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  • 1
    Digitale Medien
    Digitale Medien
    Computer-assisted study of the relationship between molecular structure and Henry's law constant (1992)
    s.l. : American Chemical Society
    Analytical chemistry 64 (1992), S. 1350-1355 
    Details
    ISSN: 1520-6882
    Quelle: ACS Legacy Archives
    Thema: Chemie und Pharmazie
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1021/ac00037a009
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  • 2
    Digitale Medien
    Digitale Medien
    General Formulation for a Quantum Free Energy Perturbation Study (1995)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 99 (1995), S. 10701-10704 
    Details
    Quelle: ACS Legacy Archives
    Thema: Chemie und Pharmazie , Physik
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1021/j100027a004
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  • 3
    Digitale Medien
    Digitale Medien
    Semiempirical molecular orbital calculations with linear system size scaling (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 104 (1996), S. 6643-6649 
    Details
    ISSN: 1089-7690
    Quelle: AIP Digital Archive
    Thema: Physik , Chemie und Pharmazie
    Notizen: Details are provided for the implementation of a density matrix divide-and-conquer approximation into the framework of molecular orbital theory on nonperiodic systems. Originally developed for density functional theory, the divide-and-conquer procedure is one of the most promising in a growing list of techniques that exhibit linear scaling with respect to the number of basis functions in the system. The key to linear scaling is the division of the electronic structure calculation into a series of calculations over a set of small, overlapping subsystems. A semiempirical molecular orbital program designed around the divide-and-conquer approach has been written and a number of tests are carried out on polyglycine structures in order to evaluate its performance. For the systems examined, linear scaling is indeed observed, and the accuracy of the calculations can be controlled quite readily by the manner in which the system is divided into its component subsystems. For very large structures, the expense associated with the computation of two-center interactions will ultimately dominate the calculation, and quadratic scaling will become apparent. Techniques to linearize this aspect of the calculation are investigated and discussed. © 1996 American Institute of Physics.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1063/1.471382
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  • 4
    Digitale Medien
    Digitale Medien
    Fast, accurate semiempirical molecular orbital calculations for macromolecules (1997)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 107 (1997), S. 879-893 
    Details
    ISSN: 1089-7690
    Quelle: AIP Digital Archive
    Thema: Physik , Chemie und Pharmazie
    Notizen: A detailed review of the semiempirical divide-and-conquer (D&C) method is given, including a new approach to subsetting, which involves dual buffer regions. Comparisons are drawn between this method and other semiempirical macromolecular schemes. D&C calculations are carried out using a basic 32 Mbyte memory workstation on a variety of peptide systems, including proteins containing up to 1960 atoms. Aspects of storage and SCF convergence are addressed, and parallelization of the D&C algorithm is discussed. © 1997 American Institute of Physics.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1063/1.474386
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  • 5
    Digitale Medien
    Digitale Medien
    Parallel implementation of a divide and conquer semiempirical algorithm (1998)
    Springer
    Theoretical chemistry accounts 99 (1998), S. 220-223 
    Details
    ISSN: 1432-2234
    Schlagwort(e): Keywords: Parallel divide and conquer ; Parallel SCF
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Chemie und Pharmazie
    Notizen: Abstract. We have implemented a parallel version of the semiempirical divide and conquer program DivCon previously developed in our laboratory. By utilizing a parallel machine we are able to leverage the linear scaling of the divide and conquer algorithm itself to perform semiempirical calculations on large bio-molecules. The utility of the implementation is demonstrated with a partial geometry optimization of hen egg white lysozyme in the gas phase.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1007/s002140050329
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  • 6
    Digitale Medien
    Digitale Medien
    Investigation of classification methods for the prediction of activity in diverse chemical libraries (1999)
    Springer
    Journal of computer aided molecular design 13 (1999), S. 533-545 
    Details
    ISSN: 1573-4951
    Schlagwort(e): chemoinformatics ; classification ; cluster analysis ; discriminant analysis ; recursive partitioning ; topological descriptors ; 2D structural keys
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Chemie und Pharmazie
    Notizen: Abstract Classification methods based on linear discriminant analysis, recursive partitioning, and hierarchical agglomerative clustering are examined for their ability to separate active and inactive compounds in a diverse chemical database. Topology-based descriptions of chemical structure from the Molconn-X and ISIS programs are used in conjunction with these classification techniques to identify ACE inhibitors, β-adrenergic antagonists, and H_2 receptor antagonists. Overall, discriminant analysis misclassifies the smallest number of active compounds, while recursive partitioning yields the lowest rate of misclassification among inactives. Binary structural keys from the ISIS package are found to generally outperform the whole-molecule Molconn-X descriptors, especially for identification of inactive compounds. For all targets and classification methods, sensitivity toward active compounds is increased by making repetitive classifications using training sets that contain equal numbers of actives and inactives. These balanced training sets provide an average numerical class membership score which may be used to select subsets of compounds that are enriched in actives.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1023/A:1008061017938
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  • 7
    Digitale Medien
    Digitale Medien
    Estimation of pKa for organic oxyacids using calculated atomic charges (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1460-1467 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A method for the estimation of pKa from empirically calculated atomic charges has been developed and tested on a diverse set of organic oxyacids. The approach involves a comparison of the atomic charges calculated for both the acid and the negative ion that is formed after loss of the acidic proton. These charges have been used in conjunction with the familiar concepts of induction and resonance to develop an accurate formula to predict pKa. Results for a set of 135 compounds, including alcohols, phenols, and carboxylic acids, yielded a fit of pKa with r = 0.993 and an rms error of 0.455. © John Wiley & Sons, Inc.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540141208
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  • 8
    Digitale Medien
    Digitale Medien
    Fast geometry optimization using a modified extended Hückel method: Results for molecules containing H, C, N, O, and F (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 733-746 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A semiempirically parameterized version of the extended Hückel molecular orbital method has been combined with an efficient quasi-Newton Broyden-Fletcher-Goldfarb-Shannon (BFGS) optimization algorithm to obtain accurate geometries for compounds containing H, C, N, O, and F. The requirement of only one matrix diagonalization per energy evaluation makes the EHNDO (Extended Hückel Neglect of Differential Overlap) method faster than semiempirical Hartree-Fock NDDO methods such as MNDO, AM1, and PM3. Geometrical results for EHNDO appear to be as good as or better than results for the widely used AM1 technique, and geometry optimization for EHNDO also requires only a fraction of the time. © 1994 by John Wiley & Sons, Inc.
    Zusätzliches Material: 3 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540150706
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  • 9
    Digitale Medien
    Digitale Medien
    Atomic charge calculations for quantitative structure - property relationships (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 492-504 
    Details
    ISSN: 0192-8651
    Schlagwort(e): Computational Chemistry and Molecular Modeling ; Biochemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A previously published empirical charge scheme has been adapted for use in studies of quantitative structure-property relationships. New parameters have been developed to allow the inclusion of nitrates, nitriles, sulfides, thiols, thiophenes, and sulfoxides. No changes have been made to the original scheme, thus preserving all previous results. A few simple additions to the program have made it possible to calculate atomic charges in a variety of ionic structures containing a formally positive nitrogen or a formally negative oxygen. The results obtained for ions are consistent with a number of concepts surrounding the familiar inductive and resonance effects.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/jcc.540130411
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