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DFT plus PCM calculation for pairing specificity of Watson–Crick‐type bases in aqueous solutions
Author(s) -
Pacureanu Liliana,
Simon Zeno
Publication year - 2010
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.22216
Subject(s) - chemistry , tautomer , aqueous solution , steric effects , hydrogen bond , base pair , enthalpy , enol , dna , computational chemistry , thermodynamics , crystallography , stereochemistry , molecule , organic chemistry , physics , biochemistry , catalysis
This study is aimed at explaining the preference for AT and CG pairings and the possible insertion of other tautomeric DNA base pairs such as G enol T, that respect energetic and steric requirements including at least two hydrogen bonds and 11 ± 0.5Å distance between the 9‐CH 3 of purine and 5‐CH 3 of pyrimidine. The calculated free energy of formation ΔΔ G at the DFT B3LYP/6‐31G*‐PCM/BEM level pointed out the CG and AT pairs as the most favored, followed closely by G enol T, in good agreement with Michaelis–Menten first order kinetics (CG ≈ AT > G enol T). Unusual DNA base pairs complexes such as AG (BEM) and CT (PCM) resulted to be stable, but it is very difficult to assume that they are likely to be included in the double strand DNA. The calculated enthalpy and dipole moments of isolated DNA bases agree well with experiment. The free energy of hydration, Δ G hyd , was found to depend on the electrostatic term, while cavitation‐dispersion components are almost constant. The stability of DNA complexes in water resulted from PCM calculations is markedly influenced by the free energy of hydration. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010