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Acta Crystallogr Sect E Struct Rep Online. 2009 December 1; 65(Pt 12): o3169.
Published online 2009 November 21. doi:  10.1107/S1600536809046492
PMCID: PMC2971831

2-Isopropyl-5-methyl­cyclo­hexyl 5-acet­oxy-1,3-oxathiol­ane-2-carboxyl­ate

Abstract

In the title compound, C16H26O5S, the oxathiol­ane ring adopts an envelope conformation, with the S atom 0.793 (3) Å out of the mean plane of the remaining four atoms. The cyclo­hexane ring of the menthol fragment adopts an almost ideal chair conformation, with all substituents in the equatorial positions. In the crystal, relatively strong, short and linear C—H(...)O hydrogen bonds link the mol­ecules into the chains along [100] direction. The chains are packed into the crystal structure by means of weak dispersive inter­actions. Inter­molecular C—H(...)S inter­actions are also observed.

Related literature

The title compound is a drug inter­mediate of lamivudine, a reverse transcriptase inhibitor used in the treatment of HIV infections. For the structures of lamivudine and its hydrate have been studied, see: Harris et al. (1997 [triangle]). For the identification of lamivudine conformers by Raman scattering measurements and quantum chemical calculations, see: Pereira et al. (2007 [triangle]). For asymmetry parameters, see: Duax & Norton (1975 [triangle]). For a description of the Cambridge Structural Database, see: Allen (2002 [triangle]).

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Object name is e-65-o3169-scheme1.jpg

Experimental

Crystal data

  • C16H26O5S
  • M r = 330.43
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-o3169-efi1.jpg
  • a = 5.329 (1) Å
  • b = 13.867 (1) Å
  • c = 23.490 (2) Å
  • V = 1735.8 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.21 mm−1
  • T = 100 K
  • 0.3 × 0.3 × 0.15 mm

Data collection

  • Oxford Diffraction Xcalibur Sapphire2 large Be window diffractometer
  • Absorption correction: multi-scan (CrysAlis Pro; Oxford Diffraction, 2009 [triangle]) T min = 0.719, T max = 1.000
  • 11503 measured reflections
  • 3632 independent reflections
  • 3175 reflections with I > 2σ(I)
  • R int = 0.025

Refinement

  • R[F 2 > 2σ(F 2)] = 0.028
  • wR(F 2) = 0.053
  • S = 1.03
  • 3632 reflections
  • 277 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.28 e Å−3
  • Δρmin = −0.18 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1435 Friedel pairs
  • Flack parameter: −0.04 (5)

Data collection: CrysAlis Pro (Oxford Diffraction, 2009 [triangle]); cell refinement: CrysAlis Pro; data reduction: CrysAlis Pro; program(s) used to solve structure: SIR92 (Altomare et al., 1993 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: Stereochemical Workstation Operation Manual (Siemens, 1989 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809046492/jh2112sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809046492/jh2112Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

CSC thanks the University of Mysore for research facilities.

supplementary crystallographic information

Comment

5-Methyl-2-(propan-2-yl)cyclohexyl 5-(acetyloxy)-1,3-oxathiolane-2-carboxylate (I, Scheme 1) is a drug intermediate of lamivudine which is a reverse transcriptase inhibitor used in the treatment of HIV infection alone or in combination with other class of Anti HIV drugs. The crystal stractures of Lamivudine and its hydrate have been studied (Harris et al., 1997). The identification of lamivudine conformers by Raman scattering measurements and quantum chemical calculations is reported (Pereira et al., 2007).

The conformation of the oxathiolane ring is close to an envelope (Fig. 1), with four atoms C13, C15, C16 and O17 almost coplanar (maximum deviation from the least-squares plane of 0.0469 (11) Å) while the fifth atom (S14) is significantly, by 0.793 (3) Å out of this plane. Also the asymmetry parameter (Duax & Norton, 1975), which describes the deviation from the ideal symmetry (in this case Cs), has relatively low value of 6.0°. Similar conformation was observed in the majority of the structures with not fused oxathiolane rings found in the Cambridge Structural Database (Allen, 2002), however different atoms occupy the out-of-plane position. The acetyloxy substituent occupies the quasi-axial position with respect to the oxathiolane ring (C13—O17—C16—O18 torsion angle is -109.18 (13) °, S14—C15—C16—O18 84.13 (12) °), the position of carboxylate group is also close to the axial one (C16—O17—C13—C12 - 97.66 (14) °, C15—S14—C13—C12 84.89 (10) °). The cyclohexyl ring is close to the typical chair conformation (maximum and minimum values of the asymmetry parameters are 0.74° for ΔCs5, and 3.96° ΔC21–6), all substituents: methyl, isopropyl and carboxylate are in equatorial positions.

