| 1. |
- Awad, Mahmoud E., et al.
(author)
-
Modeling of the adsorption of a protein-fragment on kaolinite with potential antiviral activity
- 2020
-
In: Applied Clay Science. - : Elsevier. - 0169-1317 .- 1872-9053. ; 199
-
Journal article (peer-reviewed)abstract
- 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.
|
|
| 2. |
- Escamilla-Roa, Elizabeth, et al.
(author)
-
Adsorption of methane and CO2 onto olivine surfaces in Martian dust conditions
- 2018
-
In: Planetary and Space Science. - : Elsevier. - 0032-0633 .- 1873-5088. ; 153, s. 163-171
-
Journal article (peer-reviewed)abstract
- Methane has been detected on all planets of our Solar System, and most of the larger moons, as well as in dwarf-planets like Pluto and Eric. The presence of this molecule in rocky planets is very interesting because its presence in the Earth's atmosphere is mainly related to biotic processes. Space instrumentation in orbiters around Mars has detected olivine on the Martian soil and dust. On the other hand the measurements of methane from the Curiosity rover report detection of background levels of atmospheric methane with abundance that is lower than model estimates of ultraviolet degradation of accreted interplanetary dust particles or carbonaceous chondrite material. Additionally, elevated levels of methane about this background have been observed implying that Mars is episodically producing methane from an additional unknown source, making the reasons of these temporal fluctuations of methane a hot topic in planetary research. The goal of this study is to investigate at atomic level the interactions during the adsorption processes of methane and other Mars atmospheric species (CO2, H2O) on forsterite surfaces, through electronic structure calculations based on the Density Functional Theory (DFT). We propose two models to simulate the interaction of adsorbates with the surface of dust mineral, such as binary mixtures (5CH4+5H2O/5CH4+5CO2) and as a semi-clathrate adsorption. We have obtained interesting results of the adsorption process in the mixture 5CH4+5CO2. Associative and dissociative adsorptions were observed for water and CO2 molecules. The methane molecules were only trapped and held by water or CO2 molecules. In the dipolar surface, the adsorption of CO2 molecules produced new species: one CO from a CO2 dissociation, and, two CO2 molecules chemisorbed to mineral surface forming a carbonate group. Our results suggest that CO2 has a strong interaction with the mineral surface when methane is present. These results could be confirmed after the analysis of the data from the upcoming remote and in-situ observations on Mars, as those to be performed by instruments on the ESA's ExoMars Trace Gas Orbiter and ExoMars rover.
|
|
| 3. |
- Escamilla-Roa, Elizabeth, et al.
(author)
-
Chemobrionic Fabrication of Hierarchical Self‐Assembling Nanostructures of Copper Oxide and Hydroxide
- 2019
-
In: ChemSystemsChem. - : John Wiley & Sons. - 2570-4206. ; 1:3
-
Journal article (peer-reviewed)abstract
- Copper oxide nanostructures have great potential use in a plethora of nanotechnology applications including nanoelectronics, photovoltaics, sensors, electrochemistry, and pharmacology. In the present work we show how hierarchically nano‐structured copper oxide and hydroxide may be prepared through self‐assembly from CuSO4 salt and silicate solutions using the chemobrionic growth process of a chemical garden. Procedures were explored using the cupric salt in either solid (pellet and seed growth methods) or liquid phase (fluid injection techniques). Self‐assembling nanostructures were characterized by means of environmental scanning electron microscopy (ESEM) with energy‐dispersive X‐ray spectroscopy (EDX) analysis, micro‐Raman spectroscopy and X‐ray diffraction. Our results show the formation of crystalline aggregates of copper oxide and hydroxide in complex hierarchical nanostructured forms including fans, flowers, petals, skeins, lentils, and sheaves. Analytical methods corroborate that these nanostructures may be selected in shape and chemical composition with the reaction conditions.
|
|
| 4. |
- Escamilla-Roa, Elizabeth, et al.
