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  • 1
    Electronic Resource
    Electronic Resource
    Book reviews (1992)
    Springer
    Reaction kinetics and catalysis letters 48 (1992), S. 339-347 
    Details
    ISSN: 1588-2837
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02070105
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  • 2
    Electronic Resource
    Electronic Resource
    Novel semiempirical method for quantum Monte Carlo simulation: Application to amorphous silicon (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 100 (1994), S. 3742-3746 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We propose a novel bulk phase Monte Carlo simulation technique, in which the energy is calculated by quantum mechanical methods. The semiempirical fragment self-consistent field technique applied divides the periodic simulation cell into two parts. The first is the subsystem where the important change (the random movement of an atom or molecule) takes place and the second is the environment exerting only secondary effects on the former. Expanding the electronic wave function on the basis of strictly localized molecular orbitals and/or atomic hybrid orbitals the wave function of the environment is obtained from simple coupled 2×2 secular equations. The conventional self-consistent field equations, with a perturbation term in the Fockian, have to be solved only for the subsystem. In this way the computational efforts are decreased drastically, as the dependence on the number of atoms in the environment reduces to quadratic instead of cubic or quartic as in conventional semiempirical or ab initio methods, respectively. We wrote a computer code and applied our method to amorphous silicon. Starting from a distorted tetrahedrally bonded random network model we performed Monte Carlo simulations using the fragment self-consistent field energy calculation. After equilibration we obtained distribution functions almost identical to the ones corresponding to the distortion free tetrahedrally bonded network. This finding confirms the adequacy of our method for this specific case.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.466361
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  • 3
    Electronic Resource
    Electronic Resource
    Molecular Electrostatics (1995)
    s.l. : American Chemical Society
    Chemical reviews 95 (1995), S. 829-847 
    Details
    ISSN: 1520-6890
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/cr00036a002
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  • 4
    Electronic Resource
    Electronic Resource
    Crystallization and preliminary X-ray analysis of porcine muscle prolyl oligopeptidase (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 1414-1415 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Prolyl oligopeptidase from pig muscle has been crystallized in complex with an inhibitor, using PEG 8000 and calcium acetate as precipitants. The crystals are orthorombic and the space group is P212121 with cell dimensions a = 111.8, b = 101.8, c = 72.4 Å. The asymmetric unit contains a single chain of prolyl oligopeptidase, corresponding to a specific volume of 2.55 Å3 Da−1 and a solvent content of 52%. The observed diffraction pattern extends to 2.3 Å resolution and the native crystals are well suited for structural analysis by X-ray diffraction methods.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444998004181
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  • 5
    Electronic Resource
    Electronic Resource
    Electrostatic modulation of electron transfer in the active site of heme peroxidases (1997)
    Springer
    JBIC 2 (1997), S. 135-138 
    Details
    ISSN: 1432-1327
    Keywords: Key words Heme peroxidases ; Protein electrostatics ; Free radical location ; Molecular orbital calculations
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  The heme enyzmes cytochrome c peroxidase (CCP) and pea cytosolic ascorbate peroxidase (APX) show a high level of sequence identity. The main difference near the active sites is the presence of a cation binding site in APX located about 1 nm from the Trp-179 side chain, which is hydrogen-bonded to Asp-208. It is possible that this difference in electrostatics provided by the protein environment is an essential determinant of the stabilization of the ion-pair or neutral form of the Trp...Asp couple in APX and CCP. Semiempirical molecular orbital calculations support the hypothesis that the position of the moving proton inside the couple influences the location of the free electron, leading to radical formation either on the heme or on the Trp side chain of these enzymes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007750050117
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  • 6
    Electronic Resource
    Electronic Resource
    Comparative redox and pK a calculations on cytochrome c 3 from several Desulfovibrio species using continuum electrostatic methods (1999)
    Springer
    JBIC 4 (1999), S. 73-86 
    Details
    ISSN: 1432-1327
    Keywords: Key words Protein electrostatistics ; Electron-proton coupling ; Redox-Bohr effect ; pKa calculations ; Cytochrome c3
