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)32+ 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.
Unveiling the nature and the distribution of surface sites in heterogeneous catalysts, and for the Phillips catalyst (CrO3/SiO2) in particular, is still a grand challenge despite more than 60 years ...of research. Commonly used references in Cr K-edge XANES spectral analysis rely on bulk materials (Cr-foil, Cr2O3) or molecules (CrCl3) that significantly differ from actual surface sites. In this work, we built a library of Cr K-edge XANES spectra for a series of tailored molecular Cr complexes, varying in oxidation state, local coordination environment, and ligand strength. Quantitative analysis of the pre-edge region revealed the origin of the pre-edge shape and intensity distribution. In particular, the characteristic pre-edge splitting observed for Cr(III) and Cr(IV) molecular complexes is directly related to the electronic exchange interactions in the frontier orbitals (spin-up and -down transitions). The series of experimental references was extended by theoretical spectra for potential active site structures and used for training the Extra Trees machine learning algorithm. The most informative features of the spectra (descriptors) were selected for the prediction of Cr oxidation states, mean interatomic distances in the first coordination sphere, and type of ligands. This set of descriptors was applied to uncover the site distribution in the Phillips catalyst at three different stages of the process. The freshly calcined catalyst consists of mainly Cr(VI) sites. The CO-exposed catalyst contains mainly Cr(II) silicates with a minor fraction of Cr(III) sites. The Phillips catalyst exposed to ethylene contains mainly highly coordinated Cr(III) silicates along with unreduced Cr(VI) sites.
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•Different theoretical methods in the simulation of the XANES spectra are discussed.•An extended list of available codes for XANES spectra simulation is provided.•The potential of ...operando XANES in catalysis is described with relevant examples.•Chemometric methods in the treatment of operando XANES spectra is discussed.•Machine learning approaches are used to provide structural determination from XANES.
In the last decade the appearance of progressively more sophisticated codes, together with the increased computational capabilities, has made XANES a spectroscopic technique able to quantitatively confirm (or discard) a structural model, thus becoming a new fundamental diagnostic tool in catalysis, where the active species are often diluted metal centers supported on a matrix. After providing a brief historical introduction and the basic insights on the technique, in this review article, we provide a selection of four examples where operando XANES technique has been able to provide capital information on the structure of the active site in catalysts of industrial relevance: (i) Phillips catalyst for ethylene polymerization reaction; (ii) TS-1 catalyst for selective hydrogenation reactions; (iii) carbon supported Pd nanoparticles for hydrogenation reactions; (iv) Cu-CHA zeolite for NH3-assisted selective reduction of NOx and for partial oxidation of methane to methanol. The last example testifies how the multivariate curve resolution supported by the alternating least-squares algorithm applied to a high number of XANES spectra collected under operando conditions allows to quantitatively determine different species in mutual transformation. This approach is particularly powerful in the analysis of experiments where a large number of spectra has been collected, typical of time- or space-resolved experiments. Finally, machine learning approaches (both indirect and direct) have been applied to determine, from the XANES spectra, the structure of CO, CO2 and NO adsorbed on Ni2+ sites of activated CPO-27-Ni metal-organic framework.
Gold nanoparticles represent an important class of functional nanomaterials for optoelectronics, biomedical applications, and catalysis. Therefore, controllable synthesis of nanoparticles with ...specified size and shape is important. Though reduction of gold ions is quite a simple process and may be performed with many different protocols, the reproducibility of the results and transfer of protocols between independent research groups remains a challenging task. Machine learning analysis based on statistical approaches is hardly applicable to the published data, since most of the researchers report only successful syntheses. In this work, we apply uniform sampling of the reaction parameter space. The concentrations of gold precursor, reducing agent, and surfactant were varied via an improved Latin hypercube sampling, and each run was performed under in situ UV–vis control. Based on the resulting set of optical spectra, we address the relevant chemical questions about nanoparticle formation, their shape, and period of growth. Our work demonstrates a data driven approach applied to the space of reaction parameters in a limited available set of experiments.
Microscopic tissue analysis is the key diagnostic method needed for disease identification and choosing the best treatment regimen. According to the Global Cancer Observatory, approximately two ...million people are diagnosed with colorectal cancer each year, and an accurate diagnosis requires a significant amount of time and a highly qualified pathologist to decrease the high mortality rate. Recent development of artificial intelligence technologies and scanning microscopy introduced digital pathology into the field of cancer diagnosis by means of the whole-slide image (WSI). In this work, we applied deep learning methods to diagnose six types of colon mucosal lesions using convolutional neural networks (CNNs). As a result, an algorithm for the automatic segmentation of WSIs of colon biopsies was developed, implementing pre-trained, deep convolutional neural networks of the ResNet and EfficientNet architectures. We compared the classical method and one-cycle policy for CNN training and applied both multi-class and multi-label approaches to solve the classification problem. The multi-label approach was superior because some WSI patches may belong to several classes at once or to none of them. Using the standard one-vs-rest approach, we trained multiple binary classifiers. They achieved the receiver operator curve AUC in the range of 0.80–0.96. Other metrics were also calculated, such as accuracy, precision, sensitivity, specificity, negative predictive value, and F1-score. Obtained CNNs can support human pathologists in the diagnostic process and can be extended to other cancers after adding a sufficient amount of labeled data.
