1,2,3 Tri­hydroxy­benzene–pyrimidine (1/1)11

organic papers

Acta Cryst.(2005). E61, o2981–o2983 doi:10.1107/S1600536805026012 Liliana Dobrzan´ska _C

6H6O3C4H4N2

o2981

Acta Crystallographica Section E

Structure Reports

Online

ISSN 1600-5368

1,2,3-Trihydroxybenzene–pyrimidine (1/1)

Liliana Dobrzan´ska

Department of Chemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa

Correspondence e-mail: [email protected]

Key indicators

Single-crystal X-ray study

T= 173 K

Mean(C–C) = 0.003 A˚

Rfactor = 0.052

wRfactor = 0.163

Data-to-parameter ratio = 15.4

For details of how these key indicators were automatically derived from the article, see http://journals.iucr.org/e.

#2005 International Union of Crystallography Printed in Great Britain – all rights reserved

In the title molecular co-crystal, C6H6O3C4H4N2, symmetry-related O—H N hydrogen bonds with O N distances of 2.790 (3) and 2.818 (2) A˚ link molecules of 1,2,3-trihydroxy-benzene and pyrimidine to form 18-membered rings which, in turn, are constituents of infinite chains created by O—H O hydrogen bonds between hydroxy groups in positions 1 and 2 of neighbouring 1,2,3-trihydroxybenzene molecules. The infinite chains are further stacked in stepped columns by offset - interactions, and are linked by C—H inter-actions, resulting in a herringbone pattern.

Comment

The strength and directional nature of the hydrogen bond has been a useful tool in crystal engineering as a design element of supramolecular assemblies (Etter, 1991; Lehn, 1995; Desiraju, 1989). In a search for new hydrogen-bonded motifs, we have studied hydrogen-bonded organic co-crystals comprising ’acidic’ and ‘basic’ components. The Cambridge Structural Database contains two previously reported structures with pyrogallol as a component of the adduct. In the first example, pyrogallol–hexametylenetetramine (1/1) (Tremayne & Glide-well, 2000), all hydroxyl groups of the pyrogallol act as hydrogen-bond donors. Molecules are assembled to form two distinct cyclic R4

4(18) motifs by means of only one type of synthon involving O—H N hydrogen bonds, with O N distances 2.90 (1), 2.79 (1) and 2.69 (1) A˚ . In the second example, pyrogallol–8-hydroxyquinoline (1/1) (Singh et al., 1994), the authors were primarily interested in kinetic studies, and therefore the lack of full crystallographic data precludes any insight into the resulting supramolecular assembly.

The asymmetric unit of the title compound, (I), comprises two different molecular components, viz. 1,2,3-trihydroxy-benzene and pyrimidine (Fig. 1). The two molecular building blocks are held together by O1—H1 N1 and O2—H2 N2i [symmetry code:(i) 1x, 1y, 1z] hydrogen bonds with distances 2.790 (3) and 2.818 (2) A˚ , respectively, generating an

R44(18) tetrameric arrangement with the presence of the same synthon as previously mentioned. The cyclic units are further connected to one another via O3—H3 O2ii [symmetry code:(ii) x, 1 y, 2 z] hydrogen bonds [O O = 2.858 (2) A˚ , O—H O = 137.75_{] of motif R}2

2(10), forming infinite chains along [001] (Fig. 2). The occurrence of the

second synthon in the structure leads to more efficient packing, since the hydroxyl group in the 2 position of the pyrogallol molecule also acts as a hydrogen-bond acceptor. The poor directionality of O hydrogen-bond acceptors was also noted in the case of 2-aminopyrimidine co-crystals with N—H O interactions in the range 130–144 _{(Shan et al.,}

2002). Benzene and pyrimidine rings from adjacent parallel chains interact by offset-interactions (centroid-to-centroid distance 3.674 A˚ ) to form a step-like motif (Fig. 3), which is

held together by C—H interactions [C8 (pyrogallol) 3.599 A˚ , C4 (pyrimidine) 3.711 A˚ ; measured to the centroid of the ring], resulting in a herringbone packing (Fig. 4).

Experimental

Colourless crystals suitable for single-crystal X-ray diffraction were obtained by slow evaporation of an ethanolic solution of 1,2,3-trihydroxybenzene and pyrimidine (1:1 molar ratio) at room temperature.

