过氧亚硝酸与酪氨酸的反应机理

用密度泛函理论(DFT)研究了过氧亚硝酸与酪氨酸的反应机理. 在B3LYP/6-311G(d,p)水平上对该反应体系的反应物、中间体、过渡态和产物进行了几何构型优化并计算了振动频率和能量. 计算结果表明, 过氧亚硝酸不易直接与酪氨酸反应, 而是先分解产生自由基(·OH和·NO2), 而后再与酪氨酸分步作用. 过氧亚硝酸与酪氨酸的反应生成两种主要产物, 分别为3-羟基酪氨酸和3-硝基酪氨酸, 这一结论与实验所得到的结果一致. 此外在同一计算水平上采用SCRF(PCM)方法计算了溶剂化效应, 结果表明, 极性溶剂可以增加自由基结合的稳定化能, 并降低反应通道的活化能, 有利于反应的进行.     

CH3SH与NO2的反应机理及动力学

在G3B3, CCSD(T)/6-311＋＋G(d,p)//B3LYP/6-311＋＋G(d,p)水平上详细研究了CH3SH与基态NO2的微观反应机理. 在B3LYP/6-311＋＋G(d,p)水平得到了反应势能面上所有反应物、过渡态和产物的优化构型, 通过振动频率分析和内禀反应坐标(IRC)跟踪验证了过渡态与反应物和产物的连接关系. 在CCSD(T)/6-311＋＋G(d,p)和G3B3水平计算了各物种的能量, 得到了反应势能面. 利用经典过渡态理论(TST)与变分过渡态理论(CVT)并结合小曲率隧道效应模型(SCT), 分别计算了在200～3000 K温度范围内的速率常数kTST, kCVT和kCVT/SCT. 研究结果表明, 该反应体系共存在5个反应通道, 其中N进攻巯基上H原子生成CH3S＋HNO2的通道活化势垒较低, 为主要反应通道. 动力学数据也表明, 该通道在200～3000 K计算温度范围内占绝对优势, 拟合得到的速率常数表达式为k1CVT/SCT＝1.93×10－16T0.21exp(－558.2/T) cm3&;#8226;molecule－1&;#8226;s－1.     

类硅烯H2C＝SiLiBr与RH (R＝F, OH, NH2)的插入反应

采用DFT B3LYP和QCISD方法研究了类硅烯H2C＝SiLiBr与RH (R＝F, OH, NH2)的插入反应. 在B3LYP/6- 311＋G(d,p)水平上优化了反应势能面上的驻点构型. 结果表明, H2C＝SiLiBr与HF, H2O或NH3发生插入反应的机理相同. QCISD/6-311＋＋G(d,p)//B3LYP/6-311＋G(d,p)计算的三个反应的势垒分别为148.62, 164.42和165.07 kJ•mol－1, 反应热分别为－69.63, －43.02和－28.27 kJ•mol－1. 相同条件下发生插入反应时, 反应活性都是H—F＞H—OH＞H—NH2.     

甲醇与一氧化碳合成甲酸甲酯反应机理的理论研究

用密度泛函理论(DFT)研究了甲醇与一氧化碳的微观反应机理. 在B3LYP/6-311＋＋G(d,p)水平上优化了反应物、过渡态及产物的几何构型, 并通过振动分析和内禀反应坐标方法(IRC)分别确认了过渡态的结构与反应途径. 在CCSD/6-311＋＋G(d,p)水平上进行能量校正, 并根据计算的势能面探讨了CH₃OH＋CO反应机理. 结果表明, CH₃OH＋CO反应体系有三个可能的反应通道, 产物分别为甲酸甲酯、乙酸、羟基乙醛. 在无催化条件下, 计算得到生成甲酸甲酯、乙酸和羟基乙醛的反应活化能分别是364.715, 460.775和611.402 kJ•mol^－1, 生成甲酸甲酯和羟基乙醛的反应为吸热反应, 而生成乙酸的反应为放热反应.     

