Comparison of growth methods for Si/SiO2 nanostructures as nanodot hetero-emitters for photovoltaic applications

Two different growth mechanisms are compared for the fabrication of Si/SiO₂ nanostructures on crystalline silicon (c-Si) to be used as hetero-emitter in high-efficiency solar cells: (1) The decomposition of substoichiometric amorphous SiO_x (a-SiO_x) films with 0 < x < 1.3 and (2) the dewetting of thin amorphous silicon (a-Si) layers.The grown layers are investigated with regard to their structural properties, their passivation quality for c-Si wafer substrates and their electrical properties in order to evaluate their suitability as a nanodot hetero-emitter. While by layer decomposition, no passivating nanodots could be formed, the dewetting process allows fabricating nanodot passivation layers at temperatures as low as 600 °C. The series resistance through Ag/[Si-nanodots in SiO₂]/c-Si/Al structures for dewetting is similar to nanostructured silicon rich SiO_x films. Still, a nanodot hetero-emitter which exhibits both a satisfying passivation of the substrate and induces a high band bending by doping at the same time could not be fabricated yet.     

Host-guest inclusion complex between β-cyclodextrin and paeonol: A theoretical approach

Host-guest interactions of β-cyclodextrin (β-CD) with paeonol (PAE) were simulated using semi-empirical PM3 and both ONIOM2 [(B3LYP/6-31G*:PM3), (HF/6-31G*:PM3)] methods. The results obtained with PM3 method clearly indicate that the complexes formed are energetically favored with or without solvent, the model 1 (PAE entering into the cavity of β-CD from its wide side by OCH3 group) is found more favored than the model 2 (PAE entering into the cavity of β-CD from its wide side by COCH3 group). Finally, natural bonding orbital (NBO) analysis was performed based on ONIOM2 optimized complexes to quantify the donor–acceptor interactions between PAE and β-CD.     

Prediction of the 3D structure and dynamics of human DP G-protein coupled receptor bound to an agonist and an antagonist

Prostanoids play important physiological roles in the cardiovascular and immune systems and in pain sensation in peripheral systems through their interactions with eight G-protein coupled receptors. These receptors are important drug targets, but development of subtype specific agonists and antagonists has been hampered by the lack of 3D structures for these receptors. We report here the 3D structure for the human DP G-protein coupled receptor (GPCR) predicted by the MembStruk computational method. To validate this structure, we use the HierDock computational method to predict the binding mode for the endogenous agonist (PGD2) to DP. Based on our structure, we predicted the binding of different antagonists and optimized them. We find that PGD2 binds vertically to DP in the TM1237 region with the alpha chain toward the extracellular (EC) region and the omega chain toward the middle of the membrane. This structure explains the selectivity of the DP receptor and the residues involved in the predicted binding site correlate very well with available mutation experiments on DP, IP, TP, FP, and EP subtypes. We report molecular dynamics of DP in explicit lipid and water and find that the binding of the PGD2 agonist leads to correlated rotations of helices of TM3 and TM7, whereas binding of antagonist leads to no such rotations. Thus, these motions may be related to the mechanism of activation.     

Inclusion complexes of ortho-anisidine and β-cyclodextrin: A quantum mechanical calculation

The structural aspects for the complexation of ortho-anisidine (O-AN)/β-cyclodextrin were explored by using PM6, density function theory B3LYP/6-31G*, M05-2X/6-31G*, B3PW91/6-31G*, MPW1PW91/6-31G*, HF/6-31G* methods and several combinations of ONIOM2 hybrid calculations. Calculations were performed upon the inclusion complexation of β-cyclodextrin (β-CD) with neutral (O-AN1) and cationic (O-AN2) species of ortho-anisidine. The obtained results with PM6 method clearly indicate that the formed complexes are energetically favored, the complex of O-AN2/β-CD in B orientation is significantly more favorable than the others energetically. The structures show the presence of several intermolecular hydrogen bond interactions that were studied on the basis of natural bonding orbital (NBO) analysis, employed to quantify the donor–acceptor interactions between ortho-anisidine and β-CD.     

