Chemistry and evolution of the Piperaceae

The chemistry of members of the family Piperaceae is of great interest owing to the variety of biological properties displayed. A survey of structural diversity and bioactivity reveals that groups of species specialize in the production of amides, phenylpropanoids, lignans and neolignans, benzoic acids and chromenes, alkaloids, polyketides, and a plethora of compounds of mixed biosynthetic origin. Bioassays against Cladosporium cladosporioides and C. sphaerospermun have resulted in the characterization of various amides, prenylated phenolic compounds, and polyketides as potential classes of antifungal agents. Studies on the developmental process in seedlings of Piper solmsianum have shown that phenylpropanoid are produced instead of the tetrahydrofuran lignans found in adult plants. In suspension cultures of P. cernuum and P crassinervium, phenylethylamines and alkamides predominate, whereas in the adult plants prenylpropanoids and prenylated benzoic acids are the respective major compound classes. Knowledge of the chemistry, bioactivity, and ecology of Piperaceae species provides preliminary clues for an overall interpretation of the possible role and occurrence of major classes of compounds.

The ceramic artifacts in archaeological black earth (terra preta) from Lower Amazon Region, Brazil: chemistry and geochemical evolution

Neste trabalho realizou-se a caracterização química de fragmentos de artefatos cerâmicos encontrados em sítios arqueológicos com terra preta no Baixo Amazonas (Cachoeira-Porteira, Pará, Brasil), representativos da cultura Konduri (de 900 a 400 anos AP). Esses fragmentos são constituídos de SiO₂, Al₂O₃, Fe₂O₃, Na₂O e P₂O₅, sendo que SiO₂ e Al₂O₃, juntos, perfazem mais de 80 % em peso. Os teores de P₂O,₅ são relativamente elevados (2,37 % em média) sob a forma de (Al,Fe)-fosfatos, incomuns em cerâmicas vermelhas primitivas, mas encontrados em algumas cerâmicas arqueológicas egípcias e romanas. As concentrações dos elementos traços são comparáveis ou mesmo inferiores ao nível crustal, embora a composição total seja próxima a mesma. A composição química (exceto P₂O₅) em conjunto com os dados mineralógicos e texturais indicam material saprolítico derivado de rochas ígneas félsicas ou rochas sedimentares como matéria-prima das cerâmicas. Os teores de K, Ca e Na mostram que os feldspatos e fragmentos de rochas foram adicionados ao material argiloso, como sugerido pela mineralogia. Os altos teores de sílica respondem pela presença de cauixi, cariapé e/ou areias quartzosas. Fósforo deve ter sido incorporadoà matriz argilosa da cerâmica, quando do cozimento de alimentos nos vasos cerâmicos, e ainda, em parte, durante a formação do perfil de solo tipo ABE sobre Latossolos Amarelos. A matéria prima e os temperos (cauixi, cariapé, rochas trituradas e fragmentos de vasos cerâmicos descartados) encontram-se disponíveis próximos aos sítios até a atualidade, e, portanto foram a área fonte dos mesmos para a confecção dos artefatos cerâmicos.

Lignin chemistry and topochemistry during kraft delignification of Eucalyptus globulus genotypes with contrasting pulpwood characteristics

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Molecular chemistry and the missing mass problem in planetary nebulae

Context. Detections of molecular lines, mainly from H-2 and CO, reveal molecular material in planetary nebulae. Observations of a variety of molecules suggest that the molecular composition in these objects differs from that found in interstellar clouds or in circumstellar envelopes. The success of the models, which are mostly devoted to explain molecular densities in specific planetary nebulae, is still partial however. Aims. The present study aims at identifying the influence of stellar and nebular properties on the molecular composition of planetary nebulae by means of chemical models. A comparison of theoretical results with those derived from the observations may provide clues to the conditions that favor the presence of a particular molecule. Methods. A self-consistent photoionization numerical code was adapted to simulate cold molecular regions beyond the ionized zone. The code was used to obtain a grid of models and the resulting column densities are compared with those inferred from observations. Results. Our models show that the inclusion of an incident flux of X-rays is required to explain the molecular composition derived for planetary nebulae. We also obtain a more accurate relation for the N(CO)/N(H-2) ratio in these objects. Molecular masses obtained by previous works in the literature were then recalculated, showing that these masses can be underestimated by up to three orders of magnitude. We conclude that the problem of the missing mass in planetary nebulae can be solved by a more accurate calculation of the molecular mass.

