Understanding the Reactivity of Supported Late Transition Metals on a Bare Anatase (101) Surface: A Periodic Conceptual DFT Investigation.

The rapidly growing interest for new heterogeneous catalytic systems providing high atomic efficiency along with high stability and reactivity triggered an impressive progress in the field of single-atom catalysis. Nevertheless, unravelling the factors governing the interaction strength between the support and the adsorbed metal atoms remains a major challenge. Based on periodic density functional theory (DFT) calculations, this paper provides insight into the adsorption of single late transition metals on a defect-free anatase surface. The obtained adsorption energies fluctuate, with the exception of Pd, between -3.11 and -3.80 eV and are indicative of a strong interaction. Depending on the considered transition metal, we could attribute the strength of this interaction with the support to i) an electron transfer towards anatase (Ru, Rh, Ni), ii) s-d orbital hybridisation effects (Pt), or iii) a synergistic effect between both factors (Fe, Co, Os, Ir). The driving forces behind the adsorption were also found to be strongly related to Klechkowsky's rule for orbital filling. In contrast, the deviating behaviour of Pd is most likely associated with the lower dissociation enthalpy of the Pd-O bond. Additionally, the reactivity of these systems was evaluated using the Fermi weighted density of states approach. The resulting softness values can be clearly related to the electron configuration of the catalytic systems as well as with the net charge on the transition metal. Finally, these indices were used to construct a model that predicts the adsorption strength of CO on these anatase-supported d-metal atoms. The values obtained from this regression model show, within a 95 % probability interval, a correlation of 84 % with the explicitly calculated CO adsorption energies.

A molecular understanding of citrate adsorption on calcium oxalate polyhydrates.

Calcium oxalate precipitation is a common pathological calcification in the human body, whereby crystallite morphology is influenced by the chelating properties of biological ions such as citrate. It has been suggested that citrate could steer oxalate formation towards its dihydrated form and away from the monohydrated form, which was identified as a major cause for disease. To assess the influence of the citrate ion on the resulting calcium oxalate, surface energies were calculated at the dispersion-corrected density functional level of theory for both monohydrated and dihydrated calcium oxalate. Different adsorption geometries were considered by varying the attacking angle of citrate as well as by considering the citrate ion on top of an adsorbed water layer or penetrating the water layer. The obtained results were compared to ab initio molecular dynamics simulations and experimental scanning electron microscope images. A strong preference for citrate adsorption on calcium oxalate dihydrate was observed, suggesting medical applications for the treatment of such pathological calcifications.

Synergistic Effects in the Activity of Nano-Transition-Metal Clusters Pt12 M (M=Ir, Ru or Rh) for NO Dissociation.

The dissociation of environmentally hazardous NO through dissociative adsorption on metallic clusters supported by oxides, is receiving growing attention. Building on previous research on monometallic M13 clusters [The Journal of Physical Chemistry C 2019, 123 (33), 20314-20318], this work considers bimetallic Pt12 M (M=Rh, Ru or Ir) clusters. The adsorption energy and activation energy of NO dissociation on the clusters have been calculated in vacuum using Kohn-Sham DFT, while their trends were rationalized using reactivity indices such as molecular electrostatic potential and global Fermi softness. The results show that doping of the Pt clusters lowered the adsorption energy as well as the activation energy for NO dissociation. Furthermore, reactivity indices were calculated as a first estimate of the performance of the clusters in realistic amorphous silica pores (MCM-41) through ab initio molecular dynamics simulations.

Crystalline structures of L-cysteine and L-cystine: a combined theoretical and experimental characterization.

It is assumed that genetic diseases affecting the metabolism of cysteine and the kidney function lead to two different kinds of pathologies, namely cystinuria and cystinosis whereby generate L-cystine crystals. Recently, the presence of L-cysteine crystal has been underlined in the case of cystinosis. Interestingly, it can be strikingly seen that cystine ([-S-CH2-CH-(NH2)-COOH]2) consists of two cysteine (C3H7NO2S) molecules connected by a disulfide (S-S) bond. Therefore, the study of cystine and cysteine is important for providing a better understanding of cystinuria and cystinosis. In this paper, we elucidate the discrepancy between L-cystine and L-cysteine by investigating the theoretical and experimental infrared spectra (IR), X-ray diffraction (XRD) as well as Raman spectra aiming to obtain a better characterization of abnormal deposits related to these two genetic pathologies.

