8 research outputs found
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
bisÂ(trifluoromethylsulfonyl)Âimide (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 HâO 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 CâH bonds. Individual CâH
stretching frequencies vary by 200â300 cmâ1, indicating differences in local environment of hydrogen atoms forming
CâH···O hydrogen bonds
Understanding the Structure of the Hydrogen Bond Network and Its Influence on Vibrational Spectra in a Prototypical Aprotic Ionic Liquid
Path Integral Calculation of the Hydrogen/Deuterium Kinetic Isotope Effect in Monoamine Oxidase A-Catalyzed Decomposition of Benzylamine
Comparison of the Hydrogen Bond Interaction Dynamics in the Guanine and Cytosine Crystals: Ab Initio Molecular Dynamics and Spectroscopic Study
CarâParrinello 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 CarâParrinello
molecular dynamics. The focal point of our study was simulation of
the infrared spectra of l-ascorbic acid associated with the
OâH 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 CarâParrinello 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
CarâParrinello 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 CarâParrinello
molecular dynamics. The focal point of our study was simulation of
the infrared spectra of l-ascorbic acid associated with the
OâH 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 CarâParrinello 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