Molecular mechanics parameters for

Delpeyroux and coworkers16 have developed a set of molecular mechanics parameters for nitramines (R—N—NO2) for the EMO program and used it in conjunction with MM2-85 parameters to calculate the structures of 1,4-dinitro-glycoluryl (8), 1,3-dinitro-4,6-diacetylglycoluryl (9) and 2,5,7,9-tetranitro-tetraazabicyclo(4.3.0)nonanone (10). The complete parameter list for the nitramine functionality is provided in Reference 16 but the parameterization procedure is not discussed. 

X-ray structural data for [Ru(bpy)3] " " and a wide range of other polypyridyl derivatives of Ru have been used to develop molecular mechanics parameters for these types of complex with the MM3 force field. Correlations between coordination geometry and emission properties of the Ru complexes have been examined. 

S. Grigoras and T. H. Lane,/. Comput. Chem., 9, 25 (1988). Molecular Mechanics Parameters for Organosilicon Compounds Calculated from Ab Initio Computations. 

Using Ab Initio Calculations to Develop Molecular Mechanics Parameters for Use in Biological Simulations. ... 

Blair, J.T., Levy, R.M. and Krogh-Jespersen, K. (1990) Molecular Mechanics Parameters for Electronically Excited States The (n,tr ) Singlet State of Formaldehyde, Chem. Phys. Letts. 166, 429—436. 

Since it is a non-quantum mechanical method, molecular mechanics is not intrinsically well suited to treating reaction mechanisms other than "reactions" that are simply conformational changes. That is, it would be completely unreasonable to study a bond-breaking process using a standard molecular mechanics package, because the method was not at all parameterized to treat bond-broken structures. Similarly, we might expect that an insufficient data base would exist to allow the development of reliable molecular mechanics parameters for reactive intermediates. Nevertheless, in some specific cases the method has been applied successfully to the evaluation of reaction mechanisms. 

Park S, Radmer RJ, Klein TE, Pande VS (2005) A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of coUagen-like peptides. J Comput Chem 26 1612-1616... 

The following contains portions of molecular data files generated by Insightll/discover for the various systems considered in this chapter. Only nonstandard residues are included. Molecular mechanics parameters for the standard residues are given in Reference [30]. In particular ... 

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. 

From molecular mechanics calculations4 for steric effect parameters. 

Molecular mechanics (also known as force field calculations)261 is a method for the calculation of conformational geometries.262 It is used to calculate bond angles and distances, as well as total potential energies, for each conformation of a molecule.263 Molecular orbital calculations (p. 28) can also give such information, but molecular mechanics is generally easier, cheaper (requires less computer time), and/or more accurate. In mo calculations, positions of the nuclei of the atoms are assumed, and the wave equations take account only of the electrons. Molecular mechanics calculations ignore the electrons, and study only the positions of the nuclei. Another important difference is that in an mo calculation each molecule is treated individually, but in molecular mechanics, parameters are obtained for small, simple molecules and then used in the calculations for larger or more complicated ones. 

The simple harmonic terms used to represent the energy of bond stretching in typical protein molecular mechanics force fields cannot model the making and breaking of chemical bonds. Also, molecular mechanics parameters are usually developed based on the properties of stable molecules, and so might not be applicable to transition states and intermediates. Molecular mechanics functions and parameters can be developed specifically for reactions, an approach that has been... 

This volume has two appendices. The first is a compilation by Professors Fiji Osawa and Kenny B. Lipkowitz of published molecular mechanics parameters. All too frequently, it seems, a program employing an empirical force field chokes on a structure for which it has no parameters. The tabulation in Appendix 1 will help users of molecular mechanics and molecular dynamics programs track down supplemental parameters required for their calculations. 

In the original approach, E et al 36 combined the string method with a molecular-mechanics method for the calculation of the total energy for a given structure, whereas Kanai et al 31 combined it with the parameter-free density-functional Car-Parrinello method. Below we shall present results from the latter study. 

Ab initio calculations for activated complex molecular mechanics parameters reported in paper No additional parameters necesary... 

The four-parameter model provides a crude quahtative representation of the phenomena generally observed with viscoelastie materials instantaneous elastie strain, retarded elastic strain, viscous flow, instantaneous elastie reeovery, retarded elastie reeovery, and plastic deformation (permanent set). Also, the model parameters ean be assoeiated with various molecular mechanisms responsible for the viscoelastic behavior of linear amorphous polymers under creep conditions. The analogies to the moleeular mechanism can be made as follows. 

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