Topological analysis of catalytic reaction networks: Methanol decomposition on Pt(111)

We describe our new reaction route (RR) graph approach as a powerful new tool for topological mechanistic and kinetic analysis of catalytic reaction networks, illustrated here with the help of methanol decomposition on Pt(111). In this approach a graph-theoretic network of molecular reaction steps is first constructed for the overall reaction (OR), on which each mechanistic step is represented by a directed branch interconnected at nodes, such that all conceivable reaction pathways can then be traced on it simply as walks or paths. Further, the network is consistent with the basic laws of flow graphs, so that it is suitable for a quantitative analysis. In fact, a direct analogy can be made to an equivalent wiring diagram, which allows tools of electric circuit analysis, namely, Kirchhoff's laws of current (rate) and potential (affinity), to be directly utilized for a rigorous flux analysis of the network. As a result, the dominant pathways as well as the rate-limiting steps (RLS) become transparent. This furthermore facilitates network pruning to retain only the essential steps and pathways. The RR graph approach when combined with ab initio kinetics, thus, provides a rigorous new framework for analyzing the mechanism and kinetics of catalytic reactions. It is, thus, found that methanol decomposition proceeds exclusively via the initial CH dehydrogenation step rather than through OH bond activation.     

Gas-phase kinetic of boron carbide chemical vapor deposition using BCl3+CH4+H2 mixture

A detailed chemical kinetic mechanism consisting of 472 reactions and 61 species for the gas-phase thermal decomposition of BCl₃+CH₄+H₂ mixtures is used to model the chemical vapor deposition (CVD) of boron carbide. The mechanism is constructed using a reaction mechanism generator (RMG), which is automatic and requires no or less human intervention. New functionality, considerable thermodynamic and kinetic data have been added to RMG to account for boron chemistry. The model considers all necessary reactions in the reaction pathways and reasonably predicts the experimental data available from the literature. The sensitivity analysis identifies crucial species responsible for boron carbide formation. Besides, a reduced mechanism (15 species and 26 reactions) is derived from a detailed mechanism, which could be used to expedite an effective CVD reactor design through numerical simulations. The performance of the reduced model is also evaluated concerning the complete mechanism, which shows that the reduced model can predict the reactor behavior reasonably well.     

Thiophene conversion under mild conditions over a ZSM-5 catalyst

Refiners are nowadays actively considering the post-treating FCC gasoline processes as a viable and less costly approach for meeting sulfur environmental regulations. Most promising catalytic desulfurization processes do not require hydrogen addition, including between others the use of zeolites as adsorbents/catalysts. This type of desulfurization leads to the formation of significant amounts of coke, requiring keeping high catalyst activity a continuous twin fluidized bed system (fluidized-bed reactor, fluidized bed regenerator). This study evaluates the catalytic conversion of thiophene and/or thiophene in n-octane mixtures. Catalytic experiments are carried out in the CREC riser simulator under mild conditions, using H-ZSM5 zeolite dispersed in a silica matrix. The experimental results obtained demonstrate a higher selective conversion of thiophene over n-octane. It is shown that thiophene conversion proceeds via ring opening and alkylation yielding H₂S, alkyl-thiophenes, benzothiophene, and coke, with no measurable thiophene saturation or dimerization reactions observed. The experimental results are also supported with an extensive thermodynamic analysis that includes all the possible thiophene conversion pathways over zeolites. On this basis and using as a reference the observable measurable species, a reaction network is proposed to represent the thiophene catalytic conversion under the suggested gasoline post treatment conditions.     

Cleavage of blocked isocyanates within amino-type resins: Influence of metal catalysis on reaction pathways in model systems

In the present work, a detailed account on the deblocking reactions of various blocked isocyanates in aqueous reaction media in the presence of amido- and hydroxyl-nucleophiles is given. Pyrazole- and oxime-blocked phenylisocyanate were reacted with monomethylolurea (MMU), dimethylolurea (DMU) and urea (U) in the presence of the catalysts (dibutyltin dilaurate DBTL 1, zirconium(IV)dionate 2, zinc(II)acetate 3 and manganese (III)dionate 4). Product formation was studied by kinetic analysis of either the hydrolytic or the additive reaction pathways, revealing strong differences in the reactions pathways of the used catalysts. Both zirconium(IV)dionate 2 and DBTL 1 lead to the formation of N-phenyl-N′-carbamidurea and N,N′-diphenylcarbamidurea 15 as the preferred products after reaction with urea as nucleophile, whereas zinc(II)acetate and manganese(III)dionate indicated a significantly stronger promotion of hydrolytic reaction pathways. Zirconium(IV)dionate 2 catalyst proved advantageous over DBTL 1 displaying a lower deblocking temperature.     

