Forcefield Based Simulations

A       References

Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids, Clarendon Press, Oxford Science Publications (1987).

Andersen, H. C. "Molecular dynamics simulations at constant pressure and/or temperature", J. Chem. Phys., 72, 2384 (1980).

Andersen, H. C. "Rattle: A "velocity" version of the Shake algorithm for molecular dynamics calculations", J. Comp. Physics, 52, 24-34 (1983).

Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. "Molecular dynamics with coupling to an external bath", J. Chem. Phys., 81, 3684-3690 (1984).

Born, M.; Oppenheimer, J. R. Ann. Physik, 84, 457 (1927).

Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M., J Comp. Chem., 4, 187-217 (1983).

Brooks, C. L., III; Brunger, A. T.; Karplus, M. Biopolymers, 24, 843 (1985a).

Brooks, C. L., III; Montgomery; Pettitt, B.; Karplus, M. "Structural and energetic effects of truncating long range interactions in ionic and polar fluids", J. Chem. Phys., 83, 5897-5908 (1985b).

Brown, D.; Clark, J. H. R. "A comparison of constant energy, constant temperature, and constant pressure ensembles in molecular dynamics simulation of atomic liquids", Molecular Physics, 51, 1243-1252 (1984).

Burchart, E. de Vos Studies on Zeolites; Molecular Mechanics, Framework Stability, and Crystal Growth, Ph.D. Thesis, Technische Universiteit Delft (1992).

Casewit, C. J.; Colwell, K. S.; Rappé, A. K., J. Am. Chem. Soc., 114, 10035 (1992a).

Casewit, C. J.; Colwell, K. S.; Rappé, A. K., J. Am. Chem. Soc., 114, 10046 (1992b).

Catlow, C. R. A.; Norgett, M. J. "Lattice structure and stability of ionic materials", personal communication (1976).

Dauber-Osguthorpe, P.; Roberts, V. A.; Osguthorpe, D. J.; Wolff, J.; Genest, M.; Hagler, A. T. "Structure and energetics of ligand binding to proteins: E. coli dihydrofolate reductase-trimethoprim, a drug-receptor system", Proteins: Structure, Function and Genetics, 4, 31-47 (1988).

Deem, M. W.; Newsam, J. M.; Sinha, S. K.. "The h = 0 term in Coulomb sums by the Ewald transformation", J. Phys. Chem., 94, 8356-8359 (1990).

Demontis, P.; Yashonath, S.; Klein, M. L. "Localization and mobility of benzene in sodium-Y zeolite by molecular dynamics calculations", J. Phys. Chem., 93, 5016 (1989).

Ding, H. Q.; Karasawa, N.; Goddard, W. A., III "Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions", J. Chem. Phys., 97, 4309 (1992).

Dinur, U.; Hagler, A. T. "Approaches to empirical force fields", in Reviews of Computational Chemistry, Vol. 2; Lipkwowitz, K. B.; Boyd, D. B. Eds.; VCH: New York; Chapter 4 (1991).

Ermer, O. "Calculation of molecular properties using force fields. Applications in organic chemistry", Structure and Bonding, 27, 161-211 (1976).

Ewald, P. P. Ann. d. Physik, 64, 253 (1921).

Fletcher, R. Practical Methods of Optimization, Vol. 1, Unconstrained Optimization, John Wiley & Sons: New York (1980).

Fletcher, R.; Reeves, C. M. Comput. J., 7, 149 (1964).

Garofalini, S. H. J. Amer. Ceram. Soc., 67, 133 (1984).

Garofalini, S. H.; Zirl, D. M., J. Amer. Ceram. Soc., 73, 2848 (1990).

Greengard, L.; Rokhlin, V. I. "A fast algorithm for particle simulations", J. Comp. Phys., 73, 325 (1987).

Gunsteren, W. F.; Karplus, M. J. Comp. Chem., 1, 266 (1980).

Ha, S. N.; Giammona, A.; Field, M.; Brady, J. W. "A revised potential-energy surface for molecular mechanics studies of carbohydrates", Carbohydrate Research, 180, 207-221 (1988).

Hagler, A. T.; Dauber, P.; Lifson, S. "Consistent force field studies of intermolecular forces in hydrogen bonded crystals. III. The C=O^...H-O hydrogen bond and the analysis of the energetics and packing of carboxylic acids", J. Am. Chem. Soc., 101, 5131-5141 (1979a).

Hagler, A. T.; Ewig, C. S. "On the use of quantum energy surfaces in the derivation of molecular force fields", Comp. Phys. Comm., 84, 131-155 (1994).

