N,N-二甲基-N′-(2′, 3′-二脱氧-3′-硫代胞苷)甲脒水解机理的理论研究

采用密度泛函理论B3LYP/6-31+G(d, p)方法研究了 N,N-二甲基-N′-(2′,3′-二脱氧-3′硫代胞苷)甲脒(甲脒-3TC)分子在气相和水溶液中的水解反应机理. 考虑了两条可能的反应途径: 水分子首先进攻C=N双键的途径(Path A)和先进攻C—N单键的过程(Path B). 计算结果表明气相中两条途径的第一步均是速率控制步骤, Path A比Path B更有利. 采用自洽反应场极化连续模型(CPCM模型)在B3LYP/6-31+G(d, p)水平上研究了反应体系在水溶液中的溶剂化效应. 溶液中第一条途径Path A仍是最优途径.     

N,N-二（对氟苄基）-N′-（2′,3′-二脱氧-3′-硫代胞苷）甲脒水解反应的理论研究

采用密度泛函理论方法B3LYP/6-31 G(d,p)//B3LYP/6-31G(d,p)和导体极化连续模型B3LYP/CPCM/6-31 G(d,p)方法对苯环对位上有F取代的N,N-二(对氟苄基)-N′-(2′,3′-二脱氧-3′-硫代胞苷)甲脒(FBFA-3TC)水解反应机理和溶剂效应进行了研究.考虑两条可能反应途径:水分子首先进攻CN双键的途径(PathA)和先进攻C—N单键的途径(PathB).计算结果表明,气相和水中两条途径的第一步都是速率控制步骤,PathA比PathB更有利.对优势途径PathA的第二步反应的进一步研究发现,中间体的羟基H原子转移到双键N比单键N更容易,从而形成2′,3′-二脱氧-3′-硫代胞苷(3TC)的最终水解产物.     

Theoretical study on the hydrolysis mechanism of N,N-dimethyl-N′-(2′,3′-dideoxy-3′-thiacytidine)formamidine

The hydrolysis mechanisms of N,N-dimethyl-N′-(2′,3′-dideoxy-3′-thiacytidine)formamidine (FA-3TC) in the gas phase and in aqueous solution were studied by use of the density functional theory B3LYP/6-31 G(d, p) method. Two possible reaction pathways in the title reaction were considered. In one pathway water attacks the C=N double bond first (path A) while in the other water attacks the C—N single bond first (path B). The calculated results indicate that the first step in both pathways is the rate-limiting process and path A is more favorable than path B in the gas phase. The effect of solvent water on the title reaction was assessed at the B3LYP/6-31 G(d, p) level of theory based on the po-larizable continuum model (CPCM). In water the first mechanism (path A) is also favored.     

2-(3-巯基-2-吡啶基)苯并咪唑分子内质子转移及溶剂化效应

在B3LYP/6-31G(d,p)和TD B3LYP/6-31++G(d,p)//CIS/6-31G(d,p)水平上,研究了2-(3-巯基-2-吡啶基)苯并咪唑(MPyBI)在气相和七种溶剂(环己烷、苯、三氯甲烷、乙醇、乙腈、二甲亚砜和水)中基态和激发态的分子内质子转移(GSIPT和ESIPT)过程.在基态势能面的研究中发现,该化合物存在分子内双质子转移,其中分步的双质子转移在动力学上具有优势.同时对激发态质子转移势能面及激发态转移过程中的光物理现象进行了研究,结果表明该化合物存在快速的无能垒的激发态分子内质子转移,随着溶剂极性的增强,可以降低基态过渡态的能垒,改变硫醇式与硫酮式互变异构体的比例,从而灵敏地控制荧光的强度.     

取代基对3(5)-(9-蒽基)吡唑光学性质的影响

使用密度泛函理论(DFT)B3LYP/6-31G(d)方法优化得到了3(5)-(9-蒽基)吡唑及其衍生物的基态(S₀)分子结构, 使用单激发组态相互作用(CIS)/6-31G(d)方法优化得到这些分子的第一单重激发态(S₁)的几何结构, 并使用含时密度泛函理论(TD-DFT)B3LYP/6-311++G(d,p)方法计算了它们的吸收和发射光谱. 计算结果表明, 与3(5)-(9-蒽基)吡唑相比, 无论取代基是吸电子基团还是供电子基团, 衍生物的吸收和发射峰均发生红移, 并且当取代基―R=―BH₂, ―CCl₃, ―CHO, ―NH₂时衍生物有较长的吸收波长和发射波长.     

