How Does Silica Catalyze the Amide Bond Formation under Dry Conditions? Role of Specific Surface Silanol Pairs

Reaction with Water Vapor Defines Surface Reconstruction and Membranolytic Activity of Quartz Milled in Different Molecular Environments

Industrial processing of quartz (SiO2) and quartz-containing materials produces toxic dust. Fracturing quartz crystals opens the Si‒O bond and produces highly reactive surface species which mainly react with molecules like water and oxygen. This surface-reconstruction process forms silanol (Si‒OH) on the quartz surface, which can damage biological membranes under specific configurations. To comprehend the impact of the quartz surface restructuring on membranolytic activity, the formation and reactivity of quartz radicals produced in four distinct molecular environments with electron paramagnetic resonance (EPR) spectroscopy are evaluated and their membranolytic activity is measured through in vitro hemolysis test. The four molecular environments are formulated with and without molecular water vapor and oxygen (±H2O/±O2). The absence of water favored the formation of surface radical species. In water-rich environments, diamagnetic species prevailed due to radical recombination. Quartz milled in -H2O/±O2 acquired membranolytic activity when exposed to water vapor, unlike quartz milled in +H2O/±O2. After being stabilized by reaction with water vapor, the membranolytic activity of quartz is maintained over time. It is demonstrated that the type and the reactivity of radical sites on quartz are modulated by the outer molecular environment, ultimately determining the biological activity of milled quartz dust.

Amino Acid Polymerization on Silica Surfaces

The polymerization of unactivated amino acids (AAs) is an important topic because of its applications in various fields including industrial medicinal chemistry and prebiotic chemistry. Silica as a promoter for this reaction, is of great interest owing to its large abundance and low cost. The amide/peptide bond synthesis on silica has been largely demonstrated but suffers from a lack of knowledge regarding its reaction mechanism, the key parameters, and surface features that influence AA adsorption and reactivity, the selectivity of the reaction product, the role of water in the reaction, etc. The present review addresses these problems by summarizing experimental and modeling results from the literature and attempts to rationalize some apparent divergences in published results. After briefly presenting the main types of silica surface sites and other relevant macroscopic features, we discuss the different deposition procedures of AAs, whose importance is often neglected. We address the possible AA adsorption mechanisms including covalent grafting and H-bonding and show that they are highly dependent on silanol types and density. We then consider how the adsorption mechanisms determine the occurrence and outcome of AA condensation (formation of cyclic dimers or of long linear chains), and outline some recent results that suggest significant polymerization selectivity in systems containing several AAs, as well as the formation of specific elements of secondary structure in the growing polypeptide chains.

Physico-Chemical Approaches to Investigate Surface Hydroxyls as Determinants of Molecular Initiating Events in Oxide Particle Toxicity

The study of molecular recognition patterns is crucial for understanding the interactions between inorganic (nano)particles and biomolecules. In this review we focus on hydroxyls (OH) exposed at the surface of oxide particles (OxPs) which can play a key role in molecular initiating events leading to OxPs toxicity. We discuss here the main analytical methods available to characterize surface OH from a quantitative and qualitative point of view, covering thermogravimetry, titration, ζ potential measurements, and spectroscopic approaches (NMR, XPS). The importance of modelling techniques (MD, DFT) for an atomistic description of the interactions between membranes/proteins and OxPs surfaces is also discussed. From this background, we distilled a new approach methodology (NAM) based on the combination of IR spectroscopy and bioanalytical assays to investigate the molecular interactions of OxPs with biomolecules and membranes. This NAM has been already successfully applied to SiO₂ particles to identify the OH patterns responsible for the OxPs' toxicity and can be conceivably extended to other surface-hydroxylated oxides.

