Epoxidation of acyclic chiral allylic alcohols with peroxy acids: spiro or planar butterfly transition structures? A computational DFT answer

The mechanism of the epoxidation of two chiral allylic alcohols, i.e., 3-methyl-3-buten-2-ol and (Z)-3-penten-2-ol, with peroxyformic acid has been investigated by locating 20 transition structures with the B3LYP/6-31G* method and by evaluating their electronic energy also at the B3LYP/6-311+G**@B3LYP/6-31G* theory level. Relative stability of TSs, as far as electronic energy is concerned, is basis set dependent; moreover, it also depends on entropy and solvent effects. Free enthalpies, calculated by using electronic energy at the higher theory level and with inclusion of solvent effects, indicates that syn, exo TSs, where the olefinic OH group hydrogen bonds the peroxy oxygens of the peroxy acid, outweigh syn, endo TSs, where the peroxy acid carbonyl oxygen is involved in hydrogen bonding. In the former TSs the peroxy acid moiety maintains its planar geometry while in the latter ones a strong out-of-plane distortion of peroxy acid is observed. This distortion makes it viable an unprecedented 1,2-H shift, as a possible alternative to the 1,4-H shift, for the peroxy acid hydrogen. In fact, for one syn, endo TS IRC analysis demonstrated that the 1,2-H shift mechanism is actually operative. The geometry of all TSs substantially conforms to a spiro (i.e., with the peroxy acid plane almost perpendicular to the C=C bond axis) butterfly orientation of the reactants while no TS resembles, even loosely, the planar butterfly structure. Theoretical threo/erythro epoxide ratios are in fair accord with experimental data. Calculations indicate that threo epoxides derive mostly from TSs in which the olefinic OH assumes an outside conformation while erythro epoxides originate from TSs with the OH group in an inside position. Computational findings do not support the qualitative TS models recently proposed for these reactions.     

Hexacoordinated MIV (M=Ti,Zr, Hf) Tetrachlorido Complexes with Chelating Dithienylethane Based 1,2 Diketone Ligand – π-Conjugation as Decisive Factor for Axial Chirality Mode

1,2-bis(2,5-dimethylthiophen-3-yl)ethane-1,2-dione ( 1 , DTEthane) reacts with MCl₄ metal precursors of group four (M=Ti, Zr, Hf) via coordination of the carbonyl groups. The molecular structure of complex 2–4 were determined in scXRD studies in the solid state and characterized by means of multi-nuclear and multi-dimensional NMR spectroscopy in solution. While the resulting titanium complex [TiCl₄(DTEthane)] 2 shows a monomeric structure, where 1 binds in a bidentate fashion, complexes with a Zr ( 3 ) and Hf ( 4 ) center have dimeric scaffolds in which the ligands adopt a bridging mode. Quantum chemical calculations using density functional theory (G16, B97D3/def2-TZVP) were used to evaluate the general trend of dimer formation (Ti<Zr<Hf). The molecular structures derived from both scXRD and the DFT optimized structures reveal the carbonyl groups in conjugation with the adjacent thiophene substituent. As a result, they are coplanar and rotation about the two C−C axes (C1−C7; C8−C9) is restricted allowing for only one chiral axis along C7−C8. This gains special importance with respect to previously described complexes carrying the closely related 1,2-endiolato ligand (1,2-bis(2,5-dimethylthiophen-3-yl)ethene-1,2-diolate), in which no coplanarity of the thiophene rings to their neighboring metallacycle was observed allowing for two chiral axes. Noteworthy, further DFT calculations addressing the pathway of racemization found transition states, which are characterized by contrary rotations of both thiophene rings and a loss of conjugation rather than a direct rotation around the axis C7−C8.     

