organic compounds
Methyl 5-(4-hydroxyphenyl)-6-oxo-1,6-dihydropyrazine-2-carboxylate
aDepartment of Chemistry, Rabigh College of Science and Arts, King Abdulaziz University, PO Box 344, Rabigh 21911, Saudi Arabia
*Correspondence e-mail: netaha@kau.edu.sa
The title compound, C12H10N2O4, is approximately planar, with dihedral angles of 5.53 (9) and 2.48 (13)°, respectively, between the benzene and pyrazine rings, and between the pyrazine ring and the methyl carboxylate plane. An intramolecular C—H⋯O hydrogen bond with an S(6) ring motif is observed. In the crystal, intermolecular O—H⋯O and N—H⋯O hydrogen bonds link molecules into a layer parallel to the ab plane. Adjacent layers interpenetrate each other through a π–π interaction [centroid–centroid distance of 3.4746 (11) Å].
Keywords: crystal structure; amoxicillin; antibiotics.
CCDC reference: 1510980
Structure description
The title compound was obtained unexpectedly by the reaction of amoxicillin trihydrate and copper sulfate in a mixture of methanol and water. The molecule is approximately planer, as indicated by dihedral angles 5.53 (9) and 2.48 (13)°, respectively, between the C1–C6 and C7/C8/N1/C9/C10/N2 rings, and between the C7/C8/N1/C9/C10/N2 ring and the O3/C11/O4/C12 plane. An intramolecular C5—H5⋯O3 hydrogen bond generates an S(6) ring motif (Table 1 and Fig. 1).
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In the crystal, molecules are linked through intermolecular O—H⋯O and N—H⋯O hydrogen bonds (Table 1) into a layer parallel to the ab plane (Figs. 2 and 3). Adjacent layers interpenetrate each other and a π–π stacking interaction is present between the layers. The Cg⋯Cgiii separation is 3.4746 (11) Å [symmetry code: (iii) 1 − x, −y, 1 − z]; Cg is the centroid of the C7/C8/N1/C9/C10/N2 ring.
Synthesis and crystallization
Amoxicillin trihydrate (0.5 mmol, 0.21 g) was dissolved in methanol in a round-bottomed flask, then 0.1 g copper sulfate in 5 ml water were added. The mixture was refluxed for about 2 h. The product was filtered off. Single crystals suitable for X-ray diffraction were formed on slow evaporation of the solution in a few days.
Refinement
Crystal data, data collection and structure .
details are summarized in Table 2Structural data
CCDC reference: 1510980
https://doi.org/10.1107/S2414314616016898/is4012sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314616016898/is4012Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2414314616016898/is4012Isup3.cml
