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  • Wiley-Blackwell  (3,081)
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  • 1
    Electronic Resource
    Electronic Resource
    A conformational analysis of 3′-azido-3′-deoxythymidine (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 478-491 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An extensive conformational analysis of 3′-azido-3′-deoxythymidine (AZT) was performed at the semiempirical AM1 level with full relaxation of all geometric parameters and careful consideration of furan puckering and the rotational states of the thymine - furan, furan - azide, furan - methylene, and methylene - hydroxyl bonds. The search located 70 conformers, 21 of which have relative energies within 2.5 kcal/mol of the global minimum. Several geometric features, including various forms of hydrogen bonding, within this selected lowenergy subset were examined in terms of their relative contributions to the conformational states of AZT. Hydrogen bonding of thymine's position 2 carbonyl oxygen atom to the hydroxymethyl group (O2—;HO), which until recently has not been mentioned in the literature, is observed in a few low-energy AM1 conformations; however, this form is less favored at the AM1 level than the usually depicted modes involving the thymine moiety with the oxygen atoms of the hydroxyl and furan groups (H6—;OH and H6—Ofur, as observed in the two crystallographically independent structures), as well as that involving the hydroxyl hydrogen and furan oxygen atoms (OH—Ofur, which also has not been mentioned for AZT in the literature until recently). The AM1-optimized geometries agree more closely with nuclear magnetic resonance data than with crystallographic structures and bear little resemblance to molecular mechanics results. The present study shows no evidence of a single dominant conformation or single structural parameter that determines AZT's conformational states. In contrast to our previous analogous study of cGMP, this computational study of AZT does not show strong evidence of a syn conformation with hydrogen bonding involving the base.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540130410
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  • 2
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    Comparison of ab initio, semiempirical, and molecular mechanics calculations for the conformational analysis of ring systems (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 525-532 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The potential energy surfaces of four cyclic alkanes have been examined using molecular mechanics, semiempirical, and ab initio methods to determine if they produce mutually consistent results and investigate the source of any errors between the methods. The C5 — C8 cyclic alkanes were chosen since these structures present a finite set of conformations and transition-state geometries and are still within the computational time and memory limits of the quantum mechanical approaches. We also examined several conformations of 1,2-dideoxyribose to determine the effect of heteroatoms on the results for the 5-membered ring. The molecular mechanics and ab initio calculations are consistent in the relative energies and geometries determined for the conformers of all ring systems. While the semiempirical calculations yielded geometries consistent with the other methods (except for 5-membered rings), the relative energies often deviated substantially. A decomposition analysis of the semiempirical and molecular mechanics energies revealed that the disparities are mainly due to errors in the 1-center energies of the semiempirical calculations. The 2-center bonding and nonbonding energies followed reasonable trends for the conformers. The core-repulsion function, however, is suspected of producing anomalies. A minimum in the attractive Gaussian of this term at 2.1 Å for H—H interactions partly explains the propensity of the 5-membered rings to optimize to near planarity (decreasing 1,2-diaxial hydrogen distances to 2.3 Å) and the underestimation of the relative energy of the boat structure of cyclohexane.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540130413
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  • 3
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    Alternative expressions for energies and forces due to angle bending and torsional energy (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 585-594 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have derived alternative expressions for computing the energies and forces associated with angle bending and torsional energy terms commonly used in molecular mechanics and molecular dynamics computer programs. Our expressions address the problems of singularities that are intrinsic in popular angle energy functions and that occur from other chain rule derivations of force expressions. Most chain rule derivations of expressions for Cartesian forces due to angle energies make use of relations such as \documentclass{article}\pagestyle{empty}\begin{document}$$ \frac{{\partial E}}{{\partial x}} = \frac{{\partial E}}{{\partial \phi }}\frac{{\partial \phi }}{{\partial \cos \phi }}\frac{{\partial \cos \phi }}{{\partial x}} $$\end{document} where φ is a bond or torsion angle, E(φ) is energy, and ∂/∂x represents a derivative with respect to some Cartesian coordinate. This expression leads to singularities from the middle term, -1/sin φ, when φ is 0 or π. This is a problem that prevents the use of torsional energy expressions that have phase angles, φ°, other than 0 or π, such as in E(φ) = κ[1 + cos(nφ - phsi;°)]. Our derivations make use of a different, but equivalent, form of the chain rule: \documentclass{article}\pagestyle{empty}\begin{document}$$ \frac{{\partial E}}{{\partial x}} = \frac{{\partial E}}{{\partial \phi }}\frac{{\partial \phi }}{{\partial x}} $$\end{document} This form still possesses singularities for the bond angle forces since the last factor is undefined when φ is 0 or π. However, the alternate form may be used to great advantage for the torsional angle forces where no such problem arises. The new expressions are necessary if one desires the use of torsional energy expressions with general phase angles. Even for energy expressions in common use, i.e., with phase angles of 0 or π, our force expressions are as computationally efficient as the standard ones. The new expressions are applicable to all molecular simulations that employ restrained, or phase-shifted, torsional angle energy expressions.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540130508
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  • 4
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    Conformational dependence of electrostatic potential derived charges of a lipid headgroup: Glycerylphosphorylcholine (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 622-632 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atomic monopoles are routinely determined through a least squares fit to molecular electrostatic potentials. We report studies of the variation in atomic monopoles with variation in conformation for the zwitterionic polar head group of lecithins, a common class of lipid. The monopole of one atom, a relatively buried carbon, varied by 1.3 electron units between different conformers. “Exterior” atoms, as seen previously, showed smaller changes in charge and smaller estimated standard deviations. The total charge of local groups of atoms varied less than the charge of individual atoms, indicating that shifts in charge occurred mostly between neighboring atoms. This effect might be reflected in the high correlations seen between charges of many neighboring atoms. These correlations, while present for many logical groupings of atoms (such as within methylene and methyl groups), are curiously absent between some bonded atoms. Monopoles were fit to multiple conformations simultaneously to provide a charge set that could optimally reproduce the electrostatic potential of all the conformers as a means of generating monopoles for molecular dynamics simulations or other studies where conformation varies. In some cases, the charges on chemically equivalent atoms (e.g., the hydrogen atoms in a methyl group) were different by more than their estimated error of fit. These studies lead to the suggestion that a minimum error in reported charges is on the order of 10%. All conformations show that the positive charge of the trimethylalkyl ammonium group is carried by the methyl hydrogens; the total charge on the nine hydrogens is over 2 electron units, counterbalanced by negative monopoles on the carbons. The presence of this diffuse cloud of substantial charge would appear to be a disindicator of the use of a “united” atoms approach for these methyl groups. The effects of the charge variation on intermolecular interactions is also examined.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540130512
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    Masthead (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992) 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540130601
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  • 6
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    Theoretical study of some nitriles: Intramolecular hydrogen bonds and anomeric effect (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 722-729 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An ab initio study of 3-chloro-, 3-hydroxy-, 3-mercapto-, and 3-amino-propanenitrile and 4-chloro-bu- tanenitrile was carried out at several levels of theory. The calculated stabilities and geometrical trends are interpreted in terms of the effects of intramolecular hydrogen bonds and anomeric interactions, and compared with available experimental data.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540130607
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  • 7
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    Conformational preferences for hydroxyl groups in substituted tetrahydropyrans (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 772-791 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Quantum mechanical (ab initio and semiempirical) and force field calculations are reported for representative torsion potentials in several tetrahydropyran derivatives. The overall agreement between the various methods is quite good except that the AMBER torsion profiles are sensitive to the choice of atomic point charges. Using electrostatic potential (ESP) derived atomic point charges determined with the STO-3G basis set we find that AMBER is able to match the best quantum mechanical results quite well. However, when the point charges are derived using the 6-31G* basis set we find that scaling the intramolecular electrostatic nonbond interactions is necessary. AM1 does not work very well for these compounds when compared to the ab initio methods and, therefore, should only be used in cases when ab initio calculations would be prohibitive. Based upon our results we feel that any force field that makes use of 6-31G* ESP derived atomic point charges will need to scale intramolecular interactions. Implications of scaling intramolecular interactions to the development of force fields based on 6-31G* ESP derived atomic point charges are discussed. © 1992 by John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540130611
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    Molecular electrostatic potential of substituted aromatic compounds: Factors affecting the differences between Ab Initio and semiempirical results (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 842-850 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular electrostatic potential (MEP) distribution of anisole, chlorobenzene, and fluorobenzene obtained from STO-3G, 3-21G, and 6-31G* basis set ab initio and MNDO and AM1 semiempirical wave functions is investigated to explain the differences among the MEP features obtained for polychlorodibenzo-p-dioxins. The main topological features as well as the absoltue and relative minima location obtained from ab initio calculations are independent from the choice of the basis set. MNDO calculations are in good agreement with the ab initio ones in the case of anisole and fluorobenzene, while they incorrectly describe the MEP of chlorobenzene. The AM1 fails to localize the absolute minimum of fluorobenzene and does not find the minimum above the chlorobenzene chlorine atom. The poor agreement of both semiempirical methods with ab initio for any kind of chlorinated compounds is confirmed by results obtained for chloreothylene and chloroethane. We hypothesize that the main problem concerning these methods is that they freeze a too large amount of electrons in the atomic core of elements belonging to the second row, which makes for a wrong description of the core-valence electron interactions. Results obtained by modifying the AM1 parameters related to these interactions confirm our hypothesis. © 1992 by John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540130708
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    Torsional energy levels and wave functions (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 874-882 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A numerical method for solving the approximate Schrödinger equation (SE) for a single internal motion is presented. In the SE the reduced moment of inertia I(φ) and potential energy V(φ) are expressed as functions of the torsional angle φ. Molecular examples include ethane, chloroethane, and 1,2-dichloroethane for which I(φ) and V(φ) have been derived from the HF/6-31G* optimized geometries and energies at φ increments of 30°. The resulting potential energy curves, energy levels, and wave functions are shown graphically. The calculated fundamental torsional frequencies are found to fall within 10 cm-1 of the experimental values. Approximations for the off-diagonal energy matrix elements, and numerical accuracy of torsional energy levels, are shown to be satisfactory. Attention is called to the computer programs developed for this work and their applications to torsional studies in relevant areas of spectroscopy, thermodynamics, and reaction rates. © 1992 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540130712
