organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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(4R,5S)-4-Hy­dr­oxy­meth­yl-5-[(methyl­sulfanyl)­meth­yl]-1,3-oxazolidin-2-one

aIndustrial Research Limited, PO Box 31-310, Lower Hutt, New Zealand
*Correspondence e-mail: g.gainsford@irl.cri.nz

(Received 17 May 2012; accepted 6 June 2012; online 13 June 2012)

The title compound, C6H11NO3S, crystallizes utilizing a three-dimensional set of O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds. The 1,3-oxazolidin-2-one ring adopts an envelope conformation with the C atom bearing the hy­droxy­methyl group as the flap.

Related literature

For related structures, see Evans et al. (2007[Evans, L. A., Adams, H., Barber, C. G., Caggiano, L. & Jackson, R. W. (2007). Org. Biomol. Chem. 5, 3156-3163.]); Pallavicini et al. (2004[Pallavicini, M., Bolchi, C., Di Pumpo, R., Fumagalli, L., Moroni, B., Valoti, E. & Demartin, F. (2004). Tetrahedron Asymmetry, 15, 1659-1665.]). For the synthesis, see: Clinch et al. (2012[Clinch, K., Evans, G. B., Fröhlich, R. F. G., Gulab, S. A., Gutierrez, J. A., Mason, J. M., Schramm, V. L., Tyler, P. C. & Woolhouse, A. D. (2012). Bioorg. Med. Chem. Submitted. ]). For a description of the Cambridge Structural Database, see: Allen (2002[Allen, F. H. (2002). Acta Cryst. B58, 380-388.]); For conformational analysis, see: Cremer & Pople (1975[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358.]). For hydrogen-bond motifs, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C6H11NO3S

  • Mr = 177.22

  • Monoclinic, C 2

  • a = 9.7821 (4) Å

  • b = 7.9620 (3) Å

  • c = 11.5472 (4) Å

  • β = 109.837 (2)°

  • V = 845.99 (6) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.34 mm−1

  • T = 98 K

  • 0.45 × 0.23 × 0.07 mm

Data collection
  • Bruker–Nonius APEXII CCD area-detector diffractometer

  • Absorption correction: multi-scan [Blessing (1995[Blessing, R. H. (1995). Acta Cryst. A51, 33-38.]) and SADABS (Sheldrick, 1996[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.])] Tmin = 0.854, Tmax = 0.980

  • 16080 measured reflections

  • 3172 independent reflections

  • 3091 reflections with I > 2σ(I)

  • Rint = 0.021

Refinement
  • R[F2 > 2σ(F2)] = 0.022

  • wR(F2) = 0.060

  • S = 1.07

  • 3172 reflections

  • 142 parameters

  • 2 restraints

  • All H-atom parameters refined

  • Δρmax = 0.38 e Å−3

  • Δρmin = −0.21 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1409 Friedel pairs

  • Flack parameter: 0.02 (4)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N3—H3N⋯O3i 0.829 (14) 2.029 (14) 2.8442 (9) 167.4 (14)
O3—H3O⋯O2ii 0.74 (2) 1.97 (2) 2.7018 (9) 171 (2)
C5—H5⋯O2iii 0.952 (13) 2.426 (14) 3.2264 (10) 141.6 (11)
Symmetry codes: (i) [-x+{\script{3\over 2}}, y+{\script{1\over 2}}, -z+1]; (ii) -x+2, y, -z+1; (iii) [x-{\script{1\over 2}}, y-{\script{1\over 2}}, z].

Data collection: APEX2 (Bruker, 2005[Bruker (2005). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2005[Bruker (2005). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]) and Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

This study is part of a programme aimed at preparing transition state analogue inhibitors of human methylthioadenosine phosphorylase and bacterial methylthioadenosine/S-adenosylhomocysteine nucleosidase. The title compound was produced by an unexpected rearrangement and was studied to confirm the structure and the molecular stereochemistry. The full details of the synthesis of the title compound are presented elsewhere (Clinch et al., 2012).

