Comprehensive computational automated search of barrierless reactions leading to the formation of benzene and other C6-membered rings

Cas iñei a Reis e al., Sci. Ad . 10, eadq4077 (2024) 11 Sep embe 2024
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CHEMICAL PHYSICS
Comp ehensi e compu a ional au oma ed sea ch o
ba ie less eac ions leading o he o ma ion o
benzene and o he C6- membe ed ings
Ma a Cas iñei a Reis1*, Emilio Ma ínez Núñez2, An onio Fe nández Ramos1,2*
We p esen he sys ema ic explo a ion o a ious po en ial ene gy su aces o sys ems wi h C6H6–x (x=0, 1, 2,
o 3) empi ical o mula using an au oma ic sea ch app oach. The p ima y objec i e o his s udy is o iden i y eac-
ion pa hways ha lead o he c ea ion o benzene, o- benzyne, and o he ings. These pa hways ini ia e wi h a
ba ie less ecombina ion eac ion and in ol e subsequen isome iza ion eac ions wi h subme ged ansi ion
s a es un il he inal p oduc is eached. The epo ed eac ion p o iles a e consis en wi h he exis ing condi ions
in he in e s ella medium i he ho complex o med can cool down h ough adia i e elaxa ion. Recen s udies
on he deac i a ion o polya oma ic hyd oca bons (PAHs) suppo he possibili y o hese eac ions aking place.
The C6- membe ed ings a e conside ed p ecu so s o PAHs, and ou ocus is on iden i ying pa hways o igina ing
om he ba ie less ecombina ion o eac i e molecules known o exis in he in e s ella medium, wi h po en ial
implica ions in o he en i onmen s.
INTRODUCTION
Small hyd oca bon molecules a e widely p esen in combus ion
chemis y, he a mosphe e, and he in e s ella medium (ISM). They
a e hough o play a c ucial ole in he c ea ion o mo e complex
hyd oca bon molecules, such as benzene (C6H6) (1), o- benzyne (2),
highe - o de polya oma ic hyd oca bons (PAHs) such as indene
(c- C9H8) (3, 4), o de i a i es such as 2- cyanoindene (2- C9H7CN) (5).
I is sugges ed ha a ound 10 o 25% o in e s ella ca bon exis s in he
o m o PAHs, indica ing hei subs an ial p esence in space (6, 7).
The mos accep ed hypo hesis is ha PAHs a e o med in he
ISM om benzene o he phenyl adical h ough eac ions in ol ing
ace ylene o o he ca bonaceous sca olds (8–10). Fo ins ance, he
phenyl adical may be key in he o ma ion o PAHs (10–12) and
cyanonaph halenes (9), and he 1,2,3- idihyd obenzene and he
1- hexene- 3,5- diynyl- 2 adical (l- H2H6H) ha e been ob ained in
c oss- beam expe imen s o C2 wi h inylace ylene (13). In addi ion,
1,2,3- idihyd obenzene (o 1,2,3- cyclohexa iene) due o he ing
s ain may be key in he syn hesis o complex o ganic molecules (14).
One o he pionee ing compu a ional wo ks ha explo e he o -
ma ion o benzene was ca ied ou by Mille and Klippens ein (15).
These au ho s ound ha benzene could o m by ecombina ion o
wo p opa gyl (CH2CCH) adicals a e se e al isome iza ion eac-
ions a empe a u es be ween 300 and 2200 K and di e en p es-
su es. The ecen disco e y o he p opa gyl adical in he TMC- 1
cold da k cloud (16) has s eng hened he hypo hesis ha his adi-
cal may be a key species in he o ma ion o benzene. O he species
ha ha e a di ec ela ion o dehyd ogena ed o ms o benzene, such
as o- benzyne, a e inylace ylene(bu - 1- en- 3- yne) (17) and o he
C4H4 isome s (18), which can be o med by eac ion wi h single o
iple spin s a es o he C2 molecule (13).
Because o he low densi ies o eac an s and ul alow empe a-
u es in he ISM, he ecombina ion eac ion be ween wo species
mus be ba ie less, o ming a ho in e media e ha may dissocia e
back o eac an s o ea ange o p oduce wo di e en agmen s.
This eac ion o he ype A+B → C+D may occu in a one- s ep
p ocess whe e he p oduc s a e mo e s able han he eac an s o in
a mul is ep p ocess wi h subme ged (below eac an s) ansi ion
s a es (19). In p inciple, he eac ion o wo p opa gyl adicals o
o m benzene seems highly imp obable because a ho complex is
o med ha will dissocia e back o eac an s o wo di e en p od-
uc s. Howe e , he e is also he possibili y ha he ho complex
o med by he collision o A and B loses pa o i s ene gy excess
leading o only one p oduc . T adi ionally, i has been belie ed ha
because o he low densi y o he eac ing species, he complex can-
no dissipa e i s ene gy excess and dissocia es back o eac an s.
Howe e , ecen esea ch by S ocke e al. (20) sugges s ha adia-
i e elaxa ion is mo e e ec i e han p e iously assumed. This p o-
cess allows he ho complex o cool down e icien ly, ul ima ely
o ming a cold p oduc . These indings ha e no able implica ions, as
hey explain he esilience o small PAHs, such as cyanonaph halene
and naph halene (21), om dissocia ing back o eac an s. Fu he -
mo e, his e idence opens up he possibili y o simila eac ions oc-
cu ing o o he cyclic species such as benzene and i s de i a i es.
An addi ional possibili y o his ype o eac ion o occu is on a
g ain su ace because he la e can dissipa e he ene gy excess o he
complex.
The aim o his s udy is o use au oma ed compu a ional me h-
ods o explo e he po en ial ene gy su ace o benzene, o- benzyne,
and o he C6- membe ed ings. The objec i e is o iden i y a di e se
a ie y o ba ie less bimolecula eac ions o he o m A+B → C,
which exhibi subme ged ansi ion s a es and could po en ially
lead o one o he a o emen ioned species. Ou ocus will be on
eac an s ha ha e been obse ed in he ISM o ha ha e been he-
o ized o exis , e en i hey ha e no ye been de ec ed. In his wo k,
1Cen o Singula de in es igación en Química Biolóxica e Ma e iais Molecula es
(CiQUS), Campus ida, 15782, Uni e sidade de San iago de Compos ela, C/Jena o
de la Fuen e s/n, San iago de Compos ela, Spain. 2depa amen o de Química
Física, Facul ade de Química, Campus ida, 15782, Uni e sidade de San iago de
Compos ela, A da. das Ciencias s/n, San iago de Compos ela, Spain.
*Co esponding au ho . email: ma a. cas inei a. eis@ usc. es (M.C.R.); q . amos@ usc.
es (A.F.R.)
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Au ho s, some igh s
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we iden i y all hese po en ial pa hs, bu he kine ic mechanism e-
sponsible o s abilizing he inal p oduc alls ou side he scope o
his esea ch.
Fo he gene a ion o he po en ial ene gy su aces, we ely on
so wa e o he au oma ic sea ch o s a iona y poin s. The bene i
o using an au oma ed app oach lies in i s immuni y o human bias,
he eby allowing o a mo e uninhibi ed explo a ion o he po en ial
ene gy su ace. In his con ex , se e al p og ams ha e been designed
o au oma ically ind mul is ep eac ions (22–30) and gene a e in i-
ca e eac ion ne wo ks.
He e, we ha e used Au oMeKin (22, 28, 31), which is a compu a-
ional code designed o s udy unimolecula decomposi ions. The
p og am has demons a ed i s p o iciency in analyzing sys ems o
compa able size o benzene, as e idenced by i s applica ion in s udy-
ing he decomposi ion o indole (32). The au oma ed algo i hm
iden i ies ansi ion s a e s uc u es (saddle poin s) o bo h isom-
e iza ion and decomposi ion eac ions. The equilib ium s uc u es
o hese eac ions a e ob ained by ollowing he minimum ene gy
pa h (MEP) om he ansi ion s a e in he backwa d di ec ion ( o-
wa d eac an s) and in he o wa d di ec ion ( owa d p oduc s).
