3,4,4-三甲基-1-乙酰基咪唑啉盐向邻苯二胺转移一 碳单元反应的理论研究

用PM3-MO半经验方法对叶酸辅酶模型化合物3,4,4-三甲基-1-乙酰基咪唑啉盐向邻苯二胺转移一碳单元的反应进行了理论研究。结果表明,咪唑环有两种开环方式,该反应可能通过两种途径实现,每一种途径都经历了六个反应步骤,包括两次质子转移步骤,其中第二次质子转移是限速步骤。优化计算了所有步骤的中间体和过渡态的结构,各个中间体和过渡态具有不同的构型,构象和能量。     

2，3－二甲基－1－对氯苯磺酰基咪唑啉盐与邻氨基苯酚反应的量子化学研究

用量子化学方法对叶酸辅酶模型化合物2，3－二甲基－1－对氯苯磺酰基咪唑 啉盐与邻氨基苯酚的反应进行了理论研究。结果表明，咪唑啉环有两种开环方式， 反应可以通过两种途径实现，得到较稳定的中间体或者实现一碳单元的完全转移。 通过优化计算所有步骤的中间体和过渡态的结构可知，各个中间体和过渡态具有不 同的构型、构象，有些过程的构象变化是进行下一步反应所必需的，在所有过程中 质子转移步骤过渡态的能量最高，是反应的限速步骤。     

5,10-CH+-THF向邻苯二胺转移一碳单元反应的理论研究

叶酸辅酶在酶催化的一碳单元转移过程中具有重要的作用,已有大量的实验及实验模拟对其生物学功能进行了研究分析.本文用PM3半经验方法对5,10-CH⁺-THF向邻苯二胺转移一碳单元的反应进行了理论研究.结果表明,5,10-CH⁺-THF中的咪唑啉环有两种开环方式,从而使得该反应可以通过两种途径实现,每一种途径都经历了6个反应步骤,其中包括限制速度的两次质子转移步骤.优化计算了每个步骤所有可能的中间体和过渡态的结构和能量,并通过比较分析得到了各反应阶段的最优中间体和过渡态结构.     

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.     

咪唑啉盐向邻苯二胺转移一碳单元反应的理论研究

酶催化的一碳单元转移反应在生物合成和代谢过程中具有重要的作用 ,并与抗癌药物设计和合成密切相关 .虽然催化不同一碳单元转移反应的酶不同 ,但大多数酶需要四氢叶酸作辅酶 .四氢叶酸辅酶传递一碳单元的化学与其Ｎ5,Ｎ1 0的ΔｐＫａ 密切相关 ,而与嘧啶环及谷氨酸残基部分无关 ,后两部分的作用是把辅酶结合在适当的酶蛋白表面上[1 ] .当可转移的碳处于甲酸态时 ,四氢叶酸辅酶以衍生物 5,1 0 ＣＨ+ ＴＨＦ(1 )的形式存在 ,其中可转移的碳与Ｎ5,Ｎ1 0相连形成五元环 ,是反应的活性中心 .由于酶反应体系的复杂性 ,在实验和理论研究中大多建…     

An exploration of mechanisms for the transformation of 8-oxoguanine to guanidinohydantoin and spiroiminodihydantoin by density functional theory

