Disentangling the Effects of Laser and Electron Irradiation on AgX (X = Cl, Br, and I): Insights from Quantum Chemical Calculations.

The effects on the lattice structure and electronic properties of different polymorphs of silver halide, AgX (X = Cl, Br, and I), induced by laser irradiation (LI) and electron irradiation (EI) are investigated using a first-principles approach, based on the electronic temperature (Te) within a two-temperature model (TTM) and by increasing the total number of electrons (Ne), respectively. Ab initio molecular dynamics (AIMD) simulations provide a clear visualization of how Te and Ne induce a structural and electronic transformation process during LI/EI. Our results reveal the diffusion processes of Ag and X ions, the amorphization of the AgX lattices, and a straightforward interpretation of the time evolution for the formation of Ag and X nanoclusters under high values of Te and Ne. Overall, the present work provides fine details of the underlying mechanism of LI/EI and promises to be a powerful toolbox for further cross-scale modeling of other semiconductors.

A TD-DFT-Based Study on the Attack of the OH· Radical on a Guanine Nucleotide.

Heavy charged particles induce severe damage in DNA, which is a radiobiological advantage when treating radioresistant tumors. However, these particles can also induce cancer in humans exposed to them, such as astronauts in space missions. This damage can be directly induced by the radiation or indirectly by the attack of free radicals mainly produced by water radiolysis. We previously studied the impact of a proton on a DNA base pair, using the Time Dependent-Density Functional Theory (TD-DFT). In this work, we go a step further and study the attack of the OH· radical on the Guanine nucleotide to unveil how this molecule subsequently dissociates. The OH· attack on the H1', H2', H3', and H5' atoms in the guanine was investigated using the Ehrenfest dynamics within the TD-DFT framework. In all cases, the hydrogen abstraction succeeded, and the subsequent base pair dissociation was observed. The DNA dissociates in three major fragments: the phosphate group, the deoxyribose sugar, and the nitrogenous base, with slight differences, no matter which hydrogen atom was attacked. Hydrogen abstraction occurs at about 6 fs, and the nucleotide dissociation at about 100 fs, which agrees with our previous result for the direct proton impact on the DNA. These calculations may be a reference for adjusting reactive force fields so that more complex DNA structures can be studied using classical molecular dynamics, including both direct and indirect DNA damage.

Disclosing the Biocide Activity of α-Ag2-2xCuxWO4 (0 ≤ x ≤ 0.16) Solid Solutions.

In this work, α-Ag2-2xCuxWO4 (0 ≤ x ≤ 0.16) solid solutions with enhanced antibacterial (against methicillin-resistant Staphylococcus aureus) and antifungal (against Candida albicans) activities are reported. A plethora of techniques (X-ray diffraction with Rietveld refinements, inductively coupled plasma atomic emission spectrometry, micro-Raman spectroscopy, attenuated total reflectance-Fourier transform infrared spectroscopy, field emission scanning electron microscopy, ultraviolet-visible spectroscopy, photoluminescence emissions, and X-ray photoelectron spectroscopy) were employed to characterize the as-synthetized samples and determine the local coordination geometry of Cu2+ cations at the orthorhombic lattice. To find a correlation between morphology and biocide activity, the experimental results were sustained by first-principles calculations at the density functional theory level to decipher the cluster coordinations and electronic properties of the exposed surfaces. Based on the analysis of the under-coordinated Ag and Cu clusters at the (010) and (101) exposed surfaces, we propose a mechanism to explain the biocide activity of these solid solutions.

Selective Synthesis of α-, ß-, and γ-Ag2WO4 Polymorphs: Promising Platforms for Photocatalytic and Antibacterial Materials.

