Adsorption of HCN on cosmic silicates: a periodic quantum mechanical study.

Hydrogen cyanide (HCN) represents a small but widely distributed fraction of the interstellar molecules, and it has been observed in all the environments characterizing the formation of a new planetary system. HCN can polymerize to form biomolecules, including adenine (H5C5N5), and it has drawn attention as a possible precursor of several building blocks of life due to the presence of its polymerization products in meteorites, comets and other asteroidal bodies. To elucidate the potential catalytic role that cosmic silicates have played in these processes, we have investigated, at DFT-PBE level inclusive of a posteriori dispersion correction, the energetic and spectroscopic features of the adsorption of HCN molecules on the most relevant crystalline surfaces of the mineral forsterite (Mg2SiO4), a common silicate constituent of the interstellar core grains and planetary rocky bodies. The results reveal that HCN adsorbs both in molecular and dissociative ways, within a wide range of adsorption energies (-29.4 to -466.4 kJ mol-1). Thermodynamic and kinetic results show that dissociative adsorption is dominant already at low temperatures, a fact particularly relevant at the protoplanetary conditions (i.e., the latest stages in the star system formation process). The simulated spectroscopic features of the studied adducts show a wide range of different degrees of perturbation of C-H and CN bonds. This finding agrees with previous experimental works, and our results confirm that a complex chemistry is observed when this astrochemically-relevant molecule interacts with Mg2SiO4, which may be associated with a considerable potential reactivity towards the formation of relevant prebiotic compounds.

Exploration of the Conformational Scenario for α-, ß-, and γ-Cyclodextrins in Dry and Wet Conditions, from Monomers to Crystal Structures: A Quantum-Mechanical Study.

Cyclodextrins (CDs) constitute a class of cyclic oligosaccharides that are well recognized and largely applied in the drug delivery field, thanks to their biocompatibility, low cost, and the possibility to be derivatized in order to tune and optimize the complexation/release of the specific drug. The conformational flexibility of these systems is one of their key properties and requires a cost-effective methodology to be studied by combining the accuracy of results with the possibility of exploring a large set of conformations. In the present paper, we have explored the conformational potential energy surface of the monomers and dimers of α-, ß-, and γ-cyclodextrins (i.e., 6, 7, and 8 monomeric units, respectively) by means of fast but accurate semiempirical methods, which are then refined by state-of-the-art DFT functionals. Moreover, the crystal structure is considered for a more suitable comparison with the IR spectrum experimentally recorded. Calculations are carried out in the gas phase and in water environments, applying both implicit and explicit treatments. We show that the conformation of the studied molecules changes from the gas phase to the water, even if treated implicitly, thus modifying their complexation capability.

On the stability of peptide secondary structures on the TiO2 (101) anatase surface: a computational insight.

The biological activity of proteins is partly due to their secondary structures and conformational states. Peptide chains are rather flexible so that finding ways inducing protein folding in a well-defined state is of great importance. Among the different constraint techniques, the interaction of proteins with inorganic surfaces is a fruitful strategy to stabilize selected folded states. Surface-induced peptide folding can have potential applications in different biomedicine areas, but it can also be of fundamental interest in prebiotic chemistry since the biological activity of a peptide can turn-on when folded in a given state. In this work, periodic quantum mechanical simulations (including implicit solvation effects) at the PBE-D2* level have been carried out to study the adsorption and the stability of the secondary structures (α-helix and ß-sheet) of polypeptides with different chemical composition (i.e., polyglycine, polyalanine, polyglutamic acid, polylysine, and polyarginine) on the TiO2 (101) anatase surface. The computational cost is reduced by applying periodic boundary conditions to both the surface and the peptides, thus obtaining full periodic polypeptide/TiO2 surface systems. At variance with polyglycine, the interaction of the other polypeptides with the surface takes place with the lateral chain functionalities, leaving the secondary structures almost undistorted. Results indicate that the preferred conformation upon adsorption is the α-helix over the ß-sheet, with the exception of the polyglutamic acid. According to the calculated adsorption energies, the affinity trend of the polypeptides with the (101) anatase surface is: polyarginine ≈ polylysine > polyglutamic acid > polyglycine ≈ polyalanine, both when adsorbed in gas phase and in presence of the implicit water solvent, which is very similar to the trend for the single amino acids. A set of implications related to the areas of surface-induced peptide folding, biomedicine and prebiotic chemistry are finally discussed.

