Soft X-ray spectromicroscopy for speciation, quantitation and nano-eco-toxicology of nanomaterials.

There is a critical need for methods that provide simultaneous detection, identification, quantitation and visualization of nanomaterials at their interface with biological and environmental systems. The approach should allow speciation as well as elemental analysis. Using the intrinsic X-ray absorption properties, soft X-ray scanning transmission X-ray spectromicroscopy (STXM) allows characterization and imaging of a broad range of nanomaterials, including metals, oxides and organic materials, and at the same time is able to provide detailed mapping of biological components. Thus, STXM offers considerable potential for application to research on nanomaterials in biology and the environment. The potential and limitations of STXM in this context are discussed using a range of examples, focusing on the interaction of nanomaterials with microbial cells, biofilms and extracellular polymers. The studies outlined include speciation and mapping of metal-containing nanomaterials (Ti, Ni, Cu) and carbon-based nanomaterials (multiwalled carbon nanotubes, C60 fullerene). The benefits of X-ray fluorescence detection in soft X-ray STXM are illustrated with a study of low levels of Ni in a natural river biofilm.

Advances in the detection of as in environmental samples using low energy X-ray fluorescence in a scanning transmission X-ray microscope: arsenic immobilization by an Fe(II)-oxidizing freshwater bacteria.

Speciation and quantitative mapping of elements, organic and inorganic compounds, and mineral phases in environmental samples at high spatial resolution is needed in many areas of geobiochemistry and environmental science. Scanning transmission X-ray microscopes (STXMs) provide a focused beam which can interrogate samples at a fine spatial scale. Quantitative chemical information can be extracted using the transmitted and energy-resolved X-ray fluorescence channels simultaneously. Here we compare the relative merits of transmission and low-energy X-ray fluorescence detection of X-ray absorption for speciation and quantitative analysis of the spatial distribution of arsenic(V) within cell-mineral aggregates formed by Acidovorax sp. strain BoFeN1, an anaerobic nitrate-reducing Fe(II)-oxidizing ß-proteobacteria isolated from the sediments of Lake Constance. This species is noted to be highly tolerant to high levels of As(V). Related, As-tolerant Acidovorax-strains have been found in As-contaminated groundwater wells in Bangladesh and Cambodia wherein they might influence the mobility of As by providing sorption sites which might have different properties as compared to chemically formed Fe-minerals. In addition to demonstrating the lower detection limits that are achieved with X-ray fluorescence relative to transmission detection in STXM, this study helps to gain insights into the mechanisms of As immobilization by biogenic Fe-mineral formation and to further the understanding of As-resistance of anaerobic Fe(II)-oxidizing bacteria.

Comparative study of the valence electronic excitations of N2 by inelastic x-ray and electron scattering.

Bound-state, valence electronic excitation spectra of N2 are probed by nonresonant inelastic x-ray and electron scattering. Within usual theoretical treatments, dynamical structure factors derived from the two probes should be identical. However, we find strong disagreements outside the dipole scattering limit, even at high probe energies. This suggests an unexpectedly important contribution from intramolecular multiple scattering of the probe electron from core electrons or the nucleus. These effects should grow progressively stronger as the atomic number of the target species increases.

Electron Compton-like quasielastic scattering from H2, D2, and HD.

A significant anomaly in the ratio of the cross sections for quasielastic scattering of D(2) to H(2) in a 50:50 mixture has been reported recently [Phys. Rev. Lett. 100, 043204 (2008)]. In particular, the interpretation of quasielastic scattering provided in that work predicts that the signals should be based on the elemental content and not on the molecular structure, and thus the spectrum for HD and that for the 50:50 mixture should be effectively the same, aside from minor line shape differences. In fact the signal from H in the mixture was low by 31(4)% (or that from D was correspondingly high) when compared to the signal from H in HD. Here, an attempt is made to explain this anomaly by scattering theory calculations based on the first Born and Born-Oppenheimer approximations. The relative contributions of translational, vibrational, and rotational excitations are computed for several temperatures. The computed signals are compared to the experimental spectra of HD and the 50:50 H(2)/D(2) mixture and to pure H(2) and D(2), which were reported previously. Good agreement is found for the spectral line shapes. The predicted peak positions are also found to be in good agreement with experiment except for a slight shift in the case of D(2). However the anomalous cross section ratio of D(2) to H(2) experimentally observed in the 50:50 mixture could not be explained by this approach.

