Carbon K-edge X-ray Absorption Research Articles

Experimental and Theoretical Study for Core Excitation of Firefly Luciferin in Carbon K-Edge Spectra.

Carbon (C) K-edge X-ray absorption spectra for firefly luciferin were measured and assigned using time-dependent density functional theoretical calculations for luciferin anion and dianion to elucidate the effect of hydroxy-group deprotonation. It was found that the C K-edge spectra for luciferin had four characteristic peaks. The effect of deprotonation of the hydroxy group appears in the energy difference of the first and second peaks of these spectra. This energy difference is 1.0 eV at pH 7 and 2.3 eV at pH 10. The deprotonation of the hydroxy group can be distinguished based on the soft X-ray absorption spectra.

Deconvolution of the X-ray absorption spectrum of trans-1,3-butadiene with resonant Auger spectroscopy.

High-resolution carbon K-edge X-ray photoelectron, X-ray absorption, non-resonant and resonant Auger spectra are presented of gas phase trans-1,3-butadiene alongside a detailed theoretical analysis utilising nuclear ensemble approaches and vibronic models to simulate the spectroscopic observables. The resonant Auger spectra recorded across the first pre-edge band reveal a complex evolution of different electronic states which remain relatively well-localised on the edge or central carbon sites. The results demonstrate the sensitivity of the resonant Auger observables to the weighted contributions from multiple electronic states. The gradually evolving spectral features can be accurately and feasibly simulated within nuclear ensemble methods and interpreted with the population analysis.

Core-level spectroscopy of the photodissociation process of BrCN molecule

Fewest-switches surfacing hopping (FSSH) simulations have been performed with the high-level multi-reference electronic structure method to explore the coupled electronic and nuclear dynamics upon photoexcitation of cyanogen bromide (BrCN). The potential energy surfaces (PES) of BrCN are charted as functions of the Jacobi coordinates (R, θ). An in-depth examination of the FSSH trajectories reveals the temporal dynamics of the molecule and the population changes of the lowest twelve states during BrCN’s photodissociation process, which presents a rich tapestry of dynamical information. Furthermore, the carbon K-edge x-ray absorption spectroscopy (XAS) is calculated with multi-reference inner-shell spectral simulations. The rotation of the CN fragment and the elongation of the C–Br bond are found to be the reason for the peak shifting in the XAS. Our findings offer a nuanced interpretation for inner-shell probe investigations of BrCN, setting the stage for a deeper understanding of the photodissociation process of cyanogen halides molecules.

Stacking order effects on the energetics and electronic properties of [formula omitted]-doped graphene/h-BN van der Waals heterostructures on SiC(0001)

Heterostructures based on the stacking of two-dimensional materials with different electronic properties have been the subject of several studies addressing the development of novel devices with multiple functionalities. Graphene (G)/hexagonal boron nitride (h-BN) van der Waals (vdW) systems have been extensively investigated, including studies on the large-scale synthesis of h-BN on graphene/SiC(0001) substrate. This work is a theoretical study using first-principles calculations of bilayer (G/h-BN) and trilayer (G/h-BN/G) heterostructures on SiC(0001) covered by a carbon buffer layer (SiC). The results show an energetic preference for h-BN encapsulation below a single layer of graphene on SiC, viz.: G/h-BN/SiC in the case of bilayer systems and G/h-BN/G/SiC in the case of trilayer systems. Indeed, the electronic structure calculations reveal the preservation of graphene linear energy band dispersion in the bilayer systems. The trilayer systems’ electronic structure depends on the stacking order, with the emergence of parabolic bands in energetically less stable systems. Structural characterizations of these bilayers and trilayers on SiC were carried out based on simulations of C-1s core-level-shift (CLS) and carbon K-edge X-ray absorption near edge spectroscopy (XANES) with the goal of assisting future experimental spectroscopy in these graphene/h-BN vdW systems.

Carbon K-edge x-ray absorption spectra of liquid alcohols from quantum chemical calculations of liquid structures obtained by molecular dynamics simulations.

