Simulated X-ray Absorption Spectra Research Articles

Following the Nonadiabatic Ultrafast Dynamics of Uracil via Simulated X-ray Absorption Spectra.

The nucleobase uracil exhibits high photostability due to ultrafast relaxation processes mediated by conical intersections (CoIns), where the interplay between nuclear and electron dynamics becomes crucial. In our previous study, we observed seemingly long-lived traces of electronic coherence for the relaxation process through the S2/S1 CoIn by applying our ansatz for coupled nuclear and electron dynamics in molecules (NEMol). In this work, we theoretically investigate how time-dependent transient X-ray absorption spectroscopy can be used to observe this ultrafast dynamics. Therefore, we calculated X-ray absorption spectra (XAS) for the oxygen K-edge, using a multireference protocol in combination with NEMol dynamics. Thus, we have access to both the transient XAS based on the nuclear wavepacket dynamics and the modulation of the signals caused by the electronic coherence induced by the excitation process and the presence of a CoIn seam. In both cases, we were able to qualitatively predict its influence on the resulting XAS.

Operando XANES from first-principles and its application to iridium oxide.

Efficient electro-catalytic water-splitting technologies require suitable catalysts for the oxygen evolution reaction (OER). The development of novel catalysts could benefit from the achievement of a complete understanding of the reaction mechanism on iridium oxide (IrO2), an active catalyst material that is, however, too scarce for large-scale applications. Considerable insight has already been provided by operando X-ray absorption near-edge structure (XANES) experiments, which paved the way towards an atomistic description of the catalyst's evolution in a working environment. We combine here first-principles simulations augmented with a continuum description of the solvent and electrolyte to investigate the electrochemical stability of various IrO2 interfaces and to predict the XANES cross-section for selected terminations under realistic conditions of applied potential. The comparison of computed O K-edge XANES spectra to corresponding experiments supports the formation of electron-deficient surface oxygen species in the OER-relevant voltage regime. Furthermore, surface hydroxyl groups that are found to be stable up to ∼1 V are suggested to be progressively oxidized at larger potentials, giving rise to a shift in the Ir L3-edge cross-section that qualitatively agrees with measurements.

Electronic Structure of Aqueous [Co(bpy)3]2+/3+ Electron Mediators.

We report on the electronic structure of cobalt(II) tris-2,2'-bipyridine and cobalt(III) tris-2,2'-bipyridine in aqueous solution using resonant inelastic X-ray scattering (RIXS) spectroscopy at the Co L-edge and N K-edge resonances. Partial fluorescence yield X-ray absorption spectra at both edges were obtained by signal integration of the respective RIXS spectra. Experiments are complemented by calculations of the X-ray absorption spectra for high- and low-spin configurations using density functional theory/restricted open-shell configuration interaction singles and time-dependent density functional theory methods. We find that linear combinations of the simulated X-ray absorption spectra for different spin states reproduce the experimental spectra. Best agreement is obtained for measurements at the Co L-edge, for both samples. For cobalt(II) tris-2,2'-bipyridine, our combined experimental and computational study reveals ∼40% low-spin and ∼60% high-spin state components. Much stronger low-spin character is found for cobalt(III) tris-2,2'-bipyridine, ∼80% low spin and ∼20% high spin. Prominent energy-loss features in the Co RIXS spectra are indicative of d-d excitations and charge-transfer excitations due to strong mixing between metal and ligand orbitals in both complexes. Analysis of N 1s RIXS data reveals the emission from metal dominated orbitals in the valence region, supporting the strong metal-ligand mixing.

Simulating X-ray Absorption Spectra with Linear-Response Density Cumulant Theory.

We present a new approach for simulating X-ray absorption spectra based on linear-response density cumulant theory (LR-DCT) [ Copan , A. V. ; Sokolov , A. Yu. J. Chem. Theory Comput. 2018 , 14 , 4097 - 4108 ]. Our new method combines the LR-ODC-12 formulation of LR-DCT with core-valence separation approximation (CVS) that allows us to efficiently access high-energy core-excited states. We describe our computer implementation of the CVS-approximated LR-ODC-12 method (CVS-ODC-12) and benchmark its performance by comparing simulated X-ray absorption spectra to those obtained from experiment for several small molecules. Our results demonstrate that the CVS-ODC-12 method shows good agreement with experiment for relative spacings between transitions and their intensities, but the excitation energies are systematically overestimated. When compared to results from excited-state coupled cluster methods with single and double excitations, the CVS-ODC-12 method shows a similar performance for intensities and peak separations, while coupled cluster spectra are less shifted, relative to experiment. An important advantage of CVS-ODC-12 is that its excitation energies are computed by diagonalizing a Hermitian matrix, which enables efficient computation of transition intensities.

Structural studies of spray pyrolysis synthesized oxygen deficient anatase TiO2 thin films by using X-ray absorption spectroscopy.

