organic compounds
6-Methyl-2-pyridyl N-acetyl-1-thio-β-D-glucosaminide methanol monosolvate
aFaculty of Materials Science and Chemical Engineering, Ningbo University, Zhejiang 315211, People's Republic of China
*Correspondence e-mail: lianghongze@nbu.edu.cn
In the title compound, C14H20N2O5S·CH4O, the pyranose and pyridine rings are linked through an S atom. The pyranose ring has a normal chair conformation. An intramolecular O—H⋯N hydrogen bond occurs. Intermolecular O—H⋯O, N—H⋯O, O—H⋯N and weak C—H⋯O hydrogen bonding is present in the crystal structure.
Related literature
For applications of glucopyranosides, see: Ashry et al. (2006). For the structure of an α-D-glucosaminide, see: Harrison et al. (2007).
Experimental
Crystal data
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Data collection: SMART (Bruker, 2007); cell SAINT (Bruker, 2007); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.
Supporting information
10.1107/S1600536810036238/xu5024sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536810036238/xu5024Isup2.hkl
6'-Methyl-2'-pyridyl-2,3,4,6-tetraacetyl-1-thio-β-D-glucosaminide (1.5 g, 3.3 mmol) was dissolved in MeOH (10 ml) and one equivalent MeONa was added. The process of deacetylation was monitored by 1H NMR. After removal of the solvent, the solid residue was washed with ethanol and ether, and then crystallized from H2O/MeOH to give the title compound (0.23 g) as colorless crystals.
H atoms were placed in calculated positions and treated using a riding-model, C–H = 0.93–0.98 Å with Uiso(H) = 1.2Ueq(C) or 1.5Ueq(C), N–H = 0.86 with Uiso(H) = 1.2Ueq(N), O—H = 0.82 Å with Uiso(H) = 1.5Ueq(O).
Data collection: SMART (Bruker, 2007); cell
SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).Fig. 1. A view of (I) showing the labeling of the non-H atoms and 50% probability ellipsoids. Dashed line indicates the hydrogen bonding. |
C14H20N2O5S·CH4O | F(000) = 768 |
Mr = 360.42 | Dx = 1.355 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 12040 reflections |
a = 7.3841 (15) Å | θ = 1.9–24.5° |
b = 14.041 (3) Å | µ = 0.22 mm−1 |
c = 17.038 (4) Å | T = 296 K |
V = 1766.5 (6) Å3 | Block, colourless |
Z = 4 | 0.51 × 0.27 × 0.2 mm |
Bruker SMART CCD area-detector diffractometer | 3173 independent reflections |
Radiation source: fine-focus sealed tube | 2997 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.161 |
Detector resolution: 0 pixels mm-1 | θmax = 25.2°, θmin = 1.9° |
ϕ and ω scans | h = −8→8 |
Absorption correction: multi-scan (SADABS; Bruker, 2001) | k = −16→16 |
Tmin = 0.932, Tmax = 0.950 | l = −20→20 |
12687 measured reflections |
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)] = 0.066 | H-atom parameters constrained |
wR(F2) = 0.170 | w = 1/[σ2(Fo2) + (0.1077P)2 + 0.760P] where P = (Fo2 + 2Fc2)/3 |
S = 1.05 | (Δ/σ)max = 0.003 |
3173 reflections | Δρmax = 0.56 e Å−3 |
222 parameters | Δρmin = −0.70 e Å−3 |
