The Chlorate-Iodine-Nitrous Acid Clock Reaction

A new clock reaction based on chlorate, iodine and nitrous acid is presented. The induction period of this new clock reaction decreases when the initial concentrations of chlorate, nitrous acid and perchloric acid increase, but it is independent on the initial iodine concentration. The proposed mechanism is based on the LLKE autocatalytic mechanism for the chlorite-iodide reaction and the initial reaction between chlorate and nitrous acid to produce nitrate and chlorite. This new clock reaction opens the possibility for a new family of oscillating reactions containing chlorate or nitrous acid, which in both cases has not been observed until now.     

Removal of iodine by solid phase adsorption to charcoal following iodine oxidation of acetamidomethyl-protected peptide precursors to their disulfide bonded products: oxytocin and a Pre-S1 peptide of hepatitis B virus illustrate the method.

Chemical quenching, gel filtration or liquid phase extraction procedures are currently in vogue for taking iodine off from the reaction mixtures in which it is used to cause the formation of disulfide bonds in acetamidomethyl or trityl protected peptides. It has been found that charcoal effectively, selectively and rapidly removes iodine by solid phase extraction from reaction mixtures in which it is used to convert the acetamidomethyl protected precursors of oxytocin or a peptide from the Pre-S1 region of hepatitis B virus into their intramolecularly disulfide-bonded products. The advantages of this new method, namely simplicity, rapidity, quantitative yields, freedom from side reactions, linear scalability, cost effectiveness and adsorption of iodine on to solid charcoal are discussed.     

And the segmentation clock keeps ticking

The vertebrate body is organized in segments, easily visible in the consecutive vertebrae of the skeleton. These are first defined in the embryo by the formation of somites. Somites are generated at regular intervals from the presomitic mesoderm by a combination of oscillating signals, known as the segmentation clock, which establish the pace at which new somites are formed, and signaling gradients that set the location of new intersomitic borders. Using a microarray approach, Dequéant et al. have now shown that the segmentation clock is more complex than previously thought and includes oscillating expression of genes from at least three signaling pathways organized in coordinated networks.     

Oscillating chemiluminescence with thiosemicarbazide in a batch reactor

Oscillating chemical reactions are complex systems involving a large number of chemical species. In oscillating chemical reactions, some species, usually reaction intermediates, exhibit fluctuations in their concentration. In this report, a novel slowly‐damped oscillating chemiluminescence produced by the addition of thiosemicarbazide (TSC) to the oscillating system H₂O₂–KSCN–CuSO₄–NaOH was investigated. Narrow and slightly asymmetric light pulses of 1.5 s half‐width are emitted at 440 nm, with an oscillation period of 22–363 s, an induction period of 9–397 s and an emitted light time of 700–1500 s, depending on reagent concentrations. In this study the dependence of the induction period and the oscillation period on the reagent concentrations was investigated and both parameters were plotted with respect to reagent concentrations. Copper concentration showed a significant effect on the oscillation period. A possible mechanism for the oscillating chemiluminescence reaction is discussed. Copyright © 2008 John Wiley & Sons, Ltd.     

Reactions of vitamin A with acceptors of electrons. Interactions with iodine and the formation of iodide

1. The reactions of retinol and retinoic acid with iodine were investigated since knowledge of the chemical reactions of vitamin A with acceptors of electrons may shed light on its biochemical mode of action. 2. Colloidal retinol, but not retinoic acid, reacts with iodine to yield a blue-green complex that rapidly decomposes, giving iodide and an unknown species with lambda(max.) at 870mmu. 3. In addition, both retinol and retinoic acid reduce iodine to iodide by a reaction that does not involve an intermediate coloured complex; this reaction appears to yield unstable carbonium ion derivatives of the vitamin. 4. The presence of water greatly facilitates the production of iodide from vitamin A and iodine. 5. Possible chemical pathways involved in these reactions are discussed. 6. It is suggested that the chemical properties of retinol and retinoic acid that underlie their biochemical behaviour might be apparent only when the molecules are at a lipid-water interface, and that vitamin A might be expected to react with a number of different electron acceptors in vivo.     

The Glansdorff-Prigogine thermodynamic stability criterion in the light of Lyapunov's theory.

