New Publications

An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations

Kwangho Nam, Jiali Gao, Darrin M. York
J. Chem. Theory Comput., (2005) 1, 2-13
DOI: 10.1021/ct049941i Download PDF

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Kinetic isotope effects on thio-substituted biological phosphoryl transfer reactions from density-functional theory

Yun Liu, Xabier Lopez, Darrin M. York
Chem. Commun., (2005) 31, 3909-3911
DOI: 10.1039/B502568K Download PDF

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Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes

Evelyn Mayaan, Kevin Range, Darrin M. York
J. Biol. Inorg. Chem., (2004) 9, 807-817
DOI: 10.1007/s00775-004-0608-2 Download PDF

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Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods

Jana Khandogin, Darrin M. York
Proteins, (2004) 56, 724-737
DOI: 10.1002/prot.20171 Download PDF

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Pseudorotation of natural and chemically modified biological phosphoranes: implications for RNA catalysis

Carlos Silva Lopez, Olalla Nieto Faza, Brent A. Gregersen, Xabier Lopez, Angel Rodriguez de Lera, Darrin M. York
Chem. Phys. Chem., (2004) 5, 1045-1049
DOI: 10.1002/cphc.200400091 Download PDF

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Hybrid QM/MM study of thio effects in transphosphorylation reactions: the role of solvation

Brent A. Gregersen, Xabier Lopez, Darrin M. York
J. Am. Chem. Soc., (2004) 126, 7504–7513
DOI: 10.1021/ja031815l Download PDF

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Many-body force field models based solely on pairwise Coulomb screening do not simultaneously reproduce correct gas-phase and condensed-phase polarizability limits

Timothy J. Giese, Darrin M. York
J. Chem. Phys., (2004) 120, 9903-9906
DOI: 10.1063/1.1756583 Download PDF

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Theoretical Study of the Vinyl Allene Oxide to Cyclopent-2-en-1-one Rearrangement:  Mechanism, Torquoselectivity and Solvent Effects

Carlos Silva Lopez, Olalla Nieto Faza, Darrin M. York, Angel Rodriguez de Lera
J. Org. Chem., (2004) 69, 3635-3644
DOI: 10.1021/jo049620z Download PDF

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Complete basis set extrapolated potential energy, dipole, and polarizability surfaces of alkali halide ion-neutral weakly avoided crossings with and without applied electric fields

Timothy J. Giese, Darrin M. York
J. Chem. Phys., (2004) 120, 7939
DOI: 10.1063/1.1690232 Download PDF

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The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution

Kevin Range, Matthew J. McGrath, Xabier Lopez, Darrin M. York
J. Am. Chem. Soc., (2004) 126, 1654–1665
DOI: 10.1021/ja0356277 Download PDF

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