O（~1D）与CF_2HCl反应的理论研究

用量子化学密度泛函理论（DFT）和G3B3方法，对为（~1D）与CF_2HCl的反应 进行了研究，在B3LYP/6-311+G(d)，B3LYP/6-311+G(2df,2pd)和G3B3计算水平上， 优化了反应热能面上各驻点的几何结构，通过内禀反应坐标（IRC）计算和振动分 析，对反应过渡态进行了确认，并确定了反应机理。     

O+HCNO反应势能面的理论研究

采用CCSD(T)/6-311G(d,p)//B3LYP/6-311G(d,p)+ZPVE方法对反应O＋HCNO进行了研究. 通过反应势能面揭示了该反应的机理, 通过H或O迁移等多步反应路径得到3种产物, 其中, P1(HCO+NO)为主要产物, P2(HNO+CO)和P3(NCO+OH)为次要产物. 为进一步实验研究提供了参考.     

锗烯X2Ge与环硫乙烷硫转移反应的密度泛函研究

利用量子化学密度泛函理论(DFT)的B3LYP方法, 在6-311++G(d, p)的水平上对锗烯X2Ge(X=H、CH3、F、Cl、Br、OH、OCH3)与SC2H4的硫转移反应进行了计算研究. 结果表明, 锗烯的基态是单重态, 取代基的电负性越强, 单-三态的能量差越大; 反应的活化能越高, 放热越少; 控制反应的因素是电子效应, 而不是立体效应; 该硫转移反应由两步组成, 第一步生成中间配合物, 是一个无势垒的放热过程, 第二步经过渡态生成产物. 并用组态混合模型对反应机理和势垒进行了解释. 同时讨论了该反应中环硫乙烷的C—S键解离过程.     

A computational study of the reactions of thiiranes with ammonia and amines

The relative rates of reaction of thiirane and thiirane derivatives with NH3, a series of secondary amines including aziridine, and trimethylamine were determined in the gas phase by means of B3LYP/6-31+G(d)//HF/6-31+G(d) computations and transition state theory. Convergence of the results was selectively tested using the 6-311++G(d,p) basis set. Comparison with MP2/6-31 + G(d)//MP2/6-31G(d) computations was made in model cases. These results are significant in that they supplement the only reported gas-phase experimental study of this type of reaction. The reaction rates of thiirane with secondary amines can best be rationalized by means of an interplay of steric and polarizability effects. While beta-halo substituents retard S(N)2 reactions in solution, both 2-fluorothiirane and its acyclic model react more than l0(6) times faster with NH3 than the unsubstituted compounds in the gas phase. 2-Fluorothiirane was calculated to react with NH3 at C2 by a factor of 0.142 with respect to thiirane itself; attack at C3 was found to be 3.42 x 10(6) times faster than the parent compound. 2-Methylthirane reacts with NH3 at 0. 230 the rate of thiirane with a 12.8-fold regioselectivity for C3. In the reaction of 2,2-dimethylthirane and NH3, this preference for C3 increases to a factor of 124. Ground-state destabilization of cis-2,3-dimethylthiirane is sufficient to account for its calculated rate acceleration with respect to the trans isomer.     

DFT investigation of the mechanism of CH2CO + O(3P) reaction

A detailed theoretical survey of the potential energy surface (PES) for the CH₂CO + O(³P) reaction is carried out at the QCISD(T)/6‐311+G(3df,2p)//B3LYP/6‐311+G(d,p) level. The geometries, vibrational frequencies, and energies of all stationary points involved in the reaction are calculated at the B3LYP/6‐311+G(d,p) level. More accurate energy information is provided by single‐point calculations at the QCISD(T)/6‐311+G(3df,2p) level. Relationships of the reactants, transition states, intermediates, and products are confirmed by the intrinsic reaction coordinate (IRC) calculations. The results suggest that P1(CH₂+CO₂) is the most important product. This study presents highlights of the mechanism of the title reaction. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

QM/MM Studies of the Matrix Metalloproteinase 2 (MMP2) Inhibition Mechanism of (S)-SB-3CT and its Oxirane Analogue

