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  • 1
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Biochemistry 30 (1991), S. 5826-5832 
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Biochemistry 32 (1993), S. 13830-13837 
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
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  • 5
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Accounts of chemical research 24 (1991), S. 54-61 
    ISSN: 1520-4898
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 99 (1993), S. 8063-8074 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In molecular dynamics simulations of flexible molecules, the treatment of motions that take place on different time scales (e.g., bond stretching and bond angle bending vs dihedral angle librations and overall translation and rotation) or of forces that vary differently with distance (e.g., bonding forces vs electrostatic forces) is a major consideration. The most rapidly varying quantity limits the integration time step, while the most slowly varying quantity usually determines the simulation time required. The reversible multiple time-step methods introduced by Tuckerman, Berne, and Martyna [J. Chem. Phys. 97, 1990 (1992)] allow one to use different integration time steps in the same simulation so as to treat the time development of the slow and fast motions most effectively. As a first step toward extending multiple time-step methods to macromolecules, we investigate their utility for determining the dynamics of n-alkanes as neat liquids and in aqueous solution. Because the dynamics is done in Cartesian rather than internal coordinates, the different time steps are implemented in terms of hard and soft forces acting on individual atoms; e.g., hard forces are contributed by bond stretching (and bond angle bending) terms and soft forces by the remaining intramolecular and intermolecular (van der Waals and electrostatic) terms in the additive empirical potential function used to describe these systems. Integrations with and without a Nose–Hoover thermostat are performed. Comparisons are made with ordinary single time step molecular dynamics and dynamics with constraints applied to the bonds. The stability of the integration methods and the dynamic properties are considered. It is shown that stable integrations that yield agreement with standard dynamics can be achieved with a saving of up to a factor of 5 in computer time.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 94 (1991), S. 3679-3699 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The potential energy function about the C–C single bond for the ground state 1,3-butadiene has been derived from ab initio calculations at both the Hartree–Fock (HF) level with 6-31G, 6-31G*, and 6-311G** basis sets and the second-order Møller–Plesset perturbation (MP2) level with 6-31G* basis set with the complete geometry optimizations at each of 15 fixed CCCC dihedral angles; the total energies and optimized geometries for the s-trans, gauche, and s-cis conformers were also determined at MP2 level with 6-311G* basis set and the third-order Møller–Plesset perturbation (MP3) level with 6-31G* basis set. The second stable conformer of the butadiene is predicted to be a gauche structure from all the calculations with a CCCC dihedral angle between 35° and 40° and a barrier of 0.5–1.0 kcal/mol to the s-cis transition state, and the theoretical torsional potentials are in good agreement with the experimental potential function of trans–gauche–gauche case derived by Durig et al.; by contrast, the theoretical torsional components differ significantly from the experimental results obtained from a trans–cis model. Vibrational frequencies and force field for s-trans and gauche conformers of 1,3-butadiene are determined at the Hartree–Fock and MP2 levels with 6-31G, 6-31G*, 6-311G, and 6-311G* basis sets. The mean absolute percentage deviations of the calculated frequencies from the experimental values (not corrected for anharmonicity) are ∼10%–13% and 3%–6% for the Hartree–Fock and MP2 methods, respectively. The effects of polarization functions and electron correlation on the force fields are studied, and the additivity of correlation and d function effects are discussed. Comparisons are made with other force fields, including experimental and previous ab initio results.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 94 (1991), S. 6737-6739 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In the classical time-dependent Hartree approximation (TDH), the dynamics of a single molecule is approximated by that of a "field'' (each field being N "copies'' of the molecule which are transparent to one another while interacting with the system via a scaled force). It is shown that when some molecules are represented by a field of copies, while other molecules are represented normally, the average kinetic energy of the system increases linearly with the number of copies and diverges in the limit of large N. Nevertheless, the TDH method with appropriate energy scaling can serve as a useful means of enhancing the configurational sampling for problems involving coupled systems with disparate numbers of degrees of freedom.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 96 (1992), S. 5272-5278 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The effective electronic donor/acceptor coupling (HDA) for a bridged electron transfer system is defined. An expression for HDA in terms of the bridge Green's function is developed for systems represented by a tight-binding Hamiltonian. HDA is computed exactly for two systems and the existence of a dimensionless parameter which determines whether the effective coupling oscillates or decays with increasing donor/acceptor distance is demonstrated. A numerical technique for computing HDA is developed and shown to be significantly more powerful than conventional techniques.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 93 (1990), S. 3919-3930 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The McLachlan variational principle for the time-dependent Schrödinger equation is utilized in conjunction with extant localized Guassian wave packet technology to deduce equations of motion for general multidimensional Gaussians. These equations of motion are characterized by the same simplicity as the local quadratic expansion results of Heller [J. Chem. Phys. 62, 1544 (1975)]. However, the resultant variational wave packet evolution is shown to be an improvement over its local quadratic analog as a tool for computing certain photodissociation spectra. Numerical examples drawn from the Beswick–Jortner model of ICN photodissociation [Chem. Phys. 24, 1 (1977)] are presented.
    Type of Medium: Electronic Resource
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