5-氯尿嘧啶质子转移异构化的密度泛函理论研究

采用密度泛函B3LYP/6-311+G**方法,对5-氯尿嘧啶分子内质子转移及水助催化质子转移引起的互变异构反应机理进行了计算研究,获得了互变异构过程的反应焓、活化能、活化吉布斯自由能和质子转移反应的速率常数等参数。计算结果表明,5-氯尿嘧啶无论是孤立分子还是一水合物,其双酮式CU1是最稳定异构体,由双酮式向烯醇式异构化找到3条通道(P1,P2,P3),各通道速控步骤的活化能分别为177.85、177.05和197.58kJ/mol。当水分子参与反应以双质子转移机理异构化时,活化能显著降低,各通道速控步骤的活化能依次降为66.24、69.36和77.85kJ/mol,有利于双酮式向烯醇式或酮醇式转变。计算结果还表明,氢键作用在增大5-氯尿嘧啶一水复合物稳定性、降低质子转移异构化反应活化能等方面起着重要作用。     

3-羟基哒嗪及其CH3，NO2和Cl取代衍生物质子转移过程的理论研究

用密度泛函理论(DFT)B3LYP方法,在6-311 G*基组下,对3-羟基哒嗪及其CH3,NO2和Cl取代衍生物分子醇式和酮式结构互变异构化反应进行了研究,优化化合物的几何构型,寻找反应的过渡态,通过振动分析和内禀反应坐标(IRC)分析加以证实,计算了反应的活化能.结果表明,3(2H)-哒嗪酮及其带取代基的衍生物不论是单体,还是相对应的二聚体,比其相对应的异构体能量低,表明在通常情况下是以3(2H)-哒嗪酮及其衍生物形式稳定存在的,这与前人通过实验数据对3-羟基哒嗪互变异构体的比率进行预测的结果是一致的.根据计算结果讨论了异构化反应的机理.     

3-羟基哒嗪及其CH3,NO2和CI取代衍生物质子转移过程的理论研究

用密度泛函理论(DFT)B3LYP方法,在6-311+G*基组下,对3-羟基哒嗪及其CH3,NO2和Cl取代衍生物分子醇式和酮式结构互变异构化反应进行了研究,优化化合物的几何构型,寻找反应的过渡态,通过振动分析和内禀反应坐标(IRC)分析加以证实,计算了反应的活化能.结果表明,3(2H)-哒嗪酮及其带取代基的衍生物不论是单体,还是相对应的二聚体,比其相对应的异构体能量低,表明在通常情况下是以3(2H)-哒嗪酮及其衍生物形式稳定存在的,这与前人通过实验数据对3-羟基哒嗪互变异构体的比率进行预测的结果是一致的.根据计算结果讨论了异构化反应的机理.     

胞嘧啶一水复合物质子转移异构化反应机理的理论研究

采用密度泛函B3LYP方法,在6-311＋G＊＊基组水平上对胞嘧啶一水复合物质子转移引起的氨-酮式、氨-烯醇式与亚胺-酮式互变异构反应机理进行了计算研究,获得了互变异构过程的反应焓、活化能、活化吉布斯自由能和质子转移反应速率常数等参数。将Onsager反应场溶剂模型用于水相的计算,结果表明,胞嘧啶一水复合物无论在气相中...     

3-羟基哒嗪及其CH3, NO2和Cl取代衍生物质子转移过程的理论研究

用密度泛函理论(DFT) B3LYP方法, 在6-311＋G*基组下, 对3-羟基哒嗪及其CH₃, NO₂和Cl取代衍生物分子醇式和酮式结构互变异构化反应进行了研究, 优化化合物的几何构型, 寻找反应的过渡态, 通过振动分析和内禀反应坐标(IRC)分析加以证实, 计算了反应的活化能. 结果表明, 3(2H)-哒嗪酮及其带取代基的衍生物不论是单体, 还是相对应的二聚体, 比其相对应的异构体能量低, 表明在通常情况下是以3(2H)-哒嗪酮及其衍生物形式稳定存在的, 这与前人通过实验数据对3-羟基哒嗪互变异构体的比率进行预测的结果是一致的. 根据计算结果讨论了异构化反应的机理.     

