Theoretical Studies on the Aminolysis of Ester: Effects of the Catalysis and Substituent to the Reaction of Methyl Indole-3-acetate with Ammonia

A comprehensive exploration of the aminolysis mechanism for methyl indole-3-acetate with ammonia is carried out by employing the B3 LYP/6-311++G(d,p), M06-2 X/6-311++G(d,p) and MP2/6-311++G(d,p)//M06-2 X/6-311++G(d,p) levels. Two alterative reaction channels of the concerted and addition/elimination stepwise processes including the uncatalyzed, base-catalyzed reactions are taken into consideration. Subsequently, the substituent effects and solvent effects in methanol are also evaluated at the M06-2 X/6-311++G(d,p) level. The calculated results indicate that the calculated values of M06-2 X level are quite close to those of MP2, the stepwise pathway has more advantages to the concerted one for all of the reaction processes and the catalyst facilitates the proton migration and decreases the energy barriers as well. It is shown that the most preferred mechanism is the based-catalyzed stepwise process, the substituent of NH2 group slightly accelerates all the aminolysis reaction processes, and the solvent effect does not remarkably change the mechanism of the reaction.     

Ab initio molecular orbital and density functional studies on the solvolysis of sarin and O,S-dimethyl methylphosphonothiolate, a VX-like compound

[reaction: see text] Potential energy surfaces for the alkaline hydrolysis of sarin and O,S-dimethyl methylphosphonothiolate, a VX model compound, and the perhydrolysis of the latter have been computed at the MP2/6-31+G(d)//mPW1K/MIDI! level of theory. The effect of aqueous solvation was accounted for via the integral equation formalism polarizable continuum model (IEF-PCM) at the HF/6-31+G(d) level. Excellent agreement with the experimental enthalpy of activation for alkaline hydrolysis of sarin was found. For the alkaline hydrolysis of O,S-dimethyl methylphosphonothiolate, it was found that the P-O and P-S bond cleavage processes are kinetically competitive but that the products of P-S bond cleavage are thermodynamically favored. For the perhydrolysis of O,S-dimethyl methylphosphonothiolate, it was found that P-O bond cleavage is not kinetically competitive with P-S bond cleavage. In both cases, the data support initial formation of trigonal bipyramidal intermediates and demonstrate kinetic selectivity for nucleophilic attack on the face opposite the more apicophilic methoxide ligand.     

A quantum chemical study of the interactions of uracil as a constituent of ribonucleic acid (RNA) with thiazolidinedione and rhodanine bioactive molecules: an insight into energetic and structural features

In this study, the biologically active configurations composed of Thiazolidinedione–Uracil (TU) and Rhodanine–Uracil (RU) have been fully investigated from the energetic and structural points of view, employing B3LYP and M062X functionals in combination with the different basis sets. Dispersion corrections to the interaction energy using M062X–GD3 and double hybrid density functionals (B2PLYP–GD2, B2PLYP–GD3 and mPW2PLYP–GD2) are also taking into account. The basis set superposition error-corrected interaction energy for hydrogen bonded configurations ranges from ??5.27 to ??13.53 and ??5.25 to ??12.93 kcal/mol for TU and RU complexes respectively as calculated at M062X/6–311++G(df,pd) level. The charge transfer process within all of the TU and RU configurations were analyzed using Natural Bond Orbital (NBO) calculations. The nature of the interactions is analyzed with NBO and Atoms in Molecules (AIM) analysis at M062X/6–311++G(df,pd) and energy decomposition analysis at BP86–D3/TZ2P(ZORA)//M062X/6–311++G(df,pd) level of theory. The results confirm that the nature of the interactions is nearly electrostatic, with a contribution of about 51–56% of the total interaction energy. The orbital interactions (ΔE_orb) for the considered TU and RU complexes have a contribution of about 24–38% of the total interaction energy. Based on the AIM and NBO results, the interactions were defined as electrostatic H-bonds with partially covalent character. In addition, correlation between interaction energies and vibrational frequency changes was investigated.     

