The choice of internal coordinates in complex chemical systems

This article presents several considerations for the appropriate choice of internal coordinates in various complex chemical systems. The appropriate and black box recognition of internal coordinates is of fundamental importance for the extension of internal coordinate algorithms to all fields where previously Cartesian coordinates were the preferred means of geometry manipulations. Such fields range from local and global geometry optimizations to molecular dynamics as applied to a wide variety of chemical systems. We present a robust algorithm that is capable to quickly determine the appropriate choice of internal coordinates in a wide range of atomic arrangements. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010