Vibrational spectroscopy as a tool to understand plant silicification

Die Ablagerung von Siliziumdioxid ist ein verbreitetes Phänomen, das mit der Toleranz von Pflanzen gegenüber Belastungen korreliert. Die Pflanzen akkumulieren das amorphe Siliziumdioxid in mikroskopischen Partikeln, den Phytolithen, jedoch ist der exakte Mechanismus nicht vollständig aufgeklärt. Um ein besseres Verständnis über die Ablagerung von Siliziumdioxid zu erlangen, wurden verschiedene spektroskopische Techniken an Sorghumblättern und molekularen Modellen angewandt. Festkörper Kernspinresonanz und thermogravimetrische Analysen zeigen, dass die Siliziumdioxidstruktur von der Phytolithe-Extraktion abhängt. Basierend auf Raman- und IR-Daten einzelner Phytolithe lassen sich die Änderungen dieser Strukturen ermitteln. Das deutet auf unterschiedliche biologische Prozesse der Ablagerung des Siliciumdioxids hin. Die Pflanzengewebe in denen Siliciumdioxid abgelagert ist, wurden mit einem multimodalen Ansatz charakterisiert, welcher Fluoreszenz-, Hellfeld- und Rasterelektronenmikroskopie beinhaltet. Die chemische Zusammensetzung der Pflanzengewebe wurden mit Raman- und FTIR-Mikrospektroskopie kartiert. Ein neuartiger Ansatz zur Untersuchung von Pflanzengeweben wurde verwendet, basierend auf der optischen Nahfeldmikroskopie im mittleren IR-Bereich. Dieser ermöglicht eine kombinierte Analyse von mechanischen Materialeigenschaften sowie der chemischen Zusammensetzung und Struktur. Um die Rolle der organischen Matrix zu verstehen, wurden Modellverbindungen betrachtet, die die Ablagerung von Kieselsäure in den Pflanzen induzieren können. In-vitro-Reaktionen konnten eine gleichzeitige Präzipitation von Lignin und Siliciumdioxid sowie eine Polymerisation zusammen mit Peptiden simulieren. Die Ergebnisse lassen starke Wechselwirkungen zwischen diesen Verbindungen vermuten. Neben einem besseren Verständnis verschiedener Aspekte der Silifizierung von Pflanzen werden in dieser Arbeit neue Methoden zur Charakterisierung von Pflanzenproben vorgeschlagen.Silica deposition is a common phenomenon that correlates with plant tolerance to various stresses. Plants accumulate amorphous silica in microscopic particles termed phytoliths, through yet unclear mechanisms. With the aim to gain better understanding of the processes that govern silica deposition, different vibrational techniques were used on sorghum leaves and molecular models to obtain chemical and structural information addressing different length scales. Solid-state Nuclear Magnetic Resonance and thermogravimetric analysis showed that phytolith extraction methods affect silica structure. Nevertheless, Raman and IR analysis of individual phytoliths revealed differences in the structure and composition between phytolith types, suggesting the existence of different biological pathways for silica deposition. The environment of sorghum tissues where silica is deposited was assessed using a multimodal approach consisting of fluorescence, brightfield and scanning electron microscopies, while chemical composition was mapped using Raman and Fourier transformed Infrared microspectroscopy. Scattering-type near-field optical microscopy in the mid-infrared region was used to characterize the plant tissues, in both fixed and native plant samples. The nano-IR images and the mechanical phase image enabled a combined probing of mechanical material properties together with the chemical composition and structure of both the cell walls and the phytolith structures. In vitro reactions simulating lignin-silica co-precipitation and silica polymerization with peptides revealed strong interaction between these compounds and silica, and their possible involvement in silica deposition in the plant. This thesis provides a better understanding of the chemical process that control plant silicification, suggests new methodologies to characterize plant samples, and evaluates the current methods used in plant science

Structural, mineralogical, and biochemical diversity in the lower part of the pearl layer of cultivated seawater pearls from Polynesia

A series of Polynesian pearls has been investigated with particular attention to the structural and compositional patterns of the early developmental stages of the pearl layer. These initial steps in pearl formation bear witness of the metabolic changes that have occurred during the pearl-sac formation. The resulting structurally and biochemically complex structures have been investigated using a variety of techniques that provide us with information concerning both mineral phases and the organic components. Results are discussed with respect to our understanding of the biomineralization mechanisms, as well as for the grafting process

On the roles of close shell interactions in the structure of acyl-substituted hydrazones: An experimental and theoretical approach

