York DM - Search Results

1

Molecular simulations of RNA 2'-O-transesterification reaction models in solution.

Radak BK, Harris ME, York DM. Radak BK, et al. Among authors: york dm. J Phys Chem B. 2013 Jan 10;117(1):94-103. doi: 10.1021/jp3084277. Epub 2012 Dec 24. J Phys Chem B. 2013. PMID: 23214417 Free PMC article.

2

Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer.

Range K, Riccardi D, Cui Q, Elstner M, York DM. Range K, et al. Among authors: york dm. Phys Chem Chem Phys. 2005 Aug 21;7(16):3070-9. doi: 10.1039/b504941e. Epub 2005 Jul 7. Phys Chem Chem Phys. 2005. PMID: 16186912

3

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

Gregersen BA, York DM. Gregersen BA, et al. Among authors: york dm. J Phys Chem B. 2005 Jan 13;109(1):536-56. doi: 10.1021/jp0469968. J Phys Chem B. 2005. PMID: 16851046

4

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation.

Khandogin J, Gregersen BA, Thiel W, York DM. Khandogin J, et al. Among authors: york dm. J Phys Chem B. 2005 May 19;109(19):9799-809. doi: 10.1021/jp044062d. J Phys Chem B. 2005. PMID: 16852180

5

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 2. Application to transphosphorylation thio effects in solution.

Gregersen BA, Khandogin J, Thiel W, York DM. Gregersen BA, et al. Among authors: york dm. J Phys Chem B. 2005 May 19;109(19):9810-7. doi: 10.1021/jp044061l. J Phys Chem B. 2005. PMID: 16852181

6

Theoretical studies of dissociative phosphoryl transfer in interconversion of phosphoenolpyruvate to phosphonopyruvate: solvent effects, thio effects, and implications for enzymatic reactions.

Xu D, Guo H, Liu Y, York DM. Xu D, et al. Among authors: york dm. J Phys Chem B. 2005 Jul 21;109(28):13827-34. doi: 10.1021/jp051042i. J Phys Chem B. 2005. PMID: 16852731

7

Density functional study of the in-line mechanism of methanolysis of cyclic phosphate and thiophosphate esters in solution: insight into thio effects in RNA transesterification.

Liu Y, Gregersen BA, Lopez X, York DM. Liu Y, et al. Among authors: york dm. J Phys Chem B. 2005 Oct 27;109(42):19987-20003. doi: 10.1021/jp053146z. J Phys Chem B. 2005. PMID: 16853584

8

Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes.

Formoso E, Matxain JM, Lopez X, York DM. Formoso E, et al. Among authors: york dm. J Phys Chem B. 2010 Jun 3;114(21):7371-82. doi: 10.1021/jp909004y. J Phys Chem B. 2010. PMID: 20455590 Free PMC article.

9

Characterization of the reaction path and transition states for RNA transphosphorylation models from theory and experiment.

Wong KY, Gu H, Zhang S, Piccirilli JA, Harris ME, York DM. Wong KY, et al. Among authors: york dm. Angew Chem Int Ed Engl. 2012 Jan 16;51(3):647-51. doi: 10.1002/anie.201104147. Epub 2011 Nov 11. Angew Chem Int Ed Engl. 2012. PMID: 22076983 Free PMC article. No abstract available.

10

Characterization of the Structure and Dynamics of the HDV Ribozyme at Different Stages Along the Reaction Path.

Lee TS, Giambaşu G, Harris ME, York DM. Lee TS, et al. Among authors: york dm. J Phys Chem Lett. 2011 Oct 20;2(20):2538-2543. doi: 10.1021/jz201106y. J Phys Chem Lett. 2011. PMID: 22200005 Free PMC article.

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