Data collection: APEX3 (Bruker, 2016); cell
SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXS2014 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015) and PLATON (Spek, 2015).C12H10N2O4 | F(000) = 1024 |
Mr = 246.22 | Dx = 1.486 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
a = 23.9226 (19) Å | Cell parameters from 184 reflections |
b = 7.1372 (6) Å | θ = 3.2–18.6° |
c = 13.0562 (11) Å | µ = 0.11 mm−1 |
β = 99.158 (5)° | T = 273 K |
V = 2200.8 (3) Å3 | Plate, colourless |
Z = 8 | 0.30 × 0.20 × 0.03 mm |
Bruker D8 Quest diffractometer | 1450 reflections with I > 2σ(I) |
φ and ω scans | Rint = 0.075 |
Absorption correction: multi-scan (SADABS; Bruker, 2016) | θmax = 25.4°, θmin = 3.0° |
Tmin = 0.656, Tmax = 0.745 | h = −28→28 |
20352 measured reflections | k = −8→8 |
2011 independent reflections | l = −15→15 |
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.045 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.115 | w = 1/[σ2(Fo2) + (0.0528P)2 + 1.083P] where P = (Fo2 + 2Fc2)/3 |
S = 1.07 | (Δ/σ)max < 0.001 |
2011 reflections | Δρmax = 0.14 e Å−3 |
171 parameters | Δρmin = −0.21 e Å−3 |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.27612 (6) | 0.4678 (2) | 0.63884 (13) | 0.0586 (5) | |
H1O1 | 0.2492 (12) | 0.494 (4) | 0.587 (2) | 0.095 (10)* | |
O2 | 0.45124 (6) | 0.2748 (3) | 0.32435 (10) | 0.0591 (5) | |
O3 | 0.68297 (6) | 0.0924 (2) | 0.50218 (12) | 0.0608 (5) | |
O4 | 0.64150 (5) | 0.1191 (2) | 0.33671 (11) | 0.0534 (4) | |
N1 | 0.54260 (6) | 0.2092 (2) | 0.38434 (12) | 0.0364 (4) | |
H1N1 | 0.5495 (10) | 0.216 (3) | 0.3167 (18) | 0.066 (7)* | |
N2 | 0.52255 (6) | 0.2191 (2) | 0.58370 (12) | 0.0405 (4) | |
C1 | 0.42192 (8) | 0.3329 (3) | 0.64301 (14) | 0.0428 (5) | |
H1 | 0.4536 | 0.3093 | 0.6926 | 0.051* | |
C2 | 0.37228 (8) | 0.3858 (3) | 0.67471 (15) | 0.0467 (5) | |
H2 | 0.3709 | 0.3998 | 0.7451 | 0.056* | |
C3 | 0.32447 (8) | 0.4184 (3) | 0.60294 (15) | 0.0400 (5) | |
C4 | 0.32729 (8) | 0.3998 (3) | 0.49911 (15) | 0.0472 (5) | |
H4 | 0.2952 | 0.4215 | 0.4501 | 0.057* | |
C5 | 0.37741 (8) | 0.3490 (3) | 0.46728 (15) | 0.0442 (5) | |
H5 | 0.3787 | 0.3381 | 0.3967 | 0.053* | |
C6 | 0.42609 (7) | 0.3136 (2) | 0.53830 (13) | 0.0317 (4) | |
C7 | 0.48090 (7) | 0.2593 (2) | 0.50891 (13) | 0.0326 (4) | |
C8 | 0.48888 (7) | 0.2495 (3) | 0.39935 (14) | 0.0368 (5) | |
C9 | 0.58564 (7) | 0.1695 (3) | 0.46318 (14) | 0.0357 (5) | |
C10 | 0.57426 (8) | 0.1723 (3) | 0.56099 (15) | 0.0419 (5) | |