Nearly free silanols drive the interaction of crystalline silica polymorphs with membranes: Implications for mineral toxicity

Crystalline silica (CS) is a well-known hazardous material that causes severe diseases including silicosis, lung cancer, and autoimmune diseases. However, the hazard associated to crystalline silica is extremely variable and depends on some specific characteristics, including crystal structure and surface chemistry. The crystalline silica polymorphs share the SiO₂ stoichiometry and differentiate for crystal structure. The different crystal lattices in turn expose differently ordered hydroxyl groups at the crystal surface, i.e., the silanols. The nearly free silanols (NFS), a specific population of weakly interacting silanols, have been recently advanced as the key surface feature that governs recognition mechanisms between quartz and cell membrane, initiating toxicity. We showed here that the nearly free silanols occur on the other crystalline silica polymorphs and take part in the molecular interactions with biomembranes. A set of crystalline silica polymorphs, including quartz, cristobalite, tridymite, coesite, and stishovite, was physico-chemically characterized and the membranolytic activity was assessed using red blood cells as model membranes. Infrared spectroscopy in highly controlled conditions was used to profile the surface silanol topochemistry and the occurrence of surface nearly free silanols on crystalline silica polymorphs. All crystalline silica polymorphs, but stishovite were membranolytic. Notably, pristine stishovite did not exhibited surface nearly free silanols. The topochemistry of surface silanols was modulated by thermal treatments, and we showed that the occurrence of nearly free silanols paralleled the membranolytic activity for the crystalline silica polymorphs. These results provide a comprehensive understanding of the structure-activity relationship between nearly free silanols and membranolytic activity of crystalline silica polymorphs, offering a possible clue for interpreting the molecular mechanisms associated with silica hazard and bio-minero-chemical interfacial phenomena, including prebiotic chemistry.

Polypeptide Chain Growth Mechanisms and Secondary Structure Formation in Glycine Gas-Phase Deposition on Silica Surfaces

Peptide formation by amino acids condensation represents a crucial reaction in the quest of the origins of life as well as in synthetic chemistry. However, it is still poorly understood in terms of efficiency and reaction mechanism. In the present work, peptide formation has been investigated through thermal condensation of gas-phase glycine in fluctuating silica environments as a model of prebiotic environments. In-situ IR spectroscopy measurements under a controlled atmosphere reveal that a humidity fluctuating system subjected to both temperature and water activity variations results in the formation of more abundant peptides compared to a dehydrated system subjected only to temperature fluctuations cycles. A model is proposed in which hydration steps result in the hydrolysis and redistribution of the oligomers formed during previous deposition in dry conditions. This results in the formation of self-assembled aggregates with well-defined secondary structures (especially β-sheets). Upon further monomers feeding, structural elements are conserved in newly growing chains, with indications of templated polymerization. The structural dynamics of peptides were also evaluated. Rigid self-assembled structures with a high resistance to further wetting/drying cycles and inaccessibility to isotopic exchange were present in the humidity fluctuating system compared to more flexible structures in the dehydrated system. The resistance and growth of self-assembled structures were also investigated for an extended duration of Gly deposition using isotope labeling.

Emergence of Order in Origin-of-Life Scenarios on Mineral Surfaces: Polyglycine Chains on Silica

The polymerization of amino acids (AAs) to peptides on oxide surfaces has attracted interest owing to its high importance in biotechnology, prebiotic chemistry, and origin of life theories. However, its mechanism is still poorly understood. We tried to elucidate the reactivity of glycine (Gly) from the vapor phase on the surface of amorphous silica under controlled atmosphere at 160 °C. Infrared (IR) spectroscopy reveals that Gly functionalizes the silica surface through the formation of ester species, which represent, together with the weakly interacting silanols, crucial elements for monomers activation and polymerization. Once activated, β-turns start to form as initiators for the growth of long linear polypeptides (poly-Gly) chains, which elongate into ordered structures containing both β-sheet and helical conformations. The work also points to the role of water vapor in the formation of further self-assembled β-sheet structures that are highly resistant to hydrolysis.

Building the uracil skeleton in primitive ponds at the origins of life: carbamoylation of aspartic acid

A large set of nucleobases and amino acids is found in meteorites, implying that several chemical reservoirs are present in the solar system. The "geochemical continuity" hypothesis explores how protometabolic paths developed from so-called "bricks" in an enzyme-free prebiotic world and how they affected the origins of life. In the living cell, the second step of synthesizing uridine and cytidine RNA monomers is a carbamoyl transfer from a carbamoyl donor to aspartic acid. Here we compare two enzyme-free scenarios: aqueous and mineral surface scenarios in a thermal range up to 250 °C. Both processes could have happened in ponds under open atmosphere on the primeval Earth. Carbamoylation of aspartic acid with cyanate in aqueous solutions at 25 °C gives high N-carbamoyl aspartic acid yields within 16 h. It is important to stress that, while various molecules could be efficient carbamoylating agents according to thermodynamics, kinetics plays a determining role in selecting prebiotically possible pathways.