2,6-二巯基嘌呤质子转移异构化的密度泛函理论研究

采用密度泛函B3LYP方法, 在6-311＋G(d,p)基组水平上对2,6-二巯基嘌呤质子转移引起的硫醇式与硫酮式互变异构反应进行了计算研究, 获得了互变异构过程的反应焓、活化能、活化吉布斯自由能和质子转移反应的速率常数等性质. 计算结果表明, 2,6-二巯基嘌呤无论是孤立分子还是一水合物, 其二硫酮式R是最稳定异构体. 由二硫酮式通过分子内质子转移向二硫醇式异构化共有6条反应通道, 其主通道(1)速控步骤的活化能为139.1 kJ•mol^－1, 速率常数为2.16×10^－12 s^－1; 当水分子参与反应以双质子转移机理异构化时, 活化能显著降低, 有利于硫酮式向硫醇式转变, 其主通道(7)速控步骤的活化能为61.3 kJ•mol^－1, 速率常数为1.33×10 s^－1. 计算结果还表明, 氢键作用在增大2,6-二巯基嘌呤氢键一水合物稳定性、降低质子转移异构化反应活化能等方面起着重要的作用.     

p-羟基苯丙酮酸互变异构反应机理溶剂效应的理论研究

采用密度泛函B3LYP方法,在6-31+G**基组水平上对p-羟基苯丙酮酸质子转移引起的烯醇式-酮式互变异构反应机理进行了计算研究,获得了互变异构过程的反应焓、活化能、活化吉布斯自由能和质子转移反应的速率常数等参数。Onsager反应场溶剂模型用于水相和甲醇相的计算,计算结果表明,p-羟基苯丙酮酸无论在气相还是水相、甲醇相中,其酮式异构体都是最稳定的存在形式,烯醇式异构体也会以一定量共存。气相中孤立分子内质子转移几何构型改变较显著,异构化反应需要较大的活化能,不利于发生质子转移,Onsager模型计算方法对质子转移反应的影响较小。     

2,6-硫代黄嘌呤质子互变异构反应机理的理论研究

在密度泛函B3LYP/6-311G~(**)理论水平上,对气相和水相中2,6-硫代黄嘌呤各烯醇式与酮式水助质子互变异构体及其过渡态进行几何构型全自由度优化,获得它们在气相和水相中的几何结构和电子结构,PCM反应场溶剂模型用于水相计算.结果显示在气相和水相中,水参与反应降低了互变异构质子迁移的反应活化能,对互变异构质子迁移的反应起到催化作用,但是没有改变各异构体的稳定性顺序,其顺序为W1＞W3＞W2.进一步研究了2,6-硫代黄嘌呤各烯醇式与酮式水助质子互变异构的反应机理,提出了2,6-硫代黄嘌呤各烯醇式与酮式互变异构质子迁移的反应为平面六元环的过渡态结构.探讨了溶剂化效应对互变异构体的几何结构、能量、电荷分布以及互变异构反应活化能的影响等.     

二苯甲酰甲烷互变异构反应机理溶剂效应的理论研究

采用密度泛函B3LYP方法,在6-31+G(d,p)基组水平上对二苯甲酰甲烷质子转移引起的酮式-烯醇式互变异构反应机理进行了计算研究,获得了零点能、总能量、吉布斯自由能及质子转移过程的反应焓、活化能、活化吉布斯自由能和速率常数等参数.3种非质子溶剂中的优化和频率计算采用Onsager模型进行计算.计算结果表明,不论在气相还是3种溶剂中,二苯甲酰甲烷的烯醇式较酮式稳定,烯醇式向酮式气相转变需要较高的活化能垒,在不同极性的溶剂中,随着溶剂介电常数的增大,异构化反应活化能垒减小,反应速率常数增大.     

2-硫代黄嘌呤互变异构体的密度泛函理论计算

在密度泛函B3LYP/6-311G**水平上,对14种气相和水相中可能存在的2-硫代黄嘌呤互变异构体进行了几何构型全自由度优化,并计算出它们的总能量、焓、熵、吉布斯自由能.Onsager反应场溶剂模型用于水相的计算.计算结果表明,2-硫代黄嘌呤在气相和水相中主要以酮式结构形式存在,与已有实验结果一致.在气相和水相中,酮式结构—N(7)(H)均比酮式结构—N(9)(H)更稳定.2-硫代黄嘌呤互变异构的熵效应小,对互变异构平衡没有显著的影响,而焓变对互变异构却产生了主要的影响.水溶剂化自由能与异构体的气相偶极矩存在相关性.另外,较详细地考察了2-硫代黄嘌呤与6-硫代黄嘌呤的相对稳定性.     

