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  • Computational Chemistry and Molecular Modeling  (9)
  • Wiley-Blackwell  (9)
  • American Institute of Physics (AIP)
  • Blackwell Science Pty
  • Macmillian Magazines Ltd.
Collection
Publisher
  • Wiley-Blackwell  (9)
  • American Institute of Physics (AIP)
  • Blackwell Science Pty
  • Macmillian Magazines Ltd.
Years
  • 1
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atomic partial charges for three model systems that mimic the metal-ligand moiety of the active site in the enzyme Cu, Zn superoxide dismutase (SOD) have been calculated at the ab initio level. The model systems include copper and zinc complexes with imidazole, formate and ammonia ligands. The partial charges thus obtained have been incorporated into force fields for molecular simulations. Simulations carried out with these force fields justify the need for specialized charge assignments for the metals and their ligands.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 215-219 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new algorithm for efficient evaluation of two-electron repulsion integrals (ERIs) using uncontracted geometrical-type Gaussian basis functions is presented. Integrals are evaluated by the Habitz and Clementi method. The use of uncontracted geometrical basis sets allows grouping of basis functions into shells (s, sp, spd, or spdf) and processing of integrals in blocks (shell quartets). By utilizing information common to a block of integrals, this method achieves high efficiency. This technique has been incorporated into the KGNMOL molecular interaction program. Representative timings for a number of molecules with different basis sets are presented. The new code is found to be significantly faster than the previous program. For ERIs involving only s and p functions, the new algorithm is a factor of two faster than previously. The new program is also found to be competitive when compared with other standard molecular packages, such as HONDO-8 and Gaussian 86.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A simple and efficient procedure of calculating molecular volume (VM) based on the Monte Carlo method is presented. The volume of a molecule is defined by the volume occupied by the 0.001-au electron density envelope. We have employed this method to compute the molecular volumes (VM) of a large selection of organic molecules and compare them with the corresponding molar volumes (Vm) measured in the liquid state. A strong correlation is found to exist between the VM and Vm values (VM/Vm ≈ 0.75). Using this linear relationship, the calculated molecular volume may provide an estimate of the cavity-volume parameter in solvent-effect calculations. As a chemical application of molecular volume, we have investigated the conformational equilibrium of 1,2-difluoroethane in the liquid state using the self-consistent reaction field theory. © 1995 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1003-1008 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics was used to study the hydration of superoxide (O2-). The Helmholtz free energy of hydration of O2- was estimated by the thermodynamic integration method. The diffusion of O2- and the water structure around O2- were also studied. Two water models were used in the calculations and the results were compared to experiments.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 1291-1300 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The availability of massively parallel computers with high computation rates but limited memory and input/output bandwidth prompts the reevaluation of appropriate solution schemes for the self-consistent field (SCF) equations. Several algorithms are considered which exhibit between linear and quadratic convergence using various approximations to the orbital Hessian. A prototype is developed to understand the computational expense of each approach. The optimal choice is found to be a conjugate-gradient method preconditioned with a level-shifted approximation to the orbital Hessian. This is a compromise between efficiency, stability, and low memory usage. Sample benchmarks on two parallel supercomputers are also reported. © 1995 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 6
    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: Kinetic studies of the hydrolysis of benzo[a]pyrene diol epoxides have shown that hydrolysis proceeds through an acid-catalyzed SN1 mechanism and that the rate-determining step is the formation of a benzylic carbocation. The formation of this carbocation indicates that the diol epoxide can react with nucleophilic sites on DNA as an alkylating agent. Previous work has indicated that the kinetic data could be accurately fit to kobsd = kH [H+] + k0, in which kH [H+] is the pseudo first-order rate constant for acid-catalyzed hydrolysis and k0 is the rate constant for spontaneous hydrolysis. The observation made in several laboratories, that DNA catalyzes the hydrolysis of carcinogenic diol epoxides, is of direct interest in light of our recent calculation indicating that the local environment of DNA has a high concentration of hydrogen ions. The significance of acidic domains around nucleic acids is primarily in the ability of the protons to catalyze reactions. We have hypothesized that the high concentration of hydrogen ions at the DNA surface is responsible for the catalysis and that the generation of benzylic carbocations at the DNA surface can result in either nontoxic tetraols or in mutagenic nucleotide adducts, depending on the nucleophile with which the carbocation reacts. The calculations presented here are concerned with qualitatively understanding the rate constants in terms of the mechanisms of the acid-catalyzed and the spontaneous (H2O-catalyzed) hydrolyses. © 1992 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
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  • 7
    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: The aziridine analogues of the epoxide metabolites of carcinogenic polycyclic aromatic hydrocarbons have greater mutagenic potency than the epoxides. Like their well-studied analogues, the aziridines undergo a pH-dependent decomposition that leads to a reactive carbocation intermediate. In aqueous solution the nucleophile with which the carbocation generally reacts is water. The kinetics of this pH-dependent reaction have been experimentally characterized by others. Although the effect of DNA on this reaction has not been studied, we hypothesize that, like their epoxide analogues, the aziridine derivatives of polycyclic aromatic hydrocarbons undergo a DNA-catalyzed reaction leading through a carbocation to either a DNA-adduct or a hydrolysis product. Using Poisson-Boltzmann calculations in conjunction with Metropolis Monte Carlo simulations and energy-minimized conformations, we predict the DNA-dependence of the acidcatalyzed decomposition of the K-region aziridine, phenanthrene[9,10]imine. © 1995 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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  • 8
    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: The potential energy curve describing the fragmentation of a diatomic dication AB2+ is considered as arising from an avoided crossing between an attractive diabatic curve (correlating with A2+ + B) and a repulsive diabatic curve (correlating with A+ + B+). The simplest avoided-crossing (AC) model neglects diabatic coupling and polarization and leads to useful predictions of the transition structure bond length (rTS) and the kinetic energy released (T) in fragmentations of dicationic systems in which the difference (Δ1) between the ionization energies of A+ and B is small. When Δ1 is not small, it is necessary to include diabatic coupling and polarization in the treatment. The resultant ACDCP (avoided crossing with diabatic coupling and polarization) model provides very satisfactory estimates of rTS and T for both small and large Δ1. Its implementation requires only atomic ionization energy and polarizability data and comes at virtually no computational cost. Both the AC and ACDCP models are readily generalized to fragmentations of more highly charged cations.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 9
    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 the design philosophy, structure, and supporting tool kits of the NWChem computational chemistry package. The primary purpose of this effort was to develop efficient parallel algorithms for a broad range of methods commonly used in computational chemistry. To facilitate this, we developed a shared nonuniform access memory model which simplifies parallel programming while at the same time providing for portability across both distributed- and shared-memory machines. In addition to this specific focus on parallelization, a substantial effort has been made to simplify the general problem of large-scale software development, which is common to many research groups. We find that this simplification can be achieved through judicious use of ideas from the computer science field of software engineering in the design and implementation of the program with minimal extra effort on the part of the chemist. © 1995 John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
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