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  • Atomic, Molecular and Optical Physics  (2,271)
  • 1990-1994  (1,617)
  • 1970-1974  (408)
  • 1965-1969  (246)
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  • 101
    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 “pedestrian” approach is used to enumerate the spanning trees in buckminsterfullerene. The approach is called “pedestrian” because calculations were carried out by hand and pocket calculator. The number of spanning trees obtained for buckminsterfullerene is 375,291,866,372,898,816,000, a number identical to the value reported by Brown et al. [J. Comput. Chem. 12, 1118 (1991)] who used a computationally more involved approach. © 1994 John Wiley & Sons, Inc.
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  • 102
    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 photodissociation process of argon cluster ion is studied by using the molecular dynamics method with non-adiabatic transitions. The potential energy surfaces and the electronic states are calculated with the diatomics-in-molecules (DIM) hamiltonian. The initial configurations are sampled from the classical trajectory paths on the potential energy surface of the electronic ground state. The non-adiabatic process is treated with the scheme proposed by J. C. Tully [J. Chem. Phys. 93, 1061 (1990)] with a slight modification. The method is applied to the photodissociation process of Ar7+. The calculated kinetic energy distribution and angular distribution of the photofragment are in good agreement with the ex-perimental results, but the branching ratio between Ar+ and Ar2+ fragment ions is not. © 1994 John Wiley & Sons, Inc.
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  • 103
    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.
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  • 104
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    Electronic Resource
    New York, NY : Wiley-Blackwell
    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.
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  • 105
    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.
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  • 106
    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: SC-MEH-MO calculations with electron repulsion correlation and configuration interaction included, have been carried out on Sm(Cp*)2 in both its linear and bent geometrical forms. Except for relatively small factors, there are virtually no major differences in the electronic structures of the two comfomers. In both cases, the bonding is found is to be very clost to being nearly totally ionic. An estimation of the ionic bond energy is made and discussed. © 1994 John Wiley & Sons, Inc.
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  • 107
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    New York, NY : Wiley-Blackwell
    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 self-consistent-field calculations are performed on Ga3As3, Ga3As4, and Ga4As3 clusters. Geometries, electron affinities, ionization potentials, and bondings are analyzed for these clusters. Geometry optimizations using analytic energy gradients followed by single point MP2 calculations are performed to decide for the equilibrium structure. The alternation pattern observed for the ionization potential and electron affinity are verified for these clusters after correlation energy is included. Our results are compared with previous theoretical and experimental calculations. © 1994 John Wiley & Sons, Inc.
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  • 108
    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: Electronic structure investigations on a broad range of gold compounds, including naked and ligated gold clusters, are reviewed. The calculations have been carried out with a recently introduced relativistic variant of the linear combination of Gaussian-type orbitals density-functional (LCGTO-DF) method which affords all-electron investigations for very large systems. The accuracy of the method will be evaluated for the gold dimer. Then the electronic structure of the naked cluster Au55 is studied, both in Ih and Oh symmetry. Nonrelativistic and relativistic results obtained by the present method are compared to those of the much simpler jellium model. Since triphenylphosphine is among the most common ligands in gold chemistry a series of mononuclear gold phosphine compounds MeAuPR3 with increasingly complex ligands PR3 (R = H, CH3, C5H6) is discussed. The calculations reveal the success and the limitations of simpler phosphines often employed as model ligands in theoretical studies. Some aspects of the phosphine gold interaction in these simpler compounds carry over to the main group element centered gold clusters. Thereby one arrives at a rationalization of the particularly high stability of the carbon-centered octahedral cluster cation [(R3PAu)6C]2+ as compared to the neighboring isoelectronic boron and nitrogen-centered clusters. © 1994 John Wiley & Sons, Inc.
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  • 109
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    New York, NY : Wiley-Blackwell
    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.
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  • 110
    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: Optimum equilibrium geometries, harmonic vibrational frequencies, and infrared intensities within the double harmonic approximation are computed for diborane, B2H6, dialane, Al2H6, and digallane, Ga2H6, at both the SCF level of theory and the second-order perturbation theory [E(2)] using three large basis sets: 6-311 G(d,p), 6-311G(2d,2p), and 6-311G(2df,2p). In particular, the results obtained with the latter basis set make this present work the first study to include f-type polarization functions in a systmatic investigation of the molecular structure and properties of all three molecules in the series. Because of the good agreement of the present thoretical results with experimental data and with previous theoretical studies which employed a higher treatment of electron correlation, this study serves to show that large basis sets can in part compensate for the lack of a more advanced treatment of electron correlation in these electron-deficient systems. In addition, this study establishes the level of basis set needed for future work on these systems including a thorough description of the total electronic density at a correlated level. © 1994 John Wiley & Sons, Inc.
