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

Eltayeb, N.E.

doi:10.1107/S2414314616017417

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 1| Part 11| November 2016| x161741

https://doi.org/10.1107/S2414314616017417

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

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,nasertaha90@hotmail.com

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 22 October 2016; accepted 29 October 2016; online 15 November 2016)

In the title hydrate, C₁₂H₁₀N₂O₄·H₂O, the dihedral angle between the benzene and pyrazine rings is 37.70 (10)°. In the crystal, molecules are connected by hydrogen bonds (N—H⋯O, O—H⋯O and O—H⋯O) to generate (1-10) sheets. Aromatic π–π stacking [centroid–centroid separation = 3.7070 (13) Å] links the sheets into a three-dimensional network.

Keywords: crystal structure; amoxicillin; antibiotics.

CCDC reference: 1513043

Structure description

As part of our ongoing studies of amoxicillin degradation (Eltayeb, 2016 ), we report herein the synthesis and crystal structure of the title compound (Fig. 1). The dihedral angle between the benzene and pyrazine rings is 37.70 (10)°. In the crystal, the molecules are connected by various hydrogen bonds (N1—H1N⋯O2, O1—H1O⋯O1W, O1W—H1W⋯O4 and O1W—H2W⋯N2 (Fig. 2, Table 1), which generate (1 $[\overline{1}]$ 0) sheets.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1N⋯O2ⁱ	0.94 (3)	1.88 (3)	2.805 (2)	172 (3)
O1—H1O⋯O1W	0.93 (3)	1.77 (3)	2.682 (3)	168 (3)
O1W—H1W⋯O4ⁱⁱ	0.86 (4)	2.02 (4)	2.864 (2)	167 (3)
O1W—H2W⋯N2ⁱⁱⁱ	0.90 (3)	1.97 (3)	2.838 (3)	163 (3)
Symmetry codes: (i) -x, -y+1, -z+1; (ii) x, y, z-1; (iii) -x+1, -y+2, -z.

Figure 1
The molecular structure of the title compound, shown with 50% probability displacement ellipsoids. The O—H⋯O hydrogen bond is indicated by a dashed line.

Figure 2
The crystal packing of the title compound, viewed down the a axis. Hydrogen bonds are shown as dashed lines.

Aromatic π–π stacking is also observed: Cg1⋯Cg1^iv [centroid–centroid separation = 3.7074 (13) Å] and Cg2⋯Cg2^v [centroid–centroid separation = 3.7071 (13)] [symmetry codes: (iv) −1 + x, y, x; (v) 1 + x, y, z; Cg1 is the centroid of the C7/C8/N1/C9/C10/N2 ring and Cg2 is the centroid of the C1–C6 ring]. The end result is a three-dimensional network.

Synthesis and crystallization

Amoxicillin trihydrate (0.5 mmol, 0.21 g) and 2,4-dihydroxybenzaldehyde (0.5 mmol, 0.07 g) were dissolved in methanol in a round-bottomed flask, then 0.1 g copper sulfate solution in 5 ml water was added. The mixture was refluxed for about 2 h. The product was filtered. Golden blocks of the title compound 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. The highest residual electron density peak is located at 1.78 Å from C10 and the deepest hole is located at 0.81 Å from N1.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₂H₁₀N₂O₄·H₂O
M_r	264.24
Crystal system, space group	Triclinic, P $[\overline{1}]$
Temperature (K)	100
a, b, c (Å)	3.7072 (3), 11.4251 (9), 14.3713 (13)
α, β, γ (°)	70.748 (4), 88.425 (5), 83.284 (5)
V (Å³)	570.68 (8)
Z	2
Radiation type	Mo Kα
μ (mm⁻¹)	0.12
Crystal size (mm)	0.16 × 0.12 × 0.07

Data collection
Diffractometer	Bruker D8 Quest CCD
Absorption correction	Multi-scan (SADABS; Bruker, 2016 )
T_min, T_max	0.689, 0.745
No. of measured, independent and observed [I > 2σ(I)] reflections	10223, 2091, 1556
R_int	0.079
(sin θ/λ)_max (Å⁻¹)	0.602

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.049, 0.119, 1.02
No. of reflections	2091
No. of parameters	189
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.27, −0.34
Computer programs: APEX3 and SAINT (Bruker, 2016), SHELXT2014 (Sheldrick, 2015a ), SHELXL2014 (Sheldrick, 2015b ) and PLATON (Spek, 2015 ).