This allows building a eac ion ne wo k abou he a ge species ha
includes he in e con e sion eac ions be ween di e en isome s
and he p oduc s o hei decomposi ion.
The sea ch o ba ie less decomposi ions is mo e in ol ed and
equi es an addi ional s ep, as hese eac ions do no p esen a ansi ion
s a e. We use he nudged elas ic band algo i hm (33) o in es iga e
agmen a ion pa hways o igina ing om di e en isome ic o ms
o he a ge molecule. This app oach makes i possible o iden i y
p e iously unobse ed ansi ion s a es and p ocesses wi hou ene gy
ba ie s. By con enience, we a e app oaching he p oblem om a
di e en pe spec i e, i.e., he agmen s esul ing om ba ie less
eac ions will ac as he ini ial eac an s ha combine o o m he
desi ed p oduc . No ice ha he epo ed po en ial ene gy su aces
may also se e as a u u e da abase o he s udy o he in e con e -
sion eac ions be ween isome s and hei decomposi ion in o di -
e en p oduc s. All he in o ma ion abou he di e en eac ion
ne wo ks is a ailable a Zenodo (34).
RESULTS AND DISCUSSION
We ollow a gene al scheme in which each o he C6H6–x (x=0, 1, 2,
o 3) ings a e analyzed sepa a ely, beginning wi h benzene and
ending wi h he C6H3 adicals. Fo he la e , some six- membe ed
ings and some linea ca bon chains ha e simila ene gies, so i is a
his s age when he ings s a o o m (13). The successi e addi ions
o hyd ogen a oms a e ba ie less p ocesses ha sys ema ically in-
c ease he s abili y o he ing, s a ing wi h he addi ion o he C6H3
o o m benzyne, con inuing wi h he o ma ion o he phenyl adi-
cal, and ending wi h he o ma ion o benzene. The hyd ogen addi-
ions o he ing p o ide a common g ound o a sys ema ic s udy o
hese ca bonaceous ings. In he ollowing sec ions, i s , we de-
sc ibe he o ma ion o benzene; second, he o ma ion o he phe-
nyl adical and o benzyne; and las , we deal wi h he o ma ion o
se e al isome s wi h C6H3 empi ical o mula.
Benzene
Shock- ube expe imen s ca ied ou by Wu and Ke n (35) ound
ha wo p opa gyl adicals (PR29) p oduce benzene as one o he
majo p oduc s. Mille and Melius (36) a gued ha benzene and he
phenyl adical plus a hyd ogen a om a e he i s ings o med a e
he ecombina ion o he wo p opa gyl adicals. A subsequen se-
ies o gas phase (37) and combus ion s udies (15, 38, 39) con i med
he o ma ion o benzene, as well as ha o ul ene and he phenyl
adical. In addi ion, he wo k o Wilson e al. (40) ha simula ed he
condi ions o he a mosphe e o Ti an poin ed ou ha he eac ion
o wo p opa gyl adicals is he main ou e o benzene o ma ion.
Au oMeKin ound 191 minima, 278 ansi ion s a es, and 35
p oduc s o benzene decomposi ion a he M08HX/6- 31G(d,p)
le el. The eac ion ne wo k gene a ed om hese s uc u es p e-
dic s ha he ecombina ion o wo p opa gyl adicals is a iable
pa h o benzene o ma ion. Figu e1 shows wo o hese pa hs, bu
mo e de ails a e gi en in he Supplemen a y Ma e ials. One o hem
leads o he 1,2,4,5- hexa e aene (MIN15) and hen o ul ene
(MIN2). The la e is a key species in he ecombina ion o he wo
p opa gyl adicals, al hough i is possible o ind a pa h ha a oids
ul ene and ha passes h ough he 1,2- hexadiene- 5- yne (MIN26).
Labels o s a iona y poin s o he ini ial benzene ne wo k s a wi h
MIN o TS o equilib ium o ansi ion s a e s uc u es, espec-
i ely. To dis inguish he s a iona y poin s ha o igina e om di -
e en eac ion ne wo ks, he p e ixes A, B, C, e c., a e added o he
labels wi h a gi en empi ical o mula using he ollowing con en-
ion: A (C6H5), B (C6H4), C (C6H3), D (C6H2), E (C4H4), F (C5H3),
G (C5H2), H (C5H), and I (C4H4).
Benzene can also be o med om he ba ie less eac ion o he
phenyl adical wi h a omic hyd ogen. Vinylace ylene and ace ylene
can also eac o o m benzene, bu he ini ial eac ion has a ba ie
o 31.88 kcal mol−1, so his pa h was disca ded. When inylidene
(CCH2) subs i u es ace ylene he eac ion is ba ie less. Un o u-
na ely, his ca bene emains elusi e o de ec ion in he ISM, al hough
he exis ence o his eac i e in e media e has been hypo hesized
many yea s ago (41).
We also included C5H3 species because he ecombina ion eac-
ion o his adical wi h he me hyl g oup can be ob ained om he
pho odissocia ion o benzene (42); in pa icula , he exci a ion o
benzene a 193 and 248 nm p oduces 4% o C5H3+CH3. All eac-
ions be ween hese wo agmen s in ol e he o ma ion o he
hexa- 1,2,3,4- e aene (MIN22) ha e ol es by an H- shi o a ca -
bene and unde goes ano he H- shi o o m he hexa- 1,2,3,5-
e aene (MIN11). This in e media e e ol es o a ca bene ha eac s
o o m a bicyclic species (MIN64) and he subsequen C6- membe ed
ing species (MIN21), which can e ol e o MIN44 o o m he phenyl
adical plus a omic hyd ogen o o MIN41 o yield o- benzyne plus
H2 o benzene. Howe e , he high ba ie heigh s in ol ed (nea he
dissocia ion ene gy o he wo agmen s) and he la ge numbe o
elemen a y s eps indica e ha his pa h will ma ginally con ibu e o
he o ma ion o C6- membe ed ings, a esul ha is in ag eemen
wi h expe imen al indings.
The eac ions o di e en C4H4 isome s ( inyl e hylene, bu a iene,
and me hylenecyclop opene) wi h ace ylene all ha e ini ial ba ie s.
The eac ion be ween he inyl and bu a ienyl adicals is ba ie -
less, bu none o he wo species has been de ec ed in he ISM. A
simila si ua ion occu s wi h he eac ion be ween he p opa gyl
and cyclop openyl (c- C3H3) adicals because he la e has no been
encoun e ed in he ISM.
The phenyl adical
The numbe o minima, ansi ion s a es, and p oduc s op imized a
he densi y unc ional heo y (DFT) me hod a e 181, 268, and 356,
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espec i ely. The phenyl adical (c- C6H5) can be o med om he
eac ion o he hyd ogen a om wi h o- benzyne (see Fig.2), bu he
eac ion occu s in wo s eps. The ini ial ba ie less eac ion leads o
an in e media e (A- MIN13), wi h an ene gy o 32.89 kcal mol−1 be-
low eac an s, ha easily e ol es o he inal p oduc . Howe e , o-
benzyne is no he only species wi h C6H4 empi ical o mula ha
can lead o he phenyl adical. A ull lis o he cu en ly unde ec ed
eac an s compa ible wi h he ISM condi ions is gi en in he Supple-
men a y Ma e ials. Al e na i e pa hs o he o- benzyne ou e in ol e
addi ions o a iple bond, such as he addi ion o he me hylidyne
adical, me hylene (43), me hyl adical (44), e hynyl adical (45),
and p opadienylidene (l- H2C3) (46) o C5H4, C5H3, C5H2, C4H4,
and C3H3 species, espec i ely.
