Home Physical Sciences 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
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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

  • Yi-Xin Chu ORCID logo EMAIL logo , Kai-Hao Li , Han-Huan Yang and Juan Yuan
Published/Copyright: June 10, 2020

Abstract

C38H37N5O2, monoclinic, P21/n (no. 14), a = 13.3575(2) Å, b = 16.6645(3) Å, c = 13.7678(2) Å, β = 96.4890(14)°, Z = 4, V = 3045.03(8) Å3, Rgt(F) = 0.0386, wRref(F2) = 0.1028, T = 116.2(4) K.

CCDC no.: 2007137

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 cube
Size:0.30 × 0.20 × 0.10 mm
Wavelength:Cu Kα radiation (1.54184 Å)
μ:0.65 mm−1
Diffractometer, scan mode:SuperNova, ω
θmax, completeness:71.6°, >99%
N(hkl)measured, N(hkl)unique, Rint:11880, 5759, 0.023
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 5054
N(param)refined:414
Programs:CrysAlisPRO [1], Olex2 [2], SHELX [3], [4]
Table 2:

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

AtomxyzUiso*/Ueq
O10.59614(7)0.11687(6)0.53780(7)0.0331(2)
O20.41186(7)0.45797(5)0.58019(6)0.0264(2)
N10.47335(9)0.20742(7)0.13535(8)0.0288(3)
N20.61712(9)0.26583(7)0.35445(8)0.0282(2)
N30.52523(7)0.24299(6)0.54671(7)0.0199(2)
N40.57996(9)0.48079(7)0.90132(7)0.0262(2)
H40.60900.45780.95300.031*
N50.23128(9)0.46204(6)0.26281(7)0.0261(2)
H50.20980.43630.21040.031*
C10.47825(11)0.16150(8)0.05360(9)0.0287(3)
C20.40078(12)0.16887(9)−0.02498(11)0.0366(3)
H20.34510.2011−0.01820.044*
C30.40725(14)0.12901(10)−0.11058(11)0.0431(4)
H30.35590.1344−0.16180.052*
C40.49045(14)0.08003(10)−0.12227(11)0.0429(4)
H4A0.49510.0546−0.18180.051*
C50.56448(12)0.06950(9)−0.04686(11)0.0383(4)
H5A0.61830.0356−0.05470.046*
C60.56065(11)0.10949(8)0.04333(10)0.0304(3)
C70.63411(11)0.10017(9)0.12475(11)0.0334(3)
H70.6878(13)0.0623(11)0.1201(12)0.039(4)*
C80.62715(11)0.14457(9)0.20696(10)0.0309(3)
H80.67410.13850.26170.037*
C90.54701(10)0.20002(8)0.20729(9)0.0268(3)
C100.54393(10)0.25788(8)0.28808(9)0.0271(3)
H100.48670.28940.29030.032*
C110.60798(10)0.32734(8)0.42799(9)0.0270(3)
H11A0.54430.35520.41360.032*
H11B0.66180.36620.42660.032*
C120.61351(9)0.28921(8)0.52919(9)0.0239(3)
H12A0.67200.25430.53800.029*
H12B0.62340.33130.57790.029*
C130.52623(9)0.16105(8)0.55297(9)0.0230(3)
C140.42819(9)0.13739(7)0.58508(8)0.0223(3)
C150.38985(10)0.06102(8)0.59813(9)0.0282(3)
H150.42550.01530.58410.034*
C160.29671(11)0.05547(8)0.63279(10)0.0309(3)
H160.26930.00530.64280.037*
C170.24373(10)0.12434(9)0.65275(10)0.0302(3)
H170.18160.11940.67660.036*
C180.28196(10)0.20052(8)0.63763(9)0.0257(3)
H180.24590.24640.65030.031*
C190.37501(9)0.20605(7)0.60335(8)0.0200(2)
C200.43277(9)0.28105(7)0.57964(8)0.0192(2)
C210.46151(9)0.33441(7)0.66727(8)0.0194(2)
C220.50652(9)0.30226(7)0.75580(8)0.0198(2)
H220.51020.24670.76200.024*
C230.54560(9)0.34837(7)0.83398(8)0.0202(2)
C240.53838(9)0.43341(7)0.82541(8)0.0205(2)
C250.49035(9)0.46671(7)0.73975(9)0.0225(3)
H250.48240.52200.73450.027*
C260.45421(9)0.41735(7)0.66202(8)0.0212(2)
C270.37174(9)0.41307(7)0.50106(8)0.0210(2)
C280.32571(9)0.45790(8)0.42324(9)0.0230(3)
H280.32450.51360.42740.028*
C290.28136(9)0.41976(7)0.33887(8)0.0208(2)
C300.28619(9)0.33459(7)0.33325(8)0.0207(2)
C310.33254(9)0.29329(7)0.41238(8)0.0204(2)
H310.33480.23760.40860.024*
C320.37660(9)0.33006(7)0.49832(8)0.0195(2)
C330.59719(10)0.31104(8)0.92559(9)0.0244(3)
H33A0.56040.32360.97960.037*
H33B0.66450.33170.93810.037*
H33C0.59970.25390.91760.037*
C340.57705(9)0.56747(8)0.89810(9)0.0235(3)
H34A0.50800.58570.89750.028*
H34B0.60210.58610.83860.028*
C350.64094(10)0.60239(8)0.98604(10)0.0285(3)
H35A0.71000.58710.98420.043*
H35B0.61770.58231.04490.043*
H35C0.63560.65980.98470.043*
C360.24188(10)0.29165(8)0.24233(9)0.0251(3)
H36A0.27980.30470.18930.038*
H36B0.17310.30800.22620.038*
H36C0.24440.23480.25350.038*
C370.21261(10)0.54752(8)0.26584(9)0.0246(3)
H37A0.27550.57640.26490.030*
H37B0.18480.56100.32590.030*
C380.13987(12)0.57220(9)0.17922(11)0.0361(3)
H38A0.16910.56150.12000.054*
H38B0.12570.62850.18330.054*
H38C0.07840.54230.17920.054*

