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Electron density of a cyclic tetrasaccharide composed of benzoylated galactose units

  • Peter Luger EMAIL logo and Birger Dittrich
Published/Copyright: March 8, 2023
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Zeitschrift für Naturforschung B
From the journal Zeitschrift für Naturforschung B Volume 78 Issue 3-4

Abstract

The electron density distribution (EDD) of a cyclic tetrasaccharide composed of four benzoylated galactopyranosyl units was calculated from refinement with scattering factors from the invariom library based on X-ray diffraction data downloaded from the Crystal Structural Data Base (CSD). Bond topological and atomic properties have been derived. Benzoyl substituents cause weak intermolecular interactions. These are also visible from low electron density concentrations on the Hirshfeld surface and have an influence on a low X-ray density compared to that of non-substituted carbohydrates, where hydrogen bonds allow a 20% more dense packing. On the electrostatic potential (ESP) surface, a strong polarization between the positive outer belt of 12 benzoyl groups and a negative core region composed of the four galactose sugar molecules exists. The positive benzoyl exterior establishes a repulsive wall between adjacent molecules in the structure.

Keywords: cyclic tetrasaccharide; electron density; invariom formalism; topological analysis

Dedicated to Professor Gerhard Müller on the occasion of his 70th birthday.

Corresponding author: Peter Luger, Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstraße 36a, D-14195 Berlin, Germany, E-mail:

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: None declared.

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

References

1. Allen, H. Acta Crystallogr. 2002, B58, 380–388; https://doi.org/10.1107/s0108768102003890.Search in Google Scholar PubMed

2. Groom, C. R., Bruno, I. J., Lightfood, M. P., Ward, S. C. Acta Crystallogr. 2016, B72, 171–179.10.1107/S2052520616003954Search in Google Scholar PubMed PubMed Central

3. Luger, P., Dittrich, B. Z. Naturforsch. 2022, 77b, 487–494; https://doi.org/10.1515/znb-2021-0178.Search in Google Scholar

4. Someya, H., Seki, T., Ishigama, G., Itoh, T., Saga, Y., Yamada, Y., Aoki, S. Carbohydr. Res. 2020, 487, 107888–107898.10.1016/j.carres.2019.107888Search in Google Scholar PubMed

5. Dittrich, B., Koritsanszky, T., Luger, P. Angew. Chem. Int. Ed. 2004, 43, 2718–2721; https://doi.org/10.1002/anie.200353596.Search in Google Scholar PubMed

6. Dittrich, B., Hübschle, C. B., Pröpper, K., Dietrich, F., Stolper, T., Holstein, J. J. Acta Crystallogr. 2013, B69, 91–104; https://doi.org/10.1107/s0108768113002280.Search in Google Scholar

7. Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J., Wood, P. A. J. Appl. Crystallogr. 2008, 41, 466–470; https://doi.org/10.1107/s0021889807067908.Search in Google Scholar

8. Spek, A. L. Acta Crystallogr. 2009, D65, 148–155; https://doi.org/10.1107/s090744490804362x.Search in Google Scholar

9. Lehmann, C., Luger, P. FU Berlin, 1992, unpublished study.Search in Google Scholar

10. Cremer, D., Pople, J. A. J. Am. Chem. Soc. 1975, 97, 1354–1358; https://doi.org/10.1021/ja00839a011.Search in Google Scholar

11. Sheldrick, B. Acta Crystallogr. 1976, B32, 1016–1020; https://doi.org/10.1107/s0567740876004561.Search in Google Scholar

12. Volkov, A., Macchi, P., Farrugia, L. J., Gatti, C., Mallinson, P. R., Richter, T., Koritsánszky, T. Xd2006 – A Computer Program for Multipole Refinement, Topological Analysis of Charge Densities and Evaluation of Intermolecular Energies from Experimental and Theoretical Structure Factors; University of Buffalo: NY (USA); University of Milano, (Italy); University of Glasgow, (UK); CNRISTM, Milano (Italy); Middle Tennessee State University, TN (USA), 2006.Search in Google Scholar

13. Bader, R. F. W. Atoms in Molecules-A Quantum Theory; Clarendon Press: Oxford, 1994.Search in Google Scholar

14. Bader, R. F. W. Theor. Chem. Acc. 2001, 105, 276–284.10.1038/scientificamerican0601-105Search in Google Scholar

15. Volkov, A., Gatti, C., Abramov, Y., Coppens, P. Acta Crystallogr. 2000, A56, 252–258; https://doi.org/10.1107/s0108767300001628.Search in Google Scholar

16. Hübschle, C. B., Luger, P. J. Appl. Crystallogr. 2006, 39, 901–904; https://doi.org/10.1107/s0021889806041859.Search in Google Scholar

