Methyl 5-(4-hy­droxy­phen­yl)-6-oxo-1,6-di­hydro­pyrazine-2-carboxyl­ate

Eltayeb, N.E.

doi:10.1107/S2414314616016898

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 1| Part 11| November 2016| x161689

https://doi.org/10.1107/S2414314616016898

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Methyl 5-(4-hydroxyphenyl)-6-oxo-1,6-dihydropyrazine-2-carboxylate

Naser Eltaher Eltayeb ^a ^*‡

^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

Edited by H. Ishida, Okayama University, Japan (Received 10 October 2016; accepted 21 October 2016; online 8 November 2016)

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).

Table 1
Hydrogen-bond geometry (Å, °)

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) $[x-{\script{1\over 2}}, y+{\script{1\over 2}}, z]$ ; (ii) $[-x+1, y, -z+{\script{1\over 2}}]$ .

Figure 1
The molecular structure of the title compound, shown with 50% probability displacement ellipsoids and the atom-numbering scheme. The intramolecular hydrogen bond is shown as a dashed line.

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.

Figure 2
The crystal packing of the title compound viewed down the b axis. Hydrogen bonds are shown as dashed lines and H atoms not involved in the hydrogen bonds have been omitted.

Figure 3
The crystal packing of the title compound viewed down the c axis. Hydrogen bonds are shown as dashed lines and H atoms not involved in the hydrogen bonds have been omitted.

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 refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₂H₁₀N₂O₄
M_r	246.22
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	273
a, b, c (Å)	23.9226 (19), 7.1372 (6), 13.0562 (11)
β (°)	99.158 (5)
V (Å³)	2200.8 (3)
Z	8
Radiation type	Mo Kα
μ (mm⁻¹)	0.11
Crystal size (mm)	0.30 × 0.20 × 0.03

Data collection
Diffractometer	Bruker D8 Quest
Absorption correction	Multi-scan (SADABS; Bruker, 2016 )
T_min, T_max	0.656, 0.745
No. of measured, independent and observed [I > 2σ(I)] reflections	20352, 2011, 1450
R_int	0.075
(sin θ/λ)_max (Å⁻¹)	0.602

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.045, 0.115, 1.07
No. of reflections	2011
No. of parameters	171
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.14, −0.21
Computer programs: APEX3 (Bruker, 2016), SAINT (Bruker, 2016), SHELXS2014 (Sheldrick, 2008 ), SHELXTL (Sheldrick, 2008), SHELXL2014 (Sheldrick, 2015 ) and PLATON (Spek, 2015 ).

Structural data

CCDC reference: 1510980

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314616016898/is4012sup1.cif

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

checkCIF report

Computing details top

Data collection: APEX3 (Bruker, 2016); cell refinement: 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).

Methyl 5-(4-hydroxyphenyl)-6-oxo-1,6-dihydropyrazine-2-carboxylate top

Crystal data top

C₁₂H₁₀N₂O₄	F(000) = 1024
M_r = 246.22	D_x = 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

Data collection top

Bruker D8 Quest diffractometer	1450 reflections with I > 2σ(I)
φ and ω scans	R_int = 0.075
Absorption correction: multi-scan (SADABS; Bruker, 2016)	θ_max = 25.4°, θ_min = 3.0°
T_min = 0.656, T_max = 0.745	h = −28→28
20352 measured reflections	k = −8→8
2011 independent reflections	l = −15→15

Refinement top

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(F_o²) + (0.0528P)² + 1.083P] where P = (F_o² + 2F_c²)/3
S = 1.07	(Δ/σ)_max < 0.001
2011 reflections	Δρ_max = 0.14 e Å⁻³
171 parameters	Δρ_min = −0.21 e Å⁻³

Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
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*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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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