The potential energy surface for formation of 2-amino-5-hydroxy-7,9-dihydropurine-6,8-dione (5-OH-OG), guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp) from 8-oxoguanine (8-oxoG) has been mapped out using B3LYP density functional theory, the aug-cc-pVTZ and 6-31+G(d,p) basis sets and the IEF-polarizable continuum model (PCM) solvation model. Three pathways for formation of 5-OH-OG from 8-oxoG were evaluated: (A) stepwise loss of two electrons and two protons to form the quinonoid intermediate 2-amino-7,9-dihydro-purine-6,8-dione (8-oxoG(ox)) followed by hydration; (B) stepwise loss of two electrons and one proton and net addition of hydroxide, in which the key step is nucleophilic addition to the 8-oxoG radical cation; and (C) stepwise loss of one electron and one proton and addition of hydroxyl radical to the 8-oxoG radical cation. The data suggest that all three pathways are energetically feasible mechanisms for the formation of 5-OH-OG, however, Pathway A may be kinetically favored over Pathway B. Although lower in energy, Pathway C may be of limited biological significance since it depends on the local concentration of hydroxyl radical. Pathways for hydrolysis and decarboxylation of 5-OH-OG to form Gh via either a carboxylic acid or substituted carbamic acid intermediate have been evaluated with the result that cleavage of the N1-C6 bond is clearly favored over that of the C5-C6 bond. Formation of Sp from 5-OH-OG via stepwise proton transfer and acyl migration or ring opening followed by proton transfer and ring closure have also been explored and suggest that deprotonation of the hydroxyl group facilitates a 1,2 acyl shift. Results of the calculations are consistent with experimental studies showing dependence of the Gh/Sp product ratio on pH. Under neutral and basic conditions, the data predict that formation of Sp is kinetically favored over the pathways for formation of Gh. Under acidic conditions, Gh is predicted to be the kinetically favored product.     

水分子辅助的一碳单元转移机理的密度泛函研究

The one-carbon unit transfer reaction catalysed by glycinamide ribonucleotide transformylase（GARTfase）is a key step in the de novo purine biosynthetic pathway. In order to give a theoretical research of the assumption from the experiments,the water-assisted mechanism in GAR Tfase catalysed one-carbon unit transfer reaction has been investigated by a Density Functional Theory method,B3LYP,at 6-31G* basis level. There are two possible reaction channels for the whole reaction,one is concerted（path a）and the other is stepwise（path b）. The water molecule serve as a bridge to connect the proton donor to the proton acceptor. All the transition states in both paths have a six-membered ring in their structures due to the joint of the water molecule. The calculations show that the latter is preferable to the former due to the lower energy barriers. The results have verified the presumption from experiments,and proved that the joint of a water molecule can relax the strong strain in the unstable system,so it is propitious to the whole reaction.     

别嘌醇质子迁移过程的理论研究

别嘌醇(Allopurinol)是次黄嘌呤的位置异构体,是唯一在临床上应用的黄嘌呤氧化酶抑制剂.     

喹唑啉酮互变异构的理论计算

采用密度泛函理论B3LYP/6-311+G(d,p)方法,计算并考察了喹唑啉酮进行结构互变的质子迁移过程的两种可能途径:(a)分子内质子迁移,(b)水助质子迁移.结果表明,途经b所需要的能垒小,氢键在降低反应能垒方面起重要作用.     

Understanding the fate of the oxyallyl cation following Nazarov electrocyclization: sequential Wagner-Meerwein migrations and the synthesis of spirocyclic cyclopentenones

A general reaction sequence is described that involves Nazarov cyclization followed by two sequential Wagner-Meerwein migrations, to afford spirocyclic compounds from divinyl ketones in the presence of 1 equiv of copper(II) complexes. A detailed investigation of this sequence is described including a study of substrate scope and limitations. It was found that after 4π electrocyclization, two different pathways are available to the oxyallyl cation intermediate: elimination of a proton can give the usual Nazarov cycloadduct, or ring contraction can give an alternative tertiary carbocation. After ring contraction, either [1,2]-hydride or carbon migration can occur, depending upon the substitution pattern of the substrate, to furnish spirocyclic products. The rearrangement pathway is favored over the elimination pathway when catalyst loading is high and the copper(II) counterion is noncoordinating. Several ligands were found to be effective for the reaction. Thus, the reaction sequence can be controlled by judicious choice of reaction conditions to allow selective generation of richly functionalized spirocycles. The three steps of the sequence are stereospecific: electrocyclization followed by two [1,2]-suprafacial Wagner-Meerwein shifts, the ring contraction and then a hydride, alkenyl, or aryl shift. The method allows stereospecific installation of adjacent stereocenters or adjacent quaternary centers arrayed around a cyclopentenone ring.     

