CO2 and vitamin B12 interactions determine bioactive trace metal requirements of a subarctic Pacific diatom

Phytoplankton growth can be limited by numerous inorganic nutrients and organic growth factors. Using the subarctic diatom Attheya sp. in culture studies, we examined how the availability of vitamin B(12) and carbon dioxide partial pressure (pCO(2)) influences growth rate, primary productivity, cellular iron (Fe), cobalt (Co), zinc (Zn) and cadmium (Cd) quotas, and the net use efficiencies (NUEs) of these bioactive trace metals (mol C fixed per mol cellular trace metal per day). Under B(12)-replete conditions, cells grown at high pCO(2) had lower Fe, Zn and Cd quotas, and used those trace metals more efficiently in comparison with cells grown at low pCO(2). At high pCO(2), B(12)-limited cells had ~50% lower specific growth and carbon fixation rates, and used Fe ~15-fold less efficiently, and Zn and Cd ~3-fold less efficiently, in comparison with B(12)-replete cells. The observed higher Fe, Zn and Cd NUE under high pCO(2)/B(12)-replete conditions are consistent with predicted downregulation of carbon-concentrating mechanisms. Co quotas of B(12)-replete cells were 5- to 14-fold higher in comparison with B(12)-limited cells, suggesting that >80% of cellular Co of B(12)-limited cells was likely from B(12). Our results demonstrate that CO(2) and vitamin B(12) interactively influence growth, carbon fixation, trace metal requirements and trace metal NUE of this diatom. This suggests the need to consider complex feedback interactions between multiple environmental factors for this biogeochemically critical group of phytoplankton in the last glacial maximum as well as the current and future changing ocean.

Effects of sheep and horse manure and pine bark amendments on metal distribution and chemical properties of contaminated mine soils.

Mine soils usually contain large levels of heavy metals and poor fertility conditions which limit their reclamation and the application of phyto-remediation technologies. Two organic waste materials (pine bark compost and sheep and horse manure compost), with different pHs and varying degrees of humification and nutrient contents, were applied as amendments to assess their effects on copper (Cu) and zinc (Zn) bioavailability and on fertility conditions of mine soils. Soil samples collected from two abandoned mining areas near Madrid (Spain) were mixed with 0, 30 and 60 t ha?1 of the organic amendments. The concentrations of metals among the different mineral and organic fractions of soil were determined by several extraction procedures to study the metal distribution in the solid phase of the soil affected by the organic amendments. The results showed that the manure amendment increased the soil pH and the cation exchange capacity and enhanced the nutrient levels of these soils. The pine bark amendment decreased the soil pH and did not significantly change the nutrient status of soil. Soil pH, organic matter content and its degree of humification, which were altered by the amendments, were the main factors affecting Cu fractionation. Zn fractionation was mainly affected by soil pH. The addition of manure not only improved soil fertility, but also decreased metal bioavailability resulting in a reduction of metal toxicity. Conversely, pine bark amendment increased metal ioavailability. The use of sheep and horse manure could be a cost-effective practice for the restoration of contaminated mine soils.

Phytostabilization of metals in mine soils using Brassica juncea in combination with organic amendments

Background and aims The high metal bioavailability and the poor conditions of mine soils yield a low plant biomass, limiting the application of phytoremediation techniques. A greenhouse experiment was performed to evaluate the effects of organic amendments on metal stabilization and the potential of Brassica juncea L. for phytostabilization in mine soils. Methods Plants were grown in pots filled with soils collected from two mine sites located in Central Spain mixed with 0, 30 and 60 tha?1 of pine bark compost and horse- and sheep-manure compost. Plant biomass and metal concentrations in roots and shoots were measured. Metal bioavailability was assessed using a rhizosphere-based method (rhizo), which consists of a mixture of low-molecular-weight organic acids to simulate root exudates. Results Manure reduced metal concentrations in shoots (10?50 % reduction of Cu and 40?80 % of Zn in comparison with non-amended soils), bioconcentration factor (10?50 % of Cu and 40?80 % of Zn) and metal bioavailability in soil (40?50 % of Cu and 10?30 % of Zn) due to the high pH and the contribution of organic matter. Manure improved soil fertility and was also able to increase plant biomass (5?20 times in shoots and 3?30 times in roots), which resulted in a greater amount of metals removed from soil and accumulated in roots (increase of 2?7 times of Cu and Zn). Plants grown in pine bark treatments and in non-amended soils showed a limited biomass and high metal concentrations in shoots. Conclusions The addition of manure could be effective for the stabilization of metals and for enhancing the phytostabilization ability of B. juncea in mine soils. In this study, this species resulted to be a potential candidate for phytostabilization in combination with manure, differing from previous results, in which B. juncea had been recognized as a phytoextraction plant.

