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  • 1
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 96 (1992), S. 1376-1390 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We have calculated the Kolmogorov entropy for three- and seven-particle clusters bound by Lennard-Jones potentials and for three-particle clusters bound by Morse potentials of various ranges. We have used two quite different methods, one of which is new, which give consistent results. We find that all of these systems are classically chaotic over a wide range of energies surrounding the estimated quantum-mechanical zero point energies. Furthermore, for the three-particle clusters, we can rationalize the variation in the degree of chaos with total energy in terms of the local structure of the clusters' potential energy surface.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 93 (1990), S. 8745-8756 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: By using the pairwise Morse potential as the principle vehicle we have explored the influence of the range of the pair potential on the structure of multidimensional potential-energy surfaces. A scaling relation and a set of reduced units are presented for the homoatomic pairwise-additive Morse potential. The reduced potential has one free parameter, βr0 or ρ0, regulating the range of interaction. Based on several diatomic species, the chemically important range of ρ0 is approximately 2≤ρ0≤7. The number of geometrically distinct minima and transition states depends on ρ0; the larger is ρ0, the narrower is the potential and the greater is the number of geometrically different minima. To illustrate this we found all minima and important low-energy transition states for the Morse six-and seven-particle clusters as functions of ρ0 in its chemically interesting range. From these the dominant mechanisms of isomerization of six- and seven-particle clusters are inferred and compared with experimental and theoretical results for main-group and transition-metal clusters. A nomenclature for saddle points and isomerizations is introduced. The saddle regions of the potentials reveal the dominance of diamond–square–diamond and edge-bridging mechanisms. Knowledge of the stationary points and rearrangement mechanisms allows us to determine the proper molecular symmetry groups and the topologies of the potential-energy surfaces at any arbitrary energy.
    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 117 (2002), S. 1363-1376 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A parallel searching algorithm based on eigenvector-following is used to generate databases of minima and transition states for all-atom models of Ac(ala)12NHMe and Ac(ala)16NHMe. The AMBER95 force field of Cornell et al. [J. Am. Chem. Soc. 117, 5179 (1995)] is employed both with and without a simple implicit solvent. We use a master equation approach to analyze the dynamics of both systems, and relate the results to the potential energy landscapes using disconnectivity graphs. The low-lying regions of both energy landscapes are compared and found to be remarkably similar. α-helix formation occurs via an ensemble of pathways involving both the N- and C-termini. The global minima of the two systems are also located using the CHARMM22 force field of Mackerell et al. [J. Phys. Chem. B 102, 3586 (1998)], for comparison with AMBER95. © 2002 American Institute of Physics.
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  • 4
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 116 (2002), S. 3777-3788 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The properties of higher-index saddle points have been invoked in recent theories of the dynamics of supercooled liquids. Here we examine in detail a mapping of configurations to saddle points using minimization of |∇E|2, which has been used in previous work to support these theories. The examples we consider are a two-dimensional model energy surface and binary Lennard-Jones liquids and solids. A shortcoming of the mapping is its failure to divide the potential energy surface into basins of attraction surrounding saddle points, because there are many minima of |∇E|2 that do not correspond to stationary points of the potential energy. In fact, most liquid configurations are mapped to such points for the system we consider. We therefore develop an alternative route to investigate higher-index saddle points and obtain near complete distributions of saddles for small Lennard-Jones clusters. The distribution of the number of stationary points as a function of the index is found to be Gaussian, and the average energy increases linearly with saddle point index in agreement with previous results for bulk systems. © 2002 American Institute of Physics.
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  • 5
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 113 (2000), S. 3926-3927 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: For coordinate systems with a nontrivial metric tensor covariant derivatives must be used to obtain properties that are coordinate independent. Applications to instantaneous normal mode theory and bifurcation points are presented as illustrations. © 2000 American Institute of Physics.
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  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 11070-11079 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In recent experiments on sodium chloride clusters structural transitions between nanocrystals with different cuboidal shapes were detected. Here we present results for the thermodynamics and dynamics of one of these clusters (NaCl)35Cl−. As the time scales for the structural transitions can be much longer than those accessible by conventional dynamics simulations, we use a master equation to describe the probability flow within a large sample of potential energy minima. We characterize the processes contributing to probability flow between the different nanocrystals, and obtain rate constants and activation energies for comparison with the experimental values. © 1999 American Institute of Physics.
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  • 7
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 8417-8428 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Disconnectivity graphs are used to characterize the potential energy surfaces of Lennard-Jones clusters containing 13, 19, 31, 38, 55, and 75 atoms. This set includes members which exhibit either one or two "funnels" whose low-energy regions may be dominated by a single deep minimum or contain a number of competing structures. The graphs evolve in size due to these specific size effects and an exponential increase in the number of local minima with the number of atoms. To combat the vast number of minima we investigate the use of monotonic sequence basins as the fundamental topographical unit. Finally, we examine disconnectivity graphs for a transformed energy landscape to explain why the transformation provides a useful approach to the global optimization problem. © 1999 American Institute of Physics.
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  • 8
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 8429-8437 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Stationary points and rearrangement mechanisms are characterized for protonated water trimer using a variety of basis sets and density functional theory to describe electron correlation. For the largest basis sets there are three distinct low-lying minima separated in energy by only a few wave numbers. Ten distinct transition states were found with barriers spanning nearly three orders of magnitude. Several of these mechanisms should produce observable tunneling splittings. © 1999 American Institute of Physics.
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  • 9
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 110 (1999), S. 328-334 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We perform a comprehensive survey of the potential energy landscapes of 13-atom Morse clusters, and describe how they can be characterized and visualized. Our aim is to detail how the global features of the funnel-like surface change with the range of the potential, and to relate these changes to the dynamics of structural relaxation. We find that the landscape becomes rougher and less steep as the range of the potential decreases, and that relaxation paths to the global minimum become more complex. © 1999 American Institute of Physics.
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  • 10
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
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