Benzene-1,4-diol–5-(1H-imidazol-1-yl)pyrimidine (1/1)

Abstract

The asymmetric unit of title compound, C₇H₆N₄·C₆H₆O₂, contains one 5-(1H-imidazol-1-yl)pyrimidine mol­ecule and two half benzene-1,4-diol mol­ecules; the benzene-1,4-diol mol­ecules are located on individual inversion centers. In the pyrimidine mol­ecule, the imidazole ring is twisted with respect to the pyrimidine ring at a dihedral angle of 25.73 (7)°. In the crystal, O—H⋯N hydrogen bonds link the mol­ecules to form supra­molecular chains. π–π stacking is also observed in the crystal, the centroid–centroid distance between parallel imdazole rings being 3.5543 (16) Å.

Related literature

For related structures, see: Nieuwenhuyzen et al. (1999 ▶); Clausen et al. (2010 ▶).

Experimental

Crystal data

• C₇H₆N₄·C₆H₆O₂

• M _r = 256.27

• Triclinic,

• a = 6.8219 (18) Å

• b = 9.550 (3) Å

• c = 10.449 (3) Å

• α = 108.177 (3)°

• β = 102.381 (4)°

• γ = 98.602 (4)°

• V = 614.3 (3) ų

• Z = 2

• Mo Kα radiation

• μ = 0.10 mm⁻¹

• T = 298 K

• 0.36 × 0.24 × 0.12 mm

Data collection

• Bruker SMART 1000 diffractometer

• 3103 measured reflections

• 2176 independent reflections

• 1791 reflections with I > 2σ(I)

• R _int = 0.013

Refinement

• R[F ² > 2σ(F ²)] = 0.045

• wR(F ²) = 0.115

• S = 1.04

• 2176 reflections

• 174 parameters

• H-atom parameters constrained

• Δρ_max = 0.13 e Å⁻³

• Δρ_min = −0.30 e Å⁻³

Data collection: SMART (Bruker, 2007 ▶); cell refinement: SAINT (Bruker, 2007 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supplementary Material

Supplementary material file. DOI: 10.1107/S1600536811043819/xu5356Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1A⋯N1i	0.82	1.96	2.764 (2)	168
O2—H2A⋯N4ii	0.82	2.02	2.835 (2)	174

Symmetry codes: (i) ; (ii) .

supplementary crystallographic information

Comment

The N atoms on rigid rings, such as pyridine, pyrimidine, imidazole et al., could form strong hydrogen-bond interaction and play an essential role in synthesis of supermolecular compounds. 5-(1H-Imidazol-1-yl)pyrimidine (L1) includes three such nitrogen atoms which behave as hydrogen-bond acceptors. benzene-1,4-diol (L2) is a good hydrogen-bonding donor which can form co-crystals with heterocyclic amine systems (Nieuwenhuyzen et al., 1999; Clausen et al., 2010). Here we report the co-crystal states of L1 and L2.

The molecular structure is shown in Fig. 1. The asymmetric unit contains one L1 molecule and two half of L2 in the asymmetric unit. A H-bonding driven double chain was generated from O—H···N hydrogen bonds between these molecules (Fig. 2). Imidazol ring is twisted to pyrimidine ring (the dihedral angle, 25.73 (7)°), while nearly coplanar with benzene ring of L2 (the dihedral angle, 5.54 (7)°). The π–π stacking is also observed in the crystal structure, centroids distance between parallel imdazole ring being 3.5543 (16) Å.

Experimental

A CH₂Cl₂ and CH₃CN solution (15 ml, 1:1, v/v) of 5-(1H-imidazol-1-yl)pyrimidine (15.7 mg, 0.1 mmol) and benzene-1,4-diol (11.0 mg, 0.1 mmol) was kept at room temperature. Upon slow evaporation of the solvent about 5 days, colorless crystals were obtained.

