Startseite The crystal structure of ethyl 6-(2-nitrophenyl)imidazo[2,1-b]thiazole-3-carboxylate, C14H11N3O4S
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The crystal structure of ethyl 6-(2-nitrophenyl)imidazo[2,1-b]thiazole-3-carboxylate, C14H11N3O4S

  • Yong Li ORCID logo EMAIL logo und Jingjing Wang
Veröffentlicht/Copyright: 10. April 2025

Abstract

C14H11N3O4S, monoclinic, P21/n (no. 14),a = 20.6433(8) Å, b = 6.9795(3) Å, c = 20.9482(8) Å, β = 112.440(1), V = 2789.67(19) Å3, Z = 8, R gt (F) = 0.0344, wR ref (F2) = 0.0972, T = 170 K.

CCDC no.: 2439945

1 Source of materials

A representative purification of the crude title compound was performed as follows: Ethyl 6-(2-nitrophenyl)imidazo[2,1-b]thiazole-3-carboxylate (0.3 g, 1 mmol) was dissolved in dichloromethane and washed with water under stirring for 10 min. After phase separation, the organic layer was treated with activated charcoal and filtered through a sand core funnel. Following an additional phase separation, the organic layer was concentrated under reduced pressure until precipitation occurred. The resulting viscous solid was dissolved in n-hexane and filtered in an ice-water bath, yielding a yellow solid upon evaporation that was suitable for single crystal growth (Table 1).

Table 1:

Data collection and handling.

Crystal: yellow block
Size: 0.48 × 0.26 × 0.19 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.26 mm−1
Diffractometer, scan mode: Bruker D8 Venture, φ and ω scans
θmax, completeness: 27.1°, 100 %
N(hkl)measured, N(hkl)unique, Rint: 45938, 6145, 0.036
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 5,351
N(param)refined: 399
Programs: Bruker, 1 Olex2, 2 SHELX. 3 , 4

The suitable single crystals for X-ray diffraction were obtained through the slow evaporation method.

n–Hexane solvent was added dropwise to the clean crystal growth tube containing the title compound. Care was taken to achieve near saturation of the solution. The crystal growth tube was then covered with aluminum foil, which was perforated with a needle to allow for ventilation. Subsequently, the crystal growth tube was placed in a dark cabinet to facilitate the slow evaporation of the n–hexane solvent.

During this equilibration process, yellow crystalline particles of the title compound were formed within approximately one week, and a suitable crystal was selected for X-ray crystallography.

2 Experimental details

Uiso values of hydrogen atoms were set to 1.2Ueq of the parent atoms for all C(H) groups, C(H,H) groups, and 1.5Ueq for all C(H,H,H) groups.

Secondary hydrogen atoms, were refined using riding coordinates. The phenyl hydrogen atoms, along with the imidazo[2,1-b]thiazole hydrogen atoms, wer refined as aromatic hydrogen using riding coordinates. The methyl hydrogen atoms, C14(H14A, H14B, H14C) and C14A(H14D, H14E, H14F), were refined as a idealized rotating group.

3 Comment

The title compound, a derivative of imidazothiazoles, is a high-value pharmaceutical intermediate for the synthesis of various drugs. 5

The synthesis method of the title compound has been reported in the literature. 6 , 7

The structural determination of the title compounds containing the moiety of heterocyclic imidazothiazole has been documented in several publications. 8 , 9 , 10

As part of our ongoing research interest on the structure-activity relationship about the antimicrobial agent, and understanding of hydrogen bonding schemes of related compounds, 11 , 12 , 13 , 14 this study presents the first successful preparation of single crystals of the title compound and provides a determination of its structure.

The asymmetric unit comprises two molecules of ethyl 6-(2-nitrophenyl)imidazo[2,1-b]thiazole-3-carboxylate (cf. left part of the figure).

The two molecules are indeed independent in the asymmetric unit.

First, the two molecules exhibit slightly different spatial conformations. The angle between the ring planes S1–C9–N3–C11–C10 and C9–N2–C7–C8–N3 is measured at 4.06(7), while in another molecule, the corresponding angle is 2.85(7). And, the angle between the eight-membered ring plane S1–N2–N3–C7–C8–C9–C10–C11 and the phenyl ring plane C1–C2–C3–C4–C5–C6 is 39.36(5). In contrast, in another molecule, this corresponding angle is 38.97(5).

