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2012 | OriginalPaper | Buchkapitel

Molecular Mechanics: Method and Applications

verfasst von : Valeri Poltev

Erschienen in: Handbook of Computational Chemistry

Verlag: Springer Netherlands

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Abstract

The ultimate justification for the many severe approximations and assumptions made in the present work comes from the fact that the agreement between the simple calculations and the available experimental data is as good as it is.

N. L. Allinger, J. Am. Chem. Soc., 81, 5727, 1959

A short survey of the general principles and various applications of molecular mechanics (MM) is presented. The origin of molecular mechanics and its evolution is followed starting from “pre-computer” and the first computer-aided estimations of the structure and potential energy of simple molecular systems to the modern force fields and the large system computations. The problem of “classic mechanics” description of essentially quantum properties and processes is considered. Various approaches to a selection of force field mathematical expressions and parameters are reviewed. The relation between MM simplicity and “physical nature” of the properties and events is examined. The possibility of a priori predictions of the properties of large systems is discussed in view of modern improvements of MM scheme. Quantum chemistry contributions to MM description of complex molecular and biomolecular systems are considered.

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Vorheriges Kapitel Statistical Mechanics of Force-Induced Transitions of Biopolymers

Nächstes Kapitel Molecular Structure and Vibrational Spectra

Allinger, N. L. (1959). Conformational analysis. III. Applications to some medium ring compounds. Journal of the American Chemical Society, 81, 5727.

Allinger, N. L. (2010). Molecular structure: Understanding steric and electronic effects from molecular mechanics. New Jersey: Wiley.CrossRef

Allinger, N. L., & Sprague, J. T. (1973). Calculation of the structures of hydrocarbons containing delocalized electronic systems by the molecular mechanics method. Journal of the American Chemical Society, 95, 3893.CrossRef

Antony, J., & Grimme, S. (2006). Density functional theory including dispersion corrections for intermolecular interactions in a large benchmark set of biologically relevant molecules. Physical Chemistry Chemical Physics, 8, 5287.CrossRef

Arnautova, Y. A., & Scheraga, H. A. (2008). Use of decoys to optimize an all-atom force field including hydration. Biophysical Journal, 95, 2434.CrossRef

Arnautova, Y. A., Jagielska, A., & Scheraga, H. A. (2006). A new force field (ECEPP-05) for peptides, proteins and organic molecules. Journal of Chemical Physics, 110, 5025.CrossRef

Bartell, L. S. (1960). On the effects of intramolecular van der Waals forces. Journal of Chemical Physics, 32, 827.CrossRef

Barton, D. H. R. (1948). Interaction between non-bonded atoms, and the structure of cis-Decalin. Journal of Chemical Society, 340.

Barton, D. H. R. (1950). The conformation of the steroid nucleus. Experientia, 6, 316.CrossRef

Berendsen, H. J. C., Postma, J. P. M., von Gunstaren, W. F., & Hermans, J. (1981). Interaction models for water in relation to protein hydration. In B. Pullman (Ed.), Intermolecular forces (pp. 331–342). Dordrecht: Reidel.CrossRef

Berman, H. M., Olson, W. K., Beveridge, D. l., Westbrook, J., Gelbin A., Demeny T., Hsieh S.-H., Srinivasan, A. R., & Schneider, B. (1992). The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophysical Journal, 63, 751.

Berman, H. M., Henrick, K., & Nakamura, H. (2003). Announcing the worldwide protein data bank. Nature Structural & Molecular Biology, 10, 980.CrossRef

Bernal, J. D., & Fowler, R. H. (1933). A theory of water and ionic solution, with particular reference to hydrogen and hydroxyl ions. Journal of Chemical Physics, 1, 515.CrossRef

Bordner, A. J., Cavasotto, C. N., & Abagyan, R. A. (2003). Direct derivation of van der Waals force field parameters from quantum mechanical interaction energies. The Journal of Physical Chemistry B, 107, 9601.CrossRef

Bradley, D. F., Lifson, S., & Honig, B. (1964). Theory of optical and other properties of biopolymers: Applicability and elimination of the first-neighbor and dipole–dipole approximations. In B. Pullman (Ed.), Electronic aspects of biochemistry. New York: Academic.