For reproducing the carbon K-edge x-ray absorption spectra of liquid alcohols, inner-shell quantum chemical calculations based on the Hartree-Fock method were performed with the snapshots of the liquid structures obtained by molecular dynamics simulations. The C K-edge inner-shell spectrum of liquid ethanol (EtOH) was obtained by the summation of one thousand calculated spectra of EtOH molecules including neighbor EtOH molecules within the CH2-CH2 distance of 6 Å. For the C K-edge inner-shell spectrum of liquid methanol (MeOH), we have calculated one thousand spectra of MeOH molecules including neighbor MeOH molecules within the CH3-CH3 distance of 6 Å. The calculated C K-edge inner-shell spectra of liquid alcohols well reproduced the spectral shapes of the experimentally obtained x-ray absorption spectra and the spectral changes from gas to liquid phases.

Aqueous-phase behavior of glyoxal and methylglyoxal observed with carbon and oxygen K-edge X-ray absorption spectroscopy

Abstract. Glyoxal (CHOCHO) and methylglyoxal (CH3C(O)CHO) are well-known components of atmospheric particles and their properties can impact atmospheric chemistry and cloud formation. To get information on their hydration states in aqueous solutions and how they are affected by the addition of inorganic salts (sodium chloride (NaCl) and sodium sulfate (Na2SO4)), we applied carbon and oxygen K-edge X-ray absorption spectroscopy (XAS) in transmission mode. The recorded C K-edge spectra show that glyoxal is completely hydrated in the dilute aqueous solutions, in line with previous studies. For methylglyoxal, supported by quantum chemical calculations we identified not only C–H, C=O and C–OH bonds, but also fingerprints of C–OH(CH2) and C=C bonds. The relatively low intensity of C=O transitions implies that the monohydrated form of methylglyoxal is not favored in the solutions. Instead, the spectral intensity is stronger in regions where products of aldol condensation and enol tautomers of the monohydrates contribute. The addition of salts was found to introduce only very minor changes to absorption energies and relative intensities of the observed absorption features, indicating that XAS in the near-edge region is not very sensitive to these intermolecular organic–inorganic interactions at the studied concentrations. The identified structures of glyoxal and methylglyoxal in an aqueous environment support the uptake of these compounds to the aerosol phase in the presence of water and their contribution to secondary organic aerosol formation.

Enhanced 5f-δ bonding in [U(C7H7)2]-: C K-edge XAS, magnetism, and ab initio calculations.

5f covalency in [U(C7H7)2]- was probed with carbon K-edge X-ray absorption spectroscopy (XAS) and electronic structure theory. The results revealed U 5f orbital participation in δ-bonding in both the ground- and core-excited states; additional 5f ϕ-mixing is observed in the core-excited states. Comparisons with U(C8H8)2 show greater δ-covalency for [U(C7H7)2]-.

Structural anisotropy in three dimensional macroporous graphene: A polarized XANES investigation

Three-dimensional macroporous graphene sponges with different densities were investigated by angular dependent carbon K-edge X-ray Absorption Near Edge Spectroscopy (XANES) with a linearly polarized beam. The C K-edge XANES analysis shows an unexpected anisotropic behavior of the macroporous graphene random networks. The macroporous graphene sponges expectedly show an exceedingly lower dichroic ratio compared with that of the highly oriented pyrolytic graphite, but spectra clearly points out the occurrence of oriented hexagonal carbon planes. The anisotropy of the investigated samples exhibits a linear dependence with the measured density. The XANES analysis supports the presence of graphene-like, two-dimensional planar structures inside these synthetic sponges and correlates it with different structural networks and/or density in graphene sponges.

Tetracene Ultrathin Film Growth on Hydrogen-Passivated Silicon.

Inorganic-organic interfaces are important for enhancing the power conversion efficiency of silicon-based solar cells through singlet exciton fission (SF). We elucidated the structure of the first monolayers of tetracene (Tc), an SF molecule, on hydrogen-passivated Si(111) [H-Si(111)] and hydrogenated amorphous Si (a-Si:H) by combining near-edge X-ray absorption fine structure (NEXAFS) and X-ray photoelectron spectroscopy (XPS) experiments with density functional theory (DFT) calculations. For samples grown at or below substrate temperatures of 265 K, the resulting ultrathin Tc films are dominated by almost upright-standing molecules. The molecular arrangement is very similar to the Tc bulk phase, with only a slightly higher average angle between the conjugated molecular plane normal and the surface normal (α) around 77°. Judging from carbon K-edge X-ray absorption spectra, the orientation of the Tc molecules are almost identical when grown on H-Si(111) and a-Si:H substrates as well as for (sub)mono- to several-monolayer coverages. Annealing to room temperature, however, changes the film structure toward a smaller α of about 63°. A detailed DFT-assisted analysis suggests that this structural transition is correlated with a lower packing density and requires a well-chosen amount of thermal energy. Therefore, we attribute the resulting structure to a distinct monolayer configuration that features less inclined, but still well-ordered molecules. The larger overlap with the substrate wave functions makes this arrangement attractive for an optimized interfacial electron transfer in SF-assisted silicon solar cells.

