N′-Hy­droxy­pyridine-2-carboximidamide

Suchetan, P.A.; Sreenivasa, S.; Palakshamurthy, B.S.; Madhu Chakrapani Rao, T.; Vijithkumar

doi:10.1107/S1600536813017418

organic compounds

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ISSN: 2056-9890

Volume 69| Part 7| July 2013| Page o1180

https://doi.org/10.1107/S1600536813017418

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N′-Hydroxypyridine-2-carboximidamide

P. A. Suchetan,^a S. Sreenivasa,^b ^* B. S. Palakshamurthy,^c T. Madhu Chakrapani Rao ^d and Vijithkumar ^e

^aDepartment of Studies and Research in Chemistry, U.C.S, Tumkur University, Tumkur, Karnataka 572 103, India, ^bDepartment of Studies and Research in Chemistry, Tumkur University, Tumkur, Karnataka 572 103, India, ^cDepartment of Studies and Research in Physics, U.C.S, Tumkur University, Tumkur, Karnataka 572 103, India, ^dTadimety Aromatics Pvt Ltd, Hirehally Industrial Area, Tumkur, Karnataka 572 168, India, and ^eSoild State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India
^*Correspondence e-mail: drsreenivasa@yahoo.co.in

(Received 13 June 2013; accepted 24 June 2013; online 29 June 2013)

The title molecule, C₆H₇N₃O, is almost planar (r.m.s. deviation = 0.0068 Å) and adopts an E conformation about the C=N double bond. In the crystal, molecules are linked by pairs of strong N—H⋯N hydrogen bonds, forming inversion dimers with R₂²(10) motifs. The dimers are further linked into C(3) chains through O—H⋯N hydrogen bonds.

Related literature

For the pharmaceutical and biological activity of substituted N′-hydroxybenzamidines and 1,2,4-oxadiazole derivatives, see: Kundu et al. (2012 ); Sakamoto et al. (2007 ); Tyrkov & Sukhenko (2004 ). For a related structure, see: Sreenivasa et al. (2012 )

Experimental

Crystal data

C₆H₇N₃O
M_r = 137.15
Monoclinic, C 2/c
a = 21.367 (5) Å
b = 4.6382 (11) Å
c = 13.003 (3) Å
β = 105.468 (12)°
V = 1242.0 (5) Å³
Z = 8
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 293 K
0.33 × 0.25 × 0.20 mm

Data collection

Bruker APEXII CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2009 ) T_min = 0.966, T_max = 0.979
8242 measured reflections
1086 independent reflections
982 reflections with I > 2σ(I)
R_int = 0.038

Refinement

R[F² > 2σ(F²)] = 0.031
wR(F²) = 0.081
S = 1.08
1086 reflections
103 parameters
2 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.19 e Å⁻³
Δρ_min = −0.18 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯N3ⁱ	0.903 (18)	1.859 (19)	2.7537 (14)	170.5 (17)
N2—H2N2⋯N1ⁱⁱ	0.86 (1)	2.44 (1)	3.1753 (16)	144 (1)
Symmetry codes: (i) $[-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) -x, -y, -z.

Data collection: APEX2 (Bruker, 2009); cell refinement: APEX2 and SAINT-Plus (Bruker, 2009); data reduction: SAINT-Plus and XPREP (Bruker, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2008 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536813017418/bt6916sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536813017418/bt6916Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536813017418/bt6916Isup3.cml

checkCIF report

Comment top

Substituted N'-hydroxybenzamidines are important intermediates obtained during the synthesis of pharmaceutically important 1,2,4-oxadiazole derivatives (Kundu et al., 2012). 1,2,4-Oxadiazole derivatives are well known for their biological activities such as anti-HIV (Sakamoto et al., 2007) and anti-microbial (Tyrkov et al., 2004). In this view, we synthesized the title compound to study its crystal structure.

