Application of chemical graph theory for automated mechanism generation

We present an application of the chemical graph theory approach for generating elementary reactions of complex systems. Molecular species are naturally represented by graphs, which are identified by their vertices and edges where vertices are atom types and edges are bonds. The mechanism is generated using a set of reaction patterns (sub-graphs). These subgraphs are the internal representations for a given class of reaction thus allowing for the possibility of eliminating unimportant product species a priori. Furthermore, each molecule is canonically represented by a set of topological indices (Connectivity Index, Balaban Index, Schulz TI Index, WID Index, etc.) and thus eliminates the probability for regenerating the same species twice. Theoretical background and test cases on combustion of hydrocarbons are presented.     

Microcanonical statistical study of ortho-para conversion in the reaction H3+ + H2-->(H5+)*-->H3+ + H2 at very low energies

The ortho-para conversion of H(3) (+) and H(2) in the reaction H(3) (+)+H(2)-->(H(5) (+))(*)-->H(3) (+)+H(2) in interstellar space is possible by scrambling the five protons via (H(5) (+))(*) complex formation. The product distribution of the ortho-para conversion reaction can be given by ratios of cumulative reaction probabilities (CRP) calculated by microcanonical statistical theory with conservation of energy, motional angular momentum, nuclear spin, and parity. A statistical method to calculate the state-to-state reaction probabilities for given initial nuclear spin species, rotational states, and collision energies is developed using a simple semiclassical approximation of tunneling and above-barrier reflection. A new calculation method of branching ratios for given total nuclear spins and scrambling mechanisms is also developed. The anisotropic long-range electrostatic interaction potential of H(2) in the Coulomb field of H(3) (+) is taken into account using the first-order perturbation theory in forming the complex. The CRPs and the product distribution of the ortho-para conversion reaction at very low energies with reactants in their ground vibronic and lowest rotational states for given initial nuclear spin species are presented as a function of collision energy assuming complete proton scrambling or incomplete proton scrambling. The authors show that the product distribution at very low energies (or very low temperatures) differs substantially from the high energy (or high temperature) limit branching ratios.     

Reaction rates and dissolution mechanisms of quartz as a function of pH

In this computational study, we present the dissolution rates for quartz as a function of pH at 298 K. At any given pH, the dissolution of the quartz surface depends on the distribution of protonated, deprotonated, or neutral species. The dissolution mechanism for each of these three species was investigated by ab initio electronic structure calculations to obtain the reaction profile. Using the barrier height along with the partition functions for the transition state and the reactants in the rate-limiting steps, we calculated the TST rate constants for the reactions for the temperature range of 200-500 K. At 298 K the rate constant (s-1) for the dissolution of neutral species was found to be several orders of magnitude smaller than the rate-limiting steps for the protonated and deprotonated species. The values of the rate constants were used in the rate law expression to calculate the overall dissolution rate (mol m-2 s-1) at a given pH. The calculated rates were compared to previously reported experimental and theoretical rates and were found to be in good agreement over 2-12 pH range.     

Combined DFT, QCISD(T), and G2 mechanism investigation for the reactions of carbon monophosphide CP with unsaturated hydrocarbons allene CH2CCH2 and methylacetylene CH3CCH

The possible reaction product distribution and mechanism of carbon monophosphide CP with unsaturated hydrocarbons allene CH(2)CCH(2) and methylacetylene CH(3)CCH are investigated at the B3LYP/6-311+G(d,p), QCISD(T)/6-311++G(2df,2p), and G2 levels of theory. Corresponding reactants, products, intermediates, and interconversion and dissociation transition states are located on the reaction potential energy profiles. Computation results show that in the reaction of CP with CH(2)CCH(2) the dominant reaction product should be species CH(2)CCHCP. Also, we can suggest species HCCCH(2)CP as a secondary reaction product despite of only minor contribution to reaction products. In the reaction of CP with CH(3)CCH, the primary and secondary products are suggested to be two important molecules HCCCP and CH(3)CCCP, respectively. The predicted mechanisms for the two reactions are not in parallel with the reactions of CN with allene CH(2)CCH(2) and methylacetylene CH(3)CCH given in previous studies. The present calculations provide some useful information for future possible experimental isolation and observation for some interesting unsaturated carbon-phosphorus-bearing species.     

中性水杨醛亚胺镍催化烯烃聚合反应链引发机理的密度泛函研究

采用密度泛函理论(DFT),以乙烯为模型,在B3LYP/LANL2MB水平上研究了中性水杨醛亚胺镍催化烯烃聚合反应链引发机理.通过几何构型全优化,得到了链引发阶段的反应物、产物、中间体和过渡态的最可几构型.由于该催化剂中,与中心原子N i相联接的配体不对称性,使得反应存在两条可能路径(路径A甲基位于N i—O键的对位,路径B甲基位于N i—N键的对位).分别对这两条路径进行了分析和比较.结果表明反应并不只是简单地按一条路径进行,而是通过相互竞争,最终使反应在两条路径间转换,形成一条在能量上最为有利的反应途径.     

