Ab initio molecular dynamics

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.

Anomalous dependence of particle size on supersaturation in the preparation of iron nanoparticles from iron pentacarbonyl

Iron nanoparticles were prepared by decomposing iron pentacarbonyl (Fe(CO)(5)) at 170-220°C in the presence of amine surfactant and alkane solvent and under 1-12 bar carbon monoxide (CO) pressure. It was found that the amine not only acted as a stabilizer for the growing particles but also had a critical role as a promotor in the decomposition reaction. Relatively small changes in the CO pressure had anomalous effects on the particle size distribution. Typically, monodisperse particles were obtained at 1 bar, while pressures in the 2-6 bar range led to wider and even bimodal size distributions due to an emergence of smaller particles. At still higher pressures, the larger particle size disappeared leaving the distribution monodisperse again. The CO pressure, at which the bimodal transition took place, increased with the reaction temperature. Polycrystalline particles were formed at lower pressures and monocrystalline particles at higher pressures. This indicates that increased CO pressure inhibits aggregation.

Significance of Ammonia in Growth of Atmospheric Nanoclusters

We apply accurate quantum chemistry methods to study the thermochemistry of molecular clusters containing ammonia, water, and sulfuric acid and investigate initial reaction steps in atmospheric nucleation by calculating free energies for the related reactions. The results indicate that ammonia is a key reactant enhancing the growth of small water-sulfuric acid clusters in atmospheric conditions. The role of ammonia becomes significant when the nanoclusters contain more than one or two sulfuric acid molecules. This implies a lower limit of 1:3 for the NH3/H2SO4 mole ratio of atmospheric sulfuric acid-water-ammonia clusters.

Ab initio molecular dynamics study of a mixture of HF(aq) and HCl(aq)

We have studied a mixture of HF and HCl molecules in water using Car-Parrinello ab initio molecular dynamics (CPMD). We have done simulations with 1 HF and 3 HCl molecules, 3 HF and 4 HCl, 6 HF and 8 HCl (6/8 simulation), and 14 HF molecules. All simulations consist of 32 molecules, and they were 10-96 ps long. The HF dissociation probability was around 30%, and HCl's was more than 90%. The solvation of the HF molecule was much better than the solvation of HCl. The solvation environment of F, both the F- ion and the F in HF, did not depend much on the acids concentration, whereas the Cl coordination numbers were rather sensitive to the concentration. In the 6/8 simulation, all XH-Y (X, Y = F, Cl) type molecules were observed and the FH-F was the most probable. In general, the molecular structures in mixed aqueous acid systems were similar to the pure HF(aq) and HCl(aq) systems.

Ab Initio Molecular Dynamics Study of a Mixture of HF(aq) and HCl(aq)†

We have studied a mixture of HF and HCl molecules in water using Car-Parrinello ab initio molecular dynamics (CPMD). We have done simulations with 1 HF and 3 HCl molecules, 3 HF and 4 HCl, 6 HF and 8 HCl (6/8 simulation), and 14 HF molecules. All simulations consist of 32 molecules, and they were 10-96 ps long. The HF dissociation probability was around 30%, and HCl's was more than 90%. The solvation of the HF molecule was much better than the solvation of HCl. The solvation environment of F, both the F- ion and the F in HF, did not depend much on the acids concentration, whereas the Cl coordination numbers were rather sensitive to the concentration. In the 6/8 simulation, all XH-Y (X, Y = F, Cl) type molecules were observed and the FH-F was the most probable. In general, the molecular structures in mixed aqueous acid systems were similar to the pure HF(aq) and HCl(aq) systems.