quantum theory

Summary

Summary: The theory that the radiation and absorption of energy take place in definite quantities called quanta (E) which vary in size and are defined by the equation E=hv in which h is Planck's constant and v is the frequency of the radiation.

Top Publications

  1. ncbi Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy
    Florian Weigend
    Forschungszentrum Karlsruhe GmbH, Institut fur Nanotechnologie, Postfach 3640, 76021, Karlsruhe, Germany
    Phys Chem Chem Phys 7:3297-305. 2005
  2. ncbi Structure-based calculations of optical spectra of photosystem I suggest an asymmetric light-harvesting process
    Julian Adolphs
    Institut fur Chemie und Biochemie, Freie Universitat Berlin, Fabeckstrasse 36a, D 14195 Berlin, Germany
    J Am Chem Soc 132:3331-43. 2010
  3. ncbi Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature
    Elisabetta Collini
    Department of Chemistry, Institute for Optical Sciences and Centre for Quantum Information and Quantum Control, University of Toronto, 80 St George Street, Toronto, Ontario, M5S 3H6 Canada
    Nature 463:644-7. 2010
  4. ncbi Environment-assisted quantum walks in photosynthetic energy transfer
    Masoud Mohseni
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, USA
    J Chem Phys 129:174106. 2008
  5. pmc Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions
    Orlando Acevedo
    Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
    Acc Chem Res 43:142-51. 2010
  6. ncbi The implementation of a fast and accurate QM/MM potential method in Amber
    Ross C Walker
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    J Comput Chem 29:1019-31. 2008
  7. pmc A practical guide to modelling enzyme-catalysed reactions
    Richard Lonsdale
    Centre for Computational Chemistry, University of Bristol, Cantock s Close, Bristol, BS8 1TS, UK
    Chem Soc Rev 41:3025-38. 2012
  8. pmc Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling
    Richard Lonsdale
    Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock s Close, Bristol BS8 1TS, UK
    Biochemistry 51:1774-86. 2012
  9. pmc Origin of long-lived coherences in light-harvesting complexes
    Niklas Christensson
    Faculty of Physics, University of Vienna, Strudlhofgasse 4, 1090 Vienna, Austria
    J Phys Chem B 116:7449-54. 2012
  10. pmc Long-lived quantum coherence in photosynthetic complexes at physiological temperature
    Gitt Panitchayangkoon
    Department of Chemistry and The James Franck Institute, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 107:12766-70. 2010

Detail Information

Publications385 found, 100 shown here

  1. ncbi Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy
    Florian Weigend
    Forschungszentrum Karlsruhe GmbH, Institut fur Nanotechnologie, Postfach 3640, 76021, Karlsruhe, Germany
    Phys Chem Chem Phys 7:3297-305. 2005
    ..Finally recommendations are given which type of basis set is used best for a certain level of theory and a desired quality of results...
  2. ncbi Structure-based calculations of optical spectra of photosystem I suggest an asymmetric light-harvesting process
    Julian Adolphs
    Institut fur Chemie und Biochemie, Freie Universitat Berlin, Fabeckstrasse 36a, D 14195 Berlin, Germany
    J Am Chem Soc 132:3331-43. 2010
    ..This asymmetry in light-harvesting may provide the key for understanding the asymmetric use of the two branches in primary electron transfer reactions. Experiments are suggested to check for this possibility...
  3. ncbi Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature
    Elisabetta Collini
    Department of Chemistry, Institute for Optical Sciences and Centre for Quantum Information and Quantum Control, University of Toronto, 80 St George Street, Toronto, Ontario, M5S 3H6 Canada
    Nature 463:644-7. 2010
    ....
  4. ncbi Environment-assisted quantum walks in photosynthetic energy transfer
    Masoud Mohseni
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, USA
    J Chem Phys 129:174106. 2008
    ....
  5. pmc Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions
    Orlando Acevedo
    Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
    Acc Chem Res 43:142-51. 2010
    ....
  6. ncbi The implementation of a fast and accurate QM/MM potential method in Amber
    Ross C Walker
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    J Comput Chem 29:1019-31. 2008
    ....
  7. pmc A practical guide to modelling enzyme-catalysed reactions
    Richard Lonsdale
    Centre for Computational Chemistry, University of Bristol, Cantock s Close, Bristol, BS8 1TS, UK
    Chem Soc Rev 41:3025-38. 2012
    ..Modelling protocols commonly applied in studying enzyme-catalysed reactions are outlined here, and some practical implications are considered, with cytochrome P450 enzymes used as a specific example...
  8. pmc Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling
    Richard Lonsdale
    Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock s Close, Bristol BS8 1TS, UK
    Biochemistry 51:1774-86. 2012
    ..These insights may also provide useful information for the design of novel catalysts for use in the synthesis of enantiopure compounds...
  9. pmc Origin of long-lived coherences in light-harvesting complexes
    Niklas Christensson
    Faculty of Physics, University of Vienna, Strudlhofgasse 4, 1090 Vienna, Austria
    J Phys Chem B 116:7449-54. 2012
    ..Purely electronic coherences are found to decay on a 200 fs time scale...
  10. pmc Long-lived quantum coherence in photosynthetic complexes at physiological temperature
    Gitt Panitchayangkoon
    Department of Chemistry and The James Franck Institute, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 107:12766-70. 2010
    ..The protein shapes the energy landscape and mediates an efficient energy transfer despite thermal fluctuations...
