organic compounds
rac-Methyl 4-azido-3-hydroxy-3-(2-nitrophenyl)butanoate
aInstitute of Chemistry, University of Neuchâtel, Rue Emile-Argand 11, CH-2009 Neuchâtel, Switzerland, and bInstitute of Physics, University of Neuchâtel, Rue Emile-Argand 11, CH-2009 Neuchâtel, Switzerland
*Correspondence e-mail: reinhard.neier@unine.ch
In the title compound, C11H12N4O5, the mean plane through the nitro substituent on the benzene ring is inclined to the benzene mean plane by 85.8 (2)°, which avoids steric interactions with the ortho substituents. The hydroxy group is involved in bifurcated hydrogen bonds. The first is an intramolecular O—H⋯O hydrogen bond, involving the ester carbonyl O atom, which gives rise to the formation of a boat-like hydrogen-bonded chelate ring. The second is an intermolecular O—H⋯N hydrogen bond involving the first N atom of the azide group of a symmetry-related molecule. In the this leads to the formation of a polmer chain extending in the c-axis direction.
Related literature
For literature related to the antitumor properties of rhazinilam, see: Bonneau et al. (2007). For literature related to the synthesis and structure–activity relationships of rhazinilam analogues, see: Decor et al. (2006); Baudoin et al. (2002); Ghosez et al. (2001); Rubio & Bornmann (2001); Dupont et al. (2000, 1999); Alazard et al. (1996). For details of the Mukaiyama reaction, see: Mukaiyama et al. (1974). For literature related to the synthesis of pyrrolinone precursors, see: Vallat (2004); Vallat et al. (2009).
Experimental
Crystal data
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Data collection
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Refinement
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Data collection: EXPOSE in IPDS Software (Stoe & Cie, 2000); cell CELL in IPDS Software; data reduction: INTEGRATE in IPDS Software; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97.
Supporting information
10.1107/S1600536808043857/lh2749sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536808043857/lh2749Isup2.hkl
Under an atmosphere of Ar, (1-methoxyvinyloxy)trimethylsilane (1.06 g, 7.3 mmol) was dissolved in dry CH2Cl2 (15 ml) and the temperature lowered to 243K. 2-Azido-1- (2-nitrophenyl)ethanone (0.5 g, 2.4 mmol) dissolved in dry CH2Cl2 (6 ml) was added to the reaction mixture dropwise. A solution of TiCl4 (0.13 ml, 1.2 mmol), freshly distilled over polyvinylpyridine, in dry CH2Cl2 (4 ml), was added slowly. The solution became immediately red and then dark red. The reaction mixture was stirred at 243K for 15 min and then at 258K for 30 min. The cold mixture was then poured into an aqueous solution of 2 N NaOH (2.4 ml) and extracted with chloroform. The combined organic layers were washed with brine, dried over MgSO4 and concentrated under vacuum. Purification of the residue by flash
(silica gel, CH2Cl2) followed by crystallization (ether/hexane) gave a white solid (Yield 76%). Colourless plate-like crystals, suitable for X-ray analysis, were obtained by slow evaporation of a solution in ether/hexane (v:v = 1:1)The H-atoms were located from difference Fourier maps and freely refined: O—H = 0.825 (19) Å, C—H = 0.91 (3) - 1.02 (2) Å.
