organic compounds
rac-N-[Hydroxy(4-pyridyl)methyl]picolinamide: a hemiamidal
aInstitute of Physics, University of Neuchâtel, rue Emile-Argand 11, CH-2009 Neuchâtel, Switzerland
*Correspondence e-mail: muhammad.altaf@unine.ch
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 R22(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). For solid-state reactions and solvent-free syntheses, see: Kaupp (2003, 2005). For the structure of a similar non-cyclic hemiamidal, see: Kawahara et al. (1992). For details of the Cambridge Structural Database, see: Allen (2002). For standard bond lengths, see: Allen et al. (1987). For details of hydrogen-bonding graph-set analysis, see: Bernstein et al. (1995). For the illustration and analysis of hydrogen bonding, see: Macrae et al. (2006).
Experimental
Crystal data
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Data collection
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Refinement
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Data collection: X-AREA (Stoe & Cie, 2004); cell X-AREA; data reduction: X-RED32 (Stoe & Cie, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97 and PLATON.
Supporting information
10.1107/S1600536810021756/lh5064sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536810021756/lh5064Isup2.hkl
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
were obtained.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).
Data collection: X-AREA (Stoe & Cie, 2004); cell
X-AREA (Stoe & Cie, 2004); data reduction: X-RED32 (Stoe & Cie, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).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 1 for details). |
C12H11N3O2 | F(000) = 480 |
Mr = 229.24 | Dx = 1.465 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 10944 reflections |
a = 12.1450 (13) Å | θ = 1.8–29.6° |
b = 5.6044 (4) Å | µ = 0.10 mm−1 |
c = 16.3940 (19) Å | T = 173 K |
β = 111.354 (9)° | Plate, colourless |
V = 1039.26 (18) Å3 | 0.50 × 0.41 × 0.10 mm |
Z = 4 |
Stoe IPDS-2 diffractometer | 2196 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.079 |
Graphite monochromator | θmax = 29.3°, θmin = 1.8° |
phi + ω rotation scans | h = −16→16 |
14414 measured reflections | k = −7→7 |
2823 independent reflections | l = −22→22 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.042 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.111 | w = 1/[σ2(Fo2) + (0.0672P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.04 | (Δ/σ)max < 0.001 |
2823 reflections | Δρmax = 0.37 e Å−3 |
163 parameters | Δρmin = −0.22 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.020 (4) |
C12H11N3O2 | V = 1039.26 (18) Å3 |
Mr = 229.24 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 12.1450 (13) Å | µ = 0.10 mm−1 |
b = 5.6044 (4) Å | T = 173 K |
c = 16.3940 (19) Å | 0.50 × 0.41 × 0.10 mm |
β = 111.354 (9)° |
Stoe IPDS-2 diffractometer | 2196 reflections with I > 2σ(I) |
14414 measured reflections | Rint = 0.079 |
2823 independent reflections |
R[F2 > 2σ(F2)] = 0.042 | 0 restraints |
wR(F2) = 0.111 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | Δρmax = 0.37 e Å−3 |
2823 reflections | Δρmin = −0.22 e Å−3 |
163 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | −0.08117 (8) | 1.01540 (16) | 0.21882 (6) | 0.0269 (3) | |
O2 | 0.03250 (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) | |
