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  • 101
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 186-202 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: π-Electron delocalization in neutral and protonated “doubly-extended-guanidine,” (H2N)2C=N—CH=N - CH=NH, has been studied by ab initio methods at the self-consistent field (SCF) STO-3G and 3-21G levels for a large number of tautomeric, rotameric, pseudocyclic, and monocyclic (disubstituted triazine) forms. These π systems have been characterized in terms of a number of structural and energetic parameters: degree of single/bond character from bond lengths and π bond orders, electron distributions, and tautomer, rotamer, and protonation energies. The acyclic neutral forms exhibit largely alternant single-double bond patterns as predicted by classical bonding structures but with, however, significant deviations due to conjugation. The acyclic protonated forms exhibit bond patterns consistent with resonance delocalized structures extending over the whole molecule (“doubly-extended guanidinium”) or part of the molecule (“extended-guanidinium”) or guanidinium . All systems showed alternant charge distributions with electron-deficient carbons. The energy results have been analyzed in terms of possible contributions from steric interactions, lone-pair repulsions, purportive electrostatic interactions in pseudocyclic forms, overall π-system conformation (extended, kinked, or folded), and specific through-space π-overlap interactions in some pseudocyclic forms. It was found that these other interactions usually dominate the specifically π effects so that the general concept of preferential π delocalization in straight lines does not hold for the acyclic systems. Some interesting examples of pseudocyclic forms exhibiting strongly stabilizing intramolecular interactions attributed to π through-space coupling are identified. These systems with incipient-ring characteristics present intermediate bonding models between the acyclic and closed-ring π systems. The extent of stabilization of the guanidinium-type cations by resonance delocalization in cyclic systems depended on whether it reinforced or interfered with the overall ring delocalization.
    Additional Material: 10 Ill.
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  • 102
    Electronic Resource
    Electronic Resource
    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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  • 103
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 265-283 
    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 study of systems containing the title moiety is described, with special reference to the anomeric effect. We have calculated ab initio, using Gaussian-80 with the 3-21G basis set, all basic conformations of methylene-diamine (H2N—CH2—NH2) and its N-methyl derivative with full geometry optimization of energy minima and barriers. The structural data thus obtained, were then employed to parameterize Allinger's MM2-80 force field in a procedure similar to that described for oxygen derivatives, including hydrogen-bonding effects and C—N bond shortening in tertiary amines. This modification, termed MM2-AE was then used to calculate larger molecules, including N,N′-di- and N,N,N′,N′-tetramethyl-methylenediamine, various 1,3-diazane systems, and 1,4,5,8-tetraazadecalin derivatives of established (x-ray) structures. The results are discussed in light of their verificative and predictive power and appear to validate MM2-AE as a useful computational procedure.
    Additional Material: 8 Ill.
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  • 104
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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.
    Additional Material: 2 Ill.
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  • 105
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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.
    Additional Material: 2 Ill.
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  • 106
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    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.
    Additional Material: 2 Ill.
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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: The gas-phase analogs of the classical SN1 and SN2 reactions of nucleophiles with a series of protonated oxiranes bearing the substituents CN, Cl, Me, and Ph were studied using MNDO semiempirical molecular orbital theory. The transition states for nucleophilic attack on the intact rings are calculated to become progressively more “SN1-like,” as the ability of the substituent group to stabilize the corresponding ring opened carbenium ion increases. At the same time the activation barriers become progressively smaller and their relative values for different nucleophiles approach the order expected on the basis of a purely electrostatic attraction between the reacting moieties. Exactly the opposite trends are calculated for the transition states for nucleophilic attack on the intermediate carbenium ions. As the stabilities of the latter increase the extent of bond formation, and transfer of charge to the incoming nucleophile also increase. Here, the relative barriers for attack by different nucleophiles approach the order expected on the basis of a superposition of both covalent and electrostatic interactions in which the former dominate. These results support a previously suggested rationalization for the enhanced reactivities of certain alkylating agents towards the exocyclic oxygen atoms, rather than the ring nitrogens, of the nucleic acid bases. They also suggest a new explanation for the tendencies of aralkylating electrophiles to modify the exocyclic amino groups of the nucleic acid bases: sites which are unreactive towards simple alkylating agents.
    Additional Material: 7 Ill.
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  • 108
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 603-615 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Hartree-Fock 6-31G(d) structures for the neutral, positive ion, and negative ion bimolecular complexes of NH3 with the first- and second-row hydrides AHn (AHn = NH3, OH2, FH, PH3, SH2, and ClH) have been determined. All of the stable neutral complexes except (NH3)2, the positive ion complexes with NH3 as the proton acceptor, and the negative ion complexes containing first-row anions exhibit conventional hydrogen bonded structures with essentially linear hydrogen bonds and directed lone pairs of electrons. The positive ion complex NH4+ … OH2 has the dipole moment vector of H2O instead of a lone pair directed along the intermolecular line, while the complexes of NH4+ with SH2, FH, and ClH have structures intermediate between the lone-pair directed and dipole directed forms. The negative ion complexes containing second-row anions have nonlinear hydrogen bonds. The addition of diffuse functions on nonhydrogen atoms to the valence double-split plus polarization 6-31G(d,p) basis set usually decreases the computed stabilization energies of these complexes. Splitting d polarization functions usually destabilizes these complexes, whereas splitting p polarization functions either has no effect or leads to stabilization. The overall effect of augmenting the 6-31G(d,p) basis set with diffuse functions on nonhydrogen atoms and two sets of polarization functions is to lower computed stabilization energies. Electron correlation stabilizes all of these complexes. The second-order Møller-Plesset correlation term is the largest term and always has a stabilizing effect, whereas the third and fourth-order terms are smaller and often of opposite sign. The recommended level of theory for computing the stabilization energies of these complexes is MP2/6-31+G(2d,2p), although MP2/6-31+G(d,p) is appropriate for the negative ion complexes.
    Additional Material: 3 Ill.
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  • 109
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 673-682 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new and accurate method for calculating the geometrically allowed modes of binding of a ligand molecule to a Voronoi site model is reported. It is shown that the feasibility of the binding of a group of atoms to a Voronoi site reduces to a simple set of linear and quadratic inequalities and quadratic equalities which can be solved by minimization of a simple function. Newton's numerical method of solution coupled to a line search proved to be successful. Moreover, we have developed efficient molecular and site data bases to discard quickly infeasible binding modes without time-consuming numerical calculation. The method is tested with a data set consisting of the binding constants for a series of biphenyls binding to prealbumin. After determination of the conformation space of the molecules and proposal of a Voronoi site geometry, the geometrically feasible modes are calculated and the energy interaction parameters determined to fit the observed binding energies to the site within experimental error ranges. We actually allowed these ranges to vary in order to study the influence of their broadness on the site geometry and found that as they increase, one can first model the receptor as a three-region site then as a single region site, but never as a two-region site.
