species in the

Wealden Formation, whose relative abundance recorded fluctuations in water column salinity.

The highly aliphatic algaenan characterizes the Botryococcus braunii input by a high abundance

of Ox compounds, because its selective preservation provides an efficient protection for its

oxygen-bearing groups and the proteinaceous moieties through encapsulation during early

diagenesis. The originally very small amount of proteins in the Botryococcus causes the low

abundances of N1 and N1Ox compounds. The Botryococcus input further leads to abundant very

long-chain Ox, N1 and N1Ox compounds with more than 40 carbon atoms, which were supposed

to be the degradation products of algaenan (composed of monomers on average 40 carbon atoms)

and their condensation products with the preserved proteinaceous moieties. In contrast,

dinoflagellates and other organisms adapted to the freshwater–brackish transitional conditions

of the Wealden Formation were found to be characterized by a relatively high amount of

proteins and a reduced content of very long-chain moieties with more than 40 carbon atoms.

These lacustrine microbial communities prevalent at different salinities of the Wealden

Formation were commonly featured by a high proportion of aliphatic compounds and a low

aromaticity of aromatic compounds. In addition, the amounts of medium-chain aliphatic Ox

compounds in all the Wealden extracts are comparable to or even dominant over the long-chain

species, and both show a weak carbon number preference. High amounts of the even-number

dominated aldehydes and unsaturated hydroxy fatty acids as well as the odd-number dominated

keto-diols and unsaturated diketones appeared to be primarily associated with Botryococcus

braunii, while all these diverse microorganisms could be precursors of abundant odd-number

dominated diketones.

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5.1.2 Palaeoecological and palaeoenvironmental signatures in organosulfur

compounds

5.1.2.1 Palaeoenvironmental information (levels of dissolved sulfide, oxygen, and

iron)

The iron-deficient sulfidic depositional conditions (herein, the Posidonia, the Lower

Schöneck and to a lesser extent the Upper Schöneck formations) were found to have promoted

extensive OM sulfurization (demonstrated by high amounts of both low- and high- molecular-

weight OSCs), particularly at multiple functional sites of appropriate biomolecules (illustrated

by abundant multi-sulfur bearing compounds S2Ox, S2 and S3). The high ratios of reduced versus

oxidized organosulfur forms further argue for the small amounts of oxidants such as molecular

oxygen or metal (Fe, Mn) oxides at the oxic-anoxic interfaces. Under such condition, the C20

isoprenoid alcohols in the (bacterio)chlorophylls might be preferentially sulfurized, illustrated

by enrichment of the 1 DBE S1 and S1Ox compounds containing 20 carbon atoms. The

prominently enriched S1 and S1Ox compounds containing 35 carbon atoms solely found in the

Dynow and Schöneck samples were presumed as the abiotic sulfurization products of C35

bacteriohopanepolyol derivatives such as bacteriohopanetetrol, which might reflect the low

levels of oxygen exposure prior to sulfurization during deposition of the Dynow and Schöneck

formations. Otherwise, bacteriohopanepolyol derivatives are expected to undergo oxidative

cleavage and subsequent side-chain degradation, forming short-chain derivatives rather than

preserving intact carbon skeletons.

5.1.2.2 Palaeoecological information (marine versus lacustrine biomass input)

The nitrogen-containing organosulfur compounds SzNy and SzNyOx found solely in the

marine rock extracts were assumed to record the generally high abundances of proteinaceous

moieties in marine organisms that can be sulfurized, since OSCs related to lacustrine settings

contain exclusively SzOx and/or Sz classes. In addition, marine organisms might comprise

higher proportions of sulfurizable polyoxygenated compounds relative to lacustrine organisms,

as illustrated by higher average oxygen numbers of S1Ox compounds in the marine rock extracts.

In contrast, lacustrine organisms such as Botryococcus braunii are characterized by abundant

sulfurizable aliphatic moieties.

The Sz and SzOx compounds containing 25 and 30 carbon atoms assumed as sulfurized

C25 and C30 HBI polyenes were significantly enriched only in the Upper Schöneck Formation,

indicative for a massive diatom bloom associated with a strong upwelling system, whereas the

170

precursors of C30 pentacyclic polyprenoid organosulfur compounds were assumed to be more

abundant in fresh/brackish water algae and thus a stronger enrichment occurred in the lacustrine

deposits. The prominently enriched Sz and SzOx compounds containing 40 carbon atoms

assumed as sulfurized C40 carotenoids was presumed as a sign of high primary productivity.

