Prediction of interaction between small molecule and enzyme using AdaBoost

The knowledge of whether one enzyme can interact with a small molecule is essential for understanding the molecular and cellular functions of organisms. In this paper, we introduce a classifier to predict the small molecule– enzyme interaction, i.e., whether they can interact with each other. Small molecules are represented by their chemical functional groups, and enzymes are represented by their biochemical and physicochemical properties, resulting in a total of 160 features. These features are input into the AdaBoost classifier, which is known to have good generalization ability to predict interaction. As a result, the overall prediction accuracy, tested by tenfold cross-validation and independent sets, is 81.76% and 83.35%, respectively, suggesting that this strategy is effective. In this research, we typically choose interactions between small molecules and enzymes involved in metabolism to ultimately improve further understanding of metabolic pathways. An online predictor developed by this research is available at . Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Iridium-catalyzed annulation between 1,2-diarylethanone and 3-aminopropanol toward site-specific 2,3-diaryl pyridines

An iridium-catalyzed annulation between 1,2-diarylethanone and 3-aminopropanol was developed, leading to site specific 2,3-diarylpyridines in moderate yields. 3-Aminopropanol served as both a four-atom component and solvent during this procedure, releasing water as a clean by-product. The reaction may proceed with sequential imine formation, alcohol oxidation and intramolecular cyclization by Knoevenagel reaction.     

The influence of the band structure of epitaxial graphene on SiC on the transistor characteristics

We fabricated high-mobility field-effect transistors based on epitaxial graphene synthesized by vacuum graphitization of both the Si- and C-faces of SiC. Room-temperature field-effect mobilities >4000 cm²/V s for both electrons and holes were achieved, although with wide distributions. By using a high-k gate dielectric, we were able to measure the transistor characteristics in a wide carrier density range, where the mobility is seen to decrease as the carrier density increases. We formulate a simple semiclassical model of electrical transport in graphene, and explain the sublinear dependence of conductivity on carrier density from the view point of the few-layer graphene energy band structure. Our analysis reveals important differences between the few-layer graphene energy dispersions on the SiC Si- and C-faces, providing the first evidence based on electrical device characteristics for the theoretically proposed energy dispersion difference between graphene synthesized on these two faces of SiC.     

GaAs/AlGaAs photonic crystals for VCSEL-type semiconductor lasers

The results of modelling of the influence of photonic crystal on the performance of VCSEL-type semiconductor laser structure are shown and indicate that the use of those structures would significantly improve the working parameters of the devices. The method of fabrication of photonic crystals in the Bragg mirrors of GaAs/AlGaAs-based VCSELs is presented.     

Highly enantioselective addition of phenylethynylzinc to aldehydes using aziridine-functionalized tridentate sulfinyl ligands

Diastereomerically pure tridentate heteroorganic ligands containing hydroxyl, sulfinyl and aziridine moieties as nucleophilic centers, capable of binding to various organometallic reagents, have been proven to be highly efficient catalysts in the enantioselective addition of phenylethynylzinc to aldehydes to give the desired products in very high yields (up to 95%) and with ee’s up to 90%. The influence of the stereogenic centers located on the sulfinyl sulfur atom and in the aziridine moiety on the stereochemical course of the reaction is also discussed.     

The influence of the substrate temperature on the preparation of DNA films for studies under vacuum conditions

Experiments were carried out to determine the dependence of the physical form of supercoiled DNA films on the initial temperature of the substrate. Such films are often used in irradiation experiments involving low energy particles, like electrons or photons. In order to obtain absolute values for cross sections for such experiments, the spatial distribution of the sample in the film has to be well estimated. These investigations aim to correlate the size and form of a DNA film with the initial temperature of the substrate, on which the liquid sample is deposited prior to evacuation. From our previous studies we concluded that the presence of agents preventing DNA structural water evaporation is required in order to preserve the supercoiled plasmid DNA form under vacuum conditions. Therefore, we examined the temperature dependence on films prepared from plasmid suspended in solutions containing magnesium hydroxide, Tris-Cl buffer and various concentrations of sodium hydroxide. To visualise the films we used a conventional light microscope with a CCD camera and a scanning electron microscope. The results revealed a significant influence of the temperature of the substrate on both the area of the substrate covered by the film as well as on the spatial distribution of DNA molecules. An increase in the amount of sodium hydroxide that stabilises supercoiled DNA under vacuum increases DNA aggregation. After these investigations we conclude that the best temperature of the substrate to produce uniform and thin films should be between –5 °C and -10 °C for substrates which are not atomically flat and above 0 °C for atomically flat substrates.