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  • 1
    Electronic Resource
    Electronic Resource
    Measuring the geometry of DNA grooves (1994)
    New York : Wiley-Blackwell
    Biopolymers 34 (1994), S. 337-346 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present a new method for measuring the widths and depths of the grooves formed within DNA helices. This method overcomes the limitations of simply measuring interstrand phosphate-phosphate distances and has the advantage of yielding continuous values for groove geometry along a DNA fragment. In the case of oligonucleotides, it also clearly indicates the zones in which grooves exist, bounded by two phosphodiester backbones. The methodology has been developed within the Curves algorithm for studying irregular DNA geometries and is based on the optimal, and generally curved, helical axis obtained by this analysis. © 1994 John Wiley & Sons, Inc.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360340305
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  • 2
    Electronic Resource
    Electronic Resource
    DNA flexibility as a function of allomorphic conformation and of base sequence (1992)
    New York : Wiley-Blackwell
    Biopolymers 32 (1992), S. 1077-1103 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Systematic theoretical modeling of symmetric DNA oligomers, carried out earlier for the B conformation, is now extended to A-DNA. In contrast to the previous results, it is found that A-DNA shows no multiplicity of low-energy substate conformations. The possibilities of the Jumna algorithm are subsequently applied to studying deformations of the oligomers. Controlled winding and stretching deformations are used to study how the two allomorphs and different base sequences absorb such external stress. The results help explain the internal mechanics of the DNA double helix and the extent to which fine structure influences this behavior. The results point to some differences between the A and B double helices, but also to many similarities. Sequence effects on flexibility are relatively limited compared to their impact on optimal energy conformations. It is also shown that the conformational substates detected for B-DNA oligomers are preserved under deformation, but have little influence on its energetics. © 1992 John Wiley & Sons, Inc.
    Additional Material: 22 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360320817
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  • 3
    Electronic Resource
    Electronic Resource
    The electrostatic molecular potential of tRNAPhe. V. The influence of counterion binding on the potential and the steric accessibility (1981)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 20 (1981), S. 171-183 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An investigation is carried out of the influence of counterions bound to yeast tRNAPhe on the electrostatic potential and steric accessibility of this macromolecule. Two types of cations are considered, the Mg2+ ions located in the crystal of tRNAPhe, with their waters of hydration, and Na+ ions, which are positioned by theoretical estimation. Possible effects of the counterions on the chemical reactivity of tRNAPhe are pointed out.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560200715
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  • 4
    Electronic Resource
    Electronic Resource
    Molecular electrotatic potential of a triple stranded helix: Poly(dT)·poly(dA)·poly(dT) (1983)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 23 (1983), S. 1451-1461 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The molecular electrostatic potential of the triple helix poly(dT)·tpoly(dA)·poly(dT) is calculated, and the results are examined in relation to those obtained for its component double and single helical parts. For the double helix presenting the standard Watson-Crick hydrogen bonds, the deepest potentials are formed on the side of the major groove, a situation similar to that observed in the A-DNA duplex. For the double helix presenting Hoogsteen-type hydrogen bonds the deepest potentials lie in the major groove, on the side of the pyrimidine strand. In the triple helix the deepest potentials are located in the major groove in a narrow zone over the thymine bases of the Watson-Crick pair.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560230427
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  • 5
    Electronic Resource
    Electronic Resource
    On the electrostatic properties of papain in relation to its enzymatic activity (1983)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 24 (1983), S. 353-371 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The electrostatic potentials and fields created by the thiol protease, papain, are computed on the surface envelope of the protein and in the region of its active site using a technique based on accurate multipole expansions of the electron density of appropriately chosen subunits. The effect of binding counterions to the protein is considered specifically. The possible role of the “electrostatic environment” in the functioning of the enzyme is discussed and it is found that this environment can favor the proton transfer between Cys 25 and His 159 that is thought to initiate its mode of action, but that the reasons for this appear more complicated than earlier models would suggest.
    Additional Material: 14 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560240404
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  • 6
    Electronic Resource
    Electronic Resource
    Effect of nucleic acid flexibility upon ASIF (accessible surface integrated field). Possible significance for biochemical reactivity exemplified by aflatoxin B1 binding (1984)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 26 (1984), S. 273-286 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The extent of reactivity of a guanine in B-DNA toward aflatoxin B1 depends on the base sequence surrounding that purine in the double helix. In order to account for this variability, we have computed the ASIF (accessible surface integrated field) index for the N7 atom (at which the reaction occurs) of guanine in a G—C pair surrounded on both sides by different types of base pairs in a model oligohelix. When the conformation of the helix is maintained in the B-DNA form, the correlation ASIF reactivity is limited. A study is performed showing the influence on the ASIF index of different departures from the regular B-DNA conformation, likely to occur in a double helix. It is shown that the correlation ASIF reactivity can be strongly improved by allowing some local departures from this regular arrangement.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560260729
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  • 7
    Electronic Resource
    Electronic Resource
    Model quantum chemical studies of the electronic structure and aspects of reactivity of diol epoxides of aromatic hydrocarbons (1979)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 15 (1979), S. 271-280 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This paper offers a unified presentation of the main ring conformers of the diol expoxides, triol carbonium ions, and tetrols related to the “bay-region” benzo ring of carcinogenic metabolites of PAH and brings forward quantitative information through ab initio SCF computations about their relative energies. It substantiates and evaluates the energy of the syn epoxide-OH4 hydrogen bond and, on the contrary, refutes the significance of an O⃛H—O or an O-⃛H—O bond in the triol carbonium ions. It provides an explanation for the similar rates of acid-catalyzed hydrolysis of the syn and anti diol expoxides. It evaluates the stabilization of the triol carbonium ions due to the presence of a neighboring double bond and accounts for the spontaneous opening of protonated epoxides. Finally it accounts for cis hydrolysis of the syn diol epoxide and trans hydrolysis of the anit diol epoxide under acid conditions.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560150303
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  • 8
    Electronic Resource
    Electronic Resource
    The electrostatic potential of a model phospholipid monolayer (1981)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 20 (1981), S. 161-170 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular electrostatic potentials are calculated for a single phospholipid molecule (1,2-dilauroyl-phosphatidylethanolamine) and for its model monolayer. For the single molecule the magnitudes of the positive and negative potentials associated with the amino and phosphate groups of the polar head are comparable. For the monolayer a dominantly positive surface potential is obtained.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560200714
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  • 9
    Electronic Resource
    Electronic Resource
    Theoretical model study of the reactivity of benzo(a)pyrene diol epoxide with the amino groups of the nucleic acid bases (1979)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 16 (1979), S. 175-188 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A quantum-mechanical model study, aided by classical potential calculations, of the formation of adducts between the candidate ultimate carcinogen benzo(a)pyrene diol epoxide and the amino groups of guanine, adenine, and cytosine is presented. An explanation for the preferential reactivity of guanine is proposed and conformational aspects of adduct formation are discussed for both nucleosides and B-DNA.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560160119
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  • 10
    Electronic Resource
    Electronic Resource
    Molecular electrostatic potential on the surface envelopes of macromolecules: B-DNA (1981)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 20 (1981), S. 259-272 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A procedure for calculating the molecular electrostatic potentials on surface envelopes surrounding macromolecules is presented. This new representation of potential is employed in studying B-DNA double helices and, from the results, deductions are drawn on the interaction specificities of B-DNA with electrophiles.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560200123
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