Complex organic molecules in protoplanetary disks

Context. Protoplanetary disks are vital objects in star and planet formation, possessing all the material, gas and dust, which may form a planetary system orbiting the new star. Small, simple molecules have traditionally been detected in protoplanetary disks; however, in the ALMA era, we expect the molecular inventory of protoplanetary disks to significantly increase.

Aims. We investigate the synthesis of complex organic molecules (COMs) in protoplanetary disks to put constraints on the achievable chemical complexity and to predict species and transitions which may be observable with ALMA.

Methods. We have coupled a 2D steady-state physical model of a protoplanetary disk around a typical T Tauri star with a large gas-grain chemical network including COMs. We compare the resulting column densities with those derived from observations and perform ray-tracing calculations to predict line spectra. We compare the synthesised line intensities with current observations and determine those COMs which may be observable in nearby objects. We also compare the predicted grain-surface abundances with those derived from cometary comae observations.

Results. We find COMs are efficiently formed in the disk midplane via grain-surface chemical reactions, reaching peak grain-surface fractional abundances similar to 10(-6)-10(-4) that of the H nuclei number density. COMs formed on grain surfaces are returned to the gas phase via non-thermal desorption; however, gas-phase species reach lower fractional abundances than their grain-surface equivalents, similar to 10(-12)-10(-7). Including the irradiation of grain mantle material helps build further complexity in the ice through the replenishment of grain-surface radicals which take part in further grain-surface reactions. There is reasonable agreement with several line transitions of H2CO observed towards T Tauri star-disk systems. There is poor agreement with HC3(N) lines observed towards LkCa 15 and GO Tau and we discuss possible explanations for these discrepancies. The synthesised line intensities for CH3OH are consistent with upper limits determined towards all sources. Our models suggest CH3OH should be readily observable in nearby protoplanetary disks with ALMA; however, detection of more complex species may prove challenging, even with ALMA "Full Science" capabilities. Our grain-surface abundances are consistent with those derived from cometary comae observations providing additional evidence for the hypothesis that comets (and other planetesimals) formed via the coagulation of icy grains in the Sun's natal disk.

Hybrid optimization schemes for quantum control

Optimal control theory is a powerful tool for solving control problems in quantum mechanics, ranging from the control of chemical reactions to the implementation of gates in a quantum computer. Gradient-based optimization methods are able to find high fidelity controls, but require considerable numerical effort and often yield highly complex solutions. We propose here to employ a two-stage optimization scheme to significantly speed up convergence and achieve simpler controls. The control is initially parametrized using only a few free parameters, such that optimization in this pruned search space can be performed with a simplex method. The result, considered now simply as an arbitrary function on a time grid, is the starting point for further optimization with a gradient-based method that can quickly converge to high fidelities. We illustrate the success of this hybrid technique by optimizing a geometric phase gate for two superconducting transmon qubits coupled with a shared transmission line resonator, showing that a combination of Nelder-Mead simplex and Krotov’s method yields considerably better results than either one of the two methods alone.

Coupling aerosol surface and bulk chemistry with a kinetic double layer model (K2-SUB): oxidation of oleic acid by ozone

We present a kinetic double layer model coupling aerosol surface and bulk chemistry (K2-SUB) based on the PRA framework of gas-particle interactions (Poschl-Rudich-Ammann, 2007). K2-SUB is applied to a popular model system of atmospheric heterogeneous chemistry: the interaction of ozone with oleic acid. We show that our modelling approach allows de-convoluting surface and bulk processes, which has been a controversial topic and remains an important challenge for the understanding and description of atmospheric aerosol transformation. In particular, we demonstrate how a detailed treatment of adsorption and reaction at the surface can be coupled to a description of bulk reaction and transport that is consistent with traditional resistor model formulations. From literature data we have derived a consistent set of kinetic parameters that characterise mass transport and chemical reaction of ozone at the surface and in the bulk of oleic acid droplets. Due to the wide range of rate coefficients reported from different experimental studies, the exact proportions between surface and bulk reaction rates remain uncertain. Nevertheless, the model results suggest an important role of chemical reaction in the bulk and an approximate upper limit of similar to 10(-11) cm(2) s(-1) for the surface reaction rate coefficient. Sensitivity studies show that the surface accommodation coefficient of the gas-phase reactant has a strong non-linear influence on both surface and bulk chemical reactions. We suggest that K2-SUB may be used to design, interpret and analyse future experiments for better discrimination between surface and bulk processes in the oleic acid-ozone system as well as in other heterogeneous reaction systems of atmospheric relevance.

Modelling the high-latitude ionosphere for time-varying plasma convection

The paper discusses how variations in the pattern of convective plasma flows should beincluded in self-consistent time-dependent models of the coupled ionosphere-thermosphere system. The author shows how these variations depend upon the mechanism by which the solar wind flow excites the convection. The modelling of these effects is not just of relevance to the polar ionosphere. This is because the influence of convection is not confined to high latitudes: the resultant heating and composition changes in the thermosphere are communicated to lower latitudes by the winds which are also greatly modified by the plasma convection. These thermospheric changes alter the global distribution of plasma by modulatingthe rates of the chemical reactions which areresponsible for the loss of plasma. Hence the modelling of these high-latitude processes is of relevanceto the design and operation of HF communication, radar and navigation systems worldwide.

Applications and fundamental understanding of selected analytically important chemiluminescence reactions

This thesis encompasses a series of investigations into the fundamental chemistry and spectroscopy of chemiluminescence (chemical reactions that produce light). This new knowledge enabled the development of innovative analytical methodologies for rapid chemical measurements in forensic science, industrial process monitoring and clinical diagnostics.

