New Approaches to Empirical Force Fields

[1]  L. Bartell.  REPRESENTATIONS OF MOLECULAR FORCE FIELDS. 3. GAUCHE CONFORMATIONAL ENERGY , 1977 .

[2]  H. Scheraga,et al.  Monte Carlo-minimization approach to the multiple-minima problem in protein folding. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Martin Karplus,et al.  Simulation of Protein Dynamics , 1980 .

[4]  D J Osguthorpe,et al.  Dynamics and conformational energetics of a peptide hormone: vasopressin. , 1985, Science.

[5]  A procedure for obtaining energy parameters from crystal packing , 1974 .

[6]  M. Karplus,et al.  A model for the simulation of an aqueous dipeptide solution , 1979 .

[7]  A. M. Liquori.  The stereochemical code and the logic of a protein molecule , 1969, Quarterly Reviews of Biophysics.

[8]  T. Starr,et al.  Coulombic nonbonded interatomic potential functions derived from crystal‐lattice vibrational frequencies in hydrocarbons , 1977 .

[9]  H. Scheraga,et al.  Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H...O = C hydrogen bonds from packing configurations , 1984 .

[10]  Thomas L. Starr,et al.  Calculation of the crystal structures of hydrocarbons by molecular packing analysis , 1977, Comput. Chem..

[11]  D. C. Rapaport,et al.  Evolution and stability of polypeptide chain conformation: a simulation study , 1981 .

[12]  J A McCammon,et al.  Theoretical calculation of relative binding affinity in host-guest systems. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Analytical energy derivatives and normal modes in force fields employing lone‐pair pseudoatoms , 1989 .

[14]  Norman L. Allinger,et al.  Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons , 1989 .

[15]  D. Osguthorpe,et al.  Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase‐trimethoprim, a drug‐receptor system , 1988, Proteins.

[16]  U. Dinur.  On the interpretation of infrared intensities in planar molecular systems , 1990 .

[17]  H A Scheraga,et al.  Energy parameters in polypeptides. V. An empirical hydrogen bond potential function based on molecular orbital calculations. , 1972, The Journal of physical chemistry.

[18]  F. L. Hirshfeld.  Bonded-atom fragments for describing molecular charge densities , 1977 .

[19]  N. L. Allinger.  Calculation of Molecular Structure and Energy by Force-Field Methods , 1976 .

[20]  J. Hermans,et al.  Conformational statistics of short chains of poly(L‐alanine) and poly(glycine) generated by Monte Carlo method and the partition function of chains with constrained ends , 1973 .

[21]  A. T. Hagler,et al.  Determination of atomic point charges and point dipoles from the Cartesian derivatives of the molecular dipole moment and second moments, and from energy second derivatives of planar dimers. I. Theory , 1989 .

[22]  H. Berendsen,et al.  Computer simulation of the dynamics of hydrated protein crystals and its comparison with x-ray data. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[23]  G. Fogarasi,et al.  A comparative ab initio study of amides: Part I. Force fields and vibrational assignments for formamide, acetamide and N-methylformamide , 1985 .

[24]  Arnold T. Hagler,et al.  Direct evaluation of nonbonding interactions from ab initio calculations , 1989 .

[25]  Janet E. Jones.  On the determination of molecular fields. —II. From the equation of state of a gas , 1924 .

[26]  S. Krimm,et al.  Infrared intensities of amide modes in N‐methylacetamide and poly(glycine I) from ab initio calculations of dipole moment derivatives of N‐methylacetamide , 1985 .

[27]  Norman L. Allinger,et al.  Conformational analysis. 125. The importance of twofold barriers in saturated molecules , 1977 .

[28]  J. Moult,et al.  Computer simulation of the solvent structure around biological macromolecules , 1978, Nature.

[29]  A. Warshel,et al.  Consistent Force Field Calculations. II. Crystal Structures, Sublimation Energies, Molecular and Lattice Vibrations, Molecular Conformations, and Enthalpies of Alkanes , 1970 .

[30]  S. Lifson,et al.  Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 1. Carboxylic acids, amides, and the C:O.cntdot..cntdot..cntdot.H- hydrogen bonds , 1979 .

[31]  Albert J. Cross,et al.  Influence of hamiltonian parameterization on convergence of kirkwood free energy calculations , 1986 .

[32]  T. Straatsma,et al.  THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .

[33]  H. Berendsen,et al.  A consistent empirical potential for water–protein interactions , 1984 .

[34]  C. Altona,et al.  Application of self-consistent-field ab initio calculations to organic molecules , 1976 .

[35]  C. Altona,et al.  Application of self-consistent-field ab initio calculations to organic molecules: III. Equilibrium structure of water, methanol and dimethyl ether, general valence force field of water and methanol scaled on experimental frequencies , 1976 .

[36]  Patrick W. Fowler,et al.  Do electrostatic interactions predict structures of van der Waals molecules , 1983 .

[37]  J. S. Binkley,et al.  Electron correlation theories and their application to the study of simple reaction potential surfaces , 1978 .

[38]  D. Osguthorpe,et al.  Monte Carlo simulation of water behavior around the dipeptide N-acetylalanyl-N-methylamide. , 1980, Science.

[39]  M Karplus,et al.  The internal dynamics of globular proteins. , 1981, CRC critical reviews in biochemistry.

[40]  William L. Jorgensen,et al.  Molecular dynamics of proteins with the OPLS potential functions. Simulation of the third domain of silver pheasant ovomucoid in water , 1990 .

[41]  Olga Kennard,et al.  Tables of bond lengths determined by X-ray and neutron diffraction. Part 1. Bond lengths in organic compounds , 1987 .

[42]  M. R. Peterson,et al.  A standard geometrical model for compounds of the main group elements H through I , 1985 .

[43]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

[44]  A. Hagler,et al.  Determination of atomic point charges and point dipoles from the Cartesian derivatives of the molecular dipole moment and second moments, and from energy second derivatives of planar dimers. II. Applications to model systems , 1989 .

[45]  U. Singh,et al.  Free energy perturbation calculations on binding and catalysis after mutating Asn 155 in subtilisin , 1987, Nature.

[46]  A. T. Hagler,et al.  Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 3. The C:O.cntdot..cntdot..cntdot.H-O hydrogen bond and the analysis of the energetics and packing of carboxylic acids , 1979 .

[47]  P. Gund,et al.  Three-dimensional molecular modeling and drug design. , 1980, Science.

[48]  Mark A. Spackman.  A simple quantitative model of hydrogen bonding. Application to more complex systems , 1987 .

[49]  Donald E. Williams,et al.  LONE-PAIR ELECTRONIC EFFECTS ON THE CALCULATED AB INITIO SCF-MO ELECTRIC POTENTIAL AND THE CRYSTAL STRUCTURES OF AZABENZENES , 1983 .

[50]  M. Karplus,et al.  Molecular dynamics simulations of native and substrate-bound lysozyme. A study of the average structures and atomic fluctuations. , 1986, Journal of molecular biology.

[51]  M Karplus,et al.  Dynamics of proteins: elements and function. , 1983, Annual review of biochemistry.

[52]  Anthony J. Stone,et al.  Distributed multipole analysis, or how to describe a molecular charge distribution , 1981 .

[53]  J. Andrew McCammon,et al.  Dynamics and design of enzymes and inhibitors , 1986 .

[54]  N. W. Murrall,et al.  How accurate does a force field need to be? , 1989, Comput. Chem..

[55]  Mark A. Spackman,et al.  A SIMPLE QUANTITATIVE MODEL OF HYDROGEN-BONDING , 1986 .

[56]  Donald E. Williams.  Repulsion Center of a Bonded Hydrogen Atom , 1965 .

[57]  Harold A. Scheraga,et al.  Calculations of Conformations of Polypeptides , 1968 .

[58]  A. T. Hagler,et al.  A novel decomposition of torsional potentials into pairwise interactions: A study of energy second derivatives , 1990 .

[59]  Arnold T. Hagler,et al.  COMPUTER SIMULATION OF THE CONFORMATIONAL PROPERTIES OF OLIGOPEPTIDES. COMPARISON OF THEORETICAL METHODS AND ANALYSIS OF EXPERIMENTAL RESULTS , 1979 .

[60]  E. Stevens.  Experimental electron density distribution of molecular chlorine , 1979 .

[61]  W. A. Sokalski,et al.  Correlated molecular and cumulative atomic multipole moments , 1987 .

[62]  Y. Miwa,et al.  Molecular mechanics simulations of thermodynamic functions and infrared spectra of alkanes , 1988 .