First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO2 (101) Anatase Surface Adopting a Full Periodic Approach.

Computational modeling of protein/surface systems is challenging since the conformational variations of the protein and its interactions with the surface need to be considered at once. Adoption of first-principles methods to this purpose is overwhelming and computationally extremely expensive so that, in many cases, dramatically simplified systems (e.g., small peptides or amino acids) are used at the expenses of modeling nonrealistic systems. In this work, we propose a cost-effective strategy for the modeling of peptide/surface interactions at a full quantum mechanical level, taking the adsorption of polyglycine on the TiO2 (101) anatase surface as a test case. Our approach is based on applying the periodic boundary conditions for both the surface model and the polyglycine peptide, giving rise to full periodic polyglycine/TiO2 surface systems. By proceeding this way, the considered complexes are modeled with a drastically reduced number of atoms compared with the finite-analogous systems, modeling the polypeptide structures at the same time in a realistic way. Within our modeling approach, full periodic density functional theory calculations (including implicit solvation effects) and ab initio molecular dynamics (AIMD) simulations at the PBE-D2* theory level have been carried out to investigate the adsorption and relative stability of the different polyglycine structures (i.e., extended primary, ß-sheet, and α-helix) on the TiO2 surface. It has been found that, upon adsorption, secondary structures become partially denatured because the peptide C═O groups form Ti-O═C dative bonds. AIMD simulations have been fundamental to identify these phenomena because thermal and entropic effects are of paramount importance. Irrespective of the simulated environments (gas phase and implicit solvent), adsorption of the α-helix is more favorable than that of the ß-sheet because in the former, more Ti-O═C bonds are formed and the adsorbed secondary structure results less distorted with respect to the isolated state. Under the implicit water solvent, additionally, adsorbed ß-sheet structures weaken with respect to their isolated states as the H-bonds between the strands are longer due to solvation effects. Accordingly, the results indicate that the preferred conformation upon adsorption is the α-helix over the ß-sheet.

On the Interactions of Melatonin/ß-Cyclodextrin Inclusion Complex: A Novel Approach Combining Efficient Semiempirical Extended Tight-Binding (xTB) Results with Ab Initio Methods.

Melatonin (MT) is a molecule of paramount importance in all living organisms, due to its presence in many biological activities, such as circadian (sleep-wake cycle) and seasonal rhythms (reproduction, fattening, molting, etc.). Unfortunately, it suffers from poor solubility and, to be used as a drug, an appropriate transport vehicle has to be developed, in order to optimize its release in the human tissues. As a possible drug-delivery system, ß-cyclodextrin (ßCD) represents a promising scaffold which can encapsulate the melatonin, releasing when needed. In this work, we present a computational study supported by experimental IR spectra on inclusion MT/ßCD complexes. The aim is to provide a robust, accurate and, at the same time, low-cost methodology to investigate these inclusion complexes both with static and dynamic simulations, in order to study the main actors that drive the interactions of melatonin with ß-cyclodextrin and, therefore, to understand its release mechanism.

A quantum mechanical study of dehydration vs. decarbonylation of formamide catalysed by amorphous silica surfaces.

Formamide is abundant in the interstellar medium and was also present during the formation of the Solar system through the accretion process of interstellar dust. Under the physicochemical conditions of primordial Earth, formamide could have undergone decomposition, either via dehydration (HCN + H2O) or via decarbonylation (CO + NH3). The first reactive channel provides HCN, which is an essential molecular building block for the formation of RNA/DNA bases, crucial for the emergence of life on Earth. In this work, we studied, at the CCSD(T)/cc-pVTZ level, the two competitive routes of formamide decomposition, i.e. dehydration and decarbonylation, either in liquid formamide (by using the polarization continuum model technique) or at the interface between liquid formamide and amorphous silica. Amorphous silica was adopted as a convenient model of the crystalline silica phases ubiquitously present in the primordial (and actual) Earth's crust, and also due to its relevance in catalysis, adsorption and chromatography. Results show that: (i) silica surface sites catalyse both decomposition channels by reducing the activation barriers by about 100 kJ mol-1 with respect to the reactions in homogeneous medium, and (ii) the dehydration channel, giving rise to HCN, is strongly favoured from a kinetic standpoint over decarbonylation, the latter being, instead, slightly favoured from a thermodynamic point of view.