0 restraints | Absolute structure: Flack (1983), 1334 Fiedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.01 (12) |
C14H20N2O5S·CH4O | V = 1766.5 (6) Å3 |
Mr = 360.42 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 7.3841 (15) Å | µ = 0.22 mm−1 |
b = 14.041 (3) Å | T = 296 K |
c = 17.038 (4) Å | 0.51 × 0.27 × 0.2 mm |
Bruker SMART CCD area-detector diffractometer | 3173 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2001) | 2997 reflections with I > 2σ(I) |
Tmin = 0.932, Tmax = 0.950 | Rint = 0.161 |
12687 measured reflections |
R[F2 > 2σ(F2)] = 0.066 | H-atom parameters constrained |
wR(F2) = 0.170 | Δρmax = 0.56 e Å−3 |
S = 1.05 | Δρmin = −0.70 e Å−3 |
3173 reflections | Absolute structure: Flack (1983), 1334 Fiedel pairs |
222 parameters | Absolute structure parameter: 0.01 (12) |
0 restraints |
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. |
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 | ||
S1 | 0.80502 (12) | 0.14422 (6) | 0.34312 (4) | 0.0246 (2) | |
O1 | 0.6461 (3) | 0.24215 (17) | 0.23124 (11) | 0.0209 (5) | |
O2 | 0.3258 (3) | 0.26631 (17) | 0.13049 (12) | 0.0238 (5) | |
H2A | 0.3087 | 0.2660 | 0.0829 | 0.036* | |
O3 | 0.7290 (3) | 0.28865 (18) | 0.02141 (12) | 0.0243 (5) | |
H3A | 0.6376 | 0.3204 | 0.0135 | 0.036* | |
O4 | 0.9501 (3) | 0.12909 (17) | 0.04864 (13) | 0.0237 (5) | |
H4A | 0.8695 | 0.0906 | 0.0392 | 0.036* | |
O5 | 1.0621 (4) | −0.03011 (17) | 0.24234 (16) | 0.0327 (6) | |
O6 | 0.8051 (4) | −0.00609 (19) | 0.51072 (18) | 0.0449 (8) | |
H6 | 0.7982 | 0.0517 | 0.5048 | 0.067* | |
N1 | 1.0936 (4) | 0.1246 (2) | 0.20602 (15) | 0.0221 (6) | |
H1A | 1.1689 | 0.1711 | 0.2024 | 0.027* | |
N2 | 0.8034 (4) | 0.1914 (2) | 0.49004 (14) | 0.0232 (6) | |
C1 | 0.8218 (5) | 0.2112 (2) | 0.25267 (16) | 0.0205 (6) | |
H1B | 0.9010 | 0.2665 | 0.2604 | 0.025* | |
C2 | 0.9047 (4) | 0.1441 (2) | 0.19007 (17) | 0.0191 (6) | |
H2C | 0.8369 | 0.0841 | 0.1891 | 0.023* | |
C3 | 0.8913 (4) | 0.1928 (2) | 0.10900 (16) | 0.0179 (6) | |
H3B | 0.9773 | 0.2460 | 0.1096 | 0.021* | |
C4 | 0.7073 (4) | 0.2349 (2) | 0.09201 (15) | 0.0186 (6) | |
H4B | 0.6190 | 0.1837 | 0.0837 | 0.022* | |
C5 | 0.6461 (4) | 0.2985 (2) | 0.15999 (16) | 0.0189 (6) | |
H5A | 0.7311 | 0.3516 | 0.1658 | 0.023* | |
C6 | 0.4550 (4) | 0.3376 (2) | 0.14950 (17) | 0.0211 (7) | |
H6A | 0.4181 | 0.3690 | 0.1976 | 0.025* | |
H6B | 0.4562 | 0.3850 | 0.1081 | 0.025* | |
C7 | 0.8079 (5) | 0.2318 (2) | 0.41830 (17) | 0.0220 (7) | |
C8 | 0.8187 (5) | 0.3293 (2) | 0.40626 (18) | 0.0272 (7) | |
H8A | 0.8197 | 0.3549 | 0.3559 | 0.033* | |
C9 | 0.8281 (6) | 0.3875 (3) | 0.4726 (2) | 0.0360 (9) | |
H9A | 0.8383 | 0.4532 | 0.4671 | 0.043* | |
C10 | 0.8221 (5) | 0.3470 (3) | 0.5465 (2) | 0.0343 (8) | |
H10A | 0.8265 | 0.3853 | 0.5910 | 0.041* | |
C11 | 0.8095 (5) | 0.2491 (3) | 0.55384 (17) | 0.0268 (7) | |
C12 | 0.8040 (6) | 0.2002 (3) | 0.63295 (18) | 0.0342 (8) | |