    Additional Material: 4 Ill.
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  • 110
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 698-710 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Computational algorithms are described which provide for constructing the set of associated edge-weighted directed graphs such that the average of the characteristic polynomials of the edge-weighted graphs gives the matching polynomial of the parent graph. The weights were chosen to be unities or purely imaginary numbers so that the adjacency matrix is hermitian. The computer code developed earlier by one of the authors (K.B.) is generalized for complex hermitian matrices. Applications to bridged and spirographs, some lattices and all polycyclic graphs containing up to four cycles are considered.
    Additional Material: 5 Ill.
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  • 111
    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.
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  • 112
    Electronic Resource
    Electronic Resource
    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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  • 113
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    New York, NY [u.a.] : Wiley-Blackwell
    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.
    Additional Material: 1 Ill.
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  • 114
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    New York, NY [u.a.] : Wiley-Blackwell
    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.
    Additional Material: 1 Tab.
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  • 115
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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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  • 116
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 1-13 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computer code and nonnumerical algorithm are developed to construct the edge group of a graph and to enumerate the edge colorings of graphs of chemical interest. The edge colorings of graphs have many applications in nuclear magnetic resonance (NMR), multiple quantum NMR, enumeration of structural isomers of unsaturated organic compounds, and in the construction of configurational integral expansion series in statistical mechanics. The code developed is applied to many NMR graphs, complete graphs containing up to 10 vertices, and the Petersen graph.
    Additional Material: 9 Ill.
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  • 117
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 14-16 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We report the geometry-optimized total energies and bond distances for the closo-carborane isomers 3,5-C2B6H8, 1,7-C2B7H9, and 1,2-C2B7H9 calculated by the ab initio SCF MO method using the STO-3G basis set. Relative energies are compared with those of the other carborane isomers in the 8- and 9- atom classes. These results complete the set of calculations at the same level of theory for all deltahedral carborane isomers except for those of the 11-atom class.
    Additional Material: 4 Tab.
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  • 118
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 367-375 
    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 topological properties of the electron density and the properties of an atom in a molecule are calculated by means of second-order Møller-Plesset perturbation theory (MP2) and compared with the results of configuration interaction calculations (C12) which include all single and double substitutions from the Hartree-Fock reference configuration. A software package for analyzing the effects of electron correlation on the topological properties of the electron density of molecules is described. H2CO is used to provide a numerical example and to indicate that the number of bond critical points is unaffected by the inclusion of electron correlation. Correlation leads to only a small shift in the positions of bond critical points and a small change in the electron density at bond critical points. It is further shown that the energy of an atom in a molecule can be calculated to an accuracy of 1 kcal/mol and the electron population of an atom to about 0.001e. A statistical method is used to show that the deviation of the MP2 correlation correction relative to the CI2 correlation correction for a variety of atomic properties is about 25%.
    Additional Material: 1 Ill.
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  • 119
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MM2 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.
    Additional Material: 6 Tab.
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  • 120
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    New York, NY [u.a.] : Wiley-Blackwell
    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.
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  • 121
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 718-732 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The enantioselective binding of optical analytes on chiral stationary phases used in column chromatography is investigated with molecular modeling techniques. By rolling the analytes over the van der Waals surface of the phase, configurations are sampled and free energies of transient diastereomeric complexes are computed. These free energies allow us to compute chromatographic separability factors and a linear relationship between computed and observed values is found. The intermolecular potential energy surfaces of these diastereomeric complexes are flat with gentle rolling hills and multiple minima. The binding sites are ill-defined and the analytes are found to freely slide over the chiral stationary phases. An energy partitioning algorithm is used to determine how much of the total binding energy is attributable to a given molecular fragment on the phase. It is found that the fragments of the phase bearing the stereogenic carbons are the least cognizant of differences between optical antipodes.
    Additional Material: 3 Ill.
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  • 122
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    New York, NY [u.a.] : Wiley-Blackwell
    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.
    Additional Material: 2 Ill.
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  • 123
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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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  • 124
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    New York, NY [u.a.] : Wiley-Blackwell
    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.
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  • 125
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 869-874 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In a previous article (J. Fernández Rico, R. López and G. Ramírez, J. Comp. Chem., 9, 790 (1988)) we have proposed the calculation of molecular integrals involving STOs by means of some recurrence relations which use two sets (h and H) of overlap integrals (basic matrices). In the present paper, we derive explicit expressions of these integrals employing the two-range expansion of the 0s-function. This approach yields equations for the elements of the two basic matrices in terms of two further matrices, k(x,y) and i(x,y), and some auxiliary functions. Relations between the elements of these matrices and the functions are thoroughly explored and numerical tests are included for illustrating the behavior of the method.
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  • 126
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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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  • 127
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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.
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  • 128
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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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  • 129
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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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  • 130
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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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  • 131
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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.
    Additional Material: 6 Ill.
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  • 132
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    Journal of Computational Chemistry 10 (1989), S. 295-301 
    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 case of appearance of multiple unrestricted Hartree-Fock (UHF) solutions in the SNH+ (2A') radical is reported. This kind of solution does not arise from different electron configurations or symmetry breaking effects and seem to be exclusive of the UHF method. Three solutions are found and studied on the basis of wave function stability tests and several conclusions about their origin are given.
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  • 133
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    Journal of Computational Chemistry 10 (1989), S. 287-294 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The method presented earlier [T. Kikuchi, G. Némethy, and H.A. Scheraga, (1986) J. Comput. Chem. 7, 67] for the classification of patterns of the three-dimensional folding of a covalently crosslinked polypeptide chain has been extended to nonplanar proteins. The procedure described earlier was applicable only to proteins termed planar, i.e., with a connexity of the crosslinks (e.g., disulfide bonds) that can be represented in a planar diagram. The procedure described in the present work is applicable to any (planar or nonplanar) pattern of crosslinking. The classification is based on a systematic and objective method of enumeration of spatial geometric arrangements of loops (SGAL) using no information other than the location of the disulfide bonds in the amino acid sequence. Various SGAL classes correspond to the presence of different ways of mutual penetration of loops, called thrustings and entanglements. Information on SGAL classes can be of use in structural predictions of folding patterns of proteins.
