Chi ali y-Pucke ing co ela ion and in e molecula in e ac ions in
Sphingosines: Ro a ional spec oscopy o jaspine B3 and i s
monohyd a e
Rizalina T. Sa agi
a
, Ma cos Juanes
a
, José L. Abad
b
, Ru h Pinacho
c
, José E. Rubio
c
, Albe o Lesa i
a,
⇑
a
Depa amen o de Química Física y Química Ino gánica, Facul ad de Ciencias - I.U. CINQUIMA, Uni e sidad de Valladolid, Paseo de Belén 7, Valladolid 47011, Spain
b
Resea ch Uni on BioAc i e Molecules (RUBAM), Depa amen de Química Biològica, Ins i u de Química A ançada de Ca alunya (IQAC-CSIC), Jo di Gi ona 18-26, Ba celona
08034, Spain
c
Depa amen o de Elec ónica, ETSIT, Uni e sidad de Valladolid, Paseo de Belén 11 Valladolid 47011, Spain
highligh s
In a-/in e molecula in e ac ions a
he head g oup o Jaspine B analyzed
o a ionally.
Obse a ion o six isome s o jaspine
B and he monohyd a e in he gas
phase.
In e molecula in e ac ions linked o
ing pucke ing and chi ali y, plausibly
connec ed o biological ac i i y.
g aphical abs ac
a icle in o
A icle his o y:
Recei ed 19 Augus 2021
Recei ed in e ised o m 9 Oc obe 2021
Accep ed 21 Oc obe 2021
A ailable online 16 No embe 2021
Keywo ds:
Nonco alen in e ac ions
Sphingosines
Mic osol a ion
Ring-pucke ing
Ro a ional Spec oscopy
Je spec oscopy
abs ac
Chi ali y is de e minan o sphingosine bio unc ions and pha macological ac i i y, ye he easons o
he biological chi al selec ion a e no well unde s ood. He e, we cha ac e ized he in a- and in e molec-
ula in e ac ions a he headg oup o he cy o oxic anhyd ophy osphingosine jaspine B, e ealing
chi ali y-dependen co ela ions be ween he pucke ing o he ing co e and he o ma ion o amino-
alcohol hyd ogen bond ne wo ks, bo h in he monome and he monohyd a e. Following he speci ic syn-
hesis o a sho ened 3-ca bon side-chain molecule, deno ed jaspine B3, six di e en isome s we e
obse ed in a je expansion using b oadband (chi ped-pulsed) o a ional spec oscopy. Addi ionally, a
single isome o he jaspine B3 monohyd a e was obse ed, e ealing he inse ion o wa e in be ween
he hyd oxy and amino g oups and he o ma ion o a ne wo k o O-HN-HO
ing
hyd ogen bonds. The
speci ic jaspine B3 s e eochemis y hus c ea es a double- aced molecule whe e he exposed lone-pai
elec ons may easily ca alyze he o ma ion o in e molecula agg ega es and de e mine he sphingosine
biological p ope ies.
Ó2021 The Au ho (s). Published by Else ie B.V. This is an open access a icle unde he CC BY-NC-ND
license (h p://c ea i ecommons.o g/licenses/by-nc-nd/4.0/).
1. In oduc ion
In e es in sphingolipids (SLs) is wo- old. F om a s uc u al
poin o iew SLs a e key componen s o euka yo ic cell mem-
b anes and lipid signaling messange s [1,2]. As an example, SLs
h ps://doi.o g/10.1016/j.saa.2021.120531
1386-1425/Ó2021 The Au ho (s). Published by Else ie B.V.
This is an open access a icle unde he CC BY-NC-ND license (h p://c ea i ecommons.o g/licenses/by-nc-nd/4.0/).
⇑
Co esponding au ho .
Spec ochimica Ac a Pa A: Molecula and Biomolecula Spec oscopy 267 (2022) 120531
Con en s lis s a ailable a ScienceDi ec
Spec ochimica Ac a Pa A: Molecula and
Biomolecula Spec oscopy
jou nal homepage: www.else ie .com/loca e/saa
pa icipa e wi h s e ols in he o ma ion o memb ane mic odo-
mains o lipid a s, which a e c i ically dependen on he sphin-
golipid chi ali y [3]. F om he pha macological side, some
sphingosines display s ong chi ali y-dependen an ip oli e a i e
p ope ies and can be used as an i umo o cy o oxic compounds,
exploi ing hei ole in cell p oli e a ion, mig a ion and apop osis
[4]. Phy osphingosines o m a sub-class o sphingoid bases (1,
Fig. 1), mos commonly consis ing o a 1,3,4- ihyd oxy-2-amino
head and an 18-ca bon alipha ic chain, like D- ibo-
phy osphingosine (2). Some unusual phy osphingosines de i a-
i es om ma ine o ganisms, like jaspine A (3) and jaspine B (4),
ha e impo an pha macological p ope ies. Jaspine B (pachas is-
samine), isola ed om he sponges Pachas issa sp.[5] and Jaspis sp.
[6] in 2002, is biosyn hesized om D- ibo-phy osphingosine 2by
in amolecula nucleophilic displacemen and possesses a unique
all-syn (2S,3S,4S)- isubs i u ed e ahyd o u an ing co e. Jaspine
B inhibi s he ce amide and sphingomyelin syn hases and shows
ema kable an i umo p ope ies on se e al human cance cell
lines [7–9].