The asymmetric unit and labelling is shown in Fig 1. The absolute stereochemistry with C4(R) and C5(S) was determined from the anomalous dispersion, with Hooft y value 0.028 (12). The 1,3-oxazolidin-2-one ring adopts an envelope conformation with flap atom C4 (Cremer & Pople, 1975, parameters are Q(2) 0.0980 (8) Å and φ 105.2 (5)°) with similar dimensions to the related (Allen, 2002; CSD Version 5.33, with February 2012 updates) 5-(p-tolylthiocarbonyl) (Evans et al., 2007) and 4-hydroxymethyl-2-oxazolidine (Pallavicini et al., 2004) structures.

The basic crystal packing can be described (Bernstein et al., 1995) with two C(5) motifs, corresponding to entries 1 and 3 in Table 1, which provide binding parallel to the bc and ab planes, respectively. The third interaction (entry 2, Table 1) makes an R22(14) motif in the ac plane utilizing a 2-fold axis (Figure 2). The ability of the hydroxymethyl OH group to act as both donor (through its H atom) and acceptor (to adjacent nitrogen protons) is also observed in most of the related oxazolidinone structures.

Related literature top

For related structures, see Evans et al. (2007); Pallavicini et al. (2004). For the synthesis, see: Clinch et al. (2012). For a description of the Cambridge Structural Database, see: Allen (2002); For conformational analysis, see: Cremer & Pople (1975). For hydrogen-bond motifs, see: Bernstein et al. (1995).

Experimental top

The preparation of the title compound is given by Clinch et al. (2012). Crystals were obtained by dissolving the title compound in a minimum volume of ethanol, adding hexanes until just before the turbidity point then setting aside at ambient temperature until crystallization was complete.

Refinement top

All H atoms except those on C6 were refined with isotropic thermal parameters. The O3–HO3 bond was constrained to 0.82 Å using DFIX and the three H atoms on the methyl atom C6 were refined with a common isotropic thermal parameter.

Structure description top

This study is part of a programme aimed at preparing transition state analogue inhibitors of human methylthioadenosine phosphorylase and bacterial methylthioadenosine/S-adenosylhomocysteine nucleosidase. The title compound was produced by an unexpected rearrangement and was studied to confirm the structure and the molecular stereochemistry. The full details of the synthesis of the title compound are presented elsewhere (Clinch et al., 2012).

The asymmetric unit and labelling is shown in Fig 1. The absolute stereochemistry with C4(R) and C5(S) was determined from the anomalous dispersion, with Hooft y value 0.028 (12). The 1,3-oxazolidin-2-one ring adopts an envelope conformation with flap atom C4 (Cremer & Pople, 1975, parameters are Q(2) 0.0980 (8) Å and φ 105.2 (5)°) with similar dimensions to the related (Allen, 2002; CSD Version 5.33, with February 2012 updates) 5-(p-tolylthiocarbonyl) (Evans et al., 2007) and 4-hydroxymethyl-2-oxazolidine (Pallavicini et al., 2004) structures.

The basic crystal packing can be described (Bernstein et al., 1995) with two C(5) motifs, corresponding to entries 1 and 3 in Table 1, which provide binding parallel to the bc and ab planes, respectively. The third interaction (entry 2, Table 1) makes an R22(14) motif in the ac plane utilizing a 2-fold axis (Figure 2). The ability of the hydroxymethyl OH group to act as both donor (through its H atom) and acceptor (to adjacent nitrogen protons) is also observed in most of the related oxazolidinone structures.

For related structures, see Evans et al. (2007); Pallavicini et al. (2004). For the synthesis, see: Clinch et al. (2012). For a description of the Cambridge Structural Database, see: Allen (2002); For conformational analysis, see: Cremer & Pople (1975). For hydrogen-bond motifs, see: Bernstein et al. (1995).

