Home Physical Sciences Crystal structure of (E)-2-(((5-chloro-3-methyl-1-phenyl-1H-pyrazol-4-yl)methylene)amino)-3′,6′-dihydroxyspiro[isoindoline-1,9′-xanthen]-3-one – ethanol (1/2), C35H33ClN4O6
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Crystal structure of (E)-2-(((5-chloro-3-methyl-1-phenyl-1H-pyrazol-4-yl)methylene)amino)-3′,6′-dihydroxyspiro[isoindoline-1,9′-xanthen]-3-one – ethanol (1/2), C35H33ClN4O6

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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 240 Issue 5

Abstract

C35H33ClN4O6, monoclinic, P 2 1/c (no. 14), a = 18.2808(8) Å, b = 9.0510(4) Å, c = 19.4323(7) Å, β = 93.406(10)°, V = 3209.6(2) Å3, Z = 4, R gt (F) = 0.046, wR ref (F2) = 0.129, T = 120.0 K.

CCDC no.: 2446999

The molecular structure is shown in the figure. Table 1 contains the crystallographic data and the list of the atoms including atomic coordinates and displacement parameters can be found in the cif-file attached to this article.

Table 1:

Data collection and handling.

Crystal: Light colourless block
Size: 0.28 × 0.15 × 0.10 mm
Wavelength:

μ:		 Mo Kα radiation (0.71073 Å)

0.17 mm−1
Diffractometer, scan mode:

θmax, completeness:		 Bruker APEX-II, φ and ω scans

27.5°, 99 %
N(hkl)measured, N(hkl)unique, Rint: 27117, 7343, 0.030
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 6,152
N(param)refined: 422
Programs: Bruker, 1 Olex2, 2 , 3 SHELX 4 , 5

1 Source of material

The title compound is a natural product, which has been obtained by extraction and isolation from fungal fermentation products. 6 All chemicals were of analytical grade and used as received without further purification. The preparation of the title compound is similar to the previously reported literature procedure. 6 Fluorescein hydrazide (200 mg, 577.46 μmol) and 5-chloro-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde (127.42 mg, 577.46 μmol) were mixed in ethanol (15 mL) with addition of a catalytic amount of acetic acid. The reaction mixture was refluxed at 78 °C for 2.5 h and the reaction was shown to be completed by thin layer chromatography (TLC). After cooling to room temperature, the solution was filtered, and the colorless crystals were obtained by slow evaporating in ethanol at room temperature.

2 Experimental details

The structure was treated with the Olex2 crystallographic software package, 2 , 3 solved with the SHELXT structure solution program and refined with the SHELXL refinement package. 4 , 5 Carbon-bound hydrogen atoms were placed in calculated positions and refined with riding coordinates, with Uiso(H) fixed at 1.2 times of Ueq(C) (Tables 1 and 2).

3 Comment

Fluorescein serves as an ideal fluorescent reporter for chemosensors due to its superior photophysical properties. 7 Moreover, certain fluorescein hydrazones derived from substituted benzaldehydes have demonstrated significant biological activity, by functioning as non-intercalative topoisomerase catalytic inhibitors. 8 Notably, fluorescein hydrazone derivatives incorporating aldehyde moieties have been developed as effective fluorescent probes for the detection of Hg2+, Zn2+ or Cu2+ ions. 9 , 10 , 11 Herein, we report the crystal structure of the title compound derived from fluorescein hydrazide and a substituted pyrazole-4-aldehyde, namely 5-chloro-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde.

The title compound C35H33ClN4O6 was crystallized in P21/c with one C31H21 ClN4O4 and two solvent molecules C2H6O in its asymmetric unit. The molecule structure comprises one xanthene ring and one 1-phenyl-1H-pyrazole moieties. The geometry of the title structure was characterized with the bond angles and lengths. In particular, the bond angles for C23⋯N4⋯N3, O1⋯C20⋯N1, and C22⋯C24⋯Cl1 are 106.14 (13)°, 125.74(14)° and 129.00(12)°, respectively. For another, the bond lengths for N2⋯C30, N2⋯N1, O1⋯C20, CI1⋯C24, N4⋯C23 and C22⋯C24, are 1.283(2) Å, 1.3661(17) Å, 1.2306(19) Å, 1.6973(16) Å, 1.324(2) Å and 1.377(2) Å. All bond angles and lengths of the title structure are within the expected range and comparable with those of reported fluorescein hydrazones 12 , 13 , 14 and a directly related spiro compound. 15 In the crystal, hydrazine molecules are arranged in layers by ethanol molecules via hydrogen bonds O–H⋯O and O–H⋯N, with max D–A distance 2.9 Å and minimum angle 120°.

