Intramolecular interaction energies in model alanine and glycine tetrapeptides. Evaluation of anisotropy, polarization, and correlation effects. A parallel ab initio HF/MP2, DFT, and polarizable molecular mechanics study
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Nohad Gresh | Dennis R. Salahub | Jean-François Truchon | Sherif A. Kafafi | D. Salahub | S. Kafafi | N. Gresh | Jean-François Truchon
[1] Peter Pulay,et al. Efficient elimination of basis set superposition errors by the local correlation method: Accurate ab initio studies of the water dimer , 1993 .
[2] William H. Fink,et al. Frozen fragment reduced variational space analysis of hydrogen bonding interactions. Application to the water dimer , 1987 .
[3] Enhanced intramolecular amide-amide hydrogen bonding through cooperativity , 1996 .
[4] S. Nilar,et al. Hydrogen-Bonding Capabilities Based on Polarizability Studies of Model Peptide Systems , 1995 .
[5] Sarah L. Price,et al. A TRANSFERABLE DISTRIBUTED MULTIPOLE MODEL FOR THE ELECTROSTATIC INTERACTIONS OF PEPTIDES AND AMIDES , 1990 .
[6] A. Becke. Correlation energy of an inhomogeneous electron gas: A coordinate‐space model , 1988 .
[8] Nohad Gresh,et al. A theoretical study of nonadditive effects in four water tetramers , 1998 .
[9] T. Simonson,et al. Macromolecular electrostatics: continuum models and their growing pains. , 2001, Current opinion in structural biology.
[10] Laurent Emmanuel Dardenne,et al. Reassociation of fragments using multicentered multipolar expansions: peptide junction treatments to investigate electrostatic properties of proteins , 2001, J. Comput. Chem..
[11] T. H. Dunning. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen , 1989 .
[12] N. Špačková,et al. Theoretical Study of Binding of Hydrated Zn(II) and Mg(II) Cations to 5‘-Guanosine Monophosphate. Toward Polarizable Molecular Mechanics for DNA and RNA , 2003 .
[13] R. Ludwig,et al. Quantum Cluster Equilibrium Theory of Liquids: Temperature Dependence of Hydrogen Bonding in Liquid N-Methylacetamide Studied by IR Spectra , 1998 .
[14] P. Claverie,et al. Improvements of the continuum model. 1. Application to the calculation of the vaporization thermodynamic quantities of nonassociated liquids , 1988 .
[15] B. Roux,et al. Implicit solvent models. , 1999, Biophysical chemistry.
[16] Steven J. Stuart,et al. Dynamical fluctuating charge force fields: Application to liquid water , 1994 .
[17] Dennis R. Salahub,et al. Optimization of Gaussian-type basis sets for local spin density functional calculations. Part I. Boron through neon, optimization technique and validation , 1992 .
[18] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[19] J. Perdew,et al. Accurate and simple density functional for the electronic exchange energy: Generalized gradient approximation. , 1986, Physical review. B, Condensed matter.
[20] J. Markley,et al. Theoretical Studies of Protium/Deuterium Fractionation Factors and Cooperative Hydrogen Bonding in Peptides , 1995 .
[21] Parr,et al. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.
[22] JENS ANTONY,et al. Binding of D‐ and L‐captopril inhibitors to metallo‐β‐lactamase studied by polarizable molecular mechanics and quantum mechanics , 2002, J. Comput. Chem..
[23] Nohad Gresh,et al. Energetics of Zn2+ binding to a series of biologically relevant ligands: A molecular mechanics investigation grounded on ab initio self‐consistent field supermolecular computations , 1995, J. Comput. Chem..
[24] Nohad Gresh,et al. Conformation‐dependent intermolecular interaction energies of the triphosphate anion with divalent metal cations. Application to the ATP‐binding site of a binuclear bacterial enzyme. A parallel quantum chemical and polarizable molecular mechanics investigation , 2004, J. Comput. Chem..
[25] Ioannis N. Demetropoulos,et al. Merlin - a portable system for multidimensional minimization , 1987 .
[26] P. Reinhardt. The decomposition of intermolecular interaction energies in localized orbitals — critical analysis and an invariance , 2003 .
[27] M. Alderton,et al. Distributed multipole analysis , 2006 .
[28] Robert Rein,et al. On Physical Properties and Interactions of Polyatomic Molecules: With Application to Molecular Recognition in Biology , 1973 .
[29] Ruhong Zhou,et al. Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model , 1999 .
[30] W. Goddard,et al. Charge equilibration for molecular dynamics simulations , 1991 .
[31] David Feller,et al. Hydrogen bond energy of the water dimer , 1996 .
[32] J. P. Malrieu,et al. Localization and Delocalization in Quantum Chemistry , 1975 .