Leucine on Silica: A Combined Experimental and Modeling Study of a System Relevant for Origins of Life, and the Role of Water Coadsorption

Leucine on silica constitutes an interesting system from the point of view of origins of life studies since leucine coadsorbed on SiO₂ together with glutamic acid can give rise to rather long linear polypeptides upon activation. It is also an ideal system to test methods of molecular characterization of biomolecules deposited on mineral surfaces since it combines a small-scale model of peptides and proteins, which are among the most important components of biodevices, with one of the most widely used inorganic materials. We have deposited l-leucine on a high surface fumed silica in the submonolayer range and characterized it by a multipronged approach including macroscopic information (thermogravimetry, X-ray diffraction), in situ spectroscopic methods (IR, multinuclear solid-state NMR including single-pulse and CP-MAS, 2-D HETCOR), and molecular modeling by density functional theory (DFT), including calculation of NMR parameters. Specific information can be obtained on the adsorption and interaction mechanism. Leucine is rather strongly adsorbed without any covalent bonds, through the formation of a specific lattice of H-bonds that often involve coadsorbed water molecules. Its state is indeed strongly dependent on the drying procedure: insufficient drying results in liquid-like surroundings for the leucine functional groups, while vacuum drying only retains a limited number of waters (of the order of 5 per leucine molecule). The most stable models have zwitterionic leucine interacting directly with surface silanols through their ammonium group, while the carboxylate interacts through bridging waters. Experimental NMR chemical shifts are satisfactorily predicted for these models, and leucine can be viewed as a probe for specific groups of surface sites known as silanol nests.

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.

Expeditious base-free solid-state reaction between phenyl boronates and hydrogen peroxide on silica gel

The expeditious base-free reaction between a phenyl boronate film and H2O2 vapor can be realized on a silica gel surface, playing an important role in sensor manufacturing applications and chemical production.

Water-Assisted Chemical Route Towards the Oxygen Evolution Reaction at the Hydrated (110) Ruthenium Oxide Surface: Heterogeneous Catalysis via DFT-MD and Metadynamics Simulations

Notwithstanding that RuO₂ is a promising catalyst for the oxygen evolution reaction (OER), a plethora of fundamental details on its catalytic properties are still elusive, severely limiting its large‐scale deployment. It is also established experimentally that corrosion and wettability of metal oxides can, in fact, enhance the catalytic activity for OER owing to the formation of a hydrated surface layer. However, the mechanistic interplay between surface wettability, interfacial water dynamics and OER across RuO₂, and what degree these processes are correlated are still debated. Herein, spin‐polarized Density Functional Theory Molecular Dynamics (DFT‐MD) simulations, coupled with advanced enhanced sampling methods in the well‐tempered metadynamics framework, are applied to gain a global understanding of RuO₂ aqueous interface (explicit water solvent) in catalyzing the OER, and hence possibly help in the design of novel catalysts in the context of photochemical water oxidation. The present study quantitatively assesses the free‐energy barriers behind the OER at the (110)‐RuO₂ catalyst surface revealing plausible pathways composing the reaction network of the O₂ evolution. In particular, OER is investigated at room temperature when such a surface is exposed to both gas‐phase and liquid‐phase water. Albeit a unique efficient pathway has been identified in the gas‐phase OER, a surprisingly lowest‐free‐energy‐requiring reaction route is possible when (110)‐RuO₂ is in contact with explicit liquid water. By estimating the free‐energy surfaces associated to these processes, we reveal a noticeable water‐assisted OER mechanism which involves a crucial proton‐transfer‐step assisted by the local water environment. These findings pave the way toward the systematic usage of DFT‐MD coupled with metadynamics techniques for the fine assessment of the activity of catalysts, considering finite‐temperature and explicit‐solvent effects.