N3 | 0.42324 (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) | |
C7 | 0.06900 (10) | 1.1054 (2) | 0.12781 (8) | 0.0195 (3) | |
C8 | 0.19102 (10) | 1.0180 (2) | 0.13730 (7) | 0.0202 (3) | |
C9 | 0.26572 (11) | 1.1592 (2) | 0.11155 (9) | 0.0256 (3) | |
C10 | 0.37952 (12) | 1.0795 (3) | 0.12702 (10) | 0.0318 (4) | |
C11 | 0.34982 (12) | 0.7394 (2) | 0.19001 (9) | 0.0298 (4) | |
C12 | 0.23415 (11) | 0.8019 (2) | 0.17731 (9) | 0.0258 (3) | |
H1 | −0.23290 | 0.21720 | 0.01910 | 0.0300* | |
H2 | −0.40940 | 0.24250 | 0.04240 | 0.0350* | |
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 | −0.44020 | 0.56550 | 0.12300 | 0.0360* | |
H4 | −0.29040 | 0.85360 | 0.17720 | 0.0310* | |
H7 | 0.07430 | 1.18470 | 0.18380 | 0.0230* | |
H9 | 0.23950 | 1.30840 | 0.08370 | 0.0310* | |
H10 | 0.42980 | 1.17870 | 0.10890 | 0.0380* | |
H11 | 0.37860 | 0.59140 | 0.21790 | 0.0360* | |
H12 | 0.18560 | 0.69880 | 0.19570 | 0.0310* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0345 (5) | 0.0250 (5) | 0.0274 (5) | −0.0026 (4) | 0.0186 (4) | −0.0048 (4) |
O2 | 0.0272 (4) | 0.0201 (4) | 0.0265 (4) | 0.0048 (3) | 0.0145 (4) | 0.0036 (3) |
N1 | 0.0231 (5) | 0.0199 (5) | 0.0238 (5) | 0.0013 (4) | 0.0108 (4) | 0.0005 (4) |
N2 | 0.0236 (5) | 0.0197 (5) | 0.0209 (5) | −0.0023 (4) | 0.0110 (4) | −0.0025 (4) |
N3 | 0.0246 (5) | 0.0305 (6) | 0.0421 (7) | −0.0003 (4) | 0.0107 (5) | −0.0041 (5) |
C1 | 0.0276 (6) | 0.0210 (6) | 0.0275 (6) | −0.0008 (5) | 0.0104 (5) | −0.0002 (5) |
C2 | 0.0250 (6) | 0.0279 (7) | 0.0342 (7) | −0.0042 (5) | 0.0100 (5) | 0.0012 (5) |
C3 | 0.0235 (6) | 0.0322 (7) | 0.0377 (7) | 0.0003 (5) | 0.0156 (5) | 0.0025 (6) |
C4 | 0.0255 (6) | 0.0253 (6) | 0.0290 (6) | 0.0022 (5) | 0.0141 (5) | 0.0002 (5) |
C5 | 0.0236 (5) | 0.0197 (5) | 0.0205 (5) | 0.0026 (4) | 0.0104 (4) | 0.0036 (4) |
C6 | 0.0231 (5) | 0.0187 (5) | 0.0213 (5) | 0.0028 (4) | 0.0103 (4) | 0.0019 (4) |
C7 | 0.0236 (5) | 0.0167 (5) | 0.0208 (5) | −0.0007 (4) | 0.0111 (4) | −0.0009 (4) |
C8 | 0.0220 (5) | 0.0203 (6) | 0.0191 (5) | −0.0025 (4) | 0.0086 (4) | −0.0029 (4) |
C9 | 0.0270 (6) | 0.0222 (6) | 0.0293 (6) | −0.0034 (5) | 0.0124 (5) | 0.0002 (5) |
C10 | 0.0257 (6) | 0.0312 (7) | 0.0418 (8) | −0.0051 (5) | 0.0162 (6) | −0.0008 (6) |
C11 | 0.0270 (6) | 0.0249 (6) | 0.0339 (7) | 0.0029 (5) | 0.0069 (5) | −0.0007 (5) |
C12 | 0.0264 (6) | 0.0231 (6) | 0.0279 (6) | −0.0005 (5) | 0.0099 (5) | 0.0017 (5) |
O1—C6 | 1.2226 (15) | C7—C8 | 1.5141 (18) |
O2—C7 | 1.4140 (15) | C8—C9 | 1.3807 (18) |
O2—H2O | 0.905 (19) | C8—C12 | 1.3861 (16) |
N1—C1 | 1.3348 (17) | C9—C10 | 1.385 (2) |
N1—C5 | 1.3389 (16) | C11—C12 | 1.388 (2) |
N2—C7 | 1.4452 (16) | C1—H1 | 0.9500 |
N2—C6 | 1.3443 (17) | C2—H2 | 0.9500 |
N3—C10 | 1.332 (2) | C3—H3 | 0.9500 |
N3—C11 | 1.3328 (19) | C4—H4 | 0.9500 |
N2—H2N | 0.875 (17) | C7—H7 | 1.0000 |
C1—C2 | 1.379 (2) | C9—H9 | 0.9500 |
C2—C3 | 1.382 (2) | C10—H10 | 0.9500 |
C3—C4 | 1.383 (2) | C11—H11 | 0.9500 |
C4—C5 | 1.3881 (19) | C12—H12 | 0.9500 |
C5—C6 | 1.5029 (17) | ||
C7—O2—H2O | 107.2 (11) | N3—C10—C9 | 124.42 (14) |
C1—N1—C5 | 117.60 (12) | N3—C11—C12 | 124.34 (11) |
C6—N2—C7 | 121.06 (10) | C8—C12—C11 | 118.62 (12) |
C10—N3—C11 | 115.87 (13) | N1—C1—H1 | 118.00 |
C7—N2—H2N | 117.3 (12) | C2—C1—H1 | 118.00 |
C6—N2—H2N | 120.8 (12) | C1—C2—H2 | 121.00 |
N1—C1—C2 | 123.46 (12) | C3—C2—H2 | 121.00 |
C1—C2—C3 | 118.60 (14) | C2—C3—H3 | 121.00 |
C2—C3—C4 | 118.87 (13) | C4—C3—H3 | 121.00 |
C3—C4—C5 | 118.65 (12) | C3—C4—H4 | 121.00 |
N1—C5—C4 | 122.81 (11) | C5—C4—H4 | 121.00 |
C4—C5—C6 | 118.26 (11) | O2—C7—H7 | 108.00 |
N1—C5—C6 | 118.92 (11) | N2—C7—H7 | 108.00 |
N2—C6—C5 | 115.50 (11) | C8—C7—H7 | 108.00 |
O1—C6—C5 | 120.06 (12) | C8—C9—H9 | 121.00 |
O1—C6—N2 | 124.37 (12) | C10—C9—H9 | 121.00 |
O2—C7—N2 | 111.58 (10) | N3—C10—H10 | 118.00 |
O2—C7—C8 | 108.43 (10) | C9—C10—H10 | 118.00 |
N2—C7—C8 | 111.59 (10) | N3—C11—H11 | 118.00 |
C9—C8—C12 | 117.93 (12) | C12—C11—H11 | 118.00 |
C7—C8—C9 | 120.71 (10) | C8—C12—H12 | 121.00 |
C7—C8—C12 | 121.23 (11) | C11—C12—H12 | 121.00 |
C8—C9—C10 | 118.82 (12) | ||
C5—N1—C1—C2 | 0.34 (19) | N1—C5—C6—O1 | −158.19 (12) |
C1—N1—C5—C4 | 0.59 (18) | N1—C5—C6—N2 | 24.74 (16) |
C1—N1—C5—C6 | −178.08 (11) | C4—C5—C6—O1 | 23.08 (17) |
C7—N2—C6—O1 | −4.40 (19) | C4—C5—C6—N2 | −153.99 (12) |
C7—N2—C6—C5 | 172.53 (10) | O2—C7—C8—C9 | 25.04 (15) |
C6—N2—C7—O2 | −107.33 (13) | O2—C7—C8—C12 | −159.37 (11) |
C6—N2—C7—C8 | 131.21 (12) | N2—C7—C8—C9 | 148.32 (11) |
C11—N3—C10—C9 | 0.1 (2) | N2—C7—C8—C12 | −36.09 (15) |
C10—N3—C11—C12 | 0.2 (2) | C7—C8—C9—C10 | 175.51 (12) |
N1—C1—C2—C3 | −0.7 (2) | C12—C8—C9—C10 | −0.22 (19) |
C1—C2—C3—C4 | 0.1 (2) | C7—C8—C12—C11 | −175.24 (11) |
C2—C3—C4—C5 | 0.7 (2) | C9—C8—C12—C11 | 0.47 (18) |
C3—C4—C5—N1 | −1.1 (2) | C8—C9—C10—N3 | −0.1 (2) |
C3—C4—C5—C6 | 177.56 (12) | N3—C11—C12—C8 | −0.5 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2N···N1 | 0.875 (17) | 2.468 (18) | 2.7769 (16) | 101.4 (13) |
N2—H2N···O2i | 0.875 (17) | 2.091 (17) | 2.9304 (15) | 160.7 (16) |
O2—H2O···N1ii | 0.905 (19) | 1.92 (2) | 2.8056 (16) | 167.6 (17) |
C7—H7···O1iii | 1.00 | 2.43 | 3.3694 (15) | 157 |
C12—H12···O1iv | 0.95 | 2.43 | 3.3517 (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. |
Experimental details
Crystal data | |
Chemical formula | C12H11N3O2 |
Mr | 229.24 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 173 |
a, b, c (Å) | 12.1450 (13), 5.6044 (4), 16.3940 (19) |
β (°) | 111.354 (9) |
V (Å3) | 1039.26 (18) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.50 × 0.41 × 0.10 |
Data collection | |
Diffractometer | Stoe IPDS2 diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 14414, 2823, 2196 |
Rint | 0.079 |
(sin θ/λ)max (Å−1) | 0.688 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.042, 0.111, 1.04 |
No. of reflections | 2823 |
No. of parameters | 163 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.37, −0.22 |
Computer programs: X-AREA (Stoe & Cie, 2004), X-RED32 (Stoe & Cie, 2004), SHELXS97 (Sheldrick, 2008), PLATON (Spek, 2009) and Mercury (Macrae et al., 2006), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2N···N1 | 0.875 (17) | 2.468 (18) | 2.7769 (16) | 101.4 (13) |
N2—H2N···O2i | 0.875 (17) | 2.091 (17) | 2.9304 (15) | 160.7 (16) |
O2—H2O···N1ii | 0.905 (19) | 1.92 (2) | 2.8056 (16) | 167.6 (17) |
C7—H7···O1iii | 1.00 | 2.43 | 3.3694 (15) | 157 |
C12—H12···O1iv | 0.95 | 2.43 | 3.3517 (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. |
Acknowledgements
This work was partially financed by the Swiss National Science Foundation.
References
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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).