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Reaction Networks (reaction + network)
Kinds of Reaction Networks Selected AbstractsThermal Behaviour of Selected C10H16 MonoterpenesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 15 2006Achim Stolle Abstract The presented work investigates the thermal behaviour of selected monoterpenes under various reactor temperatures and residence times (carrier gas, reactor inserts). In addition to the analysis of the liquid products by capillary GC and GC-MS, chemical derivatisation techniques (Diels,Alder reaction, hydrogenation) were used to identify the liquid-phase products. A thermal conversion of ,-pinene (1), myrcene (2) and limonene (4) in a reaction network is presented and the experimental evidence for the formation of pyrolysis products by a biradical pathway is discussed. The reaction network was modified based on the identification of additional C10H16 terpene isomers. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Cationic Ruthenium-Cyclopentadienyl-Diphosphine Complexes as Catalysts for the Allylation of Phenols with Allyl Alcohol; Relation between Structure and Catalytic Performance in O - vs.ADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 10 2009C -Allylation Abstract A new catalytic method has been investigated to obtain either O - or C -allylated phenolic products using allyl alcohol or diallyl ether as the allyl donor. With the use of new cationic ruthenium(II) complexes as catalyst, both reactions can be performed with good selectivity. Active cationic Ru(II) complexes, having cyclopentadienyl and bidentate phosphine ligands are generated from the corresponding Ru(II) chloride complexes with a silver salt. The structures of three novel (diphosphine)Ru(II)CpCl catalyst precursor complexes are reported. It appears that the structure of the bidentate ligand has a major influence on catalytic activity as well as chemoselectivity. In addition, a strong cocatalytic effect of small amounts of acid is revealed. Model experiments are described that have been used to build a reaction network that explains the origin and evolution in time of both O -allylated and C -allylated phenolic products. Some mechanistic implications of the observed structure vs. performance relation of the [(diphosphine)RuCp]+ complexes and the cocatalytic role of added protons are discussed. [source] Kinetic Study of the Asymmetric Hydrogenation of Methyl Acetoacetate in the Presence of a Ruthenium Binaphthophosphepine ComplexADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 1-2 2009Eva Öchsner Abstract The asymmetric hydrogenation of methyl acetoacetate (MAA) in methanol using dibromobis{(S)-4-phenyl-4,5-dihydro-3H -dinaphtho[2,1- c: 1,,2,- e]phosphepine}-ruthenium was studied in detail. For the determination of the reaction network, data from kinetic experiments were compared to different possible reaction networks using the kinetic software Presto Kinetics. The simulation was optimised to describe the reaction accurately with a minimal set of process parameters and reaction equations. For the best model the reaction orders, collision factors and activation energy of all reaction steps were determined. Additionally, the influence of reaction temperature and hydrogen pressure on the enantiomeric excess (ee) of the reaction was studied. It was found that high reaction temperatures and high hydrogen pressures result in increasing enantioselectivities. [source] Simulation of a slurry-bubble column reactor for Fischer-Tropsch synthesis using single-event microkineticsAICHE JOURNAL, Issue 8 2009Gisela Lozano-Blanco Abstract A single-event microkinetic model for Fischer-Tropsch synthesis including the water-gas shift reaction has been implemented in a one-dimensional, two-bubble class, heterogeneous model with axial effective diffusion to study the performance of a commercial slurry bubble column reactor. Mass balance equations are solved for every species in the reaction network in the large bubbles, small bubbles, and slurry phase, whereas the energy balance is applied to the slurry phase. The catalyst concentration profile is described by a sedimentation-dispersion model. The combination of microkinetics that generate net production rates for the individual reaction products and hydrodynamics allows describing detailed concentration profiles along the reactor axis as a function of operating conditions and design parameters. As example, the effects of catalyst loading, syngas feed flow rate, inlet temperature, or hydrogen to carbon monoxide inlet ratio on the individual hydrocarbons are investigated. To our knowledge, no reactor model in literature is able to describe detailed compositions at the level described by the reactor model developed in this work. © 2009 American Institute of Chemical Engineers AIChE J, 2009 [source] A physical organic mechanistic approach to understanding the complex reaction network of hemostasis (blood clotting)JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 10 2007Christian J. Kastrup Abstract This review focuses on how the mechanistic approach of physical organic chemistry can be used to elucidate the mechanisms behind