Weakly bound complexes of N2O: an ab initio theoretical analysis toward the design of N2O receptors

Ab initio calculations at MP2/6-311++G(2d,2p) and MP2/6-311++G(3df,3pd) computational levels have been used to analyze the interactions between nitrous oxide and a series of small and large molecules that act simultaneously as hydrogen bond donors and electron donors. The basis set superposition error (BSSE) and zero point energy (ZPE) corrected binding energies of small N2O complexes (H2O, NH3, HOOH, HOO*, HONH2, HCO2H, H2CO, HCONH2, H2CNH, HC(NH)NH2, SH2, H2CS, HCSOH, HCSNH2) vary between -0.93 and -2.90 kcal/mol at MP2/6-311++G(3df,3pd) level, and for eight large complexes of N2O they vary between -2.98 and -3.37 kcal/mol at the MP2/6-311++G(2d,2p) level. The most strongly bound among small N2O complexes (HCSNH2-N2O) contains a NH..N bond, along with S-->N interactions, and the most unstable (H2S-N2O) contains just S-->N interactions. The electron density properties have been analyzed within the atoms in molecules (AIM) methodology. Results of the present study open a window into the nature of the interactions between N2O with other molecular moieties and open the possibility to design N2O abiotic receptors.     

乙醇-水分子团簇C2H5OH(H2O)n (n=1-9)稳定结构的量子化学研究

采用密度泛函理论B3LYP方法, 在B3LYP/6-311++G(2d,2p)//B3LYP/6-311++G(d,p)基组水平上对乙醇-水分子团簇(C₂H₅OH(H₂O)_n (n=1-9))的各种性质进行研究, 如: 优化的几何构型、结构参数、氢键、结合能、平均氢键强度、自然键轨道(NBO)电荷分布、团簇的生长规律等. 结果表明, 从二维(2-D)环状结构到三维(3-D)笼状结构的过渡出现在n=5的乙醇-水分子团簇中. 此外, 利用团簇结合能的二阶差分、形成能、能隙等性质, 发现在n=6时乙醇-水分子团簇的最低能量结构稳定性较好, 可能为幻数结构. 最后, 为了进一步探讨氢键本质, 将C₂H₅OH(H₂O)_n (n=2-9)最低能量结构的各种性质与纯水分子团簇(H₂O)_n (n=3-10)比较, 结果表明前者与后者中的水分子之间氢键相似.     

HArF和HNO二聚体相互作用氢键的理论研究

The hydrogen bonding interaction of 1:1 dimer formed between HNO and HArF molecule has been completely investigated in the present study using Second-order M?ller-Plesset Perturbation (MP2) method in conjunction with 6-311+G**, 6-311++G** and 6-311++G(2d,2p) basis sets. The standard and CP-corrected calculations have been employed to determine the equilibrium structures, the vibrational frequencies and interaction energies. The interaction energies of the dimers were also calculated at G2MP2 level. Two stable structures are found as the minima. Dimer I(H···F)is a five-membered cyclic hydrogen bonded structure and is more stable than the Dimer II(H···O). The blue-shifted N-H···F hydrogen bond is confirmed with standard and CP-corrected calculations by the MP2 and DFT methods in conjunction with different basis sets. The results obtained at MP2 in conjunction with different basis sets show there is a red-shifted hydrogen bond (Ar-H···O) in the Dimer II(H···O). The topological and electronic properties, the origin of red- and blue-shifted hydrogen bonds were investigated at MP2/6-311++G(2d,2p) with CP corrected calculations. From the NBO analysis, the reasonable explanations for the red- and blue-shifted hydrogen bonds were proposed.     

气相中O3与HSO自由基间的氢键复合物

气相中O3与HSO自由基之间的相互作用及其反应在大气化学中非常重要. 在DFT-B3LYP/6-311++G**和MP2/6-311++G**水平上求得O3+HSO复合物势能面上的稳定构型, B3LYP方法得到了三种构型(复合物I, II和III), 而MP2方法只能得到一种构型(复合物II). 在复合物I和III中, HSO单元中的1H原子作为质子供体, 与O3分子中的端基O原子作为质子受体相互作用, 形成红移氢键复合物; 而在复合物II中, 虽与复合物I和III中具有相同的质子供体和质子受体, 却形成了蓝移氢键复合物. B3LYP/6-311++G**水平上计算的单体间相互作用能的计算考虑了基组重叠误差(BSSE)和零点振动能(ZPVE)校正, 其值在-3.37到-4.55 kJ·mol-1之间. 采用自然键轨道理论(NBO)对单体间相互作用的本质进行了考查, 并通过分子中原子理论(AIM)分析了三种复合物中氢键的电子密度拓扑性质.     