Data collection: EXPOSE in IPDS Software (Stoe & Cie, 2000); cell
CELL in IPDS Software (Stoe & Cie, 2000); data reduction: INTEGRATE in IPDS Software (Stoe & Cie, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).C11H12N4O5 | F(000) = 584 |
Mr = 280.25 | Dx = 1.463 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 5300 reflections |
a = 9.4772 (11) Å | θ = 2.6–25.8° |
b = 14.0710 (12) Å | µ = 0.12 mm−1 |
c = 10.1861 (12) Å | T = 153 K |
β = 110.496 (13)° | Plate, colourless |
V = 1272.4 (2) Å3 | 0.40 × 0.30 × 0.30 mm |
Z = 4 |
Stoe IPDS diffractometer | 1587 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.074 |
Graphite monochromator | θmax = 25.9°, θmin = 2.5° |
ϕ oscillation scans | h = −11→11 |
8743 measured reflections | k = −17→17 |
2451 independent reflections | l = −12→12 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.036 | All H-atom parameters refined |
wR(F2) = 0.088 | w = 1/[σ2(Fo2) + (0.0487P)2] where P = (Fo2 + 2Fc2)/3 |
S = 0.87 | (Δ/σ)max < 0.001 |
2451 reflections | Δρmax = 0.23 e Å−3 |
230 parameters | Δρmin = −0.21 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0087 (18) |
C11H12N4O5 | V = 1272.4 (2) Å3 |
Mr = 280.25 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 9.4772 (11) Å | µ = 0.12 mm−1 |
b = 14.0710 (12) Å | T = 153 K |
c = 10.1861 (12) Å | 0.40 × 0.30 × 0.30 mm |
β = 110.496 (13)° |
Stoe IPDS diffractometer | 1587 reflections with I > 2σ(I) |
8743 measured reflections | Rint = 0.074 |
2451 independent reflections |
R[F2 > 2σ(F2)] = 0.036 | 0 restraints |
wR(F2) = 0.088 | All H-atom parameters refined |
S = 0.87 | Δρmax = 0.23 e Å−3 |
2451 reflections | Δρmin = −0.21 e Å−3 |
230 parameters |
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles |
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 | ||
O1 | 0.32528 (17) | −0.00702 (10) | 0.18798 (17) | 0.0599 (6) | |
O2 | 0.39794 (16) | 0.06178 (11) | 0.39169 (15) | 0.0653 (5) | |
O3 | 0.20867 (11) | 0.19457 (8) | 0.17217 (12) | 0.0272 (4) | |
O4 | 0.13982 (13) | 0.26155 (8) | 0.41688 (11) | 0.0370 (4) | |
O5 | −0.07815 (12) | 0.34053 (9) | 0.35528 (11) | 0.0372 (4) | |
N1 | 0.30233 (17) | 0.02628 (11) | 0.28967 (16) | 0.0424 (5) | |
N2 | −0.03288 (14) | 0.22705 (10) | −0.10334 (13) | 0.0321 (4) | |
N3 | 0.08103 (17) | 0.25861 (10) | −0.12165 (13) | 0.0340 (5) | |
N4 | 0.17267 (19) | 0.29547 (14) | −0.15016 (17) | 0.0535 (6) | |
C1 | 0.1474 (2) | 0.01792 (12) | 0.29231 (16) | 0.0330 (5) | |
C2 | 0.1235 (3) | −0.06299 (14) | 0.35997 (18) | 0.0472 (7) | |
C3 | −0.0179 (3) | −0.07913 (17) | 0.3639 (2) | 0.0574 (9) | |
C4 | −0.1334 (3) | −0.01579 (16) | 0.3016 (2) | 0.0524 (8) | |
C5 | −0.1057 (2) | 0.06436 (14) | 0.23568 (19) | 0.0391 (6) | |
C6 | 0.03622 (18) | 0.08457 (11) | 0.22890 (15) | 0.0277 (5) | |
C7 | 0.05471 (16) | 0.17238 (11) | 0.14778 (15) | 0.0253 (5) | |
C8 | −0.01067 (19) | 0.14495 (13) | −0.00855 (16) | 0.0293 (5) | |
C9 | 0.02297 (16) | 0.28584 (12) | 0.32851 (16) | 0.0263 (5) | |
C10 | −0.02665 (18) | 0.25954 (13) | 0.17665 (17) | 0.0293 (5) | |
C11 | −0.0434 (3) | 0.36959 (19) | 0.4988 (2) | 0.0489 (8) | |
