Carbon K-edge Research Articles

Performance of the HERMES beamline at the carbon K-edge

Contamination of soft X-rays beamline optics due to carbon cracking and deposition under X- ray irradiation is especially critical for spectromicroscopy operations near the carbon K-absorption edge from organic materials, polymers and nanoparticles. In this paper we present the strategy and procedure followed on the HERMES beamline (Synchrotron SOLEIL) to minimize carbon contamination of the beamline optics. Measurements on a complex organic test sample are reported to demonstrate the performance of the beamline at the carbon K-edge in imaging, spectroscopy and spectromicroscopy modes.

A time-dependent atomistic reconstruction of severe irradiation damage and associated property changes in nuclear graphite

Detailed knowledge regarding the nature of and mechanisms causing neutron irradiation damage in graphite remains a scientific and technological challenge, particularly at high irradiation doses. Using electrons as a surrogate for neutron irradiation, we develop a time-dependent atomistic reconstruction strategy fed by a time series of high-resolution transmission electron microscopy (HRTEM) images, to monitor damage propagation in a graphite grain up to a dose of about one displacement per atom (i.e. well beyond the conventional irradiation simulations based on molecular dynamics). The reduction in crystalline order and the development of interlayer bonding observed in the models with increasing irradiation time induce significant modifications of the elastic constants and thermal conductivity. Homogenizing these properties to the case of isotropic polycrystalline graphite we are able to reproduce the increase in Young's modulus and decrease in thermal conductivity observed experimentally for reactor graphites with increasing dose. Further validation of the models is provided via a comparison of simulated and experimental data from irradiated material such as: HRTEM images, carbon K-edge electron energy loss spectra, dose rate and stored energies.

Compression-Induced Conformation and Orientation Changes in an n-Alkane Monolayer on a Au(111) Surface.

The influence of the preparation method and adsorbed amount of n-tetratetracontane (n-C44H90) on its orientation in a monolayer on the Au(111) surface is studied by near carbon K-edge X-ray absorption fine structure spectroscopy (C K-NEXAFS), scanning tunneling microscopy (STM) under ultrahigh vacuum, and infrared reflection-absorption spectroscopy (IRAS) at the electrochemical interface in sulfuric acid solution. The n-C44H90 molecules form self-assembled lamellar structures with the chain axis parallel to the surface, as observed by STM. For small amounts adsorbed, the carbon plane is parallel to the surface (flat-on orientation). An increase in the adsorbed amount by ∼10-20% induces compression of the lamellar structure either along the lamellar axis or alkyl chain axis. The compressed molecular arrangement is observed by STM, and induced conformation and orientation changes are confirmed by in situ IRAS and C K-NEXAFS.

Spectroscopic investigation of soil organic matter composition for shelterbelt agroforestry systems

While the role of agroforestry systems in increasing soil organic matter (SOM) storage has been studied, insufficient information is available on their effect on the chemical composition of SOM. The objective of this study was to determine the carbon (C) functional group chemistry of SOM for shelterbelts and compare it to the adjacent agricultural fields by using attenuated total reflectance Fourier transform infrared (ATR-FTIR) and Carbon K-edge X-ray absorption near edge structure (XANES) spectroscopies. ATR-FTIR spectral analysis indicated larger proportions of conjugated carboxylic and aromatic C groups for hybrid poplar, white spruce and caragana shelterbelts, phenolic C for hybrid poplar and Manitoba maple shelterbelts and aliphatic and aromatic C for Manitoba maple shelterbelts compared to the adjacent agricultural fields. Polysaccharide, ether and alcoholic C functional groups were generally lower for shelterbelts compared to agricultural fields, with the exception of hybrid poplar species. Analysis by C K-edge XANES spectroscopy on a subset of soils showed the accumulation of aromatic C, ketones and carbohydrates in the surface soil layer (0–5cm) for the shelterbelts compared to agricultural fields. Pearson correlation analysis indicated that the majority of SOM added under the shelterbelts was in the form of plant-derived aromatic, phenolic and carboxylic C groups. The results of this study suggested that the initial composition of litter and its decomposition rate had a strong influence on the composition of SOM under the shelterbelts. The higher proportion of processed forms of SOM, such as ketones, indicated that the SOM for shelterbelts was at a more advanced stage of decomposition compared to agricultural fields; likely due to the surface deposition of litter under shelterbelts.