Silver tungstate (Ag2WO4) shows structural polymorphism with different crystalline phases, namely, orthorhombic, hexagonal, and cubic structures that are commonly known as α, ß, and γ, respectively. In this work, these Ag2WO4 polymorphs were selectively and successfully synthesized through a simple precipitation route at ambient temperature. The polymorph-controlled synthesis was conducted by means of the volumetric ratios of the silver nitrate/tungstate sodium dehydrate precursors in solution. The structural and electronic properties of the as-synthesized Ag2WO4 polymorphs were investigated by using a combination of X-ray diffraction and Rietveld refinements, X-ray absorption spectroscopy, X-ray absorption near-edge structure spectroscopy, field-emission scanning electron microscopy images, and photoluminescence. To complement and rationalize the experimental results, first-principles calculations, at the density functional theory level, were carried out, leading to an unprecedented glimpse into the atomic-level properties of the morphology and the exposed surfaces of Ag2WO4 polymorphs. Following the analysis of the local coordination of Ag and W cations (clusters) at each exposed surface of the three polymorphs, the structure-property relationship between the morphology and the photocatalytic and antibacterial activities against amiloride degradation under ultraviolet light irradiation and methicillin-resistant Staphylococcus aureus, respectively, was investigated. A possible mechanism of the photocatalytic and antibacterial activity as well the formation process and growth of the polymorphs is also explored and proposed.

Excessive endosomal TLR signaling causes inflammatory disease in mice with defective SMCR8-WDR41-C9ORF72 complex function.

The SMCR8-WDR41-C9ORF72 complex is a regulator of autophagy and lysosomal function. Autoimmunity and inflammatory disease have been ascribed to loss-of-function mutations of Smcr8 or C9orf72 in mice. In humans, autoimmunity has been reported to precede amyotrophic lateral sclerosis caused by mutations of C9ORF72 However, the cellular and molecular mechanisms underlying autoimmunity and inflammation caused by C9ORF72 or SMCR8 deficiencies remain unknown. Here, we show that splenomegaly, lymphadenopathy, and activated circulating T cells observed in Smcr8-/- mice were rescued by triple knockout of the endosomal Toll-like receptors (TLRs) TLR3, TLR7, and TLR9. Myeloid cells from Smcr8-/- mice produced excessive inflammatory cytokines in response to endocytosed TLR3, TLR7, or TLR9 ligands administered in the growth medium and in response to TLR2 or TLR4 ligands internalized by phagocytosis. These defects likely stem from prolonged TLR signaling caused by accumulation of LysoTracker-positive vesicles and by delayed phagosome maturation, both of which were observed in Smcr8-/- macrophages. Smcr8-/- mice also showed elevated susceptibility to dextran sodium sulfate-induced colitis, which was not associated with increased TLR3, TLR7, or TLR9 signaling. Deficiency of WDR41 phenocopied loss of SMCR8. Our findings provide evidence that excessive endosomal TLR signaling resulting from prolonged ligand-receptor contact causes inflammatory disease in SMCR8-deficient mice.

In situ growth of Ag nanoparticles on α-Ag2WO4 under electron irradiation: probing the physical principles.

Exploiting the plasmonic behavior of Ag nanoparticles grown on α-Ag2WO4 is a widely employed strategy to produce efficient photocatalysts, ozone sensors, and bactericides. However, a description of the atomic and electronic structure of the semiconductor sites irradiated by electrons is still not available. Such a description is of great importance to understand the mechanisms underlying these physical processes and to improve the design of silver nanoparticles to enhance their activities. Motivated by this, we studied the growth of silver nanoparticles to investigate this novel class of phenomena using both transmission electron microscopy and field emission scanning electron microscopy. A theoretical framework based on density functional theory calculations (DFT), together with experimental analysis and measurements, were developed to examine the changes in the local geometrical and electronic structure of the materials. The physical principles for the formation of Ag nanoparticles on α-Ag2WO4 by electron beam irradiation are described. Quantum mechanical calculations based on DFT show that the (001) of α-Ag2WO4 displays Ag atoms with different coordination numbers. Some of them are able to diffuse out of the surface with a very low energy barrier (less than 0.1 eV), thus, initiating the growth of metallic Ag nanostructures and leaving Ag vacancies in the bulk material. These processes increase the structural disorder of α-Ag2WO4 as well as its electrical resistance as observed in the experimental measurements.

