From owner-chemistry@ccl.net Sun Dec 15 12:47:01 2013 From: "Aurora Evelyn Clark auclark!=!wsu.edu" To: CCL Subject: CCL: ChemNetworks Software Release Message-Id: <-49451-131215124120-17713-j6Ghnm4KP+NZ8m3CGAMazg[]server.ccl.net> X-Original-From: "Aurora Evelyn Clark" Date: Sun, 15 Dec 2013 12:41:19 -0500 Sent to CCL by: "Aurora Evelyn Clark" [auclark]![wsu.edu] We are pleased to announce the release of ChemNetworks, a graph-theory based analysis program for quantifying the static organizational and dynamic behavior of chemical networks defined by intermolecular interactions (for example hydrogen bond networks, ion-dipole interactions, dipole- dipole, etc.). This code processes Cartesian coordinates of chemical systems (from x-ray, QM/MM, molecular dynamics, Monte Carlo, etc.) into a network/graph formalism based upon geometric criterion for the interaction of interest, specified by the user. Following this, various topological network analyses that include Network neighborhood, the determination of geodesic paths (shortest pathways connecting molecular vertices), the degree census (distribution of the interactions), direct structural searches, and the distribution of defect states of the network can be performed. Special analyses for water have also been implemented, for example the study of the oscillation of the dipole angle as a function of time about a solute or other solvents. In this way, directed graphs that investigate for example hydrogen bond donor vs. acceptor interactions, can be studied. The properties obtained from ChemNetworks can help to understand network patterns and organization that may influence physical properties and chemical reactivity. The code is highly general, capable of converting a wide variety of systems into a chemical network formalism, including complex solutions, liquid interfaces, self-assemblies, solvated proteins, etc. ChemNetworks and its user manual is available for free download from http://aclark.chem.wsu.edu/software/