Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270112006440/gg3263sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270112006440/gg3263Isup2.hkl | |
Chemdraw file https://doi.org/10.1107/S0108270112006440/gg3263Isup3.cdx | |
Chemical Markup Language (CML) file https://doi.org/10.1107/S0108270112006440/gg3263Isup4.cml |
CCDC reference: 879441
The title compound was prepared according to an established procedure (Clark & Cooksey, 1999). Crystals suitable for X-ray analysis were obtained by slow crystallization from boiling ethyl benzoate.
The GAUSSIAN09 (Frisch et al., 2009) package of programs was used for theoretical calculations employing the B3LYP/6-31 G(2d,2p) level of theory (Jacquemin, Preat & Perpéte, 2005; Jacquemin, Preat, Wathelet & Perpéte, 2005; Jacquemin et al., 2006). Diffraction data for MBI indicated monoclinic symmetry and systematic absences consistent with the space groups Pc and P2/c. Space group Pc was used for the solution and refinement of the structure based on E statistics and structure solution. The molecules are disordered in a ratio of 0.682 (3):0.318 (3), resulting in a pseudoinversion center in the molecule. The 18 atoms which form the indigo ring occupy two sites as a result of this packing disorder, ca 0.34 Å apart, with site-occupancy factors of 0.682 (3):0.318 (3). Refining a disordered isotropic model in which two MBI molecules (one labeled A and B, and the other C and D) were used gave a model as presented in Fig. 2. The refinement was carried out with several different restraints imposed on the refinement. The one which produced the best results restrained the atoms in the two MBI molecules sharing the same position (for example, N1A and N1C) to be 0.34 (2) Å from each other. This model converged with R = 0.068 and C6A—Br6A and C6D—Br6D bond lengths of 1.93 (2) and 1.85 (3) Å, respectively, but resulted in many equivalent bond lengths, long in one ring and short in the other, and also short contacts for atom C2D. Due to the difficulty in resolving the disorder using two sites for each atom in the indigo ring, a model with one atom representing the two positions was used, and the elongated displacement parameters are a result of this positional disordering. Since the disordering of the molecule is not 0.50:0.50, the position of the one atom representing the two positions 0.34 Å apart is not the average of the two sites but a weighted average: the refined atom position is 0.08 Å from the disordered atom with 0.682 (3) occupancy and 0.26 Å from that with lower occupancy. This explains the shortening of the C6—Br6 bond lengths by 0.08 and 0.26 Å. In the final refinement, the bond lengths of the atoms in each of the two rings of the two halves of the indigo molecule were restrained to be the same length.
H atoms were placed at calculated positions, with C—H = 0.95 Å and N—H = 0.88 Å, and allowed to ride on the atom to which they were attached, with Uiso(H) = 1.2Ueq(parent atom). The crystals were twinned, with the two twin domains related to each other by a center of inversion. The final value of the Flack parameter (Flack, 1983) was 0.42 (2), indicating that the crystal was a racemic twin with approximately equal amounts of each twin component.
Data collection: APEX2 (Bruker, 2010); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008); software used to prepare material for publication: publCIF (Westrip, 2010).
