LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 137

Search options

  1. Article: On modelling disordered crystal structures through restraints from molecule-in-cluster computations, and distinguishing static and dynamic disorder.

    Dittrich, Birger

    IUCrJ

    2021  Volume 8, Issue Pt 2, Page(s) 305–318

    Abstract: Distinguishing disorder into static and dynamic based on multi-temperature X-ray or neutron diffraction experiments is the current state of the art, but is only descriptive, not predictive. Here, several disordered structures are revisited from the ... ...

    Abstract Distinguishing disorder into static and dynamic based on multi-temperature X-ray or neutron diffraction experiments is the current state of the art, but is only descriptive, not predictive. Here, several disordered structures are revisited from the Cambridge Crystallographic Data Center 'drug subset', the Cambridge Structural Database and own earlier work, where experimental intensities of Bragg diffraction data were available. Using the molecule-in-cluster approach, structures with distinguishable conformations were optimized separately, as extracted from available or generated disorder models of the respective disordered crystal structures. Re-combining these 'archetype structures' by restraining positional and constraining displacement parameters for conventional least-squares refinement, based on the optimized geometries, then often achieves a superior fit to the experimental diffraction data compared with relying on experimental information alone. It also simplifies and standardizes disorder refinement. Ten example structures were analysed. It is observed that energy differences between separate disorder conformations are usually within a small energy window of
    Language English
    Publishing date 2021-02-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252521000531
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  2. Article: Electron density of the 1:2 complex of valinomycin with calcium triflate observed in crystals of the composition (valinomycin)Ca₂(OTf)₄(THF)₅(H₂O)₄

    Luger, Peter / Dittrich, Birger

    Zeitschrift für Naturforschung. 2022 Sept. 27, v. 77, no. 9

    2022  

    Abstract: The electron density of a 1:2 complex of valinomycin with calcium triflate consisting of 10 substructures and a total of 279 atoms was examined using the invariom formalism. In addition to geometric properties, sites and strengths of hydrogen bonds were ... ...

    Abstract The electron density of a 1:2 complex of valinomycin with calcium triflate consisting of 10 substructures and a total of 279 atoms was examined using the invariom formalism. In addition to geometric properties, sites and strengths of hydrogen bonds were identified from bond topological properties and from electron density concentrations mapped onto Hirshfeld surfaces. In contrast to free valinomycin and corresponding complexes with potassium the hydrogen bonds are all intermolecular and evenly distributed over the complex. A series of electrostatic potential (ESP) surfaces show the mutual influence in the ensemble of this high Z′ structure.
    Keywords calcium ; geometry ; hydrogen ; potassium ; topology ; valinomycin
    Language English
    Dates of publication 2022-0927
    Size p. 633-641.
    Publishing place De Gruyter
    Document type Article
    ZDB-ID 2078109-X
    ISSN 1865-7117
    ISSN 1865-7117
    DOI 10.1515/znb-2022-0067
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

  3. Article: Electron density of a benzoylated tetrafructopyranose

    Luger, Peter / Dittrich, Birger

    Zeitschrift für Naturforschung. 2022 July 26, v. 77, no. 7-8

    2022  

    Abstract: The electron density distribution (EDD) of a tetrasaccharide composed of four benzoylated fructopyranosyl units was obtained by refinement with scattering factors from the invariom library. X-ray diffraction data was downloaded from the Cambridge ... ...