Hagler, A. T.; Lifson, S.; Dauber, P. "Consistent force field studies of intermolecular forces in hydrogen bonded crystals. II. A benchmark for the objective comparison of alternative force fields", J. Am. Chem. Soc., 101, 5122-5130 (1979b).

Hagler, A. T.; Stern, P. S.; Sharon, R.; Becker, J. M.; Naider, F. "Computer simulation of the conformational properties of oligopeptides. Comparison of theoretical methods and analysis of experimental results", J. Am. Chem. Soc., 101, 6842-6852 (1979c).

Halgren, T. A., J. Amer. Chem. Soc., 114, 7827-7843 (1992).

Halgren, T. A.; Nachbar, R. B. "The Merck molecular force field: IV. Conformational energies and geometries for MMFF94," J. Comp. Chem., 19, 587-615 (1996).

Halgren, T. A. J. Comput. Chem., 17, 490-519 (1996a).

Halgren, T. A. J. Comput. Chem., 17, 520-552 (1996b).

Halgren, T. A. J. Comput. Chem., 17, 553-586 (1996c).

Halgren T. A. and Robert B. Nachbar, J. Comput. Chem., 17, 587-615 (1996d).

Halgren, T. A. J. Comput. Chem., 17, 616-641 (1996e).

Halgren, T. A. J. Comput. Chem., 20, 720-729 (1999a).

Halgren, T. A. J. Comput. Chem., 20, 730-748 (1999b).

Harvey, S. C., "Treatment of electrostatic effects in macromolecular modeling", Proteins: Structure, Function, and Genetics, 5, 78-92 (1989).

Hill, J. -R.; Sauer, J. "Molecular mechanics potential for silica and zeolite catalysts based on ab initio calculations. 1. Dense and microporous silica", J. Phys. Chem., 98, 1238-1244 (1994).

Homans, S. W. "A molecular mechanical force field for the conformational analysis of oligosaccharides: Comparison of theoretical and crystal structures of Man 1-3 Man 1-4 GlcNAc", Biochemistry, 29, 9110-9118 (1990).

Hoover, W. "Canonical dynamics: Equilibrium phase-space distributions", Phys. Rev., A31, 1695-1697 (1985).

Hwang, J. K.; Warshel, A. "Semiquantitative calculations of catalytic free energies in genetically modified enzymes", Biochemistry, 26, 2669-2673 (1987).

Hwang, M.-J.; Stockfisch, T. P.; Hagler, A. T. "Derivation of Class II force fields. 2. Derivation and characterization of a Class II force field, CFF93, for the alkyl functional group and alkane molecules", J. Amer. Chem. Soc., 116, 2515-2525 (1994).

Kao, J.; Allinger, N. L., J. Amer. Chem. Soc., 99, 975 (1977).

Karasawa, N.; Goddard, W. A., III "Acceleration of convergence for lattice sums", J. Phys. Chem., 93, 7320-7327 (1989).

Karasawa, N.; Goddard, W. A., III "Force fields, structures, and properties of polyvinylidene fluoride crystals," Macromolecules, 25, 7268 (1992).

Kirkwood, J. G. "Statistical mechanics of fluid mixtures", J. Chem. Phys., 3, 300-313 (1935).

Kitson, D. H.; Hagler, A. T. "Theoretical studies of the structure and molecular dynamics of a peptide crystal", Biochemistry, 27, 5246-5257 (1988).

Kohler, A. E.; Garofalini, S. H. Langmuir, 10, 4664 (1994).

Levitt, M.; Lifson, S. J. Molec. Biol., 46, 269 (1969).

Levy, R. M.; McCammon, J. A.; Karplus, M. Chem. Phys. Lett., 64, 4 (1979).

Lifson, S.; Hagler, A. T.; Dauber, P., J. Amer. Chem. Soc., 101, 5111 (1979).

Liljefors T.; Tai, J. C.; Li, S.; Allinger, N. L., J. Comp. Chem., 8, 1051 (1987).

Maple, J.; Dinur, U.; Hagler, A. T. "Derivation of force fields for molecular mechanics and dynamics from ab initio energy surfaces", Proc. Nat. Acad. Sci. USA, 85, 5350-5354 (1988).

Maple, J. R.; Hwang, M.-J.; Stockfisch, T. P.; Dinur, U.; Waldman, M.; Ewig, C. S; Hagler, A. T. "Derivation of Class II force fields. 1. Methodology and quantum force field for the alkyl functional group and alkane molecules", J. Comput. Chem., 15, 162-182 (1994a).

