Molecular mechanics generalized coordinates

Molecular mechanics calculations are an attempt to understand the physical properties of molecular systems based upon an assumed knowledge of the way in which the energy of such systems varies as a function of the coordinates of the component atoms. While this term is most closely associated with the conformational energy analyses of small organic molecules pioneered by Allinger (1), in their more general applications molecular mechanics calculations include energy minimization studies, normal mode calculations, molecular dynamics (MD) and Monte Carlo simulations, reaction path analysis, and a number of related techniques (2). Molecular mechanics... 

Therefore, two parts of any molecular mechanics package that have a direct influence on a particular optimized structure, i. e., on the nuclear coordinates of a specific energy minimum on the calculated potential energy surface, are the mathematical functions and the corresponding parameters. The potential energy functions and the force field parameters are interrelated and, therefore, the parameters may not, in general, be transferred from one force field into another. 

Important, though not generally appreciated, problems of the application of molecular mechanics to the prediction of metal ion selectivities are the neglect of solvation and entropic effects. These have been discussed in Chapter 2, Sections 2.7 and 2.8. The sum of all the other terms mentioned above may be related to the difference in total strain energy between the metal-free and the coordinated ligand. 

The electronic ground state that a particular metal center adopts is a function of the chromophore. In many cases the ground state may be derived from chemical knowledge (e. g., octahedral cobalt(HI) ( Aig) or tetrahedral Ni(II) (3T() complexes). However, based on the molecular mechanics formalism alone, this problem cannot be solved in a general way. Let us consider coordination compounds which are close to the spin-crossover limit (for example hexacoordinate iron(II) (1Aig/5T2g)). In these cases it is not possible to assign the atom type of the metal center without further information (experimental or theoretical). Therefore, molecular mechanics alone is not always able to predict the structural properties. 

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