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New Publications

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

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

Insight into the role of Mg2+in hammerhead ribozyme catalysis from x-ray crystallography and molecular dynamics simulation

J. Chem. Theory Comput., (2007) 3, 325-327
DOI: 10.1021/ct6003142 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

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

Enzyme dynamics and tunneling enhanced by compression in the hydrogen abstraction catalyzed by soybean lipoxygenase-1

J. Phys. Chem. B., (2006) 110, 24708-24719
DOI: 10.1021/jp066263i Download PDF

Transesterification thio effects of phosphate diesters: free energy barriers and kinetic and equilibrium isotope effects from density-functional theory

Biochemistry, (2006) 45, 10043-10053
DOI: 10.1021/bi060869f 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