Ab Initio Molecular Dynamics: Basic Theory And ...
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Ab initio molecular dynamics (ab initio MD) is a computational method that uses first principles, or fundamental laws of nature, to simulate the motion of atoms in a system.[2] It is a type of molecular dynamics (MD) simulation that does not rely on empirical potentials or force fields to describe the interactions between atoms, but rather calculates these interactions directly from the electronic structure of the system using quantum mechanics.
In an ab initio MD simulation, the total energy of the system is calculated at each time step using density functional theory (DFT) or another method of quantum chemistry. The forces acting on each atom are then determined from the gradient of the energy with respect to the atomic coordinates, and the equations of motion are solved to predict the trajectory of the atoms.
In this chapter, an introduction to ab initio molecular dynamics (AIMD) has been given. Many of the basic concepts, like the Hellman-Feynman forces, the difference between the Car-Parrinello molecular dynamics and AIMD, have been explained. Also a very versatile AIMD code, the CP2K, has been introduced. On the application, the emphasis was on the aqueous systems and chemical reactions. The biochemical applications have not been discussed in depth.
Abstract:Fuel cell-based anion-exchange membranes (AEMs) and proton exchange membranes (PEMs) are considered to have great potential as cost-effective, clean energy conversion devices. However, a fundamental atomistic understanding of the hydroxide and hydronium diffusion mechanisms in the AEM and PEM environment is an ongoing challenge. In this work, we aim to identify the fundamental atomistic steps governing hydroxide and hydronium transport phenomena. The motivation of this work lies in the fact that elucidating the key design differences between the hydroxide and hydronium diffusion mechanisms will play an important role in the discovery and determination of key design principles for the synthesis of new membrane materials with high ion conductivity for use in emerging fuel cell technologies. To this end, ab initio molecular dynamics simulations are presented to explore hydroxide and hydronium ion solvation complexes and diffusion mechanisms in the model AEM and PEM systems at low hydration in confined environments. We find that hydroxide diffusion in AEMs is mostly vehicular, while hydronium diffusion in model PEMs is structural. Furthermore, we find that the region between each pair of cations in AEMs creates a bottleneck for hydroxide diffusion, leading to a suppression of diffusivity, while the anions in PEMs become active participants in the hydronium diffusion, suggesting that the presence of the anions in model PEMs could potentially promote hydronium diffusion.Keywords: anion-exchange membrane; proton exchange membranes; hydroxide diffusion mechanisms; hydronium diffusion mechanisms; low hydration; ab initio molecular dynamics; nano-confined structures
I have been studying liquid systems (particularly deep eutectic solvents) using classical molecular dynamics (MD) simulations. The main drawback of classical MD is the arbitrariness of the potential parameters and hence it doesn't give accurate results for different experiments. I am planning to pursue ab initio MD simulations for such kind of systems, but I have no experience in any kind of ab initio methods.
Thankfully, when it comes to the molecular dynamics of the situation, ab initio MD as implemented in CP2K (Born-Oppenheimer MD) works essentially the same as classical MD. The difference is really just in the force field, which is calculated on-the-fly via density functional theory methods.
In this topic, the mechanism of proton transfer in water will be discussed. Basics of ab initio molecular dynamics, and the mechanism of proton transfer in water will be presented. The mechanism in water will be compared to the one in phosphoric acid. Furthermore, influences of applied methods, solvation environment, and quantum nuclear effects should be discussed briefly.
Light weight complex metal hydrides, sodium hydride (NaH), and lithium hydride (LiH) are the last step materials during hydrogen release process of alanates and borates, which are promising candidates for hydrogen storage. We report ab initio molecular dynamics (MD) calculations based on density functional theory to study the hydrogen-deuterium exchange in NaH and LiH. We predict the single hydrogen-deuterium exchange in NaH and LiH and calculate the self-diffusion constants, >(NaH)approximate to 1.46x10(-9) m(2) s(-1) of deuterium in NaH at 420 K and >(LiH)approximate to 1.49x10(-9) m(2) s(-1) of deuterium in LiH at 550 K, which are in good agreement with the experimental values.
The sound velocity of Mo along the Hugoniot adiabat is calculated from first principles using density-functional theory based molecular dynamics. These data are compared to the sound velocity as measured in recent experiments. The theoretical and experimental Hugoniot and sound velocities are in very good agreement up to pressures of 210 GPa and temperatures of 3700 K on the Hugoniot. However, above that point the experiment and theory diverge. This implies that Mo undergoes a phase transition at about the same point. Considering that the melting point of Mo is likely much higher at that pressure, the related change in the sound velocity in experiment can be ascribed to a solid-solid transition. 781b155fdc