H10 | 0.6029 | 0.1410 | 0.6151 | 0.050* | |
C11 | 0.64207 (8) | 0.1228 (3) | 0.43776 (16) | 0.0407 (5) | |
C12 | 0.69404 (9) | 0.0771 (4) | 0.2991 (2) | 0.0649 (7) | |
H12A | 0.6877 | 0.0789 | 0.2247 | 0.097* | |
H12B | 0.7220 | 0.1693 | 0.3248 | 0.097* | |
H12C | 0.7072 | −0.0448 | 0.3231 | 0.097* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0377 (8) | 0.0876 (13) | 0.0530 (10) | 0.0142 (8) | 0.0146 (7) | 0.0015 (9) |
O2 | 0.0356 (8) | 0.1114 (14) | 0.0297 (7) | 0.0175 (8) | 0.0036 (6) | 0.0044 (8) |
O3 | 0.0334 (8) | 0.0799 (12) | 0.0665 (10) | 0.0118 (8) | −0.0006 (7) | 0.0050 (8) |
O4 | 0.0345 (8) | 0.0720 (11) | 0.0562 (10) | 0.0112 (7) | 0.0151 (7) | 0.0034 (8) |
N1 | 0.0289 (8) | 0.0481 (10) | 0.0333 (9) | 0.0019 (7) | 0.0078 (7) | 0.0035 (7) |
N2 | 0.0326 (9) | 0.0521 (11) | 0.0349 (9) | 0.0047 (7) | 0.0002 (7) | 0.0006 (7) |
C1 | 0.0336 (10) | 0.0590 (14) | 0.0343 (10) | 0.0054 (9) | 0.0011 (8) | −0.0002 (9) |
C2 | 0.0409 (11) | 0.0674 (15) | 0.0321 (10) | 0.0045 (10) | 0.0071 (9) | −0.0022 (10) |
C3 | 0.0317 (10) | 0.0442 (12) | 0.0463 (12) | 0.0018 (9) | 0.0125 (9) | 0.0003 (9) |
C4 | 0.0310 (10) | 0.0667 (15) | 0.0421 (12) | 0.0078 (10) | 0.0006 (9) | 0.0020 (10) |
C5 | 0.0369 (11) | 0.0627 (14) | 0.0328 (10) | 0.0082 (10) | 0.0047 (8) | −0.0002 (10) |
C6 | 0.0305 (9) | 0.0327 (11) | 0.0316 (9) | −0.0010 (7) | 0.0041 (7) | −0.0001 (8) |
C7 | 0.0313 (9) | 0.0324 (10) | 0.0334 (10) | −0.0004 (8) | 0.0037 (8) | 0.0015 (8) |
C8 | 0.0289 (9) | 0.0475 (12) | 0.0341 (10) | 0.0023 (8) | 0.0051 (8) | 0.0032 (9) |
C9 | 0.0272 (9) | 0.0343 (11) | 0.0443 (11) | −0.0004 (8) | 0.0020 (8) | 0.0022 (9) |
C10 | 0.0279 (9) | 0.0544 (13) | 0.0413 (11) | 0.0070 (9) | −0.0013 (8) | 0.0020 (9) |
C11 | 0.0314 (10) | 0.0378 (12) | 0.0528 (13) | 0.0014 (9) | 0.0069 (9) | 0.0033 (9) |
C12 | 0.0405 (12) | 0.0851 (18) | 0.0751 (17) | 0.0107 (12) | 0.0273 (12) | −0.0004 (14) |
O1—C3 | 1.362 (2) | C2—H2 | 0.9300 |
O1—H1O1 | 0.88 (3) | C3—C4 | 1.375 (3) |
O2—C8 | 1.234 (2) | C4—C5 | 1.379 (3) |
O3—C11 | 1.204 (2) | C4—H4 | 0.9300 |
O4—C11 | 1.317 (2) | C5—C6 | 1.391 (2) |
O4—C12 | 1.451 (2) | C5—H5 | 0.9300 |
N1—C8 | 1.361 (2) | C6—C7 | 1.475 (2) |
N1—C9 | 1.365 (2) | C7—C8 | 1.475 (3) |
N1—H1N1 | 0.92 (2) | C9—C10 | 1.348 (3) |
N2—C7 | 1.311 (2) | C9—C11 | 1.479 (3) |
N2—C10 | 1.359 (2) | C10—H10 | 0.9300 |
C1—C2 | 1.371 (3) | C12—H12A | 0.9600 |
C1—C6 | 1.393 (2) | C12—H12B | 0.9600 |
C1—H1 | 0.9300 | C12—H12C | 0.9600 |
C2—C3 | 1.378 (3) | ||
C3—O1—H1O1 | 110.3 (19) | C1—C6—C7 | 119.11 (16) |