Mechanisms of Enzyme-Catalyzed Reduction of Two Carcinogenic Nitro-Aromatics, 3-Nitrobenzanthrone and Aristolochic Acid I: Experimental and Theoretical Approaches

This review summarizes the results found in studies investigating the enzymatic activation of two genotoxic nitro-aromatics, an environmental pollutant and carcinogen 3-nitrobenzanthrone (3-NBA) and a natural plant nephrotoxin and carcinogen aristolochic acid I (AAI), to reactive species forming covalent DNA adducts. Experimental and theoretical approaches determined the reasons why human NAD(P)H:quinone oxidoreductase (NQO1) and cytochromes P450 (CYP) 1A1 and 1A2 have the potential to reductively activate both nitro-aromatics. The results also contributed to the elucidation of the molecular mechanisms of these reactions. The contribution of conjugation enzymes such as N,O-acetyltransferases (NATs) and sulfotransferases (SULTs) to the activation of 3-NBA and AAI was also examined. The results indicated differences in the abilities of 3-NBA and AAI metabolites to be further activated by these conjugation enzymes. The formation of DNA adducts generated by both carcinogens during their reductive activation by the NOQ1 and CYP1A1/2 enzymes was investigated with pure enzymes, enzymes present in subcellular cytosolic and microsomal fractions, selective inhibitors, and animal models (including knock-out and humanized animals). For the theoretical approaches, flexible in silico docking methods as well as ab initio calculations were employed. The results summarized in this review demonstrate that a combination of experimental and theoretical approaches is a useful tool to study the enzyme-mediated reaction mechanisms of 3-NBA and AAI reduction.     

Improvement of ethylene cracking reaction network with network flow analysis algorithm

Reaction network model is central to ethylene cracking process simulation. Studying an ethylene cracking reaction (ECR) network, which involves hundreds of components and thousands of reactions, becomes a difficult task. To facilitate a rapid and comprehensive reaction network analysis and improve ECR network, this paper introduced a ranking algorithm called network flow analysis algorithm (NFAA) to a reaction network analysis procedure. NFAA analyses the reaction network with comprehensive information such as network topological structure, reaction mechanism, and process model data. Following NFAA, reactions and species are ranked based on their significances. According to the ranking of reactions, unimportant reactions (lower ranking) in ECR network are removed to reduce ECR network complexity and decrease computational scale without loss of prediction accuracy. On the other hand, rankings provide guidance on adjusting parameters of ECR network. The application of NFAA makes a progress in improvement of ECR reaction network in an industrial case.     

Inference of chemical reaction networks

This paper demonstrates how, in principle, a chemical reaction mechanism (reaction network) can be inferred using relatively simple systematic mathematical and statistical analyses of experimental data obtained from chemical reactors. This method involves specifying a global ordinary differential equation (ODE) model structure capable of representing an entire set of possible chemical reactions. Mathematical and statistical tests are then used to reduce the ODE model structure to a subset of reactions. Finally, a model rationalisation procedure, relying on exploiting the basic rules of reaction chemistry, is used to obtain a consistent set of reactions which are combined to give the overall reaction network. The identification procedure is demonstrated for pure batch operation with a worked example using simulated noisy data from an extended Van de Vusse reaction network consisting of five species and four elementary reactions [Van de Vusse, J.G., 1964. Plug-flow type reactor versus tank reactor. Chemical Engineering Science 19, 994-997]. A further case study of a semi-batch (fed batch) system using simulated data from a simplified biodiesel system, with six chemical species involved in three elementary reactions, is provided. It is shown that the method is able to correctly identify the underlying structure of the network of chemical reactions and provide accurate estimates of the network rate constants.     