    Abstract The electron density distribution (EDD) of a tetrasaccharide composed of four benzoylated fructopyranosyl units was obtained by refinement with scattering factors from the invariom library. X-ray diffraction data was downloaded from the Cambridge Structural Database (CSD). Bond topological and atomic properties were obtained by application of Bader’s QTAIM formalism. From a large number of 105 C–C bonds in the molecule average bond orders for 33 single and 72 aromatic bonds were calculated yielding values of 1.33 and 1.61. Molecular Hirshfeld and electrostatic potential (ESP) surfaces show that only weak non-covalent interactions exist. The phenyl rings of the benzoyl fragments in the outer regions of the molecule generate a positive ESP shell with repulsive properties between adjacent molecules. Weak surface interactions result in a rather unusual low density around 1.3 g cm⁻³, which is understandable when compared to other carbohydrates where strong O–H⋯O hydrogen bonds allow a 20% more dense packing with densities >1.5 g cm⁻³ as determined by single crystal X-ray diffraction.
    Keywords X-ray diffraction ; databases ; hydrogen ; topology
    Language English
    Dates of publication 2022-0726
    Size p. 487-494.
    Publishing place De Gruyter
    Document type Article
    ZDB-ID 2078109-X
    ISSN 1865-7117
    ISSN 1865-7117
    DOI 10.1515/znb-2021-0178
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

  4. Article ; Online: Is there a future for topological analysis in experimental charge-density research?

    Dittrich, Birger

    Acta crystallographica Section B, Structural science, crystal engineering and materials

    2017  Volume 73, Issue Pt 3, Page(s) 325–329

    Abstract: Topological analysis using Bader and co-worker's Atoms in Molecules theory has seen many applications in theoretical chemistry and experimental charge-density research. A brief overview of successful early developments, establishing topological analysis ... ...

    Abstract Topological analysis using Bader and co-worker's Atoms in Molecules theory has seen many applications in theoretical chemistry and experimental charge-density research. A brief overview of successful early developments, establishing topological analysis as a research tool for characterizing intramolecular chemical bonding, is provided. A lack of vision in many `descriptive but not predictive' subsequent studies is discussed. Limitations of topology for providing accurate energetic estimates of intermolecular interaction energies are put into perspective. It is recommended that topological analyses of well understood bonding situations are phased out and are only reported for unusual bonding. Descriptive studies of intermolecular interactions should have a clear research focus.
    Language English
    Publishing date 2017-06-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 2020841-8
    ISSN 2052-5206 ; 1600-5740 ; 2052-5192 ; 0108-7681
    ISSN (online) 2052-5206 ; 1600-5740
    ISSN 2052-5192 ; 0108-7681
    DOI 10.1107/S2052520617006680
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  5. Article: Electron densities of two cyclononapeptides from invariom application

    Luger, Peter / Dittrich, Birger

    Zeitschrift für Naturforschung. 2019 Dec. 18, v. 74, no. 11-12

    2019  

    Abstract: The nonapeptides cyclo(Val-Leu-Pro-Ile-Leu-Leu-Leu-Val-Leu) (I) and cyclo(Val-Leu-Pro-Ala-Leu-Leu-Leu-Val-Leu) (II) were identified as promising candidates for the development as potential anti-cancer drugs. We report a re-refinement of deposited single- ... ...

    Abstract The nonapeptides cyclo(Val-Leu-Pro-Ile-Leu-Leu-Leu-Val-Leu) (I) and cyclo(Val-Leu-Pro-Ala-Leu-Leu-Leu-Val-Leu) (II) were identified as promising candidates for the development as potential anti-cancer drugs. We report a re-refinement of deposited single-crystal X-ray diffraction data with aspherical scattering factors from the invariom database. A subsequent evaluation of the molecular electron density distribution and of the differences in their molecular electrostatic potentials provides insight in their activities. The sequences differ only in residue 4, Ile in (I) and Ala in (II). Since the anti-tumor potency is reduced for the Ala peptide (II), the causes for the differences seen in activity between (I) and (II) were examined from a structural and from an electron density (ED) point of view. The exchange at residue 4 does not lead to significant changes in molecular geometry. Molecular Hirshfeld surfaces and electrostatic potential (ESP) isosurfaces show accumulations of intermolecular interactions in regions adjacent to the Ile/Ala residues indicating preferred interactions with a potential receptor in these regions. The concentrations of intermolecular interactions were localized on the Hirshfeld surfaces through an extended basin of ED concentration close to the Ile/Ala residues. Differences in the electrostatic potentials (ESPs) between (I) and (II) were only found at the Ile/Ala site and were very close to zero otherwise.
    Keywords antineoplastic agents ; basins ; chemical interactions ; databases ; electrostatic interactions ; geometry ; peptides ; X-ray diffraction
    Language English
    Dates of publication 2019-1218
    Size p. 783-789.
    Publishing place De Gruyter
    Document type Article
    ISSN 1865-7117
    DOI 10.1515/znb-2019-0154
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

