Startseite Crystal and molecular structure of 5-bromopyridine-2,3-diamine
Artikel Open Access

Crystal and molecular structure of 5-bromopyridine-2,3-diamine

  • Irina S. Konovalova ORCID logo EMAIL logo und Guido J. Reiss ORCID logo
Veröffentlicht/Copyright: 26. Juli 2024

Abstract

C5H6BrN3, orthorhombic, P212121 (no. 19), a = 3.82640(10) Å, b = 8.7336(2) Å, c = 18.6007(3) Å, V = 621.60(2) Å3, Z = 4, Rgt(F) = 0.0184, wRref = 0.0473, T = 100(2) K.

CCDC no.: 2370691

Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colourless needle
Size: 0.40 × 0.17 × 0.10 mm
Wavelength: 6.51 mm−1
μ: Mo Kα radiation (0.71073 Å)
Diffractometer, scan mode: Rigaku Xcalibur, ω
θmax, completeness: 26.0°, >99 %
N (hkl)measured, N(hkl)unique, Rint: 27,820, 1,219, 0.059
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 1,197
N(param)refined: 106
Programs: Mercury, 1 CrysAlisPRO, 2 Olex2, 3 SHELX 4
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

Atom x y z Uiso*/Ueq
Br1 0.51168 (9) 0.53612 (3) 0.47097 (2) 0.01393 (12)
N1 0.1419 (8) 0.5283 (3) 0.67852 (15) 0.0125 (6)
N2 0.0997 (8) 0.3450 (4) 0.76817 (15) 0.0133 (6)
N3 0.4117 (8) 0.1248 (3) 0.67890 (17) 0.0128 (6)
C1 0.2359 (10) 0.5708 (4) 0.61178 (19) 0.0136 (7)
C2 0.3849 (8) 0.4703 (4) 0.56441 (17) 0.0115 (6)
C3 0.4527 (9) 0.3206 (4) 0.58544 (17) 0.0097 (6)
C4 0.3601 (9) 0.2754 (4) 0.65400 (18) 0.0098 (6)
C5 0.1952 (8) 0.3838 (4) 0.69899 (17) 0.0100 (7)
H1 0.199 (11) 0.677 (5) 0.599 (2) 0.018 (11)*
H2A 0.053 (12) 0.260 (5) 0.776 (2) 0.012 (10)*
H2B −0.049 (14) 0.418 (6) 0.791 (3) 0.033 (12)*
H3 0.555 (13) 0.259 (5) 0.556 (2) 0.029 (12)*
H3A 0.479 (13) 0.119 (5) 0.724 (2) 0.028 (11)*
H3B 0.552 (13) 0.079 (5) 0.654 (2) 0.020 (12)*

1 Source of material

We thank Professor Sergiy M. Kovalenko (V. N. Karazin Kharkiv National University, Ukraine) for providing some crystals of the title compound.

2 Experimental details

Using Olex2, 3 the structure was solved by with the ShelXT 4 structure solution program. Positions of the hydrogen atoms were located from electron density difference maps and refined by riding models with Uiso = nUeq of the carrier atom (n = 1.2).

3 Comment

3.1 Introduction

Halogen derivatives of diaminopyridine are of particular interest in medicinal chemistry and organic synthesis due to its potential biological activity and its utility as a building block for the synthesis of more complex molecules. 5 Research into these derivatives is ongoing, as scientists seek to understand their properties and potential applications better. These compounds are integral to the development of new pharmaceuticals, agrochemicals, and advanced materials, offering a wide array of possibilities for innovation in various fields of chemistry and biology.

