Substituent effect of large conjugate groups on the DNA base pair derivatives: Density functional study

Abstract

AbstractThe substituent effects caused by 2‐nitro‐naphthalen (aNO2), 2‐hydroxyl‐naphthalen (aOH), 1‐nitro‐4‐vinyl‐benzene (bNO2), and 1‐hydroxyl‐4‐vinyl‐benzene (bOH) have been investigated in this report. The geometries of various substituted base pairs have been optimized using the B3LYP method at the 6‐31G* level with no constraints. The vertical ionization potential energy has been calculated. Natural bond orbital (NBO) and CHelp analyses have also been carried out on both the neutral and cationic systems at the same level. The outcomes show that the hydrogen bond lengths of these substituted base pairs are similar to unsubstituted bases, while the geometries of the substituted bases have an interesting aspect; i.e., the substituent and the substituted base are nonplanar when the substituted base is pyrimide, while it is coplanar when the substituted base is purine. The stabilization energies changed slightly as compared with the corresponding A:T or G:C base pairs. NBO analysis shows that charge transfer is the largest in aOH‐T:A, while it is small in the other derivatives. Population analysis shows that the NPA and Mulliken charge of H has a relationship with the H‐bond lengths, while that of Chelp does not. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005