H2 | 0.210 (2) | −0.1090 (17) | 0.404 (2) | 0.062 (6)* | |
H3 | −0.039 (3) | −0.1301 (18) | 0.409 (2) | 0.071 (7)* | |
H3O | 0.242 (2) | 0.2153 (14) | 0.253 (2) | 0.043 (6)* | |
H4 | −0.235 (3) | −0.0267 (16) | 0.307 (2) | 0.064 (6)* | |
H5 | −0.183 (2) | 0.1080 (15) | 0.186 (2) | 0.053 (6)* | |
H8A | 0.0553 (19) | 0.0951 (13) | −0.0298 (16) | 0.032 (4)* | |
H8B | −0.113 (2) | 0.1209 (12) | −0.0262 (17) | 0.035 (4)* | |
H10A | −0.0016 (19) | 0.3118 (13) | 0.1284 (17) | 0.037 (5)* | |
H10B | −0.133 (2) | 0.2515 (14) | 0.1442 (19) | 0.047 (5)* | |
H11A | −0.035 (3) | 0.315 (2) | 0.560 (3) | 0.084 (8)* | |
H11B | −0.128 (3) | 0.4060 (17) | 0.497 (2) | 0.067 (7)* | |
H11C | 0.044 (3) | 0.4065 (17) | 0.525 (2) | 0.062 (6)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0611 (9) | 0.0464 (10) | 0.0834 (11) | 0.0058 (7) | 0.0395 (8) | −0.0098 (8) |
O2 | 0.0494 (8) | 0.0595 (10) | 0.0596 (9) | 0.0016 (7) | −0.0151 (7) | 0.0141 (8) |
O3 | 0.0215 (6) | 0.0308 (7) | 0.0259 (6) | −0.0016 (5) | 0.0039 (4) | −0.0006 (5) |
O4 | 0.0298 (6) | 0.0426 (8) | 0.0307 (6) | 0.0080 (5) | 0.0006 (5) | −0.0054 (5) |
O5 | 0.0262 (6) | 0.0445 (8) | 0.0401 (7) | 0.0067 (5) | 0.0108 (5) | −0.0081 (5) |
N1 | 0.0440 (9) | 0.0276 (9) | 0.0482 (10) | 0.0104 (7) | 0.0069 (8) | 0.0091 (7) |
N2 | 0.0236 (7) | 0.0413 (9) | 0.0279 (7) | −0.0005 (6) | 0.0048 (5) | 0.0044 (6) |
N3 | 0.0352 (8) | 0.0377 (9) | 0.0257 (7) | 0.0053 (7) | 0.0063 (6) | 0.0049 (6) |
N4 | 0.0431 (10) | 0.0645 (12) | 0.0571 (10) | −0.0023 (9) | 0.0228 (8) | 0.0169 (9) |
C1 | 0.0452 (10) | 0.0269 (10) | 0.0264 (8) | −0.0012 (8) | 0.0118 (7) | −0.0025 (7) |
C2 | 0.0829 (15) | 0.0269 (11) | 0.0336 (10) | −0.0010 (11) | 0.0226 (10) | 0.0010 (8) |
C3 | 0.109 (2) | 0.0334 (13) | 0.0435 (12) | −0.0247 (13) | 0.0437 (13) | −0.0082 (9) |
C4 | 0.0721 (15) | 0.0475 (14) | 0.0494 (12) | −0.0280 (12) | 0.0360 (11) | −0.0173 (10) |
C5 | 0.0432 (10) | 0.0397 (11) | 0.0370 (9) | −0.0133 (9) | 0.0174 (8) | −0.0097 (9) |
C6 | 0.0341 (9) | 0.0255 (9) | 0.0229 (7) | −0.0046 (7) | 0.0091 (7) | −0.0049 (6) |
C7 | 0.0201 (7) | 0.0260 (9) | 0.0269 (8) | −0.0015 (6) | 0.0045 (6) | 0.0003 (6) |
C8 | 0.0272 (9) | 0.0297 (10) | 0.0272 (8) | −0.0021 (7) | 0.0047 (7) | −0.0003 (7) |
C9 | 0.0230 (8) | 0.0223 (9) | 0.0322 (8) | −0.0018 (7) | 0.0080 (7) | 0.0002 (7) |
C10 | 0.0226 (8) | 0.0299 (10) | 0.0304 (9) | 0.0017 (7) | 0.0032 (7) | 0.0012 (7) |
C11 | 0.0456 (12) | 0.0569 (15) | 0.0476 (12) | 0.0028 (11) | 0.0207 (10) | −0.0157 (11) |
O1—N1 | 1.224 (2) | C5—C6 | 1.400 (3) |
O2—N1 | 1.221 (2) | C6—C7 | 1.530 (2) |
O3—C7 | 1.426 (2) | C7—C10 | 1.531 (2) |
O4—C9 | 1.206 (2) | C7—C8 | 1.542 (2) |
O5—C9 | 1.330 (2) | C9—C10 | 1.497 (2) |
O5—C11 | 1.441 (2) | C2—H2 | 1.02 (2) |
O3—H3O | 0.825 (19) | C3—H3 | 0.91 (2) |
N1—C1 | 1.483 (3) | C4—H4 | 1.00 (3) |
N2—C8 | 1.473 (2) | C5—H5 | 0.95 (2) |
N2—N3 | 1.240 (2) | C8—H8A | 1.012 (19) |
N3—N4 | 1.133 (2) | C8—H8B | 0.983 (19) |
C1—C6 | 1.389 (2) | C10—H10A | 0.959 (18) |
C1—C2 | 1.390 (3) | C10—H10B | 0.95 (2) |
C2—C3 | 1.374 (4) | C11—H11A | 0.98 (3) |
C3—C4 | 1.382 (4) | C11—H11B | 0.95 (3) |
