SUPPORTING INFORMATION
A QUANTUM THEORETICAL STUDY OF MECHANISM OF THE REACTION
BETWEEN GUANINE RADICAL CATION AND CARBONATE RADICAL
ANION: FORMATION OF 8-OXOGUANINE
Amarjeet Yadav and P. C. Mishra*
Department of Physics,
Banaras Hindu University
Varanasi – 221 005, India
Two water molecules placed near N7 play an optimal catalytic role in proton transfer at
the fourth reaction step (corresponding to TS4) of scheme 1 presented in the main body
of the paper (Fig. 2). The results obtained when a single water molecule is involved in
this reaction step are found to be as follows. The reaction step relating to formation of the
product PC1 starting from IC3 via the transition state TS5 is shown in scheme S1 (Table
S1, Fig. S1). The intermediate complex IC3 of scheme S1 is the same as that of scheme 1
(Fig. 2). Scheme S1 is different from scheme 1 in the sense that in the former case at the
transition state TS5, one water molecule is involved in proton transfer from O2 to N7
while in the latter case, at the transition state TS4, this process is accomplished by two
water molecules (Fig. 2). As obtained at the MP2/AUG-cc-pVDZ level of theory in
chlorobenzene, the Gibbs free barrier energy (ΔG5b) involved in scheme S1 (12.7
kcal/mol) (Table S1) is larger than that involved in the corresponding step (ΔG4b) in
scheme 1 (6.9 kcal/mol) (Table 2). Thus two water molecules catalyze the proton transfer
reaction step in question much more efficiently than a single water molecule.
Transfer of the H8 proton from C8 can also occur directly to N7 without the involvement
of any water molecule as shown in scheme S2 (Table S2, Fig. S2). At the MP2/AUG-ccpVDZ level of theory in chlorobenzene, this process is associated with the Gibbs free
barrier energy (ΔG6b) of 11.0 kcal/mol (Fig. S2) which is 1.7 kcal/mol less than that when
the proton transfer occurs from O2 to N7 through one water molecule as discussed above
(Fig. S1) but is 4.1 kcal/mol higher than that when the proton transfer occurs through two
water molecules (Fig. 1) (Table 2). Thus we find that involvement of one water molecule
does not reduce the barrier energy of proton transfer from O2 to N7 in comparison to the
situation when no water molecule is involved in the same process while the involvement
of two water molecules does so. As discussed in the main body of the paper, one water
molecule catalyzes proton transfer from C8 to O2, the corresponding Gibbs free barrier
energy in chlorobenzene at the MP2/AUG-cc-pVDZ level of theory being 8.9 kcal/mol
(Table 2).
The reaction steps starting from IC2 to the product PC3 (8-oxoG complexed with three
water molecules) can also occur without the explicit involvement of any water molecule
in proton transfer, though with higher Gibbs free barriers than those of the Schemes 1, S1
and S2 (Figs. 1, S1, S2), as shown in Scheme S3 (Fig. S3). In scheme S3 (Table S3),
TS7, IC4 and TS8 correspond to TS3, IC3 and TS4 of scheme 1 respectively. The Gibbs
free barrier energies corresponding to TS3 and TS4 as obtained at the MP2/AUG-ccPVDZ level of theory in chlorobenzene (Table 1) are 8.9 and 6.9 kcal/mol respectively
(scheme 1) while the barrier energies corresponding to TS7 and TS8 (scheme S3, Fig. S3)
(ΔG7b, ΔG8b) are 22.8 and 37.4 kcal/mol respectively (Table S3). Thus the Gibbs free
barrier energies are significantly enhanced in going from scheme 1 to scheme S3 due to
the water molecules not being involved in proton transfer in the latter scheme.
The product complexes PC1, PC2 and PC3 are different from PC (scheme 1, Fig. 1) in
the sense that locations and orientations of the water molecules are different in these
different cases.
Table S1. Gibbs free barrier (ΔGb) and released energies (ΔGr) (kcal/mol) involved in
reaction of guanine radical cation (G.+ ) and carbonate radical anion (CO3.-) with three
water molecules in gas phase, aqueous media and chlorobenzene according to scheme
S1a.
Gibbs free
barrier and
released
energies
a
B3LYP/
6-31G**
B3LYP/
AUG-cc-pVDZ
BHandHLYP/
AUG-cc-pVDZ
MP2/
AUG-cc-pVDZ
ΔG5b
11.7(15.9)
12.4(16.7)
16.6(18.4)
11.2(13.0)[12.7]
ΔG5r
-21.2(-24.6)
-19.7(-23.4)
-23.8(-25.3)
-17.9(-18.5)[-18.0]
Quantities given in parentheses corresponds to aqueous media while those given in
brackets in the last column correspond to chlorobenzene.
Table S2. Gibbs free barrier (ΔGb) and released energies (ΔGr) (kcal/mol) involved in
reaction of guanine radical cation (G.+ ) and carbonate radical anion (CO3.-) with three
water molecules in gas phase, aqueous media and chlorobenzene according to scheme
S2a.