Monitoring the Reactivity of Formamide on Amorphous SiO2 by In-Situ UV-Raman Spectroscopy and DFT Modeling.

Formamide has been recognized in the literature as a key species in the formation of the complex molecules of life, such as nucleobases. Furthermore, several studies reported the impact of mineral phases as catalysts for its decomposition/polymerization processes, increasing the conversion and also favoring the formation of specific products. Despite the progresses in the field, in situ studies on these mineral-catalyzed processes are missing. In this work, we present an in situ UV-Raman characterization of the chemical evolution of formamide over amorphous SiO2 samples, selected as a prototype of silicate minerals. The experiments were carried out after reaction of formamide at 160 °C on amorphous SiO2 (Aerosil OX50) either pristine or pre-calcined at 450 °C, to remove a large fraction of surface silanol groups. Our measurements, interpreted on the basis of density functional B3LYP-D3 calculations, allow to assign the spectra bands in terms of specific complex organic molecules, namely, diaminomaleonitrile (DAMN), 5-aminoimidazole (AI), and purine, showing the role of the mineral surface on the formation of relevant prebiotic molecules.

Carbon monoxide adsorption at forsterite surfaces as models of interstellar dust grains: An unexpected bathochromic (red) shift of the CO stretching frequency.

Carbon monoxide (CO) is one of the most abundant species in the interstellar medium (ISM). In the colder regions of the ISM, it can directly adsorb onto exposed Mg cations of forsterite (Fo, Mg2SiO4), one of the main constituents of the dust grains. Its energetic of adsorption can strongly influence the chemico-physical evolution of cold interstellar clouds; thus, a detailed description of this process is desirable. We recently simulated the CO adsorption on crystalline Fo surfaces by computer ab initio methods and, surprisingly, reported cases where the CO stretching frequency underwent a bathochromic (red) shift (i.e., it is lowered with respect to the CO gas phase frequency), usually not experimentally observed for CO adsorbed onto oxides with non-d cations, like the present case. Here, we elucidate in deep when and under which conditions this case may happen and concluded that this red shift may be related to peculiar surface sites occurring at the morphologically complex Fo surfaces. The reasons for the red shift are linked to both the quadrupolar nature of the CO molecule and the role of dispersion interactions with surfaces of complex morphology. The present work, albeit speculative, suggests that, at variance with CO adsorption on simple oxides like MgO, the CO spectrum may exhibit features at lower frequencies than the reference gas frequency when CO is adsorbed on complex oxides, even in the absence of transition metal ions.

When the Surface Matters: Prebiotic Peptide-Bond Formation on the TiO2 (101) Anatase Surface through Periodic DFT-D2 Simulations.

The mechanism of the peptide-bond formation between two glycine (Gly) molecules has been investigated by means of PBE-D2* and PBE0-D2* periodic simulations on the TiO2 (101) anatase surface. This is a process of great relevance both in fundamental prebiotic chemistry, as the reaction univocally belongs to one of the different organizational events that ultimately led to the emergence of life on Earth, as well as from an industrial perspective, since formation of amides is a key reaction for pharmaceutical companies. The efficiency of the surface catalytic sites is demonstrated by comparing the reactions in the gas phase and on the surface. At variance with the uncatalyzed gas-phase reaction, which involves a concerted nucleophilic attack and dehydration step, on the surface these two steps occur along a stepwise mechanism. The presence of surface Lewis and Brönsted sites exerts some catalytic effect by lowering the free energy barrier for the peptide-bond formation by about 6 kcal mol-1 compared to the gas-phase reaction. Moreover, the co-presence of molecules acting as proton-transfer assistants (i.e., H2 O and Gly) provide a more significant kinetic energy barrier decrease. The reaction on the surface is also favorable from a thermodynamic standpoint, involving very large and negative reaction energies. This is due to the fact that the anatase surface also acts as a dehydration agent during the condensation reaction, since the outermost coordinatively unsaturated Ti atoms strongly anchor the released water molecules. Our theoretical results provide a comprehensive atomistic interpretation of the experimental results of Martra et al. (Angew. Chem. Int. Ed. 2014, 53, 4671), in which polyglycine formation was obtained by successive feedings of Gly vapor on TiO2 surfaces in dry conditions and are, therefore, relevant in a prebiotic context envisaging dry and wet cycles occurring, at mineral surfaces, in a small pool.