Chemistry and Chemical Education Through Text and Image: Analysis of Twentieth Century Textbooks Used in Brazilian Context

Assuming that textbooks give literary expression to cultural and ideological values of a nation or group, we propose the analysis of chemistry textbooks used in Brazilian universities throughout the twentieth century. We analyzed iconographic and textual aspects of 31 textbooks which had significant diffusion in the context of Brazilian universities at that period. As a result of the iconographic analysis, nine categories of images were proposed: (1) laboratory and experimentation, (2) industry and production, (3) graphs and diagrams, (4) illustrations related to daily life, (5) models, (6) illustrations related to the history of science, (7) pictures or diagrams of animal, vegetable or mineral samples, (8) analogies and (9) concepts of physics. The distribution of images among the categories showed a different emphasis in the presentation of chemical content due to a commitment to different conceptions of chemistry over the period. So, we started with chemistry as an experimental science in the early twentieth century, with an emphasis change to the principles of chemistry from the 1950s, culminating in a chemistry of undeniable technological influence. Results showed that reflections not only on the history of science, but on the history of science education, may be useful for the improvement of science education.

Synthesis of Modified Amino Acids and Insertion in Peptides and Mimetics. Structural Aspects and Impact on Biological Activity.

I studied the effects exerted by the modifications on structures and biological activities of the compounds so obtained. I prepared peptide analogues containing unusual amino acids such as halogenated, alkylated (S)- or (R)-tryptophans, useful for the synthesis of mimetics of the endogenous opioid peptide endomorphin-1, or 2-oxo-1,3-oxazolidine-4-carboxylic acids, utilized as pseudo-prolines having a clear all-trans configuration of the preceding peptide bond. The latter gave access to a series of constrained peptidomimetics with potential interest in medicinal chemistry and in the field of the foldamers. In particular, I have dedicated much efforts to the preparation of cyclopentapeptides containing D-configured, alfa-, or beta-aminoacids, and also of cyclotetrapeptides including the retro-inverso modification. The conformational analyses confirmed that these cyclic compounds can be utilized as rigid scaffolds mimicking gamma- or beta-turns, allowing to generate new molecular and 3D diversity. Much work has been dedicated to the structural analysis in solution and in the receptor-bound state, fundamental for giving a rationale to the experimentally determined bioactivity, as well as for predicting the activity of virtual compounds (in silico pre-screen). The conformational analyses in solution has been done mostly by NMR (2D gCosy, Roesy, VT, molecular dynamics, etc.). A special section is dedicated to the prediction of plausible poses of the ligands when bound to the receptors by Molecular Docking. This computational method proved to be a powerful tool for the investigation of ligand-receptor interactions, and for the design of selective agonists and antagonists. Another practical use of cyclic peptidomimetics was the synthesis and biological evaluation of cyclic analogues of endomorphin-1 lacking in a protonable amino group. The studies revealed that a inverse type II beta-turn on D-Trp-Phe constituted the bioactive conformation.

