摘要
质子转移(Proton Transfer,简称PT)作为化合物异构平衡和氧化还原反应中最基本的现象之一,在众多化学过程中发挥了重要的作用。质子转移广泛存在于各种化学过程和生命过程中,可存在于分子内或者分子间。大量的理论和实验研究丰富了关于质子转移在可能的反应机理、引发异构现象以及其它一些性质方面的认识。然而,由于反应体系的复杂性,目前对质子转移在反应过程中的可能机理也仅局限于猜测,或是对质子转移的深入研究没有能够很好地解释实际的反应机理。本论文采用目前研究质子转移的主要方法——量子化学计算方法,着重研究了几种经典的化学过程,探索它们的反应机理,以及一些实验无法或难以判断的性质,并得出了一些普遍性的规律。
在核酸碱基的互变异构研究方面,由于许多非经典突变的形成都是由质子转移所引起的,研究微环境对碱基异构的影响有助于我们加强对碱基诱变的认识,从而为基因突变的研究提供一个侧面依据。本论文在第三章选取了最具典型意义的尿嘧啶/5-溴尿嘧啶为研究对象,研究质子转移所导致的异构现象,探讨碱基异构的影响因素和机理。为揭示金属离子在碱基诱变过程中所起的作用,以及水分子和金属离子的协同效应,文中分别考察了含有一个Na~+、两个Na~+以及同时含有一个Na~+一个H_2O时的诱变过程,通过研究发现,微环境分别为水分子和金属离子时对尿嘧啶/5-溴尿嘧啶的诱变过程存在着差异,二者共存时存在协同效应,这样的环境相比前人的研究更接近实际生物环境,也相比前期工作有所改进。
生物素的两个NH质子近乎对称地排列于分子中,然而研究发现1位NH往往比3位NH要活泼,那么其中的原因何在?第四章从质子转移的角度对影响生物素NH质子活性的因素一一分解剖析,结果发现,在气态下3位NH质子在生物素伸展态时比1位NH质子更为活泼,而当我们进一步考虑硫原子、侧链、溶剂场等诸多因素对两个NH质子发生迁移的影响时,结果表明,以上因素均不是造成1位质子比3位质子活泼的根本原因。只有当我们综合考虑分子动力学、量子化学以及溶剂效应时,所得的结果才与实际值相吻合。生物素在溶液中存在着一个伸展态、半折叠态和折叠态之间的动态平衡,生物素中两个NH活性的比例应为三种构象下活性比例的加权平均,而硫原子、侧链、溶剂效应等都对计算的正确性起着无可替代的作用。这样的计算方法也许可以为其它生物分子的活性研究提供一个可靠的方法。
质子在顺式NMA两个原子间的跃迁可以产生动力,使得分子中两个甲基发生不同程度的转动,这样一种现象可以作为研究目前较为热门的分子马达的一个简单模型。而如何控制分子马达的转向和转速是科学家们面临的一个极大难题,第五章我们通过对质子转移所致顺式NMA甲基转动的分子动力学研究发现,当顺式NMA分子发生质子转移时,其中的两个甲基会发生转动,且转向相反。而当我们进一步通过原子中心密度矩阵传布分子运动学模型(ADMP)方法,对NMA分子以及含有水分子的NMA分子的甲基转动情况进行跟踪计算时,我们发现,水分子在NMA分子周围的不同结合位点不但可以影响其质子转移过程,而且会对其两个甲基转动发生极大的影响。水分子在NMA分子周围不同位置时,不但可以改变甲基的转动方向,而且可以停止其转动。文中对相关机理进行了分析,所报道结果可能会对控制分子机器领域起到重要作用。
由质子转移所生成的质子型离子液体是一种特殊的离子液体,其稳定性比普通的咪唑型离子液体差,分解温度比咪唑型离子液体低,那么它的性质与结构之间存在着怎样的关系,在第六章中本论文通过量子化学计算方法分析了这一现象。结果表明,由阳离子向阴离子的质子转移可能是质子型离子液体分解的先决步骤,这种无能垒的质子转移过程进一步说明了质子型离子液体没有咪唑型离子液体稳定。此外,近年来研究发现离子液体可精馏,那么质子型离子液体在气态下以何种形式存在?本论文采用实验和计算相辅助的方法来进行了探讨,发现质子型离子液体在气态下可能以离子对和中性分子对共存的形式存在,并且在离子对和中性分子对之间存在着一个平衡,这样一个平衡可能可以通过调节阴阳离子来改变,从而可以解释实验所观察到的结论之间存在的差异。
总体来说,本论文主要借助理论计算的方法,并结合一定的实验手段,从最基本的质子转移着手,多角度地探讨了几种典型的化学过程的内在机理,总结了一些具有普适性的规律,解释了一些宏观的化学现象,建立了多种研究方法相结合的基本框架,为研究更复杂的化学过程的机理提供了理论参考。
Proton transfer (PT) is the most simple and the most basic phenomenon in the isomerization balance of chemicals and oxidation-reduction reactions. It is of key importance for various kinds of chemical processes. It is a common and important reaction in different kinds of chemical and biological processes and it exists in both intra- and intermolecules. Many theoretical and experimental researches have enabled us to understand the role that proton transfer play in the possible reaction mechanisms and in the induced isomerization processes. However, because of the complexity of the reaction systems, the researches about the possible mechanism of proton transfer is only hypothesized but not demonstrated, or the deep researches of proton transfer have not been combined to explain the mechanism of the practical reactions. Therefore, the present work concentrates on several kinds of classical chemical processes so as to explore the reaction mechanism and the properties that cannot or is difficult to obtain. The commonly used quantum chemical methods are employed herein and several general rules have been obtained.