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  • 134
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    Journal of Computational Chemistry 10 (1989), S. 302-308 
    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 structure of haloperidol as free base in its C(13) - C(14) trans form is optimized using Pulay's gradient method and a 4-21G basis set without any geometrical constraints. The resulting structure is compared with the experimental structure of the free base in the C(13) - C(14) gauche form and with the experimental structure of the HBr salt of haloperidol in the C(13) - C(14) trans form. Apart from the obvious differences, the two rotameric forms of the free base show many similarities. This, together with the manner in which the differences of the two experimental structures are distributed over the haloperidol molecule, leads to the conclusion that the conspicuous differences between the experimental structures are caused by inaccuracies in the X-ray determination of the HBr salt. Deviations of phenyl ring geometries from D6h symmetry and the asymmetry of the conformation around C(1) - C(9) could be rationalized by intramolecular effects.
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  • 135
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    Journal of Computational Chemistry 10 (1989), S. 309-328 
    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 lowest singlet along with selected high spin states of three isomers of Si4H4 have been investigated, using highly correlated wave functions in conjunction with a local pseudopotential approach. Tetrasilabicyclo[1.1.0]but-1(3)-ene 1 and tetrasilatetrahedrane 3a are established as true minima by means of the harmonic vibrational frequencies. The local minimum for tetrasilacyclobutadiene is not a planar 2a but a puckered conformer 2b. Isomer 1 was found to be the most stable of the investigated isomers lying 1.96 eV below 3a and 1.04 eV below 2b. A previously examined bond stretch isomer of tetrasilatetrahedrane 3b lies only 0.2 eV above isomer 1. The Si—Si bond energies of 2b, 3a, and 3b are determined as 208, 124, and 228 kJ/mol, respectively. An explanation of the bonding situation in 1 is given.
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  • 136
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    Journal of Computational Chemistry 10 (1989), S. 344-345 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In self-consistent field (SCF) calculations the construction of the Fock matrix is most time-consuming step. The Fock matrix construction may formally be seen as a matrix-vector multiplication, where the matrix is the supermatrix,Pijkl, and the vector is the first-order density matrix, γij. This formalism should be optimal for vector machines. This is not, however, fully utilized in most programs running on computers with small core memory. The size of the P matrix, typically in the order of 106-108 elements, has forced programmers to implement other nonvectorizable methods. We will present a submatrixbased algorithm which will partition the supermatrix so that vectorizable methods can be employed. The method will also reduce the input/output.
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  • 137
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    Journal of Computational Chemistry 10 (1989), S. 346-357 
    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 proton affinity, dipole moment, and first vertical ionization potential of a number of ortho-mono-substituted pyridines are computed at the restricted Hartree-Fock level, using a number of different basis sets. Some approximations concerning the geometry, the force constants, and the basis set superposition error are introduced. The effect of both the basis set and the approximations is investigated systematically. Two nonstandard basis sets, 4-31G(*) and 4-31+G(*), in which polarization functions are only applied to heteroatoms, are defined. A qualitative explanation for the effects of electron correlation on the proton affinity is given and underbuilt with the results of some MP2 calculations. While accuracy is maintained, computational cost is reduced very substantially.
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  • 138
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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: Different highly accurate experimental determinations of molecular structures (ED: rg and r0α, MW: r0, rs, and rz, and X-ray distances) of 14 unstrained hydrocarbons have been linearly correlated with corresponding self-consistent field Hartree Fock (SCF HF) ab initio full gradient-optimized structures. From the eight applied basis sets (STO-3G, STO-6G; 3-21G, 4-31G, 6-31G, 6-311G; 6-31G*, and 6-31G**) the 6-31G basis set, although not best regarding total energies, yields statistically the most precise regression equation, which allows the prediction of ED rg CC distances as reliable as the best experimental determinations. Surprisingly the accuracy of all calculated CC distances (measured as difference Δ between calculated CC distances and experimental ED rg values) depends linearly on bond distances, with the largest deviations being observed for triple bonds. This seems to be a clear indication of different influences of correlation effects on calculated geometries which are neglected in the applied HF treatment. The linear regression equations presented here allow the prediction of any kind of experimental CC distance parameters for each of the eight basis sets considered. Even experimentally unknown re CC distances may be predicted from these single determinantal HF optimizations.
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  • 139
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    Journal of Computational Chemistry 10 (1989), S. 358-366 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The problem of the computation of the matrix elements \documentclass{article}\pagestyle{empty}\begin{document}$$ I(v,v';k) = \int_0^x {\Psi _v (r)(r - r_e )} ^k \Psi _{v'} (r)dr, $$\end{document} is considered when Ψv(r) and Ψv(r) are eigenfunctions related to a diatomic potential of the RKR type (defined by the coordinates of its turning points Pi with polynomial interpolations). The eigenfunction Ψ(r) is computed by the canonical functions method making use of the abscissas ri of Pi uniquely. This limited number of points allows the storage of ψv(ri) for all the required levels v, and reduces greatly the computational effort when v, ν′, and k are varying. The present method maintains all the advantages of a highly accurate numerical method (even for levels near the dissociation), and reduces greatly the computing time. Furthermore, it is shown that it may be extended to analytical potentials like Morse and Lennard-Jones functions, to vibrational-rotational eigenfunctions and to matrix elements between eigenfunctions related to two different potentials. Numerical applications are presented and discussed.
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  • 140
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    Journal of Computational Chemistry 10 (1989), S. 376-379 
    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 is described for rapid calculation of excluded volume of large molecules. The excluded volume is defined based on coordinates of constituent atoms as the volume of overlapping spheres, each standing for a space around an atom inaccessible for a solvent molecule. A computer program based on the algorithm has been tested on a protein, ovomucoid. The accuracy of the numerical calculation is discussed.
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  • 141
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    Journal of Computational Chemistry 10 (1989), S. 380-385 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Prolog is applied to calculate the zero- through the sixth-order molecular connectivity indexes. A description of the program is given. Enumeration of substructure fragments, which is the most time-consuming part for this calculation, can be executed quite compactly by Prolog. For this execution, molecular structures and substructures are represented by Prolog facts and rules. An example of calculation is presented for a polycyclic structure. In addition, the method to increase the calculation speed is demonstrated.
    Additional Material: 6 Ill.
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  • 142
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    Journal of Computational Chemistry 10 (1989), S. 386-391 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Comparisons have been made between relaxation methods and certain preconditioned conjugate gradient techniques for solving the system of linear equations arising from the finite-difference form of the linearized Poisson-Boltzmann equation. The incomplete Cholesky conjugate gradient (ICCG) method of Meijerink and van der Vorst has been found to be superior to relaxation methods, with at least a factor of two improvement in speed, and only a 50% increase in storage.
    Additional Material: 5 Ill.