The eac ion o he me hylidyne adical (CH) wi h 1,4- pen adiyne
[HCCCH2CCH—an isome o allenyl ace ylene, whose exis ence in
he ISM could no be es ablished (47)], allows o ming he phenyl
adical in jus h ee s eps: (i) addi ion, (ii) cycliza ion, and (iii) hyd o-
gen shi . The eac ion pa h in ol es wo low- ba ie ansi ion s a es
because, in his case, he e a e no hyd ogen shi eac ions associa ed
wi h he acyclic species.
Au oMeKin p edic s ha wo C5H3 isome s, he 1,4- pen adiynyl- 3
and he e hynyl cyclop openylidene adicals, can eac wi h me hy-
lene by an addi ion o he iple bond. The i s C5H3 isome o ms
he A- MIN14 in e media e species, which unde goes wo consecu-
i e hyd ogen shi eac ions and a u he cycliza ion o p oduce
he inal p oduc . The second C5H3 isome leads o he phenyl adi-
cal in h ee s eps: addi ion ( o o m A- MIN53), hyd ogen shi , and
cycliza ion. Mo e in o ma ion abou he mos s able C5H3 isome s is
gi en in he Supplemen a y Ma e ials.
The eac ion o he e hynyl adical wi h inylace ylene o e s
mo e possibili ies because bo h molecules p esen iple bonds.
Figu e2 shows one o he pa hs in which i is possible o ob ain he
phenyl adical in jus h ee s eps, i.e., addi ion o he iple bond,
cycliza ion, and hyd ogen ans e .
The eac ion o he p opa gyl adical wi h p opadienylidene
o ms an allenyl p opa gyl adical (A- MIN11), which, by hyd o-
gen shi , leads o he in e media e A- MIN43 ha o ms a cycle
(A- MIN15) and unde goes a new hyd ogen shi o yield (A- MIN1).
Ano he possibili y is he addi ion o he me hyl adical o pen a e -
aenylidene ha p oduces he phenyl adical in i e s eps, o which
he las h ee a e common o he eac ion s a ing wi h he wo
p opa gyl adicals.
o- Benzyne
Many pa hways may lead o o- benzyne, and he eac ion ne wo k is
o med by 278 minima, 552 ansi ion s a es, and 201 p oduc s. As
CCC
C
C
C
C
C
C
C
CC
H
H
H
H
H
H·
H
H
H
H
H
H
PR25/A-MIN1
111.2
CCC
C
C
CH
H
H
HH
MIN1
0.00
H
MIN41
90.21
TS6
90.25
TS23
106.28
TS11
94.51
CCC
C
C
C
H
H
H H
MIN21
76.34
H
HCCCC
CC
H
H
H
HH
H
MIN4
62.19
TS17
100.11
TS147
134.02 CCCC
CC
H
H
HH
H
MIN140
129.72
H
CCCCCC
H
HHH
HH
PR28
168.28
TS242
145.63
CCC
C
C
C
H
H
H
HH
MIN64
103.98
HTS223
139.22
CCCCH
H
H
H
C
C
MIN112
124.19
H
H
TS206
143.6 CCCC
CC
H
H
H
H
MIN11
70.61
HH
TS200
143.77
CCCC
CC
H
H
H
MIN149
133.95
HH
H
TS211
145.84
CCC C C
C
H
H
H
MIN22
79.89
H
H
H
CCC C C
H
H
H
PR35
149.86
·CH3
C
C
C
C
C
C
H
H
H
H
MIN33
86.99
H
H
TS199
136.22
TS241
144.98
TS219
139.07
CCCC
CC
H
H
H
H
MIN171
84.40
HH
C
C
C
C
C
C
H
H
H
H
MIN63
100.2
H
H
CCC C
C
C
H
H
H
H
H
H
PR32
178.76
H
H
CCC
HH
H
MIN26
80.02
C
C
C
H
CCC H
H
H
PR29
146.91
H
C
C
C
C
H
H
MIN31
85.24
H
TS132
130.3
H
C
C
H
TS246
144.03
PR7- dW
143.21
H
C
C
CC
H
H
H
H
C
C
H
PR7
146.04
H
C
C
C
H
H
MIN15
75.06
H
H
C
H
C
C
CC
C
C
C
C
H
H
H
H
MIN2
31.56
H
H
TS178
140.83
TS40
111.52
CC
C
C
C
C
H
H
H
MIN79
108.85
H
H
H
TS42
111.16
CC
C
C
C
C
H
H
H
MIN8
72.87
H
H
H
TS15
101.15
2
CCC
C
C
C
H
H
H
H
PR1
88.64
TS77
122.2
H2
TS44
110.0
CCC
C
C
C
H
H
H H
MIN44
92.70
H
H
Fig. 1. Mul is ep ba ie less eac ions encoun e ed by Au oMeKin leading o benzene. in g ay a e he eac i e species ha ha e no been ye de ec ed in he iSM. All
F12- CCSd( ) ela i e ene gies include he densi y unc ional heo y (dF ) ze o- poin ene gies.
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shown in Fig. 3, he mos s aigh o wa d pa h is h ough 1,2,3-
idehyd obenzene because i is a ba ie less one- s ep eac ions.
Howe e , his species has no ye been de ec ed in he ISM.
Ano he possibili y is he eac ion o he p opa gyl adical wi h
l- C3H (B- PR108) o wi h c- C3H (B- PR150). In bo h cases, he e is a
i s associa ion s ep wi h a la ge s abiliza ion and a cycliza ion o a
common species ha su e s an ini ial hyd ogen ans e o o m ul-
enylidene (B- MIN9) and a inal (nea ly ba ie less) ing expansion
o p oduce o- benzyne.
The mechanism p oposed by Kaise e al. (13) ha s a s wi h
adding C2 (single ) o he e minal ca bon o he double bond o
inylace ylene was also ound. The ecombina ion eac ion leads o
B- MIN157 [si3—nomencla u e om (13)], which, by an in e nal
C─C o a ion, leads o B- MIN55, and his species unde goes cycli-
za ion o o m ul enylidene, which easily e ol es o o- benzyne
(see Fig.3).
Figu e 3 shows ha inyldiace ylene can be o med om he
ecombina ion eac ion o he me hyl adical and pen adiynylidene
(l- C5H) (48) wi h an ene gy o 126.01 kcal mol−1 abo e o- benzyne.
Au oMeKin indica es ha l- H2C6H can be o med om hexapen ae-
nylidene (l- H2C6) (49) plus he hyd ogen a om o om bu a ienyli-
dene (l- H2C4) (50) plus he e hynyl adical (no displayed in Fig.3)
The o ma ion o o- benzyne om 1- hexene- 3,5- diynyl- 2 (l- H2C6H)
plus a omic hyd ogen leads o se e al possibili ies ha a e explained
in mo e de ailed in he Supplemen a y Ma e ials.
