Rutgers Main | CIRC | Quantitative Biology   
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Darrin M. York

New QM/MM Models for Multi-scale Simulation of Phosphoryl Transfer Reactions in Solution

DOI: 10.1002/9780470191675.ch12 Download PDF

Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms

J. Chem. Theory Comput., (2007) 3, 486-504
DOI: 10.1021/ct6002466 Download PDF

Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction

J. Phys Chem. A, (2007) 111, 10861-10873
DOI: 10.1021/jp074167r Download PDF

CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes

J. Comput. Chem., (2007) 28, 495-507
DOI: 10.1002/jcc.20474 Download PDF

Charge-dependent model for many-body polarization, exchange and dispersion interactions in hybrid QM/MM calculations

J. Chem. Phys., (2007) 127, 194101
DOI: 10.1063/1.2778428 Download PDF

Normal modes of redox-active tyrosine: conformation dependence and comparison to experiment

J. Phys. Chem. B, (2006) 110, 10970-10981
DOI: 10.1021/jp061503f Download PDF

A charge-scaling implementation of the variational electrostatic projection method

J. Comput. Chem., (2006) 27, 103-115
DOI: 10.1002/jcc.20318 Download PDF

Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems

J. Phys. Chem. B., (2006) 110, 11525-11539
DOI: 10.1021/jp0603942 Download PDF

Multi-level and density functional electronic structure calculations of proton affinities and gas-phase basicities involved in biological phosphoryl transfer

J. Phys. Chem. A, (2006) 110, 7910797
DOI: 10.1021/jp054360q Download PDF

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