Student-generated submicro diagrams : a useful tool for teaching and learning chemical equations and stoichiometry

This paper reports on a pedagogical approach to the teaching of chemical equations introduced to first year university students with little previous chemical knowledge. During the instruction period students had to interpret and construct diagrams of reactions at the submicro level, and relate them to chemical equations at the symbolic level with the aim of improving their conceptual understanding of chemical equations and stoichiometry. Students received instruction in symbol conventions, practice through graded tutorial tasks, and feedback on their efforts over the semester. Analysis of the student responses to formative test and summative exam items over consecutive years indicates that there was a consistent improvement in the abilities of the various cohorts to answer stoichiometry questions correctly. The responses provide evidence for diagrams of the submicro level being used as tools for reasoning in solving chemical problems, to recognise misconceptions of chemical formulae and to recognise the value of using various multiple representations of chemical reactions connecting the submicro and symbolic levels of representation. The student-generated submicro diagrams serve as a visualisation tool for teaching and learning abstract concepts in solving stoichiometric problems. We argue that the use of diagrams of the submicro level provides a more complete picture of the reaction, rather than a net summary of a chemical equation, leading to a deeper conceptual understanding.

The use of biodiversity as source of new chemical entities against defined molecular targets for treatment of malaria, tuberculosis, and T-cell mediated diseases: a review

The modern approach to the development of new chemical entities against complex diseases, especially the neglected endemic diseases such as tuberculosis and malaria, is based on the use of defined molecular targets. Among the advantages, this approach allows (i) the search and identification of lead compounds with defined molecular mechanisms against a defined target (e.g. enzymes from defined pathways), (ii) the analysis of a great number of compounds with a favorable cost/benefit ratio, (iii) the development even in the initial stages of compounds with selective toxicity (the fundamental principle of chemotherapy), (iv) the evaluation of plant extracts as well as of pure substances. The current use of such technology, unfortunately, is concentrated in developed countries, especially in the big pharma. This fact contributes in a significant way to hamper the development of innovative new compounds to treat neglected diseases. The large biodiversity within the territory of Brazil puts the country in a strategic position to develop the rational and sustained exploration of new metabolites of therapeutic value. The extension of the country covers a wide range of climates, soil types, and altitudes, providing a unique set of selective pressures for the adaptation of plant life in these scenarios. Chemical diversity is also driven by these forces, in an attempt to best fit the plant communities to the particular abiotic stresses, fauna, and microbes that co-exist with them. Certain areas of vegetation (Amazonian Forest, Atlantic Forest, Araucaria Forest, Cerrado-Brazilian Savanna, and Caatinga) are rich in species and types of environments to be used to search for natural compounds active against tuberculosis, malaria, and chronic-degenerative diseases. The present review describes some strategies to search for natural compounds, whose choice can be based on ethnobotanical and chemotaxonomical studies, and screen for their ability to bind to immobilized drug targets and to inhibit their activities. Molecular cloning, gene knockout, protein expression and purification, N-terminal sequencing, and mass spectrometry are the methods of choice to provide homogeneous drug targets for immobilization by optimized chemical reactions. Plant extract preparations, fractionation of promising plant extracts, propagation protocols and definition of in planta studies to maximize product yield of plant species producing active compounds have to be performed to provide a continuing supply of bioactive materials. Chemical characterization of natural compounds, determination of mode of action by kinetics and other spectroscopic methods (MS, X-ray, NMR), as well as in vitro and in vivo biological assays, chemical derivatization, and structure-activity relationships have to be carried out to provide a thorough knowledge on which to base the search for natural compounds or their derivatives with biological activity.

Stacking faults in SiCf/SiC composite obtained by chemical vapor reaction process

SiC fiber-reinforced SiC matrix composite (SiCf/SiC) is one of the leading candidates in ceramic materials for engineering applications due to its unique combination of properties such as high thermal conductivity, high resistance to corrosion and working conditions. Fiber-reinforced composites are materials which exhibit a significant improvement in properties like ductility in comparison to the monolithic SiC ceramic. The SiCf/SiC composite was obtained from a C/C composite precursor using convertion reaction under high temperature and controlled atmosphere. In this work, SiC phase presented the stacking faults in the structure, being not possible to calculate the unit cell size, symmetry and bond lengths but it seem equal card number 29-1129 of JCPDS.