SB-3CT, (4-phenoxyphenylsulfonyl)methylthiirane, is a potent, mechanism-based inhibitor of the gelatinase sub-class of the matrix metalloproteinase (MMP) family of zinc proteases. The gelatinase MMPs are unusual in that there are several examples where both enantiomers of a racemic inhibitor have comparable inhibitory abilities. SB-3CT is one such example. Here, the inhibition mechanism of the MMP2 gelatinase by the (S)-SB-3CT enantiomer and its oxirane analogue is examined computationally, and compared to the mechanism of (R)-SB-3CT. Inhibition of MMP2 by (R)-SB-3CT was shown previously to involve enzyme-catalyzed C-H deprotonation adjacent to the sulfone, with concomitant opening by β-elimination of the sulfur of the three-membered thiirane ring. Similarly to the R enantiomer, (S)-SB-3CT was docked into the active site of MMP2, followed by molecular dynamics simulation to prepare the complex for combined quantum mechanics and molecular mechanics (QM/MM) calculations. QM/MM calculations with B3LYP/6-311+G(d,p) for the QM part (46 atoms) and the AMBER force field for the MM part were used to compare the reaction of (S)-SB-3CT and its oxirane analogue in the active site of MMP2 (9208 atoms). These calculations show that the barrier for the proton abstraction coupled ring opening reaction of (S)-SB-3CT in the MMP2 active site is 4.4 kcal/mol lower than its oxirane analogue, and the ring opening reaction energy of (S)-SB-3CT is only 1.6 kcal/mol less exothermic than its oxirane analogue. Calculations also show that the protonation of the ring-opened products by water is thermodynamically much more favorable for the alkoxide obtained from the oxirane, than for the thiolate obtained from the thiirane. In contrast to (R)-SB-3CT and the R-oxirane analogue, the double bonds of the ring-opened products of (S)-SB-3CT and its S-oxirane analogue have the cis-configuration. Vibrational frequency and intrinsic reaction path calculations on a reduced size QM/MM model (2747 atoms) provide additional insight into the mechanism. These calculations yield 5.9 and 6.7 for the deuterium kinetic isotope effect for C-H bond cleavage in the transition state for the R and S enantiomers of SB-3CT, in good agreement with the experimental results.     

多通道反应O(3P)＋CH2F的理论研究

用密度泛函理论研究了氧原子与氟代甲基自由基的反应.反应中出现的所有物种的平衡构型用B3LYP方法在6-311＋＋G（2d, 2p）基组水平上进行了优化，同时对各物种进行了频率分析；在同一理论水平上计算了各反应通道的势能面变化，分析了反应物、中间体、过渡态、产物的振动模式随反应途径的变化关系，阐明了该多通道反应的反应机理.     

NO+HCCCO反应势能面的理论研究

在CCSD(T)/6-311G(d,p)//B3LYP/6-311G(d,p)+ZPVE水平下, 对反应NO＋HCCCO进行了研究. 建立了反应势能面, 揭示了该反应的反应机理, 通过O迁移、C—C键或N—O键断裂等多步反应, 得到4种产物, 其中, 最主要产物为P1(HCCO+NCO).     

CH2＝CHCl与O(3P)反应的理论研究

用量子化学密度泛函理论和QCISD (Quadratic configuration interaction calculation)方法, 对O(³P)与CH₂CHCl的反应进行了理论研究. 在UB3LYP/6-311＋＋G(d,p), UB3LYP/6-31＋＋G(3df, 3pd)计算水平上, 优化了反应物、产物、中间体和过渡态的几何构型, 并在UQCISD(T)/6-311＋＋G(2df,2pd)水平上计算了单点能量. 为了确证过渡态的真实性, 在UB3LYP/6-311＋＋G(3df,3pd)水平上进行了内禀坐标(IRC)计算和频率分析, 并确定了反应机理. 研究结果表明, 反应主要产物为CH₂CHO和Cl.     

CH_3SO+HO_2气相反应机理与主通道速率常数

在MPW1PW91/6-311G(d,p)水平上优化了标题反应各驻点物种的几何构型,并在相同水平上通过频率计算和内禀反应坐标(IRC)分析对过渡态结构及连接性进行了验证.采用QCISD(T)/6-311G(d,p)方法对所有驻点及反应路径的部分选择点进行单点能校正,分别构建了CH3SO+HO2反应体系的单、三重态反应势能剖面.研究结果表明,CH3SO+HO2反应体系存在6条反应通道7条路径,优势通道(1)R→3IM→P1(CH3SOH+3O2)发生在三重态势能面上,此通道包含两条路径,其表观活化能分别为12.01和-30.04kJ?mol-1,主路径(2)R→3IM→3TS2→P1(CH3SOH+3O2)是一个无势垒氢迁移过程.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),分别计算了主路径(2)在200～2500K温度范围内的速率常数kTST,kCVT和kCVT/SCT,在此温度区间内的表观反应速率常数三参数表达式为kCVT/SCT=4.08×10-24T3.13exp(8012.2/T)cm3imolecule-1is-1,具有负温度系数效应.速率常数计算结果显示,变分效应在计算温度段内影响较小,而量子力学隧道效应在低温段有显著影响.     

