Home Crystal structure of ethyl (E)-5-(((3′,6′-bis(ethylamino)-3-oxospiro[isoindoline-1,9′-xanthen]-2-yl)imino)methyl)-2,4-dimethyl-1H-pyrrole-3-carboxylate — ethanol (1/1), C38H45N5O5
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Crystal structure of ethyl (E)-5-(((3′,6′-bis(ethylamino)-3-oxospiro[isoindoline-1,9′-xanthen]-2-yl)imino)methyl)-2,4-dimethyl-1H-pyrrole-3-carboxylate — ethanol (1/1), C38H45N5O5

  • Xiao-Li Gao ORCID logo EMAIL logo , Shu-Shu Jia and Rui Su
Published/Copyright: February 17, 2021

Abstract

C38H45N5O5, triclinic, P1 (no. 2), a = 11.3541(16) Å, b = 12.1833(17) Å, c = 14.409(2) Å, α = 68.240(2)°, β = 76.613(3)°, γ = 88.873(3)°, V = 1796.0(4) Å3, Z = 2, Rgt(F) = 0.0620, wRref(F2) = 0.2023, T = 296 K.

CCDC no.: 2047043

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:Colorless block
Size:0.25 × 0.24 × 0.22 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.08 mm−1
Diffractometer, scan mode:Bruker APEX-II, φ and ω
θmax, completeness:25.0°, 99%
N(hkl)measured, N(hkl)unique, Rint:9253, 6305, 0.026
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 3251
N(param)refined:462
Programs:Bruker [1], SHELX [2], [3]
Table 2:

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

AtomxyzUiso*/Ueq
N1−0.0797 (2)0.0662 (2)0.38943 (18)0.0585 (7)
H1−0.07710.14230.36530.070*
N20.1181 (2)0.1667 (2)0.22061 (18)0.0557 (6)
N30.2141 (2)0.2195 (2)0.13828 (18)0.0524 (6)
N40.1356 (3)−0.1142 (3)−0.1069 (3)0.0922 (10)
H40.0951−0.0789−0.15180.111*
N50.6077 (3)−0.1031 (3)0.3494 (2)0.0888 (9)
H50.6450−0.06630.37610.107*
O1−0.1681 (2)−0.3258 (2)0.56339 (19)0.0960 (8)
O2−0.3029 (2)−0.2224 (2)0.6266 (2)0.1036 (9)
O30.1584 (2)0.40561 (19)0.12996 (18)0.0867 (8)
O40.3342 (2)−0.09311 (17)0.14233 (17)0.0679 (6)
O5−0.0600 (3)0.3229 (2)0.2949 (2)0.1240 (11)
H5Aa0.00720.32710.25670.186*
H5Bb0.00190.34270.24810.186*
C1−0.1859 (6)−0.5303 (4)0.6149 (5)0.211 (4)
H1A−0.1773−0.51120.54260.317*
H1B−0.2404−0.59980.65370.317*
H1C−0.1081−0.54510.63070.317*
C2−0.2336 (4)−0.4333 (3)0.6413 (3)0.1097 (15)
H2A−0.2229−0.44200.70850.132*
H2B−0.3196−0.43080.64340.132*
C3−0.2128 (3)−0.2240 (3)0.5655 (3)0.0704 (9)
C4−0.1380 (3)−0.1211 (3)0.4849 (2)0.0597 (8)
C5−0.0307 (3)−0.1178 (3)0.4081 (2)0.0568 (8)
C60.0027 (3)−0.0007 (3)0.3501 (2)0.0536 (8)
C7−0.1642 (3)−0.0053 (3)0.4708 (2)0.0590 (8)
C8−0.2611 (3)0.0442 (3)0.5301 (2)0.0728 (10)
H8A−0.25060.02300.59870.109*
H8B−0.33920.01250.53310.109*
H8C−0.25570.12890.49680.109*
C90.0355 (3)−0.2200 (3)0.3932 (2)0.0726 (9)
H9A0.0598−0.26650.45490.109*
H9B0.1062−0.19060.33710.109*
H9C−0.0169−0.26850.37800.109*
C100.1035 (3)0.0537 (3)0.2638 (2)0.0556 (8)
H100.15810.00710.23930.067*
C110.2259 (3)0.3413 (3)0.0970 (2)0.0613 (8)
C120.3318 (3)0.3756 (3)0.0089 (2)0.0586 (8)
C130.3817 (4)0.4868 (3)−0.0599 (3)0.0795 (10)
H130.34810.5551−0.05440.095*
C140.4827 (4)0.4933 (3)−0.1369 (3)0.0920 (12)
H140.51700.5669−0.18510.110*
C150.5334 (3)0.3911 (3)−0.1429 (3)0.0862 (11)
H150.60240.3972−0.19450.103*
C160.4836 (3)0.2806 (3)−0.0738 (2)0.0667 (9)
H160.51790.2124−0.07850.080*
C170.3823 (3)0.2738 (2)0.0019 (2)0.0517 (7)
C180.3113 (2)0.1623 (2)0.0850 (2)0.0482 (7)
C190.2605 (2)0.0870 (2)0.0376 (2)0.0513 (7)
C200.1984 (2)0.1355 (3)−0.0403 (2)0.0546 (8)
H200.18620.2159−0.06130.066*
C210.1544 (3)0.0715 (3)−0.0877 (2)0.0605 (8)
C220.1755 (3)−0.0493 (3)−0.0583 (3)0.0641 (9)
C230.2368 (3)−0.0999 (3)0.0187 (3)0.0638 (8)
H230.2505−0.18000.03940.077*
C240.2774 (3)−0.0316 (3)0.0645 (2)0.0545 (7)
C250.3975 (3)−0.0290 (3)0.1790 (2)0.0535 (7)
C260.4698 (3)−0.0941 (3)0.2420 (2)0.0631 (8)
H260.4740−0.17470.25550.076*
C270.5365 (3)−0.0399 (3)0.2853 (2)0.0621 (8)
C280.5296 (3)0.0819 (3)0.2635 (2)0.0613 (8)
C290.4573 (3)0.1431 (3)0.1992 (2)0.0564 (8)
H290.45400.22410.18400.068*
C300.3889 (2)0.0907 (2)0.1555 (2)0.0496 (7)
C310.0874 (3)0.1284 (3)−0.1694 (3)0.0815 (10)
H31A0.00680.0908−0.14760.122*
H31B0.12930.1198−0.23200.122*
H31C0.08300.2110−0.18100.122*
C320.1562 (4)−0.2349 (4)−0.0887 (4)0.1075 (14)
H32A0.2377−0.2487−0.07900.129*
H32B0.1515−0.2504−0.14920.129*
C330.0700 (4)−0.3182 (4)0.0009 (4)0.1278 (17)
H33A−0.0112−0.2971−0.00260.192*
H33B0.0857−0.31520.06260.192*
H33C0.0791−0.39690.00140.192*
C340.5948 (3)0.1427 (3)0.3128 (3)0.0869 (11)
H34A0.56150.11140.38590.130*
H34B0.58520.22630.28540.130*
H34C0.67960.12940.29850.130*
C350.6230 (4)−0.2283 (4)0.3744 (4)0.1064 (14)
H35A0.6985−0.24720.39560.128*
H35B0.6283−0.24640.31340.128*
C360.5228 (5)−0.3012 (5)0.4564 (4)0.1394 (19)
H36A0.4475−0.27940.43740.209*
H36B0.5221−0.28920.51870.209*
H36C0.5325−0.38320.46730.209*
C37a−0.2251 (11)0.4332 (15)0.3339 (12)0.178 (7)
H37Aa−0.27950.48420.29860.268*
H37Ba−0.20510.46240.38220.268*
H37Ca−0.26360.35450.37000.268*
C37Ab−0.179 (2)0.486 (2)0.2497 (18)0.226 (11)
H37Db−0.13020.53250.18280.339*
H37Eb−0.22590.53630.27920.339*
H37Fb−0.23290.43010.24360.339*
C38a−0.1137 (12)0.4308 (10)0.2588 (11)0.149 (6)
H38Aa−0.13290.44120.19400.178*
H38Ba−0.05680.49590.24660.178*
C38Ab−0.1000 (19)0.420 (2)0.3168 (15)0.164 (8)
H38Cb−0.03070.47260.30670.196*
H38Db−0.14450.39480.38830.196*
  1. aOccupancy: 0.560(16), bOccupancy: 0.440(16).

Source of material

Rhodamine 6 G hydrazide was condensed with equimolar ethyl 2,4-dimethyl-5-formylpyrrole-3-carboxylate in boiling ethanol and refluxed for 6 h. After cooling to room temperature, a white powder appeared, which was filtered off, washed with ethanol to receive the title compound. Yield: ca 80%. Single crystals of the title compound were obtained by recrystallization from ethanol solution.