In addi ion, we encoun e ed ha wo compounds wi h C5H3 em-
pi ical o mula can ecombine wi h me hylidene and lead o o-
benzyne a e a ew s eps. The i s is he 2,4- pen adiynyl- 1 adical,
al eady men ioned abo e, and he o he is he 1,4- pen adiynyl- 3
adical (HCCCHCCH). The la e can be o med om he ecombi-
na ion o he e hynyl adical plus cyclop openylidene (c- C3H2) (51),
ollowed by a ing opening and H- shi . The 1,4- pen adiynyl- 3 adical
C
C
C
C
CC
H
H
H
H
H
CC·H
C
C
H
CC
H
C
C
C
C
CC
H
H
H
H
H
H
H·
A-MIN1
0.00
MIN1
A-TS4
61.29
A-MIN13
47.61 A-PR14
80.5
C
C
C
C
CC
H
H
H
H
H
C
C
C
C
CC
H
H
H
H
H·
A-TS23
80.7
A-MIN15
47.61
C
C
C
C
CC
H
H
H
H
H
A-TS109
101.69
H H
HH
H
CCC
CC
C
A-MIN43
70.01
A-TS125
111.92
A-TS220
140.13
A-PR233
134.28
CCCCCC
H H
H
A-MIN5
44.65
H
CCC
CCC
H
H
H
H
H
H
CCCCC
H
A-PR218
140.93
H
A-TS41
89.02
A-MIN62
74.75
C
C
C
C
CC
HH
H
H
H
A-TS119
106.59
HH
H
H
H
CC
CC
A-MIN106
100.19
C
C
A-PR129
122.88
A-TS12
68.03
CCC
C
C
C
H
H
H
H
A-MIN24
47.61
H
A-TS112
105.98
CCC
H
H
H
H
A-MIN6
47.1
C
C
H
C
A-MIN65
69.93
C
C
C
C
CC
H
H
H
A-TS35
86.08
H
H
A-TS221
135.58
CC
C
C
C
C
H
H
H
A-MIN171
122.31
H
H
CH
CC
CCC
HH
A-PR330
168.27
HH
CCC
C
C
C
H
H
H
A-MIN11
47.61
H
H
H
H
·CH3
A-TS38
81.0
A-TS100
106.71
A-MIN14
47.61
A-PR150
177.83
H
C
H
CCC
H
C
CH
H
CH2
C
C
H
C
C
C
H
H
A-TS209
125.58 A-MIN68
85.78
C
C
CC
CC
HH H
H
H
A-TS204
134.1
A-MIN53
77.42
C
C
C
CCC
H
H
H
H
H
A-PR82
220.94
CH2
C
C
H
C
CC
H
H
Fig. 2. Same as Fig.1 bu o he o ma ion o he phenyl adical.
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Cas iñei a Reis e al., Sci. Ad . 10, eadq4077 (2024) 11 Sep embe 2024
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5 o 10
may also lead o m- benzyne (B- MIN2) because i is he p e ious
s ep o he o- benzyne o ma ion.
C6H3 s uc u es
The eac ion pa h connec ions be ween eac i e ISM molecules
and he mos s able C6H3 s uc u es a e gi en in Fig.4. Kaise e al.
(13) conside ed he C6H3 s uc u es “as he c ucial link be ween
ene ge ically a o ed a oma ic and esonan ly s abilized adicals
o hyd ogen- ich and poo C6Hx molecules, espec i ely.” Ce -
ainly, his is he case o he 6- bicyclo[3.1.0]hexa- 1,3,5- ienyl
adical (C- MIN1), 1,2,3- idehyd obenzene (C- MIN3), and 1,2,4-
idehyd obenzene (C- MIN4) ha a e e y close ene gy o l- H2C6H
(C- MIN2). The e o e, molecula s uc u es wi h C6H3 empi ical
o mula a e he ones wi h he leas numbe o hyd ogen a oms o
he ype C6Hx (whe e x=1, …, 6) o which he closed ing is e y
close in ene gy o he open ca bon chain (see Fig. 4). The ing
C
C
C
C
CC
H
H
H
H
H
A-MIN1/PR25
C
C
C
C
CC
H
H
H
H
B-MIN1/A-PR14
0.00
C
C
C
C
CC
H
H
H
H
B-MIN106
86.53
B-TS44
80.69
C
C
C
C
C
C
H
B-MIN74
72.54
B-TS92
88.88
H
H
H
C
C
C
C
C
C
H
B-MIN71
72.08
H
H
H
B-TS36
82.47
B-TS1
31.25
CC
C
C
CC
H
H
B-MIN9/B-MIN9*
30.84
H
H
CC
C
C
CC
H
H
B-MIN133
88.78
H
B-TS116
98.92
H
B-TS75
89.74
B-TS258
117.64
C
C
C
H
H
B-MIN36
64.61
H
H
C
CC
CC
C
C
C
C
H
B-PR108
144.33
H
H
H
CC
C
C
CC
HB-MIN19
58.72
H
H
H
CCC H
H
H
CC
C
H
B-PR150
142.49
C
C
C
C
CC
H
H
B-MIN66
69.8
B-TS33
78.42
H
H
B-TS57
87.37
B-TS97
87.81
C
CCCCC
H
B-MIN3
14.12
H
HCCCCC
B-PR141
126.01
H
B-TS14
72.03
C
C
C
C
CC
H
H
B-MIN2
15.19
HH
B-TS21
72.92
C
CC
C
C
C
H
H
H
B-MIN34
63.06
H
C
C
C
C
C
C
H
H
H
B-MIN178
101.4
H
B-TS24
80.3
C
C
C
C
CC
HH
B-MIN13
51.79
H
H
B-TS84
92.83
C
C
C
C
CC
HH
B-MIN143
95.71
H
H
B-TS455
137.81
C
C
C
C
C
C
B-MIN146
93.59
HH
HH
C
CCC
C
H
H
B-PR134
167.72
H
CH
C
C
C
C
CC
H
H
B-PR100
107.52
H
CH
H·
H·
·CH3
CCCCC
B-PR113
166.26
H
H
H
C
C
C
C
CC
H
H
B-MIN98
78.09
H
H
H
B-TS41
83.3 C
CCCCC
H
HH
HB-MIN53
66.6
B-TS304*
122.44
C
C
CH
H
B-MIN55*
73.27
C
CC
H
H
B-TS201*
116.38
C
C
C
C
CC
H
B-MIN157*
113.92
H
H
H
C
CC
C
H
B-PR213*
154.85
HH
H
CC
C
C
C
C
CC
H
B-MIN68*
74.88
H
H
H
B-TS401*
137.47
B-TS228*
97.9
H· CCCCCC
B-PR109
110.05
H
H
H
B-TS154
101.56
Fig. 3. Same as Fig.1 bu o he o ma ion o o- benzyne.
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Cas iñei a Reis e al., Sci. Ad . 10, eadq4077 (2024) 11 Sep embe 2024
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6 o 10
o ma ion is un a o able om an en opic poin o iew a high
empe a u es bu compe es wi h he o he mechanisms a ul alow
empe a u es because, in his case, he en opic con ibu ion is
negligible.
The linea l- H2C6H adical can lead o o- benzene by a u he
H- a om addi ion ( ide sup a). C ossed molecula beam expe i-
men s ca ied ou by Guo e al. (52) ound ha his molecule can
be o med om C3 (53) and allene (H2CCCH2). We ound ha he
1- hexene- 3,5- diynyl- 2 adical (Fig.4) can also be o med by he
ecombina ion o (i) hexapen aenylidene plus a omic hyd ogen
(C- PR26), (ii) pen adiynylidene plus me hylene (C- PR116), (iii)
e hynylcyclop opynylidyne (c- C3C2H) (54) plus me hylene (C-
PR191), (i ) bu a ienylidene plus he e hynyl adical (C- PR29), ( )
p opadienylidene plus p opynylidyne (C3H) (55) (C- PR95), ( i)
eac ions ha in ol e C3- membe ed ings (C- PR25, C- PR32, and
C- PR44), and ( i) o he eac an s ha go h ough he C- MIN7
adical. In pa icula , his adical is a key in e media e be ween he
open and closed o ms o C6H3 s uc u es. I can be eached by
ecombining he eac an s men ioned abo e and by o he h ee
pa hs. The mos di ec pa h is he ecombina ion o ace ylene and
he bu adiynyl adical. Ano he possibili y o he o ma ion o cy-
clic s uc u es om l- H2C6H is by di ec cycliza ion h ough C-
MIN71 and conce ed H- shi and C─C bond o ma ion leading o
he C- MIN1 bicyclic s uc u e.
The addi ion o a omic hyd ogen o 1,2,3- idehyd obenzene
and 1,2,4- idehyd obenzene may also be a sou ce o o ma ion o
o- benzyne bu no he bicyclo[3.1.0]hexa- 1,3,5- ienyl adical. Add-
ing a omic o molecula hyd ogen o he la e p esen s a ba ie
heigh . A new pa h s a s wi h he ecombina ion o he p opa gyl
adical and c- C3, bu c- C3 has no been de ec ed in he ISM (no
plo ed in Fig.4). O he possibili ies in ol e passing h ough o he
s able cyclic s uc u es (C- MIN3 o C- MIN4), bu once hey a e
o med, hei e olu ion o C- MIN1 is highly imp obable due o he
high ba ie s in ol ed.