C4—C5 | 1.384 (3) | C11—H11C | 0.93 (3) |
C9—O5—C11 | 116.57 (15) | O4—C9—C10 | 125.11 (15) |
C7—O3—H3O | 105.2 (14) | C7—C10—C9 | 113.54 (14) |
O1—N1—O2 | 125.32 (18) | C1—C2—H2 | 119.6 (12) |
O2—N1—C1 | 117.49 (15) | C3—C2—H2 | 121.7 (12) |
O1—N1—C1 | 117.11 (15) | C2—C3—H3 | 122.3 (18) |
N3—N2—C8 | 116.57 (14) | C4—C3—H3 | 117.5 (18) |
N2—N3—N4 | 171.07 (18) | C3—C4—H4 | 120.1 (13) |
N1—C1—C6 | 122.19 (15) | C5—C4—H4 | 120.3 (13) |
C2—C1—C6 | 123.7 (2) | C4—C5—H5 | 122.8 (13) |
N1—C1—C2 | 114.10 (18) | C6—C5—H5 | 114.6 (12) |
C1—C2—C3 | 118.7 (2) | N2—C8—H8A | 111.1 (10) |
C2—C3—C4 | 120.3 (2) | N2—C8—H8B | 104.2 (10) |
C3—C4—C5 | 119.6 (3) | C7—C8—H8A | 109.8 (9) |
C4—C5—C6 | 122.56 (19) | C7—C8—H8B | 106.8 (10) |
C1—C6—C7 | 125.77 (16) | H8A—C8—H8B | 111.5 (15) |
C5—C6—C7 | 118.97 (15) | C7—C10—H10A | 106.5 (11) |
C1—C6—C5 | 115.17 (16) | C7—C10—H10B | 112.4 (12) |
O3—C7—C6 | 112.72 (13) | C9—C10—H10A | 107.2 (10) |
O3—C7—C10 | 110.15 (13) | C9—C10—H10B | 107.4 (11) |
C6—C7—C8 | 105.96 (13) | H10A—C10—H10B | 109.6 (16) |
O3—C7—C8 | 104.56 (13) | O5—C11—H11A | 111.3 (17) |
C8—C7—C10 | 110.58 (13) | O5—C11—H11B | 104.1 (12) |
C6—C7—C10 | 112.49 (13) | O5—C11—H11C | 108.2 (13) |
N2—C8—C7 | 113.22 (14) | H11A—C11—H11B | 109 (2) |
O4—C9—O5 | 123.38 (14) | H11A—C11—H11C | 113 (2) |
O5—C9—C10 | 111.52 (14) | H11B—C11—H11C | 111 (2) |
C11—O5—C9—O4 | −1.0 (3) | C4—C5—C6—C1 | 0.5 (3) |
C11—O5—C9—C10 | 179.32 (17) | C4—C5—C6—C7 | 177.10 (16) |
O1—N1—C1—C2 | 91.99 (19) | C1—C6—C7—O3 | −15.3 (2) |
O1—N1—C1—C6 | −86.4 (2) | C1—C6—C7—C8 | 98.52 (18) |
O2—N1—C1—C2 | −84.7 (2) | C1—C6—C7—C10 | −140.54 (16) |
O2—N1—C1—C6 | 96.86 (19) | C5—C6—C7—O3 | 168.49 (14) |
N3—N2—C8—C7 | 78.29 (18) | C5—C6—C7—C8 | −77.74 (18) |
N1—C1—C2—C3 | −177.75 (16) | C5—C6—C7—C10 | 43.21 (19) |
C6—C1—C2—C3 | 0.6 (3) | O3—C7—C8—N2 | −73.41 (17) |
N1—C1—C6—C5 | 177.43 (15) | C6—C7—C8—N2 | 167.29 (14) |
N1—C1—C6—C7 | 1.1 (2) | C10—C7—C8—N2 | 45.12 (19) |
C2—C1—C6—C5 | −0.8 (2) | O3—C7—C10—C9 | −69.34 (17) |
C2—C1—C6—C7 | −177.19 (15) | C6—C7—C10—C9 | 57.34 (19) |
C1—C2—C3—C4 | 0.0 (3) | C8—C7—C10—C9 | 175.59 (14) |
C2—C3—C4—C5 | −0.3 (3) | O4—C9—C10—C7 | 19.8 (2) |
C3—C4—C5—C6 | 0.1 (3) | O5—C9—C10—C7 | −160.54 (14) |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3O···O4 | 0.825 (19) | 2.30 (2) | 2.9439 (16) | 135.5 (18) |
O3—H3O···N2i | 0.825 (19) | 2.27 (2) | 2.9193 (18) | 135.6 (18) |
C10—H10B···O4ii | 0.95 (2) | 2.557 (19) | 3.350 (2) | 141.0 (15) |
C11—H11B···O1iii | 0.95 (3) | 2.57 (2) | 3.268 (3) | 130.9 (16) |
Symmetry codes: (i) x+1/2, −y+1/2, z+1/2; (ii) x−1/2, −y+1/2, z−1/2; (iii) x−1/2, −y+1/2, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C11H12N4O5 |
Mr | 280.25 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 153 |
a, b, c (Å) | 9.4772 (11), 14.0710 (12), 10.1861 (12) |
β (°) | 110.496 (13) |
V (Å3) | 1272.4 (2) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.40 × 0.30 × 0.30 |
Data collection | |
Diffractometer | Stoe IPDS diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8743, 2451, 1587 |
Rint | 0.074 |
