Computational study of the aminolysis of esters. The reaction of methylformate with ammonia

The aminolysis of esters is a basic organic reaction considered as a model for the interaction of carbonyl group with nucleophiles. In the present computational study the different possible mechanistic pathways of the reaction are reinvestigated by applying higher level electronic structure theory, examining the general base catalysis by the nucleophile, and a more comprehensive study the solvent effect. Both the ab initio QCISD/6-31(d,p) method and density functional theory at the B3LYP/6-31G(d) level were employed to calculate the reaction pathways for the simplest model aminolysis reaction between methylformate and ammonia. Solvent effects were assessed by the PCM method. The results show that in the case of noncatalyzed aminolysis the addition/elimination stepwise mechanism involving two transition states and the concerted mechanism have very similar activation energies. However, in the case of catalyzed aminolysis by a second ammonia molecule the stepwise mechanism has a distinctly lower activation energy. All transition states in the catalyzed aminolysis are 10-17 kcal/mol lower than those for the uncatalyzed process.     

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.     

Computational study on the aminolysis of beta-hydroxy-alpha,beta-unsaturated ester via the favorable path including the formation of alpha-oxo ketene intermediate

The possible mechanisms of the aminolysis of N-methyl-3-(methoxycarbonyl)-4-hydroxy-2-pyridone (beta-hydroxy-alpha,beta-unsaturated ester) with dimethylamine are investigated at the hybrid density functional theory B3LYP/6-31G(d,p) level in the gas phase. Single-point computations at the B3LYP/6-311++G(d,p) and the Becke88-Becke95 1-parameter model BB1K/6-311++G(d,p) levels are performed for more precise energy predictions. Solvent effects are also assessed by single-point calculations at the integral equation formalism polarized continuum model IEFPCM-B3LYP/6-311++G(d,p) and IEFPCM-BB1K/6-311++G(d,p) levels on the gas-phase optimized geometries. Three possible pathways, the concerted pathway (path A), the stepwise pathway involving tetrahedral intermediates (path B), and the stepwise pathway via alpha-oxo ketene intermediate due to the participation of beta-hydroxy (path C), are taken into account for the title reaction. Moreover, path C includes two sequential processes. The first process is to generate alpha-oxo ketene intermediate via the decomposition of N-methyl-3-(methoxycarbonyl)-4-hydroxy-2-pyridone; the second process is the addition of dimethylamine to alpha-oxo ketene intermediate. Our results indicate that path C is more favorable than paths A and B both in the gas phase and in solvent (heptane). In path C, the first process is the rate-determining step, and the second process is revealed to be a [4+2] pseudopericyclic reaction without the energy barrier. Being independent of the concentration of amine, the first process obeys the first-order rate law.     

The DMAP-catalyzed acetylation of alcohols--a mechanistic study (DMAP = 4-(dimethylamino)pyridine)

The acetylation of tert-butanol with acetic anhydride catalyzed by 4-(dimethylamino)pyridine (DMAP) has been studied at the Becke3 LYP/6-311 + G(d,p)//Becke3 LYP/6-31G(d) level of theory. Solvent effects have been estimated through single-point calculations with the PCM/UAHF solvation model. The energetically most favorable pathway proceeds through nucleophilic attack of DMAP at the anhydride carbonyl group and subsequent formation of the corresponding acetylpyridinium/acetate ion pair. Reaction of this ion pair with the alcohol substrate yields the final product, tert-butylacetate. The competing base-catalyzed reaction pathway can either proceed in a concerted or in a stepwise manner. In both cases the reaction barrier far exceeds that of the nucleophilic catalysis mechanism. The reaction mechanism has also been studied experimentally in dichloromethane through analysis of the reaction kinetics for the acetylation of cyclohexanol with acetic anhydride, in the presence of DMAP as catalyst and triethylamine as the auxiliary base. The reaction is found to be first-order with respect to acetic anhydride, cyclohexanol, and DMAP, and zero-order with respect to triethyl amine. Both the theoretical as well as the experimental studies strongly support the nucleophilic catalysis pathway.     

