First Principles Molecular Dynamics

SmarglassI E and Madden P A 1994 Orbital-free kinetic-energy functionals for first-principles molecular dynamics Phys. Rev. B 49 5220-6... 

Gain G and Pasquarello A 1993 First-principles molecular dynamics Computer Simulation in Chemioal Physios vol 397 NATO ASI Series C ed M P Allen and D J Tildesley (Dordrecht Kluwer) pp 261-313... 

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. 

Sit, P. Marzari, N., Static and dynamical properties of heavy water at ambient conditions from first-principles molecular dynamics, Los Alamos Eprint Server 2005. cond-mat/0504146... 

Tab. 1.1 Comparison of the properties of quantum chemical electronic structure calculations (QC methods), classical molecular dynamics (Classical MD) based on empirical force fields and first-principles molecular dynamics (ab initio MD) simulations.

Fig. 7. Structures of five-coordinate Cu2+ from first principles molecular dynamics. A Berry twist mechanism for the interconversion of the two structures is shown (from left to right) the reorientation of the main axis of a square pyramidal configuration by pseudo-rotations via a trigonal bipyramidal configuration. The grey atoms in the plane of the trigonal bipyramid are all candidates for becoming apical atoms in a square pyramid.

Dissipation via Quantum Chemical Hysteresis during High-Pressure Compression A First-Principles Molecular Dynamics Study of Phosphates. 

Theoretical calculations [43] based on first principles molecular dynamics discussed in Sect. 3.2.6 have suggested that Mg Al LDHs are most stable for n = 3 (i.e. x = 0.25) and indeed many minerals, including hydrotalcite itself, have this stoichiometry [4]. It has been reported that the synthesis of LDHs (with benzoate or terephthalate anions in the interlayers) from solutions containing Mg/Al = 2, leads to LDHs having the same composition when the synthesis is carried out at moderate temperatures but LDHs with Mg/Al = 3 (plus AlOOH) when the reaction is carried out under hydrothermal conditions [44]. It was proposed that the latter ratio represents the thermodynamically most favorable product. A similar observation has been reported [45] for solutions with Ni VPe = 2, where hydrothermal preparation led to segregation of an LDH with Ni VPe = 3 and Ni Fe 204. An attempt to synthesize a Co sAl LDH resulted in partial oxidation of the Co and formation of a Co o.yCo o.s LDH with complete migration of Al " from the layers to generate interlayer aluminum oxy-species [46]. 

There have been a small number of theoretical studies of cation ordering in LDHs. First principles molecular dynamics calculations [43] on [Mg3Al(OH)8]Cl LDHs discussed in Sect. 3.2.6 suggested that structures with adjacent aluminum cations were energetically less favorable than one without, although the chosen arrangement for the latter lacked either hexagonal or rhombohedral supercell. 

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. 

Figure 3.41. Photoyield Y for H2 and D2 associative desorption from Ru(0001)(l x 1)H and Ru(0001)(lxl)D as a function of absorbed 800 nm 130fs laser pulse fluence F. (a) experimental results with circles for H2 desorption and squares for D2 desorption. Solid lines are fits to a ID friction model and dashed lines are fits to power law expressions, Y oc F28 for H2 and Y oc F3 2 for D2. From Ref. [413]. (b) Equivalent photoyields for associative desorption from 3D first principles molecular dynamics with electronic frictions. From Ref. [101].

Figure 3.43. The time dependent electronic temperature Te, lattice temperature Tq. and adsorbate temperature defined as Tads = [EH /2kB following a 130 fs laser pulse with absorbed laser fluence of 120 J/m2 centered at time t = 0. The bar graph is the rate of associative desorption dY/dt as a function of t. Te and T are from the conventional two temperature model and 7 ads and dY/dl are from 3D first principles molecular dynamics with electronic frictions. From Ref. [101].

Keywords First-Principle Molecular Dynamics, Car-Parinello Molecular Dynamics, Density... 

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

Blochl PE, Parinello M, Adiabaticity in first-principles molecular dynamics, Phys Rev B 45, 9413 (1992)... 

Canto G, Ordejon P, Cheng H, Cooper AC, Pez GP (2003) First-principles molecular dynamics study of die stretching frequencies of hydrogen molecules in carbon nanotubes. New J. Phys. 5 124.1-8... 

The fourth chapter by Michalak and Ziegler presents an excellent introduction into DFT-based first principle molecular dynamics capable of modeling complex chemical reactions. Considerable effort has been made by the authors to explain in detail the specifics of ab initio calculations wherever they differ from conventional techniques. 

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. 

In addition to the development in the methodology to compute electronic structures, there have been several attempts to handle the simulation of a chemical event in a system with a large number of degrees of freedom. The Car-Parrinello (CP) approach [5], often referred to as first-principles molecular dynamics (FPMD) method, opened the way to the molecular dynamics simulations based on the first-principles electronic structure calculations. The point of the method is to circumvent the explicit... 

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. 

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]. 

K. Uehara, M. Ishitobi, T. Oda, and Y. Hiwatari, First-principle molecular dynamics calculation of selenium clusters. Mol. Simul., 18 (1997), 385-394. 

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... 

Annealing to a moving target first-principles molecular dynamics... 

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. 

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