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Density Functional Theory has made the study of biomaterials feasible in the past years leading to better understanding of causes and possible treatments of related pathologies. Although it has been successfully applied in many fields, it has not yet consistently found its way into the field of pathological calcifications. An overview will be given of the studies where this technique has been applied in order to outline the important contributions that it can bring in the field of biomineralization. More specifically, studies on DFT calcifications from calciumoxalates and calcium phosphates, with relevance to bone formation and kidney stones, will be reviewed. Finally, a short outlook on silica mineralization will be presented as well. [ABSTRACT FROM AUTHOR]

Copper and manganese modified zeolites play key roles in selective oxidation catalytic reactions. Combining Density Functional Perturbation Theory (DFPT) implemented in VASP, and infrared spectroscopy experiments, we have studied and elucidated the incorporation of Cu2+ and Mn2+ in the framework of SiBEA zeolite. Six isomers are investigated for both models CuSiBEA and MnSiBEA. The energy stability study identified the most stable isomer in each case, which correspond to M-O2 bent moieties in the vicinity of hydroxyl groups. The isomers are then characterized by experimental and theoretical IR spectra. Both experimental and calculated IR spectra are in good agreement highlighting the presence of active sites (Cu-OH and Mn-OH) in the obtained models. The accurate molecular description of the nature of the active sites presented in this work will be important for understanding the catalysis going on and for developing novel catalytic processes. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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). [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In this paper we have presented results on spinel nano-materials considering a collection of techniques, which is considered today a state-of the-art in the field of catalyst research (characterization and study of structure/reactivity relationship). Through a selected collection of techniques, experimental as well as theoretical, we illustrate this setup of techniques on the characterization of spinels (ZnAl 2 O 4 ) through XAS and by anomalous wide angle X-ray scattering (AWAXS). The effect of Al/Zn substitution was investigated as well and related Co/Al spinels were investigated on their catalytic properties using DFT. The catalytic properties towards NO, O 2 , and NH 3 are explored for the very first time on the Co/Al spinel surfaces, and possible reaction mechanisms proposed. [ABSTRACT FROM AUTHOR]

The three forms of glycine in the solid state, α, β, and γ, are described and modeled by means of generalized-gradient approximation (GGA) ab initio calculations. In particular, the location of the protons in each structure is studied. The vibrational frequencies and the NMR chemical shifts of 1H, 13C, and 15N in the three polymorphs are calculated and compared to experimental data (IR and Raman, solid-state magic angle spinning NMR, respectively). 13C chemical shift differences on the order of 1 ppm, which constitute the most accurate way to discriminate between the three structures when X-ray diffraction is not available, can be satisfactorily predicted. The three forms of glycine in the solid state, α, β, and γ, are described and modeled by means of generalized-gradient approximation ab initio calculations. In particular, the location of the protons in each structure is studied. The vibrational frequencies and the NMR chemical shifts of 1H, 13C, and 15N in the three polymorphs are calculated and compared to experimental data (IR and Raman, solid-state magic angle spinning NMR, respectively). [ABSTRACT FROM AUTHOR]

Titanium oxide (TiO2) has been widely used in many fields, such as photocatalysis, photovoltaics, catalysis, and sensors, where its interaction with molecular H2 with TiO2 surface plays an important role. However, the activation of hydrogen over rutile TiO2 surfaces has not been systematically studied regarding the surface termination dependence. In this work, we use density functional theory (PBE+U) to identify the pathways for two processes: the heterolytic dissociation of H2 as a hydride–proton pair, and the subsequent H transfer from Ti to near O accompanied by reduction of the Ti sites. Four stoichiometric surface orientations were considered: (001), (100), (110), and (101). The lowest activation barriers are found for hydrogen dissociation on (001) and (110), with energies of 0.56 eV and 0.50 eV, respectively. The highest activation barriers are found on (100) and (101), with energies of 1.08 eV and 0.79 eV, respectively. For hydrogen transfer from Ti to near O, the activation barriers are higher (from 1.40 to 1.86 eV). Our results indicate that the dissociation step is kinetically more favorable than the H transfer process, although the latter is thermodynamically more favorable. We discuss the implications in the stability of the hydride–proton pair, and provide structures, electronic structure, vibrational analysis, and temperature effects to characterize the reactivity of the four TiO2 orientations. [ABSTRACT FROM AUTHOR]

