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

Cathode Design Based on Nitrogen Redox and Linear Coordination of Cu Center for All-Solid-State Fluoride-Ion Batteries

All-solid-state fluoride-ion batteries (FIBs) have attracted extensive attention as candidates for next-generation energy storage devices; however, promising cathodes with high energy density are still lacking. In this study, Cu3N is investigated as a cathode material for all-solid-state fluoride-ion batteries, which offers enough anionic vacancies around the 2-fold coordinated Cu center for F- intercalation, thereby enabling a multielectron-transferred fluorination process. The contribution of both cationic and anionic redox to charge compensation, in particular, the generation of molecular nitrogen species in highly charged states, has been proved by several synchrotron-radiation-based spectroscopic technologies. As a result, Cu3N exhibits a high reversible capacity of ∼550 mAh g-1, exceeding many conventional fluoride-ion cathodes. It is believed that the new charge compensation chemistry as well as the unique intercalation behaviors of novel mixed-anion Cu-N/F local structures could bring new insights into energy storage materials.

NEXAFS Spectra Simulations of Nitrogen-Bearing Heterocycles

Five-membered heterocyclic compounds containing nitrogen atoms are important biomolecule building blocks. In addition to their fundamental biological importance, these molecular structures are used in several technological applications. Consequently, it is essential to develop techniques that allow the characterization of these fundamental systems. We address this issue by performing simulations of K-edge NEXAFS spectra by applying a time-dependent density functional theory (TDDFT) and an inner-shell multiconfigurational self-consistent field (IS-MCSCF) of selected molecules. Also, vibronic coupling simulations were considered for the TDDFT computations. Surprisingly, molecular orbital binding energies do not reproduce the order of the transition energies obtained by IS-MCSCF, indicating a possible breakdown of the orbital picture concerning the NEXAFS spectrum. In general, the TDDFT and IS-MCSCF results are compatible and are in close agreement with experimental data. Moreover, vibronic coupling and vertical transition results were very similar. Finally, it is important to mention that, to the best of our knowledge, this is the first time that the IS-MCSCF method has been applied to molecular systems of this size.

Driving Forces in the Formation of Paracetamol Cocrystals and Solvate with Naphthalene, Quinoline and Acridine

Paracetamol is an important analgesic and antipyretic drug showing poor tabletability. Among the various approaches used to improve this property, understanding the forces that govern the crystal packing is revealed to be crucial. We prepared three stable compounds: (par)2∙(nap) (1), (par)∙(quin) (2), and (par)∙(acr) (3) (nap-naphthalene, quin-quinoline, acr-acridine) being cocrystals or solvate. The structural studies showed that all the reported compounds are composed of alternately arranged layers of paracetamol and coformer. Several supramolecular motifs in the paracetamol layer were identified: R44(22) in (1); R64(20) and R22(8) in (2); and R22(8), R42(12), and R44(26) rings in (3). The stability of the crystal network was studied by interactions analysis performed by Hirshfeld surface and fingerprint approaches and the energy between the closest units in the crystal network was calculated. It showed that the strongest interactions were found between blocks connected by N-H⋯O=C and O-H⋯O/N hydrogen bonds due to an important coulombic factor. The dispersive energy becomes important for tail-to-tail (and head-to-tail) arranged paracetamol units, and it prevails in the case of stacking interactions between coformer molecules. The importance of dispersive forces increases with the size of the aromatic system of the coformer. XAS studies confirmed the successful preparation of compounds and provided some details about electron structure.

Acid-Dependent Charge Transport in a Solution-Processed 2D Conductive Metal-Organic Framework

The development of conductive metal-organic frameworks (MOFs) presents a unique challenge in materials chemistry because it is unclear how to dope them. Here, we demonstrate that the inclusion of pendant amines on hexahydroxytriphenylene linkages results in two-dimensional (2D) polycrystalline frameworks Cu3(HHTATP)2, isostructural to its Cu3(HHTP)2 parent, and exhibits the highest electrical conductivity of 1.21 S/cm among 2D MOFs featuring CuO4 metal nodes. Moreover, the bulk material can be treated with acid, resulting in a protonation-dependent increase in the conductivity. By spin-coating the acidic solution, we fabricated large-area thin films and collectively demonstrated an intuitive route to solution-processable, dopable, conductive MOFs.

