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  • 1
    Electronic Resource
    Electronic Resource
    C–H...O and C–H...N interactions in RNA structures (1999)
    Springer
    Theoretical chemistry accounts 101 (1999), S. 103-113 
    Details
    ISSN: 1432-2234
    Keywords: Key words: RNA structure ; C ; H...X interactions ; Hydrogen bonds ; Statistical analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. Small molecule studies indicate that C–H...X interactions (X: O,N) constitute weak H-bonds. We have performed a comprehensive analysis of their occurrence and geometry in RNA structures. Here, we report on statistical properties of the total set of interactions identified and discuss selected motifs. The distance/angle distribution of all interactions exhibits an excluded region where the allowed C–H...X angle range increases with an increasing H...X distance. The preferred short C–H...X interactions in RNA are backbone-backbone contacts between neighbour nucleotides. Distance/angle distributions generated for various interaction types can be used for error recognition and modelling. The axial C2′(H)...O4′ and C5′(H)...O2′ interactions connect two backbone segments and form a seven-membered ring that is specific for RNA. An AA base pair with one standard H-bond and one C–H...N interaction has been identified in various structures. Despite the occurrence of short C–H...X contacts their free energy contribution to RNA stability remains to be assessed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002140050415
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Parallel dose-response curves in combination experiments (1998)
    Springer
    Bulletin of mathematical biology 60 (1998), S. 197-213 
    Details
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract A possible experimental design for combination experiments is to compare the doseresponse curve of a single agent with the corresponding curve of the same agent using either a fixed amount of a second one or a fixed dose ratio. No interaction is then often defined by a parallel shift of these curves. We have performed a systematic study for various types of doseresponse relations both for the dose-additivity (Loewe additivity) and for the independence (Bliss independence) criteria for defining zero interaction. Parallelism between doseresponse curves of a single agent and those of the same agent in the presence of a fixed amount of another one is found for the Loewe-additivity criterion for linear doseresponse relations. For nonlinear relations, one has to differentiate between effect parallelism (parallel shift on the effect scale) and dose parallelism (parallel shift on the dose scale). In the case of Loewe additivity, zero-interaction dose parallelism is found for power, Weibull, median-effect and logistic doseresponse relations, given that special parameter relationships are fulfilled. The mechanistic model of competitive interaction exhibits dose parallelism but not effect parallelism for Loewe additivity. Bliss independence and Loewe additivity lead to identical results for exponential doseresponse curves. This is the only case for which dose parallelism was found for Bliss independence. Parallelism between single-agent doseresponse relations and Loewe additivity mixture relations is found for examples with a fixed doseratio design. However, this is again not a general property of the design adopted but holds only if special conditions are fulfilled. The comparison of combination doseresponse curves with single-agent relations has to be performed taking into account both potency and shape parameters. The results of this analysis lead to the conclusion that parallelism between zero interaction combination and single-agent doseresponse relations is found only for special cases and cannot be used as a general criterion for defining zero-interaction in combined-action assessment even if the correct potency shift is taken into account.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1006/bulm.1997.0009
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    The kinetic deuterium isotope effect of proton-transfer reactions in solution. Comparison of the marcus and the quantum-statistical mechanical models (1990)
    Chichester : Wiley-Blackwell
    Journal of Physical Organic Chemistry 3 (1990), S. 62-68 
    Details
    ISSN: 0894-3230
    Keywords: Organic Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: The free energy dependence of the kinetic deuterium isotope effect of proton-transfer reactions in solution is usually analysed in terms of the Marcus model. By means of modern computer techniques, the more general quantumstatistical mechanical model is also amenable to routine application. The differnces in the basic assumptions of the two approaches concerning the kinetic isotope effect are discussed. Reaction series for which both the Brønsted relation and the free-energy dependence of the kinetic isotope effect are available are analysed by means of the two models using one set of parameters for both free-energy relations.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/poc.610030112
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    Paper (German National Licenses)
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  • 4
    Electronic Resource
    Electronic Resource
    The Marcus cross relation for hydrogen-transfer reactions (1993)
    Chichester : Wiley-Blackwell
    Journal of Physical Organic Chemistry 6 (1993), S. 281-286 
    Details
    ISSN: 0894-3230
