Publications by authors named "Martin Field"

81Publications

Hydrogen evolution reaction mediated by an all-sulfur trinuclear nickel complex.

Chem Commun (Camb) 2020 Sep 19;56(75):11106-11109. Epub 2020 Aug 19.

Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1039/d0cc04174bDOI Listing
September 2020

Modeling the Hydrolysis of Iron-Sulfur Clusters.

J Chem Inf Model 2020 02 16;60(2):653-660. Epub 2019 Dec 16.

Department of Biochemistry, Instituto de Química , Universidade de São Paulo , Av. Prof. Lineu Prestes 748 , 05508-900 São Paulo , SP , Brazil.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jcim.9b00881DOI Listing
February 2020

Electrocatalytic Hydrogen Evolution with a Cobalt Complex Bearing Pendant Proton Relays: Acid Strength and Applied Potential Govern Mechanism and Stability.

J Am Chem Soc 2020 01 19;142(1):274-282. Epub 2019 Dec 19.

Univ. Grenoble Alpes , CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, UMR 5249, 17 rue des Martyrs, 38000 Grenoble , France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jacs.9b10407DOI Listing
January 2020

Crystal structures of a GABA-receptor chimera reveal new endogenous neurosteroid-binding sites.

Nat Struct Mol Biol 2017 Nov 2;24(11):977-985. Epub 2017 Oct 2.

Department of Neuroscience, Physiology & Pharmacology, University College London, London, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nsmb.3477DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853794PMC
November 2017

Proton reduction reaction catalyzed by homoleptic nickel bis-1,2-dithiolate complexes: Experimental and theoretical mechanistic investigations.

ChemCatChem 2017 Jun 21;9(12):2308-2317. Epub 2017 Apr 21.

Inorganic Chemistry Laboratory, Chemistry Department, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou 157 71, Greece.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/cctc.201601399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5490785PMC
June 2017

An Algorithm for Adaptive QC/MM Simulations.

Authors:
Martin J Field

J Chem Theory Comput 2017 May 6;13(5):2342-2351. Epub 2017 Apr 6.

Dynamo Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale , 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jctc.7b00099DOI Listing
May 2017

Norovirus RNA-dependent RNA polymerase: A computational study of metal-binding preferences.

Proteins 2017 Aug 22;85(8):1435-1445. Epub 2017 Apr 22.

Dynamo Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, Grenoble Cedex 9, 38044, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.25304DOI Listing
August 2017

Catalytic Mechanism of Peptidoglycan Deacetylase: A Computational Study.

J Phys Chem B 2017 01 27;121(1):89-99. Epub 2016 Dec 27.

Dynamo Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale , 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jpcb.6b10625DOI Listing
January 2017

Artificial Hydrogenases Based on Cobaloximes and Heme Oxygenase.

Chempluschem 2016 Oct;81(10):1083-1089

Laboratory of Chemistry and Biology of Metals, UMR 5249, Université Grenoble Alpes, CNRS, CEA, 17 rue des Martyrs, 38054, Grenoble Cedex 9, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/cplu.201600218DOI Listing
October 2016

Structural Determinants of Improved Fluorescence in a Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins: Insights from Continuum Electrostatic Calculations and Molecular Dynamics Simulations.

Biochemistry 2016 08 29;55(31):4263-74. Epub 2016 Jul 29.

Université Grenoble Alpes , Institut de Biologie Structurale (IBS), F-38044 Grenoble, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.biochem.6b00295DOI Listing
August 2016

Hybrid Potential Simulation of the Acylation of Enterococcus faecium l,d-Transpeptidase by Carbapenems.

J Phys Chem B 2016 06 19;120(21):4767-81. Epub 2016 May 19.

RMN, UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jpcb.6b02836DOI Listing
June 2016

Aminoacetylation Reaction Catalyzed by Leucyl-tRNA Synthetase Operates via a Self-Assisted Mechanism Using a Conserved Residue and the Aminoacyl Substrate.

J Phys Chem B 2016 05 10;120(19):4388-98. Epub 2016 May 10.

Dynamo Team, DYNAMOP Group, UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale , 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jpcb.6b02387DOI Listing
May 2016

Experimental and Theoretical Insight into Electrocatalytic Hydrogen Evolution with Nickel Bis(aryldithiolene) Complexes as Catalysts.

Inorg Chem 2016 Jan 8;55(2):432-44. Epub 2015 Dec 8.