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  • 143
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    Journal of Computational Chemistry 10 (1989), S. 392-406 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A general survey of the topological properties of various phospines, phosphaalkenes, and phosphaalkynes is presented. Fifteen compounds containing carbon-phosphorus single, aromatic, double, and triple bonds were optimized at the Hartree-Fock-self-consistent field (HF-SCF) level using the 3-21G, 3-21G(*) and 6-31G* basis sets. Inclusion of d-orbitals was necessary to obtain reasonable structures. The electron densities of these compounds were analyzed using the topological method of Bader, revealing a number of trends. The value of the electron density at the P—C bond critical point correlates strongly with the bond distance and bond order. Integrated electron populations correlate with coordination number. The integrated charge indicates a strongly polarized C—P bond in all compounds. Comparisons with five C—N compounds are made.
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  • 144
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    Journal of Computational Chemistry 10 (1989), S. 417-425 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Algorithms and codes based on the method of Schur functions and Frobenius' theorem are used to generate the character tables of the symmetric groups (Sn) containing n! elements. The codes developed can generate characters of Sn up to n = 20.
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  • 145
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    Journal of Computational Chemistry 10 (1989), S. 413-416 
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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 convergence of the S matrix for the renormalized Numerov method, the original log-derivative method, and one recent version of this method is studied. A single- and a two-channel problem are analyzed and the percent relative errors for the S matrix and transition probabilities are calculated.
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  • 146
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    Journal of Computational Chemistry 10 (1989), S. 426-433 
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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 annular tautomerism of 1,2,3-triazole and 3(5)-methylpyrazole is discussed by means of a combination of theoretical calculations and experimental (ICR) gas-phase basicities and acidities. In the gas phase 1,2,3-triazole exists as the 2H-tautomer, whereas both tautomers of 3(5)-methylpyrazole are of similar energy. The solvent effects on these prototropic equilibria are discussed taking into account solvent properties as polarity/polarizability, acidity, and basicity. In nonhydrogen bonding solvents, the difference in dipole moments between both tautomers plays a role that has usually been underestimated.
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    Journal of Computational Chemistry 10 (1989), S. 434-434 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 148
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    Journal of Computational Chemistry 10 (1989) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 149
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Hydrogen exchange reactions between lithium and sodium compounds, MX (M=Li: X=H, CH3, NH2, OH, F; M=Na: X=CH3), and the corresponding hydrides, HX, have been modelled by means of ab initio calculations including electron correlation and zero point energy (ZPE) corrections. Small or no activation barriers (from the initial complexes) are encountered in systems involving lone pairs (10.8, 2.4, 0.0 kcal/mol for X=NH2, OH, F, respectively). Since the association energies of the initial complexes are much larger (21.0, 20.4, 23.5 kcal/mol, respectively; MP2/6-31+G*/6-31+G* + ZPE), such exchange reactions should occur spontaneously in the gas phase. The methyl systems (X=CH3) have the largest barriers: 26.7 (M=Li) and 31.7 (M=Na) kcal/mol (MP2/6-31+G*/6-31G* + ZPE), and the initial complexes are only weakly bound. The significance of these systems as models for hydrogen exchange reactions in complexes of electropositive transition metals is discussed. However, the gegenion-free exchange of hydrogen between CH3 and CH4 has a much lower, 11.8 kcal/mol barrier (MP2/6-31+G*/6-31+G* + ZPE). All the transition structures are highly ionic (charges on the metals 〉 +0.8). The effect of aggregation has been considered by examining the hydrogen exchange between (LiX)2 and HX(X=H, CH3, NH2, OH). Although these dimer reactions formally involve six, instead of four electrons, no “aromatic” preference is observed.
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  • 150
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    Journal of Computational Chemistry 10 (1989), S. 468-478 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Polarization and correlation effects on the nitrogen inversion barrier of some three-membered rings have been investigated. The characteristics of the barrier have been analyzed in terms of perturbation theory arguments. This analysis shows that the HOMO is the orbital that changes more dramatically along the inversion barrier. As a consequence, there is a good linear correlation between the destabilization undergone by the HOMO along the pyramidalization process and the barrier height. To obtain quantitatively meaningful barriers it is necessary to use polarized basis sets. Although polarization effects at the inverting center are dominant, a proper polarization of the remaining atoms of the ring seems also necessary. In general, with the only exception of 1H-diazirine, correlation effects on the barrier height are small if a polarized basis set is used.
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  • 151
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Notes: Proton affinities (PAs) of 2-, 3-, and 4-monosubstituted pyridines in the gas phase are calculated using the MINDO/3, MNDO, and AM1 methods. The following substituents are considered: F, Cl, CN, CH3, CF3, CHO, NO2, NH2, N(CH3)2, OCH3, and SCH3. The results are compared with experimental values. It is found that all MINDO/3 PAs are ca. 6% too high (mean value) compared to the experimental results; on the other hand, the MNDO values are ca. 7% too low (mean value). However, a much better agreement has been observed for the AM1 method where the theoretical values are only ca. 2.4% too low (mean value). Correlations between the calculated proton affinities on one hand and the charges on the acid H atom and Hammett constants on the other hand are studied. Particularly good linear relationships are found for the 4-monosubstituted compounds within the AM1 formalism.
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    Journal of Computational Chemistry 10 (1989), S. 495-502 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Basis sets ranging in size from (16, 10, 7) to (20, 14, 11) have been derived for the atoms Y-Cd. Separate sets represent the energy optimized wave functions for each of the s2dn, s1dn+1, and s0dn+2 configurations. The energies from the largest sets are within 3 mhartrees of the values obtained in numerical Hartree-Fock calculations. Reasonable Hartree-Fock s2dn- s1dn+1 and s2dn- s0dn+2 excitation energies may be obtained either using the largest basis sets, or using d-orbitals optimized for the s0dn+2 configurations. The basis sets are slightly unbalanced in favor of the s-functions and in disfavor of the d-functions, but various alternative basis sets may be derived by combining parts of the five parent sets. The convergence of radial expectation values is discussed.
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  • 153
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    Journal of Computational Chemistry 10 (1989), S. 529-551 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method for fitting a smooth ribbon representation of DNA structures is proposed. Following a review of the relevant definitions for classical linear helical DNA and generalizations to curving helices, a parameterization of smooth ribbons is given, which leads to tractable expressions. In addition it suggests a new way to define twist, tilt, and roll for a base step that is free of the ambiguities caused by noncommutativity of finite rotations. A least squares fitting criterion for ribbons is then proposed. In some cases the optimal ribbon with respect to this criterion is not unique. This problem is analyzed, and the circumstances in which it can occur are specified. To resolve the nonuniqueness problem, a variational description of the optimal ribbon is proposed, namely the ribbon of lowest elastic energy achieving a specified level of fit with respect to the least squares criterion. The appropriate level of fit is decided using distances of backbone atoms from fitted ribbon axes. Theoretical tests of the fitting methodology are presented, and as a sample application a smooth ribbon is fit to an existing experimental structure.