Since sphingoid bases acqui e biological unc ions wi h speci ic
s e eochemical con igu a ions, in e es has g own in he syn hesis
and biological assessmen o jaspine s e eoisome s [10,11] and
de i a i es [12]. He e we add ess he co ela ion be ween s e eo-
chemis y, ing-pucke ing and he in a- and in e -molecula in e -
ac ions o jaspine B and i s monohyd a es om a molecula poin
o iew, p obing he isola ed molecule in he cooled and collision-
less en i onmen o a supe sonic je expansion. Gas-phase s udies
bene i om disagg ega ion [13], ende ing in insic single-
molecule p ope ies di ec ly compa able o he in acuo molecula
o bi al compu a ions. This in o ma ion may help he a ional
design o new d ugs based on he jaspine skele on. Howe e , he
14-ca bon alipha ic chain o jaspine B would c ea e a my iad o
compe ing con o ma ions, impeding a high- esolu ion spec o-
scopic s udy. Fo his eason, we i s p epa ed a specially un-
ca ed jaspine B wi h a sho ened side chain, whe e we can
cap u e he con o ma ional and s uc u al p ope ies o he bioac-
i e pola headg oup and i s ela ion o he side chain using high-
esolu ion o a ional spec oscopy. Following chemical and spec-
oscopic conside a ions, we syn hesized he 3-ca bon alipha ic
chain jaspine analogue o (2S,3S,4S)-4-amino-2-p opyl e ahyd o
u an-3-ol, deno ed jaspine B3 (5).
Jaspine B3 is expec ed o display a ich h ee-le el-deep iso-
me ism a ising om he lexible e ahyd o u an ing, he p esence
o wo pola amino and alcohol g oups in adjacen ing a oms and
he alipha ic side chain. The e ahyd o u an i e-membe ed ing is
a common sca old in biological compounds like nucleic acids, dis-
playing unique o sional cha ac e is ics. The acile in e con e sion
be ween wis ed and en elope o ms may be desc ibed as a
monodimensional la ge-ampli ude mo ion o pseudo o a ion
[14], in which ben / wis pucke ing o a es a ound he ing a oid-
ing plana con igu a ions. Pucke ing can be e y sensi i e o ing
subs i uen s o hyd a ion and may de e mine mac omolecula
a angemen s [15–17], as in he di e en pucke ing o DNA/RNA
A o B chains. P ecise de e mina ion o he pucke ing cha ac e is-
ics is hus necessa y o speci y he pseudo o a ion pa hways, o
compa e wi h ela ed biomolecules o clus e s and o assess he
in luence o he pola and alipha ic g oups in he p e e ed s uc-
u es o jaspine B. In addi ion, he amino and alcohol adjacen
g oups o e se e al op ions o in a and in e -molecula hyd ogen
bonding, such as O-HN o N-HO[15,18]. The alipha ic side
chain, e en unca ed he e o 3 ca bons, adds se e al h ee- old
o o s which may engage wi h he ing o he pola g oups c ea ing
mul iple isome s.
The mic osol a ion o jaspine B uses one wa e molecule o
p obe he s eng h o he in amolecula o ces in he monome
and he possibili y o wa e o modula e molecula con o ma ions
o hyd ogen bonding in he isola ed molecule [13,15,19]. Speci i-
cally, wa e may ei he add o dis up he monome in amolecula
hyd ogen bonding o pucke ing, o e ing clues on he s eng h and
na u e o he in e molecula in e ac ions [20]. All hese ac o s
make jaspine B3 a es bed o examine he ela ion be ween
in a- and in e -molecula in e ac ions and con o ma ion in sphin-
gosine headg oups and o ela e o biomolecula in e ac ions. The
p esen wo k ex ends p e ious gas-phase s uc u al s udies on
mimics o sphingoid headg oups, es ic ed o small 3- o 4-
ca bon open-chain amino-alcohols like se inol [21] o he h eoni-
nol [22] and allo- h eoninol [23] dias e eoisome s. These s udies
ha e de ec ed mul iple low-ene gy isome s whe e in a-
molecula hyd ogen bonds may p oduce linea o cyclic ne wo ks
o hyd ogen bonds, e ealing ini ial connec ions be ween chi ali y
and in amolecula in e ac ions. The in es iga ion o jaspine B3
ep esen s a quali a i e leap in he p og ess owa d molecula
s udies o la ge SLs.
The spec oscopic wo k used ad anced chi ped-pulse b oad-
band mic owa e spec oscopy [24], o e ing much highe esolu-
Fig. 1. Uppe panel: Schema ics o he inse ion o sphingosine in o sphingomyelin
and in o a (simpli ied) lipidic bilaye . Lowe panel: Molecula o mulas o
sphingosine (1), D- ibo-phy osphingosine (2), jaspine A (3), jaspine B (4) and
jaspine B3 (5).
R.T. Sa agi, M. Juanes, José L. Abad e al. Spec ochimica Ac a Pa A: Molecula and Biomolecula Spec oscopy 267 (2022) 120531
2
ion (10
-7
cm
1
) han ib a ional echniques and unambiguously
disc imina ing o ame s and e en iso opologues h ough hei
momen s o ine ia. Compu a ional ools p o ided a ionaliza ion
o he expe imen .
2. Expe imen al me hods
2.1. Chemical syn hesis and spec oscopy
The molecule o jaspine B3 was ini ially p epa ed by hyd o-
gena ion and dep o ec ion o he p ope isop opylydene-Boc p o-
ec ed alkene in e media e used o he o al syn hesis o Jaspine
B[25], as de ailed in he Suppo ing In o ma ion. Jaspine B3 was
in es iga ed in a supe sonic je expansion wi h a chi ped-pulse
b oadband Fou ie - ans o m mic owa e spec ome e [24] wo k-
ing in he egion 2–8 GHz, desc ibed in he Suppo ing In o ma ion.