Computing details top

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); 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., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. Molecular structure of the asymmetric unit of (I) (Farrugia, 1997) with 50% probabilility ellipsoids.
[Figure 2] Fig. 2. Packing diagram of the unit cell showing some key interactions (see text and Table 1) (Macrae et al., 2008). Hydrogen bond interactions are shown as blue dotted lines. Symmetry (i) 3/2 - x, 1/2 + y, 1 - z (ii) 2 - x, y, 1 - z (iii) x - 1/2, 1/2 + y, z
(4R,5S)-4-Hydroxymethyl-5-[(methylsulfanyl)methyl]- 1,3-oxazolidin-2-one top
Crystal data top
C6H11NO3SF(000) = 376
Mr = 177.22Dx = 1.391 Mg m3
Monoclinic, C2Mo Kα radiation, λ = 0.71073 Å
Hall symbol: C 2yCell parameters from 6722 reflections
a = 9.7821 (4) Åθ = 3.4–34.8°
b = 7.9620 (3) ŵ = 0.34 mm1
c = 11.5472 (4) ÅT = 98 K
β = 109.837 (2)°Plate, colourless
V = 845.99 (6) Å30.45 × 0.23 × 0.07 mm
Z = 4
Data collection top
Bruker–Nonius APEXII CCD area-detector
diffractometer
3172 independent reflections
Radiation source: fine-focus sealed tube3091 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.021
Detector resolution: 8.192 pixels mm-1θmax = 34.8°, θmin = 3.4°
phi and ω scansh = 1415
Absorption correction: multi-scan
[Blessing (1995) and SADABS (Sheldrick, 1996)]
k = 1112
Tmin = 0.854, Tmax = 0.980l = 1717
16080 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.022All H-atom parameters refined
wR(F2) = 0.060 w = 1/[σ2(Fo2) + (0.0347P)2 + 0.1867P]
where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max = 0.001
3172 reflectionsΔρmax = 0.38 e Å3
142 parametersΔρmin = 0.21 e Å3
2 restraintsAbsolute structure: Flack (1983), 1409 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.02 (4)
Crystal data top
C6H11NO3SV = 845.99 (6) Å3
Mr = 177.22Z = 4
Monoclinic, C2Mo Kα radiation
a = 9.7821 (4) ŵ = 0.34 mm1
b = 7.9620 (3) ÅT = 98 K
c = 11.5472 (4) Å0.45 × 0.23 × 0.07 mm
β = 109.837 (2)°
Data collection top
Bruker–Nonius APEXII CCD area-detector
diffractometer
3172 independent reflections
Absorption correction: multi-scan
[Blessing (1995) and SADABS (Sheldrick, 1996)]
3091 reflections with I > 2σ(I)
Tmin = 0.854, Tmax = 0.980Rint = 0.021
16080 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.022All H-atom parameters refined
wR(F2) = 0.060Δρmax = 0.38 e Å3
S = 1.07Δρmin = 0.21 e Å3
3172 reflectionsAbsolute structure: Flack (1983), 1409 Friedel pairs
142 parametersAbsolute structure parameter: 0.02 (4)
2 restraints
Special details top

Experimental. One backstop screened reflection (0,0,1) was omitted in the refinement; 1 other reflection (2,0,0) within sin(theta)/lambda of 0.5 was not collected.