Inorganic Chemistry Laboratory, Chemistry Department, National and Kapodistrian University of Athens , Panepistimiopolis, Zografou 157 71, Greece.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/10.1021/acs.inorgchem.5b02000
Publisher Site
http://dx.doi.org/10.1021/acs.inorgchem.5b02000DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493980PMC
January 2016

Pcetk: A pDynamo-based Toolkit for Protonation State Calculations in Proteins.

J Chem Inf Model 2015 Oct 4;55(10):2288-96. Epub 2015 Oct 4.

Université Grenoble Alpes, IBS , F-38044 Grenoble, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jcim.5b00262DOI Listing
October 2015

Ferric-Thiolate Bond Dissociation Studied with Electronic Structure Calculations.

J Phys Chem A 2015 Oct 18;119(39):10084-90. Epub 2015 Sep 18.

Institut de Biologie Structurale (IBS), CEA/CNRS/Université Joseph Fourier , 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.jpca.5b05658DOI Listing
October 2015

Force-induced chemical reactions on the metal centre in a single metalloprotein molecule.

Nat Commun 2015 Jun 25;6:7569. Epub 2015 Jun 25.

Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms8569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491811PMC
June 2015

Dye-sensitized PS-b-P2VP-templated nickel oxide films for photoelectrochemical applications.

Interface Focus 2015 Jun;5(3):20140083

Laboratoire de Chimie et Biologie des Métaux , University Grenoble Alpes , CNRS, CEA, 17 rue des martyrs, 38000 Grenoble , France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1098/rsfs.2014.0083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410559PMC
June 2015

Technical advances in molecular simulation since the 1980s.

Authors:
Martin J Field

Arch Biochem Biophys 2015 Sep 13;582:3-9. Epub 2015 Mar 13.

Dynamo Team, DYNAMOP Group, UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.abb.2015.03.005DOI Listing
September 2015

Multiple proton relay routes in the reaction mechanism of RNAP II: assessing the effect of structural model.

Proteins 2015 Feb 18;83(2):268-81. Epub 2014 Dec 18.

Department of Chemistry, Centre for Molecular Simulation, Institute for Quantum Science and Technology, University of Calgary, Calgary, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.24732DOI Listing
February 2015

Enzymatic minimum free energy path calculations using swarms of trajectories.

J Phys Chem B 2015 Jan 17;119(3):1103-13. Epub 2014 Oct 17.

Institute of Advanced Chemistry of Catalonia (IQAC), CSIC , Jordi Girona 18-26, 08034, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jp506593tDOI Listing
January 2015

Theoretical modeling of low-energy electronic absorption bands in reduced cobaloximes.

Chemphyschem 2014 Oct 11;15(14):2951-8. Epub 2014 Aug 11.

Dynamo Team, DYNAMOP Group, Institut de Biologie Structurale-Jean-Pierre Ebel, UMR 5075, Université Grenoble 1, CNRS, CEA, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9 (France).

View Article

Download full-text PDF

Source
http://doi.wiley.com/10.1002/cphc.201402398
Publisher Site
http://dx.doi.org/10.1002/cphc.201402398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530012PMC
October 2014

QM/MM through the 1990s: The First Twenty Years of Method Development and Applications.

Isr J Chem 2014 Aug 31;54(8-9):1250-1263. Epub 2014 Jul 31.

State Key Laboratory of Theoretical and Computational Chemistry, Theoretical Chemistry Institute, Jilin University, Changchun, Jilin Province (China).

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/ijch.201400036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5788202PMC
August 2014

Cobaloxime-based artificial hydrogenases.

Inorg Chem 2014 Aug 16;53(15):8071-82. Epub 2014 Jul 16.

Laboratory of Chemistry and Biology of Metals, Université Grenoble Alpes, CNRS, CEA , 17 rue des Martyrs, F-38000 Grenoble, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ic501014cDOI Listing
August 2014

Electronic structure and hydration of tetramine cobalt hydride complexes.

J Phys Chem B 2014 May 14;118(20):5551-61. Epub 2014 May 14.

DYNAMO/DYNAMOP, Institut de Biologie Structurale (UMR5075, CEA, CNRS, Université Grenoble I ), 6 rue Jules Horowitz, 38000 Grenoble, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jp502651sDOI Listing
May 2014

The mechanism of citryl-coenzyme A formation catalyzed by citrate synthase.

J Phys Chem B 2014 May 22;118(17):4505-13. Epub 2014 Apr 22.

Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique , 91128 Palaiseau, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jp412346gDOI Listing
May 2014

Hydrolysis of DFP and the nerve agent (S)-sarin by DFPase proceeds along two different reaction pathways: implications for engineering bioscavengers.

J Phys Chem B 2014 May 21;118(17):4479-89. Epub 2014 Apr 21.

UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831-6309, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jp410422cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4010294PMC
May 2014

Simple Link Atom Saccharide Hybrid (SLASH) Treatment for Glycosidic Bonds at the QM/MM Boundary.

J Chem Theory Comput 2014 Apr;10(4):1727-38

Institut de Biologie Structurale - Jean-Pierre Ebel CEA/CNRS/UJF, 41, rue Jules Horowitz, 38027 Grenoble Cedex 1, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ct400903nDOI Listing
April 2014

Characterization of the divalent metal binding site of bacterial polysaccharide deacetylase using crystallography and quantum chemical calculations.

Proteins 2014 Jul 15;82(7):1311-8. Epub 2014 Jan 15.

PATBAC, Institut de Biologie Structurale-Jean-Pierre Ebel, Grenoble, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.24497DOI Listing
July 2014

Activation of a unique flavin-dependent tRNA-methylating agent.

Biochemistry 2013 Dec 20;52(49):8949-56. Epub 2013 Nov 20.

Laboratoire de Chimie des Processus Biologiques, CNRS-FRE 3488, Collège De France , 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi4013879DOI Listing
December 2013

Conformational compression and barrier height heterogeneity in the N-acetylglutamate kinase.

J Phys Chem B 2013 Nov 13;117(46):14261-72. Epub 2013 Nov 13.

Institute of Advanced Chemistry of Catalonia (IQAC), CSIC , Jordi Girona 18-26, 08034, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jp407016vDOI Listing
November 2013

GTKDynamo: a PyMOL plug-in for QC/MM hybrid potential simulations.

J Comput Chem 2013 Sep;34(25):2190-6

Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos–SP, Brazil.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4212890PMC
http://dx.doi.org/10.1002/jcc.23346DOI Listing
September 2013

A computational study of the mechanism of hydrogen evolution by cobalt(diimine-dioxime) catalysts.

Chemistry 2013 Nov 17;19(45):15166-74. Epub 2013 Sep 17.

Dynamo Team, DYNAMOP Group, UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale "Jean-Pierre Ebel", 41 rue Jules Horowitz, 38027 Grenoble Cedex 1 (France).

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/chem.201301860DOI Listing
November 2013

Mechanism of activation of elongation factor Tu by ribosome: catalytic histidine activates GTP by protonation.

RNA 2013 Sep 17;19(9):1218-25. Epub 2013 Jul 17.

Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1261/rna.040097.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753929PMC
September 2013

Homolytic cleavage of Fe-S bonds in rubredoxin under mechanical stress.

Angew Chem Int Ed Engl 2013 Jul 18;52(31):8144-6. Epub 2013 Jun 18.

Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, 05508-900, São Paulo, SP, Brazil.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/anie.201303462DOI Listing
July 2013

Catalytic hydrogen production by a Ni-Ru mimic of NiFe hydrogenases involves a proton-coupled electron transfer step.

Chem Commun (Camb) 2013 Jun 23;49(44):5004-6. Epub 2013 Apr 23.

Laboratoire de Chimie et Biologie des Métaux, Université Joseph Fourier, Grenoble, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1039/c3cc40987bDOI Listing
June 2013

Computational 17O-NMR spectroscopy of organic acids and peracids: comparison of solvation models.

Phys Chem Chem Phys 2013 Jan;15(4):1130-40

Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1039/c2cp43021eDOI Listing
January 2013

Combined experimental-theoretical characterization of the hydrido-cobaloxime [HCo(dmgH)2(PnBu3)].

Inorg Chem 2012 Jul 19;51(13):7087-93. Epub 2012 Jun 19.

Dynamo Team, DYNAMOP Group, UMR 5075, Université Grenoble 1, CNRS, CEA; Institut de Biologie Structurale Jean-Pierre Ebel, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ic2024204DOI Listing
July 2012

A hybrid elastic band string algorithm for studies of enzymatic reactions.

Phys Chem Chem Phys 2012 Sep 10;14(36):12544-53. Epub 2012 May 10.

Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1039/c2cp40918fDOI Listing
September 2012

Comparative DFT study to determine if α-oxoaldehydes are precursors for pentosidine formation.

