Tetra­methyl­pyrazine–endo norbornene cis 5,6 di­carboxyl­ic acid (1/2)

organic papers

Acta Cryst.(2005). E61, o731–o732 doi:10.1107/S1600536805005283 Mao-Lin Huet al. _C

9H10O40.5C8H12N2

o731

Structure Reports Online

ISSN 1600-5368

Tetramethylpyrazine–

endo

-norbornene-cis

-5,6-dicarboxylic acid (1/2)

Mao-Lin Hu,a* Zhi-Min Jin,b Ya-Juan Zhao,aDi-Mei Chen,a Shun Wangaand Xiao-Qing Caia

a_{School of Chemistry and Materials Science,}

Wenzhou Normal College, Zhejiang, Wenzhou 325027, People’s Republic of China, and

b_{College of Pharmaceutical Sciences, Zhejiang}

University of Technology, Hangzhou 310014, People’s Republic of China

Correspondence e-mail: hu403cn@yahoo.com.cn

Key indicators

Single-crystal X-ray study T= 298 K

Mean(C–C) = 0.008 A˚ Rfactor = 0.096 wRfactor = 0.326

Data-to-parameter ratio = 12.9

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 complex, 2C9H10O4C8H12N2, there is an inversion centre at the centre of the 2,3,5,6-tetramethylpyrazine mol-ecule, which is linked to two endo-norbornene-cis -5,6-di-carboxylic acid moleculesvia O—H N hydrogen bonds. In the crystal structure, O—H O and O—H N hydrogen bonds propagate a one-dimensional zigzag chain, which is extended into layers when combined with longer C—H O hydrogen bonds.

Comment

2,3,5,6-Tetramethylpyrazine (TMP) is one of the most impor-tant active ingredients of the traditional Chinese herbal medicine Ligusticum wallichii Franchat (Chung Chong) (Zhang et al., 2003). There are numerous examples of phar-macokinetic studies of the antiplatelet activity of TMP (Sheu et al., 1997; Tsai & Liang, 2001). TMP may act not only as a bridging ligand in metal complexes (Shaoet al., 2004), but also as a guest molecule in inclusion compounds (Smyth et al., 1996). We report here the structure of the title adduct, (I).

One TMP molecule, having an inversion centre at the centre of the pyrazine ring, links two endo-norbornene-cis -5,6-di-carboxylic acid (END) moleculesviaO3—H3 N3 hydrogen bonds (see Table 2 and Fig. 1). This pattern is reinforced by a C1—H1C O3 weak hydrogen bond. The TMP molecule in

Received 9 February 2005 Accepted 16 February 2005 Online 26 February 2005

Figure 1

(I) appears to be unprotonated and the C2—N1—C3 angle [119.7 (4)_{] is smaller than the corresponding angle in a} monoprotonated TMP [124.2 (3)_{] (Chenet al., 2005). The C—} O bonds in the carboxyl groups,viz. O1—C5 = 1.296 (6) A˚ and O4—C13 = 1.308 (7) A˚ differ significantly from O2—C5 = 1.215 (6) A˚ and O3—C13 = 1.201 (7) A˚, indicating that the carboxyl groups are unionized. The plane of the pyrazine ring of TMP makes angles of 59.49 (2) and 56.92 (2), respectively, with the carboxyl planes C13/O3/O4/H3 and C5/O1/O2/H1.

In the crystal structure, an O1—H1 O2ihydrogen bond forms a one-dimensional zigzag chain along the [110] direction (Fig. 2 and Table 2). The hydrogen-bonding pattern, as shown in Fig. 2, could be described in graph-set notation (Etter, 1990; Grell et al., 2000) as C2

2 (16)R2

2

(8). Neighbouring chains are interrelated by translation, and are related by a C8— H8A O4iiweak hydrogen bond to form a layer parallel to (001).

Experimental

endo-Norbornene-cis-5,6-dicarboxylic acid (2 mmol, 0.37 g) was added slowly to a solution (20 ml) of 2,3,5,6-tetramethylpyrazine (1 mmol, 0.14 g) in ethanol. The mixture was stirred for several minutes and left to stand at room temperature for about two weeks; colourless block-shaped crystals were obtained.