Modern valence-bond description of chemical reaction mechanisms: the 1,3-dipolar addition of diazomethane to ethene

The electronic mechanism for the gas-phase concerted 1,3-dipolar cycloaddition of diazomethane (CH2N2) to ethene (C2H4) is described through spin-coupled (SC) calculations at a sequence of geometries along the intrinsic reaction coordinate obtained at the MP2/6-31G(d) level of theory. It is shown that the bonding rearrangements occurring during the course of this reaction follow a heterolytic pattern, characterized by the movement of three well-identifiable orbital pairs, which are initially responsible for the pi bond in ethene and the C-N pi bond and one of the N-N pi bonds in diazomethane and are retained throughout the entire reaction path from reactants to product. Taken together with our previous SC study of the electronic mechanism of the 1,3-dipolar cycloaddition of fulminic acid (HCNO) to ethyne (C2H2) (Theor. Chim. Acc. 1998, 100, 222), the results of the present work suggest strongly that most gas-phase concerted 1,3-dipolar cycloaddition reactions can be expected to follow a heterolytic mechanism of this type, which does not involve an aromatic transition state. The more conventional aspects of the gas-phase concerted 1,3-dipolar cycloaddition of diazomethane to ethene, including optimized transition structure geometry, electronic activation energy, activation barrier corrected for zero-point energies, standard enthalpy, entropy and Gibbs free energy of activation, have been calculated at the HF/6-31G(d), B3LYP/6-31G(d), MP2/6-31G(d), MP2/6-31G(d,p), QCISD/6-31G(d) and CCD/6-31G(d) levels of theory. We also report the CCD/6-311++G(2d, 2p)//CCD/6-31G(d), MP4(SDTQ)/6-311++G(2d,2p)//CCD/6-31G(d) and CCSD(T)/6-311++G(2d, 2p)//CCD/6-31G(d) electronic activation energies.     

The substituent effects of the leaving groups on the aminolysis of phenyl acetates: DFT studies

The density functional theory B3LYP/6-31G(d, p) method is employed to study the mechanism of aminolysis reaction of p-substituted phenyl acetates (CH₃C(O)OC₆H₄X, X = H, NH₂, and NO₂) with ammonia in the gas phase. Two reaction pathways are considered: the concerted process and the stepwise pathway through neutral intermediates. The substituent effects of the leaving groups on the reactivity of phenyl acetates are discussed. The solvent effect of acetonitrile on the title reaction is also assessed by the polarizable continuum model (CPCM model) at B3LYP/6-31++G(d, p) level of theory. The calculated results show that the activation barriers of the concerted pathways are lower than those of the rate-controlling steps of the stepwise processes for all the three aminolysis reactions. This aminolysis of phenyl acetates is more favorable for X = NO₂ than for X = H and NH₂ in the gas phase and in acetonitrile.     

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.     

Theoretical investigation on the GaCl3-catalyzed ring-closing metathesis reaction of N-2,3-butadienyl-2-propynyl-1-amine: three-membered ring versus four-membered ring mechanism

The gallium chloride (GaCl(3))-catalyzed ring-closing metathesis reaction mechanism of N-2,3-butadienyl-2-propynyl-1-amine has been studied at the Becke three-parameter hybrid functional combined with Lee-Yang-Parr correlation functional (B3LYP)/6-31G(d), B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p)//B3LYP/ 6-31G(d) and the second-order M?ller-Plesset perturbation (MP2)/6-311++G(d,p)//B3LYP/6-31+G(d,p) levels. It was found that the final metathesis product can be yielded via a three-membered or four-membered ring mechanism. The three-membered ring pathway is favorable due to its low energy barrier at the rate determining step. The whole reaction is stepwise and strongly exothermic.     

DFT Studies on the Isomerization of Butene Double Bond Catalyzed by 1-Butyl-3-methyl-imidazolium in Ionic Liquid

1 INTRODUCTION Butene and its isomers are important petroleum raw materials. Isomerization reaction of butene plays a key role in the course of C4 alkylation and its reaction mechanism has captured the attention of chemists all along[1, 2]. As a green so…     

Hydride abstraction of methylamine with Cu(S) in the gas phase: A density functional theory study

The gas-phase hydride abstraction of methylamine with Cu⁺(¹S) is theoretically investigated by using density functional theory. Geometries for all the stationary points involved are fully optimized at both the B3LYP/6-311++G(d,p) and B3LYP/6-311++G(3df,2p) levels and the reaction is analyzed in terms of the topology of potential energy surface. Approach of Cu⁺ towards methylamine could form either “classical” N or “nonclassical” η¹-methyl-H attached complex with the former being the global minimum. Both complexes are found to be key intermediates for the hydride abstraction, which could transfer into each other via two parallel routes, i.e., concerted metal movement and stepwise C-H activation-rearrangement. A charge-transfer process is detected for the “nonclassical” complex converting to a precursor species (CuH-NH₂CH₂⁺), which accounts for the final products by a nonreactive dissociation.     

