organic compounds
(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
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 with the C atom bearing the hydroxymethyl group as the flap.
Related literature
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 see: Cremer & Pople (1975). For hydrogen-bond motifs, see: Bernstein et al. (1995).
Experimental
Crystal data
|
Data collection: APEX2 (Bruker, 2005); cell SAINT (Bruker, 2005); 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 (Farrugia, 1997) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009).
Supporting information
https://doi.org/10.1107/S1600536812025809/im2379sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812025809/im2379Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S1600536812025809/im2379Isup3.cml
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.
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.
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 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.
and labelling is shown in Fig 1. The absolute stereochemistry with C4(R) and C5(S) was determined from the with Hooft y value 0.028 (12). The 1,3-oxazolidin-2-one ring adopts an with flap atom C4 (Cremer & Pople, 1975, parameters are Q(2) 0.0980 (8) Å andThe 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
see: Cremer & Pople (1975). For hydrogen-bond motifs, see: Bernstein et al. (1995).Data collection: APEX2 (Bruker, 2005); cell
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).C6H11NO3S | F(000) = 376 |
Mr = 177.22 | Dx = 1.391 Mg m−3 |
Monoclinic, C2 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: C 2y | Cell parameters from 6722 reflections |
a = 9.7821 (4) Å | θ = 3.4–34.8° |
b = 7.9620 (3) Å | µ = 0.34 mm−1 |
c = 11.5472 (4) Å | T = 98 K |
β = 109.837 (2)° | Plate, colourless |
V = 845.99 (6) Å3 | 0.45 × 0.23 × 0.07 mm |
Z = 4 |
Bruker–Nonius APEXII CCD area-detector diffractometer | 3172 independent reflections |
Radiation source: fine-focus sealed tube | 3091 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.021 |
Detector resolution: 8.192 pixels mm-1 | θmax = 34.8°, θmin = 3.4° |
phi and ω scans | h = −14→15 |
Absorption correction: multi-scan [Blessing (1995) and SADABS (Sheldrick, 1996)] | k = −11→12 |
Tmin = 0.854, Tmax = 0.980 | l = −17→17 |
16080 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)] = 0.022 | All 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 reflections | Δρmax = 0.38 e Å−3 |
142 parameters | Δρmin = −0.21 e Å−3 |
2 restraints | Absolute structure: Flack (1983), 1409 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.02 (4) |
C6H11NO3S | V = 845.99 (6) Å3 |
Mr = 177.22 | Z = 4 |
Monoclinic, C2 | Mo Kα radiation |
a = 9.7821 (4) Å | µ = 0.34 mm−1 |
b = 7.9620 (3) Å | T = 98 K |
c = 11.5472 (4) Å | 0.45 × 0.23 × 0.07 mm |
β = 109.837 (2)° |
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 = 0.980 | Rint = 0.021 |
16080 measured reflections |
R[F2 > 2σ(F2)] = 0.022 | All H-atom parameters refined |
wR(F2) = 0.060 | Δρmax = 0.38 e Å−3 |
S = 1.07 | Δρmin = −0.21 e Å−3 |
3172 reflections | Absolute structure: Flack (1983), 1409 Friedel pairs |
142 parameters | Absolute structure parameter: 0.02 (4) |
2 restraints |
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. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.73433 (3) | 0.27672 (3) | 0.07622 (2) | 0.02645 (6) | |
O1 | 0.88351 (6) | 0.51738 (7) | 0.30179 (6) | 0.01702 (11) | |
O2 | 1.03771 (6) | 0.73322 (8) | 0.37235 (6) | 0.01786 (12) | |
O3 | 0.72175 (7) | 0.54658 (8) | 0.52052 (6) | 0.01844 (12) | |
N3 | 0.79288 (6) | 0.75917 (8) | 0.33788 (6) | 0.01278 (11) | |
C1 | 0.66012 (9) | 0.45196 (11) | 0.13436 (8) | 0.01841 (15) | |
C2 | 0.91379 (8) | 0.67743 (9) | 0.34084 (7) | 0.01297 (12) | |
C3 | 0.61655 (8) | 0.62734 (10) | 0.41960 (8) | 0.01628 (13) | |
C4 | 0.66762 (7) | 0.64864 (9) | 0.30976 (7) | 0.01290 (12) | |
C5 | 0.72876 (8) | 0.48658 (9) | 0.27115 (7) | 0.01284 (12) | |
C6 | 0.6659 (2) | 0.10352 (15) | 0.14198 (13) | 0.0421 (3) | |
H3O | 0.7827 (16) | 0.606 (2) | 0.5473 (14) | 0.031 (4)* | |
H3N | 0.7992 (14) | 0.8487 (18) | 0.3760 (13) | 0.018 (3)* | |
H1A | 0.5627 (16) | 0.436 (2) | 0.1172 (15) | 0.023 (3)* | |
H1B | 0.6732 (17) | 0.545 (2) | 0.0903 (15) | 0.029 (4)* | |
H3A | 0.5946 (14) | 0.7311 (17) | 0.4411 (12) | 0.018 (3)* | |
H3B | 0.5319 (15) | 0.554 (2) | 0.3952 (13) | 0.024 (3)* | |
H4 | 0.5890 (16) | 0.6908 (19) | 0.2414 (14) | 0.024 (3)* | |
H5 | 0.7184 (13) | 0.3900 (17) | 0.3160 (12) | 0.012 (3)* | |
H6A | 0.552 (2) | 0.103 (3) | 0.118 (2) | 0.052 (3)* | |
H6B | 0.693 (2) | −0.003 (3) | 0.1116 (19) | 0.052 (3)* | |
H6C | 0.713 (2) | 0.106 (3) | 0.230 (2) | 0.052 (3)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.03705 (12) | 0.02584 (11) | 0.01991 (10) | 0.00124 (9) | 0.01417 (8) | −0.00624 (8) |
O1 | 0.0122 (2) | 0.0129 (2) | 0.0260 (3) | −0.00050 (18) | 0.0066 (2) | −0.0043 (2) |
O2 | 0.0126 (2) | 0.0179 (3) | 0.0234 (3) | −0.00324 (19) | 0.0065 (2) | −0.0010 (2) |
O3 | 0.0216 (3) | 0.0178 (3) | 0.0166 (3) | −0.0059 (2) | 0.0074 (2) | 0.0020 (2) |
N3 | 0.0127 (2) | 0.0100 (3) | 0.0170 (3) | −0.0009 (2) | 0.0068 (2) | 0.0000 (2) |
C1 | 0.0219 (3) | 0.0197 (4) | 0.0134 (3) | −0.0007 (3) | 0.0057 (3) | −0.0012 (3) |
C2 | 0.0136 (3) | 0.0120 (3) | 0.0141 (3) | −0.0008 (2) | 0.0057 (2) | 0.0007 (2) |
C3 | 0.0157 (3) | 0.0161 (3) | 0.0205 (4) | −0.0008 (2) | 0.0106 (3) | −0.0003 (3) |
C4 | 0.0108 (2) | 0.0129 (3) | 0.0149 (3) | −0.0005 (2) | 0.0043 (2) | 0.0005 (2) |
C5 | 0.0121 (2) | 0.0127 (3) | 0.0139 (3) | −0.0019 (2) | 0.0047 (2) | −0.0008 (2) |
C6 | 0.0847 (11) | 0.0204 (4) | 0.0279 (6) | 0.0071 (5) | 0.0281 (7) | 0.0016 (4) |
S1—C1 | 1.8042 (9) | C1—H1A | 0.914 (15) |
S1—C6 | 1.8085 (14) | C1—H1B | 0.930 (17) |
O1—C2 | 1.3507 (9) | C3—C4 | 1.5222 (11) |
O1—C5 | 1.4538 (9) | C3—H3A | 0.909 (14) |
O2—C2 | 1.2247 (9) | C3—H3B | 0.972 (14) |
O3—C3 | 1.4201 (11) | C4—C5 | 1.5499 (10) |
O3—H3O | 0.743 (13) | C4—H4 | 0.957 (15) |
N3—C2 | 1.3402 (9) | C5—H5 | 0.952 (13) |
N3—C4 | 1.4530 (9) | C6—H6A | 1.06 (2) |
N3—H3N | 0.829 (14) | C6—H6B | 0.99 (2) |
C1—C5 | 1.5172 (11) | C6—H6C | 0.97 (2) |