17. McKinnon, J. J., Mitchell, A. S., Spackman, M. A. Chem. Eur J. 1998, 4, 2136–2141; https://doi.org/10.1002/(sici)1521-3765(19981102)4:11<2136::aid-chem2136>3.0.co;2-g.10.1002/(SICI)1521-3765(19981102)4:11<2136::AID-CHEM2136>3.0.CO;2-GSearch in Google Scholar

18. Spackman, M. A., McKinnon, J. J., Jayatilaka, D. CrystEngComm 2008, 10, 377–388.Search in Google Scholar

19. Volkov, A., King, H. F., Coppens, P., Farrugia, L. J. Acta Crystallogr. 2006, A62, 400–408; https://doi.org/10.1107/s0108767306026298.Search in Google Scholar

20. Bader, R. F. W., Bayles, D. J. Phys. Chem. 2000, A104, 5579–5589; https://doi.org/10.1021/jp9943631.Search in Google Scholar

21. Luger, P., Dittrich, B. Z. Naturforsch. 2022, 77b, 633–641; https://doi.org/10.1515/znb-2022-0067.Search in Google Scholar

22. Hübschle, C. B., Luger, P., Dittrich, B. J. Appl. Crystallogr. 2007, 40, 623–627; https://doi.org/10.1107/s0021889807016524.Search in Google Scholar

Supplementary Material

This article contains supplementary material (https://doi.org/10.1515/znb-2022-0301).

Received: 2022-11-29
Accepted: 2022-12-09
Published Online: 2023-03-08
Published in Print: 2023-03-28

© 2022 Walter de Gruyter GmbH, Berlin/Boston

Articles in the same Issue

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  4. Professor Dr. Gerhard Müller. Editor-in-Chief der Zeitschrift für Naturforschung B – Chemical Sciences. zum 70. Geburtstag
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https://doi.org/10.1515/znb-2022-0301
Keywords for this article
cyclic tetrasaccharide; electron density; invariom formalism; topological analysis

Articles in the same Issue

  1. Frontmatter
  2. In this issue
  3. Preface
  4. Professor Dr. Gerhard Müller. Editor-in-Chief der Zeitschrift für Naturforschung B – Chemical Sciences. zum 70. Geburtstag
  5. Research Articles
  6. Ferrocenylmethylation of theophylline
  7. Electron density of a cyclic tetrasaccharide composed of benzoylated galactose units
  8. Orthoamide und Iminiumsalze, CIX. Umsetzungen von Orthoamiden der Alkincarbonsäuren mit Diolen, Ethandithiol und CH-aciden Nitroverbindungen
  9. 1,4-Divinylphenylene-bridged diruthenium complexes with 2-hydroxypyridine- and 2- or 8-hydroxyquinoline-olate ligands
  10. The calcium oxidotellurates Ca2(TeIVTeVIO7), Ca2(TeIVO3)Cl2 and Ca5(TeIVO3)4Cl2 obtained from salt melts
  11. N-heterocyclic carbene-mediated oxidation of copper(I) in an imidazolium ionic liquid
  12. Synthesis, crystal structure, thermal and spectroscopic properties of ZnX2-2-methylpyrazine (X = Cl, Br, I) coordination compounds
  13. Solid-state molecular structures of Se(IV) and Te(IV) dihalides X2Se(CH3)(C6F5) and the gas-phase structure of Se(CH3)(C6F5)
  14. Ein neuartiger T-förmiger 14-Elektronen-Iridium(I)-Komplex stabilisiert durch eine agostische Ir–H-Wechselwirkung
  15. Exploring dicyanamides with two different alkali-metal cations: phase separations, solid solutions and the new compound Rb1.667Cs0.333[N(CN)2]2
  16. Eu4Al13Pt9 – a coloring variant of the Ho4Ir13Ge9 type structure
  17. Decoration of the [Nb6O19]8– cluster shell with six Cu2+-centred complexes generates the [(Cu(cyclen))6Nb6O19]4+ moiety: room temperature synthesis, crystal structure and selected properties
  18. Structure and spectroscopic properties of etherates of the beryllium halides
  19. The palladium-rich silicides RE3Pd20Si6 (RE = Sc, Y and Lu)
  20. Azido and desamino analogs of the marine natural product oroidin
  21. High-pressure high-temperature preparation of CeGe3
  22. On the synthesis and crystal structure of praseodymium(III) metaborate molybdate(VI) – PrBO2MoO4
  23. A third polymorph of the zwitterionic complex trichlorido-((dimethylphosphoryl)methanaminium-κO)zinc(II)
  24. Mechanochemical synthesis and structural evaluation of a metastable polymorph of Ti3Sn
  25. Synthesis and application of calcium silicate hydrate (C-S-H) nanoparticles for early strength enhancement by eco-friendly low carbon binders
  26. Sterically crowded di-indazolyl-pyridines: Iron(II) complexation studies
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