Crystal structure of N'-hy-droxy-pyrimidine-2-carboximidamide.

The title compound, C5H6N4O, is approximately planar, with an angle of 11.04 (15)° between the planes of the pyrimidine ring and the non-H atoms of the carboximidamide unit. The mol-ecule adopts an E configuration about the C=N double bond. In the crystal, adjacent mol-ecules are linked by pairs of N-H⋯O hydrogen bonds, forming inversion dimers with an R 2 (2)(10) ring motif. The dimers are further linked via N-H⋯N and O-H⋯N hydrogen bonds into a sheet structure parallel to the ac plane. The crystal structure also features N-H⋯O and weak C-H⋯O hydrogen bonds and offset π-π stacking inter-actions between adjacent pyrimidine rings [centroid-centroid distance = 3.622 (1) Å].

Related literature

For details of non-covalent inter­actions, see: Desiraju (2007 ▶). For the role of inter­molecular hydrogen bonds in the design of organic crystals, see: Aakeroy & Seddon (1993 ▶). For background to substituted N′-hy­droxy­benzamidines as inter­mediates in the synthesis of 1,2,4-oxa­diazole derivatives, see: Kundu et al. (2012 ▶). For the biological activity of substituted N′-hy­droxy­benzamidines and 1,2,4-oxa­diazole derivatives, see: Sakamoto et al. (2007 ▶); Tyrkov & Sukhenko (2004 ▶).

Experimental

Crystal data

C5H6N4O

M = 138.14

Monoclinic,

a = 7.4066 (7) Å

b = 8.0165 (8) Å

c = 10.2200 (9) Å

β = 101.888 (6)°

V = 593.8 (1) Å3

Z = 4

Mo Kα radiation

μ = 0.12 mm−1

T = 100 K

0.62 × 0.17 × 0.08 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer

Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.931, T max = 0.990

4073 measured reflections

1030 independent reflections

831 reflections with I > 2σ(I)

R int = 0.047

Refinement

R[F 2 > 2σ(F 2)] = 0.054

wR(F 2) = 0.181

S = 1.13

1030 reflections

103 parameters

H atoms treated by a mixture of independent and constrained refinement

Δρmax = 0.29 e Å−3

Δρmin = −0.31 e Å−3

Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶).

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536814020285/sj5423sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814020285/sj5423Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S1600536814020285/sj5423Isup3.cml

Click here for additional data file.

. DOI: 10.1107/S1600536814020285/sj5423fig1.tif

The mol­ecular structure of the title compound with atom labels. Displacement ellipsoids are shown at the 50% probability level.

Click here for additional data file.

b . DOI: 10.1107/S1600536814020285/sj5423fig2.tif

The crystal packing of the title compound viewed along the b axis die=rection. H atoms not involved in inter­molecular inter­actions (dashed lines) have been omitted for clarity.

CCDC reference: 1018015

Additional supporting information: crystallographic information; 3D view; checkCIF report

C5H6N4O	F(000) = 288
Mr = 138.14	Dx = 1.545 Mg m−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 1905 reflections
a = 7.4066 (7) Å	θ = 2.8–29.9°
b = 8.0165 (8) Å	µ = 0.12 mm−1
c = 10.2200 (9) Å	T = 100 K
β = 101.888 (6)°	Plate, colourless
V = 593.8 (1) Å3	0.62 × 0.17 × 0.08 mm
Z = 4

Bruker SMART APEXII CCD area-detector diffractometer	1030 independent reflections
Radiation source: fine-focus sealed tube	831 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.047
φ and ω scans	θmax = 25.0°, θmin = 2.8°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −8→8
Tmin = 0.931, Tmax = 0.990	k = −9→8
4073 measured reflections	l = −12→12

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)] = 0.054	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.181	H atoms treated by a mixture of independent and constrained refinement
S = 1.13	w = 1/[σ2(Fo2) + (0.093P)2 + 0.7207P] where P = (Fo2 + 2Fc2)/3
1030 reflections	(Δ/σ)max < 0.001
103 parameters	Δρmax = 0.29 e Å−3
0 restraints	Δρmin = −0.31 e Å−3

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat operating at 100.0 (1) K.

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.

	x	y	z	Uiso*/Ueq
O1	0.9616 (3)	0.4128 (2)	0.15856 (18)	0.0171 (6)
N1	0.6515 (3)	0.0148 (3)	−0.1252 (2)	0.0159 (6)
N2	0.8106 (3)	−0.0836 (3)	0.0883 (2)	0.0140 (6)
N3	0.9064 (3)	0.2423 (3)	0.1497 (2)	0.0150 (6)
N4	0.8007 (3)	0.3212 (3)	−0.0758 (2)	0.0155 (6)
C1	0.5875 (4)	−0.1406 (4)	−0.1538 (3)	0.0183 (7)
H1A	0.5107	−0.1612	−0.2389	0.022*
C2	0.6283 (4)	−0.2713 (4)	−0.0652 (3)	0.0198 (7)
H2A	0.5801	−0.3800	−0.0867	0.024*
C3	0.7425 (4)	−0.2368 (4)	0.0560 (3)	0.0183 (7)
H3A	0.7743	−0.3244	0.1191	0.022*
C4	0.7592 (3)	0.0362 (3)	−0.0043 (2)	0.0127 (6)
C5	0.8291 (3)	0.2095 (3)	0.0268 (2)	0.0126 (7)
H2N4	0.869 (4)	0.413 (4)	−0.057 (3)	0.012 (7)*
H1N4	0.784 (4)	0.281 (4)	−0.162 (3)	0.025 (8)*
H1O1	1.029 (5)	0.429 (4)	0.247 (4)	0.022 (8)*

