Chemical Similarity, Chemical Distance, and its Exact Determination

Abstract

The principle of minimum chemical distance, a modern quantitative version of the classical principle of minimum structure change, can now be applied with precision. – In this article we describe for the first time the PEMCD, a computer program for the determination of the exact minima of chemical distance. The PEMCD solves the combinatorial n!-problem for the chemically relevant cases through an approach that is based on chemical and graph theoretical reasoning. The underlying theory and algorithms of PEMCD are discussed. PEMCD does not have the flaws of the previous PMCD-program that finds the minima of chemical distance through an algebraic approximation. In some cases the prerequisites of this approximation are not met, and then the PMCD-program may find false minima of chemical distance (i.e. local minima instead of global).