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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 4.

The Gibbs energy profiles in kcal/mol of the pro-RP/pro-RP/G8/A38H+ reaction mechanism with the thio-substitution on one or both non-bridging oxygens.a

Rb TS1c IN1 TS2 IN2 TS3 P
pro-RP thio-analog 2.1 21.1 8.5 13.0 8.3 7.4 -14.5
pro-SP thio-analog 2.1 21.9 7.8 12.3 11.3 9.0 -14.6
pro-RP/pro-SP thio-analog 2.1 20.8 10.3 13.2 6.6 7.5 -15.0
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 the Supporting Information, Tables S5a, S5b, S5c) and the correction to protonation state of adenine A38.

b

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

c

The highest Gibbs energy barrier is shown in bold.