Interplay between Structural and Electronic Properties in 1,4,5,8-Naphthalenetetracarboxylic Dianhydride Films on Cu(100)

Using various surface science techniques, we have studied the properties of 1,4,5,8-naphthalenetetracarboxylic dianhydride (NTCDA) thin films on a Cu(100) surface. STM investigations suggest the high mobility of the NTCDA molecules over the surface, leading to the formation of large and well-ordered islands. In line with LEED results, two typical domains with different molecular orientations and brick-wall-like structure are revealed in the STM images. On the other hand, a fingerprint of covalent bonding at the NTCDA/Cu interface is obtained from the core level shifts measured by high-resolution XPS. As a consequence, a charge transfer process develops at the interface and enables a total filling of the π*-like lowest unoccupied orbital, which is the signature of the semiconductor character of the NTCDA layer. The carbon K-edge NEXAFS data confirm the chemisorption nature of the interaction between NTCDA and the Cu(100) surface and indicate an evolution from a flat-lying orientation of NTCDA at 1 ML to a straight-up orientation in a thick layer.

Controlling In-Plane Isotropic and Anisotropic Orientation of Organic Semiconductor Molecules on Ionic Fluoride Dielectrics

α-Sexithiophene (6T) ultrathin films have been grown on CaF2(111)/Si(111) planar surfaces and on CaF2(110)/Si(001) ridged surfaces by molecular beam epitaxy. The growth mode has been studied by means of atomic force microscopy (AFM), photoemission, and near edge X-ray absorption fine structure (NEXAFS). AFM reveals a substantial difference in the film morphology on the two substrates: on CaF2(111) large islands with flat terraces form with no in-plane preferential growth direction; on CaF2(110) narrow and elongated islands develop following the substrate corrugation. Photoemission and X-ray absorption at Ca L2,3 and F K edges indicate that the interaction with the substrate is negligible. Near-edge X-ray absorption (NEXAFS) flanked by DFT calculations of the angular-resolved absorption cross section of 6T at the carbon K-edge reveal that the molecules on both substrates have their long axis vertically oriented with respect to the substrate plane. In addition, in-plane anisotropy of the molecular orientati...

Molecular Alignment and Electronic Structure of N,N'-Dibutyl-3,4,9,10-perylene-tetracarboxylic-diimide Molecules on MoS2 Surfaces.

The molecular orientation of organic semiconductors on a solid surface could be an indispensable factor to determine the electrical performance of organic-based devices. Despite its fundamental prominence, a clear description of the emergent two-dimensional layered material-organic interface is not fully understood yet. In this study, we reveal the molecular alignment and electronic structure of thermally deposited N,N'-dibutyl-3,4,9,10-perylene-dicarboximide (PTCDI-C4) molecules on natural molybdenum disulfide (MoS2) using near-edge X-ray absorption fine structure spectroscopy (NEXAFS). The average tilt angle determination reveals that the anisotropy in the π* symmetry transition of the carbon K-edge (284-288 eV range) is present at the sub-monolayer regime. Supported by ultraviolet photoelectron spectroscopy (UPS), X-ray photoelectron spectroscopy (XPS), and resonant photoemission spectroscopy (RPES) measurements, we find that our spectroscopic measurements indicate a weak charge transfer established at the PTCDI-C4/MoS2 interface. Sterical hindrance due to the C4 alkyl chain caused tilting of the molecular plane at the initial thin film deposition. Our result shows a tunable interfacial alignment of organic molecules on transition metal dichalcogenide surfaces effectively enhancing the electronic properties of hybrid organic-inorganic heterostructure devices.

Characterization of Coke on a Pt-Re/γ-Al2O3 Re-Forming Catalyst: Experimental and Theoretical Study

The characterization of coke on spent catalysts is key to understanding deactivation mechanisms in hydrocarbon transformations. In this paper we report the comprehensive characterization (using laser Raman spectroscopy, 13C MAS NMR, temperature-programmed oxidation, XPS, and carbon K-edge NEXAFS) of coke on a series of spent Pt-Re re-forming catalysts as a function of time on stream and position in the catalytic bed. Laser Raman spectroscopy is shown to be rather insensitive to the carbon species present, while 13C MAS NMR finds that the carbon is present primarily as aromatic carbon. The TPO data are consistent with the coke being present on the alumina support and not to a large extent covering the metallic Pt-Re nanoclusters, but the data do suggest the presence of more than one type of coke present. The carbon K-edge NEXAFS data, however, clearly differentiate the types of coke species present. In the more coked samples the features ascribed to graphite become more pronounced, together with an increas...

