THORONDOR: a software for fast treatment and analysis of low-energy XAS data.

THORONDOR is a data treatment software with a graphical user interface (GUI) accessible via the browser-based Jupyter notebook framework. It aims to provide an interactive and user-friendly tool for the analysis of NEXAFS spectra collected during in situ experiments. The program allows on-the-fly representation and quick correction of large datasets from single or multiple experiments. In particular, it provides the possibility to align in energy several spectral profiles on the basis of user-defined references. Various techniques to calculate background subtraction and signal normalization have been made available. In this context, an innovation of this GUI involves the usage of a slider-based approach that provides the ability to instantly manipulate and visualize processed data for the user. Finally, the program is characterized by an advanced fitting toolbox based on the lmfit package. It offers a large selection of fitting routines as well as different peak distributions and empirical ionization potential step edges, which can be used for the fit of the NEXAFS rising-edge peaks. Statistical parameters describing the goodness of a fit such as χ2 or the R-factor together with the parameter uncertainty distributions and the related correlations can be extracted for each chosen model.

Titanium Defective Sites in TS-1: Structural Insights by Combining Spectroscopy and Simulation.

Ti silicates, and in particular, titanium silicalite-1 (TS-1), are nowadays important catalysts for several partial oxidation reactions in the presence of aqueous H2 O2 as an oxidant. Despite the numerous studies dealing with this material, some fundamental aspects are still unclear. In particular, the structure and the catalytic role of defective Ti sites, other than perfect tetrahedral sites recognized as the main active species, has not been quantitatively discussed in the literature. We assess the structural features of defective Ti sites on the basis of outcomes of electronic spectroscopies, as interpreted through quantum mechanical simulation. Strong evidence is disclosed to support the fact that the most common defective Ti sites, often reported in the TS-1 literature, are monomeric Ti centers that are embedded in the zeolite framework, and which have a distorted octahedral local symmetry.

On the structure of superbasic (MgO)n sites solvated in a faujasite zeolite.

We report the synthesis and characterisation of a HY/MgO zeolite/oxide nanocomposite material with high crystallinity and highly dispersed, highly basic MgO sites. Preparation was optimized in order to preserve sample crystallinity, to avoid the formation of mesoporosity and to minimize the formation of separate Mg-containing phases. These features were checked by means of electron microscopy, X-ray powder diffraction, porosimetry and IR spectroscopy. A highly dispersed material was obtained, comprising nanoclusters of magnesium oxide and hydroxide hosted by the microporous zeolite framework. The location and structure of the Mg-containing clusters have been studied by means of a combination of Rietveld refinement of XRPD data and high quality quantum mechanical simulations. The refinement has shown the presence of magnesium and oxygen atoms in the double six-membered ring cages, consistent with the presence of mononuclear Mg moieties. However, the composition and IR spectroscopy demonstrate that other Mg species must exist, likely located in the zeolite pores. In order to propose candidate structures for these species, several hypothetic periodic models of the material were built by placing (MgO)n clusters in different locations of the zeolite structure, taking into account the material composition and other constraints imposed by the experimental observations. Periodic structures with P1 symmetry were optimized at the B3LYP-D*/DZVP level with the CRYSTAL code and classified according to their stability. Two families of possible sites were identified: highly solvated (MgO)n units in narrow cavities and less coordinated clusters in the supercages. The stability of these clusters appears to be regulated by the ability of Mg2+ and O2- ions to interact with the pore walls and by the formation of Mg-OH species as result of the reaction of Mg-O couples with remaining acidic protons. The reactivity of four representative models with CO2 has been simulated at the B3LYP-D*/TZVP level. CO2 forms very stable linear end-on adducts with low coordinated Mg ions in most cases. Isolated sites give rise to bridge bidentate complexes in agreement with previous spectroscopic observations. The formation of hydrogen-carbonates is observed only on specific sites, through a process having a low adsorption energy because of the high deformation of the adsorption site.

Effect of Molecular Guest Binding on the d-d Transitions of Ni2+ of CPO-27-Ni: A Combined UV-Vis, Resonant-Valence-to-Core X-ray Emission Spectroscopy, and Theoretical Study.

