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  • 1985-1989  (1,638)
  • Computational Chemistry and Molecular Modeling  (1,638)
  • 101
    Electronic Resource
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    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 325-330 
    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: It is shown that configuration interaction calculations, with inclusion of the relativistic corrections, constitute an appropriate approach for the prediction of atomic energy levels and that results of experimental accuracy are possible given the availability of large-scale, fast computers. The results obtained for He through F emphasize both the practical difficulties to be encountered and the possibility of predictions with less than 1% error.
    Additional Material: 2 Ill.
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  • 102
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    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 331-337 
    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: Through a formalism developed in formr papers, some problems, set by the determination, from experimental data of the evolution equation of an n-states quantum system are considered.
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  • 103
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    International Journal of Quantum Chemistry 35 (1989), S. 495-512 
    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-body diagrammatic perturbation theory of rotation-vibration spectra is elaborated. The present approach is based on two many-body techniques, namely on the second quantization formalism (a rotating-vibrating molecule is formally treated here as a system of interacting vibrons, obeying the Bose-Einstein statistics) and the many-body diagrammatic theory of a model Hamiltonian, initially suggested in the microscopic theory of nuclei and in the last decade very frequently exploited in the accounting for the correlation effects in many electron systems. In the framework of this theory, the rotation-vibration energies are determined as the eigenvalues of a finite-dimensional model eigenproblem.
    Additional Material: 5 Ill.
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  • 104
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    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989), S. 583-584 
    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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  • 105
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    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 35 (1989) 
    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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  • 106
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    International Journal of Quantum Chemistry 35 (1989), S. 703-703 
    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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  • 107
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    International Journal of Quantum Chemistry 35 (1989), S. 709-710 
    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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  • 108
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    International Journal of Quantum Chemistry 35 (1989), S. 711-715 
    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 personal and partially anecdotal account is given of the role of the Debye-Waller factor in protein crystallography and protein dynamics.
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  • 109
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    International Journal of Quantum Chemistry 35 (1989), S. 717-719 
    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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  • 110
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    International Journal of Quantum Chemistry 35 (1989), S. 735-743 
    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: Since the overlap integral between two functions in position space is the same as the overlap integral between their counterparts in momentum space, there is an intimate connection between orthonormalization procedures in the two spaces. It is pointed out that in certain cases this situation can be used to simplify the orthogonalization.
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  • 111
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    International Journal of Quantum Chemistry 35 (1989), S. 721-734 
    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: This is the story about how knowledge of the Compton profile led to the technical development of a useful apparatus. It is also the story of interdisciplinary collaboration between condensed matter theorists and medical physicists.
    Additional Material: 7 Ill.
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  • 112
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    International Journal of Quantum Chemistry 35 (1989), S. 745-749 
    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 quantum system is repeatedly prepared in the same way and then observed in measurement processes. The following problem is stated and solved: Given the results of a series of observations, what is the best guess for a density matrix describing the ensemble of prepared systems? The corresponding classical problem and its solution are obtained as a special case.
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  • 113
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    International Journal of Quantum Chemistry 35 (1989), S. 751-760 
    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: Formulas for the energies and widths of shape resonances, i.e., quasi-stationary levels for a quantal particle moving in a spherically symmetric potential, valid also close to the top of the potential barrier, have been published by Drukarev, Fröman, and Fröman. On the basis of these formulas, in the present paper the potential is explicitly expressed in terms of experimental data on the energies and widths of the quasi-stationary states. The treatment is related to previous treatments by Wheeler and by Cole and Good, Jr., which are in turn related to the Rydberg-Klein-Rees method.
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  • 114
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    International Journal of Quantum Chemistry 35 (1989), S. 769-778 
    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: After a brief review of the historical development of the concept “antiparticle,” some recent theoretical results on CP violation are reviewed.
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  • 115
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    International Journal of Quantum Chemistry 35 (1989), S. 761-767 
    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 approximation of hyperpolarizabilities through the use of operator inequalities is sketched. Previously applied methods to ordinary polarizabilities are extended. They lead to expressions involving moments of oscillator strength distributions related through sum rules to ground state properties. Systematic applications of new formulae are suggested.
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  • 116
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    International Journal of Quantum Chemistry 35 (1989), S. 779-791 
    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: Light positive particles can be introduced in metallic lattices where they take up interstitial positions. The motion of particles between these sites is usually described as a phonon-assisted tunneling process, which at high temperatures approaches a classical over-barrier jump motion.The present paper reviews briefly the study of such phenomena at very low temperatures where phonon assistance is no longer effective. Experiments on proton transfer between certain sites in niobium metal and on positive muons which diffuse in copper or aluminium lattices show unusual temperature dependencies, which have been explained quantitatively with recent tunneling theories. These approaches take into account the simultaneous dissipation of energy to the electron bath, a phenomenon which was shown by J. Kondo to be determined by the screening electrons following the particle. The temperature dependence is essentially an effect of the Fermi distribution of the conduction electrons. The interaction of the particle with the itinerant electrons will also determine whether the particle wavefunction will be localized or form an extended (Bloch-like) state.
    Additional Material: 5 Ill.
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  • 117
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    International Journal of Quantum Chemistry 35 (1989), S. 793-799 
    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 microscopic model for nuclear dynamics has been formulated and applied to the collisions between heavy ions. It may be viewed as an extension of the collisionless time-dependent Hartree-Fock (TDHF) method to include nucleon-nucleon collisions. The collision term is written in the form of a time relaxation. The relaxation time is obtained from separate calculations. Some results are shown for the collisions between two 16O nuclei. The computations require a storage of several million words and require a super-computer. Calculations have been done on the John von Neumann Center (JVNC) CYBER-205. Future calculations are planned on the JVNC ETA-10.
    Additional Material: 4 Ill.
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  • 118
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    International Journal of Quantum Chemistry 35 (1989), S. 813-825 
    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 ground (N) state and the 1B1u(V) excited state of planar ethylene have been studied at the CPF and MR-SDCI levels of theory, using an extended CGTO basis set of the ANO type. The investigation especially addresses the near-degeneracy problem in the ground state and the coupling between the diffuse character of the π* orbital and the amount of correlation included in the wave function of the V state. The MR-SDCI results yield a vertical excitation energy in the range 7.8-8.0 eV, whereas the CPF result is 7.9 eV. The best MR-SDCI result for 〈1π*‖z2‖1π*〉 is 7.8, whereas CPF calculations based on MR-SDCI INOS give the value 6.7. It is clear from the results that these numbers have not converged and that more extended calculations than was possible in the present work would yield an even more compact wave function.
    Additional Material: 9 Ill.
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  • 119
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    International Journal of Quantum Chemistry 35 (1989), S. 839-850 
    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 generalization of the Gibbs-Bogoliubov inequality F ≤ F0 + 〈H - H0〉0 for the free energy F is studied which leads to a variation principle for this quantity that may be of importance in certain computational applications to quantum systems. This approach is coupled with a study of the perturbation expansion of the free energy for a canonical ensemble with H = H0 + λV in the general case when H0 and V do not commute. The second- and high-order derivatives of the free energy with respect to the perturbation parameter λ are calculated. From the second-order term is finally obtained a second-order correction to the previous variational minimum for the free energy.
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  • 120
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    International Journal of Quantum Chemistry 36 (1989), S. 127-140 
    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 explicit expression for the unitary group Clebsch-Gordan coefficients, which couple two fully antisymmetric single-column states into the two-column Gel'fand-Tsetlin states, is given in terms of isoscalar factors for the canonical subgroup chain U(n) ⊃ U(n - 1) ⊃ … ⊃ U(1). The isoscalar factors are expressed through the step numbers labeling canonical basis states and enable a straightforward construction of Gel'fand-Tsetlin states in the Clifford algebra unitary group approach, without the use of the tables for the symmetric group outer-product reduction coefficients.
