CONTEXT: The monoclinic L-histidine crystal is critical for protein structure and function and is also found in the myelin of brain nerve cells. This study numerically examines its structural, electronic, and optical properties. Our findings indicate that the L-histidine crystal has an insulating band gap of approximately 4.38 eV. Additionally, electron and hole effective masses range between 3.92[Formula: see text]-15.33[Formula: see text] and 4.16[Formula: see text]-7.53[Formula: see text], respectively. Furthermore, our investigation suggests that the L-histidine crystal is an excellent UV collector due to its strong optical absorption activity for photon energies exceeding 3.5 eV. METHODS: To investigate the structural, electronic, and optical properties of L-histidine crystals, we used the Biovia Materials Studio software to conduct Density Functional Theory (DFT) simulations as implemented in the CASTEP code. Our DFT calculations were performed using the generalized gradient approximation (GGA) as parameterized by the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional, with an additional dispersion energy correction (PBE [Formula: see text] TS) based on the model proposed by Tkatchenko and Scheffler to describe van der Waals interactions. Additionally, we employed the norm-conserving pseudopotential to treat core electrons.

CONTEXT: Ephrin type A receptor 2 (EphA2) is a well-known drug target for cancer treatment due to its overexpression in numerous types of cancers. Thus, it is crucial to determine the binding interactions of this receptor with both the ligand-binding domain (LBD) and the kinase-binding domain (KBD) through a targeted approach in order to modulate its activity. In this work, natural terpenes with inherent anticancer properties were conjugated with short peptides YSAYP and SWLAY that are known to bind to the LBD of EphA2 receptor. We examined the binding interactions of six terpenes (maslinic acid, levopimaric acid, quinopimaric acid, oleanolic, polyalthic, and hydroxybetulinic acid) conjugated to the above peptides with the ligand-binding domain (LBD) of EphA2 receptor computationally. Additionally, following the "target-hopping approach," we also examined the interactions of the conjugates with the KBD. Our results indicated that most of the conjugates showed higher binding interactions with the EphA2 kinase domain compared to LBD. Furthermore, the binding affinities of the terpenes increased upon conjugating the peptides with the terpenes. In order to further investigate the specificity toward EphA2 kinase domain, we also examined the binding interactions of the terpenes conjugated to VPWXE (x = norleucine), as VPWXE has been shown to bind to other RTKs. Our results indicated that the terpenes conjugated to SWLAY in particular showed high efficacy toward binding to the KBD. We also designed conjugates where in the peptide portion and the terpenes were separated by a butyl (C4) group linker to examine if the binding interactions could be enhanced. Docking studies showed that the conjugates with linkers had enhanced binding with the LBD compared to those without linkers, though binding remained slightly higher without linkers toward the KBD. As a proof of concept, maslinate and oleanolate conjugates of each of the peptides were then tested with F98 tumor cells which are known to overexpress EphA2 receptor. Results indicated that the oleanolate-amido-SWLAY conjugates were efficacious in reducing the cell proliferation of the tumor cells and may be potentially developed and further studied for targeting tumor cells overexpressing the EphA2 receptor. To test if these conjugates could bind to the receptor and potentially function as kinase inhibitors, we conducted SPR analysis and ADP-Glo assay. Our results indicated that OA conjugate with SWLAY showed the highest inhibition. METHODS: Docking studies were carried out using AutoDock Vina, v.1.2.0; Molecular Dynamics and MMGBSA calculations were carried out through Schrodinger Software DESMOND.

CONTEXT: Xanthates are organic compounds that present great interest for coordination chemistry, because they can bond in different ways to the metal ion. Thus, these compounds have several applications, being best known for their environmental application. In fact, xanthates are recognized for their application as heavy metal collector agents in aqueous environments. In view of this application, this study is aimed at showing the thermochemical and electronic parameters obtained for the reactions of substitution water molecules in the aqua zinc complexes, by xanthate ligands (n-propyl, n-butyl, and n-pentyl xanthates). In addition to their environmental application, xanthates have shown biological properties, such as anti-bacterial and anti-cancer. In recent years, xanthates have also been used in the technological area, where it participates as a precursor of sulfides for the manufacture of thin films. Our results showed complexes with distorted octahedral geometries and with negative values of enthalpy and Gibbs free energy, indicating exothermic and spontaneous processes. For all the complexes, it was observed that Zn2+ complexes have both an ionic and covalent character. However, the monosubstituted complexes showed a predominance of the ionic character. In addition, high donor-acceptor interaction energies were obtained, indicating a good superposition between the s and p orbitals involved in the Zn-S bond. METHODS: This work consists in theoretical studies of Zn2+ complexes with alkyl xanthate ligands, with different structures, where optimization and normal modes calculations were performed at different DFT levels: M06L, M06-2X, wB97XD, and B3LYP/6-311++G**+LANL2TZ, with Gaussian09 program. The process of substitution of two aqua by two xanthate ligands was analyzed in stages, forming cationic and neutral complexes, in the first and second stages, respectively. In addition, electronic energy decomposition (EDA) and natural bond orbital (NBO) analysis were performed at level M06L/6-311++G**+LANL2TZ with Gamess program.

