Current Physical Chemistry - Volume 5, Issue 4, 2015

Chinesin I and chinesin II are acylphloroglucinols of natural origin differing only by the length of their acyl chains. They exhibit antimicrobial and antiviral activities, including inhibitory effects on the replication of the vesicular stomatitis and herpes simplex viruses. Their structures (different from those of the acylphloroglucinols so far investigated computationally) combine a variety of factors with significant influence on conformational preferences: the presence of a keto O replacing one of the phenol OH ortho to the acyl chain, which removes one of the possibilities for the formation of the intramolecular hydrogen bond between the sp2 O of the acyl chain and an ortho OH, typical of acylphloroglucinols; the presence of a substituted pentagonal ring attached to the phloroglucinol moiety through a methylene bridge; and the presence of a prenyl chain, whose bond can interact with a phenol OH. Methods: The two compounds were studied at the Hartree Fock (HF/6-31G(d,p)) and Density Functional Theory (DFT/B3LYP/6-31+G(d,p)) levels, in vacuo and in three solvents – chloroform, acetonitrile and water. Calculations in solution utilized the Polarizable Continuum Model (PCM). Results: The results show fair correspondence with the patterns identified for acylphloroglucinols and, in particular, for acylphloroglucinols in which the OH at C6 is replaced by a keto O. Conclusion: The close similarities in the conformational preferences and molecular properties of the two compounds confirm scarce influence by the nature of the acyl chain, when it does not contain groups which can interact with the phloroglucinol moiety. They may also be considered responsible for the similarities in the biological activities of the two molecules.

To propose a plausible binding mode between piperine and derivatives inside acetylcholinesterase (AChE) by molecular docking simulations, which might explain the observed experimental inhibitory activity of the enzyme, the anticholinesterase activity of compounds was tested using a microplate- reader assay based on the Ellman method modified by Rhee. Docking simulations were performed with GOLD 4.1 program based on the binding mode between AChE and donepezil due to the structural similarity of this drug with piperine. Piperine, piperic acid, and piperic ester exhibit AChE in vitro inhibitory activity of 46.5, 50.6, and 63.6%, respectively. Docking simulations revealed favorable molecular interactions of these compounds within the hydrophobic binding pocket of AChE. Piperine and its derivatives seem to be a good starting point for developing novel acetylcholinesterase inhibitors with therapeutical potential in Alzheimer’s disease treatment.

Organic semiconductors have unique molecular properties that hardly ever are found in biochemical macromolecules, as charge transport and planarity of polymeric chain. The first step to understand these properties is based on reliable geometric description of these systems, where semi-empirical methodologies can provide good geometric results with low computational cost. In this study, PEDOT dimer rotational barrier was investigated by three semi-empirical methodologies (PM6, PM7 and RM1) and B3LYP/6-31+G(d,p) DFT level of theory, comparing with experimental results for bond length, dihedral angle and band-gap energy. The results show better description by DFT methodology for PEDOT dimer bond length and band-gap energy, while PM6 methodology provides better long range description, especially dihedral angle, indicating that this methodology can be used for predict geometric parameters of organic semiconductor polymeric chain.

Heptamethine Iodide and heptamethine hexafluorophosphate solutions in various solvents (chloroform, dichloromethane, ethanol and toluene) were studied spectrophotometrically and spectrofluorimetrically as X-ray and gamma-ray dosimeters for the detection of low-dose radiation. The useful dose range was found to be between 0 to 1 Gy and 1 to 30 Gy for the concentrations studied. The effects of temperature and light on the stability of response during pre-irradiation and post-irradiation storage, the effects of different solvents and dose rates on dosimetric responses of these dyes were also investigated. The results of our studies show that these dye solutions are quite stable in the dark at low as well as room temperature and could be used as dosimeters for low dose X-ray and gamma radiation in medical dosimetry for radiotherapy treatment planning. They can also be used as dosimeters in personal radiation safety applications and environmental radiation monitoring. They have constant sensitivity and their detection limit is an order of magnitude lower than recently reported in the literature. These dyes are and were used in photography industry, so they are cheap and easy to buy.

SrTiO3:Nd (0, 1 and 4%) thin films were prepared by pulsed laser deposition and chemical solution deposition techniques on (100) LaAlO3 single crystal substrates. The influence of neodymium amount as well as the influence of the deposition method on the structural and microstructural properties of the films was evaluated. All of the films are (h00) oriented and present high quality epitaxial growth. A higher short-range disorder occurs for the 4% Nd-doped films obtained by chemical solution deposition, evidenced by the presence of the TO2, LO2 and LO4 first-order Raman modes and by an increase in the intensity of the photo luminescent spectrum. A greater effect of doping is also observed on the microstructure of this film.

The band alignment mechanism for the ZnO/ZnS interface features of ZnO@ZnS core-shell structures was investigated by Density Functional Theory (DFT) calculations, using a Gaussian-type basis set and periodic boundary conditions. This study leads to an improved understanding of the unique properties of such core-shell structures, especially at the nanoscale. The band structures, energy gaps, electron charge density maps, and density of states for the ordered and disordered models were studied in order to predict the band alignment mechanism and cluster-tocluster charge transfer properties in the ZnO@ZnS core-shell structures with different degrees of crystallinity. The theoretical results show that the type-II behavior of the core-shell structures may provide an in-depth understanding of the close relationship between different coordination environments and structural characteristics, and may also reveal changes in the electronic and structural properties, which occur mainly at their interface.

DFT functionals, M06 and B3LYP, with the 6-31G(d) and LANL2DZ basis sets were used to study pyrrolopyrimidines as focal adhesion kinase (FAK) inhibitors. Thermochemistry was studied at the semi-empirical PM6 level. A set of seven molecules derived from pyrrolopyrimidine of known activity was evaluated. HOMO and LUMO orbitals were investigated for all inhibitors to understand the importance of frontier molecular orbitals for the activity. Molecular electrostatic potential maps helped in the analysis of the interaction between the amino acids in the catalytic site and their inhibitors. Interaction energies and entropic factors were also computed. Principal component analysis was performed to study the activity and their relations with theoretical properties. Theoretical results suggested the importance of electron density close to the Cys502 residue for the experimental activity.