Gibbs free
barrier and
released
energies
a
B3LYP/
6-31G**
ΔG6b
9.3(12.7)
ΔG6r
-66.9(-60.7)
B3LYP/
AUG-cc-pVDZ
8.0(9.3)
-66.4(-58.1)
BHandHLYP/
AUG-cc-pVDZ
MP2/
AUG-cc-pVDZ
11.7(13.5)
9.2(10.9)[11.0]
-72.6(-65.8)
-68.3(-60.9)[-66.1]
Quantities given in parentheses corresponds to aqueous media while those given in
brackets in the last column correspond to chlorobenzene.
Table S3. Gibbs free barrier (ΔGb) and released energies (ΔGr) (kcal/mol) involved in
reaction of guanine radical cation (G.+) and carbonate radical anion (CO3.-) with three
water molecules in gas phase, aqueous media and chlorobenzene according to scheme
S3a.
Gibbs free
barrier and
released
energies
a
B3LYP/
6-31G**
B3LYP/
AUG-cc-pVDZ
BHandHLYP/
AUG-cc-pVDZ
MP2/
AUG-cc-pVDZ
ΔG7b
26.4(26.6)
24.7(26.2)
38.8(26.2)
21.1(21.7)[22.8]
ΔG7r
-63.7(-60.1)
-64.5(-61.6)
-81.9(-61.6)
-69.6(-64.2)[-64.6]
ΔG8b
32.1(39.2)
34.0(39.6)
38.8(39.6)
39.5(41.0)[37.4]
ΔG8r
-52.5(-53.7)
-52.5(-52.9)
-57.6(-52.9)
-54.7(-56.1)[-54.6]
Quantities given in parentheses corresponds to aqueous media while those given in
brackets in the last column correspond to chlorobenzene.
C8O2=1.28
O2C1=2.86
[-0.03]
[-0.04]
N7
C1
C8
O2
N9
TS5
ΔG5b=12.7
ΔG5r=-18.0
IC3
O2C1=2.84
C8O2=1.23
C8N9=1.39
N7
O2
PC1
C8
N9
[0.12]
[-0.03]
N7
C1
C1
C8
O2
C8
N9
Scheme S1
Fig S1: Structures of intermediate complex (IC3), transition state (TS5) and product complex (PC1)
involved in reaction of guanine radical cation (G.+) and carbonate radical anion (CO3.-) along with
Gibbs free barrier energies (kcal/mol) at MP2/AUG-cc-pVDZ level of theory in chlorobenzene are
given (not to scale). Some important interatomic distances (Å) and CHelpG charges (in brackets)
are also given.
[0.03]
N7
H8
O2
N9
C8
C1
C802=1.25
C8H8=1.24
N9H8=1.51
O2C1=2.86
[-0.02]
TS6
ΔG6b= 11.0
IC2
N7
C8
ΔG6r=-66.1
O2
N9
C1
C802=1.22
O2C1=3.05
N7H8=1.00
C8N9=1.37
PC2
[0.08]
H8
[-0.02]
O2
N7
C8
C1
N9
Scheme S2
Fig S2: Structures of intermediate complexes (IC2), transition state (TS6) and product complex
(PC2) involved in reaction of guanine radical cation (G.+) and carbonate radical anion (CO3.-) along
with Gibbs free barrier energies (kcal/mol) at MP2/AUG-cc-pVDZ level of theory in chlorobenzene
are given (not to scale). Some important interatomic distances (Å) and CHelpG charges (in
brackets) are also given.
O2C1=4.5
C8H8=1.2
H8O2=1.4
C8N9=1.4
[-0.12]
C8O2=1.3
O2C1=3.4
O2H8=1.3
O2C1=3.4
N7
O2
C8
[0.02]
N9
[-0.12]
C1
TS7
N7
[-0.02]
O2
ΔG5b=22.8
C8
C1
IC2
TS8
N7
ΔG5r=-64.6
O2
C8
ΔG5b=37.4
C1
N9
ΔG5r=-54.6
C8O2=1.23
O2C1=3.30
N7H8=1.00
C8N9=1.39
IC4
[0.05]
PC3
N7
[-0.01]
[0.11]
C8 O2
C1
N9
O2
N7
C8
[-0.02]
C1
N9
C8O2=1.26
O2C1=3.21
O2H8=0.97
Scheme S3
Fig S3: Structures of intermediate complex (IC2, IC4), transition states (TS7, TS8) and product complex
(PC4) involved in reaction of guanine radical cation (G.+) and carbonate radical anion (CO3.-) along with
Gibbs free barrier energies (kcal/mol) at MP2/AUG-cc-pVDZ level of theory in chlorobenzene are given
(not to scale). Some important interatomic distances (Å) and CHelpG charges (in brackets) are also
given.