Defects on a pyrite(100) surface produce chemical evolution of glycine under inert conditions: Experimental and theoretical approaches

The presence of non-stoichiometric sites on the pyrite(100) surface makes it a suitable substrate for driving the chemical evolution of the amino acid glycine over time, even under inert conditions. Spectroscopic molecular fingerprints prove a transition process from a zwitterionic species to an anionic species over time on the monosulfide enriched surface. By combining experimental and theoretical approaches, we propose a surface mechanism where the interaction between the amino acid species and the surface will be driven by the quenching of the surface states at Fe sites and favoured by sulfur vacancies. This study demonstrates the potential capability of pyrite to act as a surface catalyst.This work has been supported by the MINECO project ESP2017-89053. The Instituto Nacional de Técnica Aeroespacial supported the work performed at CAB. EER is thankful to Javier Martin-Torres, Alfonso Hernández-Laguna and C. M. Pradier for their support and suggestions. This Project has been partially funded by the Spanish State Research Agency (AEI) Project No. MDM-2017-0737 Unidad de Excelencia “María de Maeztu”-Centro de Astrobiología (CSIC-INTA).We acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI).Peer reviewe

Ar+ ion bombardment dictates glycine adsorption on pyrite (1 0 0) surface: X-ray photoemission spectroscopy and DFT approach

Ar ion sputtering on pyrite surfaces leads to the generation of sulfur vacancies and metallic iron. Our research shows that sputtering and annealing processes drive electrostatic changes on the pyrite surface, which play an important role in the molecular adsorption of glycine. While both chemical species (anion and zwitterion) adsorb on a sputtered pyrite surface, the anionic form of glycine is favoured. Nevertheless, in both treatments (sputtered or annealed surfaces), molecules evolve from zwitterionic to anionic species over time. Quantum mechanical calculations based in Density Functional Theory (DFT) suggest the energy required to generate vacancies increases with the number of vacancies produced, and the atomic charge of the Fe atoms that is next to a vacancy increases linearly with the number of vacancies. This leads to enhanced redox processes on the sputtered pyrite surface that favour the adsorption of glycine, which is confirmed experimentally by X-ray Photoemission Spectroscopy (XPS). We have investigated theoretically the efficiency of the adsorption process of the zwitterionic glycine onto vacancies sites: this reaction is exothermic, i.e. is energetically favoured and its energy increases with the number of defects, confirming the increased reactivity observed experimentally. The experiments show a treatment-dependent molecular selectivity of the pyrite surface.This work has been supported by the MINECO projects ESP2017- 89053 and PCIN-2017-098. The Instituto Nacional de Técnica Aeroespacial supported the work performed at CAB and the S.G.M PhD Thesis. This Project has been partially funded by the Spanish State Research Agency (AEI) Project No. MDM-2017-0737 Unidad de Excelencia “María de Maeztu”- Centro de Astrobiología (CSIC-INTA)

Modeling of the adsorption of a protein-fragment on kaolinite with potential antiviral activity

This work aimed at studying the potentiality of interactions between kaolinite surfaces and a protein-fragment (350–370 amino acid units) extracted from the glycoprotein E1 in the transmembrane domain (TMD) of hepatitis C virus capsid. A computational work was performed for locating the potential electrostatic interaction sites between kaolinite aluminol and siloxane surfaces and the residues of this protein-fragment ligand, monitoring the possible conformational changes. This hydrated neutralized kaolinite/protein-fragment system was simulated by means of molecular modeling based on atomistic force fields based on empirical interatomic potentials and molecular dynamic (MD) simulations. The MD calculations indicated that the studied protein-fragment interacted with the kaolinite surfaces with an exothermic process and structural distortions were observed, particularly with the hydrophilic aluminol surface by favorable adsorption energy. The viral units isolation or trapping by the adsorption on the kaolinite nanoparticles producing structural distortion of the peptide ligands could lead to the blockage of the entry on the receptor and hence a lack of viral activity would be produced. Therefore, these findings with the proposed insights could be an useful information for the next experimental and development studies in the area of discovering inhibitors of the global challenged hepatitis and other pathogenic viruses based on the phyllosilicate surface activity. These MD studies can be extended to other viruses like the COVID-19 interacting with silicate minerals surfaces.Authors would like to acknowledge the contribution of the European COST Action CA17120 supported by the EU Framework Program Horizon 2020 and the financial support of the Andalusia Government projects [RNM1897 and RNM363, and CTS-946]; the MINECO and FEDER projects [FIS2016-77692-C2-2-P, PCIN-2017-098].Peer reviewe

DFT study of the cation arrangements in the octahedral and tetrahedral sheets of dioctahedral 2:1 phyllosilicates

Quantum mechanical calculations based on the density functional theory (DFT) are used to study the crystal structures of dioctahedral 2:1 phyllosilicates. The isomorphous cation substitution is investigated by exploring different substitutions of octahedral Al3+ by Mg2+ or Fe3+, tetrahedral substitution of Si4+ by Al3+, and different interlayer cations (IC) (Na+, K+, Ca2+, and Mg2+). Samples with different kinds of layer charges are studied: only tetrahedrally charged, only octahedrally charged, or mixed octahedral/tetrahedral charged. The effect of the relative arrangements of these substitutions on the lattice parameters and total energy is studied. The experimental observation of segregation tendency of Fe3+ and dispersion tendency of Mg2+ in the octahedral sheet is reproduced and explained with reference to the relative energies of the octahedral cation arrangements. These energies are higher than those due to the IC/tetrahedral and IC/octahedral relative arrangements. The tetrahedral and octahedral substitutions that generate charged layers also tend to be dispersed. The octahedral cation exchange potentials change with the IC-charge/ionic radius value

