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  • 2000-2004  (29)
  • 1990-1994  (3,466)
  • 1985-1989  (2,161)
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  • Computational Chemistry and Molecular Modeling  (5,670)
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  • 101
    Electronic Resource
    Electronic Resource
    Functional derivative δE/δρ in calculation of chemical potential for the Kohn-Sham electronic system (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 51 (1994), S. 569-575 
    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: A method for finding the chemical potential for an electronic system with density ρ = Σρi represented within the Kohn-Sham approximation is proposed. To find the chemical potential of the system under consideration, we propose to refer to the definition μ = δE/δρ and to apply the mathematical properties of functional derivatives. Particularly, in the case examined, the result μ = μ(r) ≠ const has been obtained, which may be explained in the framework of the calculus of variation. Taking the limit limr→∞ μ(r) as the best approximation to the proper equilibrium chemical potential of a free atom, one obtains μ = -I, where I denotes first ionization energy. A possibility of further applications of the proposed method in relation to crystalline systems is also discussed. © 1994 John Wiley & Sons, Inc.
    Additional Material: 2 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560510621
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  • 102
    Electronic Resource
    Electronic Resource
    Multicavity SCRF calculation of ion hydration energies (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 339-348 
    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: The hydration energies of the proton, hydroxyl ion, and several inorganic ions were calculated using the multicavity self-consistent reaction field (MCa SCRF) method developed for the quantum-mechanical modeling of rotationally or flexible systems in dielectric media. The ionic complexes H3O+(H2O)4, OH-(H2O)4, NH4+(H2O)4, and Hal-(H2O)4, where Hal = F, Cl, or Br, have been studied. Each complex was divided between five spheres, corresponding to the central ion and four water molecules in their first coordination sphere, respectively. Each cavity was surrounded by a polarizable medium with the dielectric permittivity of water at room temperature (80). The ionic hydration energies of ions were divided into specific and nonspecific parts. After accounting for the cavity-formation energy using scaled particle theory, good agreement between the total calculated and experimental hydration energies was obtained for all ions studied. © 1994 John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520834
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  • 103
    Electronic Resource
    Electronic Resource
    Theoretical study of the conjugation length effect on the electronic and second-order nonlinear optical properties of amino-nitro diphenylacetylenes (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 89-96 
    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 presnet a theoretical study of the effect of the conjugation length on the electronic properties and second-order molecular polarizabilities β in p-amino-p′-nitrodiphenylacetylene molecules where the number of triple bonds in the conjugated segment varies from 1 to 4. The β values are calculated via an intermediate neglect of differential overlap/single configuration interaction (INDO/SCI) sum-over-states (SOS) approach. We test the convergence of the SOS method and the validity of the two-state model to describe the β response. The results indicate that increasing the conjugation length results in a decrease of the charge transfer within the molecule. The two-state model is shown to break down as the conjugated segment extends to four triple bonds; this is due to the appearance of several low-lying nearly isoenergetic excited states that significantly contribute to the β response. The theoretical results are in excellent agreement with recent experimental data. © 1994 John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520109
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  • 104
    Electronic Resource
    Electronic Resource
    MBOHO calculations of C—H stretching frequencies in hydrocarbons and heterosubstituted hydrocarbonsThe project was supported by the National Natural Science Foundation of China and the Excellent University Teacher's Foundation of the State Education Commission. (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 109-116 
    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: Based on the generalized relationship for calculating the nuclear spin-spin coupling constants and the correlation of the bond stretching frequencies with the coupling constants, a novel generalized reationship, which includes the contributions of not only the hybrid orbitals, but also the net atomic charges, is introduced for calculation of the bond stretching frequencies and employed to elucidate the C—H stretching frequencies in hydrocarbons and heterosubstituted hydrocarbons on the basis of the MBOHO calculation employing the CNDO/2 approximation. By use of the obtained concrete realtionships, one can get different νCH value for the C—H bonds existing in different chemical environments, which is coincident with chemical intuition. The calculated numerical results show that for hydrocarbons the contribution of the net atomic charges can be neglected, but it is necessary for heterosubstituted hydrocarbons to include the contribution of the net atomic charges to the C—H stretching frequencies. The calculated C—H stretching frequencies are in good ageement with the experimental data, which shows its reasonableness. © 1994 John Wiley & Sons, Inc.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520111
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  • 105
    Electronic Resource
    Electronic Resource
    Core photoionization satellites in fullerence and related model systems (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 135-146 
    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: The so-called shake-up satellites accompanying C1s photoionization in C60 have been studied theoretically by means of INDO/CI. It is found that the lowest shake-up satellites in C60 correspond to global charge-transfer excitions that move charge from the opposite side of the fullerence cage to the core-hole region, whereas higher-energy satellites tend to move charge from regions nearer to the core hole. Analogies are drawn, with, on the one hand, smaller model molecules such as napthalene and acenaphtylene and, on the other hand, infinite systems such as graphite. © 1994 John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520114
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  • 106
    Electronic Resource
    Electronic Resource
    A vibrational Hamiltonian model for triatomic molecules based on the Kratzer and Poschl Teller potentials (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 165-175 
    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: A Hamiltonian model to describe molecular vibrations of triatomic molecules is proposed. The Hamiltonian is based on the use of the Kratzer potential variable for the stretching motions and a perturbed Poschl Teller potential for the bending one. The perturbation and variational treatments to compute the vibrational energies of this Hamiltonian can be developed using a zero-order system that includes part of the couplings between the stretching and bending motions. All the matrix elements involved in these calclations can be then evaluated in closed form. A numerical application to the HCN molecule is made. © 1994 John Wiley & Sons, Inc.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520117
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  • 107
    Electronic Resource
    Electronic Resource
    The role of the bond midpoint electron density in homonuclear molecular binding (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 247-265 
    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: Electron density theory is first employed to express the potential energy curve of the H2+ molecular ion in terms of bond midpoint properties. For heavy homonuclear diatomics, low-ordr density gradient theory is used, but now for the chemical potential, with a similar conclusion to that for H2+. Homonuclear clusters of alkali atoms are then treated in some detail. Finally the dissociation of doubly charged clusters is considered, by a study of supermolecular treated in some detail. Finally the dissociation of doubly charged clusters is considered, by a study of supermolecular ions (Na20+)2 and (K20+)2, again using a density gradient expansion in low order. The deviation between the barrier for fission and the Coulomb barrier is linear in the bond midpoint density over a substantial range of fragment separation. © 1994 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520123
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  • 108
    Electronic Resource
    Electronic Resource
    On the accuracy of molecular properties by coupled-cluster methods for some difficult examples: Oxygen atom, iron atom, and cyano radical (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 211-225 
    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: Coupled-cluster (CC) methods at the level of CCSD, CCSD+T(CCSD), CCSD(T), CCSDT-1, and CCSDT-3 are applied to calculations of the dipole moment and polarizability of the CN molecule, ionization potentials and electron affinities of the oxygen and iron atoms and CN molecule, and the energy splitting of the 5D and 5F states of the iron atom. Both UHF and ROHF references are applied. Extended basis sets are used in some comparison of CC data to experiment. All calculated atomic and molecular properties are known as challenging problems, suitable for a careful analysis of the performance of sophisticated versions of the CC approach. Attention is paid to energy terms distinguishing CCSD(T) from CCSD+T(CCSD). We exploit results from various iterative and noniterative high-level CC methods in the assessment of error bars in calculations of atomic and molecular properties. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520121
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  • 109
    Electronic Resource
    Electronic Resource
    Semiempirical studies of the interaction between metals and π-conjugated polymers: Sodium on diphenylpolyenes and aluminum on poly (p-phenylenevinylene) and derivatives (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 481-500 
    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 report some of our recent results from theoretical modeling of the interaction between metals and π-conjugated molecules. We apply the semiempirical Austin Model 1 method for the investigation of two fundamentally different systems: sodium interacting with diphenylpolyenes and aluminum interacting with poly (p-phenylenevinylene) and derivatives. In the former case, electronic-structure calculations are also performed using the nonempirical pseudopotential Valence Effective Hamiltonian (VEH) technique. For sodium interacting with diphenylpolyenes, we investigate the geometric and electronic structure modifications that are induced upon charge transfer in a series of diphenylpolyenes with an even number of carbons (from stilbene to α,ω-diphenyltetradecaheptaene, i.e., one to seven double bonds in the polyene part of the molecule). Densities of valence states generated from the VEH calculations are directly compared to experimental ultraviolet photoelectron spectroscopy valence band spectra; these are recorded during successive sodium exposure of the molecular solids. The charge-storage states in the series are discussed in terms of soliton-antisoliton-pairs and polaron-like states induced upon doping (reduction). Introducing aluminum atoms onto poly (p-phenylenevinylene) systems allows us to study the initial stages of interface formation. We find that aluminum atoms preferentially react with the vinylene linkages in both poly (p-phenylenevinylene) and poly (2,5-dimethoxy-p-phenylenevinylene). When carbonyl groups appear on the side of the chains, as in poly (2,5-dialdehyde-p-phenylenevinylene), new reactive sites are induced, leading to structures with stabilities comparable to those in the most stable configurations involving a single vinylene group. In all three systems investigated, the interaction with aluminum induces major modifications of the polymer chains with interruptions of the π-system caused by formation of sp3-like defects. © 1994 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520844
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  • 110
    Electronic Resource
    Electronic Resource
    On the interaction of cyanate and thiocyanate anions with Li+ and Mg2+ (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 553-563 
    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: The energy surfaces of Mn+/SCN- and Mn+/OCN- (M = Li+ and Mg2+) ion pairs have been calculated at the Hartree-Fock and MP2 levels of theory. The electrostatic potential and the actual binding energies are compared. Besides linear ion pairs, nonlinear ones are also found and are in some cases the most stable ones. The electrostatic potential and the actual binding to cations are compared. © 1994 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520849
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  • 111
    Electronic Resource
    Electronic Resource
    First-Principles Monte Carlo simulated annealing study of the structures and properties of hydrogenated lithium clusters (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 541-551 
    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: The minimum-energy structures and bonding properties of the hydrogenated lithium clusters, Li4H2 and Li7H, have been investigated by means of an ab initio Monte Carlo simulated annealing method. The minimum-energy structures of Li4H2 and Li7H are found to resemble those of the triangular planar (D3h) isomer of Li6 and Td isomer of Li8 clusters, respectively. © 1994 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520848
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  • 112
    Electronic Resource
    Electronic Resource
    Alternating charge densities, peierls distortion, and charge-conjugation symmetry in correlated one-dimensional diatomic systems (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 329-337 
    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: The full-optimized-APSG approach based on the MC SCF technique is developed and applied to study ground-state properties of one-dimensional correlated systems. The effects of electron-electron interactions and bond relaxation are considered for the conjugated diatomic polymer; charge distribution and bond relaxation are calculated for the N = 50 chain within a wide range of site energy and e-e integral modulation involving the case of alternancy symmetry for diatomic systems. With relation to the results obtained, the problem of the neutral-ionic transition in mixed-stack crystals is discussed. © 1994 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520208
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  • 113
    Electronic Resource
    Electronic Resource
    Disordered grown systems: Generation and fractal analysis. ElectrodepositionPresented at the 1st Congress of the International Society for Theorical Chemical Physics, Girona, Catalonia, Spain, summer 1993. (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 375-394 
    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: The basic concepts of fractal geometry are reviewed and applied to quasi-two-dimensional zinc electrodeposits. Among the different structures developed during zinc electrodeposition, we have identified the open texture (obtained at large zinc sulfate concentration and small applied potential values) as a typical fractal self-similar structure. © 1994 John Wiley & Sons, Inc.
