Determination of the structure of the violet pigment C₂₂H₁₂Cl₂N₆O₄ from a non-indexed X-ray powder diagram

The violet pigment methylbenzimidazolonodioxazine, C₂₂H₁₂Cl₂N₆O₄ (systematic name: 6,14-dichloro-3,11-dimethyl-1,3,9,11-tetrahydro-5,13-dioxa-7,15-diazadiimidazo-[4,5-b:4′,5′-m]pentacene-2,10-dione), shows an X-ray powder diagram consisting of only ca 12 broad peaks. Indexing was not possible. The structure was solved by global lattice energy minimizations. The program CRYSCA [Schmidt & Kalkhof (1999), CRYSCA. Clariant GmbH, Pigments Research, Frankfurt am Main, Germany] was used to predict the possible crystal structures in different space groups. By comparing simulated and experimental powder diagrams, the correct structure was identified among the predicted structures. Owing to the low quality of the experimental powder diagram the Rietveld refinements gave no distinctive results and it was difficult to prove the correctness of the crystal structure. Finally, the structure was confirmed to be correct by refining the crystal structure of an isostructural mixed crystal having a better X-ray powder diagram. The compound crystallizes in P, Z = 1. The crystal structure consists of a very dense packing of molecules, which are connected by hydrogen bridges of the type N—H...O=C. This packing explains the observed insolubility. The work shows that crystal structures of molecular compounds may be solved by lattice energy minimization from diffraction data of limited quality, even when indexing is not possible.

Computing details

Cell refinement: Fullprof for (I). Data reduction: Fullprof for (I). For both compounds, program(s) used to solve structure: CRYSCA (Energy minimization, M.U. Schmidt and H. Kalkhof, 1999). Program(s) used to refine structure: Fullprof for (I).

Figures

(I) 6,14-Dichlor-1,9-dimethyl-1,3,9,11-tetrahydro-diimidazo[4,5 − b:4',5'-m] triphendioxazin-2,10-dion

Crystal data

C22H12Cl2N6O4	Z = 1
Mr = 495.3	F(000) = 252
Triclinic, P1	Unit cell determined by Rietveld refinement
a = 4.2753 (15) Å	Dx = 1.742 Mg m^−3
b = 8.311 (3) Å	Cu Kα radiation, λ = 1.54059 Å
c = 14.092 (5) Å	θ = 1.5–17°
α = 107.23 (3)°	T = 293 K
β = 93.53 (2)°	Powder, dark violet
γ = 97.17 (3)°	× × mm
V = 472.0 (3) Å^3

Data collection

STOE Stadi-P, 0.7mm Capillary diffractometer	109 independent reflections
Radiation source: X-ray	θmax = 17°, θmin = 1.5°
Ge-111 monochromator	h = ?→?
Transmission scans	k = ?→?
109 measured reflections	l = ?→?

Refinement

wR(F^2) = 0.212	Primary atom site location: energy minimization
S = 11.5	Secondary atom site location: energy minimization
109 reflections	Hydrogen site location: energy minimization
9 parameters	Calc
3 restraints

Special details

Experimental. Structure determined from X-ray powder data. Synchrotron data Structure solution: by energy minimization using the program CRYSCA (Martin U. Schmidt & Holger Kalkhof, 1999). Rietveld refinement: Program GSAS, 3 rigid bodies

Geometry. Rigid body Rietveld refinement. Geometry of molecule taken from crystal structures of other compounds, and not further refined

