organic compounds
Methyl 1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylate monohydrate
aDepartment of Chemistry, Gomal University, Dera Ismail Khan, Pakistan, bApplied Chemistry Research Centre, Pakistan Council of Scientific and Industrial Research Laboratories Complex, Lahore 54600, Pakistan, cDepartment of Chemistry, University of Gujrat 50781, Gujrat, Pakistan, and dMaterials Chemistry Laboratory, Department of Chemistry, GC University, Lahore 54000, Pakistan
*Correspondence e-mail: rehman_pcsir@hotmail.com
In the structure of the title compound, C13H14N2O3·H2O, all atoms of the organic molecule except the terminal methyl group of the ethyl group attached to the N atom of the pyridinone ring are roughly coplanar, with an r.m.s. deviation of 0.0897 Å. In the crystal, C—H⋯O contacts link pairs of naphthyridine molecules into head-to-tail dimers. These are joined by strong O—H⋯O hydrogen bonds from the water molecules into infinite chains along the a axis.
Related literature
For the coordination properties of 1,8-naphthyridine ligands, see: Gavrilova & Bosnich (2004); Mintert & Sheldrick (1995). For their biological activity, see: Chen et al. (2001); Ferrarini et al. (2000); Roma et al. (2000). For related structures, see: Deeba, Khan, Zia-ur-Rehman, Çaylak & Şahin (2009); Deeba, Khan, Zia-ur-Rehman, Şahin & Çaylak (2009). For graph-set notation, see: Bernstein et al. (1995).
Experimental
Crystal data
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Data collection
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Refinement
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Data collection: APEX2 (Bruker, 2007); cell SAINT (Bruker, 2007); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and PLATON (Spek, 2009); software used to prepare material for publication: WinGX (Farrugia, 1999) and PLATON.
Supporting information
10.1107/S1600536812004333/sj5191sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812004333/sj5191Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812004333/sj5191Isup3.cml
A mixture of 1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylic acid (100.0 mmol; 23.22 g) and thionyl chloride (50 ml) was refluxed for a period of 4 h followed by distillation (under reduced pressure) of the excess thionyl chloride. After complete removal of thionyl chloride, methanol (100 ml) was slowly added and stirred for two hours followed by the addition of ice cooled water (300 ml). The contents were washed with aqueous sodium carbonate (0.5 M) and water respectively followed by crystallization from methanol to give suitable crystals. Yield: 92%.
All C-bonded H-atoms were positioned in an idealized geometry, with C—H = 0.95Å for aromatic CH and C—H =0.98Å for the methyl group. U(H) was set to 1.2Ueq for all Caromatic and 1.5Ueq for the Cmethyl & oxygen atoms. The H atoms of the water molecule were located in a difference Fourier map and refined freely with U(H) = 1.5Ueq(O).
Data collection: APEX2 (Bruker, 2007); cell
SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and PLATON (Spek, 2009); software used to prepare material for publication: WinGX (Farrugia, 1999) and PLATON (Spek, 2009).Fig. 1. The structure of (I) with 50% displacement ellipsoids. | |
Fig. 2. A crystal packing plot parallel to a with hydrogen bonds drawn as dashed lines. |
C13H14N2O3·H2O | F(000) = 560 |
Mr = 264.28 | Dx = 1.386 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 3082 reflections |
a = 4.6989 (1) Å | θ = 2.5–27.9° |
b = 23.7246 (7) Å | µ = 0.10 mm−1 |
c = 11.3635 (3) Å | T = 296 K |
β = 91.646 (1)° | Needle, white |
V = 1266.27 (6) Å3 | 0.19 × 0.09 × 0.07 mm |
Z = 4 |
Bruker Kappa APEXII CCD diffractometer | 2152 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.026 |
Graphite monochromator | θmax = 28.3°, θmin = 1.7° |
ϕ and ω scans | h = −6→6 |
12165 measured reflections | k = −29→31 |
3128 independent reflections | l = −14→15 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.047 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.163 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.98 | w = 1/[σ2(Fo2) + (0.0956P)2 + 0.2245P] where P = (Fo2 + 2Fc2)/3 |
3128 reflections | (Δ/σ)max < 0.001 |
181 parameters | Δρmax = 0.27 e Å−3 |
0 restraints | Δρmin = −0.18 e Å−3 |
C13H14N2O3·H2O | V = 1266.27 (6) Å3 |
Mr = 264.28 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 4.6989 (1) Å | µ = 0.10 mm−1 |
b = 23.7246 (7) Å | T = 296 K |
c = 11.3635 (3) Å | 0.19 × 0.09 × 0.07 mm |
β = 91.646 (1)° |
Bruker Kappa APEXII CCD diffractometer | 2152 reflections with I > 2σ(I) |
12165 measured reflections | Rint = 0.026 |
3128 independent reflections |
R[F2 > 2σ(F2)] = 0.047 | 0 restraints |
wR(F2) = 0.163 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.98 | Δρmax = 0.27 e Å−3 |
3128 reflections | Δρmin = −0.18 e Å−3 |
181 parameters |
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'s 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 > 2σ(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 | ||
C1 | 0.6664 (3) | 0.38694 (7) | 0.77501 (14) | 0.0320 (4) | |
C2 | 0.7843 (3) | 0.42644 (7) | 0.69281 (14) | 0.0309 (4) | |
C3 | 0.6891 (3) | 0.42666 (7) | 0.57746 (15) | 0.0328 (4) | |
H3 | 0.7687 | 0.4530 | 0.5274 | 0.039* | |
C4 | 0.3706 (3) | 0.35103 (7) | 0.60267 (14) | 0.0307 (4) | |
C5 | 0.4552 (3) | 0.34821 (7) | 0.72122 (14) | 0.0310 (4) | |
C6 | 0.3282 (4) | 0.30618 (7) | 0.78758 (16) | 0.0381 (4) | |
H6 | 0.3764 | 0.3023 | 0.8671 | 0.046* | |
C7 | 0.1332 (4) | 0.27070 (7) | 0.73569 (16) | 0.0398 (4) | |
H7 | 0.0481 | 0.2426 | 0.7796 | 0.048* | |
C8 | 0.0627 (3) | 0.27700 (7) | 0.61615 (15) | 0.0349 (4) | |
C9 | 1.0005 (3) | 0.46984 (7) | 0.72231 (14) | 0.0330 (4) | |
C10 | 1.2543 (4) | 0.51876 (9) | 0.87123 (18) | 0.0525 (5) | |
H10A | 1.4364 | 0.5102 | 0.8395 | 0.079* | |
H10B | 1.2713 | 0.5202 | 0.9556 | 0.079* | |
H10C | 1.1896 | 0.5546 | 0.8418 | 0.079* | |
C11 | −0.1477 (4) | 0.23821 (8) | 0.55685 (18) | 0.0448 (4) | |
H11A | −0.2117 | 0.2543 | 0.4833 | 0.067* | |
H11B | −0.3074 | 0.2329 | 0.6065 | 0.067* | |
H11C | −0.0590 | 0.2025 | 0.5428 | 0.067* | |
C12 | 0.3991 (4) | 0.39784 (8) | 0.40625 (15) | 0.0421 (4) | |
