Theoretical studies on the mechanism of acid-promoted hydrolysis of N-formylaziridine in comparison with formamide

[reaction: see text] We present an ab initio study of the acid-promoted hydrolysis reaction mechanism of N-formylaziridine in comparison with formamide. Since the rate of amide hydrolysis reactions depends on the formation of the tetrahedral intermediate, we focused our attention mainly on the reactant complex, the tetrahedral intermediate, and the transition state connecting these two stationary points. Geometries were optimized using the density functional theory, and the energetics were refined using ab initio theory including electron correlation. Solvent effects were investigated by using polarizable continuum method calculations. The proton-transfer reaction between the O-protonated and N-protonated amides was investigated. In acidic media, despite that the N-protonated species is more stable than the O-protonated one, it is predicted that both N-protonated and O-protonated pathways compete in the hydrolysis reaction of N-formylaziridine.     

Theoretical studies on the alkaline hydrolysis of N-Methylcarbamates

The reaction mechanisms of the alkaline hydrolysis of N-methylcarbamates were studied using the AM1 method by assuming two possible pathways: (1) nucleophilic attack of hydroxide ion on the carbonyl carbon to give a tetrahedral complex followed by its breakdown to carbamic acid (B_AC2); and (2) proton abstraction by hydroxide ion at the nitrogen atom followed by elimination of the alkoxide ion to form N-methyl isocyanate (E1cB). Reaction coordinate analysis showed that the reaction mechanism is determined by both the stability of an intermediate and the energy barrier for elimination.     

Theoretical studies on the acid hydrolysis of acetamide

The mechanism of the A2 hydrolysis of acetamide has been investigated theoretically using MNDO Method. Fully optimized geometries of all species at the stationary points corresponding to energy minima and energy maxima along the reaction coordinate are determined for the two reaction paths: the rate-determining nucleophilic attack of water on the carbonyl carbon (i) of the O-protonated tautomer and (ii) of the N-protonated form. Results show that the latter provides a lower energy path by 7.5 Kcal/Mol compared to the former.Tetrahedral species' found were not at the energy minima but at or near the saddle points. Optimizied structures and formal charges on heavy atoms showed that the bond interchange with the concurrent proton interchange takes place at the rate-determining step. The negative charge on N atom was found to increase in the rate-determining step relative to that of the ground state, the O-protonated acetamide, and hence substitution of electron withdrowing group on N is predicted to depress the activation energy in agreement with the experimental results.     

Theoretical studies on the hydrolysis mechanism of N-(2-oxo-1,2-dihydro-pyrimidinyl) formamide

Density functional theory (B3LYP) and ab initio (MP2) methods with the 6-31G(d,p) basis set are used to study the mechanisms for the hydrolysis of N-(2-oxo-1,2-dihydro-pyrimidinyl) formamide (PFA) in the gas phase. The direct and the water-assisted hydrolysis processes are considered, involving one and two water molecules, respectively. Three different pathways are explored in each case. In the first pathway, the O atom of water first attacks at the C atom of amide while one H atom of water transfers toward the oxygen of amide, leading to an intermediate of tetrahedral coordinated carbon with two OH groups. In the subsequent step, the hydroxyl H atom transfers to the N atom of pyrimidine ring and the C-N covalent bond of amide dissociates simultaneously. In the second path, the O and one H of water attack at the C of amide and the N of pyrimidine ring, respectively, while the C-N bond of amide dissociates. In the third path, three processes occur simultaneously: the O of water attacks at the C of amide, one H atom attacks at the N of amide, and the C-N bond of amide is broken. It is shown that the second pathway is favored for the direct hydrolysis while the first pathway is favored for the water-assisted hydrolysis. It is also shown that the water-assisted hydrolysis is slightly more favorable than the direct hydrolysis. Moreover, solvent effects on five pathways are evaluated with Monte Carlo simulation (MC) and free energy perturbation methods. It is shown that the solvent water slightly reduces the energy barrier in each pathway. The first pathway in the water-assisted hydrolysis remains the most favorable when the solvent effects of bulk water are taken into account.     

