Acta Cryst. (2010). E66, o856 [ doi:10.1107/S1600536810008330 ]
The title compound, C6H13O3PSe, was obtained in the reaction of 5,5-dimethyl-2-oxo-2-seleno-1,3,2-dioxaphosphorinane potassium salt with methyl iodide. The selenomethyl group is in the axial position in relation to the six-membered dioxaphosphorinane ring.
The title compound was obtained according to Stec, 1974. To a solution of 5,5-dimethyl-2-oxo-2-seleno-1,3,2-dioxaphosphorinane potassium salt (Rachon et al., 2005) (1 mmol) in THF (5 ml) was added methyl iodide (1 mmol) portionwise. The reaction mixture was stirred at room temperature for 15 min. Then, the solvent was evaporated and crude product crystallized from hexane. Re-crystallization from CH2Cl2 – petroleum ether (bp 40 – 60 °C) gave product in 53% yield.
Mp 90.5-92 °C, 31P NMR (THF + C6D6) δ = 11.5 ppm, 1JPSe =456 Hz, IR ν(cm-1): P=O 1258.
Literature data (Stec, 1974): mp 90.5-91.5 °C; 31P NMR (methanol) δ = 13.1 ppm, 1JPSe = 457 Hz.
Hydrogen atoms were placed in calculated positions and refined using a standard riding model. C–H bond lengths were set to 0.99 and 0.98 Å and Uiso(H) were set to 1.5 and 1.2 Ueq(C) for CH3 and CH2 groups, respectively.
The residual electron density peak is 0.83 Å from SE1, the deepest electron density hole is 1.28 Å from H5A. Absolute structure determination is unequivocal because only 189 Bijvoet pairs were measured. As the structure is not chiral, we did not attempt to elucidate it further.
Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell refinement: CrysAlis RED (Oxford Diffraction, 2009); data reduction: CrysAlis RED (Oxford Diffraction, 2009); 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 Mercury (Macrae et al., 2006); software used to prepare material for publication: WinGX (Farrugia, 1999), PLATON (Spek, 2009) and publCIF (Westrip, 2010).
![[Figure 1]](./dn2544fig1thm.gif)
| Fig. 1. The nolecular structure of (I), with the atom labeling scheme. Displacement ellipsods are drawn at the 30% probability level. H atoms are represented as small spheres of arbitrary radii. |
| C6H13O3PSe | F(000) = 488 |
| Mr = 243.09 | Dx = 1.647 Mg m−3 |
| Monoclinic, Cc | Melting point: 364(1) K |
| Hall symbol: C -2yc | Mo Kα radiation, λ = 0.71073 Å |
| a = 9.2252 (4) Å | Cell parameters from 3018 reflections |
| b = 9.4842 (4) Å | θ = 3.1–28.6° |
| c = 11.4160 (6) Å | µ = 3.96 mm−1 |
| β = 101.078 (5)° | T = 150 K |
| V = 980.22 (8) Å3 | Needless, colourless |
| Z = 4 | 0.59 × 0.41 × 0.28 mm |
| Oxford Diffraction KM-4-CCD diffractometer | 1238 independent reflections |
| Radiation source: Mo Ka radiation | 1214 reflections with I > 2σ(I) |
| graphite | Rint = 0.045 |
| Detector resolution: 8.1883 pixels mm-1 | θmax = 27°, θmin = 3.1° |
| ω scans, 0.8° width | h = −11→11 |
