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Fast approximate methods for calculating nucleic acid base pair interaction energies
Author(s) -
Sherer Edward C.,
York Darrin M.,
Cramer Christopher J.
Publication year - 2002
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.10150
Subject(s) - base (topology) , diatomic molecule , density functional theory , electronic structure , pentamer , statistical physics , computational chemistry , chemistry , computer science , mathematics , physics , quantum mechanics , molecule , mathematical analysis , biochemistry
Interaction enthalpies for six base pairs have been computed at a variety of efficient levels of electronic structure theory and compared to experiment. In addition to previously defined levels of theory, modified Hamiltonians with adjusted parameters in hybrid Hartree–Fock/density functionals and semiempirical neglect‐of‐diatomic‐differential‐overlap models were examined. Of the pure and hybrid density functional levels, m PWPW91/MIDI! performed most satisfactorily, as judged by comparison not only to the available experimental data, but also to data from more robust electronic structure methods for 22 additional base pairs. The low computational cost of the m PWPW91/MIDI! model was further exploited in an investigation of various base trimers, tetramers, and one base pentamer. A carefully reparameterized semiempirical model, PM3 BP , was able to achieve similar levels of accuracy at a still greater savings in terms of computational effort. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 57–67, 2003