Infrared harmonic features of collagen models at B3LYP-D3: From amide bands to the THz region

In this paper, we have studied the vibrational spectral features for the collagen triple helix using a dispersion corrected hybrid density functional theory (DFT-D) approach. The protein is simulated by an infinite extended polymer both in the gas phase and in a water micro-solvated environment. We have adopted proline-rich collagen models in line with the high content of proline in natural collagens. Our scaled harmonic vibrational spectra are in very good agreement with the experiments and allow for the peak assignment of the collagen amide I and III bands, supporting or questioning the experimental interpretation by means of vibrational normal modes analysis. Furthermore, we demonstrated that IR spectroscopy in the THz region can detect the small variations inherent to the triple helix helicity (10/3 over 7/2), thus elucidating the packing state of the collagen. So far, identifying the collagen helicity is only possible by means of crystal x-ray diffraction.

Mechanochemical Prebiotic Peptide Bond Formation*

The presence of amino acids on the prebiotic Earth, either stemming from endogenous chemical routes or delivered by meteorites, is consensually accepted. Prebiotically plausible pathways to peptides from inactivated amino acids are still unclear as most oligomerization approaches rely on thermodynamically disfavored reactions in solution. Now, a combination of prebiotically plausible minerals and mechanochemical activation enables the oligomerization of glycine at ambient temperature in the absence of water. Raising the reaction temperature increases the degree of oligomerization concomitantly with the formation of a commonly unwanted cyclic glycine dimer (DKP). However, DKP is a productive intermediate in the mechanochemical oligomerization of glycine. The findings of this research show that mechanochemical peptide bond formation is a dynamic process that provides alternative routes towards oligopeptides and establishes new synthetic approaches for prebiotic chemistry.

Silicon compounds as stoichiometric coupling reagents for direct amidation

Despite being one of the most frequently carried out chemical reactions in industry, there is currently no amidation protocol that is regarded as safe, high yielding, environmentally friendly and inexpensive. The direct amidation of a carboxylic acid with an amine is viewed as an inherently good solution for developing such a protocol. Since the 1960s, there has been a gradual development in the use of silicon reagents for direct amidation. This review covers the methods published to April 2021 for silicon reagent mediated direct amidation of a carboxylic acid with an amine. This review also covers the use of polymeric SiO2 to promote direct amidation.

Primordial bioenergy sources: The two facets of adenosine triphosphate

Life requires energy to exist, to reproduce and to survive. Two major hypotheses have been put forward concerning the source of this energy at the very early stages of life evolution: (i) abiotic organics either brought to Earth by comets and/or meteorites, or produced at its atmosphere, and (ii) mineral surface-dependent bioinorganic catalytic reactions. Considering the latter possibility, I propose that, besides being a precursor of nucleic acids, adenosine triphosphate (ATP), which probably was used very early to improve the fidelity of nucleic acid polymerization, played an essential role in the transition between mineral-bound protocells and their free counterparts. Indeed, phosphorylation by ATP renders carboxylate groups electrophilic enough to react with nucleophiles such as amines, an effect that, thanks to their Lewis acid character, also have dehydrated metal ions on mineral surfaces. Early ATP synthesis for metabolic processes most likely depended on substrate level phosphorylation. However, the exaptation of a hexameric helicase-like ATPase and a transmembrane H⁺ pump (which evolved to counteract the acidity caused by fermentation reactions within the protocell) generated a much more efficient membrane-bound ATP synthase that uses chemiosmosis to make ATP.

Acidity of SiO2-Supported Metal Oxides in the Presence of H2O Using the Adsorption Equilibrium Infrared Spectroscopy Method: 1. Adsorption and Coadsorption of NH3 and H2O on SiO2

The present study is dedicated to the characterization (identification, heats of adsorption, and coverages) of the adsorbed species formed by the adsorption and coadsorption of NH₃ and H₂O on two SiO₂ solids. Adsorption equilibrium infrared spectroscopy allowed us (a) to show that NH₃ and H₂O are mostly adsorbed on free SiOH groups via H bonds and (b) to determine their individual heats of adsorption: 53 and 49 kJ/mol, whatever be their coverages (Langmuir adsorption model), for NH_3ads and H₂O_ads, respectively. These values consistent with the microcalorimetry literature data explain that their coverages are decreased upon NH₃-H₂O coadsorption, considering a competitive Langmuir model. However, the temperature-programmed adsorption equilibrium procedure achieved from MS data indicated that a minor amount of other NH₃ species (not detected using Fourier-transform infrared) is more strongly adsorbed and that hydrolysis of SiOSi siloxane by H₂O could occur in parallel. NH₃-H₂O coadsorption leads to the formation of NH₄⁺ species, which involves H₂O adsorbed species. Both NH₃ and H₂O are not adsorbed above 450 K, which means that the SiO₂ contribution to the characterization of the acidity of metal oxide catalysts supported on SiO₂ using NH₃ as the probe molecule in the presence of H₂O is negligible above this temperature.

