Noncovalent Interactions in Extended Systems Described by the Effective Fragment Potential Method: Theory and Application to Nucleobase Oligomers

TitleNoncovalent Interactions in Extended Systems Described by the Effective Fragment Potential Method: Theory and Application to Nucleobase Oligomers
Publication TypeJournal Article
Year of Publication2010
AuthorsGhosh D, Kosenkov D, Vanovschi V, Williams CF, Herbert JM, Gordon MS, Schmidt MW, Slipchenko LV, Krylov AI
Journal TitleJournal of Physical Chemistry A
Volume114
Pages12739-12754
Date Published12/09
ISBN Number1089-5639
Accession NumberISI:000284738500023
Keywordsab-initio, base-pairs, BENZENE DIMER, damping functions, density-functional theory, DISTRIBUTED MULTIPOLE ANALYSIS, energy surface, molecular-dynamics, pi-pi-interactions, quantum-mechanical calculations
Abstract

The implementation of the effective fragment potential (EFP) method within the Q-CHEM electronic structure package is presented. The EFP method is used to study noncovalent pi-pi and hydrogen-bonding interactions in DNA strands. Since EFP is a computationally inexpensive alternative to high-level ab initio calculations, it is possible to go beyond the dimers of nucleic acid bases and to investigate the asymptotic behavior of different components of the total interaction energy. The calculations demonstrated that the dispersion energy is a leading component in pi-stacked oligomers of all sizes. Exchange-repulsion energy also plays an important role. The contribution of polarization is small in these systems, whereas the magnitude of electrostatics varies. Pairwise fragment interactions (i.e., the sum of dimer binding energies) were found to be a good approximation for the oligomer energy.

URL<Go to ISI>://000284738500023
DOI10.1021/Jp107557p
Alternate JournalJ Phys Chem A