Urotropin azelate: a rather unwilling co-crystal

Urotropin (U) and azelaic acid (AA) form 1:1 co-crystals (UA) that give rise to a rather complex diffraction pattern, the main features of which are diffuse rods and bands in addition to the Bragg reflections. UA is characterized by solvent inclusions, parasite phases, and high vacancy and dislocation densities. These defects compounded with the pronounced tendency of U to escape from the crystal edifice lead to at least seven exotic phase transitions (many of which barely manifest themselves in a differential scanning calorimetry trace). These involve different incommensurate phases and a peritectoid reaction in the recrystallization regime (). The system may be understood as an OD (order–disorder) structure based on a layer with layer group and cell  ≃ 4.7,  ≃ 26.1 and  ≃ 14.4 Å. At 338 K the layer stacking is random, but with decreasing temperature the build-up of an orthorhombic MDO (maximal degree of order) structure with cell a = 2a, b = b, c = c and space group is begun (at ∼301 K). The superposition structure of the OD system at T = 286 (1) K with space group and cell  = ,  =  and  =  owes its cohesion to van der Waals interactions between the AA chains and to three types of hydrogen bonds of varied strength between U—U and U—AA. Before reaching completion, this MDO structure is transformed, at 282 K, into a monoclinic one with cell a = −ac/4, b = b, c = −2, space group , spontaneous deformation ∼2°, and ferroelastic domains. This transformation is achieved in two steps: first a furtive triggering transition, which is not yet fully understood, and second an improper ferroelastic transition. At ∼233 K, the system reaches its ground state (cell  = ,  = ,  =  and space group ) via an irreversible transition. The phase transitions below 338 K are described by a model based on the interaction of two thermally activated slip systems. The OD structure is described in terms of a three-dimensional Monte Carlo model that involves first- and second-neighbour interactions along the a axis and first-neighbour interactions along the b and c axes. This model includes random shifts of the chains along their axes and satisfactorily accounts for most features that are seen in the observed diffraction pattern.

Computing details

Data collection: Stoe IPDS; cell refinement: Stoe IPDS; data reduction: Stoe IPDS; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Bruker XP; software used to prepare material for publication: Bruker SHELXTL.

(global)

Crystal data

(C6H12N4·C9H16O4)	Dx = 1.231 Mg m^−3
Mr = 328.41	Melting point: 403 K
Orthorhombic, Bmmb	Mo Kα radiation, λ = 0.71073 Å
a = 9.4157 (19) Å	Cell parameters from 721 reflections
b = 26.124 (5) Å	θ = 14.5–24.1°
c = 7.2034 (14) Å	µ = 0.09 mm^−1
V = 1771.9 (6) Å^3	T = 286 K
Z = 4	Platelet, colourless
F(000) = 712	0.72 × 0.56 × 0.04 mm

Data collection

Stoe IPDS diffractometer	539 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.053
Graphite monochromator	θmax = 25.0°, θmin = 3.6°
Detector resolution: 6.67 pixels mm^-1	h = −10→10
φ scans	k = −31→31
6062 measured reflections	l = −8→8
818 independent reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.041	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.126	H atoms treated by a mixture of independent and constrained refinement
S = 0.91	w = 1/[σ^2(Fo^2) + (0.0754P)^2 + 0.4007P] where P = (Fo^2 + 2Fc^2)/3
818 reflections	(Δ/σ)max < 0.001
110 parameters	Δρmax = 0.15 e Å^−3
0 restraints	Δρmin = −0.13 e Å^−3

Special details

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.

Authors remarks: Note that the structure is disordered, with the superposition of two acid chains and splitted carboxylic functions. This leads to problematic calculations of torsion angles, in the check-CIF procedure.

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.

