Nitrogen K-edge Research Articles

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.

Multifaceted Solution of Analytical Challenges in Complex Oilfield Materials With Synchrotron Techniques

Summary The versatility of synchrotron techniques for the solution of oilfield questions is illustrated by the application of powder X-ray diffraction (PXRD) and X-ray absorption near-edge structure (XANES) spectroscopy to a toluene-insoluble oilfield-residue sample from an alkaline/surfactant/polymer (ASP) -flood site in Taber, Alberta, Canada. The primary questions regarding the sample were the sources of the barium and nitrogen (both at levels of approximately 0.8 wt%). Synchrotron PXRD provided better signal–noise and detection limits than previously obtained laboratory PXRD data, enabling the identification of four additional crystalline minerals including heulandite, (Ba, Ca, Sr, K, Na)5 Al9 Si27 O72 (H2O)22, a tecto-silicate zeolite known for accommodation of a wide variety of cations. Heulandite provides a plausible location for barium (and strontium) observed with chemical analysis. Synchrotron XANES spectra at the nitrogen K-edge suggested that the source of the nitrogen content was a corrosion inhibitor, rather than a polyacrylamide (PAM) -based compound, as originally assumed.

Electron Microscopy Reveals Structural and Chemical Changes at the Nanometer Scale in the Osteogenesis Imperfecta Murine Pathology.

Alternations of collagen and mineral at the molecular level may have a significant impact on the strength and toughness of bone. In this study, scanning transmission electron microscopy (STEM) and electron energy-loss spectroscopy (EELS) were employed to study structural and compositional changes in bone pathology at nanometer spatial resolution. Tail tendon and femoral bone of osteogenesis imperfecta murine (oim, brittle bone disease) and wild type (WT) mice were compared to reveal defects in the architecture and chemistry of the collagen and collagen-mineral composite in the oim tissue at the molecular level. There were marked differences in the substructure and organization of the collagen fibrils in the oim tail tendon; some regions have clear fibril banding and organization, while in other regions fibrils are disorganized. Malformed collagen fibrils were loosely packed, often bent and devoid of banding pattern. In bone, differences were detected in the chemical composition of mineral in oim and WT. While mineral present in WT and oim bone exhibited the major characteristics of apatite, examination in EELS of the fine structure of the carbon K ionization edge revealed a significant variation in the presence of carbonate in different regions of bone. Variations have been also observed in the fine structure and peak intensities of the nitrogen K-edge. These alterations are suggestive of differences in the maturation of collagen nucleation sites or cross-links. Future studies will aim to establish the scale and impact of the modifications observed in oim tissues. The compositional and structural alterations at the molecular level cause deficiencies at larger length scales. Understanding the effect of molecular alterations to pathologic bone is critical to the design of effective therapeutics.

Analysis of the Electronic Structure of Aqueous Urea and Its Derivatives: A Systematic Soft X-Ray-TD-DFT Approach.

Soft X-ray emission (XE), absorption (XA), and resonant inelastic scattering (RIXS) experiments have been conducted at the nitrogen K-edge of urea and its derivatives in aqueous solution and were compared with density functional theory and time-dependent density functional theory calculations. This comprehensive study provides detailed information on the occupied and unoccupied molecular orbitals of urea, thiourea, acetamide, dimethylurea, and biuret at valence levels. By identifying the electronic transitions that contribute to the experimental spectral features, the energy gap between the highest occupied and the lowest unoccupied molecular orbital of each molecule is determined. Moreover, a theoretical approach is introduced to simulate resonant inelastic X-ray scattering spectra by adding an extra electron to the lowest unoccupied molecular orbital, thereby mimicking the real initial state of the core-electron absorption before the subsequent relaxation process.

Water-window soft x-ray high-harmonic generation up to the nitrogen K-edge driven by a kHz, 2.1 μm OPCPA source

We report the generation of coherent water-window soft x-ray harmonics in a neon-filled semi-infinite gas cell driven by a femtosecond multi-mJ mid-infrared optical parametric chirped-pulse amplification (OPCPA) system at a 1 kHz repetition rate. The cutoff energy was extended to ∼450 eV with a 2.1 μm driver wavelength and a photon flux of photons/s/1% bandwidth was obtained at 350 eV. A comparable photon flux of photons/s/1% bandwidth was observed at the nitrogen K-edge of 410 eV. This is the first demonstration of water-window harmonic generation up to the nitrogen K-edge from a kHz OPCPA system. Finally, this system is suitable for time-resolved soft x-ray near-edge absorption spectroscopy. Further scaling of the driving pulse's energy and repetition rate is feasible due to the availability of high-power picosecond Yb-doped pump laser technologies, thereby enabling ultrafast, tabletop water-window x-ray imaging.

