Computationally aided design of defect-appended aliphatic amines for CO2 activation within UiO-66.

The introduction of aliphatic amine groups in metal-organic frameworks (MOFs) can improve their ability to capture CO2 at low pressures, driven by chemisorptive formation of C-N bonds. Understanding the chemistry of amine-CO2 interaction within the confined porous space in MOFs is key to design and develop effective CO2 adsorbents. Here, we report a computational study of CO2 adsorption and subsequent formation of carbamic acid within defective UiO-66 functionalised with a series of four amino acids of varying aliphatic chain length (glycine, beta-alanine, gamma-aminobutyric acid and 5-aminovaleric acid). Periodic density functional theory (DFT) calculations suggest that CO2 can be activated by the aliphatic amines only when they are sufficiently close to each other to form hydrogen bonds and stabilise the adduct with CO2, a condition met only by UiO-66 functionalised with gamma-aminobutyric acid and 5-aminovaleric acid. The proposed mechanism involves the formation of a carbamate zwitterionic intermediate, which evolves via a simultaneous double hydrogen transfer with a proximal amine group to a carbamic acid. For the 5-aminovaleric acid case, it is suggested that even the functionalisation of just 16% of the available defective sites can be sufficient to form the CO2-amine adduct. Finally, we also investigate the effect of a possible protonation of the amine groups by the hydroxyl groups in the clusters, finding that this could lead to even more favourable interaction with CO2.

Binding energies of ethanol and ethylamine on interstellar water ices: synergy between theory and experiments.

Experimental and computational chemistry are two disciplines used to conduct research in astrochemistry, providing essential reference data for both astronomical observations and modeling. These approaches not only mutually support each other, but also serve as complementary tools to overcome their respective limitations. Leveraging on such synergy, we characterized the binding energies (BEs) of ethanol (CH3CH2OH) and ethylamine (CH3CH2NH2), two interstellar complex organic molecules (iCOMs), on crystalline and amorphous water ices through density functional theory (DFT) calculations and temperature-programmed desorption (TPD) experiments. Experimentally, CH3CH2OH and CH3CH2NH2 behave similarly, in which desorption temperatures are higher on the water ices than on a bare gold surface. Computed cohesive energies of pure ethanol and ethylamine bulk structures allow describing of the BEs of the pure species deposited on the gold surface, as extracted from the TPD curve analyses. The BEs of submonolayer coverages of CH3CH2OH and CH3CH2NH2 on the water ices cannot be directly extracted from TPD due to their co-desorption with water, but they are computed through DFT calculations, and found to be greater than the cohesive energy of water. The behaviour of CH3CH2OH and CH3CH2NH2 is different when depositing adsorbate multilayers on the amorphous ice, in that, according to their computed cohesive energies, ethylamine layers present weaker interactions compared to ethanol and water. Finally, from the computed BEs of ethanol, ethylamine and water, we can infer that the snow-lines of these three species in protoplanetary disks will be situated at different distances from the central star. It appears that a fraction of ethanol and ethylamine is already frozen on the grains in the water snow-lines, causing their incorporation in water-rich planetesimals.

Formation of Methanol via Fischer-Tropsch Catalysis by Cosmic Iron Sulphide.

Chemical reactions in the gas phase of the interstellar medium face significant challenges due to its extreme conditions (i. e., low gas densities and temperatures), necessitating the presence of dust grains to facilitate the synthesis of molecules inaccessible in the gas phase. While interstellar grains are known to enhance encounter rates and dissipate energy from exothermic reactions, their potential as chemical catalysts remain less explored. Here, we present mechanistic insights into the Fischer-Tropsch-type methanol (FTT-CH3OH) synthesis by reactivity of CO with H2 and using cosmic FeS surfaces as heterogeneous catalysts. Periodic quantum chemical calculations were employed to characterize the potential energy surface of the reactions on the (011) and (001) FeS surfaces, considering different Fe coordination environments and S vacancies. Kinetic calculations were also conducted to assess catalytic capacity and allocate reaction processes within the astrochemical framework. Our findings demonstrate the feasibility of FeS-based astrocatalysis in the FTT-CH3OH synthesis. The reactions and their energetics were elucidated from a mechanistic standpoint. Kinetic analysis demonstrates the temperature dependency of the simulated processes, underscoring the compulsory need of energy sources considering the astrophysical scenario. Our results provide insights into the presence of CH3OH in diverse regions where current models struggle to explain its observational quantity.