(sin θ/λ)max (Å−1) | 0.615 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.036, 0.088, 0.87 |
No. of reflections | 2451 |
No. of parameters | 230 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.23, −0.21 |
Computer programs: EXPOSE in IPDS Software (Stoe & Cie, 2000), CELL in IPDS Software (Stoe & Cie, 2000), INTEGRATE in IPDS Software (Stoe & Cie, 2000), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and Mercury (Macrae et al., 2006).
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3O···O4 | 0.825 (19) | 2.30 (2) | 2.9439 (16) | 135.5 (18) |
O3—H3O···N2i | 0.825 (19) | 2.27 (2) | 2.9193 (18) | 135.6 (18) |
C10—H10B···O4ii | 0.95 (2) | 2.557 (19) | 3.350 (2) | 141.0 (15) |
C11—H11B···O1iii | 0.95 (3) | 2.57 (2) | 3.268 (3) | 130.9 (16) |
Symmetry codes: (i) x+1/2, −y+1/2, z+1/2; (ii) x−1/2, −y+1/2, z−1/2; (iii) x−1/2, −y+1/2, z+1/2. |
Acknowledgements
This work was partially financed by the Swiss National Science Foundation.
References
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Rhazinilam, a natural product, has been shown to possess antitumoral properties. It induces in vitro spiralization of microtubules [vinblastin effect] and inhibits the disassembly of these microtubules [paclitaxel effect](Bonneau et al., 2007). It has shown significant in vitro cytotoxicity towards various cancer cells, but it is not active in vivo. Several groups have been interested in synthesizing and studying the structure-activity relationship of rhazinilam analogues (Decor et al., 2006; Baudoin et al., 2002; Ghosez et al., 2001; Rubia & Bornmann, 2001; Dupont et al., 2000; Dupont et al., 1999; Alazard et al., 1996).
In the synthesis of Rhazinilam analogues developed in our group the Mukaiyama reaction, a versatile synthetic tool in organic chemistry, is a key step reaction (Mukaiyama et al., 1974). In one of our retrosynthetic approaches (1-methoxyvinyloxy)trimethysilane was used as a nucleophile, 2-azido-1-(2-nitrophenyl)ethanone as an electrophile and TiCl4 as a Lewis acid, to synthesize the title hydroxyester, in high yield. This hydroxyester is a suitable precursor for the formation of the pyrrolinone required for the next step in the synthesis of Rhazinilam analogues (Vallat, 2004; Vallat et al., 2009).
The molecular structure of the title compound is illustrated in Fig. 1. The bond distances and angles are normal. The mean plane through the nitro group is inclined to the benzene mean plane by 85.8 (2)°, so avoiding steric interactions with the ortho substituents. The hydroxyl group (O3) is involved in bifurcated hydrogen bonds (Table 1). The first is an intramolecular O—H···O hydrogen bond, involving the ester carbonyl O-atom (O4), and gives rise to the formation of a boat-like hydrogen bonded chelate ring. The second is an intermolecular O—H···N hydrogen bond involving the first N-atom (N2) of the azide group (Table 1). This leads to the formation of a polymer chain extending in the c direction. (Fig. 2). There are also two weak intermolecular C—H···O interactions involving atoms O1 and O4 and the hydrogen atoms of the butanoate moiety (Table 1).