CONTEXT: The molecular structure of the compound, spectroscopic investigations (FT-IR, FT-Raman, and NMR), and the frontier energy level analysis of 5-hydroxy-3,6,7,8-tetramethoxyflavone (5HTMF) were all examined using density functional theory (DFT) methods. Comparisons were made between predicted DFT theoretical vibrational wavenumbers and observed data. The chemical reactivity of 5HTMF was studied using DFT/PBEPBE approach that included frontier orbital energies, optical characteristics, and chemical descriptors. All our theoretical calculations have been done using the Gaussian 09W package. METHODS: The cytotoxic activity of the bioactive ligand was checked against human cancer cell lines A549 and MCF-7 in vitro by the MTT assay. Hence, the docking and in vitro activity against cancer cell lines display positive results. The present ligand performance appears to be a promising way for anticancer agents with better efficacy. A molecular docking study of 5HTMF drug against Bcl-2 protein structures was performed by using the open-source AutoDock 4.2 and AutoDock Vina tools program packages.

CONTEXT: The discovery of graphene gave way to the search for new two-dimensional structures. In this regard, octa-graphene is a carbon allotrope consisting of 4- and 8-membered rings in a single planar sheet, drawing the research community's attention to study their inorganic analogs. Considering the promising properties of octa-graphene-like structures and the role of GaAs and GaP in semiconductor physics, this study aims to propose, for the first time, two novel inorganics buckled nanosheets based on the octa-graphene structure, the octa-GaAs and octa-GaP. This work investigated the structural, electronic, and vibrational properties of these novel octa-graphene-based materials. The octa-GaP and octa-GaAs have an indirect band gap transition with a valence band maximum between M and Г points and a conduction band minimum at Г point with energy of 3.05 eV and 2.56 eV, respectively. The QTAIMC analysis indicates that both structures have incipient covalent in their bonds. The vibrational analysis demonstrates the occurrence of ΓRaman = 6Ag + 6Bg and ΓRaman = 12A' + 12B″ for octa-GaP and octa-GaAs, respectively. The symmetry reduction of octa-GaAs leads to activating inactive modes observed in the octa-GaP structure. The frontier crystalline orbitals are composed by Ga(px) and P(py and pz) orbitals for octa-GaP and Ga(px and py) and As(s, py, and pz) for octa-GaAs in the valence bands while in the conduction bands by Ga(py, pz, and s) for both compounds and P(px and pz) and As(py). The phonon bands demonstrate the absence of the negative frequency modes and the structural stability of these new nanosheets. This report aims to reveal the fundamental properties of both newfound materials for stimulating experimental research groups in the search for synthesis routes to obtain this structure. METHODS: This work used the DFT/B3LYP approach implemented in the CRYSTAL17 computational package. Ga, As, and P atomic centers were described by triple-zeta valence with polarization (TZVP) basis set. The vibrational analysis was carried out via coupled-perturbed Hartree-Fock/Kohn Sham (CPHF/KS) method, and the chemical bonds were evaluated via the quantum theory of atoms in molecules and crystals (QTAIMC).

CONTEXT: Graphene has been used as reinforcement of polymeric nanocomposites to increase mechanical and electrical properties. Recently, graphene suspensions have been used for the development of nanofluids in automotive applications, where improvements in convection heat transfer coefficients and pressure drops have been reported. However, dispersions of graphene sheets in a polymeric matrix as well as in a solvent medium are difficult to achieve; that is because Van der Waals, [Formula: see text] and Coulombic interactions cause agglomerations. Surface chemical modifications have been considered as viable options to improve the graphene integration. In this work, we studied the colloidal stability of aqueous solutions of graphene sheets functionalized with (i) carboxylic groups, (ii) 3-amino-propyl tri-ethoxy silane (amphiphilic behavior), (iii) graphene oxide, and (iv) pristine graphene. Results show that the lower sedimentation velocity corresponds to the graphene functionalized with carboxylic groups, which presents the higher colloidal stability. However, the amphiphilic group enhances the interaction energy between graphene and the solvent; we believe that there is a threshold percentage of functionalization that improves the colloidal stability of graphene. METHOD: Transport properties of graphene solutions were estimated by using Non-Equilibrium Molecular Dynamics simulations to generate Poiseuille flow in an NVT ensemble. Simulations were developed in the LAMMPS code. The COMPASS Force Field was used for the graphene systems and the TIP3P for the water molecules. Bonds and angles of hydrogen atoms were kept rigid by using the shake algorithm. The molecular models were built through MedeA and visualized with the Ovito software.

