Ab initio molecular dynamics studies

Jesson B J, Foley M and Madden P A 1997 Thermal properties of the self-interstitlal In aluminum an ab initio molecular-dynamics study Pbys. Rev. B 55 4941-6... 

AokI M I and Tsumuraya K 1997 Ab initio molecular-dynamics study of pressure-induced glass-to-crystal transitions In the sodium system Pbys. Rev. B 56 2962-8... 

Meier, R.J., Van Doremaele, H.J., larlori, S., Buda, F. Ab-initio molecular dynamics study of metallocene-catalysed ethylene polymerization. J. Amer. Chem. Soc. 116 (1994) 7274-7281. 

Wang YX, Balbuena PB. 2004 Roles of proton and electric field in the electroreduction of O2 on Pt(lll) surfaces Results of an ab-initio molecular dynamics study. J Phys Chem B 108 4376-4384. 

The ab initio molecular dynamics study by Hudock et al. discussed above for uracil included thymine as well [126], Similarly to uracil, it was found that the first ultrafast component of the photoelectron spectra corresponds to relaxation on the S2 minimum. Subsequently a barrier exists on the S2 surface leading to the conical intersection between S2 and Si. The barrier involves out-of-plane motion of the methyl group attached to C5 in thymine or out-of-plane motion of H5 in uracil. Because of the difference of masses between these two molecules, kinematic factors will lead to a slower rate (longer lifetime) in thymine compared to uracil. Experimentally there are three components for the lifetimes of these systems, a subpicosecond, a picosecond and a nanosecond component. The picosecond component, which is suggested to correspond to the nonadiabatic S2/S1 transition, is 2.4 ps in uracil and 6.4 ps in thymine. This difference in the lifetimes could be explained by the barrier described above. 

Y. Kurosaki. Energy-flow dynamics in the molecular channel of propanal photodissociation, C2H5CHO -> C2H64-CO direct ab initio molecular dynamics study, J. Phys. Chem. A, 110 11230-11236(2006). 

The gas-phase model would then be tested on condensed phases. In the case of the carbonate ion, the parameters can be used to examine the structure of C02(aq), C032-(aq), and HC03 (aq) as well as the structure of, for example, siderite FeC03 and nahcolite Na(HC03). For the aqueous species, the most instructive comparisons are with the results of ab initio molecular dynamics studies of solvated ions, where the radial distribution functions can be used to check the extent of solvation. Fig. 2, for... 

Raugei, S., Klein, M. L. (2002), Hydrocarbon Reactivity in die Superacid Sbl VIIF an ab initio Molecular Dynamics Study, J. Phys. Chem. B 106, 11596-11605. 

Car, R., and M. Parrinello (1988). Structural, dynamic, and electronic properties of amorphous silicon an ab initio molecular dynamics study. Phys. Rev. Lett. 60, 204-7. 

In the case of MgO, various types of OH groups can form, depending on the sites involved in the chemisorption process. In a periodic ab initio molecular dynamics study [113], it has been shown that the faces which are energetically unfavorable in the clean MgO surface may become favored in the presence of water. The calculations indicated that there is a net stabilization upon going from the MgO(lOO) surface covered with molecularly adsorbed water to the MgO(lll) surface covered with dissociated water. This is not too surprising if we consider that brucite, Mg(OH)2, is a mineral with hexagonal structure which exhibits the (0001) face as the most stable one and that MgO is often produced by thermal decomposition of brucite. 

V. Sundararajan and V. Kumar, Ab initio molecular dynamics study of antimony clusters, J. Chem. Phys. 102,9631-9637 1995. 

Car, R., and Parrinello, M. (1988) Stinctmal, Djmianical, and Electronic Properties of Amorphous Silicon An ab initio Molecular-Dynamics Study, Phys. Rev. Lett. Vol. 60, pp.204-207. 

E. J. Meijer and M. Sprik (1998) Ab Initio Molecular Dynamics Study of the Addition Reaction of Water to Formaldehyde in Sulfuric Acid Solution. J. Am. 

M.-P. Gaigeot and M. Sprik (2004) Ab initio molecular dynamics study of uracil in aqueous solution. J. Phys. Chew,. B 108, p. 7458... 

J. Sarnthein, A. Pasquarello, and R. Car (1995) Structural and Electronic Properties of Liquid and Amorphous Si02 An Ab Initio Molecular Dynamics Study. Phys. Rev. Lett. 74, p. 4682... 

Ben Nun, M., Martinez, T. J., Ab Initio Molecular Dynamics Study of cis trans Photo isomerization in Ethylene, Chem. Phys. Lett. 1998, 298, 57 65. 

Stubbs and Marx reported Car-Parrinello ab initio molecular dynamics studies for the specific-acid-catalyzed glycosidic bond formation between a-D-glucopyranose and methanol (which corresponds to the cleavage reaction by microscopic reversibility)61,62 (Scheme 32). In this work, particular attention was paid to the role of the aqueous solvent, and as a computational study is particularly noteworthy for explicit consideration of solvent molecules. The dynamics simulations required constraints on the reaction coordinate (the methanol oxygen/oxocarbenium ion carbon distance) to ensure driving it along a productive pathway over the short time-course of the dynamics simulation, over a time period of approximately 15 ps. 

Lupton EM, Nonnenherg C, Frank I, Achenbach F, Weis J, Brauchle C (2005) Stretching siloxanes an ab initio molecular dynamics study. Chem Phys Lett 414 132-137... 

Leung K, Rempe SB (2005) Ab initio molecular dynamics study of glycine intramolecular proton transfer in water. J Chem Phys 122 184506... 

Wang, Y. Balbuena, P. B. Ab initio-molecular dynamics studies of O2 electroreduction on Pt (111) Effects of proton and electric field. J. Phys. Chem. B 2004, 108,437CA384. 

Cavazzoni, C., R. Colle, R. Farchioni, and G. Grosso. 2004. Ab initio molecular dynamics study of the structure of emeraldine base polymers. Phys Rev B 69 115213. 

Ben-Nun M, Martinez TJ (1998) Ab initio molecular dynamics study of cis-trans photoisomerization in ethylene. Chem Phys Lett 298 57... 

Ab initio molecular dynamics studies of the photodissociation of formaldehyde, H2CO—>H2+C0 Direct classical trajectory calculations by MP2 and density functional theory""... 

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