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  • 1
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 100 (1994), S. 1765-1766 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Potential barrier heights for three different hydrogen-atom migration pathways on C(111) are computed on the semiempirical hydrocarbon potential developed by Brenner [Phys. Rev. B 42, 9458 (1990)]. The barrier for diffusion to an adjacent absorption site is found to be 3.29 eV. Migration rate coefficients obtained from classical variational transition-state theory indicate that such migration processes play a minor role in diamond-film synthesis. The contribution of tunneling to the diffusion rate is shown to be negligible. The computed migration barrier to an adjacent adsorption site is in good agreement with recent results obtained by Melnik et al. using a triple-referenced, configuration interaction method.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 98 (1994), S. 6317-6323 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 104 (1996), S. 3092-3110 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We extend the matrix expansion method to study the long time dynamics for all-atom models of alkane chain internal dynamics. In order to focus on the influence of the poorly understood memory (often also termed "internal friction'') contributions, the theory is compared with Brownian dynamics simulations in which the molecular solvent is replaced by a white noise source of random and frictional forces on the individual carbon and hydrogen atoms of the alkane molecule. The interaction potentials contain torsional potentials and nonbonded interactions, and the same potentials are used for both the theory and the simulations. Hence, the comparisons between theory and simulations involve no adjustable parameters. The first order theory is equivalent to a generalized Rouse model in which harmonic forces exist, in principle, between every pair of atoms in the alkane chain, with the force constants evaluated in terms of static equilibrium correlations. The first order theory provides a decent representation of the long time (t≥100 ps) portions of the C–C motion time correlation functions (dipole and orientational), but the theory is poor for the C–H correlation functions because they have correlation times much shorter than 100 ps. Various higher order mode coupling basis sets are investigated to include the long time influences of the memory terms, and the computations consider the role of the more rapid hydrogen motions in exerting a frictional drag on the slower C–C bond motions. The truncated second order basis provides a rapidly convergent and accurate representation of the long time dynamics. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 99 (1993), S. 4748-4758 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Reaction probabilities, cross sections, rate coefficients, frequency factors, and activation energies for hydrogen-atom abstraction from a hydrogen-covered C(111) surface have been computed using quantum wave packet and classical trajectory methods on the empirical hydrocarbon #1 potential hypersurface developed by Brenner. Upper bounds for the abstraction rates, activation energies, and frequency factors have been obtained for six different chemisorbed moieties on a C(111) diamond surface using a classical variational transition-state method. For the hydrogen-covered surface, the results of the wave packet/trajectory calculations give k(T)=1.67×1014 exp(−0.46 eV/kbT) cm3/mol s, which is about a factor of 2.9 less than the gas-phase abstraction rate from tertiary carbon atoms at 1200 K. The variational calculations show that the activation energies for hydrogen-atom abstraction vary from 0.0 to 1.063 eV. Some sp2-bonded hydrogen atoms can be removed in a barrierless process if adjacent to a carbon radical. In contrast, abstractions that produce a methylene carbon are associated with much larger activation energies in the range 0.49–0.82 eV. Abstraction from nonradical chemisorbed ethylene structures of the type that might be formed by the chemisorption of acetylene at two lattice sites is a particularly slow process with a 1.063 eV activation energy. Hydrogen abstraction from sp3 carbon atoms have activation energies ∼0.4 eV. The results suggest that phenomenological growth models which assume either an equilibrium distribution between surface hydrogen/H2 or a common abstraction rate for surface hydrogen atoms are unlikely to be accurate.
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  • 5
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 99 (1993), S. 8016-8030 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Tests are introduced of one basic approximation inherent in a recent theory for long time dynamics of flexible proteins and polymers in solution. The approximation in question concerns the neglect of memory functions, which for these systems involve a memory function matrix whose properties are not readily modeled without input from simulations. The memory function matrix affects the dynamics on all time scales, but our focus is on those portions influencing mainly the long time dynamics, which is not amenable to simulation for interesting complicated systems. Thus the tests are made on a simple, yet nontrivial system for which long time simulations are possible and provide the most stringent test of the parameter free theory. The test involves Brownian dynamics simulations of united atom models for single octane and pentadecane dynamics in a structureless solvent. The octane case, for instance, yields a 7×7 memory function matrix whose properties are more complex than those of the one-dimensional Kramers model recently studied. More importantly, our computations determine those necessary ingredients of the memory function matrix for describing long time dynamics of flexible large molecules in solution. We compare the theoretical and simulation computations of the bond vector time autocorrelation functions. The leading approximation without memory functions fares remarkably well despite the frequent conformational transitions occurring during the Brownian dynamics trajectories. This approximation systematically leads to faster decay than the simulations due to the neglect of the long time frictional influence of the memory function matrix. We consider computations of these memory functions using both the Mori continued function formalism, and a generalization of the matrix methods introduced to treat the one-dimensional Kramers model. A procedure is developed to obtain the long time influence of the memory function matrix. This procedure improves agreement between theory and simulation and displays good convergence towards the simulation results at the longer times ((approximately-greater-than)100 ps) for which we are interested.
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  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 97 (1992), S. 3573-3575 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A method introduced by Stillinger for finding global minima of potential surfaces and for achieving the optimization objectives of simulated annealing is shown to require caution in some of its applications. In particular, a range parameter is varied to eliminate secondary minima on the potential surface or hypersurface of the objective function of interest. We show that in some cases, using minimizations on the simplified surface to reveal minima on the more complex surface require scrutiny of the sequences of low-energy minima, as functions of the range parameter whose variation controls the complexity of the surface.
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  • 7
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 9492-9501 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We develop methods for alleviating the major impediment in the extension to larger and more complex systems of our matrix method theory for describing the long time dynamics of flexible polymers and proteins in solution. This impediment is associated with the enormous growth in size of the required basis set with the addition of higher order mode coupling basis functions, which are needed to describe the influence on the dynamics of the "internal friction,'' or equivalently of the memory function matrices. We use the first order eigenfunctions (the generalized Rouse modes) to construct an approximate mode coupling basis. Specific applications are made to united atom models of alkanes with a white noise structureless solvent, where the theory is compared with Brownian dynamics simulations to provide a no-parameter stringent test of the theory. Good convergence is found to the full second order treatment with the new basis set whose size scales more nearly with the size of the system rather than the cube of the system with the previous full basis. These technical improvements enable us to test the need for third order contributions to the dynamics of the longer alkanes and to compute the orientational time correlation functions probed by fluorescence depolarization and NMR experiments. Additional symmetry considerations provide further reductions in the required basis set sizes. © 1995 American Institute of Physics.
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  • 8
    Publication Date: 1995-12-01
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 9
    Publication Date: 1994-01-15
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 10
    Publication Date: 1996-02-22
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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