Theoretical prediction of nanosizing effects and role of additives in the decomposition of Mg(BH4)2.

The energetic transition towards renewable resources is one of the biggest challenges of this century. In this context, the role of H2 is of paramount importance as a key source of energy that could substitute traditional fossil fuels. This technology, even if available in several manufactures, still needs to be optimized at all levels (production, storage and distribution) to be integrated on a larger scale. Among materials suitable to store H2, Mg(BH4)2 is particularly interesting due to its high content of H2 in terms of gravimetric density. Nanosizing effects and role of additives in the decomposition of Mg(BH4)2 were studied by density functional theory (DFT) modelling. Both effects were analyzed because of their contribution in promoting the decomposition of the material. In particular, to have a quantitative idea of nanosizing effects, we used thin film 2D models corresponding to different crystallographic surfaces and referred to the following reaction: Mg(BH4)2 → MgB2 + 4H2. When moving from bulk to nanoscale (2D models), a remarkable decrease in the decomposition energy (10-20 kJ mol-1) was predicted depending on the surface and the thin film thickness considered. As regards the role of additives (Ni and Cu), we based our analysis on their effect in perturbing neighboring borohydride groups. We found a clear elongation of some B-H bonds, in particular with the NiF2 additive (about 0.1 Å). We interpreted this behavior as an indicator of the propensity of borohydride towards dissociation. On the basis of this evidence, we also explored a possible reaction pathway of NiF2 and CuF2 on Mg(BH4)2 up to H2 release and pointed out the major catalytic effect of Ni compared to Cu.

Unveiling the synergy: a combined experimental and theoretical study of ß-cyclodextrin with melatonin.

Melatonin (MT) is a vital hormone controlling biorhythms, and optimizing its release in the human body is crucial. To address MT's unfavorable pharmacokinetics, we explored the inclusion complexes of MT with ß-cyclodextrin (ß-CD). Nano spray drying was applied to efficiently synthesize these complexes in three molar ratios (MT : ß-CD = 1 : 1, 2 : 1, and 1 : 2), reducing reagent use and expediting inclusion. The complex powders were characterized through thermal analyses (TGA and DSC), Fourier transform infrared spectroscopy (FTIR), and in vitro MT release measurements via high-performance liquid chromatography (HPLC). In parallel, computational studies were conducted, examining the stability of MT : ß-CD complexes by means of unbiased semi-empirical conformational searches refined by DFT, which produced a distribution of MT : ß-CD binding enthalpies. Computational findings highlighted that these complexes are stabilized by specific hydrogen bonds and non-specific dispersive forces, with stronger binding in the 1 : 1 complex, which was corroborated by in vitro release data. Furthermore, the alignment between simulated and experimental FTIR spectra demonstrated the quality of both the structural model and computational methodology, which was crucial to enhance our comprehension of optimizing MT's release for therapeutic applications.

Computational Study on the Water Corrosion Process at Schreibersite (Fe2NiP) Surfaces: from Phosphide to Phosphates.

