Origin of needle fibre calcite (NFC) : a geochemical approach

ABSTRACTNeedle fibre calcite (NFC) is one of the most widespread habits of pedogenic calcite. It is a monocrystal of calcite, in the shape of a needle, with a diameter of one micron and a length between 4 and 103 times its width. NFC occurs in soils with different macroscopic and microscopic morphologies. Macroscopically, two main habits of NFC exist: "cotton ball'Mike clusters and as "powder" coating on pebbles inside the soil. It can also act as nucleation sites for precipitation of calcite cements of purely physicochemical origin (LCC - Late Calcitic Cement). Although many studies have been conducted on needle fibre calcite, its origin remains a subject of debate. The NFC having never been reproduced in the laboratory whatever the considered approach, the processes responsible for its precipitation as a so particular morphology remain unexplained. The shift between the length orientation of the needle crystal and the normal axis of calcite growth (c-axis) is also unresolved.Samples taken in two soils observed in quarries (Villiers and Savagnier) in the Swiss Jura Mountains are used to investigate the processes involved in the formation of these calcite crystals in pedogenic environments. Three groups of microscopic morphologies are distinguished: (i) simple needles (SN), (ii) simple needles with overgrowths (SNO), and (iii) simple needles with nanofibres (SNN), nanofibres being either organic or mineral in nature. These groups correspond to different stages in the formation and evolution of NFC.Comparison of carbon and oxygen isotope compositions of NFC with LCC, in relationship with the composition of the carbonate host rock (CHR), and the carbon isotope signature of dissolved inorganic carbon (DIC) from the soil waters, indicates that both NFC and LCC are precipitated in isotopic equilibrium with the soil solution. Similar Ô13C and Ô180 values of the elongated NFC and the rhombohedral calcite crystals of the LCC suggest that the precipitation of these different calcite habits is not due to changes in physicochemical conditions. The growth of NFC crystals inside an organic mould formed by the fungal hyphae could explain the formation of calcite ciystals in the shape of a needle in isotopic equilibrium with the local environment.Strontium and calcium isotope compositions of the three microscopic groups of NFC and LCC were also studied, in order to determine the origin of calcium (Ca2+) entrapped in the calcite lattice and to elucidate the processes responsible for the precipitation of NFC. The 87Sr/86Sr ratio of the SN is closer to the 87Sr/86Sr ratio of the carbonate host rock than the LCC, SNO, and SNN. This could be another clue for the formation of SN inside fungal hyphae, because fungi are known to dissolve the rocks to release and translocate through their hyphae nutrients necessary for their growth. SN and SNN are depleted in Sr and enriched in ^Ca compared to the LCC. In the context of Villiers quarry, where the two ciystal shapes precipitate at similar temperature (in a range of 0,6°C), such variations are the result of a slower precipitation rate of NFC, which is inconsistent with a purely physicochemically precipitated elongate crystal.Finally, NFC is enriched in major and trace elements (i.e. Fe, Zn, Cu, and Mo) compared to the LCC. This enrichment is ascribed to modification in precipitation processes between the NFC and LCC. Right now, it is not possible to preclude the influence of the particular shape of NFC or the biological influence. REEs are not fractionated in NFC, contrary to LCC. Thus, NFC does not precipitate from a percolation solution circulating downward the soil, which should lead to the fractionation of the REEs. As explained above, fungi, are able to dissolve and translocate nutrients. This kind of processes allows releasing elements in the soil solution without fractionation and could explain the particular chemical signature of NFC regarding the REEs.The geochemical approach to investigate the origin of NFC presented in this study does not allow providing direct clues to the fungal origin of NFC, but brings several new insights in the understanding of the formation of such a particular mineral, calcite needles, by precluding definitively their physicochemical origin.RESUMELa calcite en aiguilles (NFC) est l'une des formes les plus ubiquiste de calcite