Bio-orthogonal labelling schemes based on inverse-electron-demand Diels-Alder (IEDDA) cycloaddition have attracted much attention in chemical biology recently. The appealing features of this reaction, such as the fast reaction kinetics, fully bio-orthogonal nature and high selectivity, have helped chemical biologists gain deeper understanding of biochemical processes at the molecular level. Lis...

BACKGROUND: The conventional solution-phase Chemical Cleavage of Mismatch (CCM) method is time-consuming, as the protocol requires purification of DNA after each reaction step. This paper describes a new version of CCM to overcome this problem by immobilizing DNA on silica solid supports. RESULTS: DNA test samples were loaded on to silica beads and the DNA bound to the solid supports underwent ...

The concept of the limiting step is extended to the asymptotology of multiscale reaction networks. Complete theory for linear networks with well separated reaction rate constants is developed. We present algorithms for explicit approximations of eigenvalues and eigenvectors of kinetic matrix. Accuracy of estimates is proven. Performance of the algorithms is demonstrated on simple examples. Appl...

Laboratory and full-scale experiments were performed in order to investigate the effect of mixing, as represented by the mean velocity gradient, G-value (Grady et al, 1999), and time dynamics in chemical phosphorus removal. The results prove that the chemical reactions occurring during phosphorus removal upon addition of trivalent metal salts (Fe, Al) cannot be described with the currently appl...

In a previous paper, Brouwers and Van Eijk [1] presented a theoretical study on the dissolution (reaction) of pulverised powder coal fly ash. This fly ash was modelled as hollow spheres, and a shrinking core model was derived for these hollow spheres that contain two regions (an outer hull and an inner region). The obtained analytical equations were applied to the dissolution experiments by Pie...

Siphons in a chemical reaction system are subsets of the species that have the potential of being absent in a steady state. We present a characterization of minimal siphons in terms of primary decomposition of binomial ideals, we explore the underlying geometry, and we demonstrate the effective computation of siphons using computer algebra software. This leads to a new method for determining wh...

A reaction between chemical species is modeled by a particular reaction pathway, in which one reaction is very fast relative to the other one. The diffusion controlled reactions of these species together with a reaction intermediate are described by a system of three transient reactiondiffusion equations over a two-dimensional spatial domain. In the asymptotic limit of the reaction parameter te...

In this paper we present recent and ongoing results of research on crystallization pressure and the reaction-driven cracking process that can result when hydration, carbonation, and/or oxidation reactions produce large changes in volume, viscosity is high (low temperature) and reaction rates are fast (large chemical potential, catalysts present, etc). Our focus is on natural processes involving...

Decarboxylation of mandelylthiamin in aqueous solution is analyzed by means of quantum mechanics/molecular mechanics simulations including solvent effects. The free energy profile for the decarboxylation reaction was traced, assuming equilibrium solvation, while reaction trajectories allowed us to incorporate nonequilibrium effects due to the solvent degrees of freedom as well as to evaluate th...

[reaction: see text] Chemical glycopeptide synthesis requires access to gram quantities of glycosylated amino acid building blocks. Hence, the efficiency of synthesis of such building blocks is of great importance. Here, we report a fast and highly efficient synthetic route to Fmoc-protected asparaginyl glycosides from unprotected sugars in three steps with high yields. The glycosylated amino a...