Theoretical Study of Tautomerization in 1,5-Dimethyl-6-Thioxo-1,3,5-Triazinane-2,4-Dione

In this work, the tautomeric transformations of a 1,5-dimethyl-6-thioxo-1,3,5-triazinane-2,4-dione molecule are explored at the M062X/6-311G(d,p) level of theory in gas and solution phases. These calculations show that the 1,5-dimethyl-6-thioxo-1,3,5-triazinane-2,4-dione isomer is more stable than its tautomer (4-hydroxy-1,5-dimethyl-6-thioxo-5,6-dihydro-1,3,5-triazin-2(1H)-one) in gas and solution phases. The frontier molecular orbitals and band gap energy calculations are performed at the M062X/6-311G(d,p) level in gas and various solvents. Solvent effects are analyzed using the self-consistent reaction field method based on the polarizable continuum model in chloroform, chlorobenzene, tetrahydrofurane, dichloromethane, and quinoline. The solvent effect on the N–H and C=O vibrations is explored. Also, natural bond orbital (NBO) analysis was used to understand the structure and bonding of the molecule.     

气相中O3与HSO自由基间的氢键复合物

气相中O3与HSO自由基之间的相互作用及其反应在大气化学中非常重要.在DFT-B3LYP/6-311++G**和MP2/6-311++G**水平上求得O3+HSO复合物势能面上的稳定构型,B3LYP方法得到了三种构型(复合物Ⅰ,Ⅱ和Ⅲ),而MP2方法只能得到一种构犁(复合物Ⅱ).在复合物Ⅰ和Ⅲ中,HSO单元中的1H原子作为质子供体.与O3分子中的端基O原子作为质子受体相互作用,形成红移氢键复合物;而在复合物Ⅱ中,虽与复合物Ⅰ和Ⅲ中具有相间的质子供体和质子受体,却形成了蓝移氢键复合物.B3LYP/6-311++G**水平上计算的单体间相互作用能的计算考虑了基组重甍误差(BSSE)和零点振动能(ZPVE)校正,其值在-3.37到-4.55 kJ·mol-1之间.采用自然键轨道理论(NBO)对单体间相互作用的本质进行了考查,并通过分子中原子理论(AIM)分析了三种复合物中氢键的电子密度拓扑性质.     

Theoretical analysis of concerted and stepwise mechanisms of Diels-Alder reactions of butadiene with silaethylene and disilene

The concerted and the stepwise mechanisms of the Diels-Alder reactions of butadiene with silaethylene and disilene were studied by ab initio MO methods. For the reaction of butadiene and silaethylene, an asymmetric concerted process that is almost stepwise and two stepwise processes were located. For the first step of the stepwise process, the C-Si bond formation is more favorable than the C-C bond formation. The activation energy barrier of the concerted transition state is only 0.89 kcal/mol lower than that of the first-step transition state of the C-Si bond formation for the stepwise process by the CASPT2 calculation level. For the reaction of butadiene and disilene, the activation energy barrier of the concerted-type transition state constrained with Cs symmetry is about 9 kcal/mol higher than that of the stepwise transition state by the CASSCF method. The energy barrier of the first step of the stepwise reaction disappears at the CASPT2/6-311++G(d,p) calculation level including the nondynamical correlation energy, although the reaction of the butadiene with disilene occurs through the stepwise-like process.     