Corresponding authors: Hong-lei Li and Fei-fei Li, Department of Pharmacy, Kangda College of Nanjing Medical University, Lianyungang 222000, People’s Republic of China, E-mail: (H.-l. Li), (F.-f. Li)

Acknowledgments

This work was supported by Jiangsu Provincial Drug Administration’s Scientific Research Program for Drugs (No. 202367), the Scientific Research Personnel Training Program of Kangda College of Nanjing Medical University (No. KD2022KYRC007), Science & Technology Funds of Kangda College of Nanjing Medical University (No. KD2023KYJJ017, KD2023KYJJ018 & KD2023KYJJ019), and the Science & Technology Funds of Lianyungang (No. JCYJ2320), Jiangsu Student’s foundation for innovation and entrepreneurship training program (No. 202413980013Y & 202413980053Y).

  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: 2025-05-20
Accepted: 2025-07-21
Published Online: 2025-07-31
Published in Print: 2025-10-27

© 2025 the author(s), published by De Gruyter, Berlin/Boston

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

Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of (S)-N-(10-((2,2-dimethoxyethyl)amino)-1,2,3-trimethoxy-9-oxo-5,6,7,9-tetrahydrobenzo[a]heptalen-7-yl)acetamide, C25H32N2O7
  4. The crystal structure of 6,6′-difluoro-3,3′-dimethyl-5,5′-di(10H-phenoxazin-10-yl)- [1,1′-biphenyl]-2,2′-dicarbonitrile, C40H24F2N4O2
  5. Crystal structure of poly[(di-ethylenediamine-κ2N,N′)cadmium(II) tetradedocyloxidohexavanadate] (V4+/V5+ = 2/1), C4H16CdN4O14V6
  6. The crystal structure of poly[bis(dimethylformamide-κ1N)-(μ4-2′,3,3″,5′-tetrakis(trifluoromethyl)-[1,1′:4′,1″-terphenyl]-4,4″-dicarboxylato-κ4 O,O′: O″,O‴)dicadmium(II)], C27H15CdF12NO5
  7. Crystal structure of bis(μ2-ferrocenylcarboxylato-O,O′)-(μ3-oxido-κ3O:O:O)-bis(μ2-salicyladoximato-κ2N,O,O′)-(μ2-isopropoxo)-tris(isopropoxy-κ1O trititanium(IV)), C48H55N2O13Fe2Ti3
  8. Crystal structure of 3-(diethylamino)-7,9,11-trimethyl-8-phenyl-6H,13H-12λ4,13λ4-chromeno[3′,4′:4,5]pyrrolo[1,2-c]pyrrolo[2,1-f][1,3,2]diazaborinin-6-one, C28H26BF2N3O2
  9. The crystal structure of catena-poly[aqua-μ2-2-nitro-benzene-1,3-dicarboxylato-κ2O,O′)-(1,10-phenanthroline-κ2N,N′)-zinc(II)], C20H13N3O7Zn
  10. Crystal structure of poly[diaqua-{μ3-1-(3-carboxylatophenyl)-4-oxo-1,4-dihydropyridazine-3-carboxylato-κ4O,O′:O′′:O′′′′}manganese(II)] hydrate
  11. Crystal structure of N′-((1-hydroxycyclohexyl)(phenyl)methyl)-2-methoxybenzohydrazide methanol solvate, C22H28N2O4
  12. The cocrystal of caffeic acid — progesterone — water (1/2/1), C51H70O9
  13. Crystal structure of (((oxido(quinolin-6-yl)methoxy)triphenyl-λ5-stibanyl)oxy)(quinolin-7-yl)methanolate
  14. Crystal structure of [(E)-6′-(diethylamino)-2-(2-(((E)-pyren-1-ylmethylene)amino)ethyl)-4′-(2-((E)-1,3,3-trimethylindolin-2-ylidene)ethylidene)-1′,2′,3′,4′-tetrahydrospiro[isoindoline-1,9′-xanthen]-3-one]-methanol, solvate C57H56N4O3