CONTEXT: CL-20/DNDAP cocrystal is a promising new type of explosive with exceptional energy density and detonation parameters. However, compared to TATB, FOX-7 and other insensitive explosives, it still has higher sensitivity. In order to decrease the sensitivity of CL20/DNDAP cocrystal explosive, in this article, a CL20/DNDAP cocrystal model was established, and six different types of polymers, including butadiene rubber (BR), ethylene-vinyl acetate copolymer (EVA), polyethylene glycol (PEG), hydroxyl-terminated polybutadiene (HTPB), fluoropolymer (F2603), and polyvinylidene difluoride (PVDF), were added to the three cleaved surfaces of (1 0 0), (0 1 0) and (0 0 1) to obtain polymer-bonded explosives (PBXs). Predict the effects of different polymers on the stability, trigger bond length, mechanical properties, and detonation performance of PBXs. Among the six PBX models, CL-20/DNDAP/PEG model exhibited the highest binding energy and the lowest trigger bond length, indicating that CL-20/DNDAP/PEG model had the best stability, compatibility, and the least sensitivity. Furthermore, although the CL-20/DNDAP/F2603 model demonstrated superior detonation capabilities, it should be noted that this model displayed low levels of compatibility. Overall, CL-20/DNDAP/PEG model exhibited the superior comprehensive properties, thereby demonstrating that PEG is a more suitable binder option for PBXs based on the CL20/DNDAP cocrystal. METHODS: The properties of CL-20/DNDAP cocrystal-based PBXs were predicted by molecular dynamics (MD) method under Materials Studio software. The MD simulation time step was set at 1fs and the total MD simulation time was 2ns. The Isothermal-isobaric (NPT) ensemble was used for the 2ns of MD simulation. The COMPASS force field was used, and the temperature was set at 295K.

CONTEXT: In this paper, we have addressed two issues that are relevant to the interaction of water in pristine and vacant graphene through first-principles calculations based on the Density Functional Theory (DFT). The results showed that for the interaction of pristine graphene with water, the DOWN configuration (with the hydrogen atoms facing downwards) was the most stable, presenting binding energies in the order of -13.62 kJ/mol at a distance of 2.375 Å in the TOP position. We also evaluated the interaction of water with two vacancy models, removing one carbon atom (Vac-1C) and four atoms (Vac-4C). In the Vac-1C system, the most favourable system was the DOWN configuration, with binding energies ranging from -20.60 kJ/mol to -18.41 kJ/mol in the TOP and UP positions, respectively. A different behaviour was observed for the interaction of water with Vac-4C; regardless of the configuration of the water, it is always more favourable for the interaction to occur through the vacancy centre, with binding energies ​​between -13.28 kJ/mol and -20.49 kJ/mol. Thus, the results presented open perspectives for the technological development of nanomembranes as well as providing a better understanding of the wettability effects of graphene sheets, whether pristine or with defects. METHOD: We evaluated the interaction of pristine and vacant graphene with the water molecule, through calculations based on Density Functional Theory (DFT); implemented by the SIESTA program. The electronic, energetic, and structural properties were analyzed by solving self-consistent Kohn-Sham equations. In all calculations, a double ζ plus a polarized function (DZP) was used for the numerical baise set. Local Density Approximation (LDA) with the Perdew and Zunger (PZ) parameterisation along with a basis set superposition error (BSSE) correction were used to describe the exchange and correlation potential (Vxc). The water and isolated graphene structures were relaxed until the residual forces were less than 0.05 eV/Å-1 in all atomic coordinates.

INTRODUCTION: Enalapril maleate is an antihypertensive ethyl ester pro-drug with two crystalline forms. A network of hydrogen bonds in both polymorphs plays an important role on solid-state stability, charge transfer process and degradation reactions (when exposed to high humidity, temperature and/or pH changes). COMPUTATIONAL PROCEDURES: Supramolecular arrangement was proposed by Hirshfeld surface using the CrystalExplorer17 software and quantum theory of atoms in molecules. The electronic structure properties were calculated using the functional hybrid M06-2X with 6-311++G** base function employing diffuse and polarization functions to improve the description of hydrogen atoms on intermolecular interactions. Also, the H+ charge transfer between enalapril and maleate molecules was performed using Car-Parrinello molecular dynamics with the Verlet algorithm. In both simulations, the temperature of the ionic system was maintained around 300 K using the Nosé-Hoover thermostat and the electronic system evolved without the use of the thermostat. RESULTS: This work evaluates the effect of maleate on the structural stability of enalapril maleate solid state. The electronic structural analysis points out a partially covalent character for N1-H∙∙∙O7 interaction; and the molecular dynamic showed a decentralized hydrogen on maleate driving a decomposition by charge transfer process while a centered hydrogen driving the stabilization. The charge transfer process and the mobility of the proton (H+) between enalapril and maleate molecules was demonstrated using supramolecular modeling analyses and molecular dynamics calculations.