The 1,2,3- idehyd obenzene adical, apa om he pa hs ha
connec wi h he C- MIN7 in e media e, can be o med om C3
C
C
C
C
CC
H
H
C-MIN3/B-PR100
0.74
H
C-TS58
66.52
CCC
C
CC
H
C-MIN7
19.09
H
H
CCCCCCH
H
H
C-MIN2/B-PR109
3.27
C-TS20
59.98
C-PR3
114.45
CCCC
H
H
CCH
C-TS88
83.86
C
CCCC
C
H
H
C-MIN22
43.77
H
C
CCC
CC
H
H
H
C-PR95
136.57
C-TS148
94.78 C
C
CC
H
C
C
H
H
C-MIN25
48.88
HC C
CCC
CH2
C-PR116
163.03
C-TS53
68.54
C-MIN14
58.44
CC
C
C
C
H
C
H
H
CCCCCC
H
H
H
C-PR26
98.69
CCH H
C-PR51
80.72
CCCC H
CCC
C
CC
C-MIN91
72.82
H
HH
C-TS63
74.54
C-TS258
120.26
C
CCC
C
C
C-MIN35
53.79
H
HH
C-TS171
100.74
CCC CH
C
C
C-MIN11
33.73
H
H
CCC
CC
C
H
H
H
C-PR25
134.28
C-TS45
72.91
H
H
C
CC
CCC
H
C-MIN46
57.5
CCH
H CCCCH
C-PR29
70.62
C
C
C
C
CC
H
H
C-MIN4/B-PR101
3.72
H
C-TS74
79.75
C-TS11
45.06
C
CC
CH
C
C
C-MIN96
79.07
H
H
C
C
HC CH
CH
C
C-MIN33
58.12
H
C-PR44
120.13
CH
CH
C
C
C
C
H
H C
C
CH
CCC
H
C-MIN5
11.65
C
C
CH
CCC
H
C-PR20
100.8
H
C-TS67
74.84
H
C
CC
CCC
H
C-MIN58
64.54
H
C-TS208
109.84
C
C
C
CCC
H
C-MIN50
57.37
H
H
CCHC
H
H
CCC
C-PR154
111.67
C-TS210
111.03
C
C
C
C
C
C
C-MIN24
50.74
H
H
H
C-PR32
122.41
CC
C
HH
CCC
H
C-TS146
99.94
C-TS79
85.89
CC
C
CC
C
C-MIN1
0.00
H
H
HC
C
C
C
CC
H
H
H
H
B-MIN1/A-PR14
(106.78)
H·
H·
C-TS43
73.88
C-TS6
41.48
C-MIN71
65.8
C-TS5
40.83
C
C
C
C
CC
H
H H
C-TS73
71.58
HC CC C
C
CH2
C-PR91
180.05
Fig. 4. Same as Fig.1 bu o he o ma ion o C6H3 s uc u es.
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plus he p opa gyl adical o om p opynylidyne (HC3) plus cyclo-
p openylidene (c- C3H2). Bo h pa hs o m he cyclic adical in h ee
s eps and ha e in common he in e media e C- MIN58 in he
las s ep.
The 1,2,4- idehyd obenzene can be o med om he ecombina-
ion o cyclop openylidene and he cyclop opanediylidenyl adical
(c- C3H) (56, 57) a e a ing opening o one o he ings, ollowed by
a ing opening o he ca bene and a u he cycliza ion. I can also be
o med om e hynylallene (HCCCHCCC) (58) plus he hyd ogen
a om in only wo s eps.
We p esen an ex ensi e analysis o bo h one- s ep and mul is ep
eac ion pa hways o he A+B → C ype o eac ions, de i ed om
a eac ion ne wo k gene a ed using au oma ed me hods. The eac-
ion p o iles ini ia e wi h he ba ie less ecombina ion o wo eac-
i e molecules, which, in he case o mul is ep eac ions, pass h ough
subme ged ansi ion s a es be o e culmina ing in he o ma ion o
aC6- membe ed ing hyd oca bon. These indings a e summa ized
in Fig.5.
Wi h his p esc ip ion, we con i med ha benzene can be o med
by associa ing wo p opa gyl adicals. In addi ion, benzene can be
eached by he eac ion o H2C5H wi h he me hyl adical o by he
eac ion o inylidene (unde ec ed) wi h inylace ylene. The mos
a o able pa h o benzene o ma ion is he ba ie less eac ion
be ween he phenyl adical and a omic hyd ogen.
The analysis o he eac ion ne wo ks o dehyd ogena ed o ms
o benzene such as he phenyl adical, o- benzyne, o di e en cyclic
C6H3 s uc u es e eals ha he o ma ion o hese ings is e y in-
ol ed and comp ises a ple ho a o eac i e species. Two enci cled
species in Fig.5, which a e he phenyl and he C6H3 adicals, ha e
no ye been encoun e ed in he ISM, bu hei exis ence has been
hypo hesized.
We ound ha se e al eac ions s a wi h di e en combina ions
o adical eac an s such as p opa gyl, cylop opynil, me hyl, o
ace yl adicals. O he pa hs ini ia e wi h he combina ion o linea
cumulenic ca bon sca olds (usually ca benes) plus a adical o a
neu al molecule, depending on he mul iplici y o he inal p oduc .
Some pa hs consis o simple hyd ogen a om addi ions o a ing; his
p o ides a common g ound o he o ma ion o di e en C6 spe-
cies. A molecule ha is e y abundan in he TMC- 1 cloud is inyl-
ace ylene, which, in ou scheme, plays a c ucial ole in he o ma ion
o o- benzyne by he addi ion o C2 [in ag eemen wi h he calcula-
ions o Kaise e al. (13)] and in he o ma ion o he phenyl adical
by he addi ion o he e hynyl adical (C2H). Ano he molecule ha
is ubiqui ous in C6 ings o ma ion is he p opa gyl adical, which
appea s in he o ma ion o benzene, he phenyl adical, o- benzyne,
and 1,2,3- idehyd obenzene by eac ion wi h ano he p opa gyl
molecule, p opadienylidene, C3H (cyclic and linea o ms), and C3,
espec i ely. This comple es he scheme depic ed in Fig. 5. Las ,
Fig. 5. Summa y scheme o di e en ISM- de ec ed (in black) and unde ec ed (in g ay) species encoun e ed by Au oMeKin as possible eac an s ha lead o
benzene and o he C6- membe ed ings. dashed a ows indica e pa hs ha in ol e se e al elemen a y s eps.
Downloaded om h ps://www.science.o g a Uni e sidade de San iago de Compos ela on Decembe 19, 2024
Cas iñei a Reis e al., Sci. Ad . 10, eadq4077 (2024) 11 Sep embe 2024
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some pa hways in ol e he eac ion o up- o- da e unde ec ed spe-
cies wi h C6H3 and C5H3 empi ical o mulas plus a small adical o
ca bene.
The ecen disco e y ha some PAHs unde go apid adia i e e-
laxa ion adds signi icance o he ecombina ion pa hs iden i ied in
his s udy. This inding may se e as a ounda ion o de eloping ki-
ne ic models ha inco po a e hese ypes o eac ions. The abundance
o iable pa hways iden i ied by Au oMeKin demons a es he e ec-
i eness o au oma ed me hods in cons uc ing eac ion ne wo ks
and unco e ing new eac ion pa hways ha may ha e ele ance in
he ISM and o he en i onmen s.