亚甲基自由基(3CH2)与So反应机理的理论研究

应用量子化学从头算和密度泛函理论(DFT),对3CH2自由基与SO分子反应的单、三重态势能面进行了研究.在UB3LYP/6-311G(d,p)水平上优化了反应通道上各驻点(反应物、中间体、过渡态和产物)的几何构型.在CCSD(T)/6-311G(d,p)水平上计算了各物种的单点能,并对总能量进行了零点能校正.研究结果表明:主要的反应通道都在单重态势能面中,反应物中自由基3CH2的C原子进攻SO分子中的O原子是主要的进攻方式,反应主产物是P1(HS HCO).反应热为-349.06kJ?mol-1.     

Quantum mechanical study of the potential energy surface of the ClO + NO2 reaction

In the study of the reaction pathways of the ClO + NO2 reaction including reliable structures of the reactants, products, intermediates, and transition states as well as energies the MP2/6-311G(d), B3LYP/6-311G(d), and G2(MP2) methods have been employed. Chlorine nitrate, ClONO2, is formed by N-O association without an entrance barrier and is stabilized by 29.8 kcal mol(-1). It can undergo either a direct 1,3 migration of Cl or OCl rotation to yield an indistinguishable isomer. The corresponding barriers are 45.8 and 7.1 kcal mol(-1), respectively. ClONO2 can further decompose into NO3 + Cl with an endothermicity of 46.4 kcal mol(-1). The overall endothermicity of the NO2 + ClO --> NO3 + Cl reaction is calculated to be 16.6 kcal mol(-1). The formation of cis-perp and trans-perp conformer of chlorine preoxynitrite, ClOONO(cp) and ClOONO(tp), are exothermic by 5.4 and 3.8 kcal mol(-1), respectively. Calculations on the possible reaction pathways for the isomerization of ClOONO to ClONO2 showed that the activation barriers are too high to account for appreciable nitrate formation from peroxynitrite isomerization. All quoted relative energies are related to G2(MP2) calculations.     

D-苯丙氨酸与Cu＋(1S0, 3d10)气相反应理论研究

用量子化学密度泛函(DFT)方法研究D-苯丙氨酸与一价基态金属阳离子Cu^＋在气相中反应的机理. 在B3LYP/6-31G*水平上, 优化了反应包含的4个反应通道的反应物、中间体、过渡态和产物的几何构型, 并采用B3LYP/DZVP, B3LYP/[6-311＋G**(C,H,O)＋Lanl2dz(Cu)], B3LYP/6-311＋G**, MP2/6-311＋G** 等方法对各驻点进行了单点能计算. 通过对计算结果的分析, 获得了其单重态反应势能面的一般轮廓、各驻点几何构型优化参数, 明确了其反应机理.     

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.     

BH2+与H2O反应机理的量子拓扑研究

采用密度泛函方法B3LYP/6-311+G(d, p)和耦合簇方法CCSD/6-311+G(d, p)研究了BH2+与H2O的气相离子-分子反应机理. 优化得到了反应途径中各驻点的几何构型, 并采用内禀反应坐标法进行追踪. 从量子拓扑学的角度, 讨论了在反应过程中各化学键的变化. 反应(I)经历了一个四元环过渡态, 找到了这个反应的能量过渡态和两个结构过渡态.     

HOSO+NO反应的机理及动力学

在B3LYP/6-311++G(d,p)水平上研究了HOSO+NO的反应机理. 优化得到了反应势能面上各驻点的几何构型, 通过内禀反应坐标(IRC)确认了反应物、中间体、过渡态和产物的相关性. 在CCSD(T)/6-311++G(d,p)水平上对计算得到的构型进行了能量校正. 应用经典过渡态理论(TST)与变分过渡态理论(CVT), 并结合小曲率隧道(SCT)效应模型校正的方法计算了标题反应在200-3000 K温度范围内的速率常数k^TST、k^CVT和k^CVT/SCT. 计算结果表明: HOSO+NO反应在单重态和三重态条件下均可发生, 其中单重态反应为主反应通道, HNO+SO₂为主产物. 并利用电子密度拓扑分析方法研究主反应通道反应过程中的化学键变化.     