We studied the electronic and magnetic properties of wurtzite GaN (w-GaN) doped with different concentrations of the 4d transition metal ions Nb, Mo, and Ru. We incorporated spin-polarized plane-wave density functional theory within an ultrasoft pseudopotential formalism. The 4d transition metals were doped at different geometrical sites to determine the geometry with the lowest total energy and the one that induced the largest magnetization. A spin-spin interaction study was performed to determine whether the doped compound was ferromagnetic or antiferromagnetic. The origin of magnetization in the transition metal-doped w-GaN compounds is due to the p-d hybridization of the nitrogen and 4d transition metals. From the bulk modulus results, we inferred that the structural integrity is preserved under compressive loads after doping w-GaN with these 4d transition metal ions. Our results indicate that these compounds can be used in spintronic applications.

CONTEXT: To apply the quantitative relationships "structure-endpoint" approach, the reliability of prediction is necessary but sometimes challenging to achieve. In this work, an attempt is made to accomplish the reliability of forecasts by creating a set of random partitions of data into training and validation sets, followed by constructing random models. A system of random models for a helpful approach should be self-consistent, giving a similar or at least comparable statistical quality of the predictions for models obtained using different splits of available data into training and validation sets. METHOD: The carried out computer experiments aimed at obtaining blood-brain barrier permeation models showed that, in principle, can be used such an approach (the Monte Carlo optimization of the correlation weights for different molecular features) for the above purpose taking advantage of specific algorithms to optimize the modelling steps with applying of new statistical criteria such as the index of ideality of correlation (IIC) and the correlation intensity index (CII). The results so obtained are good and better than what was reported previously. The suggested approach to validation of models is non-identic to traditionally applied manners of the checking up models. The concept of validation can be used for arbitrary models (not only for models of the blood-brain barrier).

CONTEXT: A remarkable change in lattice parameters and bulk modulus is achieved by the suitable addition of Al (Al1-x Lax Sb) and In (Al1-x Inx Sb) atoms in the AlSb compound. Electronic responses like band structure, the total partial density of states, and the elemental density of states are thoroughly investigated. The computed values indicate that the binary compound AlSb is an indirect band gap and an optically inactive response. After increasing the doping concentrations (0.25, 0.5, 0.75) of La and In in AlSb, the band gap changes from indirect to direct nature. Hence, Al1-0.75 La0.25 Sb, Al1-0.50 La0.50 Sb, Al1-0.75 In0.25Sb, and Al1-0.50 In0.50Sb become optically active. The illustrious roles of Al-3p and In-4d states on the band gap and nonlinear responses of these compounds are extensively explored by the comparison between the computed results of ultra-soft and norm converging pseudopotentials. The excess specific heat (CV), enthalpy of mixing (Hm), and phonon dispersion curves resulting from the concentrations "x" are estimated in order to investigate the thermodynamic stability responses of the pristine and doped AlSb. The obtained CV and thermal coefficient statistics for Al1-x Lax Sb and Al1-x Inx Sb may be useful for a good mapping of experimental results and examining these compounds' enharmonic responses. There is a valuable change in optical characteristics like dielectric functional, absorption, conductivity, and refractive index due to the addition of (La, In) impurities in AlSb. It is further observed that Al1-0.75 La0.25 Sb, Al1-0.50 La0.50 Sb, Al1-0.75 In0.25Sb, and Al1-0.50 In0.50Sb are significantly mechanically stable compared to pristine AlSb. The above results suggest that Al1-x Lax Sb and Al1-x Inx Sb are high-performance optical materials and can be promising potential candidates for optoelectronic applications. METHODS: The structural, electronic, mechanical, vibrational, and optical responses of the pure and doped Al1-0.75 La0.25 Sb, Al1-0.50 La0.50 Sb, Al1-0.75 In0.25Sb, and Al1-0.50 In0.50Sb are investigated, using Heydscuseria-Ernzerhof screened hybrid functional (HSEO6) and generalized gradient approximation (GGA) with norm-converging and ultra-soft pseudopotential techniques in the density functional theory.

CONTEXT: Several descriptors from conceptual density functional theory (cDFT) and the quantum theory of atoms in molecules (QTAIM) were utilized in Random Forest (RF), LASSO, Ridge, Elastic Net (EN), and Support Vector Machines (SVM) methods to predict the toxicity (LD50) of sixty-two organothiophosphate compounds. The A-RF-G1 and A-RF-G2 models were obtained using the RF method, yielding statistically significant parameters with good performance, as indicated by R2 values for the training set (R2Train) and R2 values for the test set (R2Test), around 0.90. METHODS: The molecular structure of all organothiophosphates was optimized via the range-separated hybrid functional ωB97XD with the 6-311 +  + G** basis set. Seven hundred and eighty-seven descriptors have been processed using a variety of machine learning algorithms: RF LASSO, Ridge, EN and SVM to generate a predictive model. The properties were obtained with Multiwfn, AIMALL and VMD programs. Docking simulations were performed by using AutoDock 4.2 and LigPlot + programs. All the calculations in this work are carried out in Gaussian 16 program package.