[33] S. Kafafi,et al. Ab initio determination of the structure of the active site of a metalloenzyme: Metal substitution in phosphotriesterase using density functional methods , 1999 .
[34] S. H. Vosko,et al. Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis , 1980 .
[35] R Rein,et al. Point charge representation of multicenter multipole moments in calculation of electrostatic properties , 1993, Theoretica chimica acta.
[36] E. Oelkers,et al. Calculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: dissociation constants for supercritical alkali metal halides at temperatures from 400 to 800.degree.C and pressures from 500 to 4000 bar , 1988 .
[37] P. Claverie,et al. The exact multicenter multipolar part of a molecular charge distribution and its simplified representations , 1988 .
[38] S. Suhai. Cooperative effects in hydrogen bonding: Fourth‐order many‐body perturbation theory studies of water oligomers and of an infinite water chain as a model for ice , 1994 .
[39] Nohad Gresh,et al. Intermolecular interactions: Elaboration on an additive procedure including an explicit charge-transfer contribution , 1986 .
[40] Nohad Gresh,et al. Joint quantum chemical and polarizable molecular mechanics investigation of formate complexes with penta‐ and hexahydrated Zn2+: Comparison between energetics of model bidentate, monodentate, and through‐water Zn2+ binding modes and evaluation of nonadditivity effects , 1999 .
[41] W. Andrzej Sokalski,et al. Intramolecular electrostatic interactions studied by cumulative atomic multipole moment expansion with improved convergence , 1994 .
[42] Nohad Gresh,et al. Conformational properties of a model alanyl dipeptide and of alanine‐derived oligopeptides: Effects of solvation in water and in organic solvents—A combined SIBFA/continuum reaction field, ab initio self‐consistent field, and density functional theory investigation , 1998 .
[43] Nohad Gresh,et al. Critical Role of Anisotropy for the Dimerization Energies of Two Protein−Protein Recognition Motifs: cis-N-Methylacetamide versus a β-Sheet Conformer of Alanine Dipeptide. A Joint ab Initio, Density Functional Theory, and Molecular Mechanics Investigation , 1999 .
[44] Nohad Gresh,et al. Modeling of Copper(II) Complexes with the SIBFA Polarizable Molecular Mechanics Procedure. Application to a New Class of HIV-1 Protease Inhibitors , 2003 .
[45] W. J. Stevens,et al. Transferability of molecular distributed polarizabilities from a simple localized orbital based method , 1989 .
[46] Nohad Gresh,et al. Comparative binding energetics of Mg2+, Ca2+, Zn2+, and Cd2+ to biologically relevant ligands: Combined ab initio SCF supermolecule and molecular mechanics investigation , 1996, J. Comput. Chem..
[47] Dennis R. Salahub,et al. Extension of the LAP functional to include parallel spin correlation , 1997 .
[48] W. A. Sokalski,et al. Correlated molecular and cumulative atomic multipole moments , 1987 .
[49] Hong Guo,et al. Cooperative Hydrogen Bonding and Enzyme Catalysis. , 1998, Angewandte Chemie.
[50] Richard A. Friesner,et al. Pseudospectral localized Mo/ller–Plesset methods: Theory and calculation of conformational energies , 1995 .
[51] Peter Pulay,et al. The local correlation treatment. II. Implementation and tests , 1988 .
[52] Ulrich Sternberg,et al. New approach to the semiempirical calculation of atomic charges for polypeptides and large molecular systems , 1994, J. Comput. Chem..
[53] Nohad Gresh,et al. Many-Body Effects in Systems of Peptide Hydrogen-Bonded Networks and Their Contributions to Ligand Binding: A Comparison of the Performances of DFT and Polarizable Molecular Mechanics , 2000 .
[54] Ulf Berg,et al. Inter‐ and intramolecular potential for the N‐formylglycinamide‐water system. A comparison between theoretical modeling and empirical force fields , 2003, J. Comput. Chem..
[55] J. Perdew,et al. Erratum: Density-functional approximation for the correlation energy of the inhomogeneous electron gas , 1986, Physical review. B, Condensed matter.
[56] P Hobza,et al. Structure, energetics, and dynamics of the nucleic Acid base pairs: nonempirical ab initio calculations. , 1999, Chemical reviews.
[57] P. Kollman,et al. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000 .
[58] Guntram Rauhut,et al. Local Treatment of Electron Correlation in Molecular Clusters: Structures and Stabilities of (H2O)n, n = 2−4 , 1998 .
[59] Martin Karplus,et al. Ab initio studies of hydrogen bonding of N-methylacetamide: structure, cooperativity, and internal rotational barriers , 1992 .
[60] Nohad Gresh,et al. Interaction of neutral and zwitterionic glycine with Zn2+ in gas phase: ab initio and SIBFA molecular mechanics calculations , 2000 .
