The thermodynamics of self-assembled monolayer formation: a computational and experimental study of thiols on a flat gold surface.

A methodology based on molecular dynamics simulations is presented to determine the chemical potential of thiol self-assembled monolayers on a gold surface. The thiol de-solvation and then the monolayer formation are described by thermodynamic integration with a gradual decoupling of one molecule from the environment, with the necessary corrections to account for standard state changes. The procedure is applied both to physisorbed undissociated thiol molecules and to chemisorbed dissociated thiyl radicals, considering in the latter case the possible chemical potential of the produced hydrogen. We considered monolayers formed by either 7-mercapto-4-methylcoumarin (MMC) or 3-mercapto-propanoic acid (MPA) on a flat gold surface: the free energy profiles with respect to the monolayer density are consistent with a transition from a very stable lying-down phase at low densities to a standing-up phase at higher densities, as expected. The maximum densities of thermodynamically stable monolayers are compared to experimental measures performed with reference-free grazing-incidence X-ray fluorescence (RF-GIXRF) on the same systems, finding a better agreement in the case of chemisorbed thiyl radicals.

A multi-edge study: investigating Co oxidation states of pristine LiNixMnyCo1-x-yO2 cathode materials by high energy-resolution X-ray spectrometry.

The investigation of Co oxidation states in pristine LiNixMnyCo1-x-yO2 (NMC) cathodes (NMC111, NMC622, NMC811) has been a subject of ongoing debate, with conflicting findings in the literature. In this study, we present a novel and comprehensive approach to address and clarify this issue using a variety of high energy-resolution X-ray spectroscopy techniques. To shed light on the Co oxidation states in NMC cathodes, we employed independent measurements including X-ray absorption spectrometry in both soft and hard X-ray ranges, as well as resonant X-ray emission spectrometry in the soft X-ray range. The investigation centered on the transition metal (TM) K and L edges, providing a thorough exploration of the electronic structure transitions. The study identified minor shifts in Co oxidation states, and theoretical calculations quantified the ratio of Co atoms undergoing oxidation state changes, which were approximately 2.05% (NMC111 to NMC622) and 3.75% (NMC111 to NMC811). Independent measurements that targeted electronic structure transitions using K-edge and L-edge absorption and emission spectrometry were strategically combined to enhance the reliability of the results. The diverse methodological approach aimed to contribute to a comprehensive understanding of Co oxidation states in NMC cathodes. This study highlights the importance of combining complementary techniques to address intricate scientific debates effectively.

Hybrid Metrology for Nanostructured Optical Metasurfaces.

Metasurfaces have garnered increasing research interest in recent years due to their remarkable advantages, such as efficient miniaturization and novel functionalities compared to traditional optical elements such as lenses and filters. These advantages have facilitated their rapid commercial deployment. Recent advancements in nanofabrication have enabled the reduction of optical metasurface dimensions to the nanometer scale, expanding their capabilities to cover visible wavelengths. However, the pursuit of large-scale manufacturing of metasurfaces with customizable functions presents challenges in controlling the dimensions and composition of the constituent dielectric materials. To address these challenges, the combination of block copolymer (BCP) self-assembly and sequential infiltration synthesis (SIS), offers an alternative for fabrication of high-resolution dielectric nanostructures with tailored composition and optical functionalities. However, the absence of metrological techniques capable of providing precise and reliable characterization of the refractive index of dielectric nanostructures persists. This study introduces a hybrid metrology strategy that integrates complementary synchrotron-based traceable X-ray techniques to achieve comprehensive material characterization for the determination of the refractive index on the nanoscale. To establish correlations between material functionality and their underlying chemical, compositional and dimensional properties, TiO2 nanostructures model systems were fabricated by SIS of BCPs. The results from synchrotron-based analyses were integrated into physical models, serving as a validation scheme for laboratory-scale measurements to determine effective refractive indices of the nanoscale dielectric materials.

Well-Defined Iron Sites in Crystalline Carbon Nitride.

