New Publications

The contribution of phosphate-phosphate repulsions to the free energy of DNA bending

Kevin Range, Evelyn Mayaan, L. J. Maher III, Darrin M. York
Nucleic Acids Res., (2005) 33, 1257-1268
DOI: 10.1093/nar/gki272 Download PDF

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Variational Electrostatic Projection (VEP) methods for efficient modeling of the macromolecular electrostatic and solvation environment in activated dynamics simulations

Brent A. Gregersen, Darrin M. York
J. Phys. Chem. B., (2005) 109, 536-556
DOI: 10.1021/jp0469968 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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Theoretical methods that help understanding the structure and reactivity of gas phase ions

J. M. Mercero, Jon M. Matxain, Xabier Lopez, Darrin M. York, A. Largo, L. A. Eriksson, J. M. Ugalde
Int. J. Mass Spectrom., (2005) 240, 37-99
DOI: 10.1016/j.ijms.2004.09.018 Download PDF

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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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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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