Source of material

All reagents and starting materials were commercially available and used as received. The title compound was synthesized from rhodmine 6G by a simple two-step Schiff base condensation reaction according to the literature [5], [6]. In first step, the intermediate rhodmine 6G amide was prepared by Schiff base condensation reaction between rhodmine 6G and ethylenediamine. The title compound was got by mixing an equimolar 2-quinolinecarbaldehyde and rhodmine 6G amide obtained in the first step.

Rhodmine 6G (5 mmol, 2.395 g) was dissolved in ethanol (60 mL). An excess of ethylenediamine (3.0 mL) was then added dropwise under vigorous stirring at room temperature. After addition, the stirred mixture was heated to reflux for 6 h, during which the white precipitate appeared. The resulting precipitate was filtered and washed several times with ethanol-water (1:1, v/v) to obtain a white powder of the intermediate rhodamine 6G amide. Yield: ca. 80%.

The intermediate rhodmine 6G amide was condensed with equimolar 2-quinolinecarbaldehyde in boiling ethanol and refluxed for 6 h, during which a yellow powder appeared. The yellow powder was filtered off, washed with ethanol-water (1:1, v/v) to obtain the crude product of the title compound, which was purified by recrystallization. Yield: ca. 85%. Single crystals of the title compound were grown from a CH2Cl2/CH3OH (1:1, v/v) solution by slow evaporation at room temperature. About one week later, light yellow cube crystals were obtained. Yield: ca. 60%.

Experimental details

The H atoms were added geometrically using riding models and refined isotropically. Their Uiso values were set to 1.2Ueq of the parent C and N atoms, and 1.5Ueq of the parent O atoms.

Comment

It is well known that quinoline skeleton and its derivatives are important units existing widely in alkaloids. Quinoline derivatives have attracted much attention due to their potential functions in molecular probes, protein binding activities and anticancer activities etc. [7], [8], [9], [10].

The title compound is probably the potential fluorescent probe, anticancer active substance or valuable ligand for transition metals. The asymmetric unit contains a neutral molecule in a ring-closed form. The amide C=O bond distance is 1.2255(16) Å, indicative of the keto form of the amide. The dihedral angle between the least-square plane of the benzamide and quinoline is 81.68°, which indicates that it is difficult for title compound to form chelate complexes in this ring-closed structure. The bond length of C10—N2 is 1.2675(17) Å, which shows the existence of the Schiff base C=N moiety. The hydrogen bond between adjacent molecules is very weak. Bond lengths are all in the expected ranges [11]. There are also no obvious pi-pi contacts.

