Cytochrome P450 enzymes (CYPs) represent an important enzyme superfamily involved in metabolism of many endogenous and exogenous small molecules. CYP2D6 is responsible for ∼15% of CYP-mediated drug metabolism and exhibits large phenotypic diversity within CYPs with over 100 different allelic variants. Many of these variants lead to functional changes in enzyme activity and substrate selectivity. Herein, a molecular dynamics comparative analysis of four different variants of CYP2D6 was performed. The comparative analysis included simulations with and without SCH 66712, a ligand that is also a mechanism-based inactivator, in order to investigate the possible structural basis of CYP2D6 inactivation. Analysis of protein stability highlighted significantly altered flexibility in both proximal and distal residues from the variant residues. In the absence of SCH 66712, *34, *17-2, and *17-3 displayed more flexibility than *1, and *53 displayed more rigidity. SCH 66712 binding reversed flexibility in *17-2 and *17-3, through *53 remained largely rigid. Throughout simulations with docked SCH 66712, ligand orientation within the heme-binding pocket was consistent with previously identified sites of metabolism and measured binding energies. Subsequent tunnel analysis of substrate access, egress, and solvent channels displayed varied bottle-neck radii. Taken together, our results indicate that SCH 66712 should inactivate these allelic variants, although varied flexibility and substrate binding-pocket accessibility may alter its interaction abilities.

Triply resonant sum frequency (TRSF) spectroscopy is a fully coherent mixed vibrational−electronic spectroscopic technique that is ideally suited for probing the vibrational−electronic couplings that become important in driving reactions. We have used cyanocobalamin (CNCbl) and deuterated aquacobalamin (D 2 OCbl + ) as model systems for demonstrating the feasibility of using the selectivity of coherent multidimensional spectroscopy to resolve electronic states within the broad absorption spectra of transition metal complexes and identify the nature of the vibrational and electronic state couplings. We resolve three short and long axis vibrational modes in the vibrationally congested 1400−1750 cm −1 region that are individually coupled to different electronic states in the 18 000−21 000 cm −1 region but have minimal coupling to each other. Double resonance with the individual vibrational fundamentals and their overtones selectively enhances the corresponding electronic resonances and resolves features within the broad absorption spectrum. This work demonstrates the feasibility of identifying coupling between different pairs of vibrational states with different electronic states that together form the reaction coordinate surface of transition metal enzymes.

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Abstract-Nonlinear multidimensional spectroscopy (MDS) is a powerful experimental technique used to interrogate complex chemical systems. MDS promises to reveal energetics, dynamics, and coupling features of and between the many quantum-mechanical states that these systems contain. In practice, simulation is typically required to connect measured MDS spectra with these microscopic physical phenomena. We present an open-source Python package, WrightSim, designed to simulate MDS. Numerical integration is used to evolve the system as it interacts with several electric fields in the course of a multidimensional experiment. This numerical approach allows WrightSim to fully account for finite pulse effects that are commonly ignored. WrightSim is made up of modules that can be exchanged to accommodate many different experimental setups. Simulations are defined through a Python interface that is designed to be intuitive for experimentalists and theorists alike. We report several algorithmic improvements that make WrightSim faster than previous implementations. We demonstrated the effect of parallelizing the simulation, both with CPU multiprocessing and GPU (CUDA) multithreading. Taken together, algorithmic improvements and parallelization have made WrightSim multiple orders of magnitude faster than previous implementations. WrightSim represents a large step towards the goal of a fast, accurate, and easy to use general purpose simulation package for multidimensional spectroscopy. To our knowledge, WrightSim is the first openly licensed software package for these kinds of simulations. Potential further improvements are discussed.