Spectroscopic Evidence of Localized Small Polarons in Low-Dimensional Ionic Liquid Lead-Free Hybrid Perovskites

Rational design is an important approach to consider in the development of low-dimensional hybrid organic-inorganic perovskites (HOIPs). In this study, 1-butyl-1-methyl pyrrolidinium (BMP), 1-(3-aminopropyl)imidazole (API), and 1-butyl-3-methyl imidazolium (BMI) serve as prototypical ionic liquid components in bismuth-based HOIPs. Element-sensitive X-ray absorption spectroscopy measurements of BMPBiBr4 and APIBiBr5 reveal distinct resonant excitation profiles across the N K-edges, where contrasting peak shifts are observed. These 1D-HOIPs exhibit a large Stokes shift due to the small polaron contribution, as probed by photoluminescence spectroscopy at room temperature. Interestingly, the incorporation of a small fraction of tin (Sn) into the APIBiBr5 (Sn/Bi mole ratio of 1:3) structure demonstrates a strong spectral weight transfer accompanied by a fast decay lifetime (2.6 ns). These phenomena are the direct result of Sn-substitution in APIBiBr5, decreasing the small polaron effect. By changing the active ionic liquid, the electronic interactions and optical responses can be moderately tuned by alteration of their intermolecular interaction between the semiconducting inorganic layers and organic moieties.

X-ray induced luminescence spectroscopy for DNA damaging intermediates aided by a monochromatic synchrotron radiation

PURPOSE

To identify the bonding sites of initial radiation interaction with DNA and to trace the following chemical reaction sequences on the pathway of damage induction, we carry out a spectroscopy XIL (X-ray induced luminescence) using soft X-ray synchrotron radiation. This is a nondestructive analysis of the excited intermediate species produced in a molecular mechanism on the damage induction pathway.

MATERIALS AND METHODS

We introduce aqueous samples of UMP (uridine-5'-monophosphate) in the vacuum by the use of a liquid micro-jet technique. The luminescence in the region of UV-VIS (from visible to ultraviolet) radiation induced after the absorption of monochromatic soft X-ray by aqueous UMP is measured with sweeping the soft X-ray energy in the region of 370-560 eV.

RESULTS

The enhanced XIL intensities for aqueous UMP in the region of soft X-ray of 410-530 eV (in "water window" region) are obtained. The enhancement of XIL intensities in the UV-VIS region, relative to the water control, is explained by the excitation and ionization of a K-shell electron of nitrogen atoms in the uracil moiety. The enhanced XIL intensities do not match the structure of XANES (X-ray absorption near-edge structure) of the aqueous UMP. This suggests that the XIL intensities reflect the quantum yields of luminescence, or the quantum yields for conversion by UMP of an absorbed X-ray into UV-VIS radiation. In this paper, spectra of luminescence are shown to be resolved by combining low pass filters. The filtered luminescence spectra are obtained at the center of gravity (λc) of the band pass wavelength regions at λc = 270nm, 295 nm, 340 nm, 385 nm, 450 nm, and 525 nm., which show a trend similar to the fluorescence of nucleobases induced by ultraviolet radiation.

CONCLUSION

It is concluded that the origin of the observed XIL is the hydrated uracil moiety in aqueous UMP, decomposition of which is suppressed by the migration of excess charge and internal energy after the double ionization due to Auger decay.

Electronic properties of DNA-related molecules containing a bromine atom

PURPOSE

To clarify the radiosensitization mechanism masking the Auger effect of the cells possessing brominated DNA, the electronic properties of DNA-related molecules containing Br were investigated by X-ray spectroscopy and specific heat measurement.

MATERIALS AND METHODS

X-ray absorption near-edge structure (XANES) and X-ray photoemission spectroscopy (XPS) were used to measure the electronic properties of the nucleotides with and without Br. We determined the specific heat of 5-bromouracil crystals with thymine as a reference molecule at low temperatures of 3-48 K to calculate the microscopic state numbers.

