Predicting olfactory receptor neuron responses from odorant structure

Background  

Olfactory receptors work at the interface between the chemical world of volatile molecules and the perception of scent in the brain. Their main purpose is to translate chemical space into information that can be processed by neural circuits. Assuming that these receptors have evolved to cope with this task, the analysis of their coding strategy promises to yield valuable insight in how to encode chemical information in an efficient way.     

Antibacterial mono- and sesquiterpene esters of benzoic acids from Iranian propolis

Background  

Propolis (bee glue) has been used as a remedy since ancient times. Propolis from unexplored regions attracts the attention of scientists in the search for new bioactive molecules.     

Structural effects on the solid-state photodimerization of 5-chloro and 5-nitro-2(1<Emphasis Type="Italic">H</Emphasis>)-pyridone in molecular compounds

Abstract  

The preparation and crystal structure of six molecular compounds consist of light-stable host molecules [(1-cyclohexyl-4-hydroxybenzene, 1,1,6,6-tetraphenyl-2,4-hexadiyne-1,6-diol, 4-((10-[4-(ethoxycarbonyl)phenoxy]decyl)oxy)benzene, 1,2,4,5-benzenetetracarboxylic acid, resorcinol] and light-sensitive guest molecules [(5-chloro-2(1H)-pyridone or 5-nitro-2(1H)-pyridone] are described in light of their failure to undergo [4 + 4] photodimerization in the solid-state upon irradiation with UV light. Unlike in many cases were pyridone and its derivatives undergo such dimerization in the solid-state due to the packing arrangement in the crystalline form in which the geometric requirement for photodimerization meet, the compounds described here failed to pack in ways to enable such photodimerization. The distances between the potentially reactive atoms ranged from 4.620 to 8.408 ? which are too long to react.     

Automated extraction of chemical structure information from digital raster images

Background  

To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated.     

DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening

Background  

Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats.     

The molecular basis of electroporation

Background  

Electroporation is a common method to introduce foreign molecules into cells, but its molecular basis is poorly understood. Here I investigate the mechanism of pore formation by direct molecular dynamics simulations of phospholipid bilayers of a size of 256 and of more than 2000 lipids as well as simulations of simpler interface systems with applied electric fields of different strengths.     

Theoretical study and atoms in molecule analysis of hydrogen bonded clusters of ammonia and isocyanic acid

Abstract  

Ab initio and density functional calculations were used to analyze the interaction between a molecule of the isocyanic acid with 1 up to 4 molecules of ammonia at the B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) computational levels. The cooperative effect is increased with the increasing size of studied clusters. Red shifts of the H–N stretching frequency for complexes involving the isocyanic acid as an H-donor were predicted. Atom in molecules was used to analyze cooperative effects on topological parameters.     

Quantum mechanical calculation of aqueuous uranium complexes: carbonate, phosphate, organic and biomolecular species

Background  

Quantum mechanical calculations were performed on a variety of uranium species representing U(VI), U(V), U(IV), U-carbonates, U-phosphates, U-oxalates, U-catecholates, U-phosphodiesters, U-phosphorylated N-acetyl-glucosamine (NAG), and U-2-Keto-3-doxyoctanoate (KDO) with explicit solvation by H₂O molecules. These models represent major U species in natural waters and complexes on bacterial surfaces. The model results are compared to observed EXAFS, IR, Raman and NMR spectra.     

Microwave assisted solvent free synthesis of 1,3-diphenylpropenones

Background  

1,3-Diphenylpropenones (chalcones) are well known for their diverse array of bioactivities. Hydroxyl group substituted chalcones are the main precursor in the synthesis of flavonoids. Till date various methods have been developed for the synthesis of these very interesting molecules. Continuing our efforts for the development of simple, eco-friendly and cost-effective methodologies, we report here a solvent free condensation of aryl ketones and aldehydes using iodine impregnated alumina under microwave activation. This new protocol has been applied to a variety of substituted aryl carbonyls with excellent yield of substituted 1,3-diphenylpropenones.     

Concise preparation of azenes by oxidation of aromatic amines with molecular oxygen in subcritical water

Abstract  

Reaction of organic substrates with molecular oxygen, the most abundant and accessible oxidant, has always been an attractive method for preparation of target molecules. In terms of green chemistry, non-metal-catalyzed oxidation of organic substrates is very attractive. This paper describes a general procedure for synthesis of azenes by oxidation of primary aromatic amines with molecular oxygen (³O₂) in subcritical water. The reactions afforded the corresponding azenes in moderate to good yield.     

Calculated conformer energies for organic molecules with multiple polar functionalities are method dependent: Taxol (case study)

Background  

Molecular mechanics (MM) and quantum chemical (QM) calculations are widely applied and powerful tools for the stereochemical and conformational investigations of molecules. The same methods have been extensively used to probe the conformational profile of Taxol (Figure 1) both in solution and at the β-tubulin protein binding site.     