The Mechanism of HDS Catalysis

The mechanism of heterogeneous catalytic reactions is much more difficult to elucidate than that of homogeneous systems. Despite the facilities provided by physical methods for investigating the surface of solids, obtaining detailed information on the structure of the active component in real heterogeneous catalysts presents difficulties due to the nonuniform chemical composition of the surface species. Some of these surface species are totally inactive in catalysis, and others can catalyze the given chemical reaction by different pathways and according to different mechanisms. This results in a change of selectivity to the desired product and the appearance of intermediates and reaction by-products. Furthermore, the effect of the reaction medium on the catalyst gains importance during a catalytic process when, at high temperature and pressure, one type of surface species is transformed into another, thus changing the mechanism and direction of the catalyzed reaction.

     

Metabolic engineering of aromatic group amino acid pathway in Bacillus subtilis for L-phenylalanine production

Metabolic control sites in the aromatic group amino acid pathway (AAAP) of Bacillus subtilis for L-Phenylalanine (Phe) overproduction were determined; and aiming pathway flux amplification, by cloning the flux controlling gene aroH to a multi-copy plasmid, the impact of single gene cloning on pathway flux distributions were investigated. The branch-point metabolites E4P and PEP+E4P supplied in vitro, enhanced Phe production and well defined perturbations were achieved on the AAAP reactions. The intracellular reaction rate distributions calculated by a mass flux balance-based stoichiometric model for B. subtilis based on the metabolic reaction network that contains 184 metabolites and 232 reaction fluxes using time profiles of glucose, dry cell, organic and amino acids, revealed that induction by E4P influenced the pathway reactions via chorismate and prephanate towards Phe by increasing the flux values. The reaction catalysed by chorismate mutase (R96) has the lowest flux value among the preceding reactions of the pathway that reduces the proceeding reaction rates towards Phe. Thus, R96 is predicted to be the primary rate-limiting step among the Phe pathway reactions. On the basis of the strategy designed, the cloning of aroH gene encoding chorismate mutase was achieved first onto the E.coli plasmid pUC19, and its expression was demonstrated to compare its performance. Thereafter, aroH was sub-cloned onto the multi-copy plasmid pMK4 and transferred into host B.subtilis mutants. The performance of r-E.coli carrying pUC19::aroH was lower than the r-B.subtilis strains carrying the pMK4::aroH; and, the highest Phe production was obtained with r-B. subtilis 1A263. The comparison of the calculated intracellular fluxes of r-B. subtilis 1A263 with that of the wild type revealed that the flux of the first reaction of the AAAP was 1.2-fold, but the engineered R96 was 7.2-fold higher in r-B.subtilis 1A263.     

Contributions of heterogeneous and homogeneous chemistry in the catalytic partial oxidation of octane isomers and mixtures on rhodium coated foams

Catalytic partial oxidation experiments with n-octane, 2,2,4-trimethylpentane (i-octane), and an n-octane:i-octane (1:1) mixture were performed on 80 and 45 ppi Rh-coated α-alumina foam supports at 2, 4, and 6 SLPM total flow rate in order to explore the effects of chemical structure for single components and binary mixtures on fuel reactivity and product distribution. When reacted as single components, the conversion of i-octane is greater than n-octane at C/O>1.1 (both fuel conversions are 100% for C/O<1.1). However, when reacted in an equimolar mixture, the conversion of n-octane is greater than i-octane. All three fuels give high selectivity to syngas (H₂ and CO) on 80 ppi supports for C/O<1. For C/O>1, n-octane produces high selectivity to ethylene while i-octane makes i-butylene and almost no ethylene. The fuel mixture produces these species proportional to the mole fractions of n-octane and i-octane within the reacting mixture. Increasing the support pore diameter decreases the selectivity to syngas and increases H₂O and olefin selectivity.The reforming of all three fuels is modeled using detailed chemistry by decoupling the heterogeneous and homogeneous chemistry in a two-zone plug flow model. Detailed homogeneous reaction mechanisms with several thousand elementary reactions steps and several hundred species are used to simulate experimentally observed olefin selectivities for all three fuels on 80 and 45 ppi monoliths at 2, 4, and 6 SLPM quite well. These results support the hypothesis that a majority of the observed olefins are made through gas-phase chemistry.     

