| Electron correlated ab initio study of amino group flexibility for improvement of molecular mechanics simulations on nucleic Acid conformations and interactions. | |
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MedLine Citation:
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PMID: 19669535 Owner: NLM Status: In-Data-Review |
Abstract/OtherAbstract:
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High level ab initio studies demonstrate substantial conformational flexibility of amino groups of nucleic acid bases. This flexibility is important for biological functions of DNA. Existing force field models of molecular mechanics do not describe this phenomenon due to a lack of quantitative experimental data necessary for an adjustment of empirical parameters. We have performed extensive calculations of nucleic acid bases at the MP2/6-31G(d,p) level of ab initio theory for broad set of amino group configurations. Two-dimensional maps of energy and geometrical characteristics as functions of two amino hydrogen torsions have been constructed. We approximate the maps by polynomial expressions, which can be used in molecular mechanics calculations. Detailed considerations of these maps enable us to propose a method for determination of numerical coefficients in the developed formulae using restricted sets of points obtained via higher-level calculations. |
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Authors:
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V I Poltev; E Gonzalez; A Deriabina; A Martinez; A Furmanchuk; L Gorb; J Leszczynski |
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Publication Detail:
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Type: Journal Article Date: 2008-07-18 |
Journal Detail:
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Title: Journal of biological physics Volume: 33 ISSN: 0092-0606 ISO Abbreviation: J Biol Phys Publication Date: 2007 Dec |
Date Detail:
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Created Date: 2009-08-11 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 0417731 Medline TA: J Biol Phys Country: Netherlands |
Other Details:
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Languages: eng Pagination: 499-514 Citation Subset: - |
Affiliation:
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Physics and Mathematics Department, Puebla Autonomous University, Puebla, 72570, Pue, Mexico, poltev@fcfm.buap.mx. |
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