Brant, D. A., & Flory, P. J. (1965). The configuration of random polypeptide chains. II. Theory. Journal of the American Chemical Society, 87, 2791.

Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., & Karplus, M. (1983). CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry, 4, 187.CrossRef

Case,D.A.,CheathamT.E.,III,Darden,T.,Gohlke, H.,Luo,R.,Merz,K.M., Jr.,Onufriev,A.,Simmerling,C.,Wang,B.,&Woods,R.J.(2005).Theamber biomolecularsimulationprograms.JournalofComputationalChemistry,26, 1668.

Case, D. A., Darden, T. A., Cheatham T. E., III, Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Walker, R. C., Zhang, W., Merz, K. M., Roberts, B., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Kolossváry, I., Wong, K. F., Paesani,F.,Vanicek, J.,Liu,J.,Wu,X.,Brozell,S.R.,Steinbrecher,T.,Gohlke, H.,Cai,Q.,Ye,X.,Wang,J.,Hsieh,M.-J.,Cui,G.,Roe,D.R.,Mathews,D.H., Seetin,M.G.,Sagui,C.,Babin,V.,Luchko,T.,Gusarov,S.,Kovalenko,A.,& Kollman, P. A. (2010). AMBER 11. San Francisco: University of California.

Chuprina, V. P., & Poltev, V. I. (1983). Possible conformations of double-helical polynucleotides containing incorrect base pairs. Nucleic Acids Research, 11, 5205.CrossRef

Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I., Merz, K., Jr., Ferguson, D., Spellmeyer, D., Fox, T., Caldwell, J., & Kollman, P. (1995). A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of the American Chemical Society, 117, 5179.CrossRef

Craig, D. P., Mason, R., Pauling, P., & Santry, D. P. (1965). Molecular packing in crystals of the aromatic hydrocarbons. Proceedings of the Royal Society A, 286, 98.CrossRef

Cramer, C. J. (2004). Essentials of computational chemistry: Theories and models. Chichester: Wiley.

Christen, M., Hunenberger, P. H., Bakowies, D., Baron, R., Burgi, R., Geerke, D. P., Heinz, T. N., Kastenholz, M. A., Krautler, V., Oostenbrink, C., Peter, C., Trzesniak, D., & Van Gunsteren, W. F. (2005). The GROMOS software for biomolecular simulation: GROMOS05. Journal of Computational Chemistry, 26, 1719.CrossRef

De Santis, P. (1992). Conformational energy calculations of macromolecules. Current Contents, 34, 8.

De Santis, P., Giglio, E., Liquori, A. M., & Ripamonti, A. (1963). Stability of helical conformations of simple linear polymers. Journal of Polymer Science Part A, 1, 1383.

De Santis, P., Giglio, E., Liquori, A. M., & Ripamonti, A. (1965). Van der Waals interaction and stability of helical polypeptide chains. Nature, 206, 456.CrossRef

De Voe, H., & Tinoco, I., Jr. (1962). The stability of helical polynucleotides: Base contributions. Journal of Molecular Biology, 4, 500.CrossRef

Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J., & Kollman, P. (2003). A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry, 24, 1999.CrossRef

Eisenberg, D. (2003). The discovery of the α-helix and β-sheet, the principal structural features of proteins. Proceedings of the National Academy of Sciences of the United States of America, 100, 11207.CrossRef

Engler, E. M., Andose, J. D., & Schleyer, P. R. (1973). Critical evaluation of molecular mechanics. Journal of the American Chemical Society, 95, 8005.CrossRef

Foloppe, N., & MacKerell, A. D., Jr. (2000). All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. Journal of Computational Chemistry, 21, 86.

Gibson, K. D., & Scheraga, H. A. (1967a). Minimization of polypeptide energy. I. Preliminary structures of bovine pancreatic ribonuclease S-peptide. Proceedings of the National Academy of Sciences of the United States of America, 58, 420.