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  • 154
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    Journal of Computational Chemistry 10 (1989) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 155
    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.
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  • 156
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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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  • 157
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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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  • 158
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    Journal of Computational Chemistry 10 (1989), S. 683-697 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm for obtaining the matching polynomial of an arbitrary catacondensed unbranched benzenoid molecule is presented. It is based on multiplication of only three 5 x 5 transfer matrices I, J, K, and an appropriate terminal vector. The choice of the matrices is dictated by the history of the growth of the hexagonal “animals” (i.e., by the pattern of the successive fusions of the benzene rings). The approach also gives the number of Kekule valance structures, the count of conjugated circuits, the values of the topological index Z, and the characteristic polynomials.
    Additional Material: 7 Ill.
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  • 159
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    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.
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  • 160
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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.
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  • 161
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    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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  • 162
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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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  • 163
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    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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  • 164
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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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  • 165
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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.
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  • 166
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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.
    Additional Material: 3 Ill.
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  • 167
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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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  • 168
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    Journal of Computational Chemistry 10 (1989), S. 35-54 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An unusual type of π-electron delocalization in Y-shaped molecules related to guanidine and its protonated form, the guanidinium ion, has been studied by ab initio methods at the STO-3G and 3-21G levels. Results are reported for tautomeric, rotameric, and protonated forms of the oxygen-substituted guanidine series (urea, carbamic, and carbonic acids); “extended-guanidine” (aminomethylene guanidine) including pseudocyclic forms; and simple ring systems in which the extended-guanidine group is incorporated (3-amino-1,2,4-triazole, 2,4-diaminopyrimidine). Both the guanidine and guanidinium type stabilizations have been characterized in terms of a number of structural and energetic parameters: degree of single/double bond character from bond lengths and π-bond orders, electron distributions, and protonation energies. The major finding is that the structural and energetic properties of the isolated extended-guanidinium group resemble those of the group when incorporated within 6-membered heterocyclic or heterobicyclic rings, although the details vary with the nature of the ring and possibility of reinforcement or interference with the substructure resonance from overall ring delocalization. The implications for stabilization of the protonated forms of some biologically important pteridines is discussed.
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  • 169
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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: Conformational equilibria of mono-, di-, and trimethylisochromanes substituted in the heterocyclic ring are calculated by the MMP2(85) force field program. The results are in generally good agreement with the experimental findings of Pihlaja et al. The accuracy of experimental studies based on vicinal coupling constants is examined.
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  • 170
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A pilot wet scrubber was examined experimentally. It is constructed like a plate column. Its plates are designed to set the gas into a whirling motion with tangential velocities of up to 25 m/s and to ensure a uniform distribution of the liquid throughout the gas flow. Particles suspended in the waste gas are collected by gas-atomized droplets to yield cut diameters between one and two microns. Energy consumption is lower than in the case of other scrubbers. The scrubbing mechanisms are analyzed by examining the measured pressure drops. Finally, methods of determining the collection efficiency are discussed and an empirical approach to its calculation is presented.
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  • 171
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    Chemical Engineering & Technology - CET 11 (1988), S. 139-148 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The suitability of any item of equipment for a given thermal separation process cannot always be judged solely in the light of efficient and loading range data. In vacuum rectification, involving a large number of theoretical stages, the vapour pressure drop per transfer unit exerts a considerable effect on the energy consumption and thus largely governs the choice of column fittings. Furthermore, the pressure drop per transfer unit determines the temperature at the bottom of a rectification column and, hence, the suitability of the equipment for the separation of heat-sensitive products. It is also an important criterion for compressor requirements in absorption processes. Another factor of considerable importance in separating heat-sensitive mixtures by distillation is the time during which the product, particularly the liquid phase, is exposed to a given temperature in the column. Therefore, a standardized liquid residence time has been adopted to evaluate the systems in their entirely. This residence time depends on the hydrodynamic conditions in the column and is thus closely related to pressure drop and efficiency. Further important factors, which may decide the selection of column internals, are the specific volume and mass of the column. Based on theoretical considerations, a flow model is derived for describing the main loading range of countercurrent packed columns; the relationships between the above mentioned parameters are presented.
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  • 172
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    Chemical Engineering & Technology - CET 11 (1988), S. 156-162 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A report is presented on the influence of liquid flow rate, NaOH concentration, column length and presence of 5 × 10-3 wt-% of the surfactant SLS on the rate of absorption of pure SO2 by aqueous NaOH solution in a sphere-and-cylinder column. The presence of sodium lauryl sulphate (SLS) prevented axial turbulence which increased mass transfer in longer columns and was almost independent of the flow rate. The enhancement factor due to the reaction between SO2 and NaOH with respect to the process of physical absorption was analyzed for the systems with excess OH- in the outflow. The results obtained in the presence of a surfactant are satisfactorily explained by film theory with a single reaction plane model. Those obtained in the absence of surfactant are best described by a two-plane model using renewal theory.
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  • 173
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    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Experimental investigation of stirring processes require the measurement of temperature changes and concentration profiles in all the zones of the mixing volume. The conversion of simultaneous chemical reactions during the mixing process depends on the local temperature and concentration. The time-dependent temperature and concentration fields can be recorded for the entire mixing volume with the use of optical tomography and correlated with time. This technique offers the possibility of continuous measurement of temperature and concentration changes during the mixing process throughout the measurement volume. In the described investigations, optical tomography is used to examine the transport and equalization processes during mixing in stirred vessels.
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  • 174
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    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Theoretical modelling of heat transfer to particle beds comprises two sequential steps: transfer from the heating surface to contacting particles followed by transfer to the interior of the bed. Two different limiting case can be formulated for the second step: unmixed and homogeneously mixed bed. In the case, heat is transferred gradually via a repeated sequence of heat transfer in the gap between adjacent particles and conduction in the particulate material. In the second case, heat is transferred to the interior of the bed by mixing of particles which have previously attained the temperature of the heating surface. On the other hand, the mixing motion maintains a homogeneous lower temperature throughout the bed. Theory predicts a significant and easily measurable difference in the behaviour of heat transfer coefficients for the two regimes at long contact times t: unmixed beds ∝ \documentclass{article}\pagestyle{empty}\begin{document}$$ \sqrt t $$\end{document} and homogeneously mixed beds ∝ 1/t. For short times t, both regimes show the same behaviour, namely of t.From a theoretical standpoint, it makes sense to differentiate further between the behaviour patterns of unmixed beds: at long times t, instantaneous heat transfer coefficients are independent of heat transfer form the heating surface to adjacent particles. Comparison with experimental result from literature shows that the derived models, which are consistent, are suitable for describing the heat transfer from submerged surfaces to unmixed and mixed beds of particles.
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  • 175
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The aim of the present paper is the discussion of the relevance of power dissipation as a criterion for the understanding and prediction of transfer and mixing efficiencies in contactors and chemical reactors. After reviewing the approach of Le Goff to the energetic efficiency of exchangers, based on the deviations from Chilton-Colburn analogy, the following processes are studied: mass transfer between a flowing fluid and a reactive solid surface, transfer to a fixed object in a stirred vessel, macro- and micromixing of miscible fluids, and mass transfer in fluid-fluid contractors (especially gas-liquid reactors). It is concluded from the various examples that a direct relationship between the dissipated power and intensity of transfer or mixing can be established only under the two following conditions: local values must be considered at the point where the actual transfer and mixing occur, and not average values over the whole device, and power dissipation must be coupled to transfer or mixing and appear physically as the driving force of the process.
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  • 176
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    Chemical Engineering & Technology - CET 11 (1988), S. 402-407 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Increasing demand for regenerable processes with SO2 recovery is to be expected. Advantages and limitations of the earlier developed citrate and adipate absorption/ steam stripping process are compared with those of the Wellman-Lord (sulphite) process. On the basis of comprehensive laboratory studies, a new process is proposed which supplements the citrate and adipate process. In this new process, the absorbent is a concentrated sodium phosphate buffer and the loaded buffer is regenerated by evaporation. The main buffer component is Na2HPO4, but NaH2PO4 is added in order to obtain a more complete stripping of SO2 during regeneration. The new process promises excellent absorption properties for SO2 with extremely low oxidation losses, regeneration with few incrustation problems and appreciable energy savings.
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  • 177
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    Chemical Engineering & Technology - CET 11 (1988) 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
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  • 178
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    Chemical Engineering & Technology - CET 11 (1988), S. 11-17 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Design and operation of a circulating fluidized bed requires the knowledge of fluid mechanics. According to heat and mass transfer as well as chemical reactions, the effect of the set superficial gas velocity on the axial pressure profile is of particular interest. The axial pressure profile was measured for a variety of solids, as a function of the superficial gas velocity, in a cylindrical circulating fluidized bed with an inner diameter of 0.19 m and an overall height of 11.5 m. Depending on the solids content and superficial gas velocity, two or one sections can be observed in the plant where the pressure gradient is constant. A pressure profile with one pressure gradient exists only at high gas velocities, so long as the acceleration pressure drop immediately above the gas distributor is negligible. Comparison of measured pressure drops in circulating fluidized beds with those measured in vertical pneumatic conveying led to a state diagram for vertical gas-solid flows. The operation behaviour of different types of circulating fluidized bed plants can be explained with the aid of this diagram.
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  • 179
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    Chemical Engineering & Technology - CET 11 (1988), S. 17-25 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Crossflow microfiltration (CMF) is a pressure driven membrane process for the separation of suspended microparticles, bacteria and emulsion droplets. The fluid to be filtered flows in parallel to the membrane surface and restricts the formation of a filter cake. This contribution explains the basic process characteristics and the combination of the crossflow technique with other membrane cleaning methods (periodic backflushing, chemical cleaning). Special attention is paid to the influence of different process parameters on the flux through the membrane. The principle of plant design and different operation modes are described. Engineering aspects such as hydrodynamics, energy requirement and selection of construction materials are discussed in some detail.
    Additional Material: 10 Ill.
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  • 180
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    Chemical Engineering & Technology - CET 11 (1988), S. 25-31 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: While two- and multiphase flows find more and more application in chemical engineering practice, and the demand for theoretical information about mass and heat transfer processes in such systems is increasing, such data or at least experimental results which could be generalized are still lacking. The following pages are concerned with mass transfer in laminar suspension tube flows normal to the main direction of flow due to the individual motions of small, inert spherical particles. On the basis of a large number of experimental data, an interpretation is attempted of the role of nearly neutrally-buoyant particles in mass transfer enhancement, and a model for a semi-empirical description is suggested. The experimental arrangement uses the mass transfer of carbon dioxide in laminar flow of salt water during the process of gas permeation through a permeable membrane tube wall.
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  • 181
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    Chemical Engineering & Technology - CET 11 (1988), S. 1-10 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Interfacial areas and gas hold-ups were determined at pressures of up to 1.7 MPa in a glass vessel, 88 mm in diameter and of standard geometry. Superficial gas velocities between 0.25 and 2.0 cm/s were used and the stirring speed varied between 4 and 30 rps. The interfacial areas were determined by the chemical method, using the model reaction between CO2 and aqueous diethanolamine (DEA). Hold-ups were determined by observation of differences in height. In contrast to literature indications, the gas hold-up was found to be independent of reactor pressure. This is also true for the interfacial area.
    Additional Material: 12 Ill.
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  • 182
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    Chemical Engineering & Technology - CET 11 (1988), S. 243-248 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Pyrolysis of propane/argon mixture in the presence of trace quantities (0.1% and 0.9%) of ethane was investigated at reflected shock wave temperatures between 1200 and 2000K. Traces of ethane accelerated propane decomposition at high temperature. However, increase in the quantity of ethane added to propane/argon mixture did not result in the same increase of its accelerating influence. Ethylene, methane and acetylene were the main hydrocarbon reaction products, with small quantities of propylene and ethane detected only at lower temperatures. Below 1500K, addition of ethane slightly enhanced the yields of ethylene and methane at the expense of propylene and ethane respectively. The selectivity for acetylene increased with increasing temperature and with the decline of those for the other products. For none of the products, did the presence of ethane alter the relationship between product formation rates and temperature. The influence of ethane addition on propane pyrolysis at high temperatures was explained in terms of increased radical concentrations, especially hydrogen atoms and vinyl radicals, formed at high conversions. These accounted for the rapid acceleration of propane decomposition and the high yield of acetylene at high temperatures.
    Additional Material: 6 Ill.
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  • 183
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    Chemical Engineering & Technology - CET 11 (1988), S. 312-320 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: This contribution presents the methods of measuring the mass transfer in centrifugal extractors and of determining it during the individual life stages of a fluid element of the dispersed liquid, i.e. drop formation, motion, coalescence and stay in the stationary layer of the dispersed phase. The experimental mass transfer coefficients of the dispersed and continuous phases are compared with well-known theoretical models developed for extraction columns in gravitational field. Due to the fast motion and coalescence of the fluid particles at high centrifugal field intensities, mass transfer in centrifugal extractors takes place during short contact times. Nevertheless, this contribution shows that mass transfer in a centrifugal field can be calculated with selected theoretical models of the gravitational field. The investigations on mass transfer are completed by a classification of the strongly deformed fluid particles in centrifugal field into regimes of circulating and oscillating drops. In addition, data on the performance of centrifugal extractors, undergoing several exchange steps, are given.