Since carotenoids are widespread in both oxygenic and anoxygenic photoautotrophs, the

strongly enriched sulfurized carotenoids could be specific to a high productivity of anoxygenic

photoautotrophs only if accompanied by hydrocarbon biomarker distributions such as abundant

isorenieratene derivatives biphenyls characteristic for PZA or PZE, for examples as shown in

the Upper Schöneck sample and the Posidonia samples, if not, it is principally linked to a high

productivity of oxygenic photoautotrophs such as in the Wealden samples.

5.1.3 Controls of lithofacies on fractionation of NSO compounds during

petroleum expulsion and migration

5.1.3.1 Fractionation during petroleum expulsion

Higher proportions of NSO compounds versus hydrocarbons in the solvent extracts from

the siliciclastic Barnett and Posidonia shales in comparison with the carbonate Niobrara

Formation indicate the generally higher retention capacities of clay minerals and biogenic

quartz for the polar compounds when compared to the carbonates. The different retention

specificities of the biogenic quartz- and clay-rich rocks were illustrated by the varying NSO

compositions in their bitumen fraction. The relatively high abundance of organonitrogen

compounds, especially multi-nitrogen bearing compounds, in the Barnett extracts was assumed

to document a selective preservation and retention of organonitrogen compounds through steric

encapsulation and adsorption by biogenic quartz such as sponge skeletons or agglutinated

foraminifera. The substantial acidic organooxygen compounds especially polyoxygenated

compounds in the Posidonia extracts might be related to their higher adsorption affinities

towards clay mineral surfaces. The observed similar abundances of the low-polarity

organooxygen compounds in the Barnett and Posidonia extracts were assumed to reflect their

comparable adsorption affinities for the clay and quartz minerals. Moreover, sulfur in OSCs

might not control their retention behaviour, instead, the retention behaviour of OSCs were

found to be primarily determined by the adsorption affinity of their contained other heteroatoms

like nitrogen and oxygen.

171

5.1.3.2 Fractionation during petroleum migration

The differences in NSO composition between the reservoir and the source rock extracts

in terms of compound class, carbon number and DBE distributions could to some extent

document the migration-induced fractionation within a petroleum system based on the type,

number and accessibility (steric hindrance induced by alkylation) of molecular active sites (i.e.,

heteroatomic functional groups), as well as, the size of molecular aromatic core structure.

Between the biogenic quartz-rich Barnett system and the carbonate-rich Niobrara system,

differences in migration-induced fractionation were found.

While the highly alkylated small acidic NSO molecules could preferably migrate out of

the Niobrara source rock units, the acidic NSO compounds irrespective of their molecule size

and alkylation degree were all strongly retained in the Barnett source showing no fractionation.

The molecular size-based fractionation of distinct low-polarity heteroatomic compound classes,

as well as, the alkylation degree-based fractionation of the low-polarity N1 compounds, were

observed in both Barnett and Niobrara petroleum systems. In contrast, the other low-polarity

NSO classes are not or less fractionated according to the degree of alkylation in the Niobrara

system in comparison with the Barnett system, which might reflect that carbonate source rock

units generally have lower retention capacity for the low-polarity NSO molecules excluding the

low-polarity N1 compounds. The low-polarity organonitrogen compounds were found to be

preferentially retained in both Niobrara and Barnett source rock units, to a lesser extent in the

Niobrara.

5.2 Perspectives

FT-ICR-MS has been applied to study organic heavy NSO compounds in sedimentary

rocks since the turn of the century, but the acquisition and deconvolution of valuable geological

messages from this vast amount of information is still in their infancy.

