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

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5,5-Di­methyl-2-methyl­seleno-1,3,2-dioxa­phospho­rinan-2-one

aChemical Faculty, Gdansk University of Technology, Narutowicza 11/12, Gdansk PL-80233, Poland
*Correspondence e-mail: jaroslaw.chojnacki@chem.pg.gda.pl

(Received 27 February 2010; accepted 4 March 2010; online 17 March 2010)

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.

Related literature

For the structures of similar methyl esters with >P(Se)OMe and >P(Se)SeMe groups, see: Grand et al. (1975[Grand, A., Martin, J., Robert, J. B. & Tordjman, I. (1975). Acta Cryst. B31, 2523-2524.]); Bartczak et al. (1987[Bartczak, T. J., Wolf, W., Swepston, P. N. & Zerong, L. (1987). Acta Cryst. C43, 1788-1790.]). For 5,5-dimethyl-2-seleno-1,3,2-dioxaphospho­rin­ane derivatives with equatorial Se atoms, see: Bartczak & Wolf (1983[Bartczak, T. J. & Wolf, W. (1983). Acta Cryst. C39, 224-227.]); Bartczak et al. (1983[Bartczak, T. J., Gałdecki, Z., Trzeźwińska, H. B. & Wolf, W. (1983). Acta Cryst. C39, 731-732.]); Wolf & Bartczak (1989[Wolf, W. M. & Bartczak, T. J. (1989). Acta Cryst. C45, 1767-1770.]) and for O-acyl derivatives with equatorial selenium, see: Cholewinski et al. (2009[Cholewinski, G., Chojnacki, J., Pikies, J. & Rachon, J. (2009). Org. Biomol. Chem. 7, 4095-4100.]). For conformers with axial Se atoms, see: Bartczak et al. (1986[Bartczak, T. J., Gałdecki, Z., Wolf, W. M., Lesiak, K. & Stec, W. J. (1986). Acta Cryst. C42, 244-246.]); Potrzebowski et al. (1994[Potrzebowski, M. J., Grossmann, G., Blaszczyk, J., Wieczorek, M. W., Sieler, J., Knopik, P. & Komber, H. (1994). Inorg. Chem. 33, 4688-4695.]); Wieczorek et al. (1995[Wieczorek, M. W., Blaszczyk, J., Potrzebowski, M. J., Skowronska, A. & Dembinski, R. (1995). Phosphorus Sulfur Silicon Relat. Elem. 102, 15-18.]). For details of the synthesis, see: Rachon et al. (2005[Rachon, J., Cholewinski, G. & Witt, D. (2005). Chem. Commun. 21, 2692-2694.]); Stec (1974[Stec, W. J. (1974). Z. Naturforsch. Teil B, 29, 109-112.]). For a description of the Cambridge Structural Database, see: Allen (2002[Allen, F. H. (2002). Acta Cryst. B58, 380-388.]).

[Scheme 1]

Experimental

Crystal data
  • C6H13O3PSe

  • Mr = 243.09

  • Monoclinic, C c

  • a = 9.2252 (4) Å

  • b = 9.4842 (4) Å

  • c = 11.4160 (6) Å

  • β = 101.078 (5)°

  • V = 980.22 (8) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 3.96 mm−1

  • T = 150 K

  • 0.59 × 0.41 × 0.28 mm

Data collection
  • Oxford Diffraction KM-4-CCD diffractometer

  • Absorption correction: analytical [CrysAlis RED (Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]), using a multifaceted crystal model based on expressions derived by Clark & Reid (1995[Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897.])] Tmin = 0.179, Tmax = 0.372

  • 3146 measured reflections

  • 1238 independent reflections

  • 1214 reflections with I > 2σ(I)

  • Rint = 0.045

Refinement
  • R[F2 > 2σ(F2)] = 0.026

  • wR(F2) = 0.065

  • S = 1.05

  • 1238 reflections

  • 103 parameters

  • 2 restraints

  • H-atom parameters constrained

  • Δρmax = 0.69 e Å−3

  • Δρmin = −0.33 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 189 Friedel pairs

  • Flack parameter: −0.009 (10)

Data collection: CrysAlis CCD (Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]); cell refinement: CrysAlis RED (Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]); data reduction: CrysAlis RED; 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 for Windows (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]) and Mercury (Macrae et al., 2006[Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453-457.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]), PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). publCIF. In preparation.]).