Maple, J. R.; Hwang, M.-J.; Stockfisch, T. P.; Hagler, A. T. "Derivation of Class II force fields. 3. Characterization of a quantum force field for the alkanes", Israel J. Chem., 34, 195 -231 (1994b).

Maple, J. R., Thacher, T. S., Dinur, U.; Hagler, A. T. "Biosym force field research results in new techniques for the extraction of inter- and intramolecular forces", Chemical Design Automation News, 5 (9), 5-10 (1990).

Mayo, S. L.; Olafson, B. D.; Goddard, W. A. III "DREIDING: A generic force field", J. Phys. Chem., 94, 8897-8909 (1990).

McCammon, J. A.; Gelin, B. R.; Karplus, M.; Wolynes, P. G. Nature, 262, 325-326 (1976).

McQuarrie, Statistical Mechanics, Harper & Row, Chapter 3 (1976).

Mezei, M.; Beveridge, D. "Free energy simulations", Ann. N.Y. Acad. Sci., 482, 1-23 (1986).

Miller, G. W.; Knaebel, K. S.; Ikels, K. G., AIChE J., 33, 194 (1987).

Momany, F. A.; Carruthers, L. M.; McGuire, R. F.; Scheraga, H. A., J. Phys. Chem., 78, 1595 (1974).

Momany, F. A.; Rone, R. J. Comp. Chem., 13, 888-900 (1992).

Némethy, G.; Pottle, M. S.; Scheraga, H. A., J. Chem. Phys., 87, 1883 (1983).

Nosé, S. "A molecular dynamics method for simulations in the canonical ensemble", Molec. Phys., 52, 255-268 (1984a).

Nosé, S. "A unified formulation of the constant temperature molecular dynamics methods", J. Chem. Phys., 81, 511-519 (1984b).

Nosé, S. "Constant temperature molecular dynamics methods", Prog. Theoret. Phys. Supplement, 103, 1-46 (1991).

Parrinello, M.; Rahman, A. "Polymorphic transitions in single crystals: A new molecular dynamics method", J. Appl. Phys., 52, 7182-7190 (1981).

Pickett, S. D.; Nowak, A. K.; Thomas, J. M.; Peterson, B. K.; Swift, J. F. P.; Cheetham, A. K.; Denouden, C. J. J.; Smit, B.; Post, M. F. M. "Mobility of adsorbed species in zeolites--A molecular dynamics simulation of xenon in silicalite", J. Phys. Chem., 94, 1233 (1990).

Powell, M. J. D. "Restart Procedure for the Conjugate Gradient Method," Mathematical Programming, 12, 241 (1977).

Press, W. H.: Flannery, B. P.; Teukolsky, S. A.; Vetterling, W. T. In Numerical Recipes, The Art of Scientific Computing; Cambridge University Press, Cambridge (1986).

Quirke, N.; Jacucci, G. "Energy difference functions in Monte Carlo simulations: Application to (1) the calculation of free energy of liquid nitrogen. II. The calculation of fluctuation in Monte Carlo averages", Mol. Phys., 45, 823-838 (1982).

Rappé, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A.; Skiff, W. M. "UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations", J. Amer. Chem. Soc., 114, 10024 (1992).

Rappé, A. K.; Colwell, K. S.; Casewit, C. J., Inorg. Chem., 32, 3438 (1993).

Rappé, A. K.; Goddard, W. A., J. Phys. Chem., 95, 3358 (1991).

Ray, J. R. Comp. Phye. Rep., 8, 109 (1988) and references therein.

Reidl, D., International Tables for Crystallography: A Space-Group Symmetry, Vol. A; Dordrecht, Holland (1983).

Rigby, D.; Sun, H.; Eichinger, B. E. "Computer simulations of poly(ethylene oxides): Force field, PVT diagram and cyclization behavior", Polymer, 44, 311 (1998).

Root, D.M., C.R. Landis, and T. Cleveland, J. Am. Chem. Soc., 1993, 115, 4201-4209.

Root, D.M., Ph.D. thesis, University of Wisconsin, Madison, 1997.

Rosenthal, A. B.; Garofalini, S. H., J. Amer. Ceram. Soc., 70, 821 (1987).

Rosenthal, A.B.; Garofalini, S. H., J. Non-Crys. Solids, 107, 65 (1988).

Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. "Numerical Integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes", J. Comp. Phys., 23, 327-341 (1977).

