DFT and molecular docking studies of self-assembly of sulfone analogues and graphene

Evodiamine and Rutaecarpine as Potential Anticancer Compounds: A Combined Computational Study

Evodiamine (EVO) and rutaecarpine (RUT) are the main active compounds of the traditional Chinese medicinal herb Evodia rutaecarpa. Here, we fully optimized the molecular geometries of EVO and RUT at the B3LYP/6-311++G (d, p) level of density functional theory. The natural population analysis (NPA) charges, frontier molecular orbitals, molecular electrostatic potentials, and the chemical reactivity descriptors for EVO and RUT were also investigated. Furthermore, molecular docking, molecular dynamics simulations, and the analysis of the binding free energies of EVO and RUT were carried out against the anticancer target topoisomerase 1 (TOP1) to clarify their anticancer mechanisms. The docking results indicated that they could inhibit TOP1 by intercalating into the cleaved DNA-binding site to form a TOP1−DNA−ligand ternary complex, suggesting that they may be potential TOP1 inhibitors. Molecular dynamics (MD) simulations evaluated the binding stability of the TOP1−DNA−ligand ternary complex. The calculation of binding free energy showed that the binding ability of EVO with TOP1 was stronger than that of RUT. These results elucidated the structure−activity relationship and the antitumor mechanism of EVO and RUT at the molecular level. It is suggested that EVO and RUT may be potential compounds for the development of new anticancer drugs.

DFT analysis of valproic acid adsorption onto Al12/B12-N12/P12 nanocages with solvent effects

Using density functional theory, the adsorption of valproic acid onto the surface of fullerene-like nanocages was investigated. Valproic acid interacts with the nanocages through the carboxylic group with energies of - 144.14, - 109.71, - 105.22, and - 84.96 kcal/mol. The frontier molecular orbital (FMO) energy levels were considerably altered upon adsorption, resulting in a reduction in energy gap and increase in electrical conductivity. This suggests that nanocages could be used as sensors as well as options for drug administration in biological systems. Solvation effects in water are also reported.

Adsorption properties of dacarbazine with graphene/fullerene/metal nanocages - Reactivity, spectroscopic and SERS analysis

Drug delivery devices are an effective way to minimize anticancer drug toxicity and nanostructures are used in the targeted drug delivery. In the present work, adsorption and interaction behavior of 4-(dimethylaminodiazenyl)-1H-imidazole-5-carboxamide (DAIC) with nano complexes (graphene, fullerene and fullerene like metal cages) are reported theoretically. From the reactivity studies, the electrophilicity index of DAIC-nanoclusters are increasing and this gives the bioactivity of the nanocluster systems. Adsorption energy is highest in the case of AlP and lowest in the case of BP clusters. Mulliken charge distribution of all systems is an evidence for chemical enhancement. DAIC adsorption over nanocages causes changes in electronic properties resulting in chemical enhancement and variation in Raman spectra which suggests that nanocages could be a good candidate for DAIC detection.

Mechanism on redistribution synthesis of dichlorodimethylsilane by AlCl3/ZSM-5(3T)@γ-Al2O3 core-shell catalyst

The redistribution method plays an important role in addressing the issue of organosilicon by-products in the direct synthesis of dichlorodimethylsilane, and the redistribution mechanism is still a topic of debate. The redistribution mechanism by the ZSM-5(3 T)@γ-Al₂O₃ core-shell catalyst and post-modified AlCl₃/ZSM-5(3 T)@γ-Al₂O₃ catalyst was technically performed using the Density functional theory (DFT) at the level of B3LYP/6-311 +  + G(3df,2pd). The results show that no. 1 active site of ZSM-5(3 T)@γ-Al₂O₃ core-shell structure has a significant effect on the activity of the catalyst. Indicating that the active center involved in the reaction is H provided by the Al-O-H bond, which is an obvious catalytic active center of Bronsted acid. Furthermore, the post-modified AlCl₃/ZSM-5(3T)@γ-Al₂O₃ catalyst is in more favor of redistribution reaction comparing with the ZSM-5(3 T)@γ-Al₂O₃ core-shell catalyst. It ascribes to the robust Lewis site of aluminum chloride favorable modification. The redistribution synthesis mechanism of dichlorodimethylsilane on the ZSM-5(3 T)@γ-Al₂O₃ core-shell catalyst and post-modified AlCl₃/ZSM-5(3 T)@γ-Al₂O₃ catalyst had been investigated by using the Density functional theory (DFT) method at the level of B3LYP/6-311 +  + G(3df,2pd). The former active center was Bronsted acidic center, while the latter one was Lewis acidic center, ascribing to the Lewis site of aluminum chloride favorable modification. The catalytic activity of the post-synthesis AlCl₃/ZSM-5(3 T)@γ-Al₂O₃ catalyst completely was consistent with experimental results.

DFT computational study of trihalogenated aniline derivative's adsorption onto graphene/fullerene/fullerene-like nanocages, X12Y12 (X = Al, B, and Y = N, P)

Adsorption of 2,4,6-tribromoaniline (BA), 2,4,6-trifluoroaniline (FA) and 2,4,6-trichloroaniline (CA) onto the surface of coronene/fullerene/fullerene-like nanocages was investigated by theoretical calculations. Due to the adsorption of BA/FA/CA, there are significant changes in chemical descriptors and nonlinear optical properties. Energy gap values of all nanoclusters are lowered, giving an increase in conductivity of complexes except for fullerene. All complex's ultraviolet visible wavenumber is blue-shifted and especially for fullerene complex, the values are very high. The enhancement of Raman intensities shows that it is possible to design a nanocage sensor for detecting these compounds by surface-enhanced Raman scattering (SERS).Communicated by Ramaswamy H. Sarma.

Spectroscopic investigations, concentration dependent SERS, and molecular docking studies of a benzoic acid derivative

Spectroscopic analysis, density functional theory (DFT) studies and surface enhanced Raman scattering of 4-((3-bromo-5-chloro-2-hydroxybenzylidene)amino)benzoic acid (BCHB) have been studied on different silver colloids concentrations in order to know the particular chemical species responsible for the spectra. For Raman and surface enhanced Raman scattering (SERS) wavenumbers, changes are observed. Observed variations in the modes of ring may be due to interaction of the π-electrons and presence of this indicated that RingII is more inclined than RingI and the BCHB assumes inclined orientation for concentration 10^-3 M. Changes in orientation are seen in SERS spectra depending on concentration. In order to determine the electron-rich and poor sites of BCHB, the molecular electrostatic potential was also constructed. The molecular docking studies show that the bindings and interactions with the receptors may be supporting evidence for further studies in design further BCHB pharmaceutical applications.