Kinetic research on heterogeneously catalysed processes: a questionnaire on the state-of-the-art in industry

On the initiative of the Working Party `Chemical Engineering in the Applications of Catalysis¿ of the European Federation of Chemical Engineering an assessment of the issues in the determination and application of kinetic data within the European industry was performed. The basis of the analysis consisted of a questionnaire put together by researchers from Dow, DSM, Shell and Eindhoven University of Technology. The 24 companies, which have responded to the questionnaire, can be classified into four groups: chemical, oil, engineering contractors and catalyst manufacturers. From the overall input it appears that there are three, equally important, utilisation areas for kinetic data: process development, process optimisation and catalyst development. There is a wide variety of kinetic data sources. Most of the respondents make use of test units which were primarily designed for development and optimisation. Avoiding transport limitation is, certainly in the case of short range projects or for complex feedstocks, not always taken care of. With respect to the modelling approaches, a common philosophy is `as simple as possible¿. Most of the respondents state that `in principle¿ one should strive for intrinsic kinetics, but the majority nevertheless does for various reasons not separate all transport phenomena from reaction kinetics. Kinetic models are mostly simple first or nth order or Langmuir-Hinshelwood type expressions. More complex kinetic models are scarcely used. Three areas were frequently identified to offer opportunities for improvement. Gathering of kinetic data is too costly and time consuming. There is no systematic approach at all for determination and application of kinetics in case of unstable catalytic performance. Furthermore, the software available for the regression of kinetic data to rate equations based on mechanistic schemes as well as software to model reactors are insufficiently user friendly. The majority of the respondents state that the problems indicated should be solved by cooperation, e.g., between companies, between industry and academia and between the catalysis and the chemical engineering community. A workshop on the above topics was held in December 1996 with 15 companies and 6 academics attending. More information can be obtained from the secretariat of the Working Party

Simplified half-life methods for the analysis of kinetic data

The analysis of reaction rate data has as its goal the determination of the order rate constant which characterize the data. Chemical reactions with one reactant and present simplified methods for accomplishing this goal are considered. The approaches presented involve the use of half lives or other fractional lives. These methods are particularly useful for the more elementary discussions of kinetics found in general and physical chemistry courses

The Tropospheric Lifetimes of Halocarbons and Their Reactions with OH Radicals: an Assessment Based on the Concentration of CO-14

Chemical reaction with hydroxyl radicals formed in the troposphere from ozone photolysis in the presence of methane, carbon monoxide and nitrogen oxides provides an important removal mechanism for halocarbons containing C-H and C = C double bonds. The isotropic distribution in atmospheric carbon monoxide was used to quantify the tropospheric hydroxyl radical distribution. Here, this methodology is reevaluated in the light of recent chemical kinetic data evaluations and new understandings gained in the life cycles of methane and carbon monoxide. None of these changes has forced a significant revision in the CO-14 approach. However, it is somewhat more clearly apparent how important basic chemical kinetic data are to the accurate establishment of the tropospheric hydroxyl radical distribution

Exchanging Experimental Kinetic Data via SabioML

The simulation of quantitative biochemical models not only requires qualitative information about the stoichiometry of the described networks, but also kinetic data describing their dynamics. Such kinetic data have to be experimentally measured, collected, systematically structured and stored to finally make them accessible. However, the dataflow from the experiment to the model is still a bottleneck, calling for systems that capture the data directly from the instrument, process and normalize it to agreed standards and finally transfer the data to publicly available databases.

SABIO-RK (http://sabio.h-its.org) is a curated database system which we have developed for bundling data referring to biochemical reactions and their kinetics. It offers data for metabolic pathways and as a novelty also for signalling reactions. Until recently, the database solely has been compiled through manual data mining of published papers and merging the kinetic data excerpt with information collected from other databases. We have designed the novel XML-based schema SabioML for exchanging experimentally derived kinetic data and corresponding metadata between programs or databases. The schema is tailored to SABIO-RK, however also could serve for transferring data between other resources. It comprises the description of kinetic laws with their parameters and relevant metadata in a structured and standardised format applying controlled vocabulary, as well as the possibility to assign annotations complying with the MIRIAM standard (Minimum Information Required In the Annotation of Models). Based on this data description format we have developed a submission interface that allows transfer of reaction kinetics data directly from the experimental instrument to the SABIO-RK database. The data can be accessed by the submitting researcher and, after release by the submitter and curation to ensure completeness of the data, also by the public, either manually via a web-based user interface or automated via web-services, both supporting the export of the data together with its annotations in SBML (Systems Biology Mark-up Language).