RESULTS

Obtained XANES and XPS spectra indicated that both the lowest unoccupied molecular orbital (LUMO) and the core-levels were not affected by the Br incorporation. The state numbers of 5-bromouracil calculated from the specific heats obtained around 25 K was about 1.5 times larger than that for thymine below 20 K, although the numbers were almost the same below 5 K.

DISCUSSION

Our results suggest that the Br atom may not contribute substantially to the LUMO and core-level electronic states of the molecule, but rather to the microscopic states related to the excitation of lattice vibrations, which may be involved in valence electronic states.

Priority Occupation of C-Sites by N-Confining P-Implantation in Pyrrodic N-Sites in NCNT@P,N-Mo2C for Highly Efficient Electrocatalytic Hydrogen Evolution

Optimizing the electronic configuration of Mo₂C by activating heteroatom(s)-neighboring carbon atoms to enhance the activity of hydrogen evolution reaction (HER) has been demonstrated. However, the development of heteroatom-doped Mo₂C to fabricate a water electrolyzer is still a challenge because of the limitation of a well-defined electronic structure of hybridization of Mo with heteroatom(s). Here, nitrogen (N) and phosphor (P) codoped Mo₂C embedded carbon nanotubes (NCNT@P,N-Mo₂C) with the priority occupation of C-sites by N, which well confines the P-implantation at the pyrrodic N-sites and brings out N-O bonding on the surface, which favorably modifies the electronic configuration of adjacent Mo, resulting in highly efficient pH-tolerant HER activity. This study not only presents a potential HER electrocatalyst candidate but also provides a strategy for the construction of a well-defined electronic structure of heteroatom(s)-neighboring carbon-based materials.

Capturing fingerprints of conical intersection: Complementary information of non-adiabatic dynamics from linear x-ray probes

Many recent experimental ultrafast spectroscopy studies have hinted at non-adiabatic dynamics indicating the existence of conical intersections, but their direct observation remains a challenge. The rapid change of the energy gap between the electronic states complicated their observation by requiring bandwidths of several electron volts. In this manuscript, we propose to use the combined information of different x-ray pump-probe techniques to identify the conical intersection. We theoretically study the conical intersection in pyrrole using transient x-ray absorption, time-resolved x-ray spontaneous emission, and linear off-resonant Raman spectroscopy to gather evidence of the curve crossing.

Tracking the interaction of drug molecules with individual mesoporous amorphous calcium phosphate/ATP nanocomposites - an X-ray spectromicroscopy study

Adenosine triphosphate (ATP) biomolecules play critial roles in the biomineralization process during the formation of amorphous calcium phosphate composites (ACPC), and ACPC is an important drug carrier due to its significant advantages of biocompatibility and biodegradability. Hence, studying the behavior of ACPC nanodrug carriers is crucial to investigate the structural regulation of biomimetic minerals and calcium phosphate (CaP)-based drug delivery systems. However, it is difficult to probe these interactions using traditional characterization methods. In this paper, XANES analysis together with STXM successfully provided a method to reveal the interaction of ATP and drug molecules with individual mesoporous ACPC. We found that the adenosine and phosphate groups of ATP biomolecules coordinated with Ca²⁺ and played critical roles in the formation of ACPC; drug molecules with the -COOH groups were linked to Ca²⁺via carboxylic acid groups primarily by electrostatic interactions, and the N-containing ring structures within the drug molecules also coordinated with Ca²⁺.

Hydration of Nucleobase as Probed by Electron Emission of Uridine-5′-Mono-Phosphate (UMP) in Aqueous Solution Induced by Nitrogen K-Shell Ionization

To identify the precise early radiation processes of DNA lesions, we measure electron kinetic energy spectra emitted from uridine-5′ monophosphate (UMP) in aqueous solution for the photoionization of the N 1s orbital electron and for the following Auger effect using a monochromatic soft X-ray synchrotron radiation at energies above the nitrogen K-shell ionization threshold. The change of photoelectron spectra for UMP in aqueous solutions at different proton concentrations (pH = 7.5 and 11.3) is ascribed to the chemical shift of the N3 nitrogen atom in uracil moiety of canonical and deprotonated forms. The lowest double ionization potentials for aqueous UMP at different pH obtained from the Auger electron spectra following the N 1s photoionization values show the electrostatic aqueous interaction of uracil moiety of canonical (neutral) and deprotonated (negatively charged) forms with hydrated water molecules.