The 2-(phenyl-hydrazono)-succinic acid dimethyl ester compound was synthesized by reacting phenylhydrazine with dimethylacetylene dicarboxylate at room temperature and characterized by elemental analysis, infrared, Raman, 1H and 13C NMR spectroscopies and mass spectrometry. Its solid state structure was determined by X-ray diffraction methods. The X-ray structure determination corroborates that the molecule is present in the crystal as the hydrazone tautomer, probably favored by a strong intramolecular N-H···O=C hydrogen bond occurring between the carbonyl (-C=O) and the hydrazone -C=N-NH- groups. A substantial fragment of the molecular skeleton is planar due to an extended π-bonding delocalization. The topological analysis of the electron densities (Atom in Molecule, AIM) allows characterization of intramolecular N-H···O interaction, that can be classified as a resonant assisted hydrogen bond (RAHB). Moreover, the Natural Bond Orbital population analysis confirms that a strong hyperconjugative lpO1 → σ∗(N2-H) remote interaction between the C2=O1 and N2-H groups takes place. Periodic system electron density and topological analysis have been applied to characterize the intermolecular interactions in the crystal. Weak intermolecular interactions determine the crystal packing, and the prevalence of non-directional dispersive contributions are inferred on topological grounds. The IR spectrum of the crystalline compound was investigated by means of density functional theory calculations carried out with periodic boundary conditions on the crystal, showing excellent agreement between theory and the experiments. The vibrational assignment is complemented with the analysis of the Raman spectrum.Fil: Saeed, Aamer. Quaid-I-Azam University; PakistánFil: Ifzan Arshad, M.. Quaid-I-Azam University; PakistánFil: Bolte, Michael. Goethe Universitat Frankfurt; AlemaniaFil: Fantoni, Adolfo Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: Delgado Espinosa, Zuly Yuliana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Química Inorgánica "Dr. Pedro J. Aymonino". Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Química Inorgánica "Dr. Pedro J. Aymonino"; ArgentinaFil: Erben, Mauricio Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Química Inorgánica "Dr. Pedro J. Aymonino". Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Química Inorgánica "Dr. Pedro J. Aymonino"; Argentin

On the roles of close shell interactions in the structure of acyl-substituted hydrazones: An experimental and theoretical approach

The 2-(phenyl-hydrazono)-succinic acid dimethyl ester compound was synthesized by reacting phenylhydrazine with dimethylacetylene dicarboxylate at room temperature and characterized by elemental analysis, infrared, Raman, 1H and 13C NMR spectroscopies and mass spectrometry. Its solid state structure was determined by X-ray diffraction methods. The X-ray structure determination corroborates that the molecule is present in the crystal as the hydrazone tautomer, probably favored by a strong intramolecular N-H···O=C hydrogen bond occurring between the carbonyl (-C=O) and the hydrazone -C=N-NH- groups. A substantial fragment of the molecular skeleton is planar due to an extended π-bonding delocalization. The topological analysis of the electron densities (Atom in Molecule, AIM) allows characterization of intramolecular N-H···O interaction, that can be classified as a resonant assisted hydrogen bond (RAHB). Moreover, the Natural Bond Orbital population analysis confirms that a strong hyperconjugative lpO1 → σ∗(N2-H) remote interaction between the C2=O1 and N2-H groups takes place. Periodic system electron density and topological analysis have been applied to characterize the intermolecular interactions in the crystal. Weak intermolecular interactions determine the crystal packing, and the prevalence of non-directional dispersive contributions are inferred on topological grounds. The IR spectrum of the crystalline compound was investigated by means of density functional theory calculations carried out with periodic boundary conditions on the crystal, showing excellent agreement between theory and the experiments. The vibrational assignment is complemented with the analysis of the Raman spectrum.Instituto de Física La PlataCentro de Química Inorgánic

Structural and chemical properties of solid organic inclusion compounds

Urea and thiourea form inclusion compounds in which organic and organometallic guest molecules are confined within non-intersecting, unidirectional tunnels within a solid urea or thiourea host structure. In this thesis, studies have been undertaken using a variety of techniques to examine the properties of urea and thiourea inclusion compounds, with a view to improving the understanding of the forces controlling the ordering of these systems on a molecular scale. From single crystal X-ray diffraction studies of urea inclusion compounds carried out at room temperature, different modes of ordering between guest molecules in adjacent tunnels, dependent on the guest species present, have been observed. Extension of these studies to low temperature, in conjunction with powder X-ray diffraction, has revealed information on phase transitions in both the host and guest substructures of urea inclusion compounds. Computer modelling, using a mathematical model developed for application to one-dimensional inclusion compounds, has been applied to model properties of n-alkane/urea and dimethylketone/urea inclusion compounds. The model has also been applied to the chlorocyclohexane/thiourea inclusion compound. EXAFS spectroscopy has been carried out on α,w-dibromoalkane/urea inclusion compounds to examine the local structural properties of the guest molecules. Halogenocyclohexane/thiourea and halogenocyclohexanes included within the pores of several zeolite-type hosts have also been investigated to determine the conformation of the guest molecules when constrained to occupy a confined environment. Additional studies have examined the potential for the polymerisation of monomeric guest molecules within the tunnels of the organic host structure of perhydrotriphenylene, and a solid state NMR investigation on the effect of magic angle spinning on the observed NMR spectrum for metallocenes

