Theoretical study on the alkaline hydrolysis of methyl thioacetate in aqueous solution

A base-catalyzed hydrolysis reaction of thiolester has been studied in both gas and solution phases using two ab initio quantum mechanics calculations such as Gaussian09 and CPMD. The free-energy surface along the reaction path is also constructed using a configuration sampling technique, namely, the metadynamics method. While there are two different reaction paths obtained for the potential profile of the base-catalyzed hydrolysis reaction for thiolester in the gas phase, a triple-well reaction path is computed for the reaction in the solution phase by two quantum mechanics calculations. Unlike the S(N)2 mechanism (a concerted mechanism) found for the gas-phase reaction, a nucleophilic attack from the hydroxide ion on the carbonyl carbon to yield a tetrahedral intermediate (a stepwise mechanism) is observed for the solution-phase reaction. Moreover, the energy profiles computed by these two theoretical calculations are found to be very comparable with those determined experimentally.     

B型DNA中鸟嘌呤-胞嘧啶碱基对内双质子转移反应

采用ONIOM(M06-2X/6-31G^*:PM3)方法研究了单个鸟嘌呤-胞嘧啶(GC)碱基对和含GC碱基对的四种排序的DNA三聚体(dATGCAT, dGCGCGC, dTAGCTA, dCGGCCG)的双质子转移反应. 通过分析其双质子转移方式、质子转移过程中各结构的能量和氢键变化, 总结出环境因素对GC碱基对双质子转移机理的影响. 气相中, dCGGCCG三聚体中发生分步双质子转移, 其它四种模型中均发生协同双质子转移. 分析发现质子转移方式受上下相邻碱基对的静电相互作用和质子接受位的质子亲和势影响, dATGCAT和dGCGCGC排序有助于质子H4a转移, 而dTAGCTA和dCGGCCG排序有助于质子H1转移, 胞嘧啶的N3位较高的质子亲和势有助于质子H1转移. 水溶剂中, 上下相邻碱基对的静电相互作用被减弱, 水溶剂稳定了分步转移过程中的单质子转移产物, 因此分步转移机理占据优势, 五种模型中均出现分步双质子转移, 在此过程中能量变化趋势相似. 溶剂效应有利于单质子转移, 却增加了双质子转移反应的反应能.     

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.     

Realistic modeling of ruthenium-catalyzed transfer hydrogenation

We report the first computational study of a fully atomistic model of the ruthenium-catalyzed transfer hydrogenation of formaldehyde and the reverse reaction in an explicit methanol solution. Using ab initio molecular dynamics techniques, we determined the thermodynamics, mechanism, and electronic structure along the reaction path. To assess the effect of the solvent quantitatively, we make a direct comparison with the gas-phase reaction. We find that the energy profile in solution bears little resemblance to the profile in the gas phase and a distinct solvation barrier is found: the activation barriers in both directions are lowered and the concerted hydride and proton transfer in the gas phase are converted into a sequential mechanism in solution with the substrate appearing as methoxide-like intermediate. Our results indicate that besides the metal-ligand bifunctional mechanism, as proposed by Noyori, also a concerted solvent-mediated mechanism is feasible. Our study gives a new perspective of the active role a solvent can have in transition-metal-catalyzed reactions.     

Ab initio aqueous thermochemistry: application to the oxidation of hydroxylamine in nitric acid solution