B ie ly, he sample was apo ized (95–110 °C) in si u a he spec-
ome e injec o , dilu ed in a s eam o neon and co-expanded
nea -adiaba ically o o m a pulsed supe sonic je in he e acua ed
expansion chambe . The es ima ed o a ional empe a u e is 2 K.
The je was hen p obed wi h chi ped mic owa e pulses (4
l
s),
exci ing he ull bandwid h by a as -passage elec ic-dipole mech-
anism [26]. The subsequen ee-induc ion decay is egis e ed in
ime scales o 40
l
s and Fou ie ans o med o he equency
domain.
2.2. Compu a ional me hods
The compu a ional me hods included a con o ma ional sea ch
and molecula o bi al calcula ions, which a e desc ibed in he Sup-
po ing In o ma ion. B ie ly, he compu a ional sea ch s a ed wi h
molecula mechanics and he MMFFs o ce ield [27], which p o-
ided an ini ial se o molecula geome ies. These con o me s
we e ully e-op imized using D3 dispe sion-co ec ed hyb id den-
si y unc ional heo y (DFT) me hods [28] and a iple- basis se
(B3LYP-D3(BJ)/de 2-TZVP), limi ing he inal sea ch o isome s
wi hin ee ene gies below 5 kJ mol
1
. The mos s able con o me s
o he monome and he monohyd a es we e addi ionally ecalcu-
la ed using a double-hyb id [29] B2PLYP-D3(BJ) unc ional and
Fig. 2. Con o ma ional landscape o jaspine B3 and p edic ed ee ene gies a 1 a m and 298 K (B3LYP-D3(BJ)/de 2-TZVP, kJ mol
1
; see Suppo ing In o ma ion o B2PLYP and
MP2 alues). The species obse ed expe imen ally a e enci cled (Ring pucke ing no a ion: T = wis , E = en elope, see Fig. 3; Side chain o ien a ions gi en by he wo dihed als
s
1
and
s
2
:A=an i, G+/G-=gauche +/-). The oxygen and ni ogen a oms a e in ed and blue colo s, espec i ely (Fo in e p e a ion o he e e ences o colou in he igu e
legends, he eade is e e ed o he web e sion o his a icle.)
Fig. 3. Ring-pucke ing diag am compa ing he ing con o ma ion o he six isome s
o jaspine B3 ( ed ci cles: 1, 2, ...6) and i s obse ed monohyd a e (blue squa e
W2). The c osses ep esen p edic ed unobse ed monome con o ma ions. The
diag am shows he pucke ing ampli ude (q) and phase (/, see Suppo ing
In o ma ion) and e eals a clus e ing o con o ma ions a ound he
3
T
4
wis and
E
5
en elope s uc u es ( ed and yellow egions, espec i ely), wi h speci ically
associa ed in amolecula in e ac ions. (Fo in e p e a ion o he e e ences o
colou in his igu e legend, he eade is e e ed o he web e sion o his a icle.)
R.T. Sa agi, M. Juanes, José L. Abad e al. Spec ochimica Ac a Pa A: Molecula and Biomolecula Spec oscopy 267 (2022) 120531
3
second-o de ab ini io pe u ba ion heo y [30] (MP2) and he
same basis se . Vib a ional equency calcula ions p o ided a ha -
monic o ce ield, cen i ugal dis o ion and ze o-poin ene gy co -
ec ions. Fo he dime , complexa ion ene gies we e co ec ed o
basis-se supe posi ion e o s wi h he coun e poise me hod [31].
3. Resul s and discussion
3.1. Po en ial ene gy su ace
The in es iga ion o jaspine B3 s a ed wi h a desc ip ion o he
po en ial ene gy su ace (PES). The compu a ional esul s a e sum-
ma ized in Tables S1-S3 (monome ) and S4-S5 (monohyd a e, Sup-
po ing In o ma ion). The calcula ions sugges ed a ich
con o ma ional landscape, gene a ing up o 52 con o me s o
he monome and 212 isome s o he monohyd a e wi hin
25 kJ mol
1
.
The con o ma ional landscape o jaspine B3 can be ca ego ized
using he ing con o ma ion and he side chain o ien a ion (dihe-
d als
s
1
= O1C2–C
a
-Cb,
s
2
= C2C
a
–CbC
c
in Scheme S1). The con o -
ma ional maps in Fig. 2 and S1-S2 (Suppo ing In o ma ion) and
he pucke ing diag am o Fig. 3 speci y ing pucke ing using he
C eme -Pople (CP) cu ilinea coo dina es [32], allowing p ecise
compa isons wi h ela ed i e-membe ed dominan ing geome-
ies, ei he wis ed
3
T
4
(con o me s 1, 3, 5, 7,10, 13) o en elope
E
5
(con o me s 2, 4, 6, 9, 11, 15), bo h wi h he alcohol poin ing
o he amino g oup. Th ee highe -ene gy isome s show a di e en
3
T
2
(8, 12) o
3
T
4
(14) wis con o ma ion, wi h he amino g oup
Fig. 4. PES scans o he sidechain o he
3
T
4
and E
5
ing con o ma ions, showing he loca ion o he mos s able con o me s. The sidechain beha io is simila o bo h
3
T
4
and
E
5
pucke ing con o ma ions, wi h p e e ence o G- and A o ien a ions (nume ical alues in Suppo ing In o ma ion). In his blue- o- ed colo scheme he smalle ene gies a e
da k blue. The isome loca ions a e ma ked 1-11.
Fig. 5. A 4 GHz sec ion o he je -cooled mic owa e spec um o Jaspine B3. Uppe ace: Expe imen al spec um; Lowe ace: Fi o he di e en con o me s 1–6 using he
o a ional pa ame e s o Table 1 and a o a ional empe a u e o 2 K.