	U11	U22	U33	U12	U13	U23
O1	0.0221 (11)	0.0123 (11)	0.0157 (11)	−0.0038 (8)	0.0012 (9)	−0.0005 (7)
N1	0.0142 (12)	0.0173 (13)	0.0169 (12)	−0.0003 (10)	0.0048 (10)	−0.0023 (9)
N2	0.0130 (12)	0.0135 (12)	0.0156 (12)	0.0008 (9)	0.0033 (10)	0.0000 (9)
N3	0.0164 (12)	0.0098 (12)	0.0185 (12)	−0.0026 (10)	0.0027 (10)	−0.0001 (9)
N4	0.0196 (13)	0.0134 (13)	0.0130 (12)	−0.0015 (11)	0.0023 (10)	0.0016 (9)
C1	0.0139 (14)	0.0209 (15)	0.0212 (14)	−0.0018 (12)	0.0058 (12)	−0.0060 (12)
C2	0.0166 (15)	0.0129 (14)	0.0319 (16)	−0.0030 (11)	0.0096 (13)	−0.0071 (12)
C3	0.0177 (15)	0.0147 (14)	0.0246 (15)	0.0015 (12)	0.0096 (12)	0.0004 (11)
C4	0.0092 (13)	0.0160 (15)	0.0138 (13)	0.0006 (11)	0.0043 (11)	−0.0032 (10)
C5	0.0099 (13)	0.0137 (14)	0.0160 (13)	0.0011 (11)	0.0065 (11)	0.0002 (10)

O1—N3	1.424 (3)	N4—H2N4	0.89 (3)
O1—H1O1	0.94 (4)	N4—H1N4	0.92 (3)
N1—C4	1.336 (3)	C1—C2	1.378 (4)
N1—C1	1.343 (4)	C1—H1A	0.9500
N2—C3	1.343 (4)	C2—C3	1.376 (4)
N2—C4	1.347 (3)	C2—H2A	0.9500
N3—C5	1.295 (3)	C3—H3A	0.9500
N4—C5	1.362 (3)	C4—C5	1.494 (4)
N3—O1—H1O1	106.1 (18)	C3—C2—H2A	121.6
C4—N1—C1	116.0 (2)	C1—C2—H2A	121.6
C3—N2—C4	116.2 (2)	N2—C3—C2	122.4 (3)
C5—N3—O1	108.7 (2)	N2—C3—H3A	118.8
C5—N4—H2N4	112.9 (18)	C2—C3—H3A	118.8
C5—N4—H1N4	118 (2)	N1—C4—N2	125.9 (2)
H2N4—N4—H1N4	117 (3)	N1—C4—C5	115.6 (2)
N1—C1—C2	122.8 (2)	N2—C4—C5	118.5 (2)
N1—C1—H1A	118.6	N3—C5—N4	125.5 (2)
C2—C1—H1A	118.6	N3—C5—C4	117.4 (2)
C3—C2—C1	116.7 (3)	N4—C5—C4	117.1 (2)
C4—N1—C1—C2	0.2 (4)	C3—N2—C4—C5	179.3 (2)
N1—C1—C2—C3	−1.1 (4)	O1—N3—C5—N4	−1.7 (3)
C4—N2—C3—C2	0.8 (4)	O1—N3—C5—C4	−179.51 (19)
C1—C2—C3—N2	0.5 (4)	N1—C4—C5—N3	168.3 (2)
C1—N1—C4—N2	1.3 (4)	N2—C4—C5—N3	−12.7 (3)
C1—N1—C4—C5	−179.8 (2)	N1—C4—C5—N4	−9.7 (3)
C3—N2—C4—N1	−1.8 (4)	N2—C4—C5—N4	169.3 (2)

D—H···A	D—H	H···A	D···A	D—H···A
N4—H2N4···O1i	0.89 (3)	2.27 (3)	2.996 (3)	139 (3)
N4—H1N4···N3ii	0.92 (3)	2.30 (3)	3.106 (3)	146 (3)
O1—H1O1···N2iii	0.95 (4)	1.85 (4)	2.783 (3)	167 (3)
C3—H3A···O1iv	0.95	2.51	3.305 (4)	141

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N4—H2N4⋯O1i	0.89 (3)	2.27 (3)	2.996 (3)	139 (3)
N4—H1N4⋯N3ii	0.92 (3)	2.30 (3)	3.106 (3)	146 (3)
O1—H1O1⋯N2iii	0.95 (4)	1.85 (4)	2.783 (3)	167 (3)
C3—H3A⋯O1iv	0.95	2.51	3.305 (4)	141

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .