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.
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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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Lopez, X., York, D. Parameterization of semiempirical methods to treat nucleophilic attacks to biological phosphates: AM1/d parameters for phosphorus. Theor Chem Acc 109, 149–159 (2003). https://doi.org/10.1007/s00214-002-0422-2
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DOI: https://doi.org/10.1007/s00214-002-0422-2