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

	x	y	z	Uiso*/Ueq	Occ. (<1)
O1	0.5913 (3)	0.37538 (12)	0.2149 (4)	0.0991 (10)	0.50
H1	0.5000	0.343 (2)	0.298 (8)	0.23 (2)*
O2A	0.3868 (10)	0.3719 (5)	0.0919 (13)	0.139 (4)	0.25
O2B	0.4232 (9)	0.3570 (3)	0.0196 (10)	0.100 (2)	0.25
N1	0.5000	0.29636 (7)	0.4327 (2)	0.0638 (5)
N2	0.62853 (18)	0.2500	0.6708 (2)	0.0706 (6)
C1	0.5000	0.38525 (9)	0.0717 (3)	0.0717 (7)
C2	0.5749 (4)	0.42167 (13)	−0.0624 (5)	0.0731 (9)	0.50
H2A	0.6151	0.4499	0.0074	0.107 (13)*	0.50
H2B	0.6526	0.4037	−0.1222	0.108 (13)*	0.50
C3	0.4764 (11)	0.44274 (12)	−0.2102 (4)	0.075 (2)	0.50
H3A	0.4282	0.4146	−0.2713	0.107 (13)*	0.50
H3B	0.4049	0.4641	−0.1519	0.101 (13)*	0.50
C4	0.5559 (4)	0.47382 (15)	−0.3530 (5)	0.0865 (12)	0.50
H4A	0.6230	0.4514	−0.4151	0.145 (19)*	0.50
H4B	0.6104	0.4998	−0.2885	0.133 (17)*	0.50
C5	0.4662 (7)	0.5000	−0.5000	0.079 (3)	0.50
H5B	0.4055	0.5252	−0.4409	0.118*	0.25
H5C	0.4055	0.4748	−0.5591	0.118*	0.25
C7	0.6267 (2)	0.29466 (8)	0.5523 (2)	0.0798 (6)
H7A	0.7111	0.2946	0.4751	0.114 (7)*
H7B	0.6293	0.3252	0.6289	0.109 (6)*
C8	0.5000	0.2500	0.7842 (4)	0.0732 (10)
H8A	0.5000	0.2800	0.8635	0.11 (6)*	0.50
H8B	0.5000	0.2200	0.8635	0.11 (6)*	0.50
C9	0.5000	0.2500	0.3177 (4)	0.0569 (7)
H9A	0.5833	0.2500	0.2385	0.06 (3)*	0.50
H9B	0.4167	0.2500	0.2385	0.08 (4)*	0.50

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.100 (2)	0.1015 (18)	0.0958 (18)	−0.0275 (16)	−0.0252 (17)	0.0294 (16)
O2A	0.074 (5)	0.232 (11)	0.111 (7)	−0.083 (6)	0.003 (5)	0.047 (7)
O2B	0.109 (6)	0.108 (4)	0.082 (4)	−0.065 (4)	−0.019 (4)	0.033 (3)
N1	0.0748 (13)	0.0618 (10)	0.0546 (9)	0.000	0.000	0.0048 (8)
N2	0.0462 (11)	0.1139 (15)	0.0517 (9)	0.000	−0.0103 (8)	0.000
C1	0.086 (2)	0.0550 (13)	0.0741 (15)	0.000	0.000	0.0046 (11)
C2	0.077 (2)	0.0646 (17)	0.0776 (19)	−0.0102 (16)	−0.0014 (16)	0.0102 (17)
C3	0.081 (7)	0.0614 (14)	0.0837 (16)	−0.005 (2)	−0.001 (2)	0.0100 (13)
C4	0.093 (3)	0.082 (2)	0.085 (2)	−0.0042 (18)	0.0022 (18)	0.028 (2)
C5	0.083 (8)	0.066 (2)	0.089 (3)	0.000	0.000	0.012 (2)
C7	0.0700 (12)	0.1003 (12)	0.0691 (10)	−0.0321 (9)	−0.0016 (9)	−0.0086 (9)
C8	0.068 (2)	0.109 (3)	0.0422 (14)	0.000	0.000	0.000
C9	0.0495 (17)	0.0789 (19)	0.0424 (12)	0.000	0.000	0.000

Geometric parameters (Å, º)

