Path Integral Calculation of the Hydrogen/Deuterium Kinetic Isotope Effect in Monoamine Oxidase A-Catalyzed Decomposition of Benzylamine

Monoamine oxidase A (MAO A) is a well-known enzyme responsible for the oxidative deamination of several important monoaminergic neurotransmitters. The rate-limiting step of amine decomposition is hydride anion transfer from the substrate α–CH2 group to the N5 atom of the flavin cofactor moiety. In this work, we focus on MAO A-catalyzed benzylamine decomposition in order to elucidate nuclear quantum effects through the calculation of the hydrogen/deuterium (H/D) kinetic isotope effect. The rate-limiting step of the reaction was simulated using a multiscale approach at the empirical valence bond (EVB) level. We applied path integral quantization using the quantum classical path method (QCP) for the substrate benzylamine as well as the MAO cofactor flavin adenine dinucleotide. The calculated H/D kinetic isotope effect of 6.5 ± 1.4 is in reasonable agreement with the available experimental values

Understanding the structure of the hydrogen bond network and its influence on vibrational spectra in a prototypical aprotic ionic liquid

Analysis of the hydrogen bond network in aprotic ionic liquid 1-ethyl-3-methylimidazolium bis­(trifluoromethylsulfonyl)­imide (EMIM-TFSI) has been performed based on structures obtained from ab initio or classical molecular dynamics simulations. Statistics of different donor and acceptor atoms and the amount of chelating or bifurcated bonds has been presented. Most of the hydrogen bonds in EMIM-TFSI are formed with oxygen atoms as hydrogen acceptors; and the most probable bifurcated bonds are those with a mixed pair of oxygen and nitrogen acceptors. Spectral graph analysis has shown that the cations may form hydrogen bonds with up to five different anions and the connectivity of the whole hydrogen bond network is supported mainly by H–O bonds. In the structures of the liquid simulated via force field-based dynamics, the number of hydrogen bonds is smaller and fluorine atoms are the most favored hydrogen acceptors. One-dimensional potential energy profiles for hydrogen atom displacements and corresponding vibrational frequencies have been calculated for selected C–H bonds. Individual C–H stretching frequencies vary by 200–300 cm–1, indicating differences in local environment of hydrogen atoms forming C–H···O hydrogen bonds

Car–Parrinello Molecular Dynamics Simulations of Infrared Spectra of Crystalline Vitamin C with Analysis of Double Minimum Proton Potentials for Medium-Strong Hydrogen Bonds

We studied proton dynamics of a hydrogen bonds of the crystalline l-ascorbic acid. Our approach was based on the Car–Parrinello molecular dynamics. The focal point of our study was simulation of the infrared spectra of l-ascorbic acid associated with the O–H stretching modes that are very sensitive to the strength of hydrogen bonding. In the l-ascorbic acid there are four kinds of hydrogen bonds. We calculated their spectra by using anharmonic approximation and the time course of the dipole moment function as obtained from the Car–Parrinello simulation. The quantization of the nuclear motion of the protons was made to perform detailed analysis of strength and properties of hydrogen bonds. We presented double minimum proton potentials with small value of barriers for medium-strong hydrogen bonds. We have also shown the difference character of medium-strong hydrogen bonds compared to weaker hydrogen bonds in the l-ascorbic acid

Car–Parrinello Molecular Dynamics Simulations of Infrared Spectra of Crystalline Vitamin C with Analysis of Double Minimum Proton Potentials for Medium-Strong Hydrogen Bonds

We studied proton dynamics of a hydrogen bonds of the crystalline l-ascorbic acid. Our approach was based on the Car–Parrinello molecular dynamics. The focal point of our study was simulation of the infrared spectra of l-ascorbic acid associated with the O–H stretching modes that are very sensitive to the strength of hydrogen bonding. In the l-ascorbic acid there are four kinds of hydrogen bonds. We calculated their spectra by using anharmonic approximation and the time course of the dipole moment function as obtained from the Car–Parrinello simulation. The quantization of the nuclear motion of the protons was made to perform detailed analysis of strength and properties of hydrogen bonds. We presented double minimum proton potentials with small value of barriers for medium-strong hydrogen bonds. We have also shown the difference character of medium-strong hydrogen bonds compared to weaker hydrogen bonds in the l-ascorbic acid