Chemiluminescence from reactions with bis-cyclometalated iridium complexes in acidic aqueous solution

Chemical reactions between certain bis-cyclometalated iridium complexes, cerium(IV) and organic reducing agents in aqueous solution produce an emission of light which in some cases is more intense than that from analogous reactions with conventional ruthenium-based reagents, thus providing a new avenue for chemically-initiated luminescence detection.

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.

Properties and one-step synthesis of (2-acetylpyridine)tetraammineruthenium(II), [Ru-II(2-acpy)(NH3)(4)](2+) and tetraammine(2-benzoylpyridine)ruthenium(II), [Ru-II(NH3)(4)(2-bzpy)](2+) Redox potentials, UV-Vis and NMR spectra

A more direct and efficient route to the syntheses of [Ru(NH3)(4)(X-Y)](BF4)(2), where X-Y can be 2-acetylpyridine (2-acpy) or 2-benzoylpyridine (2-bzpy), based on the reactions of [RuCl(NH3)(5)]Cl-2 with these ortho-substituted azines is described. The [Ru(2-acpy)(NH3)(4)](BF4)(2) and [Ru(NH3)(5)(2-bzpy)](BF4)(2) complexes have a molar conductance of 328 and 292 Ohm(-1) cm(2) mol(-1), respectively, corresponding to a 1:2 species in solution. These complexes showed two intense absorption bands around 620-650 and 380 nm, the energies of which are solvent dependent, decreasing with the increase of the Gutman's donor number of the solvent, and were assigned as metal-to-ligand charge transfer (MLCT). The complexes have oxidation potentials (Ru-II/III) of +0.380 V vs. Ag/AgCl (2-acpy) and +0.400 V vs. Ag/AgCl (2-bzpy), and reduction potentials (X-Y0/-) of -1.10 V vs. Ag/AgCl (2-acpy) and -0.950 V vs. Ag/AgCl (2-bzpy) on CF3COOH/NaCF3COO at pH=3.0, scan rate 100 mV s(-1), [Ru]=1.0x10(-3) mol l(-1). Both processes show a coupled chemical reaction. Upon oxidation of the metal center, the MLCT absorption bands are bleached and restored upon subsequent reduction. In order to confirm the structure of the complexes a detailed LH NMR investigation was performed in d(6)-acetone. Further confirmation of the structure was obtained by recording the N-15 NMR spectrum of [Ru(NH3)(4)(2-bzpy)](2+) in d(6)-DMSO using the INEPT pulse sequence improving the sensitivity of N-15 by polarization transfer from the protons to the N-15. The Nuclear Overhauser Effect (NOE) experiments were made qualitatively for [Ru(NH3)(4)(2-acpy)](2+), and showed that H-6 of the pyridine is close to a NH3 proton, which should then be in a cis position, and, hence, confirming that acpy is acting as a bidentate ligand. (C) 1999 Elsevier B.V. Ltd. All rights reserved.

Electrochemistry of organometallic compounds. Part II. Oxidations of alkyl and aryl derivatives of bis(salicylaldehyde)ethylenediimine cobalt(III) in dimethylformamide

The influence of the axial organic ligand R on the electrochemical oxidation of the compounds [RCoIII(salen)DMF)], where salen is bis(salicylaldehyde)ethylenediimine, and R CH3, C2H5, n-C3H7, n-C4H9, s-C4H9, i-C4H9, CH2Cl, CF3CH2, c-C6H11CH2, c-C6H11, C6H5, C6H5CH2, p-CH3C6H4CH2, and p-NO2C6H4CH2, was studied by means of cyclic voltametry in dimethylformamide (DMF), 0.2 M in tetraethylammonium perchlorate (TEAP), at 25 and -20°C, with a platinum disc working electrode. The above-mentioned compounds can be classified according to their electrochemical behavior. (a) The complexes with R CH3, C2H5, n-C3H7, n-C4H9, c-C6H11CH2, and C6H5 undergo a reversible one-electron oxidation in the 10-50 V s-1 potential scan range. At slower scan rates, the oxidized product decomposes chemically. At -20°C, this chemical step is slow, and a reversible one-electron electrochemical oxidation is observed. (b) The compounds with R CH2Cl, C6H5CH2, p-CH3C6H4CH2 and p-NO2C6H4CH2 undergo a quasi-reversible one-electron oxidation at room temperaure. At -20°C, the electrochemical process becomes more complex. A following chemical reactions is coupled to the quasi-reversible one-electron transfer. Two reduction peaks are observed. (c) The compounds with R i-C4H9, s-C4H9, and c-C6H11 undergo a reversible one-electron oxidation at -20°C. At room temperature, the irreversible chemical reaction following the electron transfer step is too fast to allow the isolation of the electrochemical step. (d) At -20°C, the derivatives with R C2H5, c-C6H11 CH2 and c-C6H11 are adsorbed at the electrode surface. Evidence indicates that the reagent in these reactions is the pentacoordinated species [RCoIII(salen)]. A linear free-energy relationship between E1/2 (for reversible processes) and the Taft polar parameters o* was obtained with a slope of ρ* = 0.25 ± 0.03. As expected, the benzyl derivatives which present mesomeric effects do not fit this polar correlation. The rated of the electrochemical oxidation is also affected by the nature of the ligand R. For the ligands which are strong electron-withdrawing groups and for the benzyl derivatives, the rate of the electrochemical oxidation of the metal ion decreases at room temperature. At lower temperatures, it is suggested that the oxidation to the CoIV-R species is followed by a chemical reaction in which this complex is partly transformed into a CoIII(R*) species, which is reduced at a much more cathodic potential than the Co(IV) species. © 1979.

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.

Viabilidade de uso de um misturador para a análise de propriedades reológicas de produtos alimentícios

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

Métodos eletroanalíticos e cromatográficos aplicados na análise de corantes usados como marcadores em combustíveis

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

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.