Photodissociation of benzene under collision-free conditions: An ab initio/Rice-Ramsperger-Kassel-Marcus study

The ab initio/Rice-Ramsperger-Kassel-Marcus (RRKM) approach has been applied to investigate the photodissociation mechanism of benzene at various wavelengths upon absorption of one or two UV photons followed by internal conversion into the ground electronic state. Reaction pathways leading to various decomposition products have been mapped out at the G2M level and then the RRKM and microcanonical variational transition state theories have been applied to compute rate constants for individual reaction steps. Relative product yields (branching ratios) for C6H5+H, C6H4+H-2, C4H4+C2H2, C4H2+C2H4, C3H3+C3H3, C5H3+CH3, and C4H3+C2H3 have been calculated subsequently using both numerical integration of kinetic master equations and the steady-state approach. The results show that upon absorption of a 248 nm photon dissociation is too slow to be observable in molecular beam experiments. In photodissociation at 193 nm, the dominant dissociation channel is H atom elimination (99.6%) and the minor reaction channel is H-2 elimination, with the branching ratio of only 0.4%. The calculated lifetime of benzene at 193 nm is about 11 mus, in excellent agreement with the experimental value of 10 mus. At 157 nm, the H loss remains the dominant channel but its branching ratio decreases to 97.5%, while that for H-2 elimination increases to 2.1%. The other channels leading to C3H3+C3H3, C5H3+CH3, C4H4+C2H2, and C4H3+C2H3 play insignificant role but might be observed. For photodissociation upon absorption of two UV photons occurring through the neutral hot benzene mechanism excluding dissociative ionization, we predict that the C6H5+H channel should be less dominant, while the contribution of C6H4+H-2 and the C3H3+C3H3, CH3+C5H3, and C4H3+C2H3 radical channels should significantly increase. (C) 2004 American Institute of Physics.

Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures

Bacterial chaperonin, GroEL, together with its co-chaperonin, GroES, facilitates the folding of a variety of polypeptides. Experiments suggest that GroEL stimulates protein folding by multiple cycles of binding and release. Misfolded proteins first bind to an exposed hydrophobic surface on GroEL. GroES then encapsulates the substrate and triggers its release into the central cavity of the GroEL/ES complex for folding. In this work, we investigate the possibility to facilitate protein folding in molecular dynamics simulations by mimicking the effects of GroEL/ES namely, repeated binding and release, together with spatial confinement. During the binding stage, the (metastable) partially folded proteins are allowed to attach spontaneously to a hydrophobic surface within the simulation box. This destabilizes the structures, which are then transferred into a spatially confined cavity for folding. The approach has been tested by attempting to refine protein structural models generated using the ROSETTA procedure for ab initio structure prediction. Dramatic improvements in regard to the deviation of protein models from the corresponding experimental structures were observed. The results suggest that the primary effects of the GroEL/ES system can be mimicked in a simple coarse-grained manner and be used to facilitate protein folding in molecular dynamics simulations. Furthermore, the results Sur port the assumption that the spatial confinement in GroEL/ES assists the folding of encapsulated proteins.

Ab initio modelling of basal plane oxidation of graphenes and implications for modelling char combustion

Ab initio calculations have been performed to determine the energetics of oxygen atoms adsorbed onto graphene planes and the possible reaction path extracting carbon atorns in the form of carbon monoxide. Front the energetics it is confirmed that this reaction path will not significantly contribute to the gasification of well ordered carbonaceous chars. Modelling results which explore this limit Lire presented. (C) 2002 Elsevier Science Ltd, All rights reserved.

Molecular dynamics simulation of organic-inorganic nanocomposites: Layering behavior and interlayer structure of organoclays

Isothermal-isobaric (NPT) molecular dynamics simulation has been performed to investigate the layering behavior and structure of nanoconfined quaternary alkylammoniums in organoclays. This work is focused on systems consisting of two clay layers and a number of alkylammoniums, and involves the use of modified Dreiding force field. The simulated basal spacings of organoclays agree satisfactorily with the experimental results in the literature. The atomic density profiles in the direction normal to the clay surface indicate that the alkyl chains within the interlayer space of montmorillonite exhibit an obvious layering behavior. The headgroups of long alkyl chains are distributed within two layers close to the clay surface, whereas the distributions of methyl and methylene groups are strongly dependent on the alkyl chain length and clay layer charge. Monolayer, bilayer, and pseudo-trilayer structures are found in organoclays modified with single long alkyl chains, which are identical to the structural models based on the measured basal spacings. A pseudo-quadrilayer structure, for the first time to our knowledge, is also identified in organoclays with double long alkyl chains. In the mixture structure of paraffin-type and multilayer, alkyl chains do not lie flat within a single layer but interlace, and also jump to the next layer in pseudo-trilayer as well as next nearest layer in pseudo-quadrilayer.

