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Testing the Limitations of MD-based Local Electric Fields Using the Vibrational Stark Effect in Solution: Penicillin G as a Test Case
preprintsubmitted on 21.01.2021, 08:23 and posted on 22.01.2021, 08:25 by Jacek Kozuch, Samuel Schneider, Chu Zheng, Zhe Ji, Richard T Bradshaw, Steven Boxer
Non-covalent interactions underlie nearly all molecular processes in the condensed phase from solvation to
catalysis. Their quantification within a physically consistent framework remains challenging. Experimental vibrational Stark effect (VSE)-based solvatochromism can be combined with molecular dynamics (MD) simulations to quantify the electrostatic forces in solute-solvent interactions for small rigid molecules and, by extension, when these solutes bind in enzyme active sites. While generalizing this approach towards more complex (bio)molecules, such as the conformationally flexible and charged penicillin G (PenG), we were surprised to observe inconsistencies in MD-based electric fields. Combining synthesis, VSE spectroscopy, and computational methods, we provide an intimate view on the origins of these discrepancies. We observe that the electrics fields are correlated to conformation-dependent effects of the flexible PenG side-chain, including both local solvation structure and solute conformational sampling in MD. Additionally, we identified that MD-based electric fields are consistently overestimated in 3-point water models in the vicinity of charged groups; this cannot be entirely ameliorated using polarizable force fields (AMOEBA) or advanced water models. This work demonstrates the value of the VSE as a direct method for experiment-guided refinements of MD force fields and establishes a general reductionist approach to calibrating vibrational probes for complex (bio)molecules.
Email Address of Submitting Authorjkozuch@stanford.edu
ORCID For Submitting Author0000-0002-2115-4899
Declaration of Conflict of InterestAuthors declare no conflict of interest
Read the published paper
in The Journal of Physical Chemistry B