Reactivity of Single Transition Metal Atoms on a Hydroxylated Amorphous Silica Surface: A Periodic Conceptual DFT Investigation.

The drive to develop maximal atom-efficient catalysts coupled to the continuous striving for more sustainable reactions has led to an ever-increasing interest in single-atom catalysis. Based on a periodic conceptual density functional theory (cDFT) approach, fundamental insights into the reactivity and adsorption of single late transition metal atoms supported on a fully hydroxylated amorphous silica surface have been acquired. In particular, this investigation revealed that the influence of van der Waals dispersion forces is especially significant for a silver (98 %) or gold (78 %) atom, whereas the oxophilicity of the Group 8-10 transition metals plays a major role in the interaction strength of these atoms on the irreducible SiO2 support. The adsorption energies for the less-electronegative row 4 elements (Fe, Co, Ni) ranged from -1.40 to -1.92 eV, whereas for the heavier row 5 and 6 metals, with the exception of Pd, these values are between -2.20 and -2.92 eV. The deviating behavior of Pd can be attributed to a fully filled d-shell and, hence, the absence of the hybridization effects. Through a systematic analysis of cDFT descriptors determined by using three different theoretical schemes, the Fermi weighted density of states approach was identified as the most suitable for describing the reactivity of the studied systems. The main advantage of this scheme is the fact that it is not influenced by fictitious Coulomb interactions between successive, charged reciprocal cells. Moreover, the contribution of the energy levels to the reactivity is simultaneously scaled based on their position relative to the Fermi level. Finally, the obtained Fermi weighted density of states reactivity trends show a good agreement with the chemical characteristics of the investigated metal atoms as well as the experimental data.

Towards a predictive model for polymer solubility using the noncovalent interaction index: polyethylene as a case study.

In this work we present the development of a novel, quantitative solubility descriptor based on the non-covalent interaction index. It is presented as a more insightful alternative to Hansen's solubility parameters and the COSMO model to assess and predict polymer solubility in different solvents. To this end, we studied the solvation behaviour as a function of the chain length of a single chain of arguably the most simple polymer, polyethylene, in anisole (solvent) and methanol (poor solvent) via molecular dynamics simulations. It was found that in anisole the solute maximized its interface with the solvent, whereas in methanol the macromolecule formed rod-like structures by folding on itself once the chain length surpassed a certain barrier. We assessed this behaviour - which can be related to solubility - quantitatively and qualitatively via well-known descriptors, namely the solvation free energy, and the solvent accessible surface area. In addition, we propose the non-covalent interaction (NCI) index as a versatile descriptor, providing information on the strength, as well as the nature, of the solute-solvent interactions, the solute's intramolecular interactions and on the solute's conformation, both qualitatively and quantitatively. Finally, as a quantitative measure for solubility, defined in this context as the solute's tendency to maximize its interactions with the solvent, we propose two new NCI-based descriptors: the relative integrated NCI density and the integrated NCI difference. The former represents the quantitative difference in solute-solvent interactions between a fully extended coil and the actual conformation during simulation and the latter the quantitative difference between the intermolecular (solute-solvent) and the intramolecular (in the solute) non-covalent interactions. The easy interpretation and calculation of these novel quantities open up the possibility of fast, reliable and insightful high-throughput screening of different (anti)solvent and solute combinations.

Quantified Binding Scale of Competing Ligands at the Surface of Gold Nanoparticles: The Role of Entropy and Intermolecular Forces.

A basic understanding of the driving forces for the formation of multiligand coronas or self-assembled monolayers over metal nanoparticles is mandatory to control and predict the properties of ligand-protected nanoparticles. Herein, 1 H nuclear magnetic resonance experiments and advanced density functional theory (DFT) modeling are combined to highlight the key parameters defining the efficiency of ligand exchange on dispersed gold nanoparticles. The compositions of the surface and of the liquid reaction medium are quantitatively correlated for bifunctional gold nanoparticles protected by a range of competing thiols, including an alkylthiol, arylthiols of varying chain length, thiols functionalized by ethyleneglycol units, and amide groups. These partitions are used to build scales that quantify the ability of a ligand to exchange dodecanethiol. Such scales can be used to target a specific surface composition by choosing the right exchange conditions (ligand ratio, concentrations, and particle size). In the specific case of arylthiols, the exchange ability scale is exploited with the help of DFT modeling to unveil the roles of intermolecular forces and entropic effects in driving ligand exchange. It is finally suggested that similar considerations may apply to other ligands and to direct biligand synthesis.