Theoretical studies on the acid hydrolysis of methyl carbamate

The mechanism of the A2 acid hydrolysis of methyl carbamate was investigated using MNDO method. The reaction was found to proceed in two steps: (1) the rate-determining nucleophilic attack of water on the carbonyl carbon of the N-protonated tautomer involving the tetrahedral TS; and (2) the fast subsequent proton abstraction by the leaving group, NH₃, to form products. The mechanism is similar to that involved in the A2 hydrolysis of acetamide. Effects of substituents, R¹, R², and R³ in R¹OCONR²R³, on rates can be predicted by the changes in electron densities on alkoxy oxygen and N, in complete agreement with the experimental results. We concluded that there is no need for invoking two different mechanisms for amides and carbamates since a common mechanism can easily accommodate all the experimental results.     

Theoretical study of hydrolysis mechanism of khellin

This paper describes khellin hydrolysis mechanism using semiemperical PM3 implemented in Gaussian 03 package. The calculations show that in the presence of an acidic media, an enolate molecular ion leads directly to ω-acetokhellinone while in the basic media it leads to khellinone.     

O-乙酰基-吡喃木糖热解反应机理的理论研究

为了从微观上理解半纤维素热解过程及其主要产物的形成演变机理,采用密度泛函理论方法B3LYP/6-31G++(d,p),对O-乙酰基-吡喃木糖的热解反应机理进行了量子化学理论研究。在热解过程中,O-乙酰基-吡喃木糖中的O-乙酰基首先脱出,形成乙酸和中间体IM₁,该步反应能垒为269.4 kJ/mol。IM₁进一步发生开环反应形成IM₂,开环反应能垒较低,为181.8 kJ/mol。对中间体IM₂设计了四种可能的热解反应途径,对各种反应的反应物、产物、中间体和过渡态的结构进行了能量梯度全优化,计算了各热解反应途径的热力学和动力学参数。计算结果表明,反应路径(4)和反应路径(2)是O-乙酰基-吡喃木糖热解的主要反应通道,乙酸、乙醛、乙醇醛、丙酮、CO、CO₂、CH₄等小分子产物是热解的主要产物。这与相关实验结果分析是一致的。     

Theoretical mechanism study of UF6 hydrolysis in the gas phase

The mechanism of the gas-phase reaction UF 6 + H 2O --> UOF 4 + 2HF is explored using relativistic density functional theory calculations. Initially, H 2O coordinates with UF 6 to form a 1:1 complex UF 6.H 2O. Over an activation energy barrier of about 19 kcal/mol, H 2O transfers a H atom to a nearby ligand F, resulting in UF 5OH + HF. The eliminated HF or another H 2O molecule may form a hydrogen bond with UF 5OH. Starting from UF 5OH, the second HF elimination results in UOF 4. If UF 5OH is in the isolated form, UF 5OH --> UOF 4 + HF takes place over a barrier of 24 kcal/mol. If UF 5OH is hydrogen-bonded with H 2O or HF, the conversion barrier is less than 10 kcal/mol. Once formed, the unstable UOF 4 tends to associate with additional ligands and hydrogen-bonding donors. The calculated binding energies indicate the significance of such interactions, which may have profound impact on further HF eliminating reactions. The IR spectra features can be used to indicate the formation and interaction type of the intermediates and products.     

Theoretical and structural studies on mechanism of the Stec reaction

The mechanism of the Stec reaction between phosphoroselenanilidate or phosphonoanilidate and CS₂, activated by strong bases, has been studied computationally, using DFT methods, and experimentally, by low temperature ³¹P NMR spectroscopy. From molecular calculations, the reaction pathway of the reaction has been revealed with several transition states and intermediates, including a low energy spirocyclic pentacoordinate transition state and acyclic tetracoordinate intermediates, which eventually were correlated with short living molecules detected by NMR spectroscopy.     

甲醛光催化降解反应机理的量子化学研究

分别采用B3LYP,MP2方法在6-311++G(2df,pd)水平研究了甲醛光催化降解反应的微观机理,找到了可能的反应通道,预测反应产物为HCOOH与H2O.并得到了各反应通道的反应物、中间体、过渡态和产物的优化构型、谐振频率.成功地解释了实验结论.从键长和能量的变化角度,讨论了化学反应过程中化学键的变化规律,整个反应通道中各势能面均较低,从理论角度分析该反应室温下能够进行,为空气中的甲醛降解反应的实验研究提供理论依据.     

