Force fields molecular mechanics

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. 

Geometric Optimization. The structure of the molecule as built by CHEMLAB (or a input from other methods) can be optimized through either a full force field molecular mechanics calculation (MMII) or with the semi-empirical molecular orbital methods MINDO-3 and MNDO. 

Computational chemistry, which refers to physical-chemical mathematical modeling at the molecular level and includes such topics as quantum chemistry, force fields, molecular mechanics, molecular simulations, molecular modeling, molecular design, and cheminformatics. 

Computational methodology has been used to accompany or to anticipate experimental results for many classes of compounds. Such results are particularly helpful for transient species, for rationalization of physical and structural properties, and for simulation of reaction pathways and transition states. Semiempirical valence electron (CNDO/MNDO), ab initio, and nonquantum mechanical force field (molecular mechanics) calculations have mainly been used for the examination of structure and stability of moderately strained olefins, whereas many-electron quantum-chemical methods have been used for detailed discussion of electronic aspects. Excellent reviews of molecular mechanics calculations, the principal method used to describe geometrical and energy features in distorted double bond systems, have been written by Osawa and Musso (61). 

If a structure is well modeled by the parameters in the force field, molecular mechanics provides a means to calculate its AH that is said to rival experiment for accuracy. Molecular mechanics can also be used to calculate a value for the strain energy of a structure. The strain energy of a molecule is not the same as the steric energy obtained from a molecular mechanics calculation, however, and the term strain is less precise than one might expect. "Qualitatively, organic chemists usually recognize a strained molecule when they see one," ° but strain is a parameter that can only be determined by reference to a model structure that is defined to be strain free. 

Molecular mechanics uses classical mechanics to model molecular systems. The potential energy of all systems in molecular mechanics is calculated using force fields. Molecular mechanics can be used to study small molecules as well as large biological systems or material assemblies with many thousands to millions of atoms. All-atomistic molecular mechanics methods have the following properties ... 

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