The present work focuses on synthesis and X-ray absorption studies of single phase oxygen deficient anatase TiO2 thin films. These films are prepared in a two-step method viz. the synthesis of near stoichiometric anatase TiO2 films using an open atmospheric spray pyrolysis method followed by vacuum annealing at their corresponding synthesis temperatures (Ts = 450 °C, 500 °C) for different time durations (t = 2, 4, 6, 8 hours). XRD and Raman studies of these films ascertained the formation and retention of the anatase phase post annealing, indicating that there was no phase change due to prolonged annealing. Extended X-ray absorption spectra (EXAFS) and X-ray absorption near edge spectra (XANES) revealed the presence of an oxygen vacancy and its effect on the local co-ordination. The co-ordination number obtained from EXAFS analysis revealed that the number density of the oxygen vacancy is higher in the case of thin films synthesized at 450 °C than in the case of the films synthesized at 500 °C. As the oxygen vacancy leads to changes in local co-ordination, which in turn have a profound effect on the pre-edge features of the X-ray absorption spectra (XAS), theoretically simulated XAS spectra of pure anatase TiO2 and oxygen deficient anatase TiO2 were generated using FEFF and were found to match with the experimentally observed spectra. In addition, the ambiguities in whether a change in the metal-oxygen bond length has any effect on the pre-edge features or not were delineated in the present study by comparing the pre-edge peak positions of the oxygen deficient TiO2 films. Our results matched with those of some of the researchers who have studied the rutile phase TiO2, wherein it was concluded that in the case of the titanium-oxygen system, the mean Ti-O bond length does have an effect on the pre-edge peak position. It was observed that as the Ti-O mean bond length increases, the pre-edge peak positions shift towards lower energy, which is in concurrence with the literature available for other Ti-O systems with similar geometry. The second pre-edge peak intensity, which is a measure of disorder, is higher for TiO2450 °C-2 h and TiO2500 °C-2 h thin films. This is attributed to the annealing effect, which suggests that TiO6 octahedrons are the most disordered for thin films annealed for 2 h and become more ordered upon annealing for longer times.

Impact of finite-temperature and condensed-phase effects on theoretical X-ray absorption spectra of transition metal complexes.

The impact of condensed-phase and finite-temperature effects on the theoretical X-ray absorption spectra of transition metal complexes is assessed. The former are included in terms of the all-electron Gaussian and augmented plane-wave approach, whereas the latter are taken into account by extensive ensemble averaging along second-generation Car-Parrinello ab initio molecular dynamics trajectories. We find that employing the periodic boundary conditions and including finite-temperature effects systematically improves the agreement between our simulated X-ray absorption spectra and experimental measurements. © 2018 Wiley Periodicals, Inc.

Oxygen-stabilized triangular defects in hexagonal boron nitride

Recently several experimental transmission electron microscopy (TEM) studies have reported the observation of nanoscale triangular defects in mono- and multilayer hexagonal boron nitride (h-BN). First-principles calculations are employed to study the thermodynamical stability and spectroscopic properties of these triangular defects and the chemical nature of their edge termination. Oxygen-terminated defects are found to be significantly more stable than defects with nitrogen-terminated edges. Simulated x-ray absorption spectra of the boron K edge for oxygen-terminated defects show excellent agreement with experimental x-ray absorption near-edge spectroscopy (XANES) measurements on defective h-BN films with oxygen impurities. Finally, we show that the structural model for oxygen defects in h-BN as deduced from the simulated core-level spectroscopy is intrinsically linked to the equilateral triangle shape of defects as observed in many recent electron microscopy measurements.

The solvation structure of Mg ions in dichloro complex solutions from first-principles molecular dynamics and simulated X-ray absorption spectra.

The knowledge of Mg solvation structure in the electrolyte is requisite to understand the transport behavior of Mg ions and their dissolution/deposition mechanism at electrolyte/electrode interfaces. In the first established rechargeable Mg-ion battery system [D. Aurbach et al. Nature 2000, 407, 724], the electrolyte is of the dichloro complex (DCC) solution family, Mg(AlCl2BuEt)2/THF, resulting from the reaction of Bu2Mg and EtAlCl2 with a molar ratio of 1:2. There is disagreement in the literature regarding the exact solvation structure of Mg ions in such solutions, i.e., whether Mg(2+) is tetra- or hexacoordinated by a combination of Cl(-) and THF. In this work, theoretical insight into the solvation complexes present is provided based on first-principles molecular dynamics simulations (FPMD). Both Mg monomer and dimer structures are considered in both neutral and positively charged states. We found that, at room temperature, the Mg(2+) ion tends to be tetracoordinated in the THF solution phase instead of hexacoordinated, which is the predominant solid-phase coordination. Simulating the X-ray absorption spectra (XAS) at the Mg K-edge by sampling our FPMD trajectories, our predicted solvation structure can be readily compared with experimental measurements. It is found that when changing from tetra- to hexacoordination, the onset of X-ray absorption should exhibit at least a 1 eV blue shift. We propose that this energy shift can be used to monitor changes in the Mg solvation sphere as it migrates through the electrolyte to electrolyte/electrode interfaces and to elucidate the mechanism of Mg dissolution/deposition.

Atomic and electronic structure of free niobium nanoclusters: Simulation of the M4,5-XANES spectrum of Nb13+

The atomic and electronic structure of free niobium nanoclusters has been studied on the basis of X-ray absorption near-edge structure (XANES) spectroscopy and density functional theory. M4,5-XANES spectra have been calculated for several structural models of the 13-atomic niobium cluster. The calculations have been done on the basis of both full multiple scattering theory within the muffin-tin approximation for a potential and full-potential finite difference method. The comparison of the experimental M4,5-edge XANES spectrum (Peredkov et al., J. Electron Spectros. Relat. Phenomena 184 (2011) 113–118) with the simulated X-ray absorption spectra of Nb13+ hints to a highly-symmetric icosahedral structure of the cluster. An internuclear distance of 2.2±0.1Å between neighboring “surface” atoms of the icosahedron and 2.09Å between the central “bulk” atom and “surface” atoms, respectively, has been found upon comparison of the experimental and theoretical XANES spectra.

Electronic structure of the austenitic and martensitic state of magnetocaloric Ni-Mn-In Heusler alloy films

Changes of the electronic and magnetic structure near the martensitic phase transition of Ni-Mn-In Heusler alloys doped with Co are investigated by experiment and theory. The nonstoichiometric Ni${}_{48}$Co${}_{5}$Mn${}_{35}$In${}_{12}$ epitaxial film undergoes a transition from a weakly magnetic martensitic phase below ${T}_{m}=350$ K to a ferromagnetic austenitic phase above ${T}_{m}$. Element-specific magnetic moments and the unoccupied density of states function is investigated using x-ray magnetic circular dichroism. We find an antiparallel alignment of Mn and Ni/Co magnetic moments in both phases. The electronic structure is calculated using the SPR-KKR Green's function approach considering experimental results on the atomic disorder in the sample. The good agreement of experimental and theoretically simulated x-ray absorption spectra in both phases confirms that a band Jahn-Teller like lifting of a degenerate $d$ state is the origin of the energetic preference of the martensitic phase at low temperatures.

EXAFS studies of nanostructured Finemet-type alloys

The nanostructure of nanocrystalline Fe66Cr8Cu1Nb3Si13B9 alloys has been studied using extended X-ray absorption fine structure (EXAFS) and analyzed by the cumulant method. Application of the cumulant method enables us to determine the nearest-neighbor interatomic distance and the coordination number for chromium and copper atoms, and thus we are able to obtain detailed knowledge about the role of both Cr and Cu in the structure of nanocrystals at various stages of crystallization. A detailed analysis of the distribution of alloying elements in the grains and grain boundaries reveals the accumulation of Cr in the surrounding of Fe(Si) nanocrystals. The presence of Cr in the surroundings of Fe(Si) can influence the content's arrangement of the nanograins, allowing diffusion of Si atoms in the grain boundaries. Simulated X-ray absorption spectra of the model produced by FEFF9.05 and the proposed Cu clustering of 19 atoms with average cluster size of about 0.4 nm show a good resemblance to the experimental data of the Cu k-edge.

Early precipitation stages of aluminum alloys—The role of quenched-in vacancies

We present preliminary results on the structure of nano-sized particles (clusters of solute atoms or Guinier-Preston-Bagaryatsky (GPB) zones) in aluminum alloys. Hindering the motion of dislocations, these GPB zones (precipitates) are responsible for the strength of AlCuMg-alloys – used e.g. as AA2024 – for the outer shell plates in aircraft industry. We will discuss the role of quenched-in vacancies for the formation and growth of the precipitates. Using positron annihilation (Doppler broadening together with the recently developed tool of high-momentum analysis (HMA)) and X-ray absorption spectroscopy measurements, we are able to characterize the local atomic environment in the vicinity of vacancies and selected elements (Cu) forming the precipitates. The interpretation will be based on a comparison to numerical calculations of positron lifetimes and momentum distributions as well as simulated X-ray absorption spectra. Often reliable numerical calculations of experimental quantities are possible only if relaxed atomic positions – calculated employing an ab-initio code like SIESTA – are used as input.

X-ray absorption spectroscopy, simulation and modeling of Si-DLC films

Amorphous silicon-containing diamond-like carbon (Si-DLC) films were deposited on silicon wafers by Ar+ Ion Beam Assisted Deposition (IBAD) at various energy conditions. The films were examined with X-ray Absorption Near Edge Structure (XANES) spectroscopy and Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy. The Si K-edge X-ray Absorption Spectroscopy (XAS) results indicate that Si-DLC films have an amorphous structure, where each Si atom is coordinated to four carbon atoms or CHn groups. This short-range order, where a Si atom is surrounded by four C atoms, was found in all Si-DLC films. The XANES spectra do not indicate Si coordination to oxygen atoms or phenyl rings, which are present in the precursor material. A structural model of Si-DLC is proposed based on XAS findings. Simulated X-ray absorption spectra of the model produced by FEFF8 show a good resemblance to the experimental data.