Use of a DNA film on a self-assembled monolayer for investigating the physical process of DNA damage induced by core electron ionization

Purpose: A novel two-layer sample composed of a deoxyribonucleic acid (DNA) film and self-assembled monolayer (SAM) was prepared on an inorganic surface to mimic the processes in which DNA is damaged by soft X-ray irradiation.Materials and methods: A mercaptopropyltrimethoxysilane (MPTS) SAM was formed on a sapphire surface, then oligonucleotide (OGN) molecules were adsorbed on the MPTS-SAM. The thicknesses and chemical states of the layers were determined by X-ray photoelectron spectroscopy (XPS) and near-edge X-ray fine structure (NEXAFS) around the phosphorus (P) and sulfur (S) K-edges. To induce the damage to the OGN molecules, the sample was irradiated with synchrotron soft X-rays. The chemical state of the OGN molecules before and after irradiation was examined by NEXAFS around the nitrogen (N) K-edge region.Results: The thickness of the MPTS-OGN layer was approximately 7.7 nm. The S atom of the OGN molecules was located at the bottom of the OGN layer. The peak shape of the N K-edge NEXAFS spectra of the MPTS-OGN layers clearly changed following irradiation.Conclusions: The MPTS-OGN layer formed on the sapphire surface. The chemical states and the structure of the interface were elucidated using synchrotron soft X-rays. The OGN molecules adsorbed on the MPTS films decomposed upon exposure to soft X-ray irradiation.

NEXAFS and XPS of p-Aminobenzoic Acid Polymorphs: The Influence of Local Environment

Nitrogen K-edge XPS and NEXAFS of the two polymorphic forms of para- aminobenzoic acid (PABA) are significantly different reflecting variation in hydrogen bonding. Alteration in hydrogen bonding at the amino group leads to a shift to high energy for both the XPS N 1s core level and the 3π* NEXAFS resonance with β-PABA. Participation of the amine group in the aromatic system causes the 1π* resonance to be sensitive to the nature of the intermolecular bonding at the para-carboxylic acid group, and a shift to low energy for α- PABA is observed due to hydrogen-bonded carboxylic acid dimer formation. FEFF calculations also successfully reproduce both the energy and intensity variations observed for the σ* shape resonance associated with the C-N bond, with the majority of the decrease in energy observed for b-PABA arising from the longer C-N bond.

Soil organic matter characteristics as indicator of Chernozem genesis in the Baltic Sea region

The genesis of Chernozems in the Baltic Sea region is still insufficiently understood and the composition of its organic matter may be a key for a better pedogenetic interpretation of the mollic, biogenically mixed (Axh) horizons. Therefore, we investigated the composition of soil organic matter in the Ap/Ah- and Axh-horizons from seven soil profiles at the islands of Poel, Fehmarn (Germany), and Sjalland (Denmark). In a multi-methods approach we carried out synchrotron-based X-ray absorption near edge structure (XANES) spectroscopy at the carbon (C) and nitrogen (N) K-edges, pyrolysis-field ionisation-mass spectrometry (Py-FIMS) and soil color measurements as non-specific, bulk SOM characterization methods, and quantified the benzene polycarboxylic acids (BPCAs) as specific markers for black carbon (BC). The XANES- and Py-FIMS-spectra in good agreement revealed relative enrichments of aromatic C and heterocyclic N compounds in the lower Axh- in comparison to the corresponding upper Ap/Ah-horizons. In almost all horizon pairs, the BC portions in the Axh- (7.6 to 18% of Corg) exceeded those in the Ap/Ah-horizons (6.7 to 12% of Corg) and were similar to the BC portions in typical Phaeozems and Chernozems from European loess areas. The ratios of penta- to hexacarboxylic benzoic acids (B5CA/B6CA) of 0.9 to 2.2, mean 1.2, indicated contributions of combustion residues from domestic and grassland fires. This pyrogenic organic matter and its transformation products governed the soil color, which was closely correlated to the BC portions (L*-value=−0.880 x+52.13; r2=0.539**). In summary, the enrichments of stabilized aromatic and heterocyclic compounds in the Axh-horizons derived from C- and N-XANES, Py-FIMS and the BC-determination are interpreted by an input of pyrogenic matter into the Baltic Chernozems, indicating an anthropo-pedogenesis in the period between Bronze age and the Early Middle Ages.