Mechanistic insights on N-heterocyclic carbene-catalyzed annulations: the role of base-assisted proton transfers

The density functional theory investigation on the mechanism of NHC-catalyzed cycloannulation reaction of the homoenolate derived from butenal with pentenone is studied. The M06-2X/6-31+G** and B3LYP/6-31+G** levels of theory, including the effect of continuum solvation in dichloromethane and tetrahydrofuran, are employed. Several mechanistic scenarios are examined for each elementary step by identifying the key intermediates and the corresponding transition states interconnecting them on the respective potential energy surfaces. Both assisted and unassisted pathways for important proton transfer steps are considered, respectively, with and without the explicit inclusion of base (DBU) in the corresponding transition states. The barrier for the crucial proton transfer steps involved in the formation of the Breslow intermediate as well as in the subsequent steps is found to be significantly lowered by explicit inclusion of DBU. The energetic comparison between two key pathways, depicted as path A and path B, respectively, leading to cyclopentene and cyclopentanone derivatives, is performed. The major mechanistic bifurcation has been identified as emanating from the site of enolization of the initial zwitterionic intermediate resulting from the addition of a homoenolate equivalent to enone. If the enolization occurs nearer to the NHC moiety, the reaction is likely to proceed through path A, leading to cyclopentene. The enolization away from NHC leads to cyclopentanone product through path B. The computed results are generally in good agreement with the reported experimental results.     

Hydrogen transfer vs proton transfer in 7-hydroxy-quinoline.(NH3)3: a CASSCF/CASPT2 study

Multiconfigurational CASSCF and CASPT2 calculations were performed to investigate the enol --> keto tautomerization in the lowest singlet excited state of the 7-hydroxyquinoline.(NH3)3 cluster. Two different reaction mechanisms were explored. The first one corresponds to that proposed previously by Tanner et al. (Science 2003, 302, 1736) on the basis of experimental observations and CASSCF optimizations under Cs-symmetry constraints. This mechanism comprises four consecutive steps and involves nonadiabatic transitions between the valence 1pipi* state and a pisigma* Rydberg-type state, resulting in hydrogen-atom transfer. Single-point CASPT2 calculations corroborate that for Cs-symmetry pathways hydrogen-atom transfer is clearly preferred over proton transfer. The second mechanism, predicted by CASSCF optimizations without constraints, implies proton transfer along a pathway on the 1pipi* surface in which one or more ammonia molecules depart significantly from the molecular plane defined by the hydroxyquinoline ring. The results suggest that both mechanisms may be competitive with proton transfer being somewhat favorable over hydrogen-atom transfer.     

Quantum chemical investigation on the reaction mechanism of tertiary phosphines with unsaturated carboxylic acids: An insight into kinetic data

The structures of intermediates and transition states in the reaction of tertiary phosphines with unsaturated carboxylic acids have been calculated at the B3LYP level of theory using the 6‐31+G(d,p) basis set. Analysis of the results shows that [1,3]‐intramolecular migration of carboxylic proton to carbanionic center of generated zwitterionic intermediate is strongly kinetically unfavorable, and external proton‐donor source is essential to complete quaternization. A molecular cluster of the intermediate with one molecule of water has been modeled for intermolecular reaction pathway, but even in this case, the proton transfer remains to be the rate‐determining step that is in a good agreement with previous kinetic investigations on this reaction. The data obtained for this reaction have much in common with recent studies on the mechanisms of the Morita–Baylis–Hillman reaction and phosphine‐catalyzed [3+2] cycloaddition, which revealed paramount importance of proton‐transfer steps. © 2013 Wiley Periodicals, Inc.     