Ab Initio Analysis of Metal-Ligand Bonding in An(COT)2 with An=Th, U in Their Ground- and Core-Excited States.

Relativistic multireference ab initio wave function calculations with the restricted active space second-order perturbation theory (RASPT2) were performed on thorocene and uranocene to determine the actinide N4,5 -edge and carbon K-edge X-ray absorption near-edge structure (XANES) intensities and the metal-ligand orbital mixing in the ground state and core-excited states. Calculated spectral intensities show very good agreement with the experiments and therefore allow detailed and unambiguous assignment of the observed spectral features. φ-type covalent bonding or antibonding interactions are observed for thorocene in the core-excited states, though not in the ground state. This is because the molecular orbital of φ symmetry, which is the in-phase combination of the ligand Lφ and the Th 5fφ orbitals, can be populated with electrons in core-excited states, whereas it is essentially unoccupied in the ground state. For uranocene, the XANES spectra do not reveal much information beyond multiplet broadening, despite the presence of distinct peaks in the spectra. Every core-excited peak is best characterized by its own set of bond orbitals, as the excited state covalency is clearly different from the ground state covalency.

Assessing the effect of pyrolysis temperature on the molecular properties and copper sorption capacity of a halophyte biochar

The capacity of biochar to take up heavy metals from contaminated soil and water is influenced by the pyrolysis temperature. We have prepared three biochar samples from Jerusalem artichoke stalks (JAS) by pyrolysis at 300, 500 and 700 °C, denoted as JAS300, JAS500, and JAS700, respectively. A variety of synchrotron-based techniques were used to assess the effect of pyrolysis temperature on the molecular properties and copper (Cu) sorption capacity of the samples. The content of oxygen-containing functional groups in the biochar samples decreased, while that of aromatic structures and alkaline mineral components increased, with a rise in pyrolysis temperature. Scanning transmission X-ray microscopy indicated that sorbed Cu(II) was partially reduced to Cu(I), but this process was more evident with JAS300 and JAS700 than with JAS500. Carbon K-edge X-ray absorption near edge structure spectroscopy indicated that Cu(II) cations were sorbed to biochar via complexation and Cu-π bonding. With rising pyrolysis temperature, Cu(II)-complexation weakened while Cu-π bonding was enhanced. In addition, the relatively high ash content and pH of JAS500 and JAS700 facilitated Cu precipitation and the formation of langite on the surface of biochar. The results of this investigation will aid the conversion of halophyte waste to useable biochar for the effective remediation of Cu-contaminated soil and water.

Thermal dehydrogenation of n-alkane on Au(111) and Pt(111) surface

Thermal dehydrogenation of long n-alkane on Au(111) and Pt(111) surfaces is investigated by near the carbon K-edge X-ray absorption fine structure spectroscopy (C K-NEXAFS) and scanning tunneling microscopy (STM) under ultrahigh vacuum (UHV). On Au(111), dehydrogenation and formation of unsaturated bonds start at temperatures above 480 K, ending at 650 K. This is confirmed by the decrease in the 1 s → σ*CH/R resonance (σ*CH/R resonance) and the evolution of the π*CC resonance in the C K-NEXAFS spectra. The aliphatic or non-aromatic unsaturated bonds are generated at the early stage of the dehydrogenation on the Au(111), which is examined by the reaction with bromine. The dual peaks of the π*CC resonance at 284–286 eV suggest the formation of polycyclic aromatic hydrocarbons (PAHs). These PAHs exhibit a ribbon or rosary and planer shape by heating at 800 K, which is observed by the STM. In contrast, dehydrogenation begins at RT on Pt(111), and is almost completed at 480 K. π*CC resonance exhibits a main peak at 286 eV, which corresponds to a graphene skeleton, with a sub peak or a shoulder at 284.6 eV, which is attributed to a carbon atom at an edge or defect. The main peak intensity increases as the temperature is raised up to 820 K. STM images obtained after heating at 820 K show nanodots having a diameter of ca. 2–3 nm. The final products upon heating to 1000 K on Pt(111) are graphene nanoflakes with a size of tens of nanometers. The difference between the products is related to the difference between the reaction pathways on Au(111) and Pt(111) surfaces.