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    Electronegativity and Bader's bond critical point (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 912-918 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The electronegativities () of some 36 atoms/groups (including some 6 ionic ones) X are calculated from the atomic charges in the corresponding methyl species CH3X that were obtained by applying Bader's theory of atoms in molecules. The numerical values of the for the various groups studied are reasonable and correlate linearly with the two existing experimental scales for group electronegativity, Inamoto's i scale and the 1JCC (ortho-ipso) coupling constants in the monosubstituted benzenes, to satisfactory extents. The relations between the values and some “critical properties” of the various CH3X molecules considered are also studied. It is suggested that in a molecule PX, rP/R where rP is the distance of Bader's critical point on the bond PX of length R from the atom P or the binding atom of the group P can be a very good measure of the electronegativity of the atom/group X. © 1992 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540130716
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    Improvements to the distance geometry algorithm for conformational sampling of cyclic structures (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 565-569 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Modifications to the distance geometry algorithm as embodied in the program DGEOM have been made to improve sampling capabilities. Specifically, torsion angle sampling replaces distance sampling for 1,4 atomic relationships and correlated distance sampling is disabled. The effects of these modifications are illustrated by comparing the different sets of conformations produced for butane. In addition, these changes are shown to increase the conformational sampling of two medium-sized rings, cycloheptadecane and caprylolactam. The current results for these molecules are compared to those of other conformational searching methods.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540130505
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    Kramers' restricted hartree - fock method for polyatomic molecules using ab initio relativistic effective core potentials with spin - orbit operators (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 595-601 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A two-component Kramers' restricted Hartree-Fock method (KRHF) has been developed for the polyatomic molecules with closed shell configurations. The present KRHF program utilizes the relativistic effective core potentials with spin-orbit operators at the Hartree-Fock (HF) level and produces molecular spinors obeying the double group symmetry. The KRHF program enables the variational calculation of spin-orbit interactions at the HF level. KRHF calculations have been performed for the HX, X2, XY(X, Y = I, Br), and CH3I molecules. It is demonstrated that the orbital energies from KRHF calculations are useful for the interpretation of spin-orbit splittings in photoelectron spectra. In all molecules studied, bond lengths are only slightly expanded, harmonic vibrational frequencies are reduced, and bond energies are significantly decreased by the spin-orbit interactions.
    Additional Material: 5 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540130509
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    Artificial redox enzymes. II. A computational chemistry study1 (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 614-621 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computational chemistry study of the artificial redox enzyme synthesized by covalently attaching flavin to cyclodextrins explains some of its properties. Calculations indicate that the flavin moiety covalently attached to cyclodextrin is not within the cavity of cyclodextrin. This result is consistent with the UV-vis spectrum of the artificial enzyme. The calculations also indicate hydrogen bonds formed between the carbonyl groups of the catalytic functionality and the hydroxyl groups of cyclodextrin play a role in their most stable conformation. This explains the observed overall stability of these artificial enzymes compared to riboflavin. Electrostatic energies and solvation energies play a major role in the stability of the hosts and the orientation of guests included within the artificial enzymes. The rates of oxidation of various thiols catalyzed by the artificial enzyme can be explained by the relative distances between the sulfur atom of the substrates and C(4a) of the flavin moiety.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540130511
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    Polynomial path for the calculation of liquid state free energies from computer simulations tested on liquid water (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 651-656 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The polynomial path is introduced for the calculation of liquid state free energies. The well-characterized SPC, TIP4P, and MCY water models were used to demonstrate its efficiency, as well as its range of applicability in conjunction with Monte Carlo computer simulations using thermodynamic integration based on Gaussian quadratures. The technique employed is compared with the slow-growth method (another variant of thermodynamic integration), the perturbation method, and the use of the grand-canonical ensemble.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540130515
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    Fast geometry optimizationin self-cosistent reaction field computations on solvated molecules (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 675-680 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The free energy gradient or Hessian of a molecule interacting with a liquid represented by a dielectric continuum is derived in the self-consistent reaction field formalism. An ellipsoidal approximation of the cavity is proposed with an algorithm to automatically define the ellipsoid from the nuclear coordinates of the atoms. With this approximation, geometry optimization of the solvated molecule becomes very fast. This method has been implemented in some standard ab initio or semiempirical computational codes. As a first test of the method, full geometry optimization of formamide in a high dielectric constant medium reveals that the CPU time needed for one optimization cycle is less than 3% longer for a solvated species than for the corresponding free molecule.
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    URL: http://dx.doi.org/10.1002/jcc.540130602
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    Effective internal rotation potential energy function of acryloyl fluoride, CH2 = CH — CF =O (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 718-721 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometry of acryloyl fluoride was optimized completely at the RHF/6-31G* level of theory at 10 points on the theoretical potential energy curve for internal rotation. The energies obtained were used to determine a six term cosine expansion of the torsional potential energy function. This function was then refined using the experimental torsional transition frequencies in the s-trans and s-cis wells in conjunction with the geometrical parameters optimized at the RHF/6-31G* level. The effective potential function obtained is compared with previous results. The necessity of accounting for relaxation of the geometry upon internal rotation is stressed. © 1992 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540130606
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    Electrostatic energy calculations by a Finite-difference method: Rapid calculation of charge-solvent interaction energies (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 768-771 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Finite-difference Poisson-Boltzmann (FDPB) methods allow a fast and accurate calculations of the reaction field (charge-solvent) energies for molecular systems. Unfortunately, the energy in the FDPB calculations includes the self-energies and the finite-difference approximation to the Coulombic energies as well as the reaction field energy. A second finite-difference calculation, in a uniform dielectric, is therefore necesssary to eliminate these contributions. In this article we describe a rapid and accurate method to calculate the self energy and finite-difference Coulombic energies in a uniform dielectric thus eliminating the need for a second finite-difference calculation. The computational savings for this method range from a factor of 4 for a typical protein to a factor of 103 for small molecules. © 1992 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540130610
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    Long time dynamics of a polymer with rigid body monomer units relating to a protein model: Comparison with the rouse model (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 793-798 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Simulation data from an off-lattice polymer model are compared with data from the Rouse model. The polymer model is built of sequentially connected rigid monomer units that represent the amide planes of a protein backbone. The time propagation of the dynamics of the polymer model is performed by a Monte Carlo method. The elementary Monte Carlo steps correspond to local confomational changes in a window of three consecutive monomer units. The time autocorrelation functions of end-to-end distances from segments within the linear chain molecule are considered in detail. Both models exhibit a stretched exponential decay pattern. A comparison of the data from the Rouse model and the computer simulation provide an estimate of the time unit of 15 ps for a full scan of the algorithm for local conformational changes along the chain. With a conservative estimate of the parameters governing the Rouse model this time unit is four orders of magnitude longer than the elementary time step of a conventional computer simulation of polymer dynamics based upon the classical equations of motion for all atoms. © 1992 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540130702
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    Heats of formation of organic molecules by Ab Initio calculations: Carboxylic acids and esters (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 838-841 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A bond and group equivalent scheme that allows the calculation of heats of formation for carboxylic acids and esters from ab initio 6-31G* energies has been developed. For a group of 16 compounds, the rms error for the calculated heats of formation was 0.64 kcal/mol. Heats of formation have been predicted for an additional seven compounds for which the experimental values are either unknown or suspect. © 1992 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540130707
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    NDDO fragment self-consistent field approximation for large electronic systems (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 830-837 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A semi-empirical NDDO method, generalized from a similar scheme at the CNDO/2 level developed previously, is presented to treat very large molecules. The extended molecular system is divided into a relatively small subsystem where substantial chemical changes take place and an environment remaining more-or-less unperturbed during the process. Expanding the wave function on an atomic hybrid basis an SCF procedure is performed for the subsystem in the field of the iteratively determined electronic distribution of the environment. A computer program has been written for the IBM RISC System/6000 530 computer and several test calculations were done for a variety of large classical molecules, like substituted aliphatic hydrocarbons, water oligomers, and a heptapeptide. Protonation energies, proton transfer potential curves, rotational barriers, atomic net charges, and HOMO and LUMO energies, as computed by the exact version of the NDDO method, are fairly well reproduced by our approximation if the subsystem is appropriately defined. © 1992 by John Wiley & Sons, Inc.
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    Theoretical studies of [n]paracyclophanes and their valence isomers. I. Geometries, strain energies, and enthalpies of the inter-conversions of [n]paracyclophanes and their Dewar benzee isomers (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 1047-1056 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Four semiempirical methods (AM1, MNDO, PM3, and MINDO/3) are used to calculate the deformation angles of [n]paracyclophanes and their Dewar benzene isomers for n = 3… 10. The results obtained by all these methods are in good agreement with data from X-ray studies. We have determined the strain energies that, in both series of compounds, are due to two components: (1) the strain energy of deformation of the cycle (aromatic or Dewar Benzene skeletons) and (2) the strain energy of the oligomethylene chain. In [6]paracyclophane, the strain energy [SEring(MNDO) ≍ 32.9 kcal/mol] almost compensates the resonance energy (Eresonance ≈ 36 kcal/mol) so that its chemical properties are closer to alkenes than to benzenic compounds. To better reproduce the enthalpy of the valence isomerization [n]Dewar bezene → [n]paracyclophane, which is poorly calculated with these methods, a correction is proposed and the reaction enthalpy of [6]paracyclophane is estimated to be about ΔHr ≈ 15 ± 15 kcal/mol. It is found that MNDO and MINDO/3 need the smallest corrections, but MNDO leads to better geometries than MINDO/3. In conclusion, MNDO seems to be the best technique for further studies of these compounds. © 1992 by John Wiley & Sons, Inc.