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  • 111
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    New York, NY : Wiley-Blackwell
    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 first-principles quantum molecular dynamics scheme based on density-functional theory is used to investigate the finite-temperature properties of metallic hydrogen at density 2.7 g cm-3 (rs = 1), in particular to determine melting temperature, velocity autocorrelation functions below and above melting, and the temperature dependence of proton self-diffusion in the liquid phase. A strong deviation from the prediction of the one-component plasma model is found in the value of the melting temperature. Results of simulations of the molecular phase are also presented and found to be in agreement with previous work on dense molecular hydrogen. The scheme is based, for the modeling of the electrons, on time-dependent Schrödinger equations, coupled to classical equations of motion for the protons. All numerical results were obtained using a parallel computer, and an outline of the computer program implementation is presented. © 1994 John Wiley & Sons, Inc.
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  • 112
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    New York, NY : Wiley-Blackwell
    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 iso-energy cutoff scheme is introduced for the calculation of the potential of mean force between two ions in water. The cutoff criterion is based on the optimal interaction of the water dipole with the ion pair, for which analytical expressions are derived. Formulas are also derived to characterize the solvent reorganization contribution to the potential of mean force. Treatment of the contributions from waters outside the cutoff is also discussed. © 1994 John Wiley & Sons, Inc.
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  • 113
    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.
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  • 114
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    New York, NY : Wiley-Blackwell
    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 vibration and rotation of molecules affects nuclear spin-spin coupling constants. This manifests itself as a temperature dependence of the coupling and also as an isotope effect (after allowing, where necessary, for differing magnetogyric ratios of the two nuclei involved in the isotopic substitution). Within the Born-Oppenheimer approximation, a nuclear spin-spin coupling surface can be defined for each pair of coupled nuclei. This surface is sampled by the nuclei as they undergo the excursions about equilibrium geometry that are governed by the force field. An accurate ab initio carbon-proton spin-spin coupling surface for the methane molecule has been calculated. This was obtained by summing the surfaces for each of the four contributions - Fermi contact, spin-dipolar, orbital paramagnetic, and orbital diamagnetic - expressed as power series in terms of symmetry coordinates. Preliminary calculations for 13CH4 and 13CD4 give a difference of only 6% between the calculated and observed nuclear motion contributions. The observed temperature dependence is also accounted for by the calculations. For these isotopomers, bond stretching plays the dominant role. © 1994 John Wiley & Sons, Inc.
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  • 115
    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: Using the Hartree-Fock and MP2 methods with bases of up to 6-31++G(2d, 2p) quality, the optimum geometry of the 1:2 and 2:1 (H2O)n… (HF)m complexes of water and hydrogen fluoride is searched in a systematic way. Two minimum-energy conformations are found for the 1:2 complex connected through a low-energy transition state. For the 2:1 complex, only one minimum-energy structure is obtained. The analysis of the geometries of the minima and their vibrational frequencies shows that none of them can be used to explain the existence of the H …F—H reverse complex detected experimentally. © 1994 John Wiley & Sons, Inc.
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  • 116
    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: Enantioselective hydrogenation of α-ketoesters with cinchona-modified platinum catalysts has been studied theoretically in order to rationalize the interaction between the chiral modifier and the substrate. The structure of the probable transition complex has been calculated for the system methyl pyruvate (substrate)-cinchonidine (modifier) using quantum chemistry techniques at both ab initio and semiempirical levels and molecular mechanics. The calculations indicate that crucial interaction occurs via hydrogen bonding of the quinuclidine nitrogen and the oxygen of the α-carbonyl moiety of methyl pyruvate and confirm earlier experimental evidence that the quinuclidine nitrogen of the cinchonidine is involved in the interaction leading to enantiodifferentiation. The resulting complex, which resembles to a half-hydrogenated state of the substrate, is shown to be a possible transition state for the enantioselective hydrogenation of α-ketoesters. © 1994 John Wiley & Sons, Inc.
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  • 117
    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: Unrestricted Hartree-Fock calcuations coupled with second-order Møller-Plesset correlation correction were performed to study the structures and energetics of microlusters. For (BN)2, linear and rhombus forms are almost isoenergetic, whereas cyclic forms are preferable for (BN)3 and (BN)4 clusters. As a general trend, linear isomers prefer the triplet spin state, whereas cyclic isomers prefer the singlet spin state. Total charge density plots show a strong dominace of the B—N bond, indicating that the extent of its polar character becomes stronger with the increase in the cluster size. The loss of a BN monomer is shown to be the most likely fragmentation channel for both neutral and single-ionized clusters. We find that neutral (BN)n clusters have the same structural configurations as those of their corresponding C2n counterparts. This similarity follows the isoelectronic principle and is of importance due to recent interest in the investigations of BN fullerene analogs. © 1994 John Wiley & Sons, Inc.
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  • 118
    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.
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  • 119
    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 new quantum chemical definition is proposed of the full atomic valence, VA, taking into account both the covalent and ionic parts of the chemical bonds formed by atoms in molecules and crystals. The full atomic valencies, covalencies, and charges on atoms are calculated for nickel-oxygen crystalline compounds in the CNDO band theory approximation. A comparison of the chemical bonding in nickel and copper crystalline oxides is given. © 1994 John Wiley & Sons, Inc.