Properties of aqueous nitrate and nitrite from x-ray absorption spectroscopy.

Nitrate and nitrite ions are of considerable interest, both for their widespread use in commercial and research contexts and because of their central role in the global nitrogen cycle. The chemistry of atmospheric aerosols, wherein nitrate is abundant, has been found to depend on the interfacial behavior of ionic species. The interfacial behavior of ions is determined largely by their hydration properties; consequently, the study of the hydration and interfacial behavior of nitrate and nitrite comprises a significant field of study. In this work, we describe the study of aqueous solutions of sodium nitrate and nitrite via X-ray absorption spectroscopy (XAS), interpreted in light of first-principles density functional theory electronic structure calculations. Experimental and calculated spectra of the nitrogen K-edge XA spectra of bulk solutions exhibit a large 3.7 eV shift between the XA spectra of nitrate and nitrite resulting from greater stabilization of the nitrogen 1s energy level in nitrate. A similar shift is not observed in the oxygen K-edge XA spectra of NO3 (-) and NO2 (-). The hydration properties of nitrate and nitrite are found to be similar, with both anions exhibiting a similar propensity towards ion pairing.

Energy-Specific Equation-of-Motion Coupled-Cluster Methods for High-Energy Excited States: Application to K-edge X-ray Absorption Spectroscopy

Single-reference techniques based on coupled-cluster (CC) theory, in the forms of linear response (LR) or equation of motion (EOM), are highly accurate and widely used approaches for modeling valence absorption spectra. Unfortunately, these equations with singles and doubles (LR-CCSD and EOM-CCSD) scale as O(N⁶), which may be prohibitively expensive for the study of high-energy excited states using a conventional eigensolver. In this paper, we present an energy-specific non-Hermitian eigensolver that is able to obtain high-energy excited states (e.g., XAS K-edge spectrum) at low computational cost. In addition, we also introduce an improved trial vector for iteratively solving the EOM-CCSD equation with a focus on high-energy eigenstates. The energy-specific EOM-CCSD approach and its low-scaling alternatives are applied to calculations of carbon, nitrogen, oxygen, and sulfur K-edge excitations. The results are compared to other implementations of CCSD for excited states, energy-specific linear response time-dependent density functional theory (TDDFT), and experimental results with multiple statistical metrics are presented and evaluated.

Measurement and prediction of the NEXAFS spectra of pyrimidine and purine and the dissociation following the core excitation

Near-edge X-ray absorption fine structure spectra of pyrimidine and purine at the carbon and nitrogen K-edges were measured using synchrotron radiation and a reflectron time-of-flight mass spectrometer. Spectrum assignments based on the time-dependent density functional theory calculation were presented. From the comparison of the experimental and theoretical results, the nature of various core-excitation transitions and the chemical shifts in the absorption energies were elucidated. The dissociation fragments following the core excitation were analyzed, and the enhancements on the fragment branching ratios were observed. The possible identities and dissociation mechanisms of the major fragments were discussed.

EELS analysis of the nitrogen content of carbide particles in a commercial γ′-strengthened nickel-base superalloy

Carbide particles contribute to the high strength of nickel-base superalloys. It is a long standing question whether these carbide particles contain nitrogen. Here we examine the nitrogen content of the titanium–molybdenum-carbide in the commercial superalloy NIMONIC PE16 using a combination of electron energy loss spectroscopy (EELS) with energy dispersive X-ray (EDX) analysis. Careful examination of the molybdenum M3- and M2-edges, which overlap with the nitrogen K-edge, leads to an upper limit for the nitrogen content of the carbide: 1.8 at.%.