Gibson, K. D., Scheraga, H. A. (1967b). Minimization of polypeptide energy. II. Preliminary structures of oxytocin, vasopressin, and an octapeptide from ribonuclease. Proceedings of the National Academy of Sciences of the United States of America, 58, 1317.

Gresh, N., Claverie, P., & Pullman, A. (1986). Intermolecular interactions: Elaboration on an additive procedure including an explicit charge-transfer contribution. International Journal of Quantum Chemistry, 29, 101.CrossRef

Halgren, T. A. (1996). Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. Journal of Computational Chemistry, 17, 490.

Halgren, T. A. (1999a). MMFF VI. MMFF94s option for energy minimization studies. Journal of Computational Chemistry, 20, 720.

Halgren, T. A. (1999b) MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries. Journal of Computational Chemistry, 20, 730.

Hendrickson, J. B. (1961). Molecular geometry. I. Machine computation of the common rings. Journal of the American Chemical Society, 83, 4537.

Hendrickson, J. B. (1962). Molecular geometry. II. methyl-cyclohexanes and cycloheptanes. Journal of the American Chemical Society, 84, 3355.

Hendrickson, J. B. (1973). Molecular geometry. VIII. Proton magnetic resonance studies of cycloheptane conformations. Journal of the American Chemical Society, 95, 494.

Hill, T. L. (1946). On steric effects. Journal of Chemical Physics, 14, 465.CrossRef

Hill, T. L. (1948). Sterlc effects. I. Van der Waals potential energy curves. Journal of Chemical Physics, 16, 399.

Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics, 79, 926.CrossRef

Jorgensen, W. L., & Tirado-Rives, J. (1988). The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. Journal of the American Chemical Society, 110, 1657.

Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society, 118, 11226.CrossRef

Jurecka, P., Cerny, J., Hobza, P., & Salahub, D. R. (2007). Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations. Journal of Computational Chemistry, 28, 555.

Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., & Jorgensen, W. L. (2001). Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. The Journal of Physical Chemistry B, 105, 6474.CrossRef

Khutorsky, V. E., & Poltev, V. I. (1976). Conformations of double-helical nucleic acids. Nature, 264, 483.CrossRef

Kitaigorodski, A. I. (1959). Organic chemical crystallography. New York: Consultants Bureau.

Kitaygorodsky, A. I. (1961). The interaction curve of non-bonded carbon and hydrogen atoms and its application. Tetrahedron, 14, 230.CrossRef

Kitaigorodsky, A. I. (1973). Molecular crystals and molecules. New York: Academic.

Klauda, J. B., Venable, R. M., MacKerell, A. D., Jr., & Pastor, R. W. (2008). Considerations for lipid force field development. Current Topics in Membranes, 60, 1.CrossRef

Langlet, J., Claverie, P., Caron, F., & Boeuve, J. C. (1981). Interactions between nucleic acid bases in hydrogen bonded and stacked configurations: The role of the molecular charge distribution. International Journal of Quantum Chemistry, 20, 299.CrossRef

Leach, A. R. (2001). Molecular modelling: Principles and applications. Harlow: Prentice Hall (Pearson Education).

Leach, S. J., Némethy, G., & Scheraga, H. A. (1966a). Computation of the sterically allowed conformations of peptides. Biopolymers, 4, 369.CrossRef

Leach, S. J., Némethy, G., Scheraga, H. A. (1966b). Intramolecular steric effects and hydrogen bonding in regular conformations of polyamino acids. Biopolymers, 4, 887.CrossRef

Levitt, M., & Lifson, S. (1969). Refinement of protein conformations using a macromolecular energy minimization procedure. Journal of Molecular Biology, 46, 269.CrossRef

Lifson, S., & Warshel, A. (1968). Consistent force field for calculations of conformations, vibrational spectra, and enthalpies of cycloalkane and n-alkane molecules. Journal of Chemical Physics, 49, 5116.CrossRef

Lii, L.-H., & Allinger, N. L. (1991). The MM3 force field for amides, polypeptides and proteins. Journal of Chemical Physics, 12, 186.