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520212
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  • 114
    Electronic Resource
    Electronic Resource
    Density functional studies on hydrogen-bonded complexes (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 465-478 
    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: Results of density functional calculations will be reported on a variety of hydrogen-bonded complexes, ranging from weak to strong hydrogen bonds. The charged bimolecular NH3—NH4+ complex and the dimers of water and methanol were investigated using a local approximation of the exchange-correlation potential and two different nonlocal potentials with gradient corrections. In the case of the water dimers, the dependence of the results on the extension of the atomic basis set has also been investigated. The equilibrium structures of all complexes have been determined. Dipole moments, hydrogen-bond lengths, and hydrogen-bonding energies, calculated with corrections for the basis-set superposition error using the counterpoise method, have been found to agree well with the corresponding experimental results. © 1994 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520218
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  • 115
    Electronic Resource
    Electronic Resource
    The character of the correlations in DNA sequences (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 457-463 
    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: Although several authors proposed the existence of long-range correlations in DNA sequences [W. Li and K. Kaneko, Europhys. Lett. 17, 655 (1992); R.F. Voss, Phys. Rev. Lett. 68, 3805 (1992); C.-K. Peng et al., Nature 356, 168 (1992)], we claim that the real character of the correlations remains uncertain. To corroborate long-range correlations, one should prove that the correlation functions decay as an inverse power of the distance between the nucleotides in the DNA sequence. Instead of a direct calculation of the correlation functions, one can calculate either the Fourier transforms of the sequences or the characteristics of “DNA walk.” In our previous work we pointed out that the character of the results depends upon the way the DNA sequences are chosen. When looking for the correlations separately in introns and separately in exons, we found that the resulting correlations are short range. In this work, we discuss the numerical aspects of two computational approaches: the calculation of correlation function and the evaluation of “DNA walk” characteristics. We present the analytic results for the case of exponential correlations. © 1994 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520217
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  • 116
    Electronic Resource
    Electronic Resource
    Theory of hopping conductivity of proteins (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 491-506 
    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: Quantum chemical calculations for two different kinds of native proteins (pig insulin and hen egg white lysozyme) were done by the extended negative factor counting method in which the matrix elements have been calculated at the ab initio level with the help of a minimal basis and the simulation of the aqueous solution environment. The hopping conductivities were worked out by the formulas of the random walk theory of Lax and co-workers. The electronic density of states of these native proteins confirmed the conclusions obtained previously from aperiodic model peptides chains. The results show that the ac conductivity vs. frequency curve of these native proteins lies in the range of some typical good inorganic amorphous conductors and thus confirm that proteins, if doped, are amorphous conductors. The behavior of the ac conductivities of the proteins in different ranges of frequencies are discussed. © 1994 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520220
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  • 117
    Electronic Resource
    Electronic Resource
    Thermochemical tests of a kinetic-energy dependent exchange-correlation approximation (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 625-632 
    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 test an exchange-correlation functional with explicit dependence on kinetic-energy density as well as the density, its gradient, and its Laplacian, on the Gaussian-2 thermochemical data base. With a small degree of exact-exchange mixing, we find average errors with respect to experiment of order 2 kcal/mol, 0.15 eV, and 2 kcal/mol, respectively, for atomization energies, ionization potentials, and proton affinities. © 1994 John Wiley & Sons, Inc.
    Additional Material: 4 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520855
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  • 118
    Electronic Resource
    Electronic Resource
    Density-Functional LCAO calculations for solids: Comparison between Hartree-Fock and Kohn-Sham structural properties (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 633-644 
    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: The Density-Functional method, with Linear Combination of Atomic Orbitals, has been applied to eight crystals: the lattice equilibrium parameters, and the lattice formation energies have been calculated at the Hartree-Fock level (HF), at the hybrid Hartree-Fock Density-Functional level (DFT/HF), and at the Kohn-Sham Density-Functional level (DFT). The band structures and the electronic charge distributions calculated at the DFT and HF levels are compared. © 1994 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520856
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  • 119
    Electronic Resource
    Electronic Resource
    A mass formula for the energy of metal clusters (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 767-797 
    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 obtain an analytic expression for the total energy of a metallic cluster formed by N atoms of valence v and with net charge Q, by solving variationally the extended Thomas-Fermi version of density functional theory within the spherical jellium model. The energy is expressed as an expansion (mass formula) in decreasing powers of the cluster radius RI = rsZ1/3, with Z = vN, and rs, the one electron radius of the bulk, \documentclass{article}\pagestyle{empty}\begin{document}$$ E\left( {r_s ,Z,Q} \right) = \sum\limits_{n = - 2}^3 {a_n \left( {r_s } \right)Z^{n/3} + Q\sum\limits_{n = 0}^2 {W_n \left( {r_s } \right)Z^{ - n/3} + \frac{1}{2}\frac{{Q2}}{{R_I + d\left( {r_s } \right)}},} } $$\end{document} and the coefficients of this mass formula are functions of rs. Contributions of volume (RI3), surface (RI2), curvature (RI), constant (RI0), (1/RI), and (1/RI2) are clearly separated in the formula. The Chemical potential, work function, electron affinity, and ionization potential are easily obtained for neutral and charged clusters of any electronic density in the metallic range. A general estimation of the critical size for stability against electron detachment of negatively charged clusters is also obtained. The stability of highly charged clusters against fragmentation is also studied. © John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520407
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  • 120
    Electronic Resource
    Electronic Resource
    Investigations of hydrogen-bonded systems: Local density approximation and gradient corrections (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 52 (1994), S. 957-961 
    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: The applicability of the local density approximation (LDA) and of corresponding gradient corrections (for the exchange and correlation energy) for the treatment of the hydrogen bond is investigated. As test systems, we consider the water dimer and the H2O…HX complexes (X = F, Cl, Br): Using an LCAO scheme, their equilibrium geometries and interaction energies are ćalculated and compared with experimental data and with other calculations. We obtain that the LDA gives the geometries in qualitative agreement with other data, whereas the energies are overestimated. The use of the gradient corrections (GC) according to Becke and Perdew leads to a significant improvement of the geometry, and especially of the interaction energies. The calculations indicate further that LDA + GC should also be able to describe weaker intermolecular interactions than the usual hydrogen bond. Finally, a short discussion of the charge distribution and the dipole moments of the H2O…HX complexes is performed. © 1994 John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560520421
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  • 121
    Electronic Resource
    Electronic Resource
    Masthead (1994)
    Chichester [u.a.] : Wiley-Blackwell
    Developmental Genetics 15 (1994) 
    Details
    ISSN: 0192-253X
    Keywords: Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/dvg.1020150101
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    Correlated evolution of the cis-acting regulatory elements and developmental expression of the Drosophila Gld gene in seven species from the subgroup melanogaster (1994)
    Chichester [u.a.] : Wiley-Blackwell
    Developmental Genetics 15 (1994), S. 38-50 
    Details
    ISSN: 0192-253X
    Keywords: Evolution ; Drosophila ; promoter ; glucose dehydrogenase ; development ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The tissue-specific expression patterns of glucose dehydrogenase (GLD) exhibit a high degree of inter specific variation in the adult reproductive tract among the species in the genus Drosophila. We chose to focus on the evolution of GLD expression and the evolution of the Gld promoter in seven closely related species in the mela-nogaster subgroup as a means of elucidating the relationship of changes in cis-acting regulatory elements in the Gld promoter region with changes in tissue-specific expression. Although little variation in tissue-specific patterns of GLD was found in nonreproductive tissues during development, a surprisingly high level of variation was observed in the expression of GLD in both developing and ma-ture reproductive organs. In some cases this variation is correlated with changes in sequence elements in the Gld promoter which were previously shown to direct tissue-specific expression in the reproductive tract. In particular D. teissieri adult males do not express GLD in their ejaculatory ducts, atypical of the melanogaster subgroup species. The Gld promoter region of D. teissieri specifically lacks all three of the TTAGA regulatory elements present in D. melanogaster. The TTAGA elements were previously shown to direct reporter gene expression to the ejaculatory duct. Together these data suggest the absence or presence of the TTAGA elements may be responsible for variation in the absence or presence of GLD in the ejaculatory duct among species. © 1994 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/dvg.1020150106