The system introduced here considerably facilitates the exchange of kinetic data between experimentalists and modelers. We are convinced that in systems biology it will become quite useful for the integration of the results of high throughput assays into biochemical computer models for simulation.

References:

Swainston N, Golebiewski M, et al., FEBS Journal 277(18): 3769-3779 (September 2010)

Rojas I, Golebiewski M, et al., In Silico Biology 7(2 Suppl): S37-44 (2007)
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SABIO-RK: Curated Kinetic Data of Biochemical Reactions

SABIO-RK ("http://sabio.villa-bosch.de/SABIORK/":http://sabio.villa-bosch.de/SABIORK/) is a curated, web-accessible database for modellers and wet-lab scientists to get comprehensive information about biochemical reactions and their kinetic properties. It integrates data from different origin in order to facilitate the access to reaction kinetics data and corresponding information. Since most of the kinetic data is exclusively found in the literature SABIO-RK offers data manually extracted from the literature and related information obtained from other publicly available biological databases. For instance, the kinetic data are related to reactions, organisms, tissues and cellular locations. The type of the kinetic mechanism and corresponding rate equations are presented together with their parameters and experimental conditions. Additionally, SABIO-RK also includes data about the detailed mechanism for some of the reactions based on literature information. This not only includes the graphical representation of the mechanism but also the single reaction steps with their corresponding kinetic data.

The data in SABIO-RK are extracted manually from literature and the selection of articles is not restricted to any biological source (e.g. organisms or organism classifications). All the data are curated and annotated by biological experts using a web-based input interface. To support the curation process and data integration we have implemented different constraints in the input interface and offer several controlled vocabularies as lists of values, as well as additional semi-automatic consistency checks to avoid errors and inconsistencies in the database. Controlled vocabularies and annotations to external resources and ontologies were used to identify and relate the data to their biological context. All these efforts to unify and integrate the data augment the content and the semantics of the SABIO-RK database entries to enable a comprehensive understanding and comparison of the data for the user.

SABIO-RK can be accessed via a web-based user interface or via web-services. The user interface allows the definition of complex queries by specifying reactions and reaction participants, kinetic parameters, environmental conditions or literature sources. Links to other databases based on the annotations of the
data enable the user to gather further information for example for compounds, reactions or proteins. Selected data about reactions and their kinetics, together with their annotations, can be exported in SBML (Systems Biology Mark-up Language), a widely used standard exchange format in systems biology

A study of the photocatalytic effects of aqueous suspensions of platinized semiconductor materials on the reaction rates of candidate redox reactions

The effectiveness of powdered semiconductor materials in photocatalyzing candidate redox reactions was investigated. The rate of the photocatalyzed oxidation of cyanide at platinized TiO2 was studied. The extent of the cyanide reaction was followed directly using an electroanalytical method (i.e. differential pulse polarography). Experiments were performed in natural or artificial light. A comparison was made of kinetic data obtained for photocatalysis at platinized powders with rate data for nonplatinized powders

Kinetic Study of Gluconic Acid Batch Fermentation by Aspergillus niger

Gluconic acid is one of interesting chemical products in industries such as detergents, leather, photographic, textile, and especially in food and pharmaceutical industries. Fermentation is an advantageous process to produce gluconic acid. Mathematical modeling is important in the design and operation of fermentation process. In fact, kinetic data must be available for modeling. The kinetic parameters of gluconic acid production by Aspergillus niger in batch culture was studied in this research at initial substrate concentration of 150, 200 and 250 g/l. The kinetic models used were logistic equation for growth, Luedeking-Piret equation for gluconic acid formation, and Luedeking-Piret-like equation for glucose consumption. The Kinetic parameters in the model were obtained by minimizing non linear least squares curve fitting