pédogénique. Il s'agit d'un monocrystal de calcite d'un diamètre d'un micron et d'une longueur 4 à 102 fois supérieure à sa largeur. A l'échelle macroscopique, la NFC a été observée sous deux principaux aspects : l'une « cotonneuse » et l'autre formant un mince croûte autour des graviers du sol. La NFC peut également servir de support à la nucléation de ciments secondaires précipités de manière purement physico-chimique (LCC). Malgré les nombreuses études menées sur la NFC, son origine demeure encore inconnue. A ce jour, aucune expérience en laboratoire n'a permis de créer de la calcite en aiguilles, et ce, quelque soit l'approche abordée. Par conséquent, les processus précis responsables de la précipitation calcite avec une telle morphologie restent inconnus. Le décalage existant entre l'axe d'allongement des aiguilles de calcite et l'axe normal de croissance de la calcite (axe c) reste inexpliqué.Des échantillons de NFC, LCC, roche mère, eau de pluie des différents horizons du sol ont été prélevés principalement au front de deux carrières de graviers, ainsi que dans un profil de sol adjacent à ces carrières, dans le but de mieux comprendre les processus à l'origine de la précipitation de calcite en forme d'aiguille. Trois micro-morphologies ont été distinguées: les aiguilles simples (SN), les aiguilles simples avec surcroissances calcitiques (SNO) et enfin les aiguilles simples avec nanofibres (SNN), celles-ci pouvant être de minérales ou organiques. Ces groupes, d'après nos résultats et les études antérieures pourraient correspondre à différentes étapes de formation de la calcite en aiguilles.Dans un premier temps, la comparaison des signatures isotopiques de la calcite en aiguilles, du LCC, de la roche mère et du carbone inorganique dissout dans la solution du sol (CID) indique que la NFC, tout comme le LCC, précipite en équilibre avec la solution du sol. Les valeurs similaires en Ô13C et δ180 de cristaux de calcite allongés (NFC) et rhombohédriques (LCC) formés dans un même milieu suggère que ces différences morphologiques ne peuvent pas être attribuées à des modifications purement physico-chimiques. La croissance de NFC à l'intérieur d'un moule organique comme les hyphes de champignons semble être la seule hypothèse plausible permettant d'expliquer la formation de monocrystaux allongés de calcite en équilibre avec leur environnement.La composition isotopique en strontium (Sr) et calcium (Ca) des LCC et des trois micro¬morphologies de la NFC ont été étudiées également, afin de déterminer l'origine du Ca2+ présent dans le réseau cristallin de la calcite en aiguilles, ainsi que les processus responsables de la formation de NFC. Les valeurs du rapport 87Sr/86$r de la forme SN sont les plus proches de celles de la roche mère par rapport aux formes SNN et SNO et du LCC. Ceci pourrait être un nouvel indice de l'implication des champignons dans la précipitation de calcite en aiguilles, puisqu'ils sont connus pour avoir la capacité de dissoudre les roches afin de libérer les nutriments nécessaires à leur croissance, ainsi que de les transloquer par leurs hyphes. De plus, les formes SN et SNN sont appauvries en Sr et enrichies en "Ca, comparativement au LCC. Dans le sol étudié, tous les carbonates de calcium précipitent à la même température, par conséquent, de telles variations sont dues à un taux de précipitation plus lent de SN et SNN, ce qui est contradictoire avec l'hypothèse physico-chimique. Pour finir, la NFC est enrichie en certains éléments majeurs et traces (i.e. Fe, Zn, Cu et Mo) par rapport au LCC. Ceci peut être attribué à différents processus de formation entre la NFC et le LCC. Pour le moment il est impossible d'exclure l'influence de la forme particulière de la NFC ou celle du champignon. Les terres rares (REEs) ne sont pas fractionnées dans la NFC, contrairement au LCC. Ceci peut être expliqué par le fait que la NFC précipite à partir d'une solution qui n'a pas percolé à travers le sol. Les champignons en dissolvant les roches mettent en solution éléments sans les fractionner. L'approche géochimique de l'étude de la calcite en aiguilles ne permets pas de produire des preuves directes sur sa potentielle origine fongique, mais permet de mieux comprendre comment un minéral aussi singulier que la NFC peut se former. D'autre pare cette étude permets d'exclure définitivement l'hypothèse physico-chimique de l'origine de la calcite en aiguilles

