Journal of Theoretical and Computational Chemistry

Acetylcholinesterase (AChE) is a key enzyme enhancing the cognitive disorder, leading to Alzheimer’s disease, and AChE inhibition is a crucial therapeutic mechanism against it. Matricaria recutita (MR) is widely used as a herbal medicine due to its phytotherapeutic properties. For this reason, MR flower was evaluated to identify polyphenolic compounds (PC), and then each PC is examined for AChE inhibitory activity. The ultra-performance liquid chromatography-electrospray tandem mass spectrometry UPLC-ESI-MS/MS was used to detect PC, and molecular docking was performed to insight potential inhibitory activity of PC against AChE. A series of 13 PC compounds were identified in the fractions of MR plant. Docking studies revealed that the inhibitory free energy and the position of the docked compounds in the active site are favored for the active compounds complex formed between AChE and the identified PC compounds. The accurate analysis of the docking result demonstrates that Kaempferol-3-O-rutinoside (KR) and Luteolin-8-C-glucoside (orientin) (LG) are the most significant inhibitory compounds against AChE. It can be concluded that MR is a significant source of PC compounds, and KR and LG are the most promising compounds that have high-affinity binding to AChE, based on docking outcome. Further experiments are recommended to explore in vivo enzyme compound interaction and toxicity models to establish the maximum suggested dose.

The electronic transport properties of molecular device based on photochromic diarylethene with carbon nanotube electrode are investigated by density functional theory and non-equilibrium Green’s function. The devices with open and closed configurations show a switching effect. It is found that doping of different amounts of nitrogen atoms on left electrodes results in different electronic transport properties. In addition, we discuss the observed oscillation of current in the devices induced by doping using transmission eigenstates and transmission spectra of the device. The local density of states of the device is calculated to analyze the observed rectifying behavior. The results suggest that doping of nitrogen atoms on the left electrode can be considered as a factor to modulate the electronic transport properties of molecular device.

Due to the increasing demand of Al${}_{12}$N${}_{12}$ in optoelectronics and sensing materials, we intended to investigate the adsorption behavior, electronic nature and NLO response of hydrogen and different metals decorated Al${}_{12}$N${}_{12}$ nanocages. Different systems are designed by hydrogen adsorption and encapsulation of metals (Li, Na and K) in Al${}_{12}$N${}_{12}$. Density functional theory at B3LYP functional with conjunction of 6-31G($d$, $p)$ basis set is utilized in order to gain optimized geometries. Different calculations including linear and first-order hyperpolarizability are conducted at same level of theory. Instead of chemiosorption, a phyisosorption phenomenon is seen in all hydrogen adsorbed metal encapsulated Al${}_{12}$N${}_{12}$ nanoclusters. The $Q_{\text{NBO}}$ analysis confirmed the charge separation in hydrogen adsorbed metal encapsulated nanocages. Molecular electrostatic potential (MEP) analysis cleared the different charge sites in all the systems. Similarly, frontier molecular orbitals analysis corroborated the charge densities shifting upon hydrogen adsorption on metal encapsulated AlN nanocages. HOMO–LUMO band gaps suggest effective use of H₂-M-AlN in sensing materials. Global indices of reactivity also endorsed that all hydrogen adsorbed metal encapsulated systems are better materials than pure Al${}_{12}$N${}_{12}$ nanocage for sensing applications. Lastly, linear and first hyperpolarizability of H₂-M-AlN nanocages are found to be greater than M-AlN and pure AlN nanocages. Results of these parameters recommend metal encapsulated nanocages as efficient contributors for the applications in hydrogen sensing and optoelectronic devices.