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    Embryonic expression of the single Tribolium engrailed homolog (1994)
    Chichester [u.a.] : Wiley-Blackwell
    Developmental Genetics 15 (1994), S. 7-18 
    Details
    ISSN: 0192-253X
    Keywords: Tribolium ; engrailed ; embryogenesis ; segmentation ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: We have cloned and sequenced the single Tribolium homolog of the Drosophila engrailed gene. The predicted protein contains a homeobox and several domains conserved among all engrailed genes identified to date. In addition it contains several features specific to the invected homologs of Bombyx and Drosophila, indicating that these features most likely were present in the ancestral gene in the common ancestor of holometabolous insects. We used the cross-reacting monoclonal antibody, 4D9, to follow the expression of the Engrailed protein during segmentation in Tribolium embryos. As in other insects, Engrailed accumulates in the nuclei of cells along the posterior margin of each segment. The first Engrailed stripe appears as the embryonic rudiment condenses. Then as the rudiment elongates into a germ band, Engrailed stripes appear in an anterior to posterior progression, just prior to morphological evidence of the formation of each segment. As in Drosophila (a long germ insect), expression of engrailed in Tribolium (classified as a short germ insect) is preceeded by the expression of several homologous segmentation genes, suggesting that similar genetic regulatory mechanisms are shared by diverse developmental types. © 1994 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/dvg.1020150103
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    Screen for enhancers of Polycomb and Polycomblike in Drosophila melanogaster (1994)
    Chichester [u.a.] : Wiley-Blackwell
    Developmental Genetics 15 (1994), S. 425-434 
    Details
    ISSN: 0192-253X
    Keywords: Polycomb group ; homeotic ; spalt ; devenir ; Su(Pc)37D ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: There are 11 Polycomb group genes known in Drosophila. These genes are negative regulators of homeotic gene expression, and may act by modifying chromatin structure. It is not clear how many members of the Polycomb group of genes exist. Many were discovered because of their homeotic phenotypes, or because they enhance homeotic mutations. Systematic screens for enhancers of Polycomb have identified previously known members of the Polycomb group. In an attempt to discover cytological locations of new Polycomb group genes, we crossed deletions uncovering about 20% of the genome to Polycomb-like and Polycomb and scored for enhancement of the extra sex combs phenotype. Haploidy for four regions, 36F7-37A, 43E18; 44B5-9, 70C2-6, and 70C6-15; 70D enhanced the extra sex comb phenotype associated with strong Polycomb group mutations. These regions have homeotic phenotypes either as homozygous embryos or heterozy-gous adults, or both. We also show that spalt enhances Polycomb group mutations. These results are discussed with respect to previous estimates of Polycomb group gene number. © 1994 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/dvg.1020150505
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    Developmental arrest of fertilized eggs from the B6.YDOM sex-reversed female mouse (1994)
    Chichester [u.a.] : Wiley-Blackwell
    Developmental Genetics 15 (1994), S. 435-442 
    Details
    ISSN: 0192-253X
    Keywords: Fertility ; sex-reversal ; XY ovary ; XY oocyte ; mouse ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: When the Y chromosome of a Mus musculus domesticus mouse strain is placed onto the C57BL/6J (B6) inbred background, the XY progeny develop ovaries or ovotestes but never normal testes during fetal life. While some of the hermaphroditic males become fertile, none of the XY females produces litters. Here, we examined the fertility and development of oocytes derived from the XY female mouse. With or without preceding injection of gonadotropins, female mice were mated with normal B6 males, and their embryos were recovered at various developmental stages. In vitro fertilization was performed with the eggs recovered from the oviduct after treatment with go-nadotropins. Development of embryos was examined by both light and electron microscopy. The results indicate that the oocytes released from the B6.YDOM ovary were efficiently fertilized and often initiated the first cell cleavage, but all embryos died during early preimplantation periods. Even when oocytes were fertilized in vitro, minimizing their exposure to the XY oviduct/uterus environment, most embryos died at the 1- or 2-cell stage. A few exceptional embryos reached the 4- or 8-cell stage, but abnormalities were evident in both nuclear and cytoplasmic structures of all embryos. After cleavage, neighbouring blastomeres were only loosely associated, and microvilli were abundant at the intercellular interfaces. We postulate that oocytes of the B.6.YDOM female mouse become defective during XY ovarian differentiation, and, hence, fail to proceed through normal embryonic development. © 1994 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/dvg.1020150506
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    Epigenetic effects in eukaryotic gene expression (1994)
    Chichester [u.a.] : Wiley-Blackwell
    Developmental Genetics 15 (1994), S. 458-462 
    Details
    ISSN: 0192-253X
    Keywords: Epigenetic phenomena ; chromatin structure ; eukaryotes ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: In the broadest terms, epigenetic phenomena in eukaryotes depend on the interaction of alleles or repeated sequences or on the mitotic inheritance of chromatin states or methylation patterns. One of the most exciting aspects of the study of epigenetic phenomena is the insight that can be gained into the structure and assembly of higher-order chromatin structures, an important subject that has proved refractory to current biochemical methodologies. Rapid progress in the study of gene inactivation in fungi, plants, and invertebrates will provide new hypotheses to be tested in mammals. © 1994 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/dvg.1020150603
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    Positional information and pattern formation in development (1994)
    Chichester [u.a.] : Wiley-Blackwell
    Developmental Genetics 15 (1994), S. 485-490 
    Details
    ISSN: 0192-253X
    Keywords: Pattern formation ; positional information ; periodic structures ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: A widely used mechanism for pattern formation is based on positional information: cells acquire positional identities as in a coordinate system and then interpret this information according to their genetic constitution and developmental history. In Drosophila maternal factors establish the axes and set up a maternal system of positional information on which further patterning is built. There is a cascade of gene activity which leads both to the development of periodic structures, the segments, and to their acquiring a unique identity. This involves the binding of transcription factors to regulatory regions of genes to produce sharp thresholds. Many of the genes involved in these processes, particularly the Hox complex, are also involved in specifying the body axis and limbs of vertebrates. There are striking similarities in the mechanisms for spcifying and recording positional identity in Drosophila and vertebrates. © 1994 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/dvg.1020150607
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    Experimental embryological analysis of genetic imprinting in mouse development (1994)
    Chichester [u.a.] : Wiley-Blackwell
    Developmental Genetics 15 (1994), S. 515-522 
    Details
    ISSN: 0192-253X
    Keywords: Genetic imprinting ; androgenesis ; parthenogenesis ; development ; chimeras ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/dvg.1020150610
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    Tissue-specific regulation by ecdysone: Distinct patterns of Eip28/29 expression are controlled by different ecdysone response elements (1994)
    Chichester [u.a.] : Wiley-Blackwell
    Developmental Genetics 15 (1994), S. 320-331 
    Details
    ISSN: 0192-253X
    Keywords: Drosophila melanogaster ; ecdysone ; steroid ; Eip28/29 ; EcREs ; lacZ ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: The Eip28/29 gene of Drosophila is an example of a tissue- and stage-specific ecdysone-responsive gene. Its diverse patterns of expression during the third larval instar and a synopsis of those patterns in terms of expression groups have been reported previously. Here we have studied the expression (in transgenic flies) of reporter genes controlled by Eip28/29-derived flanking DNA. During the middle and late third instar, most tissues exhibit normal expression patterns when controlled by one of two classes of regulatory sequences. Class A sequences include only 657 Np of 5′ flanking DNA from Eip28/29. Class B sequences include an extended 3′ flanking region and a minimal (≤93 Np) 5′ flanking region. The class B sequences include all those elements known to be important for ecdvsone induction in cultured cells. They are sufficient to direct the normal premetamorphic induction of Eip28/29 in the lymph glands, hemocytes, proventriculus, and Malpighian tubules. This is consistent with our suggestion that Kc cells are derived from embryonic hematopoietic cells. It is remarkable that the epidermis requires only class A sequences. These are sufficient to up-regulate expression at medinstar and to down-regulate expression at metamorphosis. It follows that the epidermis uses EcREs distinct from those that function in Kc cells. It is possible that the Upstream EcRE, which is nearly silent in Kc cells, is active in the epidermis. © 1994 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/dvg.1020150403
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    Comparison of NDDO and quasi-ab initio approaches to compute semiempirical molecular electrostatic potentials (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 12-22 
    Details
    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 suitability of the two most widely used strategies to compute semiempirical MEPs is examined. For this purpose, MEP minima, electrostatic charges, and dipoles for a large number of molecules were computed at the AM1, MNDO, and PM3 levels using both the NDDO strategy developed by Ferenczy, Reynolds, and Richards and our own quasi-ab initio method. Results demonstrate that the quasi-ab initio is preferred over the NDDO method for the computation of MEP minima. It is also found that the best set of semiempirical charges and dipoles are obtained using either the AM1 NDDO or the MNDO quasi-ab initio methods. In these two cases, the quality of the results is fully comparable with 6-31G* values. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 6 Tab.
