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  • 1
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    Women in Bioorganic Chemistry (2022)
    MDPI - Multidisciplinary Digital Publishing Institute
    Details
    Publication Date: 2024-04-11
    Description: Issues relating to the gender schism and its effect on the career advancement of women in the Academy, especially in the field of STEM disciplines, deserve our attention and the efforts of all the scientific community to mitigate the gender gap. In order to embrace gender equality, recognize the career progression of women, and to celebrate the achievements of women in the field of bioorganic chemistry, we present contributions both from highly renowned female scientists and young female researchers who are in the early stages of their careers. This Special Issue includes fifteen manuscripts, including eleven high-quality research articles and four comprehensive review articles in the area of bioorganic chemistry, published from mid-2020 to early 2022. The scope of this Special Issue covers a wide range of topics at the organic chemistry–biology interface, including the synthesis and derivatization of natural compounds and their analogues, and the investigation of their biological activities in the human health field (for instance as antitumorals, antioxidants and antimicrobial agents), as well as their possible application in the crop protection field as agrochemicals. An example of nanoparticle-based biomaterial is also included. The techniques employed, besides organic synthesis, are in silico studies (docking procedures and molecular modeling), FT-IR spectroscopy, laser diffraction, PET, fluorescence, STD-NMR studies, enzymatic evaluation, experiments on cell lines and in vivo studies on mice.
    Keywords: antibiotics ; biochemical studies ; iminosugars ; inhibitors ; insect trehalase ; trehalose ; in vivo studies ; mammalian trehalase ; natural compounds ; selectivity ; interrupted Nazarov cyclization ; pentacyclic steroids ; antiproliferative activity ; d-annulated steroids ; Lewis acid ; dental caries ; enamel remineralisation ; hydroxyapatite ; amelogenin ; amelogenin-derived peptides ; leucine-rich amelogenin peptides ; tyrosine-rich amelogenin peptides ; cannabidiol ; molecular mechanisms ; neurological diseases ; neuroprotective effects ; strigolactones ; Strigol ; anti-cancer ; antimicrobials ; sustainable agriculture ; α,α-difluorophosphonate ; deoxyxylulose phosphate reductoisomerase ; 1-deoxy-dxylulose 5-phosphate reductoisomerase (DXR) ; antimicrobial ; fosmidomycin ; isoprenoid biosynthesis ; 2-C-methyl-derythritol 4-phosphate (MEP) pathway ; multivalency ; gold nanoparticles ; enzyme inhibition ; Jack bean α-mannosidase ; aminoproline scaffold ; integrin targeting ; ligand design ; peptidomimetic synthesis ; leukocyte integrins ; BODIPY ; β-galactosidase activity ; PET ; fluorescent ; dispirooxindoles ; anticancer activity ; cytotoxicity ; 3D molecular docking ; p53/MDM2 interaction ; terpenes ; hydrazones ; penetration enhancers ; liposomes ; lipids ; stratum corneum ; laser diffraction ; fluorescence probe ; pyrene ; FT-IR spectroscopy ; heterohelicene ; chirality ; resolution ; enantiomers ; chiroptical ; screw-shaped compounds ; betulinic acid ; α-glucosidase ; inhibition mechanism ; postprandial hyperglycemia ; synergistic effect ; AMR ; persisters ; (p)ppGpp ; fragment screening ; thermal shift assay ; STD-NMR ; boron ; phthalimide ; benzamide ; glycosidase ; cancer ; boron neutron capture therapy ; n/a ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TB Technology: general issues ; thema EDItEUR::T Technology, Engineering, Agriculture, Industrial processes::TD Industrial chemistry and manufacturing technologies::TDC Industrial chemistry and chemical engineering
    Language: English
    Format: application/octet-stream
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    E-BOOK
  • 2
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    Machine Learning in Biomolecular Simulations (2021)
    Frontiers Media SA
    Details
    Publication Date: 2024-04-04
    Description: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact
    Keywords: machine learning ; molecular dynamics computer simulation ; molecular modeling ; intrinsically disordered proteins ; ligand design ; collective variable ; sampling enhancement ; non-linear dimensionality reduction ; kinetics ; thema EDItEUR::P Mathematics and Science::PD Science: general issues
