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BY 4.0 license Open Access Published by De Gruyter (O) November 25, 2021

Crystal structure of (4′E)-6′-(diethylamino)-2-[(E)-[(6-methylpyridin-2-yl)methylidene]amino]-4′-{2-[(2E)-1,3,3-trimethyl-2,3-dihydro-1H-indol-2-ylidene]ethylidene}-1′,2,2′,3,3′,4′-hexahydrospiro[isoindole-1,9′-xanthene]-3-one, C44H45N5O2

Kaihao Li, Jinping Wu, Hairong Lan, Junmin Wang and Juan Yuan ORCID logo

Abstract

C44H45N5O2, triclinic P 1 (no. 2), a = 11.2140(4) Å, b = 11.9932(5) Å, c = 14.2703(5) Å, α = 98.879(3)°, β = 102.025(3)°, γ = 91.122(3)°, Z = 2, V = 1851.98(12) Å3, R gt (F) = 0.0549, wR ref(F 2) = 0.1616, T = 293(2) K.

CCDC no.: 2119922

The asymmetric unit of the molecular structure is shown in the figure. 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: Yellow block
Size: 0.13 × 0.1 × 0.08 mm
Wavelength: Cu Kα radiation (1.54184 Å)
μ: 0.59 mm−1
Diffractometer, scan mode: Xcalibur, ω-scans
θ max, completeness: 67.1°, >99%
N(hkl)measuredN(hkl)uniqueR int: 13,570, 6625, 0.026
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 5090
N(param)refined: 476
Programs: CrysAlisPRO [1], OLEX2 [2], SHELX [3, 4]

Table 2:

