Darrin M. York

Multipolar Ewald Methods. I. Theory, Accuracy, and Performance

J. Chem. Theory Comput., (2015) 11, 436-450
DOI: 10.1021/ct5007983 Download PDF

Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

RNA, (2015) 21, 963-974
DOI: 10.1261/rna.047357.114 Download PDF

Multipolar Ewald Methods. II. Applications Using a Quantum Mechanical Force Field

J. Chem. Theory Comput., (2015) 11, 451-461
DOI: 10.1021/ct500799g Download PDF

Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations

J. Chem. Theory Comput., (2015) 11, 373-377
DOI: 10.1021/ct500776j Download PDF

Effect of Zn2+ binding and enzyme active site on the transition state for RNA 2'-O-transphosphorylation interpreted through kinetic isotope effects

Biochim. Biophys. Acta, (2015) 1854, 1795-1800
DOI: 10.1016/j.bbapap.2015.02.022. Download PDF

Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation

Curr. Opin. Chem. Biol., (2014) 21C, 96-102
DOI: 10.1016/j.cbpa.2014.06.010. Download PDF

Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions

Chem. Eur. J., (2014) 20, 14336-14343
DOI: 10.1002/chem.201403862 Download PDF

Recent advances toward a general purpose linear-scaling quantum force field

Acc. Chem. Res., (2014) 47, 2812–2820
DOI: 10.1021/ar500103g Download PDF

Linear Free Energy Relationships in RNA Transesterification: Theoretical Models to Aid Experimental Interpretations

Phys. Chem. Chem. Phys., (2014) 16, 15846-15855
DOI: 10.1039/C4CP01050G Download PDF

Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path

J. Am. Chem. Soc., (2014) 136, 7789-7792
DOI: 10.1021/ja500180q Download PDF

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