Furthermore, the crystallographic independence of the two molecules in the asymmetric unit was confirmed by Platon, 15 , 16 analysis. The ADDSYM routine, which searches for additional symmetry elements, found no missed or pseudo symmetry that could relate these two molecules. The analysis confirmed that the P21/n space group is correct and complete, with no higher symmetry possible. This crystallographic evidence, combined with the distinct conformational differences between the two molecules, conclusively proves that these are indeed two crystallographically independent molecules.

In the title compound molecule, the imidazo[2,1-b]thiazole moiety and the 2-nitrophenyl moiety form an interesting case of atropisomerism due to restricted rotation around the single bond (C6–C7) connecting them.

Our calculation using MM2 force field method, 17 shows the rotation energy barriers of the title compound is about 22 kcal/mol. According to literature, 18 , 19 the interconversion half life of this atropisomers is about 0.2 h. That means this atropisomers are usually used as mixture. But in our crystal prepared, only one atropisomeric enantiomer is present, because crystal packing forces may favor one atropisomer over another in the crystal solid state.

No classic hydrogen bonds were identified. However, two C–H⋯O nonclassic hydrogen interactions were observed (cf. right part of the figure. Some hydrogen atoms and ethyl carboxylate group are omitted for clarity).

These two hydrogen bonds (C2⋯O1A′ = 3.3250(19) Å′ = 2-x, 1-y, 2-z), and( C2A⋯O1  = 3.2934(19) Å  = 2-x, 1-y, 2-z) connect molecules in alternation layers together.

The imidazothiazole and phenyl ring planes arrange themselves in a layered configuration along the ac-plane of the crystal lattice.

Simultaneously, multiple π-π weak interactions between imidazothiazole and phenyl rings form a chain-like structure that connects the molecules along the b-axis.


Corresponding author: Yong Li, School of Chemical Engineering, Ningbo Polytechnic, No. 388, Lushan East Road, Ningbo Economic and Technological Development Zone, Beilun, Ningbo 315806, Zhejiang, People’s Republic of China; and Ningbo Key Laboratory of High Performance Petroleum Resin Preparation Engineering and Technology, No. 388, Lushan East Road, Ningbo Economic and Technological Development Zone, Beilun, Ningbo 315806, Zhejiang, People’s Republic of China, E-mail:

Acknowledgments

We gratefully acknowledge support by School of Chemical Engineering, Ningbo Polytechnic, Ningbo Polytechnic Zhejiang Collaborative Innovation Center, and Ningbo Polytechnic Academician Workstation.

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

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

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Received: 2025-02-09
Accepted: 2025-03-31
Published Online: 2025-04-10
Published in Print: 2025-06-26