Systematic study of the tautomerism of uracil induced by proton transfer. Exploration of water stabilization and mutagenicity

To systematically investigate all the possible tautomerisms from uracil (U) and its enol form (U) induced by proton transfer, we describe a study of structural tautomer interconversion in the gas phase, in a continuum solvent, and in a microhydrated environment with 1 or 2 explicit water molecules, using density functional theory (DFT) calculations by means of the B3LYP exchange and correlation functions. A total of 62 geometries including 25 transition states were optimized, and the geometrical parameters have been discussed. Some rules of the configuration variation in tautomerization were summarized. The relative stabilities of all the tautomers were established. When a proton transfers from the di-keto form to the keto-enol form, water molecules in different regions show absolutely opposite effects: some assist, whereas others hinder the tautomerization. However, when a proton transfers from the keto-enol form to the di-enol form, water molecules in different regions show similar effects: the Gibbs free energy always increases and the activation energy always decreases. Additionally, some important factors that obviously affect the activation energy and Gibbs free energy were found and discussed in detail. The reasons that water molecules can assist or prevent the proton transfer were given. Furthermore, on the basis of our calculated results, we explain why it is hard to detect the di-enol form of uracil in general experiments.     

The keto-enol tautomerization of ethyl butylryl acetate studied by LC-NMR

The keto-enol tautomerism of ethyl butylryl acetate was studied in mixed solvents under a variety of experimental conditions. The direct measurement of ketonization of the enol tautomer was performed by using the hyphenated technique LC-NMR. The keto and enol tautomers can be separated by using HPLC and their interconversion is a slow process on the NMR timescale. The ketonization reaction was found to be acid catalyzed and the solvent isotope effect, kH2O/kD2O, in an acetonitrile/water mixture, is 5.4. The ketonization rate constants were also measured at different compositions of binary solvents, such as CH3CN/D2O, CD3OD/D2O, and CH3CN/CD3OD. The rate constant and water percentage were found to have an exponential relationship. The reaction rate as a function of solvent polarity will be discussed in this paper.     

水对5-氟尿嘧啶质子转移影响规律的研究

采用密度泛函理论(DFT)B3LYP方法, 在6-311++G(d, p)基组上研究了由质子转移引起的5-氟尿嘧啶(5-FU)的异构化反应. 共研究了38个含水与不含水的构型, 其中包括15个过渡态结构. 研究发现, 在5-氟尿嘧啶周围存在两类不同的区域, 在其中一类区域中, 水分子能促进质子转移的发生；而在另一类区域中, 水分子却能阻碍质子转移的发生. 通过与尿嘧啶质子转移过程相比较, 发现在各种情况下5-氟尿嘧啶异构化为烯醇式的几率均比尿嘧啶的大, 在一定程度上解释了为什么5-氟尿嘧啶具有优良抗癌作用的同时具有一定的毒副作用.     

Theoretical Study on the Tautomerization Reaction of Formamide to Formamidic Acid Encapsulated in a Nano-sized Molecular Container

The hybrid calculations with ONIOM(B3LYP/6-31G*:AM1) method were carried out on the tautomerization reaction of formamide to formamidic acid in the microcontainer-encapsulated state. The free-state tautomerization process was also investigated with B3LYP/6-31G**//B3LYP/6-31G* method for the purpose of comparison. Bare tautomerization, H2O-assisted(single-H2O or multiple-H2O) and self-assisted mechanisms were all taken into consideration for the encapsulated state. The results show that only bare tautomerization and single-H2O catalysis mechanisms are possible to the encapsulated for-mamide tautomerization owing to the container's size confinement effect. Geometrical changes in the complexed container and guest molecules are discussed to deeply understand the complex's structural properties. The bare tautomerization barrier in the encapsulated state increases by 23.826 kJ/mol, ac-counting for 12% of the corresponding total energy barrier in the free state, and the increased values for the single-H2O catalysis process are 12.958 kJ/mol, accounting for 16% of the corresponding total energy barrier, respectively. This finding suggests that the encapsulation can make the tautomerization process slightly difficult.     

