Publications [#234888] of Weitao Yang

Journal Articles

1. Wu, P; Chaudret, R; Hu, X; Yang, W, Noncovalent Interaction Analysis in Fluctuating Environments., Journal of chemical theory and computation, vol. 9 no. 5 (May, 2013), pp. 2226-2234, ISSN 1549-9618 [doi]
   (last updated on 2026/01/16)

   Abstract:
   Noncovalent interactions play a central role in many chemical and biological systems. In a previous study, Johnson et al developed 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 S_N2 reaction in aqueous solution, charge reorganization influences over solvation structure along S_N2 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.