Carbon nitride materials can be hosts for transition metal sites, but Mössbauer studies on iron complexes in carbon nitrides have always shown a mixture of environments and oxidation states. Here we describe the synthesis and characterization of a crystalline carbon nitride with stoichiometric iron sites that all have the same environment. The material (formula C6N9H2Fe0.4Li1.2Cl, abbreviated PTI/FeCl2) is derived from reacting poly(triazine imide)·LiCl (PTI/LiCl) with a low-melting FeCl2/KCl flux, followed by anaerobic rinsing with methanol. X-ray diffraction, X-ray absorption and Mössbauer spectroscopies, and SQUID magnetometry indicate that there are tetrahedral high-spin iron(II) sites throughout the material, all having the same geometry. The material is active for electrocatalytic nitrate reduction to ammonia, with a production rate of ca. 0.1 mmol cm-2 h-1 and Faradaic efficiency of ca. 80% at -0.80 V vs RHE.

Developing Quantitative Nondestructive Characterization of Nanomaterials: A Case Study on Sequential Infiltration Synthesis of Block Copolymers.

The sequential infiltration synthesis (SIS) of inorganic materials in nanostructured block copolymer templates has rapidly progressed in the last few years to develop functional nanomaterials with controllable properties. To assist this rapid evolution, expanding the capabilities of nondestructive methods for quantitative characterization of the materials properties is required. In this paper, we characterize the SIS process on three model polymers with different infiltration profiles through ex situ quantification by reference-free grazing incidence X-ray fluorescence. More qualitative depth distribution results were validated by means of X-ray photoelectron spectroscopy and scanning transmission electron microscopy combined with energy-dispersive X-ray spectroscopy.

Quantitative Element-Sensitive Analysis of Individual Nanoobjects.

A reliable and quantitative material analysis is crucial for assessing new technological processes, especially to facilitate a quantitative understanding of advanced material properties at the nanoscale. To this end, X-ray fluorescence microscopy techniques can offer an element-sensitive and non-destructive tool for the investigation of a wide range of nanotechnological materials. Since X-ray radiation provides information depths of up to the microscale, even stratified or buried arrangements are easily accessible without invasive sample preparation. However, in terms of the quantification capabilities, these approaches are usually restricted to a qualitative or semi-quantitative analysis at the nanoscale. Relying on comparable reference nanomaterials is often not straightforward or impossible because the development of innovative nanomaterials has proven to be more fast-paced than any development process for appropriate reference materials. The present work corroborates that a traceable quantification of individual nanoobjects can be realized by means of an X-ray fluorescence microscope when utilizing rather conventional but well-calibrated instrumentation instead of reference materials. As a proof of concept, the total number of atoms forming a germanium nanoobject is quantified using soft X-ray radiation. Furthermore, complementary dimensional parameters of such objects are reconstructed.

Scan-Free GEXRF in the Soft X-ray Range for the Investigation of Structured Nanosamples.

Scan-free grazing-emission X-ray fluorescence spectroscopy (GEXRF) is an established technique for the investigation of the elemental depth-profiles of various samples. Recently it has been applied to investigating structured nanosamples in the tender X-ray range. However, lighter elements such as oxygen, nitrogen or carbon cannot be efficiently investigated in this energy range, because of the ineffective excitation. Moreover, common CCD detectors are not able to discriminate between fluorescence lines below 1 keV. Oxygen and nitrogen are important components of insulation and passivation layers, for example, in silicon oxide or silicon nitride. In this work, scan-free GEXRF is applied in proof-of-concept measurements for the investigation of lateral ordered 2D nanostructures in the soft X-ray range. The sample investigated is a Si3N4 lamellar grating, which represents 2D periodic nanostructures as used in the semiconductor industry. The emerging two-dimensional fluorescence patterns are recorded with a CMOS detector. To this end, energy-dispersive spectra are obtained via single-photon event evaluation. In this way, spatial and therefore angular information is obtained, while discrimination between different photon energies is enabled. The results are compared to calculations of the sample model performed by a Maxwell solver based on the finite-elements method. A first measurement is carried out at the UE56-2 PGM-2 beamline at the BESSY II synchrotron radiation facility to demonstrate the feasibility of the method in the soft X-ray range. Furthermore, a laser-produced plasma source (LPP) is utilized to investigate the feasibility of this technique in the laboratory. The results from the BESSY II measurements are in good agreement with the simulations and prove the applicability of scan-free GEXRF in the soft X-ray range for quality control and process engineering of 2D nanostructures. The LPP results illustrate the chances and challenges concerning a transfer of the methodology to the laboratory.