Elucidating the real-time Ag nanoparticle growth on α-Ag2WO4 during electron beam irradiation: experimental evidence and theoretical insights.

Why and how Ag is formed when electron beam irradiation takes place on α-Ag2WO4 in a vacuum transmission electron microscopy chamber? To find an answer, the atomic-scale mechanisms underlying the formation and growth of Ag on α-Ag2WO4 have been investigated by detailed in situ transmission electron microscopy (TEM) and field emission scanning electron microscopy (FE-SEM) studies, density functional theory based calculations and ab initio molecular dynamics simulations. The growth process at different times, chemical composition, size distribution and element distribution were analyzed in depth at the nanoscale level using FE-SEM, operated at different voltages (5, 10, 15, and 20 kV), and TEM with energy dispersive spectroscopy (EDS) characterization. The size of Ag nanoparticles covers a wide range of values. Most of the Ag particles are in the 20-40 nm range. The nucleation and formation of Ag on α-Ag2WO4 is a result of structural and electronic changes in the AgOx (x = 2,4, 6, and 7) clusters used as constituent building blocks of this material, consistent with metallic Ag formation. First principle calculations point out that Ag-3 and Ag-4-fold coordinated centers, located in the sub-surface of the (100) surface, are the most energetically favorable to undergo the diffusion process to form metallic Ag. Ab initio molecular dynamics simulations and the nudged elastic band (NEB) method were used to investigate the minimum energy pathways of these Ag atoms from positions in the first slab layer to outward sites on the (100) surface of α-Ag2WO4. The results point out that the injection of electrons decreases the activation barrier for this diffusion step and this unusual behavior results from the presence of a lower energy barrier process.

Adsorption of Pd, Pt, Cu, Ag, and Au monomers on NiAl(110) surface: a comparative study from DFT calculations.

First principles calculations based on periodic density functional theory (DFT) have been used to investigate the structural, energetic and electronic properties of different transition metal atoms (Pd, Pt, Cu, Ag, and Au) on the NiAl(110) surface at low coverages (0.08 and 0.25 monolayer). All adatoms prefer to adsorb on 4-fold coordinated sites interacting with two Al and two Ni atoms and forming polar and covalent bonds, respectively. The calculated negative work function changes are explained by the effect of positive surface image created after adsorption, which induces the polarization of the negatively charged adsorbates. Consequently, for metals with similar electronegativity as Ni (Ag and Cu), this polarization effect becomes more significant and leads to larger negative work function changes, but the charge transferred is small.

Coumarin derivatives for dye sensitized solar cells: a TD-DFT study.

Time dependent density functional theory (TD-DFT) calculations have been carried out to study the electronic structure and the optical properties of five coumarin based dyes: C343, NKX-2311, NKX-2586, NKX-2753 and NKX-2593. We have found out that the position and width of the first band in the electronic absorption spectra, the absorption threshold and the LUMO energy with respect to the conduction band edge are key parameters in order to establish some criteria that allow evaluating the efficiency of coumarin derivatives as sensitizers in Dye Sensitized Solar Cells (DSSC). Those criteria predict the efficiency ordering for the coumarin series in good agreement with the experimental evidence. Presumably, they might be used in the design of new efficient organic based DSSC.

Molecular modification of coumarin dyes for more efficient dye sensitized solar cells.

In this work, new coumarin based dyes for dye sensitized solar cells (DSSC) have been designed by introducing several substituent groups in different positions of the NKX-2311 structure. Two types of substitutions have been considered: the introduction of three electron-donating groups (-OH, -NH(2), and -OCH(3)) and two different substituents with steric effect: -CH(2)-CH(2)-CH(2)- and -CH(2)-HC=CH-. The electronic absorption spectra (position and width of the first band and absorption threshold) and the position of the LUMO level related to the conduction band have been used as theoretical criteria to evaluate the efficiency of the new dyes. The introduction of a -NH(2) group produces a redshift of the absorption maximum position and the absorption threshold, which could improve the cell efficiency. In contrast, the introduction of -CH(2)-CH(2)-CH(2)- does not modify significantly the electronic structure of NKX-2311, but it might prevent aggregation. Finally, -CH(2)-HC=CH- produces important changes both in the electronic spectrum and in the electronic structure of the dye, and it would be expected as an improvement of cell efficiency for these dyes.

Unraveling the MnMoO4 polymorphism: a comprehensive DFT investigation of α, ß, and ω phases.

The MnMoO4 is an environmentally friendly semiconductor material widely employed in technological devices. This material can be obtained on three different polymorphs, and although such phases were reported decades ago, some obscurity over their structure and properties is still perceived. Thus, this work provides a comprehensive DFT investigation of the α, ß, and ω phases of MnMoO4, analyzing their crystalline structure, stability, and electronic and magnetic properties. The results show that all phases of MnMoO4 are stable at room conditions connected by pressure application or long-time high-temperature treatment. The MnMoO4 phases are G-type antiferromagnetic with semiconductor bandgap and have enormous potential to develop magnetic, optical, and electronic devices and photocatalytic-based processes. The results also evidence potential antiviral and antibacterial activities of the three MnMoO4 polymorphs. Supplementary Information: The online version contains supplementary material available at 10.1007/s10853-022-07277-7.

A Theoretical Study on the Structural, Electronic, and Magnetic Properties of Bimetallic Pt13-nNin (N = 0, 3, 6, 9, 13) Nanoclusters to Unveil the Catalytic Mechanisms for the Water-Gas Shift Reaction.

In this work, first-principles calculations by using density functional theory at the GFN-xTB level, are performed to investigate the relative stability and structural, electronic, and magnetic properties of bimetallic Pt13-nNin (n = 0, 3, 6, 9, 13) nanoclusters by using corrected Hammer and Nørskov model. In addition, by employing the reaction path and the energetic span models, the energy profile and the turnover frequency are calculated to disclose the corresponding reaction mechanism of the water-gas shift reaction catalyzed by these nanoclusters. Our findings render that Ni causes an overall shrinking of the nanocluster's size and misalignment of the spin channels, increasing the magnetic nature of the nanoclusters. Pt7Ni6 nanocluster is the most stable as a result of the better coupling between the Pt and Ni d-states. Pt4Ni9 maintains its structure over the reaction cycle, with a larger turnover frequency value than Pt7Ni6. On the other hand, despite Pt10Ni3 presenting the highest value of turnover frequency, it suffers a strong structural deformation over the completion of a reaction cycle, indicating that the catalytic activity can be altered.

An experimental and theoretical approach on stability towards hydrolysis of triethyl phosphate and its effects on the microstructure of sol-gel-derived bioactive silicate glass.