Acidity of SiO2-Supported Metal Oxides in the Presence of H2O Using the AEIR Method: 2. Adsorption and Coadsorption of NH3 and H2O on TiO2/SiO2 Catalysts

Two different TiO₂/SiO₂ compounds containing TiO₂ nanodomains dispersed over SiO₂ were investigated applying the AEIR method at the adsorption equilibrium of NH₃ and H₂O from 300 to 723 K, particularly for the measurement of the individual heats of adsorption of the different species on Lewis acidic sites (LAS) and Brønsted acidic sites (BAS) as evaluation of the strength of the sites. It revealed two types of NH₃ adsorption sites: the first ones could correspond either to NH₃ species H-bonded to free OH groups or to coordinated weak LAS (named L1). The second ones (L2) were attributed to strongest LAS similar to those present at the surface of TiO₂ nanocrystallites. They also correspond to the stronger adsorption sites of H₂O. Two types of Brønsted acid sites (BAS) were additionally evidenced by the AEIR method and proposed to be specifically located on the Si-O-Ti bridging bonds at the TiO₂/SiO₂ interface. The heats of adsorption of the different adsorbed species provided by the AEIR method were consistent with literature data on average values of the heats of adsorption of NH₃ and H₂O from microcalorimetry measurements. The surface acidity of the two compounds in the presence of H₂O was determined using NH₃-H₂O coadsorption. At T ≥ 473 K, the NH₃ species on the L2 sites were not significantly displaced from the surface whatever the partial pressure of H₂O studied in agreement with the Temkin competitive model using the individual heats of adsorption of the NH₃ and H₂O species. This model also revealed the presence of a small amount of H₂O species adsorbed on L2 sites allowing H₂O dissociation or/and hydrolysis of SiOTi or TiOTi bridges, leading to the formation of a much higher amount of BAS. Therefore, this original work combining the AEIR method and the Temkin competitive model provided new insights for understanding water effects on acidic oxide catalysts.

Nearly free surface silanols are the critical molecular moieties that initiate the toxicity of silica particles

Inhalation of silica particles can induce inflammatory lung reactions that lead to silicosis and/or lung cancer when the particles are biopersistent. This toxic activity of silica dusts is extremely variable depending on their source and preparation methods. The exact molecular moiety that explains and predicts this variable toxicity of silica remains elusive. Here, we have identified a unique subfamily of silanols as the major determinant of silica particle toxicity. This population of "nearly free silanols" (NFS) appears on the surface of quartz particles upon fracture and can be modulated by thermal treatments. Density functional theory calculations indicates that NFS locate at an intersilanol distance of 4.00 to 6.00 Å and form weak mutual interactions. Thus, NFS could act as an energetically favorable moiety at the surface of silica for establishing interactions with cell membrane components to initiate toxicity. With ad hoc prepared model quartz particles enriched or depleted in NFS, we demonstrate that NFS drive toxicity, including membranolysis, in vitro proinflammatory activity, and lung inflammation. The toxic activity of NFS is confirmed with pyrogenic and vitreous amorphous silica particles, and industrial quartz samples with noncontrolled surfaces. Our results identify the missing key molecular moieties of the silica surface that initiate interactions with cell membranes, leading to pathological outcomes. NFS may explain other important interfacial processes involving silica particles.

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.

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.

Kinetic and Binding Studies Reveal Cooperativity and Off-Cycle Competition for H-Bonding Catalysis with Silsesquioxane Silanols

The catalytic activity, kinetics, and quantification of H-bonding ability of incompletely condensed polyhedral oligomeric silsesquioxane (POSS) silanols are reported. POSS-triols, a homogeneous model for vicinal silica surface sites, exhibit enhanced H-bonding compared with other silanols and alcohols as quantified using a ³¹ P NMR probe. Evaluation of a Friedel-Crafts addition reaction shows that phenyl-POSS-triol is active as an H-bond donor catalyst whereas other POSS silanols studied are not. An in-depth kinetic study (using RPKA and VTNA) highlights the concentration-dependent H-bonding behavior of POSS-triols, which is attributed to intermolecular association forming an off-cycle dimeric species. Binding constants provide additional support for reduced H-bond ability at higher concentrations, which is attributed to competitive association. POSS-triol self-association disrupts H-bond donor abilities relevant for catalysis by reducing the concentration of active monomeric catalyst.