Molecular dynamics simulation of the structural and dynamic properties of dioctadecyldimethyl ammoniums in organoclays

The structural and dynamic properties of dioctadecyldimethylammoniums (DODDMA) intercalated into 2:1 layered clays are investigated using isothermal-isobaric (NPT) molecular dynamics (MD) simulation. The simulated results are in reasonably good agreement with the available experimental measurements, such as X-ray diffraction (XRD), atom force microscopy (AFM), Fourier transform infrared (FTIR), and nuclear magnetic resonance (NMR) spectroscopies. The nitrogen atoms are found to be located mainly within two layers close to the clay surface whereas methylene groups form a pseudoquadrilayer structure. The results of tilt angle and order parameter show that interior two-bond segments of alkyl chains prefer an arrangement parallel to the clay surface, whereas the segments toward end groups adopt a random orientation. In addition, the alkyl chains within the layer structure lie almost parallel to the clay surface whereas those out of the layer structure are essentially perpendicular to the surface. The trans conformations are predominant in all cases although extensive gauche conformations are observed, which is in agreement with previous simulations on n-butane. Moreover, an odd-even effect in conformation distributions is observed mainly along the chains close to the head and tail groups. The diffusion constants of both nitrogen atoms and methylene groups in these nanoconfined alkyl chains increase with the temperature and methelene position toward the tail groups.

Comparative study of Li, Na, and K adsorptions on graphite by using ab initio method

A comprehensive study has been conducted to compare the adsorptions of alkali metals (including Li, Na, and K) on the basal plane of graphite by using molecular orbital theory calculations. All three metal atoms prefer to be adsorbed on the middle hollow site above a hexagonal aromatic ring. A novel phenomenon was observed, that is, Na, instead of Li or K, is the weakest among the three types of metal atoms in adsorption. The reason is that the SOMO (single occupied molecular orbital) of the Na atom is exactly at the middle point between the HOMO and the LUMO of the graphite layer in energy level. As a result, the SOMO of Na cannot form a stable interaction with either the HOMO or the LUMO of the graphite. On the other hand, the SOMO of Li and K can form a relatively stable interaction with either the HOMO or the LUMO of graphite. Why Li has a relatively stronger adsorption than K on graphite has also been interpreted on the basis of their molecular-orbital energy levels.

Thermal diffusion in molecular dynamics simulations of thin film diamond deposition

Molecular dynamics simulations of carbon atom depositions are used to investigate energy diffusion from the impact zone. A modified Stillinger-Weber potential models the carbon interactions for both sp2 and sp3 bonding. Simulations were performed on 50 eV carbon atom depositions onto the (111) surface of a 3.8 x 3.4 x 1.0 nm diamond slab containing 2816 atoms in 11 layers of 256 atoms each. The bottom layer was thermostated to 300 K. At every 100th simulation time step (27 fs), the average local kinetic energy, and hence local temperature, is calculated. To do this the substrate is divided into a set of 15 concentric hemispherical zones, each of thickness one atomic diameter (0.14 nm) and centered on the impact point. A 50-eV incident atom heats the local impact zone above 10 000 K. After the initial large transient (200 fs) the impact zone has cooled below 3000 K, then near 1000 K by 1 ps. Thereafter the temperature profile decays approximately as described by diffusion theory, perturbed by atomic scale fluctuations. A continuum model of classical energy transfer is provided by the traditional thermal diffusion equation. The results show that continuum diffusion theory describes well energy diffusion in low energy atomic deposition processes, at distance and time scales larger than 1.5 nm and 1-2 ps, beyond which the energy decays essentially exponentially. (C) 1998 Published by Elsevier Science S.A. All rights reserved.

Opposite roles of O-2 in NO- and N2O-carbon reactions: An ab initio study

Previous experimental studies showed that the presence of O-2 greatly enhances NO-carbon reaction while it depresses N2O-carbon reaction on carbon surfaces. A popular explanation for the rate increase is that the addition of O-2 results in a large number of reactive carbon-oxygen complexes, and decomposition of these complexes produces many more active sites. The explanation for the latter is that excess O-2 simply blocks the active sites, thus reducing the rate of N2O-carbon reaction. The contradiction is that O-2 can also occupy active sites in NO-carbon reaction and produce active sites in N2O-carbon reduction. By using ab initio calculation, we find that the opposite roles of O-2 are caused by the different manners of N2O and NO adsorption on the carbon surface. In the presence of excess O-2, most Of the active sites are occupied by oxygen groups. In the competition for the remaining active sites, NO is more likely to chemisorb in the form of NO2 and NO chemisorption is mon thermodynamically favorable than O-2 chemisorption. By contrast, the presence of excess O-2 makes N2O chemisorption much less thermally stable either on the consecutive edge sites or edge sites isolated by semiquinone oxygen. A detailed analysis and discussion of the reaction mechanism of N-2 formation from NO- and N2O-carbon reaction in the presence of O-2 is presented in this paper.

Gas-surface interactions in the thermal and sub-thermal regime: A molecular dynamics study

Molecular dynamics simulations are used to study the interaction of low-energy Ar atoms with the Ni(001) surface, Angular scattering distributions, in and out of the plane of incidence, are investigated as a function of incident energy, angles of incidence, crystallographic orientation of the incident beam and surface temperature. The results show a clear transition to the structure scattering regime at around 2 eV. However, at lower energies, two sub-regimes are revealed by the simulations, Far energies up to 250 meV, scattering is mainly diffuse, and significant trapping on the surface is observed, At energies above this level, lobular patterns start to form and trapping decreases with the increase in energy, Generally, there is a weak temperature dependence, but variations in the angle of incidence and/or changes in the crystallographic direction, generate significant changes in the scattering patterns.

Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics

Smoothing the potential energy surface for structure optimization is a general and commonly applied strategy. We propose a combination of soft-core potential energy functions and a variation of the diffusion equation method to smooth potential energy surfaces, which is applicable to complex systems such as protein structures; The performance of the method was demonstrated by comparison with simulated annealing using the refinement of the undecapeptide Cyclosporin A as a test case. Simulations were repeated many times using different initial conditions and structures since the methods are heuristic and results are only meaningful in a statistical sense.

Non-equilibrium energy and momentum accommodation coefficients of Ar atoms scattered from Ni(001) in the thermal regime: A molecular dynamics study

Molecular dynamics simulations are used to study energy and momentum transfer of low-energy Ar atoms scattered from the Ni(001) surface. The investigation concentrates on the dependence of these processes on incident energy, angles of incidence and surface temperature. Energy transfer exhibits a strong dependence on the surface temperature, at incident energies below 500 meV, and incident angles close to specular incidence. Above 500 meV, the surface temperature dependence vanishes, and a limiting value in the amount of energy transferred to the surface is attained. Momentum exchange is investigated in terms of tangential and normal components. Both components exhibit a weak surface temperature dependence, but they have opposite behaviours at all incidence angles. In each component, momentum can be lost or gained following the interaction with the surface. (C) 1997 Elsevier Science B.V.

Transition-state-theory calculations for reactions of O(3P) with halogenated olefins

The potential energy surfaces for the reactions of atomic oxygen in its ground electronic state, O(P-3), with the olefins: CF2=CCl2 and CF2=CF - CF3, have been characterized using ab initio molecular orbital calculations. Geometry optimization and vibrational frequency calculations were performed for reactants, transition states and products at the MP2 and QCISD levels of theory using the 6-31G(d) basis set. This database was then used to calculate the rate constants by means of Transition-State-Theory. To obtain a better reference and to test the reliability of the activation barriers we have also carried out computations using the CCSD(T)(fc)/6-311Gdagger, MP4(SDQ)(fc)/CBSB4 and MP2(fc)/CBSB3 single point energy calculations at both of the above levels of theory, as well as with the composite CBS-RAD procedure ( P. M. Mayer, C. J. Parkinson, D. M. Smith and L. Radom, J. Chem. Phys., 1998, 108, 604) and a modi. cation of this approach, called: CBS-RAD( MP2, MP2). It was found that the kinetic parameters obtained in this work particularly with the CBS-RAD ( MP2, MP2) procedure are in reasonable agreement with the experimental values. For both reactions it is found that the channels leading to the olefin double-bond addition predominates with respect to any other reaction pathway. However, on account of the different substituents in the alkenes we have located, at all levels of theory, two transition states for each reaction. Moreover, we have found that, for the reactions studied, a correlation exists between the activation energies and the electronic structure of the transition states which can explain the influence of the substituent effect on the reactivity of the halo-olefins.

Ab initio studies of hydrogen desorption from low index magnesium hydride surface

The low index Magnesium hydride surfaces, MgH2(001) and MgH2(110), have been studied by ab intio Density Functional Theory (DFT) calculations. It was found that the MgH2(110) surface is more stable than MgH2(001) surface, which is in good agreement with the experimental observation. The H-2 desorption barriers vary depending on the crystalline surfaces that are exposed and also the specific H atom sites involved-they are found to be generally high, due to the thermodynamic stability of the MgH2, system, and are larger for the MgH2(001) surface. The pathway for recombinative desorption of one in-plane and one bridging H atom from the MgH2(110) surface was found to be the lowest energy barrier amongst those computed (172 KJ/mol) and is in good agreement with the experimental estimates. (c) 2006 Elsevier B.V. All rights reserved.