H Lee Woodcock

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint Carbene stabilization by aryl substituents. Is bigger better?
    H Lee Woodcock
    Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602 2525, USA
    J Am Chem Soc 129:3763-70. 2007
  2. ncbi request reprint Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations
    H Lee Woodcock
    National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Comput Chem 28:1485-502. 2007
  3. pmc Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-ethoxy tetrahydropyran
    H Lee Woodcock
    Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
    Biophys J 93:1-10. 2007
  4. pmc Pathways and populations: stereoelectronic insights into the exocyclic torsion of 5-(hydroxymethyl)tetrahydropyran
    H Lee Woodcock
    Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Am Chem Soc 130:6345-7. 2008
  5. pmc Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit
    H Lee Woodcock
    Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Chem Phys 129:214109. 2008
  6. doi request reprint Characterizing the mechanism of the double proton transfer in the formamide dimer
    Jacqueline C Hargis
    Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
    J Phys Chem A 115:2650-7. 2011
  7. ncbi request reprint Exploring SCC-DFTB paths for mapping QM/MM reaction mechanisms
    H Lee Woodcock
    Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Phys Chem A 111:5720-8. 2007
  8. pmc Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H
    Edina Rosta
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    J Comput Chem 30:1634-41. 2009
  9. pmc CHARMMing: a new, flexible web portal for CHARMM
    Benjamin T Miller
    Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Chem Inf Model 48:1920-9. 2008
  10. ncbi request reprint Computation of through-space NMR shielding effects in aromatic ring pi-stacked complexes
    Ned H Martin
    Department of Chemistry and Biochemistry, University of North Carolina Wilmington, 601 S College Road, Wilmington, NC 28403 5932, USA
    J Mol Graph Model 26:1125-30. 2008

Collaborators

Detail Information

Publications11

  1. ncbi request reprint Carbene stabilization by aryl substituents. Is bigger better?
    H Lee Woodcock
    Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602 2525, USA
    J Am Chem Soc 129:3763-70. 2007
    ..e., C-C, C-H). In general, the aromaticity of the substituted rings in triplet carbenes is most affected by the presence of the unpaired electrons...
  2. ncbi request reprint Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations
    H Lee Woodcock
    National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Comput Chem 28:1485-502. 2007
    ..Our best estimate for the activation energy is 8.20 kcal/mol and for the reaction energy is -23.1 kcal/mol, both calculated at the MP2/6-31+G(d)//MP2/6-31+G(d)/C22 level of theory...
  3. pmc Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-ethoxy tetrahydropyran
    H Lee Woodcock
    Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
    Biophys J 93:1-10. 2007
    ..A comparison of vacuum and solvent-corrected one- and two-dimensional torsional surfaces indicates the equatorial form of 2-ethoxy tetrahydropyran is more sensitive to solvent than the axial...
  4. pmc Pathways and populations: stereoelectronic insights into the exocyclic torsion of 5-(hydroxymethyl)tetrahydropyran
    H Lee Woodcock
    Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Am Chem Soc 130:6345-7. 2008
    ..Solvent stabilization of theta conformations provides entropic stabilization...
  5. pmc Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit
    H Lee Woodcock
    Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Chem Phys 129:214109. 2008
    ..The VSA approach can be employed in many ways, but it will likely be most useful for estimating activation free energies in QM/MM reaction path calculations. Four examples are presented to demonstrate the utility of this method...
  6. doi request reprint Characterizing the mechanism of the double proton transfer in the formamide dimer
    Jacqueline C Hargis
    Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
    J Phys Chem A 115:2650-7. 2011
    ..The inconsistency could be assigned to the incapacity of the functional to describe delocalization effects over the whole system...
  7. ncbi request reprint Exploring SCC-DFTB paths for mapping QM/MM reaction mechanisms
    H Lee Woodcock
    Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Phys Chem A 111:5720-8. 2007
    ..For instance, RPATh can effectively use the adopted basis Newton-Raphson (ABNR) minimizer, where NEB seems to require a combination of SD and ABNR...
  8. pmc Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H
    Edina Rosta
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    J Comput Chem 30:1634-41. 2009
    ..The method used to identify important degrees of freedom, and the procedure to optimize the reaction coordinate are general and should be useful both in classical and in QM/MM free-energy calculations...
  9. pmc CHARMMing: a new, flexible web portal for CHARMM
    Benjamin T Miller
    Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Chem Inf Model 48:1920-9. 2008
    ..Although no software can replace a scientist's own judgment and experience, CHARMMing eases the introduction of newcomers to the molecular modeling discipline by providing a graphical method for running simulations...
  10. ncbi request reprint Computation of through-space NMR shielding effects in aromatic ring pi-stacked complexes
    Ned H Martin
    Department of Chemistry and Biochemistry, University of North Carolina Wilmington, 601 S College Road, Wilmington, NC 28403 5932, USA
    J Mol Graph Model 26:1125-30. 2008
    ..Finally, NMR shielding calculations were done on the optimized structure of N-phenylpyrrole dimer. The data were compared to concentration-dependent NMR shift data to estimate the percent dimer present...
  11. ncbi request reprint Advances in methods and algorithms in a modern quantum chemistry program package
    Yihan Shao
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Phys Chem Chem Phys 8:3172-91. 2006
    ....