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  • 121
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    International Journal of Quantum Chemistry 36 (1989), S. 157-167 
    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 simple semiquantitative approach to the calculation of the energy of surface states, proposed recently by the authors, is applied to high-symmetry surfaces of selected transition metal carbides, nitrides, and oxides. The results are compared with recent experimental and theoretical data. The necessity to include the changes in the potential at the crystal surface is indicated.
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  • 122
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    International Journal of Quantum Chemistry 36 (1989), S. 141-155 
    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 here a theoretical formulation of the transport of excitation energy in a three-dimensional molecular crystal containing one impurity. The excitation is assumed to be localized in the jth site at time t, and the expression for the probability of finding the excitation at some other site j′ at a later time t′ is derived. The probability is given by the correlation function \documentclass{article}\pagestyle{empty}\begin{document}$ \left\langle {\hat P_j (t)\hat P_j (0)} \right\rangle $\end{document}, where \documentclass{article}\pagestyle{empty}\begin{document}$ \left\langle {\hat P_m } \right\rangle $\end{document} represents the site projection operator, |m〉 〈m|. In our derivation we neglect the interaction among excitons of different bands, account for the presence of the impurity by adding a small perturbation term to the pure crystal Hamiltonian, and calculate the exciton solutions through first order. We consider a general impurity; that is, the trap depth is nonvanishing and may even be complex. The exciton-phonon interaction is taken to be linear in lattice displacement vectors; we assume that the short time behavior of \documentclass{article}\pagestyle{empty}\begin{document}$ \left\langle {\hat X} \right\rangle _{{\rm phonon}} $\end{document} gives the dominant contribution to the physical property X being studied and solve the dynamical problem by using a time-dependent effective potential consisting of fluctuations around the equilibrium average exciton-phonon interaction. Several limiting cases are briefly discussed.
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  • 123
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    International Journal of Quantum Chemistry 36 (1989), S. 169-178 
    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 use of a new time-dependent ket, variationally determined as a linear combination of Slater determinants associated with an electric field variant factor, provides an efficient technique for the calculation of dynamic polarizability tensors. Including electron correlation, the method is applied to the evaluation of the frequency-dependent polarizability of H2O and N2 and can be used even when the photon energy is near the excitation energy. With relatively small basis sets, calculated polarizabilities and resonance frequencies are in good agreement with experimental values for H2O but have to be improved for N2.
    Additional Material: 3 Ill.
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  • 124
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    International Journal of Quantum Chemistry 36 (1989), S. 179-186 
    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 recently proposed (semiclassical) classical path method for treating reactive scattering is reviewed. This method exploits properties of hyperspherical coordinates which allow a collision coordinate to be defined without reference to the arrangement of the particles. The coordinate space is divided into classical and quantal subspaces such that the description of the “arrangement” is quantal. Selected results are presented for the three-dimensional D + H2 → HD + H reaction.
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  • 125
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    International Journal of Quantum Chemistry 36 (1989) 
    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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  • 126
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    International Journal of Quantum Chemistry 36 (1989), S. 189-190 
    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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  • 127
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    International Journal of Quantum Chemistry 36 (1989), S. 187-188 
    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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  • 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
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  • 129
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    International Journal of Quantum Chemistry 36 (1989), S. 201-211 
    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 paper a general method for the evaluation of the matrix elements of spin-dependent operators is proposed to improve the treatment primitively suggesteed by Cooper and Musher. This approach is largely based on the recent results which the present authors have achieved in the representation theory for the inner- and outer-product reduction of the symmetric group. It is shown that the so-called outer-product coupling coefficients (OPCC) can be used to generalize the method for constructing the irreducible tensor operators of group Sn. Together with the use of inner-product coupling coefficients (IPCC), an expression for the matrix elements of spin-dependent operators is presented as the product of a Racah coefficient for Sn and a reduced matrix element which can be expressed in terms of IPCC, OPCC, and the related integrals. The treatment for one- and two-electron spin-dependent operators is discussed in detail.
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  • 130
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    International Journal of Quantum Chemistry 36 (1989), S. 213-223 
    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: Configuration interaction (CI) calculations are carried out for He atom and H2, LiH, and BH molecules in order to obtain the value of the charge density at the nucleus by the use of the Hiller-Sucher-Feinberg (HSF) identity. The HSF density also can be calculated with the double perturbation theory based on the Møller-Plesset-type theory and also on the Epstein-Nesbet type. It is found that each value of the HSF density for these perturbative corrections is very similar to the corresponding value by the CI with single- and double-electron excitations. Especially for the He atom, the HSF density value by the full-CI wave function coincides with the exact value of the charge density in three significant figures. The electron correlation effects are found to be small but cannot be ignored in the HSF density. It can be shown that the superiority of the HSF density over the usual delta-function-type density is excellently confirmed.
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  • 131
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    International Journal of Quantum Chemistry 36 (1989), S. 225-240 
    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: Analytical and numerical studies are performed concerning the exclusion of the basis set superposition error (BSSE) from the SCF calculations of intermolecular interactions. Based on these studies a new procedure is proposed, which consists of the following steps: (1) determine the orbitals by the SCF scheme based on the recent “chemical Hamiltonian approach” (CHA-SCF method), i.e., excluding the delocalization effects caused by BSSE, and then (2) calculate the usual energy expectation value. (This gives results superior to those obtained by the previous nonsymmetric CHA energy formula.) The actual numerical calculations performed for different simple systems (He2, water dimer) by using various basis sets indicate that the CHA/CE (CHA with “conventional energy” formula) potential curves are well-balanced and are close to those obtained by the Boys-Bernardi (BB) method and usually (but not necessarily) go slightly beyond the latter. So our method gives results better than (or close to) those given by the BB method by performing only a single ∼N4 calculation at each geometrical arrangement of the system.
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  • 132
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    International Journal of Quantum Chemistry 36 (1989), S. 241-253 
    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 molecular orbital methods are employed to study the low-lying states of C3H+, SiC2H+, Si2CH+, and Si3H+. Special attention is paid to a comparative study between C3H+ and Si3H+. In both cases a 3B2 state is found to lie the lowest at the HF level, although inclusion of correlation effects favor a linear structure (1Σ+ state) for C3H+, which lies 25 kcal/mol below the 3B2 state at the MP4 level, and a bent structure (1A′ state) for Si3H+, which lies just 2 kcal/mol below the 3B2 state. The proton affinities of C3, SiC2, Si2C, and Si3 are estimated at different levels of theory. Both protonation at carbon and silicon atoms are considered for SiC2 and Si2C. It is found that C3 comparatively has a low proton affinity. On the other hand, Si3 has a relatively high proton affinity compared with the protonation at silicon atom for both SiC2 and Si2C. These results are discussed on the basis of electronic structure arguments.
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  • 133
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    International Journal of Quantum Chemistry 36 (1989), S. 255-263 
    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 isotropic (aiso) and dipolar (Adip) hyperfine coupling constants of 19F2- were obtained from MRD-CI wave functions using a variety of basis sets. In series I, increasing numbers of d functions were added to a 5s4p contracted Huzinaga/Dunning basis. In series II, the 5s3p basis set was uncontracted in several steps until 9s5p was reached, to which were added from one to three d-polarization functions. CI parameters (selection thresholds and the number of reference configurations) were also varied. A study of the R dependence of aiso and Adip was performed. The best values obtained at Re are 260 G for aiso and 308 G for Adip, compared with experimental values of about 280 G for aiso and 320 G for Adip.