[63]  U. Singh,et al.  A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .

[64]  J. Kraut,et al.  Directed mutagenesis of dihydrofolate reductase. , 1983, Science.

[65]  K. Kuczera.  Uniquely defined harmonic force constants in redundant coordinates , 1987 .

[66]  Jacopo Tomasi,et al.  Electronic Molecular Structure, Reactivity and Intermolecular Forces: An Euristic Interpretation by Means of Electrostatic Molecular Potentials , 1978 .

[67]  Otto Ermer,et al.  Calculation of molecular properties using force fields. Applications in organic chemistry , 1976 .

[68]  R. Bader,et al.  Quantum Theory of Atoms in Molecules–Dalton Revisited , 1981 .

[69]  Donald E. Williams.  Representation of the molecular electrostatic potential by atomic multipole and bond dipole models , 1988 .

[70]  F. London,et al.  The general theory of molecular forces , 1937 .

[71]  U. Dinur.  Force related atomic multipoles in planar molecules. Derivation of atomic quadrupole and octupole moments , 1990 .

[72]  P. Kollman,et al.  An all atom force field for simulations of proteins and nucleic acids , 1986, Journal of computational chemistry.

[73]  U. Dinur.  "Flexible" water molecules in external electrostatic potentials , 1990 .

[74]  R. Sharon,et al.  Accurate simulation of protein dynamics in solution. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[75]  A. Hagler,et al.  Derivation of force fields for molecular mechanics and dynamics from ab initio energy surfaces. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[76]  R. Christoffersen,et al.  Development of a flexible intra‐ and intermolecular empirical potential function for large molecular systems , 1981 .

[77]  An empirical function for second neighbor interactions and its effect on vibrational modes and other properties of cyclo- and n-Alkanes , 1969 .

[78]  A. Stone,et al.  Intermolecular forces in van der waals dimers , 1986 .

[79]  H. Berendsen,et al.  Interaction Models for Water in Relation to Protein Hydration , 1981 .

[80]  P. C. Hariharan,et al.  Comparison of ab initio MODPOT interaction energy components against large basis set MBPT (4) calculations for nitromethane dimer , 1987 .

[81]  Arnold T. Hagler,et al.  Urey-Bradley force field, valence force field, and ab initio study of intramolecular forces in tri-tert-butylmethane and isobutane , 1979 .

[82]  E. Lippincott,et al.  One‐Dimensional Model of the Hydrogen Bond , 1955 .

[83]  Thomas A. Halgren,et al.  Maximally diagonal force constants in dependent angle-bending coordinates. II. Implications for the design of empirical force fields , 1990 .

[84]  S. Lifson,et al.  Born–Oppenheimer energy surfaces of similar molecules: Interrelations between bond lengths, bond angles, and frequencies of normal vibrations in alkanes , 1982 .

[85]  G. Bauer,et al.  Parameterization of site-site potentials in the spherical expansion formalism A point charge model for the electrostatic interaction of the aza-benzene molecules , 1982 .

[86]  D. E. Williams,et al.  Nonbonded potentials for azahydrocarbons: the importance of the Coulombic interaction , 1984 .

[87]  A. T. Hagler,et al.  ENERGY FUNCTIONS FOR PEPTIDES AND PROTEINS PART 2, THE AMIDE HYDROGEN BOND AND CALCULATION OF AMIDE CRYSTAL PROPERTIES , 1974 .

[88]  N. L. Allinger,et al.  An Improved Molecular Mechanics Force Field for Alcohols and Ethers , 1980 .

[89]  Norman L. Allinger,et al.  Molecular mechanics. The MM3 force field for hydrocarbons. 2. Vibrational frequencies and thermodynamics , 1989 .

[90]  W. Heisenberg,et al.  Zur Quantentheorie der Molekeln , 1924 .

[91]  M. Karplus,et al.  Dynamics of folded proteins , 1977, Nature.

[92]  A. Warshel,et al.  Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and n‐Alkane Molecules , 1968 .

[93]  Paul von Ragué Schleyer,et al.  Critical evaluation of molecular mechanics , 1973 .

[94]  Sarah L. Price,et al.  The electrostatic interactions in van der Waals complexes involving aromatic molecules , 1987 .

[95]  Donald E. Williams,et al.  Representation of the molecular electrostatic potential by a net atomic charge model , 1981 .