Lii, L.-H., Chen, K.-H., Johnson, G. P., French, A. D., & Allinger, N. L. (2005). The external-anomeric torsional effect. Carbohydrate Research, 340, 853.CrossRef

Liwo, A., Lee, J., Ripoll, D. R., Pillardy, J., & Scheraga, H. A. (1999). Protein structure prediction by global optimization of a potential energy function. Proceedings of the National Academyof Sciences of the United States of America, 96, 5482.CrossRef

MacKerell, A. D., Jr. (2004). Empirical force fields for biological macromolecules: Overview and issues. Journal of Computational Chemistry, 25, 1584.CrossRef

Mahoney, M. W., & Jorgensen, W. L. (2001). Quantum, intramolecular flexibility, and polarizability effects on the reproduction of the density anomaly of liquid water by simple potential functions. Journal of Computational Chemistry, 115, 10758.

Mason, R. (1969). The intermolecular potential and structure of crystals of aromatic molecules. Molecular Crystals and Liquid Crystals, 9, 3.CrossRef

Matsuoka, O., Clementi, E., & Yoshimine, M. (1976) CI Study of the water dimer potential surface. Journal of Chemical Physics, 64, 1351.CrossRef

McAllister, S. R., & Floudas, C. A. (2010). An improved hybrid global optimization method for protein tertiary structure prediction. Computational Optimization and Applications, 45, 377.CrossRef

McGuire, R. F., Momany, F. A., & Scheraga, H. A. (1972). Energy parameters in polypeptides. V. An empirical hydrogen bond potential function based on molecular orbital calculations. Journal of Physical Chemistry, 76, 375.

Momany, F. A., Vanderkooi, G., & Scheraga, H. A. (1968). Determination of intermolecular potentials from crystal data. I. General theory and application to crystalline benzene at several temperatures. Proceedings of the National Academy of Sciences, 61, 429.

Momany, F. A., Carruthers, L. M., & Scheraga, H. A. (1974). Intermolecular potentials from crystal data. IV. Application of empirical potentials to the packing confkgurations and lattice energies in crystals of amino acids. Journal of Physical Chemistry, 78, 1621.

Momany, F. A., McGuire, R., Burgess, A., & Scheraga, H. (1975). 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. Journal of Physical Chemistry, 79, 2361.

Nada, H., & van der Eerden, J. P. J. M. (2003). An intermolecular potential model for the simulation of ice and water near the melting point: A six-site model of H₂O. Journal of Chemical Physics, 118, 7401.CrossRef

Nash, H. A., & Bradley, D. F. (1966). Calculation of the lowest energy configurations of nucleotide base pairs on the basis of an electrostatic model. Journal of Chemical Physics, 45, 1380.CrossRef

Némethy, G., & Scheraga, H. A. (1965). Theoretical determination of sterically allowed conformations of a polypeptide chain by a computer method. Biopolymers, 3, 155.CrossRef

Némethy, G., Gibson, K. D., Palmer, K. A., Yoon, C. N., Paterlini, G., Zagari, A., Rumsey, S., & Scheraga, H. A. (1992) Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with appllcatlon to proline-containing peptides. Journal of Physical Chemistry, 96, 6472.

Oostenbrink, C., Villa, A., Mark, A. E., & van Gunsteren, W. F. (2004). A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry, 25, 1656.CrossRef

Pauling, L., & Corey, R. B. (1951). The pleated sheet, a new layer configuration of polypeptide chains. Proceedings of the National Academy of Sciences of the United States of America, 37, 251.CrossRef

Pauling, L., Corey, R. B., & Branson, H. R. (1951). The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain. Proceedings of the National Academy of Sciences of the United States of America, 37, 205.CrossRef

Perez, A., Marchan, I., Svozil, D., Sponer, J., Cheatham, T. E., Laughton, C. A., & Orozco, M. (2007). Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers. Biophysical Journal, 92, 3817.CrossRef

Polozov, R. V., Poltev, V. I., & Sukhorukov, B. I. (1973). Relation of the interactions of nucleic acid bases to the helical conformations of polynucleotides. Studia Biophysica, 40, 13.

