Computational investigation of nucleic acids.

机译：核酸的计算研究。

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In this work, various computational chemistry models are applied to problems of biochemical interest, with emphasis on nucleic acids. First various density functionals and multilevel methods are benchmarked against experimental proton affinities and gas-phase basicities. Then prediction of biologically relevant values of nucleic acids, amino acids, RNA sugar, and phosphates are made. In applied work, density functional theory is employed to help elucidate topics in lesion formation in nucleic acids. In particular the role of C5 methyl cytosine substitution is investigated through the use of various analogues and explaining NMR spectra of specific adenine lesions formed by 1,2,3,4-diepoxybutane. Finally, two works related to parameterization are given. The first is CHARMM molecular mechanical force field parameter development for the reactive intermediates of native and thio-substituted ribozymes. This work provides modifications necessary to reproduce structural aspects of transition state structures during phosphate transesterification. The second is an investigation into the appropriate solvation free energy for phosphoric acid and its anions. This includes both a review of the currently used and available data as well as a benchmark of various computational solvation models.

机译：在这项工作中，将各种计算化学模型应用于生化关注的问题，重点是核酸。首先，以实验质子亲和力和气相碱度为基准对各种密度泛函和多级方法进行基准测试。然后预测核酸，氨基酸，RNA糖和磷酸盐的生物学相关值。在应用工作中，采用密度泛函理论来帮助阐明核酸病变形成中的主题。特别是通过使用各种类似物并解释由1,2,3,4-二环氧丁烷形成的特定腺嘌呤损伤的NMR光谱，研究了C5甲基胞嘧啶取代的作用。最后，给出了与参数化有关的两项工作。首先是CHARMM分子机械力场参数开发，用于天然和硫代取代核酶的反应性中间体。这项工作提供了必要的修改，以在磷酸酯交换过程中再现过渡态结构的结构方面。第二个是对磷酸及其阴离子合适的溶剂化自由能的研究。这不仅包括对当前使用和可用数据的审查，还包括各种计算溶剂化模型的基准。

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作者
Moser, Adam Thomas.;
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作者单位

University of Minnesota.;

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授予单位 University of Minnesota.;
学科 Chemistry Physical.
学位 Ph.D.
年度 2009
页码 158 p.
总页数 158
原文格式 PDF
正文语种 eng
中图分类物理化学（理论化学）、化学物理学;
关键词
入库时间 2022-08-17 11:38:24

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1. Capillary Electrophoresis of Nucleic Acids, Vol. 1: Introduction to the Capillary Electrophoresis of Nucleic Acids. Keith R. Mitchelson and Jing Cheng, eds. Totowa, NJ: Humana Press, 2001, 484 pp., $125.00. ISBN 0-89603-779-7.Capillary Electrophoresis of Nucleic Acids, Vol. 2: Practical Applications of Capillary Electrophoresis. Keith R. Mitchelson and Jing Cheng, eds. Totowa, NJ: Humana Press, 2001, 408 pp., $125.00. ISBN 0-89603-765-7. [J] . Timothy G. Strein Clinical Chemistry: Journal of the American Association for Clinical Chemists . 2002,第4期

机译：核酸的毛细管电泳，第1：核酸毛细管电泳简介。 Keith R. Mitchelson和Jing Cheng编辑。新泽西州Totowa：Humana出版社，2001年，484页，125.00美元。 ISBN 0-89603-779-7。核酸的毛细管电泳，第2：毛细管电泳的实际应用。 Keith R. Mitchelson和Jing Cheng编辑。新泽西州Totowa：Humana出版社，2001年，408页，125.00美元。 ISBN 0-89603-765-7。
2. Chromatographic studies of nucleic acids. 4. The nucleic acid of the turnip yellow mosaic virus, including a note on the nucleic acid of the tomato bushy stunt virus [J] . J. D. Smith, R. Markham The biochemical journal . 1951,第4期

机译：核酸色谱研究。 4.萝卜黄色花叶病毒的核酸，包括关于番茄浓密特技病毒的核酸的注释
3. Interaction and cyanine dyes with nucleic acids. XXV. influence of affinity-modifying groups in the structure of benzothiazol-4-[2,6-dimethylpyridinium] dyes on the spectral properties of the dyes in the presence of nucleic acids [J] . S. M. Yarmoluk, V. B. Kovalska, D. V. Kryvorotenko, Spectrochimica acta, Part A. Molecular and biomolecular spectroscopy . 2001,第7期

机译：花青染料与核酸的相互作用。二十五。核酸存在下苯并噻唑-4- [2,6-二甲基吡啶]染料结构中亲和改性基团对染料光谱性质的影响
4. Investigating conformational changes of protein-nucleic acid and protein-ligand-nucleic acid complexes by tandem mass spectrometry [C] . Kevin B. Turner, Daniele Fabris ASMS Conference on Mass Spectrometry and Allied Topics . 2008

机译：通过串联质谱研究蛋白质 - 核酸和蛋白质 - 配体 - 核酸复合物的构象变化
5. Computational prediction of allosteric nucleic acids. [D] . Hall, Bradley. 2008

机译：变构核酸的计算预测。
6. Computation of statistical secondary structure of nucleic acids. [O] . K Yamamoto, Y Kitamura, H Yoshikura 1984

机译：核酸统计二级结构的计算。
7. Computation of statistical secondary structure of nucleic acids. [O] . Yamamoto, K, Kitamura, Y, Yoshikura, H 1984

机译：核酸统计二级结构的计算。
8. Studies on the Structure of Nucleic Acids. I. Interaction of Rosaniline with Desoxypentoss Nucleic Acid. [R] . Cavalieri, L. F., Angelos, A. 1950

机译：研究核酸的结构。 I. Rosaniline的互动与Desoxypentoss核酸。

Computational investigation of nucleic acids.

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