Proton Transfer, Hydrogen Bonding, and Disorder: Nitrogen Near-Edge X-ray Absorption Fine Structure and X-ray Photoelectron Spectroscopy of Bipyridine–Acid Salts and Co-crystals

The sensitivity of near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to Bronsted donation and the protonation state of nitrogen in the solid state is investigated through a series of multicomponent bipyridine–acid systems alongside X-ray photoelectron spectroscopy (XPS) data. A large shift to high energy occurs for the 1s → 1π* resonance in the nitrogen K-edge NEXAFS with proton transfer from the acid to the bipyridine base molecule and allows assignment as a salt (C═NH+), with the peak ratio providing the stoichiometry of the types of nitrogen species present. A corresponding binding energy shift for C═NH+ is observed in the nitrogen XPS, clearly identifying protonation and formation of a salt. The similar magnitude shifts observed with both techniques relative to the unprotonated nitrogen of co-crystals (C═N) suggest that the chemical state (initial-state) effects dominate. Results from both techniques reveal the sensitivity to identify proton transfer, hydrogen bond disorder, and even the...

Tracking of azobenzene isomerization by X-ray emission spectroscopy.

Cis-trans isomerizations are among the fundamental processes in photochemistry. In azobenzene or its derivatives this dynamics is, due to its reversibility, one of the reactions widely used in photostimulation of molecular motors or in molecular electronics. Though intensively investigated in the optical regime, no detailed study exists in the X-ray regime so far. Because the X-ray emission spectroscopy echoes the electronic structure sensitive to the geometry, this theoretical report based on the density functional theory and its time-dependent version presents different nitrogen K-edge X-ray emission spectra for cis and trans isomers with close interrelation to their electron configuration. Considering the spectrum along the isomerization path, these structural signatures can be utilized to probe the isomerization dynamics in the excited molecule. The scheme can further be generalized to the element specific photoreactions.

Nitrogen K-edge X-ray absorption near edge structure (XANES) spectra of purine-containing nucleotides in aqueous solution.

The N K-edge X-ray absorption near edge structure (XANES) spectra of the purine-containing nucleotide, guanosine 5'-monophosphate (GMP), in aqueous solution are measured under various pH conditions. The spectra show characteristic peaks, which originate from resonant excitations of N 1s electrons to π* orbitals inside the guanine moiety of GMP. The relative intensities of these peaks depend on the pH values of the solution. The pH dependence is explained by the core-level shift of N atoms at specific sites caused by protonation and deprotonation. The experimental spectra are compared with theoretical spectra calculated by using density functional theory for GMP and the other purine-containing nucleotides, adenosine 5'-monophosphate, and adenosine 5'-triphosphate. The N K-edge XANES spectra for all of these nucleotides are classified by the numbers of N atoms with particular chemical bonding characteristics in the purine moiety.

Nitrogen K-edge soft X-ray natural circular dichroism of histidine thin film

We report preliminary natural circular dichroism (NCD) spectra of amino acids, Land D-histidine, thin films in the nitrogen K-edge energy region. NCD peaks were observed at 399.9 eV and were assigned to the 1s → π* transition of the nitrogen atoms in imidazole ring. Imidazole ring is positioned at the side chain distant from the asymmetric carbon. This result suggests that NCD spectroscopy in the soft X-ray region can selectively pick up the information on local structure around specific atoms, regardless of the position of atoms in molecules. It is interesting in view of application of NCD spectroscopy in the soft X-ray region to investigation of protein structures.

Bond cleavages of adenosine 5'-triphosphate induced by monochromatic soft X-rays

To investigate which type of bond is likely to be cleaved by soft X-ray exposure to an adenosine 5'-triphosphate (ATP), we observed spectral changes in X-ray absorption near edge structure (XANES) around nitrogen and oxygen K-edge of an ATP film by soft X-ray irradiation. Experiments were performed at a synchrotron soft X-ray beamline at SPring-8, Japan. The XANES spectra around the nitrogen and oxygen .K-edge slightly varied by exposure to 560 eV soft X-rays. These changes are originated from the cleavage of C-N bonds between a sugar and a nucleobase site and of C-O, P-O or O-H bond of sugar and phosphate site. From the comparison between the change in XANES intensity of σ* peak at nitrogen and that at oxygen K-edges, it is inferred that the C-O, P-O or O-H bond of sugar and phosphate is much efficiently cleaved than the C-N of N-glycoside bond by the exposure of 560 eV soft X-ray to ATP film.