Cryo scanning transmission x-ray microscope optimized for spectrotomography.

A cryo scanning transmission X-ray microscope, the cryo-STXM, has been designed and commissioned at the Canadian Light Source synchrotron. The instrument is designed to operate from 100 to 4000 eV (λ = 12.4 - 0.31 nm). Users can insert a previously frozen sample, through a load lock, and rotate it ±70° in the beam to collect tomographic data sets. The sample can be maintained for extended periods at 92 K primarily to suppress radiation damage and a pressure on the order of 10-9 Torr to suppress sample contamination. The achieved spatial resolution (30 nm) and spectral resolution (0.1 eV) are similar to other current soft X-ray STXMs, as demonstrated by measurements on known samples and test patterns. The data acquisition efficiency is significantly more favorable for both imaging and tomography. 2D images, 3D tomograms, and 4D chemical maps of automotive hydrogen fuel cell thin sections are presented to demonstrate current performance and new capabilities, namely, cryo-spectrotomography in the soft X-ray region.

X-ray microscopy study of chromonic liquid crystal dry film texture.

Soft x-ray spectromicroscopy has been used to investigate the degree of the molecular alignment of sulfonated benzo[de]benzo[4.5]imidazo[2,1-a]isoquinoline[7,1], a lyotropic chromonic liquid crystal (LCLC). LCLC thin films cast from concentrated aqua solution (20%wt.) , aligned by shear flow and dried, show strong linear dichroism in their C-, N-, O-, S- K edge near edge x-ray spectra (NEXAFS). The carbon K edge has been used for quantitative evaluation of the orientational texture of the films at a submicron spatial scale. This has verified there is predominantly in-plane alignment of the LC director. To highlight the role of hydrophobic-hydrophilic interactions, two stereoisomers of the same dye has been synthesized with different positioning of terminal sulfonate groups, in the form of a mixture of isomers with sulfonate groups in 2,10 and 2,11 positions (Y104 compound) and in a 5,10-disulfo arrangement (Y105). Both compounds develop characteristic herringbone-type texture with similar domain sizes. Polarized optical microscopy and higher resolution x-ray microscopy show sinusoidal-like undulations of the molecular director, with occasional crisscross appearance. Such behavior is found to be consistent with earlier observation of striations, characteristic of the columnar phase. The drastic difference in the degree of undulation ( +/-15 degrees in Y104 and +/-7 degrees in Y105 films) and long period of undulation (approaching the film thickness) requires further analysis. It was also found that the degree of in-plane order within domains changes from 0.8 for Y104 to >0.9 in Y105 films.

In situ azimuthal rotation device for linear dichroism measurements in scanning transmission x-ray microscopy.

A novel miniature rotation device used in conjunction with a scanning transmission x-ray microscope is described. It provides convenient in situ sample rotation to enable measurements of linear dichroism at high spatial resolution. The design, fabrication, and mechanical characterization are presented. This device has been used to generate quantitative maps of the spatial distribution of the orientation of proteins in several different spider and silkworm silks. Specifically, quantitative maps of the dichroic signal at the C 1s-->pi* (amide) transition in longitudinal sections of the silk fibers give information about the spatial orientation, degree of alignment, and spatial distribution of protein peptide bonds. A new approach for analyzing the dichroic signal to extract orientation distributions, in addition to magnitudes of aligned components, is presented and illustrated with results from Nephila clavipes dragline spider silk measured using the in situ rotation device.

Spatially resolved TiOx phases in switched RRAM devices using soft X-ray spectromicroscopy.

