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  • Articles: DFG German National Licenses  (1,156)
  • 1985-1989  (1,156)
  • Physical Chemistry  (627)
  • Biochemistry  (529)
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  • Articles: DFG German National Licenses  (1,156)
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Year
  • 101
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 21 (1989), S. 375-386 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Kinetic studies of the transfer of hydrogen from 9,10-dihydrophenanthrene to anthracene were done at 350°C in the liquid phase. Principal products were phenanthrene and 9,10-dihydroanthracene. Autocatalysis occurred at low extents of reaction, where H-transfer from 9,10-dihydroanthracene to anthracene caused an increase in free radical concentrations. At higher extents of reaction, 9,10-dihydroanthracene inhibited rates by diverting intermediate 9-hydrophenanthryl radicals back to reactants. A quantitative kinetic model based on literature rate and thermodynamic data fits the observations well. A key net reaction is the transfer of an H-atom from a radical (9-hydrophenanthryl) to a molecule (anthracene). It is shown that this process does not involve a free H-atom intermediate. The derived rate constant for this exothermic process (7.5 × 103 M-1 s-1) is considerably greater than that for the related, but thermoneutral H-transfer between anthracene moieties (120 M-1 s-1).
    Additional Material: 2 Ill.
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  • 102
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    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 21 (1989), S. 431-437 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Rates of reaction for the alkaline hydrolysis of various hydroxamic acids in the presence of cetyltrimethylammonium bromide have been determined. Empirical reaction orders of zero, one-half, and one were found for the hydroxamic acids depending upon reaction conditions and substrate structure. N-methylhydroxamic acids exhibited only first-order kinetics. The results are consistent with the Michaelis-Menten rate equation.
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  • 103
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    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 21 (1989), S. 465-476 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Pyrogallol (1,2.3-benzentriol, 1) reacts with dioxygen in weakly alkaline solutions to form purpurogallin (2,3,4,6-tetrahydroxy-5H-benzocycloheptene-5-one, 2) which then reacts to form purpurogalloquinone (3) which then decays to a product absorbing at 440 nm. The formation of 3 requires 1.5 mol O2 per mol 1, and 1.0 mol per mol 2. No O2 is consumed during the decay of 3, and this reaction, being insensitive to O2 concentrations and the presence of both superoxide dismutase (SOD) and catalase, does not appear to be an oxidation. The first-order rate of decay of 3 decreases with increasing pH. 1 and 3 react at pH 9.0 with a second-order rate constant of ca. 100 M-1 s-1. SOD inhibits the oxidation of 1 and 2. Slight and variable apparent inhibition of the oxidation of 2 and 3 by SOD may be due to trace impurities in 2, but not contamination by 1. The peak concentration of 3 is attained more rapidly during the oxidation of 1 than during the oxidation of 2. A kinetic scheme based on parallel oxidation of 1 by dioxygen and superoxide, and it which the semiquinone of 1 oxidizes 2, is partially successful in simulating the observed kinetic behavior.
    Additional Material: 7 Ill.
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  • 104
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    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.
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  • 105
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 106
    Electronic Resource
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    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 107
    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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  • 108
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    New York, NY [u.a.] : Wiley-Blackwell
    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.
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  • 109
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 748-748 
    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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  • 110
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 798-816 
    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 finds the most probable conformational states of a protein chain is described. Single-residue conformations are represented in terms of four conformational states, α, ∊, α*, and ∊*. The conformation of the entire chain is represented by a sequence of single-residue conformational states; the distinct conformations in this representation are called “chain-states.” The first article in this series described a procedure that computes tripeptide conformational probabilities from the amino acid sequence using pattern recognition techniques. The procedure described in this article uses the tripeptide probabilities to estimate the probabilities of the chain-states. The chain-state probability estimator is a product of conditional and marginal probabilities (obtained from the tripeptide probabilities), with a penalty factor to eliminate conformations containing α-helices and ∊-strands of excessive length. The probability estimator considers short-range conformational information, medium-range sequence information and some simple long-range information (through the restrictions on helix and strand lengths). Energy minimization calculations can be carried out in the region of conformational space corresponding to a particular chain-state. By selecting the most probable chain-states, the search can be focused on the most probable, or “important,” regions of the conformational space. These energy calculations are described in the third article of the series. The complete procedure described by the three articles is called PRISM, for pattern recognition-based importance sampling minimization.
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  • 111
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    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 112
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    Journal of Computational Chemistry 10 (1989), S. 856-860 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Formulas are derived for analytical first and second energy derivatives with respect to nuclear coordinates in molecular mechanics force fields employing lone-pair pseudoatoms. These derivatives may further be used for the calculation of normal modes and vibrational frequencies while properly accounting for the presence of pseudoatoms. The equations are applied using the MM2 force field to calculate the vibrational spectrum of methanol to illustrate the applicability of the method. The results are compared to both experiment and a numerical approximation in which small masses are assigned to the lone-pair pseudoatoms.
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  • 113
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 887-895 
    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 equation is formulated on the basis of theoretical INDO/FPT calculations which describes the angular dependence of the propanic long-range coupling constant 4JMeH in substituted HCCCH3 fragments. This equation is a truncated Fourier series in the torsion angle φ, HCCMe, which takes into account the dependence of the Fourier coefficients on the bond angle θ, CCMe. The substituent effects are assumed to be additive. Some parameters in the equation may be obtained from the 4JMeH couplings in propane and neopentane derivatives. The calculated effect upon 4JMeH of changes in the bond angle θ is significant and it seems to be in part the cause of some effects which have been attributed to conformational dependence.
    Additional Material: 3 Ill.
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  • 114
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    Journal of Computational Chemistry 10 (1989), S. 911-920 
    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 conformations of various cyclic peroxides have been determined using a molecular mechanics force field developed by the authors and previously applied to linear peroxides. Comparison of the results with those of experimental and ab initio studies shows that this force field may be employed without correction for cyclic compounds.
    Additional Material: 5 Ill.
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  • 115
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 928-934 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article shows that with our Hylleras-functional based method1 for generating correlation orbitals, we can determine electronic structures for small polyatomic systems very accurately. The procedure is ab initio, uses conventional Gaussian basis sets, and solves the electronic Schrödinger equation with the coupled cluster method. A comparison is made with MRCI results obtained in equivalent basis sets for the HF, H2O, and NH3 molecules.
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  • 116
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    New York, NY [u.a.] : Wiley-Blackwell
    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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  • 117
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 939-950 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Several improvements have been made to the gradient algorithms commonly used to optimize equilibrium and transition-state geometries at the semiempirical level. A gradient algorithm derived from a combination of a variable metric method (Davidon-Fletcher-Powell/Broyden-Fletcher-Goldfarb-Shanno) and Pulay's direct inversion in the iterative subspace method for geometry optimization (GDIIS) is compared with the variable metric method combined with an accurate linear search algorithm. The latter method is used routinely in the standard semiempirical program packages, MNDO, MOPAC, and AMPAC. The combined variable metric and GDIIS algorithm is also compared with GDIIS which uses a static metric. The performance of these algorithms is examined for a wide range of systems with respect to both choice of coordinate system (for cyclic molecules) and guess for the initial Hessian. The results show that the GDIIS method is up to ca. 40% more efficient than the variable metric combined with accurate line search algorithm: however, the exact savings vary depending on the coordinate system and initial Hessian. For noncyclic systems, variable-metric GDIIS is usually equal or superior to static-metric GDIIS, and consistently performs ca. 30% more efficiently than the variable metric combined with accurate line search algorithm. For the optimization of cyclic molecules, an improved estimate of the initial Hessian has increased the efficiency by at least a factor of two. Greater efficiencies (usually 〉40%) are also obtained when static-metric GDIIS is used to refine the geometry after the initial application of a transition-state search based on the variable metric combined with line search algorithm. On the basis of these results, we recommend several changes to the algorithms as currently implemented in the standard semiempirical program packages.
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  • 118
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    Journal of Computational Chemistry 10 (1989), S. 957-962 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article the matrix elements can be grouped into classes by means of the molecular symmetry. By introducing the concepts of symmetry-matrix and symmetry-supermatrix and determining their operation rules, the storage of the supermatrix can be asymptotically reduced by a factor of ca. g2 (g is the order of the molecular symmetry group) and the calculation of Fock matrix during each SCF cycle can be reduced proportionally. Besides, by using the DIIS method combined with the symmetry-matrices, the convergence behavior for highly symmetric molecules can be improved.
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  • 119
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    Journal of Computational Chemistry 10 (1989), S. 975-981 
    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 potent neuromuscular blocker, gallamine, possesses three chemically equivalent, flexible side chains, the motion of which has been proposed as important in its mode of action on the acetylcholine receptor in vivo. The flexibility of the side chains has been investigated in the present initial study by a combination of quantum mechanics and molecular dynamics on the isolated, unsolvated molecule. Net atomic charges for the gallamine molecule have been calculated using the semiempirical program MOPAC for use in the molecular dynamics simulation. The flexibility of the side chains has been shown to correlate with the range of fluctuations in torsion angles observed in the crystal structure of gallamine.