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

Atom x y z U iso*/U eq
Cl1 −0.32807 (8) −0.58567 (6) −0.37764 (7) 0.01860 (19)
S1 −0.08434 (7) −0.51774 (6) −0.83804 (6) 0.01273 (18)
O1 0.76362 (15) 0.76100 (12) 0.06274 (10) 0.0535 (4)
O2 0.85795 (16) 1.10183 (16) 0.46464 (11) 0.0687 (5)
N1 0.79305 (15) 0.98582 (14) 0.31579 (12) 0.0444 (4)
N2 0.68178 (15) 0.95996 (14) 0.33397 (12) 0.0441 (4)
N3 0.40401 (16) 0.80511 (15) 0.22073 (14) 0.0528 (4)
N4 0.44883 (18) 0.68512 (15) −0.35587 (13) 0.0563 (5)
N5 0.9405 (2) 0.46757 (17) 0.22652 (16) 0.0699 (6)
C1 0.92517 (19) 0.77190 (18) 0.31349 (15) 0.0489 (5)
H1 0.9508 0.8226 0.3709 0.059*
C2 0.9486 (2) 0.6599 (2) 0.31324 (16) 0.0545 (5)
H2 0.9880 0.6366 0.3705 0.065*
C3 0.9139 (2) 0.57940 (18) 0.22766 (16) 0.0503 (5)
C4 0.8517 (2) 0.61967 (17) 0.14512 (15) 0.0478 (5)
H4 0.8261 0.5697 0.0873 0.057*
C5 0.82739 (18) 0.73266 (16) 0.14808 (14) 0.0424 (4)
C6 0.86455 (17) 0.81227 (16) 0.23110 (13) 0.0410 (4)
C7 0.84398 (17) 0.93617 (16) 0.22998 (14) 0.0414 (4)
C8 0.76765 (18) 0.95574 (16) 0.13445 (14) 0.0425 (4)
C9 0.73562 (18) 0.87235 (16) 0.05851 (14) 0.0425 (4)
C10 0.66598 (19) 0.88652 (17) −0.03697 (14) 0.0444 (4)
C11a 0.6399 (3) 1.0058 (4) −0.0550 (3) 0.0500 (9)
H11Aa 0.5561 1.0202 −0.0512 0.060*
H11Ba 0.6489 1.0127 −0.1201 0.060*
C12a 0.7250 (3) 1.0940 (2) 0.0179 (2) 0.0592 (8)
H12Aa 0.6969 1.1688 0.0108 0.071*
H12Ba 0.8065 1.0904 0.0049 0.071*
C13a 0.7291 (3) 1.0738 (3) 0.1218 (3) 0.0506 (9)
H13Aa 0.7863 1.1288 0.1668 0.061*
H13Ba 0.6490 1.0838 0.1366 0.061*
C14 0.87521 (19) 1.05826 (18) 0.38669 (15) 0.0477 (5)
C15 0.98309 (19) 1.07136 (17) 0.34444 (15) 0.0469 (5)
C16 0.96482 (18) 1.00598 (16) 0.25407 (15) 0.0449 (4)
C17 1.0477 (2) 1.01039 (19) 0.19607 (17) 0.0549 (5)
H17 1.0349 0.9671 0.1345 0.066*
C18 1.1515 (2) 1.0818 (2) 0.2325 (2) 0.0648 (6)
H18 1.2082 1.0875 0.1941 0.078*
C19 1.1722 (2) 1.1444 (2) 0.3245 (2) 0.0645 (6)
H19 1.2435 1.1899 0.3479 0.077*
C20 1.0885 (2) 1.1404 (2) 0.38217 (18) 0.0590 (6)
H20 1.1019 1.1825 0.4442 0.071*
C21 0.60486 (18) 0.89185 (16) 0.27227 (14) 0.0440 (4)
H21 0.6250 0.8557 0.2156 0.053*
C22 0.48291 (18) 0.87134 (16) 0.29230 (15) 0.0441 (4)
C23 0.4531 (2) 0.9201 (2) 0.37763 (17) 0.0550 (5)
H23 0.5105 0.9659 0.4251 0.066*
C24 0.3372 (2) 0.9001 (2) 0.39181 (19) 0.0654 (6)
H24 0.3149 0.9322 0.4488 0.078*
C25 0.2562 (2) 0.8323 (2) 0.3205 (2) 0.0681 (7)
H25 0.1777 0.8169 0.3288 0.082*
C26 0.2905 (2) 0.7865 (2) 0.2363 (2) 0.0605 (6)
C27 0.2009 (3) 0.7154 (3) 0.1537 (3) 0.0877 (9)
H27A 0.1378 0.7616 0.1269 0.132*
H27B 0.1652 0.6550 0.1775 0.132*
H27C 0.2428 0.6844 0.1042 0.132*
C28 0.62053 (19) 0.79443 (17) −0.10326 (15) 0.0467 (5)
H28 0.6341 0.7251 −0.0825 0.056*
C29 0.55418 (19) 0.78962 (17) −0.20126 (15) 0.0475 (5)
H29 0.5438 0.8568 −0.2262 0.057*
C30 0.50555 (19) 0.69196 (18) −0.25982 (15) 0.0468 (5)
C31 0.4975 (2) 0.57305 (19) −0.23282 (17) 0.0567 (6)
C32 0.4280 (2) 0.5057 (2) −0.32771 (18) 0.0601 (6)
C33 0.4040 (2) 0.57556 (19) −0.39718 (17) 0.0563 (6)
C34 0.3449 (2) 0.5340 (2) −0.49186 (19) 0.0703 (7)
H34 0.3297 0.5806 −0.5389 0.084*
C35 0.3091 (3) 0.4192 (3) −0.5136 (2) 0.0839 (9)
H35 0.2689 0.3889 −0.5765 0.101*
C36 0.3316 (3) 0.3502 (2) −0.4449 (3) 0.0910 (10)
H36 0.3068 0.2740 −0.4615 0.109*
C37 0.3913 (3) 0.3930 (2) −0.3506 (2) 0.0811 (9)
H37 0.4063 0.3463 −0.3036 0.097*
C38 0.4262 (3) 0.5702 (3) −0.1531 (2) 0.0877 (10)
H38A 0.4709 0.6139 −0.0937 0.132*
H38B 0.4144 0.4935 −0.1439 0.132*
H38C 0.3482 0.6014 −0.1717 0.132*
C39 0.6239 (3) 0.5242 (2) −0.2061 (2) 0.0848 (10)
H39A 0.6714 0.5377 −0.2523 0.127*
H39B 0.6140 0.4443 −0.2069 0.127*
H39C 0.6649 0.5601 −0.1423 0.127*
C40 0.4376 (3) 0.7785 (2) −0.40894 (19) 0.0762 (8)
H40A 0.3669 0.8186 −0.3990 0.114*
H40B 0.4294 0.7506 −0.4769 0.114*
H40C 0.5092 0.8285 −0.3863 0.114*
C41 1.0005 (3) 0.4261 (2) 0.3139 (2) 0.0766 (8)
H41A 1.0610 0.4831 0.3525 0.092*
H41B 1.0429 0.3591 0.2957 0.092*
C42 0.9129 (4) 0.3977 (3) 0.3746 (3) 0.1156 (14)
H42A 0.8570 0.3368 0.3387 0.173*
H42B 0.8682 0.4628 0.3907 0.173*
H42C 0.9576 0.3753 0.4332 0.173*
C43 0.9177 (3) 0.3855 (2) 0.1378 (2) 0.0679 (7)
H43A 0.8492 0.4081 0.0922 0.081*
H43B 0.8950 0.3127 0.1523 0.081*
C44 1.0243 (4) 0.3734 (4) 0.0915 (3) 0.1162 (14)
H44A 1.0063 0.3139 0.0365 0.174*
H44B 1.0938 0.3556 0.1374 0.174*
H44C 1.0418 0.4431 0.0704 0.174*
C12Ab 0.6581 (17) 1.0873 (12) 0.0434 (11) 0.0592 (8)
H12Cb 0.5822 1.0633 0.0585 0.071*
H12Db 0.6516 1.1647 0.0316 0.071*
C13Ab 0.763 (2) 1.0818 (15) 0.129 (2) 0.0506 (9)
H13Cb 0.8395 1.1111 0.1180 0.061*
H13Db 0.7476 1.1241 0.1887 0.061*
C11Ab 0.678 (2) 1.012 (2) −0.0473 (17) 0.0500 (9)
H11Cb 0.7590 1.0293 −0.0575 0.060*
H11Db 0.6187 1.0267 −0.1033 0.060*