Crystal data

C9H10O40:5C8H12N2

Mr= 250.27

Triclinic,P1 a= 6.106 (2) A˚ b= 9.293 (3) A˚ c= 11.580 (4) A˚ = 101.875 (8) = 97.890 (6) = 98.590 (8) V= 626.1 (4) A˚3

Z= 2

Dx= 1.327 Mg m

3

MoKradiation Cell parameters from 986

reflections = 2.7–24.4 = 0.10 mm1

T= 298 (2) K Block, colourless 0.220.130.12 mm

Data collection

Bruker SMART APEX area-detector diffractometer ’and!scans

Absorption correction: multi-scan (SADABS; Bruker, 2002) Tmin= 0.979,Tmax= 0.988 3212 measured reflections

2149 independent reflections 1374 reflections withI> 2(I) Rint= 0.023

max= 25.0

h=6!7 k=11!9 l=13!11

Refinement

Refinement onF2

R[F2_{> 2(F}2_{)] = 0.096}

wR(F2_{) = 0.326}

S= 1.22 2149 reflections 167 parameters

H-atom parameters constrained w= 1/[2_(F

o2) + (0.2P)2]

whereP= (Fo2+ 2Fc2)/3

(/)max< 0.001

max= 0.53 e A˚

3

min=0.45 e A˚

3

Table 1

Selected geometric parameters (A˚ ,_).

O1—C5 1.296 (6)

O2—C5 1.215 (6)

O3—C13 1.308 (7)

O4—C13 1.201 (7)

C2—N1—C3 119.7 (4)

O2—C5—O1 122.8 (5)

O4—C13—O3 123.2 (5)

Table 2

Hydrogen-bonding geometry (A˚ ,_).

D—H A D—H H A D A D—H A

O1—H1 O2i

0.82 1.88 2.696 (5) 174

O3—H3 N1 0.82 1.92 2.715 (5) 164

C1—H1C O3 0.96 2.59 3.399 (5) 142

C8—H8A O4ii

0.97 2.46 3.361 (5) 154

Symmetry codes: (i) 2x;2y;1z; (ii)x1;y;z.

All H atoms were positioned geometrically and allowed to ride on their parent atoms at distances of Csp2_{—H = 0.93 A˚ , withU}

iso = 1.2Ueq(C), Csp

3

—H = 0.96 A˚ , withUiso = 1.5Ueq(C), and O—H = 0.82 A˚ , withUiso= 1.2Ueq(O).

Data collection:SMART(Bruker, 2002); 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:

SHELXTL (Bruker, 2002); software used to prepare material for publication:SHELXL97.

This work was supported by the Wenzhou Technology Project Foundation of China (No. S2004A004), the Zhejiang Provincial Natural Science Foundation of China (No. Y404118) and the National Natural Science Foundation of China (No. 20471043).

References

Bruker (2002).SADABS (Version 2.03), SAINT (Version 6.02), SMART (Version 5.62) andSHELXTL(Version 6.10). Bruker AXS Inc., Madison, Wisconsin, USA.

Chen, D. M., Xia, F. Y., Hu, M. L., Li, L. & Jin, Z. M. (2005).Acta Cryst.E61, o419–o420.

Etter, M. C. (1990).Acc. Chem. Res.23, 120–126.

Grell, J., Bernstein, J. & Tinhofer, G. (2000).Acta Cryst.B56, 166–179. Shao, Z.-H., Luo, J., Cai, R.-F., Zhou, X.-G., Weng, L.-H. & Chen, Z.-X. (2004).

Acta Cryst.C60, m250–m253.

Sheldrick, G. M. (1997). SHELXL97 and SHELXS97. Release 97-2. University of Go¨ttingen, Germany.

Sheu, J. R., Kan, Y. C., Hung, W. C., Ko, W. C. & Yen, M. H. (1997).Thromb. Res.88, 259–270.

Smyth, M. V., Bailey, R. D. & Pennington, W. T. (1996).Acta Cryst.C52, 2170– 2173.

Tsai, T. H. & Liang, C. C. (2001).Int. J. Pharm.216, 61–66.

Figure 2

supporting information

sup-1 Acta Cryst. (2005). E61, o731–o732

supporting information

Acta Cryst. (2005). E61, o731–o732 [https://doi.org/10.1107/S1600536805005283]

Tetramethylpyrazine

–

endo

-norbornene-

cis

-5,6-dicarboxylic acid (1/2)

Mao-Lin Hu, Zhi-Min Jin, Ya-Juan Zhao, Di-Mei Chen, Shun Wang and Xiao-Qing Cai

Tetramethylpyrazine–endo-norbornene-cis-5,6-dicarboxylic acid (1/2)

Crystal data

C9H10O4·0.5C8H12N2

Mr = 250.27

Triclinic, P1 Hall symbol: -P1

a = 6.106 (2) Å

b = 9.293 (3) Å

c = 11.580 (4) Å

α = 101.875 (8)°

β = 97.890 (6)°

γ = 98.590 (8)°

V = 626.1 (4) Å3

Z = 2

F(000) = 266

Dx = 1.327 Mg m−3

Mo Kα radiation, λ = 0.71073 Å Cell parameters from 986 reflections

θ = 2.7–24.4°

µ = 0.10 mm−1

T = 298 K Block, colorless 0.22 × 0.13 × 0.12 mm

Data collection

Bruker APEX area-detector diffractometer

Radiation source: fine-focus sealed tube Graphite monochromator

φ and ω scans

Absorption correction: multi-scan (SADABS; Bruker, 2002)