C16H9BrN2O2 | F(000) = 340 |
Mr = 341.16 | Dx = 1.765 Mg m−3 |
Monoclinic, Pc | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P -2yc | Cell parameters from 1383 reflections |
a = 12.347 (3) Å | θ = 3.6–25.5° |
b = 4.6558 (12) Å | µ = 3.21 mm−1 |
c = 11.607 (3) Å | T = 173 K |
β = 105.856 (8)° | Plate, purple |
V = 641.8 (3) Å3 | 0.25 × 0.10 × 0.02 mm |
Z = 2 |
Bruker APEXII CCD area-detector diffractometer | 2180 independent reflections |
Radiation source: fine-focus sealed tube | 1558 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.056 |
ϕ and ω scans | θmax = 25.9°, θmin = 3.6° |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | h = −11→15 |
Tmin = 0.513, Tmax = 0.745 | k = −5→5 |
4715 measured reflections | l = −14→14 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.059 | H-atom parameters not refined |
wR(F2) = 0.141 | w = 1/[σ2(Fo2) + (0.0716P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.01 | (Δ/σ)max < 0.001 |
2180 reflections | Δρmax = 0.55 e Å−3 |
201 parameters | Δρmin = −0.60 e Å−3 |
23 restraints | Absolute structure: Flack (1983), with 934 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.42 (2) |
C16H9BrN2O2 | V = 641.8 (3) Å3 |
Mr = 341.16 | Z = 2 |
Monoclinic, Pc | Mo Kα radiation |
a = 12.347 (3) Å | µ = 3.21 mm−1 |
b = 4.6558 (12) Å | T = 173 K |
c = 11.607 (3) Å | 0.25 × 0.10 × 0.02 mm |
β = 105.856 (8)° |
Bruker APEXII CCD area-detector diffractometer | 2180 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | 1558 reflections with I > 2σ(I) |
Tmin = 0.513, Tmax = 0.745 | Rint = 0.056 |
4715 measured reflections |
R[F2 > 2σ(F2)] = 0.059 | H-atom parameters not refined |
wR(F2) = 0.141 | Δρmax = 0.55 e Å−3 |
S = 1.01 | Δρmin = −0.60 e Å−3 |
2180 reflections | Absolute structure: Flack (1983), with 934 Friedel pairs |
201 parameters | Absolute structure parameter: 0.42 (2) |
23 restraints |
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. |
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
Br6A | 0.72197 (10) | −0.6832 (3) | 0.16578 (9) | 0.0550 (5) | 0.682 (3) |
C4A | 0.5539 (6) | −0.1658 (19) | −0.1043 (6) | 0.045 (2) | |
H4A | 0.5619 | −0.1009 | −0.1791 | 0.054* | |
C5A | 0.6286 (7) | −0.359 (2) | −0.0391 (6) | 0.053 (3) | |
H5A | 0.6885 | −0.4313 | −0.0677 | 0.063* | |
C6A | 0.6146 (7) | −0.4514 (17) | 0.0725 (7) | 0.044 (2) | |
H6A | 0.6666 | −0.5869 | 0.1178 | 0.052* | 0.318 (3) |
C7A | 0.5299 (6) | −0.355 (2) | 0.1184 (7) | 0.045 (2) | |
H7A | 0.5221 | −0.4217 | 0.1931 | 0.055* | |
C8A | 0.4567 (6) | −0.1558 (16) | 0.0508 (6) | 0.0376 (18) | |
C9A | 0.4668 (7) | −0.0629 (19) | −0.0628 (6) | 0.046 (3) | |
C3A | 0.3802 (7) | 0.1481 (19) | −0.1069 (6) | 0.041 (2) | |