Reduction in metal-oxide thin films has been suggested as the key mechanism responsible for forming conductive phases within solid-state memory devices, enabling their resistive switching capacity. The quantitative spatial identification of such conductive regions is a daunting task, particularly for metal-oxides capable of exhibiting multiple phases as in the case of TiOx. Here, we spatially resolve and chemically characterize distinct TiOx phases in localized regions of a TiOx-based memristive device by combining full-field transmission X-ray microscopy with soft X-ray spectroscopic analysis that is performed on lamella samples. We particularly show that electrically pre-switched devices in low-resistive states comprise reduced disordered phases with O/Ti ratios around 1.37 that aggregate in a ~100 nm highly localized region electrically conducting the top and bottom electrodes of the devices. We have also identified crystalline rutile and orthorhombic-like TiO2 phases in the region adjacent to the main reduced area, suggesting that the temperature increases locally up to 1000 K, validating the role of Joule heating in resistive switching. Contrary to previous studies, our approach enables to simultaneously investigate morphological and chemical changes in a quantitative manner without incurring difficulties imposed by interpretation of electron diffraction patterns acquired via conventional electron microscopy techniques.

Effects of fullerene (C60), multi-wall carbon nanotubes (MWCNT), single wall carbon nanotubes (SWCNT) and hydroxyl and carboxyl modified single wall carbon nanotubes on riverine microbial communities.

Commercial production of nanoparticles (NP) has created a need for research to support regulation of nanotechnology. In the current study, microbial biofilm communities were developed in rotating annular reactors during continuous exposure to 500 µg L(-1) of each nanomaterial and subjected to multimetric analyses. Scanning transmission X-ray spectromicroscopy (STXM) was used to detect and estimate the presence of the carbon nanomaterials in the biofilm communities. Microscopy observations indicated that the communities were visibly different in appearance with changes in abundance of filamentous cyanobacteria in particular. Microscale analyses indicated that fullerene (C60) did not significantly (p < 0.05) impact algal, cyanobacterial or bacterial biomass. In contrast, MWCNT exposure resulted in a significant decline in algal and bacteria biomass. Interestingly, the presence of SWCNT products increased algal biomass, significantly in the case of SWCNT-COOH (p < 0.05) but had no significant impact on cyanobacterial or bacterial biomass. Thymidine incorporation indicated that bacterial production was significantly reduced (p < 0.05) by all nanomaterials with the exception of fullerene. Biolog assessment of carbon utilization revealed few significant effects with the exception of the utilization of carboxylic acids. PCA and ANOSIM analyses of denaturing gradient gel electrophoresis (DGGE) results indicated that the bacterial communities exposed to fullerene were not different from the control, the MWCNT and SWNT-OH differed from the control but not each other, whereas the SWCNT and SWCNT-COOH both differed from all other treatments and were significantly different from the control (p < 0.05). Fluorescent lectin binding analyses also indicated significant (p < 0.05) changes in the nature and quantities of exopolymer consistent with changes in microbial community structure during exposure to all nanomaterials. Enumeration of protozoan grazers showed declines in communities exposed to fullerene or MWCNT but a trend for increases in all SWCNT exposures. Observations indicated that at 500 µg L(-1), carbon nanomaterials significantly alter aspects of microbial community structure and function supporting the need for further evaluation of their effects in aquatic habitats.

Optimization of scanning transmission X-ray microscopy for the identification and quantitation of reinforcing particles in polyurethanes.

The morphology, size distributions, spatial distributions, and quantitative chemical compositions of co-polymer polyol-reinforcing particles in a polyurethane have been investigated with scanning transmission X-ray microscopy (STXM). A detailed discussion of microscope operating procedures is presented and ways to avoid potential artifacts are discussed. Images at selected photon energies in the C 1s, N 1s and O 1s regions allow unambiguous identification of styrene-acrylonitrile-based (SAN) copolymer and polyisocyanate polyaddition product-based (PIPA) reinforcing particles down to particle sizes at the limit of the spatial resolution (50 nm). Quantitative analysis of the chemical composition of individual reinforcing particles is achieved by fitting C 1s spectra to linear combinations of reference spectra. Regression analyses of sequences of images recorded through the chemically sensitive ranges of the C 1s, N 1s and O 1s spectra are used to generate quantitative compositional maps, which provide a fast and effective means of investigating compositional distributions over a large number of reinforcing particles. The size distribution of all particles determined by STXM is shown to be similar to that determined by TEM. The size distributions of each type of reinforcing particle, which differ considerably, were obtained by analysis of STXM images at chemically selective energies.

Characterisation of the dissimilatory reduction of Fe(III)-oxyhydroxide at the microbe-mineral interface: the application of STXM-XMCD.

A combination of scanning transmission X-ray microscopy and X-ray magnetic circular dichroism was used to spatially resolve the distribution of different carbon and iron species associated with Shewanella oneidensis MR-1 cells. S. oneidensis MR-1 couples the reduction of Fe(III)-oxyhydroxides to the oxidation of organic matter in order to conserve energy for growth. Several potential mechanisms may be used by S. oneidensis MR-1 to facilitate Fe(III)-reduction. These include direct contact between the cell and mineral surface, secretion of either exogenous electron shuttles or Fe-chelating agents and the production of conductive 'nanowires'. In this study, the protein/lipid signature of the bacterial cells was associated with areas of magnetite (Fe3O4), the product of dissimilatory Fe(III) reduction, which was oversaturated with Fe(II) (compared to stoichiometric magnetite). However, areas of the sample rich in polysaccharides, most likely associated with extracellular polymeric matrix and not in direct contact with the cell surface, were undersaturated with Fe(II), forming maghemite-like (γ-Fe2O3) phases compared to stoichiometric magnetite. The reduced form of magnetite will be much more effective in environmental remediation such as the immobilisation of toxic metals. These findings suggest a dominant role for surface contact-mediated electron transfer in this study and also the inhomogeneity of magnetite species on the submicron scale present in microbial reactions. This study also illustrates the applicability of this new synchrotron-based technique for high-resolution characterisation of the microbe-mineral interface, which is pivotal in controlling the chemistry of the Earth's critical zone.

Soft X-ray spectro-tomography study of cyanobacterial biomineral nucleation.

Quantitative three-dimensional (3D) chemical mapping using angle-scan spectro-tomography in a scanning transmission (soft) X-ray microscope (STXM) has been used for the first time to characterize the early stages of CaCO(3) biomineral nucleation on the surface of planktonic freshwater cyanobacterial cells of the strain Synechococcus leopoliensis PCC 7942. The apparatus for STXM angle-scan tomography is described. Aspects of sample preparation, sample mounting and data acquisition and quantitative analysis and interpretation are discussed in detail. Angle-scan tomography and chemically selective 3D imaging at multiple photon energies has been combined with a complete 2D spectromicroscopic characterization of the biochemical and mineralogical composition. This has provided detailed insights into the mechanisms of mineral nucleation, leading to development of a detailed model of CaCO(3) nucleation by the cyanobacterial strain S. leopoliensis PCC 7942. It shows that Ca is absorbed by the extracellular polymeric substances (EPS) of the cyanobacteria and that CaCO(3) with aragonite-like short-range order is precipitated rather homogeneously within the EPS. The precipitation of the thermodynamically more stable calcite polymorph then starts at Ca-rich hot spots within the EPS and close to the cyanobacteria.

Soft X-ray spectromicroscopy of nickel sorption in a natural river biofilm.

Scanning transmission X-ray microscopy (STXM) at the C 1s, O 1s, Ni 2p, Ca 2p, Mn 2p, Fe 2p, Mg 1s, Al 1s and Si 1s edges was used to study Ni sorption in a complex natural river biofilm. The 10-week grown river biofilm was exposed to 10 mg L(-1) Ni(2+) (as NiCl(2)) for 24 h. The region of the biofilm examined was dominated by filamentous structures, which were interpreted as the discarded sheaths of filamentous bacteria, as well as a sparse distribution of rod-shaped bacteria. The region also contained discrete particles with spectra similar to those of muscovite, SiO(2) and CaCO(3). The Ni(II) ions were selectively adsorbed by the sheaths of the filamentous bacteria. The sheaths were observed to be metal rich with significant amounts of Ca, Fe and Mn, along with the Ni. In addition, the sheaths had a large silicate content but little organic material. The metal content of the rod-shaped bacterial cells was much lower. The Fe on the sheath was mainly in the Fe(III) oxidation state. Mn was found in II, III and IV oxidation states. The Ni was likely sorbed to Mn-Fe minerals on the sheath. These STXM results have probed nano-scale biogeochemistry associated with bacterial species in a complex, natural biofilm community. They have implications for selective Ni contamination of the food chain and for developing bioremediation strategies.

Anomalous quasielastic electron scattering from single H2, D2, and HD molecules at large momentum transfer: indications of nuclear spin effects.

Quasielectron electron scattering from gaseous H2, D2, a 50:50 mixture of H2 and D2, and HD is investigated with 2.25 keV impact energy and a momentum transfer variant Planck's over 2piq of 19.7 a.u. The energy transfer is less than the dissociation energy. The spectral positions of the H and D recoil peaks agree with Rutherford scattering theory. Surprisingly, in the spectrum of the 50:50 H2-D2 mixture, the integrated intensity of the H peak is 31%+/-4% lower (as compared to that of D) than predicted by Rutherford scattering, despite equal screening of nuclear charges by the electrons. In contrast, the ratio of scattering intensities from H and D in HD agrees with the predictions of Rutherford scattering. Comparison is made with neutron Compton scattering results from the same systems, but at higher energy transfers causing bond breaking. Possible theoretical explanations are outlined.

Quasielastic electron scattering from methane, methane-d4, methane-d2, ethylene, and 2-methylpropane.

Quasielastic electron scattering from gaseous species at high momentum transfer was recently reported for the first time [Cooper et al., J. Electron Spectrosc. Relat. Phenom. 155, 28 (2007)]. The first results for CH(4) and CD(4) were well explained by a classical electron Compton scattering picture in which the electron scatters independently from each atom rather than the molecule as a whole. However, an alternative possible interpretation in terms of nondipole molecular vibrational excitation is suggested by previously published quantum mechanical calculations on high momentum transfer electron scattering from diatomic molecules [Bonham and de Souza, J. Chem. Phys. 79, 134 (1983)]. In order to determine which of these two interpretations best fits the experimental results, we have measured the quasielastic spectra of gaseous 2-methylpropane, ethylene, methane, and two isotopically substituted methanes, CH(2)D(2) and CD(4), at a momentum transfer of approximately 20 a.u. (2.25 keV impact energy and 100 degrees scattering angle). The experimental spectra are found to be composed of as many peaks as there are different atomic isotopes in the molecule (two for CH(4), C(2)H(4), 2-methylpropane, and CD(4) and three for CH(2)D(2)). The peak positions are predicted accurately by the independent atom electron Compton scattering model, and the relative intensities are in reasonable agreement. The experimental results thus support classical electron Compton scattering as the origin of the signal.

Soft X-ray spectromicroscopy of polymers and bipolymer interfaces.

The status of soft X-ray spectromicroscopy (near edge X-ray absorption, or NEXAFS, microscopy) is summarized, with particular emphasis on recent collaborative studies carried out by the author's group at the scanning transmission X-ray microscopy (STXM) and the photoelectron emission microscopy (PEEM) instruments at the Advanced Light Source. Results described include: characterization of phase segregation and filler particles in polyurethanes; effects of confinement on polymer self-organization; characterization of chemically structured polyurea capsule walls; and preferential interactions of proteins with chemically heterogeneous polymer surfaces. The latter is part of a systematic study of the biocompatibility of polymers used in blood contact applications.