Crystal data

C6H6O3C4H4N2

Mr= 206.20

Monoclinic,P21=c

a= 6.5952 (9) A˚

b= 13.7481 (19) A˚

c= 10.5778 (15) A˚ = 94.051 (3)

V= 956.7 (2) A˚3

Z= 4

Dx= 1.432 Mg m

3 MoKradiation Cell parameters from 2112

reflections = 3.0–27.1

= 0.11 mm1

T= 173 (2) K Block, colourless 0.300.250.20 mm

Data collection

Bruker APEX CCD area-detector diffractometer

!scans

Absorption correction: multi-scan (SADABS; Sheldrick, 1997)

Tmin= 0.745,Tmax= 0.979 5916 measured reflections

2112 independent reflections 1415 reflections withI> 2(I)

Rint= 0.030 max= 27.1

h=8!8

k=17!16

l=8!13

Refinement

Refinement onF2 R[F2_{> 2(F}2_{)] = 0.052}

wR(F2) = 0.163

S= 1.03 2112 reflections 137 parameters

H-atom parameters constrained

w= 1/[2_(F

o2) + (0.0584P)2] whereP= (Fo2+ 2Fc2)/3 (/)max< 0.001

max= 1.02 e A˚

3

min=0.27 e A˚

3

organic papers

o2982

Liliana Dobrzan´ska _C

[image:2.610.46.301.70.238.2]

6H6O3C4H4N2 Acta Cryst.(2005). E61, o2981–o2983

Figure 1

[image:2.610.312.564.72.320.2]

The asymmetric unit of (I), with atom labels and 50% probability displacement ellipsoids for non-H atoms.

Figure 2

[image:2.610.43.295.282.400.2]

Part of the infinite chain observed in the structure of the title co-crystal. Hydrogen bonds are shown as dashed lines.

Figure 3

Capped-stick representation showing the-stacking geometry of (I). Dashed red lines represent hydrogen bonds. H atoms not involved in hydrogen bonding have been omitted.

Figure 4

[image:2.610.46.297.438.588.2]

Table 1

Hydrogen-bond geometry (A˚ ,_).

D—H A D—H H A D A D—H A

O1—H1 N1i

0.84 1.98 2.790 (3) 163 O2—H2 N2ii

0.84 2.04 2.818 (2) 155 O3—H3 O2iii

0.84 2.18 2.858 (2) 138

Symmetry codes: (i)x;y;z; (ii)xþ1;yþ1;zþ1; (iii)x;yþ1;zþ2.

H atoms were positioned geometrically (C—H = 0.95 A˚ , O—H = 0.84 A˚ ) and constrained to ride on their parent atoms;Uiso(H) values

were set at 1.2 timesUeq(C). The highest peak is located 0.31 A˚ from

atom H6.

Data collection:SMART(Bruker, 2001); cell refinement:SAINT

(Bruker, 2002); data reduction: SAINT; program(s) used to solve structure: SHELXS97(Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics:

X-SEED(Atwood & Barbour, 2003; Barbour, 2001); software used to prepare material for publication:X-SEED.

The author thanks the Claude Harris Leon Foundation for financial support.

References

Atwood, J. L. & Barbour, L. J. (2003).Cryst. Growth Des.3, 3–8. Barbour, L. J. (2001).J. Supramol. Chem.1, 189–191.

Bruker (2001). SMART (Version 5.625). Bruker AXS Inc., Madison, Wisconsin, USA.

Bruker (2002).SAINT(Version 6.36a). Bruker AXS Inc., Madison, Wisconsin, USA.

Desiraju, G. R. (1989).Crystal Engineering. The Design of Organic Solids. Elsevier, Amsterdam.

Etter, M. C. (1991).J. Phys. Chem.95, 4601–4610.

Lehn, J. M. (1995).Supramolecular Chemistry, edited by U. Anton, pp. 1-171. New York: VCH.

Shan, N., Bond, A. D. & Jones, W. (2002).Tetrahedron Lett.43, 3101–3104. Sheldrick, G. M. (1997).SHELXS97,SHELXL97 andSADABS(Version

2.05). University of Go¨ttingen, Germany.

Singh, B., Singh, N. P., Amarendra Kumar, V. & Nethaji, M. (1994).J. Chem. Soc. Perkin Trans. 2, pp. 361–366.

Tremayne, M. & Glidewell, C. (2000).Chem. Commun.24, 2425–2426.

organic papers

Acta Cryst.(2005). E61, o2981–o2983 Liliana Dobrzan´ska _C

supporting information

sup-1 Acta Cryst. (2005). E61, o2981–o2983

supporting information

Acta Cryst. (2005). E61, o2981–o2983 [https://doi.org/10.1107/S1600536805026012]

1,2,3-Trihydroxybenzene

–

pyrimidine (1/1)

Liliana Dobrza

ń

ska

1,2,3-trihydroxybenzene:pyrimidine

Crystal data

C6H6O3·C4H4N2 Mr = 206.20

Monoclinic, P21/c

Hall symbol: -P2ybc

a = 6.5952 (9) Å

b = 13.7481 (19) Å

c = 10.5778 (15) Å

β = 94.051 (3)°

V = 956.7 (2) Å3 Z = 4

F(000) = 432

Dx = 1.432 Mg m−3

Mo Kα radiation, λ = 0.71073 Å Cell parameters from 2112 reflections

θ = 3.0–27.1°

µ = 0.11 mm−1 T = 173 K Block, colourless 0.30 × 0.25 × 0.20 mm

Data collection

Bruker APEX CCD area-detector diffractometer

Radiation source: fine-focus sealed tube Graphite monochromator

ω scans

Absorption correction: multi-scan (SADABS; Sheldrick, 1997)

Tmin = 0.745, Tmax = 0.979

5916 measured reflections 2112 independent reflections 1415 reflections with I > 2 σ (I)

Rint = 0.030

θmax = 27.1°, θmin = 3.0° h = −8→8

k = −17→16

l = −8→13

Refinement

Refinement on F2

Least-squares matrix: full

R[F2 _{> 2σ(F}2_{)] = 0.052} wR(F2_{) = 0.163} S = 1.03 2112 reflections 137 parameters 0 restraints

Primary atom site location: structure-invariant direct methods

Secondary atom site location: difference Fourier map

Hydrogen site location: inferred from neighbouring sites

H-atom parameters constrained

w = 1/[σ2_(F

o2) + (0.0584P)2]

where P = (Fo2 + 2Fc2)/3

(Δ/σ)max < 0.001

Δρmax = 1.02 e Å−3

Δρmin = −0.27 e Å−3

Special details

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sup-2 Acta Cryst. (2005). E61, o2981–o2983

Refinement. Refinement of F2 _{against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F}2_,

conventional R-factors R are based on F, with F set to zero for negative F2_{. The threshold expression of F}2 _{> σ(F}2_{) 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₎

x y z Uiso*/Ueq

O1 0.1911 (2) 0.43273 (12) 0.60380 (15) 0.0392 (5)

H1 0.1915 0.4200 0.5262 0.047*

O2 0.1300 (2) 0.46508 (12) 0.85521 (14) 0.0343 (4)

H2 0.2265 0.4838 0.8135 0.041*

N2 0.5207 (3) 0.43685 (13) 0.21608 (17) 0.0296 (5) N1 0.2772 (3) 0.38391 (14) 0.35728 (18) 0.0330 (5) O3 −0.2156 (3) 0.39222 (13) 0.95192 (17) 0.0435 (5)

H3 −0.1404 0.4369 0.9825 0.052*

C2 −0.0086 (3) 0.41519 (15) 0.7770 (2) 0.0274 (5) C1 0.0170 (3) 0.39868 (15) 0.6491 (2) 0.0286 (5) C9 0.2296 (3) 0.34766 (16) 0.1375 (2) 0.0317 (5)

H9 0.1525 0.3181 0.0686 0.038*

C8 0.1681 (3) 0.34391 (16) 0.2592 (2) 0.0334 (5)

H8 0.0443 0.3119 0.2740 0.040*

C3 −0.1830 (3) 0.38006 (16) 0.8283 (2) 0.0316 (5) C10 0.4084 (3) 0.39646 (16) 0.1204 (2) 0.0297 (5)

H10 0.4531 0.4015 0.0373 0.036*

C7 0.4477 (4) 0.42815 (16) 0.3298 (2) 0.0322 (5)

H7 0.5262 0.4567 0.3988 0.039*

C6 −0.1310 (3) 0.34815 (16) 0.5741 (2) 0.0355 (6)