  6. Article ; Online: Kinetic Trapping Effects in Amphiphilic Iron(II) Spin Crossover Compounds.

    Weihermüller, Johannes / Schlamp, Stephan / Dittrich, Birger / Weber, Birgit

    Inorganic chemistry

    2019  Volume 58, Issue 2, Page(s) 1278–1289

    Abstract: In this work, the synthesis of four new iron complexes with a Schiff base-like amphiphilic equatorial ligand (L) and dimethylaminopyridine (dmap) or 4,4'-bipyridine (bipy) as axial ligands is reported. Three of the complexes ([FeL(dmap) ...

    Abstract In this work, the synthesis of four new iron complexes with a Schiff base-like amphiphilic equatorial ligand (L) and dimethylaminopyridine (dmap) or 4,4'-bipyridine (bipy) as axial ligands is reported. Three of the complexes ([FeL(dmap)
    Language English
    Publishing date 2019-01-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1484438-2
    ISSN 1520-510X ; 0020-1669
    ISSN (online) 1520-510X
    ISSN 0020-1669
    DOI 10.1021/acs.inorgchem.8b02763
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article: Invariom-based comparative electron density studies of iso-sildenafil and sildenafil

    Dittrich, Birger / Peter Luger

    Zeitschrift für Naturforschung B. 2016 Dec. 8, v. 72, no. 1

    2016  

    Abstract: The title compounds have raised considerable medical and broad public interest in that sildenafil is used as an agent against male erectile dysfunction; iso-sildenafil is not in clinical use. A comparison of their structural and electronic properties ... ...

    Abstract The title compounds have raised considerable medical and broad public interest in that sildenafil is used as an agent against male erectile dysfunction; iso-sildenafil is not in clinical use. A comparison of their structural and electronic properties therefore seems of interest. The electron densities of iso-sildenafil and the cationic and neutral forms of sildenafil were examined by the application of the invariom formalism relying on diffraction data reported in the literature. The electron-density distributions obtained were subjected to topological analysis using the quantum theory of atoms in molecules (QTAIM) formalism to yield bond topological and atomic properties. Moreover, molecular Hirshfeld surfaces and electrostatic potentials (ESPs) were calculated. A number of structural and electronic differences were thus identified between sildenafil and the iso-analog. In both sildenafil structures, the phenyl ring and the pyrazolopyrimidine fragment are practically coplanar (planar conformation), whereas in the iso-analog they exhibit an angle of 44° (inclined form). Related to differences in molecular structure are completely different hydrogen bonding patterns and differences in the ESPs, the latter ones being influenced by different methylation at the pyrazolopyrimidine fragment. Iso-sildenafil is present as a hydrogen-bond dimer in the crystal, and the ESP of this dimer is dominated by a surrounding positive potential.
    Keywords hydrogen bonding ; males ; methylation ; quantum mechanics ; topology
    Language English
    Dates of publication 2016-1208
    Size p. 1-10.
    Publishing place De Gruyter
    Document type Article
    ISSN 1865-7117
    DOI 10.1515/znb-2016-0178
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

  8. Article: Contributions of charge-density research to medicinal chemistry.

    Dittrich, Birger / Matta, Chérif F

    IUCrJ

    2014  Volume 1, Issue Pt 6, Page(s) 457–469

    Abstract: This article reviews efforts in accurate experimental charge-density studies with relevance to medicinal chemistry. Initially, classical charge-density studies that measure electron density distribution via least-squares refinement of aspherical-atom ... ...