C11—O4—C12 | 118.10 (16) | N2—C7—C8 | 120.78 (16) |
C8—N1—C9 | 123.47 (16) | N2—C7—C6 | 117.73 (16) |
C8—N1—H1N1 | 116.3 (14) | C8—C7—C6 | 121.49 (15) |
C9—N1—H1N1 | 120.1 (14) | O2—C8—N1 | 120.22 (16) |
C7—N2—C10 | 120.11 (16) | O2—C8—C7 | 124.90 (16) |
C2—C1—C6 | 121.61 (17) | N1—C8—C7 | 114.88 (15) |
C2—C1—H1 | 119.2 | C10—C9—N1 | 118.02 (16) |
C6—C1—H1 | 119.2 | C10—C9—C11 | 123.04 (17) |
C1—C2—C3 | 120.41 (18) | N1—C9—C11 | 118.93 (17) |
C1—C2—H2 | 119.8 | C9—C10—N2 | 122.58 (17) |
C3—C2—H2 | 119.8 | C9—C10—H10 | 118.7 |
O1—C3—C4 | 122.84 (17) | N2—C10—H10 | 118.7 |
O1—C3—C2 | 117.92 (18) | O3—C11—O4 | 125.00 (18) |
C4—C3—C2 | 119.24 (17) | O3—C11—C9 | 123.59 (19) |
C3—C4—C5 | 120.30 (18) | O4—C11—C9 | 111.40 (16) |
C3—C4—H4 | 119.9 | O4—C12—H12A | 109.5 |
C5—C4—H4 | 119.9 | O4—C12—H12B | 109.5 |
C4—C5—C6 | 121.51 (18) | H12A—C12—H12B | 109.5 |
C4—C5—H5 | 119.2 | O4—C12—H12C | 109.5 |
C6—C5—H5 | 119.2 | H12A—C12—H12C | 109.5 |
C5—C6—C1 | 116.93 (17) | H12B—C12—H12C | 109.5 |
C5—C6—C7 | 123.96 (16) | ||
C6—C1—C2—C3 | 1.1 (3) | C9—N1—C8—C7 | 3.7 (3) |
C1—C2—C3—O1 | 179.0 (2) | N2—C7—C8—O2 | 175.80 (19) |
C1—C2—C3—C4 | −0.9 (3) | C6—C7—C8—O2 | −4.0 (3) |
O1—C3—C4—C5 | −179.8 (2) | N2—C7—C8—N1 | −4.3 (3) |
C2—C3—C4—C5 | 0.0 (3) | C6—C7—C8—N1 | 175.95 (16) |
C3—C4—C5—C6 | 0.6 (3) | C8—N1—C9—C10 | −0.7 (3) |
C4—C5—C6—C1 | −0.3 (3) | C8—N1—C9—C11 | 178.39 (18) |
C4—C5—C6—C7 | −179.86 (19) | N1—C9—C10—N2 | −2.3 (3) |
C2—C1—C6—C5 | −0.5 (3) | C11—C9—C10—N2 | 178.66 (18) |
C2—C1—C6—C7 | 179.01 (19) | C7—N2—C10—C9 | 1.7 (3) |
C10—N2—C7—C8 | 1.7 (3) | C12—O4—C11—O3 | −0.6 (3) |
C10—N2—C7—C6 | −178.52 (17) | C12—O4—C11—C9 | 179.36 (18) |
C5—C6—C7—N2 | −175.99 (19) | C10—C9—C11—O3 | −3.7 (3) |
C1—C6—C7—N2 | 4.5 (3) | N1—C9—C11—O3 | 177.29 (19) |
C5—C6—C7—C8 | 3.8 (3) | C10—C9—C11—O4 | 176.33 (18) |
C1—C6—C7—C8 | −175.72 (18) | N1—C9—C11—O4 | −2.7 (3) |
C9—N1—C8—O2 | −176.32 (19) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1O1···O3i | 0.88 (3) | 1.92 (3) | 2.770 (2) | 164 (3) |
N1—H1N1···O2ii | 0.93 (2) | 1.89 (2) | 2.792 (2) | 166 (2) |
C5—H5···O2 | 0.93 | 2.15 | 2.816 (2) | 127 |
Symmetry codes: (i) x−1/2, y+1/2, z; (ii) −x+1, y, −z+1/2. |
Footnotes
‡Thomson Reuters ResearcherID:E-9395-2011
Acknowledgements
The author acknowledges the XRD facility located at Department of Chemistry, Rabigh College of Science and Arts, King Abdulaziz University, Saudi Arabia.
References
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