Structural data

CCDC reference: 1513043

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314616017417/hb4089sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314616017417/hb4089Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314616017417/hb4089Isup3.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: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: SHELXL2014 (Sheldrick, 2015b); software used to prepare material for publication: APEX3 (Bruker, 2016) and PLATON (Spek, 2015).

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

Crystal data top

C₁₂H₁₀N₂O₄·H₂O	Z = 2
M_r = 264.24	F(000) = 276
Triclinic, P1	D_x = 1.538 Mg m⁻³
a = 3.7072 (3) Å	Mo Kα radiation, λ = 0.71073 Å
b = 11.4251 (9) Å	Cell parameters from 3588 reflections
c = 14.3713 (13) Å	θ = 2.8–25.3°
α = 70.748 (4)°	µ = 0.12 mm⁻¹
β = 88.425 (5)°	T = 100 K
γ = 83.284 (5)°	Block, gold
V = 570.68 (8) Å³	0.16 × 0.12 × 0.07 mm

Data collection top

Bruker D8 Quest CCD diffractometer	1556 reflections with I > 2σ(I)
φ and ω scans	R_int = 0.079
Absorption correction: multi-scan (SADABS; Bruker, 2016)	θ_max = 25.4°, θ_min = 2.8°
T_min = 0.689, T_max = 0.745	h = −4→4
10223 measured reflections	k = −13→13
2091 independent reflections	l = −17→16

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.049	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.119	w = 1/[σ²(F_o²) + (0.0581P)² + 0.2621P] where P = (F_o² + 2F_c²)/3
S = 1.02	(Δ/σ)_max < 0.001
2091 reflections	Δρ_max = 0.27 e Å⁻³
189 parameters	Δρ_min = −0.34 e Å⁻³
0 restraints