MATERIALS AND METHODS
The sea ch o he s a iona y poin s (minima and ansi ion s a es)
was ca ied ou wi h Au oMeKin (28). This p og am uns high-
ene gy ajec o ies combined wi h an algo i hm able o iden i y
bond- b eaking/ o ming e en s. Snapsho s along he ajec o ies
p o ide guess ansi ion s a e s uc u es ha a e u he op imized a
a low elec onic s uc u e le el. Fo he low- le el calcula ions, we
used he PM7 semiempi ical me hod (59) implemen ed in MOPAC
(60). Fo each success ully ob ained ansi ion s a e, we ollow he
MEP, so he minima ( eac an s and p oduc s) associa ed wi h ha
pa icula ansi ion s a e a e also iden i ied. In he e en ha he
cu en ansi ion s a e sea ch algo i hm ails o loca e he app op i-
a e saddle poin s, he nudged elas ic band me hod (33) is used o
alida e he absence o saddle poin s o he iden i ied ba ie less
pa hways. This ool was implemen ed in Au oMeKin in 2022 ( e i-
sion 1123). The pipeline s a s wi h a sea ch o bonds whose bond
o de is less han 1.5. The sea ch is pe o med o e e y single mini-
mum in he eac ion ne wo k. I hen uns a cons ained Lange in
dynamics simula ion wi h ex e nal o ces o b eak he selec ed bonds
wi hin each minimum ene gy s uc u e. An elemen a y s ep is con-
side ed ba ie less i i mee s he ollowing c i e ia: (i) I esul s in
wo agmen s, (ii) he ene gy o he esul ing agmen s is below a
speci ied h eshold, and (iii) no al e na i e pa hway wi h a ba ie ,
connec ing he same eac an s and p oduc s, has been ound.
Fo he eac ions wi h a ba ie , he low- le el ansi ion s a e
s uc u es a e u he op imized a a high le el, and new MEP calcu-
la ions a e pe o med o gene a e a mo e accu a e eac ion ne wo k.
All he s a iona y poin s we e op imized a he M08HX unc ional
(61) wi h he 6- 31+G(d,p) basis se excep he C2 plus inylace ylene
channel ha used he B3LYP unc ional (62) and he 6- 311G(d,p)
basis se .
All he low- le el and high- le el op imiza ion calcula ions we e
pe o med wi h MOPAC and Gaussian 16 (63), espec i ely. Fo each
DFT op imized geome y, we ha e con i med ha he wa e unc ion
was s able. High- le el Hessian calcula ions we e pe o med o check
he na u e o he s a iona y poin s. Accu a e elec onic ene gies we e
ob ained by single- poin calcula ions ca ied ou a he F12- CCSD(T)/
cc- pVTZ le el o e he DFT op imiza ions. The F12- CCSD(T) calcu-
la ions we e pe o med wi h MOLPRO (64). All epo ed ela i e
ene gies include he DFT- calcula ed ze o- poin ene gy con ibu ion
o he F12- CCSD(T) elec onic ene gy. A scaling ac o o 0.972 was
applied o he ze o- poin ene gies (65).
We ha e chosen M08HX because i has p o ided a good ep e-
sen a ion o he e y challenging ba ie less associa ion o CF2 and
he dissocia ion o C2F4 (66). In addi ion, i has been used by some
o us in he s udy o he associa ion eac ions o OH wi h me hanol
(67) and me hylamine (68), ollowed by he hyd ogen abs ac ion
eac ions. In all cases, he combina ion F12- CCSD(T)//M08HX
p oduced he mal a e cons an s in good ag eemen wi h expe i-
men . An in e es ing al e na i e o hese elec onic s uc u e calcu-
la ions could be he junChS and junChS- F12 composi e me hods o
Puzza ini and cowo ke s (69). The loca ion o eac ion pa hs inside
he eac ion ne wo k gene a ed by Au oMeKin was pe o med wi h
amk_ ools (32, 70).
The eac ion ne wo ks o he di e en po en ial ene gy su aces
we e buil inco po a ing some es ic ions. Du ing he ba ie less
agmen a ion o he molecule, Au oMeKin only examines he clea -
age o a single bond wi h a bond o de smalle han 1.5 (MOPAC
calcula es he bond o de ). Ba ie less agmen a ions ha in ol e
he clea age o mul iple bonds, as may be he case o a ca bon a om
o a C2 molecule dissocia ing om a h ee- membe ed ing, a e no
conside ed. Mo eo e , we included a spin es ic ion du ing he dis-
socia ion in o agmen s. In pa icula , he agmen s wi h an e en
numbe o elec ons ha e single spin s a es, so in e sys em c ossing
o di e en elec onic s a es ( o ins ance, iple s a es) is o bidden.
Supplemen a y Ma e ials
This PDF ile includes:
Supplemen a y ex
Figs.S1 o S4
ablesS1 o S4
Re e ences
REFERENCES AND NOTES
1. J. Ce nicha o, A. M. he as, A. G. G. M. ielens, J. R. Pa do, F. he pin, M. Guélin,
l. B. F. M. Wa e s, in a ed space obse a o y’s disco e y o C4h2, C6h2, and benzene in
CRl 618. As ophys. J. 546, l123–l126 (2001).
2. J. Ce nicha o, M. Agúndez, R. i. Kaise , C. Cabezas, B. e ce o, n. Ma celino, J. R. Pa do,
P. de icen e, disco e y o benzyne, o- C6h4, in MC- 1 wi h he QUiJO e line su ey.
As on. As ophys. 652, l9 (2021).
3. J. Ce nicha o, M. Agúndez, C. Cabezas, B. e ce o, n. Ma celino, J. R. Pa do, P. de icen e,
Pu e hyd oca bon cycles in MC- 1: disco e y o e hynyl cyclop openylidene,
cyclopen adiene, and indene. As on. As ophys. 649, l15 (2021).
4. A. M. Bu kha d , K. l. K. lee, P. B. Changala, C. n. Shingledecke , i. R. Cooke, R. A. loomis,
h. Wei, S. B. Cha nley, e. he bs , M. C. McCa hy, B. A. McGui e, disco e y o he pu e
polycyclic a oma ic hyd oca bon indene (c- C9h8) wi h GO hAM obse a ions o MC- 1.
As ophys. J. Le . 913, l18 (2021).
5. M. l. Si a, P. B. Changala, C. Xue, A. M. Bu kha d , C. n. Shingledecke , K. l. K. lee,
R. A. loomis, e. Momjian, M. A. Siebe , d. Gup a, e. he bs , A. J. Remijan, M. C. McCa hy,
i. R. Cooke, B. A. McGui e, disco e y o in e s ella 2- cyanoindene (2- C9h7Cn) in GO hAM
obse a ions o MC- 1. As ophys. J. Le . 938, l12 (2022).
6. A. G. G. M. ielens, in e s ella polycyclic a oma ic hyd oca bon molecules. Annu. Re .
As on. As ophys. 46, 289–337 (2008).
7. C. Joblin, G. Mulas, in e s ella polycylic a oma ic hyd oca bons: F om space o he
labo a o y. Eu . As on. Soc. Publ. Se . 35, 133–152 (2009).
8. Z. d. le ey, B. A. laws, S. P. Sunda , K. nau a, S. h. Kable, G. da Sil a, J. F. S an on,
. W. Schmid , PAh g ow h in lames and space: Fo ma ion o he phenalenyl adical. J.
Phys. Chem. A 126, 101–108 (2022).
9. B. A. McGui e, R. A. loomis, A. M. Bu kha d , K. l. K. lee, C. n. Shingledecke ,
S. B. Cha nley, i. R. Cooke, M. A. Co dine , e. he bs , S. Kalenskii, M. A. Siebe , e. R. Willis,
C. Xue, A. J. Remijan, M. C. McCa hy, de ec ion o wo in e s ella polycyclic a oma ic
hyd oca bons ia spec al ma ched il e ing. Science 371, 1265–1269 (2021).