C2A | 0.3165 (7) | 0.1662 (19) | −0.0131 (6) | 0.044 (2) | |
N1A | 0.3672 (5) | −0.0205 (15) | 0.0765 (5) | 0.0445 (17) | |
H1A | 0.3454 | −0.0498 | 0.1417 | 0.053* | |
O3A | 0.3581 (6) | 0.2859 (11) | −0.1988 (5) | 0.0457 (18) | |
Br6B | −0.1587 (2) | 1.2040 (7) | −0.1760 (2) | 0.0584 (13) | 0.318 (3) |
C4B | −0.0053 (7) | 0.6796 (19) | 0.0743 (8) | 0.052 (2) | |
H4B | −0.0135 | 0.6160 | 0.1492 | 0.062* | |
C5B | −0.0768 (7) | 0.8799 (17) | 0.0111 (7) | 0.053 (2) | |
H5B | −0.1355 | 0.9538 | 0.0411 | 0.064* | |
C6B | −0.0642 (8) | 0.980 (2) | −0.1006 (8) | 0.061 (3) | |
H6B | −0.1149 | 1.1197 | −0.1447 | 0.074* | 0.682 (3) |
C7B | 0.0207 (7) | 0.8760 (18) | −0.1450 (7) | 0.048 (2) | |
H7B | 0.0297 | 0.9453 | −0.2188 | 0.058* | |
C8B | 0.0919 (7) | 0.6713 (19) | −0.0813 (6) | 0.045 (2) | |
C9B | 0.0799 (6) | 0.5660 (17) | 0.0309 (6) | 0.038 (2) | |
C3B | 0.1673 (7) | 0.3641 (18) | 0.0747 (6) | 0.041 (2) | |
C2B | 0.2296 (6) | 0.3373 (17) | −0.0175 (6) | 0.0380 (18) | |
N1B | 0.1813 (5) | 0.5300 (15) | −0.1064 (5) | 0.0426 (19) | |
H1B | 0.2043 | 0.5596 | −0.1708 | 0.051* | |
O3B | 0.1913 (5) | 0.2176 (12) | 0.1692 (6) | 0.057 (2) |
U11 | U22 | U33 | U12 | U13 | U23 | |
Br6A | 0.0666 (9) | 0.0697 (8) | 0.0403 (7) | 0.0284 (10) | 0.0341 (6) | 0.0198 (9) |
C4A | 0.052 (5) | 0.062 (5) | 0.026 (4) | −0.017 (5) | 0.020 (4) | −0.003 (4) |
C5A | 0.057 (6) | 0.084 (8) | 0.027 (4) | −0.003 (6) | 0.028 (4) | −0.015 (5) |
C6A | 0.048 (5) | 0.046 (5) | 0.042 (4) | −0.005 (4) | 0.020 (4) | 0.002 (4) |
C7A | 0.039 (5) | 0.068 (6) | 0.034 (4) | −0.002 (5) | 0.018 (4) | −0.007 (4) |
C8A | 0.045 (5) | 0.043 (5) | 0.028 (4) | −0.010 (4) | 0.017 (4) | −0.005 (4) |
C9A | 0.062 (6) | 0.060 (6) | 0.025 (4) | −0.007 (5) | 0.027 (4) | −0.007 (4) |
C3A | 0.056 (6) | 0.055 (6) | 0.023 (4) | −0.018 (5) | 0.027 (4) | −0.006 (4) |
C2A | 0.063 (6) | 0.059 (5) | 0.018 (4) | −0.016 (5) | 0.025 (4) | −0.010 (4) |
N1A | 0.060 (5) | 0.060 (5) | 0.024 (3) | −0.006 (4) | 0.030 (3) | −0.004 (3) |
O3A | 0.072 (4) | 0.049 (4) | 0.028 (3) | −0.003 (3) | 0.034 (3) | −0.004 (3) |
Br6B | 0.064 (2) | 0.070 (2) | 0.0516 (19) | 0.0190 (18) | 0.0317 (17) | 0.0140 (17) |
C4B | 0.061 (6) | 0.063 (5) | 0.042 (4) | −0.005 (6) | 0.030 (4) | −0.017 (5) |
C5B | 0.060 (6) | 0.060 (6) | 0.052 (5) | −0.012 (5) | 0.035 (5) | −0.014 (4) |
C6B | 0.062 (7) | 0.080 (7) | 0.048 (6) | −0.011 (5) | 0.024 (5) | −0.029 (5) |
C7B | 0.053 (6) | 0.062 (7) | 0.030 (5) | −0.015 (5) | 0.013 (4) | −0.004 (4) |
C8B | 0.050 (5) | 0.064 (6) | 0.028 (4) | −0.012 (5) | 0.023 (4) | −0.018 (5) |
C9B | 0.048 (5) | 0.041 (5) | 0.030 (4) | −0.007 (5) | 0.022 (4) | −0.014 (4) |
C3B | 0.058 (6) | 0.047 (5) | 0.028 (4) | −0.014 (5) | 0.029 (4) | −0.013 (4) |
