Mikhail A. Soldatov

Optimized Finite Difference Method for the Full-Potential XANES Simulations: Application to Molecular Adsorption Geometries in MOFs and Metal–Ligand Intersystem Crossing Transients

Accurate modeling of the X-ray absorption near-edge spectra (XANES) is required to unravel the local structure of metal sites in complex systems and their structural changes upon chemical or light stimuli. Two relevant examples are reported here concerning the following: (i) the effect of molecular adsorption on 3d metals hosted inside metal-organic frameworks and (ii) light induced dynamics of spin crossover in metal-organic complexes. In both cases, the amount of structural models for simulation can reach a hundred, depending on the number of structural parameters. Thus, the choice of an accurate but computationally demanding finite difference method for the ab initio X-ray absorption simulations severely restricts the range of molecular systems that can be analyzed by personal computers. Employing the FDMNES code [Phys. Rev. B, 2001, 63, 125120] we show that this problem can be handled if a proper diagonalization scheme is applied. Due to the use of dedicated solvers for sparse matrices, the calculation time was reduced by more than 1 order of magnitude compared to the standard Gaussian method, while the amount of required RAM was halved. Ni K-edge XANES simulations performed by the accelerated version of the code allowed analyzing the coordination geometry of CO and NO on the Ni active sites in CPO-27-Ni MOF. The Ni-CO configuration was found to be linear, while Ni-NO was bent by almost 90°. Modeling of the Fe K-edge XANES of photoexcited aqueous [Fe(bpy)3](2+) with a 100 ps delay we identified the Fe-N distance elongation and bipyridine rotation upon transition from the initial low-spin to the final high-spin state. Subsequently, the X-ray absorption spectrum for the intermediate triplet state with expected 100 fs lifetime was theoretically predicted.

On the Origin of the Hydrogen‐Bond‐Network Nature of Water: X‐Ray Absorption and Emission Spectra of Water–Acetonitrile Mixtures

A liquid microjet was used to obtain oxygen K-edge X-ray absorption and emission spectra of water–acetonitrile mixtures of various compositions. The observed spectral changes are unambiguously related to the increasing number of broken hydrogen bonds with decreasing water concentration, and the hydrogen-bond network of liquid water can thus be addressed on purely experimental grounds without the need for theoretical modeling.

Origin of dark-channel X-ray fluorescence from transition-metal ions in water.

The nonradiative dark channels in the L-edge fluorescence spectra from transition-metal aqueous solution identify the ultrafast charge-transfer processes playing an important role in many biological and chemical systems. Yet, the exact origin of such spectral dips with respect to the X-ray transmission spectrum has remained unclear. In the present study we explore the nature of the underlying decay mechanism of 2p core-excited Co(2+) in water by probing the nonradiative Auger-type electron emission channel using photoelectron spectroscopy from a liquid microjet. Our measurements demonstrate unequivocally that metal-to-water charge transfer quenches fluorescence and will inevitably lead to a dip in the total-fluorescence-yield X-ray absorption spectrum. This is directly revealed from the resonant enhancement of valence signal intensity arising from the interference of two identical final states created by a direct and Auger-electron emission, respectively.

DMSO-Water Clustering in Solution Observed in Soft X-ray Spectra.

The significant deviation from the ideality of dimethyl sulfoxide (DMSO)/water mixtures can be addressed based on the change of the local molecular orbitals of each solvent upon mixing. Oxygen K-edge absorption and emission spectra of DMSO/water solutions were measured using the liquid microjet technique. The spectra demonstrate that the hydrogen bond network in liquid water is already influenced at small DMSO concentrations, and at the molar fraction xDMSO = 0.43 we find strong evidence of DMSO-water clustering reflected by the influence on the occupied molecular orbitals.

The Chemical Bond in Carbonyl and Sulfinyl Groups Studied by Soft X-ray Spectroscopy and ab Initio Calculations

The polar character of the sulfinyl bond, which determines many of the properties of dimethyl sulfoxide (DMSO), is a result of charge transfer in low-lying π-type orbitals. This characteristic—toge ...

Local electronic structure of aqueous zinc acetate: oxygen K-edge X-ray absorption and emission spectroscopy on micro-jets

Oxygen K-edge X-ray absorption, emission, and resonant inelastic X-ray scattering spectra were measured to site selectively gain insights into the electronic structure of aqueous zinc acetate solution. The character of the acetate ion and the influence of zinc and water on its local electronic structure are discussed.

Atomic and electronic structure of CdS-based quantum dots

The ab initio computer design of the CdS-based quantum dots and the cobalt doped CdS quantum dots is carried out. The characteristics features of the atomic and electronic structures of semiconductor colloidal quantum dots on CdS of different sizes are studied, and the effect of cobalt impurity atoms is estimated. We have proved the sensitivity of the X-ray absorption near-edge structure (XANES) method for the verification of the nanosized atomic structural parameters calculated by the methods of computer modeling for small-scale quantum dots of the CdS family, and for the determination of the local environment parameters of the cobalt atom in the quantum dot.

Electronic structure of ilmenite: X-ray absorption and DFT study

The experimental Ti K-edge X-ray absorption near edge structure (XANES) spectrum of the mineral ilmenite was recorded. The theoretical Ti K-XANES spectra of ilmenite were simulated using both the self-consistent real-space full-multiple scattering theory within the muffin-tin approximation for the potential shape and the full-potential finite difference method. The comparison of the theoretical spectra with the experimental XANES is discussed. The electronic structure of ilmenite was investigated by analyzing the distribution of the partial densities of electron states.

Potential antitumor gold drugs: DFT and XANES studies of local atomic and electronic structure

Geometry structure optimization of the potential antitumor agent Au(bipy)(OH)2 was carried out by means of density functional theory simulations. The experimental Au L3-edge X-ray absorption near edge structure (XANES) spectrum of Au(bipy)(OH)2 was obtained. The theoretical Au L3-XANES spectra of the gold(III) complex Au(bipy)(OH)2 were simulated using both the self-consistent real-space full multiple scattering theory within the muffin-tin approximation for the potential shape and the full-potential finite difference method. The comparison of the theoretical spectra with the experimental XANES is discussed. The exact local atomic structure of gold complex Au(bipy)(OH)2 has been defined by two independent ab initio methods.

X-ray spectroscopy study of the Cu(II)GHK peptide complex

The Cu(II)–Gly–His–Lys (Glycyl–Histidyl–Lysine) complex is of interest as a model peptide to test the methodology for studying the structure of metal sites in proteins, in particular, the copper binding site in amyloid-β. X-ray absorption spectra of the Cu(II)GHK aqueous solution are measured. The stability of the complex under X-ray radiation is controlled by optical spectroscopy. The structural models with different copper site coordination constructed based on the crystallographic structure are considered. Two optimal models are selected from the analysis of the theoretical X-ray absorption spectra of the constructed structures. The structural parameters of the selected models are optimized. It is found that the spectrum of the five-coordinated model with water molecules in the equatorial and axial positions “down” (with Cu–O distances of 1.97 Å and 2.31 Å respectively) has the best agreement with the experiment.