Kinetic analysis of NO-sensitized methane oxidation

The role of NO-sensitized oxidation during the product-gas entrainment of a low-NO_x, multi-jet, natural gas burner is investigated. A detailed kinetic mechanism for the NO-sensitized oxidation of CH₄, consisting of 483 reactions and 69 species, is used for the kinetic analysis. An eigenvalue-eigenvector decomposition is performed on normalized sensitivity coefficients to study the important reactions using principal component analysis (PCA), and the loadings corresponding to the largest eigenvalue are used to identify the reaction pathways of NO-sensitized oxidation. The main reaction pathway is most strongly affected by the temperature profile and equivalence ratio. Also, a reduced kinetic scheme of 110 reactions and 47 species is developed by eliminating reactions with small loadings. The temporal evolution of reactions is investigated using functional PCA, in which the functional loadings reflect the importance of reactions as a function of time. A discretization approach is used to perform the functional PCA.     

Fusion Enzymes Involved in Biosynthetic Tailoring Reactions in Fungi

Enzyme fusion, the fusion of enzymes with different domains to a single protein, has been widely recognized as a promising strategy in the development of biocatalysts. Nature has evolved gene fusion to combine different catalytic enzymes to function as a fusion enzyme, and this strategy is utilized in many natural product biosynthetic pathways. Owing to rapid advances in genome sequencing and biosynthetic pathway characterization, there is increasing interest in fusion enzymes from fungal biosynthetic pathways, particularly those involved in tailoring steps. This concept aims to provide an up-to-date overview of fusion enzymes that catalyze tailoring reactions in the biosynthesis of fungal secondary metabolites. Since fungal fusion enzymes are often associated with novel metabolites, this pioneering work may stimulate the exploration of the structural diversity of fungal natural products through genome mining of the untapped biosynthetic pathways involving fusion enzymes.     

Ru(III)/Os(VIII) Catalysed Oxidation of Gabapentin (Neurotin) Drug by Diperiodatoargentate(III) in Aqueous Alkaline Medium (Stopped Flow Technique): A Comparative Study

The kinetics of ruthenium(III) (Ru(III)) and osmium(VIII) (Os(VIII)) catalysed oxidation of neuroleptic drug, gabapentin (GBP) by diperiodatoargentate(III) (DPA) in alkaline medium at 27 °C and a constant ionic strength of 0.60 mol dm^?3 was studied spectrophotometrically. The oxidation products in both the cases are 1-(hydroxymethyl) cyclohexane acetic acid and Ag(I). The stoichiometry is the same in both the catalysed reactions i.e. [gabapentin]:[DPA] = 1:1. The reaction is of first order in Os(VIII)/Ru(III) and [DPA] and has less than unit order in both [GBP] and [alkali]. The oxidation reaction in alkaline medium has been shown to proceed via a Os(VIII)/Ru(III)-gabapentin complex, which further reacts with one mole of monoperiodatoargentate(III) (MPA) species in a rate determining step followed by other fast steps to give the products. The main products were identified by spot test and spectroscopic studies. The reaction constants involved in the different steps of the mechanism are calculated. The catalytic constant (K _c) was also calculated for both catalysed reactions at different temperatures. From the plots of log K _c versus 1/T, values of activation parameters with respect to the catalyst have been evaluated. The activation parameters with respect to slow step of the mechanism are computed and discussed and thermodynamic quantities are also determined. It has been observed that the catalytic efficiency for the present reaction is in the order of Os(VIII)>Ru(III). The probable active species of catalyst and oxidant have been identified.     

