Journal of Molecular Modeling

CONTEXT: Based on first principles, the structure, elasticity, mechanics, electronics, and optical properties of cubic K2 Pb2 O3 were studied. The structural parameters calculated by this method are close to the previous theoretical results. The elastic constant, bulk modulus, shear modulus, Young's modulus, Poisson's ratio, and mechanical stability are studied, and it is shown that cubic K2 Pb2 O3 is mechanically stable, isotropic, and brittleness. The electrical conductivity and chemical bonding of cubic K2 Pb2 O3 were analyzed based on the calculated band structure, density of states (DOS), and bond populations...

CONTENT: Ubiquitin, a ubiquitous small protein found in all living organisms, is crucial for tagging proteins earmarked for degradation and holds pivotal importance in biomedicine. Protein functionality is intricately linked to its structure. To comprehend the impact of diverse temperatures on ubiquitin protein structure, our study delved into the energy landscape, hydrogen bonding, and overall structural stability of ubiquitin protein at varying temperatures. Through meticulous analysis of root mean square deviation and root mean square fluctuation, we validated the robustness of the simulation conditions employed...

CONTEXT: Herein, we compare and contrast the dual roles of Cun clusters (n = 3, 5, and 7 atoms) in scavenging or generating RO• free radicals from ROH at the theoretical levels (where R = H, methyl, ethyl, n-propyl, i-propyl, n-butyl, t-butyl, and phenyl). This investigation is performed in water media to mimic the actual environment in the biological system. In the presence of the Cun clusters, bond dissociation energy (BDE) of RO-H and R-OH is reduced...

CONTEXT: Parkinson's disease is a neurodegenerative condition characterized by the degeneration of dopaminergic neurons, resulting in motor disabilities such as rigidity, bradykinesia, postural instability, and resting tremors. While the exact cause of Parkinson's remains uncertain, both familial and sporadic forms are often associated with the G2019S mutation found in the kinase domain of LRRK2. Roco4 is an analogue of LRRK2 protein in Dictyostelium discoideum which is an established model organism to investigate LRRK2 inhibitors...

CONTEXT: SHP2 is a non-receptor protein tyrosine phosphatase to remove tyrosine phosphorylation. Functionally, SHP2 is an essential bridge to connect numerous oncogenic cell-signaling cascades including RAS-ERK, PI3K-AKT, JAK-STAT, and PD-1/PD-L1 pathways. This study aims to discover novel and potent SHP2 inhibitors using a hierarchical structure-based virtual screening strategy that combines molecular docking and the fragment molecular orbital method (FMO) for calculating binding affinity (referred to as the Dock-FMO protocol)...

CONTEXT: This project performed quantum chemical computation, through kinetic and thermodynamic analyses to compare relative reactivity, reaction rate, and equilibrium composition from the possible pathways in connection with stabilizer-nitrodioxide reactions to determine the stability of the materials for practical application. Corresponding achievements have promoted the use of N-methyl-p-nitroaniline (MNA) and dinitrophenyl malonamide series (M3, M4, and M5) stabilizers as high priorities for selection...

CONTEXT: In this paper, the optimum coverage of 4.44% and the optimum adsorption sites were determined for the Be3 N2 adsorption system of O atoms at different coverages based on density functional theory. The electronic and optical properties of the model were investigated by applying bending deformation to the model at these coverage and adsorption sites. Adsorption of O atoms disrupts the geometrical symmetry of Be3 N2 , resulting in orbital rehybridization and lowering its band gap...

CONTEXT: Two-dimensional (2D) nanoheterostructures of materials, integrating various phase or materials into a single nanosheet have stimulated large-scale research interest for designing novel two dimensional devices. In contemporary analysis present work, we examined the structural and electronic properties of the isolated 2D BN and GaN monolayers. We have investigated the structural stability and optoelectronic and photocatalytic response of the g-GaN/BN nanoheterostructure along with its response to strain...

CONTEXT: Human estrogen-related receptor γ (hERRγ) is a key protein involved in various endocrines and metabolic signaling. Numerous environmental endocrine-disrupting chemicals (EDCs) can impact related physiological activities through receptor signaling pathways. Focused on hERRγ with 4-isopropylphenol, bisphenol-F (BPF), and BP(2,2)(Un) complexes, we executed molecular docking and multiple molecular dynamics (MD) simulations along with molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) and solvation interaction energy (SIE) calculation to study the detailed dynamical structural characteristics and interactions between them...