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C1	0.05795 (1)	−0.14104 (1)	0.03130 (1)	0.0*
C2	0.23043 (1)	0.02443 (1)	0.08370 (1)	0.0*
C3	0.15843 (1)	0.16338 (1)	0.04733 (1)	0.0*
O4	0.31404 (1)	0.32352 (1)	0.09386 (1)	0.0*
C5	0.53528 (1)	0.34715 (1)	0.17420 (1)	0.0*
C6	0.59515 (1)	0.20735 (1)	0.20612 (1)	0.0*
N7	0.43886 (1)	0.04392 (1)	0.15959 (1)	0.0*
Cl8	0.13283 (1)	−0.31079 (1)	0.07087 (1)	0.0*
C9	0.68490 (1)	0.51019 (1)	0.21830 (1)	0.0*
C10	0.90776 (1)	0.53398 (1)	0.29924 (1)	0.0*
C11	0.97645 (1)	0.39784 (1)	0.33418 (1)	0.0*
C12	0.81955 (1)	0.23540 (1)	0.28733 (1)	0.0*
N13	1.21072 (1)	0.46936 (1)	0.41602 (1)	0.0*
C14	1.27974 (1)	0.64470 (1)	0.42939 (1)	0.0*
O15	1.47337 (1)	0.74718 (1)	0.49401 (1)	0.0*
N16	1.09234 (1)	0.68229 (1)	0.35732 (1)	0.0*
C17	1.09366 (1)	0.85003 (1)	0.34613 (1)	0.0*
H18	0.63464 (1)	0.61043 (1)	0.19270 (1)	0.0*
H19	0.86889 (1)	0.13472 (1)	0.31263 (1)	0.0*
H20	1.31373 (1)	0.40765 (1)	0.45849 (1)	0.0*
H21	1.10320 (1)	0.93834 (1)	0.41628 (1)	0.0*
H22	0.89605 (1)	0.84880 (1)	0.29907 (1)	0.0*
H23	1.29311 (1)	0.87929 (1)	0.31237 (1)	0.0*

Geometric parameters (Å, º)

C1—C2	1.4349 (1)	C10—N16	1.3756 (1)
C1—Cl8	1.7207 (1)	C11—C12	1.3785 (1)
C2—C3	1.4529 (1)	C11—N13	1.4106 (1)
C2—N7	1.3070 (1)	C12—H19	1.0408 (1)
C3—O4	1.3611 (1)	N13—C14	1.4034 (1)
O4—C5	1.3803 (1)	N13—H20	1.0104 (1)
C5—C6	1.4098 (1)	C14—O15	1.2296 (1)
C5—C9	1.3666 (1)	C14—N16	1.3861 (1)
C6—N7	1.3833 (1)	N16—C17	1.4481 (1)
C6—C12	1.3912 (1)	C17—H21	1.0370 (1)
C9—C10	1.3905 (1)	C17—H22	1.0385 (1)
C9—H18	1.0409 (1)	C17—H23	1.0389 (1)
C10—C11	1.4157 (1)
C2—C1—Cl8	118.4468 (1)	C10—C11—N13	106.2138 (1)
C1—C2—C3	116.2728 (1)	C12—C11—N13	134.0398 (1)
C1—C2—N7	120.1458 (1)	C6—C12—C11	119.4672 (1)
C3—C2—N7	123.5814 (1)	C6—C12—H19	120.3846 (1)
C2—C3—O4	119.1306 (1)	C11—C12—H19	120.1482 (1)
C3—O4—C5	118.3039 (1)	C11—N13—C14	107.9976 (1)
O4—C5—C6	120.0153 (1)	C11—N13—H20	127.0901 (1)
O4—C5—C9	116.0361 (1)	C14—N13—H20	124.9123 (1)
C6—C5—C9	123.9486 (1)	N13—C14—O15	125.7657 (1)
C5—C6—N7	122.3299 (1)	N13—C14—N16	108.2848 (1)
C5—C6—C12	118.612 (1)	O15—C14—N16	125.9495 (1)
N7—C6—C12	119.0580 (1)	C10—N16—C14	108.3808 (1)
C2—N7—C6	116.6389 (1)	C10—N16—C17	126.4254 (1)
C5—C9—C10	116.0303 (1)	C14—N16—C17	125.1939 (1)
C5—C9—H18	121.8652 (1)	N16—C17—H21	108.8894 (1)
C10—C9—H18	122.1045 (1)	N16—C17—H22	109.3328 (1)
C9—C10—C11	122.1954 (1)	N16—C17—H23	108.8735 (1)
C9—C10—N16	128.6816 (1)	H21—C17—H22	112.9502 (1)
C11—C10—N16	109.1231 (1)	H21—C17—H23	109.2285 (1)
C10—C11—C12	119.7465 (1)	H22—C17—H23	107.4900 (1)

