尿酸质子转移反应的理论研究I——分子内质子转移研究

使用量子化学中的Hartree-Fock方法和密度泛函理论中的B3LYP方法，分别在3－21G^*和6－31G（d)水平上，计算了尿酸分子从三羰基异构体向三羟基异构体的转化。结果表明，转化过程经历了单羟基和双羟基异构体2种中间物和3种过渡态时的分子内质子转移（IPT），转移中的H原邻近的N，O和C原子形成了具有四元环结构的过渡态。随着IPT的进行，N－H键逐渐被削弱和断裂，O－H键则逐渐生成。3个反应的活化能分别为190.3kJ/mol,181.4kJ/mol和249.9kJ/mol(B3LYP/6-31G(d))。较高的活化能表明在室温下，无催化剂的IPT难以进行。     

鸟嘌呤受羟基自由基损伤反应机理的量子化学研究

用密度泛函理论(DFT)研究羟基自由基与鸟嘌呤分子加成反应的过渡态, 并进行内禀反应坐标(IRC)反应路径解析, 结果表明, 羟基自由基加成到鸟嘌呤碳碳双键上. 利用B3LYP/6-31++G**对反应物、反应物络合物、过渡态以及产物络合物等反应通道上各个能量驻点的能量进行了计算, 得到反应活化能E_a=28.0867 kJ/mol. AIM计算结果显示, 过渡态结构中鸟嘌呤分子碳碳双键结构被削弱, 羟基自由基氧原子与鸟嘌呤分子碳碳双键中的C4原子具有较强的相互作用, 双键中剩余的π电子离域到了环体系中.     

锰氧咔咯催化环己烷生成己二醛催化机理的理论研究

通过密度泛函理论计算,研究锰氧咔咯催化环己烷氧化成己二醛的反应,讨论该催化过程的多态反应活性.计算表明,该反应经历两步羟基化和一步C—C键断裂过程.两步羟基化都是由氢转移开始,形成碳自由基中间体,接着迅速发生的自由基反应形成二醇的中间体.C—C键断裂过程由氢转移开始,先形成氧自由基中间体,氧自由基单电子和邻近环C—C键存在强烈的相互作用,导致该C—C键活化断裂和第二个氢的协同转移.反应的速控步是第二步羟基化过程,因此碳自由基中间体的稳定性决定该反应的难易,这也解释了实验上观察到叔碳的活性大于仲碳的活性顺序.     

亮点介绍

正铑催化C—H活化-氧原子转移反应Angew.Chem.Int.Ed.2014,53,10794~10798金属催化C—H键活化官能团化是构建碳—碳和碳—杂原子键最有效的方法之一,在有机合成中发挥着非常重要的作用,并广泛应用于药物、天然产物及材料的合成.利用新型导向基实现Rh(III)催化C—H活化是近几年来C—H活化领域重要方向之一.氧化性的N—O和N—N导向基在金属催化芳烃的C—H活化中已有广泛应用,并实现了一系列的杂环化合物的合成;同时,极性N—O键也广泛用于O-原子转移的反应中(如金催化).然而这两个领     

环丁醇开环官能化反应:通过C—C键断裂区域选择性构建γ位取代脂肪酮的新策略

环丁醇开环官能化反应是制备γ位取代脂肪酮的重要策略之一。通过区域选择性的C—C键断裂和新化学键(例如:C—C、C—N、C—O、C—F键等)的构建,环丁醇开环反应可以高效地在羰基的γ位引入各种各样的取代基团。环丁醇的开环反应途径主要分为两种:1)通过过渡金属钯和铑催化的β-碳消除反应开环;2)自由基历程的环丁醇单电子氧化开环。本文依据不同的开环反应机理,对环丁醇的开环官能化反应进行了阐述和展望。     

异腈参与的惰性键活化反应研究进展

近年来,过渡金属催化的C—H键官能团化反应引起了广泛的关注并得到迅速发展.作为一个不可替代的合成子,异腈已被广泛应用于合成各类含氮杂环化合物.本综述介绍了异腈参与的惰性键活化反应的最新研究进展及其在有机合成中的应用,包括异腈对C—H键或N—H键的插入反应以及异腈参与的自由基氧化成环反应等.     