Double-level “orthogonal” dynamic combinatorial libraries on transition metal template

Dynamic combinatorial libraries are mixtures of compounds that exist in a dynamic equilibrium and can be driven to compositional self adaptation via selective binding of a specific assembly of certain components to a molecular target. We present here an extension of this initial concept to dynamic libraries that consists of two levels, the first formed by the coordination of terpyridine-based ligands to the transition metal template, and the second, by the imine formation with the aldehyde substituents on the terpyridine moieties. Dialdehyde 7 has been synthesized, converted into a variety of ligands, oxime ethers L11–L33 and acyl hydrazones L44–L77, and subsequently into corresponding cobalt complexes. A typical complex, Co(L22)22+ is shown to engage in rapid exchange with a competing ligand L11 and with another complex, Co(L22)22+ in 30% acetonitrile/water at pH 7.0 and 25°C. The exchange in the corresponding Co(III) complexes is shown to be much slower. Imine exchange in the acyl hydrazone complexes (L44–L77) is strongly controlled by pH and temperature. The two types of exchange, ligand and imine, can thus be used as independent equilibrium processes controlled by different types of external intervention, i.e., via oxidation/reduction of the metal template and/or change in the pH/temperature of the medium. The resulting double-level dynamic libraries are therefore named orthogonal, in similarity with the orthogonal protecting groups in organic synthesis. Sample libraries of this type have been synthesized and showed the complete expected set of components in electrospray ionization MS.

Oxide Semiconductors For Organic Opto-electronic Devices

Development of transparent oxide semiconductors (TOS) from Earth-abundant materials is of great interest for cost-effective thin film device applications, such as solar cells, light emitting diodes (LEDs), touch-sensitive displays, electronic paper, and transparent thin film transistors. The need of inexpensive or high performance electrode might be even greater for organic photovoltaic (OPV), with the goal to harvest renewable energy with inexpensive, lightweight, and cost competitive materials. The natural abundance of zinc and the wide bandgap ($sim$3.3 eV) of its oxide make it an ideal candidate. In this dissertation, I have introduced various concepts on the modulations of various surface, interface and bulk opto-electronic properties of ZnO based semiconductor for charge transport, charge selectivity and optimal device performance. I have categorized transparent semiconductors into two sub groups depending upon their role in a device. Electrodes, usually 200 to 500 nm thick, optimized for good transparency and transporting the charges to the external circuit. Here, the electrical conductivity in parallel direction to thin film, i.e bulk conductivity is important. And contacts, usually 5 to 50 nm thick, are optimized in case of solar cells for providing charge selectivity and asymmetry to manipulate the built in field inside the device for charge separation and collection. Whereas in Organic LEDs (OLEDs), contacts provide optimum energy level alignment at organic oxide interface for improved charge injections. For an optimal solar cell performance, transparent electrodes are designed with maximum transparency in the region of interest to maximize the light to pass through to the absorber layer for photo-generation, plus they are designed for minimum sheet resistance for efficient charge collection and transport. As such there is need for material with high conductivity and transparency. Doping ZnO with some common elements such as B, Al, Ga, In, Ge, Si, and F result in n-type doping with increase in carriers resulting in high conductivity electrode, with better or comparable opto-electronic properties compared to current industry-standard indium tin oxide (ITO). Furthermore, improvement in mobility due to improvement on crystallographic structure also provide alternative path for high conductivity ZnO TCOs. Implementing these two aspects, various studies were done on gallium doped zinc oxide (GZO) transparent electrode, a very promising indium free electrode. The dynamics of the superimposed RF and DC power sputtering was utilized to improve the microstructure during the thin films growth, resulting in GZO electrode with conductivity greater than 4000 S/cm and transparency greater than 90 %. Similarly, various studies on research and development of Indium Zinc Tin Oxide and Indium Zinc Oxide thin films which can be applied to flexible substrates for next generation solar cells application is presented. In these new TCO systems, understanding the role of crystallographic structure ranging from poly-crystalline to amorphous phase and the influence on the charge transport and optical transparency as well as important surface passivation and surface charge transport properties. Implementation of these electrode based on ZnO on opto-electronics devices such as OLED and OPV is complicated due to chemical interaction over time with the organic layer or with ambient. The problem of inefficient charge collection/injection due to poor understanding of interface and/or bulk property of oxide electrode exists at several oxide-organic interfaces. The surface conductivity, the work function, the formation of dipoles and the band-bending at the interfacial sites can positively or negatively impact the device performance. Detailed characterization of the surface composition both before and after various chemicals treatment of various oxide electrode can therefore provide insight into optimization of device performance. Some of the work related to controlling the interfacial chemistry associated with charge transport of transparent electrodes are discussed. Thus, the role of various pre-treatment on poly-crystalline GZO electrode and amorphous indium zinc oxide (IZO) electrode is compared and contrasted. From the study, we have found that removal of defects and self passivating defects caused by accumulation of hydroxides in the surface of both poly-crystalline GZO and amorphous IZO, are critical for improving the surface conductivity and charge transport. Further insight on how these insulating and self-passivating defects cause charge accumulation and recombination in an device is discussed. With recent rapid development of bulk-heterojunction organic photovoltaics active materials, devices employing ZnO and ZnO based electrode provide air stable and cost-competitive alternatives to traditional inorganic photovoltaics. The organic light emitting diodes (OLEDs) have already been commercialized, thus to follow in the footsteps of this technology, OPV devices need further improvement in power conversion efficiency and stable materials resulting in long device lifetimes. Use of low work function metals such as Ca/Al in standard geometry do provide good electrode for electron collection, but serious problems using low work-function metal electrodes originates from the formation of non-conductive metal oxide due to oxidation resulting in rapid device failure. Hence, using low work-function, air stable, conductive metal oxides such as ZnO as electrons collecting electrode and high work-function, air stable metals such as silver for harvesting holes, has been on the rise. Devices with degenerately doped ZnO functioning as transparent conductive electrode, or as charge selective layer in a polymer/fullerene based heterojunction, present useful device structures for investigating the functional mechanisms within OPV devices and a possible pathway towards improved air-stable high efficiency devices. Furthermore, analysis of the physical properties of the ZnO layers with varying thickness, crystallographic structure, surface chemistry and grain size deposited via various techniques such as atomic layer deposition, sputtering and solution-processed ZnO with their respective OPV device performance is discussed. We find similarity and differences in electrode property for good charge injection in OLEDs and good charge collection in OPV devices very insightful in understanding physics behind device failures and successes. In general, self-passivating surface of amorphous TCOs IZO, ZTO and IZTO forms insulating layer that hinders the charge collection. Similarly, we find modulation of the carrier concentration and the mobility in electron transport layer, namely zinc oxide thin films, very important for optimizing device performance.