    Language: English
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  • 3
    Electronic Resource
    Electronic Resource
    The application of three approximate free energy calculations methods to structure based ligand design: Trypsin and its complex with inhibitors (1998)
    Springer
    Journal of computer aided molecular design 12 (1998), S. 215-227 
    Details
    ISSN: 1573-4951
    Keywords: free energy calculations ; ligand design ; molecular dynamics ; Pictorial Representation of Free Energy Changes (PROFEC)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Three approximate free energy calculation methods are examined and applied to an example ligand design problem. The first of the methods uses a single simulation to estimate the relative binding free energies for related ligands that are not simulated. The second method is similar, except that it uses only first derivatives of free energy with respect to atomic parameters (most often charge, van der Waals equilibrium distance, and van der Waals well depth) to calculate free energy differences. The last method PROFEC (Pictorial Representation of Free Energy Components), generates contour maps that show how binding free energy changes when additional particles are added near the ligand. These three methods are applied to a benzamidine/trypsin complex. They each reproduce the general trends in the binding free energies, indicating that they might be useful for suggesting how ligands could be modified to improve binding and, consequently, useful in structure-based drug design.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1007905722422
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  • 4
    Electronic Resource
    Electronic Resource
    Recent Advances in Structure-Based Ligand Design Using Molecular Dynamics and Monte Carlo Methods (1998)
    Springer
    Pharmaceutical research 15 (1998), S. 368-370 
    Details
    ISSN: 1573-904X
    Keywords: docking ; scoring ; ligand design ; molecular dynamics ; free energy calculations
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1011903711265
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  • 5
    Electronic Resource
    Electronic Resource
    The Design of Selective Chelating Agents: 1,3,5-Trideoxy-1,3,5-tris-(dimethylamino)-cis-inositol, a Powerful Ligand for Hard and Highly Charged Metal Ions1,3,5-Triamino-1,3,5-trideoxy-cis-inositol, a Ligand with a Remarkable Versatility for Metal Ions, Part 7. Part 6: K. Hegetschweiler. M. Ghisletta, T. F. Fässler, R. Nesper, Angew. Chem. Int. Ed. Engl. 1993, 32, 1426. (1995)
    Weinheim : Wiley-Blackwell
    Chemistry - A European Journal 1 (1995), S. 74-88 
    Details
    ISSN: 0947-6539
    Keywords: chelate ligands ; hydrogen bonds ; ligand design ; mass spectrometry ; stability constants ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A series of compounds containing the mononuclear complexes [M(tdci)2]3+ (tdci = 1,3,5-trideoxy-1,3,5-tris(dimethylamino)-cis-inositol, M = Al, Fe, Ga, In) and [M(tdci)2]4+ (M = Ti, Ge, Sn) was prepared and characterized by elemental analysis, NMR spectroscopy, and FAB mass spectrometry. Characteristic fragmentation reactions in the mass spectra were elucidated. X-ray analysis of the AlIII, FeIII, GaIII, and InIII complexes revealed that two neutral, zwitterionic tdci ligands coordinate to the metal cation exclusively through deprotonated alkoxo groups. The six coordinated oxygen donors and the six N—H protons form a hydrophilic pocket, whereas the two cyclohexane rings and the twelve methyl groups form two hydrophobic shells. The hydrophilic pocket is filled with twelve water molecules, which are arranged as a second and a third coordination sphere around the metal cation. The reactivity in aqueous solution was investigated by potentiometric measurements. The bis complexes proved to be stable at pH 7. The evaluated formation constants show an increase of stability in the order AlIII〈InIII〈GaIII〈FeIII. The measurements established that tdci is one of the most effective tridentate ligands for small (r ≤ 0.8Å) and highly charged cations. The different chelating properties of tdci and of the unmethylated 1,3,5-triamino- 1,3,5-trideoxy-cis-inositol are discussed in terms of different steric requirements and different types of solvation of the corresponding complexes in aqueous solution.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/chem.19950010112