Suicide nucleophilic attack: Reactions of benzohydroxamate anion with bis(2,4-dinitrophenyl) phosphate

(Chemical Equation Presented) The reaction between the benzohydroxamate anion (BHO-) and bis(2,4-dinitrophenyl)phosphate (BDNPP) has been examined kinetically, and the products were characterized by mass and NMR spectroscopy. The nucleophilic attack of BHO- follows two reaction paths: (i) at phosphorus, giving an unstable intermediate that undergoes a Lossen rearrangement to phenyl isocyanate, aniline, diphenylurea, and O-phenylcarbamyl benzohydroxamate; and (ii) on the aromatic carbon, giving an intermediate that was detected but slowly decomposes to aniline and 2,4-dinitrophenol. Thus, the benzohydroxamate anion can be considered a self-destructive molecular scissor since it reacts and loses its nucleophilic ability. © 2009 American Chemical Society.

Experimental Assessment of the Sensitiveness of an Electrochemical Oscillator towards Chemical Perturbations

In this study we address the problem of the response of a (electro)chemical oscillator towards chemical perturbations of different magnitudes. The chemical perturbation was achieved by addition of distinct amounts of trifluoromethanesulfonate (TFMSA), a rather stable and non-specifically adsorbing anion, and the system under investigation was the methanol electro-oxidation reaction under both stationary and oscillatory regimes. Increasing the anion concentration resulted in a decrease in the reaction rates of methanol oxidation and a general decrease in the parameter window where oscillations occurred. Furthermore, the addition of TFMSA was found to decrease the induction period and the total duration of oscillations. The mechanism underlying these observations was derived mathematically and revealed that inhibition in the methanol oxidation through blockage of active sites was found to further accelerate the intrinsic non-stationarity of the unperturbed system. Altogether, the presented results are among the few concerning the experimental assessment of the sensitiveness of an oscillator towards chemical perturbations. The universal nature of the complex chemical oscillator investigated here might be used for reference when studying the dynamics of other less accessible perturbed networks of (bio)chemical reactions.

DNA Catalysis: The Chemical Repertoire of DNAzymes

Deoxyribozymes or DNAzymes are single-stranded catalytic DNA molecules that are obtained by combinatorial in vitro selection methods. Initially conceived to function as gene silencing agents, the scope of DNAzymes has rapidly expanded into diverse fields, including biosensing, diagnostics, logic gate operations, and the development of novel synthetic and biological tools. In this review, an overview of all the different chemical reactions catalyzed by DNAzymes is given with an emphasis on RNA cleavage and the use of non-nucleosidic substrates. The use of modified nucleoside triphosphates (dN*TPs) to expand the chemical space to be explored in selection experiments and ultimately to generate DNAzymes with an expanded chemical repertoire is also highlighted.

Ion concentration and deduced chemical compounds of the GRIP and Dome Fuji ice cores, Greenland and Antarctica

We have proposed a method of deducing the chemical compounds found in deep polar ice cores by analyzing the balance between six major ions (Cl-, NO3-, SO4**2-, Na+, Mg2+, and Ca2+). The method is demonstrated for the Holocene and last glacial maximum regions of the Dome Fuji and GRIP ice cores. The dominant compounds depend only on the ion balance and the sequence of chemical reactions. In priority order, the principle salts are calcium sulfate, other sulfates, nitrate, chloride, and carbonate. The chemical abundances deduced by this method agree well with the results of Raman spectroscopy on individual salt inclusions. The abundances in the ice cores are shown to reflect differences in climatic periods (the acidic environment of the Holocene versus the reductive environment of the last glacial maximum) and regional conditions (the marine environment of Antarctica versus the continental environment of Greenland).