活性钌、锇-配体多重键配合物研究进展

金属一配体多重键配合物的反应性研究有助人们深入理解许多重要的金属催化过程,如生物体系中的氧化和固氮及有机合成中的金属催化原子或基团转移反应．含Os=N多重键的锇（VI）氮合物在还原剂存在下发生氮偶合反应生成双核氮分子桥连配合物,为与固氮机理有关的金属氮合物氮偶合反应提供实验证据．一系列具有可调结构和氧化性含M=O,M=NR,M=CR^1R^2（M=Ru,Os）多重键的活性钌／锇氧合物,钌亚胺基配合物,钌／锇卡宾配合物（包括手性配合物）已被成功分离,其结构已通过光谱手段和x射线单晶衍射确定．这些活性金属一配体多重键配合物分别能与有机化合物发生氧原子、亚胺基、卡宾转移反应,包括烯烃环氧化、环氮化、环丙烷化、cis双羟基化,c—H键羟基化、酰胺化、卡宾插入等,从而允许直接研究相应催化过程中金属．配体多重键中间体的原子或基团转移反应,为金属催化原子或基团转移反应（包括不对称催化反应）提供重要机理信息．已发展出一系列涉及钌．配体多重键活性物种的高选择性钌催化反应,包括2,6-Cl2pyNO与烯烃的环氧化和Wacker型氧化成醛,H2O2水溶液氧化烯、炔烃和醇为羧酸或cis-二醇,PhI=NR与饱和c—H键的酰胺化,重氮化合物的卡宾偶合,分子内卡宾插入c—H键,重氮化合物、亚胺、烯／炔烃的三组分偶合,及以“PhI（OAc）2＋RNH2”为氮源的金属催化C—N键形成反应等．     

亚胺引发四肽环化反应机理的理论研究

运用密度泛函的理论方法（M06//B3LYP）对亚胺引发的关环肽环化的反应机理进行了研究. 计算结果表明,由亚胺到环肽的转化过程存在两种不同的反应机理. 一种是羰基转移-合环机理：先经历羰基转移,然后H转移与C-O合环同时进行. 另一种是H转移-合环-羰基转移-H转移机理：H原子先从O原子转移到N原子然后再进行C-O合环,随后再进行羰基转移与H原子转移. 计算结果显示,羰基转移-合环反应历程为有利路径,该反应路径中的H原子转移及C-O成环过程为整个反应的决速步骤.     

CH3CH2S自由基H迁移异构化及裂解反应的理论研究

采用密度泛函方法(B3LYP)在6-311+G(d,p)基组水平上研究了CH3CH2S自由基H迁移异构化以及裂解反应的微观动力学机理. 在QCISD(T)/6-311++G(d,p)//B3LYP/6-311+G(d,p)+ZPE水平上进行了单点能校正. 利用经典过渡态理论(TST)与变分过渡态理论(CVT)分别计算了在200~2000 K温度区间内的速率常数kTST和kCVT, 同时获得了经小曲率隧道效应模型(SCT)校正后的速率常数kCVT/SCT. 研究结果表明, CH3CH2S自由基1,2-H迁移、1,3-H迁移、C—C键断裂和β-C—H键断裂反应的势垒ΔE≠分别为149.74, 144.34, 168.79和198.29 kJ/mol. 当温度低于800 K时, 主要发生1,2-H迁移反应, 高于1800 K时, 主要表现为C—C键断裂反应, 在1300—1800 K范围内, 1,3-H迁移反应是优势通道, 在计算的整个温度段内, β-C—H键断裂反应可以忽略.     

吡啶气相光氯化反应理论研究──加成反应机理的过渡态和IRC解析

通过PM3方法研究氯自由基与吡啶分子加成反应的结果表明,生成不同产物2－氯吡啶、3－氯吡啶、4-氯吡啶的每一个反应通道都存在两个过渡态,生成2－氯吡啶反应路径主过渡态的能量及活化能最低,分别为-110293.6和139.2kJ/mol,反应优先生成2－氯吡啶,与实验结果一致.生成2－氰吡啶反应过程(IRC)相关的键长、键级和原子净电荷变化表明,吡啶环反应部位C原子与Cl加成形成C-Cl键主要与共轭双键断裂同步,而C-H键的断裂主要与共轭双键的重新形成同步.反应进程中氯原子净电荷从增加到减少的变化是氯原子诱导效应吸引电子和p－π共轭电荷平均分布等相互作用的结果.     