A comparative theoretical study on core-hole excitation spectra of azafullerene and its derivatives

The core-hole excitation spectra-near-edge x-ray absorption spectroscopy (NEXAFS), x-ray emission spectroscopy (XES), and x-ray photoelectron spectroscopy (XPS) shake-up satellites have been simulated at the level of density functional theory for the azafullerene C59N and its derivatives (C59N)(+), C59HN, (C59N)2, and C59N-C60, in which the XPS shake-up satellites were simulated using our developed equivalent core hole Kohn-Sham (ECH-KS) density functional theory approach [B. Gao, Z. Wu, and Y. Luo, J. Chem. Phys. 128, 234704 (2008)] which aims for the study of XPS shake-up satellites of large-scale molecules. Our calculated spectra are generally in good agreement with available experimental results that validates the use of the ECH-KS method in the present work. The nitrogen K-edge NEXAFS, XES, and XPS shake-up satellites spectra in general can be used as fingerprints to distinguish the azafullerene C59N and its different derivatives. Meanwhile, different carbon K-edge spectra could also provide detailed information of (local) electronic structures of different molecules. In particular, a peak (at around 284.5 eV) in the carbon K-edge NEXAFS spectrum of the heterodimer C59N-C60 is confirmed to be related to the electron transfer from the C59N part to the C60 part in this charge-transfer complex.

Chemical Bonding in Aqueous Ferrocyanide: Experimental and Theoretical X-ray Spectroscopic Study

Resonant inelastic X-ray scattering (RIXS) and X-ray absorption (XA) experiments at the iron L- and nitrogen K-edge are combined with high-level first-principles restricted active space self-consistent field (RASSCF) calculations for a systematic investigation of the nature of the chemical bond in potassium ferrocyanide in aqueous solution. The atom- and site-specific RIXS excitations allow for direct observation of ligand-to-metal (Fe L-edge) and metal-to-ligand (N K-edge) charge-transfer bands and thereby evidence for strong σ-donation and π-backdonation. The effects are identified by comparing experimental and simulated spectra related to both the unoccupied and occupied molecular orbitals in solution.

Impact of Populus trees on the composition of organic matter and the soil microbial community in Orthic Gray Luvisols in Saskatchewan (Canada)

The conversion of agriculture land to short rotation coppice (SRC) systems with hybrid poplar (Populus spp.) is becoming an important practice to store carbon and produce biomass for the fiber industry. This land-use change is likely to affect the microbial community structure, in part through the introduction of an ectomycorrhizal host, but also by changing organic matter inputs, ultimately shifting the molecular composition of soil organic matter (SOM) because these properties are crop-specific. The objective of this study was to examine the effect of different aged poplar stands growing on Orthic Gray Luvisols on these soil properties compared to an adjacent perennial crop. The site consisted of four treatments: hybrid poplar (Populus deltoides × Populus petroskyana) in SRC of 7 and 14 years age (Pop7 and Pop14), a 40-year-old aspen (Populus tremuloides) forest (Aspen), and an adjacent arable site with alfalfa (Medicago sativa). The molecular composition of SOM was determined using pyrolysis-field ionization mass spectrometry (Py-FIMS) and synchrotron-based X-ray absorption near edge spectroscopy at the nitrogen (N) K-edge (N-XANES). Phospholipid fatty acid (PLFA) profiles revealed higher concentrations of fungal but not bacterial biomarkers in poplar plantations than under alfalfa. Fungal:bacterial ratio was lower under alfalfa than under poplar trees. Overall microbial community structure also changed in response to vegetation type and the duration of woody biomass. Along the chronosequence of poplar, Py-FIMS revealed significant increases in the proportions of carbohydrates with pentose and hexose subunits, phenols and lignin monomers, alkylaromatics and peptides and significant decreases in lipids, alkanes, alkenes, bound fatty acids and alkylmonoesters and free fatty acids with increasing poplar stand age. Thermal stability of sterols decreased along the chronosequence, suggesting that poplar plantations are not involved in the build-up of these substances. Differences in the ordination were well reflected by N K-edge XANES spectra. Increased carbohydrate portions indicated a significant impact of the ectomycorrhizal host poplar on the molecular composition of SOM in arable soils. Our results demonstrate that a change in land-use from agricultural cropping to woody biomass caused shifts in microbial community structure that were lagged by a shift in SOM chemistry. These shifts impact soil functioning and should be considered in future land management strategies when SRC are harvested.