[61] Nohad Gresh,et al. Model, Multiply Hydrogen-Bonded Water Oligomers (N = 3−20). How Closely Can a Separable, ab Initio-Grounded Molecular Mechanics Procedure Reproduce the Results of Supermolecule Quantum Chemical Computations? , 1997 .
[62] A. Becke. Density-functional thermochemistry. III. The role of exact exchange , 1993 .
[63] Walter Thiel,et al. Description of peptide and protein secondary structures employing semiempirical methods , 2001 .
[64] W. Andrzej Sokalski,et al. Analysis of the transferability of atomic multipoles for amino acids in modeling macromolecular charge distribution from fragments , 2001, J. Comput. Chem..
[65] J. Dannenberg,et al. Cooperativity in amide hydrogen bonding chains: implications for protein-folding models. , 2001, Journal of the American Chemical Society.
[66] Yun-Dong Wu,et al. Theoretical study of sheets formed by β‐peptides , 2002, J. Comput. Chem..
[67] Mark S. Gordon,et al. General atomic and molecular electronic structure system , 1993, J. Comput. Chem..
[68] Y. D. Wu,et al. A theoretical study on the origin of cooperativity in the formation of 3(10)- and alpha-helices. , 2001, Journal of the American Chemical Society.
[69] P. Claverie,et al. Theoretical studies of molecular conformation. Derivation of an additive procedure for the computation of intramolecular interaction energies. Comparison withab initio SCF computations , 1984 .
[70] R. Lavery,et al. The calculation of molecular electrostatic potential from a multipole expansion based on localized orbitals and developed at their centroids: Accuracy and applicability for macromolecular computations , 1982 .
[71] Martin Karplus,et al. Solvent Influence on the Stability of the Peptide Hydrogen Bond: A Supramolecular Cooperative Effect , 1994 .
[72] Harry A. Stern,et al. Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests , 2002, J. Comput. Chem..
[73] R. Rein,et al. Quantitative examination of the approximations in the monopole and dipole theories of intermolecular interactions. , 1972, Journal of theoretical biology.
[74] Peter Pulay,et al. Fourth‐order Mo/ller–Plessett perturbation theory in the local correlation treatment. I. Method , 1987 .
[75] M. Leboeuf,et al. Energetics and Structure in Model Neutral, Anionic, and Cationic Hydrogen-Bonded Complexes: Combined Ab Initio SCF/MP2 Supermolecular, Density Functional, and Molecular Mechanics Investigation , 1994 .
[76] A Simple Coupling Scheme between Hartree−Fock and Local Spin-Density Functional Theories , 1998 .
[77] Curt M. Breneman,et al. Transferable atom equivalent multicentered multipole expansion method , 2003, J. Comput. Chem..
[78] Jay W. Ponder,et al. Accurate modeling of the intramolecular electrostatic energy of proteins , 1995, J. Comput. Chem..
[79] Hitoshi Yamamoto,et al. Solid-state13C NMR study on order → disorder phase transition in oleic acid , 2004 .
[80] D. R. Garmer,et al. Modeling of inhibitor–metalloenzyme interactions and selectivity using molecular mechanics grounded in quantum chemistry , 1998, Proteins.
[81] Harold Basch,et al. Compact effective potentials and efficient shared‐exponent basis sets for the first‐ and second‐row atoms , 1984 .
[82] Richard A. Friesner,et al. Accurate ab Initio Quantum Chemical Determination of the Relative Energetics of Peptide Conformations and Assessment of Empirical Force Fields , 1997 .
[83] R Rein,et al. Ab initio study of the electrostatic multipole nature of torsional potentials in CH3SSCH3, CH3SSH, and HOOH. , 1991, International journal of quantum chemistry. Quantum biology symposium : proceedings of the International Symposium on Quantum Biology and Quantum Pharmacology. International Symposium on Quantum Biology and Quantum Pharmacology.
[84] Nohad Gresh,et al. Intramolecular chelation of Zn2+ by α‐ and β‐mercaptocarboxamides. A parallel ab initio and polarizable molecular mechanics investigation. Assessment of the role of multipole transferability , 2001, J. Comput. Chem..
[85] Susan K. Gregurick,et al. Computation of the Electronic and Spectroscopic Properties of Carbohydrates Using Novel Density Functional and Vibrational Self-Consistent Field Methods , 1999 .
[86] Sarah L. Price,et al. Electrostatic models for polypeptides: can we assume transferability? , 1992 .
[87] Nohad Gresh,et al. Parallel ab initio and molecular mechanics investigation of polycoordinated Zn(II) complexes with model hard and soft ligands: Variations of binding energy and of its components with number and charges of ligands , 2000, J. Comput. Chem..