Refinement

All H atoms were placed in idealized positions and treated as riding, with C—H = 0.93 and O—H = 0.82 Å, U_iso(H) = 1.2U_eq(C), or 1.5U_eq(O).

Figures

Fig. 1.

The structure of the title compound with 30% probability displacement ellipsoids.(Symmetry codes: (i) -x,-y + 1,-z + 1)

Fig. 2.

A view of the hydrogen-bonded double-chain observed in the crystal structure of (1).

Crystal data

C7H6N4·C6H6O2	Z = 2
Mr = 256.27	F(000) = 268
Triclinic, P1	Dx = 1.385 Mg m−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 6.8219 (18) Å	Cell parameters from 1283 reflections
b = 9.550 (3) Å	θ = 2.3–26.8°
c = 10.449 (3) Å	µ = 0.10 mm−1
α = 108.177 (3)°	T = 298 K
β = 102.381 (4)°	Block, colourless
γ = 98.602 (4)°	0.36 × 0.24 × 0.12 mm
V = 614.3 (3) Å3

Data collection

Bruker SMART 1000 diffractometer	1791 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.013
graphite	θmax = 25.2°, θmin = 2.1°
φ and ω scans	h = −6→8
3103 measured reflections	k = −11→11
2176 independent reflections	l = −11→12

Refinement

Refinement on F2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.045	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.115	H-atom parameters constrained
S = 1.04	w = 1/[σ2(Fo2) + (0.0603P)2 + 0.0979P] where P = (Fo2 + 2Fc2)/3
2176 reflections	(Δ/σ)max = 0.002
174 parameters	Δρmax = 0.13 e Å−3
0 restraints	Δρmin = −0.30 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.

