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  • 1
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 93 (1990), S. 7137-7147 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The reaction rate and mechanism of the interconversion between a contact ion pair and solvent separated ion pair in model polar solvents is investigated by molecular dynamics (MD) simulation. The full rate constant for the model reaction is estimated from the product of the transition state theory (TST) rate constant, determined from the potential of mean force between the ions in an equilibrium solvent, and the transmission coefficient, which depends on the details of the dynamics. The collective character of the solvent motion in the reaction barrier crossing is examined in some detail, and the important role of solvent dynamics in causing the reaction rate to markedly deviate from the TST rate is discussed. The MD results are compared with the predictions of Kramers and Grote–Hynes theories.
    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 116 (2002), S. 6329-6338 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A good example of macromolecular recognition is found in the interaction of the two monomers of the dimeric superoxide dismutase protein found in Photobacterium leiognathi. We have produced, by molecular dynamics simulation techniques, a specific path for the rupture of the dimer and calculated the effective force involved in the process by extending a well established free energy calculation scheme, the molecular dynamics blue moon approach to rare events. Within this picture we have generalized the approach to a vectorial reaction coordinate and performed a number of different simulations in function of the monomer-momomer separation, at fixed relative orientation. We find a deep minimum and we compute the height of the free energy barrier to break the dimer. As for the system characterization we have found that, when the separation distance increases, the protein structure is stable and the monomer-monomer interface is uniformly hydrated. Moreover, identifying the crucial contacts for the stabilization of the dimer, we have found the sequence of the different microscopic events in the monomer-monomer recognition and we have developed a view of the process which requires a merging of standard explanations, in agreement with the recent picture of recognition as a dynamical process mixing the various mechanisms previously considered [Kimura et al., Biophys. J. 80 635 (2001)]. © 2002 American Institute of 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. 6560-6568 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Acid ionization in aprotic media is studied using molecular dynamics techniques. In particular, models for HCl ionization in acetonitrile and dimethylsulfoxide are investigated. The proton is treated quantum mechanically using Feynman path integral methods and the remaining molecules are treated classically. Quantum effects are shown to be essential for the proper treatment of the ionization. The potential of mean force is computed as a function of the ion pair separation and the local solvent structure is examined. The computed dissociation constants in both solvents differ by several orders of magnitude which are in reasonable agreement with experimental results. Solvent separated ion pairs are found to exist in dimethylsulfoxide but not in acetonitrile. Dissociation mechanisms in small clusters are also investigated. Solvent separated ion pairs persist even in aggregates composed of rather few molecules, for instance, as few as 30 molecules. For smaller clusters or for large ion pair separations cluster finite-size effects come into play in a significant fashion. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 93 (1989), S. 6261-6265 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 97 (1992), S. 378-388 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A molecular-dynamics study of adiabatic proton transfer between two ions in a polar solvent is presented. The proton is treated as a quantum particle in three dimensions and the polar solvent is composed of classical rigid, dipolar molecules. The coupled Schrödinger and Newton's equations are solved to determine the proton charge density and solvent configuration. The rate coefficient for the proton transfer is computed from correlation function expressions and corrections to transition-state theory due to recrossing of a free-energy barrier are determined. The simulation results are compared with a simple two-state model.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Journal of computer-aided materials design 2 (1995), S. 9-22 
    ISSN: 1573-4900
    Keywords: Molecular dynamics ; Microperoxidase ; Conformational calculations
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Summary Molecular dynamics simulations were performed to predict the structure of the monomeric heme-containing peptide microperoxidase-11 (MP-11). The simulations were carried out both in vacuo and in water solvent, taking as starting coordinates those of the corresponding amino acid sequence in the crystal structure of cytochrome c, since the crystallographic structure of MP-11 is not known. The structural data, including the H-bond network, are reported and visualised with the aid of graphical tools. The structure predicted is consistent with what is known experimentally on MP-11. This agreement suggests that molecular dynamics simulations might be useful in the prediction of the catalytic activity or reactivity of microperoxidases.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Journal of statistical physics 101 (2000), S. 225-242 
    ISSN: 1572-9613
    Keywords: surface-hopping dynamics ; non-adiabatic dynamics ; mixed quantum-classical dynamics ; density matrix
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract Non-adiabatic dynamics in mixed quantum-classical systems is investigated. The mixed quantum-classical system comprises a quantum system coupled to a classical environment. The starting point for the analysis is an evolution equation for the density matrix expressed in a basis of adiabatic quantum states that describes the full quantum dynamics of the subsystem and its coupling to the bath. Since the quantum dynamics influences the evolution of the “classical” degrees of freedom, a description in terms of single Newtonian trajectories is not possible. Through explicit calculations of a two-level quantum system coupled to a low dimensional bath we examine the details of mixed quantum-classical dynamics and its representation in terms of an ensemble of surface-hopping classical trajectory segments.
    Type of Medium: Electronic Resource
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  • 8
    Title: Classical and quantum dynamics in condensed phase simulation : Euroconference on Technical advances in particle-based computational material sciences ; proceedings of the international school of physics, Lerici, Italy 7-18 July, 1997
    Contributer: Berne, Bruce J. , Ciccotti, Giovanni , Coker, David F.
    Publisher: Singapore u.a. :World Scientific,
    Year of publication: 1998
    Pages: 829 S.
    Type of Medium: Book
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  • 9
    Publication Date: 2020-09-25
    Language: English
    Type: article , doc-type:article
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  • 10
    Publication Date: 2020-09-25
    Language: English
    Type: article , doc-type:article
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