Some physical and chemical proceddes in fluids

The ability to reproduce reduced gravity conditions for long periods is one of the reasons why the orbiting laboratory is so attractive. In this paper several fluid dynamics problem areas are reviewed in which zero-gravity conditions are of great importance. Although emphasis is placed on space processing, there are some older problems also in which gravity masks the phenomcna, impeding a reasonably simple approach to the solution. Three problems are considered: Thermal convection under reduced gravity. The dumping effect ofsurface gravity waves at the outset of convection induced by surface tractions is discussed in particular. The existence of convection is of concern for some satellite thermal control techniques presently used, and for most of the proposed manufacturing processes. Whereas convection should be normally avoided, problems related to the containerless stirring ofa melt constitute an exception. Secondly, gravity and chemical reactions. Although chemical reactions are independent of gravity because of the small mass of the molecules and atoms involved, in many cases the reaction rate dcpends on the arrival of the species to the reaction zone. When the arrival process is buoyancy-controlled, the net specd of the reaction will be affected by the gravity. Thirdly, two-phase flows under reduced gravity provkle interesting problems from boiling heat transfer to degasslng of melts. This part of the paper deals only with the measurement of sound veiocity in a liquid containing bubbles. It is suggested that such measurements should be mude under reduced gravity to provide reliable residís.

Peroxo-iron and oxenoid-iron species as alternative oxygenating agents in cytochrome P450-catalyzed reactions: switching by threonine-302 to alanine mutagenesis of cytochrome P450 2B4.

Among biological catalysts, cytochrome P450 is unmatched in its multiplicity of isoforms, inducers, substrates, and types of chemical reactions catalyzed. In the present study, evidence is given that this versatility extends to the nature of the active oxidant. Although mechanistic evidence from several laboratories points to a hypervalent iron-oxenoid species in P450-catalyzed oxygenation reactions, Akhtar and colleagues [Akhtar, M., Calder, M. R., Corina, D. L. & Wright, J. N. (1982) Biochem. J. 201, 569-580] proposed that in steroid deformylation effected by P450 aromatase an iron-peroxo species is involved. We have shown more recently that purified liver microsomal P450 cytochromes, including phenobarbital-induced P450 2B4, catalyze the analogous deformylation of a series of xenobiotic aldehydes with olefin formation. The investigation presented here on the effect of site-directed mutagenesis of threonine-302 to alanine on the activities of recombinant P450 2B4 with N-terminal amino acids 2-27 deleted [2B4 (delta2-27)] makes use of evidence from other laboratories that the corresponding mutation in bacterial P450s interferes with the activation of dioxygen to the oxenoid species by blocking proton delivery to the active site. The rates of NADPH oxidation, hydrogen peroxide production, and product formation from four substrates, including formaldehyde from benzphetamine N-demethylation, acetophenone from 1-phenylethanol oxidation, cyclohexanol from cyclohexane hydroxylation, and cyclohexene from cyclohexane carboxaldehyde deformylation, were determined with P450s 2B4, 2B4 (delta2-27), and 2B4 (delta2-27) T302A. Replacement of the threonine residue in the truncated cytochrome gave a 1.6- to 2.5-fold increase in peroxide formation in the presence of a substrate, but resulted in decreased product formation from benzphetamine (9-fold), cyclohexane (4-fold), and 1-phenylethanol (2-fold). In sharp contrast, the deformylation of cyclohexane carboxaldehyde by the T302A mutant was increased about 10-fold. On the basis of these findings and our previous evidence that aldehyde deformylation is supported by added H202, but not by artificial oxidants, we conclude that the iron-peroxy species is the direct oxygen donor. It remains to be established which of the many other oxidative reactions involving P450 utilize this species and the extent to which peroxo-iron and oxenoid-iron function as alternative oxygenating agents with the numerous isoforms of this versatile catalyst.

Iron isotope and chemical compositions of sediments and basalts drilled seaward of the Mariana Trench