CONTEXT: We use molecular dynamics simulations to unravel the molecular level mechanisms underlying the structure and dynamics of water and ions flowing through nanoporous starch-graphene membranes. Our findings indicate that there is a significant tendency for the formation of short-range order in close proximity to the graphene membrane surface. This leads to a greater concentration of water and ions, suggesting strong interactions between the membrane and the saltwater solution. Furthermore, we found that the starch-graphene membrane was most efficient in sieving out ions when the starch loading is 15 wt...

CONTEXT: Due to their unique photophysical properties, organic charge transfer crystals are becoming promising materials for next-generation optoelectronic devices. This research paper explores the impact of s-block metals on a charge transfer crystal of indol-2-one for enhanced nonlinear optical (NLO) responses with efficient energetic offsets. The study reveals that alkali metals can enhance NLO performance due to their free electrons. METHOD: The Perdew-Burke-Ernzerhof functional of DFT with dispersion correction (D3) was used, and the λmax values ranged between 596 and 669 nm, with the highest value for dichloromethane (DCM)...

CONTEXT: The crystal and molecular structure, electronic properties, optical parameters, and elastic properties of a 1:2 hexanitrohexaazaisowurtzitane (CL-20)/2-mercapto-1-methylimidazole (MMI) cocrystal under 0 ~ 100 GPa hydrostatic pressure were calculated. The results show that the cocrystal CL-20/MMI undergoes three structural transitions at 72 GPa, 95 GPa, and 97 GPa, respectively, and the structural transition occurs in the part of the MMI compound. Structural mutations formed new bonds S1-S2, C2-C7, and N1C5 at 72GPa, 95 GPa, and 97 GPa, respectively...

CONTEXT: To gain a deeper understanding of zinc-doped boron clusters, theoretical calculations were performed to investigate the size effects and electronic properties of zinc-doped boron clusters. The study of the electronic properties, spectral characteristics, and geometric structures of Zn <mml:math xmlns:mml="https://www.w3.org/1998/Math/MathML"><mml:msub><mml:mtext>B</mml:mtext> <mml:mi>n</mml:mi></mml:msub> </mml:math> (n = 1-15) is of great significance in the fields of semiconductor materials science, material detection, and improving catalytic efficiency...

CONTEXT: In this study, we have investigated the structure, reactivity, bonding, and electronic transitions of DPA and PDTC along with their Ni-Zn complexes using DFT/TD-DFT methods. The energy gap between the frontier orbitals was computed to understand the reactivity pattern of the ligands and metal complexes. From the energies of FMO's, the global reactivity descriptors such as electron affinity, ionization potential, hardness (η), softness (S), chemical potential (μ), electronegativity (χ), and electrophilicity index (ω) have been calculated...

CONTEXT: The electronic, discrete water solvation, and vibrational properties of zwitterionic sulfanilic acid were thoroughly investigated using periodic and non-periodic DFT approaches. The periodic-DFT results, obtained by employing the PBE-TS functional (Perdew-Burke-Ernzerhof (PBE) functional with the Tkatchenko and Scheffler (TS) dispersion correction) were first presented in order to analyze the band structures of the studied crystal. An attentive reading of the predicted band structures has shown three lowest gap energies calculated at 4...

CONTEXT: In this study, the electronic structure and diffusion barrier of Ca adsorbed MoTe2 system under different degrees of shear deformation were calculated based on the first-principles method. The results show that both the pure MoTe2 system and Ca-adsorbed MoTe2 system are affected by shear deformation. The pure MoTe2 undergoes a transition from direct to indirect band gap under shear deformation. The adsorption of Ca makes MoTe2 changes from semiconductor to quasi-metal. The results of the density of states show that Ca insertion makes the conduction band part of the adsorption system significantly enhanced...

CONTEXT: Push-pull compounds are model systems and have numerous applications. By changing their substituents, properties are modified and new molecules for different applications can be designed. The work investigates the gas-phase electronic absorption spectra of 15 derivatives of push-pull para-nitroaniline (pNA). This molecule has applications in pharmaceuticals, azo dyes, corrosion inhibitors, and optoelectronics. Both electron-donor and electron-withdrawing groups were investigated...

CONTEXT: In this study, we have developed four new chromophores (TM1-TM4) and performed quantum chemical calculations to explore their nonlinear optical properties. Our focus was on understanding the impact of electron-donating substituents on 1,3,4-oxadiazole derivative chromophores. The natural bond orbital analysis confirmed the interactions between donors and acceptors as well as provided insights into intramolecular charge transfer. We also estimated dipole moment, linear polarizability molecular electrostatic potential, UV-visible spectra, and first hyperpolarizability...

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...