Hydrogenated hydroxy-functionalized polyisoprene (H-HTPI) and isocyanurate of isophorone diisocyanates (I-IPDI): reaction kinetics study using FTIR spectroscopy

The reaction between a hydrogenated hydroxyl-functionalized polyisoprene (H-HTPI) and isophorone diisocyanate isocyanurate (I-IPDI) is followed by using direct FTIR spectroscopy. The reaction kinetics is studied using a simple model taking into consideration the I-IPDI structure. The rates of individual isocyanate groups are described by a second order equation. Influence of dibutyltin dilaurate (DBTL) concentration and temperature on selectivity, defined as the ratio between the rate constant of secondary isocyanate group and the rate constant of the primary isocyanate group, is investigated. It is observed that selectivity decreases when temperature or DBTL concentration increases. Eyring parameters are determined for the catalyzed [ΔH^*=77/35 (kJ mol⁻¹), ΔS^*=12/−100 (J mol⁻¹ K⁻¹)] and uncatalyzed reactions [ΔH^*=48/43 (kJ mol⁻¹), ΔS^*=−179/−167 (J mol⁻¹ K⁻¹)] primary and secondary isocyanate groups being differentiated.     

Are the Genes nadA and norB Involved in Formation of Aflatoxin G1?

Aflatoxins, the most toxic and carcinogenic family of fungal secondary metabolites, are frequent contaminants of foods intended for human consumption. Previous studies showed that formation of G-group aflatoxins (AFs) from O-methylsterigmatocystin (OMST) by certain Aspergillus species involves oxidation by the cytochrome P450 monooxygenases, OrdA (AflQ) and CypA (AflU). However, some of the steps in the conversion have not yet been fully defined. Extracts of Aspergillus parasiticus disruption mutants of the OYE-FMN binding domain reductase-encoding gene nadA (aflY) contained a 386 Da AFG₁ precursor. A compound with this mass was predicted as the product of sequential OrdA and CypA oxidation of OMST. Increased amounts of a 362 Da alcohol, the presumptive product of NadA reduction, accumulate in extracts of fungi with disrupted aryl alcohol dehydrogenase-encoding gene norB. These results show that biosynthesis of AFG₁ involves NadA reduction and NorB oxidation.     

Exploring flux representations of complex kinetics networks

To extract meaningful information from complex kinetic models involving a large number of species and reactions, advanced computational techniques are required. In this work, new approaches have been proposed based on element flux calculations for systematic kinetic analysis of complex reaction models. These approaches quantify element transformation flux between species to determine a metric that accurately captures the production and consumption of species. Furthermore, a graph searching procedure is employed to retrieve all possible reaction pathways from the highly complex reaction networks. Element fluxes involved in these pathways provide an indicator to quantitatively evaluate pathway activities. Based on pathway activities, a novel approach is proposed to project the totality of the information contained in pathway weights onto a single scalar, reactivity status indicator, which enables a compact representation of local chemistry. The proposed approaches are illustrated with highly complex kinetic mechanisms describing oxidation of n‐pentane, n‐heptane, and a biodiesel surrogate methyl‐butanoate. © 2011 American Institute of Chemical Engineers AIChE J, 2012     

Hydrogen assisted oxygen desorption from the V2O5(010) surface

Vanadium oxide surfaces are well known to play an active role as catalysts in hydrocarbon oxidation reactions where oxygen from different surface sites participates in the reaction. Due to the ubiquity of hydrogen in these systems, reaction steps involving (temporary) hydrogenation are possible and may influence the overall reaction scheme. This work examines structural and energetic consequences of hydrogen interacting with different oxygen sites at the V₂O₅(010) surface where the local surface environment is modeled by embedded clusters. The electronic structure and equilibrium geometries of the clusters are obtained by density functional theory (DFT) using gradient corrected functionals (RPBE) for exchange and correlation. Hydrogen is found to stabilize preferentially near oxygen sites forming surface OH and H₂O species with binding energies of 0.5–2.3 eV per H atom depending on the site and species. Hydrogen adsorption weakens the binding of the surface oxygen with its vanadium neighbors considerably where the weakening is larger for H₂O than for OH formation as evidenced by bond order analyses and results of the binding energetics. Thus, the studies suggest strongly that the presence of hydrogen at the oxide surface facilitates oxygen removal and, therefore, contributes to the enhanced yield of oxygenated products near vanadia based surfaces. This revised version was published online in August 2006 with corrections to the Cover Date.