Exploring Antiviral Drugs on Monolayer Black Phosphorene: Atomistic Theory and Explainable Machine Learning-Assisted Platform.

Favipiravir (FP) and ebselen (EB) belong to a diverse class of antiviral drugs known for their significant efficacy in treating various viral infections. Utilizing molecular dynamics (MD) simulations, machine learning, and van der Waals density functional theory, we accurately elucidate the binding properties of these antiviral drugs on a phosphorene single-layer. To further investigate these characteristics, this study employs four distinct machine learning models-Random Forest, Gradient Boosting, XGBoost, and CatBoost. The Hamiltonian of antiviral molecules within a monolayer of phosphorene is appropriately trained. The key aspect of utilizing machine learning (ML) in drug design revolves around training models that are efficient and precise in approximating density functional theory (DFT). Furthermore, the study employs SHAP (SHapley Additive exPlanations) to elucidate model predictions, providing insights into the contribution of each feature. To explore the interaction characteristics and thermodynamic properties of the hybrid drug, we employ molecular dynamics and DFT calculations in a vacuum interface. Our findings suggest that this functionalized 2D complex exhibits robust thermostability, indicating its potential as an effective and enabled entity. The observed variations in free energy at different surface charges and temperatures suggest the adsorption potential of FP and EB molecules from the surrounding environment.

Synergy of Small Antiviral Molecules on a Black-Phosphorus Nanocarrier: Machine Learning and Quantum Chemical Simulation Insights.

Favipiravir (FP) and Ebselen (EB) belong to a broad range of antiviral drugs that have shown active potential as medications against many viruses. Employing molecular dynamics simulations and machine learning (ML) combined with van der Waals density functional theory, we have uncovered the binding characteristics of these two antiviral drugs on a phosphorene nanocarrier. Herein, by using four different machine learning models (i.e., Bagged Trees, Gaussian Process Regression (GPR), Support Vector Regression (SVR), and Regression Trees (RT)), the Hamiltonian and the interaction energy of antiviral molecules in a phosphorene monolayer are trained in an appropriate way. However, training efficient and accurate models for approximating the density functional theory (DFT) is the final step in using ML to aid in the design of new drugs. To improve the prediction accuracy, the Bayesian optimization approach has been employed to optimize the GPR, SVR, RT, and BT models. Results revealed that the GPR model obtained superior prediction performance with an R2 of 0.9649, indicating that it can explain 96.49% of the data's variability. Then, by means of DFT calculations, we examine the interaction characteristics and thermodynamic properties in a vacuum and a continuum solvent interface. These results illustrate that the hybrid drug is an enabled, functionalized 2D complex with vigorous thermostability. The change in Gibbs free energy at different surface charges and temperatures implies that the FP and EB molecules are allowed to adsorb from the gas phase onto the 2D monolayer at different pH conditions and high temperatures. The results reveal a valuable antiviral drug therapy loaded by 2D biomaterials that may possibly open a new way of auto-treating different diseases, such as SARS-CoV, in primary terms.

Computational Studies of Auto-Active van der Waals Interaction Molecules on Ultra-Thin Black-Phosphorus Film.

Using the van der Waals density functional theory, we studied the binding peculiarities of favipiravir (FP) and ebselen (EB) molecules on a monolayer of black phosphorene (BP). We systematically examined the interaction characteristics and thermodynamic properties in a vacuum and a continuum, solvent interface for active drug therapy. These results illustrate that the hybrid molecules are enabled functionalized two-dimensional (2D) complex systems with a vigorous thermostability. We demonstrate in this study that these molecules remain flat on the monolayer BP system and phosphorus atoms are intact. It is inferred that the hybrid FP+EB molecules show larger adsorption energy due to the van der Waals forces and planar electrostatic interactions. The changes in Gibbs free energy at different surface charge fluctuations and temperatures imply that the FP and EB are allowed to adsorb from the gas phase onto the 2D film at high temperatures. Thereby, the results unveiled beneficial inhibitor molecules on two dimensional BP nanocarriers, potentially introducing a modern strategy to enhance the development of advanced materials, biotechnology, and nanomedicine.