In the crystal structure relatively strong (short and directional) C13—H13···O12i hydrogen bonds join the molecules into the infinite chains along [100]. These chain in turn are organized into the crystal structure by weak van der Waals - type interactions (Table 1, Fig. 2).

Experimental

To a mixture of L-menthyl-5-hydroxy-1,3-oxathiolane-2-carboxylate (1.5 g, 5.2 m mol) in pyridine (30 ml), acetic anhydride (6.4 ml) was added slowly at 273 K (Fig. 4). The mixture was allowed to attain room temperature and stirred over night, then quenched to ice cold water and extracted with ethyl acetate. The organic layer was concentrated under vacuum to obtain the product. X-ray quality crystals were grown from slow evaporation of methanol solution (m.p.: 333–335 K).

Refinement

Positional parameters of the hydrogen atoms were freely refined, the Uiso values of these atoms were set at 1.2 (1.5 for methyl groups) times Ueq of their carrier carbon atom.

Figures

Fig. 1.
Anisotropic ellipsoid representation of the compound I together with atom labelling scheme. The ellipsoids are drawn at 50% probability level, hydrogen atoms are depicted as spheres with arbitrary radii.
Fig. 2.
The hydrogen-bonded chain of molecules of I. Hydrogen bonds are shown as dashed lines.
Fig. 3.
The crystal packing as seen along the chain direction, i.e. along [100].
Fig. 4.
The preparation of the title compound.

Crystal data

C16H26O5SF(000) = 712
Mr = 330.43Dx = 1.264 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 3953 reflections
a = 5.329 (1) Åθ = 3.0–75.3°
b = 13.867 (1) ŵ = 0.21 mm1
c = 23.490 (2) ÅT = 100 K
V = 1735.8 (4) Å3Prism, colourless
Z = 40.3 × 0.3 × 0.15 mm

Data collection

Oxford Diffraction Xcalibur Sapphire2 large Be window diffractometer3632 independent reflections
Radiation source: Nova (Mo) X-ray Source3175 reflections with I > 2σ(I)
graphiteRint = 0.025
Detector resolution: 5.2679 pixels mm-1θmax = 27.8°, θmin = 2.9°
ω scansh = −6→6
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009)k = −17→19
Tmin = 0.719, Tmax = 1.000l = −18→28
11503 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.028H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.053w = 1/[σ2(Fo2) + (0.026P)2] where P = (Fo2 + 2Fc2)/3
S = 1.03(Δ/σ)max = 0.001
3632 reflectionsΔρmax = 0.28 e Å3
277 parametersΔρmin = −0.18 e Å3
0 restraintsAbsolute structure: Flack (1983), 1435 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: −0.04 (5)

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'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 > 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.

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

xyzUiso*/Ueq
C10.2221 (3)0.81153 (11)0.22603 (6)0.0144 (3)
H10.055 (3)0.7890 (12)0.2363 (5)0.017*
C20.2271 (3)0.92125 (11)0.22689 (6)0.0133 (3)
H20.402 (3)0.9383 (11)0.2176 (6)0.016*
C210.1670 (3)0.96521 (11)0.28540 (6)0.0163 (3)
H210.277 (3)0.9324 (11)0.3133 (7)0.020*
C22−0.1041 (3)0.95024 (13)0.30376 (8)0.0248 (4)
H22A−0.139 (3)0.9755 (13)0.3442 (8)0.037*
H22B−0.154 (3)0.8837 (14)0.3016 (7)0.037*
H22C−0.216 (3)0.9878 (14)0.2804 (8)0.037*
C230.2308 (3)1.07241 (12)0.28675 (7)0.0207 (4)
H23A0.126 (3)1.1091 (13)0.2621 (7)0.031*
H23B0.396 (3)1.0834 (12)0.2739 (7)0.031*
H23C0.207 (3)1.0990 (12)0.3264 (7)0.031*
C30.0559 (3)0.95554 (11)0.17848 (6)0.0193 (3)
H3A−0.122 (3)0.9338 (12)0.1888 (7)0.023*
H3B0.049 (3)1.0270 (12)0.1771 (6)0.023*
C40.1377 (3)0.91614 (12)0.12123 (7)0.0222 (4)
H4A0.300 (3)0.9392 (12)0.1134 (7)0.027*
H4B0.025 (3)0.9406 (12)0.0913 (7)0.027*
C50.1436 (3)0.80595 (12)0.12053 (6)0.0199 (4)
H5−0.025 (3)0.7843 (12)0.1282 (6)0.024*
C510.2389 (4)0.76739 (13)0.06413 (8)0.0305 (4)
H51A0.398 (4)0.7932 (14)0.0557 (7)0.046*
H51B0.137 (3)0.7914 (15)0.0335 (8)0.046*
H51C0.245 (3)0.6975 (14)0.0650 (8)0.046*
C60.3052 (3)0.76948 (11)0.16982 (6)0.0172 (3)
H6A0.478 (3)0.7877 (12)0.1612 (6)0.021*
H6B0.305 (3)0.6970 (12)0.1714 (6)0.021*
O110.39944 (16)0.77425 (7)0.26904 (4)0.0146 (2)
C120.3058 (3)0.72616 (10)0.31299 (6)0.0134 (3)
O120.08816 (18)0.70999 (9)0.32180 (4)0.0214 (2)
C130.5134 (3)0.69492 (11)0.35302 (6)0.0146 (3)
H130.672 (3)0.6830 (11)0.3325 (6)0.018*
S140.56357 (7)0.79072 (3)0.404699 (15)0.01686 (9)
C150.3109 (3)0.73820 (11)0.44548 (6)0.0176 (3)
H15A0.327 (3)0.7581 (11)0.4845 (7)0.021*
H15B0.150 (3)0.7576 (11)0.4298 (7)0.021*
C160.3439 (3)0.63111 (12)0.43767 (6)0.0189 (3)
H160.175 (3)0.5948 (11)0.4441 (6)0.023*
O170.4379 (2)0.61176 (7)0.38320 (4)0.0205 (2)
O180.52454 (18)0.59729 (7)0.47832 (4)0.0206 (2)
C190.4838 (3)0.50989 (11)0.50215 (6)0.0193 (3)
O190.3034 (2)0.46223 (9)0.49229 (6)0.0418 (4)
C200.6923 (3)0.48274 (13)0.54115 (7)0.0252 (4)
H20A0.709 (3)0.5287 (14)0.5686 (8)0.038*
H20B0.850 (3)0.4807 (13)0.5212 (8)0.038*
H20C0.659 (3)0.4227 (13)0.5576 (7)0.038*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0124 (7)0.0178 (9)0.0129 (8)−0.0003 (7)−0.0033 (6)0.0033 (6)
C20.0115 (7)0.0157 (8)0.0127 (8)−0.0026 (6)−0.0008 (6)0.0021 (6)
C210.0179 (8)0.0171 (8)0.0137 (8)0.0017 (7)−0.0020 (6)0.0002 (6)
C220.0232 (9)0.0248 (10)0.0265 (10)−0.0013 (8)0.0080 (8)−0.0066 (7)
C230.0247 (9)0.0181 (9)0.0192 (10)0.0005 (7)−0.0012 (7)−0.0027 (7)
C30.0246 (9)0.0149 (8)0.0184 (8)0.0007 (8)−0.0050 (7)0.0025 (6)
C40.0310 (10)0.0200 (9)0.0157 (8)−0.0019 (7)−0.0068 (7)0.0038 (7)
C50.0255 (8)0.0188 (9)0.0155 (8)−0.0053 (7)−0.0037 (6)−0.0011 (7)
C510.0474 (12)0.0260 (11)0.0180 (9)−0.0037 (10)−0.0045 (8)−0.0035 (8)
C60.0198 (8)0.0142 (9)0.0175 (8)0.0005 (7)0.0004 (6)−0.0005 (6)
O110.0124 (5)0.0178 (6)0.0137 (5)0.0008 (5)−0.0006 (4)0.0037 (4)
C120.0159 (8)0.0115 (8)0.0126 (8)−0.0005 (6)0.0010 (6)−0.0021 (6)
O120.0138 (5)0.0287 (6)0.0218 (6)−0.0059 (5)−0.0009 (4)0.0072 (5)
C130.0158 (8)0.0156 (8)0.0124 (7)0.0031 (6)0.0013 (5)−0.0005 (6)
S140.01923 (18)0.01732 (18)0.01403 (18)−0.00361 (17)−0.00206 (15)0.00048 (16)
C150.0176 (8)0.0250 (9)0.0101 (8)0.0018 (7)0.0015 (6)0.0009 (6)
C160.0186 (8)0.0236 (9)0.0145 (8)−0.0040 (8)−0.0029 (6)0.0058 (7)
O170.0326 (6)0.0136 (5)0.0153 (5)0.0006 (5)−0.0039 (5)0.0012 (4)
O180.0229 (6)0.0205 (6)0.0183 (5)−0.0065 (5)−0.0073 (4)0.0079 (4)
C190.0224 (8)0.0180 (8)0.0174 (8)−0.0002 (7)0.0028 (6)0.0046 (6)
O190.0291 (6)0.0330 (8)0.0632 (9)−0.0137 (6)−0.0157 (6)0.0248 (7)
C200.0335 (10)0.0230 (10)0.0193 (9)−0.0006 (8)−0.0049 (8)0.0050 (8)