  11. ncbi Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems
    Shina C L Kamerlin
    Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
    Annu Rev Phys Chem 62:41-64. 2011
    ....
  12. pmc Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study
    J Sponer
    J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
    Biophys J 73:76-87. 1997
    ..This enhancement of the total stacking interaction could contribute to the propensity of short d(CG)n sequences to adopt the Z-conformation...
  13. ncbi Vibronic enhancement of exciton sizes and energy transport in photosynthetic complexes
    Jordan M Womick
    Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    J Phys Chem B 115:1347-56. 2011
    ..This work raises the possibility that similar vibronic effects, which are often neglected, may generally have a significant influence on energy transport in molecular aggregates and photosynthetic complexes...
  14. ncbi Insights into the phosphoryl-transfer mechanism of cAMP-dependent protein kinase from quantum chemical calculations and molecular dynamics simulations
    Natalia Diaz
    Laboratoire de Dynamique Moleculaire, Institut de Biologie Structurale Jean Pierre Ebel, CEA CNRS, 41, rue Jules Horowitz, F 38027 Grenoble Cedex 1, France
    J Am Chem Soc 126:529-42. 2004
    ....
  15. ncbi 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...
  16. ncbi The role of quantum mechanics in structure-based drug design
    Kaushik Raha
    Department of Chemistry, Quantum Theory Project, University of Florida, 2328 New Physics Building, P O Box 118435, Gainesville, FL 32611 8435, United States
    Drug Discov Today 12:725-31. 2007
    ....
  17. pmc Classification and energetics of the base-phosphate interactions in RNA
    Craig L Zirbel
    Department of Mathematics and Statistics, Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
    Nucleic Acids Res 37:4898-918. 2009
    ..Bases that form BPh interactions, which are conserved in the rRNA 3D structures are also conserved in homologous rRNA sequence alignments...
  18. pmc Enzymatic mechanism and product specificity of SET-domain protein lysine methyltransferases
    Xiaodong Zhang
    Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
    Proc Natl Acad Sci U S A 105:5728-32. 2008
    ..The sequence of reactions stops at dimethylation if the conformation of Enz.Lys-N(Me)(2)H(+).(+)AdoMet has a methyl in position, which forbids the formation of the water channel...
  19. pmc Indolyne and aryne distortions and nucleophilic regioselectivites
    Paul H Y Cheong
    Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
    J Am Chem Soc 132:1267-9. 2010
    ..The regioselectivities found with other arynes are explained on the basis of distortion energies that are reflected in reactant geometries...
  20. ncbi On the origin of the stabilization of the zwitterionic resting state of cysteine proteases: a theoretical study
    Milena Mladenovic
    Institut fur Organische Chemie, Universitat Wurzburg, Am Hubland, D 97074 Wurzburg, Germany
    J Am Chem Soc 130:8696-705. 2008
    ..The active-site water molecules contribute about 30 kJ mol (-1) to the overall stabilization. Disruption of the hydrogen bonding network upon substrate binding is expected to enhance the nucleophilic reactivity of the thiolate...
  21. ncbi QM/MM methods for biomolecular systems
    Hans Martin Senn
    Department of Chemistry, WestCHEM and University of Glasgow, Glasgow G12 8QQ, UK
    Angew Chem Int Ed Engl 48:1198-229. 2009
    ..The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy...
  22. pmc The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building
    Francois Yves Dupradeau
    CNRS UMR 6219 and UFR Pharmacie, Universite de Picardie Jules Verne, 1, rue des Louvels, F 80037 Amiens Cedex 1, France
    Phys Chem Chem Phys 12:7821-39. 2010
    ..Selected results related to non-polarizable charge models are presented and discussed...
  23. ncbi Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: an ab initio QM/MM-FE study with multiple initial structures
    Po Hu
    Department of Chemistry, New York University, New York 10003, USA
    J Am Chem Soc 128:1272-8. 2006
    ..The calculation results show that the product specificity of SET7/9 as a monomethyltransferase is achieved by disrupting the formation of near-attack conformations for the dimethylation reaction...
  24. pmc CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
    K Vanommeslaeghe
    Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA
    J Comput Chem 31:671-90. 2010
    ..CGenFF thus makes it possible to perform "all-CHARMM" simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems...
  25. pmc Violation of the Leggett-Garg inequality with weak measurements of photons
    M E Goggin
    Department of Physics and Centre for Quantum Computer Technology, University of Queensland, Brisbane 4072, Australia
    Proc Natl Acad Sci U S A 108:1256-61. 2011
    ..Furthermore, we experimentally demonstrate that there is a one-to-one correlation between achieving strange weak values and violating the Leggett-Garg inequality...
  26. pmc How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by Ab initio QM/MM molecular dynamics simulations
    Po Hu
    Department of Chemistry, New York University, New York, New York 10003, USA
    J Am Chem Soc 130:3806-13. 2008
    ..These detailed insights take account of protein dynamics and are consistent with available experimental results as well as recent theoretical findings regarding the catalytic power of SET7/9...
  27. ncbi Valence tautomerism in a high-valent manganese-oxo porphyrinoid complex induced by a Lewis acid
    Pannee Leeladee
    Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
    J Am Chem Soc 134:10397-400. 2012
    ..Removal of Zn(2+) quantitatively restores the starting material. Electron-transfer and hydrogen-atom-transfer reactions are strongly influenced by the presence of Zn(2+)...