The aim of this work is to perform a computational study of the radical scavenging activity of a series of common hydroxycinnamic acids (HCAs) in polar and nonpolar solvents in order to rationalize the experimental order obtained in ethanol and to analyze the solvent effect on mechanism and radical scavenging capacity. The thermodynamics of the main mechanisms, namely, hydrogen atom transfer (HAT), sequential proton loss followed by electron transfer (SPLET), and single electron transfer followed by proton transfer (SET-PT) were investigated at the M05-2X/6-31$+$G($d,p$) level of theory using the SMD solvation model. This study shows that the SET-PT mechanism is disfavored in all media, whereas HAT is the most thermodynamically favored mechanism in gas phase and SPLET is the preferred reaction pathway in pentyl ethanoate, ethanol and water. The thermodynamically preferred site of antioxidant action and the radical scavenging order are predicted using the BDE${}_{min}$ and (PA$+$ETE)${}_{min}$ descriptors corresponding to the HAT and SPLET mechanisms, respectively. The obtained results point out that the mechanism and the radical scavenging potency are influenced by solvent polarity and our predictions are in agreement with the experimental measurements performed in ethanol giving the following descending order: caffeic $\mathrm{\text{acid}}>\mathrm{\text{sinapic}}$ $\mathrm{\text{acid}}>\mathrm{\text{ferulic}}$ $\mathrm{\text{acid}}>p$-coumaric acid. Our results also show that the ortho substitution of caffeic acid by strong electron donating groups leads to a notable increase of their radical scavenging activity and new potent HCA derivatives are designed.

Cytidine is a well-known inhibitor of DNA methyltransferase (MTN) enzyme for preventing cancer cells growth. Based on therapeutic benefits, it could be considered as a “lead compound” to be optimized through structural modification for arising better binding affinity in this case. Halogenated derivatives of cytidine were investigated in this work to examine structural and biological features employing in silico approach. To this aim, geometries of the original cytidine and four of its halogenated derivatives were minimized to prepare ligands for interacting with MTN enzyme target in molecular docking simulations. The results for singular ligand structures introduced I-cytidine as an optimized lead compound for contributing to proper interactions with MTN enzyme; the trend was confirmed by molecular docking simulations. As a final remark, I-cytidine could be considered as better ligand for complexation with the MTN enzyme in comparison with the original cytidine.

Herein, we have designed four small molecular donors (SMDs) with Donor–Acceptor–Acceptor (D–Á–A) backbone having different acceptor units for highly efficient organic solar cells (OSCs). The specific molecular modeling has been made by replacing the additional acceptor unit (A) of recently synthesized TPA-DAA-MDN molecule (R) by employing different highly efficient acceptor units in order to improve the photovoltaic performances of the molecules. A theoretical approach (DFT and TD-DFT) has been applied to investigate the photophysical, opto-electronic and photovoltaic parameters of the designed molecules (DAA1–DAA4) and compared with the reference molecule (R). The red-shifting absorption of SMDs is the most important factor for highly efficient OSCs. Our all formulated molecules showed a red shifted absorption spectrum and also exhibit near IR sensitivity. Acceptor unit modification of R molecule causes reduction in HOMO-LUMO energy gap; therefore, all designed molecules offer better opto-electronic properties as compared to R molecule. A variety of certain critical factors essential for efficient SMDs like frontier molecular orbitals (FMOs), absorption maxima, dipole moment, exciton binding energy along with transition density matrix, excitation energy, open circuit voltages and charge mobilities of (DAA1–DAA4) and R have also been investigated. Generally, low values of reorganizational energy (hole and electron) offer high charge mobility and our all designed molecules are enriched in this aspect. High open circuit voltage values, low excitation energies, large dipole moment values indicate that our designed SMDs are suitable candidates for high-efficiency OSCs. Furthermore, conceptualized molecules are superior and thus are suggested to experimentalist for out-looking future progresses of highly efficient OSCs devices.

In order to compare the influence of binders on the oily exudation of cyclotrimethylenetrinitramine (RDX) based aluminized explosives, polyvinyl acetate (EVA) and copolymer of vinylidene fluoride and perfluoropropylene (F2603) were selected as binders, which are most commonly used in the press-packed explosives. Herein, the binding energies of wax with the components of RDX-based aluminized explosives containing EVA and F2603 were predicted. Then, the migration models of wax in EVA and F2603 were constructed respectively, and the migration rate of wax in two binders was also calculated. Finally, experimental verification was carried out for wax migration in the two aluminized explosives. The results show that the binding energies of wax with other components of RDX-based composite explosive are all positive, which indicates that the physical compatibility of RDX-based aluminized explosives containing EVA and F2603 is excellent. In addition, wax interacts with the other components of RDX-based explosives mainly via Van der Waals force. However, the binding strength of wax with RDX crystals and binders decreases with the increase of temperature. The type of binders has a great influence on the migration rate of wax, and the oily exudation rate of wax in F2603 is about 4 times than that in EVA both at 298 K and 344 K. Meanwhile, the polymer configuration greatly changes the migration rate of wax. The calculated results are in good agreement with the experimental results.