O1—O2A^i	0.914 (9)	C1—C2^i	1.529 (4)
O1—C1	1.367 (3)	C1—C2	1.529 (4)
O1—O2B^i	1.493 (8)	C2—C3	1.516 (7)
O1—O1^i	1.720 (7)	C2—H2A	0.9700
O1—H1	1.34 (4)	C2—H2B	0.9700
O2A—O2B	0.735 (13)	C3—C4	1.510 (6)
O2A—O1^i	0.914 (9)	C3—H3A	0.9700
O2A—C1	1.131 (9)	C3—H3B	0.9700
O2A—C2^i	1.748 (11)	C4—C5	1.518 (5)
O2A—H7B^ii	2.7267	C4—H4A	0.9700
O2B—C1	1.100 (8)	C4—H4B	0.9700
O2B—O2B^i	1.447 (18)	C5—C4^iv	1.518 (5)
O2B—O1^i	1.493 (8)	C5—H5B	0.9700
O2B—C2^i	1.790 (8)	C5—H5C	0.9700
N1—C9	1.467 (2)	C7—H7A	0.9700
N1—C7	1.473 (2)	C7—H7B	0.9700
N1—C7^i	1.473 (2)	C8—N2^v	1.460 (2)
N2—C7^iii	1.446 (2)	C8—H8A	0.9700
N2—C7	1.446 (2)	C8—H8B	0.9700
N2—C8	1.460 (2)	C9—N1^iii	1.467 (2)
C1—O2B^i	1.100 (8)	C9—H9A	0.9700
C1—O2A^i	1.131 (9)	C9—H9B	0.9700
C1—O1^i	1.367 (3)
O2A^i—O1—C1	55.2 (6)	O2A—C1—C2^i	80.7 (6)
O2A^i—O1—O2B^i	22.4 (9)	O2A^i—C1—C2^i	135.1 (6)
C1—O1—O2B^i	45.0 (3)	O1—C1—C2^i	152.2 (3)
O2A^i—O1—O1^i	103.0 (6)	O1^i—C1—C2^i	107.69 (19)
C1—O1—O1^i	51.04 (16)	O2B—C1—C2	120.4 (4)
O2B^i—O1—O1^i	84.8 (4)	O2B^i—C1—C2	84.2 (5)
O2A^i—O1—H1	121 (2)	O2A—C1—C2	135.1 (6)
C1—O1—H1	93.0 (19)	O2A^i—C1—C2	80.7 (6)
O2B^i—O1—H1	99 (2)	O1—C1—C2	107.69 (19)
O1^i—O1—H1	50.2 (16)	O1^i—C1—C2	152.2 (3)
O2B—O2A—O1^i	129.4 (19)	C2^i—C1—C2	55.0 (3)
O2B—O2A—C1	68.5 (11)	C3—C2—C1	112.8 (4)
O1^i—O2A—C1	83.2 (8)	C3—C2—H2A	109.0
O2B—O2A—C2^i	81.2 (12)	C1—C2—H2A	109.0
O1^i—O2A—C2^i	119.7 (11)	C3—C2—H2B	109.0
C1—O2A—C2^i	59.6 (5)	C1—C2—H2B	109.0
O2B—O2A—H7B^ii	104.3	H2A—C2—H2B	107.8
O1^i—O2A—H7B^ii	98.7	C4—C3—C2	111.7 (7)
C1—O2A—H7B^ii	171.3	C4—C3—H3A	109.3
C2^i—O2A—H7B^ii	125.3	C2—C3—H3A	109.3
O2A—O2B—C1	73.1 (12)	C4—C3—H3B	109.3
O2A—O2B—O2B^i	117.8 (13)	C2—C3—H3B	109.3
C1—O2B—O2B^i	48.9 (5)	H3A—C3—H3B	107.9
O2A—O2B—O1^i	28.3 (11)	C3—C4—C5	116.2 (5)
C1—O2B—O1^i	61.5 (4)	C3—C4—H4A	108.2
O2B^i—O2B—O1^i	95.2 (4)	C5—C4—H4A	108.2
O2A—O2B—C2^i	74.9 (13)	C3—C4—H4B	108.2
C1—O2B—C2^i	58.2 (4)	C5—C4—H4B	108.2
O2B^i—O2B—C2^i	89.4 (3)	H4A—C4—H4B	107.4
O1^i—O2B—C2^i	90.5 (5)	C4—C5—C4^iv	112.3 (5)
C9—N1—C7	107.79 (12)	C4—C5—H5B	109.1
