An algorithm for the automatic deglitching of X-ray absorption spectroscopy data.

Analysis of X-ray absorption spectroscopy data often involves the removal of artifacts or glitches from the acquired signal, a process commonly known as deglitching. Glitches result either from specific orientations of monochromator crystals or from scattering by crystallites in the sample itself. Since the precise energy - or wavelength - location and the intensity of glitches in a spectrum cannot always be predicted, deglitching is often performed on a per spectrum basis by the analyst. Some routines have been proposed, but they are prone to arbitrary selection of spectral artifacts and are often inadequate for processing large data sets. Here, a statistically robust algorithm, implemented as a Python program, for the automatic detection and removal of glitches that can be applied to a large number of spectra, is presented. It uses a Savitzky-Golay filter to smooth spectra and the generalized extreme Studentized deviate test to identify outliers. Robust, repeatable, and selective removal of glitches is achieved using this algorithm.

Partitioning of copper at the confluences of Andean rivers.

The fate of copper (Cu) in rivers impacted by acid drainage remains poorly studied in waters with comparatively low Al and Fe concentrations. This work addresses the role of confluences in controlling the physical and chemical fate of Cu in a system with total molar ratio Cu/Al > 0.2 and Cu/Fe > 0.15. Two consecutive confluences were studied in the upper Mapocho watershed, a densely populated basin with intensive mining located in the Chilean Andes. The inflow had acidic conditions with seasonal variations and Cu up to 9 mg L-1. Lability measurements with diffusive gradient in thin films showed that Cu entered as a dissolved labile form. However, downstream from the confluences a higher pH shifted Cu toward nonlabile compounds and solid phases enriched with Cu. Measurements of x-ray absorption spectroscopy of freshly formed particles showed that composition was dominated by sorbed Cu and Cu(OH)2(s) precipitates, with a higher proportion of sorbed Cu downstream from confluences when pH < 5. Particle size distributions (PSD) measured in field showed that downstream from the confluences the total volume and average diameter of the suspended particles grew progressively, with estimated mean settling velocities increasing from 0.3 to 4.2 cm s-1. As a result, 7-30% of the influent Cu was removed from the river flow. These results highlight that shifts in chemical partition and PSDs in river confluences and the hydrodynamic environments at the river reach level control the mobility of Cu in systems with high Cu/Al and Cu/Fe.

Solving the problem with stannous fluoride: Formulation, stabilization, and antimicrobial action.

BACKGROUND: Stannous fluoride (SnF2) is a compound present in many commercially available dentifrices; however, oxidative decomposition negatively impacts its efficacy. Stannous oxidation is often mitigated through the addition of complexing agents or sources of sacrificial stannous compounds. The authors have found that the addition of zinc phosphate significantly improved stannous stability more effectively than other stabilization methods. The authors evaluated the chemical speciation of stannous compounds within a variety of formulations using x-ray absorption near edge spectroscopy (XANES), a technique never used before in this manner. These data were compared and correlated with several antimicrobial experiments. METHODS: XANES data of various commercially available compounds and Colgate TotalSF were performed and analyzed against a library of reference compounds to determine the tin chemical speciation. The antibacterial assays used were salivary adenosine triphosphate, short-interval kill test, plaque glycolysis, and anaerobic biofilm models. RESULTS: XANES spectra showed a diverse distribution of tin species and varying degrees of SnF2 oxidation. In vitro antimicrobial assessment indicated significant differences in performance, which may be correlated to the differences in tin speciation and oxidation state. CONCLUSIONS: Driven by the excipient ingredients, SnF2 dentifrices contain a distribution of tin species in either the SnF2 or Sn(IV) oxidation state. The addition of zinc phosphate provided significant robustness against oxidation, which directly translated to greater efficacy against bacteria. PRACTICAL IMPLICATIONS: The choice of inactive ingredients in a dentifrice with active SnF2 can dramatically impact product stability.

Effects of resuspension on the mobility and chemical speciation of zinc in contaminated sediments.

Identifying and quantifying the processes governing the mobilization of metals during resuspension events is key to assessing long-term metals efflux from sediments and associated ecological impacts. We investigated the effects of sediment resuspension on the mobilization and chemical speciation of zinc in two-week-long batch experiments using metal-contaminated sediments from Lake DePue (IL, USA). Measurements of dissolved zinc and sulfate allowed us to characterize the kinetics of metal sulfide dissolution and the resulting net release of zinc to the aqueous phase. X-ray absorption spectroscopy (XAS) provided direct insights into the chemical speciation of iron and zinc and their dynamic transformations during resuspension. While ZnS rapidly oxidized during resuspension, dissolved zinc increased only after two days of resuspension. We proposed a kinetic model to explain changes in the chemical speciation of zinc during these experiments as constrained by the dissolved species concentrations and chemical speciation as informed by XAS. Only 15% of the zinc mobilized was released to the aqueous phase while the remaining fraction repartitioned the solid phase either as a carbonate precipitate or as a sorbed species. Our results show that zinc sorption onto particle surfaces and reprecipitation of zinc minerals limit zinc solubility during resuspension of metal-sulfide sediments.