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.     

CH2F自由基与HNCO反应机理的理论研究

The reaction mechanism of CH2F radical with HNCO was investigated by density functional theory (DFT)at the B3LYP/6-311++G(d,p) level. The geometries of the reactants, the intermediates, the transition states and the products were optimized. The transition states were verified through the vibration analysis.The relative energies were calculated at the QCISD(T)/6-311++G**//B3LYP/6-311++G(d,p) level. Seven feasible reaction pathways of the reaction were studied. The results indicate that the pathway (5) is the most favorable to occur, so it is the main pathway of the reaction.     

Computational study on 1,1,3,3-tetramethylguanidine-catalyzed cyanosilylation mechanism of hypnone

The reaction mechanism of cyanosilylation of hypnone catalyzed by 1,1,3,3-tetramethylguanidine (TMG) was investigated using the density functional theory at the Becke three-parameter hybrid functional combined with Lee–Yang–Parr correlation functional (B3LYP)/6-31G(d), B3LYP/6-31G(d, p) and B3LYP/6-311++G(d, p) levels. The results show that the title reaction occurs through two processes, the formation of the intermediate five through the interaction of TMG with trimethylsilyl cyanide (TMSCN) and the reaction between the intermediate five and hypnone. The formation of intermediate five controls the whole reaction with a Gibbs free energy barrier of 31.84 kcal/mol. In addition, the results indicate that the catalyst TMG significantly promotes the title reaction and changes the mechanism. The results are in reasonable agreement with the experimental observations. Our results reveal that the overall reaction is stepwise and exoergonic in solvent-free conditions at room temperature.     

Quantum mechanical study of the ring-closing reaction of the hexatriene radical cation

The ring-closing reaction of hexatriene radical cation 1(*)(+) to 1,3-cyclohexadiene radical cation 2(*)(+) was studied computationally at the B3LYP/6-31G* and QCISD(T)/6-311G*//QCISD/6-31G* levels of theory. Both, concerted and stepwise mechanisms were initially considered for this reaction. Upon evaluation at the B3LYP level of theory, three of the possible pathways-a concerted C(2)-symmetric via transition structure 3(*)(+) and stepwise C(1)-symmetric pathways involving three-membered ring intermediate 5(*)(+) and four-membered ring intermediate 6(*)(+)-were rejected due to high-energy stationary points along the reaction pathway. The two remaining pathways were found to be of competing energy. The first proceeds through the asymmetric, concerted transition structure 4(*)(+) with an activation barrier E(a) = 16.2 kcal/mol and an overall exothermicity of -23.8 kcal/mol. The second pathway, beginning from the cis,cis,trans rotamer of 1(*)(+), proceeds by a stepwise pathway to the cyclohexadiene product with an overall exothermicity of -18.6 kcal/mol. The activation energy for the rate-determining step in this process, the formation of the intermediate bicyclo[3.1.0]hex-2-ene via transition structure 9(*)(+), was found to be 20.4 kcal/mol. More rigorous calculations of a smaller subsection of the potential energy hypersurface at the QCISD(T)//QCISD level confirmed these findings and emphasized the importance of conformational control of the reactant.     

Theoretical study of the conformational energy hypersurface of cyclotrisarcosyl

The multidimensional Conformational Potential Energy Hypersurface (PEHS) of cyclotrisarcosyl was comprehensively investigated at the DFT (B3LYP/6-31G(d), B3LYP/6-31G(d,p) and B3LYP/6-311++G(d,p)), levels of theory. The equilibrium structures, their relative stability, and the Transition State (TS) structures involved in the conformational interconversion pathways were analyzed. Aug-cc-pVTZ//B3LYP/6-311++G(d,p) and MP2/6-31G(d)//B3LYP/6-311++G(d,p) single point calculations predict a symmetric cis-cis-cis crown conformation as the energetically preferred form for this compound, which is in agreement with the experimental data. The conformational interconversion between the global minimum and the twist form requires 20.88 kcal mol-1 at the MP2/6-31G(d)//B3LYP/6-311++G(d,p) level of theory. Our results allow us to form a concise idea about the internal intricacies of the PEHSs of this cyclic tripeptide, describing the conformations as well as the conformational interconversion processes in this hypersurface. In addition, a comparative analysis between the conformational behaviors of cyclotrisarcosyl with that previously reported for cyclotriglycine was carried out     