CONTEXT: Hydrogen fluoride (HF) is extensively present in environmental and industrial pollutants. It may harm the health of humans and animals. This work evaluated the adsorption of an (HF)n linear chain (n = 1, 2, 3, and 4) onto an AlP nanocage through ab initio calculations for the evaluation of its performance in sensing and monitoring (HF)n within aqueous and gaseous media. METHODS: The present work adopted density functional theory (DFT) at the 6-311 G (d, p) basis set to analyze (HF)n linear chain adsorption onto AlP nanocages with the B3LYP functional. This paper examined the adsorption energy, configuration optimization, work function, and charge transfer. In addition, the contributions of the HF linear chain size to electronic properties and adsorption energy were measured. The dimer form of HF on the surface of AlP nanocages was found to have the highest stability based on the adsorption energy values. Once (HF)n was adsorbed onto the nanocage, the HOMO-LUMO energy gap experienced a large reduction from 3.87 to 3.03 eV, enhancing electrical conductivity. In addition, AlP nanocages may serve in the sensing of (HF)n under multiple environmental pollutants.

CONTEXT: Through experimental observations and reports, various challenges have been identified in carbon nanotubes (CNT), including Stone Wales (SW) flaws and position flaws. Among these imperfections, point vacancies are the most prevalent in the CNT lattice. However, there is currently no established method for detecting these issues, and the influence of these flaws on the vibrational properties of three-walled carbon nanotubes (TWCNTs) remains uncertain. This research paper introduces a novel approach that utilizes vibrational analysis to detect flaws in TWCNTs. By conducting the first investigation into the impact of point vacancies on the vibrational modal frequencies of TWCNTs, our study bridges these knowledge gaps. METHODS: This study examines the impact of defect quantity on various types of TWCNTs and investigates the vibrational properties of TWCNTs with point vacancies using a molecular structural mechanics technique. A total of 432 TWCNT models were simulated using molecular structural mechanics (MSM), and their modes were identified through finite element (FE) analysis. The fundamental vibration's natural frequency in TWCNTs with defects was then determined. The findings indicate that the depth of the mode shape is influenced by the TWCNTs' diameter, the extent of point vacancy defects, and the boundary condition. It was observed that as the number of vacancy defects increases from 0 to 4%, the natural frequency decreases. The study also establishes the order of TWCNTs with the highest natural vibrational frequency at 0%-point vacancy and [Formula: see text] a given attached mass, which follows the sequence of chiral, armchair, and zigzag TWCNTs.

CONTEXT: Recently, a new 2D carbon allotrope named biphenylene network (BPN) was experimentally realized. Here, we use density functional theory (DFT) calculations to study its boron nitride analogue sheet's structural, electronic, and optical properties (BN-BPN). Results suggest that BN-BPN has good structural and dynamic stabilities. It also has a direct bandgap of 4.5 eV and significant optical activity in the ultraviolet range. BN-BPN Young's modulus varies between 234.4[Formula: see text]273.2 GPa depending on the strain direction. METHODS: Density functional theory (DFT) simulations for the electronic and optical properties of BN-BPN were performed using the CASTEP package within the Biovia Materials Studio software. The exchange and correlation functions are treated within the generalized gradient approximation (GGA) as parameterized by Perdew-Burke-Ernzerhof (PBE) and the hybrid functional Heyd-Scuseria-Ernzerhof (HSE06). For convenience, the mechanical properties were carried out using the DFT approach implemented in the SIESTA code, also within the scope of the GGA/PBE method. We used the double-zeta plus polarization (DZP) for the basis set in these cases. Moreover, the norm-conserving Troullier-Martins pseudopotential was employed to describe the core electrons.

CONTEXT: Chlordecone (CLD) and β-hexachlorocyclohexane (β-HCH) are chlorinated pesticides that coexist as persistent organic pollutants in the groundwater of several countries in the Caribbean, being an environmental issue. This work evaluates theoretically the competitive formation of host-guest complexes pesticides@cyclodextrines (CDs) as an alternative for water purification and selective separation of pesticides. METHODS: Quantum mechanical calculations based on density functional theory (DFT) and classical molecular dynamics (MD) simulations were used to achieve information on geometries, energies, structure, and dynamics of guest-host complexes in the gas phase, implicit solvent medium, and in aqueous solutions. RESULTS: DFT studies showed that interactions of both pesticides with CDs are mediated by steric factors and guided by maximization of the hydrophobic interactions either with the other pesticide or with the CD cavity's inner atoms. MD results corroborate the formation of stable complexes of both pesticides with the studied CDs. α-CD exhibited a preference for the smaller β-HCH molecule over the CLD that could not perturb the formed complex. CONCLUSIONS: The simulation of competitive formation with γ-CD illustrated that this molecule could accommodate both pesticides inside its cavity. These results suggest that CDs with smaller cavity sizes such as α-CD could be used for selective separation of β-HCH from CLD in water bodies, while γ-CD could be used for methods that aim to remove both pesticides at the same time.

