Car-Parrinello and path integral molecular dynamics study of the hydrogen bond in the acetic acid dimer in the gas phase.
Summary of "Car-Parrinello and path integral molecular dynamics study of the hydrogen bond in the acetic acid dimer in the gas phase."
In the paper are described studies of the double proton transfer (DPT) processes in the cyclic dimer of acetic acid in the gas phase using Car-Parrinello (CPMD) and path integral molecular dynamics (PIMD). Structures, energies and proton trajectories have been determined. The results show the double proton transfer in 450 K. In the classical dynamics (CPMD) a clear process mechanism can be identified, where asynchronized DPT arises due to coupling between the O-H stretching oscillator and several low energy intermolecular vibrational modes. The DPT mechanism is also asynchronic when quantum tunneling has been allowed in the simulation. It has been found that the calculated values of barrier height for the proton transfer depends very strongly on the used approaches. Barrier received from the free-energy profile at the CPMD level is around 4.5 kcal mol(-1) whereas at the PIMD level is reduced to 1 kcal mol(-1). The nature of bonding in acetic acid dimer and rearrangement of electron density due to the proton movement has been also studied by the topological analysis of Electron Localization Function and Electron Localizability Indicator function.
Affiliation
Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie Str, 50-383, Wrocław, Poland, piotr@elrond.chem.uni.wroc.pl.
Journal Details
This article was published in the following journal.
Name: Journal of molecular modeling
ISSN: 0948-5023
Pages:
Links
- PubMed Source: http://www.ncbi.nlm.nih.gov/pubmed/21360182
- DOI: http://dx.doi.org/10.1007/s00894-011-1020-9
Medical and Biotech [MESH] Definitions
Molecular Dynamics Simulation
A computer simulation developed to study the motion of molecules over a period of time.
Superoxide Dismutase
An oxidoreductase that catalyzes the reaction between superoxide anions and hydrogen to yield molecular oxygen and hydrogen peroxide. The enzyme protects the cell against dangerous levels of superoxide. EC 1.15.1.1.
Nonlinear Dynamics
The study of systems which respond disproportionately (nonlinearly) to initial conditions or perturbing stimuli. Nonlinear systems may exhibit "chaos" which is classically characterized as sensitive dependence on initial conditions. Chaotic systems, while distinguished from more ordered periodic systems, are not random. When their behavior over time is appropriately displayed (in "phase space"), constraints are evident which are described by "strange attractors". Phase space representations of chaotic systems, or strange attractors, usually reveal fractal (FRACTALS) self-similarity across time scales. Natural, including biological, systems often display nonlinear dynamics and chaos.
Models, Molecular
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Hydrogen
Hydrogen. The first chemical element in the periodic table. It has the atomic symbol H, atomic number 1, and atomic weight 1. It exists, under normal conditions, as a colorless, odorless, tasteless, diatomic gas. Hydrogen ions are PROTONS. Besides the common H1 isotope, hydrogen exists as the stable isotope DEUTERIUM and the unstable, radioactive isotope TRITIUM.
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