Stability and electronic structure of magnesium hydride and magnesium deuteride under high pressure

Metal polyhydrides have attracted considerable attention because some of them become a metal under high pressure, and some undergo a phase transition into a superconductor. Some superconducting metal polyhydrides have recently been discovered with a high value of critical temperature (Tc) under pressure. In this research, we calculated the structures of MgH2, MgH3 and MgD3 under pressure between 0-300 GPa in order to determine the formation enthalpy and electronic property of their structures under high pressure by using density functional theory (DFT) based on the Quantum Espresso code. We found that the band structures reveal the metallic character of the compounds under high pressure. The energy band structures of MgHx and MgDx are exactly the same. However, their phonon dispersions are different due to the so-called isotope effect. We determined the composition stability by using the convex hull of Mg, H and the compounds. We found that MgH3 becomes thermodynamically more stable than MgH2 at around 150 GPa. The results of phonons confirm that they are dynamically stable. This finding is served as a basis for future superconducting calculations.

Theoretical and Experimental Investigation of the Electronic and Optical Properties of Pure and Interstitial Nitrogen -Doped (TiO2)n Cluster

The structural and electronic properties of pure and nitrogen-doped TiO2 nanoclusters are investigated using density functional theory (DFT) with vibrational modes. We performed numerical simulation using two methods based on theories at the Quantum Espresso/PBE and Gaussian/B3LYP/631G (d) levels. The properties of a single nitrogen-doped (TiO2)n nanocluster are also computed in this study. In both cases, interstitial and substitutional Nitrogen doping at all accessible sites was examined. For the experiment, Supersonic Cluster Beam Deposition (SCBD) was used to create pure and nitrogen-doped TiO2 films of nanocluster assemblies. Atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), UV-Vis spectroscopy, and Raman techniques were used to characterize these samples. The binding energies (Np, O2s, Ti 2p1/2, and Ti 2p3/2) of N-doped TiO2 were estimated using XPS spectral results. The UV-Vis measurement confirmed the previously stated reasoning about the quantum size effect on the band gap of the pure and nitrogen doped TiO2 nanocluster. The theoretical vibrational modes frequencies are calculated using the B3LYP/6-31G (d) functional via the Gaussian16 code's implementation algorithm. The good agreement between simulation and experimental results implies that a significant advantage of interstitial over substitutional positions. N-O vibration modes appeared in interstitial doped TiO2, and each vibration was dependent on a different cluster structure.

Structural, Electronic and Optical properties of the Inorganic Solar Perovskites XPbBr3 (X= Li or Na)

In this paper, we study the structural, electronic and optical properties of the inorganic solar perovskites XPbBr3 (X= Li or Na). We applied the two methods: the density functional theory (DFT) and time-dependent density-functional theory (TDDFT). In fact, we performed the DFT method using the Quantum Espresso package. Also, the total energies of the studied inorganic solar perovskites XPbBr3 (X= Li or Na) have been deduced as a function of the lattice parameter a (Å). The two calculation methods have been carried out under the GGA-PBE and GGA-PBESol approximations. Moreover, the total and partial density of states (DOS) and the band structure of the studied compounds have been presented and discussed for the two cases: with and without the spin orbit coupling (SOC) approximation. In addition, the DFT and TDDFT have been explored in order to elaborate the structural, the electronic and the optical properties of the inorganic perovskite CsPbI3 material for solar cell applications. When using the GGA-PBESol method without SOC approximation, we found a band gap energy value greater than that one computed when adding the SOC correction. On the other hand, the optical properties of the studied material have been studied. In particular, we found that the inorganic solar Perovskite XPbBr3 (X=Li or Na) materials exhibit a high transparency of the electromagnetic radiations in energy range between 0 eV and 33 eV.

Effect of Doping Concentration on Structural Stability and Formation Energy of the Fluorine Doped Hexagonal Molybdenum Dioxide (MoO2). A First Principle Study.

