Synchrotron X-rays reveal the modes of Fe binding and trace metal storage in the brown algae Laminaria digitata and Ectocarpus siliculosus

Funding Funding from the UK Natural Environment Research Council (NERC) through grants NE/D521522/1, NE/F012705/1, and Oceans 2025 (WP4.5) programs to FCK; the National Science Foundation (CHE-1664657) and the National Oceanic & Atmospheric Administration to CJC and FCK; and the MASTS pooling initiative (Marine Alliance for Science and Technology for Scotland, funded by the Scottish Funding Council and contributing institutions; grant reference HR09011) is gratefully acknowledged by FCK. PK would like to thank the European Commission for her postdoctoral fellowship (EC-Horizon 2020-MSCA-IF, grant no. 839151). AM and HK thank the Ministry of Education, Youth and Sports of the Czech Republic with co-financing from the European Union (grant "KOROLID", CZ.02.1.01/0.0/0.0/15_003/0000336) and the Czech Academy of Sciences (RVO: 60077344). AM, FK and HK are grateful for support from the European Community in the framework of the Access to Research Infrastructure Action of the Improving Human Potential Program to the ESRF (experiment LS-2772, beamline ID16AI). AM and HK thank Czech Government funding (Členství v European Synchrotron Radiation Facility, MŠMT – 33914/2017-1) supporting their work at the ESRF. GeoSoilEnviroCARS is supported by the National Science Foundation – Earth Sciences (EAR – 1634415) and Department of EnergyGeoSciences (DE-FG02-94ER14466). This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. Computational resources were supplied by the project "e-Infrastruktura CZ" (e-INFRA CZ LM2018140) supported by the Ministry of Education, Youth and Sports of the Czech Republic.Peer reviewedPublisher PD

Long-range chemical sensitivity in the sulfur K-edge X-ray absorption spectra of substituted thiophenes

© 2014 American Chemical Society. Thiophenes are the simplest aromatic sulfur-containing compounds and are stable and widespread in fossil fuels. Regulation of sulfur levels in fuels and emissions has become and continues to be ever more stringent as part of governments' efforts to address negative environmental impacts of sulfur dioxide. In turn, more effective removal methods are continually being sought. In a chemical sense, thiophenes are somewhat obdurate and hence their removal from fossil fuels poses problems for the industrial chemist. Sulfur K-edge X-ray absorption spectroscopy provides key information on thiophenic components in fuels. Here we present a systematic study of the spectroscopic sensitivity to chemical modifications of the thiophene system. We conclude that while the utility of sulfur K-edge X-ray absorption spectra in understanding the chemical composition of sulfur-containing fossil fuels has already been demonstrated, care must be exercised in interpreting these spectra because the assumption of an invariant spectrum for thiophenic forms may not always be valid

Reexamination of Lead(II) Coordination Preferences in Sulfur-Rich Sites: Implications for a Critical Mechanism of Lead Poisoning

Recent studies suggest that the developmental toxicity associated with childhood lead poisoning may be attributable to interactions of Pb(II) with proteins containing thiol-rich structural zinc-binding sites. Here, we report detailed structural studies of Pb(II) in such sites, providing critical insights into the mechanism by which lead alters the activity of these proteins. X-ray absorption spectroscopy of Pb(II) bound to structural zinc-binding peptides reveals that Pb(II) binds in a three-coordinate Pb(II)-S3 mode, while Zn(II) is known to bind in a four-coordinate mode in these proteins. This Pb(II)-S_3 coordination in peptides is consistent with a trigonal pyramidal Pb(II)-S_3 model compound previously reported by Bridgewater and Parkin, but it differs from many other reports in the small molecule literature which have suggested Pb(II)-S_4 as a preferred coordination mode for lead. Reexamination of the published structures of these “Pb(II)-S_4” compounds reveals that, in almost all cases, the coordination number of Pb is actually 5, 6, or 8. The results reported herein combined with this new review of published structures suggest that lead prefers to avoid four-coordination in sulfur-rich sites, binding instead as trigonal pyramidal Pb(II)-S_3 or as Pb(II)-S_(5-8). In the case of structural zinc-binding protein sites, the observation that lead binds in a three-coordinate mode, and in a geometry that is fundamentally different from the natural coordination of zinc in these sites, explains why lead disrupts the structure of these peptides and thus provides the first detailed molecular understanding of the developmental toxicity of lead

Basis sets for the calculation of core-electron binding energies

Core-electron binding energies (CEBEs) computed within a !self-consistent field approach require large basis sets to achieve convergence with respect to the basis set limit. It is shown that supplementing a basis set with basis functions from the corresponding basis set for the element with the next highest nuclear charge (Z+1) provides basis sets that give CEBEs close to the basis set limit. This simple procedure provides relatively small basis sets that are well suited for calculations where the description of a core-ionised state is important, such as time-dependent density functional theory calculations of X-ray emission spectroscopy

Determination of metal–metal distances: significance and accuracy

Nature utilises a variety of metal clusters as catalytic centers. Some of them make use of two or more metals in the catalytic site. The variation of metal-metal distances plays an important role in several processes like charge transfer and weakening of bonds. X-ray absorption spectroscopy can determine these metal-metal distances in several states (crystal, solution or amorphous). However sometimes backscattering from light elements hides the metal-metal contribution to the fine structure. Here we point out significance and accuracy of metal-metal distances in a model system. Therefore a number of different refinement protocols are applied to the data. These protocols will be discussed focusing on the significance and accuracy of the metal-metal distances extracted from the data

