Hydrogen Bond Energy Estimation in Large Molecular Clusters via the Method of Synergistic Cyclic Cooperativity: A Software Update H-BEE 2.0

Abstract

Our earlier developed software utility, H-BEE, for estimating the energies of individual hydrogen bonds (HB) in molecular clusters was implemented with three methods. These methods are: the molecular tailoring approach based (MTA-based) one, the first spherical shell (SS1), and the Fragments-in-Fragments. These methods work quite well but are still time-consuming and have certain shortcomings. Herein, our recently proposed method of synergistic cyclic cooperativity (SCC) is implemented as an update (called H-BEE 2.0) to H-BEE. The three-dimensional (3D) molecular cluster is usually made up of small cyclic structures which result from the interconnected network of HBs. Within the SCC method, the energy of a referenced HB is estimated as the sum of the cooperativity contributions (CCs) of these small cyclic structures and its energy in an isolated dimeric species. The SCC is an effective and swift method. The H-BEE 2.0 identifies all possible cyclic structures in an automatic manner and evaluates the CCs of these cycles. The H-BEE 2.0 utility has been extensively tested on a variety of molecular clusters and the results are compared with the earlier implemented methods. It also brings out the finer aspects of the strength of HBs in terms of the nature of cooperativity of small cyclic networks.