Parameters, changed molecular mechanics

Since the parameters used in molecular mechanics contain all of the electronic interaction information to cause a molecule to behave in the way that it does, proper parameters are important for accurate results. MM3(2000), with the included calculation for induced dipole interactions, should model more accurately the polarization of bonds in molecules. Since the polarization of a molecular bond does not abruptly stop at the end of the bond, induced polarization models the pull of electrons throughout the molecule. This changes the calculation of the molecular dipole moment, by including more polarization within the molecule and allowing the effects of polarization to take place in multiple bonds. This should increase the accuracy with which MM3(2000) can reproduce the structures and energies of large molecules where polarization plays a role in structural conformation. 

Head et al. developed a PLS-based model VALIDATE [47] to scale the relative contributions of entropy and enthalpy to binding affinity for a variety of complexes whose crystal structures had been determined. Molecular mechanics were used to calculate several parameters most correlated with enthalpy of binding, while changes in surface area, number of rotatable bonds fixed upon binding and other parameters more related to the entropy of binding were also included in the model. Of interest was that the principal components of the model were dominated by two terms (AH and AS,... 

Molecular structure and shape are related to orbital angular momentum and chemical change is shown to be dictated by the quantum potential. The empirical parameters used in computer simulations such as molecular mechanics and dynamics are shown to derive in a fundamental way from the relationship between covalence and the golden ratio. 

A molecule-independent, generalized force field for predictive calculations can be obtained by the inclusion of additional terms such as van der Waals and torsional angle interactions. This adds an additional anharmonic part to the potential (see below) but, more importantly, also leads to changes in the whole force field thus the force constants used in molecular mechanics force fields are not directly related to parameters obtained and used in spectroscopy. It is easy to understand this dissimilarity since in spectroscopy the bonding and angle bending potentials describe relatively small vibrations around an equilibrium geometry that, at least... 

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