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    PM3-SM3: A general parameterization for including aqueous solvation effects in the PM3 molecular orbital model (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 1089-1097 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Our recently proposed scheme for including aqueous solvation free energies in parameterized NDDO SCF models is extended to the Parameterized Model 3 semiempirical Hamiltonian. The solvation model takes accurate account of the hydrophobic effect for hydrocarbons, as well as electric polarization of the solvent, the free energy of cavitation, and dispersion interactions. Eight heteroatoms are included (along with H and C), and the new model is parameterized accurately for the water molecule itself, which allows meaningful treatments of specifically hydrogen bonded water molecules. The unphysical partial charges on nitrogen atoms predicted by the Parameterized Model 3 Hamiltonian limit the accuracy of the predicted solvation energies for some compounds containing nitrogen, but the model may be very useful for other systems, especially those for which PM3 is preferred over AM1 for the solute properties of the particular system under study. © 1992 by John Wiley & Sons, Inc.
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    General expression for the density dependence of the mori coefficients (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 1119-1124 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The particular expression that relates the first Mori coefficients of the solvent particles with the solute particles as a function of their masses m1 and m2 is generalized to the case of the solute particle also having a different volume. The resulting density relationship, in terms of the mass factor M(m2) and coupling constants CD, is also valid for the second Mori coefficients and for two- and three-dimensional system. © 1992 by John Wiley & Sons, Inc.
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    Announcement (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 1170-1170 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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    URL: http://dx.doi.org/10.1002/jcc.540130917
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    Conformational distribution of heptaalanine: Analysis using a new Monte Carlo chain growth method (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 1216-1233 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A distribution of conformations of heptaalanine is obtained using a new Monte Carlo (MC) method that grows the chain atom by atom. Resulting configurations are energy minimized and a detailed analysis is performed of the minimum-energy conformers using a method of classification that partitions φψ space. The MC-generated configurations are compared with those generated from high-temperature molecular dynamics (MD) simulations. It is found that the new method generates a wide distribution of low-energy conformers at least 10 times more quickly than the MD. An analysis of the generated energy minima demonstrates that they can be divided into clusters in the space defined by the five pairs of φ - ψ angles of the inner residues. The space occupied by the minima populating each cluster is restricted. © 1992 by John Wiley & Sons, Inc.
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    Comparison of NDDO and quasi-ab initio approaches to compute semiempirical molecular electrostatic potentials (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 12-22 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The suitability of the two most widely used strategies to compute semiempirical MEPs is examined. For this purpose, MEP minima, electrostatic charges, and dipoles for a large number of molecules were computed at the AM1, MNDO, and PM3 levels using both the NDDO strategy developed by Ferenczy, Reynolds, and Richards and our own quasi-ab initio method. Results demonstrate that the quasi-ab initio is preferred over the NDDO method for the computation of MEP minima. It is also found that the best set of semiempirical charges and dipoles are obtained using either the AM1 NDDO or the MNDO quasi-ab initio methods. In these two cases, the quality of the results is fully comparable with 6-31G* values. © 1994 by John Wiley & Sons, Inc.
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    Newton-Raphson optimization of the explicitly correlated Gaussian functions for calculations of the ground state of the helium atom (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 54-60 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Explicitly correlated Gaussian functions have been used in variational calculations on the ground state of the helium atom. The major problem of this application, as well as in other applications of the explicitly correlated Gaussian functions to compute electronic energies of atoms and molecules, is the optimization of the nonlinear parameters involved in the variational wave function. An effective Newton-Raphson optimization procedure is proposed based on analytic first and second derivatives of the variational functional with respect to the Gaussian exponents. The algorithm of the method and its computational implementation is described. The application of the method to the helium atom shows that the Newton-Raphson procedure leads to a good convergence of the optimization process. © 1994 by John Wiley & Sons, Inc.
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    General parameterization of a reaction field theory combined with the boundary element method (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 90-104 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We described various technical aspects in applying reaction field theories using continuum models to practical problems. It was investigated how solvent-dependent properties of solute molecules are influenced by the following factors: difference in quantum-chemical description of solute-solvent (continuum dielectric) interaction, difference in values of empirically determinable parameters such as atomic radii to define a size of a cavity created in a dielectric to accommodate a solute, and difference in the sophistication level of molecular orbital calculation, including electron correlation and different parameter sets (MNDO, AM1, and PM3). Through these investigations, the better parameter sets were found to evaluate accurately physicochemically important parameters such as hydration enthalpy. © 1994 by John Wiley & Sons, Inc.
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    Conformation and reactivity of α-oxo-ketenes: Ab initio and semiempirical (AM1, PM3) calculations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 132-143 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio MP2/6-31G*//MP2/6-31G* and semiempirical AM1 and PM3 calculations on a series of differently substituted α-oxo-ketenes are used to investigate E/Z-isomerism and rotational barriers in these molecules. Sterically crowded derivatives are found to exist solely as s-E conformers. The unusual stability of these derivatives thus can be attributed to their inability to adopt the s-Z conformation required for the normal α-oxo-ketene reactions. With respect to structures and energies, the PM3 method (especially in the case of highly crowded molecules) is found to be less reliable than AM1. Ab initio HF/3-21G and PM3 vibrational frequencies appear to be of sufficient accuracy for a distinction between s-Z and s-E conformers. In this respect, the AM1 method appears less reliable. © 1994 by John Wiley & Sons, Inc.
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    Atomic charges derived from a fast and accurate method for electrostatic potentials based on modified AM1 calculations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 200-207 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atomic charges derived from a recently described approach to the very rapid computation of AM1 electrostatic potentials (ESP) accurately parallel, but are ca. 20% smaller than, the corresponding HF/6-31G* values. The dipole moments computed from the AM1 charges are virtually identical to those derived directly from the wave function and in rather better agreement with the experimental values than those computed using the HF/6-31G* charges. Unlike other approaches to the semiempirical calculation of ESP-derived charges, the present method also yields near HF/6-31G* quality potentials close to the molecular periphery. For medium-sized organic molecules (40-100 basis functions), the method is approximately two orders of magnitude faster than those involving prior deorthogonalization of AM1 wave function and explicit computation of the full ESP integral matrix. © 1994 by John Wiley & Sons, Inc.
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    A ring-bracing approach to computer-assisted ligand design (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 233-240 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Rigid inhibitors suffer a smaller loss of conformational entropy when they bind to a macromolecular receptor than their acyclic counterparts. They can also be useful for elucidating pharmacophores due to their reduced conformational space and may be more amenable to synthesis. Computational approaches to rational drug design should therefore take these factors into consideration when suggesting possible compounds. We describe how an acyclic chain which links two parts of a receptor site can be ‘braced’ using ring templates. The acyclic chains may be produced from a number of sources, including lattices or the structures of known inhibitors. The resulting structures contain a rich variety of isolated and fused ring systems, which provide many useful molecular skeletons for subsequent inhibitor design. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150213
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    Force field calculations (MM3) on glyoxal, quinones, and related compounds (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 251-268 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A general force field type of calculation has been devised in connection with MM3 to treat 1,2- and 1,4-diketones, both when they are not conjugated (as in derivatives of glyoxal) and when they are conjugated (as in derivatives of ortho- and para-benzoquinone). The molecular structures, moments of inertia, dipole moments, and vibrational spectra have been examined for about 15 compounds, some in several conformations. Ab initio calculations (6-31G*) have been used to determine quantities that have not been previously defined by experiment. In general, the force field permits the calculation of the structures with high accuracy, and the spectroscopic and conformational energy data with fair accuracy. © 1994 by John Wiley & Sons, Inc.
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    A comparative study of effective core potential and full-electron calculations in Mo compounds. I. An analysis of topological properties of bond charge distribution (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 313-321 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Effective core potential (ECP) and full-electron (FE) calculations for MoS4-2, MoO4-2, and MoOCl4 compounds were analyzed. Geometry parameters, binding energies, charge distributions, and topological properties of the electronic density were studied for Mo—L bonds (L = S, O, Cl). Results clearly indicate that those approaches that include valence plus 4s and 4p electrons (ECP2 methods) are able to reproduce the topological properties of Mo—L bonds, charge distributions, and geometries with respect to those obtained by FE methods. ECP methods that consider only the 4d and 5s valence electrons (ECP1) fail in the calculation of molecular properties. The use of 5p functions in ECP1 approaches produces a negative Mulliken charge on Mo. Bader's charges give more consistent results than Mulliken's ones. A new parameter for measuring the degree of ionicity is proposed. © 1994 by John Wiley & Sons, Inc.
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    Ab initio study of low-lying electronic states of the PF2 radical (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 346-350 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The equilibrium geometries, excitation energies, force constants, and vibrational frequencies of the low-lying electronic states X2B1, 2A1, 2B2, and 2A2 of the PF2 radical have been calculated at the MRSDCI level with a double zeta plus polarization basis set. Our calculated geometry, force constants, and vibrational frequencies for the X2B1 state are in good agreement with experimental data. The electronic transition moments, oscillator strengths for the 2A1 → X2B1 and 2A2 → X2B1 transitions, and radiative lifetimes for the 2A1 and 2A2 states are calculated based on the MRSDCI wave functions. © 1994 by John Wiley & Sons, Inc.