Ocean acidification alters the calcareous microstructure of the green macro-alga Halimeda opuntia

Decreases in seawater pH and carbonate saturation state (Omega) following the continuous increase in atmospheric CO2 represent a process termed ocean acidification, which is predicted to become a main threat to marine calcifiers in the near future. Segmented, tropical, marine green macro-algae of the genus Halimeda form a calcareous skeleton that involves biotically initiated and induced calcification processes influenced by cell physiology. As Halimeda is an important habitat provider and major carbonate sediment producer in tropical shallow areas, alterations of these processes due to ocean acidification may cause changes in the skeletal microstructure that have major consequences for the alga and its environment, but related knowledge is scarce. This study used scanning electron microscopy to examine changes of the CaCO3 segment microstructure of Halimedaopuntia specimens that had been exposed to artificially elevated seawater pCO2 of 650 µatm for 45 d. In spite of elevated seawater pCO2, the calcification of needles, located at the former utricle walls, was not reduced as frequent initiation of new needle-shaped crystals was observed. Abundance of the needles was 22 %/µm**2 higher and needle crystal dimensions 14 % longer. However, those needles were 42 % thinner compared with the control treatment. Moreover, lifetime cementation of the segments decreased under elevated seawater pCO2 due to a loss in micro-anhedral carbonate as indicated by significantly thinner calcified rims of central utricles (35-173 % compared with the control treatment). Decreased micro-anhedral carbonate suggests that seawater within the inter-utricular space becomes CaCO3 undersaturated (Omega < 1) during nighttime under conditions of elevated seawater pCO2, thereby favoring CaCO3 dissolution over micro-anhedral carbonate accretion. Less-cemented segments of H. opuntia may impair the environmental success of the alga, its carbonate sediment contribution, and the temporal storage of atmospheric CO2 within Halimeda-derived sediments.

The preparation of zinc(II) and cadmium(II) complexes of the pentadentate N3S2 ligand formed from 2,6-diacetylpyridine and S-benzyldithiocarbazate (H2SNNNS) and the X-ray crystal structure of the novel dimeric [Zn2(SNNNS)2] complex

The pentadentate chelating agent, 2,6-diacetylpyridinebis(S-benzyldithiocarbazate) (H2SNNNS) reacts with zinc(II) and cadmium(II) ions forming stable complexes of empirical formula, [M(SNNNS)] (M=Zn2+, Cd2+; SNNNS2 =doubly deprotonated anionic form of the Schiff base). These complexes have been characterized by a variety of physico-chemical techniques. IR and H-1 NMR spectral evidence indicate that the Schiff base coordinates to the zinc(II) and cadmium(II) ions via the pyridine nitrogen atoms, the azomethine nitrogen atoms and the mercaptide sulfur atoms. The crystal and molecular structure of the zinc(II) complex has been determined by X-ray diffraction. The complex is a dimer in which the pyridine nitrogen atom,the azomethine nitrogen atom and the thiolate sulfur atom from one ligand coordinate to one of the zinc(II) ions whereas the azomethine and thiolate sulfur atoms from another ligand complete pentacoordination around the zinc(II) ion, the ligands being coordinated in their deprotonated forms. The coordination geometry about each zinc(II) can be considered as intermediate between a square-pyramid and trigonal-bipyramid. The cadmium(II) complex is also assigned with a dimeric structure. (C) 2003 Elsevier Ltd. All rights reserved.

