Bifurcations of dividing surfaces in chemical reactions

We study the dynamical behavior of the unstable periodic orbit (NHIM) associated to the non-return transition state (TS) of the H(2) + H collinear exchange reaction and their effects on the reaction probability. By means of the normal form of the Hamiltonian in the vicinity of the phase space saddle point, we obtain explicit expressions of the dynamical structures that rule the reaction. Taking advantage of the straightforward identification of the TS in normal form coordinates, we calculate the reaction probability as a function of the system energy in a more efficient way than the standard Monte Carlo method. The reaction probability values computed by both methods are not in agreement for high energies. We study by numerical continuation the bifurcations experienced by the NHIM as the energy increases. We find that the occurrence of new periodic orbits emanated from these bifurcations prevents the existence of a unique non-return TS, so that for high energies, the transition state theory cannot be longer applied to calculate the reaction probability.     

Bifurcations and transition states

Bifurcations of reaction channels are related to valley-ridge inflection points and it is examined what happens when these do not coincide with transition states. Under such conditions there result bifurcating regions. There exist a number of different prototypes for such regions which are discussed explicitly on the basis of the pertinent Taylor expansions. When bifurcations occur close enough to transition states then there result bifurcating transition regions. An example for a bifurcating transition region is exhibited which is obtained from a quantum mechanical ab initio calculation for the ring opening of cyclopropylidene to aliene. In general there exist no orthogonal trajectory patterns which could serve as simplified models for channel bifurcations.Operated for the U.S. Department of Energy by Iowa State University under Contract No. W-7405-ENG-82. This work was supported by the Office of Basic Energy Sciences     

Role of stereoelectronic features of imine and enamine in (S)-proline catalyzed Mannich reaction of acetaldehyde: an in silico study

A detailed mechanistic investigation of sixteen possible diastereomeric pathways for the C-C bond formation step in (S)-proline catalyzed Mannich reaction of acetaldehyde with N-acetyl protected benzaldimine in acetonitrile solvent has been carried out to understand how stereoelectronic features invoke enantioselectivity of the final product. Both kinetic and thermodynamic factors of the reaction obtained using various density functional theory methods point out that si-enantiofacial nucleophilic attack of anti-enamine on the iminium carbon of the E, s-cis N-acetyl protected imine is the stereoselective pathway. Structural features of the transition states predicted that enamine in anti conformation attacks the imine through a Burgi-Dunitz trajectory to yield the stereocenter. Computations at B3LYP-PCM/6-311++G(3df,2p)//B3LYP-PCM/6-31G(d,p) level showed a strong linear correlation between Burgi-Dunitz angle and activation energy when anti-enamine is used as nucleophile to react with all the configurations of the imine. Further, energy decomposition analysis has been carried out at B3LYP/TZ2P+ level for all the transition states, which revealed that the most dominant factor that control the enantioselectivity of the (S)-proline catalyzed Mannich reaction is steric effect. Though the less favored transition states showed high amount of stabilizing orbital interaction, the destabilizing steric effects from both Pauli repulsion and preparation energy for the reactant molecules are very high and overshadowed the stabilizing effects. However, in the most favored transition state, a balanced outcome of electronic and steric effects was observed. Solvation effect was nearly same for all the transition states and electrostatic effects showed no correlation to the rank order of the energy of the transition states.     

N-甲基b-磺内酰胺氨解反应机理的理论研究

The aminolysis and the effect of water on the aminolysis processes of n-methyl β-sultam have been studied using density functional theory （DFF） method at the B3LYP/6-31G＊ level. The stationary structures and energies have been investigated for both reactions to find two different reaction channels. Specific and general solvent effects have been evaluated and the most favored pathway was found. The presence of solvent disfavors the reaction, whereas the participation of water in the aminolysis reaction plays a positive role and reduces the activation energy greatly. All transition states in the assisted aminolysis are 35-70 kJ/mol lower than those for the non-assisted reaction.     

