Home Physical Sciences 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
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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

  • Bin Zhang , Jing Wang , Jinping Wu , Yixin Chu and Yan Wan ORCID logo EMAIL logo
Published/Copyright: August 19, 2025
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 240 Issue 5

Abstract

C57H56N4O3, monoclinic, P21/c (no. 14), a = 10.1943(2) Å, b = 25.1257(4) Å, c = 18.6057(3) Å, β = 105.462(2)°, Z = 4, V = 4593.16(14) Å3 R gt (F) = 0.0603, wR ref (F2) = 0.1869, T = 173(10) K.

CCDC no.: 2441233

The molecular structure is shown in the figure. Table 1 contains the crystallographic data. 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: Clear light yellow block
Size: 0.20 × 0.15 × 0.10 mm
Wavelength: Cu Kα radiation (1.54184 Å)
μ: 0.59 mm−1
Diffractometer, scan mode: Rigaku SuperNova, ω scan
θmax, completeness: 65.1°, 99 %
N(hkl)measured, N(hkl)unique, Rint: 29090, 7712, 0.029
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 6,280
N(param)refined: 593
Programs: Rigaku, 1 Olex2, 2 SHELX 3 , 4

1 Source of materials

All reagents were used without further purification. The title compound was synthesized via a four-step process as described in the literature. 5 , 6 , 7

Synthesis of intermediate 1: Under ice-bath conditions, cyclohexanone (0.99 mL, 4.8 mmol) was carefully dripped into concentrated sulfuric acid (10.0 mL). Subsequently, 4-diethylaminolevulinic acid (1.50 g, 4.8 mmol) was slowly added under vigorous stirring. After addition, the mixture was heated to 363 K and maintained about 4 h to promote the reaction. Then, the reaction mixture was cooled and poured into crushed ice (100.0 g). When perchloric acid (1.5 mL, 70 %) was added, a red precipitate appeared immediately, which was filtered, washed with cold water for three times and air-dried to yield a red solid, yielding 80 %, named intermediate 1. Intermediate 1 was used without further purification.

Synthesis of intermediate 2: Equimolar amounts of intermediate 1 (1.25 g, 3.33 mmol) and 2-(1,3,3–trimethylindolin-2-ylidene)acetaldehyde (0.67 g, 3.33 mmol) were successively dissolved in acetic anhydride (20.0 mL) and stirred for 30 min at room temperature. The reaction was promptly quenched by cooling it to 273 K. Then, the crude product was filtered and purified by column chromatography, ethanol-dichloromethane (CH2Cl2/CH3CH2OH = 200:1∼20:1 v/v) as the gradient eluent. At last, a dark green solid was obtained, named intermediate 2, yielding 42 %.

Synthesis of intermediate 3: Intermediate 2 (1.2 g, 2.15 mmol), PyBOP (1.4 g, 2.68 mmol) and ethylenediamine (1.07 mL, 16 mmol) were successively dissolved in dichloromethane (25 mL). And then, the mixture was stirred 10 h at room temperature. Next, the mixture was distilled under reduced pressure to obtain the crude product. Purification was performed by column chromatography, using ethanol-dichloromethane (CH2Cl2/CH3CH2OH = 200:1∼50:1 v/v) as the gradient eluent. A yellow powder was collected, which was identified as intermediate 3, yielding 30 %.

Synthesis of the title compound: Intermediate 3 (0.42 g, 0.734 mmol) and 1-pyrenecarboxaldehyde (0.25 g, 1.1 mmol) were dissolved in ethanol (20 mL) and refluxed for 3 h, during which a yellow precipitate formed. Then, the precipitate was filtered and washed thoroughly with cold water for three times and purified through column chromatography using a mixture of ethanol and dichloromethane (CH2Cl2/CH3CH2OH = 200:1∼50:1 v/v) as the eluent. The yellow powder was collected and labeled as the title compound, yielding 32 %.

2 Experimental details

The H atoms were added using riding models. Their Uiso values were set to 1.2 Ueq of the parent atoms.

3 Comment

Pyrene-based fluorophores constitute structurally versatile systems endowed with inherent chemical stability, extended radiative lifetimes, and superior quantum efficiencies. While extensive investigations have established their prominence in visible-range sensing applications, systematic exploration of near-infrared (NIR) emissive pyrene derivatives remains limited. 8 , 9 , 10 Expanding the π-conjugated system drives NIR fluorophore design. Yuan et al. pioneered xanthene-hemicyanine hybrids inducing bathochromism via extended conjugation, advancing NIR dyes. 11 , 12 , 13 Building on this, we engineered pyrene-integrated hemicyanine-xanthene fluorophores with NIR emission. 14 However, The study found that this dye exhibits low sensitivity in metal ion binding. Prompting structural optimization through precise modulation of the xanthene-pyrene interchromophoric distance. This rational design approach yielded the title compound. Cu2+ homeostasis dysfunction, implicated in Alzheimer’s, Parkinson’s, and Wilson’s diseases, drives demand for specific probes. 15 Given the potential of the title compound to bind selectively to Cu2+, it may act as a valuable Cu2+ probe, facilitating the visualization of copper dynamics in vivo and offering critical insights for disease diagnosis and therapeutic intervention.

The title compound crystallizes within the monoclinic system, belonging to the space group P21/c. The asymmetric unit of the title compound comprises a title neutral molecule and a methanol molecule. The bond lengths and angles within the crystal structure are within normal ranges. The disordered treatment was applied to the C37, revealing a statistical coexistence of two conformational states with refined occupancies of 0.837(11) and 0.163(11), respectively. Notably, the dihedral angles between the xanthene and pyrene moieties in the current structure are measured at 83.0°, and the dihedral angle between the plane of the spirolactam and the pyrene plane is merely 22.3°. In contrast, angular parameters for the previously synthesized analogs were reported as 68.6° (xanthene-pyrene) and 26.3° (spirolactam-pyrene), 14 demonstrating substantial conformational modifications in the newly designed compound. This implies that the coordination of the N and O atoms on the title compound with copper ions may trigger the ring-opening of the spirolactam, thereby conferring the compound with the ability to release near-infrared fluorescence. 16 The C17=N1 bond distance, measured as 1.255(4) Å, aligns well with the C=N double bond length of Schiff bases as reported in the literature. 12 , 14

Corresponding authors: Yan Wan and Yixin Chu, Henan University of Chinese Medicine, Zhengzhou 450046, P.R. China, E-mail: (Y. Wan), (Y. Chu)
Bin Zhang and Jing Wang contributed equally to this manuscript.

Acknowledgments

This work was supported by the National Natural Science Foundation of China (Project No.22101076), the Natural Science Foundation of Henan, China (Project No.252300420129). The authors extend their gratitude to Mr. Tian gaofeng from Scientific Compass (www.shiyanjia.com) for providing invaluable assistance with the X-ray diffraction analysis.

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Received: 2025-05-06
Accepted: 2025-08-06
Published Online: 2025-08-19
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-2025-0224
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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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