Poltev, V. I., & Bruskov, V. I. (1978) On molecular mechanisms of nucleic acid synthesis fidelity aspects 1. Contribution of base interactions. Journal of Theoretical Biology, 70, 69.

Poltev, V. I., & Shulyupina, N. V. (1986). Simulation of interactions between nucleic-acid bases by refined atom-atom potential functions. Journal of Biomolecular Structure & Dynamics, 3, 739.CrossRef

Poltev, V. I., & Sukhorukov, B. I. (1967). Theoretical examination of the physical nature of the intermolecular interactions determining the conformational state of polynucleotides. Biophysics (Moscow), 12, 879.

Poltev, V. I., & Sukhorukov, B. I. (1970). Semiempirical calculations of interaction energy of DNA nitrous bases. Studia Biophysica, 24/25, 179.

Poltev, V. I., Grokhlina, T. I., & Malenkov, G. G. (1984). Hydration of nucleic-acid bases studied using novel atom-atom potential functions. Journal of Biomolecular Structure & Dynamics, 2, 413.CrossRef

Pullman, A., & Pullman, B. (1968). Aspects of the electronic structure of the purine and pyrimidine bases of the nucleic acids and of their interactions. Advances in Quantum Chemistry, 4, 267.CrossRef

Pullman, B., Claverie, P., & Caillet, J. (1966). Van der Waals-London interactions and the configuration of hydrogen-bonded purine and pyrimidine Pairs. Proceedings of the National Academy of Sciences of the United States of America, 55, 904.CrossRef

Rae, A. I. M., & Mason, R. (1968). The intermolecular potential and the lattice energy of benzene. Proceedings of the Royal Society, 304, 487.CrossRef

Ramachandran, G. N. (1990). This week’s citation classic. Current Contents, 10, 119.

Ramachandran, G. N., Ramakrishnan, C., & Sasisekharan, V. (1963). Stereochemistry of polypeptide chain configurations. Journal of Molecular Biology, 7, 95.CrossRef

Ramachandran, K. I., Deepa, G., & Namboori, K. (2008). Computational chemistry and molecular modeling: Principles and applications. Berlin: Springer.

Raman, E. P., Guvench, O., & MacKerell, A. D., Jr. (2010). CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses. Journal of Physical Chemistry B, 114, 12981.CrossRef

Rasse, D., Warme, P. K., & Scheraga, H. A. (1974). Refinement of the Xray structure of rubredoxin by conformational energy calculations. Proceedings of the National Academy of Sciences of the United States of America, 71, 3736.CrossRef

Renugopalakrishnan, V., Lakshminarayanan, A. V., & Sasisekharan, V. (1971) Stereochemistry of nucleic acids and polynucleotides III. Electronic charge distribution. Biopolymers, 10, 1159.

Ripoll, D. R., Scheraga, H. A. (1988) On the multipleminima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method. Tests on poly(l-alanine). Biopolymers, 27, 1283.

Scheraga, H. A. (2008). From helix–coil transitions to protein folding. Biopolymers, 89, 479.CrossRef

Scheraga, H. A., Pillardy, J., Liwo, A., Lee, J., Czaplewski, C., Ripoll, D. R., Wedemeyer, W. J., & Arnautova, Y. A. (2002). Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. Journal of Computational Chemistry, 23, 28.CrossRef

Scott, R. A., & Scheraga, H. A. (1966a). Conformational analysis of macromolecules. III. Helical structures of poly-glycine and poly-l-alanine. Journal of Chemical Physics, 45, 2091.

Scott, R. A., & Scheraga, H. A. (1966b). Conformational analysis of macromolecules. II. The rotational isomeric states of the normal hydrocarbons. Journal of Chemical Physics, 44, 3054.

Shipman, L. L., Burgess, A. W., & Scheraga, H. A. (1975) A new approach to empirical intermolecular and conformational potential energy functions. I. Description of model and derivation of parameters. Proceedings of the National Academy of Sciences of the United States of America, 72, 543.