Unlocking the surface chemistry of ionic minerals: a high-throughput pipeline for modeling realistic interfaces.

A systematic procedure is introduced for modeling charge-neutral non-polar surfaces of ionic minerals containing polyatomic anions. By integrating distance- and charge-based clustering to identify chemical species within the mineral bulk, our pipeline, PolyCleaver, renders a variety of theoretically viable surface terminations. As a demonstrative example, this approach was applied to forsterite (Mg2SiO4), unveiling a rich interface landscape based on interactions with formaldehyde, a relevant multifaceted molecule, and more particularly in prebiotic chemistry. This high-throughput method, going beyond techniques traditionally applied in the modeling of minerals, offers new insights into the potential catalytic properties of diverse surfaces, enabling a broader exploration of synthetic pathways in complex mineral systems.

Gas-Phase vs. Grain-Surface Formation of Interstellar Complex Organic Molecules: A Comprehensive Quantum-Chemical Study.

Several organic chemical compounds (the so-called interstellar complex organic molecules, iCOMs) have been identified in the interstellar medium (ISM). Examples of iCOMs are formamide (HCONH2), acetaldehyde (CH3CHO), methyl formate (CH3OCHO), or formic acid (HCOOH). iCOMs can serve as precursors of other organic molecules of enhanced complexity, and hence they are key species in chemical evolution in the ISM. The formation of iCOMs is still a subject of a vivid debate, in which gas-phase or grain-surface syntheses have been postulated. In this study, we investigate the grain-surface-formation pathways for the four above-mentioned iCOMs by transferring their primary gas-phase synthetic routes onto water ice surfaces. Our objective is twofold: (i) to identify potential grain-surface-reaction mechanisms leading to the formation of these iCOMs, and (ii) to decipher either parallelisms or disparities between the gas-phase and the grain-surface reactions. Results obtained indicate that the presence of the icy surface modifies the energetic features of the reactions compared to the gas-phase scenario, by increasing some of the energy barriers. Therefore, the investigated gas-phase mechanisms seem unlikely to occur on the icy grains, highlighting the distinctiveness between the gas-phase and the grain-surface chemistry.

Ligand-Aided Glycolysis of PET Using Functionalized Silica-Supported Fe2O3 Nanoparticles.

The development of efficient catalysts for the chemical recycling of poly(ethylene terephthalate) (PET) is essential to tackling the global issue of plastic waste. There has been intense interest in heterogeneous catalysts as a sustainable catalyst system for PET depolymerization, having the advantage of easy separation and reuse after the reaction. In this work, we explore heterogeneous catalyst design by comparing metal-ion (Fe3+) and metal-oxide nanoparticle (Fe2O3 NP) catalysts immobilized on mesoporous silica (SiO2) functionalized with different N-containing amine ligands. Quantitative solid-state nuclear magnetic resonance (NMR) spectroscopy confirms successful grafting and elucidates the bonding mode of the organic ligands on the SiO2 surface. The surface amine ligands act as organocatalysts, enhancing the catalytic activity of the active metal species. The Fe2O3 NP catalysts in the presence of organic ligands outperform bare Fe2O3 NPs, Fe3+-ion-immobilized catalysts and homogeneous FeCl3 salts, with equivalent Fe loading. X-ray photoelectron spectroscopy analysis indicates charge transfer between the amine ligands and Fe2O3 NPs and the electron-donating ability of the N groups and hydrogen bonding may also play a role in the higher performance of the amine-ligand-assisted Fe2O3 NP catalysts. Density functional theory (DFT) calculations also reveal that the reactivity of the ion-immobilized catalysts is strongly correlated to the ligand-metal binding energy and that the products in the glycolysis reaction catalyzed by the NP catalysts are stabilized, showing a significant exergonic character compared to single ion-immobilized Fe3+ ions.

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.

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.

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.

Water formation on interstellar silicates: the role of Fe2+/H2 interactions in the O + H2 → H2O reaction.

