Journal of Molecular Modeling

CONTEXT: The present work deals with the linear and nonlinear optical properties such as the dipole moment, polarizability, total hyperpolarizability, electric field-induced second harmonic generation, and hyper-Rayleigh scattering first hyperpolarizability of four heterocyclic azo compounds containing the sulfonamide group considered promise in nonlinear optic. The obtained polarizability and hyperpolarizability were supported by the frontier molecular orbital analysis. The properties have been effectively estimated and thoroughly examined to shed light on the nonlinear optical activity based on the density functional theory...

INTRODUCTION: The electronic and optical properties of β-Ga2O3 have been investigated by CASTEP using first principles. It is found that β-Ga2O3 has an indirect band gap and the conduction band base is located at the Γ point. The stability of β-Ga2O3 is demonstrated by the calculation of elastic constants, and the ductility of β-Ga2O3 is demonstrated by the ratio of Poisson's ratio to shear modulus. The optical property analysis shows that β-Ga2O3 has a high absorption capacity in the ultraviolet region, but a low absorption capacity in visible and infrared light...

CONTEXT: Conjugated polymers (CPs) have been recognized as promising materials for the manufacture of electronic devices. However, further studies are still needed to enhance the electrical conductivity of these type of organic materials. The two main strategies for achieving this improvement are the doping process and chemical modification of the polymer chain. Therefore, in this article, we conduct a theoretical investigation, employing DFT calculations to evaluate the structural, energetic, and electronic properties of pristine and push-pull-derived poly(p-phenylene) oligomers (PPPs), as well as the analysis at the molecular level of the polymer doping process...

CONTEXT: Based on the first principles, the influence of S-atom doping on the electronic and optical properties of stanene is comprehensively examined in this work. The results show that pure stanene is a quasi-metal with zero bandgap. After doping with an S atom, opening the bandgap of pure stanene becomes possible and the state of the stanene is converted from quasi-metal to semiconductor. Analysis of the density of states reveals that the density of states of all doped systems is primarily made of the p-orbital of the Sn...

CONTEXT: Hydroxypropyl-β-cyclodextrin (HPβCD) is one of the derivatized cyclodextrins most widely used as an excipient in the pharmaceutical industry, for its capacity to improve certain drugs properties. Different configurations of HPβCD are possible depending on the number and location of the 2-hydroxypropyl groups substituted on the glucose rings. Rifampicin has become the most commonly clinically used antibiotic against tuberculosis in recent years, despite its low solubility and variable bioavailability...

CONTEXT: This study investigates the dynamic stability of monolayers MoS2 , WS2 , and MoS2 /WS2 van der Waals heterostructures (vdWHs) and the influence of shear strain on their electronic properties. The computational results of the binding energy and phonon dispersion demonstrate the excellent dynamic stability of MoS2 /WS2 vdWHs. The MoS2 /WS2 vdWH, with a type-II band alignment and an indirect bandgap, reduces electron-hole recombination, enhancing the efficiency and performance of optoelectronic devices...

CONTEXT: Gallium, renowned for its notably low melting point and unique property of becoming liquid at room temperature, is a valuable constituent in phase change materials. In this study, we investigate the solid-liquid phase transition of gallium using the modified embedded atom method (MEAM) potential. It addresses the technique to compute the free energy difference between the solid and liquid without using a reference state. We examine various thermodynamic and dynamic properties, including density, specific heat capacity, diffusivity, and radial distribution functions...

CONTEXT AND RESULTS: The study examines the physical characteristics of Co2 ZrZ compounds using the Wien2k code and the Anisimov and Gunnarsson approach. Results show metallic attributes in Co2 ZrBi and Co2 ZrAs, while Co2 ZrPb exhibits semi-metallic tendencies. Energy gap evaluations reveal significant infrared transitions, indicating altered electron mobility compensated by increased ultraviolet absorption. These compounds have potential in space solar energy applications due to UV light absorption capabilities, especially in Co2ZrPb...

CONTEXT: It has been reported that photoexcitation of azastilbene compounds like E-1,2-bispyrazinyl-ethylene (bpe) can undergo E → Z photoisomerization of its quaternary salts via the excited triplet state. However, experimentally it is possible to get low fluorescence and photoisomerisation quantum yields in a state with higher internal conversion than intersystem crossing. We modelled bpe and its methylated derivative (bpeMe), as well as its quaternary halogen salts (bpeMeX with X = F- , Cl- , Br- and I- ) to study levels of fluorescence, phosphorescence and excited state potential energy surfaces (PES)...

CONTEXT: BIM (Bcl-2 interacting mediator of apoptosis)-derived peptides that specifically target over-expressed Mcl-1 (myeloid cell leukemia-1) protein and induce apoptosis are potentially anti-cancer agents. Since the helicity of BIM-derived peptides has a crucial role in their functionality, a range of strategies have been used to increase the helicity including the introduction of unnatural residues and stapling methods that have some drawbacks such as the accumulation in the liver...