Ab initio molecular orbital calculations were performed and thermochemical parameters estimated for 46 species involved in the oxidation of hydroxylamine in aqueous nitric acid solution. Solution-phase properties were estimated using the several levels of theory in Gaussian03 and using COSMOtherm. The use of computational chemistry calculations for the estimation of physical properties and constants in solution is addressed. The connection between the pseudochemical potential of Ben-Naim and the traditional standard state-based thermochemistry is shown, and the connection of these ideas to computational chemistry results is established. This theoretical framework provides a basis for the practical use of the solution-phase computational chemistry estimates for real systems, without the implicit assumptions that often hide the nuances of solution-phase thermochemistry. The effect of nonidealities and a method to account for them is also discussed. A method is presented for estimating the solvation enthalpy and entropy for dilute aqueous solutions based on the solvation free energy from the ab initio calculations. The accuracy of the estimated thermochemical parameters was determined through comparison with (i) enthalpies of formation in the gas phase and in solution, (ii) Henry's law data for aqueous solutions, and (iii) various reaction equilibria in aqueous solution. Typical mean absolute deviations (MAD) for the solvation free energy in room-temperature water appear to be ~1.5 kcal/mol for most methods investigated. The MAD for computed enthalpies of formation in solution was 1.5-3 kcal/mol, depending on the methodology employed and the type of species (ion, radical, closed-shell) being computed. This work provides a relatively simple and unambiguous approach that can be used to estimate the thermochemical parameters needed to build detailed ab initio kinetic models of systems in aqueous solution. Technical challenges that limit the accuracy of the estimates are highlighted.     

Theoretical study of the neutral hydrolysis of methyl formate via a concerted and stepwise water-assisted mechanism using free-energy curves and molecular dynamics simulation

A procedure previously described by us is used for the theoretical study of chemical reactions in solution by means of molecular dynamics simulation, with solute–solvent interaction potentials LJ (12-6-1) derived from ab initio quantum calculations. We apply the procedure to the case of the neutral hydrolysis of methyl formate, HCOOCH₃ + 3H₂O → HCOOH + CH₃OH + 2H₂O in aqueous solution, via concerted and stepwise water-assisted mechanisms. We use the solvent as reaction coordinate, and the free-energy curves for the calculation of the activation energies. The theoretical calculation for the thermodynamics of this hydrolysis reaction in aqueous solution, assisted by three water molecules, is in agreement with the available experimental information. In particular our study gives values of ΔG ^≠ = 28.88 and 28.17 kcal/mol for the concerted and stepwise mechanisms, close to the experimental activation barrier of 28.8 kcal/mol, and a significant improvement over the values of 48.05 and 45.66 kcal/mol found in another similar study using the PCM model.     

Ring opening of boriranes vis‐à‐vis aziridines: An ab initio and DFT probe on the mechanisms

Borirane undergoes ring opening reaction with NOCl and HNF₂ yielding the corresponding alkenes. Ab initio and density functional investigations of this reaction with cis‐ and trans‐2,3‐dimethylboriranes reveal that these reactions take place in a single step through the formation of a prereactive complex and a transition state giving the alkene with the same stereochemistry. Calculations clearly show that the concerted cleavage of C? B bonds leads to retention of stereochemistry. Further, it shows that HNF₂ cleaves boriranes more efficiently than does NOCl. Intrinsic reaction coordinate analyses and bond order analysis describe the nature of the transition state very well and fix the reaction mechanism. Solvent effect calculations through PCM model, with acetonitrile and CCl₄ as solvents, do not alter the gas phase results significantly. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Ab initio MO study of the solvent effect on the SN2 reaction of the trimethylsulfonium cation with chloride anion

A recently developed ab initio MO theory including solvent effects has been applied to a typical cation-anion reaction, the S_N2 reaction of the trimethylsulfonium cation with the chloride anion. In the gas phase, the trimethylsulfonium and chloride ions are unstabilized, and the reaction is expected to proceed rapidly. In aqueous solution, the reactant ions are largely stabilized, and the reaction has been predicted to be endothermic, with an activation energy of 30–40 kcal/mol. This potential energy profile, which agrees with experimental results, has been well elucidated by differential solvation at several stages of the reaction path. At the transition state of this reaction, the C and H atoms in the transferring CH₃ group are almost in a plane that is perpendicular to the Cl(SINGLE BOND)C(SINGLE BOND)S line, reflecting the concerted nature of the reaction. The population analysis has shown that the electrons in the C(SINGLE BOND)S bond are mostly withdrawn by the sulfur atom at the transition state and that the electron transfer from Cl to CH₃ occurs after the transition state. The calculated activation energy for the reaction in ethanol is smaller than that in water. This agrees with experiments. © 1996 John Wiley & Sons, Inc.     