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  • 120
    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 the ground electronic state and of some special charge-transfer excited states in ionic solids is examined from the ab initio cluster model approach. Different ab initio wave functions, including a frozen orbital approach, the Hartree-Fock self-consistent field, and multireference configuration interaction wave functions, are considered and analyzed using different theoretical techniques. We explicitly consider some alkaline-earth oxides such as CaO, a more difficult case such as A12O3, a transition-metal oxide such as NiO, and a system with a more complicated structure such as KNiF3. Analysis of ab initio wave functions in terms of valence bond components shows that all these compounds are largely ionic, thus supporting the simple picture arising from the ionic model. However, the nature of the excited states is more complex. Alkaline-earth oxides lowest excited states are essentially described as charge-transfer excitations dominated by a single resonant valence bond structure and the calculated energy difference is comparable to the experimental optical gap. In the case of A12O3, the electronic spectra presents excitonic features and the local charge-transfer excitation excited states provide a reasonable representation of these phenomena. Finally, several different valence bond structures are present in the lowest electronic states of KNiF3. © 1994 John Wiley & Sons, Inc.
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  • 121
    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 new approach to the description of the formation of spherulites in a polymer solution is proposed. It is based on an analytical scheme that takes into account the mass conservation law as a fundamental evolution equation. Three physically interesting cases are considered, both which, on deterministic and stochastic levels, can reflect an asymptotic behavior characteristic for spherulites, namely, R(t) ∝ t, where R(t) is a radius of the spherulite measured at instant t. A few examples of systems similar to that under study are mentioned. © 1994 John Wiley & Sons, Inc.
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  • 122
    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.
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  • 123
    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: Geometry optimizations on molecular clusters of the five-membered heterocyclic molecules pyrrole, furane, thiophene, and selenophene were carefully carried out. It is shown that the value of the band gap cannot be related to the bond alternation in the aromatic compounds. However, a correlation of the gap value with the ionization potential of the heteroatom in the ring is found and can be explained by the different stabilizations of the LUMO energy of the heterocycle with respect to the butadiene backbone. The energy band structure including also corrections for the electron correlation effects is reported. The newly developed variational method for the calculation of static polarizabilities of polymers is reviewed and applications to cyclopropene and heteroaromatic derivatives are reported. Finally, a possible approach to treat dynamical polarizabilities of polymers based on perturbation theory is briefly outlined. © 1994 John Wiley & Sons, Inc.
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  • 124
    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.
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  • 125
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    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 many-electron system in one and two dimensions are studied within the geminal approach. The analytical expressions for the wave functions and ground-state energies are obtained for a number of 1-D and 2-D systems: conjugated polymers, organic conductors, 2-D conductors with square lattices, and others. It is shown that electron excitations of a kink type can exist in 2-D systems with mixed valency. In this case, the correlation pairing of current carriers arises as a result of correlation effects leading to superconducting properties of the system. © 1994 John Wiley & Sons, Inc.
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  • 126
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    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 multiparticle correlation expansion for the entropy of a classical monatomic liquid is presented. This entropy expresses the physical picture in which there is no free particle motion, but, rather, each atom moves within a cage formed by its neighbors. The liquid expansion, including only pair correlations, gives an excellent account of the experimental entropy of most liquid metals, of liquid argon, and of the hard-sphere liquid. The pair correlation entropy is well approximated by a universal function of temperature. Higher-order correlation entropy, due to n-particle irreducible correlations for n ≥ 3, is significant in only a few liquid metals, and its occurrence suggests the presence of n-body forces. When the liquid theory is applied to the study of melting, we discover the important classification of normal and anomalous melting, according to whether there is not or is a significant change in the electronic structure upon melting, and we discover the universal disordering entropy for melting of a monatomic crystal. Interesting directions for future research are extension to include orientational correlations of molecules, theoretical calculation of the entropy of water, application to the entropy of the amorphous state, and correlational entropy of compressed argon. We clarify the relation among different entropy expansions in the recent literature. © 1994 John Wiley & Sons, Inc.
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  • 127
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    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.
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  • 128
    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: Molecular dynamics simulations of polyethylene chains (CnH2n+2 for n = 13, 16, 28, 60) have been carried out to investigate both equilibrium and dynamic properties of polymer melts confined between flat solid surfaces. We observe an oscillatory monomer density in the direction normal to the solid surfaces, which depends on the size of the monomers (i.e., on the volume density of the system). The packing manner of monomer segments, segment orientation, and local conformations of chains are found to be independent of chain length. In addition, preferential interfacial adsorption of chain ends is observed. The chains are flattened close to the surface and many molecules assume essentially two-dimensional train configurations even in the case of C60H122 melts. The apparent self-diffusivities of the centers of mass of the molecules depend on their distance from a surface. Molecules adjacent to a surface exhibit a reduced mobility perpendicular to the surface and an increased one parallel to it. The self-diffusion constant parallel to a surface depends strongly on the size of the monomers. An increase of the united atom diameter by 10% reduces the diffusion constant by a factor of three, in good agreement with the experimental value. © 1994 John Wiley & Sons, Inc.
