Crystal structure of N′-hy­droxy­pyrimidine-2-carboximidamide

Abstract

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 mol­ecule adopts an E configuration about the C=N double bond. In the crystal, adjacent mol­ecules 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 inter­actions 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 _r = 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) ų

• 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

• Δρ_max = 0.29 e Å⁻³

• Δρ_min = −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 ▶).

Supplementary Material

CCDC reference: 1018015

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

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) .

supplementary crystallographic information

S1. Comment

Supramolecular architectures assembled via various delicate noncovalent interactions such as hydrogen bonds, π—π stacking and electrostatic interactions, have attracted intense interest in recent years because of their fascinating structural diversity and potential applications for functional materials (Desiraju, 2007). In particular, the application of intermolecular hydrogen bonding is a well known and efficient tool in the field of organic crystal design owing to their strength and directional properties (Aakeroy & Seddon, 1993). Substituted N'-hydroxybenzamidines are important intermediates obtained during the synthesis of pharmaceuticaly important 1,2,4-oxadiazole derivatives (Kundu et al., 2012). 1,2,4-oxadiazole derivatives are well known for their biological activities such as for anti-HIV (Sakamoto et al., 2007) and anti-microbial applications (Tyrkov & Sukhenko, 2004). Herein, we report the crystal structure determination of the title compound, (I).

The asymmetric unit of the title compound is shown in Fig. 1. The essentially planar pyrimidine ring [N1/N2/C1–C4, maximum deviation of 0.009 (2) Å at atom C4] forms a dihedral angle of 11.04 (15)° with the hydroxyacetimidamide (N4/C5/N3/O1). The compound adopts an E configuration across the C5═N3 double bond, as the OH group and benzene ring are on opposite sides of the double bond while the hydrogen atom of the hydroxy group is directed away from the NH₂ group. The bond lengths and angles are within normal ranges.

In the crystal packing, molecules are linked by a pair of N4—H2N4···O1ⁱ hydrogen bonds (symmetry code in Table 1) into an inversion dimer, forming an R₂²(10) ring motif. These molecules are self-assembled via N4—H1N4···N3ⁱⁱ hydrogen bonds (graph-set notation C(4); symmetry code as in Table 1), which interconnect the dimers resulting in a sheet parallel to the ac plane as shown in Fig 2. Furthermore, the crystal structure is stabilized by O1–H1O1···N2ⁱⁱⁱ and weak C3—H3A···O1^iv hydrogen bonds (symmetry code as in Table 1) and π–π stacking interactions between the pyrimidine (N1/N2/C1-C4) rings [centroid-centroid distance = 3.622 (1) Å; (symmetry code: 1-x, - y, -z)].

S2. Experimental

A hot methanol solution (20 ml) of N'-hydroxypyrimidine- 2-carboximidamide (69 mg, Aldrich) was warmed over a magnetic stirrer hotplate for a few minutes. The resulting solution was allowed to cool slowly at room temperature. Single crystals of the title compound (I) appeared from the mother liquor after a few days.

S3. Refinement

O- and N-bound H atoms were located in a difference Fourier map and refined freely [O–H = 0.94 (4) Å and N–H = 0.89 (3) Å and 0.92 (3) Å]. The remaining hydrogen atoms were positioned geometrically [C–H= 0.95 Å] and were refined using a riding model, with U_iso(H)=1.2 U_eq(C).

Figures

Fig. 1.

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

Fig. 2.

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.

Crystal data

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

Data collection

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

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

Special details

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	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)*

Atomic displacement parameters (Ų)

	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)

Geometric parameters (Å, º)

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)

Hydrogen-bond geometry (Å, º)

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) −x+2, −y+1, −z; (ii) x, −y+1/2, z−1/2; (iii) −x+2, y+1/2, −z+1/2; (iv) x, y−1, z.