Pyrimidine-2-carboxamide

Zhang, B.-Y.; Yang, Q.; Nie, J.-J.

doi:10.1107/S1600536807062770

organic compounds

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ISSN: 2056-9890

Volume 64| Part 1| January 2008| Page o105

https://doi.org/10.1107/S1600536807062770

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Pyrimidine-2-carboxamide

Bing-Yu Zhang,^a Qian Yang ^a and Jing-Jing Nie ^a ^*

^aDepartment of Chemistry, Zhejiang University, Hangzhou 310027, People's Republic of China
^*Correspondence e-mail: niejj@zju.edu.cn

(Received 23 November 2007; accepted 23 November 2007; online 6 December 2007)

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 ); Xu & Xu (2004 ); Zhang et al. (2008 ). For a similar structure, see: Zhang et al. (2007).

Experimental

Crystal data

C₅H₅N₃O
M_r = 123.12
Monoclinic, P 2₁ /c
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[F² > 2σ(F²)] = 0.038
wR(F²) = 0.107
S = 1.01
1365 reflections
82 parameters
H-atom parameters constrained
Δρ_max = 0.25 e Å⁻³
Δρ_min = −0.19 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H1A⋯O1ⁱ	0.94	2.06	2.994 (1)	172
N3—H1B⋯O1ⁱⁱ	0.96	2.04	2.986 (2)	167
Symmetry codes: (i) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ ; (ii) -x, -y, -z+1.

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

Supporting information

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

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536807062770/ng2399Isup2.hkl

checkCIF report

Comment top

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).

Related literature top

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

Experimental top

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.

Structure description top

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

Computing details top

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

Figures top

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].

pyrimidine-2-carboxamide top

Crystal data top

C₅H₅N₃O	F(000) = 256
M_r = 123.12	D_x = 1.479 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2086 reflections
a = 7.9241 (7) Å	θ = 3.0–25.5°
b = 7.3059 (7) Å	µ = 0.11 mm⁻¹
c = 9.8223 (9) Å	T = 291 K
β = 103.512 (6)°	Prism, yellow
V = 552.90 (9) Å³	0.34 × 0.26 × 0.20 mm
Z = 4

Data collection top

Rigaku R-AXIS RAPID IP diffractometer	1202 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.020
Graphite monochromator	θ_max = 28.3°, θ_min = 2.6°
ω scans	h = −10→10
7501 measured reflections	k = −9→9
1365 independent reflections	l = −12→13

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)] = 0.038	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.107	H-atom parameters constrained
S = 1.02	w = 1/[σ²(F_o²) + (0.0584P)² + 0.1258P] where P = (F_o² + 2F_c²)/3
1365 reflections	(Δ/σ)_max < 0.001
82 parameters	Δρ_max = 0.25 e Å⁻³
0 restraints	Δρ_min = −0.19 e Å⁻³

Crystal data top

C₅H₅N₃O	V = 552.90 (9) Å³
M_r = 123.12	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 7.9241 (7) Å	µ = 0.11 mm⁻¹
b = 7.3059 (7) Å	T = 291 K
c = 9.8223 (9) Å	0.34 × 0.26 × 0.20 mm
β = 103.512 (6)°