OH-与CH2CIF反应的阴离子产物通道

理论研究了羟基负离子(OH-)与氟氯代甲烷(CH2CIF)反应的阴离子产物通道.分别在B3LYP/6-31+G(d,p)和B3LYP/6-311++G(2d,p)水平上得到反应势能面上各关键物种的优化构型,进而计算得到谐振频率和零点能.基于CCSD(T)/6-311+G(3df,3dp)水平的相对能量,描述了由质子转移和双分子亲核取代(SN2)过程生成各阴离子产物的途径.各阴离子产物途径势垒的计算结果表明质子转移过程是实验中的主要产物通道,与以往实验测量的结论相符.此外,计算还显示双分子亲核取代过程得到了非典型的阴离子产物,其中动力学效应可能会导致F-的生成.     

HNO自由基与O2反应机理的理论研究

采用密度泛函理论(DFT)和从头算方法,在B3LYP/6-311++G(d,p)水平上对反应HNO+O_2做了理论计算研究。优化得到了反应物、中间体、过渡态和产物的几何构型以及相应的能量值、振动频率。通过分析反应路径的能量差异,以及异构化难易程度,发现HNO+O_2反应有2种产物通道:HOONO和HNO_3。其中过氧亚硝酸HOONO是主要产物,有3种稳定的构象。     

OH引发的正辛烷大气反应机理的理论研究

采用量子化学密度泛函理论研究了正辛烷与OH自由基的大气氧化反应机理。在B3LYP/6-31G(d)水平上对该反应体系的反应物、中间体、过渡态及产物进行了几何构型优化和频率计算,并在B3LYP/6-311＋G(3df,2p)水平上进行了单点能计算,得出了各反应通道的势能剖面图. 计算结果表明: 羟基硝酸酯和含有羟基羰基官能团的化合物是主要的反应产物,并且它们的挥发性较低,容易形成二次有机气溶胶。另外,本文将理论计算结果与可用的实验观测结果进行了比较。     

CH3SH与NO2的反应机理及动力学

在G3B3,CCSD(T)/6-311++G(d,p)//B3LYP/6-311++G(d,p)水平上详细研究了CH3SH与基态NO2的微观反应机理.在B3LYP/6-311++G(d,p)水平得到了反应势能面上所有反应物、过渡态和产物的优化构型,通过振动频率分析和内禀反应坐标(IRC)跟踪验证了过渡态与反应物和产物的连接关系.在CCSD(T)/6-311++G(d,p)和G3B3水平计算了各物种的能量,得到了反应势能面.利用经典过渡态理论(TST)与变分过渡态理论(CVT)并结合小曲率隧道效应模型(SCT),分别计算了在200～3000K温度范围内的速率常数kTST,kCVT和kCVT/SCT.研究结果表明,该反应体系共存在5个反应通道,其中N进攻巯基上H原子生成CH3S+HNO2的通道活化势垒较低,为主要反应通道.动力学数据也表明,该通道在200～3000K计算温度范围内占绝对优势,拟合得到的速率常数表达式为k1CVT/SCT=1.93×10-16T0.21exp(-558.2/T)cm3·molecule-1·s-1.     

亚甲基氰自由基(HCCN)与一氧化氮(NO)反应势能面的理论研究

在CCSD(T)/6-311G(d,p)//B3LYP/6-311G(d,p)+ZPE水平上对反应HCCN+NO的二重态反应势能面进行了计算,得到了4种产物:P1(HCN+NCO),P2(OH+NCCN),P₃[HCN+(CNO)]和P4(HCN+CNO).其中产物P1为主要产物,P2为次要产物,P₃和P4很难得到.在G2(B3LYP/MP2/CC)水平,对产物P1和P2的反应通道的单点能量进行了校正.     