The nature of reduced Cr species on silica is still under debate. In this work, combined DFT and in situ UV–vis DRS investigations of reduction of chromia–silica catalyst have been done. Advanced periodic and cluster models of amorphous silica are applied to reproduce the heterogeneity of surface Cr species. Geometrical parameters, vibrational frequencies, excitation energies, and relative stabilities of Cr sites are determined. It is predicted that reduction of monomeric Cr(VI) species to Cr(IV) sites is highly exergonic, whereas deep reduction to Cr(II) is less thermodynamically favored. Dimeric Cr(VI) species can finally be reduced to Cr(III) or Cr(II). In situ UV–vis DRS studies indicate that Cr(VI) species are selectively converted to Cr(II) under CO in dry conditions, whereas reduction with dry H 2 leads to formation of Cr(III) and Cr(II). For both reducing agents, the presence of water hampers deep reduction to Cr(II), which can be explained by reoxidation/hydrolysis processes. [ABSTRACT FROM AUTHOR]

• Pt in Au and Ag surfaces, exposed to hydrogen pressure, segregate into the bulk. • Pt in Cu and Pd surfaces, is stabilized for (Cu(1 1 1) and Cu(1 1 0) Pd(1 1 0) • Pt in Cu Pd supports is stabilized under specific H-pressures and temperatures. • Pt in Co, Rh, Ir and Ni surfaces remain stable for (200 K-1200 K and 1 Pa – 105 Pa) Single-atom alloys (SAAs) are emerging materials containing isolated metal atoms dispersed on host metal surfaces, exhibiting unique reactivity compared with the corresponding monometallic counterparts. However, the stability of the isolated atoms in the host metal has hardly been studied, although, metal segregation has been commonly observed in bimetallic nanoparticles under reaction conditions. In this work we focus on single-atom Pt anchored on various metallic support surfaces. Density Functional Theory (DFT) calculations coupled with environmental segregation energy analysis are performed to map the segregation trends of 22 different Pt-SAA surfaces under various hydrogen conditions. The results show the high stability of single-atom Pt in Ni, Co, Rh and Ir host metallic surfaces while no stability is predicted on Au and Ag surfaces. For Pd and Cu host supports, the single-atom Pt is found to be stable on specific surface facets and within definite temperature and pressure conditions. This work brings an important understanding of SAA systems through the prediction of surface atomic ordering changes under operating conditions which related to the reactivity will ultimately allow the design of more efficient catalysts. [ABSTRACT FROM AUTHOR]