  28. ncbi From red to blue to far-red in Lhca4: how does the protein modulate the spectral properties of the pigments?
    Emilie Wientjes
    Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
    Biochim Biophys Acta 1817:711-7. 2012
    ..These findings are discussed in the light of previously proposed non-photochemical quenching models...
  29. ncbi Computer simulations of enzyme catalysis: methods, progress, and insights
    Arieh Warshel
    Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
    Annu Rev Biophys Biomol Struct 32:425-43. 2003
    ..Finally, it is pointed out that although some of the issues are likely to remain controversial for some time, computer modeling approaches can provide a powerful tool for understanding enzyme catalysis...
  30. pmc Analysis of two-player quantum games in an EPR setting using Clifford's geometric algebra
    James M Chappell
    School of Chemistry and Physics, University of Adelaide, Adelaide, South Australia, Australia
    PLoS ONE 7:e29015. 2012
    ..The use of GA allows a quantum-mechanical analysis without the use of complex numbers or the Dirac Bra-ket notation, and hence is more accessible to the non-physicist...
  31. ncbi A proposal for mitochondrial processing peptidase catalytic mechanism
    Orazio Amata
    Dipartimento di Chimica, Universita della Calabria, I 87030 Arcavacata di Rende CS, Italy
    J Am Chem Soc 133:17824-31. 2011
    ..The results allowed assignment of the proper roles to some active site residues in this mechanism...
  32. pmc Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry
    Luis Manuel Frutos
    Dipartimento di Chimica, Universita di Siena, Via Aldo Moro 2, I 53100 Siena, Italy
    Proc Natl Acad Sci U S A 104:7764-9. 2007
    ..It is shown that the twisted structure achieved at decay features a momentum that provides a natural route toward the photoRh structure recently resolved by using femtosecond-stimulated Raman spectroscopy...
  33. ncbi Metal-intercalated aromatic hydrocarbons: a new class of carbon-based superconductors
    Yoshihiro Kubozono
    Research Laboratory for Surface Science, Okayama University, Okayama, Japan
    Phys Chem Chem Phys 13:16476-93. 2011
    ..The features of other carbon-based superconductors are compared to clarify the nature of hydrocarbon superconductors...
  34. ncbi Mechanism of selective halogenation by SyrB2: a computational study
    Tomasz Borowski
    Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul Niezapominajek 8, 30 239 Krakow, Poland
    J Am Chem Soc 132:12887-98. 2010
    ..CASPT2 calculations for the spin state splittings in the oxoferryl species support the conclusion that once the Fe(IV)═O intermediate is formed, the reaction proceeds on the quintet potential energy surface...
  35. ncbi Recent developments of the quantum chemical cluster approach for modeling enzyme reactions
    Per E M Siegbahn
    Department of Physics, Alba Nova, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
    J Biol Inorg Chem 14:643-51. 2009
    ..Examples are finally given from the most extensive study using the cluster model, the one of oxygen formation at the oxygen-evolving complex in photosystem II...
  36. ncbi Quantum Isostere Database: a web-based tool using quantum chemical topology to predict bioisosteric replacements for drug design
    Mike Devereux
    Manchester Interdisciplinary Biocentre MIB, Manchester M1 7DN, Great Britain
    J Chem Inf Model 49:1497-513. 2009
    ..Examples of known bioisosteric replacements correctly identified by the QID tool are given...
  37. ncbi Deciphering the influence of short-range electronic couplings on optical properties of molecular dimers: application to "special pairs" in photosynthesis
    Mohamed El Amine Madjet
    Freie Universitat Berlin, Institut fur Chemie und Biochemie, Fabeckstrasse 36a, D 14195 Berlin, Germany
    J Phys Chem B 113:12603-14. 2009
    ..8 A(-1) and another factor being in the range 0.3-0.7 A(-1) for PSI and 0.8-0.9 A(-1) for bRC. Both effects of the short-range coupling determine the excitation energy sink in the reaction centers at the special pairs...
  38. ncbi Do quantum mechanical energies calculated for small models of protein-active sites converge?
    Lihong Hu
    Department of Theoretical Chemistry, Lund University, Chemical Centre, P O Box 124, SE 221 00 Lund, Sweden
    J Phys Chem A 113:11793-800. 2009
    ..Thus, to accurately model the influence of the surroundings on enzyme reaction energies, a detailed and unbiased atomistic account of the surroundings needs to be included...
  39. pmc Exploring solvent effects upon the Menshutkin reaction using a polarizable force field
    Orlando Acevedo
    Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
    J Phys Chem B 114:8425-30. 2010
    ..The large rate accelerations observed in the reaction were correlated to an increased stabilization of the emerging charge separation at the transition state via favorable solute-solvent interactions...
  40. ncbi Theoretical study of vibrational and optical spectra of methylene-bridged oligofluorenes
    Vladimir Lukeš
    Department of Chemical Physics, Slovak University of Technology, Radlinskeho 9, SK 81 237 Bratislava, Slovakia
    J Phys Chem A 109:10232-8. 2005
    ..The decrease of the radiatiave fluorescence lifetime with the increase in the conjugation length has been discussed also...