Preparation of transition metal complexes of bicyclo[2.2.1]hept-5-ene-2-carboxylic acid (C7H9CO2H) and X-ray crystal structure of [Cu2?(±)-endo-μ-O2CC7H9?4 (CH3OH)2]·2CH3OH

Metathesis reactions were used to prepare a range of dicopper(II), monocopper(I), diruthenium(II, III), dimolybdenum(II,II) and dirhodium(II,II) complexes of either racemic or resolved forms of endo- and exo-bicyclo[2.2.1]hept-5-ene-2-carboxylic acid (C7H9CO2H). The X-ray crystal structure of [Cu2{(±)-endo-μ-O2CC7H9}4(CH3OH)2]·2CH3OH shows the two copper(II) ions bridged by two (+)-endo-bicyclo[2.2.1]hept-5-ene-2-carboxylate anions and two (−)-endo-bicyclo[2.2.1]hept-5-ene-2-carboxylate anions. Methanol molecules occupy the two trans axial sites, and there are also two methanol molecules hydrogen bonded to opposite carboxyl oxygens.

Preparation of new crystal forms via photochemical, mechanochemical and sol-gel methods

This work of thesis involves various aspects of crystal engineering. Chapter 1 focuses on crystals containing crown ether complexes. Aspects such as the possibility of preparing these materials by non-solution methods, i.e. by direct reaction of the solid components, thermal behavior and also isomorphism and interconversion between hydrates are taken into account. In chapter 2 a study is presented aimed to understanding the relationship between hydrogen bonding capability and shape of the building blocks chosen to construct crystals. The focus is on the control exerted by shape on the organization of sandwich cations such as cobalticinium, decamethylcobalticinium and bisbenzenchromium(I) and on the aggregation of monoanions all containing carboxylic and carboxylate groups, into 0-D, 1-D, 2-D and 3-D networks. Reactions conducted in multi-component molecular assemblies or co-crystals have been recognized as a way to control reactivity in the solid state. The [2+2] photodimerization of olefins is a successful demonstration of how templated solid state synthesis can efficiently synthesize unique materials with remarkable stereoselectivity and under environment-friendly conditions. A demonstration of this synthetic strategy is given in chapter 3. The combination of various types of intermolecular linkages, leading to formation of high order aggregation and crystalline materials or to a random aggregation resulting in an amorphous precipitate, may not go to completeness. In such rare cases an aggregation process intermediate between crystalline and amorphous materials is observed, resulting in the formation of a gel, i.e. a viscoelastic solid-like or liquid-like material. In chapter 4 design of new Low Molecular Weight Gelators is presented. Aspects such as the relationships between molecular structure, crystal packing and gelation properties and the application of this kind of gels as a medium for crystal growth of organic molecules, such as APIs, are also discussed.

In Situ SHINERS at Electrochemical Single-Crystal Electrode/Electrolyte Interfaces: Tuning Preparation Strategies and Selected Applications

We have studied Au(55 nm)@SiO2 nanoparticles (NPs) on two low-index phases of gold and platinum single crystal electrodes in ClO4– and SO42– ion-containing electrolytes by both electrochemical methods and in-situ shell-isolated nanoparticle enhanced Raman spectroscopy (SHINERS). We showed the blocking of the electrode with surfactants originating from the synthesis of as-prepared SHINERS NPs. We introduce an efficient procedure to overcome this problem, which provides a fundamental platform for the application of SHINERS in surface electrochemistry and beyond. Our method is based on a hydrogen evolution treatment of the SHINERS-NP-modified single-crystal surfaces. The reliability of our preparation strategy is demonstrated in electrochemical SHINERS experiments on the potential-controlled adsorption and phase formation of pyridine on Au(hkl) and Pt(hkl). We obtained high-quality Raman spectra on these well-defined and structurally carefully characterized single-crystal surfaces. The analysis of the characteristic A1 vibrational modes revealed perfect agreement with the interpretation of single-crystal voltammetric and chronoamperometric experiments. Our study demonstrates that the SHINERS protocol developed in this work qualifies this Raman method as a pioneering approach with unique opportunities for in situ structure and reactivity studies at well-defined electrochemical solid/liquid interfaces.

