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  Evaluating nonpolarizable nucleic acid force fields: A systematic comparison of the nucleobases hydration free energies and water-chloroform partition coefficients.

Wolf, M. G., & Groenhof, G. (2012). Evaluating nonpolarizable nucleic acid force fields: A systematic comparison of the nucleobases hydration free energies and water-chloroform partition coefficients. Journal of Computational Chemistry, 33(28), 2225-2232. doi:10.1002/jcc.23055.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-15E9-3 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0028-3ADD-2
Genre: Journal Article

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Wolf, M. G.1, Author              
Groenhof, G.1, Author              
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1Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society, ou_578631              

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 Abstract: Nucleic acid force fields have been shown to reproduce structural properties of DNA and RNA very well, but comparative studies with respect to thermodynamic properties are rare. As a test for thermodynamic properties, we have computed hydration free energies and chloroform-to-water partition coefficients of nucleobases using the AMBER-99, AMBER-gaff, CHARMM-27, GROMOS-45a4/53a6 and OPLS-AA force fields. A mutual force field comparison showed a very large spread in the calculated thermodynamic properties, demonstrating that some of the parameter sets require further optimization. The choice of solvent model used in the simulation does not have a significant effect on the results. Comparing the hydration free energies obtained by the various force fields to the adenine and thymine experimental values showed a very large deviation for the GROMOS and AMBER parameter sets. Validation against experimental partition coefficients showed good agreement for the CHARMM-27 parameter set. In view of mutation studies, differences in partition coefficient between two bases were also compared, and good agreement between experiments and calculations was found for the AMBER-99 parameter set. Overall, the CHARMM-27 parameter set performs best with respect to the thermodynamic properties tested here. © 2012 Wiley Periodicals, Inc.

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Language(s): eng - English
 Dates: 2012-07-102012-10-30
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1002/jcc.23055
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Title: Journal of Computational Chemistry
Source Genre: Journal
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Publ. Info: New York : Wiley.
Pages: - Volume / Issue: 33 (28) Sequence Number: - Start / End Page: 2225 - 2232 Identifier: ISSN: 0192-8651
CoNE: /journals/resource/954925489848