Phosphorus (P) is a fundamental element for whatever form of life, in the same way as the other biogenic macroelements (SONCH). The prebiotic origin of P is still a matter of debate, as the phosphates present on earth are trapped in almost insoluble solid matrixes (apatites) and, therefore, hardly available for inclusion in living systems in the prebiotic era. The most accepted theories regard a possible exogenous origin during the Archean Era, through the meteoritic bombardment, when tons of reactive P in the form of phosphide ((Fe,Ni)3P, schreibersite mineral) reached the primordial earth, reacting with water and providing oxygenated phosphorus compounds (including phosphates). In the last 20 years, laboratory experiments demonstrated that the corrosion process of schreibersite by water indeed leads to reactive phosphates that, in turn, react with other biological building blocks (nucleosides and simple sugars) to form more complex molecules (nucleotides and complex sugars). In the present paper, we study the water corrosion of different crystalline surfaces of schreibersite by means of periodic DFT (density functional theory) simulations. Our results show that water adsorbs molecularly on the most stable (110) surface but dissociates on the less stable (001) one, giving rise to further reactivity. Indeed, subsequent water adsorptions, up to the water monolayer coverage, show that, on the (001) surface, iron and nickel atoms are the first species undergoing the corrosion process and, in a second stage, the phosphorus atoms also get involved. When adsorbing up to three and four water molecules per unit cell, the most stable structures found are the phosphite and phosphate forms of phosphorus, respectively. Simulation of the vibrational spectra of the considered reaction products revealed that the experimental band at 2423 cm-1 attributed to the P-H stretching frequency is indeed predicted for a phosphite moiety attached to the schreibersite (001) surface upon chemisorption of up to three water molecules.

A Comparison between the Molecularly Imprinted and Non-Molecularly Imprinted Cyclodextrin-Based Nanosponges for the Transdermal Delivery of Melatonin.

Melatonin is a neurohormone that ameliorates many health conditions when it is administered as a drug, but its drawbacks are its oral and intravenous fast release. To overcome the limitations associated with melatonin release, cyclodextrin-based nanosponges (CD-based NSs) can be used. Under their attractive properties, CD-based NSs are well-known to provide the sustained release of the drug. Green cyclodextrin (CD)-based molecularly imprinted nanosponges (MIP-NSs) are successfully synthesized by reacting ß-Cyclodextrin (ß-CD) or Methyl-ß Cyclodextrin (M-ßCD) with citric acid as a cross-linking agent at a 1:8 molar ratio, and melatonin is introduced as a template molecule. In addition, CD-based non-molecularly imprinted nanosponges (NIP-NSs) are synthesized following the same procedure as MIP-NSs without the presence of melatonin. The resulting polymers are characterized by CHNS-O Elemental, Fourier Transform Infrared Spectroscopy (FTIR), Thermogravimetric (TGA), Differential Scanning Calorimetry (DSC), Zeta Potential, and High-Performance Liquid Chromatography (HPLC-UV) analyses, etc. The encapsulation efficiencies are 60-90% for MIP-NSs and 20-40% for NIP-NSs, whereas melatonin loading capacities are 1-1.5% for MIP-NSs and 4-7% for NIP-NSs. A better-controlled drug release performance (pH = 7.4) for 24 h is displayed by the in vitro release study of MIP-NSs (30-50% released melatonin) than NIP-NSs (50-70% released melatonin) due to the different associations within the polymeric structure. Furthermore, a computational study, through the static simulations in the gas phase at a Geometry Frequency Non-covalent interactions (GFN2 level), is performed to support the inclusion complex between ßCD and melatonin with the automatic energy exploration performed by Conformer-Rotamer Ensemble Sampling Tool (CREST). A total of 58% of the CD/melatonin interactions are dominated by weak forces. CD-based MIP-NSs and CD-based NIP-NSs are mixed with cream formulations for enhancing and sustaining the melatonin delivery into the skin. The efficiency of cream formulations is determined by stability, spreadability, viscosity, and pH. This development of a new skin formulation, based on an imprinting approach, will be of the utmost importance in future research at improving skin permeation through transdermal delivery, associated with narrow therapeutic windows or low bioavailability of drugs with various health benefits.

Computer Generated Realistic Interstellar Icy Grain Models: Physicochemical Properties and Interaction with NH3.