H12A | 0.7956 | 0.1326 | 0.6255 | 0.051* | |
H12B | 0.7005 | 0.2221 | 0.6619 | 0.051* | |
H12C | 0.9123 | 0.2149 | 0.6616 | 0.051* | |
C13 | 1.1595 (5) | 0.0380 (2) | 0.22624 (18) | 0.0258 (8) | |
C14 | 1.3633 (5) | 0.0325 (3) | 0.2284 (2) | 0.0370 (9) | |
H14A | 1.3997 | −0.0307 | 0.2431 | 0.055* | |
H14B | 1.4089 | 0.0773 | 0.2661 | 0.055* | |
H14C | 1.4111 | 0.0473 | 0.1775 | 0.055* | |
C15 | 0.9488 (6) | −0.0426 (3) | 0.4639 (3) | 0.0419 (10) | |
H15A | 1.0311 | 0.0080 | 0.4511 | 0.063* | |
H15B | 0.9002 | −0.0691 | 0.4164 | 0.063* | |
H15C | 1.0120 | −0.0912 | 0.4925 | 0.063* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0396 (5) | 0.0254 (4) | 0.0087 (4) | −0.0002 (4) | −0.0009 (3) | 0.0015 (3) |
O1 | 0.0240 (12) | 0.0320 (12) | 0.0068 (9) | 0.0013 (9) | 0.0010 (8) | 0.0021 (9) |
O2 | 0.0240 (11) | 0.0350 (12) | 0.0124 (10) | −0.0047 (10) | −0.0019 (9) | 0.0012 (9) |
O3 | 0.0243 (12) | 0.0387 (14) | 0.0100 (10) | 0.0057 (11) | 0.0008 (8) | 0.0050 (9) |
O4 | 0.0247 (11) | 0.0313 (12) | 0.0150 (10) | 0.0001 (10) | 0.0048 (9) | −0.0054 (9) |
O5 | 0.0398 (15) | 0.0250 (13) | 0.0333 (14) | 0.0013 (11) | 0.0009 (12) | 0.0023 (11) |
O6 | 0.0568 (19) | 0.0269 (13) | 0.0509 (17) | 0.0004 (15) | 0.0235 (16) | 0.0076 (12) |
N1 | 0.0221 (14) | 0.0258 (14) | 0.0184 (13) | −0.0009 (11) | −0.0029 (11) | 0.0024 (11) |
N2 | 0.0258 (14) | 0.0322 (15) | 0.0117 (12) | 0.0010 (13) | −0.0009 (11) | 0.0008 (10) |
C1 | 0.0252 (15) | 0.0290 (16) | 0.0073 (12) | 0.0010 (14) | 0.0000 (12) | −0.0004 (12) |
C2 | 0.0237 (15) | 0.0215 (15) | 0.0120 (13) | −0.0002 (13) | 0.0007 (11) | 0.0014 (12) |
C3 | 0.0224 (15) | 0.0246 (16) | 0.0068 (13) | −0.0012 (12) | 0.0020 (12) | −0.0024 (12) |
C4 | 0.0223 (16) | 0.0270 (16) | 0.0064 (13) | −0.0029 (13) | 0.0026 (11) | −0.0002 (11) |
C5 | 0.0271 (16) | 0.0219 (14) | 0.0078 (13) | −0.0031 (13) | 0.0002 (11) | 0.0009 (12) |
C6 | 0.0238 (16) | 0.0288 (16) | 0.0107 (13) | −0.0020 (13) | −0.0010 (12) | −0.0013 (12) |
C7 | 0.0218 (15) | 0.0331 (17) | 0.0111 (13) | 0.0014 (15) | 0.0003 (12) | −0.0026 (12) |
C8 | 0.0349 (18) | 0.0301 (17) | 0.0167 (15) | 0.0039 (15) | 0.0015 (15) | 0.0009 (12) |
C9 | 0.045 (2) | 0.0299 (18) | 0.0335 (19) | 0.0033 (17) | 0.0035 (18) | −0.0029 (15) |
C10 | 0.0397 (19) | 0.041 (2) | 0.0221 (16) | 0.0042 (18) | 0.0008 (16) | −0.0115 (15) |
C11 | 0.0231 (15) | 0.045 (2) | 0.0124 (14) | 0.0043 (15) | −0.0010 (13) | −0.0036 (14) |
C12 | 0.042 (2) | 0.052 (2) | 0.0090 (14) | 0.0022 (19) | −0.0021 (15) | −0.0020 (14) |
C13 | 0.039 (2) | 0.0228 (16) | 0.0155 (14) | 0.0028 (15) | −0.0014 (14) | −0.0017 (12) |
C14 | 0.036 (2) | 0.034 (2) | 0.041 (2) | 0.0059 (16) | −0.0039 (17) | 0.0026 (16) |
C15 | 0.035 (2) | 0.037 (2) | 0.054 (3) | 0.0018 (18) | 0.009 (2) | 0.0094 (19) |
S1—C7 | 1.776 (3) | C4—C5 | 1.531 (4) |
S1—C1 | 1.810 (3) | C4—H4B | 0.9800 |
O1—C1 | 1.416 (4) | C5—C6 | 1.524 (4) |
O1—C5 | 1.449 (3) | C5—H5A | 0.9800 |
