PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actaeInternational Union of Crystallographysearchopen accessarticle submissionjournal home pagethis article
 
Acta Crystallogr Sect E Struct Rep Online. 2008 January 1; 64(Pt 1): o105.
Published online 2007 December 6. doi:  10.1107/S1600536807062770
PMCID: PMC2915179

Pyrimidine-2-carboxamide

Abstract

In the crystal strucuture of the title compound, C5H5N3O, which was obtained upon recrystallization of 2-cyano­pyrimidine from aqueous sodium hydroxide, the amide group is twisted with respect to the aromatic ring by 24.9 (1)°. π–π stacking is observed between partially overlapped rings at a face-to-face separation of 3.439 (6) Å. The structure features a centrosymmetric pair of inter­molecular N—H(...)O hydrogen bonds. Another N—H(...)O hydrogen bond between adjacent mol­ecules links them into a helical chain motif.

Related literature

For general background, see: Cheng et al. (2000 [triangle]); Xu & Xu (2004 [triangle]); Zhang et al. (2008 [triangle]). For a similar structure, see: Zhang et al. (2007 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0o105-scheme1.jpg

Experimental

Crystal data

  • C5H5N3O
  • M r = 123.12
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o105-efi1.jpg
  • a = 7.9241 (7) Å
  • b = 7.3059 (7) Å
  • c = 9.8223 (9) Å
  • β = 103.512 (6)°
  • V = 552.90 (9) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.11 mm−1
  • T = 291 (2) K
  • 0.34 × 0.26 × 0.20 mm

Data collection

  • Rigaku R-AXIS RAPID IP diffractometer
  • Absorption correction: none
  • 7501 measured reflections
  • 1365 independent reflections
  • 1202 reflections with I > 2σ(I)
  • R int = 0.020

Refinement

  • R[F 2 > 2σ(F 2)] = 0.038
  • wR(F 2) = 0.107
  • S = 1.01
  • 1365 reflections
  • 82 parameters
  • H-atom parameters constrained
  • Δρmax = 0.25 e Å−3
  • Δρmin = −0.19 e Å−3

Data collection: PROCESS-AUTO (Rigaku, 1998 [triangle]); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002 [triangle]); program(s) used to solve structure: SIR92 (Altomare et al., 1993 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997 [triangle]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536807062770/ng2399sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536807062770/ng2399Isup2.hkl

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

Acknowledgments

This work was supported by the ZIJIN Project of Zhejiang University, China.

supplementary crystallographic information

Comment

In order to study the nature of π–π stacking, a series of metal complexes incorporating substituted benzoate ligand have been prepared in our laboratory (Cheng et al., 2000; Xu & Xu, 2004). As a continuing work, metal complexes with pyrimidine-2-carboxylate ligand have recently been prepared (Zhang et al., 2007). In the process of preparing pyrimidine-2-carboxylic acid from cyanopyrimidine, the title compound has been obtained.

The molecular structure of the title complex is shown in Fig. 1. The bond distances and angles are normal. The amide group is twisted with respect to the benzene ring by a dihedral angel of 24.92 (12)°. The amino group links with carbonyl groups of adjacent molecules via O—H···O hydrogen bonding (Table 1). π–π stacking is observed between parallel, partially overlapped N1-pyrimidine and Ni-pyrimidine rings (Fig. 1) [symmetry code: (i) 1 - x, 1 - y, 1 - z], face-to-face separation being 3.439 (6) Å; similar to the situation found in the pyrimidine-2-carboxylate complex of copper(II) (Zhang et al., 2007).

Experimental

2-Cyanopyrimidine (1.0 g, 9.5 mmol) was dissolved in 10 ml water, then a NaOH solution (0.1 M) was dropped to the solution until to pH = 12. Single crystals of the title compound were obtained from the solution after one week.

Refinement

Amino H atoms were located in a difference Fourier map and refined as riding in as-found relative positions with Uiso(H) = 1.5Ueq(N). Other H atoms were placed in calculated positions with C—H = 0.93 Å and refined in riding mode with Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
The molecular structure of the title compound with 30% probability displacement (arbitrary spheres for H atoms) [symmetry codes: (i) 1 - x, 1 - y, 1 - z].

Crystal data

C5H5N3OF000 = 256
Mr = 123.12Dx = 1.479 Mg m3
Monoclinic, P21/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2086 reflections
a = 7.9241 (7) Åθ = 3.0–25.5º
b = 7.3059 (7) ŵ = 0.11 mm1
c = 9.8223 (9) ÅT = 291 (2) K
β = 103.512 (6)ºPrism, yellow
V = 552.90 (9) Å30.34 × 0.26 × 0.20 mm
Z = 4