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
C1	0.3093 (3)	0.5951 (2)	0.03876 (18)	0.0443 (4)
H1	0.3309	0.6809	0.0146	0.053*
C2	0.2073 (3)	0.3702 (2)	0.02839 (19)	0.0489 (5)
H2	0.1427	0.2677	−0.0065	0.059*
C3	0.3175 (3)	0.4481 (2)	0.16172 (19)	0.0479 (5)
H3	0.3432	0.4109	0.2345	0.058*
C4	0.6323 (3)	0.83862 (19)	0.27343 (19)	0.0468 (5)
H4	0.6347	0.8351	0.1838	0.056*
C5	0.5094 (2)	0.71929 (18)	0.28759 (17)	0.0379 (4)
C6	0.5138 (3)	0.7279 (2)	0.42203 (18)	0.0470 (5)
H6	0.4334	0.6490	0.4355	0.056*
C7	0.7401 (3)	0.9551 (2)	0.5069 (2)	0.0511 (5)
H7	0.8208	1.0382	0.5843	0.061*
C8	−0.0026 (3)	0.41667 (18)	0.58820 (17)	0.0396 (4)
C9	−0.0960 (3)	0.34868 (19)	0.44598 (18)	0.0465 (5)
H9	−0.1616	0.2463	0.4087	0.056*
C10	0.0931 (3)	0.56915 (19)	0.64137 (18)	0.0459 (5)
H10	0.1561	0.6168	0.7371	0.055*
C11	0.1916 (3)	0.0311 (2)	0.09527 (17)	0.0416 (4)
C12	0.0237 (3)	0.06699 (19)	0.14148 (17)	0.0425 (4)
H12	0.0393	0.1122	0.2370	0.051*
C13	−0.1671 (3)	0.03627 (19)	0.04686 (17)	0.0415 (4)
H13	−0.2791	0.0609	0.0788	0.050*
N1	0.2027 (2)	0.46188 (16)	−0.04935 (15)	0.0475 (4)
N2	0.3850 (2)	0.59439 (15)	0.16903 (14)	0.0397 (4)
N3	0.7474 (2)	0.95816 (17)	0.38243 (17)	0.0525 (4)
N4	0.6296 (2)	0.84580 (19)	0.53321 (15)	0.0515 (4)
O1	−0.0130 (2)	0.33007 (14)	0.67005 (13)	0.0547 (4)
H1A	0.0532	0.3808	0.7513	0.082*
O2	0.3846 (2)	0.0619 (2)	0.18407 (13)	0.0668 (4)
H2A	0.3794	0.0945	0.2655	0.100*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
C1	0.0524 (11)	0.0423 (10)	0.0381 (9)	0.0075 (8)	0.0114 (8)	0.0164 (8)
C2	0.0564 (12)	0.0382 (9)	0.0478 (11)	0.0042 (8)	0.0165 (9)	0.0111 (8)
C3	0.0618 (12)	0.0412 (10)	0.0434 (10)	0.0076 (9)	0.0165 (9)	0.0194 (8)
C4	0.0538 (11)	0.0427 (10)	0.0423 (10)	0.0081 (8)	0.0140 (8)	0.0139 (8)
C5	0.0377 (9)	0.0386 (9)	0.0359 (9)	0.0106 (7)	0.0098 (7)	0.0106 (7)
C6	0.0410 (10)	0.0555 (11)	0.0398 (10)	0.0046 (8)	0.0089 (8)	0.0153 (9)
C7	0.0441 (11)	0.0489 (11)	0.0451 (11)	0.0067 (9)	0.0029 (8)	0.0045 (9)
C8	0.0418 (10)	0.0383 (9)	0.0368 (9)	0.0080 (7)	0.0118 (7)	0.0110 (8)
C9	0.0550 (11)	0.0324 (8)	0.0407 (10)	−0.0002 (8)	0.0108 (8)	0.0041 (8)
C10	0.0535 (11)	0.0426 (10)	0.0297 (9)	0.0019 (8)	0.0066 (8)	0.0046 (8)
C11	0.0441 (10)	0.0465 (10)	0.0340 (9)	0.0105 (8)	0.0081 (7)	0.0157 (8)
C12	0.0505 (11)	0.0475 (10)	0.0289 (8)	0.0139 (8)	0.0129 (8)	0.0107 (8)
C13	0.0450 (10)	0.0449 (10)	0.0403 (9)	0.0151 (8)	0.0183 (8)	0.0164 (8)
N1	0.0521 (9)	0.0459 (9)	0.0380 (8)	0.0047 (7)	0.0097 (7)	0.0112 (7)
N2	0.0446 (8)	0.0395 (8)	0.0342 (8)	0.0069 (6)	0.0121 (6)	0.0126 (6)
N3	0.0547 (10)	0.0431 (9)	0.0503 (10)	0.0038 (7)	0.0100 (8)	0.0104 (7)
N4	0.0439 (9)	0.0629 (10)	0.0371 (8)	0.0066 (8)	0.0054 (7)	0.0101 (8)
O1	0.0723 (10)	0.0434 (7)	0.0401 (7)	0.0011 (6)	0.0070 (7)	0.0149 (6)
O2	0.0464 (8)	0.1082 (12)	0.0402 (8)	0.0235 (8)	0.0075 (6)	0.0196 (8)

Geometric parameters (Å, °)