Regioselective addition of Ti enolates to conjugated enones: New insights into the mechanism based on experimental and DFT investigation

The regioselective addition mechanism of the Ti(IV) enolates derived from α-diazo-β-keto carbonyl compounds and α-diazo-β-keto phosphonates to conjugated enones has been studied on the basis of a hypothetical bridging chloride-controlled theory, by density functional theory (DFT), and experimentally. The DFT results indicate that, for the Ti(IV) enolate 3 derived from α-diazo-β-keto carbonyl compounds, the free energy of the bridging chloride-controlled 1,2-addition transition state is 2.4 kcal/mol higher than that of 1,4-addition, and the calculated enthalpies of 1,2-addition is 4.36 kcal/mol more than that of 1,4-addition. For the Ti(IV) enolate 4 derived from α-diazo-β-keto phosphonates, in contrary, the free energy of the bridging chloride-controlled 1,2-addition transition state is 1.1 kcal/mol lower than that of 1,4-addition, and the calculated enthalpy of 1,2-addition is 3.46 kcal/mol less than that of 1,4-addition. Our findings demonstrate that the nucleophilic addition of these Ti(IV) enolates to conjugated enones was carried out not only kinetically but also irreversibly for the first time.     

Density functional study of the insertion and ring-opening mechanism of MCP over Cp2LaH and Cp2LuH catalysts

The insertion and ring opening of methylenecyclopropane (MCP) catalyzed by Cp2LnH (Ln = La and Lu) was investigated using DFT method. Geometries and energies of the reactants, minima, and transition states for this reaction were obtained. The present study indicates the formation of Cp2LaH-MCP complex followed by 1,2-insertion through a tetrahedral transition state with subsequent ring opening at the proximal bond via hydrogen transfer transition state resulting in the formation of the final product.     

基态氧(3^O2)氧化硅烯的密度泛函计算研究

采用密度泛函[B3LYP(full)/6-311+G^*]方法研究了基态氧(3^O2)氧化硅烯(Si2H4)的机理。计算了三重态初始中间体(IM(T1)到单重态中间体IM2(S0)反应交叉势能面,报道了各反应中间体、产物和过渡态的构型和能量,用频率分析方法对各过渡态进行了验证,进一步用IRC方法对主要的基元反应进行了考察,确定了历经生成1,2-二氧环氧硅烷中间体的氧化过程的主要反应通道。     

气相中Cu+和Zn+与CS2反应的计算研究

以Cu⁺和Zn⁺与CS₂反应作为第一过渡金属离子与CS₂反应的范例体系. 采用密度泛函UB3LYP/6-311+G^*方法计算研究了第一过渡金属离子在基态和激发态与CS₂反应的反应机理. 全参数优化了反应势能面上各驻点的几何构型, 用频率分析方法和内禀反应坐标(IRC)方法对过渡态进行了验证. 并用UCCSD(T)/6-311G^*方法对各驻点作了单点能量校正. 在Cu⁺与CS₂反应中, 计算了单重态初始中间体¹IM1到三重态插入型中间体³IM2的反应交叉势能面. 确定了第一过渡金属离子与CS₂的反应为插入-消去反应, 找到了基态和激发态金属离子与CS₂反应的主要通道.     

气相中Sc+和Ti+与CS2反应的计算研究

以Sc⁺和Ti⁺与CS₂反应作为第一前过渡金属离子与CS₂反应的范例体系. 采用密度泛函(UB3LYP/6-311+G*)方法计算研究了Sc⁺和Ti⁺在基态和激发态与CS₂反应的反应机理. 全参数优化了反应势能面上各驻点的几何构型, 用频率分析方法和内禀反应坐标(IRC)方法对过渡态进行了验证. 计算了不同多重度下的反应交叉势能面. 确定了Sc⁺和Ti⁺与CS₂的反应为插入-消去反应, 找到了基态和激发态金属离子与CS₂反应的主要通道.     