CONTEXT: Using the molecular dynamics simulation method, the adsorption of folic acid as a drug with diphenylalanine peptide nanohole as an efficient nanodrug delivery system was investigated computationally. It focuses on the structural properties, drug loading capacity in the carrier, intermolecular interactions, and drug encapsulation behaviors. The results show that the average number of hydrogen bonds between diphenylalanine and folic acid will increase when the system reaches equilibrium. In addition, by increasing the weight concentration of folic acid from 0.3 to 0.9%, the number of hydrogen bond between them increases about 18%. In other words, hydrogen bonding can play an effective role in the binding of folic acid to the drug carrier. The results of the radial distribution function of water molecules around the carrier mass center show that its effective radius is around 1.2 nm (or 12 Å), which is in a good agreement with the results obtained from the hydrodynamic radius. METHOD: The initial structures were optimized in Amber molecular mechanics using Gaussian 09 software in aqueous medium in DFT/B3LYP/6-31 g(d). The molecular structure of folic acid was obtained from the PubChem database. The initial parameters are embedded in AmberTools. To calculate partial charges, restrained electrostatic potential (RESP) method was used. Gromacs 2021 software, modified water model (SPC/E), and Amber 03 force field have been used in all simulations. VMD software was used to view simulation photos.

CONTEXT: In contrast to un-catalyzed hydrolysis of organophosphorus (OP) compounds, metal ions or/and their complexes with chelating ligands show catalytic effects in several ways depending upon the nature of the metal, ligand, substrate, and medium. It is known that Cu(II)-en chelate containing copper complexes accelerate the hydrolysis of OP compounds. However, the mechanism for this rate enhancement in the Cu(II)-en chelate catalytic hydrolysis reaction of sarin remains unexplored. We have examined possible mechanisms involving a Cu(II)-en with hydroxide nucleophile for the reaction pathway of the hydrolysis of O-isopropyl methylphosphonofluoridate (sarin) computationally. The density functional (B3LYP) employed in this study has reproduced the experimental Gibb's free energy of activation value 15.5 kcal/mol for alkaline hydrolysis of sarin. Earlier proposal of push-pull mechanism for metal ion chelate-catalyzed hydrolysis of OP compounds has been found to be unfavorable in the present study. The role of water molecules in catalyzing the hydrolysis of sarin with Cu(II)-en chelate is crucial. The catalytic process involving Cu(II)-en chelate with one water molecule is the more plausible pathway to achieve the hydrolysis of sarin with Cu(II)-en chelate complexes. METHODS: The most popular B3LYP method was used for optimization of given geometries. Except LANL2DZ for Cu atom, all the atoms are described using the 6-31 + G(d) basis set. The stability test has been performed for the wave functions as we are dealing with the open-shell molecules in order to ensure stable electronic configuration form, and the stable wavefunction is used as the initial configuration for the subsequent optimization. Harmonic frequency calculations and thermodynamic corrections were performed at the same level of theory. PCM method has been used for solvation effects. In order to ensure that each saddle point is linked to a minimum, IRC calculations were performed in forward and reverse directions to ensure the eigenvectors associated with the unique negative eigenvalues of the Hessian matrix. All energies discussed are solvated Gibbs free energies corrected to 298.15 K for the relative stability of the chemical structure. All calculations were performed using the Gaussian 09 code.

CONTEXT: In the paper, the ORR/OER on graphene-supported nitrogen coordinated Ru-atom (Ru-N-C) is simulated. We discuss nitrogen coordination influences electronic properties, adsorption energies, and catalytic activity in a single-atom Ru active site. The over potentials on Ru-N-C are 1.12 eV/1.00 eV for ORR/OER. We calculate Gibbs-free energy (ΔG) for every reaction step in ORR/OER process. In order to gain a deeper understanding of the catalytic process on the surface of single atom catalysts, the ab initio molecular dynamics (AIMD) simulations show that Ru-N-C has a structural stability at 300 K and that ORR/OER on Ru-N-C can occur along a typical four-electron process of reaction. AIMD simulations of catalytic processes provide detailed information about atom interactions. METHODS: In this paper, we use density functional theory (DFT) with PBE functional to study the electronic properties and adsorption properties of graphene-supported nitrogen coordinated Ru-atom (Ru-N-C) Gibbs-free energy and Gibbs-free energy for very reaction step. The structural optimization and all the calculations are carried out by Dmol3 package, adopting the PNT basis set and DFT semicore pseudopotential. Ab initio molecular dynamics simulations (AIMD) were run for 10 ps. The canonical (NVT) ensemble, massive GGM thermostat, and a temperature of 300 K are taken into account. The functional of B3LYP and the DNP basis set are chosen for AIMD.