HOCl…HCOCl复合物的结构和电子性质

在DFT-B3LYP/6-311++G**水平上求得HOCl+HCOCl复合物势能面上的四种稳定构型(S1, S2, S3和S4). 其中, 在复合物S1和S3中, HOCl单体的5H原子作为质子供体, 与HCOCl单体中作为质子受体的1O原子相互作用, 形成红移氢键复合物; 在复合物S4中, HOCl单体的7Cl原子作为质子供体, 与HCOCl单体中作为质子受体的1O原子相互作用, 形成红移卤键复合物; 而在复合物S2中, 同时存在2C—3H…6O蓝移氢键和4Cl…5O相互作用. 在MP2/6-311++G**水平上计算的单体间的相互作用能考虑了基组重叠误差(BSSE)和零点振动能(ZPVE)校正, 其值在-5.05与-14.76 kJ·mol-1之间. 采用自然键轨道理论(NBO)对两种单体间相互作用的本质进行了考查, 并通过分子中原子理论(AIM)分析了复合物中氢键和卤键键鞍点处的电子密度拓扑性质.     

Mechanisms of the reactions of W AND W+ with H2O: computational studies

The mechanism of the reactions of W and W(+) with the water molecule have been studied for several lower-lying electronic states of tungsten centers at the CCSD(T)/6-311G(d,p)+SDD and B3LYP/6-31G(d,p)+SDD levels of theory. It is shown that these reactions are essentially multistate processes, during which lower-lying electronic states of the systems cross several times. They start with the formation of initial prereaction M(H(2)O) complexes with M-H(2)O bonding energies of 9.6 and 48.2 kcal/mol for M = W and W(+), followed by insertion of the metal center into an O-H bond with 20.0 and 53.3 kcal/mol barriers for neutral and cationic systems, respectively. The overall process of M + H(2)O --> t-HM(OH) is calculated to be highly exothermic, 48.4 and 48.8 kcal/mol for M = W and W(+). From the HM(OH) intermediate the reaction may proceed via several different channels, among which the stepwise HM(OH) --> HMO + H --> (H)(2)MO and concerted HM(OH) --> (H)(2)MO pathways are more favorable and can compete (energetically) with each other. For the neutral system (M = W), the concerted process is the most favorable, whereas for the charged system (M = W(+)), the stepwise pathway is slightly more favorable. From the energetically most favorable intermediate (H)(2)MO the reactions proceed via H(2)-molecule formation with a 53.1 kcal/mol activation barrier for the neutral system. For the cationic system, H-H formation and dissociation is an almost barrierless process. The overall reaction of W and W(+) with the water molecule leading to H(2) + MO formation is found to be exothermic by 48.2 and 39.8 kcal/mol, respectively. In the gas phase with the collision-less conditions the reactions W((7)S) + H(2)O --> H(2) + WO((3)Sigma(+)), and W(+)((6)D) + H(2)O --> H(2) + WO(+)((4)Sigma(+)) are expected to proceed via a 10.4 and 5.1 kcal/mol overall energy barrier corresponding to the first O-H dissociation at the TS1. On the basis of these PESs, we predict kinetic rate constants for the reactions of W and W(+) with H(2)O.     

Structures and Electronic Properties of HOCl···HCOCl Complexes

B3LYP/6-311++G** and MP2/6-311++G** calculations were used to analyze the interaction between hypochlorous acid (HOCl) and formyl chloride (HCOCl). The results showed that there were four equilibrium geometries (S1, S2, S3, and S4) optimized at B3LYP/6-311++G** level, and all the equilibrium geometries were confirmed to be in stable states by analytical frequency calculations. Complexes S1 and S3 use the 5H atom of HOCl as proton donor and the terminal 1O atom of HCOCl as acceptor to form red shift hydrogen bond systems. However, the blue-shifted hydrogen bond (2C-3H···6O) coexists with 4Cl···5O interaction in structures S2. As for S4, it uses the 7Cl atom of HOCl as proton donor and the terminal 1O atom of HCOCl as acceptor to form red shift halogen bond system. Interaction energies between monomers in the four complexes corrected with basis set superposition error (BSSE) and zero-point vibrational energy (ZPVE) lie in the range from −5.05 to −14.76 kJ·mol⁻¹ at MP2/6-311++G** level. The natural bond orbital (NBO) and atoms in molecules (AIM) theories have also been applied to explain the structures and the properties of the complexes.     

