Carbohydrate Structure Database oligosaccharide conformation tool.

Population analysis in terms of glycosidic torsion angles is frequently used to reveal preferred conformers of glycans. However, due to high structural diversity and flexibility of carbohydrates, conformational characterization of complex glycans can be a challenging task. Herein, we present a conformation module of oligosaccharide fragments occurring in natural glycan structures developed on the platform of the Carbohydrate Structure Database. Currently, this module deposits free energy surface and conformer abundance maps plotted as a function of glycosidic torsions for 194 "inter"residue bonds. Data are automatically and continuously derived from explicit-solvent molecular dynamics (MD) simulations. The module was also supplemented with high-temperature MD data of saccharides (2,403 maps) provided by GlycoMapsDB (hosted by GLYCOSCIENCES.de project). Conformational data defined by up to 4 torsional degrees of freedom can be freely explored using a web interface of the module available at http://csdb.glycoscience.ru/database/core/search_conf.html.

Three-Dimensional Structures of Carbohydrates and Where to Find Them.

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

Light-Mediated Dual Phosphine-/Copper-Catalyzed Atom Transfer Radical Addition Reaction.

The atom transfer radical addition reaction catalyzed by triphenylphosphine and copper(I) halide is described. The reaction proceeds under irradiation with 365 nm light using a light-emitting diode and was performed in regular glassware. The proposed mechanism involves the formation of quaternary phosphonium salt, which undergoes single electron reduction by copper(I) salt via photo-induced electron transfer. The method works well for terminal alkenes and activated organic halides such as esters of bromo- and iodoacetic acid and bromoacetonitrile. gem-Difluorinated styrenes, for which atom transfer reactions are rare, also proved to be good substrates for this phosphine-/copper-catalyzed protocol.

Synthesis of 3-Fluoropyridines via Photoredox-Mediated Coupling of α,α-Difluoro-ß-iodoketones with Silyl Enol Ethers.

A method for the synthesis of diversely substituted 3-fluoropyridines from two ketone components is described. The reaction involves photoredox coupling of α,α-difluoro-ß-iodoketones with silyl enol ethers catalyzed by fac-Ir(ppy)3 under blue LED irradiation with subsequent one-pot condensation with ammonium acetate. Based on cyclic voltammetry studies, it was determined that α,α-difluoro-ß-iodoketones are reduced notably easier compared to 2,2,2-trifluoro-1-iodoethane, which may be ascribed to the influence of the carbonyl group.