Odors: from chemical structures to gaseous plumes

We are immersed within an odorous sea of chemical currents that we parse into individual odors with complex structures. Odors have been posited as determined by the structural relation between the molecules that compose the chemical compounds and their interactions with the receptor site. But, naturally occurring smells are parsed from gaseous odor plumes. To give a comprehensive account of the nature of odors the chemosciences must account for these large distributed entities as well. We offer a focused review of what is known about the perception of odor plumes for olfactory navigation and tracking, which we then connect to what is known about the role odorants play as properties of the plume in determining odor identity with respect to odor quality. We end by motivating our central claim that more research needs to be conducted on the role that odorants play within the odor plume in determining odor identity

Combining multiple classifications of chemical structures using consensus clustering

Consensus clustering involves combining multiple clusterings of the same set of objects to achieve a single clustering that will, hopefully, provide a better picture of the groupings that are present in a dataset. This Letter reports the use of consensus clustering methods on sets of chemical compounds represented by 2D fingerprints. Experiments with DUD, IDAlert, MDDR and MUV data suggests that consensus methods are unlikely to result in significant improvements in clustering effectiveness as compared to the use of a single clustering method. (C) 2012 Elsevier Ltd. All rights reserved

Maximum common subgraph isomorphism algorithms for the matching of chemical structures

The maximum common subgraph (MCS) problem has become increasingly important in those aspects of chemoinformatics that involve the matching of 2D or 3D chemical structures. This paper provides a classification and a review of the many MCS algorithms, both exact and approximate, that have been described in the literature, and makes recommendations regarding their applicability to typical chemoinformatics tasks

Comparison of chemical clustering methods using graph- and fingerprint-based similarity measures

This paper compares several published methods for clustering chemical structures, using both graph- and fingerprint-based similarity measures. The clusterings from each method were compared to determine the degree of cluster overlap. Each method was also evaluated on how well it grouped structures into clusters possessing a non-trivial substructural commonality. The methods which employ adjustable parameters were tested to determine the stability of each parameter for datasets of varying size and composition. Our experiments suggest that both graph- and fingerprint-based similarity measures can be used effectively for generating chemical clusterings; it is also suggested that the CAST and Yin–Chen methods, suggested recently for the clustering of gene expression patterns, may also prove effective for the clustering of 2D chemical structures

Determination of the oxidative stability of perfluoropolyalkyl ethers and correlation with chemical structure

The oxidative stabilities of several perfluoropolyalkyl ethers (PFPAE) with related chemical structures were determined by thermal gravimetric analysis and correlated with their chemical structures. These results show that oxidative stability increases as the number of difluoroformal groups decreases and as trifluoromethyl substituents are added. They are also consistent with a recently proposed intramolecular disproportionation reaction mechanism involving coordination of successive ether oxygens to a Lewis acid. Since polytetrafluoroethylene contains no oxygen, it provides an indication of the upper limit to oxidative stability of PFPAE fluids. These results also show that oxidative decomposition of PFPAE fluids requires the presence of an active metal as well as air. Consequently, it may be possible to minimize decomposition and thus improve oxidative stability by passivating reactive metal surfaces

Clustering files of chemical structures using the Szekely-Rizzo generalization of Ward's method

Ward's method is extensively used for clustering chemical structures represented by 2D fingerprints. This paper compares Ward clusterings of 14 datasets (containing between 278 and 4332 molecules) with those obtained using the Szekely–Rizzo clustering method, a generalization of Ward's method. The clusters resulting from these two methods were evaluated by the extent to which the various classifications were able to group active molecules together, using a novel criterion of clustering effectiveness. Analysis of a total of 1400 classifications (Ward and Székely–Rizzo clustering methods, 14 different datasets, 5 different fingerprints and 10 different distance coefficients) demonstrated the general superiority of the Székely–Rizzo method. The distance coefficient first described by Soergel performed extremely well in these experiments, and this was also the case when it was used in simulated virtual screening experiments

Data Quality in Predictive Toxicology: Identification of Chemical Structures and Calculation of Chemical Descriptors

Every technique for toxicity prediction and for the detection of structure–activity relationships relies on the accurate estimation and representation of chemical and toxicologic properties. In this paper we discuss the potential sources of errors associated with the identification of compounds, the representation of their structures, and the calculation of chemical descriptors. It is based on a case study where machine learning techniques were applied to data from noncongeneric compounds and a complex toxicologic end point (carcinogenicity). We propose methods applicable to the routine quality control of large chemical datasets, but our main intention is to raise awareness about this topic and to open a discussion about quality assurance in predictive toxicology. The accuracy and reproducibility of toxicity data will be reported in another paper

Comparative study of microwave assisted and conventional synthesis of novel 2-quinoxalinone-3- hydrazone derivatives and its spectroscopic properties

A series of novel quinoxalin-2(1H)-one-3-hydrazone derivatives, 2a - 8d were synthesized via condensation of 3-hydrazinoquinoxalin-2(1H)-one, 1, with the corresponding ketones under microwave irradiation. The microwave assisted reaction was remarkably successful and gave hydrazones in higher yield at less reaction time compared to conventional heating method. The chemical structures of the compounds prepared were confirmed by analytical and spectral dat

Understanding the Chemical Structures of Polydopamine

Polydopamine (PDA) is described as a bioinspired polymer produced by a method involving the chemical oxidation of dopamine in a pH-dependent medium. It has been used for the functionalization of nanomaterials in diverse applications including drug delivery and biosensing because of its strong adhesiveness, functionality is easily modified, and biocompatibility with mammalian cells and tissues. The polymerization process is believed to be initiated by the autoxidation of dopamine to dopaminequinone. However, the repeating units, as well as the final structure of PDA, are not well understood. Hence, this work focuses on the characterizations of the PDA structures during formation and degradation under different conditions to understand how the structures affect the PDA properties and functionality. A commonly used method was chosen for the study of the PDA formation process. The synthesis of PDA was conducted in tris buffer at pH 8.5. Different microscopic and spectroscopic tools were utilized to characterize the morphology and chemical structures of the dopamine polymerization process. The results indicate that the PDA repeating units consist of dopamine, 5,6-dihydroxyindole, and indole-5,6 quinone. These repeating units are covalently bonded together forming different degrees of oligomers. Additionally, the tris base might be incorporated in the oligomers that form the PDA structure. To study the stability of the PDA structures, the degradation of the PDA was performed in hydrogen peroxide over a period of time. The resulting products mainly contain dimer and trimer units of the PDA structures that are water-soluble. Finally, the PDA formation process was used to modify the surface of silica and their subsequent use for the synthesis of metal-silica composite materials