The structural properties of undoped and Fluorine doped Hexagonal Molybdenum dioxide (MoO2) with different doping concentrations have been calculated using Density Functional Theory (DFT) within Generalized Gradient Approximation (GGA) as implemented in Quantum Espresso (QE). The calculated results were for the formation energy of 4.17%, 8.33%, 12.5%, of F doped MoO2 are 232.5eV, 463.0eV, and 698.5eV respectively, which show the variation of energy based on the increase in the doping concentration that led to having the breakage of bond in the structure of the compound. The undoped and 4.17% of F doped MoO2 have three free atoms, which maintain the stability of the structure, but when the doping concentration was increased, the bond breaks simultaneously which led to having four and five free atoms for 8.33%, and 12.5% of F doped MoO2 respectively. This makes 4.17% of F doped MoO2 with 17.09Ry more stable. Similarly, the bond length of undoped MoO2 was 2.2505pm, but when doped with 4.17% of F it changes to 2.3030pm which indicates a greater stability of the structure concentrations of the dopant above 4.17% reduced the bond length, which made the structure less stable.

Simulasi Dinamika Molekuler Senyawa Asam Ferulat dan Turunannya dari Kulit Buah Nanas (Ananas comosus) sebagai Inhibitor Enzim Tirosinase

Enzim tirosinase merupakan enzim utama pada proses pembentukan pigmen melanin. Penghambatan aktivitas enzim tirosinase secara kompetitif maupun non-kompetitif menjadi kunci utama pengembangan agen pencerah kulit. Asam ferulat merupakan salah satu senyawa antioksidan yang kuat dan mampu melindungi kulit dari dampak buruk sinar UV yang menginduksi stress oksidatif. Penelitian ini bertujuan untuk mengidentifikasi interaksi molekuler antara senyawa asam ferulat dari kulit buah nanas (Ananas comosus) dan turunannya dengan enzim tirosinase menggunakan motode dinamika molekuler. Molekul senyawa uji dimodelkan menggunakan perangkat lunak Quantum ESPRESSO v.6.6. Model terbaik dipilih untuk dilakukan studi interaksi menggunakan perangkat lunak MGLTools 1.5.6 yang dilengkapi dengan AutoDock 4.2. Konformasi terbaik hasil penambatan molekuler kemudian dikonfirmasi stabilitasnya dengan simulasi dinamika molekuler menggunakan perangkat lunak Gromacs 2016.3. Berdasarkan hasil dari penambatan molekuler, senyawa asam iso-ferulat memiliki afinitas yang paling baik, yaitu dengan nilai energi bebas ikatan −25,06 kJ/mol dan memilki ikatan dengan logam seng (Zn) pada sisi aktif enzim tirosinase. Kemudian senyawa tersebut memiki stabilitas interaksi yang baik berdasarkan grafik RMSD, RMSF, Rg, SASA, RDF, dan H-Bond. Dengan demikian, senyawa asam iso-ferulat diprediksi dapat digunakan sebagai kandidat inhibitor kompetitif dan non-kompetitif enzim tirosinase

Effect of Sr - Transition Metal Substitution on Electronic and Mechanical Properties of Mg2Si: A DFT Study

Recently, magnesium alloys have attracted scientific interest due to their technological importance in thermoelectric, piezoelectric, photo-voltaic and infrared photonics applications. The electronic and elastic properties of MgXSi (X = Mg, Sr) compounds were investigated in this work, using the density functional theory (DFT) with pseudo-potential plane-waves (PPW) approach as implemented in Quantum Espresso code. The results of the elastic constants of Mg2Si are in agreement with the previous theoretical results and favourably compared with experimental data. The electronic band structures of these semiconductors were calculated to give narrow indirect and direct band gaps of Mg2Si and MgSrSi, respectively. Our results show that the two compounds are mechanically stable. The Pugh’s ratio, B/G, indicated that Mg2Si and MgSrSi are brittle and ductile in nature. The estimated anisotropy parameter, A, shows that Mg2Si has a higher degree of elastic isotropy in comparison to MgSrSi. Three-dimensional (3D) projection of Young’s modulus and area modulus of the compounds was presented. Keywords: Electronic structure, Elastic constants, Mechanical properties, Mg2Si, MgSrSi. PACS: 31.15.A-, 62.20.F-, 71.55.-i, 71.20.Be.

