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. Author manuscript; available in PMC: 2012 Dec 1.
Published in final edited form as: J Phys Chem B. 2011 Nov 8;115(47):13911–13924. doi: 10.1021/jp206963g

Table 3.

Computed reaction Gibbs energy barriers in kcal/mol of various paths representing the proton shuttling and G8- general base reaction mechanisms (see Tables S4a, S4b in Supporting Information for the MPW1K/6-31+G(d,p) and BLYP/6-31G(d) reaction barriers without any corrections).a

Rb TS1c IN1 TS2 IN2 TS3 P
pro-RP/pro-RP/G8/A38H+ 2.1 21.0 3.3 9.6 4.7 4.5 -16.9
pro-RP/A+/G8/A38H+ 2.1 21.0 3.3 9.6 4.7 3.8 -7.4
pro-RP/pro-RP/G8t/A38H+ 2.1 25.7 3.9 10.8 5.7 6.1 -13.2
pro-RP/pro-RP/G8/A38 0.0 20.5 4.0 12.9 4.5 12.2 -12.8
pro-SP/pro-SP/G8/A38H+ 2.1 23.0 11.3 14.9 5.6 6.3 -11.6
pro-SP/pro-SP/G8t/A38H+ 2.1 30.3 14.4 16.5 8.2 5.3 -8.5
pro-SP/pro-SP/G8/A38 0.0 23.2 16.1 18.1 8.9 11.5 -8.1
G-/A+/G8/A38H+d 5.5 20.4 -13.9
a

The Gibbs energies are composed of QM/MM energy calculated at MPW1K/6-31+G(d,p):AMBER level, the Gibbs energy correction obtained from the reference reaction at MPW1K/6-31+G(d,p) level (see Methods) and the correction to respective protonation state of adenine A38 and guanine G8.

b

The energies of reactants containing protonated adenine or deprotonated guanine are corrected by the Gibbs energy required to protonate A38 or deprotonated G8, considering recent estimated adenine A38 pKa of 5.534 (2.1 kcal/mol at 300 K) and guanine G8 pKa of 9.526 (3.4 kcal/mol at 300K).

c

The highest Gibbs energy (corresponding to the rate-limiting step) is shown in bold.

d

The G8- general base reaction mechanism involves only one transition state and no intermediate.