  41. ncbi Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions
    Edina Rosta
    Department of Chemistry, University of Southern California, 3620 South McClintock Avenue, Los Angeles, California 90089 1062, USA
    J Phys Chem B 110:2934-41. 2006
    ..Our advance allows one to explore consistently various mechanistic and catalytic proposals while using ab initio (ai) QM/MM approaches...
  42. ncbi Quantum chemical simulation of excited states of chlorophylls, bacteriochlorophylls and their complexes
    Juha Linnanto
    Physical Chemistry Laboratory, University of Jyvaskyla, P O Box 35, FIN 40014, Finland
    Phys Chem Chem Phys 8:663-87. 2006
    ..Simulations for the light harvesting complexes Rhodospirillum molischianum, chlorosomes of Chlorobium tepidum and Chloroflexus aurantiacus, and LHC-II of Spinacia oleracea are presented as examples...
  43. ncbi Nuclear quantum effects in water
    Joseph A Morrone
    Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
    Phys Rev Lett 101:017801. 2008
    ..In addition, the proton momentum distribution is computed utilizing a recently developed open path-integral molecular dynamics methodology. It is shown that these results are in good agreement with experimental data...
  44. ncbi Theoretical study on the mechanism of the oxygen activation process in cysteine dioxygenase enzymes
    Devesh Kumar
    Max Planck Institut für Kohlenforschung, Kaiser Wilhelm Platz 1, D 45470 Mülheim an der Ruhr, Germany
    J Am Chem Soc 133:3869-82. 2011
    ....
  45. ncbi A QM/MM study of the phosphoryl transfer to the Kemptide substrate catalyzed by protein kinase A. The effect of the phosphorylation state of the protein on the mechanism
    Manuel Montenegro
    Institut de Biotecnologia i de Biomedicina i Departament de Química, Universitat Autonoma de Barcelona, 08193 Bellaterra Barcelona, Spain
    Phys Chem Chem Phys 13:530-9. 2011
    ..In addition, the roles of the two active site conserved residues, Asp166 and Lys168, have been analyzed for each reaction mechanism...
  46. ncbi High frequency vibrational modulations in two-dimensional electronic spectra and their resemblance to electronic coherence signatures
    N Christensson
    Electronic Properties of Materials, Faculty of Physics, University of Vienna, Strudlhofgasse 4, 1090 Vienna, Austria
    J Phys Chem B 115:5383-91. 2011
    ..Our results show that these anticorrelated oscillations occur for vibrational wavepackets and not exclusively for electronic coherences as has been assumed previously...
  47. ncbi Sugar edge/sugar edge base pairs in RNA: stabilities and structures from quantum chemical calculations
    Judit E Sponer
    Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
    J Phys Chem B 109:18680-9. 2005
    ..This likely is profitable for stabilization of SE/SE binding patterns in polar environments and could be one of the reasons why the A-minor motif is the leading type of tertiary interactions in RNAs...
  48. ncbi Reversible redox-switchable second-order optical nonlinearity in polyoxometalate: a quantum chemical study of [PW11O39(ReN)]n- (n = 3-7)
    Wei Guan
    Institute of Functional Material Chemistry, Faculty of Chemistry, Northeast Normal University, Changchun, P R China
    Inorg Chem 47:5245-52. 2008
    ..Therefore, these kinds of complexes with the facile and reversible redox states could become excellent switchable NLO materials...
  49. ncbi Quantum coherence and its interplay with protein environments in photosynthetic electronic energy transfer
    Akihito Ishizaki
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Phys Chem Chem Phys 12:7319-37. 2010
    ....
  50. ncbi Prediction and rationalization of protein pKa values using QM and QM/MM methods
    Jan H Jensen
    Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA
    J Phys Chem A 109:6634-43. 2005
    ....
  51. pmc Consequence of one-electron oxidation and one-electron reduction for aniline
    Ewa D Raczyńska
    Department of Chemistry, Warsaw University of Life Sciences SGGW, ul Nowoursynowska 159C, 02 776 Warszawa, Poland
    J Mol Model 17:3229-39. 2011
    ..The change of the tautomeric preferences for reduced aniline may partially explain the origin of the CH tautomers for reduced nucleobases (cytosine, adenine, and guanine)...
  52. ncbi The directive of the protein: how does cytochrome P450 select the mechanism of dopamine formation?
    Patric Schyman
    Institute of Chemistry and The Lise Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
    J Am Chem Soc 133:7977-84. 2011
    ..Furthermore, it is shown that external electric fields can either catalyze or inhibit the process depending on their directionality...
  53. ncbi Development of a combined protein and pharmacophore model for cytochrome P450 2C9
    Marcel J de Groot
    Department of Molecular Informatics, Structure and Design, Pfizer Global Research and Development, Sandwich Laboratories, Ramsgate Road, Sandwich, Kent CT13 9NJ, U K
    J Med Chem 45:1983-93. 2002
    ..The model has also been successful in explaining the differences in substrate specificity between CYP2C9 and CYP2C19...
  54. ncbi Compound I reactivity defines alkene oxidation selectivity in cytochrome P450cam
    Richard Lonsdale
    Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock s Close, Bristol BS8 1TS, United Kingdom
    J Phys Chem B 114:1156-62. 2010
    ..This work highlights the complexity involved in modeling these systems with QM/MM and the importance in the selection of starting geometries...