以二羧酸二苯甲醚和吡啶基三唑为配体构筑的钴(Ⅱ)配合物的合成、结构、热稳定性及DFT计算(英文)

基于V型配体4,4′-二羧酸二苯甲醚(H2oba)和刚性配体3-(3吡啶基)-5-(4′吡啶基)-1-H-1,2,4三唑(3,4′-Hbpt),在水热条件下与醋酸钴制备了一种新的配位聚合物[Co(oba)(3,4′-Hbpt)]·H2O,并对其进行X-射线单晶衍射、热重分析、元素分析和红外光谱表征。配合物为单斜晶系,P21/c空间群,完全脱质子的oba2-配体的2个羧基连接Co髤离子形成八元环,3,4′-Hbpt配体和H2oba桥连2个Co髤形成二十五元环。相邻的八元环和二十五元环进一步通过oba2-作支柱连接,形成了二维的层-孔结构。采用密度泛函理论(DFT)方法,在B3LYP/6-31*G(d)和6-31**G(d,p)水平上对配体H2oba结构进行优化计算,探讨了其稳定性,前线轨道以及最优构型,计算结果与化合物1中H2oba的构象一致。     

G3(QCI)模型化学方法

建立了非微扰外推模式下的几种G3(QCI)方法：G3(QCI/fu1)、G3(QCI/fu2)、G3(QCI/ful)//B3PW91和G3(QCI/fu2)//B3PW91.其中,电子能量用QCISD(T,FC)/G3large直接计算,芯电子相关能分别在MP2/6-31G(d)和MP2/6-31G(d,p)级别上计算,对125个G2-1 test set 的计算结果表明,总体精度与G3和G3 //B3LYP相当;平均绝对偏差分别为4.370、4.389、4.061和4.022kJ mol-1,相应G3和G3//B3LYP分别为4.27和4.05kJ mol-1.文章提出的方法排除了G3中外推办法的不确定因素,且更适用于非平衡几何构型体系能量的定量计算。     

2-(2-巯苯基)苯并噁唑分子内质子转移取代基电子效应的密度泛函理论研究

在B3LYP/6-31G(d,p)和TDB3LYP/6-31++G(d,p)//CIS/6-31G(d,p)水平上研究了2-(2-巯苯基)苯并噁唑及其衍生物基态和激发态分子内质子转移现象,并探讨取代基电子效应对分子内质子转移的影响,研究结果表明,在基态时,硫醇式异构体为优势构象,供电子取代基使基态分子内正向质子转移能垒(烯醇式→酮式)升高;而吸电子取代基则可降低能垒,有利于基态分子内质子转移并有助于硫酮式异构体的稳定.在激发态时,硫酮式结构为优势构象,所研究的2-(2-巯苯基)苯并噁唑化合物及衍生物均可以发生无能垒或低能垒(≤1.5kJ/mol)的激发态分子内质子转移.巯苯基部分是激发态失活的主要活性部分,供电子基团有利于激发态的质子转移,吸电子基团使激发态跃迁困难,不利于激发态的质子转移.     

1,3,5-三硝基苯在高岭石表面吸附的理论研究

构造了高岭石硅氧层和铝氧层的团簇模型(分别为Si₁₃O₃₇H₂₂和Al₆O₂₄H₃₀), 并分别在B3LYP/6-31G(d), MP2/6-31G(d)//B3LYP/6-31G(d)和B3LYP/6-311++G(d,p)//B3LYP/6-31G(d)理论水平上对1,3,5-三硝基苯(TNB)在高岭石表面的吸附性质(如优化的几何构型、 结构参数、 吸附能、 振动频率、 静电势和分子轨道等)进行了研究. 结果表明, TNB和硅氧层表面间的相互作用以静电和范德华相互作用为主; TNB与铝氧层间的相互作用以氢键为主, 且TNB和铝氧层间相互作用的能量更低, 结构更稳定.     

2',3'-二脱氧-2',3'-二去氢鸟嘌呤核苷构象稳定性的理论研究

采用密度泛函方法在B3LYP/6-31＋G**水平上研究了2',3'-二脱氧-2',3'-二去氢鸟嘌呤核苷分子(D4G)的构象. 分别研究在气相中的孤立分子和一水合物异构体的相对稳定性和异构体之间的相互转变过程, 分析了水分子的参与对D4G异构体的相对稳定性和几何结构参数以及自然电荷的影响. 结果表明, 孤立的D4G分子在气相中存在8种稳定构象, 其中构象d4g-2是所有构象中最稳定的, 气相中D4G主要以d4g-2存在. 气相中各构象的相对稳定性为: d4g-2＞d4g-1＞d4g-5＞d4g-3＞d4g-6＞d4g-4＞d4g-8＞d4g-7. 计算得到的各构象键长和键角数据与实验值接近. 一个水分子的加入对D4G分子的构型参数有所影响, 基本不改变D4G分子各构象的稳定性顺序, 但构象转变的能垒有所提高. 氢键在分子构象中发挥了重要作用.     

