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  • 1
    Digitale Medien
    Digitale Medien
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 62 (1997), S. 571-591 
    ISSN: 0020-7608
    Schlagwort(e): atomic correlation ; density functional ; scaling ; Hartree-Fock ; excited states ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: In the introductory section, we compare the total, kinetic, nuclear-electron, Coulomb, exchange, and correlation energies of ground-state atoms. From the analyses of the data, one can conclude that the Hartree-Fock (HF) model is notably good and might require only a small perturbation to become essentially an “accurate” model. For this reason and considering past literature, we present a semiempirical extension of the HF model. We start with a calibration of three independent models, each one with an effective Hamiltonian, which introduces a small perturbation on the kinetic, the nuclear-electron, or the Coulomb HF operators. The perturbations are expressed as very simple functions of products of orbital probability density. The three perturbations yield very equivalent results and the computed ground-state energies are reasonably near to the accurate nonrelativistic energies recently provided by E. Davidson and his collaborators for the 2-18 electron systems and the estimates by Clementi and his collaborators for the 19-54 electron systems. The first ionization potentials from He to Cs, the second ionization potentials from Li to Zn, and excitation energies for npn, 3dn, and 4s13dn configurations are used as additional verification and validation. The above three effective Hamiltonians are then combined in order to redistribute the correlation energy correction in a way which exactly satisfies the virial theorem and maintains the HF energy ratios between kinetic, nuclear-electron, and electron-electron interaction energies; the resulting effective Hamiltonian, named “virial constrained,” yields good quality data comparable to those obtained from the three independent effective operators. Concerning excitation energies, these effective Hamiltonians yield values only in modest agreement with experimental data, even if definitively superior to HF computations. To further improve the computed excitation energies, we applied an empirical scaling in the vector coupling coefficient; this correction yields very reasonable excitations for all the configurations that we have considered. We conclude that the use of effective potentials to introduce small perturbations density-dependent onto the HF model constitutes a broad class of practical and reliable semiempirical solutions to atomic many-electron problems, can provide an alternative to popular proposals from density functional theory, and should prepare the ground for “generalized HF models.” © 1997 John Wiley & Sons, Inc. Int J Quant Chem 62: 571-591, 1997
    Zusätzliches Material: 10 Ill.
    Materialart: Digitale Medien
    Bibliothek Standort Signatur Band/Heft/Jahr Verfügbarkeit
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  • 2
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 763-777 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: We report on a computer experiment in which, using Monte Carlo techniques, we considered a three-turn (30-base-pairs) B-DNA fragment as a solute and a set of 1200 water molecules and 60 sodium counterions (at a temperature of 300 K) as a solvent. From a statistical analysis of the Monte Carlo simulation (applied to the water molecules and counterions in the B-DNA field), we determined that the counterions themselves conform to two helical structures intertwined with the two strands. The strutures of the water molecules solvating both counterion helices and the two B-DNA strands are fully analyzed and described in detail. A model for base-pair recognition based on the above findings is proposed. Aspects of the unwinding mechanism are discussed.
    Zusätzliches Material: 11 Ill.
    Materialart: Digitale Medien
    Bibliothek Standort Signatur Band/Heft/Jahr Verfügbarkeit
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  • 3
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 31 (1991), S. 1017-1024 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: The conformation of cyclolinopeptide A [c-(Pro-Pro-Phe-Phe-Leu-Ile-Ile-Leu-Val)], a naturally occurring peptide with remarkable cytoprotective activity, has been investigated by means of molecular dynamics simulations in various molecular environments. Structural and dynamical properties have been analyzed and compared with those experimentally determined. A detailed analysis of hydrogen bonds is reported.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
    Bibliothek Standort Signatur Band/Heft/Jahr Verfügbarkeit
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  • 4
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: Monte Carlo simulations are reported for a system of 447 water molecules enclosing a B-DNA double-helix fragment with 12 base pairs and the corresponding sugar and phosphate units. From a detailed analysis on the interaction energies and probability distributions (at a simulated temperature of 300 K), the water molecules can be partitioned into clusters strongly interacting with (1) the phosphates, (2) the sugars, (3) the sugars and the bases, and (4) the base pairs. In addition, transgroove and interphosphate filament of hydrogen-bonded water molecules have been detected. From simulations performed with variable numbers of water molecules, a theoretical isotherm has been obtained, with the characteristic sigmoidal shape, known from absorption-desorption experiments on related systems. The expected main features for the structure of water molecules solvating B-DNA with Na+ counterions are briefly discussed at the end of the paper.
    Zusätzliches Material: 13 Ill.
    Materialart: Digitale Medien
    Bibliothek Standort Signatur Band/Heft/Jahr Verfügbarkeit
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  • 5
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: The structure of water and its interaction energy with a fragment of B-DNA composed of 12 base pairs and of the corresponding 24 sugar and 22 phosphate units and Na+ ions (one at each phosphate group) are analyzed using Monte Carlo simulations. The sample of water molecules, at the simulated temperature of 300 K, is composed of 447 water molecules. The results are discussed either in terms of statistical analyses over the 2,000,000 simulated conformations (after equilibration) or with reference to an “average configuration.” Comparison is made to a simulation previously presented for the same system but without counterions. Isotherm at different relative humidity, hydration, and reactivity scales for different sites, the hydration number at each site, the structure of intraphosphate and interphosphate hydrogen-bonded filaments of water are reported and discussed. The stabilization of the B-conformation induced by the solvent with counterion (“ion-induced compression effect”) is analyzed on the base of the above findings. A preliminary model to predict conformational transition in DNA is presented. The analyses reported are very detailed to allow refined interpretations of spectroscopic (infrared, Raman, and nmr) and scattering (x-ray and neutron beam) data on DNA insolution.
    Zusätzliches Material: 21 Ill.
    Materialart: Digitale Medien
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