The title compound, (I), crystalizes with a single molecule in the asymmetric unit. This is in contrast to (E)-3-chloro-N'-hydroxybenzene-1-carboximidamide, (II), (Sreenivasa et al., 2012) which crystalizes with two molecules in its asymmetric unit. Compound (I) adopts an E configuration across the C=N double bond, as the OH group and the benzene ring are on opposite sides of the double bond, while the H atom of the hydroxy group is directed away from the NH₂ group. This is similar as observed in (II). In the packing, the molecules are linked to one another through strong intermolecular N—H···N hydrogen bonds into R₂²(10) motifs forming inversion dimers. The dimers are further linked into C(3) chains through O—H···N hydrogen bonds.

Related literature top

For the pharmaceutical and biological activity of substituted N'-hydroxybenzamidines and 1,2,4-oxadiazole derivatives, see: Kundu et al. (2012); Sakamoto et al. (2007); Tyrkov & Sukhenko (2004). For a related structure, see: Sreenivasa et al. (2012)

Experimental top

To a solution of 2-cyanopyridine (1 mmol) in ethanol was added triethyl amine (2.5 mmol) and hydroxyl amine hydrochloride, NH₂OH.HCl (3.5 mmol). The reaction mixture was stirred at room temperature for 12hrs. (The reaction was monitored by TLC). The solvent was removed and the crude product was purified by column chromatography using hexane and ethyl acetate as the eluent.

Single crystals required for X-ray diffraction measurements were obtained from slow evaporation of the solution of the compound in a mixture of ethanol and dichloromethane (1:4).

Structure description top

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: APEX2 and SAINT-Plus (Bruker, 2009); data reduction: SAINT-Plus and XPREP (Bruker, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. Molecular structure of the title compound, showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. Packing of molecules displaying R₂²(10) loops and C(3) chains.

N'-Hydroxypyridine-2-carboximidamide top

Crystal data top

C₆H₇N₃O	F(000) = 576
M_r = 137.15	prism
Monoclinic, C2/c	D_x = 1.467 Mg m⁻³
Hall symbol: -C 2yc	Mo Kα radiation, λ = 0.71073 Å
a = 21.367 (5) Å	Cell parameters from 1088 reflections
b = 4.6382 (11) Å	θ = 2.0–25.0°
c = 13.003 (3) Å	µ = 0.11 mm⁻¹
β = 105.468 (12)°	T = 293 K
V = 1242.0 (5) Å³	Prism, colourless
Z = 8	0.33 × 0.25 × 0.20 mm

Data collection top

Bruker APEXII CCD area-detector diffractometer	1086 independent reflections
Radiation source: fine-focus sealed tube	982 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.038
Detector resolution: 1.03 pixels mm^-1	θ_max = 25.0°, θ_min = 2.0°
phi and ω scans	h = −24→24
Absorption correction: multi-scan (SADABS; Bruker, 2009)	k = −5→5
T_min = 0.966, T_max = 0.979	l = −15→15
8242 measured reflections

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)] = 0.031	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.081	H atoms treated by a mixture of independent and constrained refinement
S = 1.08	w = 1/[σ²(F_o²) + (0.0379P)² + 0.8786P] where P = (F_o² + 2F_c²)/3
1086 reflections	(Δ/σ)_max = 0.011
103 parameters	Δρ_max = 0.19 e Å⁻³
2 restraints	Δρ_min = −0.18 e Å⁻³
0 constraints

Crystal data top

C₆H₇N₃O	V = 1242.0 (5) Å³
M_r = 137.15	Z = 8
Monoclinic, C2/c	Mo Kα radiation
a = 21.367 (5) Å	µ = 0.11 mm⁻¹
b = 4.6382 (11) Å	T = 293 K
c = 13.003 (3) Å	0.33 × 0.25 × 0.20 mm
β = 105.468 (12)°

