First principles molecular dynamics simulations of

4 First principles molecular dynamics simulations of mechanically induced bond rupture 

In some respects the principle behind the first principles molecular dynamics approach to examining induced strain is similar to the static methods outlined above, in that the response of the system s configuration 

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). 

This gives the dependence of the rupture probability on force, and includes the description of the bond type through the spring constant, the length of the oligomer and temperature on the rupture force. The rupture probabilities for different length chains reproduce the trend in the simulations in that longer chains result in lower rupture forces. 

The stretching and rupture of a polyethylene glycol (PEG) fragment was examined in water to determine the impact of solvent molecules on the rupture process. The model system included water molecules in the simulation supercell and the molecule was stretched at constant velocity in the maimer described above. Two simulations were completed at 250 K and 320 K. The findings determined that both the presence of water influenced the rupture mechanism, and that the reactivity of the PEG molecule was affected by the elongation. Two reaction mechanisms were observed at 250 K and 320 K but both pathways were similar in their overall form (Fig. 12). 

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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. 

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. 

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... 

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... 

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). 

Okamoto Y (2009) First-principles molecular dynamics simulation of O2 reduction on nitrogen-doped carbon. Appl Surf Sci 256(1) 335-341... 

Okamoto reported the first-principles molecular dynamics simulation of O2 reduction on Zr02 (111) surface [92]. Density functional calculations suggested that the surface of Zr02 was poisoned by OH, which formed through three paths dissociative adsorption of H2O, H termination of O atom in Zr02 by a proton, and O2 reduction intermediate. The OH poison indicated the Z1O2 (1 1 1) surface was inactive for the ORR. However, as the author claimed in the chapter, defects such as O vacancies on the stuface may participate in ORR and contribute to a sustainable catalytic cycle. A simulation based on this reaction model might be necessary. 

Figure 7. Results of first principles molecular dynamics simulation of MgSiOs perovskite at a density of 5184 kg m and a temperature of 2000 K including a) pressme and b) the longitudinal conqjonents of the stress tensor (bold) cth, (hght) G22, (dashed) 033. The off-diagonal components of the stress tensor do not differ significantly from zero.

Figure 8. Two snapshots of a portion of the simulation cell taken from first principles molecular dynamics simulations of MgSiOs perovskite at a) 0 ps and b) 0.79 ps. The view is along [110] of the Pbnm phase.

Very recently another group has performed first principles molecular dynamics simulations of MgSiOs perovskite using methods similar to ours (Oganov et al. 2001). This group finds that the Pbnm phase is stable throughout the pressure-temperature regime of their study, which overlaps the conditions at which we find a phase transformation. The reason for this discrepancy is not clear, but may be related to differences in pseudopotential construction, run time, initial conditions, or other factors. 

Sugino, O., I. Hamada, M. Otani, Y. Morikawa, T. Dceshoji, and Y. Okamoto. 2007. First-principles molecular dynamics simulation of biased electrode/solution interface. Surface Science 601, no. 22 5237-5240. doi 10.1016/j.susc.2007.04.208. 

First-Principles Molecular Dynamics Simulations of Liquid and Glassy GeSc2... 

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