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  • 129
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    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.
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  • 130
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    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.
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  • 131
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
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    Topics: Chemistry and Pharmacology
    Notes: The relationship between surface rainbows and the onset of classical chaos in atom-surface scattering is discussed. The principal focus is the onset of chaos as a function of experimentally controllable parameters. The correspondence between the classical trapping and quantum mechanical selective adsorption resonances is briefly discussed. The connection with the more mathematical work of Grebogi and co-workers is also considered. © 1994 John Wiley & Sons, Inc.
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  • 132
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
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    Topics: Chemistry and Pharmacology
    Notes: Application of a purely algebraic least-squares approach in a spline basis to the determination of continuum orbitals in the single-electron molecular case illustrates the excellent numerical properties of the method. Initial work based on a single-center expansion is extended to an LCAO formulation within a single-particle Hamiltonian and to the full multielectron problem in the one-center scheme. Preliminary results on H2+ and He photoionization are reported. © 1994 John Wiley & Sons, Inc.
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  • 133
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An efficient method for calculating electronic matrix elements for electron-transfer reactions in biological systems is proposed. We use the tight-binding model to describe the motion of one-electron in an array representing the system: donor (D), acceptor (A), and all other atoms that compose the protein. The matrix elements |TDA|;2 is evaluated at the estimated electron energy. The essential part of the method lies in the evaluation of the off-diagonal Green function 〈I|G|F〉 between the site I neighboring with the donor and the site F with the acceptor. The recursive residue generation method is used to evaluate 〈I|G|F|〉. As an application, these matrix elements in metal-labeled myoglobin are calculated and the results are compared with those evaluated with the renormalized-perturbation-expansion approach. © 1994 John Wiley & Sons, Inc.
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  • 134
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
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  • 135
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The recently synthesized metal-encapsulated porphyrazine compound, [Sn(t-Bu)2]4-star-Ni(porphyrazine)-S8, shows very interesting structural and optical absorption features compared with other metal-centered porphyrazines, e.g., metal phthalocyanines (Pc). Using self-consistent-field local density theory, we studied the ground-state and excited-state electronic structure of this molecule and compared it with its metal phthalocyanine analog NiPc. The theoretical optical spectra including oscillator strengths are in good agreement with experimental absorption and show that the characteristic transitions at the so-called Soret band in NiPc are red-shifted in the new compound. © 1994 John Wiley & Sons, Inc.
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  • 136
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    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 and UV-visible spectra of C70 were examined using semiempirical INDO/2 and INDO/CI methods. The results obtained are in good accord with experimental results. On the basis of correct electronic spectra, calculations of the nonlinear third-order optical susceptibility (γijkl) of C70 were performed using the INDO/SDCI method combined with a sum-over-states expression. The calculated value for 〈γ〉 (-2 ω, ω, ω, O) is 0.882 × 10-33 esu (ω = 1.91 μm), which is in good agreement with observation. © 1994 John Wiley & Sons, Inc.
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  • 137
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The standard electrode potential for the quinone (Q)-hydroquinone (QH2) couple in aqueous acidic media has been explicitly calculated. Molecular geometries of Q and QH2 have been optimized. Protonation of Q, i.e., the formation of QH+ and QH22+, have been considered. Molecular geometries of these species have been thoroughly optimized. The energy of complexation of these molecules with water have been calculated by optimizing the structures of the hydrated complexes Q · 6H2O, QH2 · 6H2O, QH+ · 6H2O. and QH22+ · 6H2O. The ion-solvent interaction energy of QH+ · 6H2O, in turn, has been calculated by considering the complex QH+ · 6H2O… 2H2O, where the two extra water molecules approach the charge center of the complex QH+ · 6H2O vertically from top and bottom of the quinonoid ring. The standard reduction potential calculated by the CNDO method, 0.8548 V, is somewhat larger than the experimental potential, 0.6998 V, at 25°C. But the INDO value, 0.7085 V, is in excellent agreement with the observed potential. The electrode potential for the plastoquinone (PQ)-plastohydroquinone (PQH2) couple present in the aqueous pool in chloroplast has been calculated by the INDO method. The basic geometries of PQ, PQH+, and PQH2/sb have been synthesized by adopting the optimized geometries of Q, QH+, and QH2 and considering methyl substituents as well as an isoprenoid side chain containing up to 3 isoprene units with possible geometrical isomerism. The hydrated species PQ · 6H2O, PQH+ · 6H2O, and PQH2 · 6H2O are unstable compared to the isolated species PQ, PQH+, and PQH2, respectively. In fact, we have found that the hydration of PQH+ and PQH2 is much less extensive, and stability arises only when the hydroxyl groups in these two molecules are hydrogen-bonded to water molecules. But PQH+ is also stabilized through the association of two more water molecules in the vertical direction. For this reason, we have calculated the reduction potential of the PQ/PQH2 system from the energies of the isolated molecules PQH2 and the hydrated species PQH+ · 2H2O. The computed standard reduction potential is 0.2785 V and it yields a potential of 0.07V at pH 7 at 25°C, which is in good agreement with the reduction potential 0.11 V observed for plastoquinone in the aqueous pool in chloroplast. © 1994 John Wiley & Sons, Inc.