  15. The crystal structure of 1-(acridin-9-yl)pyrrolidine-2,5-dione, C17H22N2O2
  16. Crystal structure of N-(4-acetylphenyl)-2-(6-methoxynaphthalen-2-yl)propanamide, C22H21NO3
  17. The crystal structure of 5,10,15,20-tetrakis(4-(1H-1,2,4-triazol-1-yl)phenyl)porphyrin, C52H34N16
  18. Crystal structure of hexacarbonyl-μ2-[phenylmethanedithiolato-κ4S:S,S′:S′]diiron (Fe–Fe) C13H6Fe2O6S2
  19. Crystal structure of diiodo-bis(1-((2-propyl-1H-benzo[d]imidazol-1-yl)methyl)-1H-benzo[d][1,2,3]triazole-κ1N)cadmium(II), C34H34CdI2N10
  20. Crystal structure of (E)-(3-(3-bromophenyl)acryloyl)ferrocene, C19H15BrFeO
  21. Crystal structure of catena-poly(μ2-6-chloropyridine-2-carboxylato-κ3N,O:O′)(6-chloropyridine-2-carboxylato-κ2O,N)copper(II), C12H6Cl2N2O4Cu
  22. Crystal structure of poly[diaqua-μ 3-(5-(3,5-dicarboxy-2,4,6-trimethylbenzyl)-2,4,6-trimethylisophthalato)-κ 6O,O′:O″,O‴:O‴′,O‴″) terbium(III)-monohydrate], C23H28TbO12
  23. Crystal structure of (E)-2-(((5-chloro-3-methyl-1-phenyl-1H-pyrazol-4-yl)methylene)amino)-3′,6′-dihydroxyspiro[isoindoline-1,9′-xanthen]-3-one – ethanol (1/2), C35H33ClN4O6
  24. The crystal structure of 3-(5-amino-3-phenylisoxazol-4-yl)-4-chloro-3-hydroxyindolin-2-one, C17H12ClN3O3
  25. The crystal structure of dimethylammonium 4-[2-(4-fluorophenyl)-4, 5-diphenyl-1H-imidazol-1-yl]benzenesulfonate, C29H26FN3O3S
  26. Crystal structure of (R)-2-ammonio-3-((5-carboxypentyl)thio)propanoate
  27. Crystal structure of 4-cyclohexyl-5-(thiophen-2-yl)-2,4-dihydro-3H-1,2,4-triazole-3-thione, C12H15N3S2
  28. The crystal structure of 4,6-bis(dimethylamino)-2-fluoroisophthalonitrile, C12H13FN4
  29. Hydrogen bonding in the crystal structure of nicotin-1,1′-dium tetrabromidomanganate(II)
  30. The crystal structure of bis(2-bromobenzyl)(2-((2-oxybenzylidene)amino)-4-methylpentanoato-κ3N, O,O′)tin(IV), C27H27Br2NO3Sn
  31. Crystal structure of (E)-(3-(p-tolyl)acryloyl)ferrocene, C20H18FeO
  32. Crystal structure of (E)-7-fluoro-2-((5-(4-methylpiperazin-1-yl)pyridin-2-yl)methylene)-3,4-dihydronaphthalen-1(2H)-one, C21H22FN3O
  33. Crystal structure of (E)-7-methoxy-2-((5-(4-methylpiperazin-1-yl)pyridin-2-yl)methylene)-3,4-dihydronaphthalen-1(2H)-one, C22H25N3O2
  34. The crystal structure of poly(bis(μ2-1,3,5-tri(1H-imidazol-1-yl)benzene-κ2N:N′)-(μ2-2,3,5,6-tetrafluoroterephthalato-κ2O:O′)-manganese(II), C38H24F4N12O4Mn
  35. Crystal structure of (3,4-dimethoxybenzyl)triphenylphosphonium bromide ethanol solvate, C29H32BrO3P
  36. Crystal structure of tetraethylammonium hydrogencarbonate – (diaminomethylene)thiourea – water (2/1/3)
  37. Crystal structure of N, N-Dimethyl-N′-tosylformimidamide, C10H14N2O2S
  38. The crystal structure of ethyl 2-methyl-5-oxo-4-(2-methoxyphenyl)-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, C20H23N2O4