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    Newton-Raphson optimization of the explicitly correlated Gaussian functions for calculations of the ground state of the helium atom (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 54-60 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Explicitly correlated Gaussian functions have been used in variational calculations on the ground state of the helium atom. The major problem of this application, as well as in other applications of the explicitly correlated Gaussian functions to compute electronic energies of atoms and molecules, is the optimization of the nonlinear parameters involved in the variational wave function. An effective Newton-Raphson optimization procedure is proposed based on analytic first and second derivatives of the variational functional with respect to the Gaussian exponents. The algorithm of the method and its computational implementation is described. The application of the method to the helium atom shows that the Newton-Raphson procedure leads to a good convergence of the optimization process. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150107
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    General parameterization of a reaction field theory combined with the boundary element method (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 90-104 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We described various technical aspects in applying reaction field theories using continuum models to practical problems. It was investigated how solvent-dependent properties of solute molecules are influenced by the following factors: difference in quantum-chemical description of solute-solvent (continuum dielectric) interaction, difference in values of empirically determinable parameters such as atomic radii to define a size of a cavity created in a dielectric to accommodate a solute, and difference in the sophistication level of molecular orbital calculation, including electron correlation and different parameter sets (MNDO, AM1, and PM3). Through these investigations, the better parameter sets were found to evaluate accurately physicochemically important parameters such as hydration enthalpy. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150111
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    Conformation and reactivity of α-oxo-ketenes: Ab initio and semiempirical (AM1, PM3) calculations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 132-143 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio MP2/6-31G*//MP2/6-31G* and semiempirical AM1 and PM3 calculations on a series of differently substituted α-oxo-ketenes are used to investigate E/Z-isomerism and rotational barriers in these molecules. Sterically crowded derivatives are found to exist solely as s-E conformers. The unusual stability of these derivatives thus can be attributed to their inability to adopt the s-Z conformation required for the normal α-oxo-ketene reactions. With respect to structures and energies, the PM3 method (especially in the case of highly crowded molecules) is found to be less reliable than AM1. Ab initio HF/3-21G and PM3 vibrational frequencies appear to be of sufficient accuracy for a distinction between s-Z and s-E conformers. In this respect, the AM1 method appears less reliable. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150203
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    Atomic charges derived from a fast and accurate method for electrostatic potentials based on modified AM1 calculations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 200-207 
    Details
    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 charges derived from a recently described approach to the very rapid computation of AM1 electrostatic potentials (ESP) accurately parallel, but are ca. 20% smaller than, the corresponding HF/6-31G* values. The dipole moments computed from the AM1 charges are virtually identical to those derived directly from the wave function and in rather better agreement with the experimental values than those computed using the HF/6-31G* charges. Unlike other approaches to the semiempirical calculation of ESP-derived charges, the present method also yields near HF/6-31G* quality potentials close to the molecular periphery. For medium-sized organic molecules (40-100 basis functions), the method is approximately two orders of magnitude faster than those involving prior deorthogonalization of AM1 wave function and explicit computation of the full ESP integral matrix. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150210
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    A ring-bracing approach to computer-assisted ligand design (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 233-240 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Rigid inhibitors suffer a smaller loss of conformational entropy when they bind to a macromolecular receptor than their acyclic counterparts. They can also be useful for elucidating pharmacophores due to their reduced conformational space and may be more amenable to synthesis. Computational approaches to rational drug design should therefore take these factors into consideration when suggesting possible compounds. We describe how an acyclic chain which links two parts of a receptor site can be ‘braced’ using ring templates. The acyclic chains may be produced from a number of sources, including lattices or the structures of known inhibitors. The resulting structures contain a rich variety of isolated and fused ring systems, which provide many useful molecular skeletons for subsequent inhibitor design. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150213
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    Force field calculations (MM3) on glyoxal, quinones, and related compounds (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 251-268 
    Details
    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 general force field type of calculation has been devised in connection with MM3 to treat 1,2- and 1,4-diketones, both when they are not conjugated (as in derivatives of glyoxal) and when they are conjugated (as in derivatives of ortho- and para-benzoquinone). The molecular structures, moments of inertia, dipole moments, and vibrational spectra have been examined for about 15 compounds, some in several conformations. Ab initio calculations (6-31G*) have been used to determine quantities that have not been previously defined by experiment. In general, the force field permits the calculation of the structures with high accuracy, and the spectroscopic and conformational energy data with fair accuracy. © 1994 by John Wiley & Sons, Inc.
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    A comparative study of effective core potential and full-electron calculations in Mo compounds. I. An analysis of topological properties of bond charge distribution (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 313-321 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Effective core potential (ECP) and full-electron (FE) calculations for MoS4-2, MoO4-2, and MoOCl4 compounds were analyzed. Geometry parameters, binding energies, charge distributions, and topological properties of the electronic density were studied for Mo—L bonds (L = S, O, Cl). Results clearly indicate that those approaches that include valence plus 4s and 4p electrons (ECP2 methods) are able to reproduce the topological properties of Mo—L bonds, charge distributions, and geometries with respect to those obtained by FE methods. ECP methods that consider only the 4d and 5s valence electrons (ECP1) fail in the calculation of molecular properties. The use of 5p functions in ECP1 approaches produces a negative Mulliken charge on Mo. Bader's charges give more consistent results than Mulliken's ones. A new parameter for measuring the degree of ionicity is proposed. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 7 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540150306
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    Ab initio study of low-lying electronic states of the PF2 radical (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 346-350 
    Details
    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 equilibrium geometries, excitation energies, force constants, and vibrational frequencies of the low-lying electronic states X2B1, 2A1, 2B2, and 2A2 of the PF2 radical have been calculated at the MRSDCI level with a double zeta plus polarization basis set. Our calculated geometry, force constants, and vibrational frequencies for the X2B1 state are in good agreement with experimental data. The electronic transition moments, oscillator strengths for the 2A1 → X2B1 and 2A2 → X2B1 transitions, and radiative lifetimes for the 2A1 and 2A2 states are calculated based on the MRSDCI wave functions. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540150309
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    Free energy perturbation calculations on parallel computers: Demonstrations of scalable linear speedup (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 351-373 
    Details
    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 coarse-grain parallel implementation of the free energy perturbation (FEP) module of the AMBER molecular dynamics program is described and then demonstrated using five different molecular systems. The difference in the free energy of (aqueous) solvation is calculated for two monovalent cations ΔΔGaq(Li+ Δ Cs+), and for the zero-sum ethane-to-ethane′ perturbation ΔΔGaq(CH3—methyl—X → X—methyl—CH3), where X is a ghost methyl. The difference in binding free energy for a docked HIV-1 protease inhibitor into its ethylene mimetic is examined by mutating its fifth peptide bond, ΔG(CO—NH → CH=CH). A potassium ion (K+) is driven outward from the center of mass of ionophore salinomycin (SAL-) in a potential of mean force calculation ΔGMeOH(SAL- · K+) carried out in methanol solvent. Parallel speedup obtained is linearly proportional to the number of parallel processors applied. Finally, the difference in free energy of solvation of phenol versus benzene, ΔΔGoct(phenol → benzene), is determined in water-saturated octanol and then expressed in terms of relative partition coefficients, Δ log(Po/w). Because no interprocessor communication is required, this approach is scalable and applicable in general for any parallel architecture or network of machines. FEP calculations run on the nCUBE/2 using 50 or 100 parallel processors were completed in clock times equivalent to or twice as fast as a Cray Y-MP. The difficulty of ensuring adequate system equilibrium when agradual configurational reorientation follows the mutation of the Hamiltonian is discussed and analyzed. The results of a successful protocol for overcoming this equilibration problem are presented. The types of molecular perturbations for which this method is expected to perform most efficiently are described. © 1994 by John Wiley & Sons, Inc.
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    Transferable semiempirical quadratic force fields: The case of polythiophene and shorter oligomers (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 405-423 
    Details
    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 vibrational spectra of oligomers of thiophene are treated theoretically with the main purpose of deriving information for the interpretation of the infrared and Raman spectra of the polymer and isotopic derivatives. We report the results of a series of semiempirical MNDO calculations on the structure and vibrational properties of oligothiophenes, and we compare the calculated MNDO Pulay scaled force field of the monomer with an empirical harmonic force field that we have obtained by least squares refinement on nine isotopic derivatives. The scaling factors obtained were transferred from thiophene for the computation of the vibrational spectrum and the phonon dispersion curves of the polymer. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150405
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    Announcements (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 475-475 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150411
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  • 142
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    On the analytical calculation of van der Waals surfaces and volumes: Some numerical aspects (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 507-523 
    Details
    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 fast computer algorithm is presented for complete analytical calculation of van der Waals surfaces and volumes. Connolly's analytical algorithms, computing second- and third-order atomic spheres overlaps, are shown to give insufficient numerical approximations of the exact van der Waals surfaces and volumes. The presented algorithm computes overlaps of any order. Practical situations frequently involve six-order overlaps. Analytical computed surfaces and volumes of 63 chemicals are compared with Monte Carlo measured values. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150504
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  • 143
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    ICM - A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 488-506 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An efficient methodology, further referred to as ICM, for versatile modeling operations and global energy optimization on arbitrarily fixed multimolecular systems is described. It is aimed at protein structure prediction, homology modeling, molecular docking, nuclear magnetic resonance (NMR) structure determination, and protein design. The method uses and further develops a previously introduced approach to model biomolecular structures in which bond lengths, bond angles, and torsion angles are considered as independent variables, any subset of them being fixed. Here we simplify and generalize the basic description of the system, introduce the variable dihedral phase angle, and allow arbitrary connections of the molecules and conventional definition of the torsion angles. Algorithms for calculation of energy derivatives with respect to internal variables in the topological tree of the system and for rapid evaluation of accessible surface are presented. Multidimensional variable restraints are proposed to represent the statistical information about the torsion angle distributions in proteins. To incorporate complex energy terms as solvation energy and electrostatics into a structure prediction procedure, a “double-energy” Monte Carlo minimization procedure in which these terms are omitted during the minimization stage of the random step and included for the comparison with the previous conformation in a Markov chain is proposed and justified. The ICM method is applied successfully to a molecular docking problem. The procedure finds the correct parallel arrangement of two rigid helixes from a leucine zipper domain as the lowest-energy conformation (0.5 Å root mean square, rms, deviation from the native structure) starting from completely random configuration. Structures with antiparallel helixes or helixes staggered by one helix turn had energies higher by about 7 or 9 kcal/mol, respectively. Soft docking was also attempted. A docking procedure allowing side-chain flexibility also converged to the parallel configuration starting from the helixes optimized individually. To justdy an internal coordinate approach to the structure prediction as opposed to a Cartesian one, energy hypersurfaces around the native structure of the squash seeds trypsin inhibitor were studied. Torsion angle minimization from the optimal conformation randomly distorted up to the rms deviation of 2.2 Å or angular rms deviation of l0° restored the native conformation in most cases. In contrast, Cartesian coordinate minimization did not reach the minimum from deviations as small as 0.3 Å or 2°. We conclude that the most promising detailed approach to the protein-folding problem would consist of some coarse global sampling strategy combined with the local energy minimization in the torsion coordinate space. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 11 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150503
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    Masthead (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150601
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  • 145
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    Direct search methods for the molecular conformation problem (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 627-632 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An important area of research in computational biochemistry is the design of molecules for specific applications. The design of these molecules, which depends on the accurate determination of their three-dimensional structure, can be formulated as a global optimization problem. In this article, we present results from the application of a new conformation searching method based on direct search methods. We compare these results to some earlier results using genetic algorithms and simulated annealing. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150606
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  • 146
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    Triazene proton affinities: A comparison between density functional, Hartree-Fock, and post-Hartree-Fock methods (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 875-892 
    Details
    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 consistency of three density functional computational implementations (DMol, DGauss, and deMon) are compared with high-level Hartree-Fock and Møller-Plesset (MP) calculations for triazene (HN=NNH2) and formyl triazene (HN=NNHCOH). Proton affinities on all electronegative sites are investigated as well as the geometries of the neutral and protonated species. Density functional calculations employing the nonlocal gradient corrections show agreement with MP calculations for both proton affinities and geometries of neutral and protonated triazenes. Local spin density approximation DMol calculations using numerical basis sets must employ an extended basis to agree with other density functional codes using analytic Gaussian basis sets. The lowest energy conformation of triazene was found to be nonplanar; however, the degree of nonplanarity, as well as some bond lengths, is dependent on the basis set, electron correlation treatment, and methods used for the calculation. © 1994 by John Wiley & Sons, Inc.This article is a U.S. Government work and, as such, is in the public domain in the United States of America.
