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  • 1
    Electronic Resource
    Electronic Resource
    A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering, and visualization (2001)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 114 (2001), S. 2079-2089 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We propose an approach for summarizing the output of long simulations of complex systems, affording a rapid overview and interpretation. First, multidimensional scaling techniques are used in conjunction with dimension reduction methods to obtain a low-dimensional representation of the configuration space explored by the system. A nonparametric estimate of the density of states in this subspace is then obtained using kernel methods. The free energy surface is calculated from that density, and the configurations produced in the simulation are then clustered according to the topography of that surface, such that all configurations belonging to one local free energy minimum form one class. This topographical cluster analysis is performed using basin spanning trees which we introduce as subgraphs of Delaunay triangulations. Free energy surfaces obtained in dimensions lower than four can be visualized directly using iso-contours and -surfaces. Basin spanning trees also afford a glimpse of higher-dimensional topographies. The procedure is illustrated using molecular dynamics simulations on the reversible folding of peptide analoga. Finally, we emphasize the intimate relation of density estimation techniques to modern enhanced sampling algorithms. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1330216
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  • 2
    Electronic Resource
    Electronic Resource
    Development and assessment of new exchange-correlation functionals (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 109 (1998), S. 6264-6271 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We recently presented a new method for developing generalized gradient approximation (GGA) exchange-correlation energy functionals, using a least-squares procedure involving numerical exchange-correlation potentials and experimental energetics and nuclear gradients. In this paper we use the same method to develop a new GGA functional, denoted HCTH, based on an expansion recently suggested by Becke [J. Chem. Phys. 107, 8554 (1997)]. For our extensive training set, the new functional yields improved energetics compared to both the BLYP and B3LYP functionals [Phys. Rev. A 38, 3098 (1988); Phys. Rev. B 37, 785 (1988); J. Chem. Phys. 98, 5648 (1993); J. Phys. Chem. 98, 11623 (1994)]. The geometries of these systems, together with those of a set of transition metal compounds, are shown to be an improvement over the BLYP functional, while the reaction barriers for six hydrogen abstraction reactions are comparable to those of B3LYP. These improvements are achieved without introducing any fraction of exact orbital exchange into the new functional. We have also re-optimized the functional of Becke—which does involve exact exchange—for use in self-consistent calculations. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.477267
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Theoretical investigations of NMR chemical shifts and reactivities of oxovanadium(v) compounds (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 113-122 
    Details
    ISSN: 0192-8651
    Keywords: density-functional theory ; 51V ; chemical shift calculations ; mechanism of ethylene polymerization ; barriers for ethylene insertion ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Employing gradient-corrected levels of density-functional theory (DFT), medium-sized basis sets, and optimized geometries, chemical shifts are calculated for [VOClnF3-n] (n=0-3), VF5, [VO(OCH2CH2)3N], [V(CO)6]-, [V(CO)5(N2)]-, as well as for the model compounds [VO(OMe)nMe3-n] (n=0-3) and their AlH3 adducts. Experimental trends in δ(51V) are well reproduced with DFT-based methods; for example, the slopes of the δ(51V)calc vs. δ(51V)expt linear regression lines are 0.92 and 1.03 at the GIAO-BP86 and GIAO-B3LYP levels, respectively. Ethylene polymerization observed with [V(O⋅⋅⋅AlX3)(OR)nR′3-n] (X, R, R′=bulky alkyl, aryl, or silyl groups) is shown for model systems (X=H, R=R′=Me) to proceed by insertion of the olefin into a V - C bond via a transition state with approximate square-pyramidal coordination about vanadium. For the tri- and dialkyl derivatives (n=0, 1), similar activation barriers of ca. 19 kcal/mol are computed (BP86 level including zero-point energies), whereas that of the monoalkyl species (n=2) is predicted to be much higher, ca. 30 kcal/mol. The relevance of these results for the apparent relationship between δ(51V) and catalytic activities is discussed.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 113-122, 1998
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
  • 4
    Electronic Resource
    Electronic Resource
    Generation of pseudonative protein structures for threading (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 522-529 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; protein fold recognition ; empirical energy function ; protein folding force field ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The threading approach to protein structure prediction suffers from the limited number of substantially different folds available as templates. A method is presented for the generation of artificial protein structures, amenable to threading, by modification of native ones. The artificial structures so generated are compared to the native ones and it is shown that, within the accuracy of the pseudoenergy function or force field used, these two types of structures appear equally useful for threading. Since a multitude of pseudonative artificial structures can be generated per native structure, the pool of pseudonative template structures for threading can be enormously enlarged by the inclusion of the pseudonative artificial structures. Proteins 28:522-529, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
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