Theoretical studies on the formation of N-nitrosodimethylamine

The mechanisms of the formation of N-nitrosodimethylamine (NDMA) were studied at the MP2/6-311+G(d,p)//B3LYP/6-311+G(d,p) level of theory. We focused on the formation of NDMA from the reactions of dimethylamine (DMA) with nitrous acid and nitrite anion. Our calculations show that the reaction of DMA with nitrous acid is predicted to proceed via two distinct pathways: a concerted or a stepwise mechanism. Moreover, the energy barrier for the stepwise mechanism is somewhat higher than that for the concerted mechanism. The difference in these barriers indicates that the reaction of DMA with nitrous acid via the concerted mechanism is much more favored than that via the stepwise mechanism. In the other situation, our results demonstrate that the reaction of DMA with nitrite anion becomes feasible in the presence of carbon dioxide. Furthermore, this reaction proceeds via a stepwise pathway, in which CO₂ first attacks DMA, the result of which then reacts with nitrite anion. It is noteworthy that carbon dioxide appears to be an active catalyst to promote the formation of NDMA. Additionally, the effects of aqueous solvation on the reactions of DMA with nitrous acid and nitrite anion were investigated.     

Reactivity of phosphate monoester monoanions in aqueous solution. 1. Quantum mechanical calculations support the existence of "anionic zwitterion" MeO(+)(H)PO(3)(2-) as a key intermediate in the dissociative hydrolysis of the methyl phosphate anion

The dissociative hydrolysis reaction of the methyl phosphate monoanion has been studied for the reactant species CH(3)OPO(3)H(-) (1) and CH(3)OPO(3)H(-) x H(2)O (1a) in the gas and aqueous phases by density functional theory (B3LYP) calculations. Nonspecific solvation effects were taken into account with the polarizable continuum model PCM either by solvating the gas-phase reaction paths or by performing geometry searches directly in the presence of the solvation correction. In agreement with previous theoretical studies, our gas-phase calculations indicate that proton transfer to the methoxy group of 1 is concerted with P-O bond cleavage. In contrast, optimizations performed with the PCM solvation model establish the existence of the tautomeric form CH(3)O(+)(H)PO(3)(2-) (2) as an intermediate, indicating that proton transfer and P-O bond cleavage become uncoupled in aqueous solution. The dissociative pathway of 1a is energetically favored over the dissociative pathway of 1 only when the added water molecule plays an active catalytic role in the prototropic rearrangement 1 <--> 2. In that case, it is found that the collapse (via P-O bond cleavage) of the hydrated zwitterionic form CH(3)O(+)(H)PO(3)(2-) x H(2)O (2a) is rate-determining. This collapse may occur by a stepwise mechanism through a very short-lived metaphosphate intermediate (PO(3)(-)), or by a concerted S(N)2-like displacement through a loose metaphosphate-like transition state. The present calculations do not allow a distinction to be made between these two alternatives, which are both in excellent agreement with experiment. The present study also reveals that PO(3)(-) reacts selectively with CH(3)OH and H(2)O nucleophiles in aqueous solution. However, the observed selectivity of metaphosphate is governed by solvation effects, not nucleophilicity (water being much more effective than methanol in capturing PO(3)(-)). This arises from a better solvation of the addition product H(2)O(+)PO(3)(2-) as compared to CH(3)O(+)(H)PO(3)(2-).     

亚硝基苯与甲醛的反应机理和溶剂效应的理论研究

采用密度泛函理论方法RB3LYP/6-311＋＋G(d,p)研究了亚硝基苯与甲醛在单重态势能面上分别在气相和溶剂中的反应机理. 找到两条反应通道: 协同机理和分步机理, 均生成实验产物N-苯基氧肟酸C6H5NOHCHO. 计算结果表明: 亚硝基苯与甲醛在气相中分步机理为主要通道. 采用导电极化连续介质模型研究了反应体系在水、乙醇、乙腈、二氯甲烷、四氢呋喃、环己烷溶液中反应的溶剂化效应, 这些溶剂可降低反应的活化能, 但反应对溶剂的极性不敏感. 无论在气相还是溶剂中, 亚硝基苯与甲醛的分步机理为优势通道.     