甲酸苯酯氨解反应的机理和溶剂效应的理论研究

采用密度泛函理论方法B3LYP/6-31G(d,p)研究了甲酸苯酯与氨在气相中的反应机理. 考虑了两条可能的反应途径: 中性协同的和中性分步的机理. 采用自洽反应场极化连续模型(CPCM模型)研究了反应体系在水、乙醇和乙腈溶液中反应的溶剂化效应. 计算结果表明气相和溶液中协同机理均是最优途径. 水、乙醇和乙腈溶剂可降低协同途径的活化能, 溶剂化效应的大小对溶剂的极性不敏感.     

Aminolysis of a model nerve agent: a computational reaction mechanism study of o,s-dimethyl methylphosphonothiolate

The mechanism for the aminolysis of a model nerve agent, O,S-dimethyl methylphosphonothiolate, is investigated both at density functional level using M062X method with 6-311++G(d,p) basis set and at ab initio level using the second-order M?ller-Plesset perturbation theory (MP2) with the 6-311+G(d,p) basis set. The catalytic role of an additional NH(3) and H(2)O molecule is also examined. The solvent effects of acetonitrile, ethanol, and water are taken into account employing the conductor-like screening model (COSMO) at the single-point M062X/6-311++G(d,p) level of theory. Two possible dissociation pathways, methanethiol and methyl alcohol dissociations, along with two different neutral mechanisms, a concerted one and a stepwise route through two neutral intermediates, for each pathway are investigated. Hyperconjugation stabilization that has an effect on the stability of generated transition states are investigated by natural bond order (NBO) approach. Additionally, quantum theory of atoms in molecules analysis is performed to evaluate the bond critical (BCP) properties and to quantify strength of different types of interactions. The calculated results predict that the reaction of O,S-dimethyl methylphosphonothiolate with NH(3) gives rise to parallel P-S and P-O bond cleavages, and in each cleavage the neutral stepwise route is always favorable than the concerted one. The mechanism of NH(3) and H(2)O as catalyst is nearly similar, and they facilitate the shuttle of proton to accelerate the reaction. The steps involving the H(2)O-mediated proton transfer are the most suitable ones. The first steps for the stepwise process, the formation of neutral intermediate, are the rate-determining step. It is observed that in the presence of catalyst the reaction in the stepwise path possesses almost half the activation energy of the uncatalyzed one. A bond-order analysis using Wiberg bond indexes obtained by NBO calculation predicts that usually all individual steps of the reactions occur in a concerted fashion showing equal progress along different reaction coordinates.     

Monomer versus alcohol activation in the 4-dimethylaminopyridine-catalyzed ring-opening polymerization of lactide and lactic O-carboxylic anhydride

Model reactions for the 4-dimethylaminopyridine (DMAP)-catalyzed ring-opening polymerization of lactide and the corresponding lactic O-carboxylic anhydride (lacOCA) have been studied computationally at the B3LYP/6-31G(d) level of theory. The solvent effect of dichloromethane was taken into account through PCM/SCRF single-point calculations at the B3LYP/6-31G(d) level of theory. In marked contrast with that predicted for the reaction of alcohols with acetic anhydride, the mechanism in which nucleophilic activation of the monomer involving acylpyridinium intermediates was found to be energetically less favorable than the base activation of the alcohol through hydrogen bonding. The concerted pathway for the ring-opening of lactide and lacOCA was shown to compete with the traditional stepwise mechanism involving tetrahedral intermediates. Furthermore, DMAP is proposed to act as a bifunctional catalyst through its basic nitrogen center and an acidic ortho-hydrogen atom.     

The Dowd-Beckwith ring expansion: a theoretical study

UB3LYP/6-311++G(d,p) and ROMP2/6-311++G(d,p)//UB3LYP/6-311++G(d,p) calculations including the effect of benzene solvent through the PCM-UAHF method render a concerted mechanism without fragmentation as the most favourable one for the Dowd-Beckwith radical ring expansion of the bromomethyl adduct of methyl cyclopentanone-2-carboxylate to yield methyl cyclohexanone-3-carboxylate. The corresponding concerted TS is a bicyclic alcoxy radical.     

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.