Graphene nanoclusters (GNCs), part of the graphene family of nanomaterials, are attracting interest as promising Pt free catalysts for the Oxygen Reduction Reaction (ORR) at the cathode of the fuel cells. This investigation focuses on the theoretical prediction of their possible edge activity towards ORR determined by their shape, size and termination type. In this framework, using density functional theory (DFT) we examined the zigzag (zz) and armchair terminated (ac) triangular (T), rhombohedral (R) and hexagonal (H) GNCs of various sizes, ranging from C13 to C114. The theoretical onset overpotential (η th,onset) indicate that several GNC edges could be active for ORR. The model indicates that the zigzag edges of all triangular GNCs (C13–C46) as well as of the largest investigated rhombohedral shapes (C48, C70) are active for ORR. A correlation between the band gaps, spin densities and p-band centers of the edge carbon atoms and the adsorption energies of the ORR intermediate moieties (HOO*/O*/HO*) are discussed and which are directly related to their activity. One trend is related to the decrease of the adsorption energies with the decrease of the band gap and accordingly an increase of their ORR activities. The case studies, show that the explicit water model developed by using machine learning potentials and combined with DFT, stabilizes the ORR intermediates stronger than the implicit one, thus increasing slightly the onset overpotential. Overall, this computational study enhances our fundamental understanding of the edges of GNC for their potential application in electrocatalysis without doping. Represent the activity volcano plot the oxygen evolution reaction using as a descriptor the free energy of the first reaction step (the O2 adsorption and protonation on the carbon active sites of the graphene nanocarbons (GNC) of various shapes, sizes and terminations -- ΔG HOO* -ΔG O2) vs. the theoretical onset overpotential (η onset,th). A volcano shape plot is formed and the best ones are placed close to the top of the volcano, namely the triangular and the rhombohedral GNC structures with zigzag terminations. The best sites are marked on the top view of t each structure with "*". The reaction mechanism is pictured as an inset inside the red circle and indicates the formation of HOO*/O*/HO* intermediates on the active site (see the red filled circle). [Display omitted] [ABSTRACT FROM AUTHOR]

Abstract The stability of Ag-Pt systems: 13-atoms icosahedral cluster model (Ag 13-n Pt n) and 54-atoms (111) surface slab model (45Ag9Pt) have been systematically investigated by using Density Functional Theory within the generalized gradient approximation (DFT–GGA). Experimentally tested resistance of AgPt alloy nanoparticles supported on silica to decay upon temperature treatment (423 K–573 K in N 2 flow) have shown to correlate with theoretical results. The stability of the clusters as a function of AgPt composition decreases with increasing content of Pt. The general stability trend of the AgPt alloy was maintained, in theory and experiment, for the Ag/Pt molar ratio of 1.6–5.1. Two particularly stable Ag/Pt compositions were revealed: 1.6 and 0.4. It was also found that surface location of platinum is responsible for stabilization of the Ag-Pt nanostructured alloy. Highlights • Stability trend of AgPt nanoalloy was maintained for Ag/Pt molar ratio of 1.6–5.1. • Pt atom at the center of Ag 13-n Pt n icosahedron cluster is energetically favorable. • The most stable AgPt alloy cluster displays Ag/Pt molar ratio of 0.4 and 1.6. • AgPt alloy stability depends on the metal content and size of bimetallic particle. • Surface location of Pt in AgPt cluster results in higher stability of nanoalloy. [ABSTRACT FROM AUTHOR]

Highlights • The adsorption of GLY-PRO-GLU tripeptide on Au(110) is investigated using FF-MD and DFT. • GLY-PRO-GLU adsorption reorganizes and restructures the Au(110) surface. • A mechanism for the surface restructuration is proposed at room temperature in UHV. • The glutamic acid residue is found to be responsible for the surface reconstruction. Abstract The adsorption of GLY-PRO-GLU tripeptide on Au(110) is investigated within the frame of all atom classical mechanics simulations and Density Functional Theory, focusing on the surface reconstruction. It is shown that the tripeptide adsorption reorganizes and restructures the Au(110) surface. A mechanism for the surface restructuration is proposed for both the neutral and zwitterionic form of the peptide at room temperature in Ultra High Vacuum. Diverse residues may be involved in the Au atoms displacement, and in particular glutamic acid, triggering a double proton transfer and the formation of a zwitter ionic state, is found to be responsible for the triggering of the surface reconstruction. Graphical abstract Image, graphical abstract [ABSTRACT FROM AUTHOR]

