For recent decades, the EC (Enzyme Commission) number has been used to research various biological reactions and metabolic pathways. However, the EC classification is unsuitable for bioinformatics analyses because of the, at least, following two problems. One is inconsistent criteria for classification, utilizing reaction patterns, substrates, transfered groups, and acceptor groups in different...

We discuss the possibility to study the in-medium changes of the properties of the ω meson in reactions on ordinary nuclei with elementary electromagnetic probes. We present a tree-level calculation of the elementary γp → ωp process which is extended to describe also the photoproduction of medium-modified ω mesons in nuclear matter. Using a semi-classical transport approach we obtain results fo...

We present a method for computing thermodynamically feasible elementary flux modes (tEFMs) using equilibrium constants without need of internal metabolite concentrations. The method is compared with the method based on a binary distinction between reversible and irreversible reactions. When all reactions are reversible, adding the constraints based on equilibrium constants reduces the number of...

Diphosphine ligands are frequently used in palladium-catalyzed Suzuki–Miyaura (S-M) reactions. Despite their widespread application both academic and industrial settings, role the B-to-Pd transmetalation has not been firmly established. We combined electrochemistry, NMR spectroscopy, DFT calculations to elucidate of dppf (1,1?-bis(diphenylphosphino)ferrocene) this key elementary step S-M reacti...

We consider the problem of inferring kinetic mechanisms for biochemical reactions from time series data. Using a priori knowledge about the structure of chemical reaction kinetics we develop global nonlinear models which use elementary reactions as a basis set, and discuss model construction using top-down and bottom-up approaches.

Mechanisms of double carbonylation reactions catalyzed by palladium complexs to give a-keto amides and a-keto esters, stoichiometric double carbonylation of ally1 carbonates, and cyclization carbonylation . of 3-butenoic acid to give cyclic anhydrides are discussed as combination of elementary processes of organometallic reactions.

Potassium monopersulfate has been decomposed in aqueous solution in the presence of Co(II). The process has been simulated by means of a mechanism based on elementary reactions. Rate constants have been taken from literature reports or, alternatively, assimilated to analogous reactions occurring in Fenton ́s chemistry. Several operating conditions have been successfully applied. Keywords—Monoper...