  1. aOccupancy: 0.830(5), bOccupancy: 0.170(5).

Source of materials

All reagents and starting materials were commercially available and used as received. The title compound was synthesized according to the literature method [5], [6], [7]. The title compound was obtained from cyclohexanone by a four-step reaction.

First step: Cyclohexanone (1.98 mL) was added dropwise to concentrated sulfuric acid (20.0 mL) under ice-bath condition. Then, 2-(4-diethylamino-hydroxybenzoyl) benzoic acid (3.00 g, 9.6 mmol) was added in portions under vigorous stirring. After the addition was completed, the reaction mixture was heated at 90 °C for 3 h, cooled down and poured onto ice (150.0 g). Perchloric acid (2.0 mL, 70%) was then added and the resulting precipitate was filtered, washed several times with cold water and dried in the air to give a red solid. Yield: ca. 94%.

Both the red solid (2.5 g, 6.65 mmol) obtained in the first step and equal number of moles of fisher aldehyde (1.34 g, 6.65 mmol) were dissolved directly in acetic anhydride (35.0 mL), refluxed for 0.5 h under stirring. After that, the resulting mixture was put into the refrigerator immediately to stop the reaction and then distilled under reduced pressure to obtain a dark-green solid. The dark-green solid was further purified by silica gel chromatography (CH2Cl2/CH3CH2OH = 200:1, 20:1 v/v) to give green microcrystalline, the intermediate of the second step. Yield: ca. 50%.