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    Free energy perturbation calculations on parallel computers: Demonstrations of scalable linear speedup (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 351-373 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A coarse-grain parallel implementation of the free energy perturbation (FEP) module of the AMBER molecular dynamics program is described and then demonstrated using five different molecular systems. The difference in the free energy of (aqueous) solvation is calculated for two monovalent cations ΔΔGaq(Li+ Δ Cs+), and for the zero-sum ethane-to-ethane′ perturbation ΔΔGaq(CH3—methyl—X → X—methyl—CH3), where X is a ghost methyl. The difference in binding free energy for a docked HIV-1 protease inhibitor into its ethylene mimetic is examined by mutating its fifth peptide bond, ΔG(CO—NH → CH=CH). A potassium ion (K+) is driven outward from the center of mass of ionophore salinomycin (SAL-) in a potential of mean force calculation ΔGMeOH(SAL- · K+) carried out in methanol solvent. Parallel speedup obtained is linearly proportional to the number of parallel processors applied. Finally, the difference in free energy of solvation of phenol versus benzene, ΔΔGoct(phenol → benzene), is determined in water-saturated octanol and then expressed in terms of relative partition coefficients, Δ log(Po/w). Because no interprocessor communication is required, this approach is scalable and applicable in general for any parallel architecture or network of machines. FEP calculations run on the nCUBE/2 using 50 or 100 parallel processors were completed in clock times equivalent to or twice as fast as a Cray Y-MP. The difficulty of ensuring adequate system equilibrium when agradual configurational reorientation follows the mutation of the Hamiltonian is discussed and analyzed. The results of a successful protocol for overcoming this equilibration problem are presented. The types of molecular perturbations for which this method is expected to perform most efficiently are described. © 1994 by John Wiley & Sons, Inc.
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    Transferable semiempirical quadratic force fields: The case of polythiophene and shorter oligomers (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 405-423 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The vibrational spectra of oligomers of thiophene are treated theoretically with the main purpose of deriving information for the interpretation of the infrared and Raman spectra of the polymer and isotopic derivatives. We report the results of a series of semiempirical MNDO calculations on the structure and vibrational properties of oligothiophenes, and we compare the calculated MNDO Pulay scaled force field of the monomer with an empirical harmonic force field that we have obtained by least squares refinement on nine isotopic derivatives. The scaling factors obtained were transferred from thiophene for the computation of the vibrational spectrum and the phonon dispersion curves of the polymer. © 1994 by John Wiley & Sons, Inc.
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    Announcements (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 475-475 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150411
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    On the analytical calculation of van der Waals surfaces and volumes: Some numerical aspects (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 507-523 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A fast computer algorithm is presented for complete analytical calculation of van der Waals surfaces and volumes. Connolly's analytical algorithms, computing second- and third-order atomic spheres overlaps, are shown to give insufficient numerical approximations of the exact van der Waals surfaces and volumes. The presented algorithm computes overlaps of any order. Practical situations frequently involve six-order overlaps. Analytical computed surfaces and volumes of 63 chemicals are compared with Monte Carlo measured values. © 1994 by John Wiley & Sons, Inc.
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    ICM - A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 488-506 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An efficient methodology, further referred to as ICM, for versatile modeling operations and global energy optimization on arbitrarily fixed multimolecular systems is described. It is aimed at protein structure prediction, homology modeling, molecular docking, nuclear magnetic resonance (NMR) structure determination, and protein design. The method uses and further develops a previously introduced approach to model biomolecular structures in which bond lengths, bond angles, and torsion angles are considered as independent variables, any subset of them being fixed. Here we simplify and generalize the basic description of the system, introduce the variable dihedral phase angle, and allow arbitrary connections of the molecules and conventional definition of the torsion angles. Algorithms for calculation of energy derivatives with respect to internal variables in the topological tree of the system and for rapid evaluation of accessible surface are presented. Multidimensional variable restraints are proposed to represent the statistical information about the torsion angle distributions in proteins. To incorporate complex energy terms as solvation energy and electrostatics into a structure prediction procedure, a “double-energy” Monte Carlo minimization procedure in which these terms are omitted during the minimization stage of the random step and included for the comparison with the previous conformation in a Markov chain is proposed and justified. The ICM method is applied successfully to a molecular docking problem. The procedure finds the correct parallel arrangement of two rigid helixes from a leucine zipper domain as the lowest-energy conformation (0.5 Å root mean square, rms, deviation from the native structure) starting from completely random configuration. Structures with antiparallel helixes or helixes staggered by one helix turn had energies higher by about 7 or 9 kcal/mol, respectively. Soft docking was also attempted. A docking procedure allowing side-chain flexibility also converged to the parallel configuration starting from the helixes optimized individually. To justdy an internal coordinate approach to the structure prediction as opposed to a Cartesian one, energy hypersurfaces around the native structure of the squash seeds trypsin inhibitor were studied. Torsion angle minimization from the optimal conformation randomly distorted up to the rms deviation of 2.2 Å or angular rms deviation of l0° restored the native conformation in most cases. In contrast, Cartesian coordinate minimization did not reach the minimum from deviations as small as 0.3 Å or 2°. We conclude that the most promising detailed approach to the protein-folding problem would consist of some coarse global sampling strategy combined with the local energy minimization in the torsion coordinate space. © 1994 by John Wiley & Sons, Inc.
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    Masthead (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150601
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    Direct search methods for the molecular conformation problem (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 627-632 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An important area of research in computational biochemistry is the design of molecules for specific applications. The design of these molecules, which depends on the accurate determination of their three-dimensional structure, can be formulated as a global optimization problem. In this article, we present results from the application of a new conformation searching method based on direct search methods. We compare these results to some earlier results using genetic algorithms and simulated annealing. © 1994 by John Wiley & Sons, Inc.
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    Triazene proton affinities: A comparison between density functional, Hartree-Fock, and post-Hartree-Fock methods (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 875-892 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The consistency of three density functional computational implementations (DMol, DGauss, and deMon) are compared with high-level Hartree-Fock and Møller-Plesset (MP) calculations for triazene (HN=NNH2) and formyl triazene (HN=NNHCOH). Proton affinities on all electronegative sites are investigated as well as the geometries of the neutral and protonated species. Density functional calculations employing the nonlocal gradient corrections show agreement with MP calculations for both proton affinities and geometries of neutral and protonated triazenes. Local spin density approximation DMol calculations using numerical basis sets must employ an extended basis to agree with other density functional codes using analytic Gaussian basis sets. The lowest energy conformation of triazene was found to be nonplanar; however, the degree of nonplanarity, as well as some bond lengths, is dependent on the basis set, electron correlation treatment, and methods used for the calculation. © 1994 by John Wiley & Sons, Inc.This article is a U.S. Government work and, as such, is in the public domain in the United States of America.
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    Cluster analysis of molecular conformations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 899-916 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe a method for locating clusters of geometrically similar conformers in ensembles of chemical conformations. We first calculate the pairwise interconformational distance matrix in either torsional or Cartesian space and then use an agglomerative, single-link clustering method to define a hierarchy of clusterings in the same space. Especially good clusterings are distinguished by high values of the separation ratio: the ratio of the shortest intercluster distance to the characteristic threshold distance defining the clustering. We also discuss other statistics. The method has been embodied in a program called XCluster, which can display the distance matrix, the hierarchy of clusterings, and the clustering statistics in a variety of formats. XCluster can also write out the clustered conformations for subsequent or simultaneous viewing with a molecular visualization program. We demonstrate the sorts of insight that this approach affords with examples obtained from conformational search and molecular dynamics procedures. © 1994 by John Wiley & Sons, Inc.
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    D-CICADA: A software for conformational PES elucidation on network of workstationsThis work is dedicated to Professor M. Kratochvíl on the occasion of his seventieth birthday. (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 937-946 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The methodology of conformational potential energy (hyper)surface (PES) elucidation is the subject of this article. The decomposition of the recently developed software CICADA and its implementation in the distributed environment using PVM (parallel virtual machine) is presented. CICADA has been chosen for the parallelization because of its ability to elucidate systematically the low-energy areas of PES in polynomial time. This makes the method applicable on larger systems which are beyond the scope of the grid search. To show the level of parallelization, conformational PES of two molecules, cyclohexane and terminally blocked alanine, have been studied by the distributed version, D-CICADA, and results have been compared to those of the sequential version. D-CICADA was tested on several virtual machines composed of DEC and Sun workstations. The timing shows good efficiency for both the decomposition of the original algorithm and the PVM environment. © 1994 by John Wiley & Sons, Inc.
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    Long-time overdamped Langevin dynamics of molecular chains (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 997-1012 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a novel algorithm of constrained, overdamped dynamics to study the long-time properties of peptides, proteins, and related molecules. The constraints are applied to an all-atom model of the molecule by projecting out all components of the nonbonding interactions which tend to alter fixed bond lengths and angles. Because the overdamped dynamical equations are first order in time, the constraints are satisfied by inversion of a banded matrix at each timestep, which is computationally efficient. Thermal effects are included through a Langevin noise term in the equation of motion. Because high-frequency components of the motion have been eliminated, the timestep of the algorithm is determined by the nonbonding forces, which are two to three orders of magnitude weaker than the bonding forces. Using polyalanine as a test example, we demonstrate that trajectories simulating a microsecond of motion can be run about 103 times faster than an equivalent molecular dynamics simulation. © 1994 by John Wiley & Sons, Inc.
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    Decomposition analyses of the intermolecular interaction energies in two π—π stacking complexes: Quinhydrone and N,N,N′, N′-tetramethyl-P-diaminobenzene-chloranil complex (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1013-1018 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Although there is a similarity in the orbital interaction scheme between quinhydrone and N,N,N′,N′-tetramethyl-p-diaminobenzene-chloranil complex, the stacking conformations are different from each other. The former prefers the half-stacked conformation, whereas the latter prefers the completely stacked conformation. We have done ab initio molecular orbital calculations and decomposition analyses of the intermolecular interaction energies to clarify the origin of the different stacking conformations. It was concluded that the main origin is the difference in the steric part of the interaction energies. © 1994 by John Wiley & Sons, Inc.
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    A force field for monosaccharides and (1 → 4) linked polysaccharides (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1019-1040 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A force field for monosaccharides that can be extended to (1 → 4) linked polysaccharides has been developed for the AMBER potential function. The resulting force field is consistent with the existing AMBER force field for proteins and nucleic acids. Modifications to the standard AMBER OH force constant and to the Lennard-Jones parameters were made. Furthermore, a 10-12 nonbonded term was included between the hydroxyl hydrogen of the saccharide and the water oxygen (TIP3P, SPC/E, etc.) to reproduce better the water-saccharide intermolecular distances. STO-3G electrostatic potential (ESP) charges were used to represent the electrostatic interactions between the saccharide and its surrounding environment. To obtain charges for polysaccharides, a scheme was developed to piece together saccharide residues through 1 → 4 connections while still retaining a net neutral charge on the molecule as a whole. Free energy perturbation (FEP) simulations of D-glucose and D-mannose in water were performed to test the resulting force field. The FEP simulations demonstrate that AMBER overestimates intramolecular interaction energies, suggesting that further improvements are needed in this part of the force field. To test further the reliability of the parameters, a molecular dynamics (MD) simulation of α-D-glucose in water was also performed. The MD simulation was able to produce structural and conformational results that are in accord with experimental evidence and previous theoretical results. Finally, a relaxed conformational map of β-maltose was assembled and it was found that the present force field is consistent with available theoretical and experimental results. © 1994 by John Wiley & Sons, Inc.
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    A rapidly convergent simulation method: Mixed Monte Carlo/stochastic dynamics (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1302-1310 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Although Monte Carlo and molecular dynamics are the primary methods used for free energy simulations of molecular systems, their application to molecules that have multiple conformations separated by energy barriers of ≥ 3 kcal/mol is problematic because of slow rates of convergence. In this article we introduce a hybrid simulation method termed MC-SD which mixes Monte Carlo (MC) and stochastic dynamics (SD). This new method generates a canonical ensemble via alternating MC and SD steps and combines the local exploration strengths of dynamics with the barrier-crossing ability of large-step Monte Carlo. Using calculations on double-well potentials and long simulations (108 steps of MC and 1 μs of SD) of the simple, conformationally flexible molecule n-pentane, we find that MC-SD simulations converage faster than either MC or SD alone and generate ensembles which are equivalent to those created by classical MC or SD. Using pure SD at 300 K, the conformational populations of n-pentane are shown to be poorly converged even after a full microsecond of simulation. © 1994 by John Wiley & Sons, Inc.
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    Molecular mechanics calculations (MM2 and MM3) on enamines and aniline derivatives (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1321-1330 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MM2 and MM3 force fields have been extended to cover this class of compounds. Structures, vibrational spectra, and other data for 13 compounds were examined and can be reproduced satisfactorily by MM3. Except for the spectra, the other data can be reproduced somewhat less well by MM2. © 1994 by John Wiley & Sons, Inc.
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    A variational biorthogonal valence bond method (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1357-1364 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The details of a simple and efficient scheme for performing variational biorthogonal valence bond calculations are presented. A variational bound on the energy functional is obtained through the use of a complete configuration expansion in a well-chosen subset of orbitals. The resultant wave functions are clearly dominated by the covalent (spin-coupled) structures, with a negligible contribution from ionic structures. The orbitals obtained compare favorably with overlap enhanced atomic orbitals obtained by other valence bond approaches. The method is illustrated by calculations on water and dioxygen difluoride. © 1994 by John Wiley & Sons, Inc.
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    Stability of two-dimensional crystalline aggregates of a protein studied by molecular dynamics (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1278-1290 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two-dimensional protein (ferritin) aggregates with a square lattice symmetry, which were formed within a thin liquid layer on a mercury surface, were studied by molecular dynamics (MD) simulation. For the simulation, the ferritin molecule was modeled by an assembly of 49 spheres, and the intermolecular interactions were given by simple formulae. During the simulation, molecules were confined within a layer, which corresponds to the thin liquid layer. An annealing MD simulation was done starting from a random molecular configuration within the layer, and aggregates with the square lattice symmetry were also obtained. To study the stability of aggregates, dissociation processes of the aggregates were analyzed using MD simulations at room temperature. Interactions between the nearest-neighbor molecules were regarded as bonds. Mean bond energies and correlation coefficients between the bond energies were calculated from the MD trajectories. A decay profile according to the dissociation was obtained, yielding a dissociation rate constant. Buried bonds were stronger than peripheral bonds. The larger the aggregate size, the stronger the bond for each of the buried and peripheral bonds. A simple theoretical account, which is applicable to a general bonded network, was introduced to analyze the dynamics of the aggregates. © 1994 by John Wiley & Sons, Inc.
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    Linear dependency in the refinement of force constants with the Jacobian method (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1291-1301 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The Jacobian method in the refinement of force constants is studied. Theoretical and experimental frequencies and other observables, νs, are matched by minimizing ΣsWs(νsexp - νsth)2, where s = 1, 2, 3,…, proceeds over all normal modes and isotopes, and Ws are weighting factors. Modification of the theoretical frequencies is accomplished with the Jacobian matrix, J, with elements Jsi = ∂νs/∂ki involving each force constant or associated parameter, ki, i = 1, 2, 3,…, by Δν = JΔk. The parameters are adjusted directly with Δk = (JTWJ)-1(JW) Δν, where W is a diagonal matrix which weights the frequencies. The linear dependence problem must be addressed prior to inversion of JTWJ. The approach entails diagonalization of JT WJ, analysis of the components of the eigenvectors associated with zero and small eigenvalues, identification of the linearly dependent parameters, successive elimination of selective parameters, and a repeat of this procedure until linear dependency is removed. The Jacobian matrices are obtained by differencing the frequencies when the parameters are varied and by numerical and analytical evaluation of the derivative of the potential. The unitary transformation, U, used to calculate J = UT (∂F/∂k)U or J = UT (ΔF/Δk)U, is obtained from the diagonalization of the Hessian, Fmn = ∂2ν/∂pm∂qn, where p, q = x, y, z are the Cartesian coordinates for atoms m, n = 1, 2, 3,…, at the initial value of ki, i = 1, 2, 3,⃜ The accuracy of and the ability to evaluate the Jacobian matrix by these methods are discussed. Applications to CH4, H2CO, C2H4, and C2H6 are presented. Linearly dependent and ill-conditioned parameters are identified and removed. The procedure is general for any observable quantity. © 1994 by John Wiley & Sons, Inc.
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    Algorithms for clustering molecular dynamics configurations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1331-1340 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two traditional clustering algorithms are applied to configurations from a long molecular dynamics trajectory and compared using two sets of test data. First, a subset of atoms was chosen to present conformations which naturally fall into a number of clusters. Second, a subset of atoms was selected to span a relatively continuous region of conformational space rather than form discrete conformational classes. Of the two algorithms used, the single linkage method is inappropriate for this kind of data. The divisive hierarchical method, based on minimizing the difference between cluster centroids and extrema, is successful but also prone to imposing clustering hierarchy where none can be justified. © 1994 by John Wiley & Sons, Inc.
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    Application of a high-performance, special-purpose computer, GRAPE-2A, to molecular dynamics (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1372-1376 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The special-purpose computer GRAPE-2A accelerates the calculation of pairwise interactions in many-body systems. This computer is a back-end processor connected to a host computer through a Versa Module Europe (VME) bus. GRAPE-2A receives coordinates and other physical data for particles from the host and then calculates the pairwise interactions. The host then integrates an equation of motion by using these interactions. We did molecular dynamics simulations for two systems of liquid water: System 1 (1000 molecules), and System 2 (1728 molecules). The time spent for one step of molecular dynamics was 3.9 s (System l), and 10.2 s (System 2). The larger the molecular system, the higher the performance. The speed of GRAPE-2A did not depend on the formula describing the pairwise interaction. The cost performance was about 20 times better than that of the fastest workstations available today, and GRAPE-2A cost only $22,000. © 1994 by John Wiley & Sons, Inc.
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    Masthead (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992) 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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    MSEED: A program for the rapid analytical determination of accessible surface areas and their derivatives (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 1-11 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm for the rapid analytical determination of the accessible surface areas of solute molecules is described. The accessible surface areas as well as the derivatives with respect to the Cartesian coordinates of the atoms are computed by a program called “MSEED,” which is based in part on Connolly's analytical formulas for determining surface area. Comparisons of the CPU time required for MSEED, Connolly's numerical algorithm DOT, and a program for surface area determination (ANA) based on Connolly's analytical algorithm, are presented. MSEED is shown to be as much as 70 times faster than ANA and up to 11 times faster than DOT for several proteins. The greater speed of MSEED is achieved partially because nonproductive computation of the surface areas of internal atoms is avoided. A sample minimization of an energy function, which included a term for hydration, was carried out on MET-enkephalin using MSEED to compute the solvent-accessible surface area and its derivatives. The potential employed was ECEPP/2 plus an empirical potential for solvation based on the solvent-accessible surface area of the peptide. The CPU time required for 150 steps of minimization with the potential that included solvation was approximately twice as great as the CPU time required for 150 steps of minimization with the ECEPP/2 potential only.