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    URL: http://dx.doi.org/10.1002/jcc.540150809
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  • 147
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    Cluster analysis of molecular conformations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 899-916 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe a method for locating clusters of geometrically similar conformers in ensembles of chemical conformations. We first calculate the pairwise interconformational distance matrix in either torsional or Cartesian space and then use an agglomerative, single-link clustering method to define a hierarchy of clusterings in the same space. Especially good clusterings are distinguished by high values of the separation ratio: the ratio of the shortest intercluster distance to the characteristic threshold distance defining the clustering. We also discuss other statistics. The method has been embodied in a program called XCluster, which can display the distance matrix, the hierarchy of clusterings, and the clustering statistics in a variety of formats. XCluster can also write out the clustered conformations for subsequent or simultaneous viewing with a molecular visualization program. We demonstrate the sorts of insight that this approach affords with examples obtained from conformational search and molecular dynamics procedures. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150811
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    D-CICADA: A software for conformational PES elucidation on network of workstationsThis work is dedicated to Professor M. Kratochvíl on the occasion of his seventieth birthday. (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 937-946 
    Details
    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 methodology of conformational potential energy (hyper)surface (PES) elucidation is the subject of this article. The decomposition of the recently developed software CICADA and its implementation in the distributed environment using PVM (parallel virtual machine) is presented. CICADA has been chosen for the parallelization because of its ability to elucidate systematically the low-energy areas of PES in polynomial time. This makes the method applicable on larger systems which are beyond the scope of the grid search. To show the level of parallelization, conformational PES of two molecules, cyclohexane and terminally blocked alanine, have been studied by the distributed version, D-CICADA, and results have been compared to those of the sequential version. D-CICADA was tested on several virtual machines composed of DEC and Sun workstations. The timing shows good efficiency for both the decomposition of the original algorithm and the PVM environment. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150904
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    Long-time overdamped Langevin dynamics of molecular chains (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 997-1012 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a novel algorithm of constrained, overdamped dynamics to study the long-time properties of peptides, proteins, and related molecules. The constraints are applied to an all-atom model of the molecule by projecting out all components of the nonbonding interactions which tend to alter fixed bond lengths and angles. Because the overdamped dynamical equations are first order in time, the constraints are satisfied by inversion of a banded matrix at each timestep, which is computationally efficient. Thermal effects are included through a Langevin noise term in the equation of motion. Because high-frequency components of the motion have been eliminated, the timestep of the algorithm is determined by the nonbonding forces, which are two to three orders of magnitude weaker than the bonding forces. Using polyalanine as a test example, we demonstrate that trajectories simulating a microsecond of motion can be run about 103 times faster than an equivalent molecular dynamics simulation. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150908
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  • 150
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    Decomposition analyses of the intermolecular interaction energies in two π—π stacking complexes: Quinhydrone and N,N,N′, N′-tetramethyl-P-diaminobenzene-chloranil complex (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1013-1018 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Although there is a similarity in the orbital interaction scheme between quinhydrone and N,N,N′,N′-tetramethyl-p-diaminobenzene-chloranil complex, the stacking conformations are different from each other. The former prefers the half-stacked conformation, whereas the latter prefers the completely stacked conformation. We have done ab initio molecular orbital calculations and decomposition analyses of the intermolecular interaction energies to clarify the origin of the different stacking conformations. It was concluded that the main origin is the difference in the steric part of the interaction energies. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150909
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  • 151
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    A force field for monosaccharides and (1 → 4) linked polysaccharides (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1019-1040 
    Details
    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 force field for monosaccharides that can be extended to (1 → 4) linked polysaccharides has been developed for the AMBER potential function. The resulting force field is consistent with the existing AMBER force field for proteins and nucleic acids. Modifications to the standard AMBER OH force constant and to the Lennard-Jones parameters were made. Furthermore, a 10-12 nonbonded term was included between the hydroxyl hydrogen of the saccharide and the water oxygen (TIP3P, SPC/E, etc.) to reproduce better the water-saccharide intermolecular distances. STO-3G electrostatic potential (ESP) charges were used to represent the electrostatic interactions between the saccharide and its surrounding environment. To obtain charges for polysaccharides, a scheme was developed to piece together saccharide residues through 1 → 4 connections while still retaining a net neutral charge on the molecule as a whole. Free energy perturbation (FEP) simulations of D-glucose and D-mannose in water were performed to test the resulting force field. The FEP simulations demonstrate that AMBER overestimates intramolecular interaction energies, suggesting that further improvements are needed in this part of the force field. To test further the reliability of the parameters, a molecular dynamics (MD) simulation of α-D-glucose in water was also performed. The MD simulation was able to produce structural and conformational results that are in accord with experimental evidence and previous theoretical results. Finally, a relaxed conformational map of β-maltose was assembled and it was found that the present force field is consistent with available theoretical and experimental results. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150910
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    A rapidly convergent simulation method: Mixed Monte Carlo/stochastic dynamics (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1302-1310 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Although Monte Carlo and molecular dynamics are the primary methods used for free energy simulations of molecular systems, their application to molecules that have multiple conformations separated by energy barriers of ≥ 3 kcal/mol is problematic because of slow rates of convergence. In this article we introduce a hybrid simulation method termed MC-SD which mixes Monte Carlo (MC) and stochastic dynamics (SD). This new method generates a canonical ensemble via alternating MC and SD steps and combines the local exploration strengths of dynamics with the barrier-crossing ability of large-step Monte Carlo. Using calculations on double-well potentials and long simulations (108 steps of MC and 1 μs of SD) of the simple, conformationally flexible molecule n-pentane, we find that MC-SD simulations converage faster than either MC or SD alone and generate ensembles which are equivalent to those created by classical MC or SD. Using pure SD at 300 K, the conformational populations of n-pentane are shown to be poorly converged even after a full microsecond of simulation. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540151111
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  • 153
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    Molecular mechanics calculations (MM2 and MM3) on enamines and aniline derivatives (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1321-1330 
    Details
    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 MM2 and MM3 force fields have been extended to cover this class of compounds. Structures, vibrational spectra, and other data for 13 compounds were examined and can be reproduced satisfactorily by MM3. Except for the spectra, the other data can be reproduced somewhat less well by MM2. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 14 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540151202
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    A variational biorthogonal valence bond method (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1357-1364 
    Details
    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 details of a simple and efficient scheme for performing variational biorthogonal valence bond calculations are presented. A variational bound on the energy functional is obtained through the use of a complete configuration expansion in a well-chosen subset of orbitals. The resultant wave functions are clearly dominated by the covalent (spin-coupled) structures, with a negligible contribution from ionic structures. The orbitals obtained compare favorably with overlap enhanced atomic orbitals obtained by other valence bond approaches. The method is illustrated by calculations on water and dioxygen difluoride. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540151205
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    Stability of two-dimensional crystalline aggregates of a protein studied by molecular dynamics (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1278-1290 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two-dimensional protein (ferritin) aggregates with a square lattice symmetry, which were formed within a thin liquid layer on a mercury surface, were studied by molecular dynamics (MD) simulation. For the simulation, the ferritin molecule was modeled by an assembly of 49 spheres, and the intermolecular interactions were given by simple formulae. During the simulation, molecules were confined within a layer, which corresponds to the thin liquid layer. An annealing MD simulation was done starting from a random molecular configuration within the layer, and aggregates with the square lattice symmetry were also obtained. To study the stability of aggregates, dissociation processes of the aggregates were analyzed using MD simulations at room temperature. Interactions between the nearest-neighbor molecules were regarded as bonds. Mean bond energies and correlation coefficients between the bond energies were calculated from the MD trajectories. A decay profile according to the dissociation was obtained, yielding a dissociation rate constant. Buried bonds were stronger than peripheral bonds. The larger the aggregate size, the stronger the bond for each of the buried and peripheral bonds. A simple theoretical account, which is applicable to a general bonded network, was introduced to analyze the dynamics of the aggregates. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540151109
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    Linear dependency in the refinement of force constants with the Jacobian method (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1291-1301 
    Details
    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 Jacobian method in the refinement of force constants is studied. Theoretical and experimental frequencies and other observables, νs, are matched by minimizing ΣsWs(νsexp - νsth)2, where s = 1, 2, 3,…, proceeds over all normal modes and isotopes, and Ws are weighting factors. Modification of the theoretical frequencies is accomplished with the Jacobian matrix, J, with elements Jsi = ∂νs/∂ki involving each force constant or associated parameter, ki, i = 1, 2, 3,…, by Δν = JΔk. The parameters are adjusted directly with Δk = (JTWJ)-1(JW) Δν, where W is a diagonal matrix which weights the frequencies. The linear dependence problem must be addressed prior to inversion of JTWJ. The approach entails diagonalization of JT WJ, analysis of the components of the eigenvectors associated with zero and small eigenvalues, identification of the linearly dependent parameters, successive elimination of selective parameters, and a repeat of this procedure until linear dependency is removed. The Jacobian matrices are obtained by differencing the frequencies when the parameters are varied and by numerical and analytical evaluation of the derivative of the potential. The unitary transformation, U, used to calculate J = UT (∂F/∂k)U or J = UT (ΔF/Δk)U, is obtained from the diagonalization of the Hessian, Fmn = ∂2ν/∂pm∂qn, where p, q = x, y, z are the Cartesian coordinates for atoms m, n = 1, 2, 3,…, at the initial value of ki, i = 1, 2, 3,⃜ The accuracy of and the ability to evaluate the Jacobian matrix by these methods are discussed. Applications to CH4, H2CO, C2H4, and C2H6 are presented. Linearly dependent and ill-conditioned parameters are identified and removed. The procedure is general for any observable quantity. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540151110
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    Algorithms for clustering molecular dynamics configurations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1331-1340 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two traditional clustering algorithms are applied to configurations from a long molecular dynamics trajectory and compared using two sets of test data. First, a subset of atoms was chosen to present conformations which naturally fall into a number of clusters. Second, a subset of atoms was selected to span a relatively continuous region of conformational space rather than form discrete conformational classes. Of the two algorithms used, the single linkage method is inappropriate for this kind of data. The divisive hierarchical method, based on minimizing the difference between cluster centroids and extrema, is successful but also prone to imposing clustering hierarchy where none can be justified. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540151203