Isolation and structure elucidation of halogenated metabolites from Portieria hornemannii and Portieria tripinnata

The red marine algal genus, Portieria, is known to produce a number of potent cytotoxic compounds with anticancer potential. The most important anticancer lead produced by this genus is the compound halomon. Unfortunately, the lack of sufficient quantities of this compound hampered its further development. Two Portieria species, Portieria hornemannii and Portieria tripinnata, are found along the South African coastline. Recent studies, based on DNA analysis, suggest that Portieria hornemannii may in fact be divided into several cryptic species. The current project is part of a larger study designed to investigate the use of secondary metabolites to identify new marine algal species. In this study 1H NMR profiles of the organic extracts of selected Portieria spp were compared in order to identify new species. Selected compounds were then isolated and characterised as potential chemotaxonomic markers. Four halogenated monoterpenes were isolated from Portieria hornemannii. Two of these were new compounds 4-(3-bromo-4-chloro-4-methylpentyl)-3-chlorofuran-2(5H)-one, which were isomers of each other. The two known compounds had been previously isolated from Portieria hornemannii samples off the Madagascar coast. These compounds could prove to be useful as chemotaxonomic marker compounds, as they have never been isolated from any other species of marine algae. Three known halogenated monoterpenes were isolated from Portieria tripinnata. These compounds had been previously isolated from different species of marine algae and therefore, could not serve as chemotaxonomic marker compounds for this species of marine alga. Further work needs to be done on Portieria tripinnata, with regards to its chemistry, as it is a species of marine algae that has not been previously researched

Updates in metabolomics tools and resources: 2014-2015

Data processing and interpretation represent the most challenging and time-consuming steps in high-throughput metabolomic experiments, regardless of the analytical platforms (MS or NMR spectroscopy based) used for data acquisition. Improved machinery in metabolomics generates increasingly complex datasets that create the need for more and better processing and analysis software and in silico approaches to understand the resulting data. However, a comprehensive source of information describing the utility of the most recently developed and released metabolomics resources—in the form of tools, software, and databases—is currently lacking. Thus, here we provide an overview of freely-available, and open-source, tools, algorithms, and frameworks to make both upcoming and established metabolomics researchers aware of the recent developments in an attempt to advance and facilitate data processing workflows in their metabolomics research. The major topics include tools and researches for data processing, data annotation, and data visualization in MS and NMR-based metabolomics. Most in this review described tools are dedicated to untargeted metabolomics workflows; however, some more specialist tools are described as well. All tools and resources described including their analytical and computational platform dependencies are summarized in an overview Table

Supramolecular Nature of Multicomponent Crystals Formed from 2, 2'-Thiodiacetic Acid with 2, 6-Diaminopurine or N9-(2-Hydroxyethyl) adenine.

The synthesis and characterization of the multicomponent crystals formed by 2,2′-thiodiacetic acid (H2tda) and 2,6-diaminopurine (Hdap) or N9-(2-hydroxyethyl)adenine (9heade) are detailed in this report. These crystals exist in a salt rather than a co-crystal form, as confirmed by single crystal X-ray diffractometry, which reflects their ionic nature. This analysis confirmed proton transfer from the 2,2′-thiodiacetic acid to the basic groups of the coformers. The new multicomponent crystals have molecular formulas [(H9heade+)(Htda−)] 1 and [(H2dap+)2(tda2−)]·2H2O 2. These were also characterized using FTIR, 1H and 13C NMR and mass spectroscopies, elemental analysis, and thermogravimetric/differential scanning calorimetry (TG/DSC) analyses. In the crystal packing the ions interact with each other via O–H⋯N, O–H⋯O, N–H⋯O, and N–H⋯N hydrogen bonds, generating cyclic hydrogen-bonded motifs with graph-set notation of ��22 (16), ��22 (10), ��23 (10), ��33 (10), ��22 (9), ��23 (8), and ��24 (8), to form different supramolecular homo- and hetero-synthons. In addition, in the crystal packing of 2, pairs of diaminopurinium ions display a strong anti-parallel π,π-stacking interaction, characterized by short inter-centroids and interplanar distances (3.39 and 3.24 Å, respectively) and a fairly tight angle (17.5°). These assemblies were further analyzed energetically using DFT calculations, MEP surface analysis, and QTAIM characterization