Terminology of metal–organic frameworks and coordination polymers (IUPAC Recommendations 2013)

A set of terms, definitions, and recommendations is provided for use in the classification of coordination polymers, networks, and metal–organic frameworks (MOFs). A hierarchical terminology is recommended in which the most general term is coordination polymer. Coordination networks are a subset of coordination polymers and MOFs a further subset of coordination networks. One of the criteria an MOF needs to fulfill is that it contains potential voids, but no physical measurements of porosity or other properties are demanded per se. The use of topology and topology descriptors to enhance the description of crystal structures of MOFs and 3D-coordination polymers is furthermore strongly recommended.

Catalytic wet peroxide oxidation: a route towards the application of hybrid magnetic carbon nanocomposites for the degradation of organic pollutants. A review

Several motivations have prompted the scientific community towards the application of hybrid magnetic carbon nanocomposites in catalytic wet peroxide oxidation (CWPO) processes. The most relevant literature on this topic is reviewed, with a special focus on the synergies that can arise from the combination of highly active and magnetically separable iron species with the easily tuned properties of carbon-based materials. These are mainly ascribed to increased adsorptive interactions, to good structural stability and low leaching levels of the metal species, and to increased regeneration and dispersion of the active sites, which are promoted by the presence of the carbon-based materials in the composites. The most significant features of carbon materials that may be further explored in the design of improved hybrid magnetic catalysts are also addressed, taking into consideration the experimental knowledge gathered by the authors in their studies and development of carbon-based catalysts for CWPO. The presence of stable metal impurities, basic active sites and sulphur-containing functionalities, as well as high specific surface area, adequate porous texture, adsorptive interactions and structural defects, are shown to increase the activity of carbon materials when applied in CWPO, while the presence of acidic oxygen-containing functionalities has the opposite effect.