| Absorption correction: analytical [CrysAlis RED (Oxford Diffraction, 2009), using a multifaceted crystal model based on expressions derived by Clark & Reid (1995)] | k = −11→11 |
| Tmin = 0.179, Tmax = 0.372 | l = −5→14 |
| 3146 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)] = 0.026 | H-atom parameters constrained |
| wR(F2) = 0.065 | w = 1/[σ2(Fo2) + (0.0472P)2] where P = (Fo2 + 2Fc2)/3 |
| S = 1.05 | (Δ/σ)max = 0.005 |
| 1238 reflections | Δρmax = 0.69 e Å−3 |
| 103 parameters | Δρmin = −0.33 e Å−3 |
| 2 restraints | Absolute structure: Flack (1983), 189 Friedel pairs |
| Primary atom site location: structure-invariant direct methods | Flack parameter: −0.009 (10) |
| C6H13O3PSe | V = 980.22 (8) Å3 |
| Mr = 243.09 | Z = 4 |
| Monoclinic, Cc | Mo Kα radiation |
| a = 9.2252 (4) Å | µ = 3.96 mm−1 |
| b = 9.4842 (4) Å | T = 150 K |
| c = 11.4160 (6) Å | 0.59 × 0.41 × 0.28 mm |
| β = 101.078 (5)° |
| Oxford Diffraction KM-4-CCD diffractometer | 1238 independent reflections |
| Absorption correction: analytical [CrysAlis RED (Oxford Diffraction, 2009), using a multifaceted crystal model based on expressions derived by Clark & Reid (1995)] | 1214 reflections with I > 2σ(I) |
| Tmin = 0.179, Tmax = 0.372 | Rint = 0.045 |
| 3146 measured reflections | θmax = 27° |
| R[F2 > 2σ(F2)] = 0.026 | H-atom parameters constrained |
| wR(F2) = 0.065 | Δρmax = 0.69 e Å−3 |
| S = 1.05 | Δρmin = −0.33 e Å−3 |
| 1238 reflections | Absolute structure: Flack (1983), 189 Friedel pairs |
| 103 parameters | Flack parameter: −0.009 (10) |
| 2 restraints |
Experimental. CrysAlis RED (Oxford Diffraction, 2009), Analytical numeric absorption correction using a multifaceted crystal model based on expressions derived by Clark & Reid (1995). |
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 | ||
| Se1 | 0.50195 (3) | 0.96219 (3) | 0.92664 (3) | 0.03344 (13) | |
| P1 | 0.69226 (10) | 0.84725 (9) | 0.88178 (8) | 0.02227 (18) | |
| O1 | 0.7985 (3) | 0.9613 (2) | 0.8432 (2) | 0.0256 (6) | |
| O2 | 0.7776 (3) | 0.7862 (3) | 1.0038 (2) | 0.0268 (5) | |
| O3 | 0.6521 (3) | 0.7389 (3) | 0.7910 (3) | 0.0352 (6) | |
| C1 | 0.8748 (4) | 1.0581 (4) | 0.9339 (3) | 0.0264 (7) | |
| H1A | 0.8017 | 1.1201 | 0.9614 | 0.032* | |
| H1B | 0.9427 | 1.1185 | 0.8986 | 0.032* | |
| C2 | 0.8592 (4) | 0.8836 (4) | 1.0927 (3) | 0.0267 (7) | |
| H2A | 0.9173 | 0.8285 | 1.1592 | 0.032* | |
| H2B | 0.7882 | 0.9426 | 1.1257 | 0.032* | |
| C3 | 0.9621 (4) | 0.9780 (4) | 1.0400 (3) | 0.0234 (7) | |
| C4 | 1.0265 (5) | 1.0859 (5) | 1.1365 (4) | 0.0352 (8) | |
| H4A | 0.9463 | 1.1423 | 1.1576 | 0.053* | |
| H4B | 1.0957 | 1.1479 | 1.1061 | 0.053* | |
| H4C | 1.0785 | 1.0361 | 1.2075 | 0.053* | |
| C5 | 1.0866 (4) | 0.8934 (4) | 1.0014 (4) | 0.0317 (8) | |
| H5A | 1.1587 | 0.9584 | 0.9783 | 0.048* | |
| H5B | 1.0453 | 0.8332 | 0.9334 | 0.048* | |
| H5C | 1.1353 | 0.8345 | 1.0679 | 0.048* | |
| C6 | 0.4408 (6) | 1.0359 (5) | 0.7641 (5) | 0.0502 (13) | |