Interstellar grains are composed by a rocky core (usually amorphous silicates) covered by an icy mantle, the most abundant molecule being H2O followed by CO, CO2, NH3, and also radicals in minor quantities. In dense molecular clouds, gas-phase chemical species freeze onto the grain surface, making it an important reservoir of molecular diversity/complexity whose evolution leads to interstellar complex organic molecules (iCOMs). Many different models of water clusters have appeared in the literature, but without a systematic study on the properties of the grain (such as the H-bonds features, the oxygen radial distribution function, the dangling species present on the mantle surface, the surface electrostatic potential, etc.). In this work, we present a computer procedure (ACO-FROST) grounded on the newly developed semiempirical GFN2 tight-binding quantum mechanical method and the GFN-FF force field method to build-up structures of amorphous ice of large size. These methods show a very favorable accuracy/cost ratio as they are ideally designed to take noncovalent interactions into account. ACO-FROST program can be tuned to build grains of different composition mimicking dirty icy grains. These icy grain models allow studying the adsorption features (structure, binding energy, vibrational frequencies, etc.) of relevant species on a large variety of adsorption sites so to obtain a statistically meaningful distribution of the physicochemical properties of interest to be transferred in numerical models. As a test case, we computed the binding energy of ammonia adsorbed at the different sites of the icy grain surface, showing a broad distribution not easily accounted for by other more size limited icy grain models. Our method is also the base for further refinements, adopting the present grain in a more rigorous QM:MM treatment, capable of giving binding energies within the chemical accuracy.

Water Interaction with Fe2NiP Schreibersite (110) Surface: a Quantum Mechanical Atomistic Perspective.

Phosphorus is an element of primary importance for all living creatures, being present in many biological activities in the form of phosphate (PO4 3-). However, there are still open questions about the origin of this specific element and on the transformation that allowed it to be incorporated in biological systems. The most probable source of prebiotic phosphorus is the intense meteoritic bombardment during the Archean era, a few million years after the solar system formation, which brought tons of iron-phosphide materials (schreibersite) on the early Earth crust. It was recently demonstrated that by simple wetting/corrosion processes from this material, various oxygenated phosphorus compounds are produced. In the present work, the wetting process of schreibersite (Fe2NiP) was studied by computer simulations using density functional theory, with the PBE functional supplemented with dispersive interactions through a posteriori empirical correction. To start disentangling the complexity of the system, only the most stable (110) surface of Fe2NiP was used simulating different water coverages, from which structures, water binding energies, and vibrational spectra have been predicted. The computed (ana-)harmonic infrared spectra have been compared with the experimental ones, thus, confirming the validity of the adopted methodology and models.

Theoretical Distribution of the Ammonia Binding Energy at Interstellar Icy Grains: A New Computational Framework.

The binding energies (BE) of molecules on the interstellar grains are crucial in the chemical evolution of the interstellar medium (ISM). Both temperature-programmed desorption (TPD) laboratory experiments and quantum chemistry computations have often provided, so far, only single values of the BE for each molecule. This is a severe limitation, as the ices enveloping the grain mantles are structurally amorphous, giving rise to a manifold of possible adsorption sites, each with different BEs. However, the amorphous ice nature prevents the knowledge of structural details, hindering the development of a common accepted atomistic icy model. In this work, we propose a computational framework that closely mimics the formation of the interstellar grain mantle through a water by water accretion. On that grain, an unbiased random (but well reproducible) positioning of the studied molecule is then carried out. Here we present the test case of NH3, a ubiquitous species in the molecular ISM. We provide the BE distribution computed by a hierarchy approach, using the semiempirical xTB-GFN2 as a low-level method to describe the whole icy cluster in combination with the B97D3 DFT functional as a high-level method on the local zone of the NH3 interaction. The final ZPE-corrected BE is computed at the ONIOM(DLPNO-CCSD(T)//B97D3:xTB-GFN2) level, ensuring the best cost/accuracy ratio. The main peak of the predicted NH3 BE distribution is in agreement with experimental TPD and computed data in the literature. A second broad peak at very low BE values is also present, which has never been detected before. It may provide the solution to a longstanding puzzle about the presence of gaseous NH3 also observed in cold ISM objects.

HgBrI: a possible tecton for NLO molecular materials?