The sol-gel method is versatile and one of the well-established synthetic approaches for preparing bioactive glass with improved microstructure. In a successful approach, alkoxide precursors undergo rapid hydrolysis, followed by immediate condensation leading to the formation of three-dimensional gels. On the other hand, a slow kinetics rate for hydrolysis of one or more alkoxide precursors generates a mismatch in the progression of the consecutive reactions of the sol-gel process, which makes it difficult to form homogeneous multicomponent glass products. The amorphous phase separation (APS) into the gel is thermodynamically unstable and tends to transform into a crystalline form during the calcination step of xerogel. In the present study, we report a combined experimental and theoretical method to investigate the stability towards hydrolysis of triethyl phosphate (TEP) and its effects on the mechanism leading to phase separation in 58S bioactive glass obtained via sol-gel route. A multitechnical approach for the experimental characterization combined with calculations of functional density theory (DFT) suggest that TEP should not undergo hydrolysis by water under acidic conditions during the formation of the sol or even in the gel phase. The activation energy barrier (ΔG‡) showed a height of about 20 kcal·mol-1 for the three stages of hydrolysis and the reaction rates calculated for each stage of TEP hydrolysis were kFHR = 7.0 × 10-3s-1, kSHR = 6.8 × 10-3s-1 and kTHR = 3.5 × 10-3s-1. These results show that TEP remains in the non-hydrolyzed form segregated within the xerogel matrix until its thermal decomposition in the calcination step, when P species preferentially associate with calcium ions (labile species) and other phosphate groups present nearby, forming crystalline domains of calcium pyrophosphates permeated by the silica-rich glass matrix. Together, our data expand the knowledge about the synthesis by the sol-gel method of bioactive glass and establishes a mechanism that explains the role played by the precursor source of phosphorus (TEP) in the phase separation, an event commonly observed for these biomaterials.

Bioactive Ag3PO4/Polypropylene Composites for Inactivation of SARS-CoV-2 and Other Important Public Health Pathogens.

The current unprecedented coronavirus pandemic (COVID-19) is increasingly demanding advanced materials and new technologies to protect us and inactivate SARS-CoV-2. In this research work, we report the manufacture of Ag3PO4 (AP)/polypropylene (PP) composites using a simple method and also reveal their long-term anti-SARS-CoV-2 activity. This composite shows superior antibacterial (against Staphylococcus aureus and Escherichia coli) and antifungal activity (against Candida albicans), thus having potential for a variety of technological applications. The as-manufactured materials were characterized by XRD, Raman spectroscopy, FTIR spectroscopy, AFM, UV-vis spectroscopy, rheology, SEM, and contact angle to confirm their structural integrity. Based on the results of first-principles calculations at the density functional level, a plausible reaction mechanism for the initial events associated with the generation of both hydroxyl radical •OH and superoxide radical anion •O2- in the most reactive (110) surface of AP was proposed. AP/PP composites proved to be an attractive avenue to provide human beings with a broad spectrum of biocide activity.

Templates for wax deposition?

Molecular dynamics simulations have been used to study the behaviour of a liquid mixture of octacosane and heptane between two planar hematite surfaces; one of the surfaces was coated by a monolayer of an imidazoline-based corrosion inhibitor (CI). It was found that the octacosane could be inserted into the CI monolayer when it was aligned with the alkyl tails of the CIs, but the rate for such an insertion was slow. Potential of mean force calculations confirmed that there is a free energy barrier to insertion of octacosane into the CI film, and identified a secondary minimum about 13 A from the surface as a metastable intermediate for insertion. A much more rapid process was adsorption of the octacosane onto the exposed hematite (1012) surface, forming multiple layers and with a packing that was reminiscent of the octacosane crystal structure but with an orientation that matched the topology of the haematite surface.

Aleuritic (9,10,16-trihydroxypalmitic) acid self-assembly on mica.

Aleuritic (9,10,16-trihydroxypalmitic) acid self-assembly on mica from solution has been studied using AFM, ATR-FTIR and MD simulations. The goal of this study is to define the role of hydroxyl groups in the interaction between molecules as reference data to understand the mechanism of formation of synthetic and natural biopolyesters from polyhydroxylated long chain carboxylic acids. In a confined structure, such as the one imposed by a vertically self-assembled layer on mica, aleuritic acid has a tendency to adopt a monolayer configuration ruled by the lateral interactions between molecules via the two secondary hydroxyl groups. This (2D) growth competes with the multilayer formation (3D), which is conditioned by the terminal primary hydroxyl group. As the self-assembly spatial constraint is relaxed, MD has shown that the structure tends to become an amorphous and crosslinked phase that can be characterized by topographic and friction force AFM data.

