Novel analysis of cation solvation using a graph theoretic approach.

A new method for analyzing molecular dynamics simulation data is employed to study the solvent shell structure and exchange processes of mono-, di-, and trivalent metal cations in water. The instantaneous coordination environment is characterized in terms of the coordinating waters' H-bonding network, orientations, mean residence times, and the polyhedral configuration. The graph-theory-based algorithm provides a rapid frame-by-frame identification of polyhedra and reveals fluctuations in the solvation shell shape--previously unexplored dynamic behavior that in many cases can be associated with the exchange reactions of water between the first and second solvation shells. Extended solvation structure is also analyzed graphically, revealing details of the hydrogen bonding network that have practical implications for connecting molecular dynamics data to ab initio cluster calculations. Although the individual analyses of water orientation, residence time, etc., are commonplace in the literature, their combination with graphical algorithms is new and provides added chemical insight.

MoleculaRnetworks: an integrated graph theoretic and data mining tool to explore solvent organization in molecular simulation.

This work discusses scripts for processing molecular simulations data written using the software package R: A Language and Environment for Statistical Computing. These scripts, named moleculaRnetworks, are intended for the geometric and solvent network analysis of aqueous solutes and can be extended to other H-bonded solvents. New algorithms, several of which are based on graph theory, that interrogate the solvent environment about a solute are presented and described. This includes a novel method for identifying the geometric shape adopted by the solvent in the immediate vicinity of the solute and an exploratory approach for describing H-bonding, both based on the PageRank algorithm of Google search fame. The moleculaRnetworks codes include a preprocessor, which distills simulation trajectories into physicochemical data arrays, and an interactive analysis script that enables statistical, trend, and correlation analysis, and other data mining. The goal of these scripts is to increase access to the wealth of structural and dynamical information that can be obtained from molecular simulations.