Design and synthesis of constrained azacyclic pyrrolidine analogues of FTY720 as anticancer agents & metal coordination-controlled and bifunctional catalysis toward tertiary β-Ketols

Cette thèse se compose en deux parties: Première Partie: La conception et la synthèse d’analogues pyrrolidiniques, utilisés comme agents anticancéreux, dérivés du FTY720. FTY720 est actuellement commercialisé comme médicament (GilenyaTM) pour le traitement de la sclérose en plaques rémittente-récurrente. Il agit comme immunosuppresseur en raison de son effet sur les récepteurs de la sphingosine-1-phosphate. A fortes doses, FTY720 présente un effet antinéoplasique. Cependant, à de telles doses, un des effets secondaires observé est la bradycardie dû à l’activation des récepteurs S1P1 et S1P3. Ceci limite son potentiel d’utilisation lors de chimiothérapie. Nos précédentes études ont montré que des analogues pyrrolidiniques dérivés du FTY720 présentaient une activité anticancéreuse mais aucune sur les récepteurs S1P1 et S1P3. Nous avons soumis l’idée qu’une étude relation structure-activité (SARs) pourrait nous conduire à la découverte de nouveaux agents anti tumoraux. Ainsi, deux séries de composés pyrrolidiniques (O-arylmethyl substitué et C-arylmethyl substitué) ont pu être envisagés et synthétisés (Chapitre 1). Ces analogues ont montré d’excellentes activités cytotoxiques contre diverses cellules cancéreuses humaines (prostate, colon, sein, pancréas et leucémie), plus particulièrement les analogues actifs qui ne peuvent pas être phosphorylés par SphK, présentent un plus grand potentiel pour le traitement du cancer sans effet secondaire comme la bradycardie. Les études mécanistiques suggèrent que ces analogues de déclencheurs de régulation négative sur les transporteurs de nutriments induisent une crise bioénergétique en affamant les cellules cancéreuses. Afin d’approfondir nos connaissances sur les récepteurs cibles, nous avons conçu et synthétisé des sondes diazirine basées sur le marquage d’affinité aux photons (méthode PAL: Photo-Affinity Labeling) (Chapitre 2). En s’appuyant sur la méthode PAL, il est possible de récolter des informations sur les récepteurs cibles à travers l’analyse LC/MS/MS de la protéine. Ces tests sont en cours et les résultats sont prometteurs. Deuxième partie: Coordination métallique et catalyse di fonctionnelle de dérivés β-hydroxy cétones tertiaires. Les réactions de Barbier et de Grignard sont des méthodes classiques pour former des liaisons carbone-carbone, et généralement utilisées pour la préparation d’alcools secondaires et tertiaires. En vue d’améliorer la réaction de Grignard avec le 1-iodobutane dans les conditions « one-pot » de Barbier, nous avons obtenu comme produit majoritaire la β-hydroxy cétone provenant de l’auto aldolisation de la 5-hexen-2-one, plutôt que le produit attendu d’addition de l’alcool (Chapitre 3). La formation inattendue de la β-hydroxy cétone a également été observée en utilisant d’autres dérivés méthyl cétone. Étonnement dans la réaction intramoléculaire d’une tricétone, connue pour former la cétone Hajos-Parrish, le produit majoritaire est rarement la β-hydroxy cétone présentant la fonction alcool en position axiale. Intrigué par ces résultats et après l’étude systématique des conditions de réaction, nous avons développé deux nouvelles méthodes à travers la synthèse sélective et catalytique de β-hydroxy cétones spécifiques par cyclisation intramoléculaire avec des rendements élevés (Chapitre 4). La réaction peut être catalysée soit par une base adaptée et du bromure de lithium comme additif en passant par un état de transition coordonné au lithium, ou bien soit à l’aide d’un catalyseur TBD di fonctionnel, via un état de transition médiée par une coordination bidenté au TBD. Les mécanismes proposés ont été corroborés par calcul DFT. Ces réactions catalytiques ont également été appliquées à d’autres substrats comme les tricétones et les dicétones. Bien que les efforts préliminaires afin d’obtenir une enantioselectivité se sont révélés sans succès, la synthèse et la recherche de nouveaux catalyseurs chiraux sont en cours.

Design and synthesis of constrained azacyclic pyrrolidine analogues of FTY720 as anticancer agents & metal coordination-controlled and bifunctional catalysis toward tertiary β-Ketols