Theoretical study on the hydrolysis mechanism of N,N-dimethyl-N'-(2-oxo-1, 2-dihydro-pyrimidinyl)formamidine: water-assisted mechanism and cluster-continuum model

The hydrolysis reaction of N,N-dimethyl-N'-(2-oxo-1, 2-dihydro-pyrimidinyl)formamidine (DMPFA), a model compound of the antivirus drug amidine-3TC (3TC = 2', 3'-dideoxy-3'-thiacytidine), is investigated by the hybrid density functional theory B3LYP/6-31+G (d,p) method. The hydrolysis reaction of the title compound is predicted to undergo via two pathways, each of which is a stepwise process. Path A is the addition of H2O to the C=N double bond in the amidine group to form a tetrahedral structure in its first step, and then the transfer of the H atom of hydroxyl leads to the corresponding products via four possible channels. Path B simultaneously involves the nucleophilic attack of H2O to the C atom of the C=N bond and the proton transfer to the N atom of amino group leading to the cleavage of the C-N single bond in the amidine group. The results indicate that path A is more favorable than path B in the gas phase. Moreover, to simulate the title reaction in aqueous solution, water-assisted mechanism and the cluster-continuum model, based on the SCRF/CPCM model, are taken into account in our work. The results indicate that it is rational for two water molecules served as a bridge to assist in the first step of path A and that cytosine rather than the cytosine-substituted formamide should be released from the tetrahedral intermediate via s six-membered cycle transition state (channel 2). Our calculations exhibit that the process toward the tetrahedral intermediate is the rate-determining step both in the gas phase and in aqueous solution.     

Theoretical study on the hydrolysis mechanism of N,N -dimethyl- N ′-(2′,3′-dideoxy-3′-thiacytidine)formamidine

The hydrolysis mechanisms of N,N-dimethyl-N′-(2′,3′-dideoxy-3′-thiacytidine)formamidine (FA-3TC) in the gas phase and in aqueous solution were studied by use of the density functional theory B3LYP/6-31+G(d, p) method. Two possible reaction pathways in the title reaction were considered. In one pathway water attacks the C=N double bond first (path A) while in the other water attacks the C-N single bond first (path B). The calculated results indicate that the first step in both pathways is the rate-limiting process and path A is more favorable than path B in the gas phase. The effect of solvent water on the title reaction was assessed at the B3LYP/6-31+G(d, p) level of theory based on the polarizable continuum model (CPCM). In water the first mechanism (path A) is also favored. Supported by the National Natural Science Foundation of China (Grant Nos. 20473055 and 20773089) and the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry (Grant No. 20071108-18-15)     

DFT Study of Benzofuroxan Synthesis Mechanism from 2-Nitroaniline via Sodium Hypochlorite

The oxidative cyclization reaction of 2-nitroaniline via sodium hypochlorite to yield benzo-furoxan is investigated by the hybrid density functional theory B3LYP/6-31G(d,p) method. Solvent effects are estimated with the polarizable continuum model to optimize structures. The title reaction is predicted to undergo two pathways, each of which is a stepwise process.Path A includes four steps, namely oxidization, H-attack, hydrolysis, and cyclization. Path B involves the nucleophilic attack of OH^- to the H atom of the N-H bond and the proton transfer to the N atom of amino group leading to the cleavage of the N-H single bond in the amino group. The calculated results indicate that path A is favored mechanism for the title reaction. Furthermore, it is rational for one water molecule serving as a bridge to assist in the hydrolysis step of Path A and our calculations exhibit that this process is the rate-determining step.     

Theoretical studies on the hydrolysis mechanism of N-(2-oxo-1,2-dihydro-pyrimidinyl) formamide

Density functional theory (B3LYP) and ab initio (MP2) methods with the 6-31G(d,p) basis set are used to study the mechanisms for the hydrolysis of N-(2-oxo-1,2-dihydro-pyrimidinyl) formamide (PFA) in the gas phase. The direct and the water-assisted hydrolysis processes are considered, involving one and two water molecules, respectively. Three different pathways are explored in each case. In the first pathway, the O atom of water first attacks at the C atom of amide while one H atom of water transfers toward the oxygen of amide, leading to an intermediate of tetrahedral coordinated carbon with two OH groups. In the subsequent step, the hydroxyl H atom transfers to the N atom of pyrimidine ring and the C-N covalent bond of amide dissociates simultaneously. In the second path, the O and one H of water attack at the C of amide and the N of pyrimidine ring, respectively, while the C-N bond of amide dissociates. In the third path, three processes occur simultaneously: the O of water attacks at the C of amide, one H atom attacks at the N of amide, and the C-N bond of amide is broken. It is shown that the second pathway is favored for the direct hydrolysis while the first pathway is favored for the water-assisted hydrolysis. It is also shown that the water-assisted hydrolysis is slightly more favorable than the direct hydrolysis. Moreover, solvent effects on five pathways are evaluated with Monte Carlo simulation (MC) and free energy perturbation methods. It is shown that the solvent water slightly reduces the energy barrier in each pathway. The first pathway in the water-assisted hydrolysis remains the most favorable when the solvent effects of bulk water are taken into account.     

