Journal of Molecular Modeling

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...

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...