    Additional Material: 4 Ill.
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  • 120
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    Journal of Computational Chemistry 10 (1989), S. 982-1012 
    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 molecular mechanics force field implemented in the Sybyl program is described along with a statistical evaluation of its efficiency on a variety of compounds by analysis of internal coordinates and thermodynamic barriers. The goal of the force field is to provide good quality geometries and relative energies for a large variety of organic molecules by energy minimization. Performance in protein modeling was tested by minimizations starting from crystallographic coordinates for three cyclic hexapeptides in the crystal lattice with rms movements of 0.019 angstroms, 2.06 degrees, and 6.82 degrees for bond lengths, angles, and torsions, respectively, and an rms movement of 0.16 angstroms for heavy atoms. Isolated crambin was also analyzed with rms movements of 0.025 angstroms, 2.97 degrees, and 13.0 degrees for bond lengths, angles, and torsions respectively, and an rms movement of 0.42 angstroms for heavy atoms. Accuracy in calculating thermodynamic barriers was tested for 17 energy differences between conformers, 12 stereoisomers, and 15 torsional barriers. The rms errors were 0.8, 1.7, and 1.13 kcal/mol, respectively, for the three tests. Performance in general purpose applications was assessed by minimizing 76 diverse complex organic crystal structures, with and without randomization by coordinate truncation, with rms movements of 0.025 angstroms, 2.50 degrees, and 9.54 degrees for bond lengths, angles and torsions respectively, and an average rms movement of 0.192 angstroms for heavy atoms.
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  • 121
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    Journal of Computational Chemistry 10 (1989), S. 1031-1037 
    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 continuum and a discrete-continuum models are used to determine the solvation energies of FCH2COO-, FCH2COOH, and F2CHCOO-. For the anions, the continuum model provides results closer to the experiment, while for the acid, the addition of one water molecule improves the continuum-only energy.
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  • 122
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    International Journal of Chemical Kinetics 21 (1989), S. 1-20 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A method is described for the measurement of relative rate constants for abstraction of hydrogen from ethylene at temperatures in the region of 750 K. The method is based on the effect of the addition of small quantities of propane and isobutane on the rates of formation of products in the thermal chain reactions of ethylene. On the assumption that methane and ethane are formed by the following reactions, measurements of the ratio of the rates of formation of methane and ethane in the presence and absence of the additive gave the following results: \documentclass{article}\pagestyle{empty}\begin{document}$$\log (k_7 /k_2) = (- 0.50 \pm 0.4) + (3200 \pm 1000)/2.3T$$\end{document} \documentclass{article}\pagestyle{empty}\begin{document}$$\log (k_8 /k_3) = (- 0.20 \pm 0.4) + (2800 \pm 1000)/2.3T$$\end{document} \documentclass{article}\pagestyle{empty}\begin{document}$$\log (k_{11} /k_2) = (- 0.97 \pm 0.4) + (4600 \pm 1000)/2.3T$$\end{document} \documentclass{article}\pagestyle{empty}\begin{document}$$\log (k_{12} /k_3) = (- 2.0 \pm 0.4) + (6300 \pm 1000)/2.3T$$\end{document} Values for k2 and k3 obtained from these ratios are compared with previous measurements.
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  • 123
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    International Journal of Chemical Kinetics 21 (1989), S. 1123-1129 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using a relative rate method, rate constants for the gas-phase reactions of the OH radical with 1- and 2-propyl nitrate, 1- and 2-butyl nitrate and 1-nitrobutane have been determined in the presence of one atmosphere of air at 298 ± 2 K. Using rate constants for the reactions of the OH radical with propane and cyclohexane of 1.15 × 10-12 and 7.49 × 10-12 cm3 molecule-1 s-1, respectively, following rate constants (in units of 10-12 cm3 molecule-1 s-1) were obtained: 1-propyl nitrate, 0.62; 2-propyl nitrate, 0.41; 1-butyl nitrate, 1.78; 2-butyl nitrate, 0.93; and 1-nitrobutane, 1.35. These rate constants are compared and discussed with the literature data.
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  • 124
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    International Journal of Chemical Kinetics 21 (1989), S. 561-574 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A chemical kinetic model was constructed for the pyrolysis of butylbenzene. The mechanism was based on free radical reactions. All relevant reactions were considered, and a final selection of 60 reactions involving 29 molecules and free radicals was made. The rate constants and thermodynamic parameters were taken from the literature or estimated using accepted literature methods such as group additivity. The results from the model were compared to experimental rates and product selectivity for butylbenzene pyrolysis over a temperature range of 778 K to 868 K and to an experimental rate at 923 K. The rates agreed within a factor of two and were usually much closer. The experimental and theoretical yields of the major products, styrene, ethane, toluene, and propylene, agreed within two percentage points. The agreement for seven minor products was not quite as good, with the worst case being an overprediction of the yield of allylbenzene by a factor of 2.6.
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  • 125
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    International Journal of Chemical Kinetics 21 (1989), S. 611-619 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Rate constants have been determined for the reactions of SO4- with a series of alkanes and ethers. The SO4- radical was produced by the laser-flash photolysis of persulfate, S2O82-. For methane, only an upper limit of 1 × 106 M-1 s-1 could be determined. For ethane, propane, and 2-methylpropane, rate constants of 0.44, 4.0, and 10.5 × 107 M-1 s-1 were found. For ethyl and n-propyl ether, rate constants of 1.3 × 108 and 2.2 × 108 M-1 s-1 were found and for 1,4-dioxane and tetrahydrofuran, rate constants of 7.2 × 107 and 2.8 × 108 were obtained. The reaction of SO4- with allyl alcohol was also studied and found to have a rate constant of 1.4 × 109 M-1 s-1.
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  • 126
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    International Journal of Chemical Kinetics 21 (1989), S. 667-676 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The rate constants for the reaction of NO3· with sulfur compounds in acetonitrile have been determined by the flash photolysis method. The rate constant for dimethyl sulfone (2.7 × 104 M-1s-1 at -10°C) is larger than that of the deuterium derivative, indicating that NO3· abstracts the hydrogen atom from dimethyl sulfone. In the case of dimethyl sulfide, the rate constant was evaluated to be 1.5 × 109 M-1 s-1 at -10°C; the transient absorption band attributable to the cation radical was observed after the decay of NO3·, suggesting the electron transfer reaction from the sulfide to NO3·. For diphenyl sulfide and dimethyl disulfide, the electron transfer reactions were also confirmed. For dimethyl sulfoxide, the reaction rate constant of 1.2 × 109 M-1 s-1 (at -10°C) was not practically affected by the deuterium substitution, suggesting that NO3· adds to sulfur atom forming (CH3)2Ṡ(O)-ONO2. On the other hand, for diphenyl sulfoxide, the electron transfer reaction occurs. By the comparison of these rate constants in acetonitrile solution with the reported rate constants in the gas phase, the change of the reaction paths was revealed.
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  • 127
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    International Journal of Chemical Kinetics 21 (1989), S. 703-714 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Radical reactions involving two or more intermediates and many mutual reaction channels may lead to the specific formation of one cross-reaction product if one species is rather persistent and if transient and persistent species are produced with equal rates. A previous kinetic analysis of the phenomenon revealed that the concentrations of the intermediates and the selectivities of product formation depend critically on the relative initiation rates. The present experimental ESR studies on systems involving simultaneously generated phenoxyl radicals as persistent and alkyl radicals as transient species confirm the predicted behavior. They also lead to absolute rate constants for reactions of alkyl with phenoxyl radicals and for hydrogen atom transfer from phenols to alkyl radicals.
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  • 128
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Intermediate product of the reaction of MoOS2(S2CNR2)2 and PPh3 in dichloroethane has been detected by ESR spectroscopy. Two ESR signals have been observed at low temperature in the reaction system which was stopped by quenching it in liquid nitrogen. The g values are 2.020 ± 0.001 and 1.972 ± 0.001 respectively. The signal at g = 2.020 is attributed to a reaction intermediate with pentavalent molybdenum. A reaction mechanism has been proposed which is consistent with the observation of pentavalent molybdenum as the intermediate in the process of reaction.
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  • 129
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    International Journal of Chemical Kinetics 21 (1989), S. 21-29 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Rate constants and activation parameters of direct reaction of oxirane with certain alkyl-2-hydroxyethyl sulfides and/or successive oxyethylene adducts in the presence of basic catalyst were studied at temperatures 323-353 K. The reactions were found to be of the first order with respect to oxirane, sulfide, and catalyst concentrations. The kinetics are consistent with a termolecular mechanism.
    Additional Material: 3 Ill.