Mechanisms of formation of 8-oxoguanine due to reactions of one and two OH* radicals and the H2O2 molecule with guanine: A quantum computational study

Mechanisms of formation of the mutagenic product 8-oxoguanine (8OG) due to reactions of guanine with two separate OH* radicals and with H2O2 were investigated at the B3LYP/6-31G, B3LYP/6-311++G, and B3LYP/AUG-cc-pVDZ levels of theory. Single point energy calculations were carried out with the MP2/AUG-cc-pVDZ method employing the optimized geometries at the B3LYP/AUG-cc-pVDZ level. Solvent effect was treated using the PCM and IEF-PCM models. Reactions of two separate OH* radicals and H2O2 with the C2 position of 5-methylimidazole (5MI) were investigated taking 5MI as a model to study reactions at the C8 position of guanine. The addition reaction of an OH* radical at the C8 position of guanine is found to be nearly barrierless while the corresponding adduct is quite stable. The reaction of a second OH* radical at the C8 position of guanine leading to the formation of 8OG complexed with a water molecule can take place according to two different mechanisms, involving two steps each. According to one mechanism, at the first step, 8-hydroxyguanine (8OHG) complexed with a water molecule is formed ,while at the second step, 8OHG is tautomerized to 8OG. In the other mechanism, at the first step, an intermediate complexed (IC) with a water molecule is formed, the five-membered ring of which is open, while at the second step, the five-membered ring is closed and a hydrogen bonded complex of 8OG with a water molecule is formed. The reaction of H2O2 with guanine leading to the formation of 8OG complexed with a water molecule can also take place in accordance with two different mechanisms having two steps each. At the first step of one mechanism, H2O2 is dissociated into two OH* groups that react with guanine to form the same IC as that formed in the reaction with two separate OH* radicals, and the subsequent step of this mechanism is also the same as that of the reaction of guanine with two separate OH* radicals. At the first step of the other mechanism of the reaction of guanine with H2O2, the latter molecule is dissociated into a hydrogen atom and an OOH* group which become bonded to the N7 and C8 atoms of guanine, respectively. At the second step of this mechanism, the OOH* group is dissociated into an oxygen atom and an OH* group, the former becomes bonded to the C8 atom of guanine while the latter abstracts the H8 atom bonded to C8, thus producing 8OG complexed with a water molecule. Solvent effects of the aqueous medium on certain reaction barriers and released energies are appreciable. 5MI works as a satisfactory model for a qualitative study of the reactions of two separate OH* radicals or H2O2 occurring at the C8 position of guanine.     

HNCO与CX（X=F，Cl，Br）自由基反应机理的密度泛函理论研究

用量子化学密度泛函理论的B3LYP方法,在6-31+G~*水平上按BERNY能量梯度解 析全参数优化了HNCO与CX（X=F,Cl,Br）反应势能面上各驻点的几何构型,通过 振动频率分析确认了中间体和过渡态,内禀反应坐标（IRC）对反应物、中间体、 过渡态和产物的相关性予以证实,对各驻点进行了零点能校正（ZPE）在此基础上 计算了反应能垒。研究结果表明,与HNCO和其它小分子自由基反应不同,HNCO与 CX自由基反应首先发生分子间H原子迁移,随后N与CX的C（1）原子相互靠近成键并 生成较稳定的中间体,再发生N-C（2）键的断裂,完成N向C（1）上的迁移并进一 步解离为产物。反应按反应物→TS1→IM→TS2→产物通道进行。反应为放热反应。     

A Theoretical Investigation on N7(H)→N9(H)Tautomerization of Isolated and Monohydrated 2,6-Dithiopurine Combined with IPCM Solvent Model

The tautomerization reaction mechanism has been reported between N7(H) and N9(H) of isolated and monohydrated 2,6‐dithiopurine using B3LYP/6‐311+G(d,p). The isodensity polarized continuum model (IPCM) in the self‐consistent reaction field (SCRF) method is employed to account for the solvent effect of water on the tautomerization reaction activation energies. The results show that the two pathways P(1) (via the carbene intermediate I1) and P(2) (via the sp³‐hybrid intermediate I2) are found in intramolecular proton transfer, and each pathway is composed by two primary steps. The calculated activation energy barriers of the rate‐determining steps in isolated 2,6‐dithiopurine N7(H)→N9(H) tautomerism are 308.2 and 220.0 kJ·mol^?1 in the two pathways, respectively. Interestingly, in one‐water molecule catalyst, it dramatically lowers the N7(H)→N9(H) energy barriers by the concerted double proton transfer mechanism in P(1), favoring the formation of 2,6‐dithiopurine N9(H). However, the single proton transfer mechanism assisted with out‐of‐plane water in the first step of P(2) increases the activation energy barrier from 220.0 to 232.3 kJ·mol^?1, while the second step is the out‐of‐plane concerted double proton transfer mechanism, indicating that they will be less preferable for proton transfer. Additionally, the results also show that all the pathways are put into the aqueous solution, and the activation energy barriers have no significant changes. Therefore, the long‐range electrostatic effect of bulk solvent has no significant impact on proton transfer reactions and the interaction with explicit water molecules will significantly influence proton transfer reactions.     