Does the S-H Bond Always Break after Adsorption of an Alkylthiol on Au(111)?

The reaction mechanism for the formation of alkyl thiol self-assembled monolayers (SAM) on Au(111) is still not clearly understood. Especially, the role of defects on the chemisorption process is an important goal to be addressed. In this work, different minimum energy reaction paths for R-SH dissociation of thiols (with long and short chains and dithiol species) adsorbed on gold adatom are calculated by using periodic density functional theory (DFT). Our results show a lower energy barrier for the RS-H bond dissociation when two thiols are adsorbed per adatom. In addition, in contrast with the formation of an adatom at the Au(111) which has been shown to depend on the alkyl chain length, the activation energy of the RS-H bond dissociation of thiols adsorbed on an adatom was shown to be independent of the alkyl chain length. The presented results and derived hypothesis support the model that thiols with long alkyl chain thiols mainly adsorb molecularly on Au(111), while for short alkyl chain thiols the S-H bond breaks. This result is explained by the fact that short-chain thiols have lower interchain interaction energies and are thus more mobile compared to the long alkyl chain thiols on the Au(111) surface. This feature enables the short chains to reach adequate geometries, driven by entropy, which could deform the Au(111) more drastically and probably pull Au atoms out from surface to form adatoms. With these results a new mechanism is proposed for the formation of alkyl chain thiols on Au(111).

Porphyrins Conjugated with Peripheral Thiolato Gold(I) Complexes for Enhanced Photodynamic Therapy.

Porphyrins fused to imidazolium salts across two neighboring ß-pyrrolic positions were used as N-heterocyclic carbene (NHC) precursors to anchor AuI -Cl complexes at their periphery. Synthesis of several thiolato-AuI complexes was then achieved by substituting chloride for thiolates. Photodynamic properties of these complexes were investigated: the data obtained show that the Au-S bonds could be cleaved upon irradiation. The proposed mechanism to explain the release of thiolate moiety involves the S atom oxidation by singlet oxygen generated in the course of irradiation. In view of photodynamic therapy (PDT) applications, these porphyrins fused to NHC-AuI complexes were tested as photosensitizers to kill MCF-7 breast cancer cells. Results show the important role played by the ancillary ligands (chloride versus thiolates) on the photodynamic effect.

Experimental and Theoretical Study of the Reactivity of Gold Nanoparticles Towards Benzimidazole-2-ylidene Ligands.

The reactivity of benzimidazol-2-ylidenes with respect to gold nanoparticles (AuNPs) has been investigated using a combined experimental and computational approach. First, the grafting of benzimidazol-2-ylidenes bearing benzyl groups on the nitrogen atoms is described, and comparisons are made with structurally similar N-heterocyclic carbenes (NHCs) bearing other N-groups. Similar reactivity was observed for all NHCs, with 1) the erosion of the AuNPs under the effect of the NHC and 2) the formation of bis(NHC) gold complexes. DFT calculations were performed to investigate the modes of grafting of such ligands, to determine adsorption energies, and to rationalize the spectroscopic data. Two types of computational models were developed to describe the grafting onto large or small AuNPs, with either periodic or cluster-type DFT calculations. Calculations of NMR parameters were performed on some of these models, and discussed in light of the experimental data.

Characterization of Phosphate Species on Hydrated Anatase TiO2 Surfaces.

The adsorption/interaction of KH2PO4 with solvated (100) and (101) TiO2 anatase surfaces is investigated using periodic DFT calculations in combination with GIPAW NMR calculations and experimental IR and solid state (17)O, and (31)P NMR spectroscopies. A complete and realistic model has been used to simulate the solvent by individual water molecules. The most stable adsorption configurations are characterized theoretically at the atomic scale, and experimentally supported by NMR and IR spectroscopies. It is shown that H2PO4(-) chemisorbs on the (100) and (101) anatase surfaces, preferentially via a bidentate geometry. Dimer (H3P2O7(-)) and trimer (H4P3O10(-)) adsorption models are confronted with monomer adsorption models, in order to rationalize their occurrence.

Hydration in silica based mesoporous materials: a DFT model.

