Chemical dynamics simulations

It should be pointed out that while most of the reactions can be solved using traditional RRKM approach, experimental and theoretical studies have shown that non-RRKM dynamics is important for moderate to large-sized molecules with various barriers for unimolecular dissociation [57,58]. In these cases, non-RRKM behavior needs to be taken into account and direct chemical dynamic simulation is suggested to serve this purpose [58]. 

Whereas selective diffusion can be better investigated using classical dynamic or Monte Carlo simulations, or experimental techniques, quantum chemical calculations are required to analyze molecular reactivity. Quantum chemical dynamic simulations provide with information with a too limited time scale range (of the order of several himdreds of ps) to be of use in diffusion studies which require time scale of the order of ns to s. However, they constitute good tools to study the behavior of reactants and products adsorbed in the proximity of the active site, prior to the reaction. Concerning reaction pathways analysis, static quantum chemistry calculations with molecular cluster models, allowing estimates of transition states geometries and properties, have been used for years. The application to solids is more recent. 

Siebert, M. R. Zhang, J. Addepalli, S. V. TantiUo, D. J. Hase, W. L. The need for enzymatic steering in abietic acid biosynthesis Gas-phase chemical dynamics simulations of carbocation rearrangements on a bifurcating potential energy surface, J. Am. Chem. Soc. 2011,133, 8335-8343. 

Initiated by the chemical dynamics simulations of Bunker [37,38] for the unimolecular decomposition of model triatomic molecules, computational chemistry has had an enormous impact on the development of unimolecular rate theory. Some of the calculations have been exploratory, in that potential energy functions have been used which do not represent a specific molecule or molecules, but instead describe general properties of a broad class of molecules. Such calculations have provided fundamental information concerning the unimolecular dissociation dynamics of molecules. The goal of other chemical dynamics simulations has been to accurately describe the unimolecular decomposition of specific molecules and make direct comparisons with experiment. The microscopic chemical dynamics obtained from these simulations is the detailed information required to formulate an accurate theory of unimolecular reaction rates. The role of computational chemistry in unimolecular kinetics was aptly described by Bunker [37] when he wrote The usual approach to chemical kinetic theory has been to base one s decisions on the relevance of various features of molecular motion upon the outcome of laboratory experiments. There is, however, no reason (other than the arduous calculations involved) why the bridge between experimental and theoretical reality might not equally well start on the opposite side of the gap. In this paper... results are reported of the simulation of the motion of large numbers of triatomic molecules by... 

Intrinsic RRKM behavior is defined by Eq. (3), where an initial microcanonical ensemble of states decomposes exponentially with the RRKM rate constant [56]. Such dynamics can be investigated by computational chemical dynamics simulations. Therefore, an intrinsic non-RRKM molecule is one for which the intercept in P(t) is k(E), as a result of the initial microcanonical ensemble, but whose decomposition probability versus time is not described by k E). For such a molecule there is a bottleneck (or bottlenecks) restricting energy flow into the dissociating coordinate. Intrinsic RRKM and non-RRKM dynamics are illustrated in Fig. 15.3(a), (b), and (e). 

Chemical dynamics simulations were performed to study the unimolecular decomposition of microcanonical ensembles versus energy of the Cl — CH Br ion lipole complex.An analytic potential energy surface was used for the simulations. The complex has two unimolecular reaction paths, i.e. dissociation to C/ + CHjBr or isomerization to the CICH —Br ion iipole complex. The simulations were performed for energies of 30-80 kcal mol and the resulting non-exponential N t)IN 0) were lit by a sum of three exponentials, i.e. eqn (20.18). The resulting// and ki fitting parameters are listed in Table 20.2. 

Static (PES) and kinetic (RRKM) information can be complemented by chemical dynamics simulations, which are able to fill some aspects of gas phase reactivity not considered by the previous approaches. In particular, chemical dynamics can be used to model explicitly the collision between the ion and the target atom and thus it is possible to obtain the energy transferred in the collision and (eventually) the reactions. The molecular system, represented as an ensemble of atoms each bearing a mass i evolves on the Bom-Oppenheimer potential energy surface through Newton s equation of motirais ... 

Sun L, Base WL (2010) Comparisons of classical and Wigner sampling of transition state energy levels for quasiclassical trajectory chemical dynamics simulations. J Chem Phys 133 044313... 

Spezia R, Salpin JY, Gaigeot MP, Hase W, Song K (2009) Protonated urea collision-induced dissociation. Comparison of experiments and chemical dynamics simulations. J Phys Chem A 113 13853-13862... 

Jeanvoine Y, Gaigeot M-P, Hase WL, Song K, Spezia R (2011) Collision induced dissociation of protonated urea with a diatomic projectile effects on energy transfer and reactivity via chemical dynamics simulations, hit J Mass Spectrom 308 289-298... 

Spezia R, Cimas A, Gaigeot MP, Salpin JY, Song K, Hase WL (2012) Collision induced dissociation of doubly-charged ions Coulomb explosion vs neutral loss in [Cafurea)] " gas phase unimolecular reactivity via chemical dynamics simulations. Phys Chem Chem Phys 14 11724-11736... 

Ortiz D, Salpin JY, Song K, Spezia R (2014) Galactose 6-sulfate collisimi induced dissociation using QM-I-MM chemical dynamics simulations and ESI-MS/MS experiments. Int J Mass Spectrom 358 25-35... 

In the following section, the importance of metallic non-adiabaticity in chemical dynamics simulations will be illustrated through a few selected example applications. First, the vibrational relaxation of adsorbates at metallic surfaces will be treated in the perturbative regime. Seeond, the effect of weak non-adiabatic coupling on laser excitation simulations will be discussed. Finally, inelastic effects in scanning tunnelling mieroseopy of highly mobile species in metallic environments will be diseussed in terms of non-adiabaticity. 

Chemical dynamics simulations of the gas phase 5 2 reactions of methyl halides have been carried out at many different levels of theory and compared with experimental measurements and predictions based on transition state theory and RRKM (Rice-Ramsperger-Kassel-Marcus) theory. Although many 5 2 reactions occur by the traditional pre-reaction complex, transition state, post-reaction complex mechanism, three additional non-statistical mechanisms were detected when the F -CH3-I reaction was analysed at an atomic level (i) a direct rebound mechanism where F attacks the backside of the carbon and CH3-F separates (bounces off) from the iodine ion, (ii) a direct stripping mechanism where F approaches CH3-I from the side and strips away the CH3 group, and (iii) an indirect reaction where the pre-reaction complex activates the C-I bond causing a CH3-I rotation and then the 5 2 reaction. The presence of these processes demonstrate that three non-statistical effects, (i) recrossing of the transition state is important, (ii) the transfer of the translational energy from the reactants into the rotational and vibrational modes of the substrate is inefficient, and (iii) there is... 

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