Geometric parameters (Å, °)

C1—O111.4768 (16)C51—H51A0.94 (2)
C1—C61.510 (2)C51—H51B0.961 (18)
C1—C21.522 (2)C51—H51C0.970 (19)
C1—H10.975 (15)C6—H6A0.975 (15)
C2—C31.533 (2)C6—H6B1.006 (16)
C2—C211.537 (2)O11—C121.3264 (16)
C2—H20.986 (15)C12—O121.1991 (16)
C21—C221.522 (2)C12—C131.5155 (19)
C21—C231.525 (2)C13—O171.4122 (17)
C21—H210.990 (16)C13—S141.8193 (15)
C22—H22A1.029 (19)C13—H130.989 (15)
C22—H22B0.961 (19)S14—C151.8059 (16)
C22—H22C0.965 (18)C15—C161.507 (2)
C23—H23A0.951 (17)C15—H15A0.961 (16)
C23—H23B0.945 (18)C15—H15B0.973 (15)
C23—H23C1.009 (17)C16—O171.4000 (18)
C3—C41.515 (2)C16—O181.4345 (17)
C3—H3A1.024 (16)C16—H161.042 (16)
C3—H3B0.992 (16)O18—C191.3526 (17)
C4—C51.528 (2)C19—O191.1891 (17)
C4—H4A0.941 (18)C19—C201.489 (2)
C4—H4B0.983 (16)C20—H20A0.911 (19)
C5—C511.516 (2)C20—H20B0.961 (18)
C5—C61.529 (2)C20—H20C0.936 (18)
C5—H50.965 (15)
O11—C1—C6106.00 (11)C6—C5—H5106.3 (9)
O11—C1—C2109.26 (12)C5—C51—H51A110.6 (11)
C6—C1—C2113.12 (13)C5—C51—H51B109.9 (11)
O11—C1—H1107.7 (8)H51A—C51—H51B102.8 (15)
C6—C1—H1111.1 (8)C5—C51—H51C110.2 (11)
C2—C1—H1109.5 (10)H51A—C51—H51C110.8 (17)
C1—C2—C3106.85 (12)H51B—C51—H51C112.3 (17)
C1—C2—C21113.86 (13)C1—C6—C5111.69 (12)
C3—C2—C21114.59 (13)C1—C6—H6A111.0 (9)
C1—C2—H2104.7 (9)C5—C6—H6A106.8 (9)
C3—C2—H2108.9 (8)C1—C6—H6B110.7 (9)
C21—C2—H2107.4 (8)C5—C6—H6B111.0 (9)
C22—C21—C23109.79 (14)H6A—C6—H6B105.5 (13)
C22—C21—C2113.39 (13)C12—O11—C1117.88 (11)
C23—C21—C2111.01 (13)O12—C12—O11126.32 (13)
C22—C21—H21108.3 (9)O12—C12—C13123.07 (13)
C23—C21—H21107.6 (9)O11—C12—C13110.60 (11)
C2—C21—H21106.5 (9)O17—C13—C12109.67 (12)
C21—C22—H22A112.7 (9)O17—C13—S14107.65 (9)
C21—C22—H22B112.2 (10)C12—C13—S14108.21 (10)
H22A—C22—H22B109.0 (15)O17—C13—H13110.7 (9)
C21—C22—H22C110.8 (11)C12—C13—H13111.7 (9)
H22A—C22—H22C103.2 (14)S14—C13—H13108.8 (9)
H22B—C22—H22C108.5 (15)C15—S14—C1387.13 (7)
C21—C23—H23A112.2 (10)C16—C15—S14104.23 (11)
C21—C23—H23B111.0 (11)C16—C15—H15A112.8 (9)
H23A—C23—H23B105.6 (14)S14—C15—H15A108.9 (9)
C21—C23—H23C110.4 (10)C16—C15—H15B109.2 (9)
H23A—C23—H23C107.0 (14)S14—C15—H15B110.3 (9)
H23B—C23—H23C110.5 (14)H15A—C15—H15B111.1 (13)
C4—C3—C2112.04 (14)O17—C16—O18107.80 (12)
C4—C3—H3A111.7 (9)O17—C16—C15109.99 (12)
C2—C3—H3A106.5 (9)O18—C16—C15108.64 (12)
C4—C3—H3B110.0 (8)O17—C16—H16110.4 (8)
C2—C3—H3B110.9 (9)O18—C16—H16109.0 (8)
H3A—C3—H3B105.5 (13)C15—C16—H16111.0 (8)
C3—C4—C5112.08 (13)C16—O17—C13113.85 (11)
C3—C4—H4A108.4 (10)C19—O18—C16117.42 (11)
C5—C4—H4A108.6 (10)O19—C19—O18123.18 (13)
C3—C4—H4B109.6 (9)O19—C19—C20125.64 (15)
C5—C4—H4B110.5 (9)O18—C19—C20111.18 (13)
H4A—C4—H4B107.6 (13)C19—C20—H20A109.4 (11)
C51—C5—C4111.65 (14)C19—C20—H20B111.1 (10)
C51—C5—C6110.89 (13)H20A—C20—H20B106.0 (16)
C4—C5—C6109.53 (13)C19—C20—H20C109.6 (11)
C51—C5—H5111.4 (9)H20A—C20—H20C110.5 (16)
C4—C5—H5106.9 (10)H20B—C20—H20C110.1 (15)
O11—C1—C2—C3175.68 (11)C1—O11—C12—O12−0.5 (2)
C6—C1—C2—C357.86 (16)C1—O11—C12—C13−179.08 (11)
O11—C1—C2—C21−56.78 (16)O12—C12—C13—O1727.68 (19)
C6—C1—C2—C21−174.59 (12)O11—C12—C13—O17−153.67 (11)
C1—C2—C21—C22−68.34 (17)O12—C12—C13—S14−89.49 (16)
C3—C2—C21—C2255.10 (18)O11—C12—C13—S1489.16 (12)
C1—C2—C21—C23167.51 (14)O17—C13—S14—C15−33.57 (10)
C3—C2—C21—C23−69.05 (17)C12—C13—S14—C1584.90 (11)
C1—C2—C3—C4−57.56 (17)C13—S14—C15—C1637.16 (10)
C21—C2—C3—C4175.32 (13)S14—C15—C16—O17−33.65 (15)
C2—C3—C4—C557.98 (18)S14—C15—C16—O1884.12 (12)
C3—C4—C5—C51−176.96 (15)O18—C16—O17—C13−109.17 (13)
C3—C4—C5—C6−53.74 (19)C15—C16—O17—C139.12 (17)
O11—C1—C6—C5−177.46 (12)C12—C13—O17—C16−97.69 (14)
C2—C1—C6—C5−57.75 (17)S14—C13—O17—C1619.84 (14)
C51—C5—C6—C1176.82 (14)O17—C16—O18—C19−98.38 (14)
C4—C5—C6—C153.16 (17)C15—C16—O18—C19142.46 (13)
C6—C1—O11—C12−123.41 (13)C16—O18—C19—O19−2.4 (2)
C2—C1—O11—C12114.39 (14)C16—O18—C19—C20177.29 (13)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C13—H13···O12i0.989 (15)2.261 (15)3.1563 (18)150.0 (12)
C15—H15A···S14ii0.961 (16)3.033 (15)3.7794 (15)135.6 (11)
C20—H20B···O19i0.961 (18)2.524 (18)3.464 (2)166.0 (14)

Symmetry codes: (i) x+1, y, z; (ii) x−1/2, −y+3/2, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: JH2112).

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