Testing the Limitations of MD-based Local Electric Fields Using the Vibrational Stark Effect in Solution: Penicillin G as a Test Case

Abstract

<div>Non-covalent interactions underlie nearly all molecular processes in the condensed phase from solvation to</div><div>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.</div>

Blue Fluorescence of Cyano-tryptophan Predicts Local Electrostatics and Hydrogen Bonding in Biomolecules

“…To this end, Boxer and co-workers have recently compared the solvent electric fields estimated from FC and POL MD simulations. 60 For a small neutral molecule, they found that both levels of theory result in similar Stark tuning rates, with a small offset in the predicted electric field values. 60 Boxer's results indicate that although the predicted electric field values may be slightly overestimated in FC MD simulations, the linear correlation between since the atomic motions involved in the vibrational mode are almost totally localized on this particular bond.…”

“…60 For a small neutral molecule, they found that both levels of theory result in similar Stark tuning rates, with a small offset in the predicted electric field values. 60 Boxer's results indicate that although the predicted electric field values may be slightly overestimated in FC MD simulations, the linear correlation between since the atomic motions involved in the vibrational mode are almost totally localized on this particular bond. Interestingly, our experimental results indicate that v C N and v em are linearly correlated for aprotic solvents (Figure 2).…”

“…An electric field has been extensively used to quantify the local electrostatic forces underlying noncovalent interactions in biological systems. 30,60 The linear VSE describes the shift of the frequency of a vibrational probe arising from the interaction of its difference dipole with the electric field exerted by the environment. A particularly convenient method that provides an absolute field−frequency calibration is the combination of vibrational solvatochromism and MD simulations.…”

“…A particularly convenient method that provides an absolute field−frequency calibration is the combination of vibrational solvatochromism and MD simulations. 27,30,33,34,60 As a fluorophore's emission frequency is sensitive to the solvent polarity, 61,62 we have combined fluorescence solvatochromism of 4-cyano-tryptophan (3) and 5-cyano-tryptophan (4) with electric fields predicted from MD simulations (see Scheme 1 for the numbering of the compounds). It is important to note that the sign of the estimated electric field is negative (positive) when the solvent exerts a stabilizing (destabilizing) electric field in comparison to that in the gas phase (vacuum).…”

Nitrile IR intensities characterize electric fields and hydrogen bonding in protic, aprotic, and protein environments

“…The relative increase in peak area from hexanes to water is only 48% for ACP's -C=O but is 342% for BZN's -C≡N (Figure S4). MD simulations using the polarizable AMOEBA09 force field 31 in Tinker 8.7 32 were used to calculate the average solvent electric field, |𝐹 ⃗ |, projected onto the -C=O and -C≡N probes in the same solvents, as described previously [33][34][35][36] . We demonstrate a linear trend when correlating |𝑚 ⃗⃗⃗|, obtained from the peak areas using Equation 3, with the average |𝐹 ⃗ | exerted on ACP's -C=O (Figure 1E).…”