A new sample preparation method for biological soft X-ray microscopy: nitrogen-based contrast and radiation tolerance properties of glycol methacrylate-embedded and sectioned tissue.

We describe the preparation of a biological tissue for imaging in a transmission soft X-ray microscope. Sections of exocrine pancreas embedded in glycol methacrylate polymer, an embedding medium widely used in visible light and electron microscopy, were examined. Contrast was based primarily on the nitrogen content of the tissue, and dual-wavelength imaging at the nitrogen K-shell absorption edge was used to map the distribution and provide quantitative densitometry of both the protein and embedding matrix components of the sample. The measurements were calibrated by obtaining the absorption spectrum of protein near the nitrogen edge. The contrast was consistent and reproducible, making possible the first large-scale X-ray microscopic study on sections of plastic-embedded soft tissue. At radiation doses of up to 10(8) Gray, much more than required for routine imaging, no distortion and little mass loss were observed. This sample preparation method should permit routine imaging of tissues in X-ray microscopes, previously a difficult task, as well as multimodal imaging (using visible light, X-ray, electron, and scanned probe microscopies) on the same sample.

Towards practical soft X-ray spectromicroscopy of biomaterials.

Scanning transmission X-ray microscopy (STXM) is being developed as a new tool to study the surface chemical morphology and biointeractions of candidate biomaterials with emphasis on blood compatible polymers. STXM is a synchrotron based technique which provides quantitative chemical mapping at a spatial resolution of 50 nm. Chemical speciation is provided by the near edge X-ray absorption spectral (NEXAFS) signal. We show that STXM can detect proteins on soft X-ray transparent polymer thin films with monolayer sensitivity. Of great significance is the fact that measurements can be made in situ, i.e. in the presence of an overlayer of the protein solution. The strengths, limitations and future potential of STXM for studies of biomaterials are discussed.

Scanning transmission X-ray, laser scanning, and transmission electron microscopy mapping of the exopolymeric matrix of microbial biofilms.

Confocal laser scanning microscopy (CLSM), transmission electron microscopy (TEM), and soft X-ray scanning transmission X-ray microscopy (STXM) were used to map the distribution of macromolecular subcomponents (e.g., polysaccharides, proteins, lipids, and nucleic acids) of biofilm cells and matrix. The biofilms were developed from river water supplemented with methanol, and although they comprised a complex microbial community, the biofilms were dominated by heterotrophic bacteria. TEM provided the highest-resolution structural imaging, CLSM provided detailed compositional information when used in conjunction with molecular probes, and STXM provided compositional mapping of macromolecule distributions without the addition of probes. By examining exactly the same region of a sample with combinations of these techniques (STXM with CLSM and STXM with TEM), we demonstrate that this combination of multimicroscopy analysis can be used to create a detailed correlative map of biofilm structure and composition. We are using these correlative techniques to improve our understanding of the biochemical basis for biofilm organization and to assist studies intended to investigate and optimize biofilms for environmental remediation applications.

Variable linear polarization from an X-ray undulator.

A new X-ray undulator has been designed and constructed which produces linearly polarized X-rays in which the plane of polarization can be oriented to a user selectable angle, from horizontal to vertical. Based on the Apple-II elliptically polarizing undulator (EPU), the undulator rotates the angle of the linear polarization by a simple longitudinal motion of the undulator magnets. Combined with the circular and elliptical polarization capabilities of the EPU operating in the standard mode, this new undulator produces soft X-ray radiation with versatile polarization control. This paper describes the magnetic structure of the device and presents an analysis of the magnetic field with varying undulator parameters. The variable linear polarization capability is then exhibited by measuring the X-ray absorption spectrum of an oriented polytetrafluoroethylene thin film. This experiment, which measures the linear dichroism of the sample at two peaks near the C 1s absorption edge, demonstrates the continuous polarization rotation capabilities of the undulator.