The MCM-41 material is very commonly used as a support for catalysts. However, theoretical investigations are significantly limited due to the lack of appropriate models that well and accurately describe the real material and enable effective computation at the same time. In this work, our aim is to obtain calculable models at the DFT level of MCM-41 which are as close as possible to the real material. In particular the hydration degree has been investigated, and we present and characterize here for the first time a model for the MCM-41 unit cell filled with explicit solvent water molecules. This is particularly important, because the models developed here are aimed to be further applied in theoretical ab initio/DFT studies of adsorption or as a support for modelling active sites in catalysts.

An experimental and theoretical approach to investigate the effect of chain length on aminothiol adsorption and assembly on gold.

Despite the numerous studies on the self-assembled monolayers (SAMs) of alkylthiols on gold, the mechanisms involved, especially the nature and influence of the thiol-gold interface are still under debate. In this work the adsorption of aminothiols on Au(111) surfaces has been studied by using surface IR and X-ray photoelectron spectroscopy (XPS) as well as by density functional theory (DFT) modeling. Two aminothiols were used, cysteamine (CEA) and mercaptoundecylamine (MUAM), which contain two and eleven carbon atoms, respectively. By combining experimental and theoretical methods, it was possible to draw a molecular picture of the thiol-gold interface. The long-chain aminothiol produced better ordered SAMs, but, interestingly, the XPS data showed different sulfur binding environments depending on the alkyl chain length; an additional peak at low binding energy was observed upon CEA adsorption, which indicates the presence of sulfur in a different environment. DFT modeling showed that the positions of the sulfur atoms in the SAMs on gold with similar unit cells [(2√3×2√3)R30°] depended on the length of the alkyl chain. Short-chain alkylthiol SAMs were adsorbed more strongly than long-chain thiol SAMs and were shown to induce surface reconstruction by extracting atoms from the surface, possibly forming adatom/vacancy combinations that lead to the additional XPS peak. In the case of short alkylthiols, the thiol-gold interface governs the layer, CEA adsorbs strongly, and the mechanism is closer to single-molecule adsorption than self-assembly, whereas for long chains, interactions between alkyl chains drive the system to self-assembly, leading to a higher level of SAM organization and restricting the influence of the sulfur-gold interface.

Supported and inserted monomeric niobium oxide species on/in silica: a molecular picture.

The geometry, energetic, and spectroscopic properties of molecular structures of silica-supported niobium oxide catalysts are studied using periodic density functional calculations (DFT) and compared with experimental data. The calculations are done for Nb oxide species inserted or grafted in/on an amorphous hydroxylated silica surface. Different positions of the Nb atom/atoms in the silica structure have been investigated. By means of DFT calculations the geometry and the degree of hydration of Nb oxide species with oxidation state +5 have been studied. The local Nb geometry depends on different parameters such as the number of Nb-O-Si groups vs. Nb-O-H groups, the formation of H bonds and the distance between Nb atoms. The interaction between the oxide and silanol groups occurs by formation of Si-O-Nb bonds with chemically and thermally stable Brønsted and Lewis acid sites. UV-Vis, reflection absorption infrared vibrational spectra (RAIRS) as well as various thermodynamic properties have also been investigated in order to get a better insight into the system studied and to provide support to possible experimental studies.

Exploring the molecular structure of imidazolium-silica-based nanoparticle networks by combining solid-state NMR spectroscopy and first-principles calculations.

A DFT-based molecular model for imidazolium-silica-based nanoparticle networks (INNs) is presented. The INNs were synthesized and characterized by using small-angle X-ray scattering (SAXS), NMR spectroscopy, and theoretical ab initio calculations. (11)B and (31)P HETCOR CP MAS experiments were recorded. Calculated (19)F NMR spectroscopy results, combined with the calculated anion-imidazolium (IM) distances, predicted the IM chain density in the INN, which was also confirmed from thermogravimetric analysis/mass spectrometry results. The presence of water molecules trapped between the nanoparticles is also suggested. First considerations on possible π-π stacking between the IM rings are presented. The predicted electronic properties confirm the photoluminescence emissions in the correct spectral domain.

Characterization of two-dimensional chiral self-assemblies L- and D-methionine on Au(111).

