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  • Atomic, Molecular and Optical Physics  (4)
  • Chemistry  (2)
  • 1
    Electronic Resource
    Electronic Resource
    A molecular dynamics simulation of the (dG)6·(dC)6 minihelix including counterions and water (1990)
    New York : Wiley-Blackwell
    Biopolymers 29 (1990), S. 1027-1044 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The results of a 60 ps molecular dynamics (MD) simulation of (dG)6·(dC)6 including 10 Na+ counterions and 292 water molecules are presented. All backbone angles and helix parameters for the hexamer are reported in this paper along with trajectory plots of selected angles. Hydrogen bonding between the bases along the helical axis was observed to flucturate with time, showing the dynamic nature of the base-pairing interaction. These fluctuations gave rise to unusual hydrogen-bonding patterns. Good intrastrad base stacking and no interstrand base stacking were also observed. The hexamer minihelix retains an essentially B-DNA conformation throughout the entire simulation even though some helix parameters and backbone angles do not have strict B-DNA values. The most striking feature obtained from the simulation was a high propeller twist, which resulted in a narrow minor groove for the minihelix. It is proposed that (dG)n·(dC)n sequences are resistant to DNAase I because of this narrow minor groove in dilute aqueous solution.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360290614
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    A molecular dynamics study of the effect of G · T mispairs on the conformation of DNA in solution (1991)
    New York : Wiley-Blackwell
    Biopolymers 31 (1991), S. 211-232 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The effect of G · T mispair incorporation into a double-helical environment was examined by molecular dynamics simulation. The 60-ps simulations performed on the two hexanucleotide duplexes d (G3C3)2 and d (G3TC2)2 included 10 Na+ counterions and first hydration shell waters. The resulting backbone torsional angle trajectories were analyzed to select time spans representative of conformational domains. The average backbone angles and helical parameters of the last time span for both duplexes are reported. During the simulation the hexamers retained B-type DNA structures that differed from typical A- or B-DNA forms. The overall helical structures for the two duplexes are vary similar. The presence of G · T mispairs did not alter the overall helical structure of the oligonucleotide duplex. Large propeller twist and buckle angles were obtained for both duplexes. The purine/pyrimidine crossover step showed a large decrease in propeller twist in the normal duplex but not in the mismatch duplex. Upon the formation of wobble mispairs in the mismatched duplex, the guanines moved into the minor groove and the thymines moved into the major groove. This helped prevent purine/purine clash and created a deformation in the relative orientation of the glycosidic bonds. It also exposed the free O4 of the thymines in the major groove and N2 of the guanines in the minor groove to interactions with solvent and counterions. These factors seemed to contribute to the apparently higher rigidity of the mismatched duplex during the simulation.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360310209
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Normal-mode vibrational frequencies and thermodynamic properties of uracil and 4-hydroxyuracil (1980)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 18 (1980), S. 323-329 
    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: Normal-mode vibrational frequencies were obtained for uracil and 4-hydroxyuracil with the MINDO/3 SCF method. MINDO/3 vibrational frequencies and the moments of inertia for STO-3G optimized geometries yielded a ΔST0 for U ⇄ U* of 1.06 e.u./mol by standard statistical thermodynamic equations. ΔGT0 is then 6.29 kcal/mol in the gas phase for U ⇄ U*. The reaction field continuum model of solvent effect lowers ΔGT0 to 5.3 kcal/mol in aqueous solution. The tautomeric equilibrium constant in solution is then 1.3 × 10-4, in good agreement with experimental values.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560180146
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  • 4
    Electronic Resource
    Electronic Resource
    STO-3G study of uracil, thymine, 5-fluorouracil, 5-methoxyuracil, and their 4-hydroxytautomeric forms (1982)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 22 (1982), S. 639-647 
    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: Ab initio molecular orbital calculations with an STO-3G basis have been performed to investigate the energetics and electronic properties of some 5-substituted uracils and their 4-OH tautomer forms with R including F, CH3, and OMe. In all cases, the diketo form is more stable. An excellent linear correlation between the calculated and experimental ionization potentials was found.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560220313
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  • 5
    Electronic Resource
    Electronic Resource
    Uracil and the tautomer 4-hydroxyuracil: An ab initio study with geometry optimization (1981)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 19 (1981), S. 171-177 
    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: Ab initio STO-3G geometries and relative energies for uracil (U) and the tautomer 4-hydroxyuracil (U*) were obtained with the HONDO program utilizing the rapidly convergent method of Murtaugh and Sargent for geometry optimization. ΔE for U⇄U* is 6.61 kcal/mole. The reaction field continuum model for solvent effect indicates a preferential stabilization of U* by 1.0 kcal/mole. The calculated gas phase Kt and solution Kt for U⇄U* are 1.44×10-5 and 1.3×10-4, respectively.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560190115
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  • 6
    Electronic Resource
    Electronic Resource
    Optimum geometries and relative energies for cytosine, thymine, uracil, the imino tautomer of cytosine, the enol tautomer of thymine, and the enol tautomer of uracil by the MINDO/2 SCF MO method (1978)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 14 (1978), S. 851-860 
    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 MINDO/2 SCF MO geometry optimization of cytosine (C), thymine (T), uracil (U), the imino tautomer of cytosine (C*), the enol tautomer of thymine (T*), and the enol tautomer of uracil (U*)was made. The optimized geometries for cytosine, thymine, and uracil agree well with crystallographic data. The optimized geometries for the tautomers show the correct trends in bond lengthening and bond angle except for the C4 - O4 length and C4 - O4 - H angle of T* and U*. The energies of tautomerization were found to be 10.3, -9.0, and -14.2 kcal/mol for C⇌C*, T⇌T*, and U⇌U*, respectively, when optimized geometries are used. The overestimation of the C4 - O4 - H angle is speculated to arise because of an inadequacy in the parametrization of the one-center integrals in MINDO/2.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560140615
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