The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine-thymine and guanine-cytosine base pairs

J Comput Aided Mol Des (2010) 24:409416 DOI 10.1007/s10822-010-9348-2

The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adeninethymine and guaninecytosinebase pairs

A. Ebrahimi S. M. Habibi Khorassani

H. Delarami H. Esmaeeli

Received: 12 December 2009 / Accepted: 18 March 2010 / Published online: 30 March 2010 Springer Science+Business Media B.V. 2010

Abstract The substituent effects on the geometrical parameters and the individual hydrogen bond (HB) energies of base pairs such as Xadeninethymine (XAT), Xthymineadenine (XTA), Xguaninecytosine (X GC), and Xcytosineguanine (XCG) have been studied by the quantum mechanical calculations at the B3LYP and MP2 levels with the 6311??G(d,p) basis set. The electron withdrawing (EW) substituents (F and NO2)

increase the total binding energy (DE) of XGC derivatives and the electron donating (ED) substituent (CH3)

decreases it when they are introduced in the 8 and 9 positions of G. The effects of substituents are reversed when they are located in the 1, 5, and 6 positions of C, with exception of CH3 in the 1 position and F in the 5 position, which in both cases the DE value decreases negligibly small. With minor exceptions (X=8CH3, 8F, and 9

NO2), both ED and EW substituents increase slightly the DE values of XAT derivatives. The individual HB energies (DEHBs) have been estimated using electron densities that calculated at the hydrogen bond critical points (HBCPs) by the atoms in molecules (AIM) method. Most of changes of individual HBs are in consistent with the ED/EW nature of substituents and the role of atoms entered H-bonding. The remarkable change is observed for NO2 substituted derivative in each case.

Keywords Individual hydrogen bond Electron density

Base pair Adeninethymine Guaninecytosine

Introduction

The hydrogen bond formation in WatsonCrick type base pairs is fundamental for molecular recognition in the duplex formation of nucleic acids [1, 2]. It is also essential for the transmission of genetic information [1, 3]. Many studies have been performed on the natural nucleic acid base pairs [1, 46].

The difference in exibility between adeninethymine (AT) and guaninecytosine (GC) base pairs may be an additional factor for molecular recognition during the binding of other molecules to DNA, especially in the case of intercalation processes [7, 8]. Several ab initio molecular orbital studies on...