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ISSN: 2056-9890

Selective crystallization of indigo B by a modified sublimation method and its redetermined structure

aUniversität Leipzig, Fakultät für Chemie und Mineralogie, Institut für Anorganische Chemie, Johannisallee 29, D-04103 Leipzig, Germany, and bSpezialschulteil Mathematik/Naturwissenschaften/Informatik am, Albert-Schweitzer-Gymnasium Erfurt, Vilniuser Strasse 17a, D-99089 Erfurt, Germany
*Correspondence e-mail: krautscheid@rz.uni-leipzig.de

(Received 19 July 2011; accepted 29 September 2011; online 8 October 2011)

Good-quality single crystals of the title compound, indigo B [systematic name: 2-(3-oxoindolin-2-yl­idene)indolin-3-one], C16H10N2O2, have been prepared with high selectivity by a sublimation process. The previous structure of indigo B [Süsse & Wolf (1980[Süsse, P. & Wolf, A. (1980). Naturwissenschaften, 67, 453.]). Naturwissenschaften, 67, 453], which showed that the complete mol­ecule is generated by crystallographic inversion symmetry has been confirmed, but the present study reports more realistic geometrical parameters and modern standards of precision (e.g. σ for C—C bonds = 0.002–0.003 Å). Each mol­ecule features two intra­molecular N—H⋯O hydrogen bonds. In the crystal, mol­ecules are linked by strong face-to-face ππ stacking inter­actions involving both the six- and five-membered rings [centroid–centroid separations = 3.6290 (14) and 3.6506 (14) Å] and inter­molecular N—H⋯O hydrogen bonds.

Related literature

For background to the history and uses of indigo, see: Berger & Sicker (2009[Berger, S. & Sicker, D. (2009). Classics in Spectroscopy: Isolation and Structure Elucidation of Natural Products, pp. 577-579. Weinheim: Wiley-VCH.]); Johnson-Buck et al. (2009[Johnson-Buck, A., Kim, G., Wang, S., Hah, H. J. & Kopelman, R. (2009). Mol. Cryst. Liquid Cryst. 501, 138-144.]). For previous studies of the polymorphism of indigo, see: von Eller (1955[Eller, H. von (1955). Bull. Soc. Chim. Fr. 106, 1433-1438.]); von Eller-Pandraud (1958[Eller-Pandraud, H. von (1958). Bull. Soc. Chim. Fr. 106, 316-317.]); Süsse & Wolf (1980[Süsse, P. & Wolf, A. (1980). Naturwissenschaften, 67, 453.]); Süsse et al. (1988[Süsse, P., Steins, M. & Kupcik, V. (1988). Z. Kristallogr. 184, 269-273.]). For aromatic stacking, see: Meyer et al. (2003[Meyer, E. A., Castellano, R. K. & Dietrich, F. (2003). Angew. Chem. Int. Ed. 42, 1210-1250.]).

[Scheme 1]

Experimental

Crystal data
  • C16H10N2O2

  • Mr = 262.26

  • Monoclinic, P 21 /n

  • a = 9.799 (2) Å

  • b = 5.9064 (10) Å

  • c = 10.755 (3) Å

  • β = 106.781 (18)°

  • V = 596.0 (2) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.10 mm−1

  • T = 213 K

  • 1.00 × 0.50 × 0.30 mm

Data collection
  • Stoe IPDS 1 diffractometer

  • 4479 measured reflections

  • 1115 independent reflections

  • 896 reflections with I > 2σ(I)

  • Rint = 0.033

Refinement
  • R[F2 > 2σ(F2)] = 0.036

  • wR(F2) = 0.096

  • S = 1.03

  • 1115 reflections

  • 91 parameters

  • H-atom parameters constrained

  • Δρmax = 0.20 e Å−3

  • Δρmin = −0.16 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯Oi 0.87 2.40 2.9254 (17) 119
N1—H1⋯Oii 0.87 2.17 2.8832 (17) 139
Symmetry codes: (i) -x+1, -y, -z+1; (ii) [x+{\script{1\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}].

Data collection: X-AREA (Stoe & Cie, 2005[Stoe & Cie (2005). X-AREA. Stoe & Cie, Darmstadt, Germany.]); cell refinement: X-AREA; data reduction: X-AREA; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: DIAMOND (Brandenburg, 2004[Brandenburg, K. (2004). DIAMOND. Crystal Impact, Bonn, Germany.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]).