Sippl, M. J., Némethy, G., & Scheraga, H. A. (1984). Intermolecular potentials from crystal data. 6. Determination of empirical potentials for OH\(\cdot \) \(\cdot \) \(\cdot \)O=C hydrogen bonds from packing configurations. Journal of Physical Chemistry, 88, 6231.

Snir, J., Nemenoff, R. A., & Scheraga, H. A. (1978). A revised empirical potential for conformational, intermolecular, and solvation studies. 5. Development and testing of parameters for amides, amino acids and peptides. Journal of Physical Chemistry, 82, 2527.

Song, K., Hornak, V., de los Santos, C., Grollman, A. P., & Simmerling, C. (2008). Molecular mechanics parameters for the FapydG DNA lesion. Journal of Computational Chemistry, 29, 17.

Stillinger, F. H., & Rahman, A. (1974). Improved simulation of liquid water by molecular dynamics. Journal of Chemical Physics, 60, 1545.CrossRef

Van der Spoel, D., Lindahl, E., Hess, B., Groehof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26, 1701.CrossRef

Van Gunsteren, W., Fand, H. J., & Berendsen, C. (1987). Groningen molecular simulation (GROMOS) library manual. Groningen: BIOMOS.

Wang, J., Cieplak, P., & Kollman, P. A. (2000). How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? Journal of Computational Chemistry, 21, 1049.CrossRef

Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25, 1157.CrossRef

Wang, J., Wang, W., Kollman, P. A., & Case, D. A. (2006), Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics & Modelling, 25, 247.CrossRef

Warme, P. K., Momany, F. A., Rumball, S. V., & Scheraga, H. A. (1974). Computation of structures of homologous proteins; α-lactalbumin from lysozyme. Biochemistry, 13, 768.CrossRef

Warshel A., & Lifson, S. (1970). Consistent force field calculations. II. Crystal structures, sublimation energies, molecular and lattice vibrations, molecular conformations, and enthalpies of alkanes. Journal of Chemical Physics, 53, 582.

Watson, J. D., & Crick, F. H. C. (1953). A structure for deoxyribose nucleic acid. Nature, 171, 737.CrossRef

Weiner, P., & Kollman, P. (1981). AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions. Journal of Computational Chemistry, 2, 287.

Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta, S., Jr., & Weiner, P. (1984). A new force field for molecular mechanical simulation of nucleic acids and proteins. Journal of the American Chemical Society, 106, 765.CrossRef

Westheimer, F. H., & Mayer, J. E. (1946). The theory of the racemization of optically active derivatives of diphenyl. Journal of Chemical Physics, 14, 733.CrossRef

Williams, D. E. (1966). Nonbonded potential parameters derived from crystalline aromatic hydrocarbons. Journal of Chemical Physics, 45, 3770.CrossRef

Williams, D. E. (1967). Nonbonded potential parameters derived from crystalline hydrocarbons. Journal of Chemical Physics, 47, 4680.CrossRef

Williams, D. E., & Weller, R. R. (1983). Lone-pair electronic effects on the calculated ab initio SCF-MO electric potential and the crystal structures of azabenzenes. Journal of the American Chemical Society, 105, 4143.CrossRef

Yan, J. F., Momany, F. A., Hoffmann, R., & Scheraga, H. A. (1970). Energy parameters in polypeptides. II. Semiempirical molecular orbital calculations for model peptides. Journal of Physical Chemistry, 74, 420.

Zhurkin, V. B., Poltev, V. I., & Florentiev, V. L. (1980). Atom-atom potential functions for conformational calculations of nucleic-acids. Molecular Biology (Moscow), English Translation, 14, 882.

Titel: Molecular Mechanics: Method and Applications
verfasst von: Valeri Poltev
Verlag: Springer Netherlands
Buch: Handbook of Computational Chemistry
Print ISBN: 978-94-007-0710-8

Electronic ISBN: 978-94-007-0711-5

Copyright-Jahr: 2012
DOI: https://doi.org/10.1007/978-94-007-0711-5_9

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