Challenges of grazing emission X-ray fluorescence (GEXRF) for the characterization of advanced nanostructured surfaces.

The grazing emission X-ray fluorescence (GEXRF) technique offers a promising approach to determining the spatial distribution of various chemical elements in nanostructures. In this paper, we present a comparison with grazing incidence small-angle X-ray scattering (GISAXS), an established method for dimensional nanometrology, on periodic TiO2 nanostructures fabricated by a self-aligned double patterning (SADP) process. We further test the potential of GEXRF for process control in the presence of residual chromium on the structures. The angle-resolved fluorescence emission as well as the scattered radiation from the surface are collected with photon-counting hybrid pixel area detectors using scanning-free detection schemes. By modelling the X-ray standing wave (XSW) field in the vicinity of and inside the nanostructure, it is possible to obtain both the angle-resolved fluorescence intensities and the far-field scattering intensities from the same model. The comparison also illustrates that for ensemble photon-based measurement methods, accounting for roughness effects and imperfections can be essential when modelling advanced nanostructured surfaces.

Structure and stability of 7-mercapto-4-methylcoumarin self-assembled monolayers on gold: an experimental and computational analysis.

Self-assembled monolayers (SAM) of 7-mercapto-4-methylcoumarin (MMC) on a flat gold surface were studied by molecular dynamics (MD) simulations, reference-free grazing incidence X-ray fluorescence (GIXRF) and X-ray photoelectron spectroscopy (XPS), to determine the maximum monolayer density and to investigate the nature of the molecule/surface interface. In particular, the protonation state of the sulfur atom upon adsorption was analyzed, since some recent literature presented evidence for physisorbed thiols (preserving the S-H bond), unlike the common picture of chemisorbed thiyls (losing the hydrogen). MD with a specifically tailored force field was used to simulate either thiol or thiyl monolayers with increasing number of molecules, to determine the maximum dynamically stable densities. This result was refined by computing the monolayer chemical potential as a function of the density with the bennet acceptance ratio method, based again on MD simulations. The monolayer density was also measured with GIXRF, which provided the absolute quantification of the number of sulfur atoms in a dense self-assembled monolayer (SAM) on flat gold surfaces. The sulfur core level binding energies in the same monolayers were measured by XPS, fitting the recorded spectra with the binding energies proposed in the literature for free or adsorbed thiols and thiyls, to get insight on the nature of the molecular species present in the layer. The comparison of theoretical and experimental SAM densities, and the XPS analysis strongly support the picture of a monolayer formed by chemisorbed, dissociated thiyls.

Structural engineering and electronic state tuning optimization of molybdenum-doped cobalt hydroxide nanosheet self-assembled hierarchical microtubules for efficient electrocatalytic oxygen evolution.

Cobalt-based hydroxide are ideal candidates for the oxygen evolution reaction. Herein, we use molybdenum oxide nanorods as sacrificial templates to construct a self-supporting molybdenum-doped cobalt hydroxide nanosheet hierarchical microtubule structure based on a structural engineering strategy to improve the active area of the catalyst. X-ray-based spectroscopic tests revealed that Mo (VI) with tetrahedral coordination intercalated into the interlayer of cobalt hydroxide, promoting interlayer separation. At the same time, Mo is connected with Co through oxygen bonds, which promotes the transfer of Co charges to Mo and reduces the electron cloud density of Co ions. In 1 M KOH, optimized molybdenum-doped cobalt hydroxide nanosheet microtubules only needs an overpotential of 288 mV to drive a current density of 10 mA cm-2, which is significantly better than that of pure Co(OH)2 nanosheets and RuO2. Structural engineering and electronic state regulation can effectively improve the oxygen evolution activity of cobalt-based hydroxide, which provides a design idea for the development of efficient oxygen evolution catalysts.

Diet of breeding Eleonora's falcon Falco eleonorae in Algeria: Insights for the autumn trans-Mediterranean avian migration.