Supporting information


Comment top

Indigo, 2-(1,3-dihydro-3-oxo-2H-indol-2-ylidene)-1,2-dihydro-3H-indol-3-one, C16H10N2O2, is a powerful dye, which is used to colorize for example denim in major industrial processes (Berger & Sicker, 2009). Very important for this application is the chemical stability and the extraordinary low solubility of indigo in water and also in almost all common organic solvents. Even insoluble indigo nanoparticles have been reported recently (Johnson-Buck et al. 2009). Von Eller-Pandraud (1958) and Süsse & Wolf (1980) mentioned, that different intermolecular interactions result in two modifications with differences in the packing of indigo molecules. Indigo modification A crystallizes as centrosymmetric molecules in P 21/c with a = 9.24, b = 5.77, c = 12.22 Å, β = 117° and Z = 2 (Süsse et al., 1988). Süsse & Wolf (1980) observed indigo modification B as a minor phase with a fraction of about 10% in a mixture with indigo A after sublimation at 10 Torr. We succeeded in preparing single crystals of indigo B as almost pure phase by sublimation at 290 °C at atmospheric pressure. The structure was solved and refined in space group P 21/n, Z = 2, with a unit cell setting related to that reported by Süsse & Wolf (1980) (Table 1). Since the quality of the former data set did not allow an interpretation of bond lengths and angles, we used the new crystals to redetermine the crystal structure with improved quality.

The new data set allows a better description of the bonding situation in the indigo molecule. The new values of the bond lengths and angles are consistent with the values reported for indigo A. For example, the bond length between the carbon atoms C2 and its symmetry equivalent C2', previously determined as 1.30 Å in indigo B (1.34 Å in indigo A), which is too short for a delocalized π-system, could be corrected to a distance of 1.359 (2) Å, which is in agreement with a partial double bond. C–C distances within the six-membered ring are in the range of 1.38 to 1.41 Å, consistent with the aromatic character of the ring system.

Responsible for the low solubility of indigo is the intermolecular stabilization by face-to-face ππ-stacking of parallel aromatic rings with a distance of 3.41 Å. Furthermore, each NH and each carbonyl group form strong intermolecular hydrogen bonds N—H···O to one neighbouring unit per functional group with a N···O distance of 2.883 (2) Å (H···O 2.17 Å). In addition, weaker intramolecular hydrogen bonds are observed with N···O 2.925 (2) Å (Figure 1). In both modifications the intermolecular interactions result in almost identical arrangements of indigo molecules in layers, i.e. layers parallel (100) in indigo A and layers parallel (-101) in indigo B, respectively. This leads to edge-to-face π-interactions between indigo molecules of adjacent layers. The distance of 3.50 Å for C6 to the neighbouring ring system is in good agreement with literature data (Meyer et al., 2003). Viewing along [010], the difference in the crystal structures of both modifications can be observed as an offset in different directions in the stacking of these layers (Figure 2) (von Eller-Pandraud, 1958). As a consequence, the unit cell volume of modification B is 2.8% larger than that of indigo A, although the data set has been collected at lower temperature (-60 °C).

Powder diffraction data of crushed single crystals of indigo B do not show a phase transition by cooling to -60 °C; the diffraction pattern fits well to the simulated pattern based on our single crystal data. Additional peaks with low intensities are due to small amounts of indigo A (Figure 3).

Related literature top

For background to the history and uses of indigo, see: Berger & Sicker (2009); Johnson-Buck et al. (2009). For previous studies of the polymorphism of indigo, see: von Eller (1955); von Eller-Pandraud (1958); Süsse & Wolf (1980); Süsse et al. (1988). For aromatic stacking, see: Meyer et al. (2003).

Experimental top

Crystallization of indigo modification B was achieved by sublimation, similar to the procedure described by von Eller (1955). Indigo was heated to 290 °C in a Schlenk flask at atmospheric pressure. Although indigo is starting to decompose under these conditions, shiny, dark blue, long platelets of indigo B were formed in the cooler region of the glass tube within one hour.