[96]  H. Scheraga,et al.  Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids , 1983 .

[97]  G. N. Ramachandran,et al.  Conformation of polypeptides and proteins. , 1968, Advances in protein chemistry.

[98]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[99]  J. Hermans,et al.  Excess free energy of liquids from molecular dynamics simulations. Application to water models. , 1988, Journal of the American Chemical Society.

[100]  M. Alderton,et al.  Distributed multipole analysis , 2006 .

[101]  P. Morse.  Diatomic Molecules According to the Wave Mechanics. II. Vibrational Levels , 1929 .

[102]  N. L. Allinger,et al.  A molecular mechanics study of methyl vinyl ether an related compounds , 1982 .

[103]  Patrick W. Fowler,et al.  A model for the geometries of Van der Waals complexes , 1985 .

[104]  John C. Slater,et al.  The Van Der Waals Forces in Gases , 1931 .

[105]  J. H. Schachtschneider,et al.  A valence force field for saturated hydrocarbons , 1965 .

[106]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[107]  A. Hagler,et al.  Theoretical studies of the structure and molecular dynamics of a peptide crystal. , 1988, Biochemistry.

[108]  Z. Berkovitch-yellin,et al.  The role of Coulomb forces in the crystal packing of amides. A study based on experimental electron densities , 1980 .

[109]  R. A. Scott,et al.  Monte Carlo Calculations on Polypeptide Chains. III. Multistate per Residue Hard Sphere Models for Randomly Coiling Polyglycine and Poly‐l‐alanine , 1971 .

[110]  Norman L. Allinger,et al.  Conformational analysis. 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms , 1977 .

[111]  E. Stevens,et al.  Accurate X-Ray Diffraction and Quantum Chemistry: The Study of Charge Density Distributions , 1977 .

[112]  J Moult,et al.  Molecular dynamics study of the structure and dynamics of a protein molecule in a crystalline ionic environment, Streptomyces griseus protease A. , 1990, Biochemistry.

[113]  H. Scheraga,et al.  Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids , 1975 .

[114]  O. Tapia,et al.  Molecular dynamics simulations of the holo and apo forms of retinol binding protein. Structural and dynamical changes induced by retinol removal. , 1986, Journal of molecular biology.

[115]  A. T. Hagler,et al.  Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 2. A benchmark for the objective comparison of alternative force fields , 1979 .

[116]  R. Cramer,et al.  Validation of the general purpose tripos 5.2 force field , 1989 .

[117]  Lennart Nilsson,et al.  Empirical energy functions for energy minimization and dynamics of nucleic acids , 1986 .

[118]  Robert L. Kuczkowski,et al.  Molecular structures of gas‐phase polyatomic molecules determined by spectroscopic methods , 1979 .

[119]  Arnold T. Hagler,et al.  Crystal packing, hydrogen bonding, and the effect of crystal forces on molecular conformation , 1980 .

[120]  S. Wilson,et al.  Applications of simulated annealing to peptides , 1990, Biopolymers.

[121]  S. Lifson,et al.  Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. , 1974, Journal of the American Chemical Society.

[122]  Arieh Warshel,et al.  Incorporating electric polarizabilities in water-water interaction potentials , 1990 .

[123]  W. L. Jorgensen,et al.  Monte Carlo simulation of differences in free energies of hydration , 1985 .

[124]  P. Kollman,et al.  An approach to computing electrostatic charges for molecules , 1984 .

[125]  Sarah L. Price,et al.  A TRANSFERABLE DISTRIBUTED MULTIPOLE MODEL FOR THE ELECTROSTATIC INTERACTIONS OF PEPTIDES AND AMIDES , 1990 .

[126]  Wilfred F. van Gunsteren,et al.  Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry , 1987, J. Comput. Aided Mol. Des..

[127]  O. Teleman,et al.  Molecular dynamics simulation of interfacial water structure and dynamics in a parvalbumin solution , 1988 .

[128]  Shneior Lifson,et al.  Consistent force field calculations. III. Vibrations, conformations, and heats of hydrogenation of nonconjugated olefins , 1973 .

[129]  Peter Pulay,et al.  Combination of theoretical ab initio and experimental information to obtain reliable harmonic force constants. Scaled quantum mechanical (QM) force fields for glyoxal, acrolein, butadiene, formaldehyde, and ethylene , 1983 .