(author)
-
DFT study of electronic and redox properties of TiO2 supported on olivine for modelling regolith on Moon and Mars conditions
- 2020
-
In: Planetary and Space Science. - : Elsevier. - 0032-0633 .- 1873-5088. ; 180
-
Journal article (peer-reviewed)abstract
- Titanium dioxide TiO2 is one of the most studied oxides in photocatalysis, due to its electronic structure and its wide variety of applications, such as gas sensors and biomaterials, and especially in methane-reforming catalysis. Titanium dioxide and olivine have been detected both on Mars and our Moon. It has been postulated that on Mars photocatalytic processes may be relevant for atmospheric methane fluctuation, radicals and perchlorate productions etc. However, to date no investigation has been devoted to modelling the properties of TiO2 adsorbed on olivine surface.The goal of this study is to investigate at atomic level with electronic structure calculations based on the Density Functional Theory (DFT), the atomic interactions that take place during the adsorption processes for formation of a TiO regolith. This model is formed with different TiO films adsorbed on olivine (forsterite) surfaces, one of the most common minerals in Universe, Earth, Mars, cometary and interstellar dust. We propose three regolith models to simulate the principal phase of titanium oxide (TiO, Ti2O3 and TiO2). The models show different adsorption processes i.e. physisorption and chemisorption. Our results suggest that the TiO is the most reactive phase and produces a strong exothermic effect. Besides, we have detailed, from a theoretical point of view, the effect that has the adsorption process in the electronic properties such as electronic density of state (DOS) and oxide reduction process (redox). This theoretical study can be important to understand the formation of new materials (supports) that can be used as support in the catalytic processes that occur in the Earth, Mars and Moon. Also, it may be important to interpret the present day photochemistry and interaction of regolith and airborne aerosols in the atmosphere on Mars or to define possible catalytic reactions of the volatiles captured on the Moon regolith.
|
|
| 5. |
- Escamilla-Roa, Elizabeth, et al.
(author)
-
DFT study of the reduction reaction of calcium perchlorate on olivine surface : Implications to formation of Martian’s regolith
- 2020
-
In: Applied Surface Science. - : Elsevier. - 0169-4332 .- 1873-5584. ; 512
-
Journal article (peer-reviewed)abstract
- 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, MgO2, and in the formation of ClO3, which through photolysis is known to form ClO-O2. Because of the high UV irradiance that reaches the surface of Mars, this may be a source of O2 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.
|
|
| 6. |
- Escamilla-Roa, Elizabeth, et al.
(author)
-
Self-Assembled Structures Formed in CO2-Enriched Atmospheres: A Case-Study for Martian Biomimetic Forms
- 2022
-
In: Astrobiology. - : Mary Ann Liebert. - 1531-1074 .- 1557-8070. ; 22:7, s. 863-879
-
Journal article (peer-reviewed)abstract
- The aim of this study was to investigate the biomimetic precipitation processes that follow the chemical-garden reaction of brines of CaCl2 and sulfate salts with silicate in alkaline conditions under a Mars-type CO2-rich atmosphere. We characterize the precipitates with Environmental Scanning Electron Microscope micrography, micro-Raman spectroscopy, and X-ray diffractometry. Our analysis results indicate that self-assembled carbonate structures formed with calcium chloride can have vesicular and filamentary features. With magnesium sulfate as a reactant a tentative assignment with Raman spectroscopy indicates the presence of natroxalate in the precipitate. These morphologies and compounds appear through rapid sequestration of atmospheric CO2 by alkaline solutions of silica and salts.
|
|
| 7. |
- Galvez-Martinez, Santos, et al.
(author)
-
Ar+ ion bombardment dictates glycine adsorption on pyrite (100) surface : X-ray photoemission spectroscopy and DFT approach
- 2020
-
In: Applied Surface Science. - : Elsevier. - 0169-4332 .- 1873-5584. ; 530
-
Journal article (peer-reviewed)abstract
- 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.
|
|
| 8. |
- Galvez-Martinez, Santos, et al.
(author)
-
Defects on a pyrite(100) surface produce chemical evolution of glycine under inert conditions : experimental and theoretical approaches
- 2019
-
In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 21:44, s. 24535-24542
-
Journal article (peer-reviewed)abstract
- 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.
|
|
| 9. |
- Hernández-Laguna, Alfonso, et al.
(author)
-
Compressibility of 2M1 muscovite-phlogopite series minerals
- 2019
-
In: Journal of Molecular Modeling. - : Springer. - 1610-2940 .- 0948-5023. ; 25:11
-
Journal article (peer-reviewed)abstract
- Muscovite (Ms) and phlogopite (Phl) belong to the 2:1 dioctahedral and trioctahedral layer silicates, respectively, and are the end members of Ms-Phl series minerals. This series was studied in the 2M1 polytype and modeled by the substitution of three Mg2+ cations in the Phl octahedral sites by two Al3+ and one vacancy, increasing the substitution up to reach the Ms. The series was computationally examined at DFT level as a function of pressure to 9 GPa. Cell parameters as a function of pressure and composition, and bulk moduli as a function of the composition agrees with the existing experimental results. The mixing Gibbs free energy was calculated as a function of composition. From these data, approximated solvi were calculated at increasing pressure. A gap of solubility is found, decreasing the gap of solubility at high pressure.
|
|
| 10. |
- Mahmoud E., Awad, et al.
(author)
-
Adsorption of 5-aminosalicylic acid on kaolinite surfaces at a molecular level
- 2019
-
In: Clay minerals. - : Cambridge University Press. - 0009-8558 .- 1471-8030. ; 54:1, s. 49-56
-
Journal article (peer-reviewed)abstract
- 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.
|
|