complex biochemical networks. The dynamics of biochemical reaction networks is difficult to describe by considering their individual reactions, just as the dynamics of organic reactions is difficult to describe by considering individual electrons and atomic nuclei. Physical organic chemists have developed a useful set of tools to predict the outcome of organic reactions by separating the interacting molecules into modules (functional groups), and defining general rules for how these modules interact (mechanisms). This review shows how these tools of physical organic chemistry may be used to describe reaction networks. In addition, it describes the application of these tools to develop a mechanistic understanding of the dynamics of the complex network of hemostasis, which regulates blood clotting. Copyright © 2007 John Wiley & Sons, Ltd. [source] Transformation of antimicrobial into bradykinin-potentiating peptides during peptic hydrolysis of bovine haemoglobin: identification, release kinetics and reaction network of peptidesJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 3 2007Wei Qi Abstract The precursor cleavage of the antimicrobial peptide ,107,136 into the bradykinin-potentiating peptide ,110,125 during peptic hydrolysis of bovine haemoglobin was investigated by reverse phase high-performance liquid chromatography coupled with tandem mass spectrometry. The optimal conditions for the preparation of ,107,136 and ,110,125 were found to be low and high degrees of hydrolysis respectively. A total of six peptides were identified as being involved in the cleavage process. Moreover, the reaction network of these peptides was developed according to the sequence alignment and their release kinetics. The affinity of pepsin towards different peptide bonds of bovine haemoglobin was also compared based on data from the release kinetics of peptides. In addition, some potentially bioactive peptides were predicted by means of sequence analysis and secondary structure calculations. Copyright © 2006 Society of Chemical Industry [source] Chemical networks with inflows and outflows: A positive linear differential inclusions approachBIOTECHNOLOGY PROGRESS, Issue 3 2009David Angeli Abstract Certain mass-action kinetics models of biochemical reaction networks, although described by nonlinear differential equations, may be partially viewed as state-dependent linear time-varying systems, which in turn may be modeled by convex compact valued positive linear differential inclusions. A result is provided on asymptotic stability of such inclusions, and applied to a ubiquitous biochemical reaction network with inflows and outflows, known as the futile cycle. We also provide a characterization of exponential stability of general homogeneous switched systems which is not only of interest in itself, but also plays a role in the analysis of the futile cycle. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] Spontaneous Emergence of Homochirality via Coherently Coupled Antagonistic and Reversible Reaction CyclesCHEMPHYSCHEM, Issue 16 2008Michael Mauksch Dr. Abstract Asymmetric synthesis aims at obtaining enantio-enriched products in stereoselective reactions under a chiral influence. We demonstrate both mathematically and numerically that, even under nominally achiral conditions, fully homochiral steady states can be obtained in open reactive systems by spontaneous mirror-symmetry breaking in the homogenous solution phase when the autocatalytic reaction network is closed in the form of coherently coupled antagonistic reversible reaction cycles which, paradoxically, allow for complete recycling of the reactant. We show that the fully reversible Frank mechanism for spontaneous mirror-symmetry breaking is closely related to the Lotka,Volterra system, which models predator,prey relations in ecosystems. Amplification of total enantiomeric excess and the principle of microscopic reversibility are not in conflict for all conceivable reactions. A viable and widely applicable reaction protocol is introduced and discussed, and it permits the theoretical implications to be applied to practical laboratory examples. Implications for the possible origin of biological homochirality on early earth are discussed. [source] Kinetic Study of the Asymmetric Hydrogenation of Methyl Acetoacetate in the Presence of a Ruthenium Binaphthophosphepine ComplexADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 1-2 2009Eva Öchsner Abstract The asymmetric hydrogenation of methyl acetoacetate (MAA) in methanol using dibromobis{(S)-4-phenyl-4,5-dihydro-3H -dinaphtho[2,1- c: 1,,2,- e]phosphepine}-ruthenium was studied in detail. For the determination of the reaction network, data from kinetic experiments were compared to different possible reaction networks using the kinetic software Presto Kinetics. The simulation was optimised to describe the reaction accurately with a minimal set of process parameters and reaction equations. For the best model the reaction orders, collision factors and activation energy of all reaction steps were determined. Additionally, the influence of reaction temperature and hydrogen pressure on the enantiomeric excess (ee) of the reaction