How environmental changes are affecting bird population dynamics is one of the most challenging conservation issues. Dietary studies of top avian predators could offer scope to monitor anthropogenic drivers of ecosystem changes. We investigated the diet of breeding Eleonora's falcon in an area of Northeastern Algeria in the years 2010-2012. Feathers and insect remains originating from prey plucking behavior were analyzed, providing insights into the seasonally changing diet of this raptor, as well as the trans-Mediterranean avian migration. A total of 77 species of birds (16 Sylviidae, 11 Turdidae, and 4 Emberizidae), 3 species of insects, and 1 lizard were identified among prey remains, reflecting a diverse diet. Diet composition and prey abundance varied seasonally, faithfully correlating with the passage of migrant birds as recorded from bird ring recoveries. Our findings suggest that dietary studies of predators might be deployed to investigate changes in bird migration. We discuss our results in the context of trans-Mediterranean migration, with early-season prey mainly comprising trans-Saharan migrants (Apus apus and Merops apiaster) and late-season prey being dominated by Mediterranean winter migrants (Erithacus rubecula, Turdus philomelos, Sylvia atricapilla, and Sturnus vulgaris). Notably, we observed a significant reduction in species richness of passerine remains in 2012, potentially highlighting a decline in the diversity of avian migrants.

Reliable compositional analysis of airborne particulate matter beyond the quantification limits of total reflection X-ray fluorescence.

Knowledge on the temporal and size distribution of particulate matter (PM) in air as well as on its elemental composition is a key information for source appointment, for the investigation of their influence on environmental processes and for providing reliable data for climate models. While cascade impactors allow for time- and size-resolved collection of airborne PM, total reflection X-ray fluorescence (TXRF) allows for element-sensitive investigation of minute sample amounts thanks to its detection sensitivity. But during quantification by means of TXRF it is crucial to be aware of the linear calibration limits of TXRF in order to identify situations where collection times or pollution levels in the different size partitions were exceedingly long or high. Indeed, TXRF can only be reliably used when the amount of matter collected on the top of the substrate is sufficiently small. By means of grazing incidence X-ray fluorescence (GIXRF), where the excitation conditions are varied in a controlled and reliable manner and include also the TXRF regime, a self consistent quantification of elemental mass depositions can be performed in order to validate or falsify TXRF quantification results. For low mass depositions an agreement within a few percent for the different excitation conditions was found, while for increasing amounts of material relative errors of up to a factor of 4 were found for TXRF as compared to GIXRF. Thus, TXRF cannot be applied to all samples regardless of their coverage and threshold values for the validity of quantification results need to be determined. As a flexible solution, GIXRF allows extending the dynamic range of reliably quantifiable mass depositions beyond the linear regime of TXRF, an important advantage when variable amounts of airborne PM need to be quantified as in the case of collection with cascade impactors. The presented more reliable quantification approach can be transferred to mobile tabletop instrumentation as well. This aspect is highly relevant for air quality monitoring in terms of supporting the introduction of appropriate legislation and measures for health and climate protection as well as for supporting their enforcement.

Simultaneous Dimensional and Analytical Characterization of Ordered Nanostructures.

The spatial and compositional complexity of 3D structures employed in today's nanotechnologies has developed to a level at which the requirements for process development and control can no longer fully be met by existing metrology techniques. For instance, buried parts in stratified nanostructures, which are often crucial for device functionality, can only be probed in a destructive manner in few locations as many existing nondestructive techniques only probe the objects surfaces. Here, it is demonstrated that grazing exit X-ray fluorescence can simultaneously characterize an ensemble of regularly ordered nanostructures simultaneously with respect to their dimensional properties and their elemental composition. This technique is nondestructive and compatible to typically sized test fields, allowing the same array of structures to be studied by other techniques. For crucial parameters, the technique provides sub-nm discrimination capabilities and it does not require access-limited large-scale research facilities as it is compatible to laboratory-scale instrumentation.

Shape- and Element-Sensitive Reconstruction of Periodic Nanostructures with Grazing Incidence X-ray Fluorescence Analysis and Machine Learning.