C1—N1	1.304 (2)	C7—H7	0.9300
C1—N2	1.351 (2)	C8—O1	1.368 (2)
C1—H1	0.9300	C8—C9	1.380 (2)
C2—C3	1.340 (3)	C8—C10	1.382 (2)
C2—N1	1.367 (2)	C9—C10i	1.378 (2)
C2—H2	0.9300	C9—H9	0.9300
C3—N2	1.377 (2)	C10—C9i	1.378 (2)
C3—H3	0.9300	C10—H10	0.9300
C4—N3	1.324 (2)	C11—O2	1.368 (2)
C4—C5	1.377 (2)	C11—C13ii	1.383 (2)
C4—H4	0.9300	C11—C12	1.383 (3)
C5—C6	1.375 (2)	C12—C13	1.382 (2)
C5—N2	1.415 (2)	C12—H12	0.9300
C6—N4	1.329 (2)	C13—C11ii	1.383 (2)
C6—H6	0.9300	C13—H13	0.9300
C7—N3	1.321 (2)	O1—H1A	0.8200
C7—N4	1.329 (2)	O2—H2A	0.8200
N1—C1—N2	112.37 (16)	C10i—C9—C8	120.72 (16)
N1—C1—H1	123.8	C10i—C9—H9	119.6
N2—C1—H1	123.8	C8—C9—H9	119.6
C3—C2—N1	110.82 (15)	C9i—C10—C8	120.67 (16)
C3—C2—H2	124.6	C9i—C10—H10	119.7
N1—C2—H2	124.6	C8—C10—H10	119.7
C2—C3—N2	105.99 (16)	O2—C11—C13ii	117.69 (16)
C2—C3—H3	127.0	O2—C11—C12	122.90 (15)
N2—C3—H3	127.0	C13ii—C11—C12	119.40 (16)
N3—C4—C5	122.56 (17)	C13—C12—C11	120.52 (16)
N3—C4—H4	118.7	C13—C12—H12	119.7
C5—C4—H4	118.7	C11—C12—H12	119.7
C6—C5—C4	116.74 (16)	C12—C13—C11ii	120.08 (17)
C6—C5—N2	121.95 (15)	C12—C13—H13	120.0
C4—C5—N2	121.31 (15)	C11ii—C13—H13	120.0
N4—C6—C5	121.87 (17)	C1—N1—C2	104.87 (15)
N4—C6—H6	119.1	C1—N2—C3	105.95 (14)
C5—C6—H6	119.1	C1—N2—C5	126.48 (14)
N3—C7—N4	126.88 (17)	C3—N2—C5	127.57 (15)
N3—C7—H7	116.6	C7—N3—C4	115.79 (16)
N4—C7—H7	116.6	C7—N4—C6	116.16 (16)
O1—C8—C9	118.15 (15)	C8—O1—H1A	109.5
O1—C8—C10	123.22 (15)	C11—O2—H2A	109.5
C9—C8—C10	118.61 (16)
N1—C2—C3—N2	0.1 (2)	C3—C2—N1—C1	−0.5 (2)
N3—C4—C5—C6	−1.2 (3)	N1—C1—N2—C3	−0.7 (2)
N3—C4—C5—N2	178.71 (17)	N1—C1—N2—C5	178.84 (15)
C4—C5—C6—N4	0.4 (3)	C2—C3—N2—C1	0.3 (2)
N2—C5—C6—N4	−179.50 (16)	C2—C3—N2—C5	−179.20 (16)
O1—C8—C9—C10i	179.04 (17)	C6—C5—N2—C1	154.15 (18)
C10—C8—C9—C10i	0.3 (3)	C4—C5—N2—C1	−25.8 (3)
O1—C8—C10—C9i	−178.97 (17)	C6—C5—N2—C3	−26.4 (3)
C9—C8—C10—C9i	−0.3 (3)	C4—C5—N2—C3	153.65 (18)
O2—C11—C12—C13	178.57 (16)	N4—C7—N3—C4	−0.3 (3)
C13ii—C11—C12—C13	−0.1 (3)	C5—C4—N3—C7	1.2 (3)
C11—C12—C13—C11ii	0.1 (3)	N3—C7—N4—C6	−0.4 (3)
N2—C1—N1—C2	0.7 (2)	C5—C6—N4—C7	0.3 (3)

Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x, −y, −z.

Hydrogen-bond geometry (Å, °)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1A···N1iii	0.82	1.96	2.764 (2)	168.
O2—H2A···N4iv	0.82	2.02	2.835 (2)	174.

Symmetry codes: (iii) x, y, z+1; (iv) −x+1, −y+1, −z+1.