R.T. Sa agi, M. Juanes, José L. Abad e al. Spec ochimica Ac a Pa A: Molecula and Biomolecula Spec oscopy 267 (2022) 120531
4
owa ds he alcohol. Fo each geome y se e al side-chain o ien a-
ions a e possible. Addi ional bidimensional PES scans o he
3
T
4
and E
5
ing con o ma ions in Fig. 4 used B3LYP-D3(BJ) and show
p e e ence o a oms Cband C
c
o be o ien ed ei he an ipe iplana
(A,
s
1
180°)o gauche– (G–,
s
1
300°) espec o he ing he -
e oa om, wi h ela i ely small ene gy di e ences be ween he
lowes -lying con o me s and close simila i y be ween he
3
T
4
and
E
5
ing con o ma ions.
3.2. Jaspine B3 monome
The compu a ional p edic ions we e assessed in ou spec-
oscopy expe imen . The dense o a ional spec um in Fig. 5
immedia ely sugges ed he p esence o mul iple compe ing iso-
me s. The spec um was hen sea ched i e a i ely using simula-
ions wi h he ial o a ional cons an s in Tables S1 (B3LYP), S2
(B2PLYP) and S3 (MP2) in he Suppo ing In o ma ion. Mos ansi-
ions exhibi ed small (<1 MHz) nuclea quad upole coupling
e ec s (Figu es S3-S4, Suppo ing In o ma ion), so he spec um
was analyzed wi h a Wa son’s semi igid- o o Hamil onian wi h
quad upole e ms app op ia e o he
14
N nucleus (nuclea spin
I=1)[33]. Bo h he global spec al pa e ns and he indi idual
hype ine e ec s we e ex emely sensi i e o molecula geome y,
leading o an unambiguous s uc u al iden i ica ion. The p ocess
was epea ed i e a i ely and inally a o al o six di e en con o m-
e s we e posi i ely iden i ied, wi h he expe imen al pa ame e s
and measu ed ansi ions p esen ed in Table 1 and S6-S12 (Sup-
po ing In o ma ion). The compa ison o expe imen and heo y
con i med he de ec ion o all six jaspine B3 isome s wi h con o -
ma ional ene gies below 3 kJ mol
1
(ou lined in Fig. 2). Di e ences
be ween he expe imen al and heo e ical o a ional cons an s
we e below 0.8% o B3LYP and B2PLYP, while MP2 o e ed wo se
esul s (<2.8%). Rela i e in ensi ies on a common se o
l
a
ansi-
ions ga e es ima ions o he je popula ions o 2:1:3:4:6:5 = 1.0
> 0.69(6) > 0.34(3) 0.34(3) > 0.09(1) > 0.06(1), indica ing ha iso-
me 2 is he mos popula ed. Howe e , popula ion a ios canno be
ansla ed in o ene gy di e ences as con o ma ional elaxa ion is
o en obse ed in he je in case o low (<5–10 kJ mol
1
) in e con-
e sion ba ie s [34,35]. We explo ed plausible con e sions
be ween non-obse ed and de ec ed species in Figu es S5-S8 (Sup-
po ing In o ma ion), ob aining ba ie s in he ange 6.9–17.3 kJ m
ol
1
e en o changes limi ed o he side chain o ien a ion. The
smalle ba ie s exchanging con o me s 10 and 3 o 9 and 2 (6.9
and 7.1 kJ mol
1
, espec i ely) may be su moun able in he je ,
explaining he absence o addi ional speci ic isome s.
The expe imen ally obse ed isome s o jaspine B3 comp ise
h ee
3
T
4
wis (1, 3, 5) and h ee E
5
en elope (2, 4, 6) con o ma-
ions. Topological analyses o he educed elec onic densi y wi h
NCI plo s [36] in Figu es S9-S10 (Suppo ing In o ma ion) and
he s uc u al da a in Tables S13-S18 (Suppo ing In o ma ion)
con i med he p esence o in amolecula hyd ogen bonds in all
Table 1
Expe imen al o a ional pa ame e s o he six obse ed isome s o jaspine B3 and he dime (jaspine B3)-wa e . See Suppo ing In o ma ion o heo e ical alues.
Sys em Jaspine B3 Jaspine B3-
wa e
Isome 1 2 3 4 5 6 W2
Pucke ing
3
T
4
E
53
T
4
E
53
T
4
E
53
T
4
Side chain AA G
-
AG
-
AAAG
-
G
-
G
-
G
-
AA
A/ MHz
a
2795.4709(11)
c
2243.8144(10) 3174.6108(18) 2462.18(14) 2901.8114(71) 2298.2034(14) 1382.331(28)
B/ MHz 741.10679(29) 801.63564(35) 686.67666(33) 804.3406(12) 750.5540(14) 857.91008(53) 667.2511(10)
C/ MHz 645.70568(22) 704.55488(32) 616.73418(28) 696.1520(11) 677.8354(14) 743.21068(50) 485.6647(10)
3/2
aa
1.569(16) 2.2950(97) 3.090(17) 0.392(52) 4.04(13) 2.897(35) 3.355(47)
1/4 (
bb
-
cc
) 0.3322(51) 1.7099(27) 0.2650(49) 1.314(13) 0.585(32) 1.6560(90) 0.893(40)
D
J
/ kHz [ 0.0]
d
0.1626(66) [ 0.0] [ 0.0] [0.0] 0.3314(62) [0.]
D
JK
/ kHz [ 0.0] 0.754(11) [ 0.0] [ 0.0] [0.0] [ 0.0] [0.]