Temperature-Dependent Structural Changes in Liquid Benzene.

Benzene is the simplest aromatic molecule with intermolecular π-π interactions. Because ordered liquids are key structures used to study chemical and biological phenomena in the liquid state, ordered structures of benzene confined in nanopores have been extensively studied, whereas those in the liquid state are still unknown. In this study, we address fundamental questions regarding whether ordered structures of benzene are formed in the liquid state by using carbon K-edge X-ray absorption spectroscopy (XAS) as a sensitive local probe. By comparing unexpected temperature behaviors of the π* peak in XAS spectra with model calculations, we have investigated temperature-dependent changes of ordered structures in liquid benzene caused by the increase in abundance of the parallel sandwich orientation relative to parallel displaced structures for the higher temperature. These results are confirmed by infrared spectroscopy with additional support of vibrational mode calculations.

In situ characterization of change in superficial organic components of thermoacidophilic archaeon Acidianus manzaensis YN-25

For the first time, synchrotron radiation (SR) -based carbon K-edge X-ray absorption near edge structure (XANES) spectroscopy in-situ characterization was conducted to evaluate the evolution of superficial (about 10 nm) organic components of extracellular polymeric substances (EPS) of thermoacidophilic archaeon Acidianus manzaensis YN-25 acclimated with different energy substrates (FeS2, CuFeS2, S0, FeSO4). The atomic force microscopy (AFM) morphology scanning showed that the strain acclimated with different energy substrates varied a lot in EPS amount. XANES results showed clear associations between the energy substrates and the changes in organic composition in terms of typical function groups (CO, CO and CN). The chalcopyrite- and pyrite-acclimated cells contained higher proportion of proteins but less proportion of polysaccharides than the S0-acclimated cells. The FeSO4-acclimated cells contained the highest proportion of proteins, while the S0-acclimated cells contained more lipids and polysaccharides. The results of linear-combination and peak fitting of the K-edge XANES for the extracellular superficial organic component C is consistent with the trend in comparison with the results of FTIR and spectrophotometric determination, but there are significant differences in the values. These differences are caused by the inconsistencies of measurement depth between XANES and the latter two characterization methods.

Intercalation of Iron Atoms under Graphene Formed on Silicon Carbide

The intercalation of iron under a graphene monolayer grown on 4H-SiC(0001) is studied. The experiments have been carried out in situ under conditions of ultrahigh vacuum by low-energy electron diffraction, high-energy-resolution photoelectron spectroscopy using synchrotron radiation, and near carbon K-edge X-ray absorption spectroscopy. The deposited iron film thicknesses have been varied within 0.1–2 nm and the sample temperatures from room temperature to 700°C. It is shown that the intercalation process begins at temperatures higher than ~350°C. In this case, it is found that intercalated iron atoms are localized not only between graphene and a buffer layer coating SiC, but also under the buffer layer itself. The optimal conditions of the intercalation are realized in the range 400–500°C, because, at higher temperatures, the system becomes unstable due to the chemical interaction of the intercalated iron with silicon carbide. The inertness of the intercalated films to action of oxygen is demonstrated.

Tetrahedral hydrocarbon nanoparticles in space: X-ray spectra

It has been proposed, or confirmed, that diamond nanoparticles exist in various environments in space: close to active galactic nuclei, in the vicinity of supernovae and pulsars, in the interior of several planets in the Solar system, in carbon planets and other exoplanets, carbon-rich stars, meteorites, in X-ray active Herbig Ae/Be stars, and in the interstellar medium. Using density functional theory methods we calculate the carbon K-edge X-ray absorption spectrum of two large tetrahedral nanodiamonds: C26H32 and C51H52. We also study and test our methods on the astrophysical molecule CH4, the smallest C-H tetrahedral structure. A possible detection of nanodiamonds from X-ray spectra by future telescopes, such as the project Arcus, is proposed. Simulated spectra of the diffuse interstellar medium using Cyg X-2 as a source show that nanodiamonds studied in this work can be detected by Arcus, a high resolution X-ray spectrometer mission selected by NASA for a Phase A concept study.