    Additional Material: 13 Ill.
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  • 184
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    Chemical Engineering & Technology - CET 11 (1988), S. 392-402 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The kinetics of heterogeneously catalyzed methacrylic acid synthesis from isobutyric acid has been investigated. Initial catalyst screening pointed to 10-molybdo-2-vanado-phosphoric acid and its Cs-salts as the most promising catalysts. A model describing the reaction behaviour of all the different hetropoly-compounds used in this work was developed. A relationship was found between model parameters and composition of different catalysts. First insight was gained into the catalyst deactivation phenomena. Deactivation appears to be caused mainly by loss of molybdenum with simultaneous collapse of the Keggin structure.
    Additional Material: 18 Ill.
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  • 185
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Transient diffusion of inert gases into Zeolon 900 H, a zeolite of the mordenite type, was studied by the chromatographic method. Experiments were performed with argon and helium either as tracer or as carrier gas. The diffusion of argon was also studied in a carrier gas containing methanol at a low temperature (75°C, no reaction) and at higher temperatures (up to 130°C) when some dehydration of methanol to dimethyl ether takes place. The adsorption isotherm of argon is linear. In the absence of methanol, its penetration into microcrystals of zeolite is equally well represented either by an effective diffusion coefficient D′μ = 7.4 × 10-8exp(-2873/T)m2s-1 or by a mass transfer coefficient at the crystallite surface keμ = 1.9 × 10-4 exp(-1324/T) ms-1. A small amount of methanol in the carrier gas considerably slows down the transfer of argon (by a factor of 40 for D′μ and 550 for keμ) showing the “blocking” effect of adsorbed methanol. In addition, transient adsorption can no longer be accounted for by a single transfer time. The size distribution of microcrystals, determined from Scanning Electron Microscope photographs leads to a Transfer Time Distribution which account well for experimental breakthrough curves without any parameter fitting. This interpretation is supported by experiments under reaction conditions where transport of argon within crystallites increases faster with temperature than in the absence of reaction due to the transformation of methanol into dimethyl ether, which is less adsorbed and thus provides lesser hindrance to argon diffusion.
    Additional Material: 8 Ill.
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  • 186
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Fischer-Tropsch catalysts (Fe/V oxides with ZnO and K2CO3 as promoters) were exposed to CHCl3, thereby producing surface and bulk chlorides. The effect of this exposure on activity and selectivity was studied in a continuous recycle reactor at a total pressure of 10 bar (CO/H2 in most experiments: ca 1:1) in a temperature range between 200 and 343°C. CHCl3 was introduced in amounts of up to 1 × 10-2 mol chlorine per g catalyst. The catalyst samples were characterized by internal surface area, pore-size distribution and adsorption capacities for CO, H2 and C2H4. Prior to synthesis, the catalysts were reduced by H2. Catalyst exposure to CHCl3 resulted in a decrease of activity and considerable changes in product distribution. Hydrogenation and isomerization of 1-olefins were partly suppressed; the chain length of the products was slightly increased. Deactivation of the catalysts due to chlorine addition was partly reversible during operation, while olefin formation was not significantly altered with time-on-stream. The effect of chlorine on activity and selectivity is explained by dissociation of CO as the chain initiating step and CO insertion into a carbon/metal bond as a possible chain propagation step. Since adsorption capacity for H2 decreases on the addition of chlorine, this may also contribute to lower activity and change in selectivity, compared to the unexposed catalyst.
    Additional Material: 7 Ill.
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  • 187
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    Chemical Engineering & Technology - CET 11 (1988), S. 50-56 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The performance characteristic of a packed bed reactor has been analyzed by considering diffusional resistance of the biofilm. Model equations were solved by the method of orthogonal collocation for various classical enzyme inhibition kinetics, including partially non-competitive, partially competitive, partially uncompetitive, partially mixed and fully mixed. For all considered modes of inhibition, an increase in the inlet substrate concentration decreases the steady state conversion in the reactor. However, an increase in the Peclet number has been found to improve the conversion. The effects of various other process variables of physical importance were also investigated parametrically.
    Additional Material: 15 Ill.
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  • 188
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    Chemical Engineering & Technology - CET 11 (1988), S. 63-72 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Asymptotes are known to be useful, but their potential in interpreting and correlating chemical and physical behaviour is seldom exploited fully. The derivation and selection of asymptotes for particular as well as limiting cases is described. The evaluation of the range of validity and applicability, if any, of asymptotes is also considered. Asymptotes are shown to be uniquely useful in the identification of groupings of variables which minimize parameteric variations, as upper and lower bounds, as trial functions in the method of weighted residuals, and most especially as components of correlating equations.
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  • 189
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    Chemical Engineering & Technology - CET 11 (1988), S. 57-62 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A single variable pole-placement self-tuning controller (PPSTC) is used to simulate examples typical of chemical processes; i.e., open-loop stable, unstable, and unstable non-minimum phase systems with unknown varying process dead time. The PPSTC is shown to be effective in each case. Set-point tracking and rejection of randomly occurring deterministic disturbances for all three types of processes are achieved. Simultaneous estimation of process parameters and process time delay is realized by using a recursive extended least squares method.
    Additional Material: 10 Ill.
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  • 190
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: An important parameter influencing the crystal size distribution in mass crystallization from solution is the mechanical stress exerted on crystals in the crystallizer. This contribution presents the study of the influence of mechanical stress and attrition of the system potassium nitrate-water in an FC-crystallizer and in various draft-tube crystallizers, fitted with different types of impellers. The intensity of stress is a newly defined variable which is used to describe the level of stress in crystallizers. The reduction of crystal size by attrition is described by the linear attrition rate. The influence of impeller design and crystal hold-up on crystal size distribution and scale-up rules is discussed.
    Additional Material: 16 Ill.
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  • 191
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    Chemical Engineering & Technology - CET 11 (1988), S. 80-88 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The mean crystal size of coarse crystalline products is determined by secondary nucleation and crystal growth. Secondary unclei are mainly produced by contacts of crystals with parts of the crystallizer or with other crystals. As a consequence, attrition effects are very important. In this paper, a model is proposed in order to calculate the attrition rate of crystals, depending on the physical properties of the crystalline product, the geometry of the crystallizer and on the operating conditions such as the stirrer speed or the suspension density. The effective rate of secondary nucleation can be expressed in terms of the attrition rate by introducing effective values for number and size of attrition particles. Finally, a scale-up criterion based on this model is derived. This criterion allows to predict effective rates of secondary nucleation and mean crystal sizes if data obtained in a laboratory crystallizer are available.
