organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890
Volume 70| Part 10| October 2014| Pages o1107-o1108

Crystal structure of N′-hy­dr­oxy­pyrimidine-2-carboximidamide

aSchool of Chemistry, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
*Correspondence e-mail: tommtrichy@yahoo.co.in

Edited by J. Simpson, University of Otago, New Zealand (Received 7 September 2014; accepted 9 September 2014; online 13 September 2014)

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 R22(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 ππ stacking inter­actions between adjacent pyrimidine rings [centroid–centroid distance = 3.622 (1) Å].

1. Related literature

For details of non-covalent inter­actions, see: Desiraju (2007[Desiraju, G. R. (2007). Angew. Chem. Int. Ed. 46, 8342-8356.]). For the role of inter­molecular hydrogen bonds in the design of organic crystals, see: Aakeroy & Seddon (1993[Aakeroy, C. B. & Seddon, K. R. (1993). Chem. Soc. Rev. 22, 397-407.]). For background to substituted N′-hy­droxy­benzamidines as inter­mediates in the synthesis of 1,2,4-oxa­diazole derivatives, see: Kundu et al. (2012[Kundu, M., Singh, B., Ghosh, T., Maiti, B. C. & Maity, T. K. (2012). Indian J. Chem. Sect. B, 51, 493-497.]). For the biological activity of substituted N′-hy­droxy­benzamidines and 1,2,4-oxa­diazole derivatives, see: Sakamoto et al. (2007[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.]); Tyrkov & Sukhenko (2004[Tyrkov, A. G. & Sukhenko, L. T. (2004). Pharm. Chem. J. 38, 30-38.]).

[Scheme 1]

2. Experimental

2.1. Crystal data

  • C5H6N4O

  • Mr = 138.14

  • Monoclinic, P 21 /c

  • 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

2.2. Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.931, Tmax = 0.990

  • 4073 measured reflections

  • 1030 independent reflections

  • 831 reflections with I > 2σ(I)

  • Rint = 0.047

2.3. Refinement

  • R[F2 > 2σ(F2)] = 0.054

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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+{\script{1\over 2}}, z-{\script{1\over 2}}]; (iii) [-x+2, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]; (iv) x, y-1, z.

Data collection: APEX2 (Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

Supramolecular architectures assembled via various delicate noncovalent interactions such as hydrogen bonds, ππ 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 C5N3 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···O1iv hydrogen bonds (symmetry code as in Table 1) and ππ stacking interactions between the pyrimidine (N1/N2/C1-C4) rings [centroid-centroid distance = 3.622 (1) Å; (symmetry code: 1-x, - y, -z)].

Related literature top

For details of non-covalent interactions, see: Desiraju (2007). For the role of intermolecular hydrogen bonds in organic crystal design, see: Aakeroy & Seddon (1993). For the importance of substituted N'-hydroxybenzamidines as intermediates in the synthesis of pharmaceutically important 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 top

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.

Refinement top

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 Uiso(H)=1.2 Ueq(C).

Computing details top

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

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound with atom labels. Displacement ellipsoids are shown at the 50% probability level.
[Figure 2] 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.
N'-Hydroxypyrimidine-2-carboximidamide top
Crystal data top
C5H6N4OF(000) = 288
Mr = 138.14Dx = 1.545 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 1905 reflections
a = 7.4066 (7) Åθ = 2.8–29.9°
b = 8.0165 (8) ŵ = 0.12 mm1
c = 10.2200 (9) ÅT = 100 K
β = 101.888 (6)°Plate, colourless
V = 593.8 (1) Å30.62 × 0.17 × 0.08 mm
Z = 4
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
1030 independent reflections
Radiation source: fine-focus sealed tube831 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.047
ϕ and ω scansθmax = 25.0°, θmin = 2.8°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 88
Tmin = 0.931, Tmax = 0.990k = 98
4073 measured reflectionsl = 1212
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.054Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.181H 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 parametersΔρmax = 0.29 e Å3
0 restraintsΔρmin = 0.31 e Å3
Crystal data top
C5H6N4OV = 593.8 (1) Å3
Mr = 138.14Z = 4
Monoclinic, P21/cMo Kα radiation
a = 7.4066 (7) ŵ = 0.12 mm1
b = 8.0165 (8) ÅT = 100 K
c = 10.2200 (9) Å0.62 × 0.17 × 0.08 mm
β = 101.888 (6)°
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
1030 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
831 reflections with I > 2σ(I)
Tmin = 0.931, Tmax = 0.990Rint = 0.047
4073 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0540 restraints
wR(F2) = 0.181H atoms treated by a mixture of independent and constrained refinement
S = 1.13Δρmax = 0.29 e Å3
1030 reflectionsΔρmin = 0.31 e Å3
103 parameters
Special details top

