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. 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
  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. 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
  9. 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
  10. pmc Web-based computational chemistry education with CHARMMing III: Reduction potentials of electron transfer proteins
    B Scott Perrin
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Comput Biol 10:e1003739. 2014

Collaborators

  • Stefan Boresch
  • Jing Kong
  • Alejandro Toro-Labbe
  • Wenjun Zheng
  • Peter M W Gill
  • Gerhard Hummer
  • An Ghysels
  • Alexander D MacKerell
  • Jeffery B Klauda
  • Joseph E Subotnik
  • Nicholas A Besley
  • WanZhen Liang
  • Andreas Heyden
  • John M Herbert
  • Michael S Lee
  • N H Martin
  • Benjamin T Miller
  • Bernard R Brooks
  • Vinushka Schalk
  • Edina Rosta
  • Toshiko Ichiye
  • Frank C Pickard
  • B Scott Perrin
  • Jacqueline C Hargis
  • Rishi P Singh
  • Henry F Schaefer
  • Yihan Shao
  • Carrie S Miller
  • Jingjun Sun
  • Yuri Pevzner
  • Michael G Lerner
  • Esteban Vöhringer-Martinez
  • Milan Hodoscek
  • Brian Austin
  • Anna I Krylov
  • Emil I Proynov
  • Ross D Adamson
  • Daniel M Chipman
  • Troy Van Voorhis
  • Gregory J O Beran
  • Ching Yeh Lin
  • Jon Baker
  • Young Min Rhee
  • Robert A DiStasio
  • Paul E Maslen
  • Arup K Chakraborty
  • Andrew T B Gilbert
  • Holger Dachsel
  • Rohini C Lochan
  • Yousung Jung
  • Aaron M Lee
  • Frerich J Keil
  • Jim Ritchie
  • Martin Head-Gordon
  • Darragh P O'Neill
  • Itay Lotan
  • Lyudmila V Slipchenko
  • Chao Ping Hsu
  • Thomas R Furlani
  • So Hirata
  • Vitaly A Rassolov
  • Andreas Dreuw
  • Christian Ochsenfeld
  • Shawn T Brown
  • Robert J Doerksen
  • Siu Hung Chien
  • Rustam Z Khalliulin
  • Anthony D Dutoi
  • Steven R Gwaltney
  • Arieh Warshel
  • Alexis T Bell
  • Nikhil Nair
  • Piotr A Pieniazek
  • Sergey V Levchenko
  • Warren J Hehre
  • Prakashan P Korambath
  • Alex Sodt
  • Laszlo Fusti Molnar
  • Baron Peters
  • Phil Klunzinger
  • Edward F C Byrd
  • C David Sherrill
  • Ryan P Steele
  • Gary Kedziora
  • Tao Wang
  • Weimin Zhang
  • Andrew C Simmonett
  • Barry D Dunietz
  • Jörg Kussmann

Detail Information

Publications14

  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. 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...
  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. 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...
  9. 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...
  10. pmc Web-based computational chemistry education with CHARMMing III: Reduction potentials of electron transfer proteins
    B Scott Perrin
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Comput Biol 10:e1003739. 2014
    ..This demonstration is valuable to both computational chemistry students and researchers interested in predicting sequence determinants of E° for mutagenesis. ..
  11. pmc Web-based computational chemistry education with CHARMMing I: Lessons and tutorial
    Benjamin T Miller
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America
    PLoS Comput Biol 10:e1003719. 2014
    ..In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance. ..
  12. pmc Web-based computational chemistry education with CHARMMing II: Coarse-grained protein folding
    Frank C Pickard
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Comput Biol 10:e1003738. 2014
    ..The CG model builder and its accompanying lesson should be a valuable tool to chemistry students, teachers, and modelers in the field...
  13. 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...
  14. 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
    ....