C2B | 0.043 (5) | 0.044 (4) | 0.037 (4) | −0.008 (5) | 0.028 (4) | −0.012 (4) |
N1B | 0.063 (5) | 0.047 (4) | 0.024 (4) | −0.001 (4) | 0.022 (4) | 0.002 (3) |
O3B | 0.072 (6) | 0.073 (4) | 0.036 (3) | −0.002 (3) | 0.032 (4) | 0.004 (3) |
Br6A—C6A | 1.820 (8) | Br6B—C6B | 1.631 (11) |
C4A—C5A | 1.361 (10) | C4B—C5B | 1.354 (10) |
C4A—C9A | 1.378 (9) | C4B—C9B | 1.390 (9) |
C4A—H4A | 0.9500 | C4B—H4B | 0.9500 |
C5A—C6A | 1.419 (9) | C5B—C6B | 1.425 (10) |
C5A—H5A | 0.9500 | C5B—H5B | 0.9500 |
C6A—C7A | 1.372 (8) | C6B—C7B | 1.376 (9) |
C6A—H6A | 0.9500 | C6B—H6B | 0.9500 |
C7A—C8A | 1.380 (9) | C7B—C8B | 1.368 (10) |
C7A—H7A | 0.9500 | C7B—H7B | 0.9500 |
C8A—N1A | 1.374 (8) | C8B—N1B | 1.383 (9) |
C8A—C9A | 1.426 (8) | C8B—C9B | 1.436 (9) |
C9A—C3A | 1.439 (10) | C9B—C3B | 1.416 (9) |
C3A—O3A | 1.210 (9) | C3B—O3B | 1.256 (10) |
C3A—C2A | 1.508 (8) | C3B—C2B | 1.485 (8) |
C2A—C2B | 1.327 (9) | C2B—N1B | 1.374 (8) |
C2A—N1A | 1.369 (9) | N1B—H1B | 0.8800 |
N1A—H1A | 0.8800 | ||
C5A—C4A—C9A | 120.7 (7) | C5B—C4B—C9B | 120.8 (7) |
C5A—C4A—H4A | 119.6 | C5B—C4B—H4B | 119.6 |
C9A—C4A—H4A | 119.6 | C9B—C4B—H4B | 119.6 |
C4A—C5A—C6A | 118.3 (7) | C4B—C5B—C6B | 120.1 (8) |
C4A—C5A—H5A | 120.9 | C4B—C5B—H5B | 120.0 |
C6A—C5A—H5A | 120.9 | C6B—C5B—H5B | 120.0 |
C7A—C6A—C5A | 123.5 (8) | C7B—C6B—C5B | 120.6 (9) |
C7A—C6A—Br6A | 118.1 (6) | C7B—C6B—Br6B | 122.0 (7) |
C5A—C6A—Br6A | 118.1 (6) | C5B—C6B—Br6B | 117.3 (7) |
C7A—C6A—H6A | 118.3 | C7B—C6B—H6B | 119.7 |
C5A—C6A—H6A | 118.3 | C5B—C6B—H6B | 119.7 |
C6A—C7A—C8A | 116.7 (7) | C8B—C7B—C6B | 119.0 (8) |
C6A—C7A—H7A | 121.7 | C8B—C7B—H7B | 120.5 |
C8A—C7A—H7A | 121.7 | C6B—C7B—H7B | 120.5 |
N1A—C8A—C7A | 128.7 (6) | C7B—C8B—N1B | 130.5 (7) |
N1A—C8A—C9A | 109.9 (6) | C7B—C8B—C9B | 121.2 (6) |
C7A—C8A—C9A | 121.4 (7) | N1B—C8B—C9B | 108.3 (7) |
C4A—C9A—C8A | 119.4 (7) | C4B—C9B—C3B | 134.4 (7) |
C4A—C9A—C3A | 133.5 (7) | C4B—C9B—C8B | 118.3 (7) |
C8A—C9A—C3A | 106.9 (6) | C3B—C9B—C8B | 107.2 (6) |
O3A—C3A—C9A | 129.9 (7) | O3B—C3B—C9B | 130.5 (6) |
O3A—C3A—C2A | 124.7 (8) | O3B—C3B—C2B | 122.6 (7) |
C9A—C3A—C2A | 105.4 (6) | C9B—C3B—C2B | 106.9 (6) |
C2B—C2A—N1A | 127.4 (5) | C2A—C2B—N1B | 127.0 (6) |
C2B—C2A—C3A | 125.5 (6) | C2A—C2B—C3B | 126.6 (7) |
N1A—C2A—C3A | 107.0 (7) | N1B—C2B—C3B | 106.4 (6) |
C2A—N1A—C8A | 110.7 (6) | C2B—N1B—C8B | 111.1 (6) |
C2A—N1A—H1A | 124.6 | C2B—N1B—H1B | 124.5 |
C8A—N1A—H1A | 124.6 | C8B—N1B—H1B | 124.5 |
C9A—C4A—C5A—C6A | −0.3 (14) | C5B—C6B—C7B—C8B | 1.0 (14) |
C4A—C5A—C6A—C7A | −0.1 (14) | Br6B—C6B—C7B—C8B | −174.8 (8) |
C4A—C5A—C6A—Br6A | −174.2 (7) | C6B—C7B—C8B—N1B | 178.8 (9) |
C5A—C6A—C7A—C8A | −0.7 (14) | C6B—C7B—C8B—C9B | −0.5 (13) |
Br6A—C6A—C7A—C8A | 173.4 (6) | C5B—C4B—C9B—C3B | 178.5 (9) |