3.2 Structural comment

The asymmetric unit of the title structure contains one complete molecule (see the figure). The molecular structure of the title compound shows that the molecule is nearly planar with r.m.s deviation from the mean plane of all non-hydrogen atoms of 0.01/Å. Bond lengths are all in the expected ranges 6 and they are similar with bond lengths of 5-chloro-pyridine-2,3-diamine. 7 A more general search in the Cambridge Structural database yielded some related structures that consists of a 5-bromo-pyridine moiety with 2 and 3 positions substituted by an amino group and a halogen substituent, respectively. 8 , 9 , 10

Both amino groups in the title structure have pyramidal configuration (the sum of valence angles centered on the nitrogen atom are for N2 346.8°, for N3 334.2°) and they can both participate in hydrogen bonds formation as donor and acceptor of proton (see left part of the figure). In the crystal phase molecules of the titled compound form zig–zag columns along the crystallographic c axis (see the figure right side) due to the N2–H2A⋯N1 (H⋯N 2.32 Å, N–H⋯N 167°), N2–H2B⋯N3 (H⋯N 2.35 Å, N–H⋯N 167°) and face-to-face stacking interactions.


Corresponding author: Irina S. Konovalova, SSI “Institute for Single Crystals” NAS of Ukraine, Nauky Ave., 60, Kharkiv, 61072, Ukraine; and Institut für Anorganische Chemie und Strukturchemie, Lehrstuhl II: Bioanorganische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany, E-mail:

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

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

  3. Research funding: This project has received funding through the MSCA4Ukraine project, which is funded by the European Union. Furthermore this study was supported by the Ministry of Innovation, Science and Research of North-Rhine Westphalia; the German Research Foundation (DFG): Xcalibur diffractometer; INST 208/533-1, project no. 162659349.

References

1. Macrae, C. F.; Sovago, I.; Cottrell, S. J.; Galek, P. T. A.; McCabe, P.; Pidcock, E.; Platings, M.; Shields, G. P.; Stevens, J. S.; Towler, M.; Wood, P. A. Mercury 4.0: From Visualization to Analysis, Design and Prediction. J. Appl. Crystallogr. 2020, 53, 226–235; https://doi.org/10.1107/S1600576719014092.Suche in Google Scholar PubMed PubMed Central

2. Oxford Diffraction CrysAlisPRO (Version 1.171.41.93a); Oxford Diffraction Ltd.: Oxford, UK, 2020.Suche in Google Scholar

3. Dolomanov, O. V.; Bourhis, L. J.; Gildea, R. J.; Howard, J. A. K.; Puschmann, H. OLEX2: A Complete Structure Solution, Refinement and Analysis Program. J. Appl. Cryst. 2009, 42, 339–341; https://doi.org/10.1107/s0021889808042726.Suche in Google Scholar

4. Sheldrick, G. M. A Short History of SHELX. Acta Crystallogr. 2008, A64, 112–122; https://doi.org/10.1107/s0108767307043930.Suche in Google Scholar PubMed

5. Sedehizadeh, S.; Keogh, M.; Maddison, P. The Use of Aminopyridines in Neurological Disorders. Clin. Neuropharmacol. 2012, 35, 191–200; https://doi.org/10.1097/WNF.0b013e31825a68c5.Suche in Google Scholar PubMed

6. Groom, C. R.; Bruno, I. J.; Lightfoot, M. P.; Ward, S. C. The Cambridge Structural Database. Acta Crystallogr. 2016, B72, 171–179. https://doi.org/10.1107/S2052520616003954.Suche in Google Scholar PubMed PubMed Central

7. Sulovari, A.; Tanski, J. M. Crystallographic and Spectroscopic Characterization of 5-chloropyridine-2,3-diamine. Acta Crystallogr. 2017, E73, 1213–1217; https://doi.org/10.1107/S2056989017010489.Suche in Google Scholar PubMed PubMed Central

8. Jiao, Z.-J.; Huang, S.-S.; Li, C.-X.; Diao, Y. P. Crystal Structure of 3,5-dibromopyridin-2-amine, C5H4Br2N2. Z. Kristallogr. N. Cryst. Struct. 2012, 227, 515–516; https://doi.org/10.1524/ncrs.2012.0246.Suche in Google Scholar