Experimental details

The structure was solved by direct methods and refined with the SHELX crystallographic software package [3]. The C37/C38 atoms occupied two positions, with the occupancy value of C37(C38)/C37A(C38A) being 0.56/0.44. All hydrogen atoms were placed at calculated positions and refined as riding atoms with isotropic displacement parameters.

Comment

Rhodamine derivatives have attracted much attention in the design of chemosensors or chemodosimeters for metal ions [4]. Particularly, rhodamine hydrazones bearing a pyrrole unit may act as fluorescent probes for Cu2+ or Cd2+ [5], [6]. Herein, we report the crystal structure of the title compound derived from rhodamine 6 G hydrazide and a substituted pyrrole-2-aldehyde, which is related to the anticancer drug Sunitinib.

The asymmetric unit contains a neutral hydrazone molecule in a ring-closed form and one ethanol molecule. The C11=O3 bond distance is 1.229(3) Å, indicating the keto form of the amide. The bond length of C10–N2 is 1.279(4) Å, suggesting the existence of the Schiff base C=N moiety. All bond lengths are in the expected ranges [7], [8] and comparable with those of rhodamine 6 G hydrazones containing pyrrole ring [5], [6]. The benzamide and pyrrole ring are almost coplanar with the dihedral angle of 0.83°. The torsion angle of N1–C6–C10–N2 is −0.8(4)°, which reveals that the title compound might form chelate complexes with metal ions in this ring closed structure [6]. As expected, the intermolecular N–H…O, O–H…O and O–H…N hydrogen bonds are present between the hydrazone molecules and crystal ethanol molecules.


Corresponding author: Xiao-Li Gao, Department of Chemistry, Taiyuan Normal University, Jinzhong, 030619, P. R. China, E-mail:

Award Identifier / Grant number: 21671124

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

  2. Research funding: National Natural Science Foundation of China (grant no. 21671124).

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

References

1. Bruker. Smart and Saint; Bruker AXS Inc.: Madison, Wisconsin, USA, 2007.Search in Google Scholar

2. Sheldrick, G. M. SHELXT-integrated space-group and crystal-structure determination. Acta Crystallogr. 2015, A71, 3–8; https://doi.org/10.1107/s2053273314026370.Search in Google Scholar

3. Sheldrick, G. M. Crystal structure refinement with SHELX. Acta Crystallogr. 2015, C71, 3–8; https://doi.org/10.1107/s2053229614024218.Search in Google Scholar

4. Chen, X. Q., Pradhan, T., Wang, F., Kim, J. S., Yoon, J. Fluorescent chemosensors based on spiroring-opening of xanthenes and related derivatives. Chem. Rev. 2012, 112, 1910–1956; https://doi.org/10.1021/cr200201z.Search in Google Scholar

5. Puangploy, P., Smanmoo, S., Surareungchai, W. A new rhodamine derivative-based chemosensor for highly selective and sensitive determination of Cu2+. Sens. Actuators, B 2014, 193, 679–686; https://doi.org/10.1016/j.snb.2013.12.037.Search in Google Scholar

6. Wang, Y., Chang, H.-Q., Wu, W.-N., Peng, W.-B., Yan, Y.-F., He, C.-M., Chen, T.-T., Zhao, X.-L., Xu, Z.-Q. Rhodamine 6G hydrazone bearing pyrrole unit: ratiometric and selective fluorescent sensor for Cu2+ based on two different approaches. Sens. Actuators, B 2016, 228, 395–400; https://doi.org/10.1016/j.snb.2016.01.052.Search in Google Scholar

7. Yuan, J., Cheng, D. Crystal structure of (E)-3′,6′-bis(ethylamino)-2′,7′-dimethyl-2-((pyridin-2-ylmethylene)amino) spiro[isoindoline-1,9′-xanthen]-3-one, C32H31N5O2. Z. Kristallogr. NCS 2019, 234, 149–151.10.1515/ncrs-2018-0239Search in Google Scholar

8. Chu, Y., Li, K., Yang, H., Yuan, J. Crystal structure of (E)-3′,6′-bis(ethylamino)-2′,7′-dimethyl-2-(2-((quinolin-2-ylmethylene)amino) ethyl)spiro[isoindoline-1,9′-xanthen]-3-one, C38H37N5O2. Z. Kristallogr. NCS 2020, 235, 1175–1177; https://doi.org/10.1515/ncrs-2020-0233.Search in Google Scholar

Received: 2020-11-09
Accepted: 2020-11-29
Published Online: 2021-02-17
Published in Print: 2021-03-26

© 2020 Xiao-Li Gao et al., published by De Gruyter, Berlin/Boston

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

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