title: Noncovalent Interaction Analysis in Fluctuating Environments.
abstract: Noncovalent interactions play a central role in many chemical and biological systems. In a previous study, Johnsonet aldeveloped a NonCovalent Interaction (NCI) index to characterize and visualize different types of weak interactions. To apply the NCI analysis to fluctuating environments as in solution phase, we here develop a new Averaged NonCovalent Interaction (i.e., aNCI) index along with a fluctuation index to characterize magnitude of interactions and fluctuations. We applied aNCI for various systems including solute-solvent and ligand-protein noncovalent interactions. For water and benzene molecules in aqueous solution, solvation structures and the specific hydrogen bond patterns were visualized clearly. For the Cl-+CH3Cl SN2 reaction in aqueous solution, charge reorganization influences over solvation structure along SN2 reaction were revealed. For ligand-protein systems, aNCI can recover several key fluctuating hydrogen bond patterns that have potential applications for drug design. Therefore, aNCI, as a complementary approach to the original NCI method, can extract and visualize noncovalent interactions from thermal noise in fluctuating environments.
authors.affiliation: Department of Chemistry, Duke University, Durham, NC 27708.
authors.forename: Pan
authors.initials: P
authors.lastname: Wu
authors.forename: Robin
authors.initials: R
authors.lastname: Chaudret
authors.forename: Xiangqian
authors.initials: X
authors.lastname: Hu
authors.forename: Weitao
authors.initials: W
authors.lastname: Yang
keywords: fluctuating environment; hydrogen bond; ligand-protein binding; noncovalent interaction; solvation structure
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