J Phys Chem A 2012 Mar 7;116(11):2986-96. Epub 2012 Mar 7.

Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, Evin, 19839-63113, Tehran, Iran.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/10.1021/jp2104165
Publisher Site
http://dx.doi.org/10.1021/jp2104165DOI Listing
March 2012

Sampling the conformational energy landscape of a hyperthermophilic protein by engineering key substitutions.

Mol Biol Evol 2012 Jun 19;29(6):1683-94. Epub 2012 Jan 19.

Dynamop Group, Institut de Biologie Structurale J.-P. Ebel, CEA CNRS UJF, UMR 5075, Grenoble cedex 01, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/mss015DOI Listing
June 2012

The nature of transient dark states in a photoactivatable fluorescent protein.

J Am Chem Soc 2011 Nov 31;133(46):18586-9. Epub 2011 Oct 31.

Institut de Biologie Structurale (IBS)-Jean-Pierre Ebel, CEA/CNRS/ Université Joseph Fourier, 41, rue Jules Horowitz, 38027 Grenoble Cedex 1, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ja2085355DOI Listing
November 2011

Cross-linking mechanisms of arginine and lysine with α,β-dicarbonyl compounds in aqueous solution.

J Phys Chem A 2011 Nov 26;115(46):13542-55. Epub 2011 Oct 26.

Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, Tehran, Iran.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jp205558dDOI Listing
November 2011

Efficient solvent boundary potential for hybrid potential simulations.

Phys Chem Chem Phys 2011 Jun 8;13(22):10503-9. Epub 2011 Mar 8.

Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale Jean-Pierre Ebel (CEA, CNRS UMR5075, Université Joseph Fourier-Grenoble I), 41 rue Jules Horowitz, 38027 Grenoble, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1039/c0cp02828bDOI Listing
June 2011

Diffusion pathways of oxygen species in the phototoxic fluorescent protein KillerRed.

Photochem Photobiol Sci 2010 Oct 31;9(10):1342-50. Epub 2010 Aug 31.

Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, Université Joseph Fourier, 41 rue Jules Horowitz, F-38027, Grenoble, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1039/c0pp00141dDOI Listing
October 2010

A structural and functional mimic of the active site of NiFe hydrogenases.

Chem Commun (Camb) 2010 Aug 12;46(32):5876-8. Epub 2010 Jul 12.

Laboratoire de Chimie et Biologie des Métaux, Université Joseph Fourier, Grenoble, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1039/c001675fDOI Listing
August 2010

Pentacoordinated phosphorus revisited by high-level QM/MM calculations.

Proteins 2010 Aug;78(11):2405-11

Departament de Química Biològica i Modelització Molecular, Institut de Química Avançada de Catalunya (CSIC), Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.22758DOI Listing
August 2010

Mechanism of hydrogen evolution catalyzed by NiFe hydrogenases: insights from a Ni-Ru model compound.

Dalton Trans 2010 Mar 14;39(12):3043-9. Epub 2009 Dec 14.

Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale Jean-Pierre Ebel, UMR CNRS/UJF/CEA 5075, 41 rue Jules Horowitz F-38027, Grenoble cedex 1, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1039/b912690bDOI Listing
March 2010

Editing mechanism of aminoacyl-tRNA synthetases operates by a hybrid ribozyme/protein catalyst.

J Am Chem Soc 2010 Mar;132(8):2751-8

Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba Science City, Ibaraki 305-8577, Japan.

View Article

Download full-text PDF

Source
http://pubs.acs.org/doi/abs/10.1021/ja9095208
Publisher Site
http://dx.doi.org/10.1021/ja9095208DOI Listing
March 2010

Photoconversion of the fluorescent protein EosFP: a hybrid potential simulation study reveals intersystem crossings.

J Am Chem Soc 2009 Nov;131(46):16814-23

CNRS, UMR5075, Institut de Biologie Structurale Jean-Pierre Ebel, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ja905380yDOI Listing
November 2009

Intrinsic dynamics in ECFP and Cerulean control fluorescence quantum yield.

Biochemistry 2009 Oct;48(42):10038-46

Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS-CEA-Universite Joseph Fourier, F-38027 Grenoble Cedex 1, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi901093wDOI Listing
October 2009

Cyclopentadienyl ruthenium-nickel catalysts for biomimetic hydrogen evolution: electrocatalytic properties and mechanistic DFT studies.