Generally, the canonical nucleic acid bases exist as the main forms in the double helix. However, the enol form tautomers of the base can also be formed by proton transfer and the tautomers may cause the nucleic acid bases mispairing, which has been proven to be one of the origins of gene mutation. The base tautomerizing processes of uracil/5-bromouracil were investigated in a microcosmic environment with both H_2O and Na~+ (W-M environment). It was found that uracil was more stable in the W-M environment than in the microcosmic environment with only water, which suggested that the metal ions and water work cooperated to maintain the classical nucleic acid bases. However, 5-bromouracil, a chemical mutagen, was found to be less stable than uracil in the W-M environment. The systems here are more important components for the real biological environment. The results obtained here allow us to have a new insight into the structural tautomer interconversion of uracil/5-bromouracil.
Though the two NH protons of biotin are placed almost symmetrically, only the 1-NH proton is selectively deprotonated and substituted by the carboxyl group. Even in vitro, the 1-NH protons are also found by various IR and NMR investigations, namely, saturation transfer method and temperature dependence measurements, to be more active than that of 3-NH. Activity differences of the two amide protons of biotin were first visited via perspective from proton transfer in the gas phase and our results reveal that for different conformation of biotin, the activity of the two amide is different: the 3-NH proton was more active than that of 1-NH for extended biotin, while less active for folded conformation, which indicated that the 1 -NH proton of biotin is not always more active than the 3-NH proton. The effects of the sulfur atom, the side chain and the solvent effects are further investigated. It is suggested that the relative proportion of the three different conformations of biotin in diverse solutions were responsible for the activity ratio differences of the two amide protons of biotin in various solutions. The method for computing the relative activity of the two amide protons of biotin in water here may be used to predict the relative activity in other solutions.
Methyl rotation induced by proton transfer was found for cis-N-methylacetamide (NMA). More interestingly, the methyl rotation was found to be controlled by the microenvironment. The atom-centered density matrix propagation (ADMP) method, a recently developed ab initio molecular dynamics, was further carried out to depict the trajectories for methyl rotation of NMA. Moreover, trajectories for methyl rotation of NMA complexed with water molecules were also calculated, and water molecules at the two different sites of NMA were found to reverse or cease the rotational direction of the methyl groups of NMA. This finding that microenvironment can not only control rotational direction of methyl groups, but can also cease the rotation may be of significant importance for the control of molecular machines.
Ionic liquids (ILs) are receiving an upsurge of interest in multidisciplinary areas, but the past researches focused mainly on imidazolium-based ILs. The present work concentrates on a kind of protic ionic liquid that results form proton transfer. The theoretical results here will help to understand the fundamental properties of these ILs. It is found that the H proton is not stable on the cation and tends to transfer to the anion to form neutral molecule pairs. Moreover, the neutral pairs are more stable than the ion pairs and the ion pairs tend to tautomerize to neutral pairs without barriers. It suggested that the transformation from the ion pairs to neutral pairs may be the first step for the decomposition of protoc ionic liquids. Furthermore, the ionic liquids have been illustrated to be volatilizable, the species of ionic liquids in the gas phase is still controversial. Therefore, the present work investigate a kind of protic ionic liquid, using the mass spectroscopy experiments combined with the quantum chemical calculations, so as to find which kinds of species exist in the gas phase of the protic ionic liquid. Both the MS spectra and the quantum chemical results have suggested the coexistence of the ion pairs and the neutral molecule pairs of the ionic liquid in the gas phase. The results here may contribute to the resolve of the above controversy.
To sum up, the quantum chemical calculation and experiment are combined to investigate the simple proton transfer processes in several classical chemical processes. The mechanisms of the chemical processes have been analyzed and some rules on the interactions and the mechanisms are discovered. We expect it can provide a base for the future development of the research on the mechanisms for the chemical processes.
引文
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