Data collection top

Bruker APEXII CCD area-detector diffractometer	1086 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2009)	982 reflections with I > 2σ(I)
T_min = 0.966, T_max = 0.979	R_int = 0.038
8242 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.031	2 restraints
wR(F²) = 0.081	H atoms treated by a mixture of independent and constrained refinement
S = 1.08	Δρ_max = 0.19 e Å⁻³
1086 reflections	Δρ_min = −0.18 e Å⁻³
103 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
O1	0.19134 (4)	0.1826 (2)	0.26040 (7)	0.0207 (3)
H1N2	0.0896 (7)	0.225 (3)	0.1797 (12)	0.027 (4)*
H2N2	0.0456 (6)	0.081 (3)	0.0861 (11)	0.027 (4)*
H1	0.2316 (9)	0.260 (4)	0.2779 (14)	0.043 (5)*
C1	0.12315 (6)	−0.2716 (3)	0.03188 (9)	0.0154 (3)
C2	0.17439 (6)	−0.4236 (3)	0.01036 (10)	0.0189 (3)
H2	0.2167	−0.3964	0.0520	0.023*
C3	0.16144 (6)	−0.6149 (3)	−0.07361 (10)	0.0208 (3)
H3	0.1949	−0.7164	−0.0904	0.025*
C4	0.09770 (6)	−0.6536 (3)	−0.13259 (10)	0.0211 (3)
H4	0.0874	−0.7834	−0.1891	0.025*
C5	0.05004 (6)	−0.4948 (3)	−0.10538 (10)	0.0203 (3)
H5	0.0073	−0.5229	−0.1449	0.024*
C6	0.13390 (5)	−0.0595 (3)	0.12070 (9)	0.0147 (3)
N1	0.06133 (5)	−0.3023 (2)	−0.02561 (8)	0.0176 (3)
N2	0.08163 (5)	0.0824 (2)	0.13540 (9)	0.0179 (3)
N3	0.19228 (5)	−0.0259 (2)	0.18081 (8)	0.0175 (3)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0156 (5)	0.0240 (5)	0.0199 (5)	−0.0027 (4)	0.0004 (4)	−0.0070 (4)
C1	0.0157 (6)	0.0151 (6)	0.0149 (6)	−0.0009 (5)	0.0032 (5)	0.0048 (5)
C2	0.0152 (6)	0.0215 (7)	0.0186 (6)	0.0008 (5)	0.0022 (5)	0.0038 (5)
C3	0.0225 (7)	0.0210 (7)	0.0205 (7)	0.0050 (5)	0.0087 (5)	0.0035 (5)
C4	0.0276 (7)	0.0199 (7)	0.0157 (6)	0.0005 (5)	0.0055 (5)	−0.0008 (5)
C5	0.0175 (6)	0.0231 (7)	0.0173 (6)	−0.0017 (5)	−0.0006 (5)	−0.0008 (5)
C6	0.0142 (6)	0.0154 (6)	0.0141 (6)	0.0000 (5)	0.0029 (5)	0.0046 (5)
N1	0.0155 (5)	0.0193 (6)	0.0162 (5)	−0.0008 (4)	0.0012 (4)	0.0004 (4)
N2	0.0130 (6)	0.0216 (6)	0.0162 (6)	0.0013 (5)	−0.0009 (5)	−0.0031 (5)
N3	0.0163 (5)	0.0177 (6)	0.0169 (5)	−0.0009 (4)	0.0018 (4)	−0.0017 (4)

Geometric parameters (Å, º) top

O1—N3	1.4201 (13)	C4—C5	1.3773 (18)
O1—H1	0.903 (18)	C4—H4	0.9300
C1—N1	1.3407 (16)	C5—N1	1.3408 (16)
C1—C2	1.3918 (17)	C5—H5	0.9300
C1—C6	1.4878 (17)	C6—N3	1.2928 (16)
C2—C3	1.3765 (18)	C6—N2	1.3532 (16)
C2—H2	0.9300	N2—H1N2	0.862 (13)
C3—C4	1.3849 (19)	N2—H2N2	0.859 (13)
C3—H3	0.9300