The characterization of nanostructured surfaces with sensitivity in the sub-nm range is of high importance for the development of current and next-generation integrated electronic circuits. Modern transistor architectures for, e.g., FinFETs are realized by lithographic fabrication of complex, well-ordered nanostructures. Recently, a novel characterization technique based on X-ray fluorescence measurements in grazing incidence geometry was proposed for such applications. This technique uses the X-ray standing wave field, arising from an interference between incident and the reflected radiation, as a nanoscale sensor for the dimensional and compositional parameters of the nanostructure. The element sensitivity of the X-ray fluorescence technique allows for a reconstruction of the spatial element distribution using a finite element method. Due to a high computational time, intelligent optimization methods employing machine learning algorithms are essential for timely provision of results. Here, a sampling of the probability distributions by Bayesian optimization is not only fast, but it also provides an initial estimate of the parameter uncertainties and sensitivities. The high sensitivity of the method requires a precise knowledge of the material parameters in the modeling of the dimensional shape provided that some physical properties of the material are known or determined beforehand. The unknown optical constants were extracted from an unstructured but otherwise identical layer system by means of soft X-ray reflectometry. The spatial distribution profiles of the different elements contained in the grating structure were compared to scanning electron and atomic force microscopy and the influence of carbon surface contamination on the modeling results were discussed. This novel approach enables the element sensitive and destruction-free characterization of nanostructures made of silicon nitride and silicon oxide with sub-nm resolution.

Grazing incidence-x-ray fluorescence for a dimensional and compositional characterization of well-ordered 2D and 3D nanostructures.

The increasing importance of well-controlled ordered nanostructures on surfaces represents a challenge for existing metrology techniques. To develop such nanostructures and monitor complex processing constraints fabrication, both a dimensional reconstruction of nanostructures and a characterization (ideally a quantitative characterization) of their composition is required. In this work, we present a soft x-ray fluorescence-based methodology that allows both of these requirements to be addressed at the same time. By applying the grazing-incidence x-ray fluorescence technique and thus utilizing the x-ray standing wave field effect, nanostructures can be investigated with a high sensitivity with respect to their dimensional and compositional characteristics. By varying the incident angles of the exciting radiation, element-sensitive fluorescence radiation is emitted from different regions inside the nanoobjects. By applying an adequate modeling scheme, these datasets can be used to determine the nanostructure characteristics. We demonstrate these capabilities by performing an element-sensitive reconstruction of a lamellar grating made of Si3N4, where GIXRF data for the O-Kα and N-Kα fluorescence emission allows a thin oxide layer to be reconstructed on the surface of the grating structure. In addition, we employ the technique also to three dimensional nanostructures and derive both dimensional and compositional parameters in a quantitative manner.

Speciation of iron sulfide compounds by means of X-ray Emission Spectroscopy using a compact full-cylinder von Hamos spectrometer.

We present experimental and theoretical X-ray emission spectroscopy (XES) data of the Fe Kß line for Iron(II)sulfide (FeS) and Iron(II)disulfide (FeS2). In comparison to X-ray absorption spectroscopy (XAS), XES offers different discrimination capabilities for chemical speciation, depending on the valence states of the compounds probed and, more importantly in view of a a broader, laboratory-based use, a larger flexibility with respect to the excitation source used. The experimental Fe Kß XES data was measured using polychromatic X-ray radiation and a compact full-cylinder von Hamos spectrometer while the calculations were realized using the OCEAN code. The von Hamos spectrometer used is characterized by an energy window of up to 700 eV and a spectral resolving power of E/ΔE = 800. The large energy window at a single position of the spectrometer components is made profit of to circumvent the instrumental sensitivity of wavelength-dispersive spectrometers to sample positioning. This results in a robust energy scale which is used to compare experimental data with ab initio valence-to-core calculations, which are carried out using the ocean package. To validate the reliability of the ocean package for the two sample systems, near edge X-ray absorption fine structure measurements of the Fe K absorption edge are compared to theory using the same input parameters as in the case of the X-ray emission calculations. Based on the example of iron sulfide compounds, the combination of XES experiments and ocean calculations allows unravelling the electronic structure of different transition metal sulfides and qualifying XES investigations for the speciation of different compounds.

Core-level nonlinear spectroscopy triggered by stochastic X-ray pulses.

Stochastic processes are highly relevant in research fields as different as neuroscience, economy, ecology, chemistry, and fundamental physics. However, due to their intrinsic unpredictability, stochastic mechanisms are very challenging for any kind of investigations and practical applications. Here we report the deliberate use of stochastic X-ray pulses in two-dimensional spectroscopy to the simultaneous mapping of unoccupied and occupied electronic states of atoms in a regime where the opacity and transparency properties of matter are subject to the incident intensity and photon energy. A readily transferable matrix formalism is presented to extract the electronic states from a dataset measured with the monitored input from a stochastic excitation source. The presented formalism enables investigations of the response of the electronic structure to irradiation with intense X-ray pulses while the time structure of the incident pulses is preserved.