Nitrogen-rich compounds constitute an increasing proportion of organic matter with depth in Oi-Oe-Oa-A horizons of temperate forests

Soil organic matter (SOM) in O horizons of temperate forests forms a natural gradient of increasing decomposition, as operationally separated into the Oi (leaf litter), Oe (partially decomposed), and Oa (highly decomposed) sub-horizons. This study determines the contribution of extractable nitrogen (N)-rich biomolecules and characterizes changes in SOM composition within O horizon decomposition gradients and in underlying A horizons of three temperate forest stands. Four biomolecules were chosen for this investigation: chlorophyll, protein, DNA, and chitin; combined, they represent the majority of identifiable N-rich organic compound classes present in soils. Selective chemical extractions and purification methods provide estimates of concentrations of each distinct biomolecule class, while short-term respiration measurements provide insight into possible relationships with microbial activity. Changes in the molecular character of SOM are probed using Fourier Transform Infrared (FTIR) and Carbon K-edge X-ray Absorption Near Edge Structure (C-XANES) spectroscopies. Differences in biomolecule concentrations and respiration by horizon reveal two contrasting trends with increasing decomposition and depth: chlorophyll and respiration decrease, whereas protein, DNA and chitin increase. Increasing contribution of these three extractable N-rich biomolecules with progressive decomposition and depth at all sites correspond to decreasing concentrations of C and N and to increases in C:N ratio. These trends are consistent with FTIR spectral results, which indicate a relative increase of NH bending and aromatic CN vibrations, and with C-XANES spectral results, which show a relative increase of aromatic CN transitions. These multiple lines of evidence demonstrate that extractable N-rich biomolecules constitute a growing proportion of the organic C and N content within an organic matter decomposition gradient and that this trend continues into the underlying mineral soil. We posit that the persistence of these intact N-containing biomolecules represents a growing contribution from the microbial biomass pool, but also from non-specific interactions among biomolecules in the Oe and Oa horizons and from biomolecule-mineral interactions in mineral soils. The results of this investigation (increases in the proportion of extractable N-rich biomolecules) also provide valuable insight into the potential bioavailability and biochemical structure of SOM in relation to degree of decomposition.

On the Electronic Structure of Cu Chlorophyllin and Its Breakdown Products: A Carbon K-Edge X-ray Absorption Spectroscopy Study.

Using near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, the carbon backbone of sodium copper chlorophyllin (SCC), a widely used chlorophyll derivative, and its breakdown products are analyzed to elucidate their electronic structure and physicochemical properties. Using various sample preparation methods and complementary spectroscopic methods (including UV/Vis, X-ray photoelectron spectroscopy), a comprehensive insight into the SCC breakdown process is presented. The experimental results are supported by density functional theory calculations, allowing a detailed assignment of characteristic NEXAFS features to specific C bonds. SCC can be seen as a model system for the large group of porphyrins; thus, this work provides a novel and detailed description of the electronic structure of the carbon backbone of those molecules and their breakdown products. The achieved results also promise prospective optical pump/X-ray probe investigations of dynamic processes in chlorophyll-containing photosynthetic complexes to be analyzed more precisely.

<i>In Situ</i> Characterization of Superficial Organic Composition Changes of Thermoacidophilic Archaea <i>Acidianus manzaensis</i> YN-25 in Response to Energy Substrate

The differences of superficial (about 10 nm) extracellular polymeric substances (EPS) composition of thermoacidophilic archaea Acidianus manzaensis YN-25 acclimated with different energy substrates (FeS2, CuFeS2, S0, FeSO4) were analyzed in situ for the first time by synchrotron radiation (SR) based carbon K-edge X-ray absorption near edge structure (XANES) spectroscopy. The results showed that there are clear associations between the energy substrates and the changes in organic composition in terms of typical function groups (-C=O, -C-O and -C-N). The archaea acclimated with chalcopyrite and pyrite contain higher proportion of proteins but less polysaccharides compared to cells acclimated with S0.The archaea acclimated with FeSO4 contains the highest proportion of protein which is positively associated with the iron oxidation process, while archaea acclimated with S0 contains more lipids and polysaccharides, which may be favorable to the hydrophobic S0 adsorption and utilization processes.

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.