Theoretical investigation study based on PM3MM and ONIOM2 calculations of β-Cyclodextrin complexes with diphenylamine

The inclusion complex of β-cyclodextrin (β-CD) and diphenylamine (DPA) was investigated by using PM3MM, DFT, HF and ONIOM2 methods. The most stable structure was obtained at the optimum position and angle. The results indicate that the inclusion complex formed by DPA entering into the cavity of β-CD from its wide side (the secondary hydroxyl group side) is more stable than that formed by DPA entering into the cavity of β-CD from its narrow side (the primary hydroxyl group side). The structures show the presence of several intermolecular hydrogen bond interactions that were studied on the basis of natural bonding orbital (NBO) analysis, employed to quantify the donor–acceptor interactions between diphenylamine and β-CD. A study of these complexes in solution was carried out using the CPCM model to examine the influence of solvation on the stability of the diphenylamine β-CD complex.     

Allosteric antagonist binding sites in class B GPCRs: corticotropin receptor 1

The 41 amino acid neuropeptide, corticotropin-releasing factor (CRF) and its associated receptors CRF₁-R and CRF₂-R have been targeted for treating stress related disorders. Both CRF₁-R and CRF₂-R belong to the class B G-protein coupled receptors for which little information is known regarding the small molecule antagonist binding characteristics. However, it has been shown recently that different non-peptide allosteric ligands stabilize different receptor conformations for CRF₁-R and hence an understanding of the ligand induced receptor conformational changes is important in the pharmacology of ligand binding. In this study, we modeled the receptor and identified the binding sites of representative small molecule allosteric antagonists for CRF₁-R. The predicted binding sites of the investigated compounds are located within the transmembrane (TM) domain encompassing TM helices 3, 5 and 6. The docked compounds show strong interactions with H228 on TM3 and M305 on TM5 that have also been implicated in the binding by site directed mutation studies. H228 forms a hydrogen bond of varied strengths with all the antagonists in this study and this is in agreement with the decreased binding affinity of several compounds with H228F mutation. Also mutating M305 to Ile showed a sharp decrease in the calculated binding energy whereas the binding energy loss on M305 to Leu was less significant. These results are in qualitative agreement with the decrease in binding affinities observed experimentally. We further predicted the conformational changes in CRF₁-R induced by the allosteric antagonist NBI-27914. Movement of TM helices 3 and 5 are dominant and generates three degenerate conformational states two of which are separated by an energy barrier from the third, when bound to NBI-27914. Binding of NBI-27914 was predicted to improve the interaction of the ligand with M305 and also enhanced the aromatic stacking between the ligand and F232 on TM3. A virtual ligand screening of ~13,000 compounds seeded with ~350 CRF₁-R specific active antagonists performed on the NBI-27914 stabilized conformation of CRF₁-R yielded a 44% increase in enrichment compared to the initially modeled receptor conformation at a 10% cutoff. The NBI-27914 stabilized conformation also shows a high enrichment for high affinity antagonists compared to the weaker ones. Thus, the conformational changes induced by NBI-27914 improved the ligand screening efficiency of the CRF₁-R model and demonstrate a generalized application of the method in drug discovery.     

Molecular docking study on β-cyclodextrin Interactions of metobromuron and [3-(p-bromophenyl)-1-methoxy-1-methylurea]

The inclusion process involving β-cyclodextrin (β-cyclodextrin-CD) and phenylurea herbicide metobromuron (MB) has been investigated by using the MM+, PM3, B3LYP, HF, ONIOM2 and NBO methods. The binding and complexation energies for both orientations considered in this research are reported. The geometry of the most stable complex shows that the aromatic ring is deeply self-included inside the hydrophobic cavity of β-CD also an intermolecular hydrogen bond is established between host and guest molecules. This suggests that hydrophobic effect and hydrogen bond play an important role in the complexation process. The statistical thermodynamic calculations by PM3 demonstrate that 1:1?MB/β-CD complex is favored by a negative enthalpy change. Moreover, NBO calculations proved also that are a very useful means to quantify the interaction energies of the hydrogen bonds.