Computing details top

Data collection: X-AREA (Stoe & Cie, 2005); cell refinement: X-AREA (Stoe & Cie, 2005); data reduction: X-AREA (Stoe & Cie, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2004); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top
[Figure 1] Fig. 1. a) Molecular structure of indigo B (50% probability displacement ellipsoids); b) packing diagram of indigo B showing ππ-stacking interactions, inter- (N···O 2.883 (2) Å) and intramolecular (N···O 2.925 (2) Å) hydrogen bonds.
[Figure 2] Fig. 2. Packing of the indigo layers in indigo B (top) and indigo A (bottom), showing the different offset of the layers; view along [010].
[Figure 3] Fig. 3. Comparison of the experimental powder diffraction pattern of crushed indigo crystals (bottom, -60 °C, Cu—Kα1) with simulated powder patterns of both indigo modifications, A (top, room temperature, Süsse et al. 1988) and B (middle, -60 °C), based on single-crystal data.
2-(3-oxoindolin-2-ylidene)indolin-3-one top
Crystal data top
C16H10N2O2F(000) = 272
Mr = 262.26Dx = 1.461 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 3816 reflections
a = 9.799 (2) Åθ = 1.9–26.0°
b = 5.9064 (10) ŵ = 0.10 mm1
c = 10.755 (3) ÅT = 213 K
β = 106.781 (18)°Fragment of long platelet, dark blue
V = 596.0 (2) Å31.00 × 0.50 × 0.30 mm
Z = 2
Data collection top
Stoe IPDS 1
diffractometer
896 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.033
Graphite monochromatorθmax = 26.0°, θmin = 1.9°
ω scansh = 1211
4479 measured reflectionsk = 66
1115 independent reflectionsl = 1313
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.036 w = 1/[σ2(Fo2) + (0.0607P)2]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.096(Δ/σ)max < 0.001
S = 1.03Δρmax = 0.20 e Å3
1115 reflectionsΔρmin = 0.16 e Å3
91 parameters
Crystal data top
C16H10N2O2V = 596.0 (2) Å3
Mr = 262.26Z = 2
Monoclinic, P21/nMo Kα radiation
a = 9.799 (2) ŵ = 0.10 mm1
b = 5.9064 (10) ÅT = 213 K
c = 10.755 (3) Å1.00 × 0.50 × 0.30 mm
β = 106.781 (18)°
Data collection top
Stoe IPDS 1
diffractometer
896 reflections with I > 2σ(I)
4479 measured reflectionsRint = 0.033
1115 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0360 restraints
wR(F2) = 0.096H-atom parameters constrained
S = 1.03Δρmax = 0.20 e Å3
1115 reflectionsΔρmin = 0.16 e Å3
91 parameters
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
N10.51536 (12)0.2222 (2)0.62685 (11)0.0300 (3)
H10.59260.19630.68970.036*
C20.46722 (14)0.0924 (3)0.51583 (13)0.0275 (4)
C30.32960 (14)0.1920 (3)0.43595 (13)0.0291 (4)
C3a0.30488 (14)0.3864 (3)0.50987 (14)0.0306 (4)
C40.19548 (16)0.5474 (3)0.48631 (16)0.0386 (4)
H40.11760.53910.41110.046*
C50.20430 (18)0.7188 (3)0.57588 (17)0.0419 (4)
H50.13100.82690.56220.050*
C60.32189 (17)0.7325 (3)0.68710 (16)0.0387 (4)
H60.32610.85130.74630.046*
C70.43206 (16)0.5759 (3)0.71239 (15)0.0342 (4)
H70.51080.58720.78680.041*
C7a0.42120 (14)0.4009 (3)0.62272 (14)0.0284 (4)
O0.25789 (11)0.1165 (2)0.32944 (10)0.0380 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0249 (6)0.0319 (8)0.0282 (6)0.0016 (5)0.0003 (4)0.0006 (5)
C20.0234 (6)0.0297 (10)0.0270 (7)0.0025 (5)0.0034 (5)0.0038 (6)
C30.0241 (7)0.0322 (10)0.0280 (7)0.0018 (6)0.0028 (5)0.0053 (6)
C3a0.0279 (7)0.0317 (10)0.0311 (8)0.0006 (6)0.0068 (6)0.0041 (6)
C40.0327 (7)0.0423 (11)0.0382 (8)0.0080 (7)0.0064 (6)0.0058 (7)
C50.0413 (9)0.0378 (12)0.0489 (10)0.0121 (7)0.0164 (7)0.0053 (7)
C60.0440 (9)0.0322 (11)0.0447 (9)0.0008 (7)0.0202 (7)0.0045 (7)
C70.0339 (7)0.0351 (11)0.0334 (8)0.0048 (6)0.0091 (6)0.0021 (6)
C7a0.0267 (6)0.0294 (10)0.0289 (7)0.0014 (6)0.0079 (5)0.0044 (6)
O0.0321 (5)0.0408 (8)0.0320 (6)0.0019 (5)0.0051 (4)0.0010 (5)
Geometric parameters (Å, º) top
N1—C21.3821 (19)C4—C51.383 (3)
N1—C7a1.394 (2)C4—H40.9400
N1—H10.8700C5—C61.403 (3)
C2—C2i1.359 (3)C5—H50.9400
C2—C31.4944 (19)C6—C71.387 (2)
C3—O1.2409 (18)C6—H60.9400
C3—C3a1.456 (2)C7—C7a1.397 (2)
C3a—C41.400 (2)C7—H70.9400
C3a—C7a1.407 (2)
C2—N1—C7a109.55 (12)C3a—C4—H4120.6
C2—N1—H1125.2C4—C5—C6120.45 (15)
C7a—N1—H1125.2C4—C5—H5119.8
C2i—C2—N1126.43 (16)C6—C5—H5119.8
C2i—C2—C3125.83 (16)C7—C6—C5121.99 (15)
N1—C2—C3107.74 (13)C7—C6—H6119.0
O—C3—C3a130.39 (13)C5—C6—H6119.0
O—C3—C2124.47 (15)C6—C7—C7a117.26 (14)
C3a—C3—C2105.14 (12)C6—C7—H7121.4
C4—C3a—C7a120.14 (15)C7a—C7—H7121.4
C4—C3a—C3132.53 (14)N1—C7a—C7128.36 (13)
C7a—C3a—C3107.31 (12)N1—C7a—C3a110.21 (13)
C5—C4—C3aA118.71 (14)C7—C7a—C3a121.43 (14)
C5—C4—H4120.6
Symmetry code: (i) x+1, y, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···Oi0.872.402.9254 (17)119
N1—H1···Oii0.872.172.8832 (17)139
Symmetry codes: (i) x+1, y, z+1; (ii) x+1/2, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC16H10N2O2
Mr262.26
Crystal system, space groupMonoclinic, P21/n
Temperature (K)213
a, b, c (Å)9.799 (2), 5.9064 (10), 10.755 (3)
β (°) 106.781 (18)
V3)596.0 (2)
Z2
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)1.00 × 0.50 × 0.30
Data collection
DiffractometerStoe IPDS 1
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
4479, 1115, 896
Rint0.033
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.036, 0.096, 1.03
No. of reflections1115
No. of parameters91
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.20, 0.16