Microscopic origin of ultra-low friction coefficient between the wear track formed on carbon nitride coating and transfer layer on sliding ball in friction tests under dry N2

Carbon nitride (CNx) coatings have been found to exhibit an ultra-low friction coefficient (less than 0.01) after repeated sliding against a silicon nitride (Si3N4) ball in a dry nitrogen gas (N2) atmosphere. However, the mechanism for this has not yet been fully elucidated with respect to analyzing changes in the space structure of CNx. In the present study, we examined the microscopic structural changes in the near-surface structural transition layers of the wear track in the CNx coating and the transfer layer of the Si3N4 ball, using scanning transmission electron microscopy and electron energy-loss spectroscopy. We investigated the nitrogen concentration, density, and curvature of fragmented graphitic planes in the structural transition layers of both the CNx coating and the transfer layer of the Si3N4 ball by analyzing the plasmon peak and carbon K-edge. In addition, we theoretically examined the chemical bonding states of nitrogen doping in various model clusters using an ab initio molecular orbital method to clarify the role of nitrogen in the ultra-low friction behavior. The mechanism behind the ultra-low friction behavior is explained by nano-graphitization of the fragmented carbon structure with optimal nitrogen concentration passivating the contacting counter surfaces of the coating and ball formed during sliding.

Time-resolved x-ray absorption spectroscopy with a water window high-harmonic source.

Time-resolved x-ray absorption spectroscopy (TR-XAS) has so far practically been limited to large-scale facilities, to subpicosecond temporal resolution, and to the condensed phase. We report the realization of TR-XAS with a temporal resolution in the low femtosecond range by developing a tabletop high-harmonic source reaching up to 350 electron volts, thus partially covering the spectral region of 280 to 530 electron volts, where water is transmissive. We used this source to follow previously unexamined light-induced chemical reactions in the lowest electronic states of isolated CF4+ and SF6+ molecules in the gas phase. By probing element-specific core-to-valence transitions at the carbon K-edge or the sulfur L-edges, we characterized their reaction paths and observed the effect of symmetry breaking through the splitting of absorption bands and Rydberg-valence mixing induced by the geometry changes.

Structure of nanoscale-pitch helical phases: blue phase and twist-bend nematic phase resolved by resonant soft X-ray scattering.

Periodic structures of phases with orientational order of molecules but homogenous electron density distribution: a short pitch cholesteric phase, blue phase and twist-bend nematic phase, were probed by resonant soft X-ray scattering (RSoXS) at the carbon K-edge. The theoretical model shows that in the case of a simple heliconical nematic structure, two resonant signals corresponding to the full and half pitch band should be present, while only the full pitch band is observed experimentally. This suggests that the twist-bend nematic phase has a complex structure with a double-helix built of two interlocked, shifted helices. We confirm that the helical pitch in the twist-bend nematic phase is in a 10 nm range for both the chiral and achiral materials. We also show that the symmetry of the blue phase can be unambiguously determined through a resonant enhancement of the X-ray diffraction signals, by including polarization effects, which are found to be an important indicator in phase structure determination.

Synchrotron based NEXAFS study on nitrogen doped hydrothermal carbon: Insights into surface functionalities and formation mechanisms

Synchrotron-based Near-Edge X-ray Absorption Fine Structure (NEXAFS) studies have been conducted on two hydrothermally produced carbon (HTC) structures and their main surface structural features are reported. The two HTCs were produced respectively from sucrose, and sucrose with added (NH4)2SO4, under subcritical water conditions. The NEXAFS carbon K-edge spectra reveal the presence of CC, COC (furan), CO and COH functionalities on the surface of the sucrose derived HTC. For the nitrogen-doped HTC, the carbon K-edge spectra indicate an increase in CC and COH functionalities, as well as the inclusion of CN and CN functionalities. Additionally, the nitrogen K-edge for the doped hydrothermal carbon displayed characteristic peaks for pyridinic, pyrrolic and tertiary amine nitrogen surface groups. Furthermore, a mechanistic pathway to inclusion of nitrogen atoms in the HTC-SAS structure is postulated.