过氧烷基自由基分子内氢迁移反应类速率常数的计算

过氧烷基自由基分子内氢迁移是低温燃烧反应中的一类重要基元反应. 本文用等键反应方法计算了该类反应的动力学参数. 所有反应物、过渡态、产物的几何结构均在B3LYP/6-311+G(d,p)水平下优化得到. 本文提出了用过渡态反应中心几何结构守恒作为反应类判据, 并将该分子内氢迁移反应分为四类, 包括(1,3)、(1,4)、(1,5)、(1,n) (n=6, 7, 8)氢迁移类. 分别将这4 类反应类中最小反应体系作为类反应的主反应, 并分别在B3LYP/6-311+G(d,p)低水平和CBS-QB3 高水平下得到其近似能垒和精确能垒. 其余氢迁移反应作为目标反应, 在B3LYP/6-311+G(d,p)低水下计算得到其近似能垒, 再采用等键反应方法校正得到目标反应的精确反应势垒和精确速率常数. 研究表明, 采用等键反应方法只需在低水平用从头算计算就可以得到大分子反应体系的高精度能垒和速率常数值, 且本文按等键反应本质的分类方法更能揭示反应类的本质, 并对反应类的定义给出了客观标准. 本文的研究为碳氢化合物低温燃烧模拟中重要的过氧烷基分子内氢迁移反应提供了准确的动力学参数.     

Transition state structure and energetics of the N(2)O + X (X = Cl,Br) reactions

The structural and vibrational properties of the transition state of the N(2)O + X (X = Cl,Br) reactions have been characterized by ab initio methods using density functional theory. We have employed Becke's hybrid functional (B3LYP), and transition state optimizations were performed with 6-31G(d), 6-311G(2d,2p), 6-311+G(3d,2p), and 6-311+G(3df,2p) basis sets. For the chlorine atom reaction the coupled-cluster method (CCSD(T)) with 6-31G(d) basis set was also used. All calculations resulted in transition state structures with a planar cis arrangement of atoms for both reactions. The geometrical parameters of transition states at B3LYP are very similar, and the reaction coordinates involve mainly the breaking of the N-O bond. At CCSD(T)/6-31G(d) level a contribution of the O-Cl forming bond is also observed in the reaction coordinate. In addition, several highly accurate ab initio composite methods of Gaussian-n (G1, G2, G3), their variations (G2(MP2), G3//B3LYP), and complete basis set (CBS-Q, CBS-Q//B3LYP) series of models were applied to compute reaction energetics. All model chemistries predict exothermic reactions. The G3 and G2 methods result in the smallest deviations from experiment, 1.8 and 0 kcal mol(-1), for the enthalpies of reaction for N(2)O reaction with chlorine and bromine, respectively. The G3//B3LYP and G1 methods perform best among the composite methods in predicting energies of the transition state, with a deviation of 1.9 and 3.0 kcal mol(-1), respectively, in the activation energies for the above processes. However, the B3LYP/6-311+G(3df,2p) method gives smaller deviations of 0.4 and -1.0 kcal mol(-1), respectively. The performance of the methodologies applied in predicting transition state energies was analyzed.     

NMR spectra, GIAO and charge density calculations of five-membered aromatic heterocycles

The B3LYP/6-31+G(d) molecular geometry optimized structures of 17 five-membered heterocycles were employed together with the gauge including atomic orbitals (GIAO) density functional theory (DFT) method at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p) and B3LYP/6-311+G(2d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants. The method of geometry optimization for pyrrole (1), N-methylpyrrole (2) and thiophene (7) using the larger 6-311++G(d,p) basis sets at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,p) and B3LYP/cc-pVTZ levels of theory gave little difference between calculated and experimental values of coupling constants. In general, the (1)H and 13C chemical shifts for all compounds are in good agreement with theoretical calculations using the smaller 6-31 basis set. The values of nJHH(n=3, 4, 5) and rmnJ(CH)(n=1, 2, 3, 4) were predicted well using the larger 6-31+G(d,p) and 6-311++G(d,p) basis sets and at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,2p) levels of theory. The computed atomic charges [Mülliken; Natural Bond Orbital Analysis (NBO); Merz-Kollman (MK); CHELP and CHELPG] for the B3LYP/6-311++G(d,p) geometry optimized structures of 1-17 were used to explore correlations with the experimental proton and carbon chemical shifts.     