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    Application of a high-performance, special-purpose computer, GRAPE-2A, to molecular dynamics (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1372-1376 
    Details
    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 special-purpose computer GRAPE-2A accelerates the calculation of pairwise interactions in many-body systems. This computer is a back-end processor connected to a host computer through a Versa Module Europe (VME) bus. GRAPE-2A receives coordinates and other physical data for particles from the host and then calculates the pairwise interactions. The host then integrates an equation of motion by using these interactions. We did molecular dynamics simulations for two systems of liquid water: System 1 (1000 molecules), and System 2 (1728 molecules). The time spent for one step of molecular dynamics was 3.9 s (System l), and 10.2 s (System 2). The larger the molecular system, the higher the performance. The speed of GRAPE-2A did not depend on the formula describing the pairwise interaction. The cost performance was about 20 times better than that of the fastest workstations available today, and GRAPE-2A cost only $22,000. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540151207
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  • 159
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    Hydrating peptides using a sprouting technique (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 23-27 
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    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 scheme for generating water coordinates, whose proton orientations are random, and simultaneously generating side chain coordinates of peptides, preparatory to studying solvation of peptides using molecular dynamics schemes is presented in an X-PLOR context. Examples from the Integrin and Tropomyosin systems are used to illustrate the procedure. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150104
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  • 160
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    Simulations of the solution structure of HIV-1 protease in the presence and absence of bound zinc (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 61-71 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Zinc ions have been shown to inhibit human immunodeficiency virus type 1 (HIV-1) protease in vitro at neutral pH [Zhang et al. Biochemistry, 36, 8717 (1991)]. Kinetic data from this study support a reversible binding mechanism of zinc in the active site. Preliminary calculations of the ion-protein potential energy based on the geometry of the crystallographic structure [Wlodawer et al. Science, 245, 616 (1989)] are consistent with this proposed mechanism. To examine the structure of HIV-1 protease with zinc bound in the active site, molecular dynamics simulations in the presence and absence of zinc at this site have been carried out to 200 ps. These simulations suggest zinc remains stably bound to the catalytic aspartate residues without disruption of the dimer or significant alteration of the active site structure. These data are consistent with those observed by Zhang et al. (1991), and together give strong evidence that this is the binding site that leads to inactivation. A proposed model of zinc binding at the active site based on quantum mechanical calculations indicates Zn+2 coordination is monodentate with each catalytic aspartate, leaving at least two ligand positions potentially free (occupied by water molecules in the calculations). © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150108
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    Masthead (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150201
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  • 162
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    Parallel algorithm for calculating ro-vibrational states of diatomic molecules (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 144-148 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article, we develop and implement an algorithm for calculating the rovbrational states of diatomic molecules optimized for multiple instructions multiple data computers of distributed memory. The method is based upon the p-version of the finite element method and has been implemented on an INTEL iPSC/2 machine with 16 processors. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540150204
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  • 163
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    Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 162-182 
    Details
    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 method for deriving force fields for molecular simulations has been developed. It is based on the derivation and parameterization of analytic representations of the ab initio potential energy surfaces. The general method is presented here and used to derive a quantum mechanical force field (QMFF) for alkanes. It is based on sampling the energy surfaces of 16 representative alkane species. For hydrocarbons, this force field contains 66 force constants and reference values. These were fit to 128,376 quantum mechanical energies and energy derivatives describing the energy surface. The detailed form of the analytic force field expression and the values of all resulting parameters are given. A series of computations is then performed to test the ability of this force field to reproduce the features of the ab initio energy surface in terms of energies as well as the first and second derivatives of the energies with respect to molecular deformations. The fit is shown to be good, with rms energy deviations of less than 7% for all molecules. Also, although only two atom types are employed, the force field accounts for the properties of both highly strained species, such as cyclopropane and methylcyclopropanes, as well as unstrained systems. The information contained in the quantum energy surface indicates that it is significantly anharmonic and that important intramolecular coupling interactions exist between internals. The representation of the nature of these interactions, not present in diagonal, quadratic force fields (Class I force fields), is shown to be important in accounting accurately for molecular energy surfaces. The Class II force field derived from the quantum energy surface is characterized by accounting for these important intramolecular forces. The importance of each 4.2 to 18.2%. This fourfold increase in the second derivative error dramatically demonstrates the importance of bond anharmonicity in the ab initio potential energy surface. The Class II force field derived from the quantum energy surface is characterized by accounting for these important intramolecular forces. The importance of each of the interaction terms of the potential energy function has also been assessed. Bond anharmonicity, angle anharmonicity, and bond/angle, bond/torsion, and angle/angle/ torsion cross-term interactions result in the most significant overall improvement in distorted structure energies and energy derivatives. The implications of each energy term for the development of advanced force fields is discussed. Finally, it is shown that the techniques introduced here for exploring the quantum energy surface can be used to determine the extent of transferability and range of validity of the force field. The latter is of crucial importance in meeting the objective of deriving a force field for use in molecular mechanics and dynamics calculations of a wide range of molecules often containing functional groups in novel environments. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150207
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  • 164
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    Eclipsed and staggered conformations of (SIH3)2F+: An ab initio study (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 69-90 
    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: Ab initio calculations at 6-31G**, 6-31++G**, and MP2/6-31G** levels were performed on disilyl-fluoronium, (SiH3)2F+, with the SiH3 group eclipsed or staggered. Optimized geometries, total energies, dipole moments, atomic charges, electronic density, and vibrational frequencies were computed. The results were compared with calculated structural parameters and vibrational frequencies of H3SiF, H2SiF+, H2SiF-, and H4SiF+ ions. The basis-set effects were studied. Several thermochemistry parameters - ZPE, thermal energy, rotational constants, and entropies - were also calculated. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500106
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  • 165
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    Announcement (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 91-91 
    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
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500107
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  • 166
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    Masthead (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994) 
    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
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500201
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  • 167
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    Ab initio studies on the mechanism of the cycloaddition reaction between ketene and alleneThis project was supported by the national natural science fund of china. (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 93-99 
    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: The mechanism of the cycloaddition reaction between ketene and allene to form methylene-cyclobutanones has been studied theoretically by HF/3-21G and MP2/3-21G. These two reactions are believed to be unsynchronous and concerted, taking place through the twisted transition states. Four orbitals are mainly involved in each reaction, which is a “2 × [1 + 1]”-type cycloaddition. The activated barrier for the two reactions are 27.2 and 27.1 kcal/mol, respectively, at the level of MP2/6-31G* based on the MP2/3-21G geometries, i.e., these two reactions are compatible. © 1994 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500202
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  • 168
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    Analytic properties of connected moments expansions (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 101-107 
    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: The derivation of the connected moments expansion (CMX) is examined as well as the singularities that arise in the series expansion for the ground-state energy. Explicit analytic results are presented that show a canceling of these singularities. Also, an alternate moments expansion (AMX) is derived that closely models the CMX but displays a varied computational range. © 1994 John Wiley & Sons, Inc.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500203
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  • 169
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    Origin of steric hindrance in ethane (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 109-112 
    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: Steric hindrance has been regarded as a result of nonbonding atomic repulsion and measured in terms of empirically obtained van der Waals radii. The authors sought the cause of steric hindrance using the partial derivatives of the energy-components with respect to a nuclear coordinate. The results show that electrostatic interactions do not produce steric hindrance but the restriction on electron-movement does. Namely, the kinetic energy pressure is the first cause of steric hindrance. © 1994 John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500204
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  • 170
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    Numerical computation of bounded states for schröudinger operators (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 113-134 
    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: A method developed previously for computing eigenfunctions of one-dimensional Schrödinger operators is extended to Schrödinger operators in L2(R3N). It is known that in many cases these operators have not a compact resolvent; therefore, the convergence in L2(R3N) of the more used methods for computing the eigenfunctions is not guaranteed. The idea of the present method consists of replacing the eigenvalue problem in L2(R3N) by one corresponding to the system confined into a box Ω with impenetrable walls [Dirichlet problem in L2(Ω)]. It is shown that the eigenfunctions of the unbounded system can be approximated by those of the confined system when the box Ω is expanded. On the other hand, it is proved that the Schrödinger operator associated to the confined system has a compact resolvent and its corresponding sesquilinear form is bounded and elliptic in the Sobolev space W2,10(Ω). These properties guarantee the convergence in L2(Ω) of the standard methods to solve the Dirichlet problem: the Ritz method as well as the finite-element and finite-difference methods. Therefore, the eigenfuncions of the unbounded system can be approximated in L2(R3N) by means of the numerical solutions of the Dirichlet problem in L2(Ω) with sufficiently large Ω. This property guarantees the accurate computation of the true expectation values. © 1994 John Wiley & Sons, Inc.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500205
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  • 171
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    Calculation of electric dipole transition moments using quasi-degenerate variational perturbation theory and averaged coupled-pair functional theory (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 135-149 
    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: Results are reported from calculations of electric dipole transition moments for various electronic transitions in Be, CH2, and A1H using multireference singles and doubles configuration interaction, quasi-degenerate variational perturbation theory, and multireference averaged coupled pair functional theory. A simple normalization scheme is used for the quasi-degenerate variational perturbation theory and multireference averaged coupled pair functional theory wave functions. In all cases, comparison is made with full configuration interaction results in the valence space. For Be and CH2, all methods are of comparable quality in calculating the transition moments and excitation energies, with averaged coupled-pair functional theory yielding slightly quicker convergence of the excitation energies and transition moments in most cases. For AlH, multireference singles and doubles configuration interaction is somewhat more accurate for the calculation of the transition moment. Factors that affect the accuracy of the methods are discussed. © 1994 John Wiley & Sons, Inc.