C6A—C7A—C8A—N1A | −178.4 (8) | C5B—C4B—C9B—C8B | 1.5 (13) |
C6A—C7A—C8A—C9A | 1.9 (13) | C7B—C8B—C9B—C4B | −0.7 (13) |
C5A—C4A—C9A—C8A | 1.5 (13) | N1B—C8B—C9B—C4B | 179.8 (8) |
C5A—C4A—C9A—C3A | 176.3 (9) | C7B—C8B—C9B—C3B | −178.5 (8) |
N1A—C8A—C9A—C4A | 177.9 (8) | N1B—C8B—C9B—C3B | 2.0 (9) |
C7A—C8A—C9A—C4A | −2.4 (13) | C4B—C9B—C3B—O3B | 2.3 (17) |
N1A—C8A—C9A—C3A | 1.8 (9) | C8B—C9B—C3B—O3B | 179.7 (9) |
C7A—C8A—C9A—C3A | −178.5 (8) | C4B—C9B—C3B—C2B | 179.7 (10) |
C4A—C9A—C3A—O3A | 3.8 (17) | C8B—C9B—C3B—C2B | −3.0 (9) |
C8A—C9A—C3A—O3A | 179.1 (8) | N1A—C2A—C2B—N1B | 178.0 (9) |
C4A—C9A—C3A—C2A | −176.9 (10) | C3A—C2A—C2B—N1B | −0.4 (11) |
C8A—C9A—C3A—C2A | −1.6 (9) | N1A—C2A—C2B—C3B | −0.1 (12) |
O3A—C3A—C2A—C2B | −1.1 (13) | C3A—C2A—C2B—C3B | −178.5 (9) |
C9A—C3A—C2A—C2B | 179.5 (7) | O3B—C3B—C2B—C2A | −1.0 (12) |
O3A—C3A—C2A—N1A | −179.8 (8) | C9B—C3B—C2B—C2A | −178.6 (7) |
C9A—C3A—C2A—N1A | 0.9 (9) | O3B—C3B—C2B—N1B | −179.4 (8) |
C2B—C2A—N1A—C8A | −178.4 (7) | C9B—C3B—C2B—N1B | 3.0 (9) |
C3A—C2A—N1A—C8A | 0.2 (9) | C2A—C2B—N1B—C8B | 179.8 (7) |
C7A—C8A—N1A—C2A | 179.0 (8) | C3B—C2B—N1B—C8B | −1.8 (9) |
C9A—C8A—N1A—C2A | −1.3 (9) | C7B—C8B—N1B—C2B | −179.5 (9) |
C9B—C4B—C5B—C6B | −1.0 (14) | C9B—C8B—N1B—C2B | −0.1 (10) |
C4B—C5B—C6B—C7B | −0.3 (14) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1A—H1A···O3Ai | 0.88 | 2.12 | 2.916 (8) | 150 |
N1A—H1A···O3B | 0.88 | 2.37 | 2.895 (8) | 119 |
N1B—H1B···O3Bii | 0.88 | 2.09 | 2.890 (9) | 150 |
N1B—H1B···O3A | 0.88 | 2.38 | 2.913 (9) | 119 |
Symmetry codes: (i) x, −y, z+1/2; (ii) x, −y+1, z−1/2. |
Experimental details
Crystal data | |
Chemical formula | C16H9BrN2O2 |
Mr | 341.16 |
Crystal system, space group | Monoclinic, Pc |
Temperature (K) | 173 |
a, b, c (Å) | 12.347 (3), 4.6558 (12), 11.607 (3) |
β (°) | 105.856 (8) |
V (Å3) | 641.8 (3) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 3.21 |
Crystal size (mm) | 0.25 × 0.10 × 0.02 |
Data collection | |
Diffractometer | Bruker APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2005) |
Tmin, Tmax | 0.513, 0.745 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4715, 2180, 1558 |
Rint | 0.056 |
(sin θ/λ)max (Å−1) | 0.614 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.059, 0.141, 1.01 |
No. of reflections | 2180 |
No. of parameters | 201 |
No. of restraints | 23 |
H-atom treatment | H-atom parameters not refined |
Δρmax, Δρmin (e Å−3) | 0.55, −0.60 |
Absolute structure | Flack (1983), with 934 Friedel pairs |
Absolute structure parameter | 0.42 (2) |
Computer programs: APEX2 (Bruker, 2010), SAINT (Bruker, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), XP in SHELXTL (Sheldrick, 2008), publCIF (Westrip, 2010).