Water is the most abundant molecule in the solid state of the interstellar medium, and its presence is critically important for life in space. Interstellar water is thought to be effectively synthesised by reactions occurring on the surfaces of interstellar grains, as gas-phase reactions are not efficient enough to justify its high abundance. In the present work, DFT simulations have been performed to investigate the formation of interstellar water through the O + H2 → H2O reaction on olivinic silicate surfaces that contain Fe2+ cations. The surfaces have been modeled adopting both periodic and cluster approaches. This study focuses on: (i) the stability of the surface models as a function of the electronic states (i.e., quintuplet, triplet and singlet) arising from the presence of the Fe2+ centers, (ii) the adsorption of H2 on the silicate surfaces and its likely activation due to the Fe2+/H2 interactions, and (iii) characterising the energy profiles of the H2O formation reaction complemented with kinetics that include tunneling effects. The results indicate that quintuplet is the most stable electronic state in all the bare surface models. H2 adsorption, however, does not show a clear trend on the relative stabilities of the H2/surface complexes with the electronic states, which is in general more favourable on singlet state surfaces. Finally, reactions simulated on the periodic surfaces show elementary high energy barriers but the reaction is kinetically feasible (considering the long lifetime of interstellar clouds) due to the dominance of tunnelling. In contrast, in the nanocluster models, tunneling effects cannot contribute due to the presence of endoenergetic elementary steps. It is predicted that the reactions on the nanoclusters are only possible if the energy released during the adsorption of the O atom is used to overcome the energy barriers.

Tracing the Primordial Chemical Life of Glycine: A Review from Quantum Chemical Simulations.

Glycine (Gly), NH2CH2COOH, is the simplest amino acid. Although it has not been directly detected in the interstellar gas-phase medium, it has been identified in comets and meteorites, and its synthesis in these environments has been simulated in terrestrial laboratory experiments. Likewise, condensation of Gly to form peptides in scenarios resembling those present in a primordial Earth has been demonstrated experimentally. Thus, Gly is a paradigmatic system for biomolecular building blocks to investigate how they can be synthesized in astrophysical environments, transported and delivered by fragments of asteroids (meteorites, once they land on Earth) and comets (interplanetary dust particles that land on Earth) to the primitive Earth, and there react to form biopolymers as a step towards the emergence of life. Quantum chemical investigations addressing these Gly-related events have been performed, providing fundamental atomic-scale information and quantitative energetic data. However, they are spread in the literature and difficult to harmonize in a consistent way due to different computational chemistry methodologies and model systems. This review aims to collect the work done so far to characterize, at a quantum mechanical level, the chemical life of Gly, i.e., from its synthesis in the interstellar medium up to its polymerization on Earth.

Non-energetic Formation of Ethanol via CCH Reaction with Interstellar H2O Ices. A Computational Chemistry Study.

Ethanol (CH3CH2OH) is a relatively common molecule, often found in star-forming regions. Recent studies suggest that it could be a parent molecule of several so-called interstellar complex organic molecules (iCOMs). However, the formation route of this species remains under debate. In the present work, we study the formation of ethanol through the reaction of CCH with one H2O molecule belonging to the ice as a test case to investigate the viability of chemical reactions based on a "radical + ice component" scheme as an alternative mechanism for the synthesis of iCOMs, beyond the usual radical-radical coupling. This has been done by means of DFT calculations adopting two clusters of 18 and 33 water molecules as ice models. Results indicate that CH3CH2OH can potentially be formed by this proposed reaction mechanism. The reaction of CCH with H2O on the water ice clusters can be barrierless (because of the help of boundary icy water molecules acting as proton-transfer assistants), leading to the formation of vinyl alcohol precursors (H2CCOH and CHCHOH). Subsequent hydrogenation of vinyl alcohol yielding ethanol is the only step presenting a low activation energy barrier. We finally discuss the astrophysical implications of these findings.

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.

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.

Prebiotic Peptide Bond Formation Through Amino Acid Phosphorylation. Insights from Quantum Chemical Simulations.

Condensation reactions between biomolecular building blocks are the main synthetic channels to build biopolymers. However, under highly diluted prebiotic conditions, condensations are thermodynamically hampered since they release water. Moreover, these reactions are also kinetically hindered as, in the absence of any catalyst, they present high activation energies. In living organisms, in the formation of peptides by condensation of amino acids, this issue is overcome by the participation of adenosine triphosphate (ATP), in which, previous to the condensation, phosphorylation of one of the reactants is carried out to convert it as an activated intermediate. In this work, we present for the first time results based on density functional theory (DFT) calculations on the peptide bond formation between two glycine (Gly) molecules adopting this phosphorylation-based mechanism considering a prebiotic context. Here, ATP has been modeled by a triphosphate (TP) component, and different scenarios have been considered: (i) gas-phase conditions, (ii) in the presence of a Mg2+ ion available within the layer of clays, and (iii) in the presence of a Mg2+ ion in watery environments. For all of them, the free energy profiles have been fully characterized. Energetics derived from the quantum chemical calculations indicate that none of the processes seem to be feasible in the prebiotic context. In scenarios (i) and (ii), the reactions are inhibited due to unfavorable thermodynamics associated with the formation of high energy intermediates, while in scenario (iii), the reaction is inhibited due to the high free energy barrier associated with the condensation reactions. As a final consideration, the role of clays in this TP-mediated peptide bond formation route is advocated, since the interaction of the phosphorylated intermediate with the internal clay surfaces could well favor the reaction free energies.

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.

Silicate-mediated interstellar water formation: A theoretical study.

Water is one of the most abundant molecules in the form of solid ice phase in the different regions of the interstellar medium (ISM). This large abundance cannot be properly explained by using only traditional low temperature gas-phase reactions. Thus, surface chemical reactions are believed to be major synthetic channels for the formation of interstellar water ice. Among the different proposals, hydrogenation of atomic O (i.e., 2H + O → H2O) is a chemically "simple" and plausible reaction toward water formation occurring on the surfaces of interstellar grains. Here, novel theoretical results concerning the formation of water adopting this mechanism on the crystalline (010) Mg2SiO4 surface (a unequivocally identified interstellar silicate) are presented. The investigated reaction aims to simulate the formation of the first water ice layer covering the silicate core of dust grains. Adsorption of the atomic O as a first step of the reaction has been computed, results indicating that a peroxo ( O 2 2 - ) group is formed. The following steps involve the adsorption, diffusion and reaction of two successive H atoms with the adsorbed O atom. Results indicate that H diffusion on the surface has barriers of 4-6 kcal mol-1, while actual formation of OH and H2O present energy barriers of 22-23 kcal mol-1. Kinetic study results show that tunneling is crucial for the occurrence of the reactions and that formation of OH and H2O are the bottlenecks of the overall process. Several astrophysical implications derived from the theoretical results are provided as concluding remarks.

Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies.

There is a consensus that the interaction of organic molecules with the surfaces of naturally-occurring minerals might have played a crucial role in chemical evolution and complexification in a prebiotic era. The hurdle of an overly diluted primordial soup occurring in the free ocean may have been overcome by the adsorption and concentration of relevant molecules on the surface of abundant minerals at the sea shore. Specific organic⁻mineral interactions could, at the same time, organize adsorbed molecules in well-defined orientations and activate them toward chemical reactions, bringing to an increase in chemical complexity. As experimental approaches cannot easily provide details at atomic resolution, the role of in silico computer simulations may fill that gap by providing structures and reactive energy profiles at the organic⁻mineral interface regions. Accordingly, numerous computational studies devoted to prebiotic chemical evolution induced by organic⁻mineral interactions have been proposed. The present article aims at reviewing recent in silico works, mainly focusing on prebiotic processes occurring on the mineral surfaces of clays, iron sulfides, titanium dioxide, and silica and silicates simulated through quantum mechanical methods based on the density functional theory (DFT). The DFT is the most accurate way in which chemists may address the behavior of the molecular world through large models mimicking chemical complexity. A perspective on possible future scenarios of research using in silico techniques is finally proposed.

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.

Interaction of organic compounds with chondritic silicate surfaces. Atomistic insights from quantum chemical periodic simulations.

The interaction of 14 different probe organic molecules with the crystalline (010) forsterite Mg2SiO4 surface has been studied at quantum chemical level by means of B3LYP-D2* periodic simulations. The probe molecules are representatives of the class of soluble organic compounds found in carbonaceous meteorites, namely: aliphatic and aromatic hydrocarbons, alcohols, carbonyl compounds, amines, amides, nitrogen heterocycles, carboxylic and hydroxycarboxylic acids, sulfonic and phosphonic acids, amino acids, and carbohydrates. With the exception of the aliphatic and aromatic hydrocarbons, the interaction takes place mainly between the O and N electron donor atoms of the molecules and the outermost Mg surface cations, and/or by hydrogen bonds of H atoms of the molecules with O surface atoms. Dispersion also contributes to the final interaction energies. Each surface/molecule complex has also been characterized by computing its harmonic vibrational spectrum, in which the most significant frequency perturbations caused by the surface interaction are described. With the calculated interaction energies, a trend of the intrinsic affinity of the probe molecules with the silicate surface has been obtained. However, this affinity scale does not correlate with the experimental abundances of the class of compounds found in the Murchison meteorite. A brief discussion of this lack of correlation and the factors that can help us to understand the abundances is provided.