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Acta Crystallogr Sect E Struct Rep Online. 2010 July 1; 66(Pt 7): o1640.
Published online 2010 June 16. doi:  10.1107/S1600536810021756
PMCID: PMC3006802

rac-N-[Hy­droxy(4-pyrid­yl)meth­yl]picolinamide: a hemiamidal

Abstract

The title compound, C12H11N3O2, a hemiamidal, was synthesized by solvent-free aldol condensation at room temperature by grinding picolinamide with isonicotinaldehyde in a 1:1 molar ratio. In the mol­ecule, the two pyridine rings are inclined to one another by 58.75 (6)°. They are linked, at positions 2 and 4, by the hemiamidal bridge (–CO—NH—CHOH–). The NH-group H atom forms an intra­molecular hydrogen bond with the N atom of the picolinamide pyridine ring. In the crystal, symmetry-related mol­ecules are linked via N—H(...)O hydrogen bonds, involving the NH group H atom of the hemiamidal bridge and the hy­droxy O atom, forming inversion-related dimers, with graph-set R 2 2(8). Adjacent mol­ecules are also linked via O—H(...)N hydrogen bonds, involving the hy­droxy substituent and the 4-pyridine N atom. Together these inter­actions lead to the formation of double-stranded ribbon-like hydrogen-bonded polymers propagating in [010]. The latter are further connected via C—H(...)O hydrogen bonds involving the carbonyl O atom, so forming a two-dimensional network in (011).

Related literature

For background to green synthesis, see: Raston & Scott (2000 [triangle]). For solid-state reactions and solvent-free syntheses, see: Kaupp (2003 [triangle], 2005 [triangle]). For the structure of a similar non-cyclic hemiamidal, see: Kawahara et al. (1992 [triangle]). For details of the Cambridge Structural Database, see: Allen (2002 [triangle]). For standard bond lengths, see: Allen et al. (1987 [triangle]). For details of hydrogen-bonding graph-set analysis, see: Bernstein et al. (1995 [triangle]). For the illustration and analysis of hydrogen bonding, see: Macrae et al. (2006 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o1640-scheme1.jpg

Experimental

Crystal data

  • C12H11N3O2
  • M r = 229.24
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o1640-efi3.jpg
  • a = 12.1450 (13) Å
  • b = 5.6044 (4) Å
  • c = 16.3940 (19) Å
  • β = 111.354 (9)°
  • V = 1039.26 (18) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 173 K
  • 0.50 × 0.41 × 0.10 mm

Data collection

  • Stoe IPDS-2 diffractometer
  • 14414 measured reflections
  • 2823 independent reflections
  • 2196 reflections with I > 2σ(I)
  • R int = 0.079

Refinement

  • R[F 2 > 2σ(F 2)] = 0.042
  • wR(F 2) = 0.111
  • S = 1.04
  • 2823 reflections
  • 163 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.37 e Å−3
  • Δρmin = −0.22 e Å−3

Data collection: X-AREA (Stoe & Cie, 2004 [triangle]); cell refinement: X-AREA; data reduction: X-RED32 (Stoe & Cie, 2004 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: PLATON (Spek, 2009 [triangle]) and Mercury (Macrae et al., 2006 [triangle]); software used to prepare material for publication: SHELXL97 and PLATON.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810021756/lh5064sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810021756/lh5064Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

This work was partially financed by the Swiss National Science Foundation.

supplementary crystallographic information

Comment

Green chemistry is a well established field of research, enhanced by its numerous applications in high technology industries and because of the need for environmentally friendly syntheses. The perfect green reaction has been described as one which: proceeds at room temperature, requires no organic solvent, is highly selective and exhibits high atom efficiency, yet produces no waste products (Raston & Scott, 2000). In recent decades, numerous reactions using mechanical activation have been reported to give 100% yield (Kaupp, 2005). This procedure has a number of advantages, such as rapid and qualitatively solvent free synthesis and no necessary work up procedure (Kaupp, 2003). On the other hand, there are some disadvantages, such as the use of harmful sodium hydroxide, or other sodium salts, as intermediates in the reaction work up. The title compound was synthesized by grinding picolinamide with isonicotinaldehyde in a molar ratio of 1:1 giving a brown gelatinous material. On drying in air a brown microcrystalline powder was obtained, which proved to be the title compound. The compound is a result of the combination of green chemistry and mechanical activation.

