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

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

Complexation and Toxicity of Copper in Higher Plants. I. Characterization of Copper Accumulation, Speciation, and Toxicity in Crassula helmsii as a New Copper Accumulator

The amphibious water plant Crassula helmsii is an invasive copper (Cu)-tolerant neophyte in Europe. It now turned out to accumulate Cu up to more than 9,000 ppm in its shoots at 10 microm (=0.6 ppm) Cu(2+) in the nutrient solution, indicating that it is a Cu hyperaccumulator. We investigated uptake, binding environment, and toxicity of Cu in this plant under emerged and submerged conditions. Extended x-ray absorption fine structure measurements on frozen-hydrated samples revealed that Cu was bound almost exclusively by oxygen ligands, likely organic acids, and not any sulfur ligands. Despite significant differences in photosynthesis biochemistry and biophysics between emerged and submerged plants, no differences in Cu ligands were found. While measurements of tissue pH confirmed the diurnal acid cycle typical for Crassulacean acid metabolism, Delta(13)C measurements showed values typical for regular C3 photosynthesis. Cu-induced inhibition of photosynthesis mainly affected the photosystem II (PSII) reaction center, but with some unusual features. Most obviously, the degree of light saturation of electron transport increased during Cu stress, while maximal dark-adapted PSII quantum yield did not change and light-adapted quantum yield of PSII photochemistry decreased particularly in the first 50 s after onset of actinic irradiance. This combination of changes, which were strongest in submerged cultures, shows a decreasing number of functional reaction centers relative to the antenna in a system with high antenna connectivity. Nonphotochemical quenching, in contrast, was modified by Cu mainly in emerged cultures. Pigment concentrations in stressed plants strongly decreased, but no changes in their ratios occurred, indicating that cells either survived intact or died and bleached quickly

Architecture of a protein central to iron homeostasis: crystal structure and spectroscopic analysis of the ferric uptake regulator

Iron is an essential element for almost all organisms, although an overload of this element results in toxicity because of the formation of hydroxyl radicals. Consequently, most living entities have developed sophisticated mechanisms to control their intracellular iron concentration. In many bacteria, including the opportunistic pathogen Pseudomonas aeruginosa, this task is performed by the ferric uptake regulator (Fur). Fur controls a wide variety of basic physiological processes including iron uptake systems and the expression of exotoxin A. Here, we present the first crystal structure of Fur from P. aeruginosa in complex with Zn2+ determined at a resolution of 1.8 Å. Furthermore, X-ray absorption spectroscopic measurements and microPIXE analysis were performed in order to characterize the distinct zinc and iron binding sites in solution. The combination of these complementary techniques enables us to present a model for the activation and DNA binding of the Fur protein

Complexation and Toxicity of Copper in Higher Plants. II. Different Mechanisms for Copper versus Cadmium Detoxification in the Copper-Sensitive Cadmium/Zinc Hyperaccumulator Thlaspi caerulescens (Ganges Ecotype)

The cadmium/zinc hyperaccumulator Thlaspi caerulescens is sensitive toward copper (Cu) toxicity, which is a problem for phytoremediation of soils with mixed contamination. Cu levels in T. caerulescens grown with 10 microm Cu(2+) remained in the nonaccumulator range (<50 ppm), and most individuals were as sensitive toward Cu as the related nonaccumulator Thlaspi fendleri. Obviously, hyperaccumulation and metal resistance are highly metal specific. Cu-induced inhibition of photosynthesis followed the "sun reaction" type of damage, with inhibition of the photosystem II reaction center charge separation and the water-splitting complex. A few individuals of T. caerulescens were more Cu resistant. Compared with Cu-sensitive individuals, they recovered faster from inhibition, at least partially by enhanced repair of chlorophyll-protein complexes but not by exclusion, since the content of Cu in their shoots was increased by about 25%. Extended x-ray absorption fine structure (EXAFS) measurements on frozen-hydrated leaf samples revealed that a large proportion of Cu in T. caerulescens is bound by sulfur ligands. This is in contrast to the known binding environment of cadmium and zinc in the same species, which is dominated by oxygen ligands. Clearly, hyperaccumulators detoxify hyperaccumulated metals differently compared with nonaccumulated metals. Furthermore, strong features in the Cu-EXAFS spectra ascribed to metal-metal contributions were found, in particular in the Cu-resistant specimens. Some of these features may be due to Cu binding to metallothioneins, but a larger proportion seems to result from biomineralization, most likely Cu(II) oxalate and Cu(II) oxides. Additional contributions in the EXAFS spectra indicate complexation of Cu(II) by the nonproteogenic amino acid nicotianamine, which has a very high affinity for Cu(II) as further characterized here