Mixed mercury(II) halogenides have been known for a long time as good NLO (non-linear optic) materials. The NLO properties are due to the halogen disposition in the solid state and the electron distribution among the bonds formed by soft elements. We investigated the possibility of using HgBrI as a asymmetric tecton in the preparation of noncentrosymmetric crystalline compounds, by exploiting the coordinating power of Hg(II) toward N-donor ligands, and seven coordination complexes have been obtained. To unravel the nature of these complex systems we combined the data from different techniques: Raman spectroscopy, SC-XRD and Second Harmonic Generation, supported by a periodic DFT computational approach. In HgBrI crystalline products with low symmetry, the presence of substitutional disorder leads to a lack of the inversion center conferring NLO activity, which is absent in analogous complexes of Hg(II) halogenides. These results indicate HgBrI as an interesting tecton to obtain metallorganic NLO materials.

Anion···Anion [AuI4]-···[AuI2]- Complex Trapped in the Solid State by Tetramethylammonium Cations.

A discrete π-hole···σ-hole dimer is synthesized and X-ray characterized. It presents a perfect thumbtack geometry where the σ-hole of the linear [AuI2]- anion points to the π-hole located above the central Au-atom of the [AuI4]- anion. Such discrete π-hole···σ-hole dimers are unprecedented in literature, since all mixed-valence gold(I/III) iodide compounds reported to date form infinite ···([AuI4]-···[AuI2]-) n ·· chains in the solid state. If an excess of iodine is used for the synthesis, triiodide [I3]- ions are partially incorporated into the [AuI2]- sites, forming infinite chains. The nature of the anion···anion interaction has been studied considering two possibilities: (i) a π-hole coinage bond or (ii) σ-hole halogen bond using high-level density functional theory calculations, the quantum theory of atoms in molecules, and the noncovalent interaction plot index.

Elucidating the Nature of Interactions in Collagen Triple-Helix Wrapping.

Collagen is the most abundant protein family in the animal kingdom. Its structural motif envisages three polypeptide chains coiled in the so-called collagen triple helix. Depending on the triplet amino acid sequence of the chains, collagen has different helical arrangements. Such atomic-scale structural variations have a large impact on the large-scale structure of collagen. In this Letter, we elucidate the interactions that are responsible for a specific helical pattern of the collagen protein by means of DFT-D-based computer simulations. We demonstrate that interchain interactions and solvation effects stabilize compact helices over elongated ones. Conversely, elongated helices are stabilized by less geometrical strain and entropic factors. Our computational procedure predicts the collagen helical pattern in agreement with the experimental evidence.

Water Adsorption on MO2 (M = Ti, Ru, and Ir) Surfaces. Importance of Octahedral Distortion and Cooperative Effects.

Understanding metal oxide MO2 (M = Ti, Ru, and Ir)-water interfaces is essential to assess the catalytic behavior of these materials. The present study analyzes the H2O-MO2 interactions at the most abundant (110) and (011) surfaces, at two different water coverages: isolated water molecules and full monolayer, by means of Perdew-Burke-Ernzerhof-D2 static calculations and ab initio molecular dynamics (AIMD) simulations. Results indicate that adsorption preferably occurs in its molecular form on (110)-TiO2 and in its dissociative form on (110)-RuO2 and (110)-IrO2. The opposite trend is observed at the (011) facet. This different behavior is related to the kind of octahedral distortion observed in the bulk of these materials (tetragonal elongation for TiO2 and tetragonal compression for RuO2 and IrO2) and to the different nature of the vacant sites created, axial on (110) and equatorial on (011). For the monolayer, additional effects such as cooperative H-bond interactions and cooperative adsorption come into play in determining the degree of deprotonation. For TiO2, AIMD indicates that the water monolayer is fully undissociated at both (110) and (011) surfaces, whereas for RuO2, water monolayer exhibits a 50% dissociation, the formation of H3O2 - motifs being essential. Finally, on (110)-IrO2, the main monolayer configuration is the fully dissociated one, whereas on (011)-IrO2, it exhibits a degree of dissociation that ranges between 50 and 75%. Overall, the present study shows that the degree of water dissociation results from a delicate balance between the H2O-MO2 intrinsic interaction and cooperative hydrogen bonding and adsorption effects.