was studied. It was found that high reaction temperatures and high hydrogen pressures result in increasing enantioselectivities. [source] Solid-solid reactions in series: A modeling and experimental studyAICHE JOURNAL, Issue 9 2009A. K. Suresh Abstract Reactions among particulate solid phases are important and abundant in many materials, chemical, and metallurgical process industries. Many of these are reaction networks, and not single-step reactions as normally assumed. There is no theoretical framework available for the analysis of such systems, and single-reaction models derived from the gas,solid literature continue to be used. Formation of cement clinker in the rotary cement kiln is a prime example of the genre, in which mechanistic aspects play an important role in determining energy efficiency and the composition and nature of the phases that form. In the present study, we formulate a model within the ambit of the "shrinking core" class of models, for reactions in series among solid phases. The model shows the presence of one or two moving fronts in the reacting particle, depending on the relative rates of the processes involved. A single Thiele-type parameter controls the model behavior, at once describing the relative rates of the intermediate formation and consumption processes, and the diffusion-reaction competition for the product formation step. The model has been shown to reduce to the well known single reaction models at the limits of low and high values of the Thiele parameter. Experimental data have been obtained on the calcia-alumina system, an important one in cement manufacture, in the temperature range 1150,1250°C. The model has been fitted to these data and the kinetic parameters determined. The comparison bears out the salient features of the theory, and shows that a degree of diffusion limitation exists for the intermediate conversion step under these conditions. The diffusivity values estimated are in the range of 10,19 to 10,18 m2/s and agree with values found in the literature for similar systems. The rate constant for the intermediate conversion step is of the order of 10,6 s,1. This being among the first such determinations, this value awaits confirmation from other studies. © 2009 American Institute of Chemical Engineers AIChE J, 2009 [source] Lexicography of kinetic modeling of complex reaction networksAICHE JOURNAL, Issue 8 2005Linda J. Broadbelt First page of article [source] A physical organic mechanistic approach to understanding the complex reaction network of hemostasis (blood clotting)JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 10 2007Christian J. Kastrup Abstract This review focuses on how the mechanistic approach of physical organic chemistry can be used to elucidate the mechanisms behind complex biochemical networks. The dynamics of biochemical reaction networks is difficult to describe by considering their individual reactions, just as the dynamics of organic reactions is difficult to describe by considering individual electrons and atomic nuclei. Physical organic chemists have developed a useful set of tools to predict the outcome of organic reactions by separating the interacting molecules into modules (functional groups), and defining general rules for how these modules interact (mechanisms). This review shows how these tools of physical organic chemistry may be used to describe reaction networks. In addition, it describes the application of these tools to develop a mechanistic understanding of the dynamics of the complex network of hemostasis, which regulates blood clotting. Copyright © 2007 John Wiley & Sons, Ltd. [source] Computational framework for predictive biodegradationBIOTECHNOLOGY & BIOENGINEERING, Issue 6 2009Stacey D. Finley Abstract As increasing amounts of anthropogenic chemicals are released into the environment, it is vital to human health and the preservation of ecosystems to evaluate the fate of these chemicals in the environment. It is useful to predict whether a particular compound is biodegradable and if alternate routes can be engineered for compounds already known to be biodegradable. In this work, we describe a computational framework (called BNICE) that can be used for the prediction of novel biodegradation pathways of xenobiotics. The framework was applied to 4-chlorobiphenyl, phenanthrene, ,-hexachlorocyclohexane, and 1,2,4-trichlorobenzene, compounds representing various classes of xenobiotics with known biodegradation routes. BNICE reproduced the proposed biodegradation routes found experimentally, and in addition, it expanded the biodegradation reaction networks through the generation of novel compounds and reactions. The novel reactions involved in the biodegradation of 1,2,4-trichlorobenzene were studied in depth, where pathway and thermodynamic analyses were performed. This work demonstrates that BNICE can be applied to generate novel pathways to degrade xenobiotic compounds that are thermodynamically feasible alternatives to known biodegradation routes and attractive targets for metabolic engineering. Biotechnol. Bioeng. 