    Additional Material: 11 Ill.
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  • 192
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    Chemical Engineering & Technology - CET 11 (1988), S. 95-104 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Settling characteristics of four different suspensions were measured by batch settling tests (glass spheres in glycerol-water mixtures and CaCO3) and by continuous settling test in a bench-scale vertical flow tank (activated sludge and kaolin in water), including the measurement of solids concentrations inside the tank. The characteristics could be described by different correlation functions which now include all the information about the settling behaviour of ideal suspensions. Continuous settling experiments in a bench-scale vertical flow tank were carried out with the same four material systems. These results correspond with sufficient accuracy to those from the theory of limiting flux if the settling characteristics determined earlier are considered.
    Additional Material: 15 Ill.
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  • 193
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    Chemical Engineering & Technology - CET 11 (1988), S. 113-119 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Thermal deactivation can be described either by deactivation kinetics or by the isokinetic effect. The latter expression is used synonymously with the “compensation effect” and the “Theta-Rule”. An examination of the original literature shows that only the compensation effect is applicable to thermal deactivation but not the Theta-Rule. The introduction of the preparation temperature as a parameter of the compensation effect results in a “modified Theta-Rule”, which describes the experimental data and is proposed for the non-separable kinetics. The consequence of the observed deviations from the validity range of the Theta-Rule is that the activation energy cannot be used as a universal activity criterion.
    Additional Material: 1 Ill.
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  • 194
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    Chemical Engineering & Technology - CET 11 (1988), S. 89-94 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A number of topped crude oil residues were subjected to mild thermal cracking in the temperature range between 613 and 673K at N2 pressure of one atmosphere. It was found that the thermal stability of the six topped crude oils decreased in the order Brent 〈 Piper 〈 Auk 〈 Saudi Arabian 〈 Romashkinskaya 〈 Tia Juana Pesado. This was measured in terms of light end production (C1-C5 hydrocarbons). The asphaltene, sulphur and metal (nickel and vanadium) contents were also determined. The production of light ends, exemplified by methane, was found to be related to the metal asphaltene content of the crude oils, but the sulphur content exerted a moderating influence upon the extent of cracking. Hence, metal asphaltenes, probably as metal porphyrins, catalyse cracking but the presence of sulphur reduces that catalytic activity and can inhibit cracking. If cracking of long chain hydrocarbons is to be minimized, metal asphaltenes should be removed (preferably) or reduced in concentration or poisoned, in order to decrease their catalytic activity.
    Additional Material: 5 Ill.
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  • 195
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    Chemical Engineering & Technology - CET 11 (1988), S. 120-126 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The kinetics of non-catalytic as well as catalytic oxidation of Isobutyraldehyde has been investigated. Reaction rate equations for the formation of the main product isobutyric acid and of the side products acetone, CO and CO2 were derived. Kinetic parameters, namely the order of reaction, preexponential factor and activation energy were estimated by non-linear regression. The influence of selectivity and activity of the different type of catalysts employed was investigated quantitatively.
    Additional Material: 11 Ill.
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  • 196
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    Chemical Engineering & Technology - CET 11 (1988), S. 228-236 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The interpretation of the term “compensation” obscures a logical contradiction, the catalytic paradox, which is caused by inconsistent validity ranges of the Arrhenius parameters, the pre-exponential factor and the activation energy. For this reason, a theory which contains the Arrhenius parameters cannot be established for the entire system (whole temperature range) on the basis of classical logic. Only the subsystems can be consistent and complete. One subsystem is the range of the topocatalytic concept which is relevant for thermal deactivation, thermal bistability and for all reactions with surface dependence of activity. The other is the range of the energetic concept which is preferred in fundamental research. In order to complete the subsystems, new consistent symbols are introduced. The change of particle size caused by thermal deactivation can result in four possible particle size effects, two of which have been discussed in the literature.
    Additional Material: 4 Ill.
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  • 197
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Thermal radiation of gas/solid mixtures in high-temperature heat exchangers is of considerable importance for the design of heat exchange surfaces. Therefore, an experimental plant was constructed to measure solid particle emissivities, since there is a lack of relevant data in the existing literature. A theoretical equation was derived to describe the solid particle emissivity as a function of layer thickness, specific solid surface area, solid loading and absorption and scatter coefficients. Measurements were carried out for fluidized bed ash and quartz sand. The emissivities of these particle fractions increase with increasing layer thickness, slid loading, specific solid surface area and temperature. The description of these data by the derived model equation is very satisfactory. No dependence on wavelength was observed. The ash components do exert some influence which, for the present, cannot be described exactly.
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  • 198
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    Chemical Engineering & Technology - CET 11 (1988), S. 213-227 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A report is presented on the performance of modern dumped and structured packings for application in the field of thermal separation processes. The evaluation of the results is based on extensive experimental investigations of rectification, absorption, and desorption systems. The following are indicated: the efficiency in terms of the number of theoretical stages per unit height or in terms of the height of transfer unit or volumetric mass transfer coefficient, the pressure drop per unit height as well as per theoretical stage or per gas phase transfer unit, and the liquid hold-up, whereby either the gas capacity factor or the liquid load was adopted as influencing parameter, and finally the maximum gas capacity factor as a function of the flow parameter. The results are presented in diagrams and tables.
    Additional Material: 25 Ill.
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  • 199
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    Chemical Engineering & Technology - CET 11 (1988), S. 249-251 
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: It is shown that the volumetric mass transfer coefficients, presented recently by Schmitz et al. [1] for viscous solutions of carboxymethyl cellulose (CMC) in aqueous sodium sulphite, are considerably underestimated as a result of unjustified neglect of the oxygen back pressure during oxygen absorption. Schmitz et. al. [1] found a decrease in the exponent n in the relationship between the oxygen mass transfer coefficient, kla, and the power dissipated per unit volume of the liquid phase, e (kla ∝ en), and ascribed it to viscosity effects. However, no such decrease is observed, provided that the actual oxygen back pressure is taken into account.
    Additional Material: 2 Ill.
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  • 200
    ISSN: 0930-7516
    Keywords: Chemistry ; Industrial Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: NOx emissions from different commercial gas burners for metal heat treatment applications were measured for a research project of the Gaswärme-Institut. The burners, rated at up to 50 kW, were installed for the tests in a laboratory combustion chamber operated at temperatures of up to 1400°C. The air for combustion was preheated to maximum temperature of 600°C. Following the tests, the potentials of different NOx control techniques were investigated. Methods explored included staged combustion air injection, staged fuel injection and fuel gas injection into the flue for NOx reduction. The results showed that it is feasible to reduce the NOx content of flue gases by as much as 90%.
    Additional Material: 16 Ill.
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