Automatic Conformational Search of Transition States for Catalytic Reactions Using Genetic Algorithm.

With the ever-increasing computational power available to carry out expensive quantum mechanics calculations and the ever-increasing complexity of transition state conformational search problems, a program performing an automatic conformational search will be a valuable tool for computational and experimental chemists. In this manuscript, we report the development and testing of a computational program (QMTSDock) that can automatically search the conformational space of a noncovalent interaction catalyzed transition state or molecular clusters, using quantum mechanics (QM) methods. This program adopts a docking approach using the genetic algorithm (GA). The program allows users to choose the QM method and permits the use of multiple catalysts. New interesting cluster structures were obtained for the GA studies of water heptamer and benzene trimer, while new mechanistic insights have been gained from the GA studies of asymmetric Strecker reaction and asymmetric methanolysis of mesocyclic anhydride reaction.