Offspring Microbiomes Differ Across Breeding Sites in a Panmictic Species.

High dispersal rates are known to homogenize host's population genetic structure in panmictic species and to disrupt host local adaptation to the environment. Long-distance dispersal might also spread micro-organisms across large geographical areas. However, so far, to which extent selection mechanisms that shape host's population genetics are mirrored in the population structure of the enteric microbiome remains unclear. High dispersal rates and horizontal parental transfer may homogenize bacterial communities between breeding sites (homogeneous hypothesis). Alternatively, strong selection from the local environment may differentiate bacterial communities between breeding sites (heterogeneous hypothesis). Furthermore, selection from age-specific environmental or physiological factors may differentiate the microbiome between juveniles and adults. Here, we analyzed the cloacal bacterial 16S rRNA gene of fledgling greater flamingos, Phoenicopterus roseus, across nine western Mediterranean breeding sites and four breeding seasons (n = 731) and adult birds (n = 27) from a single site. We found that fledgling cloacal microbiome, as measured by alpha diversity, beta diversity, the relative abundance of assigned sequence variants (ASVs) belonging to a phylum and genus composition within phylum, varied significantly between sampling sites and across time within site despite high adult dispersal rates. The spatio-temporal effects were stronger on individual ASV absence/presence than on ASV abundance (i.e., than on core microbiome composition). Spatial effects had a stronger effect than temporal effects, particularly on ASV abundance. Our study supports the heterogeneous hypothesis whereby local environmental conditions select and differentiate bacterial communities, thus countering the homogenizing effects of high-dispersing host species. In addition, differences in core microbiome between adult vs. fledgling samples suggests that differences in age-specific environmental and/or physiological factors result in differential selection pressure of core enteric microbiome between age classes, even within the same environment. In particular, the genus Corynebacterium, associated with both seasonal fat uptake and migration in previous studies, was much more abundant in high-dispersing fledglings than in more resident adults. To conclude, selection mechanisms that shape the host's genetic structure cannot be extended to the genetic structure of the enteric microbiome, which has important implications regarding our understanding of both host local adaptation mechanisms and enteric microbiome population genetics.

Mechanism of hydrolysis of a platinum(IV) complex discovered by atomic telemetry.

Herein we report on the hydrolysis mechanism of [Pt{N(p-HC6F4)CH2}2(NC5H5)2(OH)2], a platinum(IV) complex that exhibits anti-cancer properties. Atomic telemetry, an in situ technique based on electron structure sensitive X-ray spectroscopy, revealed that hydrolysis preceded any reduction of the metal center. The obtained results are complemented with 19F NMR measurements and theoretical calculations and support the observation that this PtIV complex does not reduce spontaneously to PtII in HEPES buffer solution at pH 7.4 and after 24 h incubation. These results are of importance for the design of novel Pt-based coordination complexes as well as understanding their behavior under physiological conditions.

Element sensitive reconstruction of nanostructured surfaces with finite elements and grazing incidence soft X-ray fluorescence.

The geometry of a Si3N4 lamellar grating was investigated experimentally with reference-free grazing-incidence X-ray fluorescence analysis. While simple layered systems are usually treated with the matrix formalism to determine the X-ray standing-wave field, this approach fails for laterally structured surfaces. Maxwell solvers based on finite elements are often used to model electrical field strengths for any 2D or 3D structures in the optical spectral range. We show that this approach can also be applied in the field of X-rays. The electrical field distribution obtained with the Maxwell solver can subsequently be used to calculate the fluorescence intensities in full analogy to the X-ray standing-wave field obtained by the matrix formalism. Only the effective 1D integration for the layer system has to be replaced by a 2D integration of the finite elements, taking into account the local excitation conditions. We will show that this approach is capable of reconstructing the geometric line shape of a structured surface with high elemental sensitivity. This combination of GIXRF and finite-element simulations paves the way for a versatile characterization of nanoscale-structured surfaces.