Neutral zinc(II) O,O-di-alkyldithiopho- sphates-variable temperature 31P NMR and quantum chemical study of the ZDDP monomer-dimer equilibrium

A full line-shape analysis of the VT 31P NMR spectra was carried out for the monomer-dimer equilibrium of neutral ZDDP. The energy surface and the energetics of the monomer-dimer equilibrium (DeltaH degrees , DeltaG degrees , Ea, DeltaH(not equal), and DeltaG(not equal)) are reported for three variants wherein the alkyl groups in the ZDDP are 2-ethylhexyl, isopropyl, and isobutyl. We explored a reaction pathway between the monomer and dimer form by means of density functional theory (DFT). The linear combination of atomic orbitals (LCAO) code DMol3 was used together with a synchronous transient method to effectively locate transition states. Vibrational eigenmodes of all intermediates were computed to capture finite temperature effects. Methyl and ethyl were considered as alkyl groups. Two novel intermediates were located-a four-membered ring and a six-membered ring intermediate along the reaction coordinate. Comparison of the experimentally derived and computed energy surfaces was carried out.     

Substituent effects in pericyclic reactions of radical cations: the ring opening of 3-substituted cyclobutene radical cations

The substituent effects on the ring-opening reaction of cyclobutene radical cations have been studied at the Becke3LYP/6-31G* level of theory. The effect on the reaction energies and activation energies of the concerted and stepwise pathways of electron-donating substituents such as methyl and methoxy as well as electron-withdrawing substituents such as nitrile and carboxaldehyde in the 3-position of the cyclobutene is discussed. The exothermicity of the reaction correlates well with the ability of the substituent to stabilize the 1,3-butadiene radical cation by electron donation or conjugation. The relative stability of the (E) and (Z) isomers of the resulting 1,3-butadiene radical cations depends largely on steric effects. Similarly, steric effects are responsible for the relative energies of the different diastereomeric transition structures. The cyclopropyl carbinyl intermediate of the stepwise pathway resembles the nonclassical carbocation and is stabilized by electron-donating substituents. In the case of electron-donating substituents, this species becomes a minimum on the potential energy hypersurface, whereas unstabilized or destabilized cyclopropyl carbinyl radical cations are not minima on the hypersurface. The stabilization of the cyclopropyl carbinyl radical cation by substituents correlates qualitatively with the Brown-Okamoto substituent parameter sigma+. However, in all cases studied here, the concerted mechanism is the lowest energy pathway.     

6-甲基-4-羟基嘧啶单体及二聚体质子转移过程的理论研究

应用密度泛函理论的B3LYP/6-311+G(d)方法研究了6-甲基-4-羟基嘧啶单体及二聚体质子转移的异构化反应.对反应势能面的研究发现,该化含物可能存在9种单体异构体,对其最稳定的单体构型进行分析.各单体间异构化反应的过渡态共有9种,反应的活化能最小为22.06 kJ/mol,最大为356.55 kJ/mol,最可能的反应路径在室温下即可进行. 研究了2种二聚体及其异构化反应的过渡态,发现二聚体均比其对应的单体稳定,而且质子转移所需要的活化能仅为20.13 kJ/mol,比单体低很多. 氢键在这种变化中起了主要作用,由单体和二聚体的总能量计算了氢键的键能.     

Computational elucidation of the transition state shape selectivity phenomenon

The most commonly cited example of a transition state shape selective reaction, m-xylene disproportionation in zeolites, is examined to determine if the local spatial environment of a reaction can significantly alter selectivity. In the studied reaction, ZPE-corrected rate limiting energy barriers are 136 kJ/mol for the methoxide-mediated pathway and 109 to 145 kJ/mol for the diphenylmethane-mediated pathway. Both pathways are likely to contribute to selectivity and disfavor one product isomer (1,3,5-trimethylbenzene), but relative selectivity to the other two isomers varies with pore geometry, mechanistic pathway, and inclusion of entropic effects. Most importantly, study of one pathway in three different common zeolite framework types (FAU, MFI, and MOR) allows explicit and practically oriented consideration of pore shape. Variation of the environment shape at the critical transition states is thus shown to affect the course of reaction. Barrier height shifts on the order of 10-20 kJ/mol are achievable. Observed selectivities do not agree with the transition state characteristics calculated here and, hence, are most likely due to product shape selectivity. Further examination of the pathways highlights the importance of mechanistic steps that do not result in isomer-defining bonds and leads to a more robust definition of transition state shape selectivity.     