Core charge distribution and self assembly of columnar phases: the case of triphenylenes and azatriphenylenes

Background  

The relation betweeen the structure of discotic molecules and columnar properties, a crucial point for the realization of new advanced materials, is still largely unknown. A paradigmatic case is that hexa-alkyl-thio substituted triphenylenes present mesogenic behavior while the corresponding azatriphenylenes, similar in shape and chemical structure, but with a different core charge distribution, do not form any liquid crystalline mesophase. This study is aimed at investigating, with the help of computer simulations techniques, the effects on phase behaviour of changes of the charge distribution in the discotic core.     

Prion protein self-peptides modulate prion interactions and conversion

Background  

Molecular mechanisms underlying prion agent replication, converting host-encoded cellular prion protein (PrP^C) into the scrapie associated isoform (PrP^Sc), are poorly understood. Selective self-interaction between PrP molecules forms a basis underlying the observed differences of the PrP^C into PrP^Sc conversion process (agent replication). The importance of previously peptide-scanning mapped ovine PrP self-interaction domains on this conversion was investigated by studying the ability of six of these ovine PrP based peptides to modulate two processes; PrP self-interaction and conversion.     

A laser desorption ionization/matrix‐assisted laser desorption ionization target system applicable for three distinct types of instruments (LinTOF/curved field RTOF,LinTOF/RTOF and QqRTOF) with different performance characteristics from three vendors

Rationale

We have developed a target system which enables the use of only one target (i.e. target preparation set) for three different laser desorption ionization (LDI)/matrix‐assisted laser desorption ionization (MALDI) mass spectrometric instruments. The focus was on analysing small biomolecules with LDI for future use of the system for the study of meteorite samples (carbonaceous chondrites) using devices with different mass spectrometric performance characteristics.

Methods

Three compounds were selected due to their potential presence in meteoritic chondrites: tryptophan, 2‐deoxy‐d ‐ribose and triphenylene. They were prepared (with and without MALDI matrix, i.e. MALDI and LDI) and analysed with three different mass spectrometers (LinTOF/curved field RTOF, LinTOF/RTOF and QqRTOF). The ion sources of two of the instruments were run at high vacuum, and one at intermediate pressure. Two devices used a laser wavelength of 355 nm and one a wavelength of 337 nm.

Results

The developed target system operated smoothly with all devices. Tryptophan, 2‐deoxy‐d ‐ribose and triphenylene showed similar desorption/ionization behaviour for all instruments using the LDI mode. Interestingly, protonated tryptophan could be observed only with the LinTOF/curved field RTOF device in LDI and MALDI mode, while sodiated molecules were observed with all three instruments (in both ion modes). Deprotonated tryptophan was almost completely obscured by matrix ions in the MALDI mode whereas LDI yielded abundant deprotonated molecules.

Conclusions

The presented target system allowed successful analyses of the three compounds using instruments from different vendors with only one preparation showing different analyser performance characteristics. The elemental composition with the QqRTOF analyser and the high‐energy 20 keV collision‐induced dissociation fragmentation will be important in identifying unknown compounds in chondrites.

     

Synthesis of nicotinonitrile derivatives and study of their photophysical properties

Abstract  

A convenient route was developed for the synthesis of novel nicotinonitrile derivatives by a three-component Dimroth reaction of chalcones, malononitrile, and secondary heterocyclic amines or sodium alcoholate. Nicotinonitrile derivatives are obtained in fair to good yields. The structures of all new compounds were established by spectroscopic characteristics and their photophysical properties were studied.     

DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0

Background  

Small-molecule docking is an important tool in studying receptor-ligand interactions and in identifying potential drug candidates. Previously, we developed a software tool (DOVIS) to perform large-scale virtual screening of small molecules in parallel on Linux clusters, using AutoDock 3.05 as the docking engine. DOVIS enables the seamless screening of millions of compounds on high-performance computing platforms. In this paper, we report significant advances in the software implementation of DOVIS 2.0, including enhanced screening capability, improved file system efficiency, and extended usability.     

Cloning and characterisation of hAps1 and hAps2, human diadenosine polyphosphate-metabolising Nudix hydrolases

Background  

The human genome contains at least 18 genes for Nudix hydrolase enzymes. Many have similar functions to one another. In order to understand their roles in cell physiology, these proteins must be characterised.     

Pickering emulsions stabilized by anatase nanoparticles

Abstract  

Oil-in-water emulsions can be stabilized by solid particles. These so-called Pickering emulsions are regularly used in many technological applications. Here we describe the efficiency of sol–gel-synthesized anatase nanoparticles with a diameter of 6 nm in stabilizing emulsions. Key parameters were the surface charge of the particles—depending on pH and salt concentration—and their contact angle—depending on the surface groups and the polarity of the oil phase. The effect of these properties on the stability of the emulsions was investigated. The sol–gel nanoparticles were most efficient in stabilizing emulsions at pH 3 (depending on the salt and particle concentration). Highly apolar oil phases (cyclohexane, n-hexane) were required to obtain stable emulsions with the investigated system and addition of salt or hydrophobic coupling molecules in the oil phase, such as long alkyl chain containing phosphonates, increased the stability of the emulsions.