Optical Absorption and Reflectivity of Four 2D Materials: MoS2, MoP2, NbS2, and NbP2

We calculated the energy band structure and the optical absorption and reflectivity for each of the ultrathin 2D hexagonal materials MoS2, MoP2, NbS2, and NbP2. Our simulations included density functional theory, generalized gradient approximation (GGA), and the Quantum Espresso code. Other researchers already synthesized the first three materials. We obtained that NbP2 should be another hexagonal 2D material. In all cases in the infrared and visible ranges, the absorptions present much larger concerning graphene. However, the absorptions for MoP2, NbP2, and NbS2, are far more prominent concerning MoS2. In the ultraviolet region, the absorptions are like each other and differ from graphene. In all cases, the reflectivities are similar to each other and vary from graphene.

A Newly Developed Dispersive Interaction Approach, DFT-D3, To The Three-Dimensional Topological Host Material Sb2Te3

Antimony Telluride (Sb2Te3), a topological insulator is a layered semiconductor material with hexagonal unit cell similar to graphene. The characteristic presence of their conducting edges or surfaces with self-induced protection, promise for remarkable future applications. In this exertion based on the first principle approach, the structural and electronic properties of Sb2Te3 compound have been investigated for both without and with spin orbit coupling (SOC). Lattice structure, band structure, total density of states (TDOS), partial density of states (PDOS), energy bands of surface states are determined within Quantum Espresso simulation package. Furthermore, dispersive interactions, induced due to the presence of van-der-Waals forces have also been taken care of. The newly developed method of DFT-D3 has been incorporated for accurate predictions of band gap and lattice parameters. A proficient model, The Slab Model, has been used to observe the presence of single Dirac cone on the surface. To our knowledge, our theoretical investigations are valid and are found to be congruous with the observed data.

Measuring Shared Electrons in Extended Molecular Systems: Covalent Bonds from Plane-Wave Representation of Wave Function

In the study of materials and macromolecules by first-principle methods, the bond order is a useful tool to represent molecules, bulk materials and interfaces in terms of simple chemical concepts. Despite the availability of several methods to compute the bond order, most applications have been limited to small systems because a high spatial resolution of the wave function and an all-electron representation of the electron density are typically required. Both limitations are critical for large-scale atomistic calculations, even within approximate density-functional theory (DFT) approaches. In this work, we describe our methodology to quickly compute delocalization indices for all atomic pairs, while keeping the same representation of the wave function used in most compute-intensive DFT calculations on high-performance computing equipment. We describe our implementation into a post-processing tool, designed to work with Quantum ESPRESSO, a popular open-source DFT package. In this way, we recover a description in terms of covalent bonds from a representation of wave function containing no explicit information about atomic types and positions.

Biological activity, molecular docking, and ADME predictions of amphibine analogues of Ziziphus spina-christi towards SARS-CoV-2 Mpro

The main protease of the SARS-CoV-2 virus, SARS-CoV-2 Mpro, can be discovered as a promising target to treat the COVID-19 pandemic. The peptide-based inhibitors may present better options than small molecules for inhibits SARS-CoV-2 Mpro. Ziziphus spina-christi species reported have a peptide-based of alkaloids group, i.e. Amphibine that the analogues can be identified the potential as an inhibitor of SARS-CoV-2 Mpro. The compound structure was drawn and optimized using semi-empirical AM-1 method using Quantum ESPRESSO v.6.6, then the biological activity using PASS Prediction server and molecular docking simulation using MGLTools 1.5.6 with AutoDock 4.2 were performed. Afterward, the ADME profiles were predicted using the SWISS-ADME server. PASS server was predicting Amphibine B-F and H showed potency both as antiviral and as a protease inhibitor. The molecular docking simulation of Amphibine analogues showed lower binding energy than the native ligand. The binding energy of the native ligand was −7.69 Kcal/mol compared to the lowest binding energy of Amphibine analogues was −10.10 Kcal/mol (Amphibine-F). The ADME prediction showed, as an oral drug Amphibine-F has the best bioavailability, Amphibine-B, C, and D have good bioavailability, and Amphibine-E and H have poor bioavailability. Concluded, Amphibine B-F and H of Amphibine analogues showed potency as COVID-19 treatment targeting SARS-CoV-2 Mpro.