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 (Å2) top
xyzUiso*/Ueq
O10.9616 (3)0.4128 (2)0.15856 (18)0.0171 (6)
N10.6515 (3)0.0148 (3)0.1252 (2)0.0159 (6)
N20.8106 (3)0.0836 (3)0.0883 (2)0.0140 (6)
N30.9064 (3)0.2423 (3)0.1497 (2)0.0150 (6)
N40.8007 (3)0.3212 (3)0.0758 (2)0.0155 (6)
C10.5875 (4)0.1406 (4)0.1538 (3)0.0183 (7)
H1A0.51070.16120.23890.022*
C20.6283 (4)0.2713 (4)0.0652 (3)0.0198 (7)
H2A0.58010.38000.08670.024*
C30.7425 (4)0.2368 (4)0.0560 (3)0.0183 (7)
H3A0.77430.32440.11910.022*
C40.7592 (3)0.0362 (3)0.0043 (2)0.0127 (6)
C50.8291 (3)0.2095 (3)0.0268 (2)0.0126 (7)
H2N40.869 (4)0.413 (4)0.057 (3)0.012 (7)*
H1N40.784 (4)0.281 (4)0.162 (3)0.025 (8)*
H1O11.029 (5)0.429 (4)0.247 (4)0.022 (8)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0221 (11)0.0123 (11)0.0157 (11)0.0038 (8)0.0012 (9)0.0005 (7)
N10.0142 (12)0.0173 (13)0.0169 (12)0.0003 (10)0.0048 (10)0.0023 (9)
N20.0130 (12)0.0135 (12)0.0156 (12)0.0008 (9)0.0033 (10)0.0000 (9)
N30.0164 (12)0.0098 (12)0.0185 (12)0.0026 (10)0.0027 (10)0.0001 (9)
N40.0196 (13)0.0134 (13)0.0130 (12)0.0015 (11)0.0023 (10)0.0016 (9)
C10.0139 (14)0.0209 (15)0.0212 (14)0.0018 (12)0.0058 (12)0.0060 (12)
C20.0166 (15)0.0129 (14)0.0319 (16)0.0030 (11)0.0096 (13)0.0071 (12)
C30.0177 (15)0.0147 (14)0.0246 (15)0.0015 (12)0.0096 (12)0.0004 (11)
C40.0092 (13)0.0160 (15)0.0138 (13)0.0006 (11)0.0043 (11)0.0032 (10)
C50.0099 (13)0.0137 (14)0.0160 (13)0.0011 (11)0.0065 (11)0.0002 (10)
Geometric parameters (Å, º) top
O1—N31.424 (3)N4—H2N40.89 (3)
O1—H1O10.94 (4)N4—H1N40.92 (3)
N1—C41.336 (3)C1—C21.378 (4)
N1—C11.343 (4)C1—H1A0.9500
N2—C31.343 (4)C2—C31.376 (4)
N2—C41.347 (3)C2—H2A0.9500
N3—C51.295 (3)C3—H3A0.9500
N4—C51.362 (3)C4—C51.494 (4)
N3—O1—H1O1106.1 (18)C3—C2—H2A121.6
C4—N1—C1116.0 (2)C1—C2—H2A121.6
C3—N2—C4116.2 (2)N2—C3—C2122.4 (3)
C5—N3—O1108.7 (2)N2—C3—H3A118.8
C5—N4—H2N4112.9 (18)C2—C3—H3A118.8
C5—N4—H1N4118 (2)N1—C4—N2125.9 (2)
H2N4—N4—H1N4117 (3)N1—C4—C5115.6 (2)
N1—C1—C2122.8 (2)N2—C4—C5118.5 (2)
N1—C1—H1A118.6N3—C5—N4125.5 (2)
C2—C1—H1A118.6N3—C5—C4117.4 (2)
C3—C2—C1116.7 (3)N4—C5—C4117.1 (2)
C4—N1—C1—C20.2 (4)C3—N2—C4—C5179.3 (2)
N1—C1—C2—C31.1 (4)O1—N3—C5—N41.7 (3)
C4—N2—C3—C20.8 (4)O1—N3—C5—C4179.51 (19)
C1—C2—C3—N20.5 (4)N1—C4—C5—N3168.3 (2)
C1—N1—C4—N21.3 (4)N2—C4—C5—N312.7 (3)
C1—N1—C4—C5179.8 (2)N1—C4—C5—N49.7 (3)
C3—N2—C4—N11.8 (4)N2—C4—C5—N4169.3 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H2N4···O1i0.89 (3)2.27 (3)2.996 (3)139 (3)
N4—H1N4···N3ii0.92 (3)2.30 (3)3.106 (3)146 (3)
O1—H1O1···N2iii0.95 (4)1.85 (4)2.783 (3)167 (3)
C3—H3A···O1iv0.952.513.305 (4)141
Symmetry codes: (i) x+2, y+1, z; (ii) x, y+1/2, z1/2; (iii) x+2, y+1/2, z+1/2; (iv) x, y1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H2N4···O1i0.89 (3)2.27 (3)2.996 (3)139 (3)
N4—H1N4···N3ii0.92 (3)2.30 (3)3.106 (3)146 (3)
O1—H1O1···N2iii0.95 (4)1.85 (4)2.783 (3)167 (3)
C3—H3A···O1iv0.95002.51003.305 (4)141.00
Symmetry codes: (i) x+2, y+1, z; (ii) x, y+1/2, z1/2; (iii) x+2, y+1/2, z+1/2; (iv) x, y1, z.
 

Acknowledgements

NJJ thanks the UGC–SAP for the award of an RFSMS. PTM thanks the UGC for a one-time BSR grant.

References

First citationAakeroy, C. B. & Seddon, K. R. (1993). Chem. Soc. Rev. 22, 397–407.  CrossRef CAS Web of Science Google Scholar
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First citationSakamoto, 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
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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 70| Part 10| October 2014| Pages o1107-o1108
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