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Likozar B.,Slovenian National Institute of Chemistry | Levec J.,University of Ljubljana
Fuel Processing Technology | Year: 2014

Detailed reaction kinetics of oil transesterification were studied based on mechanism and reaction scheme of individual triglyceride, diglyceride, monoglyceride, glycerol and fatty acid methyl ester containing different combinations of gadoleic, linoleic, linolenic, oleic, palmitic and stearic acids determined by high-performance liquid chromatography. Pre-exponential factors and activation energies were correlated with molecular structure in terms of chain lengths and double bonds by response surface models. The activation energies of forward reactions were 47-61 kJ mol- 1 with backward ones being 31-49 kJ mol- 1, depending on component structure. Mass transfer during initial emulsion phase was acknowledged by determining diffusivities, distribution coefficients, molar volumes, boiling points and viscosities of individual components. Model was validated for a wide range of temperatures, hydrodynamic conditions, dispersed and continuous phase ratios, and methanolysis catalyst concentrations. Rotational speed had the most profound influence on the duration of transport phenomena-limited region spanning the latter to 27 min upon use of 100 rpm. Economics of the process were finally evaluated in terms of alcoholysis cost and price breakdown. Proposed methodology may be usefully applied to transesterification syntheses employing heterogeneous catalysis and enzymes, as well as various renewable resources such as microalgae lipids, waste oils, bioethanol and biobutanol. © 2014 Elsevier B.V. Source


Konc J.,Slovenian National Institute of Chemistry | Janezic D.,University of Primorska
Nucleic Acids Research | Year: 2014

The ProBiS-ligands web server predicts binding of ligands to a protein structure. Starting with a protein structure or binding site, ProBiS-ligands first identifies template proteins in the Protein Data Bank that share similar binding sites. Based on the superimpositions of the query protein and the similar binding sites found, the server then transposes the ligand structures from those sites to the query protein. Such ligand prediction supports many activities, e.g. drug repurposing. The ProBiS-ligands web server, an extension of the ProBiS web server, is open and free to all users at http://probis.cmm.ki. si/ligands. © 2014 The Author(s). Source


Randic M.,Slovenian National Institute of Chemistry
Chemical Physics Letters | Year: 2014

For a selection of smaller benzenoid hydrocarbons we calculated ring bond orders (RBO) by adding the Pauling bond orders for CC bonds forming individual benzene rings. The RBO show full parallelism with qualitative expectations based on Clar's intuitive sextet theory. The highest RBO values belong to sextets of a single Clar structure, intermediate values to 'migrating' sextets and the smallest values to the 'empty' rings, and rings involving essentially single CC bond. This novel quantitative upgrading of the Clar structural formulas of aromatic benzenoid hydrocarbons offers numerical characterization of individual benzene rings as fully aromatic, intermediate, and weakly aromatics. © 2014 Published by Elsevier B.V. Source


Randic M.,Slovenian National Institute of Chemistry
Chemical Physics Letters | Year: 2010

We consider calculation of induced currents of π-electrons over the molecular network when molecules are placed in a magnetic field. The approach is based on consideration of current contributions arising from conjugated circuits within each individual Kekulé valence structure. The calculation is illustrated for an isomer of coronene C 24H 12 for which ab initio computations of π-electron current densities are available. Agreement is found between the quantum chemical ab initio computations that make no assumptions on ring contributions and the graph theoretical models based on conjugated circuit currents. © 2010 Elsevier B.V. All rights reserved. Source


Konc J.,Slovenian National Institute of Chemistry | Konc J.,U.S. National Institutes of Health | Janezic D.,University of Primorska
Current Opinion in Structural Biology | Year: 2014

While structural genomics resulted in thousands of new protein crystal structures, we still do not know the functions of most of these proteins. One reason for this shortcoming is their unique sequences or folds, which leaves them assigned as proteins of 'unknown function'. Recent advances in and applications of cutting edge binding site comparison algorithms for binding site detection and function prediction have begun to shed light on this problem. Here, we review these algorithms and their use in function prediction and pharmaceutical discovery. Finding common binding sites in weakly related proteins may lead to the discovery of new protein functions and to novel ways of drug discovery. © 2013 Elsevier Ltd. Source

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