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    Ab initio and molecular mechanics calculations on imine derivatives: A study of the rotational barriers and the development of MM2 parameters (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 57-65 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The application of molecular mechanics methods for the study of structures has become a standard approach to conformational analysis. The MM2 force field has been extended to include imines. In general, a diverse group of aliphatic and aromatic imine structures can now be treated. The rotational energy profiles and barriers to N-substituted imines about the Csp2—Csp2 single bonds adjacent to C=N functional group were calculated via ab initio MO theory. Information obtained from the quantum mechanical calculations at the 3-21G, 6-31G*, and MP4/6-31G* //6-31G* levels was used both to study the phenomena involved and to parameterize MM2. The syn-anti isomerization was also studied, and the mechanistic pathways have been evaluated. In cases where the comparison with experimental data can be made, the agreements are good.
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    Application of SINDO1 to organo-transition metal compounds (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 93-101 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The recently extended SINDO1 method is used to study geometries, electronic structures, and chemical bonding of transition metal organometallic compounds. The optimized distances and angles between metal atoms and organic ligands are in fair agreement with experimental data and are comparable to ab initio results. The comparison of orbital energies between the current method and ab initio methods shows that the method can give a correct description of electronic structure and bonding patterns of organometallic compounds. The method is also used to calculate atomic and bond valence, which are defined in terms of appropriate combinations of first-order density matrix elements for molecules. The valence indices provide a straightforward and easy-to-interpret way to analyze the magnitude of metal-carbon and metal-metal bonds.
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    On the numerical solution of the multidimensional vibrational time-independent Schroedinger equation (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 135-141 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A preliminary study of the capability of the finite difference and finite element methods (FDM, FEM) to evaluate eigenvalues of one-, two-, and three-dimensional self-adjoint operators is reported with reference to applications dealing with the description of vibrational levels. Results of harmonic oscillator model potentials and ab initio PES for the water molecule are obtained by using the FDM. In spite of the large matrices used, low accuracy, nonvariational results are found. A different method, based on FEM and normal coordinates, is therefore proposed. Two nearly harmonic cases are studied and it is shown that variational results with higher accuracy can be obtained with a moderate cost. The vibrational levels of the water molecule are also calculated in order to compare the results with those of the FDM treatment.
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    A coarse-grain parallel implementation of the direct SCF method (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 160-164 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A coarse-grain, parallel approach to direct Hartree-Fock calculations is presented and discussed. The suggested scheme allows for a near asymptotic speedup involving a very low parallelization overhead without compromising the vector performance of vector-parallel architectures. A shared-memory MIMD implementation, for which very high speeds of computation have been achieved, is discussed in detail.
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    New realization of loop driven direct CI (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 187-198 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article we report a newly developed direct CI program and its preliminary applications. This program is based mainly on the relationship between direct and exchange type loops and the rederivation of the external loop shapes.
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    Microscopic models for quantum mechanical calculations of chemical processes in solutions: LD/AMPAC and SCAAS/AMPAC calculations of solvation energies (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 199-213 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Our previously developed approaches for integrating quantum mechanical molecular orbital methods with microscopic solvent models are refined and examined. These approaches consider the nonlinear solute-solvent coupling in a self-consistent way by incorporating the potential from the solvent dipoles in the solute Hamiltonian, while considering the polarization of the solvent by the potential from the solute charges. The solvent models used include the simplified Langevin Dipoles (LD) model and the much more expensive surface constrained All Atom Solvent (SCAAS) model, which is combined with a free energy pertubation (FEP) approach. Both methods are effectively integrated with the quantum mechanical AMPAC package and can be easily combined with other quantum mechanical programs. The advantages of the present approaches and their earlier versions over macroscopic reaction field models and supermolecular approaches are considered. A LD/MNDO study of solvated organic ions demonstrates that this model can yield reliable solvation energies, provided the quantum mechanical charges are scaled to have similar magnitudes to those obtained by high level ab initio methods. The incorporation of a field-dependent hydrophobic term in the LD free energy makes the present approach capable of evaluating the free energy of transfer of polar molecules from non polar solvents to aqueous solutions. The reliability of the LD approach is examined not only by evaluating a rather standard set of solvation energies of organic ions and polar molecules, but also by considering the stringent test case of sterically hindered hydrophobic ions. In this case, we compare the LD/MNDO solvation energies to the more rigorous FEP/SCAAS/MNDO solvation energies. Both methods are found to give similar results even in this challenging test case. The FEP/SCAAS/AMPAC method is incorporated into the current version of the program ENZYMIX. This option allows one to study chemical reactions in enzymes and in solutions using the MNDO and AM1 approximations. A special procedure that uses the EVB method as a reference potential for SCF MO calculations should help in improving the reliability of such studies.
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    PEFF: A program for the development of empirical force fields (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 257-267 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: PEFF is a new computer program designed to assist in the development of empirical force fields used in molecular mechanics calculations. Its main features are: constrained and unconstrained energy minimization available with four different techniques, rigid group refinement, crystal lattice summations, calculation of normal modes, thermodynamic functions and crystallographic temperature factors, vibrational corrections of calculated crystal structures, and a multidimensional driver to scan the energy hypersurface. Used in force field optimization mode, the program employs a least-squares method to fit the force field parameters to a set of experimental data.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540130302
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    Charge distributions of phosphorylcholine and its derivatives (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 318-328 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Hartree-Fock self-consistent field calculations on the 3-21G(*) level of approximation have been performed to phosphorylcholine and its derivatives in a geometry close to an X-ray structure of an antibody/antigen complex. Wave functions have been analyzed using different methods for derivation of atomic charges used as Coulomb charges in empirical force fields for molecular dynamics simulations. Among the three applied methods - Mulliken population analysis, natural population analysis, and electrostatical fit - the natural population analysis seems to give best results for these molecules.
    Additional Material: 2 Ill.
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    Free energy perturbation calculations involving potential function changes (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 362-370 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The solvation free energies of thymine and adenine were calculated using free energy methods to examine the effect of applying Lennard-Jones 6-12 and 10-12 perturbations to the hydrogen-bonding groups. The calculations were performed using a new free energy algorithm developed for the AMBER 4.0 program package that allows an interaction described by a Lennard-Jones 6-12 potential to be changed into one described by a hydrogen bond 10-12 potential. The algorithm applied allows this change to occur smoothly without the generation of more extrema on the potential surface. Results using this algorithm have been compared with those determined using the standard AMBER 3.0 Revision A program package, which provides for 6-12 to 6-12 parameter perturbations only. We have also developed a procedure to perform pyrimidine to purine nucleoside mutations to calculate the relative free energies of solvation directly. The theoretical results are compared to experimental energies derived from solvation and vaporization data taken from the literature. The free energies calculated using the new algorithm show good agreement with the derived experimental values. This is also true for the calculations that employ the 6-12 function only, but with 6-12 parameters modified to reflect the correct hydrogen-bonding interactions. However, perturbation of the “standard” 6-12 parameters without changing the functional form proves to be less effective in determining solvation free energies correctly, and demonstrates the importance of accurate hydrogen bond descriptions in free energy simulations.
    Additional Material: 4 Ill.
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    Methods for the calculation of Voh in OH—O hydrogen bonds (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 399-407 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio calculations are reported for dimerization-induced changes, Δk, in the harmonic force constant k of the H-bonded OH in water dimer. Two dimer geometries are considered. Δk is obtained by considering the perturbation of a given monomer OH potential by the interaction energy in the dimer in question. The interaction energy is partitioned to identify the role of the various contributions to Δk. The sensitivity of Δk to the choice of the one-electron basis set is studied by using five different basis sets, some of which have a set of bond functions in the H—O bond. At the correlated level, correction for basis set superposition error is found to be essential. A comparison is made of the correlation contribution to Δk as given by the CEPA1, MP2, MP3, and MP4 methods. Of these, MP2 gives exaggerated results. Nevertheless, for economical and reasonably accurate calculations on large systems the MP2 approach in the ESPB basis set is advocated. The most accurate calculations yield a shift Δv0-;1 of - 121 cm-1 for the uncoupled donor O-H vibrational frequency in water dimer.
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    Parallelization of quantum mechanical integral calculations (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 414-422 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In ab initio Hartree - Fock crystal orbital calculations of chemical and physical properties of polymers, the huge number of two-electron integrals restricts the size of the elementary cell. Therefore, the question arises how the storage and computation resources of modern parallel supercomputers can be exploited. In this work, we report the parallelization of the one- and two-electron integral programs, respectively, for the parallel computer SUPRENUM. A short description of the hardware and software environment of this supercomputer is given. The results are discussed with respect to speed-up and efficiency.
