ReaxFF Parameter Optimization with Monte-Carlo and Evolutionary Algorithms: Guidelines and Insights.

ReaxFF is a computationally efficient force field to simulate complex reactive dynamics in extended molecular models with diverse chemistries, if reliable force-field parameters are available for the chemistry of interest. If not, they must be optimized by minimizing the error ReaxFF makes on a relevant training set. Because this optimization is far from trivial, many methods, in particular, genetic algorithms (GAs), have been developed to search for the global optimum in parameter space.

Francisella tularensis Periprosthetic Joint Infections Diagnosed with Growth in Cultures.

Tularemia caused by is a zoonotic infection of the Northern Hemisphere that mainly affects the skin, lymph nodes, bloodstream, and lungs. Other manifestations of tularemia are very rare, especially those with musculoskeletal involvement. Presenting in 2016, we diagnosed two cases of periprosthetic knee joint infections (PJI) caused by in Europe (one in Switzerland and one in the Czech Republic).

Automated Training of ReaxFF Reactive Force Fields for Energetics of Enzymatic Reactions.

Computational studies of the reaction mechanisms of various enzymes are nowadays based almost exclusively on hybrid QM/MM models. Unfortunately, the success of this approach strongly depends on the selection of the QM region, and computational cost is a crucial limiting factor. An interesting alternative is offered by empirical reactive molecular force fields, especially the ReaxFF potential developed by van Duin and co-workers.

Different QM/MM Approaches To Elucidate Enzymatic Reactions: Case Study on ppGalNAcT2.

Hybrid QM/MM computational studies can provide invaluable insight into the mechanisms of enzymatic reactions that can be exploited for rational drug design. Various approaches are available for such studies. However, their strengths and weaknesses may not be immediately apparent.

Stepwise catalytic mechanism via short-lived intermediate inferred from combined QM/MM MERP and PES calculations on retaining glycosyltransferase ppGalNAcT2.

The glycosylation of cell surface proteins plays a crucial role in a multitude of biological processes, such as cell adhesion and recognition. To understand the process of protein glycosylation, the reaction mechanisms of the participating enzymes need to be known. However, the reaction mechanism of retaining glycosyltransferases has not yet been sufficiently explained.

Spectroscopic, morphological, and mechanistic investigation of the solvent-promoted aggregation of porphyrins modified in meso-positions by glucosylated steroids.

Solvent-driven aggregation of a series of porphyrin derivatives was studied by UV/Vis and circular dichroism spectroscopy. The porphyrins are characterised by the presence in the meso positions of steroidal moieties further conjugated with glucosyl groups. The presence of these groups makes the investigated macrocycles amphiphilic and soluble in aqueous solvent, namely, dimethyl acetamide/water.

Thiosugars--derivatization agents for chiral resolution of homoleucines.

o-Phthaldialdehyde was used in combination with a series of six thiosugars for the pre-column chiral derivatization of selected primary amino acids. The diastereomers were resolved on a conventional reversed-phase column and with fluorescence detection. A surprisingly effective resolution of 1-isoindolyl-(1-thioglycosides) derived from 1-thio-beta-L-fucose was observed.

Copper-ligand complex for the decolorization of synthetic dyes.

The reaction system containing Cu(II), hydrogen peroxide and D-arabinono-1,4-lactone was found to be effective in the decolorization and reduction of toxicity of azo, thiazine-, triphenylmethane- and anthraquinone-based synthetic dyes. More than 85% decolorization was obtained with 100ppm Acridine Orange, Azure B, Chicago Sky Blue 6B, Crystal Violet, Evans Blue, Poly B-411, Reactive Blue 2, Reactive Blue 5, and Remazol Brilliant Blue R incubated for 24h in the presence of 10mM CuSO(4), 20mM D-arabinono-1,4-lactone and 80 mM H(2)O(2). The rate of decolorization was not affected by pH in the range of 3-9.

Decolorization of synthetic dyes using a copper complex with glucaric acid.

Selected azo, acridine, triphenyl methane, anthraquinone and thiazine-based dyes were decolorized using a catalytic system consisting of Cu(II)/glucaric acid/H(2)O(2). More than 90% decolorization was obtained with 100 ppm Acridine Orange, Azure B, Chicago Sky Blue, Crystal Violet, Methyl Orange, Poly B-411, Reactive Black 5, Reactive Blue 2, and Remazol Brilliant Blue R within 24 h. Seventy to eighty percent decolorization was achieved within the first 6 h.