We used Ni K-edge resonant-valence-to-core X-ray emission spectroscopy (RVtC-XES, also referred to as direct RIXS), an element-selective bulk-sensitive synchrotron-based technique, to investigate the electronic structure of the CPO-27-Ni metal-organic framework (MOF) upon molecular adsorption of significant molecular probes: H2O, CO, H2S, and NO. We compare RVtC-XES with UV-vis spectroscopy, and we show that the element selectivity of RVtC-XES is of strategic significance to observe the full set of d-d excitations in Ni2+, which are partially overshadowed by the low-energy π-π* transitions of the Ni ligands in standard diffuse-reflectance UV-vis experiments. Our combined RVtC-XES/UV-vis approach provides access to the whole set of d-d excitations, allowing us a complete discussion of the changes undergone by the electronic configuration of the Ni2+ sites hosted within the MOF upon molecular adsorption. The experimental data have been interpreted by multiplet ligand-field theory calculations based on Wannier orbitals. This study represents a step further in understanding the ability of the CPO-27-Ni MOFs in molecular sorption and separation applications.

X-ray Computed Tomography Analysis of Historical Woodwind Instruments of the Late Eighteenth Century.

In this work, two historical flutes of the late eighteenth century were analysed by means of X-ray computed tomography (CT). The first one is a piccolo flute whose manufacturer is unknown, though some features could suggest an English or American origin. The second musical instrument is a baroque transverse flute, probably produced by Lorenzo Cerino, an Italian instrument maker active in Turin (Italy) in the late eighteenth century. Analyses carried out provided information on manufacturing techniques, materials and conservation state, and are suitable to plan restoration intervention. In particular, through the CT images, it was possible to observe the presence of defects, cracks, fractures and previous restorations, as well as indications of the tools used in the making of the instruments. Particular attention was directed towards extracting metrological information about the objects. In fact, this work is the first step of a study with a final aim of determining an operative protocol to enable the making of precise-sounding copies of ancient instruments starting from CT images, that can be used to plan a virtual restoration, consisting in the creation of digitally restored copies with a 3D printer.

FTIR spectroscopy and thermodynamics of CO and H(2) adsorbed on gamma-, delta- and alpha-Al(2)O(3).

The adsorption of CO and H(2) at the surface of transitional (gamma and delta) and corundum (alpha) phases of Al(2)O(3) is studied by means of FTIR spectroscopy at temperature variable in the 293-60 K (CO) and 293-20 K (H(2)) intervals with the aims of better clarifying the nature of the surface Lewis centres and evaluate the thermodynamics of the adsorption process.

Stability and reactivity of grafted Cr(CO)3 species on MOF linkers: a computational study.

The possibility to modulate Cr(CO)(3) properties by grafting it onto metal-organic framework (MOF) linkers of different natures has been investigated using density functional methods. MOF linkers were modeled using clusters constituted by benzene rings doubly substituted in the para position. The effect of the electron-donor or electron-acceptor nature of benzene substituents on the stability of the (eta(6)-arene)Cr(CO)(3) adduct and on the shift of the CO bands has been considered. Different electron-donor (-NH(2), -CH(3), -OH, -COONa) and electron-acceptor (-F, -COOH, -CN, -CF(3)) substituents have been used and the results compared with the bare benzene. C(6)H(4)(COOZnOH)(2) and C(6)H(4)(Zn(4)O(13)C(6)H(5))(2) clusters have also been adopted as models of the MOF-5 benzene rings. The possibility of modulating the stability and the reactivity of Cr(CO)(3) species by grafting them to MOFs with different organic linkers was verified. In particular, this study indicates that electron-acceptor (e.g., C(6)H(4)(COOH)(2)) substituted MOF linkers facilitate the substitution of CO by incoming molecules, whereas the use of electron-donor ones (e.g., C(6)H(4)(OH)(2)) would improve the stability of the Cr(CO)(3) adduct and the ring acidity. Furthermore, an almost linear dependence of the Cr(CO)(3) binding energies on the calculated structural and vibrational features of the tricarbonyl was found, suggesting that the stability of the Cr(CO)(3) adduct can be inferred experimentally from vibrational and diffraction data. In the end, on the basis of the results obtained, it was possible to successfully explain the experimental shift of the CO IR stretching features of grafted Cr(CO)(3) on the UiO-66, CPO-27-Ni, and MOF-5 aromatic linkers and on the benzene rings of poly(ethylstyrene-co-divinylbenzene). The sign of the Delta nu(CO) shift with respect to C(6)H(6)Cr(CO)(3) has been found to be strongly dependent on higher/lower electron density on the ring.