CONTEXT: Alzheimer's disease (AD) is a chronic progressive neurodegenerative syndrome, which adversely disturbs cognitive abilities as well as intellectual processes and frequently occurs in the elderly. Inhibition of cholinesterase is a valuable approach to upsurge acetylcholine concentrations in the brain and persuades the development of multi-targeted ligands against cholinesterases. METHODS: The current study aims to determine the binding potential accompanied by antioxidant and anti-inflammatory activities of stilbenes-designed analogs against both cholinesterases (Acetylcholinesterase and butyrylcholinesterase) and neurotrophin targets for effective AD therapeutics. Docking results have shown that the WS6 compound exhibited the least binding energy - 10.1 kcal/mol with Acetylcholinesterase and - 7.8 kcal/mol with butyrylcholinesterase. The WS6 also showed a better binding potential with neurotrophin targets that are Brain-derived Neurotrophic Factor, Neurotrophin 4, Nerve Growth Factor, and Neurotrophin 3. The tested compounds particularly WS6 revealed significant antioxidant and anti-inflammatory activities through the comparative docking analysis with Fluorouracil and Melatonin as control drugs of antioxidants while Celecoxib and Anakinra as anti-inflammatory. The bioinformatics approaches including molecular docking calculations followed by the pharmacokinetics analysis and molecular dynamic simulations were accomplished to explore the capabilities of designed stilbenes as effective and potential leads. Root mean square deviation, root mean square fluctuations, and MM-GBSA calculations were performed through molecular dynamic simulations to extract the structural and residual variations and binding free energies through the 50-ns time scale.

CONTEXT: The property transition between metal and semiconductor is the key to improving the properties of transition metal dichalcogenides (TMDCs). The adsorption of the NbS2 compound in the defect state was adjusted for the first time. The hybrid system overwrites the original surface mechanism of NbS2 and induces indirect band gaps. This modulation mode makes NbS2 convert into a semiconductor and effectively improves the catalytic activity of the material in the system. In addition, the original local magnetic moment of the compound is concentrated in the vacancy region and is improved. The optical properties of the adsorption system indicate that NbS2 compounds can be effectively applied in visible and low-frequency ultraviolet regions. This provides a new idea for the design of the NbS2 compound as a two-dimensional photoelectric material. METHODS: In the study, we assume that only one atom is adsorbed on the NbS2 supercell of the defect, and the distance between the two adjacent atoms exceeds 12.74 Å, so the interaction between atoms is ignored in the study. Adsorbed atoms include nonmetallic elements (H, B, C, N, O, F), metallic elements (Fe, Co), and noble metal elements (Pt, Au, Ag). The density functional theory (DFT) was used in the experiment. The non-conservative pseudopotential method was used in the calculation to optimize the crystal structure geometrically. The approximate functional is Heyd-Scuseria-Ernzerhof (HSE06). The calculation method includes the spin-orbit coupling (SOC) effect. The crystal relaxation optimization uses a 7 × 7 × 1 k point grid to calculate niobium disulfide's photoelectric and magnetic properties. A vacuum space of 15Å is introduced in the direction outside the plane, and the free boundary condition is adopted to avoid the interaction between atomic layers. For the convergence parameter setting, the interatomic force of all composite systems is less than 0.03 eV/Å, and the lattice stress is less than 0.05 Gpa.

CONTEXT: This study aims to tune the transport properties of tetracene single-molecule junctions with the proper choice and placement of side and anchoring groups. For the operationalization of the molecule that was anchored with thiol or isocyanide groups, two different side groups, amine and nitro, in two different positions, were taken into consideration. For unperturbed tetracene molecule, a prominent negative differential resistance (NDR) feature at 1.8 V was observed with the isocyanide anchoring group while the thiol anchoring group exhibits a plateau region over a bias voltage of 2.2 to 3.2 V. At a bias voltage that is dependent on the chemical or structural change of side or anchoring groups, NDR feature of varying degree was seen in all configurations. Results show that the current flowing through the thiol-anchored molecule perturbed with the amine group at S' position is relatively larger than other configurations because of the smaller HOMO-LUMO gap and broader transmission peaks resulting in a peak to valley current ratio (PVCR) of 1.22. In addition, multiple NDR regions were realized in nitro-perturbed isocyanide-anchored molecule at S position. These results suggest their promising applications in switches, logic cells, and storage devices. METHODS: The modeling and simulation of side-group mediated anchored tetracene molecule through two electrodic systems were studied using density functional theory (DFT) combined with non-equilibrium Green's function (NEGF) in Virtual NanoLab-AtomistixToolkit (ATK). The electron transport properties were calculated using Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) exchange-correlation function. To optimize computing time, gold electrodes were single zeta polarized whereas the molecule, anchor groups, and side groups were double zeta polarized.