9. Aakeroy, C. B.; Rajbanshi, A.; Li, Z. J.; Desper, J. Mapping Out the Synthetic Landscape for Re-crystallization, Co-crystallization and Salt Formation. CrystEngComm 2010, 12, 4231–4239; https://doi.org/10.1039/c0ce00052c.Suche in Google Scholar

10. Bunker, K. D.; Sach, N. W.; Nukui, S.; Rheingold, A. L.; Yanovsky, A. 3-amino-5-bromo-2-iodopyridine. Acta Crystallogr. 2009, E65, o28; https://doi.org/10.1107/S1600536808040452.Suche in Google Scholar PubMed PubMed Central

Received: 2024-05-24
Accepted: 2024-07-15
Published Online: 2024-07-26
Published in Print: 2024-10-28

© 2024 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

Artikel in diesem Heft

  1. Frontmatter
  2. Editorial
  3. Editorial 2024 – New developments and changes of Zeitschrift für Kristallographie – New Crystal Structures
  4. New Crystal Structures
  5. Hydrogen bonding and π⋅⋅⋅halogen interactions in the crystal structure of bis(theophyllinium) hexachloridoplatinate(IV) monohydrate
  6. The crystal structure of 6-amino-2-carboxypyridin-1-ium perchlorate, C6H7ClN2O6
  7. Crystal structure of poly[(μ4-(3-amino-1H-1,2,4-triazol-1-yl)benzene-1,3-dicarboxylato-κ 4 N:O:O':O')(1-methylpyrroldin-2-one-κ1O)dicopper(II)] – 1-methylpyrroldin-2-one (1/3), C40H48Cu2N12O12
  8. The crystal structure of 18-crown-6-k6O6(2,4,5-trinitroimidazol-1-ido-k1O)potassium(I)
  9. Crystal structure of poly[tetraaqua-bis(μ2-5-bromoisophthalato-κ3O,O:O)-(μ2-1,5-bis(imidazol-2-methyl)pentane-κ2N:N)dicadmium(II)] dihydrate
  10. Crystal structure of (5R,6S,E)-5-acetoxy-2-methyl-6-((2aR,3R,5aS,5bS,11aR,12aS)-2a,5a,8,8-tetramethyl-9-oxotetradecahydro-1H,12H-cyclopenta[a]cyclopropa[e]phenanthren-3-yl)hept-2-enoic acid, C32H48O5
  11. The crystal structure of poly[diaqua-bis(μ2 -thiocyanato-κ2N:O)cobalt(II) monohydrate
  12. The crystal structure of 1,3,5-tri(1H-imidazol-1-yl)benzene–2,3,5,6-tetrachlorobenzene-1,4-dicarboxylic acid (1/1)
  13. Crystal structure of dichlorido-bis(1-[(2-ethyl-benzimidazole-1-yl)methyl]-1H–benzotriazole) cadmium(II), C32H32CdN10OCl2
  14. The crystal structure of N′-(tert-butyl)-N′-(3,5-dimethylbenzoyl)-3-methoxy-N,2-dimethylbenzohydrazide, C23H30N2O3
  15. Crystal stucture of 3-benzamido-N-(2-bromo-4-(perfluoropropan-2-yl)-6-(trifluoromethyl)phenyl)-2-fluorobenzamide
  16. Crystal structure of bis(μ-benzeneselenolato)-(tetracarbonyl)-{μ-[N-(diphenylphosphanyl)-N-(3-ethynylphenyl)-P,P-diphenylphosphinous amide]} diiron, C48H35Fe2NO4P2Se2
  17. The crystal structure of 2′-(p-tolyl)-4′H-spiro[isochromane-1,1′-naphthalene]-3,4′-dione, C25H18O3