Transmetalation reactions from Fischer carbene complexes to late transition metals: a DFT study

Transmetalation reactions from chromium(0) Fischer carbene complexes to late-transition-metal complexes (palladium(0), copper(I), and rhodium(I)) have been studied computationally by density functional theory. The computational data were compared with the available experimental data. In this study, the different reaction pathways involving the different metal atoms have been compared with each other in terms of their activation barriers and reaction energies. Although the reaction profiles for the transmetalation reactions to palladium and copper are quite similar, the computed energy values indicate that the process involving palladium as catalyst is more favorable than that involving copper. In contrast to these transformations, which occur via triangular heterobimetallic species, the transmetalation reaction to rhodium leads to a new heterobimetallic species in which a carbonyl ligand is also transferred from the Fischer carbene to the rhodium catalyst. Moreover, the structure and bonding situation of the so far elusive heterobimetallic complexes are briefly discussed.     

Evaluation of potential reaction mechanisms leading to the formation of coniferyl alcohol α-linkages in lignin: a density functional theory study

Five potential reaction mechanisms, each leading to the formation of an α-O-4-linked coniferyl alcohol dimer, and one scheme leading to the formation of a recently proposed free-radical coniferyl alcohol trimer were assessed using density functional theory (DFT) calculations. These potential reaction mechanisms were evaluated using both the calculated Gibbs free energies, to predict the spontaneity of the constituent reactions, and the electron-density mapped Fukui function, to determine the most reactive sites of each intermediate species. The results indicate that each reaction in one of the six mechanisms is thermodynamically favorable to those in the other mechanisms; what is more, the Fukui function for each free radical intermediate corroborates with the thermochemical results for this mechanism. This mechanism proceeds via the formation of two distinct free-radical intermediates, which then react to produce the four α-O-4 stereoisomers.     

Molecular emission characteristics of various fluorides in a low-temperature-hydrogen diffusion flame

A capillary burner supporting a nitrogen/hydrogen diffusion flame has been evaluated as a possible means of detection for several volatile fluorides after their gas-chromatographic separation. The fluorides of As, B, C, Ge, I, Mo, P, Re, S, Sb, Se, Si, Te and W were formed by the reaction of the element with chlorine trifluoride, and the intense molecular emission given by each was recorded. An attempt was made to identify the emitting species.     

Structure, bonding, and aggregation of selenium-containing organolithium species

1,3-Dioxo compounds can be prepared from selenium-mediated carbonylation of lithium enolates in the presence of carbon monoxide. Intermediates in this reaction include several organic species that contain both selenium and lithium. The first step in understanding the detailed reaction mechanism is to understand the structure of these intermediates. Like most organolithium compounds, these species can exist as aggregates in solution. The B3LYP density functional theory (DFT) method was used to examine the gas phase and THF solvated structures of these compounds. The calculations showed that each of the compounds forms dimers or higher aggregates in the gas phase. Aggregates are also formed in THF solution, although solvation favors lower aggregates as compared to the gas phase.     

The mechanism of C--X (X=F, Cl, Br, and I) bond activation in CX4 by a stabilized dialkylsilylene

The potential-energy surfaces for the abstraction and insertion reactions of dialkylsilylene with carbon tetrahalides (CX4) have been characterized in detail using density functional theory (B3LYP), including zero-point corrections. Four CX4 species, CF4, CCl(4), CBr4, and CI(4), were chosen as model reactants. The theoretical investigations described herein suggest that of the three possible reaction paths, the one-halogen-atom abstraction (X abstraction), the one-CX3-group abstraction (CX3 abstraction), and the insertion reaction, the X-abstraction reaction is the most favorable, with a very low activation energy. However, the insertion reaction can lead to the thermodynamically stable products. Moreover, for a given stable dialkylsilylene, the chemical reactivity has been found to increase in the order CF4相似文献   

苯胺和乙二醇生成吲哚反应机理的DFT理论研究

利用传统过渡态理论研究了苯胺和乙二醇生成吲哚反应的机理,设计了四种可能的反应通道.优化计算了反应物、产物和每个通道中可能的中间体和过渡态的几何构型,找出并确认了每个反应通道中各基元反应的可能过渡态和活化能.经分析对比给出该反应可能的主反应通道.同时初步探讨了在经过渡态TS1的基元反应中加入催化剂Ag后的反应机理.加入催化剂后,反应的活化能降低.     

丁烯自由基和O2反应机理的理论研究

应用量子化学密度泛函理论(DFT)对丁烯自由基C₄H₇和O₂的反应机理进行了研究. 在B3LYP/6-31G(d,p)水平上优化了反应通道上的反应物、中间体、过渡态和产物的几何构型, 并计算出它们的振动频率和零点能(ZPVE), 并对能量进行了零点能校正. 计算结果表明, C₄H₇和O₂形成三种氧环中间体, 再分别分解, 这是主要的反应形式. 生成物主要为羰基化合物, 其次还有一定比例的CO.     