X-ray Absorption Spectroscopy of an Investigational Anticancer Gallium(III) Drug: Interaction with Serum Proteins, Elemental Distribution Pattern, and Coordination of the Compound in Tissue

Tris(8-quinolinolato)gallium(III) (1, KP46) is a very promising investigational anticancer drug. Its interaction with serum proteins, elemental distribution, and coordination in tissue were investigated with X-ray absorption (XAS) methods. Model compounds with mixed O, N, and/or S donor atoms are reported. The coordination and structure of 1 in cell culture medium (minimum essential medium, MEM) and fetal calf serum (FCS) were probed by XANES and EXAFS. The interaction of 1 with the serum proteins apotransferrin (apoTf) and human serum albumin (HSA) was addressed as well. By application of micro-XAS to tissue samples from mice treated with 1, the gallium distribution pattern was analyzed and compared to those of physiological trace elements. The complex 1 turned out to be very stable under physiological conditions, in cell culture media and in tissue samples. The coordination environment of the metal center remains intact in the presence of apoTf and HSA. The gallium distribution pattern in tumor and liver tissue revealed high similarities to the distribution patterns of Zn and Fe, minor similarities to Cu and Ni, and no similarity to Ca

K ss Detected High-Resolution XANES of FeII and FeIII Models of the 2-His-1-Carboxylate Motif : Analysis of the Carboxylate Binding Mode

Proteins sharing the same 2-His-1-carboxylate structural motif have little amino acid sequence similarity and are able to perform many different reactions. Many factors have been cited to explain their different specificity and turnover rates, like protein environment, coordinated ligand geometry, electronic structure of the active site, etc. In this paper, we present a combined approach applying high-resolution XANES spectroscopy and theory simulations to different model complexes that mimic the binding modes of the amino acids to the metal site. Experiments were performed on three compounds showing three metal sites: ferrous hexacoordinate, ferric pentacoordinate and ferrous pentacoordinate. The first two compounds bear an N,N,O-tridentate 3,3-bis(1-alkylimidazol-2-yl)propionate ligand that features a monodentate carboxylate group. These complexes mimic the activity of extradiol dioxygenases but also exhibit intradiol cleavage activity. The third compound features a bidentate terphenylcarboxylate ligand and a sterically hindered bidentate N,N-donor, thus providing a good structural mimic of the ternary enzyme-tetrahydrobiopterin-substrate complex in pterin-dependent phenylalanine hydroxylase, which also contains a bidentate carboxylate. Modeling of high-resolution XANES on well-defined model complexes of different geometry can aid in protein structure elucidation. XANES gives the oxidation state and coordination number of the metal in the non-crystallized protein at natural pH. The accuracy of the results is limited by the core-hole and experimental broadenings. We found that high-resolution XANES experiments give increased resolution at the pre-edges, but limited improvement at the main edge. These high-resolution pre-edges can be accurately simulated by using crystal field multiplet theory (CFM). We show that by combining modelling and XANES simulations with FEFF8, detailed structural and chemical information can be obtained. We found that a short O2metal distance for the carboxylate oxygen atom not bound to the metal causes a higher white line in FeII, which is similar to the results obtained for the pterin-dependent hydroxylase, tyrosine hydroxylase (TYH). Full-potential FDMNES simulations for each sample confirm the accuracy of the main results with muffin-tin approximation (FEFF8)