Mineral chemistry and structural relationships of inclusions in diamond samples

Diamant ist das härteste Mineral – und dazu ein Edelstein -, das unter höchstem Druck und hohen Temperaturen in tiefen kontinentalen Regionen der Erde kristallisiert. Die Mineraleinschlüsse in Diamanten werden durch die physikalische Stabilität und chemische Beständigkeit der umgebenden – eigentlich metastabilen -Diamant-Phase geschützt. Aufgrund der koexistierenden Phasenkombination ermöglichen sie, die Mineral-Entwicklung zu studieren, während deren der Einschlüssen und die Diamanten kristallisierten. rnDie Phasenkombinationen von Diamant und Chrom-Pyrop, Chrom-Diopsid, Chromit, Olivin, Graphit und Enstatit nebeneinander (teilweise in Berührungsexistenz) mit Chrom-Pyrop Einschlüssen wurden von neunundzwanzig Diamant-Proben von sechs Standorten in Südafrika (Premier, Koffiefontein, De Beers Pool, Finsch, Venetia und Koingnaas Minen) und Udachnaya (Sibirien/Russland) identifiziert und charakterisiert. Die Mineraleinschlüsse weisen z.T. kubo-oktaedrische Form auf, die unabhängig von ihren eigenen Kristallsystemen ausgebildet werden können. Das bedeutet, dass sie syngenetische Einschlüsse sind, die durch die sehr hohe Formenergie des umgebenden Diamanten morphologisch unter Zwang stehen. Aus zweidiemnsionalen Messungen der ersten Ordnung von charakteristischen Raman-Banden lassen sich relative Restdrucke in Diamanten zwischen Diamant und Einschlussmineral gewinnen; sie haben charakteristische Werte von ca. 0,4 bis 0,9 GPa um Chrom-Pyrop-Einschlüsse, 0,6 bis 2,0 GPa um Chrom-Diopsid-Einschlüsse, 0,3 bis 1,2 GPa um Olivin-Einschlüsse, 0,2 bis 1,0 GPa um Chromit-Einschlüsse, beziehungsweise 0,5 GPa um Graphit Einschlüsse.rnDie kristallstrukturellen Beziehung von Diamanten und ihren monomineralischen Einschlüssen wurden mit Hilfe der Quantifizierung der Winkelkorrelationen zwischen der [111] Richtung von Diamanten und spezifisch ausgewählten Richtungen ihrer mineralischen Einschlüsse untersucht. Die Winkelkorrelationen zwischen Diamant [111] und Chrom-Pyrop [111] oder Chromit [111] zeigen die kleinsten Verzerrungen von 2,2 bis zu 3,4. Die Chrom-Diopsid- und Olivin-Einschlüsse zeigen die Missorientierungswerte mit Diamant [111] bis zu 10,2 und 12,9 von Chrom-Diopsid [010] beziehungsweise Olivin [100].rnDie chemische Zusammensetzung von neun herausgearbeiteten (orientiertes Anschleifen) Einschlüssen (drei Chrom-Pyrop-Einschlüsse von Koffiefontein-, Finsch- und Venetia-Mine (zwei von drei koexistieren nebeneinander mit Enstatit), ein Chromit von Udachnaya (Sibirien/Russland), drei Chrom-Diopside von Koffiefontein, Koingnaas und Udachnaya (Sibirien/Russland) und zwei Olivin Einschlüsse von De Beers Pool und Koingnaas) wurden mit Hilfe EPMA und LA-ICP-MS analysiert. Auf der Grundlage der chemischen Zusammensetzung können die Mineraleinschlüsse in Diamanten in dieser Arbeit der peridotitischen Suite zugeordnet werden.rnDie Geothermobarometrie-Untersuchungen waren aufgrund der berührenden Koexistenz von Chrom-Pyrop- und Enstatit in einzelnen Diamanten möglich. Durchschnittliche Temperaturen und Drücke der Bildung sind mit ca. 1087 (± 15) C, 5,2 (± 0,1) GPa für Diamant DHK6.2 von der Koffiefontein Mine beziehungsweise ca. 1041 (± 5) C, 5,0 (± 0,1) GPa für Diamant DHF10.2 von der Finsch Mine zu interpretieren.rn

Preparation and functional characterisation of recombinant silicatein-alpha from the sponge Suberites domuncula