Chemistry 2009 Sep;15(37):9350-64

Laboratoire de Chimie et Biologie des Métaux, Université Joseph Fourier, Grenoble, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/chem.200900854DOI Listing
September 2009

A minima hopping study of all-atom protein folding and structure prediction.

J Phys Chem B 2009 May;113(20):7315-21

Departement Physik, Universität Basel, Klingelbergstr. 82, 4056 Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jp8106793DOI Listing
May 2009

Structural characterization of IrisFP, an optical highlighter undergoing multiple photo-induced transformations.

Proc Natl Acad Sci U S A 2008 Nov 18;105(47):18343-8. Epub 2008 Nov 18.

European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, BP 220, 38043 Grenoble Cedex, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0805949105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2587625PMC
November 2008

The pDynamo Program for Molecular Simulations using Hybrid Quantum Chemical and Molecular Mechanical Potentials.

Authors:
Martin J Field

J Chem Theory Comput 2008 Jul;4(7):1151-61

Laboratoire de Dynamique Moléculaire Institut de Biologie Structurale - Jean-Pierre Ebel (CEA/CNRS/UJF - UMR 9075), 41 Rue Jules Horowitz, F - 38027 Grenoble, Cedex 01, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ct800092pDOI Listing
July 2008

A QM/MM study of proton transport pathways in a [NiFe] hydrogenase.

Proteins 2008 Oct;73(1):195-203

Laboratoire de Dynamique Moléculaire, IBS (Institut de Biologie Structurale-Jean-Pierre Ebel), CEA, CNRS, Université Joseph Fourier, F-38027 Grenoble, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.22045DOI Listing
October 2008

The enamine intermediate may not be universal to thiamine catalysis.

Angew Chem Int Ed Engl 2008 ;47(4):628

Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale Jean-Pierre Ebel, CEA; CNRS; UJF, 41 rue Jules Horowitz, 38027 Grenoble, France, Fax: (+33)4-3878-4217.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/anie.200890003DOI Listing
March 2008

The enamine intermediate may not be universal to thiamine catalysis.

Angew Chem Int Ed Engl 2007 ;46(47):9019-22

Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, 41 rue Jules Horowitz, 38027 Grenoble, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/anie.200702993DOI Listing
January 2008

Binding of calcium and other metal ions to the EF-hand loops of calmodulin studied by quantum chemical calculations and molecular dynamics simulations.

J Phys Chem B 2007 Aug 28;111(33):10012-22. Epub 2007 Jul 28.

Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale-Jean-Pierre Ebel, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jp0716583DOI Listing
August 2007

Improving the efficiency of the NEB reaction path finding algorithm.

J Comput Chem 2008 Jan;29(1):139-43

IBS, Institut de Biologie Structurale, Jean-Pierre Ebel, 41 rue Jules Horowitz, F-38027, Grenoble, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/jcc.20780DOI Listing
January 2008

A transition path sampling study of the reaction catalyzed by the enzyme chorismate mutase.

J Phys Chem B 2007 May 3;111(20):5708-18. Epub 2007 May 3.

Departament de Química Orgànica Biologica Institut de Investigaciones Químiques i Ambientals de Barcelona, Consejo Superior de Investigaciones Cientificas, Jordi Girona 18, 08034 Barcelona, Catalonia, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jp067629uDOI Listing
May 2007

New insights into the reaction mechanism catalyzed by the glutamate racemase enzyme: pH titration curves and classical molecular dynamics simulations.

J Phys Chem B 2007 Mar 8;111(9):2385-97. Epub 2007 Feb 8.

Departament de Química and Institut de Biotecnologia i de Biomedicina, Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/jp066350aDOI Listing
March 2007

A comparative QM/MM simulation study of the reaction mechanisms of human and Plasmodium falciparum HG(X)PRTases.

J Am Chem Soc 2006 Aug;128(31):10096-102

Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale--Jean-Pierre Ebel (CEA/CNRS/UJF), 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ja060823+DOI Listing
August 2006

A computational study of the deacylation mechanism of human butyrylcholinesterase.

Biochemistry 2006 Jun;45(24):7529-43

Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006 Oviedo, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/bi052176pDOI Listing
June 2006

An implementation of the nudged elastic band algorithm and application to the reaction mechanism of HGXPRTase from Plasmodium falciparum.

J Mol Graph Model 2005 Oct 13;24(2):102-10. Epub 2005 Jun 13.