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  • 134
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    International Journal of Quantum Chemistry 36 (1989), S. 265-275 
    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: Hyperfine coupling constants (HFCC) of the 19F and 35Cl atoms and the 19F2- and 35Cl2- radical anions have been calculated by the unrestricted Hartree-Fock (UHF) method using polarization and diffuse functions with contracted double-zeta as well as uncontracted basis sets. The Adip values are fairly insensitive to changes in the basis set and show good accordance with experimental and other theoretical studies. The isotropic HFCCS aN of 19F, 19F2-, and 35Cl2- show strong dependence on d functions and the state of contraction of the s, p set. Spin-projected UHF wave functions lead to better agreement with experiment.
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  • 135
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    International Journal of Quantum Chemistry 36 (1989), S. 277-285 
    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 effect of electron correlation on the results of pseudopotential calculations was examined using a simple analytical semiempirical pseudopotential and a correlated floating-type one-center wave function. Investigations were performed for the XH alkali metal hydride molecules (X = Na, K, Rb, Cs). The inclusion of the electron correlation in the ground state proved important for the calculation of the dissociation and ionization energies, but it is less significant for the determination of the equilibrium nuclear distances. The ground state potential energy curves are also determined.
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  • 136
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    International Journal of Quantum Chemistry 36 (1989), S. 287-298 
    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 empirical potential is introduced that is suitable for calculation of the interaction enegies of biomolecules with thousands of atoms. The potential consists of electrostatic, repulsion, and dispersion energy terms. The approach used for parametrization of the potential is entirely different from that used with other existing potentials. Namely, all the terms were parametrized independently to retain their physical significance. The sum of the electrostatic and repulsion terms mimic the SCF interaction energy calculated using Huzinaga's minimal basis set MINI-1. The dispersion energy is very important and is usually predominant for the interactions of large (polar) molecules in the gas phase as well as in the liquid phase.
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  • 137
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    International Journal of Quantum Chemistry 36 (1989), S. 319-323 
    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 solitonic models of proton transfer in a molecular hydrogen-bonded chain have been examined with respect to the shape of protonic interaction potential. The kink-like excitations with quadratic, quartic, Morse, and Toda interactions are reported and analyzed.
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  • 138
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    International Journal of Quantum Chemistry 36 (1989), S. 299-312 
    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 mechanical calculations have been used to study the reaction mechanism of human carbonic anhydrase-catalyzed hydration of CO2. This reaction is responsible for fast metabolism of CO2 in the human body. For each of the reaction steps, possible catalytic effects of active site residues are examined. The pertinent results are as follows. (1) For CO2 binding, the experimentally observed 2.5 cm-1 frequency shift of the asymmetic stretching frequency between measurements taken in the aqueous solution and in the enzyme is reproduced in our theoretical calculations. Our results suggest that CO2 binds to the zinc ion within the hydrophobic pocket. (2) No energy barrier is found for the nucleophilic attack from Zn2+-bound OH- to C of CO2 to form Zn2+-bound HCO3-. (3) For the internal proton transfer within zinc-bound HCO3-, the barrier of 35.6 kcal/mol for the direct internal proton transfer is reduced to 3.5 and 1.4 kcal/mol, respectively, when one or two water molecules are included for proton relay. (4) Displacement of Zn2+-bound HCO3- by H2O is facilitated by the presence of the negatively charged Glu 106-Thr 199 chain and by the association and the subsequent ionization of a fifth water ligand. (5) For the intramolecular proton transfer between Zn2+-bound H2O and His 64, the Zn2+ ion lowers the pKa of Zn2+-bound water and repels the proton. His 64, or a similar proton receptor with a larger proton affinity than H2O, functions as proton receiver; and the active site water molecules visualized by x-ray crystallography are important for the proton relay function. In summary, it is demonstrated that in order to achieve effective catalysis, a sequence of precisely coordinated catalytic events among all participating catalytic elements in the enzyme's active site is essential.
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  • 139
    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 pi interaction in complexes of (S)-methyl N-(2-naphthyl)alaninate with (S)- and (R)-N-(3,5-dinitrobenzoyl)leucine n-propylamide was investigated with Hartree-Fock and second-order Møller-Plesset perturbation theory calculations using the STO-3G basis set. For each complex, the geometry of the model of the pi interaction (i.e., naphthalene and 1,3-dinitrobenzene) was derived directly from the complex geometry which was relaxed by the semiempirical quantum-mechanical AM1 method. At the level of treatment used herein, our results are in agreement with our earlier AM1 interaction energy calculations in which the pi interaction, one of the three primary interactions proposed in models of the aforementioned complexes, is attractive and of equal strength (ca. 0.8 kcal/mol) in both complexes.
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  • 140
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    International Journal of Quantum Chemistry 36 (1989), S. 341-351 
    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 alternative scheme for ab initio polymer band structure calculations based on a Filon-type quadrature is proposed. This scheme avoids the explicit calculation and the storage of the “troublesome” Fourier transforms of the LCAO density matrix elements and is a first step towards a better control of the convergence of the different lattice sums appearing in the configuration space LCAO-SCF-CO method. The potential of the proposed technique is illustrated by a minimal basis set calculations on an infinite chain of H atoms.
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  • 141
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    International Journal of Quantum Chemistry 36 (1989), S. 325-339 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We describe an efficient new algorithm which extends the range of feasible shell model calculations. This algorithm is applicable to single shell and multiple shell configurations, where two or more quantum numbers (e.g., L and S) are required to label the states within each shell. The algorithm proceeds by factoring the shell model Hilbert space into a product of subspaces, one for each angular momentum. N-particle wave functions are built up recursively from N - 1 particle wave functions. Three kinds of N - 1- to N-particle coefficients are required to carry out the construction of N-particle electron (or fermion) states from N - 1 particle states. These are (1) coefficients of fractional parentage (CFPs) within a single shell, (2) outerproduct isoscalar factors (OISFs) within a single angular momentum subspace, and (3) innerproduct isoscalar factors (IISFs) which describe how multishell states within the complementary angular momentum subspaces are combined to form totally antisymmetric wave functions. All three types of N - 1- to N-particle coefficients are generated recursively using a single powerful and efficient matrix diagonalization algorithm. Matrix elements of single particle creation and annihilation operators are expressed in terms of single particle CFPs, OISFs, and IISFs. We also describe an efficient algorithm for computing matrix elements of products of creation and anihilation operators by inserting and summing over complete sets of intermediate states. This is the Feynman-like sum over path overlaps procedure. Timing benchmarks are presented comparing the new Drexel University shell model (DUSM) code with a state of the art shell model code.
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  • 142
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    International Journal of Quantum Chemistry 36 (1989), S. 369-377 
    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: Experimental works suggest the existence of an oscillating complex in the collisional quenching of Na with N2 molecules. Until now, however, few efforts have been dedicated to the study of these possible complexes. In this work, a diabatic and diabatic-configuration interaction method are proposed in order to investigate the existence of these quasibound levels. The results and their comparison with other available data are presented and discussed.
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  • 143
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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: Recently we extended our strategy for MRD-CI (multireference double excitation-configuration interaction) calculations based on localized/local orbitals and an “effective” CI Hamiltonian for molecular decompositions of large molecules to breaking a chemical bond in a molecule in a crystal or other solid environment. Our technique involves solving a quantum chemical ab-initio SCF explicitly for a system of a reference molecule surrounded by a number of other molecules in the multipole environment of more distant neighbors. The resulting canonical molecular orbitals are then localized and the localized occupied and virtual orbitals in the region of interest are included explicitly in the MRD-CI with the remainder of the occupied localized orbitals being folded into an “effective” CI Hamiltonian. The MRD-CI calculations are carried out for breaking a bond in the reference molecule. This method is completely general. The space treated explicitly quantum chemically and the surrounding space can have voids, defects, deformations, dislocations, impurities, dopants, edges and surfaces, boundaries, etc. We previously applied this procedure successfully to the H3C—NO2 bond dissociation of nitromethane in a nitromethane crystal with extensive testing of the number of molecules that have to be included explicitly in the SCF and how many molecules have to be represented by more distant multipoles. The results indicated that it took more energy to dissociate the H3C—NO2 bond when the nitromethane molecule was in the crystal than it did to dissociate that bond in the free nitromethane molecule. In this present study we have investigated the effect of voids (both in the nitromethane molecules treated explicitly in the SCF and those in the environment represented by multipoles) on the calculated H3C—NO2 bond dissociation energies.