  55. ncbi Conical intersection dynamics of the primary photoisomerization event in vision
    Dario Polli
    IFN CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza L da Vinci 32, 20133 Milano, Italy
    Nature 467:440-3. 2010
    ..Taken together, these findings constitute the most compelling evidence to date for the existence and importance of conical intersections in visual photochemistry...
  56. ncbi Structural study of selected polyhalogenated benzimidazoles (protein kinase CK2 inhibitors) by nuclear quadrupole double resonance, X-ray, and density functional theory
    J N Latosińska
    Faculty of Physics, Adam Mickiewicz University Umultowska 85, 61 614 Poznan, Poland
    J Phys Chem A 114:563-75. 2010
    ..NQDR and DFT results suggest the presence of the prototropic annular tautomerism 50:50, which is in a good agreement with the X-ray and (1)H NMR data...
  57. pmc Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9
    Shenglong Wang
    Department of Chemistry, New York University, New York, New York 10003, USA
    J Phys Chem B 111:3758-64. 2007
    ..Meanwhile, we find that the transition state in the enzyme reaction is a little more dissociative than that in solution...
  58. ncbi Electronic structure of compound I in human isoforms of cytochrome P450 from QM/MM modeling
    Christine M Bathelt
    Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock s Close, Bristol BS8 1TS United Kingdom
    J Am Chem Soc 127:12900-8. 2005
    ....
  59. pmc Atomistic study of the long-lived quantum coherences in the Fenna-Matthews-Olson complex
    Sangwoo Shim
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
    Biophys J 102:649-60. 2012
    ..This work thus presents, to our knowledge, one of the first steps to explain the role of excitonic quantum coherence in photosynthetic light-harvesting complexes based on their atomistic and molecular description...
  60. ncbi Electronic structures of metal sites in proteins and models: contributions to function in blue copper proteins
    Edward I Solomon
    Department of Chemistry, Stanford University, Stanford, California 94305, USA
    Chem Rev 104:419-58. 2004
  61. ncbi Mechanisms and free energies of enzymatic reactions
    Jiali Gao
    Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
    Chem Rev 106:3188-209. 2006
  62. ncbi Two-dimensional electronic spectroscopy of bacteriochlorophyll a in solution: Elucidating the coherence dynamics of the Fenna-Matthews-Olson complex using its chromophore as a control
    Kelly A Fransted
    Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
    J Chem Phys 137:125101. 2012
    ..Our results suggest that the beating observed in spectra of FMO is of a radically different character than the signals observed here and can therefore be attributed to electronic coherences or intermolecular degrees of freedom...
  63. ncbi QM/MM modeling of benzene hydroxylation in human cytochrome P450 2C9
    Christine M Bathelt
    Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantocks Close, Bristol BS8 1TS, UK
    J Phys Chem A 112:13149-56. 2008
    ..This suggests that overall, the competition between formation of epoxide and phenol final products in P450 oxidation of aromatic substrates is quite finely balanced...
  64. pmc Witnessing Quantum Coherence: from solid-state to biological systems
    Che Ming Li
    Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan
    Sci Rep 2:885. 2012
    ..These robust quantum indicators may assist in reducing the experimental overhead in unambiguously verifying quantum coherence in complex systems...
  65. pmc Theoretical examination of quantum coherence in a photosynthetic system at physiological temperature
    Akihito Ishizaki
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 106:17255-60. 2009
    ..A potential role of quantum coherence is to overcome local energetic traps and aid efficient trapping of electronic energy by the pigments facing the reaction center complex...
  66. ncbi Why urease is a di-nickel enzyme whereas the CcrA β-lactamase is a di-zinc enzyme
    Crystal E Valdez
    Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095 1569, United States
    J Phys Chem B 116:10649-56. 2012
    ..Thus, β-lactamases operate by the principle of "good enough"; i.e., the choice for Zn in them leads to a performance that is just satisfactory for its biological purpose but can be evolutionarily improved via replacement of Zn with Ni...
  67. ncbi QM/MM studies of enzymes
    Hans Martin Senn
    Max Planck Institut fur Kohlenforschung, D 45470 Mulheim an der Ruhr, Germany
    Curr Opin Chem Biol 11:182-7. 2007
    ..Methodological advances include improved QM/MM schemes, in particular new approaches for an effective treatment of the QM-MM electrostatic interactions, and the incorporation of new efficient and accurate QM methods in QM/MM schemes...
  68. pmc Hybrid dynamics simulation engine for metalloproteins
    Manuel Sparta
    Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
    Biophys J 103:767-76. 2012
    ..The change is facilitated by the backbone adjustment. QM/DMD is ideal and fast for providing this level of structural insight...
  69. ncbi Mechanism for N₂O generation in bacterial nitric oxide reductase: a quantum chemical study
    Margareta R A Blomberg
    Department of Physics, AlbaNova University Center, and Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE 106 91 Stockholm, Sweden
    Biochemistry 51:5173-86. 2012
    ....
  70. pmc Structural evolution of the chromophore in the primary stages of trans/cis isomerization in photoactive yellow protein
    Karsten Heyne
    Max Born Institut fur Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D 12489 Berlin, Germany
    J Am Chem Soc 127:18100-6. 2005
    ....