© 2025 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. New Crystal Structures
  3. Crystal structure of 5,5′-bis(2,4,6-trinitrophenyl)-2,2′-bi(1,3,4-oxadiazole), C16H4N10O14
  4. Crystal structure of catena-poly[(μ3-4,4′-oxydibenzoato- κ5 O,O: O,O:O)-bis(2,4,6-tri(3-pyridine)-1,3,5-triazine-κ1 N)cadmium(II)], C50H32CdN12O5
  5. The crystal structure of 1,4-diazepane-1,4-diium potassium trinitrate, C5H14KN5O9
  6. The crystal structure of benzyl 2,2,5,5-tetramethylthiazolidine-4-carboxylate, C15H21NO2S
  7. Crystal structure of 2-hydroxyethyl-triphenylphosphonium tetracyanidoborate, C24H20BN4OP
  8. The crystal structure of 1-methyl-3-(N-methylnitrous amide–N-methylene) imidazolidine-2,4,5-trione
  9. Crystal structure of N-((3-cyano-1-(2,6-dichloro-4-(trifluoromethyl)phenyl)-4-(2,2,2-trifluoroacetyl)-1H-pyrazol-5-yl)carbamoyl)-2,6-difluorobenzamide, C20H7Cl2F8N5O3S
  10. Crystal structure of 5-(2,2-difluoropropyl)-5-methylbenzo[4,5]imidazo[2,1-a] isoquinolin-6(5H)-one, C20H18F2N2O
  11. The crystal structure of N′,N″-[1,2-bis(4-chlorophenyl)ethane-1,2-diylidene]bis(furan-2- carbohydrazide), C24H16Cl2N4O4
  12. Crystal structure of [(4-bromobenzyl)triphenylphosphonium] tetrabromoantimony(III), [C25H21BrP]+[SbBr4]
  13. Crystal structure of [(4-bromobenzyl)triphenylphosphonium] tetrabromidoindium(III), [C25H21BrP]+[InBr4]
  14. The crystal structure of 4-carboxy-2-oxobutan-1-aminium chloride, C5H10ClNO3
  15. Crystal structure of (4-(4-chlorophenyl)-1H-pyrrole-3-carbonyl)ferrocene, C21H16ClFeNO
  16. The crystal structure of dichlorido(η6-p-cymene)(triphenylarsine)ruthenium(II), C28H29AsCl2Ru
  17. Crystal structure of (Z)-2-hydroxy-N′-(1-(o-tolyl)ethylidene)benzohydrazide, C16H16N2O2
  18. The crystal structure of 10-(1-bromoethyl)-14-(bromomethyl)dibenzo[a, c]acridine, C24H17NBr2
  19. Synthesis and crystal structure of 6-methoxy-7-[(4-methoxyphenyl)methoxy]-2H-1-benzopyran-2-one, C18H16O5
  20. Synthesis and crystal structure of ethyl 4-((4-trifluoromethylbenzyl)amino)benzo, C17H16F3NO2
  21. The crystal structure of (Z)-2-(tert-butyl)-6-(7-(tert-butyl)-5-methylbenzo[d][1,3]oxathiol-2-ylidene)-4-methylcyclohexa-2,4-dien-1-one, C23H28O2S
  22. The crystal structure of (R)-2-aminobutanamide hydrochloride, C4H11ClN2O
  23. Crystal structure of bromido[hydridotris(3-tert-butyl-5-isopropylpyrazolyl)borato-κ3 N,N′,N″]copper(II), C30H52BBrCuN6
  24. Crystal structure of chlorido{hydridotris[3-mesityl-5-methyl-1H-pyrazol-1-yl-κN3]borato}-copper(II) dichloromethane monosolvate
  25. Crystal structure of 4-[3,5-bis(propan-2-yl)-1H-pyrazol-4-yl]pyridine, C14H19N3
  26. Crystal structure of ((4-(4-bromophenyl)-1H-pyrrol-3-yl)methyl)ferrocene, C21H16BrFeNO
  27. Crystal structure of [(4-chlorobenzyl)triphenylphosphonium] dichloridocopper(I), {[C25H21ClP]+[CuCl2]}n
  28. The crystal structure of {Cu(2,9-diisopropyl-4,7-diphenyl-1,10-phenanthroline)[4,5-bis(diphenylphosphino)-9,9-dimethylxanthene]}+ PF6·1.5(EtOAC)
  29. Crystal structure of 3,5-bis(t-butyl)-1H-pyrazol-4-amine, C11H21N3
  30. Crystal structure of [(2,4-dichlorobenzyl)triphenylphosphonium] trichloridocopper(II), [C25H20Cl2P]+[CuCl3]
  31. The crystal structure of dipotassium sulfide, K2S
  32. Crystal structure of (4-(4-methoxyphenyl)-1H-pyrrole-3-carbonyl)ferrocene, C22H19FeNO2