甲苯-2,4-二异氰酸酯与仲胺类化合物反应中的质子转移过程

采用密度泛函理论B3LYP/6-31+G(d,p)方法研究了甲苯-2,4-二异氰酸酯(2,4-TDI)与仲胺类化合物反应过程中的质子转移效应. 研究发现甲醇分子对反应有显著的催化效应,可使反应能垒大幅降低,这表明含活泼氢的化合物会加速质子转移过程,从而加快反应速率. 2,4-TDI与甲基-N-甲基氨基甲酸酯的催化加成反应为一步反应,其反应过渡态呈六元环结构;而2,4-TDI与N-甲基对硝基苯胺、二苯胺、1,2-二氢-2,2,4-三甲基喹啉等芳香胺类化合物的催化加成反应经历了两步反应,其中第一步为速率控制步骤. 研究表明,在与2,4-TDI的反应中,芳胺化合物的活性高于甲基-N-甲基氨基甲酸酯的活性,计算的反应活性顺序与实验结果一致.     

Cross-linking mechanisms of arginine and lysine with α,β-dicarbonyl compounds in aqueous solution

Cross-linking in proteins by α,β-dicarbonyl compounds is one of the most damaging consequences of reactive carbonyl species in vivo and in foodstuffs. In this article we investigate computationally the cross-linking of glyoxal and methylglyoxal with lysine and arginine residues using density functional theory and the wB97XD dispersion-corrected functional. Five pathways, A-E, have been characterized. In pathways A and B, the reaction proceeds via formation of the Schiff base, aldimine, followed by addition of arginine. In contrast, in pathways C-E, direct addition of arginine to the dicarbonyl compounds occurs first, leading to a dihydroxyimidazolidine intermediate, which then reacts with lysine after dehydration and proton transfer reactions. The results reveal that pathways A, C, and E are competitive whereas reactions via pathways B and D are much less favorable. Inclusion of up to five explicit water molecules in the proton transfer and dehydration steps is found to lower the energy barriers in the feasible pathways by about 5-20 kcal/mol. Comparison of the mechanisms of methylglyoxal-derived imidazolium cross-linking (MODIC) and glyoxal-derived imidazolium cross-linking (GODIC) shows that the activation barriers are lower for GODIC than MODIC, in agreement with experimental observations.     

Intramolecular hydroamination/cyclisation of aminoallenes mediated by a neutral zirconocene catalyst: a computational mechanistic study

The complete catalytic cycle for the intramolecular hydroamination/cyclisation (IHC) of 4,5-hexadien-1-ylamine (1) by a prototypical [ZrCp(2)Me(2)] precatalyst (2) has been scrutinized by employing a reliable DFT method. The present study conducted by means of a detailed computational characterisation of structural and energetic aspects of alternative pathways for all of the relevant elementary steps complements the mechanistic insights revealed from experimental results. The operative mechanism entails an initial transformation of precatalyst 2 into the thermodynamically prevalent, but dormant, bis(amido)-Zr compound in the presence of aminoallene 1. This complex undergoes a reversible, rate-determining alpha-elimination of 1 to form the imidoallene-Zr complex. The substrate-free form, which contains a chelating imidoallene functionality, is the catalytically active species and is rapidly transformed into azazirconacyclobutane intermediates through a [2+2] cycloaddition reaction. This highly facile process does not proceed regioselectively because the alternative pathways for the formation of five- and six-membered azacycles have comparable probabilities. Degradation of cyclobutane intermediates by following the most feasible pathway occurs through protonolysis of the metallacycle moiety and subsequent proton transfer from the Zr-NHR moiety onto the azacycle. The five-membered allylamine is generated through protonation at carbon atom C(6) followed by alpha-hydrogen elimination, whereas protonolysis of the cyclobutane moiety at the Zr-N bond followed by proton transfer onto carbon atom C(5) is the dominant route for the six-membered product. Of the two consecutive proton transfer steps, the second one determines the overall kinetics of the entire protonation sequence. This process is predicted to be substantially slower than the cycloaddition reaction. The factors that regulate the composition of the cycloamine products have been elucidated.     