D
K
/ kHz [ 0.0] 3.24(13) [ 0.0] [ 0.0] [0.0] [ 0.0] [0.]
|
l
a
| / D +++
e
+++ +++ +++ ++ + +++
|
l
b
|/D + ++ + – – ++ –
|
l
c
|/D ++ + ++ – – – –
N
b
161 168 103 62 36 56 45
/ kHz 15.2 10.2 13.4 12.5 13.5 15.7 12.4
a
Ro a ional cons an s (A,B,C), nuclea quad upole coupling pa ame e s (
a
,
b
,
c
), Wa son’s S- educ ion cen i ugal dis o ion cons an s (D
J
,D
JK
,D
K
; he cons an s d
1
and
d
2
we e ixed o ze o) and elec ic dipole momen s (
l
a
,
a
=a,b,c).
b
Numbe o i ed ansi ions (N) and ms de ia ion (
) o he i .
c
S anda d e o s in pa en heses uni s o
he las digi .
d
Values in squa e b acke s we e ixed o ze o.
e
One o mo e posi i e signs indica es he obse a ion and in ensi y o he co esponding ansi ions.
Fig. 6. Con o ma ional landscape o he mos s able (jaspine B3)-wa e monohy-
d a es W1 o W5 (T = wis , E = en elope), wi h p edic ed ee ene gies a 1 a m and
298 K (B3LYP-D3, kJ mol
1
; see Suppo ing In o ma ion o B2PLYP and MP2
alues). The obse ed species is enci cled.
R.T. Sa agi, M. Juanes, José L. Abad e al. Spec ochimica Ac a Pa A: Molecula and Biomolecula Spec oscopy 267 (2022) 120531
5

isome s. The wis ed
3
T
4
isome s display a single O-HN hyd ogen
bond, as his ing con o ma ion inc eases he dis ance be ween he
amino g oup and he ing oxygen (B3LYP: (O-HN) = 2.07 Å). Con-
e sely, he E
5
con o me s may es ablish a ne wo k o wo consec-
u i e O-HN-HO
ing
hyd ogen bonds, since he ing pe mi s a
close app oach o one o he amino N-H bonds owa ds he ing
he e oa om. These isome s combine a ela i ely sho O-HN
hyd ogen bond ( (O-HN) = 1.94–1.99 Å) wi h a long N-HO
ing
con ac ( (N-H O
ing
) = 2.59–2.61 Å). All in amolecula in e ac-
ions a e cons ained by he ing geome y bu all wi hin he s a-
is ical bounds o hese hyd ogen bonds [15,18].
3.3. Jaspine B3 monohyd a e
The addi ion o wa e o he ca ie gas line pe mi ed he
obse a ion o new ansi ions om he monohyd a ed dime
(Table S19, Suppo ing In o ma ion). Figu e S11 (Suppo ing In o -
ma ion) shows he nuclea quad upole coupling hype ine e ec s
o some ypical o a ional ansi ions, which we e well ep oduced
wi h a semi igid- o o model. The expe imen al esul s in Table 1
and Table S20 (Suppo ing In o ma ion) can be compa ed wi h cal-
cula ions o he con o ma ional landscape in Tables S4 (B3LYP) and
S5 (B2PLYP and MP2, Suppo ing In o ma ion), which p edic ed
Fig. 7. Uppe panel: NCI plo mapping he in e - and in amolecula in e ac ions in he obse ed monohyd a e o jaspine B3. The blue and g een shades indica e s ongly and
weakly a ac i e in e ac ions, espec i ely (see Suppo ing In o ma ion), cha ac e izing he hyd ogen bonds. Lowe panel: Plo o he educed elec onic densi y g adien s
¼
1
23
p
2
ðÞ
1=3
q
jj
q
4=3

s. he signed elec onic densi y compa ing con o me 1 (=
3
T
4
AA, ed ace) and he wa e dime W2 (=
3
T
4
AA, blue ace). A ac i e c i ical poin s a e
shown as nega i e minima o he cu e (see Suppo ing In o ma ion). The compa ison shows he o ma ion o new in e ac ions in he dime . (Fo in e p e a ion o he
e e ences o colou in his igu e legend, he eade is e e ed o he web e sion o his a icle.)
R.T. Sa agi, M. Juanes, José L. Abad e al. Spec ochimica Ac a Pa A: Molecula and Biomolecula Spec oscopy 267 (2022) 120531
6
hi een di e en isome s below 5 kJ mol
1
. The expe imen al da a
unequi ocally co espond o isome W2 o Fig. 6-7 and Figu e S12
(Suppo ing In o ma ion), associa ed o a
3
T
4
ing pucke ing con-
o ma ion. A ew ansi ions we e en a i ely assigned o isome
W1, bu he small da ase did no pe mi a de ini i e con i ma ion.
Consis en ly, he W2 monohyd a e shows he la ges complexa ion
ene gy (B2PLYP: 49.5 kJ mol
1
). The obse ed W2 monohyd a e
can be a ionalized as esul o he inse ion o a wa e molecule
in be ween he alcohol and amino g oups o he monome
3
T
4
glo-
bal minimum, also p edic ed o isome W3 (E
4
). Con e sely, iso-
me s W1, W4 and W5 would co espond o a common pa e n o
addi ion o he ing oxygen o h ee di e en pucke ings. The
pucke ing plo o Fig. 3 e idences small ing dis o ions o isome
W2 espec o he monome , so he wa e ole is o ein o ce he
cha ac e is ic ne wo k o hyd ogen bonds in which wa e always
pa icipa es simul aneously as p o on dono and accep o . NCI
plo s in Fig. 7 and s uc u al da a in Table S21 (Suppo ing In o -
ma ion) con i med he complemen a i y and o ma ion o new
in a- and in e molecula in e ac ions in he dime . The
3
T
4
dime
exhibi s wo cha ac e is ic O-HO
w
-HN-H hyd ogen bonds,
while o he hyd a es may show up o h ee consecu i e O-HN-
HO
w
-HO hyd ogen bonds. The addi ion o wa e o he ing
oxygen gi es he sho es hyd ogen bond (B3LYP: (O
w
-HO
)=
1.83–1.85 Å). Wa e also beha es as p o on dono o he amino
g oup when inse ing in be ween he pola g oups in he ing
( (O
w
-HN) = 1.90 Å), con i ming he amino g oup as be e hyd o-
gen bond accep o and poo e dono , as obse ed in se inol [21]
and h eoninol [22,23].