Modeling CO and N2 adsorption at Cr surface species of Phillips catalyst by hybrid density functionals: effect of Hartree-Fock exchange percentage.

In this article, we present a computational study of the structure and vibrational properties of the species formed by the interaction between Cr sites of Phillips catalyst and probe molecules (CO, N(2)). The vibrational properties of these surface species, intensively investigated in the past, form a very rich and ideal set of experimental data to test computational approaches. By adopting the X(4)Si(2)O(3)Cr (X = H, OH, F) cluster as a simplified model of the ([triple bond]SiO)(2)Cr(II) species present at the surface of the real catalyst, we found that the B3LYP hybrid functional (containing 20% of Hartree-Fock exchange), when applied to this model, is unable to reproduce with reasonable accuracy the currently available experimental data (principally coming from IR spectroscopy). Better agreement is obtained when the percentage of Hartree-Fock exchange is increased (up to 35-40%).

Role of exposed metal sites in hydrogen storage in MOFs.

The role of exposed metal sites in increasing the H2 storage performances in metal-organic frameworks (MOFs) has been investigated by means of IR spectrometry. Three MOFs have been considered: MOF-5, with unexposed metal sites, and HKUST-1 and CPO-27-Ni, with exposed Cu(2+) and Ni(2+), respectively. The onset temperature of spectroscopic features associated with adsorbed H2 correlates with the adsorption enthalpy obtained by the VTIR method and with the shift experienced by the H-H stretching frequency. This relationship can be ascribed to the different nature and accessibility of the metal sites. On the basis of a pure energetic evaluation, it was observed that the best performance was shown by CPO-27-Ni that exhibits also an initial adsorption enthalpy of -13.5 kJ mol(-1), the highest yet observed for a MOF. Unfortunately, upon comparison of the hydrogen amounts stored at high pressure, the hydrogen capacities in these conditions are mostly dependent on the surface area and total pore volume of the material. This means that if control of MOF surface area can benefit the total stored amounts, only the presence of a great number of strong adsorption sites can make the (P, T) storage conditions more economically favorable. These observations lead to the prediction that efficient H2 storage by physisorption can be obtained by increasing the surface density of strong adsorption sites.

Interaction of Hydrogen with MOF-5.

Hydrogen storage is among the most demanding challenges in the hydrogen-based energy cycle. One proposed strategy for hydrogen storage is based on physisorption on high surface area solids such as metal-organic frameworks (MOFs). Within this class of materials, MOF-5 has been the first structure studied for hydrogen storage. The IR spectroscopy of adsorbed H2 performed at 15 K and ab initio calculations show that the adsorptive properties of this material are mainly due to dispersive interactions with the internal wall structure and to weak electrostatic forces associated with O13Zn4 clusters. Calculated and measured binding enthalpies are between 2.26 and 3.5 kJ/mol, in agreement with the H2 rotational barriers reported in the literature. A minority of binding sites with higher adsorption enthalpy (7.4 kJ/mol) is also observed. These species are probably associated with OH groups on the external surfaces present as termini of the microcrystals.

Maya blue: a computational and spectroscopic study.

