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ISSN: 2056-9890

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

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. ππ 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[Nieuwenhuyzen, M., Keirse, R., Shaw, B. & Vos, J. G. (1999). Acta Cryst. C55, 264-266. ]); Clausen et al. (2010[Clausen, H. F., Chevallier, M. S., Spackman, M. A. & Iversen, B. B. (2010). New J. Chem. 34, 193-199.]).

[Scheme 1]

Experimental

Crystal data
  • C7H6N4·C6H6O2

  • Mr = 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)

  • Rint = 0.013

Refinement
  • R[F2 > 2σ(F2)] = 0.045

  • wR(F2) = 0.115

  • S = 1.04

  • 2176 reflections

  • 174 parameters

  • H-atom parameters constrained

  • Δρmax = 0.13 e Å−3

  • Δρmin = −0.30 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Bruker (2007). SAINT and SMART. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2007[Bruker (2007). SAINT and SMART. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information


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 ππ 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.

Refinement top

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

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
[Figure 1] Fig. 1. The structure of the title compound with 30% probability displacement ellipsoids.(Symmetry codes: (i) -x,-y + 1,-z + 1)
[Figure 2] 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·C6H6O2Z = 2
Mr = 256.27F(000) = 268
Triclinic, P1Dx = 1.385 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.8219 (18) ÅCell parameters from 1283 reflections
b = 9.550 (3) Åθ = 2.3–26.8°
c = 10.449 (3) ŵ = 0.10 mm1
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 tubeRint = 0.013
Graphite monochromatorθmax = 25.2°, θmin = 2.1°
ϕ and ω scansh = 68
3103 measured reflectionsk = 1111
2176 independent reflectionsl = 1112
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.045Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.115H-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 parametersΔρmax = 0.13 e Å3
0 restraintsΔρmin = 0.30 e Å3
Crystal data top
C7H6N4·C6H6O2γ = 98.602 (4)°
Mr = 256.27V = 614.3 (3) Å3
Triclinic, P1Z = 2
a = 6.8219 (18) ÅMo Kα radiation
b = 9.550 (3) ŵ = 0.10 mm1
c = 10.449 (3) ÅT = 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 reflectionsRint = 0.013
2176 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0450 restraints
wR(F2) = 0.115H-atom parameters constrained
S = 1.04Δρmax = 0.13 e Å3
2176 reflectionsΔρmin = 0.30 e Å3
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
xyzUiso*/Ueq
C10.3093 (3)0.5951 (2)0.03876 (18)0.0443 (4)
H10.33090.68090.01460.053*
C20.2073 (3)0.3702 (2)0.02839 (19)0.0489 (5)
H20.14270.26770.00650.059*
C30.3175 (3)0.4481 (2)0.16172 (19)0.0479 (5)
H30.34320.41090.23450.058*
C40.6323 (3)0.83862 (19)0.27343 (19)0.0468 (5)
H40.63470.83510.18380.056*
C50.5094 (2)0.71929 (18)0.28759 (17)0.0379 (4)
C60.5138 (3)0.7279 (2)0.42203 (18)0.0470 (5)
H60.43340.64900.43550.056*
C70.7401 (3)0.9551 (2)0.5069 (2)0.0511 (5)
H70.82081.03820.58430.061*
C80.0026 (3)0.41667 (18)0.58820 (17)0.0396 (4)
C90.0960 (3)0.34868 (19)0.44598 (18)0.0465 (5)
H90.16160.24630.40870.056*
C100.0931 (3)0.56915 (19)0.64137 (18)0.0459 (5)
H100.15610.61680.73710.055*
C110.1916 (3)0.0311 (2)0.09527 (17)0.0416 (4)
C120.0237 (3)0.06699 (19)0.14148 (17)0.0425 (4)
H120.03930.11220.23700.051*
C130.1671 (3)0.03627 (19)0.04686 (17)0.0415 (4)
H130.27910.06090.07880.050*
N10.2027 (2)0.46188 (16)0.04935 (15)0.0475 (4)
N20.3850 (2)0.59439 (15)0.16903 (14)0.0397 (4)
N30.7474 (2)0.95816 (17)0.38243 (17)0.0525 (4)
N40.6296 (2)0.84580 (19)0.53321 (15)0.0515 (4)
O10.0130 (2)0.33007 (14)0.67005 (13)0.0547 (4)
H1A0.05320.38080.75130.082*
O20.3846 (2)0.0619 (2)0.18407 (13)0.0668 (4)
H2A0.37940.09450.26550.100*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0524 (11)0.0423 (10)0.0381 (9)0.0075 (8)0.0114 (8)0.0164 (8)
C20.0564 (12)0.0382 (9)0.0478 (11)0.0042 (8)0.0165 (9)0.0111 (8)
C30.0618 (12)0.0412 (10)0.0434 (10)0.0076 (9)0.0165 (9)0.0194 (8)
C40.0538 (11)0.0427 (10)0.0423 (10)0.0081 (8)0.0140 (8)0.0139 (8)
C50.0377 (9)0.0386 (9)0.0359 (9)0.0106 (7)0.0098 (7)0.0106 (7)
C60.0410 (10)0.0555 (11)0.0398 (10)0.0046 (8)0.0089 (8)0.0153 (9)
C70.0441 (11)0.0489 (11)0.0451 (11)0.0067 (9)0.0029 (8)0.0045 (9)
C80.0418 (10)0.0383 (9)0.0368 (9)0.0080 (7)0.0118 (7)0.0110 (8)
C90.0550 (11)0.0324 (8)0.0407 (10)0.0002 (8)0.0108 (8)0.0041 (8)
C100.0535 (11)0.0426 (10)0.0297 (9)0.0019 (8)0.0066 (8)0.0046 (8)
C110.0441 (10)0.0465 (10)0.0340 (9)0.0105 (8)0.0081 (7)0.0157 (8)
C120.0505 (11)0.0475 (10)0.0289 (8)0.0139 (8)0.0129 (8)0.0107 (8)
C130.0450 (10)0.0449 (10)0.0403 (9)0.0151 (8)0.0183 (8)0.0164 (8)
N10.0521 (9)0.0459 (9)0.0380 (8)0.0047 (7)0.0097 (7)0.0112 (7)
N20.0446 (8)0.0395 (8)0.0342 (8)0.0069 (6)0.0121 (6)0.0126 (6)
N30.0547 (10)0.0431 (9)0.0503 (10)0.0038 (7)0.0100 (8)0.0104 (7)
N40.0439 (9)0.0629 (10)0.0371 (8)0.0066 (8)0.0054 (7)0.0101 (8)
O10.0723 (10)0.0434 (7)0.0401 (7)0.0011 (6)0.0070 (7)0.0149 (6)
O20.0464 (8)0.1082 (12)0.0402 (8)0.0235 (8)0.0075 (6)0.0196 (8)
Geometric parameters (Å, º) top
C1—N11.304 (2)C7—H70.9300
C1—N21.351 (2)C8—O11.368 (2)
C1—H10.9300C8—C91.380 (2)
C2—C31.340 (3)C8—C101.382 (2)
C2—N11.367 (2)C9—C10i1.378 (2)
C2—H20.9300C9—H90.9300
C3—N21.377 (2)C10—C9i1.378 (2)
C3—H30.9300C10—H100.9300
C4—N31.324 (2)C11—O21.368 (2)
C4—C51.377 (2)C11—C13ii1.383 (2)
C4—H40.9300C11—C121.383 (3)
C5—C61.375 (2)C12—C131.382 (2)
C5—N21.415 (2)C12—H120.9300
C6—N41.329 (2)C13—C11ii1.383 (2)
C6—H60.9300C13—H130.9300
C7—N31.321 (2)O1—H1A0.8200
C7—N41.329 (2)O2—H2A0.8200
N1—C1—N2112.37 (16)C10i—C9—C8120.72 (16)
N1—C1—H1123.8C10i—C9—H9119.6
N2—C1—H1123.8C8—C9—H9119.6
C3—C2—N1110.82 (15)C9i—C10—C8120.67 (16)
C3—C2—H2124.6C9i—C10—H10119.7
N1—C2—H2124.6C8—C10—H10119.7
C2—C3—N2105.99 (16)O2—C11—C13ii117.69 (16)
C2—C3—H3127.0O2—C11—C12122.90 (15)
N2—C3—H3127.0C13ii—C11—C12119.40 (16)
N3—C4—C5122.56 (17)C13—C12—C11120.52 (16)
N3—C4—H4118.7C13—C12—H12119.7
C5—C4—H4118.7C11—C12—H12119.7
C6—C5—C4116.74 (16)C12—C13—C11ii120.08 (17)
C6—C5—N2121.95 (15)C12—C13—H13120.0
C4—C5—N2121.31 (15)C11ii—C13—H13120.0
N4—C6—C5121.87 (17)C1—N1—C2104.87 (15)
N4—C6—H6119.1C1—N2—C3105.95 (14)
C5—C6—H6119.1C1—N2—C5126.48 (14)
N3—C7—N4126.88 (17)C3—N2—C5127.57 (15)
N3—C7—H7116.6C7—N3—C4115.79 (16)
N4—C7—H7116.6C7—N4—C6116.16 (16)
O1—C8—C9118.15 (15)C8—O1—H1A109.5
O1—C8—C10123.22 (15)C11—O2—H2A109.5
C9—C8—C10118.61 (16)
N1—C2—C3—N20.1 (2)C3—C2—N1—C10.5 (2)
N3—C4—C5—C61.2 (3)N1—C1—N2—C30.7 (2)
N3—C4—C5—N2178.71 (17)N1—C1—N2—C5178.84 (15)
C4—C5—C6—N40.4 (3)C2—C3—N2—C10.3 (2)
N2—C5—C6—N4179.50 (16)C2—C3—N2—C5179.20 (16)
O1—C8—C9—C10i179.04 (17)C6—C5—N2—C1154.15 (18)
C10—C8—C9—C10i0.3 (3)C4—C5—N2—C125.8 (3)
O1—C8—C10—C9i178.97 (17)C6—C5—N2—C326.4 (3)
C9—C8—C10—C9i0.3 (3)C4—C5—N2—C3153.65 (18)
O2—C11—C12—C13178.57 (16)N4—C7—N3—C40.3 (3)
C13ii—C11—C12—C130.1 (3)C5—C4—N3—C71.2 (3)
C11—C12—C13—C11ii0.1 (3)N3—C7—N4—C60.4 (3)
N2—C1—N1—C20.7 (2)C5—C6—N4—C70.3 (3)
Symmetry codes: (i) x, y+1, z+1; (ii) x, y, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···N1iii0.821.962.764 (2)168
O2—H2A···N4iv0.822.022.835 (2)174
Symmetry codes: (iii) x, y, z+1; (iv) x+1, y+1, z+1.

Experimental details

Crystal data
Chemical formulaC7H6N4·C6H6O2
Mr256.27
Crystal system, space groupTriclinic, 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)
V3)614.3 (3)
Z2
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.36 × 0.24 × 0.12
Data collection
DiffractometerBruker SMART 1000
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
3103, 2176, 1791
Rint0.013
(sin θ/λ)max1)0.600
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.045, 0.115, 1.04
No. of reflections2176
No. of parameters174
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.13, 0.30

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

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···N1i0.821.962.764 (2)168.2
O2—H2A···N4ii0.822.022.835 (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

First citationBruker (2007). SAINT and SMART. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationClausen, H. F., Chevallier, M. S., Spackman, M. A. & Iversen, B. B. (2010). New J. Chem. 34, 193–199.  Web of Science CSD CrossRef CAS Google Scholar
First citationNieuwenhuyzen, M., Keirse, R., Shaw, B. & Vos, J. G. (1999). Acta Cryst. C55, 264–266.   Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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