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    • MM2 Energy Minimization with hindered rotation

    • Presenter: Jesse Gordon , Company: PerkinElmer Informatics
    • Duration: 3 min
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  • MM2 energy minimizations can identify more than one stable molecular conformation.

    The MM2 force field method is available in all versions of ChemBio3D. MM2 is most commonly used for calculating properties of organic molecular models.

    In ChemBio3D 11.0 and 12.0, the MM2 atom type is used for force field calculations. In earlier versions, MM2 was used only in building models.

    This video demonstrates:

    • Running an MM2 energy-minimization on a molecule with steric hindrance preventing a freely rotatable bond.
    • The MM2 energy-minimization results in two different conformations, depending on the starting point around the hindered bond.
    • The Dihedral Driver tool can analyze the conformations, including the steric hindrance.
    • ChemBio3D 12.0 includes a new implementation of Norman L. Allinger's MM2 force field based in large measure on work done by Jay W. Ponder of Washington University.
    • For a review of MM2 and applications of molecular mechanics methods in general, see Molecular Mechanics, by U. Burkert and N. L. Allinger, ACS, Washington, D.C., USA, 1982. Computational Chemistry, by T. Clark, Wiley, N.Y., USA, 1985, also contains an excellent description of molecular mechanics.
    • For a description of the TINKER system and the detailed rationale for Ponder's additions to the MM2 force field, visit the TINKER home page.
    • For a description and review of molecular dynamics, see Dynamics of Proteins and Nucleic Acids, J. Andrew McCammon and Stephen Harvey, Cambridge University Press, Cambridge, UK, 1987. Despite its focus on biopolymers, this book contains a cogent description of molecular dynamics and related methods, as well as information applicable to other molecules.


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