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	0.5384 (5)	0.72898 (15)	−0.07116 (12)	0.0208 (4)
O2	0.1695 (4)	0.53640 (13)	0.38440 (11)	0.0185 (4)
O1W	0.2759 (5)	0.93868 (16)	−0.21323 (13)	0.0215 (4)
O3	0.0237 (4)	0.68091 (13)	0.65526 (11)	0.0166 (4)
O4	0.2049 (5)	0.87280 (14)	0.61292 (11)	0.0198 (4)
N1	0.1665 (5)	0.65746 (16)	0.48160 (14)	0.0125 (4)
N2	0.4133 (5)	0.84534 (16)	0.32977 (13)	0.0137 (4)
C1	0.3041 (6)	0.84329 (19)	0.13426 (16)	0.0133 (5)
H1	0.2106	0.9183	0.1458	0.016*
C2	0.3441 (6)	0.84230 (19)	0.03887 (16)	0.0143 (5)
H2	0.2730	0.9157	−0.0149	0.017*
C3	0.4887 (6)	0.7337 (2)	0.02149 (16)	0.0145 (5)
C4	0.5883 (6)	0.6262 (2)	0.09990 (16)	0.0154 (5)
H4	0.6897	0.5523	0.0879	0.018*
C5	0.5405 (6)	0.62616 (19)	0.19544 (16)	0.0147 (5)
H5	0.6038	0.5516	0.2489	0.018*
C6	0.3997 (6)	0.73496 (19)	0.21435 (16)	0.0123 (5)
C7	0.3548 (6)	0.74126 (19)	0.31435 (16)	0.0128 (5)
C8	0.2279 (6)	0.63618 (19)	0.39424 (16)	0.0115 (5)
C9	0.2278 (6)	0.76628 (19)	0.49603 (16)	0.0121 (5)
C10	0.3518 (6)	0.85802 (19)	0.42030 (16)	0.0137 (5)
H10	0.3972	0.9332	0.4303	0.016*
C11	0.1537 (6)	0.78086 (19)	0.59361 (16)	0.0137 (5)
C12	−0.0733 (6)	0.6846 (2)	0.75253 (17)	0.0179 (5)
H12A	−0.1903	0.6103	0.7886	0.027*
H12B	−0.2415	0.7596	0.7466	0.027*
H12C	0.1462	0.6863	0.7883	0.027*
H1N	0.070 (8)	0.593 (3)	0.531 (2)	0.043 (9)*
H1O	0.451 (9)	0.807 (3)	−0.114 (2)	0.056 (10)*
H1W	0.224 (9)	0.914 (3)	−0.261 (3)	0.049 (10)*
H2W	0.388 (9)	1.008 (3)	−0.238 (2)	0.048 (9)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0321 (10)	0.0195 (9)	0.0097 (9)	0.0020 (7)	0.0026 (7)	−0.0052 (7)
O2	0.0303 (10)	0.0138 (8)	0.0131 (9)	−0.0090 (7)	0.0062 (7)	−0.0054 (7)
O1W	0.0334 (11)	0.0164 (9)	0.0145 (10)	−0.0058 (7)	0.0007 (8)	−0.0038 (7)
O3	0.0252 (9)	0.0146 (8)	0.0116 (9)	−0.0058 (7)	0.0059 (7)	−0.0056 (6)
O4	0.0313 (10)	0.0151 (9)	0.0152 (9)	−0.0061 (7)	0.0014 (7)	−0.0069 (7)
N1	0.0165 (10)	0.0102 (9)	0.0103 (10)	−0.0025 (7)	0.0026 (8)	−0.0026 (8)
N2	0.0169 (10)	0.0117 (9)	0.0113 (10)	−0.0004 (7)	−0.0010 (8)	−0.0026 (8)
C1	0.0131 (12)	0.0117 (11)	0.0152 (12)	−0.0004 (8)	−0.0007 (9)	−0.0047 (9)
C2	0.0162 (12)	0.0130 (11)	0.0113 (12)	−0.0011 (9)	−0.0009 (9)	−0.0008 (9)
C3	0.0150 (12)	0.0187 (12)	0.0105 (12)	−0.0034 (9)	0.0011 (9)	−0.0054 (9)
C4	0.0156 (12)	0.0140 (11)	0.0167 (13)	0.0018 (9)	0.0027 (9)	−0.0066 (10)
C5	0.0157 (12)	0.0127 (11)	0.0132 (12)	−0.0012 (9)	−0.0006 (9)	−0.0008 (9)
C6	0.0109 (11)	0.0142 (11)	0.0116 (12)	−0.0045 (8)	0.0017 (9)	−0.0029 (9)
C7	0.0108 (11)	0.0127 (11)	0.0131 (12)	−0.0012 (8)	0.0004 (9)	−0.0019 (9)
C8	0.0117 (11)	0.0116 (11)	0.0104 (12)	−0.0007 (9)	0.0009 (9)	−0.0029 (9)
C9	0.0112 (11)	0.0124 (11)	0.0129 (12)	0.0002 (8)	−0.0014 (9)	−0.0047 (9)
C10	0.0151 (12)	0.0120 (11)	0.0152 (13)	−0.0014 (9)	−0.0006 (9)	−0.0060 (9)
C11	0.0145 (12)	0.0126 (12)	0.0136 (12)	−0.0003 (9)	−0.0004 (9)	−0.0042 (9)
C12	0.0212 (13)	0.0217 (13)	0.0110 (12)	−0.0027 (10)	0.0053 (10)	−0.0061 (10)

Geometric parameters (Å, º) top

O1—C3	1.357 (3)	C2—C3	1.390 (3)
O1—H1O	0.93 (3)	C2—H2	0.9500
O2—C8	1.238 (2)	C3—C4	1.385 (3)
O1W—H1W	0.86 (4)	C4—C5	1.380 (3)
O1W—H2W	0.90 (3)	C4—H4	0.9500
O3—C11	1.326 (3)	C5—C6	1.398 (3)
O3—C12	1.447 (3)	C5—H5	0.9500
O4—C11	1.208 (3)	C6—C7	1.466 (3)
N1—C8	1.364 (3)	C7—C8	1.475 (3)
N1—C9	1.371 (3)	C9—C10	1.352 (3)
N1—H1N	0.94 (3)	C9—C11	1.480 (3)
N2—C7	1.322 (3)	C10—H10	0.9500
N2—C10	1.366 (3)	C12—H12A	0.9800
C1—C2	1.378 (3)	C12—H12B	0.9800
C1—C6	1.401 (3)	C12—H12C	0.9800
C1—H1	0.9500