甲醇和氨对腺嘌呤水解脱氨机理的影响(英文)

用密度泛函理论在B3LYP/6-311G(d,p)水平上研究了甲醇和氨辅助的腺嘌呤水解脱氨机理,结果表明该反应首先是在水的亲核进攻下形成一个四面体结构中间体,然后该中间体通过构象变化得到两个不同构象,从而找到两条不同反应路径.在路径a中,辅助分子参与了过渡态的形成,起到转移氢原子的作用;而在路径b中,辅助分子仅作为介质,没有参与过渡态的形成.在氨辅助的情况下,腺嘌呤在亲核反应前发生了胺-亚胺异构化,而在甲醇辅助机理中则未发生该异构化.能量结果表明甲醇辅助腺嘌呤脱氨反应具有与水辅助类似的势垒,而氨辅助反应的势垒则比水辅助的高.     

Hiscotropic rearrangements: hybrids of electrocyclic and sigmatropic reactions

An unusual reaction manifold for cyclopropylcarbinyl cations, uncovered using B3LYP and MP2 calculations, is described. This reaction is a hybrid of a [1,2] sigmatropic hydrogen shift and a two-electron electrocyclic ring opening. These two processes occur through a single transition structure (i.e., they are concerted), although they are not synchronous. We call these reactions "hiscotropic" rearrangements. The potential energy surfaces for these reactions are often complicated, in some cases involving flat plateaus and bifurcations. Torquoselectivity occurs in some cases as a result of favorable orbital interactions between the breaking C-C and C-H bonds.     

Theoretical study of mechanism of forming a silapolycyclic compound between methylenesilylene and acetone

The mechanism of the cycloaddition reaction of forming a silapolycyclic compound between singlet methylenesilylene and acetone has been investigated with MP2/6‐31G* method, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. The energies of the different conformations are calculated by CCSD(T)//MP2/6‐31G* method. From the potential energy profile, we predict that the cycloaddition reaction of forming a silapolycyclic compound between singlet methylenesilylene and acetone has two competitive dominant reaction pathways. First dominant reaction pathway consists of four steps: (I) the two reactants (R1, R2) first form an intermediate (INT1) through a barrier‐free exothermic reaction of 46.2 kJ/mol; (II) intermediate (INT1) then isomerizes to a planar four‐membered ring product (P3) via transition state (TS3) with an energy barrier of 47.1 kJ/mol; (III) planar four‐membered ring product (P3) further reacts with acetone (R2) to form an intermediate (INT4), which is also a barrier‐free exothermic reaction of 40.0 kJ/mol; (IV) intermediate (INT4) isomerizes to a silapolycyclic compound (P4) via transition state (TS4) with an energy barrier of 57.0 kJ/mol. Second dominant reaction pathway consists of three steps: (I) the two reactants (R1, R2) first form a four‐membered ring intermediate (INT2) through a barrier‐free exothermic reaction of 0.5 kJ/mol; (II) INT2 further reacts with acetone (R2) to form an intermediate (INT5), which is also a barrier‐free exothermic reaction of 45.4 kJ/mol; (III) intermediate (INT5) isomerizes to a silapolycyclic compound (P5) via transition state (TS5) with an energy barrier of 49.3 kJ/mol. P4 and P5 are isomeric compounds. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