Theoretical study on the mechanism of the thermal decarboxylation of acrylic and benzoic acids. Models for aqueous solution

The mechanism of acrylic and benzoic acid decarboxylation in aqueous solution has been investigated by ab initio methods using the STO-3G and 3-21G basis sets. In those reactions, the solvent is represented successively by one and two water molecules. Their active participation as a proton relay in the chemical process is demonstrated by the large decrease in the activation energy with respect to the reaction studied in the absence of water. In the absence of any intermediate found along the reaction pathway, the proposed mechanism is the concerted process; the free acid being the species that undergoes decarboxylation via a pseudounimolecular mechanism by interaction with a chain of water molecules. At the transition state, the carboxylic hydrogen transfer to one water molecule, the reorganization of the chain of water molecules through which the proton is transferred and the cleavage of the C? C bond are much more advanced than the proton transfer from the last water molecule to the α-carbon atom of the carboxyl group.     

The influence of hydrogen bonding interactions on the C-H bond activation step in class I ribonucleotide reductases

In order to model the C-H bond activation step in ribonucleotide reductases the hydrogen atom abstraction reaction from cis-tetrahydrofuran-2,3-diol (7) by methylthiyl (8) radical has been studied with theoretical methods. In order to identify an appropriate theoretical method for this system, the hydrogen transfer reaction between radical 8 and methanol (9) to give methanol radical (10) and methyl thiol (11) has been studied at several different levels of theory. While the reaction energy for this process is predicted equally well by the Becke3LYP and BH and HLYP hybrid functional methods, the reaction barrier is predicted to be significantly lower by the former. Compared to results obtained at CCSD(T)/cc-pVTZ level the BH and HLYP functional is better suited for the calculation of activation barriers for hydrogen abstraction reactions. This latter method was subsequently used to study the reaction of radical 8 with cis-tetrahydrofuran-2,3-diol 7 in the absence and in the presence of additional functional groups (acetate and acetamide) as models for the substrate reaction of class I ribonucleotide reductases (RNRs). The reaction barrier is lowest in those systems, in which acetate forms a double hydrogen bonded complex with the hydroxy groups of diol 7 (+8.2 kcal mol-1) and increases somewhat for side-on complexes between substrate 7 and acetate featuring only one hydrogen bond (+10.5 kcal mol-1). The barrier reduction of 6.5 kcal mol-1 obtained through complexation of diol 7 with acetate appears to be due to the formation of short strong hydrogen bonds in the transition. These effects can also be found in reactions of thiyl radical 8 with complexes of diol 7 with acetamide, but to a much smaller extent. The lowest reaction barrier is in this case calculated for the side-on complex (+11.2 kcal mol-1), while the bridging orientation between diol 7 and acetamide leads to a reaction barrier (+13.4) that is only slightly lower than that for the uncatalyzed process (+14.7 kcal mol-1). With respect to the structure of the active site of the RNR R1 subunit, only the side-on complexes appear to be relevant for the enzyme-catalyzed process. Under this condition the influence of the E441 side chan and thus the impact of the E441Q mutation in the initial C-H bond activation step will be rather small.     

硅杂苯与亲二烯体的Diels-Alder反应

采用密度泛函理论(DFT)在B3LYP/6-311G(d,p)水平上研究了硅杂苯与一些亲二烯体的两类可能的Diels-Alder反应的微观机理、势能剖面、取代基效应和溶剂化效应. 计算结果表明, 所研究反应均以协同的方式进行. 亲二烯体分子碳原子上的苯基取代基对两个新键形成的非同步性和反应的活化能垒的影响取决于苯基在产物中的相对位置, 而硅杂苯分子中硅原子上的CCl3取代基有利于杂Diels-Alder反应的进行. 形成一个C—Si键的杂Diels-Alder反应在热力学和动力学上均远比相应的全碳Diels-Alder反应容易进行, 实验观察到的杂Diels-Alder反应中的区域选择性由动力学因素所控制. 硅杂苯与烯烃的反应比与相应炔烃的反应在动力学上容易进行一些, 但在热力学上后者远比前者容易进行. 苯溶剂对所研究反应的势能剖面影响较小.     