Maya Blue pigment, used in pre-Colombian America by the ancient Mayas, is a complex between the clay palygorskite and the indigo dye. The pigment can be manufactured by mixing palygorskite and indigo and heating to T > 120 degrees C. The most quoted hypothesis states that the dye molecules enter the microchannels which permeate the clay structure, thus creating a stable complex. Maya Blue shows a remarkable chemical stability, presumably caused by interactions formed between indigo and clay surfaces. This work aims at studying the nature of these interactions by means of computational and spectroscopic techniques. The encapsulation of indigo inside the clay framework was tested by means of molecular modeling techniques. The calculation of the reaction energies confirmed that the formation of the clay-organic complex can occur only if palygorskite is heated at temperatures well above the water desorption step, when the release of water is entropically favored. H-bonds between the clay framework and the indigo were detected by means of spectroscopic methods. FTIR spectroscopy on outgassed palygorskite and freshly synthesized Maya Blue samples showed that the presence of indigo modifies the spectroscopic features of both structural and zeolitic water, although no clear bands of the dye groups could be observed, presumably due to its very low concentration. The positions and intensities of delta(H2O) and nu(H2O) modes showed that part of the structural water molecules interact via a hydrogen bond with the C=O or N-H groups of indigo. Micro-Raman spectra clearly evidenced the presence of indigo both in original and in freshly synthesized Maya Blue. The nu(C=O) symmetric mode of Maya Blue red-shifts with respect to pure indigo, as the result of the formation of H-bonds with the nearest clay structural water. Ab initio quantum methods were applied on the indigo molecule, both isolated and linked through H-bonds with water, to calculate the magnitude of the expected vibrational shifts. Calculated and experimental vibrational shifts appeared to be in good agreement. The presence of a peak at 17.8 ppm and the shift of the N-H signal in the 1H MAS NMR spectrum of Maya Blue provide evidence of hydrogen bond interactions between indigo and palygorskite in agreement with IR and ab initio methods.

Cu+(H2) and Na+(H2) adducts in exchanged ZSM-5 zeolites.

Cu(I) ions in Cu-ZSM-5 form Cu+(H2) complexes, stable at room temperature and sub-atmospheric H2 pressure, which do not have any homogeneous analogue except for matrix-isolated [Cu(eta2-H2)Cl]. Comparison with the unstable Na+(H2) adducts formed in the parent Na-ZSM-5 zeolite allow the conclusion that the Cu(I)/H2 bond is governed by sigma-pi overlap forces.

Tailoring metal-organic frameworks for CO2 capture: the amino effect.

Carbon dioxide capture from processes is one of the strategies adopted to decrease anthropogenic greenhouse gas emissions. To lower the cost associated with the regeneration of amine-based scrubber systems, one of the envisaged strategies is the grafting of amines onto high-surface-area supports and, in particular, onto metal-organic frameworks (MOFs). In this study, the interaction between CO(2) and aliphatic and aromatic amines has been characterized by quantum mechanical methods (MP2), focusing attention both on species already reported in MOFs and on new amine-based linkers, to inspire the rational synthesis of new high-capacity MOFs. The calculations highlight binding-site requisites and indicate that CO(2) vibrations are independent of the adsorption energy and monitoring them in probe-molecule experiments is not a suitable marker of efficient adsorption.

Structure and nuclearity of active sites in Fe-zeolites: comparison with iron sites in enzymes and homogeneous catalysts.