Schmidt, K. E.; Lee, M. A. "Implementing the fast multipole method in three dimensions", J. Stat. Phys., 63, 1223 (1991).

Shi, S.; Yan, L.; Yang, Y.; Fisher, J. ESFF Forcefield Project Report II; MSI, San Diego.

Singh, U. C; Brown, F. K.; Bash, P. A.; Kollman, P. A. "An approach to the application of free energy perturbation methods using molecular dynamics: Applications to the transformations of methanol to ethane, oxonium to ammonium, glycine to alanine, and alanine to phenylalanine in aqueous solution and to H₃O⁺(H₂O)₃ NH₄⁺(H₂O)₃ in the gas phase", J. Am. Chem. Soc., 109, 1607-1614 (1987).

Soules, T. F., J.Chem. Phys., 71, 4570 (1979).

Soules, T. F.; Varshneya, A. K., J. Amer. Ceram. Soc., 64, 145 (1981).

Sprague, J. T.; Tai, J. C.; Yuh, Y.; Allinger, N. L., J. Comp. Chem., 8, 581 (1987).

Straatsma, T. P.; Berendsen, H. J. C.; Postma, J. P. M. "Free energy of hydrophobic hydration: A molecular dynamics study of noble gases in water", J. Chem. Phys., 85, 6720-6727 (1986).

Sun, H. J. Comp. Chem., 15, 752 (1994).

Sun, H. "Ab initio calculations and force field development for computer simulation of polysilanes", Macromolecules, 28, 701 (1995).

Sun, H. "The parameterization and validation of a condensed-phase optimized ab initio forcefield" (in preparation).

Sun, H.; Mumby, S. J.; Maple, J. R.; Hagler, A. T. "An ab initio CFF93 all-atom force field for polycarbonates", J. Amer. Chem. Soc., 116, 2978-2987 (1994).

Sun, H.; Rigby, D. "Polydimethylsiloxane: Ab initio force field: Structural, conformational and thermophysical properties", Spectrochimica Acta (in press).

Sun, H.; Ren, P.; Fried, J. R. "The COMPASS Force Field: Parameterization and Validation for Polyphosphazenes" Computational and Theoretical Polymer Science, 8 (1/2), 229 (1998).

Sun, H. "COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase Applications - Overview with Details on Alkane and Benzene Compounds" J. Phys. Chem., (1998 in press).

Tembe, B. L.; McCammon, J. A. "Ligand-receptor interactions", Comput. Chem., 8, 281-283 (1984).

Tesar, A. A.; Varshneya, A. K. J. Chem. Phys., 87, 2986 (1987).

Tosi, M. P., Solid State Physics, 16, 107 (1964).

van Beest, B. W. H.; Kramer, G. J.; van Santen, R. A., Phys. Rev. Lett., 64, 1955 (1990).

Verlet, L. "Computer experiments on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules", Phys. Rev., 159, 98-103 (1967).

Waldman, M.; Hagler, A. T. "New combining rules for rare gas van der Waals parameters", J. Comput. Chem., 14, 1077-1084 (1993).

Warshel, A.; Sussman, F.; King, G. "Free energy of charges in solvated proteins: Microscopic calculations using a reversible charging process", Biochemistry, 25, 8368-8372 (1986).

Watanabe, K.; Austin, N.; Stapleton M. R. "Investigation of the air separation properties of zeolites types A, X, and Y by Monte Carlo simulations," Molec. Sim., 15, 197-221 (1995).

Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S. Jr.; Weiner, P. "A new force field for molecular mechanical simulation of nucleic acids and proteins", J. Am. Chem. Soc., 106, 765-784 (1984).

Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. "An all atom forcefield for simulations of proteins and nucleic acid", J. Comp. Chem., 7, 230-252 (1986).

Wiberg, K. B.; Murcko, M. A., J. Am. Chem. Soc., 111, 4821 (1989).

Williams, D. E., J. Phys. Chem., 45, 3370 (1966).

Wilson, E. B.; Decius, J. C.; Cross, P. C. Molecular Vibrations, Dover, New York (1980).

Woodcock, L. V., Advances in Molten Salt Chemistry; Plenum, New York (1975).

Yashonath, S.; Thomas, J. M.; Nowak, A. K.; Cheetham, A. K. "The siting, energetics and mobility of saturated hydrocarbons inside zeolitic cages--Methane in zeolite-Y", Nature, 331, 601 (1988).

Zirl, D. M.; Garofalini, S. H. Phys. Chem. Glasses, 30, 155 (1989).