N3—O1—H1	104.9 (11)	C3—C4—H4	120.9
N1—C1—C2	123.03 (11)	N1—C5—C4	124.19 (12)
N1—C1—C6	115.35 (10)	N1—C5—H5	117.9
C2—C1—C6	121.61 (11)	C4—C5—H5	117.9
C3—C2—C1	118.91 (12)	N3—C6—N2	123.75 (11)
C3—C2—H2	120.5	N3—C6—C1	118.26 (10)
C1—C2—H2	120.5	N2—C6—C1	117.97 (10)
C2—C3—C4	118.86 (12)	C1—N1—C5	116.69 (10)
C2—C3—H3	120.6	C6—N2—H1N2	116.3 (10)
C4—C3—H3	120.6	C6—N2—H2N2	119.9 (10)
C5—C4—C3	118.28 (12)	H1N2—N2—H2N2	118.9 (14)
C5—C4—H4	120.9	C6—N3—O1	108.89 (9)

N1—C1—C2—C3	−0.07 (18)	N1—C1—C6—N2	−0.29 (16)
C6—C1—C2—C3	−179.35 (11)	C2—C1—C6—N2	179.05 (11)
C1—C2—C3—C4	−1.19 (18)	C2—C1—N1—C5	1.51 (17)
C2—C3—C4—C5	0.96 (18)	C6—C1—N1—C5	−179.17 (10)
C3—C4—C5—N1	0.6 (2)	C4—C5—N1—C1	−1.77 (18)
N1—C1—C6—N3	178.22 (10)	N2—C6—N3—O1	−0.96 (16)
C2—C1—C6—N3	−2.45 (17)	C1—C6—N3—O1	−179.38 (9)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···N3ⁱ	0.903 (18)	1.859 (19)	2.7537 (14)	170.5 (17)
N2—H2N2···N1ⁱⁱ	0.86 (1)	2.44 (1)	3.1753 (16)	144 (1)

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

Experimental details

Crystal data
Chemical formula	C₆H₇N₃O
M_r	137.15
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	293
a, b, c (Å)	21.367 (5), 4.6382 (11), 13.003 (3)
β (°)	105.468 (12)
V (Å³)	1242.0 (5)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.33 × 0.25 × 0.20

Data collection
Diffractometer	Bruker APEXII CCD area-detector
Absorption correction	Multi-scan (SADABS; Bruker, 2009)
T_min, T_max	0.966, 0.979
No. of measured, independent and observed [I > 2σ(I)] reflections	8242, 1086, 982
R_int	0.038
(sin θ/λ)_max (Å⁻¹)	0.594

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.031, 0.081, 1.08
No. of reflections	1086
No. of parameters	103
No. of restraints	2
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.19, −0.18

Computer programs: APEX2 (Bruker, 2009), APEX2 and SAINT-Plus (Bruker, 2009), SAINT-Plus and XPREP (Bruker, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), Mercury (Macrae et al., 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···N3ⁱ	0.903 (18)	1.859 (19)	2.7537 (14)	170.5 (17)
N2—H2N2···N1ⁱⁱ	0.859 (13)	2.438 (14)	3.1753 (16)	144.3 (13)

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

Acknowledgements

The authors thank Dr S. C. Sharma, Ex-Vice Chancellor, Tumkur University, Tumkur, for his constant encouragement, and Professor T. N. Guru Row, S. S. C. U, Indian Institute of Science, Bangalore, for his guidance and support.

References

Bruker (2009). APEX2, SADABS, SAINT-Plus and XPREP. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Kundu, M., Singh, J., Singh, B., Ghosh, T., Maiti, B. C. & Maity, T. K. (2012). Indian J. Chem. Sect. B, 51, 493–497. Google Scholar
Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466–470. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Sakamoto, T., Cullen, M. D., Hartman, T. L., Watson, K. M., Buckheit, R. W., Pannecouque, C., DeClercq, E. & Cushman, M. (2007). J. Med. Chem. 50, 3314–3319. Web of Science CrossRef PubMed CAS Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sreenivasa, S., ManojKumar, K. E., Suchetan, P. A., Mohan, N. R. & Palakshamurthy, B. S. (2012). Acta Cryst. E68, o3402. CSD CrossRef IUCr Journals Google Scholar
Tyrkov, A. G. & Sukhenko, L. T. (2004). Pharm. Chem. J.. 38(7), 30–38. Google Scholar