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  • 1
    Electronic Resource
    Electronic Resource
    Electron density redistribution in the stabilization of a molecular stacking complex: The nature and correction of basis set superposition errors (1981)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 73-82 
    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 effect of the basis set superposition error (BSSE) on the calculated electronic structure of a molecular stacking complex is analyzed with the counterpoise correction method. The complex between para-hydroxyaniline (PHA) and formamidinium cation (FAM) is calculated ab initio with the STO-3G and Whitman-Hornback minimal bases, and with two split valence basis sets: 4-31G and STO-3G(D). When the counterpoise correction is applied, the charge redistribution in the PHA/FAM complex calculated with all four basis sets suggests that the complex is electrostatic in nature and that the main polarization is from the PHA toward FAM. The FAM cation is polarized away from the intermolecular region, thus causing further increase in the electrostatic interaction. This picture is not evident with the STO-3G related bases if the counterpoise correction is not applied. Thus, the BSSE in the charge redistribution is shown to be particularly large in the STO-3G basis and in the diffuse, split valence, STO-3G(D). Both these basis sets suffer from an inappropriate description of the core region. Where there is an improved description of the electron density in the core region, as in the calculations with the energy-optimized Whitman-Hornback basis and with the 4-31G basis, the counterpoise correction has only a very small effect on the charge redistribution. After the counterpoise correction is applied, the two minimal basis sets yield nearly identical charge redistribution results, as do the two split valence bases. It is therefore suggested that basis sets used in the calculation of molecular complexes might be classifiable according to criteria such as the degree of contraction and the quality of the description of angular polarization. This would help in the comparative evaluation of results obtained with different bases since minimal basis sets (or split valence bases) would become directly identifiable as groups yielding qualitatively similar results.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540020113
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  • 2
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540130410
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  • 3
    Electronic Resource
    Electronic Resource
    Comparison of the use of the MNDO and MINDO/3 methods with ab initio methods to study tautomerism in histamine, 2- and 4-methylhistamine (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 142-148 
    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 semiempirical MNDO and MINDO/3 methods are used to study the various tautomeric forms of histamine, 2-methylhistamine, and 4-methylhistamine. Comparisons of the optimized structures and tautomerization energies are made with values obtained from ab initio Hartree-Fock calculations using the 3-21G and STO-3G basis sets. Based on these results and previous comparisons of STO-3G results with x-ray structures, the present results indicate that while there are some differences in the values of the structural parameters, the changes in structure upon tautomerization and/or protonation are very similar. Further analysis of the MNDO and MINDO/3 structures by means of their utilization in 3-21G and STO-3G calculations indicates that either of these semiempirical methods provides reliable values for the structural parameters. Both methods give good qualitative agreement with the ab initio calculations for the relative energies of the various tautomers in the three compounds. In these studies the MNDO method appears to give better quantitative agreement with the 3-21G and STO-3G results than the MINDO/3 method.
    Additional Material: 4 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080206
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  • 4
    Electronic Resource
    Electronic Resource
    3S- Versus 1s-type Gaussian primitives: Modifications of the 3-21G(*) basis set for the sulfur atom (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 660-672 
    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 complete set of second-order Gaussian functions (6D) includes a totally symmetric second-order Gaussian function (3s-type) in addition to the five d-type functions. This 3s-type function in the 3-21G(*) basis set for the sulfur atom is described (1) in terms of its geometric and electronic effects observed in the sulfur atom and in four sulfur-containing molecules and (2) by the ability of a single zero-order 1s-type Gaussian function (with various exponents) to replace it in ab initio Hartree-Fock calculations. The geometry of the molecules (dihydrogen sulfide, dihydrogen thioketone, dihydrogen disulfide, and methanesulfonamide) were obtained using various semiempirical and ab initio methods. It is found that the 3s-type function lowers the energy relative to that calculated with the 3-21G(*) basis set with only five second-order Gaussian functions by ca. 46-48 kcal/mol per sulfur atom. Only small changes in geometry are observed when the latter basis set is augmented with a 3s or 1s function. When the exponent of the 1s replacement function is chosen so that the resulting function has a location similar to that of the 3s function as measured by the degree of overlap or the coincidence of radial distribution maxima, the corresponding drop in energy is less than 8 kcal/mol per sulfur atom. However, when the shape of the radial distribution of the 1s function is similar to that of the 3s, i.e., when the value of the 1s exponent is ca. equal to that of the 3s function (a local maximum in the 1s energy profile), the energy lowering is similar to that produced with the 3s function. The electronic effects observed in the molecules differ from those in the atom, the largest deviations being found in the methanesulfonamide calculations.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100508
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