  33. Crystal structure of (E)-6-(4-methylpiperazin-1-yl)-2-(4-(trifluoromethyl)benzylidene)-3, 4-dihydronaphthalen-1(2H)-one, C23H23F3N2O
  34. Crystal structure of (E)-6-morpholino-2-(4-(trifluoromethyl)benzylidene)-3,4-dihydronaphthalen-1(2H)-one, C22H20F3NO2
  35. Crystal structure of Ce9Ir37Ge25
  36. The crystal structure of ethyl 6-(2-nitrophenyl)imidazo[2,1-b]thiazole-3-carboxylate, C14H11N3O4S
  37. Crystal structure of (4-(4-isopropylphenyl)-1H-pyrrol-3-yl)(ferrocenyl)methanone, C24H23FeNO
  38. Crystal structure of bis(methylammonium) tetrathiotungstate(VI), (CH3NH3)2[WS4]
  39. Crystal structure of 6,11-dihydro-12H-benzo[e]indeno[1,2-b]oxepin-12-one, C17H12O2
  40. Crystal structure of 3-[(4-phenylpiperidin-1-yl)methyl]-5-(thiophen-2-yl)-2,3-dihydro-1,3,4- oxadiazole-2-thione, C18H19N3OS2
  41. Crystal structure of N-isopropyl-1,8-naphthalimide C15H13NO2
  42. TiNiSi-type EuPdBi
  43. Crystal structure of 1-(p-tolylphenyl)-4-(2-thienoyl)-3-methyl-1H-pyrazol-5-ol, C16H14N2O2S
  44. The crystal structure of 3-(3-carboxypropyl)-2-nitro-1H-pyrrole 1-oxide, C7H9N3O5
  45. The crystal structure of tetraaqua-bis(2-(2-methyl-5-nitro-1H-imidazol-1-yl)acetato-k2O:N)-tetrakis(2-(2-methyl-5-nitro-1H-imidazol-1-yl)acetato-k1N)trizinc(II) hexahydrate C36H52N18O32Zn3
  46. The crystal structure of 4-(3-carboxy-1-ethyl-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)piperazin-1-ium 4-hydroxy-3,5-dimethoxybenzoate monohydrate, C25H30FN3O9
  47. Crystal structure of bis(DL-1-carboxy-2-(1H-indol-3-yl)ethan-1-aminium) oxalate — acetic acid (1/2)
  48. Crystal structure of methyl (E)-4-((4-methylphenyl)sulfonamido)but-2-enoate, C12H15NO4S
  49. The crystal structure of actarit, C10H11NO3
  50. The crystal structure of bicyclol, C19H18O9
  51. The crystal structure of topiroxostat, C13H8N6
  52. Crystal structure of 2,2-dichloro-N-methyl-N-(4-p-tolylthiazol-2-yl)acetamide, C13H12Cl2N2OS
  53. Crystal structure of 4-(trifluoromethyl)-7-coumarinyl trifluoromethanesulfonate C11H4F6O5S
  54. Crystal structure of (1,4,7,10,13,16-hexaoxacyclooctadecane-κ6O6)-((Z)-N,N′-bis(2-(dimethylamino)phenyl)carbamimidato-κ1N)potassium(I)
  55. Crystal structure of (Z)-2-(5-((4-(dimethylamino)naphthalen-1-yl)methylene)-4-oxo-2-thioxothiazolidin-3-yl)acetic acid, C18H16N2O3S2
  56. Crystal structure of (4-fluorobenzyl)triphenylphosphonium bromide, C25H21BrFP
  57. The crystal structure of dichlorido-[6-(pyridin-2-yl)phenanthridine-κ2N, N′]zinc(II)-chloroform (1/1), C19H13N2ZnCl5
  58. Crystal structure of (E)-(3-(2,4-dichlorophenyl)acryloyl)ferrocene, C19H14Cl2FeO
  59. The crystal structure of (E)-7-chloro-1-cyclopropyl-6-fluoro-3-((2-hydroxybenzylidene)amino)quinolin-4(1H)-one, C19H14ClFN2O2
  60. Crystal structure of 2-bromo-11-(((fluoromethyl)sulfonyl)methyl)-6-methyl-6,11-dihydrodibenzo[c,f][1,2]thiazepine 5,5-dioxide, C16H13BrFNO4S2
  61. Crystal structure of 2-chloro-11-(((fluoromethyl)sulfonyl)methyl)-6-methyl-6,11-dihydrodibenzo[c,f][1,2]thiazepine 5,5-dioxide, C16H13ClFNO4S2
  62. Crystal structure of 5-(2,2-difluoropropyl)-5-methyl-6-oxo-5,6-dihydrobenzo[4,5]imidazo[2,1-a]isoquinoline-3-carbonitrile, C20H15F2N3O
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