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  • 144
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    International Journal of Quantum Chemistry 36 (1989), S. 379-389 
    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, the Hamiltonian for the scattering of the He + H2 system is given by using the interaction potential V(X, Y, Θ) determined by experiments and the semiclassical method. From this Hamiltonian we find a dynamical algebra h6. The statistical expectation of the energy and the transition probability of H2, Pn→m, are derived; therefore, selection rules have been found easily.
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  • 145
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    International Journal of Quantum Chemistry 36 (1989), S. 417-425 
    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 magnetooptical properties (B terms) vibronically induced have been calculated for a series of carbonyl compounds in the region of the first absorption band. The rules deduced experimentally for the signs and sizes of the B terms induced by vibrations of different symmetry are generally confirmed by these calculations.
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  • 146
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    International Journal of Quantum Chemistry 36 (1989), S. 391-415 
    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 short review of the recent development of the stochastic approach to chemical reactions in condensed media is made. The relations of this approach to a general formulation of chemical kinetics are discussed on the basis of a many-frequency oscillator model. It is shown that the classical transition-state theory is not a particular case of the stochastic theory neither in the case of small viscosity nor in the case of large viscosity. The recent quantum generalizations of the stochastic theory are identical to earlier results of a quantum transition-state theory that correspond to the case of large viscosity. Such generalizations based on previous results of a collision theory are made for the case of small viscosity. It is shown that these quantum generalizations of the stochastic theory are possible only in the temperature range of moderate tunneling defined in terms of a characteristic temperature.
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  • 147
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    International Journal of Quantum Chemistry 36 (1989), S. 427-427 
    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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  • 148
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    International Journal of Quantum Chemistry 36 (1989) 
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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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  • 149
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    International Journal of Quantum Chemistry 36 (1989), S. 429-453 
    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 particularly compact form of the orthogonally spin-adapted coupled-cluster equations involving all singly and doubly excited clusters is derived for the general case of a non-Hartree-Fock closed-shell reference determinant. The diagrammatic approach based on the graphical methods of spin algebras is applied. The relationship of different diagrammatic procedures for spin-adaptation, employing both bare and spin-adapted two-electron interaction vertices, is discussed. A comparison with the results obtained with algebraic spin-adaption approaches is also given.
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  • 150
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    International Journal of Quantum Chemistry 36 (1989), S. 473-486 
    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: It is shown that doubly excited states play an important role in calculations of the optical activity of molecules with well-conjugated electron systems, such as the DNA bases. In some significant cases it is necessary to include a large number of excited states in the configuration interaction (CI) to obtain a reliable, converging result. A new version of the CNDO/OPTIC method, which includes doubly excited states in the CI, is proposed. As an application, the electric transition moments in different pyrimidines are considered. The calculated results agree with experimental data and results obtained from ab initio calculations and INDO calculations using doubly excited states in the CI.
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  • 151
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    International Journal of Quantum Chemistry 36 (1989), S. 455-472 
    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: Electronegativity χ and hardness η for 54 atoms and their positive and negative ions are calculated by means of self-interaction-corrected DFT including correlation terms. The exchange potential energy is treated by local spin density approximation corrected to account for self-interaction effects as suggested by Rae. The highest occupied orbital eigenvalues for ions are identified to the chemical potential μ± for positive and negative charged atoms depending upon the developing charge process. Values of χ±δ and η± for the different ionic species are given for several values of δ. Average values for 〈χ〉 and 〈η〉 in the sense of Mulliken finite formula for neutral atoms are also tabulated and compared with Mulliken values from experimental data. The agreement among them is almost quantitative.
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  • 152
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    International Journal of Quantum Chemistry 36 (1989), S. 487-501 
    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 mathematically well-defined measure of localization is presented based on Mulliken's orbital populations. It is shown that this quantity equals 1 for core- and lone-pair orbitals, 2 for two-atomic bonds, 6 for benzene rings, etc., and it is applicable for delocalized canonical HF orbitals as well. The definition of this quantity is general in the sense that ab initio MOS with overlapping AO expansion, and semiempirical wave functions using the ZDO approximation as well, can be treated. The localization quantity is essentially “intrinsic,” i.e., no subdivision of the molecule is required. For N-electron wave functions, mean delocalization can be defined. This measure is not invariant to unitary transformations of the one-electron orbitals, characterizing in this way the localized or extended representation of the N-electron wave function. It can be proven, however, that for unitary transformed wave functions a maximum delocalization exists which depends only on the physical (N-electron) properties of the molecule. It is shown that inhomogeneous charge distribution can cause strong electron localization in molecular systems. The delocalization of the canonical Hartree-Fock orbitals, the Parr-Chen circulant orbitals, and the optimum delocalized orbitals is studied by numerical calculations in extended systems.
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  • 153
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    International Journal of Quantum Chemistry 36 (1989), S. 503-524 
    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 graphical approach to the configuration interaction in the basis of pure Slater determinants is presented. The formulation based on the spin-separated two-slope graph (SSTSG), enabling the selection of determinants with the fixed Ms value, has a direct relation to the well-known concept of the group-function product. The commonly used excitation criterion and the spatial (Abelian) symmetry properties are analyzed in terms of the graph's internal structure. The Slater formulae for the Hamiltonian matrix elements between determinants, in the particle-hole formalism and in the spin-separated form, are related to different classes of loops within graphs. Some aspects of implementation within both the matrix-element-driven (ME) and integral driven (ID, direct) CI algorithms are discussed. The presented formulation, of a general complete active space (CAS) CI type, is a basis of the Graphical Determinantal Configuration Interaction (GDCI) computer program.
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  • 154
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    International Journal of Quantum Chemistry 36 (1989), S. 533-533 
    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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  • 155
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    International Journal of Quantum Chemistry 36 (1989), S. 525-531 
    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 derivative of the electron-electron potential energy Uee with respect to internuclear separation R is studied for light homonuclear diatomic molecules at equilibrium. It is readily related to nuclear-nuclear potential energy Unn, the force constant K, and the electron-nuclear potential energy Uen. An approximate expression, based on the simplest form of density functional theory, is then used to eliminate dUen/dR|Re. The result thus obtained for dUee/dR|Re transcends an earlier proposal of Kryachko by including a term 2/3ReK, with K the force constant. Numerical tests at SCF-RHF level are presented for nine homonuclear diatomic molecules.
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  • 156
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    International Journal of Quantum Chemistry 36 (1989), S. 535-535 
    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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  • 157
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    International Journal of Quantum Chemistry 36 (1989), S. 537-537 
    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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  • 158
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    International Journal of Quantum Chemistry 36 (1989), S. 541-541 
    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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  • 159
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    International Journal of Quantum Chemistry 36 (1989) 
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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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  • 160
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    International Journal of Quantum Chemistry 36 (1989), S. 545-552 
    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: Oxygen clusters of the equilateral ring types On and their negative ions On- are studied by the recently developed pictorial-topological quantum chemistry method, VIF (valency interaction formulas), of this author. The species are found to be of high energy relative to separated oxygen atoms, the cause being evident from the VIF pictures. The odd n rings should be at local minima but are not likely to have observable negative ions. The even n rings have distortional instabilities, yet their negative ions are more likely to be observed as transients in beam experiments.
