The influence of the cation structure on the basicity-related polarity of ionic liquids.

UV/Vis absorption data of (E)-4-(2-[5-{4,4,5,5-tetramethyl-1,3,2-dioxaborolane-2-yl}thiene-2-yl]vinyl)-2-(dicyano-methylene)-3-cyano-5,5-dimethyl-2,5-dihydrofuran (ThTCF) as a solvatochromic probe is applied to examine the anion coordination strength (e.g. of N(CN)2, BF4, PF6, N(Tf)2, CF3COO) as a function of the cation structure of ionic liquids. Several 1-n-alky-3-methylimidazolium- and tetraalkylammonium CH3-NR3+-based ILs with different n-alkyl chain lengths (R = -C4H9, -C6H11, -C8H17, -C10H21) are considered. UV/Vis absorption data of ThTCF show subtle correlations with hydrogen bond accepting (HBA) ability-related measurands such as Kamlet-Taft ß, Freire's EHB, and Laurence ß1 parameter as a function of anion and cation structure. The different influence of the n-alkyl chain length of imidazolium- and tetraalkylammonium-based ILs on the dipolarity and HBA strength is confirmed by comparison with the 14N isotropic hyperfine coupling constants (Aiso) of a positively (CATI) and negatively charged spin probe (TSKCr) of TEMPO-type [(2,2,6,6-tetramethylpiperidin-1-yl)oxyl] and quantum chemically derived dipoles of the cations. The Aiso values correlate with the absorption energy of ThTCF and EHB, but in different ways depending on the anion or charge of the spin probe. In a final discussion of the ß, EHB, and ß1 scales in relation to ThTCF, the importance of the molar concentration N of ionic liquids for the physical significance of the respective parameters is discussed.

Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb.

BACKGROUND: A protein annotation database, such as the Universal Protein Resource knowledge base (UniProtKb), is a valuable resource for the validation and interpretation of predicted 3D structure patterns in proteins. Existing studies have focussed on point mutation extraction methods from biomedical literature which can be used to support the time consuming work of manual database curation. However, these methods were limited to point mutation extraction and do not extract features for the annotation of proteins at the residue level. RESULTS: This work introduces a system that identifies protein residues in MEDLINE abstracts and annotates them with features extracted from the context written in the surrounding text. MEDLINE abstract texts have been processed to identify protein mentions in combination with taxonomic species and protein residues (F1-measure 0.52). The identified protein-species-residue triplets have been validated and benchmarked against reference data resources (UniProtKb, average F1-measure of 0.54). Then, contextual features were extracted through shallow and deep parsing and the features have been classified into predefined categories (F1-measure ranges from 0.15 to 0.67). Furthermore, the feature sets have been aligned with annotation types in UniProtKb to assess the relevance of the annotations for ongoing curation projects. Altogether, the annotations have been assessed automatically and manually against reference data resources. CONCLUSION: This work proposes a solution for the automatic extraction of functional annotation for protein residues from biomedical articles. The presented approach is an extension to other existing systems in that a wider range of residue entities are considered and that features of residues are extracted as annotations.