A combination of XPS, in situ RAIRS, LEED, and STM experiments together with ab initio DFT calculations were used to elucidate the self-assembly properties at the atomic level, and enabled the interpretation of the expression of surface chirality upon adsorption of both enantiomers of methionine on a clean Au(111) surface under UHV conditions. The combination of experimental results, in particular, LEED and STM data with quantum chemical calculations is shown to be a successful setup strategy for addressing this challenge. It was found that the methionine molecular self-assembly consists of the first molecule lying parallel to the gold surface and the second interacting with the first methionine through a 2D H-bond network. The interaction with the gold surface is weak. The stability of the assembly is mainly due to the presence of intermolecular H bonds, resulting in the formation of ziplike dimer rows on the Au(111) surface. The methionine molecules interact with each other via their amino acid functional groups. The assembly shows an asymmetric pattern due to a slightly different orientation of the methionine molecules with respect to the surface. Simulations of the STM image of methionine assemblies were consistent with the experimental STM image. The present study shows another example of Au(111) stabilizing a self-assembled biological layer, which is not chemically perturbed by the surface.

Characterization of molybdenum monomeric oxide species supported on hydroxylated silica: a DFT study.

Periodic DFT calculations have been performed on molybdenum(VI) oxide species supported on the hydroxylated amorphous silica surface. The Mo grafting site has been investigated systematically for the type of silanol (geminate, vicinal, isolated or in a nest) accessible on the surface, as well as its effect on H-bond formation and stabilization, with the Mo-oxide species. Different grafting geometries, combined with different degrees of hydration of the Mo species are investigated using atomistic thermodynamics. The most stable Mo(VI) oxide species resulting from these calculations are confronted with experiment. Finally, calculated vibrational frequencies confirm the experimental evidence of the dominant presence of di grafted di-oxo Mo(VI) species on silica up to 700 K.

Raman Characterization of Plastics: A DFT Study of Polystyrene.

Plastic materials are ubiquitous and raise concerns about their impact on health and the environment. To address these concerns, it is crucial to characterize the structural, size, and textural properties of plastics throughout their lifecycle from production to degradation. Raman spectroscopy appears as a valuable tool for this purpose, offering speed, robustness, and sensitivity to nanoscale and amorphous particles. In order to be properly used for plastics, the Raman response of reference materials needs to be carefully assessed, with the literature on such assessments being scarce. This study addresses this gap by using theoretical calculations to generate ab initio spectra for polystyrene, a reference material. The aim is to explain the origins of the spectral peaks and their consistency across various compositions and structures using linear ordered polymeric and finite amorphous models. The CRYSTAL package is employed to obtain full Raman spectra based on a careful benchmark of computational settings. While some peaks are present across all spectra and can serve for calibration, others exhibit structure-dependent behavior, enabling polymer identification. We conclude that Raman spectroscopy is a well-suited technique for plastics characterization provided that a careful analysis of signal origin is conducted to fully interpret the spectra and deploy applications.

Unraveling the self-assembly of the (S)-glutamic acid "flower" structure on Ag(100).

(S)-Glutamic acid adsorbed on Ag(100) organizes in different self-assembled structures depending on surface temperature [Smerieri, M.; Vattuone, L.; Kravchuk, T.; Costa, D.; Savio, L. (S)-Glutamic Acid on Ag(100): Self-Assembly in the Nonzwitterionic Form. Langmuir2011, 27, 2393-2404]. In particular, two of these structures, referred to as "square" and "flower" geometries, are found to coexist on the surface upon deposition at T = 350 K. The former assembly was fully resolved at the atomic level in the work of Smerieri et al. [Smerieri, M.; Vattuone, L.; Costa, D.; Tielens, F.; Savio, L. Self-Assembly of (S)-Glutamic Acid on Ag(100): A Combined LT-STM and Ab Initio Investigation. Langmuir2010, 26, 7208-7215], in which we proved that the driving force for adsorption is the van der Waals interactions between the molecules and the Ag surface, that is, that molecules are in a physisorbed state. In this paper, we complete our work by presenting the characterization of the "flower" structure. In contrast to the case of the "square" assembly, a strong chemical bond between glutamic acid radicals and the surface is at the basis of the "flowers" geometry. Whereas the chemisorbed central GLU tetramer interacts strongly with the surface, the physisorbed surrounding GLU molecules conserve some degree of freedom in the layer which counterbalances the weak adsorption energy. The "flower" and the "square" assemblies have similar dispersion energy and H-bond interaction energy; as a consequence of the different chemical state of the GLU molecules, however, such contributions have a very different relative weight in the stabilization of the two structures.

Special Issue "Theoretical Calculation and Molecular Modeling of Nanomaterials".

The continuous advancement of computational chemistry and the chemical modeling of materials is closely aligned with the ever-evolving computational power and related techniques [...].