The identification of suitable molecular proxies to measure a specific

palaeoenvironmental or palaeoecological parameter or describe a certain geological process is

of particular value. In this study, a series of proxies was developed based on relative abundances

of certain NSO compound classes or individual NSO compounds obtained by direct infusion

FT-ICR-MS, to provide palaeoenvironmental information (levels of dissolved sulfide, oxygen,

and iron), to differentiate lacustrine, marine and terrestrial palaeoecosystems, as well as, to

distinguish petroleum expulsion and migration processes that occurred in biogenic quartz-,

biogenic carbonate-, and detrital clay-rich petroleum systems. Since direct infusion FT-ICR-

172

MS data cannot distinguish isomers, the structural discussions and suggestions for the detected

species in this study are speculative based on the unambiguous molecular formulas provided

by FT-ICR-MS and the selectivity of the applied ionization modes. Although these speculations

have also been indirectly supported by the results obtained by methods such as GC-MS, GC-

FID and the open system Py-GC, the observations and conclusions made in this dissertation

still await further verification, not only by larger databases of NSO inventories in more diverse

sedimentary rocks, but also by combining preparation procedures (derivatization steps or

chromatography, including ion mobility approaches, etc.) with FT-ICR-MS to actually extract

structural information or analysis specific compound class. Hopefully, they may consequence

more important implications.

The proxies developed in this study for assessing palaeoenvironment, palaeoecology or

petroleum retention were not based on correlations in just a few particular geographic regions;

they were formulated in a way that are also meaningful in terms of known biomolecular

compositions, early diagenetic responses (e.g., abiotic sulfurization), or molecular mobility, to

ensure that they have a relatively strong scientific underpinning and thus can translate well to

other depositional setting or unconventional petroleum systems. However, most of the

sedimentary heavy NSO compounds become amenable to study at the molecular level only

using ultrahigh resolution FT-ICR-MS, lacking an understanding of their individual source

specificity or molecular mobility. As a consequence, most proxies were proposed based on

elemental than molecular information, i.e., at the compound class level rather than at the

compounds level; only a small portion of the molecular-level information on sedimentary heavy

NSO compounds were developed as palaeoenvironmental or palaeoecological proxies with a

relatively robust scientific underpinning. The future development of new proxies for

palaeoenvironmental or palaeoecological assessment requires the introduction of FT-ICR-MS

for comprehensive analysis of organisms of geochemical interest as a scientific footing,

including biochemical compositions, cellular/organismal biosynthetic responses,

species/community responses, and diagenetic reactions.

To properly deconvolute the effects of each geological factor of interest on sedimentary

NSO composition, appropriate sample series were selected to ensure that the differences

between their NSO inventories were primarily controlled by the geological factors of interest.

However, the impact of confounding factors (i.e., other than those a given proxy is intended to

measure) need to be considered. For instance, importance of organo-lithologic interactions for

understanding the composition of resins in source rocks and associated reservoir rocks in the

173

peak–late oil window was discussed in this study, other factors that influence the composition

of the polar fraction have not been thoroughly tested. Matrix porosity and pore size distributions,

specific surface areas (in addition to general mineralogical surface properties), organic

porosity/kerogen-product interactions, and compositional differences between kerogens (even

if all samples contain roughly similar oil-prone marine type II organic matter) are all factors

that have a role to play in expulsion and migration within shale petroleum systems. A future

comprehensive study looking at samples from these or other formations over a wide range of

thermal maturities including FT-ICR-MS results, kerogen compositional/spectroscopic data,

and surface area-pore type/size distribution information could potentially delineate the relative

influence of these factors.

Several interesting trends were observed but not thoroughly tested as they were not

the focus of interest in this dissertation. Future works on them are expected to have important

implications. For instance, similarities in the retention behavior of biogenic carbonate- and

biogenic quartz-rich petroleum systems were described in this work, e.g., the preferential

retention of large low-polarity NSO compounds (i.e., high DBE species). Thus, DBE

distributions of the low-polarity NSO compounds might have the potential to be established as

common indicators for migration regardless of lithofacies. Further case studies on more diverse

petroleum systems utilizing (+)-APPI FT-ICR-MS are needed to verify their applicability.

The observations and conclusions in this dissertation were only based on the NSO

inventories in sedimentary rocks that are extractable in azeotropic mixtures. Ion-mobility based

mass spectrometry imaging, e.g., matrix-assisted laser desorption ionization FT-ICR-MS, could

directly measure solid-phase samples without extraction steps and would make the insoluble

NSO compounds in rocks accessible. Its application should consequence more important

implications, especially given that it can visualize the detailed, sub-millimetre spatial

distribution of analytes, thus enabling the exploration of target compounds at an unprecedented

fine scale and level of detail. The high-resolution images of how NSO compounds are

distributed on sample surfaces could open up the way to calculate palaeoenvironmental or

palaeoecological biomarker proxies or trace the petroleum expulsion and migration at an

unprecedented spatial resolution.

174

175

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