Skip to main content
SpringerLink
Log in

Molecular Mechanics: Principles, History, and Current Status

  • Living reference work entry
  • First Online:
Handbook of Computational Chemistry

Abstract

A short survey of the general principles and selected 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 software for the computations of large biomolecules and their complexes. Analysis of the current state of physicochemical study of biological processes suggests that MM simulations based on empirical force fields have an ever-increasing impact on understanding the structure and functions of biomolecules. 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. Quantum chemistry contributions to MM description of complex molecular systems and MM contribution to quantum mechanics computations of such systems are considered.

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. Amer. Chem. Soc., 81, 5727, 1959

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

Similar content being viewed by others

Bibliography

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

    Article  CAS  Google Scholar 

  • Allinger, N. L. (2010). Molecular structure: Understanding steric and electronic effects from molecular mechanics. Hoboken: Willey.

    Book  Google Scholar 

  • Allinger, N. L. (2011). Understanding molecular structure from molecular mechanics. Journal of Computer-Aided Molecular Design, 25, 295.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Allinger, N. L., Tribble, M. T., Miller, M. A., & Wertz, D. W. (1971). Conformational analysis. LXIX. Improved force field for the calculation of the structures and energies of hydrocarbons. Journal of the American Chemical Society, 93, 1637.

    Article  CAS  Google Scholar 

  • Allinger, N. L., Yuh, Y. H., & Lii, J. H. (1989). Molecular mechanics. The MM3 force field for hydrocarbons. Journal of the American Chemical Society, 111, 8551.

    Article  CAS  Google Scholar 

  • Allinger, N. L., Chen, K., & Lii, J. H. (1996). An improved force field (MM4) for saturated hydrocarbons. Journal of Computational Chemistry, 17, 642.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Baker, C. M., Anisimov, V. M., & MacKerell, A. D., Jr. (2011). Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model. The Journal of Physical Chemistry B, 115, 580.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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.

    Chapter  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Best, R. B., Zhu, X., Shim, J., Lopes, P. E. M., Mittal, J., Feig, M., & MacKerell, A. D., Jr. (2012). Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ1 and χ2 dihedral angles. Journal of Chemical Theory and Computation, 8, 3257.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Google Scholar 

  • Brandenburg, J. G., & Grimme, S. (2014). Accurate modeling of organic molecular crystals by dispersion-corrected density functional tight binding (DFTB). The Journal of Physical Chemistry Letters, 5, 1785.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Case, D. A., Cheatham, T. E., III, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computation Chemistry, 26, 1668.

    Article  CAS  Google Scholar 

  • 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.

    Google Scholar 

  • Case, D. A., Berryman, J. T., Betz, R. M., Cerutti, D. S., Cheatham, T. E., III, Darden, T., Duke, R. E., Giese, T. J., Gohlke, H., Goetz, A. W., Homeyer, N., Izadi, S., Janowski, P., Kaus, J., Kovalenko, A., Lee, T. S., LeGrand, S., Li, P., Luchko, T., Luo, R., Madej, B., Merz, K. M., Monard, G., Needham, P., Nguyen, H., Nguyen, H. T., Omelyan, I., Onufriev, A., Roe, D. R., Roitberg, A., Salomon-Ferrer, R., Simmerling, C. L., Smith, W., Swails, J., Walker, R. C., Wang, J., Wolf, R. M., Wu, X., York, D. M., & Kollman, P. A. (2015). AMBER 2015. San Francisco: University of California.

    Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

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

    Google Scholar 

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

    Google Scholar 

  • 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.

    Google Scholar 

  • De Santis, P., Giglio, E., Liquori, A. M., & Ripamonti, A. (1965). Interaction and stability of helical polypeptide chains. Nature, 206, 456.

    Article  Google Scholar 

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

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Golas, E., Maisuradze, G. G., Senet, P., Oldziej, S., Czaplewski, C., Scheraga, H. A., & Liwo, A. (2012). Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics. Journal of Chemical Theory and Computation, 8, 1750.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Grimme, S. (2004). Accurate description of van der Waals complexes by density functional theory including empirical corrections. Journal of Computational Chemistry, 25, 1463.

    Article  CAS  Google Scholar 

  • Grimme, S. (2011). Density functional theory with London dispersion corrections. WIREs Computational Molecular Science, 1, 211.

    Article  CAS  Google Scholar 

  • Grubišić, S., Brancato, G., & Barone, V. (2013). An improved AMBER force field for α, α-dialkylated peptides: Intrinsic and solvent-induced conformational preferences of model systems. Physical Chemistry Chemical Physics, 15, 17395.

    Article  CAS  Google Scholar 

  • Guo, X., Wang, Z., Zuo, L., Zhou, Z., Guo, X., & Sun, T. (2014). Quantitative prediction of enantioseparation using b-cyclodextrin derivatives as chiral selectors in capillary electrophoresis. Analyst, 139, 6511.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Hart, K., Foloppe, N., Baker, C. M., Denning, E. J., Nilsson, L., & MacKerell, A. D., Jr. (2012). Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. Journal of Chemical Theory and Computation, 8, 348.

    Article  CAS  Google Scholar 

  • He, Y., Maciejczyk, M., Oldziej, S., Scheraga, H. A., & Liwo, A. (2013). Mean-field interactions between nucleic-acid-base dipoles can drive the formation of the double helix. Physical Review Letters, 110, 098101.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Huang, J., & MacKerell, A. D., Jr. (2014). Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide. Biophysical Journal, 107, 991.

    Article  CAS  Google Scholar 

  • Huang, J., Lopes, P. E. M., Roux, B., & MacKerell, A. D., Jr. (2014). Recent advances in polarizable force fields for macromolecules: Microsecond simulations of proteins using the classical Drude oscillator model. The Journal of Physical Chemistry Letters, 5, 3144.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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, 11225.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Google Scholar 

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

    Google Scholar 

  • Kitaygorodsky, A. I. (1960). Calculation of conformations of organic molecules. Tetrahedron, 9, 183.

    Article  Google Scholar 

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

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Lam, A. R., Rodriguez, J. J., Rojas, A., Scheraga, H. A., & Mukamel, S. (2013). Tracking the mechanism of fibril assembly by simulated two-dimensional ultraviolet spectroscopy. The Journal of Physical Chemistry A, 117, 342.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Laury, M. L., Wang, L.-P., Pande, V. S., Head-Gordon, T. L., & Ponder, J. W. (2015). Revised parameters for the AMOEBA polarizable atomic multipole water model. Journal of Physical Chemistry B. doi:10.1021/jp510896n.

    Google Scholar 

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

    Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Lewars, E. G. (2011). Computational chemistry. Introduction to the theory and applications of molecular and quantum mechanics (2nd ed.). Dordrecht/Heidelberg/London/New York: Springer.

    Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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 Academy of Sciences of the United States of America, 96, 5482.

    Article  CAS  Google Scholar 

  • Lorecchio, C., Venanzi, M., Mazzuca, C., Lettieri, R., Palleschi, A., Thi, T. H. N., Cardová, L., Drasar, P., & Monti, D. (2014). Tuning the chiroptical and morphological properties of steroidal-porphyrin aggregates: A mechanistic, structural, and MM investigation. Organic & Biomolecular Chemistry, 12, 3956.

    Article  CAS  Google Scholar 

  • Maciejczyk, M., Spasic, A., Liwo, A., & Scheraga, H. A. (2010). Coarse-grained model of nucleic acid bases. Journal of Computational Chemistry, 31, 1644.

    CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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. The Journal of Chemical Physics, 115, 10758.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  • 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. The Journal of Physical Chemistry, 76, 375.

    Article  CAS  Google Scholar 

  • 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 of the United States of America, 61, 429.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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. The Journal of Physical Chemistry, 79, 2361.

    Article  CAS  Google Scholar 

  • 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. The Journal of Chemical Physics, 118, 7401.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  • 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 application to proline-containing peptides. The Journal of Physical Chemistry, 96, 6472.

    Article  Google Scholar 

  • Ogata, K., & Nakamura, S. (2015). Improvement of parameters of the AMBER potential force field for phospholipids for description of thermal phase transitions. The Journal of Physical Chemistry. doi:10.1021/acs.jpcb.5b01656.

    Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Pawar, S., Sawant, S., Nerkar, A., & Bhosale, A. (2014). In silico design, synthesis and pharmacological screening of novel 2-(6-substituted benzo [d] thiazol-2-yl) isoindoline-1, 3-diones as potential COX-2 inhibitors for anti-inflammatory activity. International Journal of Pharmacy and Pharmaceutical Sciences, 6, 353.

    Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kale, L., & Klaus Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26, 1781.

    Article  CAS  Google Scholar 

  • Pinilla, C., Irani, A. H., Nicola Seriani, N., & Scandolo, S. (2012). Ab initio parameterization of an all-atom polarizable and dissociable force field for water. The Journal of Chemical Physics, 136, 114511.

    Article  CAS  Google Scholar 

  • Pol-Fachin, L., Hugo Verli, H., & Lins, R. D. (2014). Extension and validation of the GROMOS 53A6glyc parameter set for glycoproteins. Journal of Computational Chemistry, 35, 2087.

    Article  CAS  Google Scholar 

  • 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.

    Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Google Scholar 

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

    Google Scholar 

  • 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 Stucture & Dynamics, 2, 413.

    Article  CAS  Google Scholar 

  • Ponder, J. W. (2015). TINKER – Software tools for molecular design. http://dasher.wustl.edu/tinker/

  • 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.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Ren, P., & Ponder, J. W. (2003). Polarizable atomic multipole water model for molecular mechanics simulation. The Journal of Physical Chemistry B, 107, 5933.

    Article  CAS  Google Scholar 

  • Ren, P., & Ponder, J. W. (2004). Temperature and pressure dependence of the AMOEBA water model. The Journal of Physical Chemistry B, 108, 13427.

    Article  CAS  Google Scholar 

  • Ren, P., Wu, C., & Ponder, J. W. (2011). Polarizable atomic multipole-based molecular mechanics for organic molecules. Journal of Chemical Theory and Computation, 7, 314.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Rojas, A. V., Liwo, A., & Scheraga, H. A. (2011). A study of the α-helical intermediate preceding the aggregation of the amino-terminal fragment of the β amyloid peptide (Aβ1–28). The Journal of Physical Chemistry B, 115, 12978.

    Article  CAS  Google Scholar 

  • Savelyev, A., & MacKerell, A. D., Jr. (2014a). Balancing the interactions of ions, water and DNA in 1314 the Drude polarizable force field. The Journal of Physical Chemistry B, 118, 6742.

    Article  CAS  Google Scholar 

  • Savelyev, A., & MacKerell, A. D., Jr. (2014b). All-atom polarizable force field for DNA based on 1317 the classical Drude oscillator model. Journal of Computational Chemistry, 35, 1219.

    Article  CAS  Google Scholar 

  • Sawant, R. L., Hardas, D. B., Pawa, K. K., & Shinde, A. K. (2014). QSAR analysis of structurally similar 1, 3, 4-oxadiazole/thiadiazole and 1, 2, 4-triazole derivatives of biphenyl-4-yloxy acetic acid as antiinflammatoryagents. World Journal of Pharmaceutical Research, 3, 1844.

    CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Scheraga, H. A. (2015). My 65 years in protein chemistry. Quarterly Reviews of Biophysics, 48, 117.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Shi, Y., Xia, Z., Zhang, J., Best, R., Wu, C., Ponder, J. W., & Ren, P. (2013). Polarizable atomic multipole-based AMOEBA force field for proteins. Journal of Chemical Theory and Computation, 9, 4046.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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. The Journal of Physical Chemistry, 82, 2527.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Tröster, P., Lorenzen, K., & Tavan, P. (2014). Polarizable six-point water models from computational and empirical optimization. The Journal of Physical Chemistry B, 118, 1589.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

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

    Google Scholar 

  • Vanommeslaeghe, K., & MacKerell, A. D., Jr. (2015). CHARMM additive and polarizable force fields for biophysics and computer-aided drug design. Biochimica et Biophysica Acta, General Subjects, 1850, 861.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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 & Modeling, 25, 247.

    Article  CAS  Google Scholar 

  • Wang, L.-P., Chen, J., & van Voorhis, T. (2013a). Systematic parametrization of polarizable force fields from quantum chemistry data. Journal of Chemical Theory and Computation, 9, 452.

    Article  CAS  Google Scholar 

  • Wang, L.-P., Head-Gordon, T., Ponder, J. W., Ren, P., Chodera, J. D., Eastman, P. K., Martinez, T. J., & Pande, V. S. (2013b). Systematic improvement of a classical molecular model of water. The Journal of Physical Chemistry B, 117, 9956.

    Article  CAS  Google Scholar 

  • Warme, P. K., & Scheraga, H. A. (1974). Refinement of the X-ray structure of lysozyme by complete energy minimization. Biochemistry, 13, 757.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Wiberg, K. B. (1965). A scheme for strain energy minimization. Application to the cycloalkanes. Journal of the American Chemical Society, 87, 1070.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Yilmazer, N. D., & Korth, M. (2015). Enhanced semiempirical QM methods for biomolecular interactions. Computational and Structural Biotechnology Journal, 13, 169.

    Article  Google Scholar 

  • Yin, Y., Sieradzan, A. K., Liwo, A., He, Y., & Scheraga, H. A. (2015). Physics-based potentials for coarse-grained modeling of protein-DNA interactions. Journal of Chemical Theory and Computation, 11, 1792.

    Article  CAS  Google Scholar 

  • Yu, W., Lopes, P. E. M., Roux, B., & MacKerell, A. D. (2013). Six-site polarizable model of water based on the classical Drude oscillator. The Journal of Chemical Physics, 138, 034508.

    Article  CAS  Google Scholar 

  • Zgarbova, M., Otyepka, M., Sponer, J., Mladek, A., Banas, P., Cheatham, T. E., & Jurecka, P. (2011). Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles. Journal of Chemical Theory and Computation, 7, 2886.

    Article  CAS  Google Scholar 

  • Zgarbova, M., Luque, F. J., Sponer, J., Cheatham, T. E., Otyepka, M., & Jurecka, P. (2013). Toward improved description of DNA backbone: Revisiting epsilon and zeta torsion force field parameters. Journal of Chemical Theory and Computation, 9, 2339.

    Article  CAS  Google Scholar 

  • 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.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Autonomous University of Puebla, Puebla, Mexico

    Valeri Poltev

Authors
  1. Valeri Poltev
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Valeri Poltev .

Editor information

Editors and Affiliations

  1. Jackson State University, Jackson, Mississippi, USA

    Jerzy Leszczynski

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media Dordrecht

About this entry

Cite this entry

Poltev, V. (2015). Molecular Mechanics: Principles, History, and Current Status. In: Leszczynski, J. (eds) Handbook of Computational Chemistry. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6169-8_9-2

Download citation

  • DOI: https://doi.org/10.1007/978-94-007-6169-8_9-2

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, Dordrecht

  • Online ISBN: 978-94-007-6169-8

  • eBook Packages: Springer Reference Chemistry and Mat. ScienceReference Module Physical and Materials ScienceReference Module Chemistry, Materials and Physics

Publish with us

Policies and ethics

Search

Navigation