Force field, molecular modelling

Many of the molecular modelling force fields in use today for molecular systems can be interpreted in terms of a relatively simple four-component picture of the intra- and inter-molecular forces within the system. Energetic penalties are associated with the deviation of bonds and angles away from their reference or equilibrium values, there is a function... 

DMA models have also been incorporated into the molecular modeling force field program MOMO, ° which was used to study host-guest complexes, such as benzene in a hexaoxacyclophane host. The difficult problem of accurately modeling the intramolecular electrostatic energy of proteins has also used distributed-multipole-type models. ... 

The model of the interactions in molecular mechanics is simple and the Bom-Oppenheimer approximation must be applicable. The most common molecular modelling force fields are based on the very simple picture of intra- and intermolecular forces. The energy is expressed as a function of a series of reference values for the bond lengths and angles. The electrostatic interactions can also be considered in this framework. 

Keywords Molecular modeling Force field Numerical optimization High-performance computing Modular software packages... 

Computer Graphics and Molecular Modeling Force Fields A General Discussion Internet Internet-based Computational Chemistry Tools Molecular Models Visualization Symmetry in Chemistry Teaching Computational Chemistry to Undergraduate Students. 

Landis C R, D M Root and T Cleveland 1995. Molecular Mechanics Force Fields for Modeling Inorgani and Organometallic Compounds. In Lipkowitz K B and D B Boyd (Editors). Reviews in Compute tional Chemistry Volume 6. New York, VCH Publishers, pp. 73-148. 

AMBER (assisted model building with energy refinement) a molecular mechanics force field... 

The original molecular-mechanics force field was developed by Allinger, and is generally referred to as MM. You should read the definitive text by Burkert and Allinger (1982) for more details. This model was followed by the MM2 model (Allinger, 1977), and I thought that you might like to read the synopsis. 

Bernardo DN, Ding YB, Kroghjespersen K, Levy RM (1994) An anisotropic polarizable water model - incorporation of all-atom polarizabilities into molecular mechanics force-fields. J Phys Chem 98(15) 4180-4187... 

Bret C, Field MJ, Hemmingsen L (2000) A chemical potential equalization model for treating polarization in molecular mechanical force fields. Mol Phys 98(11) 751— 763... 

Molecular mechanics force fields rest on four fundamental principles. The first principle is derived from the Bom-Oppenheimer approximation. Electrons have much lower mass than nuclei and move at much greater velocity. The velocity is sufficiently different that the nuclei can be considered stationary on a relative scale. In effect, the electronic and nuclear motions are uncoupled, and they can be treated separately. Unlike quantum mechanics, which is involved in determining the probability of electron distribution, molecular mechanics focuses instead on the location of the nuclei. Based on both theory and experiment, a set of equations are used to account for the electronic-nuclear attraction, nuclear-nuclear repulsion, and covalent bonding. Electrons are not directly taken into account, but they are considered indirectly or implicitly through the use of potential energy equations. This approach creates a mathematical model of molecular structures which is intuitively clear and readily available for fast computations. The set of equations and constants is defined as the force... 

Clark R. Landis, Daniel M. Root, and Thomas Cleveland, Molecular Mechanics Force Fields for Modeling Inorganic and Organometallic Compounds. 

Figure 3. Structural representation of the computational models A-F. Models B, D, and E are combined QM/MM models where the regions enclosed in the dotted polygons represent the QM region. The regions outside the polygons are treated by a molecular mechanics force field. For the electronic structure calculation of the QM region, the covalent bonds that traverse the QM/MM boundary (the dotted polygon), have been capped with hydrogen atoms. In model A the atoms labelled 1 through 4 are the atoms that have been fixed in the calculations of models A through E.

Park, H. and Lee, S. (2004) Homology modeling, force field design, and free energy simulation studies to optimize the activities of histone deacetylase inhibitors. Journal of Computer-Aided Molecular Design, 16, 375—388. 

A classical force-field is developed to represent the conformational characteristics of PC based upon recent experimental and quantum mechanical data. This force field is an improvement upon previously published molecular mechanics force fields because it allows for rotation about all the single bonds in the PC repeat unit. An RIS model of PC is obtained using the force field results. 

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