H12A | 0.4415 | 0.4358 | 0.3801 | 0.051* | |
H12B | 0.1945 | 0.3926 | 0.3994 | 0.051* | |
C13 | 0.5409 (5) | 0.35647 (9) | 0.32742 (18) | 0.0560 (6) | |
H19A | 0.4711 | 0.3616 | 0.2479 | 0.084* | |
H19B | 0.4995 | 0.3188 | 0.3527 | 0.084* | |
H19C | 0.7430 | 0.3625 | 0.3311 | 0.084* | |
N1 | 0.1777 (3) | 0.31671 (6) | 0.55030 (12) | 0.0346 (3) | |
N2 | 0.4905 (3) | 0.39199 (6) | 0.53125 (12) | 0.0331 (3) | |
O1 | 0.7306 (3) | 0.38354 (6) | 0.88110 (11) | 0.0449 (4) | |
O2 | 1.1179 (3) | 0.49770 (6) | 0.64973 (12) | 0.0529 (4) | |
O3 | 1.0520 (3) | 0.47558 (6) | 0.83641 (11) | 0.0483 (4) | |
O4 | 0.2506 (4) | 0.38795 (8) | 0.03949 (15) | 0.0678 (5) | |
H4B | 0.099 (7) | 0.3912 (13) | −0.025 (3) | 0.102* | |
H4A | 0.394 (7) | 0.3865 (14) | −0.003 (3) | 0.102* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0303 (8) | 0.0350 (9) | 0.0306 (8) | 0.0031 (6) | −0.0017 (6) | 0.0001 (7) |
C2 | 0.0285 (8) | 0.0320 (8) | 0.0322 (8) | 0.0010 (6) | −0.0005 (6) | −0.0023 (7) |
C3 | 0.0334 (8) | 0.0311 (8) | 0.0339 (9) | −0.0009 (6) | 0.0000 (6) | 0.0004 (7) |
C4 | 0.0294 (8) | 0.0304 (8) | 0.0321 (8) | 0.0033 (6) | −0.0007 (6) | −0.0006 (6) |
C5 | 0.0301 (8) | 0.0305 (8) | 0.0324 (8) | 0.0020 (6) | 0.0002 (6) | 0.0006 (7) |
C6 | 0.0403 (9) | 0.0399 (10) | 0.0341 (9) | −0.0007 (7) | 0.0005 (7) | 0.0025 (7) |
C7 | 0.0406 (9) | 0.0368 (9) | 0.0421 (10) | −0.0045 (7) | 0.0036 (7) | 0.0030 (8) |
C8 | 0.0291 (8) | 0.0325 (8) | 0.0433 (9) | 0.0011 (6) | 0.0029 (7) | −0.0062 (7) |
C9 | 0.0301 (8) | 0.0349 (9) | 0.0338 (9) | 0.0015 (7) | −0.0019 (6) | −0.0006 (7) |
C10 | 0.0581 (12) | 0.0563 (12) | 0.0427 (11) | −0.0220 (10) | −0.0066 (9) | −0.0083 (9) |
C11 | 0.0428 (10) | 0.0412 (10) | 0.0505 (11) | −0.0069 (8) | 0.0010 (8) | −0.0079 (8) |
C12 | 0.0480 (10) | 0.0434 (10) | 0.0342 (9) | −0.0084 (8) | −0.0126 (8) | 0.0078 (8) |
C13 | 0.0709 (14) | 0.0609 (13) | 0.0361 (10) | −0.0118 (11) | −0.0036 (9) | −0.0068 (9) |
N1 | 0.0317 (7) | 0.0341 (7) | 0.0377 (8) | −0.0003 (6) | −0.0017 (6) | −0.0028 (6) |
N2 | 0.0348 (7) | 0.0347 (8) | 0.0296 (7) | −0.0011 (6) | −0.0041 (5) | 0.0011 (6) |
O1 | 0.0472 (7) | 0.0558 (8) | 0.0313 (7) | −0.0130 (6) | −0.0069 (5) | 0.0055 (6) |
O2 | 0.0583 (8) | 0.0615 (9) | 0.0388 (7) | −0.0266 (7) | −0.0020 (6) | 0.0047 (6) |
O3 | 0.0571 (8) | 0.0544 (8) | 0.0331 (7) | −0.0227 (6) | −0.0046 (6) | −0.0034 (6) |
O4 | 0.0642 (10) | 0.0912 (13) | 0.0477 (9) | −0.0087 (9) | −0.0003 (8) | 0.0004 (8) |
C1—O1 | 1.237 (2) | C9—O3 | 1.319 (2) |
C1—C2 | 1.445 (2) | C10—O3 | 1.445 (2) |
C1—C5 | 1.472 (2) | C10—H10A | 0.9600 |
C2—C3 | 1.373 (2) | C10—H10B | 0.9600 |
C2—C9 | 1.478 (2) | C10—H10C | 0.9600 |
C3—N2 | 1.340 (2) | C11—H11A | 0.9600 |
C3—H3 | 0.9300 | C11—H11B | 0.9600 |
C4—N1 | 1.344 (2) | C11—H11C | 0.9600 |
C4—N2 | 1.395 (2) | C12—N2 | 1.479 (2) |
C4—C5 | 1.395 (2) | C12—C13 | 1.498 (3) |
C5—C6 | 1.395 (2) | C12—H12A | 0.9700 |
C6—C7 | 1.366 (2) | C12—H12B | 0.9700 |
C6—H6 | 0.9300 | C13—H19A | 0.9600 |
C7—C8 | 1.397 (2) | C13—H19B | 0.9600 |
C7—H7 | 0.9300 | C13—H19C | 0.9600 |
C8—N1 | 1.328 (2) | O4—H4B | 1.01 (4) |