Chemical behavior of the biradicaloid (HO...ONO) singlet states of peroxynitrous acid. The oxidation of hydrocarbons, sulfides, and selenides

Various high levels of theory have been applied to the characterization of two higher lying biradicaloid metastable singlet states of peroxynitrous acid. A singlet minimum (cis-2) was located that had an elongated O-O distance (2.17 A) and was only 12.2 kcal/mol [UB3LYP/6-311+G(3df,2p)+ZPVE] higher in energy than its ground-state precursor. A trans-metastable singlet (trans-2) was 10.9 kcal/mol higher in energy than ground-state HO-ONO. CASSCF(12,10)/6-311+G(d,p) calculations predict the optimized geometries of these cis- and trans-metastable singlets to be close to those obtained with DFT. Optimization of cis- and trans-2 within the COSMO solvent model suggests that both exist as energy minima in polar media. Both cis- and trans-2 exist as hydrogen bonded complexes with several water molecules. These collective data suggest that solvated forms of cis-2.3H(2)O and trans-2.3H(2)O represent the elusive higher lying biradicaloid minima that were recently (J. Am. Chem. Soc. 2003, 125, 16204) advocated as the metastable forms of peroxynitrous acid (HOONO). The involvement of metastable trans-2 in the gas phase oxidation of methane and isobutane is firmly established to take place on the unrestricted [UB3LYP/6-311+G(d,p)] potential energy surface (PES) with classical activations barriers for the hydrogen abstraction step that are 15.7 and 5.9 kcal/mol lower than the corresponding activation energies for producing products methanol and tert-butyl alcohol formed on the restricted PES. The oxidation of dimethyl sulfide and dimethyl selenide, two-electron oxidations, proceeds by an S(N)2-like attack of the heteroatom lone pair on the O-O bond of ground-state peroxynitrous acid. No involvement of metastable forms of HO-ONO was discernible.     

丁烯和丁烷自由基阳离子的分子结构和超精细结构的 理论研究

用密度函数理论B3LYP方法和6-31G(d,p),6-311G(d,p)及6-311+G(d,p)基组，分别对1-C4H^+~8,2-C4H^+~8和C4H^+~10进行了构型优化和频率分析计算，预言1-C4H^+~8具有非平面构型，与以往报道的从头算和密度函数理论计算结果不同。在各自由基阳离子的B3LYP构型上，进行了B3LYP、MP2及MRSDCI方法的超精细偶合常数计算，得到了比以往更好的结果，特别是MP2/B3LYP计算值是至今与实验值符合得最好的理论计算结果。     

类锗烯H2C=GeLiCl与RH(R=F,OH, NH2)的插入反应

采用DFT B3LYP和QCISD方法研究了不饱和类锗烯H2C=GeLiCl与RH(R=F, OH, NH2)的插入反应. 在B3LYP/6-311+G(d,p)水平上优化了反应势能面上的驻点构型. 结果表明, H2C=GeLiCl与HF、H2O 或NH3发生插入反应的机理相同. QCISD/6-311++G(d,p)//B3LYP/6-311+G(d,p)计算的三个反应的势垒分别为173.53、194.48和209.05 kJ·mol-1, 反应热分别为60.18、72.93和75.34 kJ·mol-1. 相同条件下发生插入反应时, 反应活性顺序都是H—F>H—OH>H—NH2.     

o-Quinone methide as alkylating agent of nitrogen, oxygen, and sulfur nucleophiles. The role of H-bonding and solvent effects on the reactivity through a DFT computational study