| H6A | 0.4241 | 0.9573 | 0.7075 | 0.075* | |
| H6B | 0.5184 | 1.0973 | 0.7449 | 0.075* | |
| H6C | 0.3493 | 1.0901 | 0.7588 | 0.075* |
| U11 | U22 | U33 | U12 | U13 | U23 | |
| Se1 | 0.02636 (18) | 0.0350 (2) | 0.0420 (2) | 0.00387 (16) | 0.01415 (14) | −0.0031 (2) |
| P1 | 0.0210 (4) | 0.0227 (4) | 0.0225 (4) | 0.0011 (3) | 0.0029 (3) | −0.0025 (4) |
| O1 | 0.0235 (13) | 0.0358 (15) | 0.0182 (11) | −0.0015 (9) | 0.0056 (10) | 0.0014 (10) |
| O2 | 0.0287 (12) | 0.0229 (11) | 0.0273 (12) | −0.0058 (9) | 0.0014 (10) | 0.0014 (11) |
| O3 | 0.0294 (13) | 0.0375 (13) | 0.0351 (14) | 0.0044 (12) | −0.0027 (11) | −0.0129 (13) |
| C1 | 0.0289 (18) | 0.0251 (15) | 0.0266 (17) | −0.0075 (14) | 0.0088 (15) | 0.0013 (15) |
| C2 | 0.0282 (16) | 0.0323 (17) | 0.0189 (14) | −0.0088 (13) | 0.0029 (13) | 0.0021 (14) |
| C3 | 0.0240 (17) | 0.0262 (17) | 0.0210 (15) | −0.0061 (13) | 0.0065 (14) | −0.0029 (14) |
| C4 | 0.039 (2) | 0.0370 (19) | 0.0292 (18) | −0.0188 (17) | 0.0060 (15) | −0.0077 (18) |
| C5 | 0.0253 (18) | 0.039 (2) | 0.0296 (18) | 0.0000 (14) | 0.0021 (14) | −0.0003 (18) |
| C6 | 0.044 (3) | 0.054 (3) | 0.050 (3) | 0.026 (2) | 0.003 (2) | 0.005 (2) |
| Se1—C6 | 1.962 (6) | C2—H2B | 0.99 |
| Se1—P1 | 2.2094 (9) | C3—C5 | 1.534 (5) |
| P1—O3 | 1.456 (3) | C3—C4 | 1.537 (5) |
| P1—O2 | 1.574 (3) | C4—H4A | 0.98 |
| P1—O1 | 1.579 (3) | C4—H4B | 0.98 |
| O1—C1 | 1.460 (4) | C4—H4C | 0.98 |
| O2—C2 | 1.468 (4) | C5—H5A | 0.98 |
| C1—C3 | 1.523 (5) | C5—H5B | 0.98 |
| C1—H1A | 0.99 | C5—H5C | 0.98 |
| C1—H1B | 0.99 | C6—H6A | 0.98 |
| C2—C3 | 1.512 (5) | C6—H6B | 0.98 |
| C2—H2A | 0.99 | C6—H6C | 0.98 |
| C6—Se1—P1 | 93.09 (15) | C1—C3—C5 | 110.1 (3) |
| O3—P1—O2 | 112.74 (15) | C2—C3—C4 | 107.1 (3) |
| O3—P1—O1 | 111.84 (16) | C1—C3—C4 | 108.2 (3) |
| O2—P1—O1 | 105.49 (14) | C5—C3—C4 | 110.3 (3) |
| O3—P1—Se1 | 114.08 (12) | C3—C4—H4A | 109.5 |
| O2—P1—Se1 | 105.16 (11) | C3—C4—H4B | 109.5 |
| O1—P1—Se1 | 106.89 (10) | H4A—C4—H4B | 109.5 |
| C1—O1—P1 | 118.3 (2) | C3—C4—H4C | 109.5 |
| C2—O2—P1 | 119.0 (2) | H4A—C4—H4C | 109.5 |
| O1—C1—C3 | 111.1 (3) | H4B—C4—H4C | 109.5 |
| O1—C1—H1A | 109.4 | C3—C5—H5A | 109.5 |
| C3—C1—H1A | 109.4 | C3—C5—H5B | 109.5 |
| O1—C1—H1B | 109.4 | H5A—C5—H5B | 109.5 |
| C3—C1—H1B | 109.4 | C3—C5—H5C | 109.5 |
| H1A—C1—H1B | 108 | H5A—C5—H5C | 109.5 |
| O2—C2—C3 | 112.1 (3) | H5B—C5—H5C | 109.5 |
| O2—C2—H2A | 109.2 | Se1—C6—H6A | 109.5 |
| C3—C2—H2A | 109.2 | Se1—C6—H6B | 109.5 |
| O2—C2—H2B | 109.2 | H6A—C6—H6B | 109.5 |
| C3—C2—H2B | 109.2 | Se1—C6—H6C | 109.5 |
| H2A—C2—H2B | 107.9 | H6A—C6—H6C | 109.5 |
| C2—C3—C1 | 109.6 (3) | H6B—C6—H6C | 109.5 |
| C2—C3—C5 | 111.5 (3) | ||
| C6—Se1—P1—O3 | −61.8 (2) | P1—O1—C1—C3 | 54.9 (4) |
| C6—Se1—P1—O2 | 174.2 (2) | P1—O2—C2—C3 | −51.4 (4) |
| C6—Se1—P1—O1 | 62.4 (2) | O2—C2—C3—C1 | 56.3 (4) |
| O3—P1—O1—C1 | −166.5 (2) | O2—C2—C3—C5 | −65.9 (4) |