First in-flight synchrotron X-ray absorption and photoemission study of carbon soot nanoparticles.

Many studies have been conducted on the environmental impacts of combustion generated aerosols. Due to their complex composition and morphology, their chemical reactivity is not well understood and new developments of analysis methods are needed. We report the first demonstration of in-flight X-ray based characterizations of freshly emitted soot particles, which is of paramount importance for understanding the role of one of the main anthropogenic particulate contributors to global climate change. Soot particles, produced by a burner for several air-to-fuel ratios, were injected through an aerodynamic lens, focusing them to a region where they interacted with synchrotron radiation. X-ray photoelectron spectroscopy and carbon K-edge near-edge X-ray absorption spectroscopy were performed and compared to those obtained for supported samples. A good agreement is found between these samples, although slight oxidation is observed for supported samples. Our experiments demonstrate that NEXAFS characterization of supported samples provides relevant information on soot composition, with limited effects of contamination or ageing under ambient storage conditions. The highly surface sensitive XPS experiments of airborne soot indicate that the oxidation is different at the surface as compared to the bulk probed by NEXAFS. We also report changes in soot’s work function obtained at different combustion conditions.

Morphology and mixing of black carbon particles collected in central California during the CARES field study

Abstract. Aerosol absorption is strongly dependent on the internal heterogeneity (mixing state) and morphology of individual particles containing black carbon (BC) and other non-absorbing species. Here, we examine an extensive microscopic data set collected in the California Central Valley during the CARES 2010 field campaign. During a period of high photochemical activity and pollution buildup, the particle mixing state and morphology were characterized using scanning transmission X-ray microscopy (STXM) at the carbon K-edge. Observations of compacted BC core morphologies and thick organic coatings at both urban and rural sites provide evidence of the aged nature of particles, highlighting the importance of highly aged particles at urban sites during periods of high photochemical activity. Based on the observation of thick coatings and more convex BC inclusion morphology, either the aging was rapid or the contribution of fresh BC emissions at the urban site was relatively small compared to background concentrations. Most particles were observed to have the BC inclusion close to the center of the host. However, host particles containing inorganic rich inclusions had the BC inclusion closer to the edge of the particle. These measurements of BC morphology and mixing state provide important constraints for the morphological effects on BC optical properties expected in aged urban plumes.

Carbon K-edge electron-energy-loss near-edge structure in the reflection mode on graphene/Ni(111)

Electron-energy-loss near-edge structure (ELNES) in the transmission mode is a useful tool to investigate the properties of materials, in conjunction with transmission electron microscope (TEM) imaging. The ELNES technique has been extensively applied on graphene and other carbon-based materials. Of course, such method is applicable only on thin systems; thus, it cannot be used to investigate the properties of massive samples, or thin layers adsorbed on thick substrates, for example, graphene on metal supports. Here, we show that it is possible to use electron energy loss in the reflection mode to measure the fine structure of the carbon K-edge in monolayer graphene on Ni(111), thus demonstrating that reflection ELNES is a very sensitive tool, particularly useful in cases where the TEM-based ELNES cannot be applied.

Fast Time-Dependent Density Functional Theory Calculations of the X-ray Absorption Spectroscopy of Large Systems.

The computational cost of calculations of K-edge X-ray absorption spectra using time-dependent density functional (TDDFT) within the Tamm-Dancoff approximation is significantly reduced through the introduction of a severe integral screening procedure that includes only integrals that involve the core s basis function of the absorbing atom(s) coupled with a reduced quality numerical quadrature for integrals associated with the exchange and correlation functionals. The memory required for the calculations is reduced through construction of the TDDFT matrix within the absorbing core orbitals excitation space and exploiting further truncation of the virtual orbital space. The resulting method, denoted fTDDFTs, leads to much faster calculations and makes the study of large systems tractable. The capability of the method is demonstrated through calculations of the X-ray absorption spectra at the carbon K-edge of chlorophyll a, C60 and C70.