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    Automated docking with grid-based energy evaluation (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 505-524 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The ability to generate feasible binding orientations of a small molecule within a site of known structure is important for ligand design. We present a method that combines a rapid, geometric docking algorithm with the evaluation of molecular mechanics interaction energies. The computational costs of evaluation are minimal because we precalculate the receptor-dependent terms in the potential function at points on a three-dimensional grid. In four test cases where the components of crystallographically determined complexes are redocked, the “force field” score correctly identifies the family of orientations closest to the experimental binding geometry. Scoring functions that consider only steric factors or only electrostatic factors are less successful. The force field function will play an important role in our efforts to search databases for potential lead compounds.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540130412
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    Protein calculations on parallel processors. I. Parallel algorithm for the potential energy (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 533-538 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We investigate and test an algorithm suitable for the parallel calculation of the potential energy of a protein, or its spatial gradient, when the protein atoms interact via pair potentials. This algorithm is similar to one previously proposed, but it is more efficient, having half the interprocessor communications costs. For a given protein, we show that there is an optimal number of processors that gives a maximum speedup of the potential energy calculation compared to a sequential machine. (Using more than the optimum number of processors actually increases the computation time). With the optimum number the computation time is proportional to the protein size N. This is a considerable improvement in performance compared to sequential machines, where the computation time is proportional to N2. We also show that the dependence of the maximum speedup on the message latency time is relatively weak.
    Additional Material: 2 Ill.
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    Conformational analysis of 4h-1,3,2-benzodioxaphosphorin 2-sulfides with ab initio molecular orbital calculations (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 560-564 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Among some 2-substituted 4H-1,3,2-benzodioxaphosphorin 2-sulfides, the 2-OMe derivative has the sulfur atom mainly in the quasiequatorial position. On the other hand, the conformation in which the sulfur is quasiaxial is favored in the 2-NHMe and 2-Et derivatives. We have done ab initio molecular orbital calculations for the model compounds, and such a substituent effect was reproduced. Moreover, the effect was discussed in terms of the intramolecular electrostatic interactions and the degree of charge distribution.
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    Locally implicit solution of a reaction-diffusion system with stiff kinetics (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 570-578 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The Tyson-Fife reaction-diffusion equations are solved numerically using a locally implicit approach. Since the variables evolve at very different time scales, the resulting system of equations is stiff. The reaction term is responsible for the stiffness and the time step is increased by using an implicit method. The diffusion operator is evaluated explicitly and the system of implicit nonlinear equations is decoupled. The method is particularly useful for parameter values in which the equations are very stiff, such as the values obtained directly from the experimental reaction rate constants. Previous efforts modified the parameters on the equations to avoid stiffness. The equations then become a simplified model of excitable media and, for those cases, the locally implicit method gives a faster although less accurate solution. Nevertheless, since the modified equations no longer represent a particular chemical system an accurate solution is not as important. The algorithm is applied to observe the transition from simple motion to compound motion of a spiral tip.
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    Masthead (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992) 
    Details
    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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    URL: http://dx.doi.org/10.1002/jcc.540130701
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    Hydrating peptides using a sprouting technique (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 23-27 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A scheme for generating water coordinates, whose proton orientations are random, and simultaneously generating side chain coordinates of peptides, preparatory to studying solvation of peptides using molecular dynamics schemes is presented in an X-PLOR context. Examples from the Integrin and Tropomyosin systems are used to illustrate the procedure. © 1994 by John Wiley & Sons, Inc.
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    Simulations of the solution structure of HIV-1 protease in the presence and absence of bound zinc (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 61-71 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Zinc ions have been shown to inhibit human immunodeficiency virus type 1 (HIV-1) protease in vitro at neutral pH [Zhang et al. Biochemistry, 36, 8717 (1991)]. Kinetic data from this study support a reversible binding mechanism of zinc in the active site. Preliminary calculations of the ion-protein potential energy based on the geometry of the crystallographic structure [Wlodawer et al. Science, 245, 616 (1989)] are consistent with this proposed mechanism. To examine the structure of HIV-1 protease with zinc bound in the active site, molecular dynamics simulations in the presence and absence of zinc at this site have been carried out to 200 ps. These simulations suggest zinc remains stably bound to the catalytic aspartate residues without disruption of the dimer or significant alteration of the active site structure. These data are consistent with those observed by Zhang et al. (1991), and together give strong evidence that this is the binding site that leads to inactivation. A proposed model of zinc binding at the active site based on quantum mechanical calculations indicates Zn+2 coordination is monodentate with each catalytic aspartate, leaving at least two ligand positions potentially free (occupied by water molecules in the calculations). © 1994 by John Wiley & Sons, Inc.
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    Masthead (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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    URL: http://dx.doi.org/10.1002/jcc.540150201
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    Parallel algorithm for calculating ro-vibrational states of diatomic molecules (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 144-148 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article, we develop and implement an algorithm for calculating the rovbrational states of diatomic molecules optimized for multiple instructions multiple data computers of distributed memory. The method is based upon the p-version of the finite element method and has been implemented on an INTEL iPSC/2 machine with 16 processors. © 1994 by John Wiley & Sons, Inc.
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    Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 162-182 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new method for deriving force fields for molecular simulations has been developed. It is based on the derivation and parameterization of analytic representations of the ab initio potential energy surfaces. The general method is presented here and used to derive a quantum mechanical force field (QMFF) for alkanes. It is based on sampling the energy surfaces of 16 representative alkane species. For hydrocarbons, this force field contains 66 force constants and reference values. These were fit to 128,376 quantum mechanical energies and energy derivatives describing the energy surface. The detailed form of the analytic force field expression and the values of all resulting parameters are given. A series of computations is then performed to test the ability of this force field to reproduce the features of the ab initio energy surface in terms of energies as well as the first and second derivatives of the energies with respect to molecular deformations. The fit is shown to be good, with rms energy deviations of less than 7% for all molecules. Also, although only two atom types are employed, the force field accounts for the properties of both highly strained species, such as cyclopropane and methylcyclopropanes, as well as unstrained systems. The information contained in the quantum energy surface indicates that it is significantly anharmonic and that important intramolecular coupling interactions exist between internals. The representation of the nature of these interactions, not present in diagonal, quadratic force fields (Class I force fields), is shown to be important in accounting accurately for molecular energy surfaces. The Class II force field derived from the quantum energy surface is characterized by accounting for these important intramolecular forces. The importance of each 4.2 to 18.2%. This fourfold increase in the second derivative error dramatically demonstrates the importance of bond anharmonicity in the ab initio potential energy surface. The Class II force field derived from the quantum energy surface is characterized by accounting for these important intramolecular forces. The importance of each of the interaction terms of the potential energy function has also been assessed. Bond anharmonicity, angle anharmonicity, and bond/angle, bond/torsion, and angle/angle/ torsion cross-term interactions result in the most significant overall improvement in distorted structure energies and energy derivatives. The implications of each energy term for the development of advanced force fields is discussed. Finally, it is shown that the techniques introduced here for exploring the quantum energy surface can be used to determine the extent of transferability and range of validity of the force field. The latter is of crucial importance in meeting the objective of deriving a force field for use in molecular mechanics and dynamics calculations of a wide range of molecules often containing functional groups in novel environments. © 1994 by John Wiley & Sons, Inc.
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    Impressum (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992) 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/ange.19921040102
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    Feldeffekttransistoren als Sensoren neuronaler Systeme (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 47-49 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/ange.19921040106
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    Optisch anomale Kristalle (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 1-28 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Die optische Symmetrie vieler Kristalle ist niedriger als aufgrund ihrer äußeren Form und der Röntgenbeugungsdaten zu erwarten wäre. Heute schreibt man solche optischen Anomalien Nichtgleichgewichtsstrukturen zu, die durch kinetisch kontrolliertes Kristallwachstum entstehen. Verunreinigungen werden an Positionen, die normalerweise im Kristallverband über Symmetrieoperationen ineinander überführt werden könnten, in unterschiedlichem Ausmaß in die Oberfläche eingebaut. Die optisch anomalen Kristalle waren nach ihrer Entdeckung durch Brewster im Jahre 1815 während des gesamten 19. Jahrhunderts Gegenstand einer lebhaften Diskussion zwischen den wichtigsten Pionieren auf dem Gebiet der Kristallographie, darunter Biot, Berzelius, Herschel, Mitscherlich, Frankenheim, Pasteur, Mallard, Klein, Groth, Wyrouboff, Barlow, Brauns, Rinne, Pockels und Friedel. Aus dem Nebel wilder Spekulation tauchten zwei sich widersprechende Postulate auf: Zum einen wurde die symmetrische Form auf die zufällige Zwillingsbildung mehrerer Segmente niedrigerer Symmetrie zurückgeführt, zum anderen erklärte man die optischen Besonderheiten mit Spannungen, die man auf Verunreinigungen oder äußere Störungen zurückführte. Keines dieser Postulate entspricht der heutigen Betrachtungsweise. Um die Jahrhundertwende schwand allmählich das Interesse an diesem Forschungsgebiet, und nach 1917 griff niemand Tammanns neue und richtige Erkenntnisse auf. Das Problem der anomalen Doppelbrechung blieb - bis zu seiner Lösung in jüngster Zeit - mehr als ein halbes Jahrhundert unbeachtet. In dieser Übersicht werden sowohl mineralische als auch organische Systeme diskutiert, wobei das Hauptaugenmerk auf dem Phyllosilicat Apophyllit und auf 1,5-Dichlor-2,3-dinitrobenzol liegt. Das Studium optisch anomaler Nichtgleichgewichtsstrukturen kann dabei helfen, Fragen zu Kristallordnung, Kristallwachstum, molekularen Erkennungsmechanismen und der Entwicklung neuer Werkstoffe zu beantworten. Auch soll dieser Beitrag deutlich machen, wie wertvoll das Polarisationsmikroskop nach wie vor für die chemische Forschung ist.