H6 −0.1132 0.3369 0.4870 0.043*

C5 −0.3014 (4) 0.31500 (18) 0.6268 (3) 0.0407 (6)

H5 −0.4028 0.2816 0.5754 0.049*

C4 −0.3279 (4) 0.32936 (17) 0.7536 (3) 0.0406 (6)

H4 −0.4453 0.3045 0.7895 0.049*

Atomic displacement parameters (Å2₎

U11 _U22 _U33 _U12 _U13 _U23

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sup-3 Acta Cryst. (2005). E61, o2981–o2983

C7 0.0318 (12) 0.0374 (12) 0.0276 (12) −0.0056 (9) 0.0036 (10) −0.0047 (10) C6 0.0313 (12) 0.0354 (12) 0.0395 (13) −0.0013 (10) 0.0012 (10) −0.0050 (10) C5 0.0327 (13) 0.0387 (13) 0.0508 (16) −0.0084 (10) 0.0041 (11) −0.0110 (11) C4 0.0289 (12) 0.0347 (12) 0.0599 (17) −0.0093 (10) 0.0149 (12) 0.0008 (12)

Geometric parameters (Å, º)

O1—C1 1.358 (3) C9—C10 1.380 (3)

O1—H1 0.8400 C9—C8 1.378 (3)

O2—C2 1.373 (3) C9—H9 0.9500

O2—H2 0.8400 C8—H8 0.9500

N2—C7 1.332 (3) C3—C4 1.385 (3)

N2—C10 1.332 (3) C10—H10 0.9500

N1—C7 1.329 (3) C7—H7 0.9500

N1—C8 1.338 (3) C6—C5 1.368 (3)

O3—C3 1.351 (3) C6—H6 0.9500

O3—H3 0.8400 C5—C4 1.378 (4)

C2—C1 1.394 (3) C5—H5 0.9500

C2—C3 1.393 (3) C4—H4 0.9500

C1—C6 1.398 (3)

C1—O1—H1 109.5 O3—C3—C2 121.8 (2)

C2—O2—H2 109.5 C4—C3—C2 120.5 (2)

C7—N2—C10 115.54 (18) N2—C10—C9 122.6 (2)

C7—N1—C8 115.8 (2) N2—C10—H10 118.7

C3—O3—H3 109.5 C9—C10—H10 118.7

O2—C2—C1 123.05 (18) N1—C7—N2 127.2 (2)

O2—C2—C3 118.13 (19) N1—C7—H7 116.4

C1—C2—C3 118.8 (2) N2—C7—H7 116.4

O1—C1—C2 116.71 (19) C5—C6—C1 119.7 (2)

O1—C1—C6 123.0 (2) C5—C6—H6 120.2

C2—C1—C6 120.2 (2) C1—C6—H6 120.2

C10—C9—C8 116.8 (2) C6—C5—C4 120.9 (2)

C10—C9—H9 121.6 C6—C5—H5 119.6

C8—C9—H9 121.6 C4—C5—H5 119.6

N1—C8—C9 122.1 (2) C5—C4—C3 119.8 (2)

N1—C8—H8 118.9 C5—C4—H4 120.1

C9—C8—H8 118.9 C3—C4—H4 120.1

O3—C3—C4 117.7 (2)

O2—C2—C1—O1 1.5 (3) C7—N2—C10—C9 −0.8 (3) C3—C2—C1—O1 −178.84 (19) C8—C9—C10—N2 1.3 (3) O2—C2—C1—C6 −179.3 (2) C8—N1—C7—N2 0.1 (4)

C3—C2—C1—C6 0.3 (3) C10—N2—C7—N1 0.1 (3)

C7—N1—C8—C9 0.5 (3) O1—C1—C6—C5 179.2 (2)

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sup-4 Acta Cryst. (2005). E61, o2981–o2983

O2—C2—C3—C4 179.9 (2) O3—C3—C4—C5 −180.0 (2)

C1—C2—C3—C4 0.2 (3) C2—C3—C4—C5 −1.2 (4)

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A

O1—H1···N1 0.84 1.98 2.790 (3) 163

O2—H2···N2i _{0.84 2.04 2.818 (2) 155}

O3—H3···O2ii _{0.84 2.18 2.858 (2) 138}