【作者】 黄志坚；

【导师】 林子敬；

【作者基本信息】 中国科学技术大学 ， 凝聚态物理， 2006， 博士

【摘要】 本论文的研究方向是通过密度泛函理论和从头算方法研究气相氨基酸的构型和性质。近年来，随着计算方法的发展和计算能力的提高，电子结构理论以及基于第一性原理的科学计算方法，已经成为许多科学问题的强有力的工具，它被广泛应用到化学、生物化学、环境科学和材料科学等诸多学科领域的科学研究中。另一方面，蛋白质和多肽的结构组成单元—氨基酸是目前研究的热点。木论文对芳香型氨基酸和精氨酸进行了理论研究，研究的性质包括几何结构、电子结构、构刑分布、电离能和电子亲和势、质子化过程、红外谱、紫外谱以及分子内相互作用等方面。第一章简要介绍了量子化学的基本原理和几种用于量化计算的理论方法，主要包括多体微扰理论、组态相互作用、耦合簇理论和密度泛函理论。同时，介绍了本论文使用到的含时密度泛函理论、分子中的原子理论以及自然键轨道理论。本章最后还介绍了本论文所用的软件包和本论文的研究目的。第二章首先简要介绍了氨基酸的物理和化学性质。由于芳香型氨基酸具有紫外发色基团，通过对蛋白质残基中芳香型氨基酸的光谱研究可以探测蛋白质的空间结构，因而芳香型氨基酸的光谱性质是目前研究的热点。本章系统地研究了芳香型氨基酸的势能面并计算了构型性质和构型平衡分布，解释芳香型氨基酸的光谱现象。另外，应用分子中的原子理论研究芳香型氨基酸构型的分子内相互作用。第三章研究了气相精氨酸分子的构型和性质。由于其众多的自由度而成为氨基酸理论计算中很富有挑战性的一个氨基酸。由于精氨酸中含有胍基侧链，在20种氨基酸中它的碱性最强。一般认为，气相中精氨酸的双电性和中性构型可以共存。同时由于精氨酸中存在众多能参与形成氢键的氢原子，研究精氨酸分子内相互将会非常有意思。本章应用高精度的从头计算和密度泛函理论计算，以及利用分子中的原子理论和自然键轨道理论，揭示了精氨酸分子内存在的相互作用。第四章研究了气相组氨酸及其相关离子的构型和性质。组氨酸残基的咪唑侧链频繁地作为酸和碱参与蛋白质催化剂作用和络合生物必需的金属离子过程。研究组氨酸和其相关离子的结构和性质对于理解在大生物体系中它们的静态或动态的性质有着极其重要的意义。本章通过高精度的密度泛函理论计算揭示气相组氨酸的质子化和去质子化过程。另外，应用含时密度泛函理论计算了中性和质子化组氨酸的电子谱，去理解溶液和蛋白质中组氨酸残基的电子光谱特性以及质子化组氨酸的解离过程。更多还原

【Abstract】 The dissertation is devoted to the study of conformations and properties of amino acids in the gas phase using the DFT and ab initio calculations. With the progress in computational methods and enhancement of computational ability, molecular electronic structure theory and computational method based first-principles calculation have been widely used in chemistry, biochemistry, environmental science and material science. Meanwhile, amino acids have become a research focus as they are the units of building blocks of proteins and peptides. We thorough search the stable conformers of aromatic amino acids and arginine and examine the properties of the stable conformers using ab initio and DFT methods. The properties examined include the characteristics of intramolecular interactions, IR and UV spectra, temperature dependent conformer distributions, electron attachment and ionization energies, protonation/deprotonation processes.In chapter 1, we introduce the basic principles of quantum chemistry and computational methods including Many-Body Perturbation Theory, Configuration Interaction, Coupled Cluster and Density Functional Theory. We also introduce the Time-dependent DFT, Atoms in Molecules and Natural Bond Orbital. At the end of this chapter, we briefly introduce two simulation packages used in the dissertation and the aim of the study.In chapter 2, we first introduce the physical and chemical properties of amino acids. Tryptophan, tyrosine, phenylalanine and histidine have aromatic UV chromophores, and thus have been the subject of most laser spectroscopic studies on amino acids. We systematically explore the conformational potential energy surfaces of aromatic amino acids and calculate the conformational properties, explaining the experimental UV spectra of aromatic amino acids. In addition, the intramolecular interactions of aromatic amino acids are characterized using AIM theory. In chapter 3, we study the conformations and properties of arginine in the gas phase. The conformational study of arginine is the most challenging due to its large number of rotational degrees of freedom. Arginine is also the most basic natural amino acid due to its extremely basic guanidine side chain. It is speculated that the zwitterionic form of arginine exists in the gas phase. Due to a large number of hydrogens in the molecule, the study of the intramolecular interaction of arginine is very interesting. We reveal the intramolecular interaction of arginine using the ab initio and DFT calculations as well as AIM and NBO.In chapter 4, we study the conformations and properties of histidine and its related ions. The imidazole side chain of histidine frequently serves as a general acid or base in catalysis and in ligation of essential metal ions. Detailed knowledge of the structures and properties of histidine and the related molecules is important for our understanding of their static and dynamic properties in larger bio-systems. We reveal the protonation and deprotonation processes of gaseous histidine molecule using the DFT calculations. In addition, we calculated the electronic spectra of neutral and protonated histidine using the TDDFT method in order to understand the UV feature spectra of histidine residue in solution and protein and the dissociation processes of protonated histidine on UV excitation.更多还原