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    Isocyanidruthenate - Analoga von TetracarbonylferratDiese Arbeit wurde von der U.S. National Science Foundation (Nr. 8722424) gefördert. Dr. Garry Warnock und Patricia Leach danken wir für anregende Diskussionen. (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 55-57 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/ange.19921040110
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    Unerwartete oxidative Ringöffnung eines (Octadehydrocorrinato)nickel(II)-Salzes zu einem Chlorophin-DerivatDiese Arbeit wurde von den National Institutes of Health (GM 34468 und GM 36520) an der Michigan State University und vom National Science Council (NSC) der Republik China (NSC80-0208-M002-58) gefördert. C. K. C. dankt dem NSC und der National Taiwan University für die Gastprofessur. (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 61-64 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/ange.19921040114
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    Titelbild (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. cpi 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/ange.19921040101
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    Synthese optisch aktiver Makromoleküle mit löslichen Metallocen-Katalysatoren (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 49-50 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1002/ange.19921040107
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    Cycloalkadiine  -  von der gebogenen Dreifachbindung bis zur gespannten KäfigstrukturProfessor Heinz A. Staab zum 65. Geburtstag gewidmet (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 29-46 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Cycloalkadiine (“cyclische Dialkine”) mittlerer Ringgröße lassen sich durch Ringschluß- und Eliminierungsreaktionen herstellen. Die Konformation der Ringe und die transanulare Wechselwirkung der Dreifachbindungen können durch Röntgenstrukturuntersuchungen an Einkristallen und durch Photoelektronenspektren bestimmt werden. Verglichen mit den unkomplexierten Verbindungen zeigen AgI- und CuI-Komplexe nur geringe Strukturänderungen, die Strukturen von Bis(hexacarbonyldicobalt)-Komplexen unterscheiden sich dagegen deutlich. Die Reaktion von Cycloalkadiinen mit Dicarbonyl(η5-cyclopentadienyl)cobalt ergibt inter- und intramolekulare Cyclobutadien-Komplexe. Das durch intermolekulare Reaktion entstehende Superphan des Cyclobutadiens kann in eine Reihe hochgespannter Käfigverbindungen überführt werden. Die Palette der Käfigverbindungen kann noch durch die Reaktion von cyclischen Diacetylenen mit Aluminiumchlorid und Acetylendicarbonsäureester erweitert werden. Sie führt über zweifach verbrückte Dewar-Benzole zu Propellaprismanen.
    Additional Material: 15 Ill.
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    URL: http://dx.doi.org/10.1002/ange.19921040105
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    1-O-(2-Acetoxyhexadec-1-enyl)choliniodid, ein neues Cytostaticum (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 54-55 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Tab.
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    URL: http://dx.doi.org/10.1002/ange.19921040109
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    Ein synthetischer Rezeptor für cyclo-AdenosinmonophosphatDiese Arbeit wurde von den U.S. National Institutes of Health gefördert. G. D. dankt dem kanadischen Natural Sciences and Engineering Research Council für ein Postdoc-Stipendium. Wir danken Dr. Marta Bruix (C. S. I. C., Madrid) für die Durchführung der ROESY-Experimente. (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 58-60 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/ange.19921040112
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    Synthese und Struktur eines ungewöhnlichen Uranpentachlorid-DerivatsProfessor Oskar Glemser zum 80. Geburtstag gewidmetDiese Arbeit wurde von der Deutschen Forschungsgemeinschaft (Gewährung eines Habilitationsstipendiums für F. T. E.) gefördert. Herrn Prof. Dr. H. W. Roesky danken wir für Unterstützung. (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 64-65 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/ange.19921040115
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    [Ni4(SC3H7)8Br] und [Ni4(SC3H7)8I]: gemischtvalente Nickelthiolate mit ganzzahligen bzw. gebrochenen MetalloxidationsstufenProfessor Peter Sartori zum 60. Geburtstag gewidmetDiese Arbeit wurde von der Deutschen Forschungsgemeinschaft, dem Bundesministerium für Forschung und Technologie und dem Fonds der Chemischen Industrie gefördert. (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 71-72 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/ange.19921040119
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    Die Stabilität von Buckminsterfulleren C60; Experimentelle Bestimmung der BildungswärmeDiese Arbeit wurde von der Deutschen Forschungsgemeinschaft, der US National Science Foundation und dem Fonds der Chemischen Industrie gefördert. (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 69-70 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Tab.
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    URL: http://dx.doi.org/10.1002/ange.19921040118
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    Lithiodiphenylmethylisocyanid-(  -  )-Spartein-Bis(tetrahydrofuran): Kristallstruktur eines lithiierten IsocyanidsProfessor Ulrich Schöllkopf gewidmetDiese Arbeit wurde vom Fonds der Chemischen Industrie und von der Deutschen Forschungsgemeinschaft (SFB 260) gefördert. (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 80-81 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/ange.19921040124
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  • 92
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    Wasser als Ligand in lithiierten organischen Verbindungen: [LiCH(CN)2 · H2O · TMEDA]∞Diese Arbeit wurde von der Deutschen Forschungsgemeinschaft und dem Fonds der Chemischen Industrie gefördert. Wir danken Dr. R. Snaith, Dr. D. S. Wright und D. Hoffmann für die zahlreichen Anregungen und ganz besonders Dr. W. Bauer für die Aufnahme eines HOESY-Spektrums. TMEDA = N, N, N′, N′-Tetramethylethylendiamin. (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 78-79 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/ange.19921040123
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    Stabile Zwischenstufen bei der Addition von BuSnCl3 an Molybdänzentren und bei seiner Eliminierung unter Spaltung bzw. Knüpfung einer Sn-Cl-Bindung: die Struktur von [Mo(CO)2(PCy3)(μ-Cl)(μ-S2CPCy3)-(BuSnCl2)]·CH2Cl2Diese Arbeit wurde von der spanischen Dirección General de Investigación Científica y Técnica (DGICYT) (Projekt PB88-0467), der Metalúrgica del Nalón S.A. und der Fundación de Investigación Científica y Técnica (FICYT) gefördert, J.A.P.-M. dankt der FICYT für ein Stipendium. Cy = Cyclohexyl. (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 81-83 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/ange.19921040125
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    [Et4N]2[{MO(S2)2}2(μ2-S7)(μ2-H2NNH2)] (M = Mo, W) - zweifach verbrückte Komplexe mit einem S72- und einem doppelt end-on-gebundenen H2NNH2-BrückenligandenDiese Arbeit wurde vom Structural Chemistry Research Laboratory des Fujian Institute of Research on Structure of Matter, von der Chinese Academy of Sciences und der National Science Foundation of China gefördert. (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 83-84 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/ange.19921040126
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    Eintopfsynthese von Tagatose-1,6-bisphosphat durch diastereoselektive enzymatische AldoladditionEnzyme in der Organischen Synthese, 2. Mitteilung. Diese Arbeit wurde von der Deutschen Forschungsgemeinschaft (Projekt Fe 244/2-1), der Wissenschaftlichen Gesellschaft Freiburg und dem Fonds der Chemischen Industrie gefördert. Wir danken Prof. Dr. J. W. Lengeler, Universität Osnabrück, für die Überlassung von Bakterienstämmen und Frau Dipl.- Chem. G. Sinerius für auf chemischem Weg [7] synthetisiertes 1. - 1. Mitteilung: [2]. (1992)
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    Zeitschrift für die chemische Industrie 104 (1992), S. 76-78 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/ange.19921040122
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    Ein Germaniumsesquisulfid der Zusammensetzung (tBuGe)4S6 ohne AdamantanstrukturDiese Arbeit wurde vom japanischen Ministerium für Erziehung, Wissenschaft und Kultur mit Mitteln des Fonds für Hochschulforschung gefördert. Wir danken dem Asai Germanium Institut für eine Spende von Tetrachlorgerman. (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 84-85 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/ange.19921040127
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    Die Struktur der Thioschwefelsäure H2S2O3 und ihres Monoanions HS2O3-Schwefelverbindungen, 147. Mitteilung. - 146. Mitteilung: R. Steudel, M. Papavassiliou, F. Baumgart, Z. Naturforsch. B 1991, 46, 1674-1678. (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 87-89 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/ange.19921040129
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    Ein ungewöhnliches Wechselspiel zwischen makromolekularer und supramolekularer Helicität bei in einem chiralen Flüssigkristall gelösten PolyisocyanatenDiese Arbeit wurde an der Temple und an der Polytechnic University von der National Science Foundation (Stipendien DMR 89-17833 bzw. CHE 90-02536) sowie an der Polytechnic University von IBM (Almaden Laboratory) und von der Petroleum Research Foundation, verwaltet von der American Chemical Society, gefördert. (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 86-87 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/ange.19921040128
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    Ungewöhnliche Koordination des 1,3-Diphosphacyclobutadiens (iPr2NCP)2 an zwei [Ni(CO)3]-KomplexfragmenteReaktive E=C(p-p)π-Systeme, 29. Mitteilung. Diese Arbeit wurde von der Deutschen Forschungsgemeinschaft und dem Fonds der Chemischen Industrie gefördert.-28. Mitteilung: J. Grobe, D. Le Van, T. Großpietsch, Z. Naturforsch. B 1991, 46, 978-984. (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 94-96 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/ange.19921040132
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    Drei unabhängige Moleküle in der Elementarzelle eines Phosphor-Ylids; Änderungen der Molekülgeometrie bei der Rotation um die Phosphor-Kohlenstoff-YlidbindungDiese Arbeit wurde von Prof. W. Sundermeyer, Prof. G. Huttner, der Deutschen Forschungsgemeinschaft, dem Fonds der Chemischen Industrie und der Dr.-Otto-Röhm-Gedächtnisstiftung gefördert. (1992)
    Weinheim : Wiley-Blackwell
    Zeitschrift für die chemische Industrie 104 (1992), S. 92-94 
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    ISSN: 0044-8249
    Keywords: Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/ange.19921040131
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