  18. The crystal structure of poly[hexaqua-tetrakis(μ4-pyridine-2,4-dicarboxylate-κ5N: O: O′: O″: O‴)-bi(μ2-pyridine-2,4-dicarboxylate-κ3N: O: O′)-digadolinium(III)tricopper (II)], [Gd2Cu3(C7H3NO4)6(H2O)6] n
  19. Crystal structure of poly[bis(4-(4-(pyridin-4-yl)phenyl)pyridin-1-ium-κ1N)-(μ4-benzene-1,2,4,5-tetracarboxylato-κ5O:O′: O″:O‴:O⁗)-(μ2-2,5-dicarboxyterephthalato-κ2O:O′)dizinc(II)], C52H32N4O16Zn2
  20. The crystal structure of 4-(3-carboxy-1-ethyl-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)piperazin-1-ium 2-carboxy-6-nitrobenzoate monohydrate, C24H25FN4O10
  21. Crystal structure of dichlorido-(1-((3,5-dimethyl-2,3-dihydro-1H-1,2,3-triazol-1-yl)methyl)-1H-benzo[d][1,2,3]triazole-k1N)zinc(II), C22H24ZnN12Cl2
  22. The crystal structure of (3-chlorothiophene-2-carboxylato-κ2O, O′)-(2,2′-dipyridyl-κ2N,N′)lead(II), C20H12Cl2N2O4S2Pb
  23. Synthesis and crystal structure of (Z)-4-((1-(3-fluorophenyl)-1H-1,2,3-triazol-4-yl)methylene)-5-methyl-2-phenyl-2,4-dihydro-3H-pyrazol-3-one, C19H14FN5O
  24. The crystal structure of the coordination compound catena-poly[(18-crown-6-ether-κ6O6)(4,5-dinitroimidazolato-κ1O)potassium(I)]
  25. Crystal structure of 7-(diethylamino)-3-(trifluoroacetyl)-2H-chromen-2-one, C15H14F3NO3
  26. Crystal structure of dichlorido-1-[(2-ethylimidazole-1-yl)methyl]-1H–benzotriazole κ1N zinc(II), C24H26ZnN10Cl2
  27. Crystal and molecular structure of 5-bromopyridine-2,3-diamine
  28. Crystal structure of catena-poly[bis(μ2-1-(3-carboxyphenyl)-5-methyl-4-oxo-1,4-dihydropyridazine-3-carboxylato-k3-O,O:O)hexaqua-dicobalt tetrahydrate], C26H36N4O20Co2
  29. Crystal structure of thiocyanate-κ1N-bis(μ1-2,6-diformyl-4-methylphenol oxime-κ2N,O)-manganese(III) acetonitrile solvate, C21H21MnN6O6S
  30. The crystal structure of pyrrolidin-1-yl pivalate, C9H13NO4
  31. The crystal structure of 2,2′-(2,2-diphenylethene-1,1-diyl)bis(1,4-dimethoxybenzene), C30H28O4
  32. Crystal structure of bis(benzyltrimethylammonium) tetrathiotungstate(VI), {(C6H5CH2)(CH3)3N}2[WS4]
  33. The crystal structure of ethyl (Z)-2-(ethoxymethylene)-3-oxobutanoate, C9H14O4
  34. The crystal structure of (E)-6-bromo-3,5-dimethyl-2-(1-phenylprop-1-en-2-yl)-3Himidazo[4,5b]pyridine, C17H16BrN3
  35. Crystal structure of (3S,3′S,4R,4′S)-3′-(furan-3-yl)-3-hydroxy-4′-methyl-3,5,6′,7′-tetrahydro-1H,3′H-4,5′-spirobi[isobenzofuran]-1,1′(4′H)-dione-methanol (1/1), C21H22O7
  36. Cocrystal structure of progesterone-isophthalic acid, C25H33O4
  37. The crystal structure of 3-(6-fluoro-1H-indol-3-yl)-1-methylquinoxalin-2(1H)-one, C17H12FN3O