Computer programs: X-AREA (Stoe & Cie, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2004), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···Oi0.872.402.9254 (17)119
N1—H1···Oii0.872.172.8832 (17)139
Symmetry codes: (i) x+1, y, z+1; (ii) x+1/2, y+1/2, z+1/2.
Relationship between unit cell dimensions of the indigo modifications (Å, °, A3) top
Indigo AaIndigo BbIndigo BcIndigo Bd
a9.24 (3)9.799 (2)10.84 (1)9.85 (1)
b5.77 (2)5.906 (1)5.887 (6)5.887 (6)
c12.22 (3)10.755 (3)12.28 (1)10.84 (1)
β117.0106.78 (2)130.02 (5)107.38 (5)
a580596.0600600
space groupP 21/cP 21/nP 21/cP 21/n
Notes: (a) von Eller (1955); (b) -60°C, this work; (c) Süsse & Wolf (1980), original setting; (d) Süsse & Wolf (1980), transformed setting.
 

Acknowledgements

Support by Universität Leipzig and the Fonds der Chemischen Industrie are gratefully acknowledged.

References

First citationBerger, S. & Sicker, D. (2009). Classics in Spectroscopy: Isolation and Structure Elucidation of Natural Products, pp. 577–579. Weinheim: Wiley-VCH.  Google Scholar
First citationBrandenburg, K. (2004). DIAMOND. Crystal Impact, Bonn, Germany.  Google Scholar
First citationEller, H. von (1955). Bull. Soc. Chim. Fr. 106, 1433–1438.  Google Scholar
First citationEller-Pandraud, H. von (1958). Bull. Soc. Chim. Fr. 106, 316–317.  Google Scholar
First citationFarrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838.  CrossRef CAS IUCr Journals Google Scholar
First citationJohnson-Buck, A., Kim, G., Wang, S., Hah, H. J. & Kopelman, R. (2009). Mol. Cryst. Liquid Cryst. 501, 138–144.  Google Scholar
First citationMeyer, E. A., Castellano, R. K. & Dietrich, F. (2003). Angew. Chem. Int. Ed. 42, 1210–1250.  Web of Science CrossRef CAS Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationStoe & Cie (2005). X-AREA. Stoe & Cie, Darmstadt, Germany.  Google Scholar
First citationSüsse, P., Steins, M. & Kupcik, V. (1988). Z. Kristallogr. 184, 269–273.  Google Scholar
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