  71. ncbi Type-II quantum dots: CdTe/CdSe(core/shell) and CdSe/ZnTe(core/shell) heterostructures
    Sungjee Kim
    Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
    J Am Chem Soc 125:11466-7. 2003
    ..The enhanced control over carrier distribution afforded by these type-II materials may prove useful for many applications, such as photovoltaics and photoconduction devices...
  72. ncbi Ab initio QM/MM calculations show an intersystem crossing in the hydrogen abstraction step in dealkylation catalyzed by AlkB
    Dong Fang
    Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
    J Phys Chem B 117:6410-20. 2013
    ..These conserved residues are proposed as targets for experimental mutagenesis studies...
  73. pmc A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands
    Akash Khandelwal
    Department of Pharmaceutical Sciences and Center for Protease Research, North Dakota State University, Fargo, North Dakota 58105, USA
    J Med Chem 48:5437-47. 2005
    ..08 to 349 nM, with the average unassigned error of 0.318 log units. The structural and energetic information obtained from the time-averaged MD simulation results helped understand the differences in binding modes of related compounds...
  74. ncbi Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps
    Jiri Sponer
    Intitute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
    Chemistry 12:2854-65. 2006
    ..The reference calculations are complemented by continuum-solvent assessment of solvent-screening effects...
  75. ncbi Quantum mechanical/molecular mechanical study on the mechanism of the enzymatic Baeyer-Villiger reaction
    Iakov Polyak
    Max Planck Institut fur Kohlenforschung, Kaiser Wilhelm Platz 1, D 45470 Mulheim an der Ruhr, Germany
    J Am Chem Soc 134:2732-41. 2012
    ....
  76. ncbi How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study
    Yuhui Cheng
    Howard Hughes Medical Institute, Department of Chemistry and Biochemistry and Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093 0365, USA
    J Am Chem Soc 127:1553-62. 2005
    ....
  77. ncbi Demonstration and interpretation of significant asymmetry in the low-resolution and high-resolution Q(y) fluorescence and absorption spectra of bacteriochlorophyll a
    Margus Rätsep
    Institute of Physics, University of Tartu, Riia 142, 51014 Tartu, Estonia
    J Chem Phys 134:024506. 2011
    ..Most other semi-empirical, density-functional, and ab initio computational methods severely overestimate the electron-vibrational coupling and its asymmetry. It is shown that the asymmetry arises primarily through Duschinsky rotation...
  78. ncbi Real-world predictions from ab initio molecular dynamics simulations
    Barbara Kirchner
    Wilhelm Ostwald Institute of Physical and Theoretical Chemistry, University of Leipzig, Linnestr 2, 04103 Leipzig, Germany
    Top Curr Chem 307:109-53. 2012
    ..Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented...
  79. ncbi A DFT comparison of the neutral and cationic Heck pathways
    Carina Bäcktorp
    Department of Chemistry, University of Gothenburg, Kemigården 4, 8076, SE 412 96, Goteborg, Sweden
    Dalton Trans 40:11308-14. 2011
    ..The geometries and energies of the selectivity-determining transitions states are analyzed in detail...
  80. ncbi A critical view on transport and entanglement in models of photosynthesis
    Markus Tiersch
    Institute for Quantum Optics and Quantum Information, Austrian Academy of Sciences, Technikerstrasse 21a, 6020 Innsbruck, Austria
    Philos Trans A Math Phys Eng Sci 370:3771-86. 2012
    ....
  81. ncbi Ultralong spin coherence time in isotopically engineered diamond
    Gopalakrishnan Balasubramanian
    Physikalisches Institut, Universitat Stuttgart, 70550 Stuttgart, Germany
    Nat Mater 8:383-7. 2009
    ..We also show that single electron spins in the same isotopically engineered CVD diamond can be used to detect external magnetic fields with a sensitivity reaching 4 nT Hz(-1/2) and subnanometre spatial resolution...
  82. ncbi Theoretical study of the electronic-vibrational coupling in the Q(y) states of the photosynthetic reaction center in purple bacteria
    Yuanyuan Jing
    Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
    J Phys Chem B 116:1164-71. 2012
    ..The large amplitude of the static disorder indicates that a large portion of the spectral density and their correlations may still be hidden in the inhomogeneous broadening due to the finite MD simulation time...
  83. ncbi Influence of environment induced correlated fluctuations in electronic coupling on coherent excitation energy transfer dynamics in model photosynthetic systems
    Pengfei Huo
    Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
    J Chem Phys 136:115102. 2012
    ..We find that the relative sign of the different correlations can have profound influence on decoherence time and energy transfer rate and can provide sensitive control of relaxation in these complex quantum dynamical open systems...
  84. ncbi All-atom semiclassical dynamics study of quantum coherence in photosynthetic Fenna-Matthews-Olson complex
    Hyun Woo Kim
    Institute of Theoretical and Computational Chemistry, Department of Chemistry, Pohang University of Science and Technology, Pohang 790 784, Korea
    J Am Chem Soc 134:11640-51. 2012
    ..Our results indicate that a description of both chromophore coupling strengths and their fluctuations is crucial to better understand coherent EET processes in photosynthetic systems...
  85. ncbi QM/MM nonadiabatic decay dynamics of 9H-adenine in aqueous solution
    Zhenggang Lan
    Max Planck Institut fur Kohlenforschung, Kaiser Wilhelm Platz 1, D 45470 Mulheim an der Ruhr, Germany
    Chemphyschem 12:1989-98. 2011
    ..The simulations yield ultrafast S(2)-S(1) decay within 40 fs and S(1)-S(0) internal conversion to the ground state within 410 fs, which is consistent with recent experimental results from time-resolved spectroscopy...
  86. pmc Nature of light correlations in ghost imaging
    Sammy Ragy
    School of Mathematical Sciences, The University of Nottingham, University Park, Nottingham NG7 2RD, UK
    Sci Rep 2:651. 2012
    ..We further demonstrate that the total correlations in the thermal source beams effectively determine the quality of the imaging, as quantified by the signal-to-noise ratio...
  87. ncbi A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution
    Michael A Crawford
    Imperial College, Department of Cancer and Surgery, Division of Reproductive Physiology, Obstetrics and Gynaecology, Room 334, Chelsea and Westminster Hospital Campus, 369 Fulham Road, London SW10 9NH, UK
    Prostaglandins Leukot Essent Fatty Acids 88:5-13. 2013
    ....
  88. pmc Molecular response in one-photon absorption via natural thermal light vs. pulsed laser excitation
    Paul Brumer
    Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 3H6
    Proc Natl Acad Sci U S A 109:19575-8. 2012
    ..Emphasis is placed on resolving confusions regarding this issue that are shown to arise from aspects of quantum measurement and from a lack of appreciation of the proper description of the absorbed photon...
  89. ncbi Acidity of anilines: calculations vs experiment
    Lauri Lipping
    Institute of Chemistry, University of Tartu, 14a Ravila St, 50411 Tartu, Estonia
    J Phys Chem A 115:10335-44. 2011
    ..The method proved to be rather accurate for showing pK(a) trends (R(2)=0.980 in DMSO). However, the predicted absolute pK(a) values were all somewhat lower (rmsd=2.49 kcal·mol(-1)) than the respective experimental values...
  90. ncbi Modelling enzyme reaction mechanisms, specificity and catalysis
    Adrian J Mulholland
    Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
    Drug Discov Today 10:1393-402. 2005
    ..Some recent applications to enzymes of pharmacological interest are also covered, showing the types of problems that can be tackled and the insight they can give...
  91. ncbi Fragment molecular orbital calculations on red fluorescent proteins (DsRed and mFruits)
    Naoki Taguchi
    Department of Chemistry and Research Center for Smart Molecules, Rikkyo University, Toshima ku, Tokyo 171 8501, Japan
    J Phys Chem B 113:1153-61. 2009
    ..It was theoretically revealed that the electrostatic interactions play a dominant role in the DsRed chromophore, whereas the color tunings in mFruits are controlled in a more delicate fashion...
  92. ncbi Accurate modelling of Pd(0) + PhX oxidative addition kinetics
    Claire L McMullin
    School of Chemistry, University of Bristol, Cantock s Close, Bristol, UK BS8 1TS
    Dalton Trans 39:10833-6. 2010
    ..Barrios-Landeros, B. P. Carrow and J. F. Hartwig, J. Am. Chem. Soc., 2009, 131, 8141-8154). The calculated activation free energies agree near-quantitatively with experimentally observed rate constants...
  93. ncbi Structural basis for the role of LYS220 as proton donor for nucleotidyl transfer in HIV-1 reverse transcriptase
    Servaas Michielssens
    Departement of Chemistry and INPAC Institute of Nanoscale Physics and Chemistry, Katholieke Universiteit Leuven, Belgium
    Biophys Chem 157:1-6. 2011
    ..A combination of quantum mechanical and molecular mechanics methods was used to validate the different modes of interaction...
  94. pmc Quest for spatially correlated fluctuations in the FMO light-harvesting complex
    Carsten Olbrich
    School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
    J Phys Chem B 115:758-64. 2011
    ..Depending on the level of theory employed, also correlations between the fluctuations of site energies and the fluctuations in electronic couplings are discernible...
  95. ncbi Photodynamics of azomethane: a nonadiabatic surface-hopping study
    Bernhard Sellner
    Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A 1090 Vienna, Austria
    J Phys Chem A 114:8778-85. 2010
    ..Our results favor a statistical model with trans-AZM moving to the ground-state minima before the first CN dissociation takes place. A detailed discussion in comparison to recent experimental and theoretical data is presented...
  96. ncbi Halide ligated iron porphines: a DFT+U and UB3LYP study
    Pooja M Panchmatia
    Department of Physics and Astronomy, Uppsala University, Box 516, S 751 20 Uppsala, Sweden
    J Phys Chem A 114:13381-7. 2010
    ..This observation is also supported by our UB3LYP calculations...
  97. ncbi Insight into the electronic structure of the CP47 antenna protein complex of photosystem II: hole burning and fluorescence study
    Bhanu Neupane
    Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA
    J Am Chem Soc 132:4214-29. 2010
    ..The above findings provide important constraints and parameters for future excitonic calculations, which in turn should offer new insight into the excitonic structure and composition of low-energy absorption traps...
  98. ncbi Specific formation of negative ions from leucine and isoleucine molecules
    Peter Papp
    Department of Experimental Physics, Comenius University, 842 48 Bratislava, Slovakia
    J Chem Phys 132:014301. 2010
    ..23 eV. Additional negative ions with m/z=115, 114, 113, 112, 84, 82, 74, 45, 26, and 17 have been detected...