O2—C6 | 1.420 (4) | C6—H6A | 0.9700 |
O2—H2A | 0.8200 | C6—H6B | 0.9700 |
O3—C4 | 1.429 (3) | C7—C8 | 1.386 (5) |
O3—H3A | 0.8200 | C8—C9 | 1.397 (5) |
O4—C3 | 1.431 (4) | C8—H8A | 0.9300 |
O4—H4A | 0.8200 | C9—C10 | 1.382 (5) |
O5—C13 | 1.227 (4) | C9—H9A | 0.9300 |
O6—C15 | 1.423 (5) | C10—C11 | 1.383 (5) |
O6—H6 | 0.8200 | C10—H10A | 0.9300 |
N1—C13 | 1.355 (4) | C11—C12 | 1.513 (4) |
N1—C2 | 1.447 (4) | C12—H12A | 0.9600 |
N1—H1A | 0.8600 | C12—H12B | 0.9600 |
N2—C7 | 1.348 (4) | C12—H12C | 0.9600 |
N2—C11 | 1.357 (4) | C13—C14 | 1.507 (6) |
C1—C2 | 1.550 (4) | C14—H14A | 0.9600 |
C1—H1B | 0.9800 | C14—H14B | 0.9600 |
C2—C3 | 1.545 (4) | C14—H14C | 0.9600 |
C2—H2C | 0.9800 | C15—H15A | 0.9600 |
C3—C4 | 1.510 (5) | C15—H15B | 0.9600 |
C3—H3B | 0.9800 | C15—H15C | 0.9600 |
C7—S1—C1 | 104.68 (15) | O2—C6—H6A | 108.9 |
C1—O1—C5 | 112.5 (2) | C5—C6—H6A | 108.9 |
C6—O2—H2A | 109.5 | O2—C6—H6B | 108.9 |
C4—O3—H3A | 109.5 | C5—C6—H6B | 108.9 |
C3—O4—H4A | 109.5 | H6A—C6—H6B | 107.7 |
C15—O6—H6 | 109.5 | N2—C7—C8 | 123.4 (3) |
C13—N1—C2 | 124.3 (3) | N2—C7—S1 | 111.3 (2) |
C13—N1—H1A | 117.9 | C8—C7—S1 | 125.3 (2) |
C2—N1—H1A | 117.9 | C7—C8—C9 | 117.5 (3) |
C7—N2—C11 | 118.3 (3) | C7—C8—H8A | 121.3 |
O1—C1—C2 | 111.8 (2) | C9—C8—H8A | 121.3 |
O1—C1—S1 | 108.4 (2) | C10—C9—C8 | 119.6 (3) |
C2—C1—S1 | 107.3 (2) | C10—C9—H9A | 120.2 |
O1—C1—H1B | 109.8 | C8—C9—H9A | 120.2 |
C2—C1—H1B | 109.8 | C9—C10—C11 | 119.5 (3) |
S1—C1—H1B | 109.8 | C9—C10—H10A | 120.2 |
N1—C2—C3 | 108.2 (2) | C11—C10—H10A | 120.2 |
N1—C2—C1 | 111.5 (3) | N2—C11—C10 | 121.6 (3) |
C3—C2—C1 | 108.7 (2) | N2—C11—C12 | 116.2 (3) |
N1—C2—H2C | 109.5 | C10—C11—C12 | 122.2 (3) |
C3—C2—H2C | 109.5 | C11—C12—H12A | 109.5 |
C1—C2—H2C | 109.5 | C11—C12—H12B | 109.5 |
O4—C3—C4 | 112.3 (2) | H12A—C12—H12B | 109.5 |
O4—C3—C2 | 110.2 (2) | C11—C12—H12C | 109.5 |
C4—C3—C2 | 113.7 (2) | H12A—C12—H12C | 109.5 |
O4—C3—H3B | 106.7 | H12B—C12—H12C | 109.5 |
C4—C3—H3B | 106.7 | O5—C13—N1 | 123.1 (3) |
C2—C3—H3B | 106.7 | O5—C13—C14 | 122.6 (3) |
O3—C4—C3 | 105.5 (2) | N1—C13—C14 | 114.3 (3) |
O3—C4—C5 | 111.2 (2) | C13—C14—H14A | 109.5 |
C3—C4—C5 | 110.4 (2) | C13—C14—H14B | 109.5 |
O3—C4—H4B | 109.9 | H14A—C14—H14B | 109.5 |
C3—C4—H4B | 109.9 | C13—C14—H14C | 109.5 |
C5—C4—H4B | 109.9 | H14A—C14—H14C | 109.5 |
O1—C5—C6 | 107.1 (2) | H14B—C14—H14C | 109.5 |
O1—C5—C4 | 108.3 (2) | O6—C15—H15A | 109.5 |
C6—C5—C4 | 113.2 (3) | O6—C15—H15B | 109.5 |
O1—C5—H5A | 109.3 | H15A—C15—H15B | 109.5 |
C6—C5—H5A | 109.3 | O6—C15—H15C | 109.5 |
C4—C5—H5A | 109.3 | H15A—C15—H15C | 109.5 |
O2—C6—C5 | 113.3 (3) | H15B—C15—H15C | 109.5 |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···O2i | 0.86 | 2.15 | 2.925 (4) | 149 |
O2—H2A···O3ii | 0.82 | 2.02 | 2.794 (3) | 156 |
O3—H3A···O4ii | 0.82 | 1.88 | 2.646 (3) | 155 |
O4—H4A···O6iii | 0.82 | 1.82 | 2.637 (4) | 176 |
O6—H6···N2 | 0.82 | 1.98 | 2.795 (4) | 175 |
C8—H8A···O5iv | 0.93 | 2.48 | 3.329 (4) | 151 |