10. e. Reize , B. iskolcz, B. Fise , Fo ma ion and g ow h mechanisms o polycyclic a oma ic
hyd oca bons: A mini- e iew. Chemosphe e 291, 132793 (2022).
11. X. Gu, R. i. Kaise , Reac ion dynamics o phenyl adicals in ex eme en i onmen s: A
c ossed molecula beam s udy. Acc. Chem. Res. 42, 290–302 (2009).
12. R. i. Kaise , d. S. n. Pa ke , F. Zhang, A. lande a, . . Kislo , A. M. Mebel, Pah o ma ion
unde single collision condi ions: Reac ion o phenyl adical and 1,3- bu adiene o o m
1,4- dihyd onaph halene. J. Phys. Chem. A 116, 4248–4258 (2012).
13. R. i. Kaise , M. Goswami, P. Maksyu enko, F. Zhang, Y. S. Kim, A. lande a, A. M. Mebel, A
c ossed molecula beams and abini io s udy on he o ma ion o C6h3 adicals. An
Downloaded om h ps://www.science.o g a Uni e sidade de San iago de Compos ela on Decembe 19, 2024
Cas iñei a Reis e al., Sci. Ad . 10, eadq4077 (2024) 11 Sep embe 2024
SCienCe Ad AnCeS | ReSeARCh AR iCle
9 o 10
in e ace be ween esonan ly s abilized and a oma ic adicals. J. Phys. Chem. A 115,
10251–10258 (2011).
14. A. . Kelleghan, A. S. Bulge , d. C. Wi kowski, n. K. Ga g, S ain- p omo ed eac ions o
1,2,3- cyclohexa iene and i s de i a i es. Na u e 618, 748–754 (2023).
15. J. A. Mille , S. J. Klippens ein, he ecombina ion o p opa gyl adicals and o he eac ions
on a C6h6 po en ial. J. Phys. Chem. A 107, 7783–7799 (2003).
16. M. Agúndez, C. Cabezas, B. e ce o, n. Ma celino, J. d. Gallego, P. de icen e, J. Ce nicha o,
disco e y o he p opa gyl adical (Ch2CCh) in MC- 1: One o he mos abundan adicals
e e ound and a key species o cycliza ion o benzene in cold da k clouds. As on.
As ophys. 647, l10 (2021).
17. J. Ce nicha o, M. Agúndez, C. Cabezas, n. Ma celino, B. e ce o, J. R. Pa do, J. d. Gallego,
F. e ce o, J. A. lópez- Pé ez, P. de icen e, disco e y o Ch2ChCCh and de ec ion o
hCCn, hC4n, Ch3Ch2Cn, and, en a i ely, Ch3Ch2CCh in MC- 1. As on. As ophys. 647,
l2 (2021).
18. A. M. Mebel, . . Kislo , R. i. Kaise , Ab ini io/Rice- Ramspe ge - Kassel- Ma cus s udy o he
single C4h4 po en ial ene gy su ace and o he eac ions o C2 (
X1
Σ
+
g
) wi h C4h4 ( X
1
A
+
1
g
)
and C (1d) wi h C3h4 (allene and me hylace ylene). J. Chem. Phys. 125, 133113 (2006).
19. C. Puzza ini, Gas- phase chemis y in he in e s ella medium: he ole o labo a o y
as ochemis y. F on . As on. Space Sci. 8, 811342 (2022).
20. M. h. S ocke , J. n. Bull, h. Cede quis , S. ind aji h, M. Ji, J. e. na a o na a e e,
h. . Schmid , h. Ze e g en, B. Zhu, e icien s abiliza ion o cyanonaph halene by as
adia i e cooling and implica ions o he esilience o small pahs in in e s ella clouds.
Na . Commun. 14, 395 (2023).
21. M. Sai o, h. Kubo a, K. Yamasa, K. Suzuki, . Majima, h. suchida, di ec measu emen o
ecu en luo escence emission om naph halene ions. Phys. Re . A 102, 012820 (2020).
22. e. Ma ínez- núñez, An au oma ed me hod o ind ansi ion s a es using chemical
dynamics simula ions. J. Compu . Chem. 36, 222–234 (2015).
23. C. W. Gao, J. W. Allen, W. h. G een, R. h. Wes , Reac ion mechanism gene a o : Au oma ic
cons uc ion o chemical kine ic mechanisms. Compu . Phys. Commun. 203, 212–225
(2016).
24. P. l. Bhoo asigh, B. l. Slakman, F. S. Khanshan, J. Y. Cain, R. h. Wes , Au oma ed ansi ion
s a e heo y calcula ions o high- h oughpu kine ics. J. Phys. Chem. A 121, 6896–6904
(2017).
25. C. Ca allo i, M. Pelucchi, Y. Geo gie skii, S. J. Klippens ein, eS ok P: elec onic s uc u e
o empe a u e- and p essu e- dependen a e cons an s - A code o au oma ically
p edic ing he he mal kine ics o eac ions. J. Chem. Theo y Compu . 15, 1122–1145
(2019).
26. i. ismail, h. B. . A. S u a o d- Fowle , C. Ochan Ashok, C. Robe son, S. habe shon,
Au oma ic p oposal o mul is ep eac ion mechanisms using a g aph- d i en sea ch.
J.Phys. Chem. A 123, 3407–3417 (2019).
27. R. an de ij e , J. Zádo , Kinbo : Au oma ed s a iona y poin sea ch on po en ial ene gy
su aces. Compu . Phys. Commun. 248, 106947 (2020).
28. e. Ma ínez- núñez, G. l. Ba nes, d. R. Glowacki, S. Kopec, d. Peláez, A. Rod íguez,
R. Rod íguez- Fe nández, R. J. Shannon, J. J. P. S ewa , P. G. ahoces, S. A. azquez,
Au oMeKin2021: An open- sou ce p og am o au oma ed eac ion disco e y. J. Compu .
Chem. 42, 2036–2048 (2021).
29. C. Robe son, R. hyland, A. J. d. lacey, S. ha ens, S. habe shon, iden i ying ba ie less
mechanisms o benzene o ma ion in he in e s ella medium using pe mu a ionally
in a ian eac ion disco e y. J. Chem. Theo y Compu . 17, 2307–2322 (2021).
30. J. Zádo , C. Ma í, R. an de ij e , S. l. Johansen, Y. Yang, h. A. Michelsen, h. n. najm,
Au oma ed eac ion kine ics o gas- phase o ganic species o e mul iwell po en ial
ene gy su aces. J. Phys. Chem. A 127, 565–588 (2023).
31. e. Ma ínez- núñez, An au oma ed ansi ion s a e sea ch using classical ajec o ies
ini ialized a mul iple minima. Phys. Chem. Chem. Phys. 17, 14912–14921 (2015).
32. d. Ga ay- Ruiz, M. Ál a ez Mo eno, C. Bo, e. Ma ínez- núñez, new ools o aming
complex eac ion ne wo ks: he unimolecula decomposi ion o indole e isi ed. ACS
Phys. Chem. Au 2, 225–236 (2022).
33. G. henkelman, h. Jónsson, imp o ed angen es ima e in he nudged elas ic band
me hod o inding minimum ene gy pa hs and saddle poin s. J. Chem. Phys. 113,
9978–9985 (2000).
34. M. Cas inei a Reis, e. Ma inez-nunez, A. Fe nandez-Ramos, Comp ehensi e
compu a ional au oma ed sea ch o ba ie less eac ions leading o he o ma ion o
benzene and o he C6-membe ed ings (2024). h ps://zenodo.o g/ eco ds/11175641.
35. C. h. Wu, R. d. Ke n, Shock- ube s udy o allene py olysis. J. Phys. Chem. 91, 6291–6296
(1987).
36. J. A. Mille , C. F. Melius, Kine ic and he modynamic issues in he o ma ion o a oma ic
compounds in lames o alipha ic uels. Combus . Flame 91, 21–39 (1992).