C9—N1—C7^i	107.79 (12)	C4^iv—C5—H5B	109.1
C7—N1—C7^i	108.26 (18)	C4—C5—H5C	109.1
C7^iii—N2—C7	107.62 (18)	C4^iv—C5—H5C	109.1
C7^iii—N2—C8	108.71 (12)	H5B—C5—H5C	107.9
C7—N2—C8	108.71 (12)	N2—C7—N1	112.28 (14)
O2B—C1—O2B^i	82.3 (10)	N2—C7—H7A	109.1
O2B—C1—O2A	38.4 (7)	N1—C7—H7A	109.1
O2B^i—C1—O2A	117.2 (8)	N2—C7—H7B	109.1
O2B—C1—O2A^i	117.2 (8)	N1—C7—H7B	109.1
O2B^i—C1—O2A^i	38.4 (7)	H7A—C7—H7B	107.9
O2A—C1—O2A^i	140.9 (13)	N2—C8—N2^v	112.0 (2)
O2B—C1—O1	123.0 (5)	N2—C8—H8A	109.2
O2B^i—C1—O1	73.6 (4)	N2^v—C8—H8A	109.2
O2A—C1—O1	115.9 (6)	N2—C8—H8B	109.2
O2A^i—C1—O1	41.6 (5)	N2^v—C8—H8B	109.2
O2B—C1—O1^i	73.6 (4)	H8A—C8—H8B	107.9
O2B^i—C1—O1^i	123.0 (5)	N1—C9—N1^iii	111.3 (2)
O2A—C1—O1^i	41.6 (5)	N1—C9—H9A	109.4
O2A^i—C1—O1^i	115.9 (6)	N1^iii—C9—H9A	109.4
O1—C1—O1^i	77.9 (3)	N1—C9—H9B	109.4
O2B—C1—C2^i	84.2 (5)	N1^iii—C9—H9B	109.4
O2B^i—C1—C2^i	120.4 (4)	H9A—C9—H9B	108.0
O1^i—O2A—O2B—C1	−60.7 (19)	O1^i—O2A—C1—O1	26.1 (12)
C2^i—O2A—O2B—C1	60.7 (3)	C2^i—O2A—C1—O1	156.5 (4)
H7B^ii—O2A—O2B—C1	−174.9	H7B^ii—O2A—C1—O1	−76.7
O1^i—O2A—O2B—O2B^i	−40 (3)	O2B—O2A—C1—O1^i	−137.3 (19)
C1—O2A—O2B—O2B^i	20.4 (8)	C2^i—O2A—C1—O1^i	130.4 (9)
C2^i—O2A—O2B—O2B^i	81.1 (8)	H7B^ii—O2A—C1—O1^i	−102.8
H7B^ii—O2A—O2B—O2B^i	−154.5	O2B—O2A—C1—C2^i	92.3 (12)
C1—O2A—O2B—O1^i	60.7 (19)	O1^i—O2A—C1—C2^i	−130.4 (9)
C2^i—O2A—O2B—O1^i	121 (2)	H7B^ii—O2A—C1—C2^i	126.8
H7B^ii—O2A—O2B—O1^i	−114.2	O2B—O2A—C1—C2	83.6 (16)
O1^i—O2A—O2B—C2^i	−121 (2)	O1^i—O2A—C1—C2	−139.2 (6)
C1—O2A—O2B—C2^i	−60.7 (3)	C2^i—O2A—C1—C2	−8.8 (8)
H7B^ii—O2A—O2B—C2^i	124.4	H7B^ii—O2A—C1—C2	118.1
O2A—O2B—C1—O2B^i	155.8 (11)	O2A^i—O1—C1—O2B	95.1 (13)
O1^i—O2B—C1—O2B^i	127.8 (4)	O2B^i—O1—C1—O2B	69.0 (10)
C2^i—O2B—C1—O2B^i	−121.8 (4)	O1^i—O1—C1—O2B	−61.1 (6)
O2B^i—O2B—C1—O2A	−155.8 (11)	O2A^i—O1—C1—O2B^i	26.1 (13)
O1^i—O2B—C1—O2A	−28.0 (12)	O1^i—O1—C1—O2B^i	−130.1 (5)
C2^i—O2B—C1—O2A	82.4 (13)	O2A^i—O1—C1—O2A	138.8 (18)
O2A—O2B—C1—O2A^i	139.2 (17)	O2B^i—O1—C1—O2A	112.7 (9)
O2B^i—O2B—C1—O2A^i	−16.6 (7)	O1^i—O1—C1—O2A	−17.4 (8)
