On chirality or planality controle in molecular mchanics

Abstract

We propose a new form of penalty function to constrain molecular structural chirality or planelity in molecular mechanics calculation. By using the signed volume of tetrahedral structure spanned with four unit vectors arround centered chiral carbon atom as a single variable index of the chirality, all chemical bonds are treated as symmetrically equivalent, and any form of single variable function is available for the constraint penalty function. The index of chirality can be extended for the three chemical bond case, and can be used as symmetrical planer constraint penalty functions.