The molecule structure of the title molecule is illustrated in Fig. 1. The bond distances are normal (Allen et al., 1987) and the bond angles in the hemiamidal bridge (–CO—NH-CHOH–) are similar to those observed in (1-hydroxybut-2-yl)ammonium N-benzoyl-α-hydroxyglycine (Kawahara et al., 1992). Interestingly, here the authors showed that Peptidylglycine-hydroxylating monooxygenase (PHM), converted N-benzoylglycine stereoselectively to S-N-benzoyl-hydroxyglycine. The latter is the only non-cyclic example of such a (–CO—NH-CHOH–) unit that was found during a search of the Cambridge Crystal Structure Database (CSD, V5.31, last update May 2010; Allen et al., 2002).

In the title molecule the two pyridine rings are inclined to one another by 58.75 (6) °, and the NH H-atom (H2N) forms an intramolecular hydrogen bond with the picolinamide N-atom (N1) (Fig. 1 and Table 1).

In the crystal molecules are linked via N—H···O and O—H···O hydrogen bonds (Table 1). The N—H···O hydrogen bonds, involving the hemiamidal NH group and the hydroxyl O-atom, lead to the formation of inversion dimers, graph-set R22(8) (Fig. 2) (Bernstein et al., 1995). Adjacent molecules are linked via O—H···N hydrogen bonds involving the hydroxyl H-atom (H2O) and the adjacent pyridine N-atom, N2 (Table 1). Together with molecules related by an inversion center these interactions lead to a graph-set of R44(14) (Fig. 3). Finally these hydrogen bonding interactions lead to the formation of double-stranded ribbon-like polymers propagating in [010]. They are further linked via C—H···O interactions, involving the C═O O-atom, leading to the formation of two dimensional networks stacking along [100] (Fig. 4 and Table 1).

Experimental

The synthesis of the title compound was carried out by mixing by hand in a mortar a 1:1 molar ratio of picolinamide with isonicotinaldehyde. A viscous brown mixture was obtained which on drying in air gave a brown micro-crystalline powder (Yield 98.78%). Elemental analysis (%) for C12H11N3O2: C, 62.88; H, 4.80; N, 18.34. Found: C, 62.75; H, 4.91; N, 18.54. IR (cm-1): 3471.51, 3288.31, 3025.77, 1676.26, 1616.03, 1590.90, 1569.42, 1412.63, 1156.79, 922.55, 747.07, 581.52. Crystals suitable for X-ray analysis were obtained during a failed attempt of complex formation with MnCl2.6H2O in a methanol/water solution. The colourless reaction solution obtained was filtered and the filtrate left undisturbed at RT for slow evaporation. After five days colourless plate-like crystals, suitable for X-ray diffraction analysis, were obtained.

Refinement

The NH and OH H-atoms were located in a difference electron-density map and were freely refined: O—H = 0.905 (19) Å, N—H = 0.875 (17) Å. The C-bound H-atoms were included in calculated positions and treated as riding atoms: C—H = 0.95 Å for H-aromatic, and 1.00 Å for H-methine, with Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
A view of the molecular structure of the title molecule, with dispacement ellipsoids drawn at the 50% probability level [The intramolecular N—H···N hydrogen bond is shown as a dashed line].
Fig. 2.
A view of the hydrogen bonded inversion dimers in the crystal of the title compound; graph-set R22(8)>b>b (Mercury: Macrae et al., 2006).
Fig. 3.
A view of the hydrogen bonded R44(14)a>b>a>b graph-set, involving adjacent molecules and those related by an inversion center, in the crystal structure of the title compound (Mercury: Macrae et al., 2006).
Fig. 4.
A view along the b-axis of the crystal packing of the title compound, with the N—H···O, O—H···N and C—H···O hydrogen bonds shown as dashed lines (see Table ...