C8—C11 | 1.497 (2) | O4—H4A | 0.84 (3) |
C9—O2 | 1.203 (2) | ||
O1—C1—C2 | 125.82 (15) | H10A—C10—H10B | 109.5 |
O1—C1—C5 | 120.43 (15) | O3—C10—H10C | 109.5 |
C2—C1—C5 | 113.75 (14) | H10A—C10—H10C | 109.5 |
C3—C2—C1 | 119.95 (14) | H10B—C10—H10C | 109.5 |
C3—C2—C9 | 114.64 (14) | C8—C11—H11A | 109.5 |
C1—C2—C9 | 125.38 (14) | C8—C11—H11B | 109.5 |
N2—C3—C2 | 125.18 (15) | H11A—C11—H11B | 109.5 |
N2—C3—H3 | 117.4 | C8—C11—H11C | 109.5 |
C2—C3—H3 | 117.4 | H11A—C11—H11C | 109.5 |
N1—C4—N2 | 116.27 (14) | H11B—C11—H11C | 109.5 |
N1—C4—C5 | 124.62 (15) | N2—C12—C13 | 113.02 (16) |
N2—C4—C5 | 119.10 (14) | N2—C12—H12A | 109.0 |
C6—C5—C4 | 116.23 (15) | C13—C12—H12A | 109.0 |
C6—C5—C1 | 121.03 (15) | N2—C12—H12B | 109.0 |
C4—C5—C1 | 122.75 (14) | C13—C12—H12B | 109.0 |
C7—C6—C5 | 119.97 (16) | H12A—C12—H12B | 107.8 |
C7—C6—H6 | 120.0 | C12—C13—H19A | 109.5 |
C5—C6—H6 | 120.0 | C12—C13—H19B | 109.5 |
C6—C7—C8 | 119.43 (16) | H19A—C13—H19B | 109.5 |
C6—C7—H7 | 120.3 | C12—C13—H19C | 109.5 |
C8—C7—H7 | 120.3 | H19A—C13—H19C | 109.5 |
N1—C8—C7 | 122.34 (15) | H19B—C13—H19C | 109.5 |
N1—C8—C11 | 117.19 (16) | C8—N1—C4 | 117.42 (14) |
C7—C8—C11 | 120.48 (16) | C3—N2—C4 | 119.21 (14) |
O2—C9—O3 | 122.85 (15) | C3—N2—C12 | 119.92 (14) |
O2—C9—C2 | 123.56 (15) | C4—N2—C12 | 120.87 (13) |
O3—C9—C2 | 113.58 (14) | C9—O3—C10 | 116.29 (14) |
O3—C10—H10A | 109.5 | H4B—O4—H4A | 99 (3) |
O3—C10—H10B | 109.5 | ||
O1—C1—C2—C3 | −178.42 (16) | C3—C2—C9—O2 | −10.8 (2) |
C5—C1—C2—C3 | 2.3 (2) | C1—C2—C9—O2 | 171.14 (17) |
O1—C1—C2—C9 | −0.5 (3) | C3—C2—C9—O3 | 168.67 (15) |
C5—C1—C2—C9 | −179.75 (14) | C1—C2—C9—O3 | −9.3 (2) |
C1—C2—C3—N2 | −0.6 (2) | C7—C8—N1—C4 | 0.8 (2) |
C9—C2—C3—N2 | −178.77 (15) | C11—C8—N1—C4 | −178.85 (14) |
N1—C4—C5—C6 | 0.4 (2) | N2—C4—N1—C8 | 179.33 (14) |
N2—C4—C5—C6 | −179.72 (14) | C5—C4—N1—C8 | −0.8 (2) |
N1—C4—C5—C1 | −179.66 (14) | C2—C3—N2—C4 | −1.5 (2) |
N2—C4—C5—C1 | 0.2 (2) | C2—C3—N2—C12 | 177.86 (16) |
O1—C1—C5—C6 | −1.5 (2) | N1—C4—N2—C3 | −178.45 (14) |
C2—C1—C5—C6 | 177.77 (14) | C5—C4—N2—C3 | 1.7 (2) |
O1—C1—C5—C4 | 178.56 (15) | N1—C4—N2—C12 | 2.2 (2) |
C2—C1—C5—C4 | −2.1 (2) | C5—C4—N2—C12 | −177.68 (15) |
C4—C5—C6—C7 | 0.0 (2) | C13—C12—N2—C3 | 99.01 (19) |
C1—C5—C6—C7 | −179.89 (16) | C13—C12—N2—C4 | −81.6 (2) |
C5—C6—C7—C8 | 0.0 (3) | O2—C9—O3—C10 | 1.6 (3) |
C6—C7—C8—N1 | −0.4 (3) | C2—C9—O3—C10 | −177.90 (15) |
C6—C7—C8—C11 | 179.24 (16) |
D—H···A | D—H | H···A | D···A | D—H···A |
O4—H4B···O1i | 1.01 (4) | 2.02 (4) | 2.994 (2) | 163 (3) |
O4—H4A···O1ii | 0.84 (3) | 2.09 (3) | 2.928 (2) | 176 (3) |
O4—H4B···O3i | 1.01 (4) | 2.56 (3) | 3.224 (2) | 124 (2) |
C3—H3···O2iii | 0.93 | 2.40 | 3.293 (2) | 160 |
C11—H11C···O4iv | 0.96 | 2.59 | 3.539 (3) | 168 |
Symmetry codes: (i) x−1, y, z−1; (ii) x, y, z−1; (iii) −x+2, −y+1, −z+1; (iv) x, −y+1/2, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C13H14N2O3·H2O |
Mr | 264.28 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 296 |
a, b, c (Å) | 4.6989 (1), 23.7246 (7), 11.3635 (3) |
β (°) | 91.646 (1) |
V (Å3) | 1266.27 (6) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.19 × 0.09 × 0.07 |