Tmin = 0.979, Tmax = 0.988

3212 measured reflections 2149 independent reflections 1374 reflections with I > 2σ(I)

Rint = 0.023

θmax = 25.0°, θmin = 1.8°

h = −6→7

k = −11→9

l = −13→11

Refinement

Refinement on F2 Least-squares matrix: full

R[F2 _{> 2σ(F}2_{)] = 0.096}

wR(F2_{) = 0.326}

S = 1.22 2149 reflections 167 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) + (0.2P)2] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max < 0.001

Δρmax = 0.53 e Å−3 Δρmin = −0.45 e Å−3

Special details

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 0.7089 (7) 0.8995 (5) 0.4539 (4) 0.0539 (13)

H1 0.8045 0.9480 0.5108 0.081*

O2 0.9940 (7) 0.9262 (5) 0.3574 (4) 0.0554 (12)

O3 0.9186 (7) 0.5820 (5) 0.3271 (4) 0.0553 (13)

H3 1.0315 0.5501 0.3491 0.083*

O4 1.0845 (7) 0.5991 (5) 0.1714 (4) 0.0601 (13)

N1 1.3035 (7) 0.5209 (5) 0.4383 (4) 0.0409 (12)

C1 1.2874 (11) 0.7434 (7) 0.5853 (7) 0.064 (2)

H1A 1.3829 0.8360 0.5868 0.096*

H1B 1.2590 0.7423 0.6647 0.096*

H1C 1.1475 0.7340 0.5326 0.096*

C2 1.4009 (9) 0.6153 (6) 0.5414 (5) 0.0380 (13)

C3 1.4009 (9) 0.4064 (5) 0.3933 (5) 0.0368 (13)

C4 1.2833 (11) 0.3014 (6) 0.2791 (5) 0.0525 (17)

H4A 1.1758 0.3481 0.2387 0.079*

H4B 1.2071 0.2120 0.2960 0.079*

H4C 1.3912 0.2764 0.2288 0.079*

C5 0.7984 (9) 0.8772 (5) 0.3581 (5) 0.0352 (13)

C6 0.6339 (9) 0.7887 (6) 0.2482 (5) 0.0382 (14)

H6 0.4921 0.7526 0.2725 0.046*

C7 0.5854 (10) 0.8841 (6) 0.1529 (5) 0.0461 (15)

H7 0.4896 0.9580 0.1732 0.055*

C8 0.4866 (9) 0.7569 (6) 0.0413 (5) 0.0465 (16)

H8A 0.3588 0.6890 0.0529 0.056*

H8B 0.4494 0.7927 −0.0306 0.056*

C9 0.8013 (11) 0.9424 (7) 0.1205 (6) 0.0554 (18)

H9 0.8732 1.0420 0.1412 0.067*

C10 0.8775 (10) 0.8277 (7) 0.0559 (6) 0.0509 (16)

H10 1.0100 0.8324 0.0246 0.061*

C11 0.7036 (9) 0.6914 (6) 0.0455 (5) 0.0408 (14)

H11 0.7036 0.6070 −0.0210 0.049*

C12 0.7108 (8) 0.6539 (5) 0.1701 (5) 0.0381 (14)

H12 0.5919 0.5667 0.1603 0.046*

C13 0.9272 (9) 0.6120 (5) 0.2222 (5) 0.0399 (14)

Atomic displacement parameters (Å2₎

U11 _U22 _U33 _U12 _U13 _U23

O1 0.053 (3) 0.054 (3) 0.041 (3) −0.0001 (19) 0.001 (2) −0.008 (2)

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sup-3 Acta Cryst. (2005). E61, o731–o732

O3 0.041 (2) 0.069 (3) 0.060 (3) 0.022 (2) −0.008 (2) 0.025 (2)

O4 0.042 (3) 0.084 (3) 0.062 (3) 0.032 (2) 0.008 (2) 0.021 (2)

N1 0.041 (3) 0.040 (3) 0.041 (3) 0.015 (2) −0.003 (2) 0.007 (2)

C1 0.058 (4) 0.044 (4) 0.080 (5) 0.029 (3) −0.006 (4) −0.008 (3)

C2 0.042 (3) 0.034 (3) 0.037 (3) 0.017 (2) 0.003 (2) 0.000 (2)

C3 0.039 (3) 0.032 (3) 0.037 (3) 0.008 (2) 0.001 (2) 0.006 (2)

C4 0.064 (4) 0.047 (3) 0.041 (4) 0.017 (3) −0.004 (3) 0.002 (3)

C5 0.041 (3) 0.035 (3) 0.029 (3) 0.014 (2) 0.003 (2) 0.003 (2)

C6 0.029 (3) 0.042 (3) 0.040 (3) 0.008 (2) 0.002 (2) 0.003 (2)