| O2—P1—O1—C1 | −43.6 (3) | O2—C2—C3—C4 | 173.4 (3) |
| Se1—P1—O1—C1 | 68.0 (3) | O1—C1—C3—C2 | −58.0 (4) |
| O3—P1—O2—C2 | 163.9 (3) | O1—C1—C3—C5 | 65.0 (4) |
| O1—P1—O2—C2 | 41.6 (3) | O1—C1—C3—C4 | −174.5 (3) |
| Se1—P1—O2—C2 | −71.2 (3) |
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The title compound, 5,5-dimethyl-2-methylseleno-2-oxo-1,3,2-dioxaphosphorinane, forms molecular crystals (Fig. 1). No stronger intermolecular interactions beside weak C–H···O=P contacts (the shortest H6c···O3 distance is 2.387 Å) can be found. Bonds P–Se and Se–C in the selenomethyl group are almost perpendicular, which is expected for selenium compounds. For comparison: in related compound bearing >P(Se)SeMe moiety (Bartczak et al., 1987) the relevant angle is ca two degrees wider (95.17°). Rather long P–Se bond length of ca 2.2 Å is typical for selenium with the coordination number two.
Selenium atom can adopt axial or equatorial positions in the chair conformation of the six-membered ring in derivatives of 5,5-dimethyl-2-seleno-1,3,2-dioxaphosphorinane. Search of CSD data (Allen, 2002) reveals both possibilities can be realised in the solid state structures. Derivatives, which are substituted at P atom by –NH–aryl group, often have equatorial Se atoms (Bartczak et al., 1983, Bartczak & Wolf, 1983, Wolf & Bartczak, 1989 and Grand et al., 1975). Recently, we reported on several O-acyl derivatives with equatorial Se, but also –NH2 and NH–C(O)tBu derivatives, which contain selenium atom in axial positions (Cholewinski et al., 2009). More precisely, the last derivative contains both conformers - axial and equatorial - in the unit cell. Conformers with axial Se atoms were found also for –NHEt derivative (Bartczak et al., 1986), and for two compounds with double P=O or P=S bonds: the bisselenide and the bisdiselenide, respectively (Wieczorek et al., 1995 and Potrzebowski et al., 1994). In the case of 5,5-dimethyl-2-methylseleno-1,3,2-dioxaphosphorinane-2-selenide the group –SeMe is aligned in the axial position and P=Se positioned equatorially (Bartczak et al., 1987). In 5,5-dimethyl-2-methoxy-2-seleno-1,3,2-dioxaphosphorinane –OMe is axial, so Se atom adopts the equatorial position (Grand et al., 1975).
In our previous study (Cholewinski et al., 2009) we described a correlation between the anomeric iteractions nO → σ*P–X (where X is O or NH) and axial / equatorial conformer distribution in >P(Se)XR systems. However, those orbital systems were different - contained single P–X bond and the selenium atom was linked only to P atom, formally by a double bond. The reasoning derived there cannot be applied to prediction of conformation for systems with double P=O and single P–Se bonds, like the present case or to bisselenides. In fact, the doubly bonded oxygen atoms tend to occupy equatorial position in relation to the six-membered ring.