Data collection | |
Diffractometer | Bruker Kappa APEXII CCD diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 12165, 3128, 2152 |
Rint | 0.026 |
(sin θ/λ)max (Å−1) | 0.667 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.047, 0.163, 0.98 |
No. of reflections | 3128 |
No. of parameters | 181 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.27, −0.18 |
Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997) and PLATON (Spek, 2009), WinGX (Farrugia, 1999) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
O4—H4B···O1i | 1.01 (4) | 2.02 (4) | 2.994 (2) | 163 (3) |
O4—H4A···O1ii | 0.84 (3) | 2.09 (3) | 2.928 (2) | 176 (3) |
O4—H4B···O3i | 1.01 (4) | 2.56 (3) | 3.224 (2) | 124 (2) |
C3—H3···O2iii | 0.93 | 2.40 | 3.293 (2) | 160.4 |
C11—H11C···O4iv | 0.96 | 2.59 | 3.539 (3) | 168.4 |
Symmetry codes: (i) x−1, y, z−1; (ii) x, y, z−1; (iii) −x+2, −y+1, −z+1; (iv) x, −y+1/2, z+1/2. |
Acknowledgements
The authors are grateful to the Higher Education Commission of Pakistan for the purchase of the X-ray Diffractometer at the Material Science Laboratories, Department of Chemistry, Government College University, Lahore, Pakistan.
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1,8-Naphthyridines have been cited in the literature for their interesting complexation properties due to the possibility of their bonding with metals in several coordination modes. These include monodendate, chelating bidendate and dinuclear bridging coordination (Gavrilova & Bosnich, 2004; Mintert & Sheldrick, 1995). These compounds are also biologically active with anti-bacterial (Chen et al., 2001), anti-hypertensive (Ferrarini et al., 2000) and anti-inflammatory (Roma et al., 2000) properties. In a continuation of our work on the synthesis, biological activity and crystal structures of various 1,8-naphthyridines (Deeba, Khan, Zia-ur-Rehman, Çaylak & Şahin, 2009; Deeba, Khan, Zia-ur-Rehman, Şahin & Çaylak, 2009), we herein report the synthesis and crystal structure of the title compound (I) (Fig. 1; Scheme 1).
The two fused aromatic rings (C1/C2/C3/N2/C4/C5) & (C4/C5/C6/C7/C8/N1) are co-planar with root mean square (r. m. s.) deviations of 0.0103 Å & 0.0023 Å and are twisted at a dihedral angle of 1.20 (10)°. The methyl ester unit attached to the pyridinone ring is also planar with an r. m. s. deviation of 0.0051 Å and oriented at dihedral angles of 10.97 (15)° & 11.41 (15)° with respect to the pyridinone and pyridine rings respectively. In addition, a solvent water molecule is also present and stabilizes the crystal structure through intermolecular hydrogen bonding interactions. The molecule exhibits C—H···O type weak intermolecular hydrogen bonding and forms dimers through the formation of ten membered ring motif R22(10) (Bernstein, et al., 1995). These are further connected via water molecules along the a axis to form infinite chains. On the other hand, one of the hydrogen atoms of water molecule is also involved in the formation of six membered ring motif with O atoms of pyridinone ring and the ester (Fig. 2, Table. 1).