Fe-ZSM-5 and Fe-silicalite zeolites efficiently catalyse several oxidation reactions which find close analogues in the oxidation reactions catalyzed by homogeneous and enzymatic compounds. The iron centres are highly dispersed in the crystalline matrix and on highly diluted samples, mononuclear and dinuclear structures are expected to become predominant. The crystalline and robust character of the MFI framework has allowed to hypothesize that the catalytic sites are located in well defined crystallographic positions. For this reason these catalysts have been considered as the closest and best defined heterogeneous counterparts of heme and non heme iron complexes and of Fenton type Fe(2+) homogeneous counterparts. On this basis, an analogy with the methane monooxygenase has been advanced several times. In this review we have examined the abundant literature on the subject and summarized the most widely accepted views on the structure, nuclearity and catalytic activity of the iron species. By comparing the results obtained with the various characterization techniques, we conclude that Fe-ZSM-5 and Fe-silicalite are not the ideal samples conceived before and that many types of species are present, some active and some other silent from adsorptive and catalytic point of view. The relative concentration of these species changes with thermal treatments, preparation procedures and loading. Only at lowest loadings the catalytically active species become the dominant fraction of the iron species. On the basis of the spectroscopic titration of the active sites by using NO as a probe, we conclude that the active species on very diluted samples are isolated and highly coordinatively unsaturated Fe(2+) grafted to the crystalline matrix. Indication of the constant presence of a smaller fraction of Fe(2+) presumably located on small clusters is also obtained. The nitrosyl species formed upon dosing NO from the gas phase on activated Fe-ZSM-5 and Fe-silicalite, have been analyzed in detail and the similarities and differences with the cationic, heme and non heme homogeneous counterparts have been evidenced. The same has been done for the oxygen species formed by N(2)O decomposition on isolated sites, whose properties are more similar to those of the (FeO)(2+) in cationic complexes (included the [(H(2)O)(5)FeO](2+)"brown ring" complex active in Fenton reaction) than to those of ferryl groups in heme and non heme counterparts.

Direct observation and modelling of ordered hydrogen adsorption and catalyzed ortho-para conversion on ETS-10 titanosilicate material.

Hydrogen physisorption on porous high surface materials is investigated for the purpose of hydrogen storage and hydrogen separation, because of its simplicity and intrinsic reversibility. For these purposes, the understanding of the binding of dihydrogen to materials, of the structure of the adsorbed phase and of the ortho-para conversion during thermal and pressure cycles are crucial for the development of new hydrogen adsorbents. We report the direct observation by IR spectroscopic methods of structured hydrogen adsorption on a porous titanosilicate (ETS-10), with resolution of the kinetics of the ortho-para transition, and an interpretation of the structure of the adsorbed phase based on classical atomistic simulations. Distinct infrared signals of o- and p-H2 in different adsorbed states are measured, and the conversion of o- to p-H2 is monitored over a timescale of hours, indicating the presence of a catalyzed reaction. Hydrogen adsorption occurs in three different regimes characterized by well separated IR manifestations: at low pressures ordered 1:1 adducts with Na and K ions exposed in the channels of the material are formed, which gradually convert into ordered 2:1 adducts. Further addition of H2 occurs only through the formation of a disordered condensed phase. The binding enthalpy of the Na+-H2 1:1 adduct is of -8.7+/-0.1 kJ mol(-1), as measured spectroscopically. Modeling of the weak interaction of H2 with the materials requires an accurate force field with a precise description of both dispersion and electrostatics. A novel three body force field for molecular hydrogen is presented, based on the fitting of an accurate PES for the H2-H2 interaction to the experimental dipole polarizability and quadrupole moment. Molecular mechanics simulations of hydrogen adsorption at different coverages confirm the three regimes of adsorption and the structure of the adsorbed phase.

Theoretical characterization of dihydrogen adducts with halide anions.

The interaction between a hydrogen molecule and the halide anions F(-), Cl(-), Br(-), and I(-) has been studied at different levels of theory and with different basis sets. The most stable configurations of the complexes have a linear geometry, while the t-shaped complexes are saddle points on the potential energy surface, opposite to what is observed for alkali cations. An electrostatic analysis conducted on the resulting adducts has highlighted the predominance of the electrostatic term in the complexation energy and, in particular, of the quadrupole- and dipole-polarizability dependent contributions. Another striking difference with respect to the positive ions, is the fact that although the binding energies have similar values (ranging between 25 and 3 kJ /mol for F(-) and I(-), respectively), the vibrational shift of the nu(H-H) and in general the perturbation of the hydrogen molecule in complexes are much greater in the complexes with anions (Delta nu(H-H) ranges between -720 and -65 cm(-1)). Another difference with respect to the interaction with cations is a larger charge transfer from the anion to the hydrogen molecule. The Delta nu is the result of the cooperative role of the electrostatics and of the charge transfer in the interaction. The correlation between binding energies and vibrational shift is far from linear, contrary to what is observed for cation complexes, in accordance with the higher polarizability and dynamic polarizability of the molecule along the molecular axis. The observed correlation may be valuable in the interpretation of spectra and thermodynamic properties of adsorbed H(2) in storage materials.