Kinetic and theoretical studies on the mechanism of alkaline hydrolysis of DNA

The reaction mechanism of alkaline hydrolysis of DNA has been investigated by kinetic analysis and density-functional-theory calculation. The rates of hydrolysis of thymidine 3'-monophosphate esters (including thymidylyl(3'-5')thymidine (Tp-OT)) monotonically decrease as the leaving groups get poorer. According to the theoretical calculation in which the solvent effects are incorporated, no intermediate is formed in the course of the reaction. In the alkaline hydrolysis of the activated Tp-OT analogues having good leaving groups, the 3',5'-cyclic monophosphate of thymidine is concurrently formed through the intramolecular attack by the 5'-alkoxide ion. In the hydrolysis of the native dinucleotide, however, this side reaction does not occur, since the transition state leading to the departure of its poor leaving group cannot be formed due to conformational restraint. These arguments are supported by the theoretical analysis on the hydrolysis of both dimethyl phosphate and its O(bridging)-->S substituted analogue.     

Theoretical studies of reaction mechanism in chemistry

After defining reaction mechanism, reaction path, reaction coordinate, reaction profile, and classical trajectories, dynamic and static approaches suitable (or promising) for analysis of reaction mechanism are critically discussed.     

Theoretical studies on the isomerization mechanism of the ortho-green fluorescent protein chromophore

We present a systematic theoretical investigation on the overall ground state and excited-state isomerization reaction mechanism of ortho-green fluorescent protein chromophore (o-HBDI) using the density functional theory and the multireference methods. The calculated results and subsequent analysis suggest the possible isomerization mechanism for o-HBDI. By comparison with experimental observation and detailed analysis, it is concluded that as initiated by the excited-state intramolecular proton transfer reaction, the conical intersection between the ground state and the excited state along the C4-C5 single-bond rotational coordinate is responsible for the rapid deactivation of o-HBDI.     

Theoretical study on the reaction mechanism for the hydrolysis of esters and amides under acidic conditions

The mechanisms underlying the hydrolysis of methyl acetate and acetamide under acidic conditions were investigated using the MP2/6-311+G(d,p)//MP2/6-31+G(d,p) level of theory. It was necessary to include two water molecules as reactants to obtain a tetrahedral (TD) intermediate for the A_AC2 mechanism that Ingold classified for the hydrolysis of methyl acetate. This mechanism includes two TS structures, one for the formation of the TD intermediate and the other for its decomposition. Since the activation energies were calculated to be 15.7 and 18.3 kcal mol⁻¹, the second step determines the rate of hydrolysis. The calculated value was close to that observed at ∼16 kcal mol⁻¹. It was confirmed that the A_AC2 mechanism had a barrier lower by 9.9 kcal mol⁻¹ than the A_AL2 mechanism. The A_AC2 mechanism is also applicable to the acid-catalyzed hydrolysis of acetamide. It is not the TD intermediate with which the NH₃⁺ moiety forms, but one further step is required to produce the final products, acetic acid and ammonium ion.     

Theoretical evaluation of the substrate-assisted catalysis mechanism for the hydrolysis of phosphate monoester dianions

Quantum chemistry methods coupled with a continuum solvation model have been applied to evaluate the substrate-assisted catalysis (SAC) mechanism recently proposed for the hydrolysis of phosphate monoester dianions. The SAC mechanism, in which a proton from the nucleophile is transferred to a nonbridging phosphoryl oxygen atom of the substrate prior to attack, has been proposed in opposition to the widely accepted mechanism of direct nucleophilic reaction. We have assessed the SAC proposal for the hydrolysis of three representative phosphate monoester dianions (2,4-dinitrophenyl phosphate, phenyl phosphate, and methyl phosphate) by considering the reactivity of the hydroxide ion toward the phosphorus center of the corresponding singly protonated monoesters. The reliability of the calculations was verified by comparing the calculated and the observed values of the activation free energies for the analogous S_N2(P) reactions of F⁻ with the monoanion of the monoester 2,4-dinitrophenyl phosphate and its diester analogue, methyl 2,4-dinitrophenyl phosphate. It was found that the orientation of the phosphate hydrogen atom has important implications with regard to the nature of the transition state. Hard nucleophiles such as OH⁻ and F⁻ can attack the phosphorus atom of a singly protonated phosphate monoester only if the phosphate hydrogen atom is oriented toward the leaving-group oxygen atom. As a result of this proton orientation, the SAC mechanism in solution is characterized by a small Brønsted coefficient value (β_lg=−0.25). This mechanism is unlikely to apply to aryl phosphates, but becomes a likely possibility for alkyl phosphate esters. If oxyanionic nucleophiles of pK_a<11 are involved, as in alkaline phosphatase, then the S_N2(P) reaction may proceed with the phosphate hydrogen atom oriented toward the nucleophile. In this situation, a large negative value of β_lg (−0.95) is predicted for the substrate-assisted catalysis mechanism.     