  39. Crystal structure of bis(μ2-1,5-bis[(E)-1-(2-hydroxyphenyl)ethylidene] thiocarbonohydrazide)-bis(dimethylformamide)-dizinc(II) dimethylformamide solvate, C40H46N10O6S2Zn2⋅C3H7NO
  40. Crystal structure of azido-κ1N{hydridotris(3-tert-butyl-5-methylpyrazol-1-yl)borato-κ3N,N′,N″}copper(II), C24H40BCuN9
  41. The crystal structure of fac-tricarbonyl(1,10-phenanthroline-κ2N,N′)-(azido-κ1N)rhenium(I), C15H8N5O3Re
  42. Crystal structure of 4-((triphenylphosphonio)methyl)pyridin-1-ium tetrachloridozincate(II), C24H22Cl4NPZn
https://doi.org/10.1515/ncrs-2025-0236
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of (S)-N-(10-((2,2-dimethoxyethyl)amino)-1,2,3-trimethoxy-9-oxo-5,6,7,9-tetrahydrobenzo[a]heptalen-7-yl)acetamide, C25H32N2O7
  4. The crystal structure of 6,6′-difluoro-3,3′-dimethyl-5,5′-di(10H-phenoxazin-10-yl)- [1,1′-biphenyl]-2,2′-dicarbonitrile, C40H24F2N4O2
  5. Crystal structure of poly[(di-ethylenediamine-κ2N,N′)cadmium(II) tetradedocyloxidohexavanadate] (V4+/V5+ = 2/1), C4H16CdN4O14V6
  6. The crystal structure of poly[bis(dimethylformamide-κ1N)-(μ4-2′,3,3″,5′-tetrakis(trifluoromethyl)-[1,1′:4′,1″-terphenyl]-4,4″-dicarboxylato-κ4 O,O′: O″,O‴)dicadmium(II)], C27H15CdF12NO5
  7. Crystal structure of bis(μ2-ferrocenylcarboxylato-O,O′)-(μ3-oxido-κ3O:O:O)-bis(μ2-salicyladoximato-κ2N,O,O′)-(μ2-isopropoxo)-tris(isopropoxy-κ1O trititanium(IV)), C48H55N2O13Fe2Ti3
  8. Crystal structure of 3-(diethylamino)-7,9,11-trimethyl-8-phenyl-6H,13H-12λ4,13λ4-chromeno[3′,4′:4,5]pyrrolo[1,2-c]pyrrolo[2,1-f][1,3,2]diazaborinin-6-one, C28H26BF2N3O2
  9. The crystal structure of catena-poly[aqua-μ2-2-nitro-benzene-1,3-dicarboxylato-κ2O,O′)-(1,10-phenanthroline-κ2N,N′)-zinc(II)], C20H13N3O7Zn
  10. Crystal structure of poly[diaqua-{μ3-1-(3-carboxylatophenyl)-4-oxo-1,4-dihydropyridazine-3-carboxylato-κ4O,O′:O′′:O′′′′}manganese(II)] hydrate
  11. Crystal structure of N′-((1-hydroxycyclohexyl)(phenyl)methyl)-2-methoxybenzohydrazide methanol solvate, C22H28N2O4
  12. The cocrystal of caffeic acid — progesterone — water (1/2/1), C51H70O9
  13. Crystal structure of (((oxido(quinolin-6-yl)methoxy)triphenyl-λ5-stibanyl)oxy)(quinolin-7-yl)methanolate
  14. Crystal structure of [(E)-6′-(diethylamino)-2-(2-(((E)-pyren-1-ylmethylene)amino)ethyl)-4′-(2-((E)-1,3,3-trimethylindolin-2-ylidene)ethylidene)-1′,2′,3′,4′-tetrahydrospiro[isoindoline-1,9′-xanthen]-3-one]-methanol, solvate C57H56N4O3
  15. The crystal structure of 1-(acridin-9-yl)pyrrolidine-2,5-dione, C17H22N2O2
  16. Crystal structure of N-(4-acetylphenyl)-2-(6-methoxynaphthalen-2-yl)propanamide, C22H21NO3
  17. The crystal structure of 5,10,15,20-tetrakis(4-(1H-1,2,4-triazol-1-yl)phenyl)porphyrin, C52H34N16
  18. Crystal structure of hexacarbonyl-μ2-[phenylmethanedithiolato-κ4S:S,S′:S′]diiron (Fe–Fe) C13H6Fe2O6S2
  19. Crystal structure of diiodo-bis(1-((2-propyl-1H-benzo[d]imidazol-1-yl)methyl)-1H-benzo[d][1,2,3]triazole-κ1N)cadmium(II), C34H34CdI2N10