37. l. Zhao, W. lu, M. Ahmed, M. . Zagidullin, . n. Azyazo , A. n. Mo ozo , A. M. Mebel,
R. i. Kaise , Gas- phase syn hesis o benzene ia he p opa gyl adical sel - eac ion. Sci.
Ad . 7, eab 0360 (2021).
38. W. ang, R. S. an e , K. B ezinsky, isome ic p oduc dis ibu ions om he sel - eac ion o
p opa gyl adicals. J. Phys. Chem. A 109, 6056–6065 (2005).
39. M. e. law, P. R. Wes mo eland, . A. Cool, J. Wang, n. hansen, C. A. aa jes, . Kaspe ,
Benzene p ecu so s and o ma ion ou es in a s oichiome ic cyclohexane lame. P oc.
Combus . Ins . 31, 565–573 (2007).
40. e. h. Wilson, S. K. A eya, A. Cous enis, Mechanisms o he o ma ion o benzene in he
a mosphe e o i an. J. Geophys. Res. Plane s 108, 5014 (2003).
41. S. G een, e. he bs , Me as able isome s: A new class o in e s ella molecules. As ophys. J.
229, 121 (1979).
42. A. Yokoyama, X. Zhao, e. J. hin sa, R. e. Con ine i, Y. . lee, Molecula beam s udies o
hepho odissocia ion o benzene a 193 and 248 nm. J. Chem. Phys. 92, 4222–4233
(1990).
43. J. M. hollis, P. R. Jewell, F. J. lo as, Con i ma ion o in e s ella me hylene. As ophys. J.
438, 259 (1995).
44. h. Feuch g ube , F. P. helmich, e. F. an dishoeck, C. M. W igh , de ec ion o in e s ella
Ch3. As ophys. J. 535, l111–l114 (2000).
45. K. d. ucke , M. l. Ku ne , P. haddeus, he e hynyl adical C2h–A new in e s ella
molecule. As ophys. J. 193, l115–l119 (1974).
46. J. Ce nicha o, C. A. Go lieb, M. Guélin, . C. Killian, G. Paube , P. haddeus, J. M. ilek,
As onomical de ec ion o h2CCC. As ophys. J. 368, l39 (1991).
47. J. Ce nicha o, C. Cabezas, M. Agúndez, B. e ce o, n. Ma celino, J. R. Pa do, F. e ce o,
J. d. Gallego, J. A. lópez- Pé ez, P. de icen e, disco e y o allenyl ace ylene, h2CCChCCh,
in MC- 1. A s udy o he isome s o C5h4. As on. As ophys. 647, l3 (2021).
48. J. Ce nicha o, M. Guelin, C. M. Walmsley, de ec ion o he hype ine s uc u e o he C5h
adical. As on. As ophys. 172, l5 (1987).
49. W. d. lange , . elusamy, . B. h. Kuipe , R. Peng, M. C. McCa hy, M. J. a e s, A. Ko ács,
C. A. Go lieb, P. haddeus, Fi s as onomical de ec ion o he cumulene ca bon chain
molecule h2C6 in MC- 1. As ophys. J. 480, l63 (1997).
50. J. Ce nicha o, C. A. Go lieb, M. Guélin, . C. Killian, G. Paube , P. haddeus, J. M. ilek,
As onomical de ec ion o h2CCCC. As ophys. J. 368, l43 (1991).
51. P. haddeus, J. M. ilek, C. A. Go lieb, P. haddeus, J. M. ilek, C. A. Go lieb, labo a o y
and as onomical iden i ica ion o cyclop openylidene, C3H2. As ophys. J. 299, l63
(1985).
52. Y. Guo, X. Gu, F. Zhang, A. M. Mebel, R. i. Kaise , A c ossed molecula beam s udy on he
o ma ion o hexenediynyl adicals (h2CCCCCCh; C6h3 (X2A′)) ia eac ions o ica bon
molecules, C3 (
X1
Σ
+
g
), wi h allene (h2CCCh2; X1A1) and me hylace ylene (Ch3CCh; X1A1).
Phys. Chem. Chem. Phys. 9, 1972 (2007).
53. K. W. hinkle, J. J. Keady, P. F. Be na h, de ec ion o C3 in he ci cums ella shell o
iRC+10216. Science 241, 1319–1322 (1988).
54. C. Cabezas, M. Agúndez, R. Fuen e aja, Y. endo, n. Ma celino, B. e ce o, J. R. Pa do,
P. de icen e, J. Ce nicha o, disco e y o he cyclic C5h adical in MC- 1. As on. As ophys.
663, l2 (2022).
55. P. haddeus, C. A. Go lieb, A. hjalma son, l. e. B. Johansson, W. M. i ine, P. F ibe g,
R. A. linke, As onomical iden i ica ion o he C3h adical. As ophys. J., Le . Ed. 294,
l49–l53 (1985).
56. S. Yamamo o, S. Sai o, M. Ohishi, h. Suzuki, S.- i. ishikawa, n. Kai u, A. Mu akami,
labo a o y and as onomical de ec ion o he cyclic C3h adical. As ophys. J. 322, l55
(1987).
57. J. G. Mangum, A. Woo en, Obse a ions o he cyclic C3h adical in he in e s ella
medium. As on. As ophys. 239, 319 (1990).
58. R. Fuen e aja, M. Agúndez, C. Cabezas, B. e ce o, n. Ma celino, J. R. Pa do, P. de icen e,
J. Ce nicha o, disco e y o wo new in e s ella molecules wi h QUiJO e: hCCChCCC and
hCCCCS. As on. As ophys. 667, l4 (2022).
59. J. J. P. S ewa , Op imiza ion o pa ame e s o semiempi ical me hods i: Mo e
modi ica ions o he nddO app oxima ions and e- op imiza ion o pa ame e s. J. Mol.
Model. 19, 1–32 (2013).
60. J. J. P. S ewa , “MOPAC2016,” 2016; h p://openmopac.ne /MOPAC2016.h ml; 10 h May 2024.
61. Y. Zhao, d. G. uhla , explo ing he limi o accu acy o he global hyb id me a densi y
unc ional o main- g oup he mochemis y, kine ics, and nonco alen in e ac ions.
J.Chem. Theo y Compu . 4, 1849–1868 (2008).
62. A. d. Becke, densi y- unc ional he mochemis y. iii. he ole o exac exchange. J. Chem.
Phys. 98, 5648–5652 (1993).
63. M. J. F isch, G. W. ucks, h. B. Schlegel, G. e. Scuse ia, M. A. Robb, J. R. Cheeseman,
G. Scalmani, . Ba one, G. A. Pe e sson, h. naka suji, X. li, M. Ca ica o, A. . Ma enich,
J. Bloino, B. G. Janesko, R. Gompe s, B. Mennucci, h. P. h a chian, J. . O iz, A. F. izmaylo ,
J. l. Sonnenbe g, d. Williams- Young, F. ding, F. lippa ini, F. egidi, J. Goings, B. Peng,
A. Pe one, . hende son, d. Ranasinghe, . G. Zak zewski, J. Gao, n. Rega, G. Zheng,
W. liang, M. hada, M. eha a, K. oyo a, R. Fukuda, J. hasegawa, M. ishida, . nakajima,
Y. honda, O. Ki ao, h. nakai, . e en, K. h ossell, J. A. Mon gome y, J ., J. e. Pe al a,
F. Oglia o, M. J. Bea pa k, J. J. heyd, e. n. B o he s, K. n. Kudin, . n. S a o e o , . A. Kei h,
R. Kobayashi, J. no mand, K. Ragha acha i, A. P. Rendell, J. C. Bu an , S. S. iyenga ,
J. omasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, J. W. Och e ski,
R. l. Ma in, K. Mo okuma, O. Fa kas, J. B. Fo esman, d. J. Fox, Gaussian 16 Re ision B.01
(Gaussian inc., 2016).
Downloaded om h ps://www.science.o g a Uni e sidade de San iago de Compos ela on Decembe 19, 2024