Data collection

Rigaku R-AXIS RAPID IP diffractometer1202 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.020
Monochromator: graphiteθmax = 28.3º
T = 293(2) Kθmin = 2.6º
ω scansh = −10→10
Absorption correction: nonek = −9→9
7501 measured reflectionsl = −12→13
1365 independent reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.038H-atom parameters constrained
wR(F2) = 0.107  w = 1/[σ2(Fo2) + (0.0584P)2 + 0.1258P] where P = (Fo2 + 2Fc2)/3
S = 1.02(Δ/σ)max < 0.001
1365 reflectionsΔρmax = 0.25 e Å3
82 parametersΔρmin = −0.19 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

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 (Å2)

xyzUiso*/Ueq
N10.35320 (14)0.45375 (15)0.64547 (11)0.0431 (3)
N20.18202 (13)0.54314 (14)0.42171 (10)0.0383 (3)
O10.13605 (12)0.15236 (12)0.61860 (8)0.0431 (3)
N30.07527 (15)0.18634 (15)0.38330 (10)0.0435 (3)
H1A0.09490.24770.30430.065*
H1B0.00390.07830.36750.065*
C10.23238 (14)0.42647 (15)0.52761 (11)0.0315 (2)
C20.43153 (18)0.6167 (2)0.65658 (14)0.0495 (3)
H20.51930.64120.73550.059*
C30.38709 (19)0.74967 (19)0.55555 (15)0.0502 (3)
H30.44050.86380.56590.060*
C40.26039 (18)0.70681 (18)0.43855 (14)0.0462 (3)
H40.22790.79440.36860.055*
C50.14304 (14)0.24129 (15)0.51331 (11)0.0325 (3)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0446 (6)0.0418 (6)0.0383 (5)−0.0037 (4)0.0002 (4)−0.0014 (4)
N20.0417 (5)0.0350 (5)0.0375 (5)0.0003 (4)0.0080 (4)0.0046 (4)
O10.0602 (6)0.0366 (5)0.0316 (4)−0.0065 (4)0.0087 (4)0.0025 (3)
N30.0593 (7)0.0389 (6)0.0304 (5)−0.0120 (5)0.0065 (4)−0.0018 (4)
C10.0325 (5)0.0315 (5)0.0311 (5)0.0019 (4)0.0085 (4)−0.0016 (4)
C20.0478 (7)0.0501 (8)0.0473 (7)−0.0108 (6)0.0046 (5)−0.0103 (6)
C30.0530 (8)0.0377 (7)0.0628 (9)−0.0123 (5)0.0194 (6)−0.0072 (6)
C40.0506 (7)0.0367 (6)0.0538 (7)0.0001 (5)0.0175 (6)0.0084 (5)
C50.0362 (5)0.0304 (5)0.0302 (5)0.0018 (4)0.0067 (4)−0.0001 (4)

Geometric parameters (Å, °)

N1—C11.3336 (14)N3—H1B0.9622
N1—C21.3355 (18)C1—C51.5182 (15)
N2—C11.3319 (14)C2—C31.374 (2)
N2—C41.3397 (17)C2—H20.9300
O1—C51.2335 (13)C3—C41.374 (2)
N3—C51.3265 (14)C3—H30.9300
N3—H1A0.9406C4—H40.9300
C1—N1—C2115.46 (11)C3—C2—H2118.8
C1—N2—C4115.41 (10)C2—C3—C4117.18 (12)
C5—N3—H1A122.9C2—C3—H3121.4
C5—N3—H1B119.6C4—C3—H3121.4
H1A—N3—H1B117.5N2—C4—C3122.26 (12)
N2—C1—N1127.28 (11)N2—C4—H4118.9
N2—C1—C5116.74 (9)C3—C4—H4118.9
N1—C1—C5115.99 (10)O1—C5—N3124.08 (11)
N1—C2—C3122.37 (12)O1—C5—C1120.20 (9)
N1—C2—H2118.8N3—C5—C1115.72 (9)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N3—H1A···O1i0.942.062.994 (1)172
N3—H1B···O1ii0.962.042.986 (2)167

Symmetry codes: (i) x, −y+1/2, z−1/2; (ii) −x, −y, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: NG2399).

References

  • Altomare, A., Cascarano, G., Giacovazzo, C. & Guagliardi, A. (1993). J. Appl. Cryst.26, 343–350.
  • Cheng, D.-P., Zheng, Y., Lin, J., Xu, D. & Xu, Y. (2000). Acta Cryst. C56, 523–524. [PubMed]
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Farrugia, L. J. (1999). J. Appl. Cryst.32, 837–838.
  • Rigaku (1998). PROCESS-AUTO Rigaku Corporation, Tokyo, Japan.
  • Rigaku/MSC (2002). CrystalStructure Version 3.00. Rigaku/MSC, The Woodlands, Texas, USA.
  • Sheldrick, G. M. (1997). SHELXL97 University of Göttingen, Germany. [PubMed]
  • Xu, T.-G. & Xu, D.-J. (2004). Acta Cryst. E60, m1131–m1133.
  • Zhang, B.-Y., Yang, Q. & Nie, J.-J. (2008). Acta Cryst. E64, m7. [PMC free article] [PubMed]

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography