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

Jiang, Y.-K.; Hou, G.-G.

doi:10.1107/S1600536811043819

organic compounds

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Volume 67| Part 11| November 2011| Page o3073

doi:10.1107/S1600536811043819

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

Yan-Ke Jiang ^a and Gui-Ge Hou ^b ^*

^aResearch Center of Medical Chemisty and Chemical Biology, Chongqing Technology and Business University, Chongqing 400067, People's Republic of China, and ^bCollege of Pharmacy, Binzhou Medical University, Yantai 264003, People's Republic of China
^*Correspondence e-mail: guigehou@163.com

(Received 19 October 2011; accepted 21 October 2011; online 29 October 2011)

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, $[P \overline 1]$
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) Å³
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[F² > 2σ(F²)] = 0.045
wR(F²) = 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

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) x, y, z+1; (ii) -x+1, -y+1, -z+1.

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.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811043819/xu5356sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811043819/xu5356Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811043819/xu5356Isup3.cml

checkCIF report

Comment top

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.

Related literature top

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

Experimental top

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.

Computing details top

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

Figures top

	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).

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

Crystal data top

C₇H₆N₄·C₆H₆O₂	Z = 2
M_r = 256.27	F(000) = 268
Triclinic, P1	D_x = 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 top

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

Refinement top

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(F_o²) + (0.0603P)² + 0.0979P] where P = (F_o² + 2F_c²)/3
2176 reflections	(Δ/σ)_max = 0.002
174 parameters	Δρ_max = 0.13 e Å⁻³
0 restraints	Δρ_min = −0.30 e Å⁻³

Crystal data top

C₇H₆N₄·C₆H₆O₂	γ = 98.602 (4)°
M_r = 256.27	V = 614.3 (3) Å³
Triclinic, P1	Z = 2
a = 6.8219 (18) Å	Mo Kα radiation
b = 9.550 (3) Å	µ = 0.10 mm⁻¹
c = 10.449 (3) Å	T = 298 K
α = 108.177 (3)°	0.36 × 0.24 × 0.12 mm
β = 102.381 (4)°

Data collection top

Bruker SMART 1000 diffractometer	1791 reflections with I > 2σ(I)
3103 measured reflections	R_int = 0.013
2176 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.045	0 restraints
wR(F²) = 0.115	H-atom parameters constrained
S = 1.04	Δρ_max = 0.13 e Å⁻³
2176 reflections	Δρ_min = −0.30 e Å⁻³
174 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.

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 (Å²) top

	x	y	z	U_iso*/U_eq
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 (Å²) top

	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, º) top

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, º) top

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···N4^iv	0.82	2.02	2.835 (2)	174

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

Experimental details

Crystal data
Chemical formula	C₇H₆N₄·C₆H₆O₂
M_r	256.27
Crystal system, space group	Triclinic, P1
Temperature (K)	298
a, b, c (Å)	6.8219 (18), 9.550 (3), 10.449 (3)
α, β, γ (°)	108.177 (3), 102.381 (4), 98.602 (4)
V (Å³)	614.3 (3)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.10
Crystal size (mm)	0.36 × 0.24 × 0.12

Data collection
Diffractometer	Bruker SMART 1000 diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	3103, 2176, 1791
R_int	0.013
(sin θ/λ)_max (Å⁻¹)	0.600

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.045, 0.115, 1.04
No. of reflections	2176
No. of parameters	174
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.13, −0.30

Computer programs: SMART (Bruker, 2007), SAINT (Bruker, 2007), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1A···N1ⁱ	0.82	1.96	2.764 (2)	168.2
O2—H2A···N4ⁱⁱ	0.82	2.02	2.835 (2)	174.2

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

Acknowledgements

The authors thank the Scientific Research Project of Chongqing Education Committee (grant Nos. KJ100720 and KJTD201020), Chongqing Technology and Business University (grant No. 2010-56-07), and Binzhou Medical University, China.

References

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