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) top
xyzUiso*/Ueq
S10.73433 (3)0.27672 (3)0.07622 (2)0.02645 (6)
O10.88351 (6)0.51738 (7)0.30179 (6)0.01702 (11)
O21.03771 (6)0.73322 (8)0.37235 (6)0.01786 (12)
O30.72175 (7)0.54658 (8)0.52052 (6)0.01844 (12)
N30.79288 (6)0.75917 (8)0.33788 (6)0.01278 (11)
C10.66012 (9)0.45196 (11)0.13436 (8)0.01841 (15)
C20.91379 (8)0.67743 (9)0.34084 (7)0.01297 (12)
C30.61655 (8)0.62734 (10)0.41960 (8)0.01628 (13)
C40.66762 (7)0.64864 (9)0.30976 (7)0.01290 (12)
C50.72876 (8)0.48658 (9)0.27115 (7)0.01284 (12)
C60.6659 (2)0.10352 (15)0.14198 (13)0.0421 (3)
H3O0.7827 (16)0.606 (2)0.5473 (14)0.031 (4)*
H3N0.7992 (14)0.8487 (18)0.3760 (13)0.018 (3)*
H1A0.5627 (16)0.436 (2)0.1172 (15)0.023 (3)*
H1B0.6732 (17)0.545 (2)0.0903 (15)0.029 (4)*
H3A0.5946 (14)0.7311 (17)0.4411 (12)0.018 (3)*
H3B0.5319 (15)0.554 (2)0.3952 (13)0.024 (3)*
H40.5890 (16)0.6908 (19)0.2414 (14)0.024 (3)*
H50.7184 (13)0.3900 (17)0.3160 (12)0.012 (3)*
H6A0.552 (2)0.103 (3)0.118 (2)0.052 (3)*
H6B0.693 (2)0.003 (3)0.1116 (19)0.052 (3)*
H6C0.713 (2)0.106 (3)0.230 (2)0.052 (3)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.03705 (12)0.02584 (11)0.01991 (10)0.00124 (9)0.01417 (8)0.00624 (8)
O10.0122 (2)0.0129 (2)0.0260 (3)0.00050 (18)0.0066 (2)0.0043 (2)
O20.0126 (2)0.0179 (3)0.0234 (3)0.00324 (19)0.0065 (2)0.0010 (2)
O30.0216 (3)0.0178 (3)0.0166 (3)0.0059 (2)0.0074 (2)0.0020 (2)
N30.0127 (2)0.0100 (3)0.0170 (3)0.0009 (2)0.0068 (2)0.0000 (2)
C10.0219 (3)0.0197 (4)0.0134 (3)0.0007 (3)0.0057 (3)0.0012 (3)
C20.0136 (3)0.0120 (3)0.0141 (3)0.0008 (2)0.0057 (2)0.0007 (2)
C30.0157 (3)0.0161 (3)0.0205 (4)0.0008 (2)0.0106 (3)0.0003 (3)
C40.0108 (2)0.0129 (3)0.0149 (3)0.0005 (2)0.0043 (2)0.0005 (2)
C50.0121 (2)0.0127 (3)0.0139 (3)0.0019 (2)0.0047 (2)0.0008 (2)
C60.0847 (11)0.0204 (4)0.0279 (6)0.0071 (5)0.0281 (7)0.0016 (4)
Geometric parameters (Å, º) top
S1—C11.8042 (9)C1—H1A0.914 (15)
S1—C61.8085 (14)C1—H1B0.930 (17)
O1—C21.3507 (9)C3—C41.5222 (11)
O1—C51.4538 (9)C3—H3A0.909 (14)
O2—C21.2247 (9)C3—H3B0.972 (14)
O3—C31.4201 (11)C4—C51.5499 (10)
O3—H3O0.743 (13)C4—H40.957 (15)
N3—C21.3402 (9)C5—H50.952 (13)
N3—C41.4530 (9)C6—H6A1.06 (2)
N3—H3N0.829 (14)C6—H6B0.99 (2)
C1—C51.5172 (11)C6—H6C0.97 (2)
C1—S1—C6100.40 (5)H3A—C3—H3B111.4 (12)
C2—O1—C5109.43 (6)N3—C4—C3111.81 (6)
C3—O3—H3O107.9 (13)N3—C4—C5100.96 (5)
C2—N3—C4112.43 (6)C3—C4—C5114.50 (6)
C2—N3—H3N119.9 (9)N3—C4—H4110.7 (9)
C4—N3—H3N123.0 (9)C3—C4—H4109.1 (9)
C5—C1—S1115.86 (6)C5—C4—H4109.6 (9)
C5—C1—H1A108.2 (10)O1—C5—C1109.90 (6)
S1—C1—H1A109.3 (10)O1—C5—C4105.14 (6)
C5—C1—H1B109.3 (10)C1—C5—C4111.91 (6)
S1—C1—H1B105.2 (10)O1—C5—H5107.4 (7)
H1A—C1—H1B108.7 (14)C1—C5—H5109.2 (8)
O2—C2—N3127.40 (7)C4—C5—H5113.1 (8)
O2—C2—O1121.61 (7)S1—C6—H6A113.8 (13)
N3—C2—O1110.98 (6)S1—C6—H6B108.9 (12)
O3—C3—C4112.51 (6)H6A—C6—H6B107.0 (17)
O3—C3—H3A111.1 (8)S1—C6—H6C108.3 (13)
C4—C3—H3A107.6 (9)H6A—C6—H6C111.1 (17)
O3—C3—H3B106.0 (9)H6B—C6—H6C107.7 (17)
C4—C3—H3B108.3 (8)
C6—S1—C1—C571.48 (8)C2—O1—C5—C1115.03 (7)
C4—N3—C2—O2173.09 (8)C2—O1—C5—C45.56 (8)
C4—N3—C2—O17.65 (9)S1—C1—C5—O158.29 (8)
C5—O1—C2—O2179.83 (7)S1—C1—C5—C4174.71 (5)
C5—O1—C2—N30.86 (9)N3—C4—C5—O19.13 (7)
C2—N3—C4—C3111.84 (7)C3—C4—C5—O1111.14 (7)
C2—N3—C4—C510.33 (8)N3—C4—C5—C1110.13 (7)
O3—C3—C4—N364.24 (8)C3—C4—C5—C1129.59 (7)
O3—C3—C4—C549.80 (9)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3N···O3i0.829 (14)2.029 (14)2.8442 (9)167.4 (14)
O3—H3O···O2ii0.74 (2)1.97 (2)2.7018 (9)171 (2)
C5—H5···O2iii0.952 (13)2.426 (14)3.2264 (10)141.6 (11)
Symmetry codes: (i) x+3/2, y+1/2, z+1; (ii) x+2, y, z+1; (iii) x1/2, y1/2, z.