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  • 130
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    International Journal of Chemical Kinetics 21 (1989) 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 131
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    International Journal of Chemical Kinetics 21 (1989), S. 233-243 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: It is shown that kinetic data on the polymerization of acetylene to vinyl acetylene and benzene can be reconciled with the formation of a 1,4 biradical which can isomerize by a 1-3, H-atom shift to the molecular product. Since the biradicals have a negligibly small life-time in the system the overall process appears to be a concerted bimolecular reaction. The labile isomer CH2 = C: which had been suggested as being the reactive intermediate, is argued on energy considerations not to be a plausible intermediate.Data on the reverse pyrolysis of vinyl acetylene to acetylene are consistent with the model. Extending the model to butadiene explains the observed molecular nature of its decomposition to ethylene and acetylene.Reactions of other oligomers of acetylene are discussed.
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  • 132
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Studies of the kinetics of thermal unimolecular decomposition of methylcyclopentane, methylcyclohexane, ethynylcyclopentane, and ethynylcyclohexane have been carried out at temperatures in the range 861-1218 K using the technique of very low-pressure pyrolysis (VLPP). Multiple reaction pathways and secondary decomposition of primary products results in a complex array of reaction products. VLPP rate data (fall-off regime) were obtained for the overall decompositions and interpreted via the application of RRKM theory. The data for methylcyclopentane and methylcyclohexane were interpreted in terms of ring-opening bond fission pathways and bond fission to methyl and cycloalkyl radicals. By selecting Arrhenius parameters consistent with the analogous pathways in open-chain alkanes, a good fit to the overall decomposition is obtained. The data for ethynylcyclopentane and ethynylcyclohexane were interpreted in terms of ring-opening bond fission and alkyne to allene isomerization. The A factors for ring opening were based on known values for C-C fission in open-chain alkynes and the Arrhenius parameters for isomerization were chosen to be consistent with previously reported alkyne to allene isomerizations. The VLPP data are consistent with the following high-pressure rate expressions (at 〈 T 〉 = 1100 K) for the dominant primary reaction channel of ring opening adjacent to the substitutent group: \documentclass{article}\pagestyle{empty}\begin{document}$$\log (k/s^{ - 1} ) = (16.4 \pm 0.3) - (341 \pm 10)/\theta {\rm for methylcyclopentane,}$$\end{document} \documentclass{article}\pagestyle{empty}\begin{document}$$\log (k/s^{ - 1} ) = (16.4 \pm 0.3) - (345 \pm 10)/\theta {\rm for methylcyclopentane,}$$\end{document} \documentclass{article}\pagestyle{empty}\begin{document}$$\log (k/s^{ - 1} ) = (16.0 \pm 0.3) - (304 \pm 10)/\theta {\rm for ethynylcyclpentane, and}$$\end{document} \documentclass{article}\pagestyle{empty}\begin{document}$$\log (k/s^{ - 1} ) = (16.0 \pm 0.3) - (303 \pm 10)/\theta {\rm for ethynylcyclohexane,}$$\end{document} where θ = 2.303RT kJ mol-. Comparison of the activation energies for the ethynyl-cycloalkanes with those for the methyl-cycloalkanes shows that the effect of the ethynyl substituent is consistent with the propargyl resonance energy. This evidence supports the assumption of a biradical mechanism for ring opening in these cycloalkanes.
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  • 133
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    International Journal of Chemical Kinetics 21 (1989), S. 297-314 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Starting from Smoluchowski's hypothesis, a simple algorithm is developed in order to obtain the apparent rate constant at large values of time, t, with some physical and chemical processes, as in the case of diffusion controlled reactions. Some practical examples are illustrated, assuming nonuniform distribution function, space-dependent diffusion coefficient or short-range interaction leading to an asymptotic analytical expression of the form α + β/√t, where α and β are constants function of the system of interest.
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  • 134
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    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: N-chloro-3-aminopropanol was obtained in aqueous solution by mixing the amine with the hypochlorite. The first order decomposition kinetics of the N-chloramine in strongly alkaline media are explained by a mechanism in which the rate controlling step is the formation of an imine which is subsequently hydrolyzed. Spectrophotometry of the reaction in acid media showed that under these conditions dichloramines are formed: the second order experimental kinetics of this process are explained by a mechanism in which the rate-controlling step is a reaction between the protonated and free forms of the N-chloramine.
    Additional Material: 5 Ill.
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  • 135
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    International Journal of Chemical Kinetics 21 (1989), S. 367-371 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The elimination kinetics of 2-chloropropionic acid have been studied over the temperature range of 320-370.2°C and pressure range of 79-218.5 torr. The reaction in seasoned vessel and in the presence of the free radical suppressor cyclohexene, is homogeneous, unimolecular, and obeys a first-order rate law. The dehydrochlorination products are acetaldehyde and carbon monoxide. The rate coefficient is expressed by the following Arrhenius equation: log k1(s-1) = (12.53 ± 0.43) - (186.9 ± 5.1) kJ mol-1 (2.303RT)-1. The hydrogen atom of the carboxylic COOH appears to assist readily the leaving chloride ion in the transition state, suggesting an intimate ion pair mechanism operating in this reaction.
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  • 136
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    International Journal of Chemical Kinetics 21 (1989), S. 399-421 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The kinetics of oxidation of 2,2′-azinobis-(3-ethylbenzothiazole-6-sulphonate) (ABTS) by the inorganic peroxides, peroxomonosulphate, peroxodisulphate, peroxodiphosphate, and hydrogen peroxide were investigated in aqueous solution. The kinetics of formation of the radical cation, ABTS.+, on one-electron abstraction by these peroxides and the further reaction of ABTS.+ with higher concentrations of these peroxides at longer time scale were studied by following the growth and decay of the radical cation, ABTS.+ at 417 nm. The rate of formation of ABTS.+ was found to obey a total second-order, first-order each in [ABTS] and [peroxide], except for H2O2, which reacted through Michaelis-Menten kinetics. All the peroxides investigated were found to react with ABTS.+; however peroxodisulphate alone oxidized ABTS.+ to the dication (ABTS++), the other peroxides reacted via ionic mechanism, probably forming sulphoxide and sulphone as products. The kinetics of decay of the radical cation, ABTS.+, was also found to follow a total second-order, first-order each in [ABTS.+] and [peroxide], except peroxodiphosphate the reaction of which obeyed Michaelis-Menten kinetics. The effect of pH and temperature were also investigated in all the systems and the kinetic and thermodynamic parameters were evaluated and discussed with suitable reaction mechanisms.
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  • 137
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    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Rate coefficients were calculated for vibrational relaxation and collision-induced dissociation of ground state xenon fluoride in neon at temperatures between 300 and 1000 K for each of nine vibrational levels. These coefficients were calculated using a pairwise additive potential energy surface, which consists of a Morse function for the XeF interaction and Lennard-Jones functions for the NeXe and NeF interactions. Rate coefficients are provided for both temperature and v- dependences. The vibrational relaxation and dissociation processes occur by multiquanta transitions. Dissociation can take place from all v-levels provided that the internal energy of the XeF molecule is close to the rotationless dissociation limit. The order of increase effectiveness of the various forms of energy in promoting dissociation in XeF was found to be translation-rotation-vibration. At room temperature, neon atoms were found to be more efficient than helium atoms in the dissociation processes; helium atoms were found to be more efficient than neon atoms in the vibrational relaxation of XeF. Strong vibration-rotation coupling in both vibrational relaxation and in the dissociation processes is demonstrated.
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  • 138
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    International Journal of Chemical Kinetics 21 (1989), S. 1049-1067 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The high temperature kinetics of NH in the pyrolysis of isocyanic acid (HNCO) have been studied in reflected shock wave experiments. Time histories of the NH(X3Σ-) radical were measured using a cw, narrow-linewidth laser absorption diagnostic at 336 nm. The second-order rate coefficients of the reactions: were determined to be: \documentclass{article}\pagestyle{empty}\begin{document}$$k_{1{\rm a}} = 9.84\,\, \times \,\,10^{15} \,\,\exp (- 43000/T,{\rm K})\,\,\,\,\,\,(f = 0.65,F = 1.50)\,\,\,\,\,\,T = 1830 - 3340\,\,{\rm K,}$$\end{document} \documentclass{article}\pagestyle{empty}\begin{document}$$k_{\rm 2} = 5.1\,\, \times \,\,10^{13} \,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,(f = 0.7,F = 1.3)\,\,\,\,\,\,T = 2070 - 2730\,\,{\rm K,}$$\end{document} \documentclass{article}\pagestyle{empty}\begin{document}$$k_{\rm 3} = 2.65\,\, \times \,\,10^{14} \,\,\,\exp (- 38000/T,{\rm K})\,\,\,\,\,\,(f = 0.5,F = 1.4)\,\,\,\,\,\,T = 3140 - 3320\,\,{\rm K,}$$\end{document} cm3-mol-1-s-1, where f and F define the lower and upper uncertainty limits, respectively. The data for k1a are somewhat better fit by: \documentclass{article}\pagestyle{empty}\begin{document}$$k_{{\rm 1a}} = 3.26\,\, \times \,\,10^{35} T^{ - 5.11} \,\,\exp (- 55300/T,{\rm K})\,\,\,{\rm cm}^{\rm 3} {\rm - mol}^{{\rm - 1}} {\rm - s}^{{\rm - 1}} .$$\end{document}
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  • 139
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    International Journal of Chemical Kinetics 21 (1989), S. 1095-1100 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The kinetics and products of the decomposition of 9-diazofluorene by tris (p-bromophenyl) aminium hexachloroantimonate in acetonitrile solvent has been investigated. The reaction is first order with respect to the concentration of both 9-diazofluorene and tris (p-bromophenyl) aminium hexachloroantimonate. A reaction mechanism has also been proposed.
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  • 140
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    International Journal of Chemical Kinetics 21 (1989), S. 1131-1139 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The pressure-jump method has been used to determine the rate constants for the formation and dissociation of nickel(II) and cobalt(II) complexes with cinchomeronate in aqueous solution at zero ionic strength. The forward and reverse rate constants obtained are kf = 2.27 × 106 M-1 s-1 and kr = 3.81 × 101 s-1 for the nickel(II) complex and kf = 1.23 × 107 M-1 s-1 and kr = 2.66 × 102 s-1 for the cobalt(II) complex at 25°C. The activation parameters of the reactions have also been obtained from the temperature variation study. The results indicate that the rate determining step of the reaction is a loss of a water molecule from the inner coordination sphere of the cation for the nickel(II) complex and the chelate ring closure for the cobalt(II) complex. The influence of the pyridine ring nitrogen atom of the cinchomeronate ligand on the complexation of cobalt(II) ion is also discussed.
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  • 141
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    International Journal of Chemical Kinetics 21 (1989), S. 485-498 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Reactions of the hydroxyl radical, OH, with several reactants have been studied near 1200 K in shock tube experiments in which UV absorption was used to monitor the OH concentration. The values of the rate coefficients were found to be 2.7 × 1012, 2.6 × 1012, 2.8 × 1013, and 1.26 × 1013 cm3/mol-s for the reactions of OH with hydrogen, methane, cyclopentane, and isobutane, respectively. These measured values are compared with previous experimental results and transition-state theory calculations.
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  • 142
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    International Journal of Chemical Kinetics 21 (1989), S. 535-546 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The near U-V photolysis of t-butyl nitrite has been studied over the temperature range 303-393 K. Under these conditions t-butyl nitrite was shown to be a very clean photochemical source of t-butoxy radicals. This allows a study of the decomposition of the t-butoxy radical to be made over this temperature range (3). Extrapolation of the rate constants k3 to high pressure and combination with our previous thermal data give the results: \documentclass{article}\pagestyle{empty}\begin{document}$$k_3 (\infty)/{\rm s}^{{\rm - 1}} = 10^{14.04 \pm 0.37} \exp (- 7519 \pm 70.5/T)$$\end{document}
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  • 143
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    International Journal of Chemical Kinetics 21 (1989), S. 575-591 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The title reaction has been studied in a static quartz reaction vessel between 587 and 658 K at pressures between 40 and 152 torr. The dehydrochlorination is the only significant reaction and is autoaccelerated by the produced HCl. Numerical modelling indicates that the Rice-Herzfeld mechanism, generally used for describing the pyrolysis of halogenated ethanes, has to be completed in the case of CC13CH3 with additional transfer reactions converting “dead” radicals into chain carriers and vice-versa. The numerical simulation fits the experimental results, in the absence as well as in the presence of different amounts of added HCl. The dehydrochlorination is also accelerated by the addition of CCl4, which can be explained in terms of additional elementary steps involving · CCl3 radicals.
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  • 144
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    International Journal of Chemical Kinetics 21 (1989), S. 643-666 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Propyne (p-C3H4) or allene (a-C3H4) mixtures, highly diluted with Ar, were heated to the temperature range 1200-1570 K at pressures of 1.7-2.6 atm behind reflected shock waves. The thermal decompositions of propyne and allene were studied by both measuring the profiles of the IR emission at 3.48 μm or 5.18 μm and analyzing the concentrations of reacted gas mixtures. The mechanism and the rate constant expressions were discussed from both the profiles and the concentrations of reactant and products obtained. The rate constant expressions for reactions, (1) p-C3H4 → a-C3H4, (-1) a-C3H4 → p-C3H4, and (5) p-C3H4 + H → CH3 + C2H2 were evaluated.
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  • 145
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    International Journal of Chemical Kinetics 21 (1989), S. 621-633 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Kinetics of oxidation of thiocyanate ion (NCS-) by iodine monochloride and iodine has been studied in aqueous perchloric acid medium. The rates of oxidations followed the rate laws: \documentclass{article}\pagestyle{empty}\begin{document}$$ \begin{array}{*{20}c} {- \frac{{d[{\rm ICl]}}}{{dt}} = \frac{{k[{\rm ICl][NCS}^ -][{\rm H}^ +]}}{{l + {\rm K[NCS}^ -][{\rm H}^ +]}}} \\ {- \frac{{d[{\rm I}_{\rm 2}]}}{{dt}} = \frac{{k'[{\rm I}_{\rm 3} ^ -][{\rm NCS}^ -][{\rm H}^ +]}}{{[{\rm I}^ -][1 + {\rm K'[H}^ +]]}}{\rm at low [H}^ +]} \\ {{\rm and} - \frac{{d[{\rm I}_{\rm 2}]}}{{dt}} = \frac{{k''[{\rm I}_{\rm 2}]}}{{k'' + [{\rm H}^ +][{\rm I}^ -]}}{\rm at high [H}^ +]} \\ \end{array} $$\end{document} Variations in ionic strength and dielectric constant of the medium had little effects on the rates of reactions with both the oxidants. Mechanisms consistent with the observed rate laws have been suggested. Rate limiting steps have been identified and the constants of some of these steps have been evaluated by varying [NCS-] at each temperature. Activation parameters were computed from the Arrhenius plots. The rate constants predicted from the rate law as [NCS-], and [H+], varied in iodine monochloride oxidation, are in good agreement with the experimental values providing support to the proposed mechanism.
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  • 146
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    International Journal of Chemical Kinetics 21 (1989), S. 689-701 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The thermal decomposition of propane was studied behind reflected shock waves over the temperature range 1100-1450 K and the pressure range 1.5-2.6 atm, by both monitoring the time variations of absorption at 3.39 μm and analyzing the concentrations of the reacted gas mixtures. The rate constants of the elementary reactions were discussed from the results. The rate constant expressions, k1 = 1.1 × 1016 exp (-84 kcal/RT) s-1 and k4 = 9.3 × 1013 exp(-8 kcal/RT) cm3 mol-1 s-1, of reactions C3H8 → CH3 + C2H5 and C3H8 + H → n-C3H7 + H2 were evaluated, respectively.
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  • 147
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    International Journal of Chemical Kinetics 21 (1989), S. 715-727 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The UV absorption spectrum and the kinetics of the self combination reaction of the CCl3 radical were studied by flash photolysis in the temperature range 253-623 K. Experiments were performed at the atmospheric pressure, except for a few runs at the highest temperatures, which were performed between 30 and 760 torr. CCl3 radicals were generated by flash photolysis of molecular chlorine in the presence of chloroform. The UV spectrum exhibits a strong unstructured band between 195 and 260 nm with a maximum at 211 ± 2 nm. The absorption cross section, measured relative to σ(HO2), is σ(CCl3) = (1.45 ± 0.35) × 10-17 cm2 molecule-1 at the maximum. This value takes into account the uncertainty in σ(HO2) which was taken equal to (4.9 ± 0.7) × 10-18 cm2 molecule-1. The absolute rate constant for the CCl3 mutual combination was determined by computer simulation of the transient decays. The rate constant, which exhibits a slight negative temperature coefficient, can be expressed as: \documentclass{article}\pagestyle{empty}\begin{document}$$ k_6 = (3.3 \pm 0.8) \times 10^{- 12} (T/298)^{- 1.0 \pm 0.2} {\rm cm}^{\rm 3} {\rm molecule}^{- 1} {\rm s}^{- 1} {\rm at 760 torr}{\rm.} $$\end{document}The study of the pressure dependence showed that only a slight fall-off behavior could be observed at the highest temperature (623 K). This result was corroborated by RRKM calculations which showed that the rate constant is at the high pressure limit under most experimental conditions below 600 K.
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  • 148
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    International Journal of Chemical Kinetics 21 (1989), S. 765-774 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Pulsed laser photolysis/laser-induced fluorescence (LIF) is utilized to measure absolute rate constants of CH radical reactions as a function of temperature and pressure. Multiphoton dissociation of CHBr3 at 266 nm is employed for the generation of CH (X2Π) radicals. The CH radical relative concentration is monitored by exciting fluorescence on the R1(2) line of the (A2Δ - X2Π) transition at 429.8 nm. A resistively heated cell allows temperature studies to be performed from room temperature to ≈670 K. The following Arrhenius equations are derived: \documentclass{article}\pagestyle{empty}\begin{document}$${\rm CH}\,{\rm + }\,{\rm N}_{\rm 2} {\rm O,}\,\,\,\,\,\,\,\,k = (1.59 \pm 0.20)\, \times \,\,10^{ - 11} \,\,\exp [(500 \pm 45)/T]{\rm cm}^{\rm 3} {\rm s}^{{\rm - 1}};$$\end{document} \documentclass{article}\pagestyle{empty}\begin{document}$${\rm CH}\,{\rm + }\,{\rm SO}_{\rm 2} {\rm ,}\,\,\,\,\,\,\,\,k = (1.32 \pm 0.17)\, \times \,\,\,10^{ - 10} \,\,\exp [(250 \pm 45)/T]\,\,{\rm cm}^{\rm 3} {\rm s}^{{\rm - 1}};$$\end{document} \documentclass{article}\pagestyle{empty}\begin{document}$${\rm CH}\,{\rm + }\,{\rm OCS,}\,\,\,\,\,\,\,\,k = (1.99 \pm 0.11)\, \times \,\,\,10^{ - 10} \,\,\exp [(190 \pm 20)/T]\,\,{\rm cm}^{\rm 3} {\rm s}^{{\rm - 1}};$$\end{document} \documentclass{article}\pagestyle{empty}\begin{document}$${\rm CH}\,{\rm + }\,{\rm CS}_{\rm 2} {\rm ,}\,\,\,\,\,\,\,\,k = (3.49 \pm 0.36)\, \times \,\,\,10^{ - 10} \,\,\exp [- (40 \pm 35)/T]\,\,{\rm cm}^{\rm 3} {\rm s}^{{\rm - 1}};$$\end{document} \documentclass{article}\pagestyle{empty}\begin{document}$${\rm CH}\,{\rm + }\,{\rm SF}_{\rm 6} {\rm ,}\,\,\,\,\,\,\,\,k 〈 5\,\,\, \times \,\,\,10^{ - 17} {\rm cm}^{\rm 3} {\rm s}^{{\rm - 1}} .$$\end{document} With the exception of SF6, the reactions of sulfur containing species proceed at rates that are near the theoretical gas kinetic collision frequency. Additionally, these reactions all have activation energies that are near zero or slightly negative. These observations are consistent with an insertion-decomposition mechanism being dominant under these conditions.
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    New York, NY : Wiley-Blackwell
    International Journal of Chemical Kinetics 21 (1989), S. 847-858 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Second order rate constants for C2H2 or C2D2 polymerizations into vinylacetylene and higher CnHn products have been measured in a static reactor by dynamic mass spectrometry between 770-980 K. They are nearly identical within experimental error (±50%). It is shown that these results are consistent with the participation of thermally equilibrated vinylidene H2C = C: as a reactive intermediate: since this assumption only introduces a modest reverse equilibrium isotope effect (KiH/KiD ca. 0.48 in this range) into overall rate constants. At the same time they seem to discriminate in general against alternative mechanisms in which the required H-atom transfers take place in rate determining steps. Present evidence, in conjunction with an updated analysis of relevant issues such as experimental and theoretical vs. termochemical estimates of the heat of formation of H2C=C:, the nature of the transition states of singlet vinylidene addition reactions and the likelihood of discrete biradical intermediates in C2H2 dimerization, seems to lend further support to the notion that acetylene behaves as a singlet carbene at high temperatures.
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  • 150
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Measurements from previous studies have shown that when hydroxyl radicals react with various chlorinated hydrocarbons under atmospheric conditions, free chlorine atoms can be produced. In one such study (Edney et al., [3]) from an analysis of the rate equations under a strict set of assumptions, Cl-atom yields could be inferred. Since the approach was indirect, a more direct method for obtaining these yields has been developed. The technique described in this study involves scavenging Cl atoms produced by the reaction (using ethylene or propylene as the scavenger) and then measuring the yield of the stable chlorinated product generated. Cl-atom yields were determined for allyl chloride, vinyl chloride, vinylidene chloride, trichloroethylene, and benzyl chloride. The experiments were performed by irradiating mixtures of CH3ONO/NO/chlorinated hydrocarbon/alkene in air in 150-L Teflon chambers. The yields for the reaction of Cl atoms with the alkenes generating the stable products were determined in seperate experiments. Yields for the formation of Cl atoms upon reaction with hydroxyl radicals are as follows (with 1 σ deviation): allyl chloride: 0.37 ± 0.10, vinyl chloride: 0.04 ± 0.01, vinylidene chloride: 0.23 ± 0.09, trichloroethylene: 0.63 ± 0.34, and benzyl chloride: 0.08 ± 0.03.
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  • 151
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    International Journal of Chemical Kinetics 21 (1989), S. 959-966 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The transient diaryl disulfide radical anions (RSSR-) were produced in nonaqueous solutions at room temperature by the flash photolysis of a solution of arylthiolate ion pair in the presence of the excess corresponding disulfide. The transient spectra were almost identical with those obtained from γ-radiolysis of the disulfides in 77 K 2-methyl-tetrahydrofuran (MTHF) glassy matrix. The spectra of disulfide radical anions in nonaqueous solutions were changed by cations, solvents, and para-substituents depending on the ion pair properties. The tighter ion pairs showed a shift of absorption band to the shorter wavelength. The disulfide radical anions decay by a unimolecular dissociation reaction to yield thiolate anion and thiyl radical. The decay kinetics were first-order in the initial time region. The rate constants obtained were changed by the counter cations in the order Na+ 〉 K+ 〉 Cs+ 〉 Li+, and by solvents. The tighter ion pairs of the disulfide radical anions showed faster dissociation reaction. This is due to stabilization of a transition state with the counter cation.
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  • 152
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    International Journal of Chemical Kinetics 21 (1989), S. 1015-1027 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The thermal reaction of CH2O with NO2 has been investigated in the temperature range of 393-476 K by means of FTIR product analysis. Kinetic modeling of the measured CH2O, NO, CO, and CO2 concentration time profiles under varying reaction conditions gave rise to the rate constants for the following key reactions: and The error limits shown represent only the scatter (±1 σ) of the modeled values. In the modeling, the total rate constant for the CHO + NO2 reaction, k2 + k3, was not varied and the value reported by Gutman and co-workers (ref. [8]) was used for the whole temperature range investigated here. The proposed reaction mechanism, employing these newly established rate constants, can quantitively account for nearly all measured product yields, including the [CO]/([CO] + [CO2]) ratios reported by earlier workers.
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  • 153
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    International Journal of Chemical Kinetics 21 (1989), S. 1077-1089 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Fourier transform infrared spectroscopy was used to identify and quantify products of the self reaction of ethylperoxy radicals, C2H5O2, formed in the photolysis of Cl2/C2H6 mixtures in 700 torr total pressure of synthetic air at 295 K. From these measurements, branching ratios for the reaction channels of k1a/(k1a + k1b) = 0.68 and k1c/(k1a + k1b + k1c) ≤ 0.06 were established. Additionally, using the relative rate technique, the rate constant for the reaction of Cl atoms with C2H5OOH was determined to be (1.07 ± 0.07) × 10-10 × cm3 molecule-1 s-1. Results are discussed with respect to the previous kinetic and mechanistic studies of C2H5O2 radicals.
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  • 154
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    International Journal of Chemical Kinetics 21 (1989), S. 1101-1112 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The gas phase reaction of OH radicals with dimethyl sulfide (CH3SCH3, DMS) has been studied using both an absolute and a relative technique at 295 ± 2 K and a total pressure of 1 atm. The absolute rate technique of pulse radiolysis combined with kinetic spectroscopy was applied. Using this technique a rate constant of (3.5 ± 0.2) × 10-12 cm3 molecule-1 s-1 was obtained. For the relative rate method, rate constants for the reaction of OH with DMS were found to increase with increasing concentrations of added NO. These results are compared with the large body of kinetic and mechanistic data previously reported in the literature.
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  • 155
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    International Journal of Chemical Kinetics 21 (1989), S. 1141-1152 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The gas-phase reaction of methyl vinyl ketone with the OH radical, in the presence of NOx, was investigated at 298 ± 2 K and atmospheric pressure of air. Glycolaldehyde and methylglyoxal were observed to be the major products, with a combined yield of 0.89 ± 0.16. The sum of the yields of the two other main products, formaldehyde and peroxyacetyl nitrate, were found to be essentially unity. The product yield data for glycolaldehyde and methylglyoxal indicate that OH radical addition to the terminal carbon atom of the 〉C=C〈 bond accounts for 72 ± 21% of the overall reaction, with the remaining 28 ± 9% proceeding via addition to the inner carbon atom of the double bond.
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  • 156
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    International Journal of Chemical Kinetics 21 (1989), S. 207-218 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The photo-oxidation of n-heptane in synthetic air containing methyl nitrite and nitric oxide has been ivestigated in an atmospheric flow reactor. By measuring the total yields of heptyl nitrate products, relative to the depletion of the n-heptane, the rate constant ratio, k3b/k3a has been determined for the reactions: Over the temperature range 253-325 K and at a total pressure of 730 Torr, the following relative Arrhenius equation has been obtained from the present study together with literature data: \documentclass{article}\pagestyle{empty}\begin{document}$$k_{3b} /k_{3a} = (1.4 \pm 1.1) \times 10^{ - 3} \exp [1640 \pm 250)/T]$$\end{document} These results confirm that the formation of alkyl nitrates from the photo-oxidation of n-alkanes arise from a primary reaction between the alkylperoxy radicals and nitric oxide. Furthermore the present experiments show that the lifetime of the intermediate in this type of reaction, presumed to be an alkyl peroxynitrite, ROONO, must be less than a few seconds.
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  • 157
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    International Journal of Chemical Kinetics 21 (1989), S. 245-250 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Rate constants for the reactions of tert-butoxy radicals (generated by the thermal decomposition of di-tert-butylperoxyoxalate) with several sulfur containing compounds have been measured at 310 K in benzene. Hexanethiol (k = 6.5 × 107M-1s-1) reacts considerably faster than alkyl sulfides and disulfides. For these compounds the reaction rate constants are slightly dependent on the α-hydrogen type, changing (when it is expressed per hydrogen atom) only a factor 5 for sulfides and 3 for disulfides when the α-hydrogen is changed from primary (methyl) to tertiary (isopropyl). The data obtained are compared to those found for the deactivation of the benzophenone triplet. Values of ktert-butoxy/kbenzophenone range from ca 10-3 (di-tert-butyl disulfide) to 7.5 (hexanethiol). The results obtained are rationalized in terms of bond strength, steric hindrance, and charge transfer contributions to the critical configuration energies.
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  • 158
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    International Journal of Chemical Kinetics 21 (1989), S. 355-365 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using a relative rate method, rate constants have been determined at 296 ± 2 K for the gas-phase reactions of the OH radical with toluene, the xylenes, and the trimethylbenzenes. Using the recommended literature rate constant for the reaction of OH radicals with propene of (2.66 ± 0.40) × 10-11 cm3 molecule-1 s-1, the following rate constants (in units of 10-12 cm3 molecule-1 s-1) were obtained: toluene, 5.48 ± 0.84; o-xylene, 12.2 ± 1.9; m-xylene, 23.0 ± 3.5; p-xylene, 13.0 ± 2.0; 1,2,3-trimethylbenzene, 32.7 ± 5.3; 1,2,4-trimethylbenzene, 32.5 ± 5.0; and 1,3,5-trimethylbenzene, 57.5 ± 9.2. These data are compared with the literature values.
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  • 159
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    International Journal of Chemical Kinetics 21 (1989), S. 387-397 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The decomposition of 1-chloro-1,1-difluoroethane by a radical chain reaction has been studied in a flow reactor in the temperature range from 503 to 773 K. For the initiation of the chain small amounts of added chlorine were photolyzed with a XeCl laser (λ = 308 nm). The formation of the dehydrochlorination and chlorination products, vinylidene fluoride, and 1,2-dichloro-1,1-difluoroethane respectively, is described by a kinetic model. Arrhenius parameters for the two abstraction reactions \documentclass{article}\pagestyle{empty}\begin{document}$${\rm CI + CH}_{\rm 3} {\rm CCIF}_{\rm 2} {\hbox to 25pt{\rightarrowfill}} {\hskip-18pt ^{K_2 }}{\hskip1em} {\rm HCI + CH}_{\rm 2} {\rm CCIF}_{\rm 2}$$\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$${\rm CI + CH}_{\rm 2} {\rm CICCIF}_{\rm 2} {\hbox to 25pt{\rightarrowfill}} {\hskip-18pt ^{K_7 }}{\hskip1em} {\rm HCI + CHCICCIF}_{\rm 2}$$\end{document} were determined by a competition method: \documentclass{article}\pagestyle{empty}\begin{document}$$\log _{10} (k_2 /cm^3 {\rm mol}^{{\rm - 1}} {\rm s}^{{\rm - 1}} = (13.6 \pm 0.1) - (9200 \pm 300)/4.576T$$\end{document} \documentclass{article}\pagestyle{empty}\begin{document}$$\log _{10} (k_7 /cm^3 {\rm mol}^{{\rm - 1}} {\rm s}^{{\rm - 1}} = (13.7 \pm 0.1) - (6500 \pm 200)/4.576T$$\end{document} Experimental and modeling results are discussed with respect to former studies on the thermal reaction of 1-chloro-1,1-difluoroethane.
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  • 160
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The kinetics of reaction of substituted 2-aminobenzothiazoles and phenacyl bromide have been followed conductometrically and in some cases, argentometrically. Both the methods produced almost the same rate constants. Substituents at position 5 of the benzothiazole nucleus behave like para substituents of the benzene ring. A correlation with Hammett σp substituent constants has been obtained with a rho value of -1.04. The rate data of quaternization reaction of 4, 5, and 6 substituted 2-aminobenzothiazoles with phenacyl bromide have been correlated with Fk, Rk, and Vw values by multiple regression analysis with the equation suggested by Williams and Norrington and modified by us. The values are found to correlate well with the equation, log k = -4.4979 - 0.4815fjFk + 0.5933rjRk - 0.0277Vw.
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  • 161
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    International Journal of Chemical Kinetics 21 (1989), S. 519-533 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A kinetic study of uncatalyzed and Ru(III) catalyzed oxidation of indigo carmine(IC) (disodium 3,3′-dioxobi-indolin-2,2′-ylidene-5,5′-disulphonate) by iodate ion in aqueous sulphuric acid solution is reported. The uncatalyzed reaction order was found to be four; one each with respect to IC and iodate ion and second order with H+ ion. The Ru(III) catalyzed reaction was of fifth order, second order with respect to H+ and first order with respect to reductant, oxidant, and catalyst. Stoichiometric ratios of both reactions were the same with a 3:2 reductant-oxidant ratio. In both uncatalyzed and catalyzed reactions isatin-5-monosulphonic acid (2,3-dioxoindoline-5-sulphonic acid) was observed as the oxidation product. Rate constants for both the reactions are reported. Reaction mechanisms consistent with the experimental data are suggested.Further, a fixed time method is described for the determination of Ru(III), based on its ability to catalyze the oxidation of IC by acidic iodate. Using [H+] 2.25M, [iodate] 1.00 × 10-3M and [IC] 5.0 × 10-5M, in presence of Ru(III), the reaction followed first order kinetics with respect to IC. The interference of various cations, neutral salts, and potassium iodide on the determination of Ru(III) was studied using synthetic mixtures. The selectivity of the method and the recommended procedure are described.
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  • 162
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    International Journal of Chemical Kinetics 21 (1989), S. 885-908 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Generalized models for steady state catalytic processes are presented in matrix form. Multistep reaction rate control is assumed. Numerical algorithms for solving of the created linear and nonlinear equation systems are developed and tested. Four examples are considered: an Eley-Rideal-mechanism, a Langmuir-Hinshelwood mechanism, a dual route, dual site mechanism, and a monomolecular decomposition with steady state multiplicity. The overall reaction rates are simulated as a function of the reactant concentrations.A maximum reaction rate is obtained in the case of a Langmuir-Hinshelwood mechanism (example 2), the location of the rate maximum in the concentration domain is shifted towards the concentration of the reactant with the lowest adsorption constants. An Eley-Rideal mechanism (example 1) has always monotonously increasing rate curves. In the case of steady state multiplicity (example 4) all steady states could be simulated with the proposed algorithm. The computation of reaction rate surfaces is important in investigating the behavior of complicated catalytic systems (e.g., systems with multistep rate control and/or steady state multiplicity), in planning of experiments and in chemical reactor simulation.
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  • 163
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    International Journal of Chemical Kinetics 21 (1989), S. 1029-1047 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The rate of V → R, T energy relaxation following pulsed ir laser excitation is measured by employing an optoacoustic single pulse method. Under present experimental conditions the operation of convolution applies. The experimental optoacoustic waveform can be viewed as the convolution of the kinetic relaxation waveform with an optoacoustic waveform obtained under very fast energy relaxation conditions. A discrete Fourier transform deconvolution method is applied to optoacoustic measurements on SF6 in argon to obtain the time constant, τ, for energy transfer. The present method gives τP = 182 ± 15 μs torr, in good agreement with other methods. These results were obtained without requiring either a theoretical description of the pressure waveform or an assumed laser irradiation geometry. For convolution to apply, the differential equation describing the pressure pulse must be linear under the conditions of the experiment. The linearity of the system can usually be tested experimentally.
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  • 164
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    International Journal of Chemical Kinetics 21 (1989) 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 165
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    International Journal of Chemical Kinetics 21 (1989), S. 1113-1122 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Using Fourier transform infrared spectroscopy, the ethene yield from the reaction of C2H5 radicals with O2 has been determined to be 1.50 ± 0.09%, 0.85 ± 0.11%, and 〈0.1% at total pressures of 25, 50, and 700 torr, respectively. Additionally, the rate constant of the reaction of C2H5 radicals with molecular chlorine was measured relative to that with molecular oxygen. A ratio k6/k7 = 1.99 ± 0.14 was measured at 700 torr total pressure which, together with the literature value of k7 = 4.4 × 10-12 cm3 molecule-1s-1, yields k6 = (8.8 ± 0.6) × 10-12 cm3 molecule-1s-1. Quoted errors represent 2σ. These results are discussed with respect to previous kinetic and mechanistic studies of C2H5 radicals.
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  • 166
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    International Journal of Chemical Kinetics 21 (1989), S. 1161-1172 
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The reactions Br + NO2 + M → BrNO2 + M (1) and I + NO2 + M → INO2 + M (2) have been studied at low pressure (0.6-2.2 torr) at room temperature and with helium as the third body by the discharge-flow technique with EPR and mass spectrometric analysis of the species. The following third order rate constants were found k1(0) = (3.7 ± 0.7) × 10-31 and k2(0) = (0.95 ± 0.35) × 10-31 (units are cm6 molecule-2 s-1). The secondary reactions X + XNO2 → X2 + NO2 (X = Br, I) have been studied by mass spectrometry and their rate constants have been estimated from product analysis and computer modeling.
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  • 167
    ISSN: 0538-8066
    Keywords: Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Calculations were carried out on several data sets to study the mechanism of hydrogen abstraction from phenols by peroxy radicals: Rate constants, k values, were collected for the reactions of cumyl-, 1-phenylethyl- and tert-butyl-peroxy radicals with ortho-para-substituted phenol inhibitors. The rate constants were recalculated for the same temperature. Solvent effects were neglected because the solvents used were similar in nature. The phenol ortho substituents were characterized by an indicator variable ItBu accounting for the presence or absence of di-tert-butyl groups. The phenol para substituents were characterized by Charton's σI, σR, and σR+ substituent constants.The dependence of log k values on Itbu, σI, σR, σR+ was investigated using stepwise linear regression analysis. The combined data set of 32 reactions gives: \documentclass{article}\pagestyle{empty}\begin{document}$$\log \,\,k_{(333{\rm K)}} = - 0.801\sigma _I - 2.483\sigma _{\rm R} + 3.766\,\,\,\,\,\,\,\,\,(r = 0.851)$$\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$$\log \,\,k_{(333{\rm K)}} = - 0.932\sigma _1 - 2.302\sigma _R^ + + 3.802\,\,\,\,\,\,\,\,\,(r = 0.848)$$\end{document}The results suggest that hydrogen abstraction from phenols by peroxy radicals proceeds by an electrophilic mechanism, and that neither the peroxy-radical nor the ortho-di-tert-butyl groups have considerable effect on the rate of reaction (1).
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  • 168
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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.
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  • 169
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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.
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  • 170
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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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  • 171
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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.
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  • 172
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    Journal of Computational Chemistry 10 (1989), S. 903-910 
    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 recently reported Random Incremental Pulse Search (RIPS) technique has been used to probe the conformational energy surface of cyclononane. The stochastic method permits searching of the potential energy surface for all minimum-energy conformations. The search located all previously reported structures together with three additional conformations that were not found by earlier, primitive searching techniques. Two of these structures are high-nergy skew forms, and the third is a low-energy conformer that should contribute significantly to the overall equilibrium set of cyclononane conformations. The global minimum has been found to be the D3 symmetrical twist chair-boat (TBC) form in accordance with previous studies. The newly discovered low-energy structure, which lies only 2.2 kcal/mol above the global minimum, has been designated twist chair-twist chair (TCTC). The two higher energy conformers are skewed chair-chair (SCC) and skewed boat-boat (SBB) forms that are 5.7 kcal/mol and 10.4 kcal/mol above the global minimum, respectively. The seven reported conformations were reanalyzed quantum mechanically (AM1), and a comparison between MM2 and AM1 results is presented.
    Additional Material: 3 Ill.
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  • 173
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    Journal of Computational Chemistry 10 (1989), S. 479-487 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab Initio charge distributions for amino acid dipeptides are derived utilizing two medium-sized basis sets. Peptide charges differ in two ways from those of existing force fields: the magnitude of the peptide dipole and the dependency on the residue type. The merging of charge distributions of side chain and backbone fragments within a semiclassical model including polarization is investigated. Polarization plays a small, but distinct role in improving the correspondence with ab initio data derived for the complete dipeptide. A description in terms of partly overlapping, interacting fragments correlates well with the ab initio data. The method can be used to derive the electrostatic properties of biological macromolecules by combining accurate descriptions of short range interactions (using good quality basis sets on not too small fragments) with good classical models of long range interactions (using multicenter multipole expansions and atomic polarizability tensors). Factors limiting the accuracy of the present representations are discussed.
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  • 174
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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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  • 175
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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 MM2 potential functions for amides and peptides have been further extended by examining the experimental crystal structures for cyclo-(-Ala-Ala-Gly-Gly-Ala-Gly-), I, and cyclo-(-Ala-Ala-Gly-Ala-Gly-Gly-), II. The force field obtained was then applied to a study of the structure of the hydrophobic protein Crambin, for which a high resolution crystal structure is available. The energy minimization was carried out using a version of MM2 adapted to the CYBER 205.
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  • 176
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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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  • 177
    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 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.
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  • 178
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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.
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  • 179
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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.
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  • 180
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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.
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  • 181
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    Journal of Computational Chemistry 10 (1989), S. 770-797 
    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 uses pattern recognition techniques to compute tripeptide conformational probabilities is described. The procedure differs in several respects from the many “secondary structure” prediction algorithms that have been published over the last 20 years. First, the procedure classifies tripeptides into 64 different conformational types, rather than just α, β and coil, as is commonly done. Thus, the procedure can attempt to predict regions of irregular structure. Second, the procedure uses the methods of pattern recognition, which are powerful but conceptually simple. In this approach, amino acid properties are used to map peptide sequences into a multivariate property space. Particular tripeptide conformations tend to map to particular regions of the property space. These regions are represented by multivariate gaussian distributions, where the parameters of the distributions are determined from tripeptides in the protein X-ray data bank. Finally, rather than making simple predictions, the procedure computes probabilities. Tripeptide conformational probabilities are calculated in the multivariate property space using the gaussian distributions. In a prediction, the procedure might find that a particular tripeptide in a protein has a 36% chance of being in the ααα conformation, a 17% chance of being αα∊, a 14% chance of being ααα*, etc. The α-helical conformation is thus the most probable, but, in predicting the structure of the protein, a search algorithm should also consider some of the other possibilities. The values of the probability provide a rational basis for selecting from among the possible conformations. The second article of this series describes a procedure that uses the probabilities to direct a search through the conformational space of a protein. The third article of the series describes a procedure that generates actual three-dimensional structures, and minimizes their energies. The three articles together describe a complete procedure, termed “pattern recognition-based importance-sampling minimization” (PRISM), for predicting protein structure from amino acid sequence.
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  • 182
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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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  • 183
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    Journal of Computational Chemistry 10 (1989), S. 863-868 
    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 steric energy difference (ΔEst) between tertiary carbenium ions (R+) and the corresponding alcohols has been calculated by MM2 for a series of tertiary nonbridgehead substrates and correlated with their rate of solvolytic reactivity. Satisfactory correlation is obtained, except for p-nitrobenzoates of highly congested substrates. The slope and intercept of the correlations remain almost unchanged if bridge-head substrates are included in the plot. However, the quality of the fit is better for bridgehead substrates alone.
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  • 184
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    Journal of Computational Chemistry 10 (1989), S. 875-886 
    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 effect of the parent basis set on the basis set superposition error caused by bond functions is investigated systematically. An important difference between BSSE at the SCF and correlated levels is pointed out. Three new basis sets are defined, denoted 6-311 + G(d,p)B, 6-311 + G(2d,p)B, and 6-311 + G(2df,p)B. BSSE for the first-row hydrides seems to increase uniformly with increasing atomic number of the central atom. Expansion of the valence part of the basis set from 6-31G to 6-311G, as well as adding f functions, has a significant effect on the BSSE. Additional BSSEs incurred by bond functions are less than or equal to 1 kcal/mol for the 6-311 + G(2df,p)B basis set. For the dissociation energies of the first-row hydride species, agreement with experiment within only a few kcal/mol can be obtained even without resorting to isogyric reaction cycles. For high-quality calculations, adding bond functions seems to have definite advantages over expanding the polarization space beyond the [2d1f] level.
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  • 185
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    Journal of Computational Chemistry 10 (1989), S. 921-927 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new algorithm is proposed for the evaluation of nonbonded interactions in Molecular Dynamics simulations. The algorithm is based on a grid search and on partitioning of the atoms into boxes rather than on calculations of distances. The effort associated with the generation of the box list grows only linearly with the number of atoms. The algorithm is particularly advantageous for solvated systems. Test calculations show significant savings in CPU time and storage compared to commonly used algorithms for systems containing in excess of ca. 600 atoms.
    Additional Material: 5 Ill.
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  • 186
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    Journal of Computational Chemistry 10 (1989), S. 935-938 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Explicit formulas are given for the characters of symmetric and antisymmetric powers of an arbitrary representation up to the sixth, and a general method for obtaining the higher ones is described. The results allow, among others, the determination of nonvanishing higher force constants in symmetrical molecules. The benzene molecule, for instance, has 237 nonvanishing cubic and 1890 quartic force constants. Other potential applications are a general method for the symmetry species of vibrational overtones, the determination of the number of independent centrifugal distortion constants, and the symmetry classification of vibrational multiplets.
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  • 187
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    Journal of Computational Chemistry 10 (1989), S. 965-974 
    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 modified scheme of a previously developed concept of atomic valence numbers in molecules is presented. The relation to population analysis is demonstrated. The scheme is suitable for ab initio wave functions with extended basis sets. The procedure involved a combination of symmetric orthogonalization and contraction of the basis set. The method is used for a systematic investigation of a series of compounds with first-row atoms from Li to F. The predicted atomic charges and valence numbers are in line with results from infrared spectroscopy and multipole moment analysis.
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  • 188
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    Journal of Computational Chemistry 10 (1989), S. 951-956 
    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 recipe for calculating and differentiating cosine of bond angle and dihedral angle expressions. The resulting formulas can be incorporated in a straightforward manner into the bond angle and dihedral angle components of potential energy functions. These formulas rely only on expressions and derivatives of dot products, and, in particular, they avoid cross products as well as excessive Fortran function references. Consequently, the expressions derived in this article can be written compactly and evaluated rapidly.
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  • 189
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    Journal of Computational Chemistry 10 (1989), S. 1013-1015 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two new methods of bivariate interpolation suitable for experimental designs are summarized. The methods use experimental data obtained in usual manner. The programs are short and rapid and are often more accurate on test functions than the standard method.
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  • 190
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    Journal of Computational Chemistry 10 (1989), S. 1016-1030 
    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 analytical representation of atom valence state energy (E(nj), j = 1,…4; E(nj) is a nonlinear function of orbital occupancy numbers nj) is proposed and explicitly derived for H—Ar; the values of electronegativity calculated based on E(nj) agree within truncation error with those of Hinze and Jaffe. However, in our representation, orbital electronegativity χ and hardness parameters η of a given orbital always include nonlinear contributions from other orbitals, hence accounting for their influence on χ and η. An atomic charge calculation procedure based on E(nj) is also described and shown to perform well.
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  • 191
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    Journal of Computational Chemistry 10 (1989), S. 1038-1052 
    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 of molecular mechanics is used to investigate the structural and electrostatic features of molecular recognition by β-cyclodextrin and capped β-cyclodextrin models of α-chymotrypsin. Since capped β-cyclodextrin has been shown to be the more effective biomimetic catalyst, these features of molecular recognition can be interpreted in terms of the relationship between molecular structure and catalytic function. Calculations in vacuo show that the addition of an N-methylformamide “cap” substituent to each glucose unit appears to change the relative orientation of some glucose fragments from that found in the X-ray structure of the β-cyclodextrin macrocycle. These results indicate that certain structural components of molecular recognition, such as the orientation of the secondary hydroxyls and the related orientation of the caps, may be implicated in the catalysis. In addition, the electrostatic component of molecular recognition was investigated by the analysis of molecular electrostatic potential maps calculated in planes parallel to the average plane of the glycosidic oxygen atoms. The results indicate that the addition of the caps to the β-cyclodextrin macrocycle subtly alters the pattern of the maps in each plane. However, the general qualitative features of electrostatic recognition by β-cyclodextrin and capped β-cyclodextrin are similar.
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  • 192
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    Journal of Computational Chemistry 10 (1989), S. 514-519 
    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 charge on oxygen for a series of compounds was obtained using Mulliken population, natural population analysis (NPA), integrated projected electron population (IPP) analysis, and Bader's topological density analysis, “integrated Bader populations” (IBP). The orbital-based methods (Mulliken and NPA) predict oxygen charges of about -0.6 whereas the spatial-based methods (IPP and IBP) predict charges of about - 1.2 to - 1.3. The differences are ascribed primarily to the nuclear-centered basis sets used in the orbital methods that minimize local atomic polarization effects. Accordingly, such population analyses should be used for electronic structure considerations only with due circumspection. The IPP method as an approximation to IBP shows gross similarities; small but significant differences vary in a nonsystematic manner and IPP values must also be used with care.
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  • 193
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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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  • 194
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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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  • 195
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    Journal of Computational Chemistry 10 (1989), S. 648-659 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Calculations of chemical shifts have been carried out using “locally dense” basis sets for the resonant atom of interest, and smaller, attenuated sets on other atoms in the molecule. For carbon, calculations involving a 6-311G(d) triply split valence set with polarization on the resonant atom and 3-21G atomic bases on other heavy atoms result in good agreement with experiment, and are virtually identical to those found employing the larger basis on all atoms. For species such as nitrogen, oxygen, and fluorine where standard balanced basis sets do not agree well with experiment, use of attenuated sets fail as well. The use of locally dense basis sets permits calculations previously impractical, and the successful application to carbon suggests that the chemical shift is most dependent on the local basis set, and less so on whether or not a balanced or unbalanced calculation is being carried out.
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  • 196
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    Journal of Computational Chemistry 10 (1989), S. 711-717 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Empirical intermolecular force field parameters for the fluorine atom of the 4-fluorophenyl group have been generated for use in molecular mechanics programs. Partial charges on the ring system were obtained by Mulliken population analysis of wave functions generated by molecular orbital calculations in the STO-3G approximation. Fluorine van der Waals parameters were obtained by non-linear least-squares fitting of crystallographic data following the procedure of Hagler and Lifson. The parameters developed are compared to fluorine parameters reported previously.
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  • 197
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    Journal of Computational Chemistry 10 (1989), S. 628-634 
    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 the computation and representation of van der Waals surfaces and volumes of supermolecules (several overlapping molecules) by a set of grid points originating from an equidistant lattice is described in detail. The grid points in this set belong either to the “outer” surface of the van der Waals body or to a layer just below that outer surface. By means of this double layer (outer and inner) it is possible to represent the volume via the surface without referring to grid points lying inside the body. The algorithm is based on the octree concept, which means that the final relevant lattice points are derived by the successive refinement of an initial coarse lattice. The main features of the algorithm are the automatic elimination of inner atoms irrelevant for the surface definition and the association of any surface point with only those atoms which define the surface in the vicinity of these points. The most remarkable consequence of these features is that the amount of computation is almost independent of the number of atoms in the supermolecule. The algorithm can be used in solving problems arising in drug design, protein folding, molecular graphics, etc.
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  • 198
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    Journal of Computational Chemistry 10 (1989), S. 660-672 
    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 complete set of second-order Gaussian functions (6D) includes a totally symmetric second-order Gaussian function (3s-type) in addition to the five d-type functions. This 3s-type function in the 3-21G(*) basis set for the sulfur atom is described (1) in terms of its geometric and electronic effects observed in the sulfur atom and in four sulfur-containing molecules and (2) by the ability of a single zero-order 1s-type Gaussian function (with various exponents) to replace it in ab initio Hartree-Fock calculations. The geometry of the molecules (dihydrogen sulfide, dihydrogen thioketone, dihydrogen disulfide, and methanesulfonamide) were obtained using various semiempirical and ab initio methods. It is found that the 3s-type function lowers the energy relative to that calculated with the 3-21G(*) basis set with only five second-order Gaussian functions by ca. 46-48 kcal/mol per sulfur atom. Only small changes in geometry are observed when the latter basis set is augmented with a 3s or 1s function. When the exponent of the 1s replacement function is chosen so that the resulting function has a location similar to that of the 3s function as measured by the degree of overlap or the coincidence of radial distribution maxima, the corresponding drop in energy is less than 8 kcal/mol per sulfur atom. However, when the shape of the radial distribution of the 1s function is similar to that of the 3s, i.e., when the value of the 1s exponent is ca. equal to that of the 3s function (a local maximum in the 1s energy profile), the energy lowering is similar to that produced with the 3s function. The electronic effects observed in the molecules differ from those in the atom, the largest deviations being found in the methanesulfonamide calculations.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 199
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 733-747 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Several general procedures for the derivation and analysis of a Fourier-series expansion V(φ) over computed torsional energies E(φi) are formulated. STO-3G energy values in n-butane, 1-chloropropane, and 1,2-dichloroethane are used as test data for deriving V(φ) with the numerical methods of interpolation and least squares. The accuracy of each derived V(φ) is assessed on the basis of calculated conformational properties, mean and rms deviations, and an error curve, V(φ)-V(φ)ref, where V(φ)ref represents a reference set of E(φi). Results indicate that given the same number of expansion terms, interpolation and least squares yield functions of comparable accuracy; however, interpolation is a more efficient procedure for monitoring the accuracy of a function in regions of interest. In cases where there are too few input energies to achieve the desired accuracy, energy derivatives can be employed effectively for expanding the input set. In designing special-purpose functions, the error curve can be used meaningfully as a guide; an example for producing functions that are especially well behaved in regions for gauche conformations is provided. The present study continues to add systematics and rigor to the fitting of an internal rotation potential function from energy data.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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  • 200
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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).
    Additional Material: 29 Tab.
    Type of Medium: Electronic Resource
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