  38. Crystal structure of S-(4-carboxybutyl)- l -cysteine
  39. The cocrystal of 2,2′-(hydrazine-1,1-diyl)bis(1H-imidazole-4,5-dicarbonitrile)– methanol (2/3)
  40. Crystal structure of (1′R,2′S,4′R,6′S)-4,6-dihydroxy-1′,8′,8′-trimethyl-3-(3-methylbutanoyl)-4′,8′,6′,1′,7,2′-hexahydro-1H-4′,6′-methanoxanthene-8-carbaldehyde, C23H30O5
  41. Crystal structure of (3,6-di(2-pyridyl)-4-methylphenyl pyridazine-k 2 N,N′)-bis(1-phenyl-pyrazole-κ 2 C,N) iridium(III) hexafluorophosphate, C39H29F6IrN8P
  42. Crystal structure of 1,5-bis[(E)-1-(2-hydroxyphenyl)ethylidene]thiocarbonohydrazide dimethyl sulfoxide monosolvate, C17H18N4O2S·C2H6OS
  43. Crystal structure of (S)-4-(2-(4-(2-acetyl-5-chlorophenyl)-3-methoxy-6-oxopyridazin-1(6H)-yl)-3-phenylpropanamido)benzoic acid monohydrate, C29H26ClN3O7
  44. The crystal structure of 1,3-bis(2,4-dinitro-1H-imidazol-1-yl)propane
  45. Crystal structure of 4-chlorobenzyl (S)-2-(6-methoxynaphthalen-2-yl)propanoate, C21H19ClO3
  46. Crystal structure of 1-(5-(benzo[d][1,3]dioxol-5-yl)-4-benzyl-1-(4-bromophenyl)-4,5-dihydro-1H-1,2,4-triazol-3-yl)ethan-1-one, C24H20BrN3O3
  47. The crystal structure of (Z)-3′-(2-(1-(3,4-dimethyl-phenyl)-3-methyl-5-oxo-1,5-dihydro-4H-pyrazol-4-ylidene)hydrazinyl)-2′-hydroxy-[1,1′-biphenyl]-3-carboxylicacid ─ methanol (1/1), C26H26N4O5
  48. Crystal structure of (S)-1-phenylpropan-1-aminium (S)-(1-phenylpropyl)carbamate C19H26N2O2
  49. Synthesis and crystal structure of methyl 2-((5-bromo-4-(4-cyclopropylnaphthalen-1-yl)-4H-1,2,4-triazol-3-yl)thio)acetate, C18H16BrN3O2S
  50. The crystal structure of trichlorobis(pyridine-2,6-dithio-κS-carbomethylamido)antimony(III), [SbCl3(C9H11N3S2)2]
  51. Crystal structure of 1,8-dihydroxy-3-{[(triphenylstannyl)oxy]carbonyl} anthracene-9,10-dione, C33H22O6Sn
  52. The crystal structure of (E)-4-(2-(pyridin-4-ylmethylene)hydrazine-1-carbonyl)pyridin-1-ium-2-olate dihydrate, C12H14N4O4
  53. The crystal structure of 6-amino-pyridinium-2-carboxylate, C6H6N2O2
  54. The crystal structure of catena-poly[aqua-nitrato-κ3O,O:O′′-(1,10-phenanthroline-κ2N,N)sodium(I)], C24H18N6O7Na2
  55. Retractions
  56. Retraction of: Crystal structure of bis[diaquaisonicotinatosamarium(III)]-µ-isonicotinato-[diisonicotinatocopper(II)], CuSm2(C6H4NO2)8(H2O)4
  57. Retraction of: Crystal structure of aqua(2,2-bipyridine-k 2 N:N′)(nitrato)-(4-aminobenzoato)cadmium(II) nitrate, [Cd(H2O)(NO3)(C10H8N2)(C7H7NO2)][NO3]
Heruntergeladen am 28.9.2025 von https://www.degruyterbrill.com/document/doi/10.1515/ncrs-2024-0221/html
Button zum nach oben scrollen