D—H···A | D—H | H···A | D···A | D—H···A |
N1A—H1A···O3Ai | 0.88 | 2.12 | 2.916 (8) | 149.7 |
N1A—H1A···O3B | 0.88 | 2.37 | 2.895 (8) | 118.7 |
N1B—H1B···O3Bii | 0.88 | 2.09 | 2.890 (9) | 150.0 |
N1B—H1B···O3A | 0.88 | 2.38 | 2.913 (9) | 119.1 |
Symmetry codes: (i) x, −y, z+1/2; (ii) x, −y+1, z−1/2. |
In nature, the violet 6-bromoindigo dye (commonly abbreviated as MBI, monobromoindigo) is an important colorant and one of three indigoids in the purple and violet pigments produced from the Hexaplex (= Murex) trunculus species of the Muricidae family of sea snails (Koren, 2008a). In antiquity, these and related Mediterranean molluscs were used for the production of red–purple or Tyrian Purple woollen dyes, as well as blue–purple dyes, for kings, emperors and high priests. MBI, which can be the major component of a purple molluscan pigment, is a chromatic marker for the H. trunculus snail, and thus detecting a significant quantity of it in an archaeological pigment indicates that the malacological provenance of that pigment is the H. trunculus snail (Koren, 2008a). This colorant has been found, together with others, in pigments and dyes on archaeological artifacts dating back to nearly four millennia ago as, for example, a paint pigment (Karapanagiotis, 2006; Karapanagiotis et al., 2006; Sotiropoulou & Karapanagiotis, 2006; Koren, 2008a), as a residual pigment in a Phoenician dye vat (Koren, 1995) and as a textile dye (Koren, 1997, 2008b). The composition of MBI in the purple pigment, present together with the other two indigoids, the blue–violet indigo (IND) and the red–purple 6,6'-dibromoindigo (DBI) dyes, thus affects the final color of the raw pigment and of dyes produced from it.
MBI has been studied chromatographically and spectrometrically (Wouters & Verhecken, 1991; Clark & Cooksey, 1999; Cooksey, 2001; Koren, 2006, 2008a,c; Nowik et al., 2011) and colorimetrically (Clark & Cooksey, 1999). However, although the crystal structures of unsubstituted indigo (Reis & Schneider, 1928; von Eller, 1952, 1955; Gribova et al. 1956; Süsse & Wolf, 1980; Süsse et al., 1988) and DBI (Süsse & Krampe, 1979; Larsen & Watjen, 1980; Süsse, 1983) have been determined, the exact structure of crystalline MBI has not been previously established. A preliminary study of MBI was reported by Ziderman et al. (2004) and the first X-ray structure of MBI (Fig. 1) to be detailed is reported herein.
Within the crystal structure, the MBI molecule is oriented in one direction with an occupancy of 0.682 (3), as depicted in Fig. 1, and in the other direction with an occupancy of 0.318 (3), so that the Br atom would be located near C6B. This is not a simple disordering, but, due to packing forces involving the Br atom, there is a slippage of the indigo ring so that all the atoms occupy two sites, which are displaced by about 0.34 Å between the two orientations. In Fig. 2, the indigo ring-atom disorder [0.682 (3):0.319 (3)] can be observed. The positions of the refined atoms in Fig. 1 are the weighted averages of the two positions in Fig. 2. Because all the atoms within the ring are shifted uniformly, the distances within the ring are similar to those found in DBI (Süsse & Krampe, 1979; Larsen & Watjen, 1980; Süsse, 1983), but the C—Br bond lengths are 0.077 and 0.26 Å shorter than those found in DBI. When the Br atom is attached to atom C6A, all the other atoms in the indigo ring are shifted 0.077 Å from the refined position of C6A (away from the Br atom to the right in Fig. 1), while when the Br atom is attached to atom C6B, all the atoms in the ring are shifted 0.26 Å in the opposite direction (to the left in Fig. 1) from their refined positions. This disorder is too small to resolve but is reflected in the elongated displacement parameters of the atoms in the indigo ring. The Br atom is displaced by 0.28 (2) Å from the 18-atom mean plane [±0.04 (2) Å]. In DBI, the same 18 atoms are also planar (±0.04 Å) but the Br atom is only 0.09 Å out of this plane. The out-of-plane distortion of Br6A in MBI results in a decrease in the distance found in the Br6A···C6B interaction which is described below.