Thermodynamic Impact of Mineral Surfaces on Amino Acid Polymerization: Aspartate Dimerization on Goethite

This article presents a thermodynamic predictive scheme for amino acid polymerization in the presence of minerals as a function of various environmental parameters (pH, ionic strength, amino acid concentration, and the solid/water ratio) using l-aspartate (Asp) and goethite as a model combination. This prediction is enabled by the combination of the surface adsorption constants of amino acid and its polymer, determined from the extended triple layer model characterization of the corresponding experimental results, with the thermodynamic data of these organic compounds in water reported in the literature. Calculations for the Asp-goethite system showed that the goethite surface drastically shifts the Asp monomer-dipeptide equilibrium toward the dipeptide side; when the dimerization of 0.1 mM Asp was considered in the presence of 10 m² L^-1 of goethite, an Asp dipeptide concentration around 10⁵ times larger was computed to be thermodynamically attainable compared with that in the absence of goethite at acidic pH (4-5) and low ionic strength (0.1 mM NaCl). Under this condition, the dipeptide-to-monomer molecular ratio in the adsorbed state reached 20%. In contrast, no significant enhancement by goethite was predicted at alkaline pH (>8), where the electrostatic interactions of the goethite surface with Asp and Asp dipeptide are weak. Thus, mineral surfaces should have had a significant impact on the thermodynamics of prebiotic peptide bond formation on the early Earth, although the influences likely depended largely on the environmental conditions. Future experimental studies for various amino acid-mineral interactions using our proposed methodology will provide a quantitative constraint on favorable geochemical settings for the chemical evolution on Earth. This approach can also offer important clues for future exploration of extraterrestrial life.

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.

Facile Peptide Bond Formation: Effective Interplay between Isothiazolone Rings and Silanol Groups at Silver/Iron Oxide Nanocomposite Surfaces

Proportional to considerable progress in protein-drug conjugations, attention to the efficient peptide coupling reagents is being increased. Hence, in this study, a versatile heterogeneous nanoscale reagent is presented for chemical, biological, and medical purposes. A combination of silver and silica-coated iron oxide nanoparticles (Ag/Fe₃O₄) has been well functionalized with isothiazolone rings via a silver-modified Heck mechanism. An appropriate condition is provided for peptide bond formation through the surface interplay between silanol groups and the loaded isothiazolone rings. A logical mechanism including a series of successive covalent bonds onto the surface of Ag/Fe₃O₄ nanocomposites is suggested for this catalyzed peptide bond formation. Accurate comparisons have been made to obtain the optimum value of the nanocatalyst and suitable conditions. As an additional application, the biological activity of the desired product has also been investigated through antibacterial assay tests. The results showed that our desired product could also be used as an effective heterogeneous nanoscale antibacterial agent for different purposes. In this regard, all of the essential structural and practical analyses have been carried out and precisely interpreted.

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.

Formamide Adsorption at the Amorphous Silica Surface: A Combined Experimental and Computational Approach

Mineral surfaces have been demonstrated to play a central role in prebiotic reactions, which are understood to be at the basis of the origin of life. Among the various molecules proposed as precursors for these reactions, one of the most interesting is formamide. Formamide has been shown to be a pluripotent molecule, generating a wide distribution of relevant prebiotic products. In particular, the outcomes of its reactivity are strongly related to the presence of mineral phases acting as catalysts toward specific reaction pathways. While the mineral–products relationship has been deeply studied for a large pool of materials, the fundamental description of formamide reactivity over mineral surfaces at a microscopic level is missing in the literature. In particular, a key step of formamide chemistry at surfaces is adsorption on available interaction sites. This report aims to investigate the adsorption of formamide over a well-defined amorphous silica, chosen as a model mineral surface. An experimental IR investigation of formamide adsorption was carried out and its outcomes were interpreted on the basis of first principles simulation of the process, adopting a realistic model of amorphous silica.