Experimental details

Crystal data
Chemical formulaC6H11NO3S
Mr177.22
Crystal system, space groupMonoclinic, C2
Temperature (K)98
a, b, c (Å)9.7821 (4), 7.9620 (3), 11.5472 (4)
β (°) 109.837 (2)
V3)845.99 (6)
Z4
Radiation typeMo Kα
µ (mm1)0.34
Crystal size (mm)0.45 × 0.23 × 0.07
Data collection
DiffractometerBruker–Nonius APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
[Blessing (1995) and SADABS (Sheldrick, 1996)]
Tmin, Tmax0.854, 0.980
No. of measured, independent and
observed [I > 2σ(I)] reflections
16080, 3172, 3091
Rint0.021
(sin θ/λ)max1)0.803
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.022, 0.060, 1.07
No. of reflections3172
No. of parameters142
No. of restraints2
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å3)0.38, 0.21
Absolute structureFlack (1983), 1409 Friedel pairs
Absolute structure parameter0.02 (4)

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXS97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and Mercury (Macrae et al., 2008), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3N···O3i0.829 (14)2.029 (14)2.8442 (9)167.4 (14)
O3—H3O···O2ii0.742 (16)1.966 (16)2.7018 (9)171.4 (16)
C5—H5···O2iii0.952 (13)2.426 (14)3.2264 (10)141.6 (11)
Symmetry codes: (i) x+3/2, y+1/2, z+1; (ii) x+2, y, z+1; (iii) x1/2, y1/2, z.
 

Acknowledgements

We thank Dr J. Wikaira of the University of Canterbury, New Zealand, for the data collection. This work was supported by the New Zealand Foundation for Research, Science & Technology under contract C08X0701.

References

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