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  • 138
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
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    Topics: Chemistry and Pharmacology
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  • 139
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
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  • 140
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Three representative isomerization reactions (HNC → HCN, CH3NC → CH3CN, and N2H2 trans → cis and sin) have been studied using both the LCGTO-LSD and LCGTO-NLSD density functional methods and employing a new algorithm for the search and the refinement of the transition-state structures. The inclusion of the nonlocal corrections and the use of large basis sets improve the reliability of the energetic parameters. Results are in good agreement with previous accurate first-principle computations and available experimental data. © John Wiley & Sons, Inc.
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  • 141
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In computational studies to understand the interaction of polycyclic aromatic hydrocarbons (PAHs) with biomolecular systems, the semiempirical method AM1 has been used previously to determine the geometry of the PAH and its metabolites and relevant intermediates. A number of studies have shown that AM1 provides geometries for parent PAHs that are acceptably close to experimentally determined structures. However, many of the properties that determine the manner by which PAHs interact with biological nucleophiles depend on the structure of metabolites and reactive intermediates where less experimental information is available. In a previous study, we used AM1 to obtain the molecular geometries of reactive intermediates of cyclopenta-PAHs (cPAHs) and then used single-point Hartree-Fock calculations, with the gaussian 3-21g basis set, to obtain molecular energies and charge distributions, in order to predict the direction of epoxide ring opening. Recent advances in the availability of computational hardware and software have provided other, more rigorous, methods for approaching this problem. In this study, we used hartree-fock methods in the gaussian series of programs employing the 3-21g and 6-31g basis sets and the local density functional method Dmol to obtain molecular geometries, energies, and charge distributions of the epoxides and the two potential hydroxycarbocations that could result from protonated ring opening, for a series of cPAHs. We have also performed the same calculations with AMSOL/SM2, a semiempirical method that adds the effect of the aqueous environment to the AM1 Hamiltonian. The division of the cPAHs into classes is not altered by these more rigorous calculations. The inclusion of water in the Hamiltonian has a greater effect on the results than using the ab initio methods to obtain the structure. © 1994 John Wiley & Sons, Inc.
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  • 142
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
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    Topics: Chemistry and Pharmacology
    Notes: An analysis of the integrand occurring in current density functional calculations is presented, concentrating attention on correlation energy functionals and the atomic regions, i.e., the regions of space surrounding atomic centers. The analysis follows the structure of a previously proposed numerical integration scheme for three-dimensional integrals occurring in electronic structure calculations. The scheme is based on the choice of density-based weight functions that naturally partition the space into «atomic» volumes (in which the integration is performed in terms of spherical coordinates) and «diatomic» volumes (in which the integration is performed in terms of confocal elliptical coordinates). From this analysis, a simplified procedure for the atomic «internal» integrations is developed, whereas preliminary results are discussed for the atomic and diatomic «external» integrations. The numerical tests are performed on the C60 molecule in the symmetrical configuration. © John Wiley & Sons, Inc.
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  • 143
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    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this work, we carry out an analysis of the gradient-corrected density functionals in molecules that are used in the Kohn-Sham density functional approach. We concentrate on the special features of the exchange and correlation energy densities and exchange and correlation potentials in the bond region. By comparing to the exact Kohn-Sham potential, it is shown that the gradient-corrected potentials build in the required peak in the bond midplane, but not completely correctly. The gradient-corrected potentials also exhibit wrong asymptotic behavior. Contributions from different regions of space (notably bond and outer regions) to nonlocal bonding energy contributions are investigated by integrating the exchange and correlation energy densities in various spatial regions. This provides an explanation of why the gradient corrections reduce the local density approximation (LDA) overbinding of molecules. It explains the success of the presently used nonlocal corrections, although it is possible that there is a cancellation of errors, too much repulsion being derived from the bond region and too little from the outer region. © John Wiley & Sons, Inc.
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  • 144
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    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.