Adsorption of 5-aminosalicylic acid on kaolinite surfaces at a molecular level

The application of clay minerals in therapeutics is becoming important due to their structural and surface physicochemical properties. 5-aminosalicylic acid (5-ASA) is a very common pharmaceutical drug and is used worldwide. The interactions between the 5-ASA molecule and both the aluminol and siloxane surfaces of kaolinite are studied by means of atomistic calculations using force fields based on empirical interatomic potentials and quantum mechanics calculations based on density functional theory. A conformational analysis of 5-ASA has been performed and the anion of 5-ASA was also studied. The calculated adsorption energy values indicate that 5-ASA is likely to be adsorbed on the kaolinite surfaces with greater affinity to the aluminol surface. Hence, kaolinite may be considered as a promising pharmaceutical carrier of 5-ASA

DFT study of the reduction reaction of calcium perchlorate on olivine surface: Implications to formation of Martian's regolith

Perchlorates have been found widespread on the surface of Mars, their origin and degradation pathways are not understood to date yet. We investigate here, from a theoretical point of view, the potential redox processes that take place in the interaction of Martian minerals such as olivine, with anhydrous and hydrated perchlorates. For this theoretical study, we take as mineral substrate the (1 0 0) surface of forsterite and calcium perchlorate salt as adsorbate. Our DFT calculations suggests a reduction pathway to chlorate and chlorite. When the perchlorate has more than 4 water molecules, this mechanism, which does not require high-temperature or high energy sources, results in parallel with the oxidation of the mineral surface, forming magnesium peroxide, MgO, and in the formation of ClO, which through photolysis is known to form ClO-O. Because of the high UV irradiance that reaches the surface of Mars, this may be a source of O on Mars. Our results suggest that this process may be a natural removal pathway for perchlorates from the Martian regolith, which in the presence of atmospheric water for salt hydration, can furthermore lead to the production of oxygen. This mechanism may thus have implications on the present and future habitability of the Martian surface.Authors would like to acknowledge the contribution of the European COST Action CA17120 supported by the EU Framework Programme Horizon 2020, and the Spanish MINECO projects CGL2014-55230-R, FIS2016-77692-C2, PCIN-2017-098. MPZ acknowledges the partial support of the Spanish State Research Agency (AEI) Project No. MDM-2017-0737. E. E. acknowledges to Rafael Esteso for his help with the Graphical Abstract

Molecular structure and ammonia gas adsorption capacity of a Cu(II)-1,10-phenanthroline complex intercalated in montmorillonite by DFT simulations

A hydrated complex of 1,10-phenanthroline with Cu2+ cation was intercalated in the interlayer space of montmorillonite. This intercalation occurs initially by through a cation exchange mechanism in which the charge of the complex cation compensates the excess of the negative charge of the interlayer, then, once the cation exchange capacity (CEC) value has been reached, by direct adsorption of the sulfate salt of this complex (i.e. the cation together with its sulfate counterion). This material has showed interesting entrapping properties of gaseous phases and a peculiar chemical reactivity. However, the complete characterization and explanation of the formation of these materials is difficult with only experimental techniques. Hence, we used computational methods at atomic level to know how are the molecular structure of these complexes and their adsorption capacity of ammonia inside the interlayer confined space of montmorillonite for a better understanding of the experimental behaviour. First Principles calculations were performed based on Density Functional Theory (DFT). The intercalation of the phenanthroline-Cu(II) complex inside the nanoconfined interlayer of montmorillonite is energetically favourable in the relative proportion observed experimentally, being a cation exchange process. The further adsorption of the sulfate salt of the phenanthroline-Cu complex is also energetically possible. The adsorption of ammonia molecules in these montmorillonite-phenanthroline-Cu complexes was also favourable according with experimental behaviour

DFT study of the cation arrangements in the octahedral and tetrahedral sheets of dioctahedral 2:1 phyllosilicates

Quantum mechanical calculations based on the density functional theory (DFT) are used to study the crystal structures of dioctahedral 2:1 phyllosilicates. The isomorphous cation substitution is investigated by exploring different substitutions of octahedral Al3+ by Mg2+ or Fe3+, tetrahedral substitution of Si4+ by Al3+, and different interlayer cations (IC) (Na+, K+, Ca2+, and Mg2+). Samples with different kinds of layer charges are studied: only tetrahedrally charged, only octahedrally charged, or mixed octahedral/tetrahedral charged. The effect of the relative arrangements of these substitutions on the lattice parameters and total energy is studied. The experimental observation of segregation tendency of Fe3+ and dispersion tendency of Mg2+ in the octahedral sheet is reproduced and explained with reference to the relative energies of the octahedral cation arrangements. These energies are higher than those due to the IC/tetrahedral and IC/octahedral relative arrangements. The tetrahedral and octahedral substitutions that generate charged layers also tend to be dispersed. The octahedral cation exchange potentials change with the IC-charge/ionic radius value