Crystal data

C12H11N3O2F(000) = 480
Mr = 229.24Dx = 1.465 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 10944 reflections
a = 12.1450 (13) Åθ = 1.8–29.6°
b = 5.6044 (4) ŵ = 0.10 mm1
c = 16.3940 (19) ÅT = 173 K
β = 111.354 (9)°Plate, colourless
V = 1039.26 (18) Å30.50 × 0.41 × 0.10 mm
Z = 4

Data collection

Stoe IPDS-2 diffractometer2196 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.079
graphiteθmax = 29.3°, θmin = 1.8°
phi + ω rotation scansh = −16→16
14414 measured reflectionsk = −7→7
2823 independent reflectionsl = −22→22

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.042H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.111w = 1/[σ2(Fo2) + (0.0672P)2] where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max < 0.001
2823 reflectionsΔρmax = 0.37 e Å3
163 parametersΔρmin = −0.22 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.020 (4)

Special details

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles
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)

xyzUiso*/Ueq
O1−0.08117 (8)1.01540 (16)0.21882 (6)0.0269 (3)
O20.03250 (8)1.27719 (16)0.06003 (6)0.0233 (2)
N1−0.15978 (9)0.51231 (18)0.08046 (7)0.0216 (3)
N2−0.01442 (9)0.91083 (19)0.11117 (7)0.0206 (3)
N30.42324 (10)0.8732 (2)0.16564 (8)0.0328 (3)
C1−0.24525 (11)0.3491 (2)0.05116 (9)0.0253 (3)
C2−0.35054 (11)0.3619 (3)0.06494 (9)0.0293 (4)
C3−0.36862 (11)0.5519 (3)0.11228 (10)0.0299 (4)
C4−0.28077 (11)0.7220 (2)0.14387 (9)0.0254 (3)
C5−0.17819 (10)0.6966 (2)0.12589 (8)0.0206 (3)
C6−0.08534 (10)0.8875 (2)0.15735 (8)0.0204 (3)
C70.06900 (10)1.1054 (2)0.12781 (8)0.0195 (3)
C80.19102 (10)1.0180 (2)0.13730 (7)0.0202 (3)
C90.26572 (11)1.1592 (2)0.11155 (9)0.0256 (3)
C100.37952 (12)1.0795 (3)0.12702 (10)0.0318 (4)
C110.34982 (12)0.7394 (2)0.19001 (9)0.0298 (4)
C120.23415 (11)0.8019 (2)0.17731 (9)0.0258 (3)
H1−0.232900.217200.019100.0300*
H2−0.409400.242500.042400.0350*
H2N−0.0255 (14)0.824 (3)0.0645 (11)0.026 (4)*
H2O−0.0220 (16)1.371 (3)0.0699 (12)0.038 (5)*
H3−0.440200.565500.123000.0360*
H4−0.290400.853600.177200.0310*
H70.074301.184700.183800.0230*
H90.239501.308400.083700.0310*
H100.429801.178700.108900.0380*
H110.378600.591400.217900.0360*
H120.185600.698800.195700.0310*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0345 (5)0.0250 (5)0.0274 (5)−0.0026 (4)0.0186 (4)−0.0048 (4)
O20.0272 (4)0.0201 (4)0.0265 (4)0.0048 (3)0.0145 (4)0.0036 (3)
N10.0231 (5)0.0199 (5)0.0238 (5)0.0013 (4)0.0108 (4)0.0005 (4)
N20.0236 (5)0.0197 (5)0.0209 (5)−0.0023 (4)0.0110 (4)−0.0025 (4)
N30.0246 (5)0.0305 (6)0.0421 (7)−0.0003 (4)0.0107 (5)−0.0041 (5)
C10.0276 (6)0.0210 (6)0.0275 (6)−0.0008 (5)0.0104 (5)−0.0002 (5)
C20.0250 (6)0.0279 (7)0.0342 (7)−0.0042 (5)0.0100 (5)0.0012 (5)
C30.0235 (6)0.0322 (7)0.0377 (7)0.0003 (5)0.0156 (5)0.0025 (6)
C40.0255 (6)0.0253 (6)0.0290 (6)0.0022 (5)0.0141 (5)0.0002 (5)
C50.0236 (5)0.0197 (5)0.0205 (5)0.0026 (4)0.0104 (4)0.0036 (4)
C60.0231 (5)0.0187 (5)0.0213 (5)0.0028 (4)0.0103 (4)0.0019 (4)
C70.0236 (5)0.0167 (5)0.0208 (5)−0.0007 (4)0.0111 (4)−0.0009 (4)
C80.0220 (5)0.0203 (6)0.0191 (5)−0.0025 (4)0.0086 (4)−0.0029 (4)
C90.0270 (6)0.0222 (6)0.0293 (6)−0.0034 (5)0.0124 (5)0.0002 (5)
C100.0257 (6)0.0312 (7)0.0418 (8)−0.0051 (5)0.0162 (6)−0.0008 (6)
C110.0270 (6)0.0249 (6)0.0339 (7)0.0029 (5)0.0069 (5)−0.0007 (5)
C120.0264 (6)0.0231 (6)0.0279 (6)−0.0005 (5)0.0099 (5)0.0017 (5)

