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Polarizable model potential function for nucleic acid bases
KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
2007 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 28, no 9, 1538-1550 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2007. Vol. 28, no 9, 1538-1550 p.
Keyword [en]
polarized one-electron potential, polarizable force field, ab initio molecular orbital calculation, multicenter polarizability, nucleic acid bases
National Category
Chemical Sciences
Identifiers
URN: urn:nbn:se:kth:diva-37088DOI: 10.1002/jcc.20643ISI: 000246575500008PubMedID: 17342710Scopus ID: 2-s2.0-34249821931OAI: oai:DiVA.org:kth-37088DiVA: diva2:432046
Note

QC 20110728

Available from: 2011-07-28 Created: 2011-07-28 Last updated: 2017-12-08Bibliographically approved

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