4. Conclusion
The obse a ion o six isome s and he mos s able monohyd a e
o jaspine B3 p o ides an accu a e desc ip ion o he con o ma-
ional landscape and mic osol a ion p ope ies. As obse ed in
o he biomolecules wi h a e ahyd o u an co e, in pa icula
nucleo ides, ing pucke ing u ns undamen al, as ela i ely small
pucke ing di e ences a e ampli ied by he ing subs i uen s, condi-
ioning in e molecula in e ac ions and la ge-scale molecula
beha iou [15]. Pucke ing p e e ences a e ela i ely unchanged
o he monome and hyd a es and speci ically dependen on he
ing subs i uen s, as obse ed in u anosides [37]. This esul con-
i ms p e ious obse a ions ha molecula s abili y a ises om
an in e play o in insic hype conjuga i e elec onic e ec s and
in amolecula in e ac ions [16,17]. Simila i ies in he side chain
o di e en pucke ing con o ma ions sugges a seconda y ole o
he alipha ic g oup, as in amino acids [38]. As a esul , he speci ic
jaspine s e eochemis y, which loca es he pola g oups on he
same side o he ing, is de e minan o i s in a- and in e molecula
in e ac ions, c ea ing a double- aced molecule whe e he exposed
lone-pai elec ons on he subs i uen s ace may easily ca alyze
he o ma ion o in e molecula agg ega es. The mic osol a ion o
jaspine B3 shows mul iple hyd a ion pa e ns by p o on dona ion
o he oxygen ing o he amino g oup, c ea ing chi ali y-
dependen hyd ogen bond ne wo ks amilia in suga hyd a ion
[39,40], which may be ins umen al o he jaspine biological ole.
Finally, he impo ance o gas-phase molecula s udies o comple-
men c ys al di ac ion o liquid NMR in o ma ion o biochemical
building blocks should be ou lined, ma king u u e ou es o in e-
g a ed s udies co e ing om he ba e molecule o he in eg a ion
o biomolecula uni s in he hyd a ed biological en i onmen .
CRediT au ho ship con ibu ion s a emen
Rizalina T. Sa agi: Valida ion, Fo mal analysis, In es iga ion,
Da a cu a ion, W i ing – o iginal d a , W i ing – e iew & edi ing,
Visualiza ion. Ma cos Juanes: Valida ion, In es iga ion, W i ing –
e iew & edi ing. José L. Abad: Concep ualiza ion, Me hodology,
Resou ces, In es iga ion, W i ing – e iew & edi ing. Ru h Pina-
cho: So wa e, Resou ces, W i ing – e iew & edi ing. José E.
Rubio: So wa e, Resou ces, W i ing – e iew & edi ing. Albe o
Lesa i: Concep ualiza ion, Me hodology, Resou ces, Da a cu a ion,
W i ing – o iginal d a , W i ing – e iew & edi ing, Supe ision,
P ojec adminis a ion, Funding acquisi ion.
Decla a ion o Compe ing In e es
The au ho s decla e ha hey ha e no known compe ing inan-
cial in e es s o pe sonal ela ionships ha could ha e appea ed
o in luence he wo k epo ed in his pape .
Acknowledgemen s
Funding suppo om he Spanish MICINN-FEDER (g an
PGC2018-098561-B-C22) is g a e ully acknowledged. M.J. and R.
T.S. a e hank ul o p edoc o al con ac s om he MICINN and
UVa, espec i ely.
Appendix A. Supplemen a y ma e ial
Supplemen a y da a o his a icle can be ound online a
h ps://doi.o g/10.1016/j.saa.2021.120531.
Re e ences
[1] B. Cinque, L. Di Ma zio, C. Cen i, C. Di Rocco, C. Ricca di, M.G. Ci one,
Sphingolipids and he immune sys em, Pha macol. Res. 47 (2003) 421–437,
h ps://doi.o g/10.1016/S1043-6618(03)00051-3.
[2] T. A iga, W.D. Ja is, R.K. Yu, Role o sphingolipid-media ed cell dea h in
neu odegene a i e diseases, J. Lipid Res. 39 (1) (1998) 1–16, h ps://doi.o g/
10.1016/S0022-2275(20)34198-5.
[3] K. Simons, E. Ikonen, Func ional a s in cell memb anes, Na u e. 387 (6633)
(1997) 569–572.
[4] J. Pad ón, Sphingolipids in An icance The apy, Cu . Med. Chem. 13 (2006)
755–770, h ps://doi.o g/10.2174/092986706776055553.
[5] I. Ku oda, M. Musman, I.I. Oh ani, T. Ichiba, J. Tanaka, D.G. G a alos, T. Higa,
Pachas issamine, a cy o oxic anhyd ophy osphingosine om a ma ine
sponge, Pachas issa sp, J. Na . P od. 65 (10) (2002) 1505–1506, h ps://doi.
o g/10.1021/np010659y.
[6] V. Led oi , C. Debi us, C. La aud, G. Massio , Jaspines A and B: wo new
cy o oxic sphingosine de i a i es om he ma ine sponge Jaspis sp,
Te ahed on Le . 44 (2) (2003) 225–228, h ps://doi.o g/10.1016/S0040-
4039(02)02541-8.