  20. Crystal structure of (E)-(3-(3-bromophenyl)acryloyl)ferrocene, C19H15BrFeO
  21. Crystal structure of catena-poly(μ2-6-chloropyridine-2-carboxylato-κ3N,O:O′)(6-chloropyridine-2-carboxylato-κ2O,N)copper(II), C12H6Cl2N2O4Cu
  22. Crystal structure of poly[diaqua-μ 3-(5-(3,5-dicarboxy-2,4,6-trimethylbenzyl)-2,4,6-trimethylisophthalato)-κ 6O,O′:O″,O‴:O‴′,O‴″) terbium(III)-monohydrate], C23H28TbO12
  23. Crystal structure of (E)-2-(((5-chloro-3-methyl-1-phenyl-1H-pyrazol-4-yl)methylene)amino)-3′,6′-dihydroxyspiro[isoindoline-1,9′-xanthen]-3-one – ethanol (1/2), C35H33ClN4O6
  24. The crystal structure of 3-(5-amino-3-phenylisoxazol-4-yl)-4-chloro-3-hydroxyindolin-2-one, C17H12ClN3O3
  25. The crystal structure of dimethylammonium 4-[2-(4-fluorophenyl)-4, 5-diphenyl-1H-imidazol-1-yl]benzenesulfonate, C29H26FN3O3S
  26. Crystal structure of (R)-2-ammonio-3-((5-carboxypentyl)thio)propanoate
  27. Crystal structure of 4-cyclohexyl-5-(thiophen-2-yl)-2,4-dihydro-3H-1,2,4-triazole-3-thione, C12H15N3S2
  28. The crystal structure of 4,6-bis(dimethylamino)-2-fluoroisophthalonitrile, C12H13FN4
  29. Hydrogen bonding in the crystal structure of nicotin-1,1′-dium tetrabromidomanganate(II)
  30. The crystal structure of bis(2-bromobenzyl)(2-((2-oxybenzylidene)amino)-4-methylpentanoato-κ3N, O,O′)tin(IV), C27H27Br2NO3Sn
  31. Crystal structure of (E)-(3-(p-tolyl)acryloyl)ferrocene, C20H18FeO
  32. Crystal structure of (E)-7-fluoro-2-((5-(4-methylpiperazin-1-yl)pyridin-2-yl)methylene)-3,4-dihydronaphthalen-1(2H)-one, C21H22FN3O
  33. Crystal structure of (E)-7-methoxy-2-((5-(4-methylpiperazin-1-yl)pyridin-2-yl)methylene)-3,4-dihydronaphthalen-1(2H)-one, C22H25N3O2
  34. The crystal structure of poly(bis(μ2-1,3,5-tri(1H-imidazol-1-yl)benzene-κ2N:N′)-(μ2-2,3,5,6-tetrafluoroterephthalato-κ2O:O′)-manganese(II), C38H24F4N12O4Mn
  35. Crystal structure of (3,4-dimethoxybenzyl)triphenylphosphonium bromide ethanol solvate, C29H32BrO3P
  36. Crystal structure of tetraethylammonium hydrogencarbonate – (diaminomethylene)thiourea – water (2/1/3)
  37. Crystal structure of N, N-Dimethyl-N′-tosylformimidamide, C10H14N2O2S
  38. The crystal structure of ethyl 2-methyl-5-oxo-4-(2-methoxyphenyl)-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, C20H23N2O4
  39. Crystal structure of bis(μ2-1,5-bis[(E)-1-(2-hydroxyphenyl)ethylidene] thiocarbonohydrazide)-bis(dimethylformamide)-dizinc(II) dimethylformamide solvate, C40H46N10O6S2Zn2⋅C3H7NO
  40. Crystal structure of azido-κ1N{hydridotris(3-tert-butyl-5-methylpyrazol-1-yl)borato-κ3N,N′,N″}copper(II), C24H40BCuN9
  41. The crystal structure of fac-tricarbonyl(1,10-phenanthroline-κ2N,N′)-(azido-κ1N)rhenium(I), C15H8N5O3Re
  42. Crystal structure of 4-((triphenylphosphonio)methyl)pyridin-1-ium tetrachloridozincate(II), C24H22Cl4NPZn
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