CH3S与HO2气相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CH3S自由基与HO2自由基的微观反应机理, 全参数优化了反应势能面上各驻点的几何构型, 振动分析和内禀反应坐标(IRC)分析结果证实了中间体和过渡态的真实性, 计算所得的键鞍点电荷密度的变化情况也确认了反应过程. 找到了五条可能的反应通道, 对结果的分析表明: 单线态反应通道(5) CH3S＋HO2→CH3SOOH (1P), 是所有通道中的主要反应通道. 该通道不需要克服过渡态能垒, 属于放热反应, 在动力学和热力学上都是最为有利的. 对于三线态反应通道来说, 通道(1)CH3S＋HO2→COM11→TS1→COM12→CH3SH＋O2 (3P)为主要反应通道, 控制步骤的活化能为53.5 kJ/mol, 能垒最低, 属于放热反应, 在动力学和热力学上都是有利的.     

Theoretical studies on the gas-phase pyrolysis of 2-phenoxycarboxylic acids: an ONIOM approach

Various ONIOM combinations-ONIOM(HF/6-31G*: PM3), ONIOM(B3LYP/6-31G*: PM3), ONIOM(MP2/6-31G*: PM3), and ONIOM(MP2/6-31G*: HF/3-21G)--were applied to investigate thermal decomposition mechanisms of four 2-phenoxycarboxylic acids (2-phenoxyacetic acid, 2-phenoxypropionic acid, 2-phenoxybutyric acid, and 2-phenoxyisobutyric acid) in the gas phase. All the transition states and intermediates of the reaction paths were optimized. The reaction pathway of four reactants yielding the phenol, CO, and the corresponding carbonyl compound was characterized on the potential energy surface and found to proceed stepwise. The first step corresponds to the elimination of phenol and the formation of alpha-lactone intermediate through a five-membered ring transition state, and the second step is the cycloreversion process of alpha-lactone intermediate to form CO and the corresponding carbonyl compound. The reaction pathway of latter three compounds to produce the carboxylic acid and phenol via a four-membered cyclic transition structure was also examined theoretically. Comparison with experiment indicates that the activation parameters for the fist reaction channel are accurately predicted at the ONIOM(MP2/6-31G*: HF/3-21G) level of theory.     

A growing string method for determining transition states: comparison to the nudged elastic band and string methods

Interpolation methods such as the nudged elastic band and string methods are widely used for calculating minimum energy pathways and transition states for chemical reactions. Both methods require an initial guess for the reaction pathway. A poorly chosen initial guess can cause slow convergence, convergence to an incorrect pathway, or even failed electronic structure force calculations along the guessed pathway. This paper presents a growing string method that can find minimum energy pathways and transition states without the requirement of an initial guess for the pathway. The growing string begins as two string fragments, one associated with the reactants and the other with the products. Each string fragment is grown separately until the fragments converge. Once the two fragments join, the full string moves toward the minimum energy pathway according to the algorithm for the string method. This paper compares the growing string method to the string method and to the nudged elastic band method using the alanine dipeptide rearrangement as an example. In this example, for which the linearly interpolated guess is far from the minimum energy pathway, the growing string method finds the saddle point with significantly fewer electronic structure force calculations than the string method or the nudged elastic band method.     

The importance of hydrogen's potential-energy surface and the strength of the forming R-H bond in surface hydrogenation reactions

An understanding of surface hydrogenation reactivity is a prevailing issue in chemistry and vital to the rational design of future catalysts. In this density-functional theory study, we address hydrogenation reactivity by examining the reaction pathways for N+H-->NH and NH+H-->NH(2) over the close-packed surfaces of the 4d transition metals from Zr-Pd. It is found that the minimum-energy reaction pathway is dictated by the ease with which H can relocate between hollow-site and top-site adsorption geometries. A transition state where H is close to a top site reduces the instability associated with bond sharing of metal atoms by H and N (NH) (bonding competition). However, if the energy difference between hollow-site and top-site adsorption energies (DeltaE(H)) is large this type of transition state is unfavorable. Thus we have determined that hydrogenation reactivity is primarily controlled by the potential-energy surface of H on the metal, which is approximated by DeltaE(H), and that the strength of N (NH) chemisorption energy is of less importance. DeltaE(H) has also enabled us to make predictions regarding the structure sensitivity of these reactions. Furthermore, we have found that the degree of bonding competition at the transition state is responsible for the trend in reaction barriers (E(a)) across the transition series. When this effect is quantified a very good linear correlation is found with E(a). In addition, we find that when considering a particular type of reaction pathway, a good linear correlation is found between the destabilizing effects of bonding competition at the transition state and the strength of the forming N-H (HN-H) bond.     