    Abstract This article reviews efforts in accurate experimental charge-density studies with relevance to medicinal chemistry. Initially, classical charge-density studies that measure electron density distribution via least-squares refinement of aspherical-atom population parameters are summarized. Next, interaction density is discussed as an idealized situation resembling drug-receptor interactions. Scattering-factor databases play an increasing role in charge-density research, and they can be applied both to small-molecule and macromolecular structures in refinement and analysis; software development facilitates their use. Therefore combining both of these complementary branches of X-ray crystallography is recommended, and examples are given where such a combination already proved useful. On the side of the experiment, new pixel detectors are allowing rapid measurements, thereby enabling both high-throughput small-molecule studies and macromolecular structure determination to higher resolutions. Currently, the most ambitious studies compute intermolecular interaction energies of drug-receptor complexes, and it is recommended that future studies benefit from recent method developments. Selected new developments in theoretical charge-density studies are discussed with emphasis on its symbiotic relation to crystallography.
    Language English
    Publishing date 2014-09-23
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252514018867
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  9. Article ; Online: Hydrogen ADPs with Cu Kα data? Invariom and Hirshfeld atom modelling of fluconazole.

    Orben, Claudia M / Dittrich, Birger

    Acta crystallographica. Section C, Structural chemistry

    2014  Volume 70, Issue Pt 6, Page(s) 580–583

    Abstract: For the structure of fluconazole [systematic name: 2-(2,4-difluorophenyl)-1,3-bis(1H-1,2,4-triazol-1-yl)propan-2-ol] monohydrate, C13H12F2N6O·H2O, a case study on different model refinements is reported, based on single-crystal X-ray diffraction data ... ...

    Abstract For the structure of fluconazole [systematic name: 2-(2,4-difluorophenyl)-1,3-bis(1H-1,2,4-triazol-1-yl)propan-2-ol] monohydrate, C13H12F2N6O·H2O, a case study on different model refinements is reported, based on single-crystal X-ray diffraction data measured at 100 K with Cu Kα radiation to a resolution of sin θ/λ of 0.6 Å(-1). The structure, anisotropic displacement parameters (ADPs) and figures of merit from the independent atom model are compared to `invariom' and `Hirshfeld atom' refinements. Changing from a spherical to an aspherical atom model lowers the figures of merit and improves both the accuracy and the precision of the geometrical parameters. Differences between results from the two aspherical-atom refinements are small. However, a refinement of ADPs for H atoms is only possible with the Hirshfeld atom density model. It gives meaningful results even at a resolution of 0.6 Å(-1), but requires good low-order data.
    MeSH term(s) Copper/chemistry ; Crystallography, X-Ray ; Fluconazole/chemistry ; Hydrogen/chemistry ; Models, Molecular ; X-Ray Diffraction
    Chemical Substances Copper (789U1901C5) ; Hydrogen (7YNJ3PO35Z) ; Fluconazole (8VZV102JFY)
    Language English
    Publishing date 2014-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 2025703-X
    ISSN 2053-2296 ; 1600-5759 ; 0108-2701
    ISSN (online) 2053-2296 ; 1600-5759
    ISSN 0108-2701
    DOI 10.1107/S2053229614010195
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  10. Article ; Online: Photochemical C(

    Görlich, Tim / Frost, Daniel S / Boback, Nico / Coles, Nathan T / Dittrich, Birger / Müller, Peter / Jones, William D / Müller, Christian

    Journal of the American Chemical Society

    2021  Volume 143, Issue 46, Page(s) 19365–19373

    Abstract: The photochemical activation of the C( ...

    Abstract The photochemical activation of the C(
    Language English
    Publishing date 2021-11-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.1c07370
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

To top