References

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Received: 2020-05-16
Accepted: 2020-06-02
Published Online: 2020-06-10
Published in Print: 2020-08-26

©2020 Yi-Xin Chu 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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  60. Crystal structure of tetrakis(1H-benzo[d]imidazol-3-ium) bis(μ5-phenylphosphonato)-pentakis(μ2-oxido)-decaoxo-penta-molybdenum dihydrate, C40H42Mo5N8O23P2
  61. Structure of 7-(3,3,4,4,5,5-hexafluoro-2-(2-methylbenzo[b]thiophen-3-yl)cyclopent-1-en-1-yl)-8-methylquinoline, C24H15F6NS
  62. Crystal structure of monocarbonyl[2-((cyclopentylmethylene)amino)-5-methylphenolato-κ2N,O] (tricyclohexylphosphine)rhodium(I), C32H48NO2PRh
  63. The crystal structure of fac-tricarbonyl(1,10-phenanthroline-κ2N,N′)-(pyrazole-κN)rhenium(I)nitrate, C18H12O3N4Re
  64. Crystal structure of poly[diaqua-bis(μ2-4-(3-(pyridin-3-yl)-1H-1,2,4-triazol-5-yl)benzoato-κ2N:O)nickel(II)], C28H22O6N8Ni
  65. Crystal structure of 4,4′-bis(pyridin-1-ium-4-yl)biphenyl poly[bis(μ2-4,4′-bis(pyrid-4-yl)biphenyl-K2N:N′)-tetrakis(μ4-4′-methyl-[1,1′-biphenyl]-3,5-dicarboxylato-K4O,O′:O′′:O′′′)-bis[[μ2-1,1′-biphenyl]-3-carboxyl-5-carboxylato-K2O:O′]tetracobalt(II)]— [1,1′-biphenyl]-3,5-dicarboxylic acid (1/2), C93H68N3O16Co2
  66. The crystal structure of 4a-formyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydro-1-2-6a,6b,9,9,12a-heptamethylpicen-10-yl acetate, C32H50O3
  67. Crystal structure of 3,3′-(1,2-phenylenebis(methylene))bis(1-methyl-1H-imidazol-3-ium) bis(hexafluoridophosphate), C16H20F12N4P2
  68. Crystal structure of catena-poly[diaqua-(μ2-tartrato-κ4O,O′:O′′,O′′′)zinc(II)], C4H8O8Zn
  69. The crystal structure of (6aR,6bS,8aS,8bR,9S,11aS,12aS,12bS)-10-(4-acetoxy-3-methylbutyl)-6a,8a,9-trimethyl-3,4,5,6,6a,6b,7,8,8a,8b,9,10,11a,12,12a,12b-hexadecahydro-1H-naphtho[2′,1′:4,5]indeno[2,1-b]furan-4-yl acetate, C31H48O5
  70. Crystal structure of 4,4′-(oxybis(methylene))bis(bromobenzene), C14H12Br2O
  71. Crystal structure of (N,N-dimethylsulphoxide)-[N-(3-ethoxy-2-(oxide)benzylidene)-3-methoxybenzenecarbohydrazonato-κ3N,O,O′]-dioxo-molybdenum(VI), C19H22MoN2O7S
  72. Crystal structure of dichlorido-bis(dimethyl sulphoxide-κO)-bis(4-methylbenzyl-κC1)tin(IV), C20H30Cl2O2S2Sn
  73. Crystal structure of (E)-2-amino-N′-(2-hydroxy-4-(2-(piperidin-1-yl)ethoxy)benzylidene)benzohydrazide monohydrate, C21H26N4O3 ⋅ H2O
  74. Crystal structure of chloridotris(4-chlorophenyl)(dimethyl sulfoxide-κO)tin(IV), C20H18Cl4OSSn
  75. Crystal structure of catena{di-aqua-sodium-[N-(hydroxyethyl), N-isopropyl-dithiocarbamato]}n, [C6H16NNaO2S2]n
  76. Crystal structure of 2,2,4,4,6,6-hexakis(4-chlorophenyl)-1,3,5,2,4,6-trithiatristanninane, C36H24Cl6S3Sn3
  77. Crystal structure of 6-methoxy-3-(5-(3-methoxyphenyl)-1,3,4-oxadiazol-2-yl)-4H-chromen-4-one-methanol (1/1), C20H18N2O6
  78. Crystal structure of hexanedihydrazide, C6H14N4O2
  79. Crystal structure of tert-butyl 2-(hydroxymethyl)-5-{4-[(methoxycarbonyl)amino]phenyl}-2,5-dihydro-1H-pyrrole-1-carboxylate, C18H24N2O5
  80. Crystal structure of [(Z)-O-isopropyl N-(4-nitrophenyl)thiocarbamato-κS]-(triphenylphosphine-κP)-gold(I), C28H26AuN2O3PS
  81. Crystal structure of [O-ethyl N-(4-nitrophenyl)thiocarbamato-κS](tri-4-tolylphosphine-κP)gold(I) tetrahydrofuran solvate, C30H30AuN2O3PS, C4H8O
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