    Keywords: Organic Chemistry ; Physical Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: The Marcus cross relation provides a tool to calculate cross rates from the corresponding identity rates and the equilibrium constant. Assumptions made in deriving the Marcus cross relation and conclusions which can be drawn from agreement or disagreement between experimental and calculated cross rates are discussed. For a small variation in identity rate constants, agreement between experimental and calculated cross rates are discussed. For a small variation in identity rate constants, agreement between experimental and calculated cross rates simply means that the rate constant of a hypothetical thermoneutral cross reaction has a value within the range covered by the identity rates. Whether or not this value corresponds to the mean value of logarithmic identity rate constants can only be checked for a large variation in identity rates. Therefore, a newly defined index M is used to relate the difference in experimental and calculated logarithmic rate constants to the variation in the logarithmic identity rates. Provided that the Marcus cross relation is not obeyed, this indicates non-additivity of kinetic parameters. Applying this analysis to protontransfer reactions between different transition metal acids and between 9-alkylflourenes and (9-alkylfluorenyl)lithium shows that claims about agreement or disagreement of experimental rate constants with the rate constants calculated by means of the Marcus cross relation have to be revised in part.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/poc.610060505
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    Paper (German National Licenses)
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  • 5
    Electronic Resource
    Electronic Resource
    Gleichgewichtsgeometrie und spektroskopische Eigenschaften des Biphenyls im S0-und S1-Zustand (1978)
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 61 (1978), S. 2100-2107 
    Details
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Equilibrium geometry and spectroscopic properties of biphenyl in the S0 and S1 stateEquilibrium geometries for the S0 and S1 state of biphenyl were determined by minimization of the total energy with respect to all cartesian coordinates. The molecule is twisted in the S0 state (20°), but becomes planar in the S1 state. Using these results, an interpretation of the fluorescence and absorption spectra can be given. In passing from the S0 to the S1 state equilibrium geometry a remarkable change of the state ordering occurs.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/hlca.19780610617
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    Paper (German National Licenses)
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  • 6
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    Unknown
    Density functional study of isoguanine tetrad and pentad sandwich complexes with alkali metal ions (2007)
    Details
    Publication Date: 2016-06-30
    Language: English
    Type: article , doc-type:article
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    OPUS
  • 7
    facet.materialart.
    Unknown
    Density functional study of guanine and uracil quartets and of guanine quartet metal/ion complexes (2000)
    Details
    Publication Date: 2014-02-26
    Description: The structures and interaction energies of guanine and uracil quartets have been determined by B3LYP hybrid density functional calculations. The total interaction energy $\Delta$E$^{T}$ of the $\it{C}$$_{4h}$-symmetric guanine quartet consisting of Hoogsteen type base pairs with two hydrogen bonds between two neighbour bases is -66.07 kcal/mol at the highest level. The uracil quartet with C6-H6...O4 interactions between the individual bases has only a small interaction energy of -20.92 kcal/mol and the interaction energy of -24.63 kcal/mol for the alternative structure with N3-H3...O4 hydrogen bonds is only slightly more negative. Cooperative effects contribute between 10 and 25 \% to all interaction energies. Complexes of metal ions with G-quartets can be classified into different structure types. The one with Ca$^{2+}$ in the central cavity adopts a $\it{C}$$_{4h}$-symmetric structure with coplanar bases, whereas the energies of the planar and non-planar Na$^{+}$ complexes are almost identical. The small ions Li$^{+}$, Be$^{2+}$, Cu$^{+}$ and Zn$^{2+}$ prefer a non-planar $\it{S}$$_{4}$-symmetric structure. The lack of co-planarity prevents probably a stacking of these base quartets. The central cavity is too small for K$^{+}$ ions and therefore this ion favours in contrast to all other investigated ions a $\it{C}$$_{4}$-symmetric complex, which is 4.73 kcal/mol more stable than the $\it{C}$$_{4h}$-symmetric one. The distance 1.665 {\AA} between K$^{+}$ and the root mean squares plane of the guanine bases is approximately half of the distance between two stacked G-quartets. The total interaction energy of alkaline earth ion complexes exceeds the ones with alkali ions. Within both groups of ions the interaction energy decreases with an increasing row position in the periodic table. The B3LYP and BLYP methods lead to similar structures and energies. Both methods are suitable for hydrogen-bonded biological systems. Compared with the before mentioned methods the HCTH functional leads to longer hydrogen bonds and different relative energies for two U-quartets. Finally we calculated also structures and relative energies with the MMFF94 forcefield. Contrary to all DFT methods, MMFF94 predicts bifurcated C-H...O contacts in the uracil quartet. In the G-quartet the MMFF94 hydrogen bond distances N2-H22...N7 are shorter than the DFT distances, whereas the N1-H1...O6 distances are longer.
    Keywords: ddc:000
    Language: English
    Type: reportzib , doc-type:preprint
    Format: application/postscript
    Format: application/pdf
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