Electrochemical pinning of the Fermi level: mediation of photoluminescence from gallium nitride and zinc oxide

Charge transfer between diamond and an electrochemical redox couple in an adsorbed water film has recently been shown to pin the Fermi level in hydrogen-terminated diamond. Here we show that this effect is a more general phenomenon and influences the properties of other semiconductors when the band lineup between the ambient and electronic states in the semiconductor is appropriate. We find that the luminescent intensities from GaN and ZnO change in different, but predictable, ways when exposed to HCl and NH3 vapors in humid air. The effect is reversible and has been observed on single crystals, nanowires, flakes, and powders. These observations are explained by electron exchange between the oxygen electrochemical redox couple in an adsorbed water film and electronic states in the semiconductor. This effect can take place in parallel with other processes such as defect formation, chemisorption, and surface reconstruction and may play an important, but previously unrecognized, role when electronic and optical measurements are made in air.     

Laser photoacoustic spectroscopy of iodine molecule: Single and two-photon absorption

Photoacoustic spectroscopy of iodine molecule has been studied in gas phase using nitrogen laser-pumped tunable dye laser. The experiment yielded the vibrational spectrum corresponding toX ¹Σ⁺(0 _g ⁺ )→B ³Π(0 _g ⁺ ) transition up to the convergence limit. The photo-acoustic spectrum in the region 17580–18850 cm⁻¹ is presented along with the vibrational analysis. Five of the vibrational bands reported earlier by Venkateswarlu, Kumar and McGlynn have been partially resolved and the structure of one of them has been analyzed and shown to be due to an overlap of (14, 2) and (12, 1) bands. The analysis was based on a comparison with the highly resolved spectrum of Gerstenkorn and Luc. The structure observed in the region 20200–20750 cm⁻¹ which is beyond the convergence limit of the transitionX ¹Σ⁺(0 _g ⁺ )→B ³Π(0 _u ⁺ ) has been analyzed as due to two-photon absorption. Most of the bands could be assigned to two transitions both originating in the ground state and terminating in two different electronic states 1 _g andE(0 _g ⁺ ), atT _e=40821 cm⁻¹ (orT ₀=41355 cm⁻¹) andT _e=41411 cm⁻¹ (orT ₀=41355 cm⁻¹) respectively.     

Synthesis of indolo[2,3-a]quinolizine and hexahydro-1H-indolizino[8,7-b]indole derivatives by cascade condensation, cyclization, and Pictet-Spengler reaction: an application to the synthesis of (±)-harmicine

Synthesis of indole alkaloid related compounds using Schiff base formation, intramolecular cyclization (or N-alkylation), and Pictet-Spengler reaction as a cascade one pot condensation has been reported. The cascade chemistry has been applied to the synthesis of (±)-harmicine as a key step.     

Molecular mechanics methods for predicting protein-ligand binding

Ligand binding affinity prediction is one of the most important applications of computational chemistry. However, accurately ranking compounds with respect to their estimated binding affinities to a biomolecular target remains highly challenging. We provide an overview of recent work using molecular mechanics energy functions to address this challenge. We briefly review methods that use molecular dynamics and Monte Carlo simulations to predict absolute and relative ligand binding free energies, as well as our own work in which we have developed a physics-based scoring method that can be applied to hundreds of thousands of compounds by invoking a number of simplifying approximations. In our previous studies, we have demonstrated that our scoring method is a promising approach for improving the discrimination between ligands that are known to bind and those that are presumed not to, in virtual screening of large compound databases. In new results presented here, we explore several improvements to our computational method including modifying the dielectric constant used for the protein and ligand interiors, and empirically scaling energy terms to compensate for deficiencies in the energy model. Future directions for further improving our physics-based scoring method are also discussed.     

Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening

We demonstrate that using an all-atom molecular mechanics force field combined with an implicit solvent model for scoring protein-ligand complexes is a promising approach for improving inhibitor enrichment in the virtual screening of large compound databases. The rescoring method is evaluated by the extent to which known binders for nine diverse, therapeutically relevant enzymes are enriched against a background of approximately 100,000 drug-like decoys. The improvement in enrichment is most robust and dramatic within the top 1% of the ranked database, that is, the first thousand compounds; below the first few percent of the ranked database, there is little overall improvement. The improved early enrichment is likely due to the more realistic treatment of ligand and receptor desolvation in the rescoring procedure. We also present anecdotal but encouraging results assessing the ability of the rescoring method to predict specificity of inhibitors for structurally related proteins.     

L‐Proline‐Catalyzed Asymmetric Direct Aldol Reaction of Heteroaromatic Aldehydes and Acetone: Improvement of Catalytic Efficiency in Ionic Liquid bmim [BF4]

l‐proline in bmim [BF₄] ionic liquid has been successfully used as an efficient and reusable catalyst for the direct asymmetric aldol reaction of acetone with different heteroaromatic aldehydes to afford higher selectivity of the aldol products with good enantioselectivity.     

A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series

We introduce the "Prime-ligand" method for ranking ligands in congeneric series. The method employs a single scoring function, the OPLS-AA/GBSA molecular mechanics/implicit solvent model, for all stages of sampling and scoring. We evaluate the method using 12 test sets of congeneric series for which experimental binding data is available in the literature, as well as the structure of one member of the series bound to the protein. Ligands are "docked" by superimposing a common stem fragment among the compounds in the series using a crystal complex from the Protein Data Bank and sampling the conformational space of the variable region. Our results show good correlation between our predicted rankings and the experimental data for cases in which binding affinities differ by at least 1 order of magnitude. For 11 out of 12 cases, >90% of such ligand pairs could be correctly ranked, while for the remaining case, Factor Xa, 76% of such pairs were correctly ranked. A small number of compounds could not be docked using the current protocol because of the large size of functional groups that could not be accommodated by a rigid receptor. CPU requirements for the method, involving CPU minutes per ligand, are modest compared with more rigorous methods that use similar force fields, such as free energy perturbation. We also benchmark the scoring function using series of ligands bound to the same protein within the CSAR data set. We demonstrate that energy minimization of ligands in the crystal structures is critical to obtain any correlation with experimentally determined binding affinities.     

Parallel synthesis enablement of 2-pyridyl-5-cyano-pyrimidine-6-ones—a novel class of HIF-hydroxylase inhibitors

The synthesis of various substituted 2-pyridyl-5-cyano-pyrimidine-6-ones was accomplished via a three-step protocol. The key aspects of this parallel protocol was the preparation of amidines from nitriles under mild conditions followed by cyclization with ethyl (ethoxymethylene)cyanoacetate.     

Studies on sorption of uranium on chitin: a solid-state extractant application for removal of uranium from ground water

Studies were carried out to remove uranium from aqueous systems based on the solid phase extraction of uranium by powdered chitin. The effects of various parameters like pH, contact time, and amount of chitin for quantitative sorption of uranium on chitin have been studied. The sorption studies with spiked water samples and natural ground water samples showed that uranium was easily sorbed onto powdered chitin between pH 3 and 6. The effects of various cations and anions, which are present in the water samples, were studied. The method is simple, fast and environmental friendly and it is unaffected by the other ions present in the natural waters. The accuracy of the method was evaluated by applying the present method on ground water samples containing uranium in the range of 100–2,200 μg/L. The uranium remained in water samples is <20 μg/L after treatment with chitin, which is below the AERB limits given for uranium in drinking water. The values are an average of five replicate measurements, with an RSD of ±10 μg/L at 100 μg/L uranium in water samples.