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  1. Article ; Online: Carbohydrate Structure Database oligosaccharide conformation tool.

    Scherbinina, Sofya I / Frank, Martin / Toukach, Philip V

    Glycobiology

    2022  Volume 32, Issue 6, Page(s) 460–468

    Abstract: 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 ... ...

    Abstract 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.
    MeSH term(s) Carbohydrate Conformation ; Carbohydrates/chemistry ; Glycosides ; Molecular Conformation ; Oligosaccharides/chemistry ; Polysaccharides/chemistry
    Chemical Substances Carbohydrates ; Glycosides ; Oligosaccharides ; Polysaccharides
    Language English
    Publishing date 2022-03-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1067689-2
    ISSN 1460-2423 ; 0959-6658
    ISSN (online) 1460-2423
    ISSN 0959-6658
    DOI 10.1093/glycob/cwac011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  2. Article ; Online: Three-Dimensional Structures of Carbohydrates and Where to Find Them.

    Scherbinina, Sofya I / Toukach, Philip V

    International journal of molecular sciences

    2020  Volume 21, Issue 20

    Abstract: 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 ... ...

    Abstract 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.
    MeSH term(s) Carbohydrates/chemistry ; Databases, Protein ; Imaging, Three-Dimensional ; Molecular Conformation ; Molecular Dynamics Simulation ; Reproducibility of Results
    Chemical Substances Carbohydrates
    Keywords covid19
    Language English
    Publishing date 2020-10-18
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms21207702
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Light-Mediated Dual Phosphine-/Copper-Catalyzed Atom Transfer Radical Addition Reaction.

    Fedorov, Oleg V / Scherbinina, Sofya I / Levin, Vitalij V / Dilman, Alexander D

    The Journal of organic chemistry

    2019  Volume 84, Issue 17, Page(s) 11068–11079

    Abstract: 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 ... ...

    Abstract 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.
    Language English
    Publishing date 2019-08-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 123490-0
    ISSN 1520-6904 ; 0022-3263
    ISSN (online) 1520-6904
    ISSN 0022-3263
    DOI 10.1021/acs.joc.9b01649
    Database MEDical Literature Analysis and Retrieval System OnLINE

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

    Fedorov, Oleg V / Scherbinina, Sofya I / Levin, Vitalij V / Dilman, Alexander D

    Journal of organic chemistry. 2019 Aug. 14, v. 84, no. 17

    2019  

    Abstract: 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 ... ...

    Abstract 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.
    Keywords alkenes ; catalytic activity ; chemical structure ; copper ; electron transfer ; esters ; iodoacetic acid ; irradiation ; light emitting diodes ; phosphine ; ultraviolet radiation
    Language English
    Dates of publication 2019-0814
    Size p. 11068-11079.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 123490-0
    ISSN 1520-6904 ; 0022-3263
    ISSN (online) 1520-6904
    ISSN 0022-3263
    DOI 10.1021/acs.joc.9b01649
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: Synthesis of 3-Fluoropyridines via Photoredox-Mediated Coupling of α,α-Difluoro-β-iodoketones with Silyl Enol Ethers

    Scherbinina, Sofya I / Fedorov Oleg V / Levin Vitalij V / Kokorekin Vladimir A / Struchkova Marina I / Dilman Alexander D

    Journal of organic chemistry. 2017 Dec. 15, v. 82, no. 24

    2017  

    Abstract: 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-β-iodoketones with silyl enol ethers catalyzed by fac-Ir(ppy)₃ under blue LED ... ...

    Abstract 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-β-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-β-iodoketones are reduced notably easier compared to 2,2,2-trifluoro-1-iodoethane, which may be ascribed to the influence of the carbonyl group.
    Keywords ammonium acetate ; irradiation ; moieties ; organic chemistry ; redox reactions ; silyl enol ethers
    Language English
    Dates of publication 2017-1215
    Size p. 12967-12974.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 123490-0
    ISSN 1520-6904 ; 0022-3263
    ISSN (online) 1520-6904
    ISSN 0022-3263
    DOI 10.1021%2Facs.joc.7b02467
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Synthesis of 3-Fluoropyridines via Photoredox-Mediated Coupling of α,α-Difluoro-β-iodoketones with Silyl Enol Ethers.

    Scherbinina, Sofya I / Fedorov, Oleg V / Levin, Vitalij V / Kokorekin, Vladimir A / Struchkova, Marina I / Dilman, Alexander D

    The Journal of organic chemistry

    2017  Volume 82, Issue 24, Page(s) 12967–12974

    Abstract: 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-β-iodoketones with silyl enol ethers catalyzed by fac-Ir(ppy) ...

    Abstract 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-β-iodoketones with silyl enol ethers catalyzed by fac-Ir(ppy)
    Language English
    Publishing date 2017--15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 123490-0
    ISSN 1520-6904 ; 0022-3263
    ISSN (online) 1520-6904
    ISSN 0022-3263
    DOI 10.1021/acs.joc.7b02467
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 4473: Show issues Location:
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