Reaction mechanisms molecular dynamics principles

Eucken discovered that the molecular heat of hydrogen falls at low temperatures from 5 to 3. This and other variations in specific heats with temperature can only be interpreted in terms of quantum dynamics, and the subjection of mechanical processes taking place among gas molecules to quantum principles must be taken into consideration in theories of chemical reaction mechanisms. 

An often-overlooked aspect of standard reaction mechanistic thought is that it really addresses only half of the picture. We talk about the positions of the atoms during the course of the reaction and the relative energies of points along the reaction path, but no mention is made of the time evolution of this process. In classical mechanics, description of a reactive system requires not just the particle positions but their momenta as well. The same is true for a quantum mechanical description, though one must keep in mind the limits imposed by the Heisenberg Uncertainty Principle. A complete description of a molecular reaction requires knowledge of both the position and the momenrnm of every atom for the entire time it takes for reactants to convert into products. This kind of description falls under the term molecular dynamics (MD). 

Progress was also reported in modeling the reaction and transportation processes on fuel cell catalysts and through membranes, using multiple paradigms as well as starting from first principle quantum mechanics to train a reactive force field that can be applied for large scale molecular dynamics simulations. It is expected that the model would enable the conception, synthesis, fabrication, characterization, and development of advanced materials and structures for fuel cells . 

First principles approaches are important as they avoid many of the pitfalls associated with using parameterized descriptions of the interatomic interactions. Additionally, simulation of chemical reactivity, reactions and reaction kinetics really requires electronic structure calculations [108]. However, such calculations were traditionally limited in applicability to rather simplistic models. Developments in density functional theory are now broadening the scope of what is viable. Car-Parrinello first principles molecular dynamics are now being applied to real zeolite models [109,110], and the combined use of classical and quantum mechanical methods allows quantum chemical methods to be applied to cluster models embedded in a simpler description of the zeoUte cluster environment [105,111]. 

There has been a variety of studies using Car-Parrinello simulations to determine the structure and energetics of adsorbates on semiconductor and insulating surfaces. Studies on metal surfaces are much rarer, and as far as I know, first-principles molecular dynamics simulations have not yet been used to study reactive processes on metals. The reason is primarily one of computational expense, because metals require the inclusion of a large number of k-points. Tliere is, of course, a substantial body of work which uses static quantum mechanical calculations to study reactions on metal surfaces. 

There are continuous theoretical attempts to describe the mechanism of CVD-diamond synthesis including mechanisms of surface reactions, diamond nucleation, and film growth. To achieve this aim various phenomenological or first-principles models, molecular dynamics and Monte Carlo simulations have been used [57,58]. 

Although new reaction pathways may become favorable on the application of mechanical force, this does not necessarily mean that the rupture process proceeds by this path. Simulations on the molecular scale using first principles molecular dynamics simulations can follow the evolution of the electronic structure as the molecule is forced along a specific pathway at finite temperature, which captures the response of the molecule in terms of adjustments in bond parameters as mechanical energy is added to the system. By adjusting the length of the molecule and the pulling rate, the impact of molecular parameters and the means by which the force is applied can be accurately determined. The modification of the electronic structure as rupture occurs is also described. 

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