1. 5-环辛二烯-3, 7-二炔(C~8H~4)结构和光谱性质的理论研究

采用量子化学从头算方法研究了1,5-环辛二烯-3,7-二炔(C~8H~4)的结构和光谱性质,根据等键反应分析和自然键轨道方法研究了它的稳定性、成键情况和共轭性。结果表明1,5-环辛二烯-3,7-二炔(C~8H~4)分子为平面刚性结构,可能稳定存在。分子中C≡C键与C=C键存在一定程度的共轭,可能具有芳香性。     

Chemistry of naphthazarin derivatives 13. Conformational analysis of 3-(alk-1-enyl)-2-hydroxy-1,4-naphthoquinones by quantum chemistry methods

The molecular structures of various conformers of 2-hydroxy-1,4-naphthoquinone; 3-(alk-1-enyl)-2-hydroxy-1,4-naphthoquinones; 2,5,8-trihydroxy-1,4-naphthoquinone; and 3-(alk-1-enyl)-2,5,8-trihydroxy-1,4-naphthoquinones were studied by density functional theory (B3LYP/6-31(d), B3LYP/6-31(d, p)) and ab initio (MP2/6-31G, MP2/6-31(d)) methods. The strengths of the intramolecular hydrogen bonds formed by the β-hydroxy group with the O atom at C(1) and with the double bond π-electrons of the alkenyl substituents in the quinonoid rings were estimated. The compounds studied mainly exist as rotamers with the former-type hydrogen bonds. The splitting of the quinonoid bands of the stretching vibrations of the β-hydroxy group in the IR spectra of 3-(alk-1-enyl)-2-hydroxy-1,4-naphthoquinones and 3-(alk-1-enyl)-2,5,8-trihydroxy-1,4-naphthoquinones in hexane solutions is due to the existence of rotamers formed upon internal rotation of the alkenyl substituent. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1667–1673, October, 2006.     

Spectroscopic characterization and single molecule structures of N,N-bis-(3-phthalimidopropyl)-N-(2-hydroxyethyl)-N-propylammonium salts and their hydrates

N,N-Bis-(3-phthalimidopropyl)-N-(2-hydroxyethyl)-N-propylammonium salts and their hydrates have been characterized by FTIR, Raman and NMR spectroscopy. Also B3LYP and PM5 calculations have been carried out. The optimized bond lengths, bond angles and torsion angles calculated by B3LYP/6-31G(d,p) approach have been compared with the spectroscopic data. The screening constants for ¹³C and ¹H atoms have been calculated by the GIAO/B3LYP/6-31G(d,p) approach and analyzed. Linear correlations between the experimental ¹H and ¹³C chemical shifts and the computed screening constants confirm the optimized geometry.     

The molecular structure and vibrational spectra of 3-acetyl-4-[N-(2'-aminopyridinyl)-3-amino]-3-buten-2-one by Hartree-Fock and density functional theory calculations

The molecular structure and vibrational spectra of 3-acetyl-4-[N-(2'-aminopyridinyl)-3-amino]-3-buten-2-one (C(11)H(13)N(3)O(2)) in the ground state have been investigated by Hartree-Fock and density functional method (B3LYP and BLYP) with 6-31G(d) basis set. The optimized geometric bond lengths and bond angles obtained by using HF and DFT show the best agreement with the experimental data. Comparison of the observed fundamental vibrational frequencies of title compound and calculated results by HF and DFT methods indicate that B3LYP is superior to the scaled HF approach for molecular problems.     

Reaction of Isatoic Anhydride,Amine, and N,N′-Dialkyl Carbodiimides Under Solvent-Free Conditions: New and Efficient Synthesis of 3-Alkyl-2-(alkylamino)quinazolin-4(3H)-ones

Heating a mixture of isatoic anhydride, amines, and N,N′-dialkyl carbodiimides under solvent-free conditions provided novel 3-alkyl-2-(alkylamino)quinazolin-4(3H)-one derivatives for the first time. The products were obtained in moderate to good yields without formation of any by-products.

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