Elucidating esterification reaction during deposition of cutin monomers from classical molecular dynamics simulations.

The structural behavior of some cutin monomers, when deposited on mica support, was extensively investigated by our research group. However, other events, such as esterification reaction (ER), are still a way to explore. In this paper, we explore possible ER that could occur when these monomers adsorb on support. Although classical molecular dynamics simulations are not able to capture reactive effects, here, we show that they become valuable strategies to analyze the initial structural configurations to predict the most favorable reaction routes. Thus, when depositing aleuritic acid (ALE), it is observed that the loss of capacity to form self-assembled (SA) systems favors different routes to occur ER. In pure ALE bilayers systems, an ER is given exclusively through the -COOH and primary -OH groups. In pure ALE monolayers systems, the ER does not happen when the system is self-assembled. However, for disorganized systems, it is able to occur by two possible routes: -COOH and primary -OH (route 1) and -COOH and secondary -OH (route 2). When palmitic acid (PAL) is added in small quantities, ALE SAMs can now form an ER. In this case, ER occurs mostly through the -COOH and secondary -OH groups. However, when the presence of PAL is dominant, ER can occur with either of both possibilities, that is, routes 1 and 2. Graphical abstract.

Unraveling the relationship between exposed surfaces and the photocatalytic activity of Ag3PO4: an in-depth theoretical investigation.

Over the years, the possibility of using solar radiation in photocatalysis or photodegradation processes has attracted remarkable interest from scientists around the world. In such processes, due to its electronic properties, Ag3PO4 is one of the most important semiconductors. This work delves into the photocatalytic activity, stability, and reactivity of Ag3PO4 surfaces by comparing plane waves with projector augmented wave and localized Gaussian basis set simulations, at the atomic level. The results indicate that the (110) surface, in agreement with previous experimental reports, displays the most suitable characteristics for photocatalytic activity due to its high reactivity, i.e. the presence of a large amount of undercoordinated Ag cations and a high value work function. Beyond the innovative results, this work shows a good synergy between both kinds of DFT approaches.

Electron beam irradiation for the formation of thick Ag film on Ag3PO4.

This study demonstrates that the electron beam irradiation of materials, typically used in characterization measurements, could be employed for advanced fabrication, modification, and functionalization of composites. We developed irradiation equipment using an electron beam irradiation source to be applied in materials modification. Using this equipment, the formation of a thick Ag film on the Ag3PO4 semiconductor is carried out by electron beam irradiation for the first time. This is confirmed by various experimental techniques (X-ray diffraction, field-emission scanning electron microscopy, Raman spectroscopy, and X-ray photoelectron spectroscopy) and ab initio molecular dynamics simulations. Our calculations demonstrate that, at the earlier stages, metallic Ag growth is initiated preferentially at the (110) surface, with the reduction of surface Ag cations forming metallic Ag clusters. As the (100) and (111) surfaces have smaller numbers of exposed Ag cations, the reductions on these surfaces are slower and are accompanied by the formation of O2 molecules.

Understanding segregation processes in SAMs formed by mixtures of hydroxylated and non-hydroxylated fatty acids.

In this paper, we focus on the segregation processes emerging when preparing mixtures with different compositions of aleuritic (9,10,16 trihydroxyhexadecanoic) (ALE) and palmitic (hexadecanoic) (PAL) acids. The combination of atomic force microscopy (AFM) and molecular dynamics (MD) simulations enabled us to prove the role of the functional groups in the formation of self-assembled monolayers (SAMs) on muscovite mica surfaces. MD simulations indicate that segregation processes are favored in high ALE composition mixtures in agreement with the experimental evidence, whereas low ALE compositions promote the co-existence between segregated and dispersed systems. The secondary hydroxyl groups play a central role in the self-assembling mechanism because they control the formation of hydrogen bonding networks guarantying system stability.