Solvation‐Induced Changes in the Mechanism of Alcohol Oxidation at Gold/Titania Nanocatalysts in the Aqueous Phase versus Gas Phase

Gold/titania catalysts are widely used for key reactions, notably including the selective oxidation of alcohols in the liquid phase. Our large‐scale ab initio simulations disclose that the liquid‐phase reaction mechanism is distinctly different from that in the gas phase because of active participation of water molecules. While concerted charge transfers related to O₂ splitting and abstraction of both protonic and hydridic hydrogens are enforced under dry conditions, stepwise charge transfer is preferred in the condensed phase. Dissociation of reactive water molecules and subsequent Grotthuss migration of protonic defects, H⁺(aq), allows for such a decoupling of the oxidation process, both in time and space. It is expected that these observations are paradigmatic for heterogeneous catalysis in aqueous phases.     

A semiempirical study of 2,2′-dichlorodiethyl sulfide SN2 and neighboring group hydrolysis reaction mechanisms in the gas phase and in aqueous solution

A PM3 and SM3-PM3 semiempirical molecular orbital study of the 2,2′-dichlorodiethyl sulfide conventional S_N2 and neighboring group hydrolysis reaction mechanisms in the gas phase and in aqueous solution is described. The calculations predict substantially faster reactions in aqueous solution, with the neighboring group mechanism always being preferred. Detailed consideration is given to the geometries, relative energies, and partial atomic charges of all species involved in the reaction mechanisms considered and the extent to which aqueous solvation impacts these quantities. The results are consistent with expectation and with reported calculations concerning the intramolecular S_N2 reaction of 2-chloroethyl methyl sulfide. We also present the lowest energy mustard chlorohydrin structures according to PM3 and AM1 conformational analysis.     

Comparison of AM1 and PM3 semiempirical to ab initio methods in the study of Diels-Alder reactions of butadiene and cyclopentadiene with cyanoethylenes

Assuming a concerted synchronous mechanism with one transition state of the Diels-Alder reactions, the structures of the transition states and the activation energies for the reactions of butadiene and cyclopentadiene with cyanoethylenes were calculated by AM1 and PM3 semiempirical methods. The structural parameters were compared with those obtained by high level Gaussian calculations, whereas the activation energies were compared both with the ab initio calculations and those obtained experimentally. The structural properties calculated with PM3 methods are in general in better agreement with the ab initio calculations. The low level ab initio calculations are in many cases worse than the semiempirical methods. All predicted activation energies with both semiempirical methods are up to 300% higher than the experimental values. The predicted reactivity is also opposite to the experimental data. Only the very high level Gaussian calculations are in good correlation with experimental results. The predicted selectivity of the reaction is also opposite to the experimental facts. Two explanations are offered for this discrepancy: AM1 and PM3 methods cannot handle the calculation of the concerted Diels-Alder transition states and are not recommended to be used for that purpose, or this Diels-Alder reaction is not concerted but is stepwise.     

Potential energy surface of the reaction of imidazole with peroxynitrite: Density functional theory study