The preparation and characterization of tin(IV) complexes of 2-quinolinecarboxaldehyde Schiff bases of S-methyl- and S-benzyldithiocarbazates and the X-ray crystal and molecular structures of the 2-quinolinecarboxaldehyde Schiff base of S-benzyldithi

New tin(IV) complexes of empirical formula, Sn(NNS)I-3 (NNS = anionic forms of the 2-quinolinecarboxaldehyde Schiff bases of S-methyl- and S-benzyldithiocarbazate) have been prepared and characterized by a variety of physico-chemical techniques. In the solid state, the Schiff bases exist as the thione tautomer but in solution and in the presence of tin(IV) iodide they convert to the thiol tautomer and coordinate to the tin atom in their deprotonated thiolate forms. The structures of the free ligand, Hqaldsbz and its triiodotin(IV) complex, [Sn(qaldsbz)I-3] have been determined by X-ray diffraction. The complex, [Sn(qaldsbz)I-3] has a distorted octahedral structure with the Schiff base coordinated to the tin atom as a uninegatively charged tridentate chelating agent via the quinoline nitrogen atom, the azomethine nitrogen atom and the thiolate sulfur atom. The three iodo ligands are coordinated meridionally to the tin atom. The distortion from an ideal octahedral geometry of [Sn(qaldsbz)I-3] is attributed to the restricted bite size of the tridentate Schiff base ligand. (C) 2004 Elsevier Ltd. All rights reserved.

The preparation and characterization of seven-coordinate tin(IV) complexes of the 2,6-diacetylpyridine Schiff bases of S-alkyl/aryl-dithiocarbazates and the X-ray crystal structure of the [Sn(dapsme)I-2] complex (dapsme=doubly deprotonated form of the 2,6

New tin(IV) complexes of empirical formula, Sn(SNNNS)I-2 (SNNNS = anionic form of the 2,6-diacetylpyridine Schiff bases of S-methyl- or S-benzyldithiocarbazate) have been prepared and characterized by a variety of physico-chemical techniques. The structure of Sn(dapsme)I-2 has been determined by single crystal X-ray crystallographic structural analysis. The complex has a seven-coordinate distorted pentagonal-bipyramidal geometry with the Schiff base coordinated to the tin(IV) ion as a dinegatively charged pentadentate chelating agent via the pyridine nitrogen atom, the two azomethine nitrogen atoms and the two thiolate sulfur atoms. The ligand occupies the equatorial plane and the iodo ligands are coordinated to the tin(IV) ion at axial positions. The distortion from an ideal pentagonal bipyramidal geometry is attributed to the restricted bite size of the pentadentate ligands. (C) 2004 Elsevier Ltd. All rights reserved.

XAS characterization of the RuO(2)-Ta(2)O(5) system local (crystal) structure

The influence of the preparation method on the structural properties of the RuO(2)-Ta(2)O(5) system was investigated. Both thin films on Ti substrates and powder samples of nominal composition Ti/RuO(2)-Ta(2)O(5) (Ru:Ta = 100:0, 90:10, 80:20, 30:70, and 0:100 at.%) were prepared through thermal decomposition of polymeric precursors (DPP). The thin films and powder samples were investigated using X-ray absorption spectroscopy (XAS). XANES analyses showed that Ru and Ta are present in the Ru(IV) and Ta(V) oxidation states. EXAFS signals of all the samples were analyzed, to obtain the average bond length (r), coordination number, and the Debye-Waller factor (sigma(2)) for each Ru-O, Ru-Ru, Ta-O nearest-neighbor. The first shell Ru-O distance was found at 1.91-1.92 angstrom with coordination number of 1.8-2.1, and at 2.01-2.02 angstrom with coordination number of 3.9-4.1. The Ta-O distance obtained for all the samples and in both modes (transmission and fluorescence) had significantly different values from the theoretical ones. The results revealed that the local structure around both the Ru and Ta sites are similar, and that they consist of distorted M-O(6) octahedra (where M = Ru or Ta). (C) 2010 Elsevier B.V. All rights reserved.