Theoretical Study on the Mechanism of CF2 Reaction with CH2O

The insertion reaction mechanism of CF2 with CH2O was investigated at the B3LYP/6-311G（d）//MP2/6-311G（d） level. The geometric conformations at each stationary point in reaction potential surface were fully optimized and the transition states were verified by intrinsic reaction coordinate （IRC） and frequency analysis. The energies of all reactants were calculated with CCSD（T）/6-311G（d）//G2MP2 methods. Results indicated that the P1 reaction route with difuoroaldehyde as product is the dominant reaction pathway, which exhibits nucleophilic character. According to NBO analysis, the starting point of insertion reaction is the interaction between carbene LP（C3） and formaldehyde π（Cl-O2）. Besides, the thermodynamic and dynamic properties of dominated reaction （1） at different temperature were studied with statistic thermodynamic method and Eyring transition state theory adjusted by Wigner means, from which the proper temperature （500- 1200 K） of reaction （1） could be estimated. Finally, the thermo- dynamic and dynamic properties of insertion reaction mechanisms （CF2, CX2 （X = Cl, Br） with CH2O） were compared and discussed.     

氮原子与卤代甲烷反应的直接氢抽提过程研究

利用B3LYP理论研究了N(~4S)+CH_3X(X = H, F, Cl)反应体系的直接氢抽提过 程，分别得到了各反应物、产物和过渡态的优化构型和谐振频率。同时应用了6- 31G(d), 6-311+G(d,p)和6-311+ + G(2d,2p)基组，考察其大小对反应体系中各物 种构型及能量的影响。理论计算表明，随着基组的增加，反应势垒逐渐降低，反应 吸热减少。对比取代甲烷的情形，结果表明反应过程中卤素原子具有典型的诱导效 应，降低了抽提势垒。     

H2CCF自由基与HNCO反应机理的理论研究

采用密度泛函理论的B3LYP方法, 在6-311＋＋G(d,p)基组水平上研究了H₂CCF自由基与HNCO的微观反应机理, 优化了反应过程中的反应物、中间体、过渡态和产物, 为了获得更精确的能量信息, 还在QCISD(T)/6-311＋＋G(d,p)基组水平上计算了各物质的能量．振动分析结果和IRC分析结果证实了中间体和过渡态的真实性, 计算所得的成键临界点电荷密度的变化也确认了反应过程．对于H₂CCF自由基与HNCO反应, 我们找到了六条可行的反应通道, 结果分析表明通道H₂CCF＋HNCO→IM3→TS5→H₂CCFH＋NCO控制步骤活化能最低, 是该反应的主要通道, 在此反应过程中有稳定的氢键复合物IM3生成, 还表现出氢原子迁移的反应特征．     

Theoretical study of mechanism of extraction reaction between germylene carbene and its derivatives and thiirane

The mechanism of the sulfur extraction reaction between singlet germylene carbene and its derivatives [X₂Ge?C: (X = H, F, Cl, CH₃)] and thiirane has been investigated with density functional theory, including geometry optimization and vibrational analyses for the involved stationary points on the potential energy surface. The energies of the different conformations are calculated by B3LYP/6‐311G(d,p) method. From the potential energy profile, it can be predicted that the reaction pathway of this kind consists two steps: (1) the two reactants firstly form an intermediate (INT) through a barrier‐free exothermic reaction; (2) the INT then isomerizes to a product via a transition state (TS). This kind reaction has similar mechanism, when the germylene carbene and its derivatives [X₂Ge?C: (X = H, F, Cl, CH₃)] and thiirane get close to each other, the shift of 3p lone electron pair of S in thiirane to the 2p unoccupied orbital of C in X₂Ge = C: gives a p → p donor–acceptor bond, leading to the formation of INT. As the p → p donor–acceptor bond continues to strengthen (that is the C? S bond continues to shorten), the INT generates product (P + C₂H₄) via TS. It is the substituent electronegativity that mainly affects the extraction reactions. When the substituent electronegativity is greater, the energy barrier is lower, and the reaction rate is greater. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011