The purpose of this work is to study the mobility and budget of Fe isotopes in the oceanic crust and in particular during low-temperature interaction of seawater with oceanic basalt. We carried out this investigation using samples from Ocean Drilling Program (ODP) Site 801C drilled during Leg 129 and Leg 185 in Jurassic Pacific oceanic crust seaward of the Mariana Trench. The site comprises approximately 450 m of sediment overlying a section of 500 m of basalt, which includes intercalated pelagic and chemical sediments in the upper basaltic units and two low-temperature (10-30°C) ocherous Si-Fe hydrothermal deposits. Fe was chemically separated from 70 selected samples, and 57Fe/54Fe ratios were measured by MC-ICP-MS Isoprobe. The isotopic ratios were measured relative to an internal standard solution and are reported relative to the international Fe-standard IRMM-14. Based on duplicate measurements of natural samples, an external precision of 0.2? (2 sigma) has been obtained. The results indicate that the deep-sea sediment section has a restricted range of d57Fe, which is close to the igneous rock value. In contrast, large variations are observed in the basaltic section with positive d57Fe values (up to 2.05?) for highly altered basalts and negative values (down to ?2.49?) for the associated alteration products and hydrothermal deposits. Secondary Fe-minerals, such as Fe-oxyhydroxides or Fe-bearing clays (celadonite and saponite), have highly variable d57Fe values that have been interpreted as resulting from the partial oxidation of Fe(2+) leached during basalt alteration and precipitated as Fe(3+)-rich minerals. In contrast, altered basalts at Site 801C, which are depleted in Fe (up to 80%), display an increase in d57Fe values relative to fresh values, which suggest a preferential leaching of light iron during alteration. The apparent fractionation factor between dissolved Fe(2+) and Fe remaining in the mineral is from 0.5? to 1.3? and may be consistent with a kinetic isotope fractionation where light Fe is stripped from the minerals. Alternatively, the formation of secondary clays minerals, such as celadonite during basalt alteration may incorporate preferentially the heavy Fe isotopes, resulting in the loss of light Fe isotopes in the fluids. Because microbial processes within the oceanic crust are of potential importance in controlling rates of chemical reactions, Fe redox state and Fe-isotope fractionation, we evaluated the possible effect of this deep biosphere on Fe-isotope signatures. The Fe-isotope systematics presented in this study suggest that, even though iron behavior during seafloor weathering may be mediated by microbes, such as iron-oxidizers, d57Fe variations of more than 4? may also be explained by abiotic processes. Further laboratory experiments are now required to distinguish between various processes of Fe-isotope fractionation during seafloor weathering.

A dictionary of chemical equations.

Mode of access: Internet.

Toxicity reduction through chemical and biological modification of spent pulp bleaching liquors /

Mode of access: Internet.

Industrial uses of isotopes, chemical reaction mechanisms and kinetics, and radiochemistry : a selected list of references /

This bibliography contains 417 annotated references on uses of isotopes in industry and in chemical reaction mechanisms and kinetics. The references were taken from the 1957-1958 open literature. Also included are a list of journals from which the references were selected, an author index, an isotope index, and a graphical depiction of typical applications.

A multi-scaled approach for simulating chemical reaction systems

In this paper we give an overview of some very recent work, as well as presenting a new approach, on the stochastic simulation of multi-scaled systems involving chemical reactions. In many biological systems (such as genetic regulation and cellular dynamics) there is a mix between small numbers of key regulatory proteins, and medium and large numbers of molecules. In addition, it is important to be able to follow the trajectories of individual molecules by taking proper account of the randomness inherent in such a system. We describe different types of simulation techniques (including the stochastic simulation algorithm, Poisson Runge–Kutta methods and the balanced Euler method) for treating simulations in the three different reaction regimes: slow, medium and fast. We then review some recent techniques on the treatment of coupled slow and fast reactions for stochastic chemical kinetics and present a new approach which couples the three regimes mentioned above. We then apply this approach to a biologically inspired problem involving the expression and activity of LacZ and LacY proteins in E. coli, and conclude with a discussion on the significance of this work.

Chemical kinetic investigation of a commercial batch reactor process

The aim of this investigation was to study the chemical reactions occurring during the batchwise production of a butylated melamine-formaldehyde resin, in order to optimise the efficiency and economics of the batch processes. The batch process models are largely empirical in nature as the reaction mechanism is unknown. The process chemistry and the commercial manufacturing method are described. A small scale system was established in glass and the ability to produce laboratory resins with the required quality was demonstrated, simulating the full scale plant. During further experiments the chemical reactions of methylolation, condensation and butylation were studied. The important process stages were identified and studied separately. The effects of variation of certain process parameters on the chemical reactions were also studied. A published model of methylolation was modified and used to simulate the methylolation stage. A major result of this project was the development of an indirect method for studying the condensation and butylation reactions occurring during the dehydration and acid reaction stages, as direct quantitative methods were not available. A mass balance method was devised for this purpose and used to collect experimental data. The reaction scheme was verified using this data. The reactions stages were simulated using an empirical model. This has revealed new information regarding the mechanism and kinetics of the reactions. Laboratory results were shown to be comparable with plant scale results. This work has improved the understanding of the batch process, which can be used to improve product consistency. Future work has been identified and recommended to produce an optimum process and plant design to reduce the batch time.