The significance of thermodynamic coupling in chemical reactions—which recently has been questioned on thermodynamic grounds—is examined from the point of view of kinetics. It is shown that considerations of stoichiometry lead to a meaningful definition of velocity for elementary and certain elementary-complex reactions, whereas the non-equilibrium thermodynamic definition of reaction velocity is ambiguous in multireaction systems. Based on rate laws which include the effects of nonideality, it is proven that elementary-type reactions are not coupled thermodynamically and concluded that thermodynamic coupling has no kinetic significance. A discussion is given to show that this result is compatible with coupling in both biochemical systems and oscillating reactions.     

Wnt3a plays a major role in the segmentation clock controlling somitogenesis

The vertebral column derives from somites generated by segmentation of presomitic mesoderm (PSM). Somitogenesis involves a molecular oscillator, the segmentation clock, controlling periodic Notch signaling in the PSM. Here, we establish a novel link between Wnt/beta-catenin signaling and the segmentation clock. Axin2, a negative regulator of the Wnt pathway, is directly controlled by Wnt/beta-catenin and shows oscillating expression in the PSM, even when Notch signaling is impaired, alternating with Lfng expression. Moreover, Wnt3a is required for oscillating Notch signaling activity in the PSM. We propose that the segmentation clock is established by Wnt/beta-catenin signaling via a negative-feedback mechanism and that Wnt3a controls the segmentation process in vertebrates.     

(Per)chlorate reduction at high temperature: Physiological study of Archaeoglobus fulgidus and potential implications for novel souring mitigation strategies

The recent finding that Archaeoglobus fulgidus is able to couple (per)chlorate reduction to growth expanded this trait to the hyperthermophilic range of life. This sulfate-reducing archaeon is considered to be one of the major contributors to souring in hot oil reservoirs. Therefore, it is important to study its physiology in depth, particularly in view of novel souring mitigation strategies. A. fulgidus does not possess the classical (per)chlorate reduction pathway, as it lacks the key enzyme chlorite dismutase. Rather, the microorganism seems to couple (per)chlorate reduction to sulfur metabolism. Growth experiments show the strict necessity of sulfur compounds to sustain perchlorate reduction. Furthermore, the chemical formation of elemental sulfur was observed during perchlorate reduction, a compound that is biologically reduced again. Additional experiments showed that tetrathionate, but not elemental sulfur and polysulfide, serves as an electron acceptor for growth by A. fulgidus. Taken together these results provide further evidence for the importance of chemical and biological redox reactions involving sulfur compounds during (per)chlorate reduction. In non-reduced media also, nitrate could be reduced by A. fulgidus, though not coupled to growth. This observation and the fact that A. fulgidus had prolonged adaptation phases on sulfate after long-lasting growth on perchlorate are of interest in the development of new souring mitigation strategies using nitrate and/or (per)chlorate.     

Studies of visible oscillating chemiluminescence with a luminol–H2O2–KSCN–CuSO4–NaOH system in batch reactor

Oscillating chemical reactions are complex systems involving a large number of chemical species. In oscillating chemical reactions some species, usually reaction intermediates, exhibit fluctuation in concentration. Visible oscillating chemiluminescence, produced by the addition of luminol (3‐aminophthalhydrazide) to the oscillating system H₂O₂–KSCN–CuSO₄–NaOH, was investigated. In this study the effect of varying the concentration of H₂O₂, KSCN, CuSO₄, NaOH and luminol was investigated in a batch reactor. We showed that the concentration of all components involved in the oscillating chemilumenscent reaction influenced the light intensity and the oscillation period. Copyright © 2002 John Wiley & Sons, Ltd.     

Stomatal uptake and stomatal deposition of ozone in isoprene and monoterpene emitting plants

Volatile isoprenoids were reported to protect plants against ozone. To understand whether this could be the result of a direct scavenging of ozone by these molecules, the stomatal and non-stomatal uptake of ozone was estimated in plants emitting isoprene or monoterpenes. Ozone uptake by holm oak (Quercus ilex, a monoterpene emitter) and black poplar (Populus nigra, an isoprene emitter) was studied in whole plant enclosures (continuously stirred tank reactors, CSTR). The ozone uptake by plants was estimated measuring ozone concentration at the inlet and outlet of the reactors, after correcting for the uptake of the enclosure materials. Destruction of ozone at the cuticle or at the plant stems was found to be negligible compared to the ozone uptake through the stomata. For both plant species, a relationship between stomatal conductance and ozone uptake was found. For the poplar, the measured ozone losses were explained by the uptake of ozone through the stomata only, and ozone destruction by gas phase reactions with isoprene was negligible. For the oak, gas phase reactions of ozone with the monoterpenes emitted by the plants contributed significantly to ozone destruction. This was confirmed by two different experiments showing a) that in cases of high stomatal conductance but under low CO(2) concentration, a reduction of monoterpene emission was still associated with reduced O(3) uptake; and b) that ozone losses due to the gas phase reactions only can be measured when using the exhaust from a plant chamber to determine the gas phase reactivity in an empty reaction chamber. Monoterpenes can therefore relevantly scavenge ozone at leaf level contributing to protection against ozone.     