The green microcrystalline (1.2 g, 2.15 mmol), PyBOP (1.4 g, 2.68 mmol) and hydrazine hydrate (2.4 mL) were dispersed in CH2Cl2 (25 mL), and stirred at room temperature for 4 h. Then, the resulting mixture was distilled under reduced pressure to give a crude product, which was further purified by neutral alumina column chromatography (CH2Cl2/CH3CH2OH = 200:1, 50:1 v/v) to yield yellow powder, the intermediate of the third step. Yield: ca. 45%.

The ethanol solution of the yellow powder (0.5 g, 0.87 mmol) obtained from the above step and the ethanol solution of 6-methyl-2-pyridine carboxaldehyde (0.16 g, 1.31 mmol) were mixed and refluxed for 10 h. Then, the resulting mixture was concentrated by vacuum distillation to give the crude product of the title compound, which was further purified by neutral alumina column chromatography (CH2Cl2/CH3CH2OH = 200:1, 50:1 v/v) to give a yellow powder product, the title compound. Yield: ca. 20%.

Single crystals of the title compound were grown from a methanol solution by slow evaporation at room temperature. About one week later, light yellow block crystals were appeared. Yield: ca. 75%.

Experimental details

The H atoms were added using riding models. Their U iso values were set to 1.2 U eq of the parent atoms.

Comment

Rhodamine fluorescent dyes based on xanthene are widely used as fluorescent probes to track target molecules, because of the advantages of large molar extinction coefficient, high fluorescence quantum efficiency and good optical stability [8, 9]. At present, most of fluorescent probes based on xanthene are mainly concentrated in the visible region. Visible light imaging technology has some problems such as strong background fluorescence, photobleaching, phototoxicity and limited tissue penetration, which limits the application of fluorescent probes in chemical biology and clinical diagnostics. While near-infrared fluorescent probes have many advantages, such as long emission wavelength, little damage to cells, strong tissue penetration and low spontaneous emission background, which is widely used in detection, tracing and imaging of biomolecules in complex biological systems such as cells and tissues [1013]. In this work, a near-infrared rhodamine-derived compound was reported, which may be a potential near-infrared fluorescent probe for the good coordination ability to transition metal ions and rare-earth metal ions [14, 15].

The asymmetric unit of the title compound contains one molecule in a ring-closed form (see the figure). The amide C=O bond distance is 1.209(3) Å, indicative of the keto form of the amide. The bond length of C21–N2 is 1.273(3) Å, which shows the existence of the Schiff base C=N [16]. The dihedral angle between the aroylhydrozone plane and the pyridyl plane is 8.62°. While, the xanthene least-square plane and pyridylaroyl hydrozone group are almost perpendicular, the dihedral angle is 82.97°. All geometric parameters are in the expected ranges.


Corresponding authors: Junmin Wang and Juan Yuan, Henan University of Chinese Medicine, Zhengzhou 450046, P. R. China, E-mail: , (J. Yuan)

Funding source: National Natural Science Foundation of China

Award Identifier / Grant number: 22101076

Award Identifier / Grant number: 21771115

Funding source: Natural Science Foundation of Henan

Award Identifier / Grant number: 202300410261

Funding source: Henan University of Chinese Medicine

Award Identifier / Grant number: BSJJ2020-01

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

  2. Research funding: This work was supported by the National Natural Science Foundation of China (Project Nos. 22101076 and 21771115), the Natural Science Foundation of Henan, China (Project No. 202300410261) and the Startup Foundation for Doctors of Henan University of Chinese Medicine (Project No. BSJJ2020-01).

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

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Received: 2021-09-17
Accepted: 2021-11-02
Published Online: 2021-11-25
Published in Print: 2022-02-23

© 2021 Kaihao Li et al., published by De Gruyter, Berlin/Boston

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