Polarizable model potential function for nucleic acid bases

✍ Scribed by Setsuko Nakagawa

• Publisher: John Wiley and Sons
• Year: 2007
• Tongue: English
• Weight: 643 KB
• Volume: 28
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.20643

✦ Synopsis

Abstract

A polarizable model potential (PMP) function for adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) is developed on the basis of ab initio molecular orbital calculations at the MP2/6‐31+G* level. The PMP function consists of Coulomb, van der Waals, and polarization terms. The permanent atomic charges of the Coulomb term are determined by using electrostatic potential (ESP) optimization. The multicenter polarizabilities of the polarization term are determined by using polarized one‐electron potential (POP) optimization in which the electron density changes induced by a test charge are target. Isotropic and anisotropic polarizabilities are adopted as the multicenter polarizabilities. In the PMP calculations using the optimized parameters, the interaction energies of Watson–Crick type A‐T and C‐G base pairs were −15.6 and −29.4 kcal/mol, respectively. The interaction energy of Hoogsteen type A‐T base pair was −17.8 kcal/mol. These results reproduce well the quantum chemistry calculations at the MP2/6‐311++G(3df,2pd) level within the differences of 0.6 kcal/mol. The stacking energies of A‐T and C‐G were −9.7 and −10.9 kcal/mol. These reproduce well the calculation results at the MP2/6‐311++G (2d,2p) level within the differences of 1.3 kcal/mol. The potential energy surfaces of the system in which a sodium ion or a chloride ion is adjacent to the nucleic acid base are calculated. The interaction energies of the PMP function reproduced well the calculation results at the MP2/6‐31+G* or MP2/6‐311++G(2d,2p) level. The reason why the PMP function reproduces well the high‐level quantum mechanical interaction energies is addressed from the viewpoint of each energy terms. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007