Thyroglobulin-mediated one- and two-electron oxidations of glutathione and ascorbate in thyroid peroxidase systems

The one- or two-electron oxidation of thyroglobulin by the thyroid peroxidase system was found to be regulated by the iodine content of thyroglobulin. The catalytic intermediate of thyroid peroxidase observed at steady state of the reaction was Compound I and II when the iodine content in thyroglobulin was 0.2 and 0.7%, respectively, apparent rate constants for the rate-limiting steps being estimated at 4.7 x 10(7) and 4.8 x 10(4) M-1 S-1. The thyroglobulin-mediated oxidation of GSH occurred by way of two-electron transfer at 0.2% iodine content and by way of one-electron transfer at 0.7% iodine content. The spin-trapping experiment with 5,5-dimethyl-1-pyrroline-N-oxide showed that glutathione radicals were formed in the latter reaction but not in the former. In the reactions of thyroid peroxidase, the one- and two-electron oxidations of ascorbate were also mediated by 0.2 and 0.7% iodine thyroglobulins, respectively. The reactions were analyzed and mimicked with the use of p-cresol and p-acetaminophenol as a mediator in the reactions of lactoperoxidase and thyroid peroxidase.     

The reaction stoichiometry between ozone and unsaturated fatty acids in an aqueous environment

The light absorption of ozone in an air stream allowed the monitoring of reactions of ozone with unsaturated fatty acids in solution. The kinetics for the reaction of ozone with linolenic acid was found to be of a pseudo-first-order after the first few minutes and did not vary with the concentration of ozone introduced into the solution. The reaction of ozone with linolenic acid in solution was found to be exceedingly rapid.When various combinations of polyunsaturated fatty acids were injected simultaneously, they reacted independently. The stoichiometry of ozone reacted to number of double bonds present in the fatty acid was one for mono- and diunsaturated; however, for triunsaturated fatty acid the stoichiometry was about 0.70.Malondialdehyde was produced upon the reaction of ozone with di- and triunsaturated fatty acids, as shown by both the thiobarbituric acid test and the characteristic UV absorption of malondialdehyde in solution. The true yield of malondialdehyde for the reaction of polyunsaturated fatty acids with ozone was found to be about 2%. In addition, other species, absorbing at 290–300 nm, were formed in solution during ozonolysis.     

Modelling of multi-component immunoassay kinetics — A new node-based method for simulation of complex assays

The behaviour of binding reactions in immunoassays can be predicted and studied by modelling methods. Simple antibody-analyte binding reaction kinetics can be simulated by e.g. a mechanistic assay model based on differential equations. However, the mathematical modelling becomes more complicated if multivalent-structured components are involved and the number of binding complexes increases.In this paper, a new node-based method to model complex binding reactions is introduced. The principle of this method is to construct a network of the initial components, reaction intermediates and end-products by forming a network of nodes. This network is then solved, node by node, breaking the initial problem into smaller partial problems, still obeying the laws of chemical reaction kinetics and without ignoring any parts of the problem.This method provides an easy and quick way to study complex binding reactions since simulation networks are simple to construct directly from the reaction scheme. This presented new “NODE”-method is compared with the well known mechanistic assay model.     

Analysing the role of soil properties, initial biomass and ozone on observed plant growth variability in a lysimeter study

This simulation study is based on a lysimeter experiment with juvenile beech trees (Fagus sylvatica L.) which were grown under ambient or doubled ambient atmospheric ozone concentrations. The aim of the study was to analyze the role of differences in soil properties, differences in initial biomass and ozone impacts on observed plant growth variability at the eight lysimeters of this experiment. For this purpose, we established a new simulation model based on the model system Expert-N by coupling soil water and nitrogen transport models with the plant growth model PLATHO, which was already tested and applied for juvenile beech. In order to parameterize the soil model, for all lysimeters soil hydraulic parameters as well as carbon and nitrogen stocks were measured. Simulation results reveal that the observed decreased growth rates under elevated ozone are due to ozone impacts on plant growth, whereas the high plant growth variability between lysimeters is to a major part the consequence of differences in soil hydraulic properties. Differences in initial biomass are of minor importance to explain plant growth variability in this experiment.     