O1^i—O2B—C1—O2A^i	111.2 (7)	O2B^i—O1—C1—O2A^i	−26.1 (13)
C2^i—O2B—C1—O2A^i	−138.4 (6)	O1^i—O1—C1—O2A^i	−156.2 (11)
O2A—O2B—C1—O1	91.2 (14)	O2A^i—O1—C1—O1^i	156.2 (11)
O2B^i—O2B—C1—O1	−64.7 (4)	O2B^i—O1—C1—O1^i	130.1 (5)
O1^i—O2B—C1—O1	63.2 (5)	O2A^i—O1—C1—C2^i	−98.8 (11)
C2^i—O2B—C1—O1	173.5 (4)	O2B^i—O1—C1—C2^i	−124.8 (7)
O2A—O2B—C1—O1^i	28.0 (12)	O1^i—O1—C1—C2^i	105.1 (5)
O2B^i—O2B—C1—O1^i	−127.8 (4)	O2A^i—O1—C1—C2	−52.1 (11)
C2^i—O2B—C1—O1^i	110.4 (3)	O2B^i—O1—C1—C2	−78.2 (5)
O2A—O2B—C1—C2^i	−82.4 (13)	O1^i—O1—C1—C2	151.8 (3)
O2B^i—O2B—C1—C2^i	121.8 (4)	O2B—C1—C2—C3	41.6 (7)
O1^i—O2B—C1—C2^i	−110.4 (3)	O2B^i—C1—C2—C3	119.1 (5)
O2A—O2B—C1—C2	−125.6 (12)	O2A—C1—C2—C3	−4.1 (11)
O2B^i—O2B—C1—C2	78.6 (5)	O2A^i—C1—C2—C3	157.8 (7)
O1^i—O2B—C1—C2	−153.6 (3)	O1—C1—C2—C3	−170.2 (3)
C2^i—O2B—C1—C2	−43.2 (4)	O1^i—C1—C2—C3	−72.5 (6)
O1^i—O2A—C1—O2B	137.3 (19)	C2^i—C1—C2—C3	−14.7 (3)
C2^i—O2A—C1—O2B	−92.3 (12)	C1—C2—C3—C4	−173.7 (3)
H7B^ii—O2A—C1—O2B	34.5	C2—C3—C4—C5	−175.7 (3)
O2B—O2A—C1—O2B^i	−27.1 (13)	C3—C4—C5—C4^iv	−174.8 (4)
O1^i—O2A—C1—O2B^i	110.1 (11)	C7^iii—N2—C7—N1	59.7 (2)
C2^i—O2A—C1—O2B^i	−119.5 (5)	C8—N2—C7—N1	−57.90 (19)
H7B^ii—O2A—C1—O2B^i	7.3	C9—N1—C7—N2	−59.39 (18)
O2B—O2A—C1—O2A^i	−67 (2)	C7^i—N1—C7—N2	57.0 (2)
O1^i—O2A—C1—O2A^i	70 (2)	C7^iii—N2—C8—N2^v	−58.44 (10)
C2^i—O2A—C1—O2A^i	−159.6 (16)	C7—N2—C8—N2^v	58.44 (10)
H7B^ii—O2A—C1—O2A^i	−32.8	C7—N1—C9—N1^iii	58.33 (11)
O2B—O2A—C1—O1	−111.2 (11)	C7^i—N1—C9—N1^iii	−58.33 (11)

Symmetry codes: (i) −x+1, y, z; (ii) x−1/2, y, z−1/2; (iii) x, −y+1/2, z; (iv) x, −y+1, −z−1; (v) −x+1, −y+1/2, z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···N1	1.34 (4)	1.56 (6)	2.732 (3)	140 (2)
C7—H7B···O2A^vi	0.97	2.73	3.185 (10)	110
C7—H7A···O2B^vi	0.97	2.60	3.240 (8)	124
C8—H8B···O2B^vii	0.97	2.41	3.348 (9)	161
C9—H9B···N2^ii	0.97	2.76	3.654 (2)	154
C2—H2B···O1^viii	0.97	2.78	3.730 (5)	166

Symmetry codes: (ii) x−1/2, y, z−1/2; (vi) x+1/2, y, z+1/2; (vii) x, −y+1/2, z+1; (viii) −x+3/2, y, z−1/2.