Theoretical studies on the mechanism of chlorination reaction of trichlorogermyl acrylic acid

The mechanism of the chlorination reaction of trichlorogermyl acrylic acid has been studied systematically using quantum chemistry methods. Geometries of reactants, transition states and products have been optimized at the B3LYP/6-311G(d,p) level. Vibrational frequencies, IR intensities and relative energies for various stationary points have been determined. The reaction pathways have been identified by intrinsic reaction coordinate (IRC) calculations. Theoretical analysis provides conclusive evidence that the process proceeds through two and three pathways for the first and second reaction steps, respectively.     

Theoretical studies on the hydrolysis of mono-phosphate and tri-phosphate in gas phase and aqueous solution

Phosphate hydrolysis by GTPases plays an important role as a molecular switch in signal transduction and as an initiator of many other biological processes. Despite the centrality of this ubiquitous reaction, the mechanism is still poorly understood. As a first step to understand the mechanisms of this process, the nonenzymatic hydrolysis of mono-phosphate and tri-phosphate esters were systematically studied in gas phase and aqueous solution using hybrid density functional methods. The dielectric effect of the environment on the energetics of these processes was also explored. Theoretical results show that for mono-phosphate ester, the dissociative pathway is much more favorable than the associative pathway. However, the reaction barriers for the dissociative and associative pathways of tri-phosphate hydrolysis are very close in aqueous solution, though the dissociative pathway is more favorable in the gas phase. High dielectric solvents, such as water, significantly lower the activation barrier of the associative pathway due to the greater solvation energy of the associative transition states than that of the reactant complex. By contrast, the barrier of the dissociative pathway, with respect to the gas phase, is less sensitive to the surrounding dielectric. In the associative hydrolysis pathway of the tri-phosphate ester, negative charge is transferred from the gamma-phosphate to beta-phosphate through the bridging ester oxygen and results in Pgamma-O bond dissociation. No analogous charge transfer was observed in the dissociative pathway, where Pgamma-O bond dissociation resulted from proton transfer from the gamma-phosphate to the bridge oxygen. Finally, the active participation of local water molecules can significantly lower the activation energy of the dissociative pathway for both mono-phosphate and tri-phosphate.     

Kinetic and theoretical studies on the mechanism of intramolecular catalysis in phenyl ester hydrolysis

The kinetic study of the hydrolysis reaction of Z-substituted phenyl hydrogen maleates (Z = H, m-CH3, p-CH3, m-Cl, p-Cl and m-CN) was carried out in aqueous solution, and the results were complemented with theoretical studies. Under some experimental conditions, two kinetic processes were observed. One of them was ascribed to maleic anhydride formation and the other to the anhydride hydrolysis. The Br?nsted-type plot for the leaving-group dependence was linear with slope beta(lg) = -1. The experimental results are consistent with a mechanism that involves significant bond breaking in the rate-limiting transition state (alpha(lg) = 0.64). Theoretical results for the reaction in the gas phase showed an excellent Br?nsted-type dependence with a beta(lg) of -1.03. A tetrahedral intermediate (TI) could not be found through DFT gas-phase studies (B3LYP/6-311+G*). Calculations carried out within a continuous solvation model or with discrete water molecules failed to find a stable TI. With both models, a flat region on the potential-energy surface is found and a tight optimization of the structures led back to starting materials. The theoretical results do not discard the possible existence of an unstable intermediate on the free-energy surface, but the analysis of the whole body of results compared with other acyl transfer reactions lead us to suggest that an enforced concerted mechanism is the most appropriate to describe these reactions.     

硫代双烯酮与硫甲醛环加成反应机理的理论研究

采用从头算HF/6-31G^*和密度泛函B3LYP/6-31++G^*^*方法研究了硫代双烯酮与硫甲醛两种可能的环加成反应的机理,并对反应各驻点进行了电子密度拓扑分析研究.结果表明,这两个生成不同四元杂环产物的平行反应均为有一两性离子中间体的分步反应.两个反应均较易进行,但反应(1)更容易一些,结果与实验一致.