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A chemical system is a collection of atomic nuclei and accompanying electrons interacting by electromagnetic forces and organized into one or more lattices, molecules, and transient structures. A general problem is to devise a mathematical representation of conformation which is useful in further mechanical analysis. Through dihedral rotations of bonds and relative motion of structures, many chemical systems can attain an infinite number of conformations. A scheme partitioning these into a finite number of sets can assist in comprehension and calculation.
At the macroscopic level, kinematics can describe the progress of a reaction. There it is a part of chemical kinetics. At the microscopic level, is the emerging field of molecular kinematics named by Stefan Fischer and also studied in the Kavraki group.
For a given macromolecule, the problem of finding the conformation with a potential energy near the global minimum is particularly interesting and notoriously difficult. A partitioning scheme can assist in finding such a special conformation. More generally, a partitioning of conformations is fundamental to a microscopic understanding of a chemical process. The complexity of any non-trivial chemical process necessitates involvement of computation in microscopic understanding.
The above publication contains a flaw, first reported by T.F. Havel in a personal communication. In principle, the flaw has been resolved.
Sequel to "Classifying the Conformations of a Chemical System ...". May not be published during my life.
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