Simulation and theory of hybrid aligned liquid crystal films

We present a study of the effects of nanoconfinement on a system of hard Gaussian overlap particles interacting with planar substrates through the hard-needle-wall potential, extending earlier work by two of us [D. J. Cleaver and P. I. C. Teixeira, Chem. Phys. Lett. 338, 1 (2001)]. Here, we consider the case of hybrid films, where one of the substrates induces strongly homeotropic anchoring, while the other favors either weakly homeotropic or planar anchoring. These systems are investigated using both Monte Carlo simulation and density-functional theory, the latter implemented at the level of Onsager's second-virial approximation with Parsons-Lee rescaling. The orientational structure is found to change either continuously or discontinuously depending on substrate separation, in agreement with earlier predictions by others. The theory is seen to perform well in spite of its simplicity, predicting the positional and orientational structure seen in simulations even for small particle elongations.

Biochemical, immunological and toxicological characteristics of the crystal proteins of Bacillus thuringiensis subsp. medellin

Characterization of the insecticidal and hemolytic activity of solubilized crystal proteins of Bacillus thuringiensis (Bt) subsp. medellin (Btmed) was performed and compared to solubilized crystal proteins of isolates 1884 of B. thuringiensis subsp. israelensis (Bti) and isolate PG-14 of B. thuringiensis subsp. morrisoni (Btm). In general, at acid pH values solubilization of the Bt crystalline parasporal inclusions (CPI) was lower than at alkaline pH. The larvicidal activity demonstrated by the CPI of Btmed indicated that optimal solubilization of CPI takes place at a pH value of 11.3, in Bti at pH values from 5.03 to 11.3 and in Btm at pH values from 9.05 to 11.3. Hemolytic activity against sheep red blood cells was mainly found following extraction at pH 11.3 in all Bt strains tested. Polyacrylamide gel electrophoresis under denaturing conditions revealed that optimal solubilization of the CPI in all Bt strains takes place at the alkaline pH values from 9.05 to 11.3. An enriched preparation of Btmed crystals was obtained, solubilized and crystal proteins were separated on a size exclusion column (Sephacryl S-200). Three main protein peaks were observed on the chromatogram. The first peak had two main proteins that migrate between 90 to 100 kDa. These proteins are apparently not common to other Bt strains isolated to date. The second and third peaks obtained from the size exclusion column yielded polypeptides of 68 and 28-30 kDa, respectively. Each peak independently, showed toxicity against 1st instar Culex quinquefasciatus larvae. Interestingly, combinations of the fractions corresponding to the 68 and 30 kDa protein showed an increased toxicity. These results suggest that the 94 kDa protein is an important component of the Btmed toxins with the highest potency to kill mosquito larvae. When crystal proteins of Bti were probed with antisera raised independently against the three main protein fractions of Btmed, the only crystal protein that showed cross reaction was the 28 kDa protein. These data suggest that Btmed could be an alternative bacterium for mosquito control programs in case mosquito larval resistance emerges to Bti toxic proteins.

Preparation and management of complications in prostate biopsies

Transrectal ultrasonography-guided biopsy plays a key role in prostate sampling for cancer detection. Among interventional procedures, it is one of the most frequent procedures performed by radiologists. Despite the safety and low morbidity of such procedure, possible complications should be promptly assessed and treated. The standardization of protocols and of preprocedural preparation is aimed at minimizing complications as well as expediting their management. The authors have made a literature review describing the possible complications related to transrectal ultrasonography-guided prostate biopsy, and discuss their management and guidance to reduce the incidence of such complications.