Parameterization of semiempirical methods to treat nucleophilic attacks to biological phosphates: AM1/d parameters for phosphorus |
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Authors: | Xabier Lopez Darrin M York |
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Institution: | (1) Kimika Fakultatea, Euskal Herriko Unibertsitatea, P.K. 1072, 20080 Donostia, Euskadi, Spain, ES;(2) Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA, US |
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Abstract: | This paper reports a new AM1/d model for phosphorus that can be used to model nucleophilic attack of phosphates relevant
for biological phosphate hydrolysis reactions. The parameters were derived from a quantum dataset calculated with hybrid density-functional
theory B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p)] of phosphates and phosphoranes in various charge states, and on transitions
states for nucleophilic attacks. A suite of non-linear optimization methods is outlined for semiempirical parameter development
based on integrated evolutionary (genetic), Monte Carlo simulated annealing and direction set minimization algorithms. The
performance of the new AM1/d model and the standard AM1 and MNDO/d models are compared with the density-functional results.
The results demonstrate that the strategy of developing semiempirical parameters specific for biological reactions offers
considerable promise for application to large-scale biological problems.
Received: 15 January 2002 / Accepted: 6 September 2002 / Published online: 28 March 2003
Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American
Chemical Society, 2001
Correspondence to: D.M. York e-mail: york@chem.umn.edu
Acknowledgements. D.M.Y. is grateful for financial support provided by the National Institutes of Health (grant 1R01-GM62248-01A1) and the
Donors of The Petroleum Research Fund, administered by the American Chemical Society, and the Minnesota Supercomputing Institute
through a 6-month research scholar award (X.L.). Computational resources were provided by the Minnesota Supercomputing Institute. |
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Keywords: | : Semiempirical model – AMI/d parameters for phosphorus – Nucleophilic reaction – Phosphate |
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