(calc) 6,14-Dichlor-1,9-dimethyl-1,3,9,11-tetrahydro-diimidazo[4,5 − b:4',5'-m] triphendioxazin-2,10-dion

Crystal data

C22H12Cl2N6O4	γ = 95.1180 (1)°
Mr = 495.3	V = 481.93 (1) Å^3
Triclinic, P1	Z = 1
a = 4.3346 (1) Å	Crystal structure calculated by lattice energy minimization without reference to experimental data.
b = 8.4193 (1) Å	Cu Kα radiation, λ = 1.54059 Å
c = 13.9057 (1) Å	T = 293 K
α = 106.9467 (1)°	Powder, dark violet
β = 92.9106 (1)°	× × mm

Data collection

STOE Stadi-P, 0.7mm Capillary diffractometer	θmax = 17°, θmin = 1.5°
Radiation source: X-ray	h = ?→?
Ge-111 monochromator	k = ?→?
Transmission scans	l = ?→?

Refinement

Primary atom site location: lattice energy minimization	Calc
Secondary atom site location: lattice energy minimization
Hydrogen site location: lattice energy minimization

Special details

Experimental. Crystal structure calculated by lattice energy minimization using the program CRYSCA (Martin U. Schmidt & Holger Kalkhof, 1999). without any reference to experimental data. The simulated powder diagram of the calculated structure is similar to the experimental X-ray powder diagram (no fit). No Rietveld refinement.

Geometry. Rigid molecule. Geometry of molecule taken from crystal structures of other compounds, and not further optimized

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C1	0.06106 (1)	−0.13993 (1)	0.03139 (1)	0.0*
C3	0.22942 (1)	0.02065 (1)	0.08267 (1)	0.0*
C2	0.15438 (1)	0.15873 (1)	0.04628 (1)	0.0*
O1	0.30602 (1)	0.31430 (1)	0.09177 (1)	0.0*
C5	0.52628 (1)	0.33430 (1)	0.17113 (1)	0.0*
C4	0.58923 (1)	0.19557 (1)	0.20313 (1)	0.0*
N1	0.43699 (1)	0.03676 (1)	0.15764 (1)	0.0*
Cl1	0.13968 (1)	−0.30841 (1)	0.07105 (1)	0.0*
C6	0.67187 (1)	0.49282 (1)	0.21421 (1)	0.0*
C7	0.89375 (1)	0.51295 (1)	0.29416 (1)	0.0*
C8	0.96542 (1)	0.37770 (1)	0.32913 (1)	0.0*
C9	0.81254 (1)	0.21988 (1)	0.28333 (1)	0.0*
N10	1.19759 (1)	0.44472 (1)	0.40982 (1)	0.0*
C11	1.26246 (1)	0.61657 (1)	0.42248 (1)	0.0*
O11	1.45336 (1)	0.71473 (1)	0.48604 (1)	0.0*
N2	1.07457 (1)	0.65643 (1)	0.35111 (1)	0.0*
C16	1.07205 (1)	0.82180 (1)	0.33951 (1)	0.0*
H6	0.61942 (1)	0.59240 (1)	0.18858 (1)	0.0*
H9	0.86409 (1)	0.11987 (1)	0.30866 (1)	0.0*
H10	1.30181 (1)	0.38234 (1)	0.45200 (1)	0.0*
H161	1.08264 (1)	0.90885 (1)	0.41051 (1)	0.0*
H162	0.87597 (1)	0.82358 (1)	0.29368 (1)	0.0*
H163	1.26595 (1)	0.84749 (1)	0.30325 (1)	0.0*