CONTEXT AND RESULTS: This study aimed to obtain potential energy curves within a multireference 4-component relativistic method and to present spectroscopic constants (R[Formula: see text],[Formula: see text],[Formula: see text]x[Formula: see text],[Formula: see text]y[Formula: see text], D[Formula: see text], D[Formula: see text], B[Formula: see text],[Formula: see text],[Formula: see text],[Formula: see text] ), accurate extended Rydberg analytical form, and rovibrational levels for the 6 low-lying states of the I[Formula: see text] anion. For these states, some spectroscopic constants, rovibrational levels, and an accurate analytical form are presented for the first time in literature, and they are of interest for femtosecond and dynamics experiments of I[Formula: see text] as well as for electron attachment of I[Formula: see text]. This study suggests that the inclusion of relativistic and correlation effects treated at the MRCISD+Q level is needed to obtain reliable results, specially for D[Formula: see text]. COMPUTATIONAL AND THEORETICAL TECHNIQUES: The potential energy curves of the ground and the excited states of the molecular iodine anion (I[Formula: see text]) were investigated at multireference configuration interaction (MRCISD) with Davidson size-extensivity correction (denoted as +Q) within a fully relativistic four-component relativistic framework including Breit interaction.

CONTEXT: Herein, we have studied progressively novel metal lead-free halide double perovskite renewable energy materials. Due to their potential use in electronic devices, researchers have investigated these materials with a lot of interest. From the electronic structure, we have found that these are the indirect band gap semiconductors within the range between 1.273 and 3.986 eV. Optical parameters such as dielectric constant, electrical conductivity, and absorption coefficient have also been investigated, which have shown that these materials have potential use in photovoltaics. We have checked stability issues by thermodynamic parameters and phonon spectra. We have found them thermally stable; however, the phonon spectra show their dynamical instability and except for Na2AgSbF6 and Na2AgSbI6, the remaining compounds are weak in mechanical stability. For another futuristic purpose, thermoelectric parameters such as Seebeck coefficient, power factor, and figure of merit have also been calculated, which again verifies that these materials may be very useful in thermoelectric devices. Most of the parameters have been computed for the first time. METHODS: We have performed this computational work using WIEN2k simulation code, which is based on the full-potential linearized augmented plane wave (FP-LAPW) technique. It is one of the most reliable techniques to calculate the photovoltaic properties of semiconducting perovskites. The interaction between ion-core and valence electrons was dealt with within the PAW technique as implemented in Vienna Ab initio Simulation Package (VASP).

CONTEXT: Fullerenes are of high significance due to their unique chemical properties and various applications in technology, particularly materials science, drug delivery, electronics, and nanoelectronics. In the recent years, many attempts have been focused to introduce new heteroatom-doped fullerenes having advanced chemical properties and tunable electronic traits, which make them a potential candidate for application in many branches of sciences. In this study, a novel C50N10 azafullerene with a fascinating structure of chained nitrogen atoms on a buckyball pole, with different electronic and optical properties compared to its other analogs, is introduced and trace of N-N substructures on the surface of C60 fullerene cage is investigated. For this molecule, four structural isomers including 3 structures with chain N atoms on a fullerene buckyball pole (NP isomers) and one isomer with separated N atoms (SN isomer) have been studied. All isomers have been studied with and without symmetry constraints, and the symmetry influence on the structure and stability of each isomer has been investigated. Although the studied NP structures have lower stability than the SN isomer, some reasons (such as their more all-carbon hexagonal rings, breaking some of their N-N bonds for partial opening of the cage and creating bigger rings in order to get rid of the unfavorable strain, as well as decreasing the N-N lone pair repulsions) lead to the acceptable stability of these structures with the bonded N atoms. The results of atomization energy and vibrational frequency calculations indicate that isomers with the bonded N atoms have acceptable stabilities and do not decompose into their constituent components. Investigation on the structural parameters demonstrates important roles of the number of all-carbon hexagonal rings, the number of N-N junction, and the molecule symmetry in the stability of the structures with the bonded N atoms. Study on the electronic and optical properties indicates that the target structures exhibit high electronic polarizability, relatively small HOMO/LUMO gap, high first- and second-order hyperpolarizability, and also large third-order nonlinear optical properties. METHODS: All calculations have been performed using Gaussian G09 software using density functional theory (DFT) approach. Three-parameter Beck hybrid exchange functional (B3) hybridized with nonlocal correlation functional of Lee, Yang, and Parr (LYP) has been employed as the level of DFT calculations. All optimizations have been performed at double-zeta polarized (DZP) split valence 6-31G(d,p) and also at split valence TZP 6-311G(d,p) basis sets. The global minimum structures have been confirmed by frequency calculations at the same level of optimizations. The natural bond orbital (NBO) analyses, frontier orbital surfaces imaging, atomic charges, and charge transfer analyses have been achieved by GenNBO program package.