The marine world is an immense source of biodiversity that provides substances with striking potentials in medicinal chemistry and biotechnology. Sponges (Porifera) are marine animals that represent the most impressive example of organisms possessing the ability to metabolise silica through a family of enzymes known as silicateins. Complex skeletal structures (spicules) made of pure biogenic silica (biosilica) are produced under physiological conditions. Biosilica is a natural material comprising inorganic and organic components with unique mechanical, optical, and physico-chemical properties, including promising potential to be used for development of therapeutic agents in regenerative medicine. Unravelling the intimate physiological mechanisms occurring in sponges during the construction of their siliceous spicules is an on-going project, and several questions have been addressed by the studies proposed by our working group. In this doctoral work, the recombinant DNA technology is exploited for functional and structural characterisation of silicatein. Its precursors are produced as fusion proteins with a chaperone tag (named TF-Ps), and a robust method for the overexpression of native soluble proteins in high concentrations has been developed. In addition, it is observed and proven experimentally that the maturation of silicatein is an autocatalytic event that: (i) can be modulated by rational use of protease inhibitors; (ii) is influenced by the temperature of the environment; (iii) only slightly depends on the pH. In the same experimental framework, observations on the dynamics in the maturation of silicateins allow a better understanding of how the axial filaments form during the early stages of spicule construction. In addition, the definition of new distinct properties of silicatein (termed “structure-guiding” and “structure-forming”) is introduced. By homology models and through comparisons with similar proteins (the cathepsins), domains with significant surface hydrophobicity are identified as potential self-assembly mediators. Moreover, a high-throughput screening showed that TF-Ps could generate crystals under certain conditions, becoming promising for further structural studies. With the goal of optimise the properties of the recombinant silicatein, implementation of new production systems are tried for the first time. Success in the expression of silicatein-type proteins in insect and yeast cells, constitute a promising basis for further development, towards the establishment of an efficient method for the production of a high-value pure and soluble protein.

Comparison of Model Chemistry and Density Functional Theory Thermochemical Predictions with Experiment for Formation of Ionic Clusters of the Ammonium Cation Complexed with Water and Ammonia; Atmospheric Implications

The G2, G3, CBS-QB3, and CBS-APNO model chemistry methods and the B3LYP, B3P86, mPW1PW, and PBE1PBE density functional theory (DFT) methods have been used to calculate ΔH° and ΔG° values for ionic clusters of the ammonium ion complexed with water and ammonia. Results for the clusters NH4+(NH3)n and NH4+(H2O)n, where n = 1−4, are reported in this paper and compared against experimental values. Agreement with the experimental values for ΔH° and ΔG° for formation of NH4+(NH3)n clusters is excellent. Comparison between experiment and theory for formation of the NH4+(H2O)n clusters is quite good considering the uncertainty in the experimental values. The four DFT methods yield excellent agreement with experiment and the model chemistry methods when the aug-cc-pVTZ basis set is used for energetic calculations and the 6-31G* basis set is used for geometries and frequencies. On the basis of these results, we predict that all ions in the lower troposphere will be saturated with at least one complete first hydration shell of water molecules.

Homo-DNA templated chemistry and its application to nucleic acid sensing

We have investigated the homo-DNA templated Staudinger reduction of the profluorophore rhodamine azide and have applied this reaction to the detection of natural DNA with a hybrid homo-DNA/DNA molecular beacon. In this system the sensing and the reporting unit are bioorthogonal to each other which facilitates sequence design and increases fidelity.

The recoil transfer chamber - An interface to connect the physical preseparator TASCA with chemistry and counting setups

Performing experiments with transactinide elements demands highly sensitive detection methods due to the extremely low production rates (one-atom-at-a-time conditions). Preseparation with a physical recoil separator is a powerful method to significantly reduce the background in experiments with sufficiently long-lived isotopes (t1/2≥0.5 s). In the last years, the new gas-filled TransActinide Separator and Chemistry Apparatus (TASCA) was installed and successfully commissioned at GSI. Here, we report on the design and performance of a Recoil Transfer Chamber (RTC) for TASCA—an interface to connect various chemistry and counting setups with the separator. Nuclear reaction products recoiling out of the target are separated according to their magnetic rigidity within TASCA, and the wanted products are guided to the focal plane of TASCA. In the focal plane, they pass a thin Mylar window that separates the ∼1 mbar atmosphere in TASCA from the RTC kept at ∼1 bar. The ions are stopped in the RTC and transported by a continuous gas flow from the RTC to the ancillary setup. In this paper, we report on measurements of the transportation yields under various conditions and on the first chemistry experiments at TASCA—an electrochemistry experiment with osmium and an ion exchange experiment with the transactinide element rutherfordium.