DFT computational studies on rotation barriers,tautomerism, intramolecular hydrogen bond,and solvent effects in 8‐hydroxyquinoline

Intramolecular hydrogen binding interactions in 8‐hydroxyquinoline, both in its zwitterionic tautomer and in the rotamer without the intramolecular hydrogen bond (IHB), have been computed using the B3LYP and MPW1K density functionals. The rotation of the O? H bond and intramolecular proton transfer reactions were studied theoretically. The following theory levels have been applied: B3LYP/6‐31G(d,p), B3LYP/6‐311++G(d,p), MPW1K/6‐311++G(d,p), and MPW1K/6‐311++G(2d,3p)//MPW1K/6‐311++G(d,p). Natural bond orbital (NBO) analysis has also been carried out. The effect of medium (benzene, chloroform, tetrahydrofuran, 1,2‐dichloroethane, acetone, water) was simulated using the self‐consistent reaction field (SCRF) method within the framework of the polarizable continuum model (PCM), at the MPW1K/6‐311++G(d,p) level. The evolution of geometry, relative energies, heights of rotation (around the O? H bond) and tautomerization barriers, IHB energies, and ΔG(solv) have been systematically investigated. The results obtained have shown the failure to neglect some changes of the above characteristics in polar media with respect to the gaseous phase. The series of stability of the forms under study in the gaseous phase remains the same in solution. Thus, in spite of the important role of the solvent electrostatic effects, the intrinsic stability of those species overcomes the solvent effects. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Role of base assisted proton transfer in N-heterocyclic carbene-catalyzed intermolecular Stetter reaction

The mechanism of the NHC-catalyzed intermolecular Stetter reaction between benzaldehyde and cyclopropene has been investigated using the PCM-M062X/6-311++G(3df,2p)//M062X/6-31+G(d,p) level of DFT. Compared to the direct reaction, a substantial reduction in the activation free energy by 10.6–14.4 kcal/mol is observed when the reaction is performed in the presence of water, 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD), and 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU). The bases promote the proton transfer step of the reaction to yield the Breslow intermediate. An early concerted transition state has been located for the stereocontrolling C–C bond formation step (ΔG^# = 26.6 kcal/mol) which is used to explain the diastereomeric ratio observed in the experiment.     

3-硝基-1,2,4-三唑-5-酮与NH3及H2O分子间相互作用的理论研究

在DFT—B3LYP／6—311 G^**水平上,求得3-硝基-1,2,4-三唑-5-酮(NTO)／NH3和NTO／H2O两种超分子体系势能面上5种全优化构型．经基组叠加误差(BSSE)和零点能(ZPE)校正,求得NTO与NH3和H2O的分子间最大相互作用能依次为-37．58和-30．14kJ／mol,表明NTO与NH3的分子问相互作用强于与H2O的作用．超分子体系中电子均由NH3或H2O向NTO转移,相互作用能主要由强氢键所贡献,由自然键轨道分析揭示了相瓦作用的本质．对优化构型进行振动分析,并基于统计热力学求得200．0～800．0K温度范围从单体形成超分子的热力学性质变化．发现由NTO和NH3形成超分子Ⅱ和Ⅲ在常温下可自发进行;而NTO和H2O只在低温下才能自发形成Ⅳ,Ⅴ和Ⅵ超分子．     

HOCl…HCOCl复合物的结构和电子性质

在DFT-B3LYP/6-311++G**水平上求得HOCl+HCOCl复合物势能面上的四种稳定构型(S1,S2,S3和S4).其中,在复合物S1和S3中,HOCl单体的5H原子作为质子供体,与HCOCl单体中作为质子受体的10原子相互作用,形成红移氢键复合物;在复合物S4中,HOCl单体的7Cl原子作为质子供体,与HCOCl单体中作为质子受体的IO原子相互作用,形成红移卤键复合物;而在复合物S2中,同时存在2C-3H…6O蓝移氢键和4Cl…5O相互作用.在MP2/6-311++G**水平上计算的单体间的相互作用能考虑了基组重叠误差(BSSE)和零点振动能(ZPVE)校正,其值在-5.05与-14.76 kJ·mol-1之间.采用自然键轨道理论(NBO)对两种单体间相互作用的本质进行了考查,并通过分子中原子理论(AIM)分析了复合物中氢键和卤键键鞍点处的电子密度拓扑性质.     