2009; 104: 1086,1097. © 2009 Wiley Periodicals, Inc. [source] An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis,BIOTECHNOLOGY & BIOENGINEERING, Issue 3 2008Jamey D. Young Abstract Nonstationary metabolic flux analysis (NMFA) is at present a very computationally intensive exercise, especially for large reaction networks. We applied elementary metabolite unit (EMU) theory to NMFA, dramatically reducing computational difficulty. We also introduced block decoupling, a new method that systematically and comprehensively divides EMU systems of equations into smaller subproblems to further reduce computational difficulty. These improvements led to a 5000-fold reduction in simulation times, enabling an entirely new and more complicated set of problems to be analyzed with NMFA. We simulated a series of nonstationary and stationary GC/MS measurements for a large E. coli network that was then used to estimate parameters and their associated confidence intervals. We found that fluxes could be successfully estimated using only nonstationary labeling data and external flux measurements. Addition of near-stationary and stationary time points increased the precision of most parameters. Contrary to prior reports, the precision of nonstationary estimates proved to be comparable to the precision of estimates based solely on stationary data. Finally, we applied EMU-based NMFA to experimental nonstationary measurements taken from brown adipocytes and successfully estimated fluxes and some metabolite concentrations. By using NFMA instead of traditional MFA, the experiment required only 6 h instead of 50 (the time necessary for most metabolite labeling to reach 99% of isotopic steady state). Biotechnol. Bioeng. 2008;99: 686,699. © 2007 Wiley Periodicals, Inc. [source] Exploring multiplicity conditions in enzymatic reaction networksBIOTECHNOLOGY PROGRESS, Issue 3 2009Irene Otero-Muras Abstract In this work, a novel algorithmic approach to detect multiplicity of steady states in enzymatic reaction networks is presented. The method exploits the structural properties of networks derived from the Chemical Reaction Network Theory. In first instance, the space of parameters is divided in different regions according to the qualitative behavior induced by the parameters in the long term dynamics of the network. Once the regions are identified, a condition for the appearance of multiplicities is checked in the different regions by solving a given optimization problem. In this way, the method allows the characterization of the whole parameter space of biochemical networks in terms of the appearance or not of multistability. The approach is illustrated through a well-known case of enzymatic catalysis with substrate inhibition. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] Chemical networks with inflows and outflows: A positive linear differential inclusions approachBIOTECHNOLOGY PROGRESS, Issue 3 2009David Angeli Abstract Certain mass-action kinetics models of biochemical reaction networks, although described by nonlinear differential equations, may be partially viewed as state-dependent linear time-varying systems, which in turn may be modeled by convex compact valued positive linear differential inclusions. A result is provided on asymptotic stability of such inclusions, and applied to a ubiquitous biochemical reaction network with inflows and outflows, known as the futile cycle. We also provide a characterization of exponential stability of general homogeneous switched systems which is not only of interest in itself, but also plays a role in the analysis of the futile cycle. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] Preliminary Studies on the In Silico Evolution of Biochemical NetworksCHEMBIOCHEM, Issue 10 2004Anastasia Deckard Abstract Due to the variety and importance of roles performed by signalling networks, understanding their function and evolution is of great interest. Signalling networks allow organisms to process and react to changes in their internal and external environment. Current estimates suggest that two to three percent of all genomes code for proteins involved in signalling networks. The study of signalling networks is hindered by the complexities of the networks and difficulties in ascribing function to form. For example, a very complex dense network might comprise eighty or more densely connected proteins. In the majority of cases there is very little understanding of how these networks process signals. Unlike in electronics, where there is a broad practical and theoretical understanding of how to construct devices that can process almost any kind of signal, in biological signalling networks there is no equivalent theory. Part of the problem stems from the fact that in most cases it is unknown what particular signal processing circuits would look like in a biological form. This paper describes the evolutionary methods used to generate networks with particular signal- and computational-processing capabilities. The techniques involved are described, and the approach is illustrated by evolving computational circuits such as multiplication, radicals and logarithmic functions. The experiments also illustrate the evolution of modularity within biochemical reaction networks. [source] | |||||||||||||