This article presents a theoretical investigation of the reaction mechanism of imidazole nitration by peroxynitrite using density functional theory calculations. Understanding this reaction mechanism will help in elucidating the mechanism of guanine nitration by peroxynitrite, which is one of the assumed chemical pathways for damaging DNA in cells. This work focuses on the analysis of the potential energy surface (PES) for this reaction in the gas phase. Calculations were carried out using Hartree–Fock (HF) and density functional theory (DFT) Hamiltonians with double‐zeta basis sets ranging from 6‐31G(d) to 6‐31++G(d,p), and the triple‐zeta basis set 6‐311G(d). The computational results reveal that the reaction of imidazole with peroxynitrite in gas phase produces the following species: (i) hydroxide ion and 2‐nitroimidazole, (ii) hydrogen superoxide ion and 2‐nitrosoimidazole, and (iii) water and 2‐nitroimidazolide. The rate‐determining step is the formation of a short‐lived intermediate in which the imidazole C₂ carbon is covalently bonded to peroxynitrite nitrogen. Three short‐lived intermediates were found in the reaction path. These intermediates are involved in a proton‐hopping transport from C₂ carbon to the terminal oxygen of the ? O? O moiety of peroxynitrite via the nitroso (ON? ) oxygen. Both HF and DFT calculations (using the Becke3–Lee–Yang–Parr functional) lead to similar reaction paths for proton transport, but the landscape details of the PES for HF and DFT calculations differ. This investigation shows that the reaction of imidazole with peroxynitrite produces essentially the same types of products (nitro‐ and nitroso‐) as observed experimentally in the reaction of guanine with peroxynitrite, which makes the former reaction a good model to study by computation the essential characteristics of the latter reaction. Nevertheless, the computationally determined activation energy for imidazole nitration by peroxynitrite in the gas phase is 84.1 kcal/mol (calculated at the B3LYP/6‐31++G(d,p) level), too large for an enzymatic reaction. Exploratory calculations on imidazole nitration in solution, and on the reaction of 9‐methylguanine with peroxynitrite in the gas phase and solution, show that solvation increases the activation energy for both imidazole and guanine, and that the modest decrease (15 kcal mol^?1) in the activation energy, due to the adjacent six member ring of guanine, is counterbalanced by solvation. These results lead to the speculation that proton tunneling may be at the origin of experimentally observed high reaction rate of guanine nitration by peroxynitrite in solution. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Relative basicities of carboxylate lone pairs in aqueous solution

Relative basicities of the lone pairs of the acetate ion have been determined using ab initio calculations for the gas phase and Monte Carlo simulations for the aqueous phase. The syn lone pair is found to be more basic by only 1.25 pK_a units. This small difference is the result of a large intrinsic preference for the syn conformer of the conjugate acid in the gas phase, offset by an almost equally large preferential solvation of the anti conformer in the aqueous phase. The better solvation of the anti conformer is due to stronger solute–solvent interactions. © 1993 John Wiley & Sons, Inc.     

Two-state model based on the block-localized wave function method

The block-localized wave function (BLW) method is a variant of ab initio valence bond method but retains the efficiency of molecular orbital methods. It can derive the wave function for a diabatic (resonance) state self-consistently and is available at the Hartree-Fock (HF) and density functional theory (DFT) levels. In this work we present a two-state model based on the BLW method. Although numerous empirical and semiempirical two-state models, such as the Marcus-Hush two-state model, have been proposed to describe a chemical reaction process, the advantage of this BLW-based two-state model is that no empirical parameter is required. Important quantities such as the electronic coupling energy, structural weights of two diabatic states, and excitation energy can be uniquely derived from the energies of two diabatic states and the adiabatic state at the same HF or DFT level. Two simple examples of formamide and thioformamide in the gas phase and aqueous solution were presented and discussed. The solvation of formamide and thioformamide was studied with the combined ab initio quantum mechanical and molecular mechanical Monte Carlo simulations, together with the BLW-DFT calculations and analyses. Due to the favorable solute-solvent electrostatic interaction, the contribution of the ionic resonance structure to the ground state of formamide and thioformamide significantly increases, and for thioformamide the ionic form is even more stable than the covalent form. Thus, thioformamide in aqueous solution is essentially ionic rather than covalent. Although our two-state model in general underestimates the electronic excitation energies, it can predict relative solvatochromic shifts well. For instance, the intense pi-->pi* transition for formamide upon solvation undergoes a redshift of 0.3 eV, compared with the experimental data (0.40-0.5 eV).     

氧杂环丁烷热解机理的量子化学研究

本文利用半经验分子轨道理论研究了氧杂环丁烷热解为甲醛和乙烯的反应机理计算是采用半经验方法AM1进行的, 各种驻点全部运用Berny梯度方法优化. 同时, 对过渡态的结构进行了振动分析的确证. 计算表明: 1)不存在协同的同面-同面反应途径的过渡态, 其驻点只是一个二级鞍点; 2) 协同的同面-异面反应途径需要经过一个能量很高的过渡态; 3)有利的反应途径是包含了双自由基中间体的分步过程。