Geometric parameters (Å, °)

O1—C61.2226 (15)C7—C81.5141 (18)
O2—C71.4140 (15)C8—C91.3807 (18)
O2—H2O0.905 (19)C8—C121.3861 (16)
N1—C11.3348 (17)C9—C101.385 (2)
N1—C51.3389 (16)C11—C121.388 (2)
N2—C71.4452 (16)C1—H10.9500
N2—C61.3443 (17)C2—H20.9500
N3—C101.332 (2)C3—H30.9500
N3—C111.3328 (19)C4—H40.9500
N2—H2N0.875 (17)C7—H71.0000
C1—C21.379 (2)C9—H90.9500
C2—C31.382 (2)C10—H100.9500
C3—C41.383 (2)C11—H110.9500
C4—C51.3881 (19)C12—H120.9500
C5—C61.5029 (17)
C7—O2—H2O107.2 (11)N3—C10—C9124.42 (14)
C1—N1—C5117.60 (12)N3—C11—C12124.34 (11)
C6—N2—C7121.06 (10)C8—C12—C11118.62 (12)
C10—N3—C11115.87 (13)N1—C1—H1118.00
C7—N2—H2N117.3 (12)C2—C1—H1118.00
C6—N2—H2N120.8 (12)C1—C2—H2121.00
N1—C1—C2123.46 (12)C3—C2—H2121.00
C1—C2—C3118.60 (14)C2—C3—H3121.00
C2—C3—C4118.87 (13)C4—C3—H3121.00
C3—C4—C5118.65 (12)C3—C4—H4121.00
N1—C5—C4122.81 (11)C5—C4—H4121.00
C4—C5—C6118.26 (11)O2—C7—H7108.00
N1—C5—C6118.92 (11)N2—C7—H7108.00
N2—C6—C5115.50 (11)C8—C7—H7108.00
O1—C6—C5120.06 (12)C8—C9—H9121.00
O1—C6—N2124.37 (12)C10—C9—H9121.00
O2—C7—N2111.58 (10)N3—C10—H10118.00
O2—C7—C8108.43 (10)C9—C10—H10118.00
N2—C7—C8111.59 (10)N3—C11—H11118.00
C9—C8—C12117.93 (12)C12—C11—H11118.00
C7—C8—C9120.71 (10)C8—C12—H12121.00
C7—C8—C12121.23 (11)C11—C12—H12121.00
C8—C9—C10118.82 (12)
C5—N1—C1—C20.34 (19)N1—C5—C6—O1−158.19 (12)
C1—N1—C5—C40.59 (18)N1—C5—C6—N224.74 (16)
C1—N1—C5—C6−178.08 (11)C4—C5—C6—O123.08 (17)
C7—N2—C6—O1−4.40 (19)C4—C5—C6—N2−153.99 (12)
C7—N2—C6—C5172.53 (10)O2—C7—C8—C925.04 (15)
C6—N2—C7—O2−107.33 (13)O2—C7—C8—C12−159.37 (11)
C6—N2—C7—C8131.21 (12)N2—C7—C8—C9148.32 (11)
C11—N3—C10—C90.1 (2)N2—C7—C8—C12−36.09 (15)
C10—N3—C11—C120.2 (2)C7—C8—C9—C10175.51 (12)
N1—C1—C2—C3−0.7 (2)C12—C8—C9—C10−0.22 (19)
C1—C2—C3—C40.1 (2)C7—C8—C12—C11−175.24 (11)
C2—C3—C4—C50.7 (2)C9—C8—C12—C110.47 (18)
C3—C4—C5—N1−1.1 (2)C8—C9—C10—N3−0.1 (2)
C3—C4—C5—C6177.56 (12)N3—C11—C12—C8−0.5 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2N···N10.875 (17)2.468 (18)2.7769 (16)101.4 (13)
N2—H2N···O2i0.875 (17)2.091 (17)2.9304 (15)160.7 (16)
O2—H2O···N1ii0.905 (19)1.92 (2)2.8056 (16)167.6 (17)
C7—H7···O1iii1.002.433.3694 (15)157
C12—H12···O1iv0.952.433.3517 (17)163

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH5064).

References

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  • Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst.39, 453–457.
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