Impacts of Conformational Geometries in Fluorinated Alkanes

Research of blood substitute formulations and their base materials is of high scientific interest. Especially fluorinated microemulsions based on perfluorocarbons, with their interesting chemical properties, offer opportunities for applications in biomedicine and physical chemistry. In this work, carbon K-edge absorption spectra of liquid perfluoroalkanes and their parent hydrocarbons are presented and compared. Based on soft X-ray absorption, a comprehensive picture of the electronic structure is provided with the aid of time dependent density functional theory. We have observed that conformational geometries mainly influence the chemical and electronic interactions in the presented liquid materials, leading to a direct association of conformational geometries to the dissolving capacity of the presented perfluorocarbons with other solvents like water and possibly gases like oxygen.

Understanding the F 1s NEXAFS Dichroism in Fluorinated Organic Semiconductors

The analysis of NEXAFS spectra acquired at the absorption edge of heteroatoms like fluorine, nitrogen, or oxygen enables the determination of the molecular orientation of individual compounds even in multinary structures. Such an analysis requires detailed knowledge about the nature of the corresponding electronic excitations, especially because 1s-π* and 1s-σ* excitations frequently feature disparate transition dipole moments in planar molecules. Unlike intuitively assumed, the resulting dichroisms of both excitation types in planar systems are, however, not necessarily inverted. Instead, both the structure of the molecules and their alignment on the substrate determine the actual dichroisms. In this study, the NEXAFS signature and dichroisms of thin films of the organic n-type semiconductor perfluoropentacene (PFP) in different crystalline orientations at the carbon and fluorine absorption K-edge are thoroughly analyzed. For lying molecular orientations, an inverted dichroism at the fluorine K-edge compared to the carbon K-edge is found. In contrast, for upright molecular configurations the dichroisms at both absorption edges are similar. With the help of density functional theory methods, this behavior is explained by the different nature of the excitations. While at the carbon K-edge 1s-π* excitations are most prominent, 1s-σ*-related signals are dominant at the fluorine K-edge. Computations of the NEXAFS signatures and corresponding excitations at different levels of theory are compared with particular focus on electronic relaxation. Energetic positions and oscillator strengths, especially for resonances of σ*-type, depend strongly on the theoretical approach whereas the π*-related signals are barely affected by the methods applied in the present work. Similar effects were also found for the analysis of the smaller perfluoronaphthalene and are explained by the different relaxation effects for 1s-σ*- and 1s-π*-type excitations. As the investigated acenes are representative model systems for π-conjugated molecular semiconductors, the present findings are important for the understanding of the electronic properties and the application of NEXAFS for structural analysis in such materials.

Hybrid Complex Polarization Propagator/Molecular Mechanics Method for Heterogeneous Environments.

We introduce a hybrid complex polarization propagator/molecular mechanics method for the calculation of near-resonant and resonant response properties of molecules in heterogeneous environments, which consist of a metallic surface, or nanoparticle, and a solvent. The applicability and performance of the method is demonstrated by computations of linear absorption spectra of p-nitroaniline physisorbed at a gold/dimethyl sulfoxide interface in the UV/vis and near-carbon-K-edge regions of the spectrum. It is shown that the shift of absorption cross-section induced by the heterogeneous environment varies significantly depending on the nature of the excited states encountered in the targeted frequency region as well as on the actual size of the resonant frequencies, and that the solvent component of the heterogeneous environment is responsible for the major part of the environmental shift, especially in the higher frequency range of the carbon K-edge region.

X-ray natural linear dichroism of graphitic materials across the carbon K-edge: Correction for perturbing high-order harmonics

Reflectivity measurements on graphitic materials such as graphene at energies across the carbon K-edge are frustrated by significant intensity loss due to adventitious carbon on beamline mirrors. Such intensity reduction enhances effects due to perturbing high-order harmonics in the beam. These effects distort the actual structure of the reflectance curve. In order to overcome this limitation, a correction technique has been developed and demonstrated first with measurements for highly ordered pyrolytic graphite. The same approach may be applied to other graphitic materials such as graphene and it may be used with other synchrotron beamlines. The fraction of high-order harmonics was determined by passing the incident beam through a 87 nm thin silicon nitride absorber that can be well modeled. Using the corrected measurements the x-ray natural linear dichroism of the sample has been determined.