C1—S1—C6 | 100.40 (5) | H3A—C3—H3B | 111.4 (12) |
C2—O1—C5 | 109.43 (6) | N3—C4—C3 | 111.81 (6) |
C3—O3—H3O | 107.9 (13) | N3—C4—C5 | 100.96 (5) |
C2—N3—C4 | 112.43 (6) | C3—C4—C5 | 114.50 (6) |
C2—N3—H3N | 119.9 (9) | N3—C4—H4 | 110.7 (9) |
C4—N3—H3N | 123.0 (9) | C3—C4—H4 | 109.1 (9) |
C5—C1—S1 | 115.86 (6) | C5—C4—H4 | 109.6 (9) |
C5—C1—H1A | 108.2 (10) | O1—C5—C1 | 109.90 (6) |
S1—C1—H1A | 109.3 (10) | O1—C5—C4 | 105.14 (6) |
C5—C1—H1B | 109.3 (10) | C1—C5—C4 | 111.91 (6) |
S1—C1—H1B | 105.2 (10) | O1—C5—H5 | 107.4 (7) |
H1A—C1—H1B | 108.7 (14) | C1—C5—H5 | 109.2 (8) |
O2—C2—N3 | 127.40 (7) | C4—C5—H5 | 113.1 (8) |
O2—C2—O1 | 121.61 (7) | S1—C6—H6A | 113.8 (13) |
N3—C2—O1 | 110.98 (6) | S1—C6—H6B | 108.9 (12) |
O3—C3—C4 | 112.51 (6) | H6A—C6—H6B | 107.0 (17) |
O3—C3—H3A | 111.1 (8) | S1—C6—H6C | 108.3 (13) |
C4—C3—H3A | 107.6 (9) | H6A—C6—H6C | 111.1 (17) |
O3—C3—H3B | 106.0 (9) | H6B—C6—H6C | 107.7 (17) |
C4—C3—H3B | 108.3 (8) | ||
C6—S1—C1—C5 | 71.48 (8) | C2—O1—C5—C1 | 115.03 (7) |
C4—N3—C2—O2 | −173.09 (8) | C2—O1—C5—C4 | −5.56 (8) |
C4—N3—C2—O1 | 7.65 (9) | S1—C1—C5—O1 | 58.29 (8) |
C5—O1—C2—O2 | 179.83 (7) | S1—C1—C5—C4 | 174.71 (5) |
C5—O1—C2—N3 | −0.86 (9) | N3—C4—C5—O1 | 9.13 (7) |
C2—N3—C4—C3 | 111.84 (7) | C3—C4—C5—O1 | −111.14 (7) |
C2—N3—C4—C5 | −10.33 (8) | N3—C4—C5—C1 | −110.13 (7) |
O3—C3—C4—N3 | −64.24 (8) | C3—C4—C5—C1 | 129.59 (7) |
O3—C3—C4—C5 | 49.80 (9) |
D—H···A | D—H | H···A | D···A | 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+3/2, y+1/2, −z+1; (ii) −x+2, y, −z+1; (iii) x−1/2, y−1/2, z. |
Experimental details
Crystal data | |
Chemical formula | C6H11NO3S |
Mr | 177.22 |
Crystal system, space group | Monoclinic, C2 |
Temperature (K) | 98 |
a, b, c (Å) | 9.7821 (4), 7.9620 (3), 11.5472 (4) |
β (°) | 109.837 (2) |
V (Å3) | 845.99 (6) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.34 |
Crystal size (mm) | 0.45 × 0.23 × 0.07 |
Data collection | |
Diffractometer | Bruker–Nonius APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan [Blessing (1995) and SADABS (Sheldrick, 1996)] |
Tmin, Tmax | 0.854, 0.980 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 16080, 3172, 3091 |
Rint | 0.021 |
(sin θ/λ)max (Å−1) | 0.803 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.022, 0.060, 1.07 |
No. of reflections | 3172 |
No. of parameters | 142 |
No. of restraints | 2 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.38, −0.21 |
Absolute structure | Flack (1983), 1409 Friedel pairs |
Absolute structure parameter | 0.02 (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).
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3N···O3i | 0.829 (14) | 2.029 (14) | 2.8442 (9) | 167.4 (14) |
O3—H3O···O2ii | 0.742 (16) | 1.966 (16) | 2.7018 (9) | 171.4 (16) |
C5—H5···O2iii | 0.952 (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) x−1/2, y−1/2, 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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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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.