C3—O1—H1O	106 (2)	C5—C6—C7	122.84 (19)
H1W—O1W—H2W	108 (3)	C1—C6—C7	118.6 (2)
C11—O3—C12	116.91 (16)	N2—C7—C6	118.44 (19)
C8—N1—C9	123.15 (19)	N2—C7—C8	121.0 (2)
C8—N1—H1N	115.4 (18)	C6—C7—C8	120.44 (18)
C9—N1—H1N	121.4 (18)	O2—C8—N1	121.07 (19)
C7—N2—C10	120.27 (19)	O2—C8—C7	124.0 (2)
C2—C1—C6	120.7 (2)	N1—C8—C7	114.90 (18)
C2—C1—H1	119.6	C10—C9—N1	119.0 (2)
C6—C1—H1	119.6	C10—C9—C11	121.71 (19)
C1—C2—C3	119.9 (2)	N1—C9—C11	119.30 (19)
C1—C2—H2	120.1	C9—C10—N2	121.63 (19)
C3—C2—H2	120.1	C9—C10—H10	119.2
O1—C3—C4	118.0 (2)	N2—C10—H10	119.2
O1—C3—C2	121.90 (19)	O4—C11—O3	125.3 (2)
C4—C3—C2	120.1 (2)	O4—C11—C9	123.6 (2)
C5—C4—C3	120.1 (2)	O3—C11—C9	111.11 (18)
C5—C4—H4	119.9	O3—C12—H12A	109.5
C3—C4—H4	119.9	O3—C12—H12B	109.5
C4—C5—C6	120.6 (2)	H12A—C12—H12B	109.5
C4—C5—H5	119.7	O3—C12—H12C	109.5
C6—C5—H5	119.7	H12A—C12—H12C	109.5
C5—C6—C1	118.6 (2)	H12B—C12—H12C	109.5

C6—C1—C2—C3	−1.5 (3)	C9—N1—C8—C7	−2.0 (3)
C1—C2—C3—O1	−178.9 (2)	N2—C7—C8—O2	−179.8 (2)
C1—C2—C3—C4	0.8 (3)	C6—C7—C8—O2	3.6 (3)
O1—C3—C4—C5	−179.5 (2)	N2—C7—C8—N1	2.1 (3)
C2—C3—C4—C5	0.7 (3)	C6—C7—C8—N1	−174.48 (19)
C3—C4—C5—C6	−1.5 (3)	C8—N1—C9—C10	0.7 (3)
C4—C5—C6—C1	0.8 (3)	C8—N1—C9—C11	−179.89 (19)
C4—C5—C6—C7	−177.9 (2)	N1—C9—C10—N2	0.7 (3)
C2—C1—C6—C5	0.7 (3)	C11—C9—C10—N2	−178.7 (2)
C2—C1—C6—C7	179.5 (2)	C7—N2—C10—C9	−0.5 (3)
C10—N2—C7—C6	175.74 (19)	C12—O3—C11—O4	1.8 (3)
C10—N2—C7—C8	−0.9 (3)	C12—O3—C11—C9	−177.80 (18)
C5—C6—C7—N2	143.9 (2)	C10—C9—C11—O4	−1.6 (3)
C1—C6—C7—N2	−34.8 (3)	N1—C9—C11—O4	179.0 (2)
C5—C6—C7—C8	−39.4 (3)	C10—C9—C11—O3	178.00 (19)
C1—C6—C7—C8	141.9 (2)	N1—C9—C11—O3	−1.4 (3)
C9—N1—C8—O2	179.85 (19)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···O2ⁱ	0.94 (3)	1.88 (3)	2.805 (2)	172 (3)
O1—H1O···O1W	0.93 (3)	1.77 (3)	2.682 (3)	168 (3)
O1W—H1W···O4ⁱⁱ	0.86 (4)	2.02 (4)	2.864 (2)	167 (3)
O1W—H2W···N2ⁱⁱⁱ	0.90 (3)	1.97 (3)	2.838 (3)	163 (3)

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

Footnotes

‡Thomson Reuters ResearcherID: E-9395-2011.

Acknowledgements

The author acknowledges the XRD facility located at the Department of Chemistry, Rabigh College of Science and Arts, King Abdulaziz University, Saudi Arabia.

References

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Sheldrick, G. M. (2015a). Acta Cryst. A71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2015b). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Spek, A. L. (2015). Acta Cryst. C71, 9–18. Web of Science CrossRef IUCr Journals Google Scholar

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