Vibrational and thermodynamic properties of Ar, N2, O2, H2 and CO adsorbed and condensed into (H,Na)-Y zeolite cages as studied by variable temperature IR spectroscopy.

The adsorption of Ar, H2, O2, N2 and CO on (H,Na)-Y zeolite (Si/Al = 2.9, H+/Na+ approximately 5) has been studied at variable-temperature (90-20 K) and sub-atmospheric pressure (0-40 mbar) by FTIR spectroscopy. Unprecedented filling conditions of the zeolite cavities were attained, which allowed the investigation of very weakly adsorbed species and of condensed, liquid-like or solid-like, phases. Two pressure regimes were singled out, characterized by: (i) specific interaction at low pressure of the probe molecules (P) with the internal Brønsted and Lewis sites, and (ii) multilayer adsorption at higher pressure. In the case of CO the perturbation of the protonic sites located inside the sodalite cages was also observed. As the molecule is too large to penetrate the sodalite cage, the perturbation is thought to involve a proton jump tunneling mechanism. The adsorption energy for the (HF)OH...P (P = Ar, H2, O2, N2 and CO) specific interaction involving the high frequency Brønsted acid sites exposed in the supercages was derived following the VTIR (variable temperature infrared spectroscopy) method described by E. Garrone and C. Otero Areán (Chem. Soc. Rev., 2005, 34, 846).

Theoretical maximal storage of hydrogen in zeolitic frameworks.

Physisorption and encapsulation of molecular hydrogen in tailored microporous materials are two of the options for hydrogen storage. Among these materials, zeolites have been widely investigated. In these materials, the attained storage capacities vary widely with structure and composition, leading to the expectation that materials with improved binding sites, together with lighter frameworks, may represent efficient storage materials. In this work, we address the problem of the determination of the maximum amount of molecular hydrogen which could, in principle, be stored in a given zeolitic framework, as limited by the size, structure and flexibility of its pore system. To this end, the progressive filling with H2 of 12 purely siliceous models of common zeolite frameworks has been simulated by means of classical molecular mechanics. By monitoring the variation of cell parameters upon progressive filling of the pores, conclusions are drawn regarding the maximum storage capacity of each framework and, more generally, on framework flexibility. The flexible non-pentasils RHO, FAU, KFI, LTA and CHA display the highest maximal capacities, ranging between 2.86-2.65 mass%, well below the targets set for automotive applications but still in an interesting range. The predicted maximal storage capacities correlate well with experimental results obtained at low temperature. The technique is easily extendable to any other microporous structure, and it can provide a method for the screening of hypothetical new materials for hydrogen storage applications.

Theoretical characterization of dihydrogen adducts with alkaline cations.

As part of an extended fundamental study on the interaction of molecular hydrogen with the surfaces of potential storage materials, this work describes the interaction of dihydrogen with bare alkaline cations (Li(+),Na(+),K(+),Rb(+)) by means of ab initio and density functional calculations. The effects of method and basis set are evaluated, and an estimate of the electrostatic contributions to the binding energy is evaluated. All methods predict a t-shaped coordination geometry, in accord with the quadrupolar nature of the molecule. The binding energies at the MP2/aug-cc-pVQZ (MP2-Møller-Plesset method truncated at second order) level ranges between 24 kJ/mol for Li(+) and 5 kJ/mol for Rb(+). Basis set size has minor effect on the binding energy of the complexes, although the poorer sets have severe limitations in the description of the electrostatics of the isolated molecule. The electrostatic contribution to the binding energy calculated from the electrostatic properties of the isolated molecule are in fact strongly basis set dependent. Their careful analysis shows that the predominant terms of the interaction are those due to the quadrupole and dipole-polarizability terms. The vibrational spectra of the adducts are evaluated and compared with a large set of experimental and theoretical results from the literature. This review highlights a linear correlation between the frequency shift and the binding energy, which is valuable in the understanding of adsorption phenomena by means of spectroscopic methods.