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  • 145
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The first implementation of the intrinsic reaction coordinate (IRC) method within the density functional theory (DFT) framework is presented. The implementation has been applied to four different types of chemical reactions represented by the isomerization process, HCN = HNC (A); the SN2 process, H- + CH4 = CH4 + H- (B); the exchange process, H· + HX = HX + H· (X = F,Cl) (C); and the elimination process, C2H5Cl = C2H4 + HCl (D). The present study presents for each process optimized structures and calculated harmonic vibrational frequencies for the reactant(s), the transition state, and the product(s) along with the IRC path connecting the stationary points. The calculations were carried out within the local density approximation (LDA) as well as the LDA/NL scheme where the LDA energy expression is augmented by Perdew's and Becke's nonlocal (NL) corrections. The LDA and LDA/NL results are compared with each other as well as the best available ab initio calculations and experimental data. For reaction (D), ab initio calculations based on MP2 geometries and MP4SDTQ energies have been added due to the lack of accurate published post-HF calculations on this process. A detailed discussion is provided on the efficiency of the IRC algorithms, the relative accuracy of the DFT and ab initio schemes, as well as the reaction mechanisms of the four reactions. It is concluded that the LDA/NL scheme affords the same accuracy as does the MP4 method. The post-HF methods seem to overestimate activation energies, whereas the corresponding LDA/NL estimates are too low. The LDA activation energies are even lower than the LDA/NL counterparts. The incorporation of the IRC method into the DFT framework provides a promising and reliable tool for probing the chemical reaction path on the potential energy surfaces, even for large-size systems. IRC calculations by ab initio methods of an accuracy similar to the LDA/NL scheme, such as the MP4 scheme, are not feasible. © John Wiley & Sons, Inc.
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  • 146
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: There is an increasing number of applications using methods based on density functional theory (DFT) describing a large variety of systems of chemical interest. All these calculations are performed through evaluations of integrals of exchange and correlation contributions to the energy and the potential, which depend on the density and also on its first and second derivatives (nonlocal functionals). Within our DF program, the integrand is decomposed into single-center components, through the introduction of weight functions, and its radial and angular dependence can be chosen. In this article, we give a brief description of these features, with compared performances of different grids for the evaluation of different integrals, such as the total number of electrons and the exchange and correlation energies. More complex properties, such as total energies and equilibrium geometries, are also studied with respect to the choice of the grid of points, in order to determine the most favorable radial and angular quadrature schemes. The incidence of this choice is analyzed in the case of the metal-metal bond of the Ru2, Rh2, and Pd2 dimers. Finally, the use of an extended grid of points is shown necessary for systems involving weak interactions, such as the Ar2 molecule. © John Wiley & Sons, Inc.
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  • 147
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    Topics: Chemistry and Pharmacology
    Notes: The first discussion of the dynamics of Jahn-Teller systems in terms of the electronic density as the fundamental variable was given by W.J. Clinton in 1960, where the degenerate electronic configuration of a Jahn-Teller molecule was interpreted in terms of the infinite number of ways in which the charge distribution can be oriented for the same energy. The moving nuclear framework serves as the perturbation necessary to define the orientation of the charge density, with no activation energy required to put the charge cloud into motion. Recently, this notion of the electronic charge cloud in a Jahn-Teller molecule sweeping out the potential surface over which the nuclei move has found mathematical expression in our work in terms of a generalized electronic current density in nuclear-coordinate space [N. Sukumar and B.M. Deb, Int. J. Quantum Chem. 40, 501 (1991)]. The introduction of the electronic phase as a function of both electronic and nuclear coordinates, in addition to the electronic density, is a crucial component of this formulation. In the present work, the density-based treatment is extended to the nonadiabatic situation, with the Born couplings interpreted as nonadiabatic currents in parameter space. Abelian and non-Abelian gauge transformations of these currents are discussed. © John Wiley & Sons, Inc.
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  • 148
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    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The minimization of the energy functional of the first-order density matrix γ(r,r') is achieved using unitary transformations applied to γ. Equivalently, such transformations can be carried out also on one-electron orbitals (natural orbitals) and their occupation (integer or non-integer) numbers. The conventional local density approximation based on the electron density p(r) is then considered as a special case. The direct minimization of the energy functional of p with respect to the parameters of the unitary transformation leads to stationary conditions that are all equivalent to the Kohn-Sham equations. Preliminary numerical tests show that the proposed algorithms for the direct minimization of the energy work in a satisfactory manner. © John Wiley & Sons, Inc.
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  • 149
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    International Journal of Quantum Chemistry 52 (1994), S. 1219-1228 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Two cases of bilinear coupling of a particle to a medium are compared. They differ in that one of the mediums does not modify the particle potential, whereas the other does. Two corresponding kramers-type rate equations for adiabatic reactions are derived directly from a dynamic rate theory and interpreted from the view of the stochastic theory. Both equations become identical in the weak coupling limit. Their relations to transition-state theory are also discussed. Corresponding results for nonadiabatic reactions are considered. © 1994 John Wiley & Sons, Inc.
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    International Journal of Quantum Chemistry 52 (1994), S. 1245-1245 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
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    Topics: Chemistry and Pharmacology
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  • 151
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    International Journal of Quantum Chemistry 52 (1994), S. 1247-1247 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 152
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    International Journal of Quantum Chemistry 52 (1994), S. 1267-1271 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An extended Rayleigh-Ritz method for computing two-sided eigenvalue bounds of the one-dimensional Schrödinger equation without using a complementary method is presented. The method is based on the B-spline approximation over the truncated domain, which results in a generalized banded matrix eigenvalue problem. Numerical results for two multiminima potentials of different natures are presented. © 1994 John Wiley & Sons, Inc.
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  • 153
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    Topics: Chemistry and Pharmacology
    Notes: A method is proposed how to calculate the correct density matrix of an infinite polymeric chain from that of a standard finite supercell calculation. The density matrix of the finite supercell is transformed into k-space for all k-values allowed by the periodic boundary conditions. The k-dependent matrices are then unitarily transformed, with each unitary matrix being represented by a set of complex rotation matrices. It is shown that the corresponding angles can be interpolated and extrapolated toward the zone boundaries in a straghtforward manner and that this extrapolation can be done from any finite supercell with reasonable accuracy. This gives rise to an infinite system density matrix for which all fundamental properties are guaranteed by construction. This infinite system density matrix may be used to construct a corrected density matrix for the finite supercell calculation. © 1994 John Wiley & Sons, Inc.
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  • 154
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Calculations of finite atomic clusters based on the Hartree-Fock self-consistent field theory are modified to model more closely the ideal behavior of the infinite system. The density matrix of the standard finite supercell calculation is extrapolated to an infinite supercell so that it contains information from a continuum of k points in the first Brillouin zone. This modification is incorporated into the self-consistency loop of the MOPAC quantum chemistry program and leads to improved results compared to a standard finite supercell calculation. Heats of formation, bond lenghts, and electronic properties converge more quickly to the correct ground-state values. For polyacetylene, we obtain a reduced bond-length alternation of Δr = 0.084 Å, which is in agreement with more sophisticated calculations containing electron correlation effects. © 1994 John Wiley & Sons, Inc.
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  • 155
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    International Journal of Quantum Chemistry 52 (1994), S. 1317-1328 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Photoenolization of a ketone in its lowest triplet state was examined using the AM1 semiempirical molecular orbital method with complete geometry optimization at the configuration interaction level in the restricted Hartree-Fock frame. The theoretical barrier fits with a polynomial given by Eq. (1) and the probability of tunneling of hydrogen was calculated by the WKB method. The density of states above the zero-point level was estimated by the Whitten-Rabinovitch approximation. Rate constants for the hydrogen and deuterium-abstraction processes via tunneling were then computed at different temperatures. © 1994 John Wiley & Sons, Inc.
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  • 156
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    International Journal of Quantum Chemistry 52 (1994), S. 1301-1316 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This article deals with a dynamical system that generalizes the Kepler-Coulomb system and the Hartmann system. It is shown that the Schrödinger equation for this generalized Kepler-Coulomb system can be separated in prolate spheroidal coordinates. The coefficients of the interbasis expansions between three bases (spherical, parabolic, and spheroidal) are studied in detail. It is found that the coefficients for the expansion of the parabolic basis in terms of the spherical basis, and vica versa, can be expressed through the Clebsch-Gorden coefficients for the group SU(2) analytically continued to real values of their arguments. The coefficients for the expansions of the spheroidal basis in terms of the spherical and parabolic bases are proved to satisfy three-term recursion relations. © 1994 John Wiley & Sons, Inc.
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  • 157
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    Topics: Chemistry and Pharmacology
    Notes: Results of CASSCF state-averaged calculations on the lowest electronic states of LaO and LaO+ are reported in this work. For comparison, some low-lying electronic states of AlO and AlO+ are also reported. The ground state of LaO was found to be the X2Σ+ (Re = 1.987 Å, ωe = 794 cm-1) with a low-lying A2Δ excited state. Five more excited states below 26000 cm-1 were found. The first ionization potential (IP) is found at 5.16 eV, resulting in an X1Σ+ ground state for the LaO+ diatom, in opposition to AlO+ for which an X3 Π ground state has been found. Analysis of the wave functions, dipole moments, and Mulliken populations reveal that the bonding is quite ionic in both systems. © 1994 John Wiley & Sons, Inc.
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  • 158
    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 spectra of free water molecules were measured at scattering angles 2θ ranging from 10.5° to 75.7°, using an angle-dispersive-type diffractometer and synchrotron radiation as an X-ray source. A silicon (111) monochrometer was used to obtain incident X-rays with the wavelengths of (1.543/n) Å (n = 1,3,4,5). Observed inelastic scattering peaks are clearly separated from eleastic ones at s values [s = (4π/λ) sin Å] larger than 8 Å-1. The increase of the separation with an increasing s value was consistent with the classical theory of the Compton shift. The total (elastic plus inelastic) intensities were obtained over a range of s = 0.74-5.0 Å-1. Experimental difference intensities Δσee and Δσne were obtained separately by combining the X-ray and high-energy electron scattering data. The experimental results are in reasonable agreement with the theoretical intensities calculated from SCF and CI molecular wave functions with a basis set of double-zeta plus polarization functions. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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  • 159
    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
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  • 160
    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 semiclassical density functional approach is used to evaluate the smooth part of the variation of the Hartree-Fock (HF) binding energy in atoms, from helium through xenon. The energy density functional is chosen with an improved form for the kinetic energy functional (KEF). The variation of the HF binding energy is split into smooth and oscillating (shell-structure) parts, in accordance with Strutinskyøs self-consistent averaging procedure, which is equivalent to a semiclassical ħ-expansion of the KEF. This enables a well-grounded evaluation of the oscillating part of the HF binding energy, which displays a quasi-periodic behavior expressing clearly the shell structure of atoms. © 1994 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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  • 161
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    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
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  • 162
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    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
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  • 163
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    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 previously demonstrated capacity to utilize the hydrophobic folding and assembly transition in designed model proteins to perform diverse energy conversions is formalized in terms of three postulates with an associated 15 corollaries. Each corollary defines one of the 15 pairwise free-energy transductions involving the six intensive variables: mechanical force, temperature, pressure, chemical potential, electrochemical potential, and electromagnetic radiation. The first postulate directly involves the input of thermal energy to raise the temperature from below to above that temperature required to drive hydrophobic folding and assembly, with the resultant capacity to perform useful mechanical work. The second postulate considers the energy inputs that can lower or raise the temperature range over which the hydrophobic folding transition occurs; these energy inputs can thereby perform mechanical work. The third postulate treats the energy conversions not involving mechanical force, whereby a pair of functional groups becomes coupled by each being a part of the same hydrophobic association process with each functional group being able individually to drive the hydrophobic folding transition and thereby to change the state of the second functional group in an energy-conversion process. It is then shown how a model protein can be so designed as to function in a second-order process treated by Postulate III and how the efficiency of energy conversion can be enhanced. Finally, these energy-conversion studies using the hydrophobic folding and assembly transition in model proteins are related to a theoretical model for cooperative hydrophobic folding and to experimental studies suggesting a central role for hydrophobic folding in the general problem of protein folding. © 1994 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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  • 164
    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 use molecular dynamics, electrostatic, and quantumchemical calculations to discuss chromophore and protein structural changes as well as proton transfer pathways in the first half of the bacteriorhodopsin photocycle. A model for the molecular mechanism is presented, which accounts for the complex pH dependence of the proton release and uptake pattern found for the M intermediates. The results suggest that transient transfer of the Schiff base proton to a nearby tightly bound water molecule is the primary step, which is accompanyied by dissipation of free energy to the protein. From there, the energetically most favorable proton transfer is to aspartate D85. Arginine R82 is involved in the protein reorientation switch, which catalyzes the pKa reduction of glutamate E204. This residue is, therefore, identified as extracellular proton release group whose acid base equilibrium regulates the pH-dependent splitting of the photocycle. © 1994 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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  • 165
    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 new class of calcium antagonists (dibenzotricyclic compounds) is studied by means of reaction field ab initio calculations and molecular dynamics simulations. The central ring of these tricyclic molecules is found to be more important to the calcium antagonistic potency than the two phenyl rings. The central ring with antagonistic potency shows hydrophobic character, thus the interaction between the drug and the binding sites is assumed to be dominated by hydrophobic interactions. Variation of the flexure angle, the angle between the two phenyl rings, does not change the hydrophobic property of the central ring significantly, therefore it is not expected to affect the interaction between the drug and binding site directly. The effect of the flexure angle on calcium antagonistic potency, the relation between drug affinity of these tricyclic molecules and their ionization energies, and the interaction of calcium ions with the central ring are discussed. © 1994 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
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  • 166
    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: Triglycerides, the major components of neutral lipids, are important biomaterials, as they take part in the edification of membranes. In this perspective, the consideration of biological membranes at a molecular level requires detailed knowledge of the preferred conformations of the triglycerides in their various polymorphic forms. In this context, we adapted a molecular modeling approach, which allows the simulation the three-dimensional structure of the different polymorphic forms (α, β′, and β) valid for any triglyceride. Their conformational analysis is based on molecular mechanics calculations, as follows: First, a large number of isolated molecular structures were generated in a systematic structuretree analysis. For their generation, atomic charges within the Mulliken scheme, calculated at the ab initio RHF-LCAO-MO-SCF level (6-31G), were considered. The lowest-energy conformers were, next, correlated with experimental data (NMR, powder X-ray diffraction) in order to select α, β′, or β structures. Then, in a second step, these selected conformers were assembled, in head-to-tail dimers in order to form a monolayer. For this step, the use of potential-derived atomic charges is known to be more suitable. In this study, we consider triglycerides derived from the predominant fatty acids, i.e., stearic, elaidic, and oleic acids. © 1994 John Wiley & Sons, Inc.
    Additional Material: 12 Ill.
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  • 167
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    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 consider the paradoxical situation arising in the standard multiple regression analysis in that as the standard error of prediction decreases by introduction of additional variables (descriptors) at the same time the standard error of the coefficients of the regression analysis increases, often to the point of the coefficients having no statistical validity. We trace the origin of this paradoxical situation to intercorrelation of the variables. A remedy to this curve-fitting paradox is in the introduction of orthogonal variables or descriptors. © 1994 John Wiley & Sons, Inc.
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  • 168