A Peculiar Binding Characterization of DNA (RNA) Nucleobases at MoOS-Based Janus Biosensor: Dissimilar Facets Role on Selectivity and Sensitivity.

Distinctive properties of Janus monolayer have drawn much interest in biotechnology applications. For this purpose, it has explored theoretically all sensing possibilities of nucleobases molecules (DNA/RNA) by Janus MoOS monolayer on both oxygen and sulfur terminations by means of rigorous first-principles calculation. Indeed, differences in interaction energy between nucleobases indicate that a monolayer can be used for DNA sequencing. Exothermic interaction energy range for DNA/RNA molecules with both oxygen and sulfur sides of the Janus MoOS surfaces have been found to range between (0.61-0.91 eV), and (0.63-0.88 eV), respectively, and the binding distances indicate that these molecules bind to both facets by physisorption. The exchange of weak electronic charges between the MoOS monolayer and the nucleobases molecules has been studied by means of Hirshfeld-I charge analysis. It has been observed that the introduction of DNA/RNA nucleobases molecules alters the electronic properties of both oxygen and sulfur atomic layers of the Janus MoOS complex systems as determined by plotting the 3D Kohn-Sham frontier orbitals. A good correlation has been found between the interaction energy, van der Waals energy, Hirshfeld-I, and d-band center as a function of the nucleobase's affinity, and the interaction energy, suggesting adsorption dominated by van der Waals interactions driven by molybdenum d-orbital. Moreover, the lowering in the adsorption energy leads to an active interaction of the DNA/RNA with the surfaces, accordingly its conduct to shorter the recovery time. The selectivity of the biosensor modulation device has illustrated a significant sensitivity for the nucleobases on both the oxygen and sulfur layer sides of the MoOS monolayer. This finding reveals that apart from graphene, dichalcogenides-Janus transition metal may also be adequate for identifying DNA/RNA bases in applied biotechnology.

Ethers on Si(001): A Prime Example for the Common Ground between Surface Science and Molecular Organic Chemistry.

By using computational chemistry it has been shown that the adsorption of ether molecules on Si(001) under ultrahigh vacuum conditions can be understood with classical concepts of organic chemistry. Detailed analysis of the two-step reaction mechanism-1) formation of a dative bond between the ether oxygen atom and a Lewis acidic surface atom and 2) nucleophilic attack of a nearby Lewis basic surface atom-shows that it mirrors acid-catalyzed ether cleavage in solution. The O-Si dative bond is the strongest of its kind, and the reactivity in step 2 defies the Bell-Evans-Polanyi principle. Electron rearrangement during C-O bond cleavage has been visualized with a newly developed method for analyzing bonding, which shows that the mechanism of nucleophilic substitutions on semiconductor surfaces is identical to molecular SN 2 reactions. Our findings illustrate how surface science and molecular chemistry can mutually benefit from each other and unexpected insight can be gained.

Ab-Initio Investigations of Magnetic Properties and Induced Half-Metallicity in Ga1-xMnxP (x = 0.03, 0.25, 0.5, and 0.75) Alloys.

Ab-initio calculations are performed to examine the electronic structures and magnetic properties of spin-polarized Ga1-xMnxP (x = 0.03, 0.25, 0.5, and 0.75) ternary alloys. In order to perceive viable half-metallic (HM) states and unprecedented diluted magnetic semiconductors (DMSs) such as spintronic materials, the full potential linearized augmented plane wave method is utilized within the generalized gradient approximation (GGA). In order to tackle the correlation effects on 3d states of Mn atoms, we also employ the Hubbard U (GGA + U) technique to compute the magnetic properties of an Mn-doped GaP compound. We discuss the emerged global magnetic moments and the robustness of half-metallicity by varying the Mn composition in the GaP compound. Using GGA + U, the results of the density of states demonstrate that the incorporation of Mn develops a half-metallic state in the GaP compound with an engendered band gap at the Fermi level (EF) in the spin-down state. Accordingly, the half-metallic feature is produced through the hybridization of Mn-d and P-p orbitals. However, the half-metallic character is present at a low x composition with the GGA procedure. The produced magnetic state occurs in these materials, which is a consequence of the exchange interactions between the Mn-element and the host GaP system. For the considered alloys, we estimated the X-ray absorption spectra at the K edge of Mn. A thorough clarification of the pre-edge peaks is provided via the results of the theoretical absorption spectra. It is inferred that the valence state of Mn in Ga1-xMnxP alloys is +3. The predicted theoretical determinations surmise that the Mn-incorporated GaP semiconductor could inevitably be employed in spintronic devices.