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  A comparative study of the pH-dependent redox mechanisms of several members of the cytochrome c 3 family has been carried out. In a previous work, the molecular determinants of this dependency (the so-called redox-Bohr effect) were investigated for one species using continuum electrostatic methods to find groups with a titrating range and strength of interaction compatible with a mediating role in the redox-Bohr effect. Here we clarify these aspects in the light of new and improved pK a calculations, our findings supporting the hypothesis of propionate D from heme I being the main effector in the pH-dependent modulation of the cytochrome c 3 redox potentials in all the c 3 molecules studied here. However, the weaker (but significant) role of other titrating groups cannot be excluded, their importance and identity changing with the particular molecule under study. We also calculate the relative redox potentials of the four heme centers among the selected members of the c 3 family, using a continuum electrostatic method that takes into account both solvation and interaction effects. Comparison of the calculated values with available data for the microscopic redox potentials was undertaken, the quality of the agreement being dependent upon the choice of the dielectric constant for the protein interior. We find that high dielectric constants give best correlations, while low values result in better magnitudes for the calculated potentials. The possibility that the crystallographic calcium ion in c 3 from Desulfovibrio gigas may be present in the solution structure was tested, and found to be likely.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007750050291
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  • 7
    Electronic Resource
    Electronic Resource
    Transferability of the -COOH...−OOC- dyad Geometry from the gas phase to crystals and proteins (1995)
    Springer
    Theoretical chemistry accounts 90 (1995), S. 41-50 
    Details
    ISSN: 1432-2234
    Keywords: Carboxyl ; Carboxylate dyad ; Geometry ; Transferability ; Crystals ; Proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Simple models of the -COO− ... HOOC- moiety were studied byab initio and semiempirical MNDO/PM3 methods combined with retrieval from the Cambridge Crystallographic Database and Protein Data Bank in order to check transferability of the non-bonded geometry. We found that the gas-phase O ... O distance (252 pm) elongates in crystals and proteins to 256±14 and 262±27 pm, respectively. C-O ... O-C dihedral angles are much more variable, however, energetically excluded values appear only exceptionally in crystals and less frequently in proteins. Most probably due to packing effects -COO− ... HOOC-conformations, preferred in the gas phase, are poorly populated in crystals
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01119781
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  • 8
    Electronic Resource
    Electronic Resource
    Editorial foreword (1992)
    Springer
    Journal of mathematical chemistry 10 (1992), S. vii 
    Details
    ISSN: 1572-8897
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Mathematics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01169167
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  • 9
    Electronic Resource
    Electronic Resource
    The molecular transform as a similarity measure (1993)
    Springer
    Journal of mathematical chemistry 13 (1993), S. 343-357 
    Details
    ISSN: 1572-8897
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Mathematics
    Notes: Abstract We propose to quantify molecular similarity through various forms of molecular transforms directly related to experimental measurements. Various metric distances between molecular transforms are introduced in measuring similarity which can be used in quantitative structure-activity relationships. For simpler classes of compounds like aliphatic alcohols good correlations are obtained between the abstract distance from a lead compound and various physical and pharmalogical properties. For substituted phenols the correlation is worse; however, the predictive power of the descriptors derived from the molecular transform is yet acceptable. For trypsin inhibitors, a class of compounds having very different molecular formulae, the net atomic charge is introduced as a parameter in the generalized form of the molecular transform. Though a poor regression equation is obtained for the differences in the inhibitory power, inactive compounds within a set can be reliably selected.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01165574
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  • 10
    Electronic Resource
    Electronic Resource
    Computational chemistry on a PC (1990)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 38 (1990), S. 163-171 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We describe a package of some IBM PC programs that may find application in computer-aided molecular design. PCGEOM constructs and visualizes molecular models from bond lengths, bond angles, and dihedral angles, from Cartesian coordinates, or from stored fragments. It may prepare output files to be used as input for other programs, like CNDOB (conventional CNDO/2) or PCMEP using the bond increment (BI) method for the calculation of molecular electrostatic potentials. PCPROT is in preparation and will use Protein Data Bank coordinates to visualize and manipulate protein molecular models. Starting from these, it will calculate electrostatic potentials using the BI method and/or monopoles adjusted to reproduce ab initio values for amino acid residues. FSCF is based on a CNDO-type approximation and uses strictly localized molecular orbitals in order to partition large molecules into a central fragment, a polarizable region, and a fully transferable environment. The partition allows one to handle relatively large systems with up to 200 atoms. To illustrate applications, we present estimation of relative inhibitory potencies of a series of substituted triazines on chicken liver dihydrofolate reductase.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560380211
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