Structure of diepoxide–diamine network polymers. II. Soluble chemical species

Gel permeation chromatography has been used to separate diepoxide–diamine oligomers, produced at a variety of stoichiometric ratios, into individual chemical species. Probability theory has been applied to calculate expressions for the amounts of each of these compounds and close agreement has been found with the experimental results. In conjunction with previous conclusions, this provides compelling evidence in favor of a purely random reaction mechanism, contrary to the inhomogeneous network-forming mechanism suggested by other workers. The effect of adding an inert diluent prior to reaction has been investigated and it is evident that the fraction of intramolecularly formed bonds increases as the concentration of polymer decreases.     

Reaction Mechanisms and Kinetics of the Melt Transesterification of Bisphenol‐A and Diphenyl Carbonate

The catalyzed and uncatalyzed reaction mechanisms of the melt transesterification process of bisphenol‐A and diphenyl carbonate are proposed based on nucleophilic substitution at the carbonyl group of the reactants. The reaction paths and energy barriers of the melt transesterification reaction were predicted and identified via density functional theory (DFT) calculations. The calculations reveal that the different oligomers with only one repeating unit are formed through different thermal processes. The theoretical evaluation further indicates that the basic hydroxide catalysts can reduce the energy barrier for the transesterification reaction, which allows subsequent nucleophilic attack to easily occur. Furthermore, the reaction kinetics of transesterification using tetraethyl ammonium hydroxide as a catalyst were investigated experimentally over a temperature range of 155–175°C. The reaction rate constants and equilibrium constants were determined based on the functional group model, and the equilibrium constants decreased with increasing reaction temperature. A detailed molecular species model with a specific repeating unit (n = 3) was developed and applied to predict the change in the reactants, oligomers, and phenol, and the experimental data and model calculation agree quite well. The standard curves of the oligomer were reversely derived, which provide intuitive insight into the concentration change of each oligomer. Both the DFT calculations and experimental results indicate that the C1 oligomer is first formed, and some of which are then converted to other types or higher molecular weight oligomers.     

Theoretical study of thermal rearrangements of 1-hexen-5-yne, 1,2,5-hexatriene, and 2-methylenebicyclo[2.1.0]pentane

In this research, a comprehensive theoretical investigation of the thermal rearrangements of 1-hexen-5-yne, 1,2,5-hexatriene, and 2-methylenebicyclo[2.1.0]pentane is carried out employing density functional theory (DFT) and high level ab initio methods, such as the complete active space self-consistent field (CASSCF), multireference second-order M?ller-Plesset perturbation theory (MRMP2), and coupled-cluster singles and doubles with perturbative triples [CCSD(T)]. The potential energy surface (PES) for the relevant system is explored to provide a theoretical account of pyrolysis experiments by Huntsman, Baldwin, and Roth on the target system. The rate constants and product distributions are calculated using theoretical kinetic modelings. The rate constant for each isomerization reaction is computed using the transition state theory (TST). The simultaneous first-order ordinary-differential equations are solved numerically for the relevant system to obtain time-dependent concentrations, hence the product distributions at a given temperature. Our computed energy values (reaction energies and activation parameters) are in agreement with Roth's experiments and the product distributions of Huntsman's experiments at 340 and 385 °C with various reaction times, while simulated product fractions are in qualitative accordance with Baldwin's experiment.     

Monitoring of chemical reactions within microreactors using an inverted Raman microscopic spectrometer

An inverted Raman microscope spectrometer has been used to profile the spatial evolution of reactant and product concentrations for a chemical reaction within a microreactor operating under hydrodynamic flow control. The Raman spectrometer was equipped with a laser source at wavelength of 780 nm, confocal optics, a holographic transmission grating, and a charge-coupled device (CCD) detector. The microreactor consisted of a T-shaped channel network etched within a 0.5 mm thick glass bottom plate that was thermally bonded to a 0.5 mm thick glass top plate. The ends of the channel network were connected to reagent reservoirs that were linked to a syringe pump for driving the solutions by hydrodynamic pumping within the channels. The microchannels were 221 micro m wide and 73 micro m deep. The synthesis of ethyl acetate from ethanol and acetic acid was investigated as a model system within the microreactor as Raman scattering bands for each reactant and product species were clearly resolved. Raman spectral intensities of each band were proportional to concentration for each species and hence all concentrations could be quantitatively measured after calibration. By scanning specific Raman bands within a selected area in the microchannel network at given steps in the X-Y plane, spatially resolved concentration profiles were obtained under steady-state flow conditions. Under the flow conditions used, different positions within the concentration profile correspond to different times after contact and mixing of the reagents, thereby enabling one to observe the time dependence of the product formation. Raman microscopy provides a useful complementary technique to UV/VIS absorbance and fluorescence methods for the in situ monitoring and analysis of chemical reaction species having their lowest S(0)-S(1) absorption bands too far in the UV to be of use, due to their probable overlap with the bands from other reactant, product and solvent molecules.     

O2-coverage-dependent CO oxidation on reduced TiO2(110): A first principles study

First principles periodic slab calculations based on gradient-corrected density functional theory have been performed to investigate CO oxidation on rutile TiO2(110) at varying O2 coverages (theta = 1, 2, and 3, where theta is defined as the number of O2 per oxygen vacancy). For each coverage we only present the reaction of CO with oxygen species in the most stable configuration. Our results show a significant variation in the oxidation activation energy with O2 coverage.