Patterning embryos with oscillations: structure, function and dynamics of the vertebrate segmentation clock

The segmentation clock is an oscillating genetic network thought to govern the rhythmic and sequential subdivision of the elongating body axis of the vertebrate embryo into somites: the precursors of the segmented vertebral column. Understanding how the rhythmic signal arises, how it achieves precision and how it patterns the embryo remain challenging issues. Recent work has provided evidence of how the period of the segmentation clock is regulated and how this affects the anatomy of the embryo. The ongoing development of real-time clock reporters and mathematical models promise novel insight into the dynamic behavior of the clock.     

Ozonolysis of 2'-Deoxycytidine: Isolation and Identification of the Main Oxidation Products

The ozone-mediated oxidation of 2'-deoxycytidine (dCyd) was investigated on the basis of final product identification. The oxidation reaction gave rise to five major modified nucleosides which were isolated and characterized on the basis of extensive ¹H NMR and mass spectrometry measurements. The comparison with the current knowledge of the hydroxyl radical mediated oxidation reactions of 2'-deoxycytidine in aerated aqueous solution, indicates that the formation of ozone oxidation products may be mostly explained by the opening of the pyrimidine C₅-C₆ double bond. Thus, the formation of the identified products obtained by ozonolysis of 2'-deoxycytidine is accounted for by the initial generation of an ozonide.     

Ozonolysis of Thymidine: Isolation and Identification of the Main Oxidation Products

The ozone-mediated oxidation of thymidine was investigated on the basis of final product identification. The oxidation reaction gave rise to five major modified nucleosides which were isolated and characterised from extensive H NMR and mass spectrometry studies. The comparison with the current knowledge of the hydroxyl radical-mediated oxidation reactions of thymidine in aerated aqueous solution indicates that the formation of ozone oxidation products may be mostly explained in terms of initial generation of an ozonide. Indeed, the identified products obtained by ozonolysis of thymidine resulted from the opening of the pyrimidine C5-C5 bond.     

Reaction of ozone with nicotinamide and its derivatives

Reaction of ozone with NADH eliminated the 340 nm absorbance. The 260 nm absorbance increased initially and then slowly declined. Equimolar amounts of NADH and ozone reacted. Products were separated by ion exchange chromatography and were shown to contain only traces of NAD. The products were not active in the alcohol dehydrogenase assay and did not form cyanide complexes. There was no reaction of NAD with ozone. NADPH and NADP showed the same reactivities as NADH and NAD. The reactions were not influenced by pH in the range 4.6–9.0. When NADH and tryptophan, or NADH and methionine, or NADH and glutathione (at low concentration) were competitors for available ozone, NADH was preferentially oxidized. Treatment of aqueous solutions of 1,4-dihydro-1-methyl nicotinamide with ozone caused changes in the absorbance spectrum consistent with ozonolysis of the 5,6 double bond. The product has been isolated after ozonolysis in methylene chloride and characterized by uv, ir, mass spectroscopy, and elemental analysis. Results were consistent with the reaction:

Further ozonolysis cleaved the 2,3 double bond. Reaction of NADH with ozone resulted in analogous reactions. The adenine moiety was resistant to ozonolysis, but this reaction was pH dependent, being greater at neutral and alkaline pH.     

Plasmachemical and heterogeneous processes in ozonizers with oxygen activation by a dielectric barrier discharge

Plasmachemical and heterogeneous processes of generation and loss of ozone in the atmosphericpressure dielectric barrier discharge in oxygen are studied theoretically. Plasmachemical and electronic kinetics in the stage of development and decay of a single plasma filament (microdischarge) are calculated numerically with and without allowance for the effects of ozone vibrational excitation and high initial ozone concentration. The developed analytical approach is applied to determine the output ozone concentration taking into account ozone heterogeneous losses on the Al₂O₃ dielectric surface. Using the results of quantummechanical calculations by the method of density functional theory, a multistage catalytic mechanism of heterogeneous ozone loss based on the initial passivation of a pure Al₂O₃ surface by ozone and the subsequent interaction of O₃ molecules with the passivated surface is proposed. It is shown that the conversion reaction 2O₃ → 3O₂ of a gas-phase ozone molecule with a physically adsorbed ozone molecule can result in the saturation of the maximum achievable ozone concentration at high specific energy depositions, the nonstationarity of the output ozone concentration, and its dependence on the prehistory of ozonizer operation.