Mössbauer study of Fe oxides and hydroxides : application to the study of soils

Se estudian la mineralogia de los compuestos de Fe y la estabilidad de los compuestos magnéticos de tipo espinel en dos suelos de mineralogía y condiciones de manejo del suelo muy diferentes, y bajo la acción de climas y regímenes hídricos muy distintos (Molisoles de Bahía Blanca y Ultisoles de un yerbatal de Misiones) usando la espectroscopía Mossbauer a temperatura ambiente y a 15K. También se realizan mediciones de magnetización y se llevan a cabo las técnicas tradicionales para el estudio de suelos: DRX y los métodos químicos de disolución selectiva. Se hacen sugerencias para la implementación de la espectroscopía Mossbauer al estudio de los suelos pobres en Fe (Molisoles) y se estudia la eficiencia del tratamiento de disolución de Fe Ditionito -EDTA en comparación con los tratamientos químicos tradicionales. No obstante el bajo contenido de Fe del Molisol, los resultados obtenidos por la espectroscopía Mossbauer indican que los óxidos de Fe se presentan en tamaños pequeños pero sin ser superparamagnéticos y podrían estar cementando otras particulas no ferrosas. Los resultados para los Ultisoles sugieren que la mineralogía del Fe se ve afectada por las modificaciones del ecosistema en un proceso muy dinámico. A su vez en esta tesis se ha verificado la estabilidad de la magnetita en los Ultisoles de Misiones proporcionando elementos acerca de la controversia en la literatura sobre la estabilidad de la magnetita derivada de rocas maficas en suelos tropicales de areas vecinas de Brasil. Resultados similares se encuentran para la magnetita de un suelo muy poco desarrollado como es el Molisol.The mineralogy of the Fe compounds and the stability of the spinel magnetic compounds are studied in two soils making use of the Mossbauer spectroscopy at room temperature and 15K. These soils with different mineralogy and management conditions are under different climates and hidric regime (Molisols from Bahia Blanca and Ultisoles from a Yerba Mate plantation from Misiones). Moreover, measurements of magnetization are done and traditional techniques for the study of soils like XRD and chemical dissolution treatments are carried out. Suggestions for the implementation of Mossbauer spectroscopy applied to the study of the poor- Fe soils (Molisols) are done. The performance of the Fe dissolution treatment Ditionite- EDTA is compared with the traditional chemical treatments. In spite of the low Fe content of the Molisol, the obtained results by Mössbauer spectroscopy show that small sized particles of Fe oxides are present in the soil without being superparamagnetic but probably agglutinating non- ferrous particles. The results suggest that the Fe mineralogy is affected by the modifications of the ecosystem in a very dynamic process. A result is obtained about the controversy related to the stability of magnetite derived form mafic rocks in the tropical soils of neighbour areas in Brazil; the stability of magnetite in Ultisols from Misiones is verified in this thesis. Similar results are obtained for the magnetite of a less developed soil like the Molisol.Fil:Mijovilovich, Ana Esther. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina

Simulating the XANES of metalloenzymes – a case study

The analysis of XANES patterns is very indicative for screening samples. Powerful X-ray absorption spectroscopy data-analysis programs can simulate these patterns. Here, a case study on two structural motifs is presented: a non-heme Fe site (2-His-1-carboxylate motif) and the metallo [beta]-lactamase dinuclear Zn site. Simulations of the edge shapes for different structural models will be compared with experimental results, pointing out limitations and challenges. The influence of single neighbouring atoms in the first and second shell on the resulting XANES pattern is discussed. Insights into catalytic mechanisms and the requirements for future theory development are addressed

Tissue- and Age-Dependent Differences in the Complexation of Cadmium and Zinc in the Cadmium/Zinc Hyperaccumulator Thlaspi caerulescens (Ganges Ecotype) Revealed by X-Ray Absorption Spectroscopy

Extended x-ray absorption fine structure measurements were performed on frozen hydrated samples of the cadmium (Cd)/zinc (Zn) hyperaccumulator Thlaspi caerulescens (Ganges ecotype) after 6 months of Zn(2+) treatment with and without addition of Cd(2+). Ligands depended on the metal and the function and age of the plant tissue. In mature and senescent leaves, oxygen ligands dominated. This result combined with earlier knowledge about metal compartmentation indicates that the plants prefer to detoxify hyperaccumulated metals by pumping them into vacuoles rather than to synthesize metal specific ligands. In young and mature tissues (leaves, petioles, and stems), a higher percentage of Cd was bound by sulfur (S) ligands (e.g. phytochelatins) than in senescent tissues. This may indicate that young tissues require strong ligands for metal detoxification in addition to the detoxification by sequestration in the epidermal vacuoles. Alternatively, it may reflect the known smaller proportion of epidermal metal sequestration in younger tissues, combined with a constant and high proportion of S ligands in the mesophyll. In stems, a higher proportion of Cd was coordinated by S ligands and of Zn by histidine, compared with leaves of the same age. This may suggest that metals are transported as stable complexes or that the vacuolar oxygen coordination of the metals is, like in leaves, mainly found in the epidermis. The epidermis constitutes a larger percentage of the total volume in leaves than in stems and petioles. Zn-S interaction was never observed, confirming earlier results that S ligands are not involved in Zn resistance of hyperaccumulator plants