A DFT Study on the Binuclear Copper(I)-Catalyzed Synthesis Mechanism of 1,2,3-Triazolo[1,5-c]Pyrimidine via Interrupted Click and Ketenimine Rearrangement

In this paper, the mechanism of the full catalytic cycle for binuclear Cu(I)-catalyzed sulfonyl azide-alkyne cycloaddition reaction for the synthesis of triazolopyrimidines was rationalized by density functional theoretical (DFT) calculations. The computed reaction route consists of: (a) formation of dicopper intermediates, including C−H activation of terminal alkyne, 3+2 ring cycloaddition and ring-reducing reaction and transmetalation, (b) interrupted CuAAC reaction, including di-copper catalyzed ring-opening of 2H-azirines and C−C bond formation to generate the copper-triazoles and -ketenimines, (c) two-step C−N cross-coupling and following (d) multi-step hydrogen transfer by the hydrogen bonding chain of water to promote the C−N formation and another C−N cleavage through the removal of p-tolyl sulfonamides. Our DFT results indicate that the multi-step hydrogen transfer process is the rate-determining step along the potential energy surface profile. The explicit water model was used for systematic determination of barrier for C−C cross-coupling, C−N bond formation and cleavage, and p-tolylsulfonamide removal. A critical insight in the interrupted CuAAC reaction was proposed. Further prediction interprets H₂O hydrogen bond chain plays an important role in C−N bond formation and cleavage, and the removal of p-tolylsulfonamide. This may have fundamental guidance on the design of 1, 5-herterocyclic functionalized triazolopyrimidines via interrupted CuAAC rearrangement reaction, as well as hydrogen bond chain of water.     

Isoguanine formation from adenine

Several possible mechanisms underlying isoguanine formation when OH radical attacks the C(2) position of adenine (A?C?2) are investigated theoretically for the first time. Two steps are involved in this process. In the first step, one of two low-lying A?C?2???OH reactant complexes is formed, leading to C(2)-H(2) bond cleavage. Between the two reactant complexes there is a small isomerization barrier, which lies well below separated adenine plus OH radical. The complex dissociates to free molecular hydrogen and an isoguanine tautomer (isoG?1 or isoG?2). The local and activation barriers for the two pathways are very similar. This evidence suggests that the two pathways are competitive. After dehydrogenation, there are two possible routes for the second step of the reaction. One is direct hydrogen transfer, via enol-keto tautomerization, which has high local barriers for both tautomers and is not favored. The other option is indirect hydrogen transfer involving microsolvation by one water molecule. The water lowers the reaction barrier by over 20?kcal mol(-1) , indicating that water-mediated hydrogen transfer is much more favorable. Both A+OH(?) →isoG+H(?) reactions are exothermic and spontaneous. Among four isoguanine tautomers, isoG?1 has the lowest energy. Our findings explain why only the N(1)H and O(2)H tautomers of isolated isoguanine and isoguanosine have been observed experimentally.     

Rh(Xantphos)L催化氢化肉桂醛和降冰片二烯间转移加氢甲酰化反应的理论研究

采用密度泛函理论方法 M11-L/6-31G(d,p)对氢化肉桂醛与降冰片二烯(nbd)在活化催化剂a[Rh(Xantphos)L,L=苯甲酸根,Xantphos=4,5-双二苯基膦-9,9-二甲基氧杂蒽]催化下发生转移加氢甲酰化反应生成主产物苯乙烯(3)的反应机理进行理论研究.结果表明,参与反应的醛类化合物在α碳(α-C)上应至少连接一个氢原子,这可以减少醛类反应物和抗衡离子的空间排斥作用.通过反应能垒图可见,受体nbd发生加氢甲酰化反应,促进了脱氢甲酰化反应的进行,进而促使整个转移加氢甲酰化循环不可逆进行.还研究了氢化肉桂醛发生脱羰化生成少量副产物苯乙烷(4)的机理过程.结果表明,苯甲酸根作为抗衡离子抑制了脱羰化反应的竞争,理论计算得到脱氢甲酰化反应的选择性为苯乙烯(3)∶苯乙烷(4)99∶1.简单醛(如丙醛)在活化催化剂a催化下更易于发生脱羰反应而不是脱氢甲酰化反应.     

Modeling hydrogen evolution from the Fe4S4 and Fe8S9X (X = N,C) clusters. Can a Fe?S high‐spin cluster serve as a surrogate for the FeMo cofactor?

A high-spin model of nitrogenase with a Fe(8)S(9)X(+) cluster (X = nitrogen or carbon) is used to test a mechanism for molecular hydrogen production, which is known to accompany ammonia production. The reaction proceeds with a series of protonation-reduction (PR) steps which are considered to be spontaneous if the calculated hydrogen-cluster bond energy exceeds 35-40 kcal/mol. The novel features of this mechanism include the opening of the cluster when one of the bridging sulfides undergoes two PR steps and the direct participation of the central atom when it undergoes a PR step. After the sixth PR step, a cluster is formed which has a low barrier for loss of molecular hydrogen in an exothermic reaction step. The central atom (nitrogen or carbon) has only a minor effect on the reaction steps.