Institut d'Investigacions Químiques i Ambientals de Barcelona (CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmgm.2005.05.003DOI Listing
October 2005

A quantum chemical study of the reaction mechanism of acetyl-coenzyme a synthase.

J Am Chem Soc 2005 Mar;127(8):2776-84

Laboratoire de Dynamique Moléculaire and Laboratoire de Cristallographie et Cristallogenèse des Protéines, Institut de Biologie Structurale - Jean-Pierre Ebel, CEA/CNRS/UJF, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 01, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ja0439221DOI Listing
March 2005

Molecular dynamics simulations of human butyrylcholinesterase.

Proteins 2005 Apr;59(1):104-17

Departamento de Química Física y Analítica, Universidad de Oviedo, Oviedo, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.20398DOI Listing
April 2005

Development and testing of a de novo drug-design algorithm.

J Comput Aided Mol Des 2003 Oct;17(10):621-41

Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale-Jean-Pierre Ebel-CEA/CNRS, 41 Rue Jules Horowitz, F-38027 Grenoble Cedex 01, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1023/b:jcam.0000017362.66268.d5DOI Listing
October 2003

Transition events in one dimension.

Phys Rev E Stat Nonlin Soft Matter Phys 2004 Jan 12;69(1 Pt 1):012101. Epub 2004 Jan 12.

Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale-Jean-Pierre Ebel (CEA-CNRS), Grenoble Cedex 1, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.69.012101DOI Listing
January 2004

Insights into the phosphoryl-transfer mechanism of cAMP-dependent protein kinase from quantum chemical calculations and molecular dynamics simulations.

J Am Chem Soc 2004 Jan;126(2):529-42

Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale-Jean-Pierre Ebel, CEA/CNRS, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 1, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ja037277uDOI Listing
January 2004

A computational study of the open and closed forms of the N-lobe human serum transferrin apoprotein.

Biophys J 2003 Dec;85(6):3485-501

Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale Jean-Pierre Ebel, Commissariat à l'Energie Atomique, and the Centre National de Recherche Scientifique, Grenoble, France.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1303656PMC
http://dx.doi.org/10.1016/S0006-3495(03)74769-9DOI Listing
December 2003

Understanding the acylation mechanisms of active-site serine penicillin-recognizing proteins: a molecular dynamics simulation study.

Proteins 2003 Oct;53(1):88-100

Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale Jean-Pierre Ebel, CEA/CNRS Grenoble, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.10450DOI Listing
October 2003

Comment on "Action-derived molecular dynamics in the study of rare events".

Phys Rev Lett 2003 Feb 26;90(8):089801; author reply 089802. Epub 2003 Feb 26.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevLett.90.089801DOI Listing
February 2003

Initial catalytic events in class 3 aldehyde dehydrogenase: MM and QM/MM simulations.

Chem Biol Interact 2003 Feb;143-144:75-84

Pittsburgh Supercomputing Center, Biomedical Initiative Group, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/s0009-2797(02)00175-8DOI Listing
February 2003

Parametrization of a force field for metals complexed to biomacromolecules: applications to Fe(II), Cu(II) and Pb(II).

J Comput Aided Mol Des 2002 Aug-Sep;16(8-9):635-51

Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec, Canada H3C 3J7.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1023/a:1021962616650DOI Listing
August 2003

Molecular dynamics study of Desulfovibrio africanus cytochrome c3 in oxidized and reduced forms.

Biophys J 2002 Dec;83(6):3049-65

Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale J.P. Ebel, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1302385PMC
http://dx.doi.org/10.1016/S0006-3495(02)75310-1DOI Listing
December 2002

Reaction mechanism of the HGXPRTase from Plasmodium falciparum: a hybrid potential quantum mechanical/molecular mechanical study.

J Am Chem Soc 2002 Oct;124(42):12432-8

Laboratoire de Dynamique Moléculaire Institut de Biologie Structurale Jean-Pierre Ebel, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 01, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/ja0206846DOI Listing
October 2002

Simulating enzyme reactions: challenges and perspectives.

Authors:
Martin J Field

J Comput Chem 2002 Jan;23(1):48-58

Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale, Grenoble, France.

View Article

Download full-text PDF

Source
https://www.csb.pitt.edu/BBSI/2005/jc_paper/caster.pdf
Web Search
http://doi.wiley.com/10.1002/jcc.1156
Publisher Site
http://dx.doi.org/10.1002/jcc.1156DOI Listing
January 2002