烷基咪唑型卤盐类离子液体的合成机理研究

用密度泛函理论考察了甲基咪唑和一系列的卤代烷烃(氯乙烷,氯丁烷,溴乙烷,溴丁烷)反应合成咪唑类离子液体的反应机理. 在B3LYP/6-31++G**//B3LYP/6-31G*基组水平上找到了两条反应路径：路径A(反应物→TS1→P1)和路径B(反应物→TS2→P2). 在路径A中, 卤素离子和咪唑环C2上的氢质子形成氢键；在路径B中, 卤素离子和咪唑环C5上的氢质子形成氢键. 计算发现, 氢键的形成在反应中起到了非常重要的作用, 特别是咪唑环C2上的氢质子在和卤素离子成氢键后形成了一个五员环结构的过渡态, 该过渡态能量较低. 经过渡态TS1的反应途径其活化能要低于经过渡态TS2的反应途径, 反应路径A为主要的反应通道. 计算结果表明, 经过渡态TS1的反应途径是一放热过程, 这和实验观察现象一致.     

乙烯自由基与臭氧反应的DFT计算研究

采用密度泛函B3LYP/6-311G**水平计算研究了O3氧化乙烯基（C2H3）的机理,全参数优化了反应势能面上各驻点的几何构型,用内禀反应坐标（IRC）计算和频率分析方法,对过渡态进行了验证.结果表明，乙烯基（C2H3）与O3之间有很强的反应活性.     

羰基氧化物环化反应动力学的计算研究

用密度泛函（DFT）方法计算了羰基氧化物（H2COO、HFCOO、F2COO和Me2COO）环化反应的动力学信息，优化了反应物和产物的几何构型，优化搜索了各反应的过渡态结构，并用频率分析和内禀坐标法(IRC)验证了各鞍点构型和反应路径.计算了不同温度下经零点能校正的活化热力学量、反应过程热力学改变量，反应速率常数及频率因子.计算表明，电负性较大的取代基对环化反应有促进作用.     

Theoretical Study on the Photodegradation Mechanism of Pyrethroid Insecticide Fenvalerate in Water

The photodegradation mechanism of fenvalerate in water has been investigated by density functional theory(DFT).The geometries of reactants,transition states,intermediates and products are optimized at the B3LYP/6-31G* level.The calculated results indicate that the reaction process mainly includes the nucleophilic attack and the substitution reaction by hydroxyl radical to the carbonyl group.By vibrational frequency analysis and intrinsic reaction coordinate(IRC) method,the transition state and its reaction pathway are confirmed.Moreover,the changes of natural population analysis(NPA),calculated using the Natural bond orbital(NBO) method,are analyzed along with the degradation reaction which can explain the variation of chemical bonds.Additionally,the solvent effect is also investigated and the results show that the reaction preferably takes place in water.     

Stereochemistry of 1,2-elimination reactions at the E2-E1cB interface--tert-butyl 3-tosyloxybutanoate and its thioester

Experimental data on the stereoselectivity of base-catalyzed 1,2-elimination reactions that produce conjugated carbonyl compounds are scarce in spite of the importance of these reactions in organic and biochemistry. As part of a comprehensive study in this area, we have synthesized stereospecifically-deuterated beta-tosyloxybutanoate esters and thioesters and studied the stereoselectivity of their elimination reactions under non-ion pairing conditions. With the availability of both the (2R*,3R*) and (2R*,3S*) diastereomers the innate stereoselectivity could be determined unambiguously. (1)H and (2)H NMR data show that these substrates produce 5-6% syn elimination, the usual amount for acyclic substrates undergoing E2 reactions. Contrary to earlier suggestions, activation by a carbonyl group has virtually no influence upon the stereoselectivity. Elimination of the (2R*,3R*) diastereomer of the beta-tosyloxyester and thioester produces 21-25% of the (Z)-alkene, much more than observed with a poorer beta-nucleofuge. A relatively large amount of (Z)-alkene product seems to be a good marker for an E2 pathway, in which the transition state is E1cB-like, rather than an E1cB(irrev) mechanism. Syn KIE values were higher than those for anti elimination for the esters as well as the thioesters. Experimental challenges to the synthesis of stereospecifically-deuterated beta-tosyloxyesters are discussed.     