    Additional Material: 12 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500206
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  • 172
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    Masthead (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994) 
    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
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500301
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  • 173
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    Ab initio study of the inversion barrier in NF3+This paper was originally submitted for inclusionin the paper symposium dedicated to Prof. Robert G. Parr. (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 151-160 
    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: Ab initio Hartree-Fock, Møller-Plesset perturbation theory (MP2), and quadratic configuration interaction, using single and double substitutions (QCISD), calculations were carried out for the NF3+ ion. Optimized structures were examined at the various levels of theory. Calculation of the inversion barrier height shows the importance of optimizing the geometry at the post-Hartree-Fock level and the inclusion of polarization functions. The best calculated inversion barrier was 13.3 kcal/mol, compared to an experimental value of 17.3 kcal/mol. The dissociation transition state was computed to determine the well depth of the NF3+ ion and its stability toward dissociation. The computed well depth was 28 and 48 kcal/mol at the SCF and MP2 levels, respectively. © 1994 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500207
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  • 174
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    Theoretical prediction of the Infrared and Raman spectra of O-ethyl S-2-diisopropylaminoethylmethylphosphonothiolateThis paper was originally submitted for inclusion in the paper symposium dedicated to Prof. Robert G. Parr. (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 161-172 
    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 have extended our computations of the structure and of the infrared and Raman spectra of methylphosphonates and related compounds to the O-ethyl S-2-diisopropylaminoethylmethylphosphonothiolate molecule (we abbreviate the name to ESD). We have computed the optimized geometry and the vibrational infrared and Raman frequencies of ESD by means of the Guassian 92 Program Package using 6-31G* basis sets. We assign the vibrational frequencies and we correct each frequency by multiplying it with a previously derived 6-31G* correction factor. The result is a computer-generated prediction of the IR and Raman spectra of ESD. The agreement between our theoretical predictions and the experimental IR spectrum of ESD is surprisingly good. © 1994 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500208
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  • 175
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    Quantum chemistry study on B14, B142-, and B14H142- (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 173-179 
    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: The structure of B14, B142-, and B14H142- in octahedral symmetry has been investigated by ab initio calculations at the STO-3G and 4-31G levels. The relationship of molecular orbitals among them has been analyzed and it can be found that the number of valence bonding orbitals of high borane obeys the Wade rule. The similarities and difference between boron clusters and carbon clusters are also discussed. © 1994 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500302
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  • 176
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    Aromaticity in metallacyclobutadienes from the perspective of the valence bond theory (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 189-196 
    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: The valence bond method has been implemented for the study of π-electron systems using a semiempirical CNDO-type Hamiltonian. The algorithm used is based on the Clifford algebra realization of the Rumer-Weyl basis presented by Paldus et al. Using this version of the CNDO-VB approach, the effect of the metal hybridization in the electronic delocalization of metallacyclobutadienes is discussed. © 1994 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500304
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  • 177
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    Orbital binding effect in molecular orbital theory (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 197-205 
    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: Based on the virial theorem and the virial function, a description of the orbital binding effect and the definition of orbital bond order are developed within the framework of molecular orbital theory for both diatomic and polyatomic molecules. Orbital binding effect calculations for N2, CH4, C2H4, C2H2, and C4H4 molecules show that the definition is reasonable. © 1994 John Wiley & Sons, Inc.
    Additional Material: 5 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500305
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  • 178
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    Quantum chemical study of catalysts based on oxides of transition metals (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 181-188 
    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: Catalysts based on oxides of transition metals were studied by Xα-DV calculations. The chemical composition and electronic structure of surface layers for platinum(IV) oxide catalysts modified under percompound electrosynthesis were determined by X-ray photoelectron spectroscopic, quantum chemical, and electrochemical data. The main regularities in electronic structure change under the transition from solid pure oxide PtO2 to its, in part, N-substituted PtO2-xNx were analyzed. Then, we looked for perspective catalysts, calculating the electronic structure for analogous compounds of Ir(III), Ir(IV), Rh(III), and Pd(II). We found that the changes in electronic structure of rhodium oxide under O - N-substitution allowed us to predict the excellent properties of its compound as a catalyst for percompound electrosynthesis reactions. © 1994 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500303
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  • 179
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    Masthead (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994) 
    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
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500401
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  • 180
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    Quasi-Spin and the pseudo-orthogonal group in the hubbard model (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 207-231 
    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: In this article, we demonstrate a complementarity between the quasi-spin SU(2) algebra of the Hubbard model and the pseudo-orthogonal group O(m,m), where n = 2m is the number of lattice sites. It is shown that all N-electron states for the one-dimensional Hubbard model, corresponding to given values of spin and quasi-spin, give rise to an irreducible representation of O(m,m). Moreover, the cyclic group Cn symmetry of the Hamiltonian is investigated and the O(m,m) ↓ Cn branching rules are determined with the use of the U(n) q-dimension formula. © 1994 John Wiley & Sons, Inc.
    Additional Material: 2 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500306
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  • 181
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    Band structures of al-doped superconductors YBa2Cu3-xALxO7 + δ (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 233-242 
    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: Based on the EHMO approach, an approximate treatment of electronic energy-band structures is suggested. By employing this treatment, computations of the band structures for the Al-doped superconductors YBa2Cu3-xAlxO7 + δ were carried out. It is shown by analysis of the band structures and the density of states that the 2D Cu-O planes in the Y—Ba-Cu—O superconducting system play a dominant role in superconductivity, whereas the 1D Cu—O ribbons have indirectly an influence on superconductivity through the connection of the O(4) atoms to two Cu—O planes. © 1994 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500402
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  • 182
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    On multireference superdirect configuration interaction in third order (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 243-271 
    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: The superdirect configuration interaction (Sup-CI) method has the usual versatility and stability of the CI methods with computational efficiency typical to that of the many-body methods, such as the many-body perturbation theory (MBPT). The Hamilton operator is projected into a space of a few trial vectors, such as Krylov, Nesbet, or Møller-Plesset correction vectors. In this space, Hamiltonian matrix elements may be directly computed in the many-body fashion, as weighted sums of integral products over orbital indices. The variation-perturbation method based on the first-order wave function is equivalent to the Sup-CI method with a single correction vector of the Møller-Plesset type. Different points of view on the superdirect CI method are discussed and a version in which third-order contributions are computed for a relatively small (10-100) space of reference and correction vectors is tested. Selection of the best “effective first-order spaces” and size-extensivity corrections in Sup-CI are briefly discussed. Møoller-Plesset, Epstein-Nesbet, and other correction vectors are included in the model calculations on the symmetric stretch of bonds in water, acetylene, and the NH2 molecule. Errors are almost independent of molecular geometry and the method appears to be superior than the multireference second-order perturbation methods. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500403
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  • 183
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    Antiaromaticity in relation to 1,3,5,7-cyclooctatetraene structures (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 273-277 
    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: An isodesmic energy analysis has been carried out at the MP2/6-31G*//HF/3-21G level for the nonplanar ground state (1) of 1,3,5,7-cyclooctateraene and for two planar forms, one having complete π delocalization (2) and the other having alternating single and double bonds (3). 1 is found to have a considerable degree of stabilization, which is attributed to limited π delocalization. The polyene 3 is the more stable of the two planar forms; it is a transition state in the inversion between two possible nonplanar structures. 2 is found to be a triplet at the Hartree-Fock level and is a critical point on an alternate pathway between the two possible arrangements of alternating single and double bonds in 3. Both 2 and 3 have negative isodesmic energies, indicating the presence of stabilizing factors. Our results for 3 show that an “antiaromatic” system need not necessarily show a net destabilization. © 1994 John Wiley & Sons, Inc.