C7 0.054 (4) 0.042 (3) 0.040 (3) 0.022 (3) −0.004 (3) 0.004 (3)

C8 0.042 (3) 0.049 (3) 0.041 (3) 0.012 (2) −0.012 (3) 0.003 (3)

C9 0.058 (4) 0.044 (3) 0.056 (4) −0.003 (3) −0.016 (3) 0.019 (3)

C10 0.038 (3) 0.066 (4) 0.049 (4) 0.010 (3) −0.007 (3) 0.021 (3)

C11 0.036 (3) 0.039 (3) 0.040 (3) 0.008 (2) −0.004 (2) 0.000 (2)

C12 0.028 (3) 0.026 (3) 0.047 (3) −0.002 (2) −0.011 (2) −0.004 (2)

C13 0.039 (3) 0.028 (3) 0.045 (3) 0.007 (2) −0.015 (3) 0.005 (2)

Geometric parameters (Å, º)

O1—C5 1.296 (6) C5—C6 1.509 (7)

O1—H1 0.8200 C6—C12 1.560 (7)

O2—C5 1.215 (6) C6—C7 1.576 (8)

O3—C13 1.308 (7) C6—H6 0.9800

O3—H3 0.8200 C7—C9 1.476 (9)

O4—C13 1.201 (7) C7—C8 1.541 (8)

N1—C2 1.329 (7) C7—H7 0.9800

N1—C3 1.343 (7) C8—C11 1.538 (8)

C1—C2 1.500 (7) C8—H8A 0.9700

C1—H1A 0.9600 C8—H8B 0.9700

C1—H1B 0.9600 C9—C10 1.352 (9)

C1—H1C 0.9600 C9—H9 0.9300

C2—C3i _{1.401 (7) C10—C11 1.499 (8)}

C3—C2i _{1.401 (7) C10—H10 0.9300}

C3—C4 1.488 (7) C11—C12 1.548 (8)

C4—H4A 0.9600 C11—H11 0.9800

C4—H4B 0.9600 C12—C13 1.515 (7)

C4—H4C 0.9600 C12—H12 0.9800

C5—O1—H1 109.5 C8—C7—C6 99.7 (4)

C13—O3—H3 109.5 C9—C7—H7 115.4

C2—N1—C3 119.7 (4) C8—C7—H7 115.4

C2—C1—H1A 109.5 C6—C7—H7 115.4

C2—C1—H1B 109.5 C11—C8—C7 93.0 (4)

H1A—C1—H1B 109.5 C11—C8—H8A 113.1

C2—C1—H1C 109.5 C7—C8—H8A 113.1

H1A—C1—H1C 109.5 C11—C8—H8B 113.1

H1B—C1—H1C 109.5 C7—C8—H8B 113.1

N1—C2—C1 117.2 (5) C10—C9—C7 109.0 (5)

C3i_{—C2—C1 121.8 (5) C10—C9—H9 125.5}

N1—C3—C2i _{119.2 (5) C7—C9—H9 125.5}

N1—C3—C4 117.9 (5) C9—C10—C11 105.5 (6)

C2i_{—C3—C4 122.7 (5) C9—C10—H10 127.2}

C3—C4—H4A 109.5 C11—C10—H10 127.2

C3—C4—H4B 109.5 C10—C11—C8 101.5 (5)

H4A—C4—H4B 109.5 C10—C11—C12 108.9 (4)

C3—C4—H4C 109.5 C8—C11—C12 98.1 (5)

H4A—C4—H4C 109.5 C10—C11—H11 115.4

H4B—C4—H4C 109.5 C8—C11—H11 115.4

O2—C5—O1 122.8 (5) C12—C11—H11 115.4

O2—C5—C6 124.0 (5) C13—C12—C11 116.0 (5)

O1—C5—C6 113.2 (5) C13—C12—C6 116.2 (4)

C5—C6—C12 116.6 (4) C11—C12—C6 104.3 (4)

C5—C6—C7 112.5 (4) C13—C12—H12 106.5

C12—C6—C7 100.6 (4) C11—C12—H12 106.5

C5—C6—H6 108.9 C6—C12—H12 106.5

C12—C6—H6 108.9 O4—C13—O3 123.2 (5)

C7—C6—H6 108.9 O4—C13—C12 124.7 (5)

C9—C7—C8 100.5 (5) O3—C13—C12 111.9 (6)

C9—C7—C6 108.3 (5)

Symmetry code: (i) −x+3, −y+1, −z+1.

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A

O1—H1···O2ii _{0.82 1.88 2.696 (5) 174}

O3—H3···N1 0.82 1.92 2.715 (5) 164

C1—H1C···O3 0.96 2.59 3.399 (5) 142

C8—H8A···O4iii _{0.97 2.46 3.361 (5) 154}