[7] F. Cingolani, F. Simba i, J.L. Abad, M. Casasampe e, G. Fab ias, A.H. Fu e man, J.
Casas, Jaspine B induces nonapop o ic cell dea h in gas ic cance cells
independen ly o i s inhibi ion o ce amide syn hase, J. Lipid Res. 58 (8) (2017)
1500–1513, h ps://doi.o g/10.1194/jl .M072611.
[8] Y. Yoshimi su, S. Oishi, J. Miyagaki, S. Inuki, H. Ohno, N. Fujii, Pachas issamine
(jaspine B) and i s s e eoisome s inhibi sphingosine kinases and a ypical
p o ein kinase C, Bioo g. Med. Chem. 19 (18) (2011) 5402–5408, h ps://doi.
o g/10.1016/j.bmc.2011.07.061.
[9] Y. Salma, E. La on , N. The ille, S. Ca pen ie , M.-J. Bonna é, T. Le ade, Y.
Génisson, N. And ieu-Abadie, The na u al ma ine anhyd ophy osphingosine,
Jaspine B, induces apop osis in melanoma cells by in e e ing wi h ce amide
me abolism, Biochem. Pha macol. 78 (5) (2009) 477–485, h ps://doi.o g/
10.1016/j.bcp.2009.05.002.
[10] D. Canals, D. Mo meneo, G. Fab iàs, A. Lleba ia, J. Casas, A. Delgado, Syn hesis
and biological p ope ies o Pachas issamine (jaspine B) and
dias e eoisome ic jaspines, Bioo ganic, Med. Chem. 17 (1) (2009) 235–241,
h ps://doi.o g/10.1016/j.bmc.2008.11.026.
[11] M. Ma inko á, J. Gonda, Syn he ic analogues o ma ine cy o oxic jaspine B
and i s s e eoisome s, Ca bohyd . Res. 482 (2019) 107737, h ps://doi.o g/
10.1016/j.ca es.2019.06.016.
[12] H. Yang, Y. Li, H. Chai, T. Yaku a, B.o. Liu, Q. Yao, Syn hesis and biological
e alua ion o 2-epi-jaspine B analogs as selec i e sphingosine kinase 1
inhibi o s, Bioo g. Chem. 98 (2020) 103369, h ps://doi.o g/10.1016/j.
bioo g.2019.103369.
[13] J.-P. Sche mann, Spec oscopy and Modeling o Biomolecula Building Blocks,
Else ie (2008), h ps://doi.o g/10.1016/B978-0-444-52708-0.X5001-1.
[14] A.H. Mamlee , L.N. Gunde o a, R.V. Galee , Mic owa e spec um and hinde ed
pseudo o a ion o e ahyd o u an, J. S uc . Chem. 42 (2001) 365–370,
h ps://doi.o g/10.1023/A:1012448618502.
R.T. Sa agi, M. Juanes, José L. Abad e al. Spec ochimica Ac a Pa A: Molecula and Biomolecula Spec oscopy 267 (2022) 120531
7
[15] G.A. Je ey, W. Saenge , Hyd ogen Bonding in Biological S uc u es, Sp inge ,
Be lin Heidelbe g, Be lin, Heidelbe g (1991), h ps://doi.o g/10.1007/978-3-
642-85135-3.
[16] P. Écija, I. U ia e, L. Spada, B.G. Da is, W. Camina i, F.J. Bas e e xea, A. Lesa i,
E.J. Cocine o, Fu anosic o ms o suga s: Con o ma ional equilib ium o me hyl
b-d- ibo u anoside, Chem. Commun. 52 (2016) 6241–6244, h ps://doi.o g/
10.1039/c6cc01180b.
[17] C. Calab ese, I. U ia e, A. Insaus i, M. Vallejo-López, F.J. Bas e e xea, S.A.
Coch ane, B.G. Da is, F. Co zana, E.J. Cocine o, Obse a ion o he Unbiased
Con o me s o Pu a i e DNA-Sca old Ribosuga s, ACS Cen . Sci. 6 (2) (2020)
293–303, h ps://doi.o g/10.1021/acscen sci.9b01277.
[18] G.A. Je ey, An In oduc ion o Hyd ogen Bonding, Ox o d Uni e si y P ess,
Ox o d, 1997.
[19] M. Juanes, R.T. Sa agi, W. Camina i, A. Lesa i, The Hyd ogen Bond and Beyond:
Pe spec i es o Ro a ional In es iga ions o Non-Co alen In e ac ions, Chem.
- A Eu . J. 25 (49) (2019) 11402–11411, h ps://doi.o g/10.1002/chem.
25.4910.1002/chem.201901113.
[20] M. Juanes, R.T. Sa agi, R. Pinacho, J.E. Rubio, A. Lesa i, Sul u hyd ogen bonding
and in e nal dynamics in he monohyd a es o henyl me cap an and henyl
alcohol, Phys. Chem. Chem. Phys. 22 (22) (2020) 12412–12421, h ps://doi.
o g/10.1039/D0CP01706J.
[21] D. Lo u, I. Peña, J.L. Alonso, M. Eugenia Sanz, In amolecula in e ac ions in he
pola headg oup o sphingosine: Se inol, Chem. Commun. 52 (18) (2016)
3615–3618, h ps://doi.o g/10.1039/C5CC09423B.
[22] V. Vaque o-Va a, D. Zhang, B.C. Dian, D.W. P a , T.S. Zwie , Delica e balance o
hyd ogen bonding o ces in D- h eoninol, J. Phys. Chem. A. 118 (2014) 7267–
7273, h ps://doi.o g/10.1021/jp410859n.