    Additional Material: 2 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500404
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  • 184
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    Masthead (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994) 
    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
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500501
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  • 185
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    Companions in the search (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 49 (1994), S. 739-770 
    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
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560490515
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  • 186
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    Electron correlations and transport effective mass in narrow-band systems and the Hubbard model (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 49 (1994), S. 727-738 
    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: The Hubbard model is rederived from a tight-binding band calculation, showing that, as long as parameters are properly chosen, the model is justified for calculating electronic properties of narrow-band systems. The treatment is extended by including correlations and it was found that bound solutions called dimers exist. The concept of dimers is found to be very powerful for understanding the unusual properties of heavy fermion systems. However, a Mott-Hubbard-like model may be required to calculate properties of high Tc cuprates. © 1994 John Wiley & Sons, Inc.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560490514
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  • 187
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    Addendum (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 49 (1994), S. 771-771 
    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
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560490516
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  • 188
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    Electronic Resource
    Masthead (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 49 (1994) 
    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
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560490601
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  • 189
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    Electronic Resource
    Ab initio study of the low-lying electronic states of the CH2NO2 radical (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 49 (1994), S. 781-788 
    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: Ab initio electronic structures calculations are reported for the four low-lying electronic states X 2B1, 2B2, 2A2, and 2A1 of the CH2NO2 radical. The geometric parameters for the ground-state X 2B1 are predicted by MRSDCI calculations with a double zeta plus polarization basis set. The vertical excitations energies for these electronic states are determined using MRSDCI/DZ+P calculations at the ground-state equilibrium geometry and in agreement with the recent experimental data obtained via PES of the CH2NO2- anion. The oscillator strenghts and the radiative lifetimes for these electronic states and the spin properties for the ground state are calculated based on the MRSDCI wave functions, predicting results in good agreement with available experimental data. © 1994 John Wiley & Sons, Inc.
    Additional Material: 4 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560490603
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  • 190
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    Electronic Resource
    Feynman path integral representation for many-fermion interacting systems (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 49 (1994), S. 789-804 
    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: A many-fermion interacting system is investigated within the scenario of the Feynman path integral representation of quantum mechanics. Short-time propagator algorithms and a basis set, closely related to the coherent states, are used to obtain the many-body analytic propagator. A second-quantized Hamiltonian involving a restricted set of two-body interactions and the whole set of Coulomb interactions are separately and shown to lead to an exact and an approximate propagator, respectively. In the latter case, use of a grand canonical ensemble allows the grand partition function and the density operator matrix to be readily obtained. No further approximations are required in the calculation of the trace of the evolution operator involved in the evaluation of statistical expectation values. © 1994 John Wiley & Sons, Inc.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560490604
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  • 191
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    A “canonical functions” approach to the eigenvalues of a system of two coupled Schrödinger equation (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 49 (1994), S. 773-780 
    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: The problem of the determination of eigenvalues for two coupled Schrödinger equations is considered. A new method to solve this problem is presented. This method replaces the use of the wave functions (with unknown initial values) by eight canonical functions αij and βij (i = 1,2; j = 1,2) having well-defined initial values at an arbitrary “origin” r0. These functions are collected in four couples; each one is the solution of the given coupled equations. For a given E, an “eigenvalue functions” D(E) is defined by an analytical expression depending on αij (r) and βij (r) at r = 0 and r = ∞ only. The successive eigenvalues En of the given system are precisely the successive intersection of the graph D(E) with the E-axis. The present method eliminates the conventional use of wave function initial values as well as the conventional problem of the prior guess of the limit points; it determines these points automatically. It eliminates also the use of trial values for E and the need of iterations for its correction. The numerical application of a standard example used by Friedman and co-workers (1990) shows that the eigenvlues computed by the present method are highly accurate for low and high levels; the average relative discrepancy between computed and exact levels is about 3.4 × 10 -15 (this discrepancy never exceeds 1.6 × 10 -14), which is almost the precision of the computer. © 1994 John Wiley & Sons, Inc.
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560490602
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  • 192
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    Electronic Resource
    Equilibrium geometry and electronic structure of benzylidene, arylethylidene, and heterocyclic arylidene malononitriles (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 49 (1994), S. 805-816 
    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: The equilibrium geometry of some benzylidene, arylethylidene, and heterocyclic arylidene malononitriles has been calculated within the framework of the MNDO-MO formalism. Various structural factors are analyzed and discussed in terms of localized and delocalized MOS and π-interaction between methylene malononitrile (MMN) and aryl moieties. The possibility of charge transfer (CT) from aryl to MMN moieties has been examined. The presence of a heterocyclic ring introduces a small perturbation into the MMN nuclear frame. p-Substituents have a pronounced effect on the magnitude and direction of the dipole moment. The variation of ionization potentials and bond order with the Hammet σ p are examined and a straight-line relationship is obtained. The correlation between physiological activity and quantum mechanical properties is analyzed in terms of heat of formation, ionization potential, dipole moment, and charge density on the aryl ring. © 1994 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560490605
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  • 193
    Electronic Resource
    Electronic Resource
    Brueckner coupled cluster response functions (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 49 (1994), S. 835-848 
    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: A derivation of the linear response function for the Brueckner coupled cluster method is presented that enables the calculation of second-order molecular properties such as frequency-dependent polarizabilities. By using the Brueckner orbital variant of coupled cluster theory, the spurious pole structure inherent in the standard coupled cluster approach with orbital relaxation is avoided. © 1994 John Wiley & Sons, Inc.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560490607
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  • 194
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    Electronic Resource
    Optimized triple-zeta Gaussian basis sets for use with relativistic effective potentials (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 49 (1994), S. 817-833 
    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: Contracted split valence 311 Gaussian basis sets optimized for the averaged relativistic effective potentials (AREP) of Christiansen et al. are developed for the main-group elements B—Ne, Al—Ar, and Ga—Kr. These triple-zeta basis sets are intended for use in valence-only molecular calculations with inclusion of correlation. The performance of the optimized basis functions is first analyzed in HF atomic calculations and compared with HF-limit results. Molecular calculations at the HF, MP2, and CISD levels of theory are performed for some selected diatomics, using these potentials and the optimized sets supplemented by one standard d-type polarization function. Results are reported for bond lenghts, harmonic vibrational frequencies, dipole moments, atomization energies, and ionization energies and compared with all-electron reference calculations and experimental data. © 1994 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560490606
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  • 195
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    Electronic Resource
    Long-range Casimir forces - theory and recent experiments on atomic systems. Series edited by F. S. Levin and D. A. Micha, Vol. 1, Finite Systems and Multiparticle Dynamics, Plenum Press, New York, London, 1993 (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 49 (1994), S. 877-878 
    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
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560490609
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  • 196
    Electronic Resource
    Electronic Resource
    Electronic structure of DNA dimer units, d(AG) · d, (CT), d(TG) · d(CA), · d(GT), and d(GA), in A and B conformations by DV-Xα cluster calculations (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 49 (1994), S. 849-875 
    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: The electronic structure of d(AG) · d(CT), d(TG) · d(CA), d(AC) · d(GT), and d(TC) · d(GA), which are stacked base pairs in the DNA double helix, are elucidated for A and B conformations in detail by DV-Xα cluster calculations. By using the S̃r values of the O2 (and O3) of each phosphate in the clusters together with those calculated in previous articles, it becomes possible to treat chemical reactivities of phosphates as recognition sites for all DNA fragments. Contour maps of the wave function of the HOMO and LUMO for bases differ subtly among the clusters and show the various fields around the P ion induced by the respective stacking constructed from four kinds of bases. © 1994 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560490608
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  • 197
    Electronic Resource
    Electronic Resource
    Announcement (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 49 (1994), S. 879-881 
    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
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560490610
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  • 198
    Electronic Resource
    Electronic Resource
    Masthead (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994) 
    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
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500101
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  • 199
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    Electronic Resource
    A new single-center method to compute molecular integrals of quantum chemistry in slater-type orbital basis of functions (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 21-42 
    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: The present work is dedicated to the introduction of a new single-center expansion method derived from the Barnett and Coulson approach leading to reliable numerical algorithms. The basic concept lies in the use of the integral representations of the modified Bessel functions Iλ+1/2 and Kλ+1/2, rather than employing their closed analytical expressions that are known to involve large numbers that usually make the numerical calculation worthless. It is applied to two-center overlap and Coulomb integrals as well as to three-center nuclear attraction integrals useful in density functional theory. © 1994 John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500103
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  • 200
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    Electronic Resource
    Molecular cyclicity and centricity of polycyclic graphs. I. Cyclicity based on resistance distances or reciprocal distances (1994)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 50 (1994), S. 1-20 
    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: Rules for molecular cyclicity based on the global indices resulting from reciprocal distances (Harary number, H) or from resistance distances (Kirchhoff number, Kf) were tested in comparison with those elaborated earlier by means of the Wiener index, W. The Harary number and the Wiener number were found to match molecular cyclicity in an almost identical manner. The Kirchhoff number also generally follows cyclicity trends described previously. H is slightly less degenerate than is W, but Kf has practically no degeneracy in the graphs investigated here. Being much more discriminating than the Wiener number (i.e., practically nondegenerate), Kf allowed the formulation of new rules for systems formed from linearly condensed ribbons of even-membered rings with different sizes as well as for branched ribbons. The topological cyclicity patterns are thus reformulated in an extended basis, proceeding from three different graph metrics. © 1994 John Wiley & Sons, Inc.
    Additional Material: 8 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560500102
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