Ti-based molecules and materials are ubiquitous and play a major role in both homogeneous and heterogeneous catalytic processes. Understanding the electronic structures of their active sites ...(oxidation state, local symmetry, and ligand environment) is key to developing molecular-level structure-property relationships. In that context, X-ray absorption spectroscopy (XAS) offers a unique combination of elemental selectivity and sensitivity to local symmetry. Commonly, for early transition metals such as Ti, K-edge XAS is applied for in situ characterization and subsequent structural analysis with high sensitivity toward tetrahedral species. Ti L
-edge spectroscopy is in principle complementary and offers specific opportunities to interrogate the electronic structure of five-and six-coordinated species. It is, however, much more rarely implemented because the use of soft X-rays implies ultrahigh vacuum conditions. Furthermore, the interpretation of the data can be challenging. Here, we show how Ti L
-edge spectroscopy can help to obtain unique information about both homogeneous and heterogeneous epoxidation catalysts and develop a molecular-level relationship between spectroscopic signatures and electronic structures. Toward this goal, we first establish a spectral library of molecular Ti reference compounds, comprising various coordination environments with mono- and dimeric Ti species having O, N, and Cl ligands. We next implemented a computational methodology based on multiplet ligand field theory and maximally localized Wannier orbitals benchmarked on our library to understand Ti L
-edge spectroscopic signatures. We finally used this approach to track and predict the spectra of catalytically relevant intermediates, focusing on Ti-based olefin epoxidation catalysts.
We present an extension of an ab initio numerical tool calculating X-ray absorption spectroscopies and crystal orbital overlap populations at the same time. Density functional theory is used to ...calculate the electronic structure in both occupied (valence to core X-ray emission spectroscopy) and nonoccupied states (i.e., X-ray absorption near the edge structure and X-ray magnetic circular dichroism) and to evaluate the orbital overlap typifying the covalency between neighboring atoms. We show how the different features in the experimental spectra can be correlated to the chemical bonds around the absorbing atoms in several examples including acrylonitrile molecules, rutile TiO2, Li2RuO3 high-energy density cathode, ZnO, and anti-ferromagnetic V2O3.
Ti-based molecules and materials are ubiquitous and play a major role in both homogeneous and heterogeneous catalytic processes. Understanding the electronic structures of their active sites ...(oxidation state, local symmetry, and ligand environment) is key to developing molecular-level structure–property relationships. In that context, X-ray absorption spectroscopy (XAS) offers a unique combination of elemental selectivity and sensitivity to local symmetry. Commonly, for early transition metals such as Ti, K-edge XAS is applied for in situ characterization and subsequent structural analysis with high sensitivity toward tetrahedral species. Ti L2,3-edge spectroscopy is in principle complementary and offers specific opportunities to interrogate the electronic structure of five-and six-coordinated species. It is, however, much more rarely implemented because the use of soft X-rays implies ultrahigh vacuum conditions. Furthermore, the interpretation of the data can be challenging. Here, we show how Ti L2,3-edge spectroscopy can help to obtain unique information about both homogeneous and heterogeneous epoxidation catalysts and develop a molecular-level relationship between spectroscopic signatures and electronic structures. Toward this goal, we first establish a spectral library of molecular Ti reference compounds, comprising various coordination environments with mono- and dimeric Ti species having O, N, and Cl ligands. We next implemented a computational methodology based on multiplet ligand field theory and maximally localized Wannier orbitals benchmarked on our library to understand Ti L2,3-edge spectroscopic signatures. We finally used this approach to track and predict the spectra of catalytically relevant intermediates, focusing on Ti-based olefin epoxidation catalysts.
Element selectivity and possibilities for in situ and operando applications make X-ray absorption spectroscopy a powerful tool for structural characterization of catalysts. While determination of ...coordination numbers and interatomic distances from extended spectral region is rather straightforward, analysis of X-ray absorption near-edge structure (XANES) spectra remains a highly debated and topical problem. The latter region of spectra is shaped depending on the local 3D geometry and electronic structure. However, there is no straightforward procedure for the unambiguous extraction of these parameters. This work gives a critical vision on the amount of information that can be practically extracted from Pd
K
-edge XANES spectra measured under in situ and operando conditions, in which adsorption of reactive molecules at the surface of palladium with further formation of subsurface and bulk palladium carbides are expected. We investigate how particle size, concentration of carbon impurities, and their distribution in the bulk and at the surface of palladium particles affect Pd
K
-edge XANES features and to which extend they should be implemented in the theoretical model to adequately reproduce experimental data. Then, we show how the step-by-step increasing the complexity of the theoretical model improves the agreement with experiment. Finally, we suggest a set of formal descriptors relevant to possible structural diversity and construct a library of theoretical spectra for machine-learning-based analysis of the experimental data.
We present a new ab initio way to calculate X-ray Raman scattering spectra within the independent electron approximation. Our approach avoids any approximation about the shape of the used potential ...and leads to good agreement between experiment and theory. We show that the momentum transfer dependence in two typical cases, the F K-edge in LiF and the B and N K-edges in hexagonal BN, is well-reproduced. A more in-depth analysis of the electronic states and of the local atomic structure around the absorbing atoms is at hand.
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