First-principles molecular dynamics simulations

Using the first-principles molecular-dynamics simulation, Munejiri, Shimojo and Hoshino studied the structure of liquid sulfur at 400 K, below the polymerization temperature [79]. They found that some of the Ss ring molecules homolytically open up on excitation of one electron from the HOMO to the LUMO. The chain-like diradicals S " thus generated partly recombine intramolecularly with formation of a branched Sy=S species rather than cyclo-Ss- Furthermore, the authors showed that photo-induced polymerization occurs in liquid sulfur when the Ss chains or Sy=S species are close to each other at their end. The mechanism of polymerization of sulfur remains a challenging problem for further theoretical work. 

Rovira, C., and Parrinello, M. 2000. First-principles molecular dynamics simulations of models of the myoglobin active center. Int. J. Quantum Chem. 80 1172-80. 

Michalak A, Ziegler T, First-principle molecular dynamic simulations along the intrinsic reaction paths, J Phys Chem A, 105, 4333—4343 (2001)... 

It is known that first principles molecular dynamics may overcome the limitations related to the use of an intermolecular interaction model. However, it is not clear that the results for the structure of hydrogen bonding liquids predicted by first principles molecular dynamics simulations are necessarily in better agreement with experiment than those relying on classical simulations, and recent first principles molecular dynamics simulations of liquid water indicated that the results are dependent on the choice of different approximations for the exchange-correlation functional [50], Cluster calculations are an interesting alternative, although surface effects can be important and extrapolation to bulk phase remains a controversial issue. 

The first principles molecular dynamics simulation has been applied, based on the linearized-augmented-plane-wave (LAPW) method, to Seg and Seg+ clusters. The equilibrium structures have been obtained for Se8 and Se8+ clusters for the ionized cluster Seg-, a remarkable change from that for the neutral cluster has been found, which reflects the strong electron-lattice coupling in the cluster <1997MI1660, 1997MI75, 1997MI472>. 

Boero M, Parrinello M, Terakura K, Ikeshoji T, Liew CC. (2003) First-principles molecular-dynamics simulations of a hydrated electron in normal and supercritical water. Phys Rev Lett 90 226403-1 to 226403-4. 

McHale JM, Auroux A, Perrotta AJ, Navrotsky A (1997) Surface energies and thermodynamic phase stability in nanocrystalline aluminas. Science 277 788-791 Molteni C, Martonak R, Parrinello M (2001) First principles molecular dynamics simulations of pressure-induced stiuctural transformations in silicon clusters. J Chem Phys 114 5358-5365 Murray CB, Norris DJ, Bawendi MG (1993) Synthesis and characterization of nearly monodisperse CdE (E = S, Se, Te) semiconductor nanocrystallites. J Am Chem Soc 115 8706-8715 Onodera A (1972) Kinetics of polymorphic transitions of cadmium chalcogenides under high pressure. Rev Phys Chem Japan 41 1... 

Successful first-principles molecular dynamics simulations in the Car-Paxrinello framework requires low temperature for the annealed electronic parameters while maintaining approximate energy conservation of the nuclear motion, all without resorting to unduly small time steps. The most desirable situation is a finite gap between the frequency spectrum of the nuclear coordinates, as measured, say, by the velocity-velocity autocorrelation function. 

The review of models and applications in this section proceeds from few- to many-electron systems. This is not historically accurate, since the first first-principles molecular dynamics simulations were performed on larger systems. However, applications to solids, amorphous materials and liquids have been stressed in other reviews [44-47], so we will take the opportunity to place more emphasis on systems of chemical interest. 

In empirical force-fields calculations, the information about the electronic system is entirely contracted in the data of the ground state potential energy surface and forces acting on the nuclei. Model potentials and forces are then used to propagate the ionic dynamics, instead of performing an electronic structure calculation. This on the fly quantum calculation is the challenging part of first-principle Molecular Dynamics simulations. 

In this section we will quickly discuss the special case of plane wave basis sets, as they have been often used in first-principle Molecular Dynamics simulations. 

M. Boero, M. Parrinello, K. Terakura, T. Ikeshoji, and C. C. Liew (2003) First-Principles Molecular-Dynamics Simulations of a Hydrated Electron in Normal and Supercritical Water. Phys. Rev. Lett. 90, p. 226403... 

M. Pohhnaim, M. Benoit, and W. Kob (2004) First-principles molecular-dynamics simulations of a hydrous silica melt Structural properties and hydrogen diffusion mechanism. Phys. Rev. B 70, p. 184209... 

Abstract Theoretical investigations of ionic liquids are reviewed. Three main categories are discussed, i.e., static quantum chemical calculations (electronic structure methods), traditional molecular dynamics simulations and first-principles molecular dynamics simulations. Simple models are reviewed in brief. 

V. van Speybroeck and R. J. Meier, A recent development in computational chemistry Chemical reactions from first principles molecular dynamics simulations, Chem. Soc. Rev., 32 (2003) 151-157. 

X. Biarmes, J. Nieto, A. Planas, and C. Rovira, Substrate distortion in the Michaelis complex of Bacillus 1,3-1,4-/i-glucanase. Insight from first principles molecular dynamics simulations, J. Biol. Chem., 281 (2006) 1432-1441. 

Finally, we refer to a quite recent paper where a first- principles molecular dynamics simulation of amorphous and liquid Si02 was performed [14]. This work confirmed that computer simulation based on the quantum-mechanical calculation of interatomic energy gives basically the same atomic structure of amorphous Si02 as mentioned above simulations based on semiempirical potential of Eq. (1). 

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. 

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. 

First principles molecular dynamics simulations of mechanically induced bond rupture... 

The work by Kruger et al. was initiated by an investigation into the influence of mechanical force on the thiolate - gold interaction which was relevant to mechanical break junctions. In this review we focus on the aspects of this work which relate to mechanochemistry, and not to the mechanical strength of gold nanowires. Their research applied first principles molecular dynamics simulations to investigate the abstraction of an ethylthiolate molecule from an Au(211) substrate, thus investigating the response of the substrate - molecule interaction to an external force applied to the surface normal (Fig. 7). 

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