Cette thèse se compose en deux parties: Première Partie: La conception et la synthèse d’analogues pyrrolidiniques, utilisés comme agents anticancéreux, dérivés du FTY720. FTY720 est actuellement commercialisé comme médicament (GilenyaTM) pour le traitement de la sclérose en plaques rémittente-récurrente. Il agit comme immunosuppresseur en raison de son effet sur les récepteurs de la sphingosine-1-phosphate. A fortes doses, FTY720 présente un effet antinéoplasique. Cependant, à de telles doses, un des effets secondaires observé est la bradycardie dû à l’activation des récepteurs S1P1 et S1P3. Ceci limite son potentiel d’utilisation lors de chimiothérapie. Nos précédentes études ont montré que des analogues pyrrolidiniques dérivés du FTY720 présentaient une activité anticancéreuse mais aucune sur les récepteurs S1P1 et S1P3. Nous avons soumis l’idée qu’une étude relation structure-activité (SARs) pourrait nous conduire à la découverte de nouveaux agents anti tumoraux. Ainsi, deux séries de composés pyrrolidiniques (O-arylmethyl substitué et C-arylmethyl substitué) ont pu être envisagés et synthétisés (Chapitre 1). Ces analogues ont montré d’excellentes activités cytotoxiques contre diverses cellules cancéreuses humaines (prostate, colon, sein, pancréas et leucémie), plus particulièrement les analogues actifs qui ne peuvent pas être phosphorylés par SphK, présentent un plus grand potentiel pour le traitement du cancer sans effet secondaire comme la bradycardie. Les études mécanistiques suggèrent que ces analogues de déclencheurs de régulation négative sur les transporteurs de nutriments induisent une crise bioénergétique en affamant les cellules cancéreuses. Afin d’approfondir nos connaissances sur les récepteurs cibles, nous avons conçu et synthétisé des sondes diazirine basées sur le marquage d’affinité aux photons (méthode PAL: Photo-Affinity Labeling) (Chapitre 2). En s’appuyant sur la méthode PAL, il est possible de récolter des informations sur les récepteurs cibles à travers l’analyse LC/MS/MS de la protéine. Ces tests sont en cours et les résultats sont prometteurs. Deuxième partie: Coordination métallique et catalyse di fonctionnelle de dérivés β-hydroxy cétones tertiaires. Les réactions de Barbier et de Grignard sont des méthodes classiques pour former des liaisons carbone-carbone, et généralement utilisées pour la préparation d’alcools secondaires et tertiaires. En vue d’améliorer la réaction de Grignard avec le 1-iodobutane dans les conditions « one-pot » de Barbier, nous avons obtenu comme produit majoritaire la β-hydroxy cétone provenant de l’auto aldolisation de la 5-hexen-2-one, plutôt que le produit attendu d’addition de l’alcool (Chapitre 3). La formation inattendue de la β-hydroxy cétone a également été observée en utilisant d’autres dérivés méthyl cétone. Étonnement dans la réaction intramoléculaire d’une tricétone, connue pour former la cétone Hajos-Parrish, le produit majoritaire est rarement la β-hydroxy cétone présentant la fonction alcool en position axiale. Intrigué par ces résultats et après l’étude systématique des conditions de réaction, nous avons développé deux nouvelles méthodes à travers la synthèse sélective et catalytique de β-hydroxy cétones spécifiques par cyclisation intramoléculaire avec des rendements élevés (Chapitre 4). La réaction peut être catalysée soit par une base adaptée et du bromure de lithium comme additif en passant par un état de transition coordonné au lithium, ou bien soit à l’aide d’un catalyseur TBD di fonctionnel, via un état de transition médiée par une coordination bidenté au TBD. Les mécanismes proposés ont été corroborés par calcul DFT. Ces réactions catalytiques ont également été appliquées à d’autres substrats comme les tricétones et les dicétones. Bien que les efforts préliminaires afin d’obtenir une enantioselectivité se sont révélés sans succès, la synthèse et la recherche de nouveaux catalyseurs chiraux sont en cours.

(Table 2) Trace metal ratios of various benthic foraminifera shells

Benthic foraminiferal d13C and Cd/Ca studies suggest that deep Atlantic circulation during the Last Glacial Maximum was very different from today, with high-nutrient (low d13C, high Cd) deep Southern Ocean Water (SOW) penetrating far into the North Atlantic. However, if some glacial d13C values are biased by productivity artifacts and/or air-sea exchange processes, then the existing d13C data may be consistent with the continual dominance of North Atlantic Deep Water (NADW). Cibicidoides wuellerstorfi Cd/Ca results presented here indicate that the glacial North Atlantic was strongly enriched in dissolved Cd below ~2500 m depth. If NADW formation was still vigorous relative to SOW formation, these data could be explained by either increased preformed nutrient levels in the high-latitude North Atlantic or by increased organic matter remineralization within lower NADW. High glacial Zn/Ca values in the same samples, however, are best explained by a substantially increased mixing with Zn-rich SOW. The cause was most likely a partial replacement of NADW by less dense Glacial North Atlantic Intermediate Water. This reorganization also lowered deep North Atlantic [CO3]2- concentrations by perhaps 10 to 15 µmol/kg.