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Noncovalent Interaction Analysis in Fluctuating Environments
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DOI：10.1021/ct4001087.png)
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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 the solution phase, we here developed a new averaged noncovalent interaction (i.e., aNCI) index along with a fluctuation index to characterize the 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(N)2 reaction in aqueous solution, charge reorganization influences over solvation structure along S(N)2 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.
Keyword:
LIQUID WATER
INTERACTION REGIONS
ELECTRON-DENSITY
BENZENE
INHIBITOR
DYNAMICS
HSP90
MECHANISM
DISCOVERY
HYDRATION
期刊
IF:
5.5
论文数:
1.1W
被引数:
5.4W
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