Computational study of the aminolysis of 2-benzoxazolinone

Three possible mechanisms (zwitterionic, neutral stepwise, and neutral concerted) of the ring-opening reaction of 2-benzoxazolinone (BO) upon aminolysis with methylamine were studied at the B3LYP/6-31G* level. In the gas phase, the neutral concerted mechanism is shown to be most favorable, which proceeds via a rate-determining barrier of 28-29 kcal/mol. The transition state, CTS, associated with this barrier is a four-centered one, where 1,2-addition of the N[bond]H of methylamine to the C[bond]O of BO ring occurs. The rate-determining barrier of the neutral stepwise pathway is found to be ca. 42 kcal/mol. The inclusion of solvent effects by a polarizable continuum model (PCM) does not change the conclusions based on the gas-phase study; the barrier at CTS is reduced to 20, 20, and 22 kcal/mol in water, ethanol, and acetonitrile, respectively.     

Computational study of the aminolysis of anhydrides: effect of the catalysis to the reaction of succinic anhydride with methylamine in gas phase and nonpolar solution

Different possible pathways of the aminolysis reaction of succinic anhydride were investigated by applying high level electronic structure theory, examining the general base catalysis by amine and the general acid catalysis by acetic acid, and studying the effect of solvent. The density functional theory at the B3LYP/6-31G(d) and B3LYP/6-311++G(d,p) levels was employed to investigate the reaction pathways for the aminolysis reaction between succinic anhydride and methylamine. The single point ab initio calculations were based on the second-order M?ller-Plesset perturbation theory (MP2) with 6-31G(d) and 6-311++G(d,p) basis sets and CCSD(T)/6-31G(d) level calculations for geometries optimized at the B3LYP/6-311++G(d,p) level of theory. A detailed analysis of the atomic movements during the process of concerted aminolysis was further obtained by intrinsic reaction coordinate calculations. Solvent effects were assessed by the polarized continuum model method. The results show that the concerted mechanism of noncatalyzed aminolysis has distinctly lower activation energy compared with the addition/elimination stepwise mechanism. In the case of the process catalyzed by a second methylamine molecule, asynchronous proton transfer takes place, while the transition vectors of the acid-catalyzed transition states correspond to the simultaneous motion of protons. The most favorable pathway of the reaction was found through the bifunctional acid catalyzed stepwise mechanism that involves formation of eight-membered rings in the transition state structures. The difference between the activation barriers for the two mechanisms averages 2 kcal/mol at various levels of theory.     

N2O…HOCl复合物结构和性质的理论研究

分别在DFT-B3LYP和MP2/6-311++G**水平上求得HOCl + N2O复合物势能面上的六种(S1, S2, S3, S4, S5和S6)和四种(S1, S2, S4和S5)构型. 频率分析表明,其中的S1和S3为过渡态,其它为稳定构型. 在复合物S3, S5 和S6中,HOCl 单体的σ*(5O-6H)作为质子供体,与N2O单体中作为质子受体的3O原子相互作用,形成氢键结构,而在氢键复合物S2中, 质子受体为N2O单体中的端1N原子;复合物S1中,HOCl分子的σ*(5O-4Cl)作为质子供体与N2O分子中的端1N原子(质子受体)相互作用,形成卤键结构,而复合物S4中的卤键结构的质子受体为N2O分子中的端3O原子. 经B3LYP/6-311++G**水平上的计算,考虑了基组重叠误差(BSSE)校正的单体间相互作用能在-1.56 ~ -8.73 kJ·mol-1之间. 采用自然键轨道理论(NBO)对两种单体间相互作用的本质进行了考查,并通过分子中原子理论(AIM)分析了复合物中氢键和卤键键鞍点处的电子密度拓扑性质.