CONTEXT: Nucleophilic substitution reactions of aliphatic amines with alkyl halides represent a simple and direct mechanism for obtaining higher-order aliphatic amines. However, it is well known that these reactions suffer from low selectivity due to multiple alkylations, which is attributed to the higher reactivity of the newly formed amine. In order to provide a detailed explanation for this kind of system, we have investigated the reactivity of primary and secondary amines with 1-bromopropane and 2-bromopropane...

CONTEXT: The reactions of radicals with O2 play the important role in the biological, medicinal, and industrial processes. The mechanism of this reaction is studied previously for the alkane, alkene, alkyne, phenols, and close-related radicals. According to these studies, the formation of intermediates in these reactions is predicted only for the aromatic radicals. Thus, the Van der Waals complexes of O2 with phenyl or benzyl radicals are predicted, as well as the π-π cluster for benzene...

CONTEXT: Electronic durable behavior on the material surface was accompanied by a class of antipsychotic drugs (APD) to describe the surface modification in the designed adsorption model. Hierarchically Zn-MOF system was utilized for estimating its capacity for drug molecule removal. Geometrically optimized strategy on the studied systems was performed using DFT/GGA/PBE. FMOs analysis was depicted based on the same level of calculations, and molecular electrostatic potential surface (MEP) was generated for unadsorbed and adsorbed systems to illustrate the variation in the surface-active sites...

CONTEXT: The nitro group was introduced into the nitrogen heterocycle of 1H-benzotriazole to design a total of 31 derivatives. To estimate the thermal stability of these derivatives, the heat of formation (HOF) is calculated based on the isodesmic reaction. The bond dissociation energy (BDE) was also predicted based on the homolytic reaction to further evaluate the dynamic stability. To evaluate the possibility of utilizing as high energy density compounds (HEDCs), the detonation parameters including the detonation pressure (P), detonation velocity (D), and explosive heat (Q) are predicted by taking advantage of the Kamlet-Jacobs empirical equation...

CONTEXT: Monoamine oxidase B (MAO-B), an enzyme of significant relevance in the realm of neurodegenerative disorders, has garnered considerable attention as a potential target for therapeutic intervention. Natural compounds known as chalcones have shown potential as MAO-B inhibitors. In this particular study, we employed a multimodal computational method to evaluate the inhibitory effects of chalcones on MAO-B. METHODS: Molecular docking methods were used to study and assess the complicated binding interactions that occur between chalcones and MAO-B...

The characterization of normal mode (CNM) procedure coupled with an adiabatic connection scheme (ACS) between local and normal vibrational modes, both being a part of the Local Vibrational Mode theory developed in our group, can identify spectral changes as structural fingerprints that monitor symmetry alterations, such as those caused by Jahn-Teller (JT) distortions. Employing the PBE0/Def2-TZVP level of theory, we investigated in this proof-of-concept study the hexaaquachromium cation case, <mml:math xmlns:mml="https://www...

CONTEXT: Choline-based surfactants are interesting both from the practical point of view to obtaining environmental-friendly surfactants as well as from the theoretical side since the interactions between the choline and surfactants can help to understand self-assembly phenomena in deep eutectic solvents. Although no significant change was noticed in the micelle size and shape due to the exchange of the sodium counter-ion by choline in our simulations, the adsorption of the choline cation over the micelle surface is stronger than the adsorption of the sodium, which leads to a reduction of the exposed surface area of the micelle and remarkable effects over the electrostatic potential...

CONTEXT: A comparative study of the change in different properties of electronic and structural of the free 1H-indole-2,3-dione molecule and its complexes has been obtained. HOMA analysis was performed to investigate the effects of lithium sodium and potassium cations on the aromaticity of lithium sodium and potassium complexes of 1H-indole-2,3-dione. METHODS: Several 1H-indole-2,3-dione complexes with lithium, sodium, and potassium cations were optimized at the B3LYP/6-311G(d,p) level...

CONTEXT: The new equations have been developed for the structural and electronic properties using the plasmon calculations for the first time for 2-D MoX2 structures. Literature shows still an extensive study is required on the stability and optical properties of MoX2 under different hydrostatic pressures and thermal properties under different temperatures using the first principles, for electronic industrial applications. The stability is analyzed using binding energy and phonon calculations...

CONTEXT: Various 7H,7'H-[6,6'-bi[1,2,4]triazolo[4,3-b][1,2,4]triazole]-3,3',7,7'-tetramine (A) based nitrogen-rich energetic salts were designed and their properties explored. All energetic salts possess relatively high nitrogen content (> 48%), positive heats of formation (> 429 kJ/mol) and stability owing to a significant contribution from fused backbone. The cationic component shows a very high heat of formation (2516 kJ/mol); therefore, it is highly suitable for enthalpy enhancement in new energetic salts...