Complex surface chemistry of an otherwise inert solvent molecule: tetrahydrofuran on Si(001).

The reaction of tetrahydrofuran (THF), an otherwise inert solvent molecule, on Si(001) was experimentally studied in ultra-high vacuum. Using scanning tunneling microscopy (STM) and photoelectron spectroscopy at variable temperature, we could both isolate a datively bound intermediate state of THF on Si(001), as well as the final configuration that bridges two dimer rows of the Si(001) surface after ether cleavage. The latter configuration implies splitting of the OC bond, which is typically kinetically suppressed. THF thus exhibits a hitherto unknown reactivity on Si(001).

Size-dependent permittivity and intrinsic optical anisotropy of nanometric gold thin films: a density functional theory study.

Physical properties of materials are known to be different from the bulk at the nanometer scale. In this context, the dependence of optical properties of nanometric gold thin films with respect to film thickness is studied using density functional theory (DFT). We find that the in-plane plasma frequency of the gold thin film decreases with decreasing thickness and that the optical permittivity tensor is highly anisotropic as well as thickness dependent. Quantitative knowledge of planar metal film permittivity's thickness dependence can improve the accuracy and reliability of the designs of plasmonic devices and electromagnetic metamaterials. The strong anisotropy observed may become an alternative method of realizing indefinite media.

A first-principles characterization of water adsorption on forsterite grains.

Numerical simulations examining chemical interactions of water molecules with forsterite grains have demonstrated the efficacy of nebular gas adsorption as a viable mechanism for water delivery to the terrestrial planets. Nevertheless, a comprehensive picture detailing the water-adsorption mechanisms on forsterite is not yet available. Towards this end, using accurate first-principles density functional theory, we examine the adsorption mechanisms of water on the (001), (100), (010) and (110) surfaces of forsterite. While dissociative adsorption is found to be the most energetically favourable process, two stable associative adsorption configurations are also identified. In dual-site adsorption, the water molecule interacts strongly with surface magnesium and oxygen atoms, whereas single-site adsorption occurs only through the interaction with a surface Mg atom. This results in dual-site adsorption being more stable than single-site adsorption.

A multiscale physical model for the transient analysis of PEM water electrolyzer anodes.

Polymer electrolyte membrane water electrolyzers (PEMWEs) are electrochemical devices that can be used for the production of hydrogen. In a PEMWE the anode is the most complex electrode to study due to the high overpotential of the oxygen evolution reaction (OER), not widely understood. A physical bottom-up multi-scale transient model describing the operation of a PEMWE anode is proposed here. This model includes a detailed description of the elementary OER kinetics in the anode, a description of the non-equilibrium behavior of the nanoscale catalyst-electrolyte interface, and a microstructural-resolved description of the transport of charges and O(2) at the micro and mesoscales along the whole anode. The impact of different catalyst materials on the performance of the PEMWE anode, and a study of sensitivity to the operation conditions are evaluated from numerical simulations and the results are discussed in comparison with experimental data.

Nature of adhesion of condensed organic films on platinum by first-principles simulations.

Understanding the nature of the adhesion of an organic liquid on a metal surface is of paramount importance for elucidating the stability and chemical reactivity at these complex interfaces. However, to date, the morphology, layering and chemical properties at organic liquid metal interfaces have been rarely known. Using semi-empirical dispersion corrected density functional theory calculations and ab initio molecular dynamics simulations, we show that carbon tetrachloride and ethanol films confined to a platinum surface alter their intrinsic properties and exhibit interfacial reactivity. A few interface carbon tetrachloride (ethanol) molecules adsorb dissociatively (molecularly) on platinum thanks to the surrounding medium. The adsorption strength of the interfacial molecules is consequently increased in the condensed phase as compared to the gas phase. This remarkable effect is rationalized by an interaction energy decomposition model and an electrostatic potential analysis.