In the context of copper corrosion passivation, the adsorption of benzotriazole ( BTAH ) and its derivatives: 5-Methyl, 5-Amine, 1-Amine, 1-Methyl on a Cu(1 1 1) surface was investigated using periodic density functional (DFT) calculations. The results were contrasted with experimental ASTM protocols. Adsorption of BTAH and radical ( BTA● ) forms, as well as solvent effect were evaluated. The Cu-N interaction provides stable complexes with adsorption over top sites. Radical forms yielded more stable complex. Their adsorption energies correlate with the substituent position and electronic features. And finally, a strong interaction was obtained when the charge transfer goes from surface to adsorbate. [ABSTRACT FROM AUTHOR]

[Display omitted] • AgTi 2 (PO 4) 3 efficient photocatalyst for degradation of RhB was synthesized. • Theoretical results based on DFT calculations complemented the experimental results. • The photocatalytic activity was ascribed to the formation of Ag0 in situ. • The mechanism for RhB degradation by AgTi 2 (PO 4) 3 was proposed. Ag-based semiconductors have attracted significant attention as promising visible-light photocatalysts for environmental purification. In this study, electronic and photocatalytic properties of AgTi 2 (PO 4) 3 NASICON-type phosphate, have been addressed in detail, combining experimental results and theoretical calculations. The as-prepared sample was characterized for its morphological, structural and optical properties by various techniques. The generalized gradient approximation by Perdew-Burke-Ernzerhof (GGA-PPE) within density functional theory (DFT) was used to investigate the electronic structure. We have applied corrective Hubbard U terms to Ti 3d orbitals in order to better reproduce the experimental band gap of 2.6 eV. The photocatalytic activity has then been performed for rhodamine B dye degradation under visible light illumination. Efficient dye degradation up to 97.2 % was achieved in 120 min. In addition, the catalyst exhibited good stability over four consecutive cycles. Finally, combining experimental and theoretical findings, the origin of the photocatalytic activity was identified and a photodegradation mechanism was proposed. [ABSTRACT FROM AUTHOR]

Bimetallic catalysts have manifold technological applications; their reactivity can greatly exceed that of the original single metals. In this work, we investigate an ideal model-system consisting of a complete monolayer of Pd underneath the surface of Au(111). First, we investigate the stability of this system, and then its interaction with hydrogen. We analyze in detail the energetics and the electronic interactions for the Volmer step of the hydrogen evolution reaction (HER), and the further absorption below the surface layer of gold. We combine Density Functional Theory based on computational techniques with the theory of electrocatalysis. [ABSTRACT FROM AUTHOR]

• Adsorption of Ag+, Cu2+, and Co2+ ions on faujasite-type zeolite Y was analyzed. • Physicochemical interpretation of adsorption mechanism was obtained via a physical model. • Characterization of the adsorption interactions was performed with DFT and statistical physics. This work evaluated the potential of a synthesized faujasite-type zeolite Y as an adsorbent for the removal of relevant heavy metals such as silver (Ag+), copper (Cu2+), and cobalt (Co2+). The adsorption data of Ag+, Cu2+, and Co2+ ions were determined experimentally at pH 6 and temperatures of 298, 308, and 318 K. Two theoretical approaches have been applied based on statistical physics modeling and density functional theory (DFT) to understand and characterize the ion exchanges involved in the removal of all metals. Results showed that this zeolite was more efficient for the adsorption of Ag+ via cation-exchange. Based on the physical modelling, the removal of heavy metals on this zeolite was mono and multi-ionic (simple and multi-interactions), where the ions interacted via one and two adsorption sites. It was also noted that the temperature increment generated more available functional groups of the zeolite, facilitating the access to the smaller cavities and the interactions with the adsorbent. Adsorption energies for removing these metals with tested zeolite were slightly endothermic and were consistent with the typical values reported for ion exchange systems of heavy metals + zeolites. DFT results demonstrated that these cationic exchange energies depend on the nature of precursor salt, but with the same ranking. Both statistical and DFT approaches agreed that exchange Ag+ in zeolite Y was easier than Cu2+ and Co2+. Overall, the application of both theoretical approaches provided a reliable interpretation of the adsorption mechanism. [ABSTRACT FROM AUTHOR]