As in the IND and DBI structures, the molecules in MBI exhibit an infinite stacking interaction along the b axis at a distance of 3.375 (5) Å between the best-fit planes [closest contacts C2B···C7Bi = 3.372 (11) Å and C9B···C6Bi = 3.384 (12) Å; symmetry code: (i) x, y - 1, z], which is similar to the distances found in DBI [3.452 (1) Å; Süsse, 1983] and IND [3.345 (1) (Süsse et al., 1988) and 3.401 (1) Å (Süsse & Wolf, 1980)].
MBI has two intramolecular hydrogen bonds between the imine H atom on one half of the molecule and the carbonyl O atom on the other half (see Table 1 for details). There are also intermolecular hydrogen bonds between the two imine H atoms and two carbonyl O atoms on symmetry-related molecules (Table 1). These hydrogen bonds connect molecules related by the c-glide. Each indigo molecule is hydrogen bonded to four others. This is a feature also found in IND and DBI. The major differences among the three structures are in the interactions made by the groups attached to C6A and C6B.
In IND, C5 and C6 have an interaction with an H atom on a symmetry-related molecule, with H···C distances of 2.81 (3) and 2.88 (3) Å, respectively. In DBI, atom Br6 exhibits two close contacts with the Br atoms of neighboring molecules. The Br···Br contact distances are each 3.531 (2) Å and the two C6—Br6···Br angles are 92.6 (1) and 167.6 (1)°, making both contacts type 2 (Pedireddi et al., 1994). As shown in Fig. 3, in MBI, one of these Br···Br contacts is replaced by a Br6A···C6B interaction with a distance of 3.510 (9) Å and a Br6A···H6B contact of 3.25 Å. This replaces the other Br···Br contact. As mentioned previously, atom Br6 is bent out of the plane of the indigo ring towards atom C6B of a symmetry-related molecule at (x + 1, -y, z + 1/2), which results in the close contact between atoms Br6A and C6B. In DBI, the corresponding distance is 4.083 (4) Å.
The asymmetry of the MBI molecule causes a different crystal packing from IND and DBI. Monomer, dimer and tetramer units were modeled in the gas phase and their wave functions were used to obtain Bader electron atomic charges (Bader & Zou, 1992; Bader & Matta, 2004). In each of these cases, the crystal structure geometry was maintained. Additionally, optimization of a single MBI molecule was performed.
To understand the nature of the short-contact interactions within the MBI crystal structure, we calculated the corresponding bond paths, which are definitive characteristics of all bonding interactions. The quantum theory of atoms in molecules (QTAIM) calculations performed using the AIMALL software package (Keith, 2010) reveal the presence of a C6B···Br6A bond path, which indicates attractive forces between atoms Br6A and C6B. Analysis of the electron density ρ(r) contour plot (Fig. 4) shows that the C6B area has low electron density relative to that around atom Br6A. (Note, for example, the relatively greater number of contour lines around Br6A versus C6B.) There is less positive charge on C6B compared with neighboring atoms. Fig. 5 presents the calculated magnitude of MBI short-contact interactions as an indication of the stabilization which must occur in the experimental structure. The interaction energy I1 between two individual monomer units was computed as: I1 = E(dimer) - 2E(monomer). The interaction energy I2 for C6B···Br6A and H6B···Br6A contacts combined was computed as: I2 = E(trimer) - E(dimer) - E(monomer). These calculations gave I1 = -0.92 kcal mol-1 and I2 = -0.79 kcal mol-1 (1 kcal mol-1 = 4.184 kJ mol-1). Thus, the experimental geometry of the MBI crystal structure results in attractive binding interactions, as expected.
For the first time, suitable crystals of MBI were obtained of sufficient quality for X-ray diffraction. These data complete the structural knowledge of naturally derived molecules with the same framework, namely IND, MBI and DBI. Such structural information opens possibilities for further studies of MBI behavior and its properties as a colorant.