Force fields molecular modeling

Keywords Fluctuating charges Charge equilibration Electronegativity equalization Chemical hardness Force fields Molecular models Water models... 

Keywords aminosilane, ab initio, DFT, force field, molecular modeling... 

AMBER force field, molecular modelling 77 anchoring 12... 

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. 

Molecular Dynamics and Monte Carlo Simulations. At the heart of the method of molecular dynamics is a simulation model consisting of potential energy functions, or force fields. Molecular dynamics calculations represent a deterministic method, ie, one based on the assumption that atoms move according to laws of Newtonian mechanics. Molecular dynamics simulations can be performed for short time-periods, eg, 50—100 picoseconds, to examine localized very high frequency motions, such as bond length distortions, or, over much longer periods of time, eg, 500—2000 ps, in order to derive equiUbrium properties. It is worthwhile to summarize what properties researchers can expect to evaluate by performing molecular simulations ... 

Molecular modeling itself can be simply described as the computer-assisted calculation, modulation, and visualization of realistic 3D-molecular structures and their physical-chemical properties using force fields/ molecular mechanics. 

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

Table 7 compares free energies of hydration125 produced by the two types of solvent models that have been presented discrete molecular and continuum. The discrete molecular involved classical force field molecular dynamics (MD) and a free energy perturbation (FEP) technique whereby the solute molecule is annihilated to dummy atoms, so that absolute AGhydration are obtained the continuum were SCRF/PCM calculations, with Claverie-Pierotti Gcavilatlon and Floris-Tomasi Gvdw. The... 

A potentially much more adaptable technique is force-field vibrational modeling. In this method, the effective force constants related to distortions of a molecule (such as bond stretching) are used to estimate unknown vibrahonal frequencies. The great advantage of this approach is that it can be applied to any material, provided a suitable set of force constants is known. For small molecules and complexes, approximate force constants can often be determined using known (if incomplete) vibrational specha. These empirical force-field models, in effect, represent a more sophisticated way of exhapolating known frequencies than the rule-based method. A simple type of empirical molecular force field, the modified Urey-Bradley force field (MUBFF), is introduced below. 

Landis CR, Root DM, Cleveland T. Molecular mechanics force fields for modeling inorganic and organometallic compounds. In Lipkowitz KB, Boyd DB, eds. Reviews in Computational Chemistry. Vol. 6. New York VCH, 1995 73-148. 

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... 

Molecular mechanics force fields for modeling inorganic and organometallic compounds . 

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