C12—H12C···O1v | 0.96 | 2.58 | 3.520 (4) | 165 |
C15—H15C···O3vi | 0.96 | 2.56 | 3.367 (5) | 142 |
Symmetry codes: (i) x+1, y, z; (ii) x−1/2, −y+1/2, −z; (iii) −x+3/2, −y, z−1/2; (iv) −x+2, y+1/2, −z+1/2; (v) x+1/2, −y+1/2, −z+1; (vi) −x+2, y−1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C14H20N2O5S·CH4O |
Mr | 360.42 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 296 |
a, b, c (Å) | 7.3841 (15), 14.041 (3), 17.038 (4) |
V (Å3) | 1766.5 (6) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.22 |
Crystal size (mm) | 0.51 × 0.27 × 0.2 |
Data collection | |
Diffractometer | Bruker SMART CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2001) |
Tmin, Tmax | 0.932, 0.950 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 12687, 3173, 2997 |
Rint | 0.161 |
(sin θ/λ)max (Å−1) | 0.599 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.066, 0.170, 1.05 |
No. of reflections | 3173 |
No. of parameters | 222 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.56, −0.70 |
Absolute structure | Flack (1983), 1334 Fiedel pairs |
Absolute structure parameter | 0.01 (12) |
Computer programs: SMART (Bruker, 2007), SAINT (Bruker, 2007), SHELXTL (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···O2i | 0.86 | 2.15 | 2.925 (4) | 149 |
O2—H2A···O3ii | 0.82 | 2.02 | 2.794 (3) | 156 |
O3—H3A···O4ii | 0.82 | 1.88 | 2.646 (3) | 155 |
O4—H4A···O6iii | 0.82 | 1.82 | 2.637 (4) | 176 |
O6—H6···N2 | 0.82 | 1.98 | 2.795 (4) | 175 |
C8—H8A···O5iv | 0.93 | 2.48 | 3.329 (4) | 151 |
C12—H12C···O1v | 0.96 | 2.58 | 3.520 (4) | 165 |
C15—H15C···O3vi | 0.96 | 2.56 | 3.367 (5) | 142 |
Symmetry codes: (i) x+1, y, z; (ii) x−1/2, −y+1/2, −z; (iii) −x+3/2, −y, z−1/2; (iv) −x+2, y+1/2, −z+1/2; (v) x+1/2, −y+1/2, −z+1; (vi) −x+2, y−1/2, −z+1/2. |
Acknowledgements
This project was sponsored by the Cultivation Program of Young and Middle-aged Academic Leaders in Zhejiang Higher Education Institutions, the Natural Science Foundation of Ningbo City (Nos. 2009 A610047 and 2010 A610027) and the K. C. Wong Magna Fund of Ningbo University. We thank Professor X. Li for help with the structural analysis.
References
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Thioglycosides are widely employed as biological inhibitors, glycosyl donors and enzyme resistant ligands for affinity chromatography (Ashry et al., 2006). Here we report the crystal structure of the title compound (Scheme 1). The title compound crystallizes exclusively as the β anomer. The molecule contains a pyranose ring and a pyridine ring linked by a sulfur atom. The pyranose ring has a normal chair conformation, similar to that found in an α-D-glucosaminide (Harrison et al. 2007). The extensive hydrogen bonding network is present in the crystal structure, involving O—H···O, O—H···N and N—H···O hydrogen bonding (Table 1). Weak intermolecular C—H···O hydrogen bonding is also present in the crystal structure.