DFT法研究离子液中EMIM+催化丁烯双键异构反应机理(II)

用密度泛函理论(DFT)在B3LYP/6-31G(d, p)的计算水平上研究了离子液中1-乙基-3-甲基咪唑阳离子(EMIM⁺)的4-H和5-H原子催化丁烯双键异构反应的可能途径，优化了反应体系的平衡态和过渡态的几何构型，分析了反应过程中键参数的变化，通过振动分析对平衡态和过渡态进行了验证. 计算结果表明, 离子液中的EMIM⁺首先通过4-H和5-H原子吸附丁烯, 进而催化丁烯的双键异构反应, EMIM⁺的4-H和5-H催化1-丁烯异构为2-丁烯的正反应活化能分别为204.2和207.3 kJ•mol^-1，逆反应活化能约为220.9和223.8 kJ•mol^-1， 反应为基元反应.     

双[1,2-二(三氟甲基)乙烯-1,2-二硫基]镍与丁二烯反应的溶剂效应

采用密度泛函理论(DFT)在B3LYP/6-31G(d)水平上研究了双[1,2-二(三氟甲基)乙烯-1,2-二硫基]镍(Ni[S2C2(CF3)2]2)与丁二烯的反应机理.采用极化连续介质模型(PCM),考察了溶剂对各反应驻点的电荷分布、偶极矩、溶剂化自由能的影响.计算结果表明:Ni[S2C2(CF3)2]2与丁二烯的反应为前线轨道对称性匹配的协同反应,溶剂介电常数的增大有利于稳定各反应驻点.同时在同种溶剂中,过渡态和产物稳定的程度大于反应物,从而反应更加容易进行.     

Stereoselective synthesis of cyclopropanes based on a 1,2-chirality transfer

A stereoselective route to enantiomerically enriched bicyclic cyclopropane derivatives 13 is described which is based on a conceptually novel 1,2-chirality transfer approach. The hyperconjugative interaction of an electronically excited carbonyl group with the sigma* orbital of an adjacent C--X bond in the transition state of a hydrogen abstraction causes the preference of a certain conformation and consequently the differentiation between two diastereotopic methylene groups. The 1,2-chirality transfer is completed by a subsequent HX elimination which destroys the only stereogenic center in the reactants 12. Furthermore, it was found that contrary enthalpic and entropic influences result in the existence of an inversion temperature T 0. Upon crossing T 0 the stereoselectivity is reversed. Considering this temperature dependency, chirality transfer efficiencies of up to 83 % could be achieved. The absolute configuration of most products could be unambiguously determined by VCD spectroscopy combined with DFT calculations.     

化学反应的内禀反应坐标法(Ⅷ)——甲基叠氮热解反应的反应路径解析

采用内禀反应坐标法完成了对甲基叠氮热解反应途径的微观动力学解析.结果表明甲基叠氮的热解是以伴随N₂消除后发生1,2-H迁移的协同方式完成的,属协同的非同步反应,此机制可解释(H₃C)nH_3-nC-N₃(n=0～2)烷基叠氮系列热解温度的光电子能谱结果.     

Mechanism of cooperative catalysis in a lewis Acid promoted nickel-catalyzed dual C-h activation reaction

The mechanism of cooperativity offered by AlMe(3) in a Ni-catalyzed dehydrogenative cycloaddition between substituted formamides and an alkyne is investigated by using DFT(SMD(toluene)/M06/6-31G**) methods. The preferred pathway is identified to involve dual C-H activation, with first a higher barrier formyl C(sp(2))-H oxidative insertion followed by benzylic methyl C(sp(3))-H activation. The cooperativity is traced to be of kinetic origin as evidenced by stabilized transition states when AlMe(3) is bound to the formyl group, particularly in the oxidative insertion step.     