Enantiomerization Mechanism of Thalidomide and the Role of Water and Hydroxide Ions

The significance of the molecular chirality of drugs has been widely recognized due to the thalidomide tragedy. Most of the new drugs reaching the market today are single enantiomers, rather than racemic mixtures. However, many optically pure drugs, including thalidomide, undergo enantiomerization in vivo, thus negating the single enantiomers’ benefits or inducing unexpected effects. A detailed atomic level understanding of chiral conversion, which is still largely lacking, is thus critical for drug development. Herein, we use first‐principle density function theory (DFT) to explore the mechanism of enantiomerization of thalidomide. We have identified the two most plausible interconversion pathways for isolated thalidomide: 1) proton transfer from the chiral carbon center to an adjacent carbonyl oxygen atom, followed by isomerization and rotation of the glutarimide ring (before the proton hops back to the chiral carbon atom); and 2) a pathway that is the same as “1”, but with the isomerization of the glutarimide ring occurring ahead of the initial proton transfer reaction. There are two remarkable energy barriers, 73.29 and 23.59 kcal mol^?1, corresponding to the proton transfer and the rotation of the glutarimide ring, respectively. Furthermore, we found that water effectively catalyzes the interconversion by facilitating the proton transfer with the highest energy barrier falling to approximately 30 kcal mol^?1, which, to our knowledge, is the first time that this important role of water in chiral conversion has been demonstrated. Finally, we show that the hydroxide ion can further lower the enantiomerization energy barrier to approximately 24 kcal mol^?1 by facilitating proton abstraction, which agrees well with recent experimental data under basic conditions. Our current findings highlight the importance of water and hydroxide ions in the enantiomerization of thalidomide and also provide new insights into the mechanism of enantiomerization at an atomic level.     

2-巯基吡啶质子迁移过程的理论研究

采用密度泛函理论,在B3LYP/6-311G**基组水平上,计算并考察了2-巯基吡啶分子硫醇式结构和硫酮式结构进行结构互变质子迁移过程中的4种可能途径:(a)分子内质子迁移,(b)水助质子迁移,(c)同种二聚体双质子迁移和(d)异种二聚体间双质子迁移.计算结果表明,途经c所需要的活化能最小(9.73 kJ.mol-1,逆反应则为55.28 kJ.mol-1),而过程a所需要的活化能最大(106.02 kJ.mol-1),途径b和d的活化能居中间(分别为32.05和15.91 kJ.mol-1).研究还表明,氢键在降低反应活化能方面起着重要的作用.     

4(3H)-嘧啶酮及其类似物互变异构的理论研究

采用密度泛函理论,在B3LYP/6-311G**基组水平上,计算并考察了4(3H)-嘧啶酮及其类似物(5-氟-4(3H)-嘧啶酮、4-巯基嘧啶和5-氟-4-巯基嘧啶)醇式结构和酮式结构进行结构互变质子迁移过程中的2种可能途径:(a)分子内质子迁移;(b)水助质子迁移.计算结果表明,途经b所需要的活化能较小.研究还表明,氢键在降低反应活化能方面起着重要的作用.     

Addition Mechanisms of Phenol toward Formaldehyde under Acidic Condition： a Theoretical Investigation

The reaction mechanisms of phenol with formaldehyde in the first and second addition at the ortho- and para-position in acid solution were theoretically investigated at the PW91/DNP level with solvent effects included. The reaction of phenol with protonated methanediol firstly forms an adduct intermediate, via a SN2 mechanism with a water molecule as the leaving group. From the adduct intermediate, there are two reaction channels involving a proton transfer to form the addition products. One is that a proton directly transfers via a four-membered ring transition state with a notable energy barrier (Four-member mechanism). Another mechanism involving a water molecule as catalyst to mediate the proton transfer (WCP mechanism), is a barrierless process, indicating that the formation of the adduct intermediate, the first reaction step, is rate-limiting. The reaction products are free hydroxymethyl phenols and/or hydroxybenzy carbocation (HOC6H4CH2+) which plays an important role in the following formation of methylene and methylene ether linkages. The second addition reactions between formaldehyde and hydroxymethyl phenol at all possible reaction sites of the phenol ring in acid solution were also investigated and discussed.