  99. ncbi Nonadiabatic hybrid quantum and molecular mechanic simulations of azobenzene photoswitching in bulk liquid environment
    Marcus Böckmann
    Lehrstuhl fur Theoretische Chemie, Ruhr Universitat Bochum, 44780 Bochum, Germany
    J Phys Chem A 114:745-54. 2010
    ..The main molecular motions responsible for nonadiabatic coupling have been identified as the oscillations in the NN and CN bond lengths, the CNN bond angles, and the CNNC dihedral angle...
  100. ncbi Resonance electron capture by serine
    Jaroslav Kocisek
    Department of Experimental Physics, Comenius University Bratislava, Mlynska Dolina F2, 84248, Bratislava, Slovak Republic
    J Phys Chem A 114:1677-83. 2010
    ..We have found that the second OH group influences some dissociative channels. Quantum chemical calculations were applied to interpret products of the DEA reaction channels...
  101. pmc New light on NO bonding in Fe(III) heme proteins from resonance Raman spectroscopy and DFT modeling
    Alexandra V Soldatova
    Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
    J Am Chem Soc 132:4614-25. 2010
    ..Implications for biologically important processes, including NO binding, reductive nitrosylation, and NO reduction, are discussed...

Research Grants19

  1. Local Quantum Theory for Large Molecular Systems
    Jing Kong; Fiscal Year: 2005
    ..The new hybrid models will enable Q-Chem to reach a much larger market where high-level quantum modeling is desired but is currently prohibitively expensive. ..
  2. Structure and Function of Tau
    David Eliezer; Fiscal Year: 2008
    ..This work may also have broader implications for understanding and treating other protein aggregation diseases. ..
  3. Substrate Binding and Catalysis of Subclass B2 beta-Lactamases
    Hua Guo; Fiscal Year: 2007
    ..The proposed research is fundamental in nature, but will impact public health by providing a solid foundation for designing novel and effective drugs to combat bacterial infections. [unreadable] [unreadable] [unreadable]..
  4. PORPHYRIN SYNTHETIC METHODS FOR BIOORGANIC APPLICATIONS
    JONATHAN LINDSEY; Fiscal Year: 2007
    ....
  5. Stable cationic bacteriochlorins for antimicrobial photodynamic therapy
    JONATHAN LINDSEY; Fiscal Year: 2008
    ..The two best performing bacteriochlorins will then be tested in a mouse model of a potentially lethal wound infection and monitored by bioluminescence imaging. [unreadable] [unreadable] [unreadable]..
  6. Studies of redox-active sites in Photosystem II
    Victor S Batista; Fiscal Year: 2010
    ..abstract_text> ..
  7. TRIPLE QUADRUPOLE MASS SPECTROMETER
    Jeffrey Jones; Fiscal Year: 2001
    ..T specific DNA-binding properties of a human protein; and quantitation and identification of isoprostane biomarkers of oxidative stress. ..
  8. High Performance Computer System for Molecular Modeling
    Benoit Roux; Fiscal Year: 2004
    ....
  9. 2007 Electron Distribution & Chemical Bonding Gordon Research Conference
    Carlo Gatti; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  10. Hierarchical Bayes Methods for Serial Dilution Assays
    Andrew Gelman; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  11. CYTOCHROME P450 MODELS FOR RISK ASSESSMENT
    Jeffrey Jones; Fiscal Year: 2007
    ..Thus, this proposal also helps to train scientists in the use of multidisciplinary approaches, at the chemical/biological interface, to understanding a given scientific problem. [unreadable] [unreadable] [unreadable]..
  12. Structure and Function of Alpha-Synuclein
    David Eliezer; Fiscal Year: 2010
    ....
  13. Structure and Interactions of Gas Vesicles by SSNMR
    Judith Herzfeld; Fiscal Year: 2007
    ....
  14. Cognitive Modeling of Risky Decisions in Drug Abusers
    Jerome Busemeyer; Fiscal Year: 2008
    ..unreadable] [unreadable]..
  15. ENZYMATIC MECHANISMS OF SULFUR NUCLEOSIDE METABOLISM
    GEORGE MARKHAM; Fiscal Year: 2008
    ..These studies will unmask why nature conserves use of a pyruvoyl cofactor for this metabolic function instead of adopting the common pyridoxal cofactor. ..
  16. Comparing Models of Function Learning
    Jerome Busemeyer; Fiscal Year: 2006
    ..This last line of research is designed to test the basic learning mechanisms underlying almost all connectionist-learning approaches. [unreadable] [unreadable]..
  17. Chemical Mechanism of Guanine Deamination
    Rainer Glaser; Fiscal Year: 2003
    ..5. The computational studies will include studies of the bimolecular reaction mechanisms for dediazoniation of the nucleobase diazonium ions. ..
  18. Image Reconstruction Algorithms for Optical Tomography
    JOHN SCHOTLAND; Fiscal Year: 2009
    ..We will utilize the parallel plate imaging geometry which is often employed in optical mammography. The results of this research are expected to impact the design of clinically useful instruments for noncontact optical tomography. ..
  19. X-RAY AND CHEMICAL STUDIES OF METALLOPORPHYRINS
    W Robert Scheidt; Fiscal Year: 2010
    ..The effect of pressure will be investigated through the measurement of the NRVS spectrum at pressures up to about 8 GPa. Whenever possible, these measurements will be made on an oriented crystal specimen. ..