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  • 6
    Electronic Resource
    Electronic Resource
    Ligand Design for Securing Ferromagnetic Exchange Coupling in Multimetallic Complexes (1995)
    Weinheim : Wiley-Blackwell
    Chemistry - A European Journal 1 (1995), S. 528-537 
    Details
    ISSN: 0947-6539
    Keywords: exchange coupling ; ferromagnetic properties ; ligand design ; magnetic properties ; multimetallic complexes ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An approach is suggested for using ligands to control exchange coupling in multinuclear ions. The idea arose from structural, EPR, and magnetic studies of [PPh4]3 (Scheme 1). Ferromagnetic coupling has been found between the CoII and each CoIII in 3 with J = -22 ± 5 cm-1 (JS1 · S2). It is suggested that dominant antiferromagnetic superexchange is absent because of the strong σ-donor capacity of the tetradentate ligand [k4-PAC*]4- (Fig. 1). The ligand interacts at CoIII primarily with a single d orbital; it is thus best able to participate in superexchange. The interaction makes the unique d orbital strongly σ-antibonding and empty for each d6, S = 1, CoIII ion in 3, that is, unavailable for antiferromagnetic coupling, but available for ferromagnetic pathways by a Goodenough-Kanamori mechanism. By corollary, when any [k4-PAC*]4--type ligand with any magnetic ion Ma in the tetradentate site binds any magnetic ion Mb in the bidentate site, ferromagnetic coupling should be favored provided Ma is not a d9 ion.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/chem.19950010806
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  • 7
    Electronic Resource
    Electronic Resource
    Heterocyclic Carbenes:Heterocyclic Carbenes, Part 6. Part 5: ref. [8] A High-Yielding Synthesis of Novel, Functionalized N-Heterocyclic Carbenes in Liquid Ammonia (1996)
    Weinheim : Wiley-Blackwell
    Chemistry - A European Journal 2 (1996), S. 1627-1636 
    Details
    ISSN: 0947-6539
    Keywords: carbenes ; heterocycles ; ligand design ; structure elucidation ; transition metal complexes ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: To date the only free carbenes of the imidazoline-2-ylidene type to have been described in the literature are those bearing simple hydrocarbon or haloalkyl and -aryl substituents. We report here a novel, versatile and high-yielding method for the synthesis of N-heterocyclic carbenes in a mixture of liquid ammonia and aprotic organic solvents. Deprotonation of the imidazolium precursor salts proceeds under mild conditions within a few minutes at temperatures below -30°C, and side reactions are thus avoided. The imidazolium salts are much more soluble in organic solvents if liquid ammonia is added. Furthermore, the acidity of the C-2 protons appears to be enhanced by hydrogen bonding. Not only are the known free ylidenes conveniently and quantitatively accessible by this procedure, but also novel functionalized derivatives that are not accessible by known procedures. Imidazoline-2-ylidenes with linear, branched, cyclic, heteroatom-substituted (O, N, P) and chiral hydrocarbon residues are accessible through the novel route. Stable carbene-metal “adducts” are conveniently obtained by treating the free carbenes with chloro- or acetato-bridged dinuclear metal complexes, or by displacement of coordinated ligands such as carbon monoxide, THF or acetonitrile by the free carbenes. The syntheses of novel imidazolium salts. N-heterocyclic carbenes and carbene adducts of RuII, RHI, W0 and sulfur are reported, and the structures of five products analysed by single-crystal X-ray diffraction. N-Heterocyclic carbenes bearing functionalized side chains are important because a number of these complexes show excellent activity in catalytic reactions. They do not show the typical reactivity of metal-carbon “double bonds” and are remarkably stable both thermally and chemically. For a number of reasons, they are best viewed as donor adducts of the highly Lewis basic imidazoline-2-ylidene ligands and the Lewis acidic organometallic fragments. The new synthetic procedure reported here makes N-heterocylic carbenes a generally accessible class of useful ligands in coordination chemistry and catalysis.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/chem.19960021222
