A molecular dynamics simulation study of chloroform

Three different chloroform models have been investigated using molecular dynamics computer simulation. The thermodynamic, structural and dynamic properties of the various models were investigated in detail. In particular, the potential energies, diffusion coefficients and rotational correlation times obtained for each model are compared with experiment. It is found that the theory of rotational Brownian motion fails in describing the rotational diffusion of chloroform. The force field of Dietz and Heinzinger was found to give good overall agreement with experiment. An extended investigation of this chloroform model has been performed. Values are reported for the isothermal compressibility, the thermal expansion coefficient and the constant volume heat capacity. The values agree well with experiment. The static and frequency dependent dielectric permittivity were computed from a 1·2 ns simulation conducted under reaction field boundary conditions. Considering the fact that the model is rigid with fixed par...

[1]  M. Karplus,et al.  Protein dynamics in solution and in a crystalline environment: a molecular dynamics study. , 1982, Biochemistry.

[2]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

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

[4]  W F van Gunsteren,et al.  An NMR‐based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution , 1989, Proteins.

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

[6]  Michael P. Allen,et al.  Computer simulation in chemical physics , 1993 .

[7]  R. Levy,et al.  Molecular dynamics simulation of solvated protein at high pressure. , 1992, Biochemistry.

[8]  D. Hartsough,et al.  Protein dynamics and solvation in aqueous and nonaqueous environments , 1993 .

[9]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[10]  J. Goodfellow Computer Simulation of Macromolecules , 1990 .

[11]  J. Kirkwood Statistical Mechanics of Fluid Mixtures , 1935 .

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

[13]  Evans,et al.  Relationship between McQuarrie and Helfand equations for the determination of shear viscosity from equilibrium molecular dynamics. , 1993, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[14]  H. Berendsen,et al.  Simulations of Proteins in Water a , 1986, Annals of the New York Academy of Sciences.

[15]  J. C. Martin,et al.  Domain communication in the dynamical structure of human immunodeficiency virus 1 protease. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[16]  K. Heinzinger,et al.  Structure of Liquid Chloroform. A Comparison between Computer Simulation and Neutron Scattering Results , 1984 .

[17]  Alan E. Mark,et al.  Dielectric properties of trypsin inhibitor and lysozyme calculated from molecular dynamics simulations , 1993 .

[18]  H. Berendsen,et al.  Conformational flexibility of aqueous monomeric and dimeric insulin: a molecular dynamics study. , 1991, Biochemistry.

[19]  R. C. Weast CRC Handbook of Chemistry and Physics , 1973 .

[20]  Ronald M. Levy,et al.  Molecular dynamics simulations of water with Ewald summation for the long range electrostatic interactions , 1991 .

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

[22]  W F van Gunsteren,et al.  On the dependence of molecular conformation on the type of solvent environment: A molecular dynamics study of cyclosporin A , 1990, Biopolymers.

[23]  The chemical potential of water: molecular dynamics computer simulation of the CF and SPC models , 1992 .

[24]  M. Neumann The dielectric constant of water. Computer simulations with the MCY potential , 1985 .

[25]  Bernard R. Brooks,et al.  The effects of environment and hydration on protein dynamics: A simulation study of myoglobin , 1991 .

[26]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[27]  Allen,et al.  Comment on "Use of the McQuarrie equation for the computation of shear viscosity via equilibrium molecular dynamics" , 1994, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[28]  Arnold Weissberger,et al.  Organic solvents;: Physical properties and methods of purification , 1970 .

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

[30]  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.

[31]  M. Levitt,et al.  A molecular dynamics simulation of the C-terminal fragment of the L7/L12 ribosomal protein in solution , 1991 .

[32]  C. P. Smyth,et al.  Microwave Absorption and Molecular Structure in Liquids. LIII. Hydrogen Bonding and Dielectric Properties in Chloroform Mixtures , 1964 .

[33]  W F van Gunsteren,et al.  Computer simulation as a tool for tracing the conformational differences between proteins in solution and in the crystalline state. , 1984, Journal of molecular biology.

[34]  William L. Jorgensen,et al.  Relative partition coefficients for organic solutes from fluid simulations , 1990 .

[35]  W. F. Gunsteren,et al.  A comparison of the structure and dynamics of avian pancreatic polypeptide hormone in solution and in the crystal , 1985, European Biophysics Journal.

[36]  Roger Impey,et al.  Spectroscopic and transport properties of water , 1982 .

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

[38]  Max L. Berkowitz,et al.  Isothermal compressibility of SPC/E water , 1990 .

[39]  M Levitt,et al.  A model of the molten globule state from molecular dynamics simulations. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[40]  M. Evans A review and computer simulation of the structure and dynamics of liquid chloroform , 1983 .

[41]  A. Laaksonen,et al.  Molecular dynamics simulation of liquid mixtures of acetonitrile and chloroform , 1990 .

[42]  W F van Gunsteren,et al.  Simulation of the thermal denaturation of hen egg white lysozyme: trapping the molten globule state. , 1992, Biochemistry.

[43]  H. Böhm,et al.  Molecular dynamics simulation of liquid CH2Cl2 and CHCl3 with new pair potentials , 1985 .

[44]  M. P. Allen,et al.  SOME NOTES ON EINSTEIN RELATIONSHIPS , 1993 .

[45]  Martin Neumann,et al.  Dipole moment fluctuation formulas in computer simulations of polar systems , 1983 .

[46]  C L Brooks,et al.  Characterization of "native" apomyoglobin by molecular dynamics simulation. , 1992, Journal of molecular biology.

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

[48]  Harold A. Scheraga,et al.  Intermolecular potentials from crystal data. III. Determination of empirical potentials and application to the packing configurations and lattice energies in crystals of hydrocarbons, carboxylic acids, amines, and amides , 1974 .

[49]  K. Heinzinger,et al.  A molecular dynamics study of liquid chloroform , 1985 .

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