Structural characterization of metal complexes in aqueous solutions: a XAS study of stannous fluoride.

The identity and structure of tin(ii)-fluoride complexes formed in aqueous solutions is determined by combining X-ray absorption spectroscopy, thermodynamic modeling and quantum mechanical calculations. Spectroscopic measurements confirm the presence of 3 stannous fluoride complexes, SnF+, SnF02 and SnF3-, with mean Sn-F bond distances that increase linearly, from 1.98 to about 2.04 Å, as a function of the coordination number. Computational ab initio calculations indicate that the stannous fluoride complexes form localized σs-p bonds, with the stereochemically active lone pair of the Sn(ii) atom distorting the geometry of the complexes. In addition, the SnF3- complex exhibits loosely coordinated water, which is removed upon addition of glycerol to lower the solvent activity. Our results provide spectroscopic confirmation of the stannous fluoride complexes proposed in the literature, and explain why glycerol additions stabilize solutions of Sn(ii) against oxidation.

Copper Corrosion and Biocorrosion Events in Premise Plumbing.

Corrosion of copper pipes may release high amounts of copper into the water, exceeding the maximum concentration of copper for drinking water standards. Typically, the events with the highest release of copper into drinking water are related to the presence of biofilms. This article reviews this phenomenon, focusing on copper ingestion and its health impacts, the physicochemical mechanisms and the microbial involvement on copper release, the techniques used to describe and understand this phenomenon, and the hydrodynamic effects. A conceptual model is proposed and the mathematical models are reviewed.

Conformational changes during permeation of Na+ through a modified cyclic peptide nanotube promote energy landscape roughness.

Using a metadynamics approach, we investigate the potential of mean force for Na+ permeation inside a cyclic peptide nanotube (CPN) with modified interior as a function of ion position, coordination number, and lumen chemistry. We show that functionalizing the lumen of a CPN with a methyl-benzoic acid group introduces non-periodic variations in the internal energy of the nanotube, which dictate the overall free energy roughness during the permeation of Na+. These non-periodic variations arise from the structural dynamics of the functional group, where changes in the dihedral angles induced by the proximity of the ion give rise to conformational changes that increase landscape roughness and thereby decrease transport rate. Our computational framework emphasizes the advantages of using the coordination number as a collective variable to investigate the available conformations during ion permeation through CPNs, and reveals new structure-function relations for chemically tunable CPNs, paving the way for rational design of nano-porous systems with tunable selectivity and flux.

Multi-technique approach to assess the effects of microbial biofilms involved in copper plumbing corrosion.

Microbially influenced corrosion (MIC) is recognized as an unusual and severe type of corrosion that causes costly failures around the world. A microbial biofilm could enhance the copper release from copper plumbing into the water by forming a reactive interface. The biofilm increases the corrosion rate, the mobility of labile copper from its matrix and the detachment of particles enriched with copper under variable shear stress due to flow conditions. MIC is currently considered as a series of interdependent processes occurring at the metal-liquid interface. The presence of a biofilm results in the following effects: (a) the formation of localized microenvironments with distinct pH, dissolved oxygen concentrations, and redox conditions; (b) sorption and desorption of labile copper bonded to organic compounds under changing water chemistry conditions; (c) change in morphology by deposition of solid corrosion by-products; (d) diffusive transport of reactive chemical species from or towards the metal surface; and (e) detachment of scale particles under flow conditions. Using a multi-technique approach that combines pipe and coupon experiments this paper reviews the effects of microbial biofilms on the corrosion of copper plumbing systems, and proposes an integrated conceptual model for this phenomenon supported by new experimental data.

Enhanced copper release from pipes by alternating stagnation and flow events.

Traditional studies of copper release in plumbing systems assume that the water extracted from a pipe follows a plug-type flow and that the pipe surface does not interact with the bulk water under flow conditions. We characterized actual stagnation-flushing cycles in a household pipe undergoing corrosion in the presence of a microbial biofilm. The mass of copper released in 10 experiments was on average 8 times the value estimated by using the plug-flow assumption. The experimental copper release pattern was explained by an advection-diffusion model only if a high copper concentration occurs near the pipe surface after stagnation. Microscopic examination of the pipe surface showed a complex assemblage of biotic and abiotic features. X-ray diffraction analyses identified only malachite, while X-ray absorption spectroscopy also revealed cupric hydroxide and cuprite. These results indicate that the surface serves as a storage compartment of labile copper that may be released under flow conditions. Thus, the diffusive transport from the pipe surface to the bulk during stagnation is not the only control of the flux of copper to the tap water when porous reactive microstructures cover the pipe. Our results highlight the need for models that consider the interaction between the hydrodynamics, chemistry, and structure at the solid-water interface to predict the release of corrosion byproducts into drinking water.