[23] D.i. Zhang, S. Bockli z, T.S. Zwie , B oadband Mic owa e Spec oscopy o
P o o ypical Amino Alcohols and Polyamines: Compe i ion be ween H-Bonded
Cycles and Chains, J. Phys. Chem. A. 120 (1) (2016) 55–67, h ps://doi.o g/
10.1021/acs.jpca.5b1065010.1021/acs.jpca.5b10650.s001.
[24] S.T. Shipman, B.H. Pa e, New Techniques in Mic owa e Spec oscopy, in: F.
Me k , M. Quack (Eds.), Handb. High-Resolu ion Spec osc., John Wiley & Sons,
L d, New Yo k, 2011: pp. 801–828. h ps://doi.o g/10.1002/9780470749593.
h s036.
[25] A.K. Jana, G. Panda, S e eoselec i e syn hesis o Jaspine B and i s C2 epime
om Ga ne aldehyde, RSC Ad . 3 (2013) 16795–16801, h ps://doi.o g/
10.1039/c3 a41778 .
[26] J.C. McGu k, T.G. Schmalz, W.H. Flyga e, Fas passage in o a ional
spec oscopy: Theo y and expe imen , J. Chem. Phys. 60 (11) (1974) 4181–
4188, h ps://doi.o g/10.1063/1.1680886.
[27] T.A. Halg en, MMFF VI. MMFF94s op ion o ene gy minimiza ion s udies, J.
Compu . Chem. 20 (1999) 720–729. h ps://doi.o g/10.1002/(SICI)1096-987X
(199905)20:7<720::AID-JCC7>3.0.CO;2-X.
[28] H. Sch öde , A. C eon, T. Schwabe, Re o mula ion o he D3(Becke-Johnson)
Dispe sion Co ec ion wi hou Reso ing o Highe han C6 Dispe sion
Coe icien s, J. Chem. Theo y Compu . 11 (7) (2015) 3163–3170, h ps://doi.
o g/10.1021/acs.jc c.5b00400.
[29] S. G imme, F. Neese, Double-hyb id densi y unc ional heo y o exci ed
elec onic s a es o molecules, J. Chem. Phys. 127 (2007) 1–18, h ps://doi.o g/
10.1063/1.2772854.
[30] Ch . Mølle , M.S. Plesse , No e on an App oxima ion T ea men o Many-
Elec on Sys ems, Phys. Re . 46 (7) (1934) 618–622, h ps://doi.o g/10.1103/
PhysRe .46.618.
[31] S.F. Boys, F. Be na di, The calcula ion o small molecula in e ac ions by he
di e ences o sepa a e o al ene gies. Some p ocedu es wi h educed e o s,
Mol. Phys. 19 (4) (1970) 553–566, h ps://doi.o g/10.1080/
00268977000101561.
[32] D. C eme , J.A. Pople, Gene al de ini ion o ing pucke ing coo dina es, J. Am.
Chem. Soc. 97 (6) (1975) 1354–1358, h ps://doi.o g/10.1021/ja00839a011.
[33] W. Go dy, R.L. Cook, Mic owa e Molecula Spec a, John Wiley & Sons Inc, New
Yo k, NY, 1984.
[34] P.D. God ey, R.D. B own, P opo ions o species obse ed in je spec oscopy-
ib a ional-ene gy e ec s: His amine au ome s and con o me s, J. Am. Chem.
Soc. 120 (1998) 10724–10732, h ps://doi.o g/10.1021/ja980560m.
[35] F. Xie, N.A. Sei e , M. Hege , J. Thomas, W. Jäge , Y. Xu, The ich
con o ma ional landscape o pe illyl alcohol e ealed by b oadband
o a ional spec oscopy and heo e ical modelling, Phys. Chem. Chem. Phys.
21 (28) (2019) 15408–15416, h ps://doi.o g/10.1039/C9CP03028J.
[36] E.R. Johnson, S. Keinan, P. Mo i-Sánchez, J. Con e as-Ga cía, A.J. Cohen, W.
Yang, Re ealing nonco alen in e ac ions, J. Am. Chem. Soc. 132 (18) (2010)
6498–6506, h ps://doi.o g/10.1021/ja100936w.
[37] H.A. Taha, M.R. Richa ds, T.L. Lowa y, Con o ma ional analysis o u anoside-
con aining mono- and oligosaccha ides, Chem. Re . 113 (3) (2013) 1851–1876,
h ps://doi.o g/10.1021/c 300249c.
[38] E.J. Cocine o, A. Lesa i, J.-U. G abow, J.C. López, J.L. Alonso, The shape o
leucine in he gas phase, ChemPhysChem. 8 (4) (2007) 599–604, h ps://doi.
o g/10.1002/(ISSN)1439-764110.1002/cphc. 8:410.1002/cphc.200600730.
[39] E.J. Cocine o, A. Lesa i, P. Écija, F.J. Bas e e xea, J.-U. G abow, J.A. Fe nández,
F. Cas año, Ribose ound in he gas phase, Angew. Chemie - In . Ed. 51 (13)
(2012) 3119–3124, h ps://doi.o g/10.1002/anie. 51.1310.1002/
anie.201107973.
[40] E.J. Cocine o, A. Lesa i, P. Écija, Á. Cimas, B.G. Da is, F.J. Bas e e xea, J.A.
Fe nández, F. Cas año, F ee uc ose is con o ma ionally locked, J. Am. Chem.
Soc. 135 (7) (2013) 2845–2852, h ps://doi.o g/10.1021/ja312393m.
R.T. Sa agi, M. Juanes, José L. Abad e al. Spec ochimica Ac a Pa A: Molecula and Biomolecula Spec oscopy 267 (2022) 120531
8