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  • 8
    Electronic Resource
    Electronic Resource
    A Pyrrole-Imidazole Polyamide Motif for Recognition of Eleven Base Pair Sequences in the Minor Groove of DNADedicated to Dieter Seebach on the occasion of his 60th birthday (1997)
    Weinheim : Wiley-Blackwell
    Chemistry - A European Journal 3 (1997), S. 1600-1607 
    Details
    ISSN: 0947-6539
    Keywords: DNA recognition ; hydrogen bonds ; ligand design ; molecular recognition ; sequence-specificity ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new upper limit of binding site size is defined for the 2:1 overlapped polyamide: DNA motif. Eight-ring polyamides composed of four-ring subunits containing pyrrole (Py) and imidazole (Im) amino acids linked by a central β-alanine (β) spacer („4-β-4 ligands“) were designed for recognition of eleven base pair sequences as antiparallel dimer (4-β-4)2.DNA complexes in the minor groove. The DNA binding properties of three polyamides, ImPyPyPy-β-PyPyPyPy-β-Dp, ImImPyPy-β-PyPyPyPy-β-Dp, and ImImImPy-β-PyPyPyPy-β-Dp, were analyzed by footprinting experiments on DNA fragments containing the respective match sites 5'-AGTAATTTACT-3', 5'-AGGTATTACCT-3', and 5'-AGGGATTCCCT-3' (Dp = dimethylaminopropylamide). Quantitative footprint titrations reveal that each polyamide binds its respective target site with subnanomolar affinity and 7-fold to over 30-fold specificity over double-base-pair mismatch sites. A 20-fold decrease in binding affinity is observed for placement of a side-by-side β-β pairing opposite G.C/C.G relative to placement opposite a A.T/T.A base pair. The use of side-by-side antiparallel β-alanine residues as an A.T/T.A-specific DNA binding element provides a new pairing rule for polyamide design. Expanding the DNA binding site size targeted by pyrrole-imidazole polyamides represents an important step in the development of cell-permeable synthetic ligands for the control of gene-specific regulation.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/chem.19970031009
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  • 9
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    Advanced Synthesis and Catalysis
    Wiley
    Online: 1(1).1834 –
    Details
    Formerly as: Journal für Praktische Chemie / Chemiker-Zeitung  (1834–2000)
    Publisher: Wiley
    Description: Advanced Synthesis & Catalysis (ASC) is the leading primary journal in organic, organometallic, and applied chemistry. The high impact of ASC can be attributed to the unique focus of the journal, which publishes exciting new results from academic and industrial labs on efficient, practical, and environmentally friendly organic synthesis. While homogeneous, heterogeneous, organic, and enzyme catalysis are key technologies to achieve green synthesis, significant contributions to the same goal by synthesis design, reaction techniques, flow chemistry, and continuous processing, multiphase catalysis, green solvents, catalyst immobilization, and recycling, separation science, and process development are also featured in ASC.
    Print ISSN: 0021-8383 , 0368-301X , 0941-1216 , 1436-9966 , 1615-4150
    Electronic ISSN: 1521-3897 , 1615-4169
    Topics: Chemistry and Pharmacology
    Keywords: Präparative Chemie ; Katalyse ; Organische Synthese ; organic chemistry ; inorganic chemistry ; organometallic chemistry ; green chemistry ; homogeneous catalysis ; heterogeneous catalysis ; organocatalysis ; enzyme catalysis ; asymmetric catalysis ; multiphase catalysis ; organic synthesis ; asymmetric synthesis ; synthetic methods ; supported catalysts ; ligand design
    Acronym: ASC
    Abbreviation: Adv Synth Catal
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    JOURNAL
  • 10
    Journal cover
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    Quaestiones Geographicae
    De Gruyter | Institute of Geography, Adam Mickiewicz University, Poznań, Poland
    Online: 29(1).2010 –
    Details
    Publisher: De Gruyter , Institute of Geography, Adam Mickiewicz University, Poznań, Poland
    Corporation: Institute of Geography, Adam Mickiewicz University 〈Poznań, Poland〉
    Print ISSN: 0137-477X
    Electronic ISSN: 2081-6383
    Topics: Geography
    Keywords: Allgemeine Geographie
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    JOURNAL
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