Data collection top

Rigaku R-AXIS RAPID IP diffractometer	1202 reflections with I > 2σ(I)
7501 measured reflections	R_int = 0.020
1365 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.038	0 restraints
wR(F²) = 0.107	H-atom parameters constrained
S = 1.02	Δρ_max = 0.25 e Å⁻³
1365 reflections	Δρ_min = −0.19 e Å⁻³
82 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
N1	0.35320 (14)	0.45375 (15)	0.64547 (11)	0.0431 (3)
N2	0.18202 (13)	0.54314 (14)	0.42171 (10)	0.0383 (3)
O1	0.13605 (12)	0.15236 (12)	0.61860 (8)	0.0431 (3)
N3	0.07527 (15)	0.18634 (15)	0.38330 (10)	0.0435 (3)
H1A	0.0949	0.2477	0.3043	0.065*
H1B	0.0039	0.0783	0.3675	0.065*
C1	0.23238 (14)	0.42647 (15)	0.52761 (11)	0.0315 (2)
C2	0.43153 (18)	0.6167 (2)	0.65658 (14)	0.0495 (3)
H2	0.5193	0.6412	0.7355	0.059*
C3	0.38709 (19)	0.74967 (19)	0.55555 (15)	0.0502 (3)
H3	0.4405	0.8638	0.5659	0.060*
C4	0.26039 (18)	0.70681 (18)	0.43855 (14)	0.0462 (3)
H4	0.2279	0.7944	0.3686	0.055*
C5	0.14304 (14)	0.24129 (15)	0.51331 (11)	0.0325 (3)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0446 (6)	0.0418 (6)	0.0383 (5)	−0.0037 (4)	0.0002 (4)	−0.0014 (4)
N2	0.0417 (5)	0.0350 (5)	0.0375 (5)	0.0003 (4)	0.0080 (4)	0.0046 (4)
O1	0.0602 (6)	0.0366 (5)	0.0316 (4)	−0.0065 (4)	0.0087 (4)	0.0025 (3)
N3	0.0593 (7)	0.0389 (6)	0.0304 (5)	−0.0120 (5)	0.0065 (4)	−0.0018 (4)
C1	0.0325 (5)	0.0315 (5)	0.0311 (5)	0.0019 (4)	0.0085 (4)	−0.0016 (4)
C2	0.0478 (7)	0.0501 (8)	0.0473 (7)	−0.0108 (6)	0.0046 (5)	−0.0103 (6)
C3	0.0530 (8)	0.0377 (7)	0.0628 (9)	−0.0123 (5)	0.0194 (6)	−0.0072 (6)
C4	0.0506 (7)	0.0367 (6)	0.0538 (7)	0.0001 (5)	0.0175 (6)	0.0084 (5)
C5	0.0362 (5)	0.0304 (5)	0.0302 (5)	0.0018 (4)	0.0067 (4)	−0.0001 (4)

Geometric parameters (Å, º) top

N1—C1	1.3336 (14)	N3—H1B	0.9622
N1—C2	1.3355 (18)	C1—C5	1.5182 (15)
N2—C1	1.3319 (14)	C2—C3	1.374 (2)
N2—C4	1.3397 (17)	C2—H2	0.9300
O1—C5	1.2335 (13)	C3—C4	1.374 (2)
N3—C5	1.3265 (14)	C3—H3	0.9300
N3—H1A	0.9406	C4—H4	0.9300

C1—N1—C2	115.46 (11)	C3—C2—H2	118.8
C1—N2—C4	115.41 (10)	C2—C3—C4	117.18 (12)
C5—N3—H1A	122.9	C2—C3—H3	121.4
C5—N3—H1B	119.6	C4—C3—H3	121.4
H1A—N3—H1B	117.5	N2—C4—C3	122.26 (12)
N2—C1—N1	127.28 (11)	N2—C4—H4	118.9
N2—C1—C5	116.74 (9)	C3—C4—H4	118.9
N1—C1—C5	115.99 (10)	O1—C5—N3	124.08 (11)
N1—C2—C3	122.37 (12)	O1—C5—C1	120.20 (9)
N1—C2—H2	118.8	N3—C5—C1	115.72 (9)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H1A···O1ⁱ	0.94	2.06	2.994 (1)	172
N3—H1B···O1ⁱⁱ	0.96	2.04	2.986 (2)	167

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

Experimental details

Crystal data
Chemical formula	C₅H₅N₃O
M_r	123.12
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	291
a, b, c (Å)	7.9241 (7), 7.3059 (7), 9.8223 (9)
β (°)	103.512 (6)
V (Å³)	552.90 (9)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.34 × 0.26 × 0.20

Data collection
Diffractometer	Rigaku R-AXIS RAPID IP
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	7501, 1365, 1202
R_int	0.020
(sin θ/λ)_max (Å⁻¹)	0.667

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.038, 0.107, 1.02
No. of reflections	1365
No. of parameters	82
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.25, −0.19

Computer programs: PROCESS-AUTO (Rigaku, 1998), CrystalStructure (Rigaku/MSC, 2002), SIR92 (Altomare et al., 1993), SHELXL97 (Sheldrick, 1997), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H1A···O1ⁱ	0.94	2.06	2.994 (1)	172
N3—H1B···O1ⁱⁱ	0.96	2.04	2.986 (2)	167

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

Acknowledgements

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

References

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