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  • 161
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    Journal of Computational Chemistry 10 (1989) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 162
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    Journal of Computational Chemistry 10 (1989), S. 35-54 
    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 unusual type of π-electron delocalization in Y-shaped molecules related to guanidine and its protonated form, the guanidinium ion, has been studied by ab initio methods at the STO-3G and 3-21G levels. Results are reported for tautomeric, rotameric, and protonated forms of the oxygen-substituted guanidine series (urea, carbamic, and carbonic acids); “extended-guanidine” (aminomethylene guanidine) including pseudocyclic forms; and simple ring systems in which the extended-guanidine group is incorporated (3-amino-1,2,4-triazole, 2,4-diaminopyrimidine). Both the guanidine and guanidinium type stabilizations have been characterized in terms of a number of structural and energetic parameters: degree of single/double bond character from bond lengths and π-bond orders, electron distributions, and protonation energies. The major finding is that the structural and energetic properties of the isolated extended-guanidinium group resemble those of the group when incorporated within 6-membered heterocyclic or heterobicyclic rings, although the details vary with the nature of the ring and possibility of reinforcement or interference with the substructure resonance from overall ring delocalization. The implications for stabilization of the protonated forms of some biologically important pteridines is discussed.
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  • 163
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    Journal of Computational Chemistry 10 (1989), S. 99-103 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: For a series of simple alkyldisilanes, 3-21G (*) full gradient geometry optimizations have been performed to yield both structural and conformational energy data which was suitable for calibrating the MM2 force field for disilanes. We have examined several model structures which yielded sufficient information about the rotational potential around the Si-Si bond to enable us to revise and augment those reported by Frierson. These parameters were questioned by us in the course of MM2 studies of 1,2-disilacyclobutanes. We report new Si-Si torsion parameters as well as pertinent structural data from 3-21G(*) geometry optimizations and relative conformational energies derived from Møller-Plesset (MP2/MP3) calculations at the 6-31(*)/3-21G(*) level. The new parameters were applied to the 1,2-dimethyl-1,2-disilacyclohexane system and those results are also reported.
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  • 164
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    Journal of Computational Chemistry 10 (1989), S. 136-136 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 165
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    Journal of Computational Chemistry 10 (1989), S. 118-135 
    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 theory of atoms in molecules defines an unambiguous partitioning of the three-dimensional electron density into atomic basins based on the zero-flux surfaces of the gradient of the electron density, ∇(r). Integrations of the electron density within such basins yield integrated Bader populations (IBP) that have a rigorous foundation in quantum mechanics. In the density integration technique based on the two-dimensional electron density projection function, P(x,z), integrated projection populations (IPP) are obtained by integration within regions demarked by steepest descent lines Dp of P(x,z). These density integration techniques are compared by an analysis of the electron density of diatomic molecules that is based on the properties of the zero-flux surface that partitions the electron density between the atoms. The conventional method for the partitioning of regions of P(x,z) approximates the virial partitioning. Differences between IPP and IBP can be quantitatively described by two terms. One term reflects the error intrinsic to projection populations as a result of the loss of all information about the electron distribution in the third dimension in the calculation of P(x,z). The second term accounts for the effects of the displacement of the demarcation lines Dp toward the less polarizable atom compared with the cross-section of the density with the plane of projection, Dd. The analysis suggests the definition of a projection population IPP2 that is based on the cross-section Dd instead of the demarcation lines Dp. Relations between the populations IPP, IPP2, and IBP are derived for diatomic molecules and numerical results are presented for a series of diatomic molecules. Several polyatomic anions are also discussed. The values of IPP are found to be good approximations of IBP in highly polar diatomic molecules. In cases where the bonding involves comparatively little intramolecular charge transfer IPP2 is the better and equally satisfactory projection population. In the intermediate semipolar bonding situations projection populations provide qualitatively correct descriptions of the charge distributions but the numerical agreement with the IBP values is less satisfactory.
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  • 166
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    Journal of Computational Chemistry 10 (1989), S. 344-345 
    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 self-consistent field (SCF) calculations the construction of the Fock matrix is most time-consuming step. The Fock matrix construction may formally be seen as a matrix-vector multiplication, where the matrix is the supermatrix,Pijkl, and the vector is the first-order density matrix, γij. This formalism should be optimal for vector machines. This is not, however, fully utilized in most programs running on computers with small core memory. The size of the P matrix, typically in the order of 106-108 elements, has forced programmers to implement other nonvectorizable methods. We will present a submatrixbased algorithm which will partition the supermatrix so that vectorizable methods can be employed. The method will also reduce the input/output.
    Additional Material: 2 Ill.
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  • 167
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    Journal of Computational Chemistry 10 (1989), S. 358-366 
    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 problem of the computation of the matrix elements \documentclass{article}\pagestyle{empty}\begin{document}$$ I(v,v';k) = \int_0^x {\Psi _v (r)(r - r_e )} ^k \Psi _{v'} (r)dr, $$\end{document} is considered when Ψv(r) and Ψv(r) are eigenfunctions related to a diatomic potential of the RKR type (defined by the coordinates of its turning points Pi with polynomial interpolations). The eigenfunction Ψ(r) is computed by the canonical functions method making use of the abscissas ri of Pi uniquely. This limited number of points allows the storage of ψv(ri) for all the required levels v, and reduces greatly the computational effort when v, ν′, and k are varying. The present method maintains all the advantages of a highly accurate numerical method (even for levels near the dissociation), and reduces greatly the computing time. Furthermore, it is shown that it may be extended to analytical potentials like Morse and Lennard-Jones functions, to vibrational-rotational eigenfunctions and to matrix elements between eigenfunctions related to two different potentials. Numerical applications are presented and discussed.
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  • 168
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    Journal of Computational Chemistry 10 (1989), S. 380-385 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Prolog is applied to calculate the zero- through the sixth-order molecular connectivity indexes. A description of the program is given. Enumeration of substructure fragments, which is the most time-consuming part for this calculation, can be executed quite compactly by Prolog. For this execution, molecular structures and substructures are represented by Prolog facts and rules. An example of calculation is presented for a polycyclic structure. In addition, the method to increase the calculation speed is demonstrated.
    Additional Material: 6 Ill.
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  • 169
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    Journal of Computational Chemistry 10 (1989), S. 495-502 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Basis sets ranging in size from (16, 10, 7) to (20, 14, 11) have been derived for the atoms Y-Cd. Separate sets represent the energy optimized wave functions for each of the s2dn, s1dn+1, and s0dn+2 configurations. The energies from the largest sets are within 3 mhartrees of the values obtained in numerical Hartree-Fock calculations. Reasonable Hartree-Fock s2dn- s1dn+1 and s2dn- s0dn+2 excitation energies may be obtained either using the largest basis sets, or using d-orbitals optimized for the s0dn+2 configurations. The basis sets are slightly unbalanced in favor of the s-functions and in disfavor of the d-functions, but various alternative basis sets may be derived by combining parts of the five parent sets. The convergence of radial expectation values is discussed.
    Additional Material: 8 Tab.
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  • 170
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    Journal of Computational Chemistry 10 (1989), S. 529-551 
    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 method for fitting a smooth ribbon representation of DNA structures is proposed. Following a review of the relevant definitions for classical linear helical DNA and generalizations to curving helices, a parameterization of smooth ribbons is given, which leads to tractable expressions. In addition it suggests a new way to define twist, tilt, and roll for a base step that is free of the ambiguities caused by noncommutativity of finite rotations. A least squares fitting criterion for ribbons is then proposed. In some cases the optimal ribbon with respect to this criterion is not unique. This problem is analyzed, and the circumstances in which it can occur are specified. To resolve the nonuniqueness problem, a variational description of the optimal ribbon is proposed, namely the ribbon of lowest elastic energy achieving a specified level of fit with respect to the least squares criterion. The appropriate level of fit is decided using distances of backbone atoms from fitted ribbon axes. Theoretical tests of the fitting methodology are presented, and as a sample application a smooth ribbon is fit to an existing experimental structure.
    Additional Material: 11 Ill.
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  • 171
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An SCF calculation has been performed on C63H113N11O12, a derivative of the immuno-suppressive drug cyclosporin, using a 3-21G basis set and a Direct SCF method. A distributed multipole analysis has been performed on the resulting charge density to give a set of multipoles at each atomic site, which are used to calculate the electrostatic potential around the molecule. The potential maxima and minima on the accessible surface of the molecule are compared with those predicted using the corresponding Mulliken charges, and also using a potential-derived point-charge model based on the force-field of Kollman et al. The Mulliken charges give a misleading picture of the electrostatic potential around this peptide. The potential-derived charges give results which are in far better agreement with the ab initio distributed multipole model, despite being derived from calculations on smaller molecules with different basis sets and geometries. The limitations of point-charge models for describing the electrostatic interactions of polypeptides are discussed.
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  • 172
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    Journal of Computational Chemistry 10 (1989), S. 17-34 
    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 procedure for deorthogonalization (D) of atomic orbitals in the semiempirical CNDO approach is reviewed. For comparative studies, CNDO/2, CNDO/2D, and STO-3G calculations of molecular dipole moments and Mulliken populations are carried out on 35 prototype molecules containing H, C, N, O, and F atoms. The calculated values are assessed on the basis of how well they agree with experimental trends, chemical bonding theories, and ab initio molecular orbital (MO) values. Results of analyses indicate that the CNDO/2D values for dipole moments are in reasonable agreement with experimental values, and those for net atomic charges and electron populations bear greater resemblance to the ab initio (STO-3G and 6-31G**) values than the original CNDO/2 values. These findings, together with those of previous investigators, demonstrate unequivocally the advantages of incorporating deorthogonalization into routine CNDO/2 or INDO calculations as a means to obtain reasonable estimates of charge distributions.
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  • 173
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    Journal of Computational Chemistry 10 (1989), S. 63-76 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Matrix elements for the first and second derivatives of the internal coordinates with respect to Cartesian coordinates are reported for stretching, linear, nonlinear, and out-of-plane bending and torsional motion. Derivatives of the energy with respect to the Cartesian coordinates are calculated with the chain rule. Derivatives of the energy with respect to the internal coordinates are straightforward, but the calculation of the derivatives of the internal coordinates with respect to the Cartesian coordinates can be simplified by the following two steps outlined in this article. First, the number of terms in the analytical functions can be reduced or will vanish when the derivatives of the bond length, bond angle, and torsion angle are reported in a local coordinate system in which one bond lies on an axis and an adjacent bond lies in the plane of two axes or is projected onto perpendicular planes for linear and out-of-plane bending motion. Second, a simple rotation transforms these derivatives to the appropriate orientation in the space-fixed molecular coordinate system. Functions of the internal coordinates are invariant with respect to translation and rotation. The translational invariance and the symmetry of the second derivatives for a system with L atoms are used to select L-1- and L(L-1)/2-independent first and second derivatives, respectively, of which approximately half of the latter vanish in the local coordinate system. The rotational invariance permits the transformation of the simplified derivatives in the local coordinate system to any orientation in space. The approach outlined in this article simplifies the formulas by expressing them in a local coordinate system, identifies the most convenient independent elements to compute, from which the dependent ones are calculated, and defines a transformation to the space-fixed molecular coordinate system.
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  • 174
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    Journal of Computational Chemistry 10 (1989), S. 77-93 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Radial dielectric constant (permittivity) functions for ionic solute, polar solvent systems of the type obtainable from the Lorentz-Debye continuum field formulations are reexamined. Major interest is focused on the assumptions underlying these formulations and their expression in limiting field behavior. The analysis is extended to dipolar solutes and the importance of two types of corrections are evaluated. The first draws connections with the concept of the reaction field as employed by Onsager. This correction is shown to be significant as regards range of predicted saturation effects and for dipole moment self-consistency, for the same type molecule serving as solute and solvent. The second type correction involves the phenomenon of electrostriction whose effects appear much more limited both in range and on the intensity of the fields necessary for its observation. Application of the permittivity functions developed to compute modified Born model hydration energies for a variety of ions is illustrated. Excellent asymptotic approximations for all radial permittivity equations of interest are also presented which should enhance their future utility.
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  • 175
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    Journal of Computational Chemistry 10 (1989), S. 104-111 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Three improvements on the direct self-consistent field method are proposed and tested which together increase CPU-efficiency by about 50%: (i) selective storage of costly integral batches; (ii) improved integral bond for prescreening; (iii) decomposition of the current density matrix into a linear combination of previous density matrices - for which the two-electron contributions to the Fock matrix are available - and a remainder ΔD, which is minimized; construction of the current Fock matrix only requires processing of the small ΔD which enhances prescreening.
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  • 176
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    Journal of Computational Chemistry 10 (1989), S. 137-137 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 177
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    Journal of Computational Chemistry 10 (1989) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 178
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    Journal of Computational Chemistry 10 (1989), S. 488-494 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Monte Carlo simulations have been performed to study the conformations of the pentapeptide fragments of normal adult (Thr-Pro-Glu-Glu-Lys) and sickle-like anemia hemoglobin (Thr-Pro-Val-Glu-Lys). The results show that the energy optimized conformation of normal adult hemoglobin-fragment agrees with the X-ray experiment and the theoretically determined conformation of the sickle-like anemia hemoglobin-fragment is identical with the conformation of the normal adult hemoglobin-fragment.
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  • 179
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    Journal of Computational Chemistry 10 (1989), S. 520-528 
    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 method for calculating the number of rotamers of a linear alkane and of the number of rotamers with a given number of gauche conformations along the chain as a function of the total number of atoms in the chain, using general equations, is presented. A graphical method for generating individual rotamers was applied to the homologs up to decane, which has 1134 rotamers. The steric energies calculated by molecular mechanics (MM2 force field) were used as measures of the heat of formation for the coiled conformations relative to the anti conformer for each molecule, whereas the statistical entropy differences were calculated for classes of coiled rotamers grouped by the number of gauche bonds and steric energy. The free energy values calculated from these components show that already at 400 K hexane exists preferentially in conformations containing gauche bonds. For larger chains the free energy advantage for the coiled chains increases very steeply. The implications for the question of reactions of linear alkanes occurring on the surface or inside the channels of small- and medium-pore zeolites are briefly examined.
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  • 180
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The gas-phase analogs of the classical SN1 and SN2 reactions of nucleophiles with a series of protonated oxiranes bearing the substituents CN, Cl, Me, and Ph were studied using MNDO semiempirical molecular orbital theory. The transition states for nucleophilic attack on the intact rings are calculated to become progressively more “SN1-like,” as the ability of the substituent group to stabilize the corresponding ring opened carbenium ion increases. At the same time the activation barriers become progressively smaller and their relative values for different nucleophiles approach the order expected on the basis of a purely electrostatic attraction between the reacting moieties. Exactly the opposite trends are calculated for the transition states for nucleophilic attack on the intermediate carbenium ions. As the stabilities of the latter increase the extent of bond formation, and transfer of charge to the incoming nucleophile also increase. Here, the relative barriers for attack by different nucleophiles approach the order expected on the basis of a superposition of both covalent and electrostatic interactions in which the former dominate. These results support a previously suggested rationalization for the enhanced reactivities of certain alkylating agents towards the exocyclic oxygen atoms, rather than the ring nitrogens, of the nucleic acid bases. They also suggest a new explanation for the tendencies of aralkylating electrophiles to modify the exocyclic amino groups of the nucleic acid bases: sites which are unreactive towards simple alkylating agents.
    Additional Material: 7 Ill.
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  • 181
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    Journal of Computational Chemistry 10 (1989), S. 616-627 
    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 simple computational method for the evaluation of solute-solvent dispersion energy contributions in dilute isotropic solutions, supplementing the method with an analysis of its sensitivity with respect to several parameters (or features of the solvation model) which are left free in the general formulation. The method is a natural complement of the electrostatic solvation procedure described in preceding articles.
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  • 182
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    Journal of Computational Chemistry 10 (1989), S. 683-697 
    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 algorithm for obtaining the matching polynomial of an arbitrary catacondensed unbranched benzenoid molecule is presented. It is based on multiplication of only three 5 x 5 transfer matrices I, J, K, and an appropriate terminal vector. The choice of the matrices is dictated by the history of the growth of the hexagonal “animals” (i.e., by the pattern of the successive fusions of the benzene rings). The approach also gives the number of Kekule valance structures, the count of conjugated circuits, the values of the topological index Z, and the characteristic polynomials.
    Additional Material: 7 Ill.
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  • 183
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    Journal of Computational Chemistry 10 (1989), S. 698-710 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Computational algorithms are described which provide for constructing the set of associated edge-weighted directed graphs such that the average of the characteristic polynomials of the edge-weighted graphs gives the matching polynomial of the parent graph. The weights were chosen to be unities or purely imaginary numbers so that the adjacency matrix is hermitian. The computer code developed earlier by one of the authors (K.B.) is generalized for complex hermitian matrices. Applications to bridged and spirographs, some lattices and all polycyclic graphs containing up to four cycles are considered.
    Additional Material: 5 Ill.
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  • 184
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    Journal of Computational Chemistry 10 (1989), S. 718-732 
    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 enantioselective binding of optical analytes on chiral stationary phases used in column chromatography is investigated with molecular modeling techniques. By rolling the analytes over the van der Waals surface of the phase, configurations are sampled and free energies of transient diastereomeric complexes are computed. These free energies allow us to compute chromatographic separability factors and a linear relationship between computed and observed values is found. The intermolecular potential energy surfaces of these diastereomeric complexes are flat with gentle rolling hills and multiple minima. The binding sites are ill-defined and the analytes are found to freely slide over the chiral stationary phases. An energy partitioning algorithm is used to determine how much of the total binding energy is attributable to a given molecular fragment on the phase. It is found that the fragments of the phase bearing the stereogenic carbons are the least cognizant of differences between optical antipodes.
    Additional Material: 3 Ill.
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  • 185
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    Journal of Computational Chemistry 10 (1989), S. 753-769 
    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 well-tempered Gaussian basis sets (14s 10p) for atoms from lithium to neon were contracted and used in restricted Hartree-Fock calculations on 13 systems: Li2(Σ), B2(Σ), C2(Σ), N2(Σ), O2(Σ), F2(Σ), Ne2(Σ), LiF(Σ), BeO(Σ), BF(Σ), CN-(Σ), CO(Σ), and NO+(Σ). Spectroscopic constants (Re, ωe, ωexe, Be, αe, and ke) and one-electron properties (dipole, quadrupole, and octupole moments at the center of mass and electric field, electric field gradient, potential, and electron density at the nuclei) were evaluated and compared with the Hartree-Fock results. The largest contracted basis set (7s6p3d) gives results very close to the Hartree-Fock values; the remaining differences are attributed to the absence of the f functions in the present basis sets. For Ne2, the interaction energy was calculated; the magnitude of the basis-set superposition error was found to be very small (less than 3 μEh at 2.8 a0 and less than 2 μEh at 5.0 a0).
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  • 186
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    Journal of Computational Chemistry 10 (1989), S. 817-831 
    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 procedure that generates random conformations of a protein chain, and then applies energy minimization to find the structure of lowest energy, is described. Single-residue conformations are represented in terms of four conformational states, α, ∊, α*, and ∊*. Each state corresponds to a rectangular region in the φ, ψ map. The conformation of an entire chain is then represented by a sequence of single-residue conformational states. The distinct “chain-states” in this representation correspond to multidimensional rectangular regions in the conformational space of the whole protein. A set of highly-probable chain-states can be predicted from the amino acid sequence using the pattern recognition procedure developed in the first two articles of this series. The importance-sampling minimization procedure of the present article is then used to explore the regions of conformational space corresponding to each of these chain-states. The importance-sampling procedure generates a number of random conformations within a particular multidimensional rectangular region, sampling most densely from the most probable, or “important,” sections of the φ, ψ map. All values of φ and ψ are allowed, but the less-probable values are sampled less often. To achieve this, the random values of φ and Φ are generated from bivariate gaussian distributions that are determined from known X-ray structures. Separate gaussian distributions are used for proline residues in the α and ∊ states, for glycine residues in the α, ∊, α*, and ∊* states, and for ordinary residues involved in 29 different tripeptide conformations. Energy minimization is then applied to the randomly-generated structures to optimize interactions and to improve packing. The final energy values are used to select the best structures. The importance-sampling minimization procedure is tested on the avian pancreatic polypeptide, using chain-states predicted from the amino acid sequence. The conformation having the lowest energy is very similar to the X-ray conformation.
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  • 187
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    Journal of Computational Chemistry 10 (1989), S. 832-849 
    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 geometries, relative conformational energies, and dipole moments of mono and polychlorosilanes have been calculated using ab initio molecular orbital (MO) theory. Calculations at the HF/3-21G(*) level, with the exception of dipole moments, give reasonable agreement with experimental data. A new MM2 force field for chlorosilanes, which includes terms for bond length shortening and bond angle compression due to the attachment of electronegative Cl atoms, has been developed on the basis of experimental and ab initio results. The new force field is generally successful in predicting structural parameters, but is unable to reproduce the dipole moments of several model systems. While dipole moment predictions are not the authors' main interest, this failure defines a shortcoming in the MM2 method. The new parameters have been applied to problems in the prediction of stereochemistries of cyclic systems, and compared with experimental results where data are available.
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  • 188
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    Journal of Computational Chemistry 10 (1989), S. 869-874 
    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 a previous article (J. Fernández Rico, R. López and G. Ramírez, J. Comp. Chem., 9, 790 (1988)) we have proposed the calculation of molecular integrals involving STOs by means of some recurrence relations which use two sets (h and H) of overlap integrals (basic matrices). In the present paper, we derive explicit expressions of these integrals employing the two-range expansion of the 0s-function. This approach yields equations for the elements of the two basic matrices in terms of two further matrices, k(x,y) and i(x,y), and some auxiliary functions. Relations between the elements of these matrices and the functions are thoroughly explored and numerical tests are included for illustrating the behavior of the method.
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    Journal of Computational Chemistry 10 (1989), S. 896-902 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: There are many methods in the literature for calculating conformations of a molecule subject to geometric constraints, such as those derived from two-dimensional NMR experiments. One of the most general ones is the EMBED algorithm, based on distance geometry, where all constraints except chirality are converted into upper and lower bounds on interatomic distances. Here we propose a variation on this where the molecule is assumed to have fixed bond lengths, vicinal bond angles and chiral centers; and these holonomic constraints are enforced separately from the experimental constraints by being built into the mathematical structure of the problem. The advantages of this approach are: (1) for molecules having large rigid groups of atoms, there are substantially fewer variables in the problem than all the atomic coordinates; (2) rigid groups achieve in the end more accurate local geometry (e.g., planar aromatic rings are truly planar, chiral centers always have their correct absolute chirality); (3) it is easier to detect inconsistencies between the holonomic and the experimental constraints; and (4) when generating a random sampling of conformers consistent with all constraints, the probability of achieving satisfactory structures tends to be greater.
    Additional Material: 1 Ill.
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  • 190
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    Journal of Computational Chemistry 10 (1989), S. 163-175 
    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 potential energy surfaces for the proton transfer processes in H+(H2O)n with n=2 ∼ 11 have been studied using the semiempirical AM1 method. Two model systems were adopted: branched and linear systems. The branched system showed a tendency to form a bulk cluster, while the linear system showed a tendency toward a constant barrier height with increasing number of water molecules in the model system. The potential energy surfaces were discussed using Marcus theory. In the case of H+ (H2O)n with n=10 and 11, the intrinsic barrier to the proton transfer was found to be around 1.0 kcal/mol.
    Additional Material: 10 Ill.
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  • 191
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    Journal of Computational Chemistry 10 (1989) 
    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
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  • 192
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    Journal of Computational Chemistry 10 (1989), S. 287-294 
    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 method presented earlier [T. Kikuchi, G. Némethy, and H.A. Scheraga, (1986) J. Comput. Chem. 7, 67] for the classification of patterns of the three-dimensional folding of a covalently crosslinked polypeptide chain has been extended to nonplanar proteins. The procedure described earlier was applicable only to proteins termed planar, i.e., with a connexity of the crosslinks (e.g., disulfide bonds) that can be represented in a planar diagram. The procedure described in the present work is applicable to any (planar or nonplanar) pattern of crosslinking. The classification is based on a systematic and objective method of enumeration of spatial geometric arrangements of loops (SGAL) using no information other than the location of the disulfide bonds in the amino acid sequence. Various SGAL classes correspond to the presence of different ways of mutual penetration of loops, called thrustings and entanglements. Information on SGAL classes can be of use in structural predictions of folding patterns of proteins.
    Additional Material: 5 Ill.
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  • 193
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    Journal of Computational Chemistry 10 (1989), S. 1-13 
    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 computer code and nonnumerical algorithm are developed to construct the edge group of a graph and to enumerate the edge colorings of graphs of chemical interest. The edge colorings of graphs have many applications in nuclear magnetic resonance (NMR), multiple quantum NMR, enumeration of structural isomers of unsaturated organic compounds, and in the construction of configurational integral expansion series in statistical mechanics. The code developed is applied to many NMR graphs, complete graphs containing up to 10 vertices, and the Petersen graph.
    Additional Material: 9 Ill.
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  • 194
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    Journal of Computational Chemistry 10 (1989), S. 14-16 
    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 report the geometry-optimized total energies and bond distances for the closo-carborane isomers 3,5-C2B6H8, 1,7-C2B7H9, and 1,2-C2B7H9 calculated by the ab initio SCF MO method using the STO-3G basis set. Relative energies are compared with those of the other carborane isomers in the 8- and 9- atom classes. These results complete the set of calculations at the same level of theory for all deltahedral carborane isomers except for those of the 11-atom class.
    Additional Material: 4 Tab.
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  • 195
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular recognition in Rebek's cleft was studied with the MM2 force field. A new computational protocol was used to determine the free energies of substrate binding to this topologically unique model receptor. The energies and structural features of substrate-receptor complexes reveal that molecular recognition involves ammonium ion binding to the interior of the cleft and aromatic π-stacking on the exterior of the cleft.
    Additional Material: 6 Ill.
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  • 196
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    Journal of Computational Chemistry 10 (1989), S. 603-615 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Hartree-Fock 6-31G(d) structures for the neutral, positive ion, and negative ion bimolecular complexes of NH3 with the first- and second-row hydrides AHn (AHn = NH3, OH2, FH, PH3, SH2, and ClH) have been determined. All of the stable neutral complexes except (NH3)2, the positive ion complexes with NH3 as the proton acceptor, and the negative ion complexes containing first-row anions exhibit conventional hydrogen bonded structures with essentially linear hydrogen bonds and directed lone pairs of electrons. The positive ion complex NH4+ … OH2 has the dipole moment vector of H2O instead of a lone pair directed along the intermolecular line, while the complexes of NH4+ with SH2, FH, and ClH have structures intermediate between the lone-pair directed and dipole directed forms. The negative ion complexes containing second-row anions have nonlinear hydrogen bonds. The addition of diffuse functions on nonhydrogen atoms to the valence double-split plus polarization 6-31G(d,p) basis set usually decreases the computed stabilization energies of these complexes. Splitting d polarization functions usually destabilizes these complexes, whereas splitting p polarization functions either has no effect or leads to stabilization. The overall effect of augmenting the 6-31G(d,p) basis set with diffuse functions on nonhydrogen atoms and two sets of polarization functions is to lower computed stabilization energies. Electron correlation stabilizes all of these complexes. The second-order Møller-Plesset correlation term is the largest term and always has a stabilizing effect, whereas the third and fourth-order terms are smaller and often of opposite sign. The recommended level of theory for computing the stabilization energies of these complexes is MP2/6-31+G(2d,2p), although MP2/6-31+G(d,p) is appropriate for the negative ion complexes.
    Additional Material: 3 Ill.
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  • 197
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    Journal of Computational Chemistry 10 (1989), S. 635-647 
    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 molecular mechanics calculations reported earlier for nitrogen heterocycles have now been extended to include the title compounds, and related molecules. It is in general possible to calculate these structures with an accuracy that compares favorably with experiment.
    Additional Material: 2 Ill.
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  • 198
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    Journal of Computational Chemistry 10 (1989), S. 673-682 
    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 and accurate method for calculating the geometrically allowed modes of binding of a ligand molecule to a Voronoi site model is reported. It is shown that the feasibility of the binding of a group of atoms to a Voronoi site reduces to a simple set of linear and quadratic inequalities and quadratic equalities which can be solved by minimization of a simple function. Newton's numerical method of solution coupled to a line search proved to be successful. Moreover, we have developed efficient molecular and site data bases to discard quickly infeasible binding modes without time-consuming numerical calculation. The method is tested with a data set consisting of the binding constants for a series of biphenyls binding to prealbumin. After determination of the conformation space of the molecules and proposal of a Voronoi site geometry, the geometrically feasible modes are calculated and the energy interaction parameters determined to fit the observed binding energies to the site within experimental error ranges. We actually allowed these ranges to vary in order to study the influence of their broadness on the site geometry and found that as they increase, one can first model the receptor as a three-region site then as a single region site, but never as a two-region site.
    Additional Material: 4 Ill.
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  • 199
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    Journal of Computational Chemistry 10 (1989), S. 417-425 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Algorithms and codes based on the method of Schur functions and Frobenius' theorem are used to generate the character tables of the symmetric groups (Sn) containing n! elements. The codes developed can generate characters of Sn up to n = 20.
    Additional Material: 5 Tab.
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  • 200
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 426-433 
    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 annular tautomerism of 1,2,3-triazole and 3(5)-methylpyrazole is discussed by means of a combination of theoretical calculations and experimental (ICR) gas-phase basicities and acidities. In the gas phase 1,2,3-triazole exists as the 2H-tautomer, whereas both tautomers of 3(5)-methylpyrazole are of similar energy. The solvent effects on these prototropic equilibria are discussed taking into account solvent properties as polarity/polarizability, acidity, and basicity. In nonhydrogen bonding solvents, the difference in dipole moments between both tautomers plays a role that has usually been underestimated.
    Additional Material: 2 Ill.
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