Molecular Dynamics of Polyatomic Systems

Ryckaert, Jean-Paul

doi:10.1007/978-94-011-3546-7_3

Cited by 6 publications

(2 citation statements)

References 17 publications

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“…For this purpose eq 1 is rewritten as where G(n) ) (I x I y I z ) 1/2 (I R are the principal values of the inertia tensor of a given conformer) reflects the dependence of the molecular moment of inertia on conformation. It results from averaging over the dynamical variables associated with the rotational kinetic energy of the conformer as a whole; 15,16 it has only small effects on the final results. U(n,Ω) represents the total potential defined by eq 13, and D ij (n,Ω) is where θ ij denotes the angle between the internuclear vector, r ij , between the two proton spins, and the applied magnetic field.…”

Section: Model and Simulation Methodsmentioning

confidence: 99%

Conformational Distribution of n-Hexane in a Nematic Liquid Crystal Obtained from Nuclear Spin Dipolar Couplings by Monte Carlo Sampling

1996

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Motionally averaged proton-proton dipolar couplings measured by nuclear magnetic resonance (NMR) spectroscopy can provide information about the conformations and orientations sampled by partially oriented molecules. In this study, the measured dipolar couplings between pairs of protons on n-hexane dissolved in a nematic liquid crystal solvent are used as constraints in a Monte Carlo sampling of the conformations and orientations of n-hexane. Rotation about each carbon-carbon bond in the molecule is modeled by the complete sinusoidal torsional potential of Ryckaert and Bellemans rather than by the three-state rotational isomeric states (RIS) model that has been used in previous studies. Comparison of the results of the simulations using the Ryckaert-Bellemans potential and the RIS model indicates little difference in the values of the adjustable parameters and the quality of the fits to the experimental data. The primary difference between the models appears in the calculated conformer probability distributions for n-hexane, highlighting the importance of the exact shape of the torsional potential used to model carbon-carbon bond rotation in organic molecules.

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Section: Model and Simulation Methodsmentioning

confidence: 99%

Conformational Distribution of n-Hexane in a Nematic Liquid Crystal Obtained from Nuclear Spin Dipolar Couplings by Monte Carlo Sampling

1996

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“…However, this is not feasible if the reaction of interest has a high barrier compared to k&T, where k% is Boltzmann's constant and T is temperature, unless one employs infrequent event sampling and/or a constraint on the reaction coordinate. In such a case, one can show that it is still possible to obtain statistical information about a given reaction along a reaction coordinate by using umbrella sampling or by enforcing a constrained reaction coordinate and employing generalized normal mode analysis, thermodynamic integration, or free energy perturbation theory where the incremental charge in the reaction coordinate is the perturbation (1)(2)(3)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28). In this approach, one selects (or "distinguishes") a specific RC that most conveniently leads the system through an area of interest, for instance the transition state region.…”

Section: Transition State Theorymentioning

confidence: 99%

Quantum Catalysis: The Modeling of Catalytic Transition States

Hall

Margl

Náray-Szabó

et al. 1999

ACS Symposium Series

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We present an introduction to the computational modeling of transition states for catalytic reactions. We consider both homogeneous catalysis and heterogeneous catalysis, including organometallic catalysts, enzymes, zeolites and metal oxides, and metal surfaces. We summarize successes, promising approaches, and problems. We attempt to delineate the key issues and summarize the current status of our understanding of these issues. Topics covered include basis sets, classical trajectories, cluster calculations, combined quantum -mechanical/molecular-mechanical (QM/MM) methods, density functional theory, electrostatics, empirical valence bond theory, free energies of activation, frictional effects and nonequilibrium solvation, kinetic isotope effects, localized orbitals at surfaces, the reliability of correlated electronic structure calculations, the role of d orbitals in transition metals, transition state geometries, and tunneling.Computational chemistry has achieved great strides in recent years, and it has become a strong partner with experimental methods, displacing purely analytic theory almost completely. The essential element in computational chemistry is the use of very general theoretical frameworks that can be applied broadly across a number of fields. Examples are molecular orbital theory, molecular mechanics, transition state theory, 2

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Molecular Dynamics of Polyatomic Systems

Cited by 6 publications

References 17 publications

Conformational Distribution of n-Hexane in a Nematic Liquid Crystal Obtained from Nuclear Spin Dipolar Couplings by Monte Carlo Sampling

Conformational Distribution of n-Hexane in a Nematic Liquid Crystal Obtained from Nuclear Spin Dipolar Couplings by Monte Carlo Sampling

Quantum Catalysis: The Modeling of Catalytic Transition States

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