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．     

The Kinetic Isotope Effect as a Probe of Spin Crossover in the CH Activation of Methane by the FeO+ Cation

Two‐state reactivity (TSR) is often used to explain the reaction of transition‐metal–oxo reagents in the bare form or in the complex form. The evidence of the TSR model typically comes from quantum‐mechanical calculations for energy profiles with a spin crossover in the rate‐limiting step. To prove the TSR concept, kinetic profiles for C? H activation by the FeO⁺ cation were explored. A direct dynamics approach was used to generate potential energy surfaces of the sextet and quartet H‐transfers and rate constants and kinetic isotope effects (KIEs) were calculated using variational transition‐state theory including multidimensional tunneling. The minimum energy crossing point with very large spin–orbit coupling matrix element was very close to the intrinsic reaction paths of both sextet and quartet H‐transfers. Excellent agreement with experiments were obtained when the sextet reactant and quartet transition state were used with a spin crossover, which strongly support the TSR model.     

The IRC method in chemical reactions: Reaction ergodography for the addition of LiH to acetylene

The ab initio calculation have been performed on the addition of LiH to acetylene at RHF/3-21G basis set. The geometries and energies of the isolated reactant, molecular complex, transition state and product have been determined on the singlet potential energy surface of the ground state. Our results indicate that there is a meta stable molecular complex near the isolated reactant in the reaction pathway. The process from isolated reactant to molecular complex is a non-bonding-exchanging reaction process, and the process from molecular complex to product is the rate-controlling step of the reaction. We also estimate the activated entropy and the frequency factor of the rate-controlling step by using the RRKM theory. The FMO analysis for the transition state reveals the HOMO of transition state to be formed from both HOMO-LUMO and HOMO-HOMO interactions.     

3-甲基环状乙撑磷酸二酯醇解的反应途径研究

采用密度泛函理论和MP2方法研究了3-甲基环状乙撑磷酸二酯(MEP)与甲醇的反应途径: (I) CH3O－＋MEP; (II) CH3OH＋MEP; (III) CH3O－＋HMEP (MEP的质子化形式); (IV) CH3OH＋HMEP. 在B3LYP/6-31＋＋G(d,p)水平上优化了四条反应途径的反应物、中间体、过渡态及产物的几何构型, 并在同水平上进行了自然电荷分析, 然后在MP2/6-311＋＋G(3df,2p)水平上计算了各驻点的单点能. 采用极化连续介质模型(PCM)研究了各途径在苯、甲醇和水溶液中的溶剂化效应. 计算结果表明, 溶剂效应使途径(I)的自由能垒降低, 而使途径(II)和(IV)的决速步骤的自由能垒升高. 在气相和苯溶剂中途径(IV)是反应的优势途径, 在甲醇和水溶剂中途径(I)则成为最优. 研究结果进一步表明实验条件下途径(II)与(IV)对总醇解反应的贡献相当.     

Inorganic‐Base‐Mediated Hydroamination of Alkenyl Oximes for the Synthesis of Cyclic Nitrones

A method based on hydroamination mediated by inorganic base was developed for the synthesis of cyclic nitrones from alkenyl oximes. DFT calculations of the reaction pathway suggested that this hydroamination could proceed through an unprecedented nucleophilic amination of the unactivated alkene by the oxime nitrogen atom. The transition state of this reaction is stabilized by an ionic interaction between a metal cation such as K⁺ and the oxime oxygen and negatively charged alkene moiety.