DFT investigation on the mechanism of the deacetylation reaction catalyzed by LpxC

LpxC is a key enzyme in the biochemical synthesis of Lipid A, an important outer cell-membrane component found in a number of pathogenic bacteria. Using DFT, we have investigated the binding of the substrate within its active site as well as the deacetylation mechanism it catalyzes. The substrate is found to preferentially coordinate to the active site Zn2+ via its carbonyl oxygen between a Zn2+-bound H2O and an adjacent threonine (Thr191). Furthermore, upon substrate binding a nearby Glu78 residue is found to readily deprotonate the remaining Zn2+-bound H2O. Unlike several related metallopeptidases, the mechanism of LpxC is found to proceed via four steps; (i) initial hydroxylation of the substrates' carbonyl carbon to give a gem-diolate intermediate, (ii) protonation of the amide nitrogen by the histidine His265-H+, (iii) a barrier-less change in the active site-intermediate hydrogen-bond network and finally, (iv) C-N bond cleavage. Notably, the rate-determining step of the mechanism of LpxC is found to be the initial hydroxylation while the final C-N bond cleavage occurs with an overall barrier of 23.6 kJ mol-1. Furthermore, LpxC uses a general acid/base pair mechanism as indicated by the fact that both His265-H+ and Glu78 are accordingly involved.     

Lewis acid mediated [2,3]-sigmatropic rearrangement of allylic alpha-amino amides

Boron trifluoride and BBr(3) mediated [2,3]-sigmatropic rearrangements of allylic alpha-amino amides have been developed affording secondary amines in good yields. (E)-Crotyl and (E)-cinnamyl alpha-amino amides 2b and 2c exhibit excellent syn-diastereoselectivity upon rearrangement with either Lewis acid. The allylic amine 2a forms upon treatment with BF(3) or BBr(3) a five-membered heterocylic complex in which a single halide anion has been displaced by the carbonyl oxygen atom. The structures of the Lewis acid-amine complexes were elucidated using NMR spectroscopy. A plausible reaction mechanism, based on DFT calculations, is presented. Thus, BF(3)- or BBr(3)-complexed allylic amines 2 are shown to preferentially proceed, after deprotonation, via an endo transition state.     

Combined charge and spin density experimental study of the yttrium(III) semiquinonato complex Y(HBPz3)2(DTBSQ) and DFT calculations

High-resolution X-ray diffraction and polarized neutron diffraction experiments have been performed on the Y-semiquinonate complex, Y(HBPz3)2(DTBSQ), in order to determine the charge and spin densities in the paramagnetic ground state, S = (1/2). The aim of these combined studies is to bring new insights to the antiferromagnetic coupling mechanism between the semiquinonate radical and the rare earth ion in the isomorphous Gd(HBPz3)2(DTBSQ) complex. The experimental charge density at 106 K yields detailed information about the bonding between the Y3+ ion and the semiquinonate ligand; the topological charge of the yttrium atom indicates a transfer of about 1.5 electrons from the radical toward the Y3+ ion in the complex, in agreement with DFT calculations. The electron density deformation map reveals well-resolved oxygen lone pairs with one lobe polarized toward the yttrium atom. The determination of the induced spin density at 1.9 K under an applied magnetic field of 9.5 T permits the visualization of the delocalized magnetic orbital of the radical throughout the entire molecule. The spin is mainly distributed on the oxygen atoms [O1 (0.12(1) mu B), O2(0.11(1) mu B)] and the carbon atoms [C21 (0.24(1) mu B), C22(0.20(1) mu B), C24(0.16(1) mu B), C25(0.12(1) mu B)] of the carbonyl ring. A significant spin delocalization on the yttrium site of 0.08(2) mu B is observed, proving that a direct overlap with the radical magnetic orbital can occur at the rare earth site and lead to antiferromagnetic coupling. The DFT calculations are in good quantitative agreement with the experimental charge density results, but they underestimate the spin delocalization of the oxygen toward the yttrium and the carbon atoms of the carbonyl ring.