The reactivity of the alkylating agent o-quinone methide (o-QM) toward NH(3), H(2)O, and H(2)S, prototypes of nitrogen-, oxygen-, and sulfur-centered nucleophiles, has been studied by quantum chemical methods in the frame of DF theory (B3LYP) in reactions modeling its reactivity in water with biological nucleophiles. The computational analysis explores the reaction of NH(3), H(2)O, and H(2)S with o-QM, both free and H-bonded to a discrete water molecule, with the aim to rationalize the specific and general effect of the solvent on o-QM reactivity. Optimizations of stationary points were done at the B3LYP level using several basis sets [6-31G(d), 6-311+G(d,p), adding d and f functions to the S atom, 6-311+G(d,p),S(2df), and AUG-cc-pVTZ]. The activation energies calculated for the addition reactions were found to be reduced by the assistance of a water molecule, which makes easier the proton-transfer process in these alkylation reactions by at least 12.9, 10.5, and 6.0 kcal mol(-1) [at the B3LYP/AUG-cc-pVTZ//B3LYP/6-311+G(d,p) level], for ammonia, water, and hydrogen sulfide, respectively. A proper comparison of an uncatalyzed with a water-catalyzed reaction mechanism has been made on the basis of activation Gibbs free energies. In gas-phase alkylation of ammonia and water by o-QM, reactions assisted by an additional water molecule H-bonded to o-QM (water-catalyzed mechanism) are favored over their uncatalyzed counterparts by 5.6 and 4.0 kcal mol(-1) [at the B3LYP/6-311+G(d,p) level], respectively. In contrast, the hydrogen sulfide alkylation reaction in the gas phase shows a slight preference for a direct alkylation without water assistance, even though the free energy difference (DeltaDeltaG(#)) between the two reaction mechanisms is very small (by 1.0 kcal mol(-1) at the B3LYP/6-311+G(d,p),S(2df) level of theory). The bulk solvent effect, evaluated by the C-PCM model, significantly modifies the relative importance of the uncatalyzed and water-assisted alkylation mechanism by o-QM in comparison to the case in the gas phase. Unexpectedly, the uncatalyzed mechanism becomes highly favored over the catalyzed one in the alkylation reaction of ammonia (by 7.0 kcal mol(-1)) and hydrogen sulfide (by 4.0 kcal mol(-1)). In contrast, activation induced by water complexation still plays an important role in the o-QM hydration reaction in water as solvent.     

戊烯自由基阳离子的密度泛函理论研究

使用密度泛函理论B3LYP方法和6-31G(d,p)、6-31＋G(d,p)、6-311G(d,p)及6-311＋G(d,p)基组，分别对2-C5H10＋和1-C5H10＋的各种构象进行了几何构型优化，并用B3LYP/6-311G(d,p)进行了频率分析计算.计算预言1-C5H10＋具有非平面构型，与以往报导的从头算计算结论相反.在两个自由基阳离子的各种构象的B3LYP几何构型上，进行了B3LYP和UMP2(full)方法的超精细偶合常数计算，得到了比以往更好的结果.     

On the flexibility of beta-peptides

The full conformational space was explored for an achiral and two chiral beta-peptide models: namely For-beta-Ala-NH2, For-beta-Abu-NH2, and For-beta-Aib-NH2. Stability and conformational properties of all three model systems were computed at different levels of theory: RHF/3-21G, B3LYP/6-311++G(d,p)//RHF/3-21G, B3LYP/6-311++G(d,p), MP2//B3LYP/6-311++G(d,p), CCSD//B3LYP/6-311++G(d,p), and CCSD(T)//B3LYP/6-311++G(d,p). In addition, ab initio E = E(phi, micro, psi) potential energy hypersurfaces of all three models were determined, and their topologies were analyzed to determine the inherent flexibility properties of these beta-peptide models. Fewer points were found and assigned than expected on the basis of Multidimensional Conformational Analysis (MDCA). Furthermore, it has been demonstrated, that the four-dimensional surface, E = E(phi, mu, psi), can be reduced into a three-dimensional one: E = E[phi, f(phi), psi]. This reduction of dimensionality of freedom of motion suggests that beta-peptides are less flexible than one would have thought. This agrees with experimental data published on the conformational properties of peptides composed of beta-amino acid residues.     

Structural elucidation of nitro-substituted five-membered aromatic heterocycles utilizing GIAO DFT calculations

The GIAO (Gauge Including Atomic Orbitals) DFT (Density Functional Theory) method is applied at the B3LYP/6-31+G(d,p)//B3LYP/6-31+G(d), B3LYP/6-311++G(d,p)//B3LYP/6-31+G(d), B3LYP/6-311+G (2d,p)//B3LYP/6-31+G(d) and B3LYP/6-311++G(d,p)//B3LYP/6-311++G(d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants for 25 nitro-substituted five-membered heterocycles. Difference (1D NOE) spectra in combination with long-range gHMBC experiments were used as tools for the structural elucidation of nitro-substituted five-membered heterocycles. The assigned NMR data (chemical shifts and coupling constants) for all compounds were found to be in good agreement with theoretical calculations using the GIAO DFT method. The magnitudes of one-bond (1JCH) and long-range (nJCH, n>1) coupling constants were utilized for unambiguous differentiation between regioisomers of nitro-substituted five-membered heterocycles.