NOVEL ANALYTICAL STUDY FOR REACTION INTERMEDIATES IN THE PRIMARY RADIATION INTERACTION OF DNA USING A SYNCHROTRON RADIATION-INDUCED LUMINESCENCE SPECTROSCOPY

To identify the precise molecular processes to induce DNA lesions, we attempt a novel spectroscopy of X-ray induced luminescence (XIL) using soft X-ray synchrotron radiation, which is a non-destructive analysis of the reaction intermediates in the elementary reaction pathway of damage induction and self-organized restoration. Using a liquid micro-jet technique to introduce aqueous samples in a vacuum chamber, we measure UV-visible luminescence from nucleotide solution as a function of the soft X-ray energy from the nitrogen to oxygen K-edge region. The XIL intensities for the nucleotide solutions are significantly enhanced in the soft X-ray region (410-530 eV) which is ascribed to the K-shell excitation/ionization of nitrogen atoms in the nucleobases. Furthermore, the XIL spectra do not show any signature of X-ray absorption near-edge structure (XANES) of the nucleobases. This is because the luminescence intensities collected from the integral area of the micro-jet only reflect the quantum yield of luminescence of the absorbed X-ray into UV-visible light irrespective of the absorption cross sections, i.e. of XANES. Thus the present result is the first evidence of luminescence as a result of X-ray absorption of aqueous nucleotides.

Chemical Modification of Graphene Oxide by Nitrogenation: An X-ray Absorption and Emission Spectroscopy Study

Nitrogen-doped graphene oxides (GO:N_x) were synthesized by a partial reduction of graphene oxide (GO) using urea [CO(NH₂)₂]. Their electronic/bonding structures were investigated using X-ray absorption near-edge structure (XANES), valence-band photoemission spectroscopy (VB-PES), X-ray emission spectroscopy (XES) and resonant inelastic X-ray scattering (RIXS). During GO:N_x synthesis, different nitrogen-bonding species, such as pyrrolic/graphitic-nitrogen, were formed by replacing of oxygen-containing functional groups. At lower N-content (2.7 at%), pyrrolic-N, owing to surface and subsurface diffusion of C, N and NH is deduced from various X-ray spectroscopies. In contrast, at higher N-content (5.0 at%) graphitic nitrogen was formed in which each N-atom trigonally bonds to three distinct sp²-hybridized carbons with substitution of the N-atoms for C atoms in the graphite layer. Upon nitrogen substitution, the total density of state close to Fermi level is increased to raise the valence-band maximum, as revealed by VB-PES spectra, indicating an electron donation from nitrogen, molecular bonding C/N/O coordination or/and lattice structure reorganization in GO:N_x. The well-ordered chemical environments induced by nitrogen dopant are revealed by XANES and RIXS measurements.

Nitrogen K-edge x-ray absorption near edge structure of pyrimidine-containing nucleotides in aqueous solution

X-ray absorption near edge structure (XANES) was measured at energies around the N K-edge of the pyrimidine-containing nucleotides, cytidine 5'-monophosphate (CMP), 2'-deoxythymidine 5'-monophosphate (dTMP), and uridine 5'-monophosphate (UMP), in aqueous solutions and in dried films under various pH conditions. The features of resonant excitations below the N K-edge in the XANES spectra for CMP, dTMP, and UMP changed depending on the pH of the solutions. The spectral change thus observed is systematically explained by the chemical shift of the core-levels of N atoms in the nucleobase moieties caused by structural changes due to protonation or deprotonation at different proton concentrations. This interpretation is supported by the results of theoretical calculations using density functional theory for the corresponding nucleobases in the neutral and protonated or deprotonated forms.