Ab initio direct dynamics

Ab initio direct dynamics trajectory calculations were performed at the B3LYP/6-311+G(d,p) level of theory.39 The trajectories were initiated at the separated reactants, TS (HOOCH3- F ), and the CII 2( 011)0 H- F region on IRC, with quasiclassical sampling including ZPE. The trajectories from the reactants were started at 15 A separation of the two species with small attractive potentials of -0.21 or -0.13 kcalmol-1. The collision impact parameter was chosen randomly between zero and maximum. The initial CH3OOH vibrational and rotational degrees of freedom were selected from their 300 K Boltzmann distributions. 

The ring-opening reaction of cyclopropyl radical [Equation (7)] was shown to occur at 174°C to give ally radical, but the product stereochemistry was unclear. Ab initio direct dynamics study was carried out to clarify the stereochemical course of the reaction.40 Trajectories were initiated at the ringopening TS obtained at CASSCF(3,3)/6-31G(d), with quasiclassical normal sampling at the experimental temperature of 174°C. ZPE was included, and thermal vibrational energy was sampled from the normal-mode Boltzmann distribution. A rotational energy of RT/2 was added toward the allyl radical product. 

Scheme 1.10 Trajectories observed during Ab initio direct dynamics trajectory caicuiations.

For the alternative low level, we used an ab initio direct dynamics calculation at the MP2/6-31G [42] level. 

Park K, Song K, Hase WL (2007) An ab initio direct dynamics simulation of protonated glycine surface-induced dissociation, hit J Mass Spectrom 265 326-336... 

Karplus employed this level of theory to study the photoisomerization of 2-butene. The first ab initio direct dynamics study is that by Leforestier for the + CH4 CH4 + Sn2 nucleophilic substitution reaction. 

Carbene Formation in Its Lower Singlet State from Photoexcited 3H-Diazirine or Diazomethane. A Combined CASPT2 and Ab Initio Direct Dynamics Trajectory Study. 

Microsolvated Sn2 Reaction of F (H20) with CH3CI A Full Dimensional Ab Initio Direct Dynamics Study. 

Arenas, J.F., Lopez-Tocon, I., Otero, J.C., and Soto, J., Carbene Formation in Its Lower Singlet State from Photoexcited 3H-Diazirine or Diazomethane. A Combined CASPT2 and Ab Initio Direct Dynamics Trajectory Study, /. Am. Chem. Soc., 124,1728, 2002. 

Ultimately we may want to make direct comparisons with experimental measurements made on specific materials, in which case a good model of molecular interactions is essential. The aim of so-called ab initio molecular dynamics is to reduce the amount of fitting and guesswork in this process to a minimum. On the other hand, we may be interested in phenomena of a rather generic nature, or we may simply want to discriminate between good and bad theories. When it comes to aims of this kind, it is not necessary to have a perfectly realistic molecular model one that contains the essential physics may be quite suitable. 

The second approach used in first-principles tribological simulations focuses on the behavior of the sheared fluid. That is, the walls are not considered and the system is treated as bulk fluid, as discussed. These simulations are typically performed using ab initio molecular dynamics (AIMD) with DFT and plane-wave basis sets. A general tribological AIMD simulation would be run as follows. A system representing the fluid would be placed in a simulation cell repeated periodically in all three directions. Shear or load is applied to the system using schemes such as that of Parrinello and Rahman, which was discussed above. In this approach, one defines a (potentially time-dependent) reference stress tensor aref and alters the nuclear and cell dynamics, such that the internal stress tensor crsys is equal to aref. When crsys = aref, the internal and external forces on the cell vectors balance, and the system is subject to the desired shear or load. 

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). 

Direct ab initio molecular dynamic simulations starting at the reactant with total Maxwell-Boltzmann equipartitioned thermal kinetic energy of 26kcalmol however, demonstrated that the reaction pathway did not follow the IRC (dotted line in Fig. 1) on the PES, but that it was rather... 

However, these discussions based on the MO calculations are only relevant for the reaction at 0 K, and the interpretation of the reaction mechanism ought to rely on reaction dynamics at finite temperature. Ab initio direct MD calculations are a means to obtain the desired dynamical characterization. 

According to traditional interpretation of chemical reactivity, the reaction rate and hence the product selectivity are governed by the energy of the TS and its variation. However, ab initio direct MD simulation studies described in this chapter revealed that this is not universally true and that the organic reactivity theory must consider the effect of dynamics explicitly. 

We have presented nonadiabatic ab initio molecular dynamics simulations of the photophysical properties of a variety of nucleobases and base pairs. In addition to the canonical tautomers a number of rare tautomers have been investigated. Moreover, effects of substitution and solvation have been studied in detail. The simulations of nonradiative decay in aqueous solution, in particular, demonstrate the strength of the na-AIMD technique employed here as it permits the treatment of solute and solvent on an equal footing. Condensed phase calculations can be directly compared with those in the gas phase because the same computational setup can be used. 

Ab Initio Direct Molecular Dynamics Studies of Atmospheric Reactions Interconversion of Nitronium Ions and Nitric Acid in Small Clusters (Y. Ishikawa R. C. Binning, Jr.)... 

---