Density functional study of the conformations and intramolecular proton transfer in thiohydroxamic acids

The conformational preferences of thiohydroxamic acids (N-hydroxythioamides) are investigated by the density functional B3LYP/6-311++G(3df,3pd)//B3LYP/6-31G(d) method in this work. Unlike hydroxamic acids, the thione and thiol forms are found to be equally stable in the gas phase, and the reaction pathways for the interconversion between the thione and thiol forms have been deduced to involve rotation about the C[double bond, length as m-dash]N bond of the thiol tautomer in the rate-determining step. The effect of aqueous solvation on the reactions has also been investigated. It is found that inclusion of a few explicit water molecules in an implicit solvent calculation is necessary in order to accurately account for hydrogen bonding effects. Thiohydroxamic acids, like their hydroxamic acid analogues, are found to be N-acids, both in the gas phase and in aqueous solution.     

Tautomeric Transformations and Reactivity of Polyfunctional Hydroxypyrimidines: IV. Effects of Tautomer Structure and Acidity and Solvent Nature on the State of Tautomeric Equilibria in the Series of 5-Nitro Derivatives of 2,4,6-Pyrimidinetrione

Tautomeric equilibria of 5-nitrobarbituric acid and 1,3-dimethyl-5-nitrobarbituric acid were studied by NMR, UV, and IR spectroscopy, as well as by quantum-chemical methods. These compounds were found to exist in the gas phase, in solutions in water and DMSO, and in crystal as the corresponding enol tautomers. In trifluoroacetic and chloroform solutions, an equilibrium mixture of the ketone and enol forms was detected. The parameters determining the state of the tautomeric equilibrium are the total energy of a tautomer, its deprotonation energy, and a component of the latter, which relates to electrostatic interaction between the mobile proton and the rest of the molecule. Proton-donor and proton-acceptor properties of the solvent and 5-nitro-2,4,6-pyrimidinetrione derivatives are the main factors responsible for displacement of the tautomeric equilibrium in solution; electrostatic solvation and tautomer stabilization via hydrogen bonding are less significant.     

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

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.     

溶剂分子对甲酰胺及其衍生物分子内氢转移催化作用的研究

在B3LYP/6-311+ +G* * 水平下,通过计算所形成二元团簇的能量来研究水、氨、甲醇、氟化氢等溶剂分子对甲酰胺及其衍生物分子内氢原子转移的催化作用.简单描绘了在有水、氨、甲醇和氟化氢等溶剂分子存在时,甲酰胺及其衍生物分子内氢原子转移的过程.结果表明,当有水、氨、甲醇、氟化氢等溶剂分子存在时,从甲酰胺甲酰胺酸转变的能垒会降低.而且不同的溶剂分子对甲酰胺(FA)、 N-甲基甲酰胺(MF)和N,N-二甲基甲酰胺(DMF)的催化能力各不相同.在这四种溶剂分子中,氟化氢的催化作用最强.     

Examination of formamide,formamidic acid,amidine dimers,and the double proton transfer transition states involving these dimers

Structures and relative energies were obtained for the hydrogen bonded dimers of formamide and formamidic acid using the 3-21G basis set. A double proton transfer transition state is claimed to link these two dimers. While the structure of the transition state was intermediate between those of the two dimers, the energy was only 7.6 kJ/mol greater than the less stable formamidic acid dimer. The activation energy from the formamide dimer side of the reaction was found to be 125 kJ/mol of dimer. A similar transition state was found for the amidine dimer system. The activation energy for this model reaction was found to be 66.9 kJ/mol of dimer.     

Substituent effects on the stability of 1,4‐benzodiazepin‐2‐one tautomers: A density functional study

The relative stability of 1,4‐benzodiazepin‐2‐one tautomers in the gas phase and model solvents was calculated at the M06 and ωB97XD levels of theory. The two density functionals were benchmarked earlier and demonstrated as excellent models to study tautomerism in a vast array of chemical systems. A number of commercially available 1,4‐benzodiazepin‐2‐ones were investigated computationally for the first time. In addition, some biologically active and newly devised benzodiazepines were considered, which may be important in designing structures with desired (bio)chemical features. Special attention was paid to determine substituent effects on the Gibbs free energies of keto, enol, and iminol forms for each respective benzodiazepine. It was demonstrated that (i) the replacement of the benzene ring by the heterocyclic ring in the benzodiazepine system may stabilize the iminol tautomer, and (ii) the electron‐withdrawing substituent at the C3‐position of the respective benzodiazepine may stabilize the enol tautomer relative to the parent keto form. It is concluded that substituent effects may govern the chemical reactivity and biological properties of selected benzodiazepines.