Polyspherical Coordinate Systems on Orbit Spaces with Applications to Biomolecular Shape

Abstract

A general theory of molecular internal coordinates of valence type is presented based on the concept of a Z-system. The Z-system can be considered as a discrete mathematical generalization of the Z-matrix (a molecular geometry file format familiar to chemists) which avoids the principal disadvantage of Z-matrices. Z-matrices are usually only employed for small molecules because there is no easy way to glue two Z-matrices together to get the Z-matrix of a larger molecule. It is shown that Z-matrices are simply Z-systems together with additional extraneous structures and that the Z-systems for any two molecules can be naturally glued together to obtain a Z-system for the combined molecule. A general mathematical framework suitable for the detailed study of molecular geometry is introduced and applied to five and six-membered molecular rings. A classification of shapes of hexagons with opposite sides and angles congruent is given with explicit parameterizations of the flexible and rigid solutions. The entire mathematical formalism generalizes to a theory of polyspherical coordinate systems on orbit spaces of the group of \(n\)-dimensional rigid motions acting on finite collections of points in \(n\)-dimensional Euclidean space. The \(n\)-dimensional Z-system is a new discrete structure related to abstract simplicial complexes, graded posets, and iterated line graphs. Complete proofs of all the \(n\)-dimensional results are given, and connections to other areas of mathematics are noted.