Supporting information


Comment top

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.

Related literature top

For the structures of similar methyl esters with >P(Se)OMe and >P(Se)SeMe groups, see: Grand et al. (1975); Bartczak et al. (1987). For 5,5-dimethyl-2-seleno-1,3,2-dioxaphosphorinane derivatives with equatorial Se atoms, see: Bartczak & Wolf (1983); Bartczak et al. (1983); Wolf & Bartczak (1989) and for O-acyl derivatives with equatorial selenium, see: Cholewinski et al. (2009). For conformers with axial Se atoms, see: Bartczak et al. (1986); Potrzebowski et al. (1994); Wieczorek et al. (1995). For details of the synthesis, see: Rachon et al. (2005); Stec (1974). For a description of the Cambridge Structural Database, see: Allen (2002).

Experimental top

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.

Refinement top

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.

Computing details top

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).

Figures top
[Figure 1] 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.
5,5-Dimethyl-2-methylseleno-1,3,2-dioxaphosphorinan-2-one top
Crystal data top
C6H13O3PSeF(000) = 488
Mr = 243.09Dx = 1.647 Mg m3
Monoclinic, CcMelting point: 364(1) K
Hall symbol: C -2ycMo Kα radiation, λ = 0.71073 Å
a = 9.2252 (4) ÅCell parameters from 3018 reflections
b = 9.4842 (4) Åθ = 3.1–28.6°
c = 11.4160 (6) ŵ = 3.96 mm1
β = 101.078 (5)°T = 150 K
V = 980.22 (8) Å3Needless, colourless
Z = 40.59 × 0.41 × 0.28 mm
Data collection top
Oxford Diffraction KM-4-CCD
diffractometer
1238 independent reflections
Radiation source: Mo Ka radiation1214 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.045
Detector resolution: 8.1883 pixels mm-1θmax = 27°, θmin = 3.1°
ω scans, 0.8° widthh = 1111
Absorption correction: analytical
[CrysAlis RED (Oxford Diffraction, 2009), using a multifaceted crystal model based on expressions derived by Clark & Reid (1995)]
k = 1111
Tmin = 0.179, Tmax = 0.372l = 514
3146 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)] = 0.026H-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 reflectionsΔρmax = 0.69 e Å3
103 parametersΔρmin = 0.33 e Å3
2 restraintsAbsolute structure: Flack (1983), 189 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.009 (10)
Crystal data top
C6H13O3PSeV = 980.22 (8) Å3
Mr = 243.09Z = 4
Monoclinic, CcMo Kα radiation
a = 9.2252 (4) ŵ = 3.96 mm1
b = 9.4842 (4) ÅT = 150 K
c = 11.4160 (6) Å0.59 × 0.41 × 0.28 mm
β = 101.078 (5)°
Data collection top
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 = 0.372Rint = 0.045
3146 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.026H-atom parameters constrained
wR(F2) = 0.065Δρmax = 0.69 e Å3
S = 1.05Δρmin = 0.33 e Å3
1238 reflectionsAbsolute structure: Flack (1983), 189 Friedel pairs
103 parametersAbsolute structure parameter: 0.009 (10)
2 restraints
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Se10.50195 (3)0.96219 (3)0.92664 (3)0.03344 (13)
P10.69226 (10)0.84725 (9)0.88178 (8)0.02227 (18)
O10.7985 (3)0.9613 (2)0.8432 (2)0.0256 (6)
O20.7776 (3)0.7862 (3)1.0038 (2)0.0268 (5)
O30.6521 (3)0.7389 (3)0.7910 (3)0.0352 (6)
C10.8748 (4)1.0581 (4)0.9339 (3)0.0264 (7)
H1A0.80171.12010.96140.032*
H1B0.94271.11850.89860.032*
C20.8592 (4)0.8836 (4)1.0927 (3)0.0267 (7)
H2A0.91730.82851.15920.032*
H2B0.78820.94261.12570.032*
C30.9621 (4)0.9780 (4)1.0400 (3)0.0234 (7)
C41.0265 (5)1.0859 (5)1.1365 (4)0.0352 (8)
H4A0.94631.14231.15760.053*
H4B1.09571.14791.10610.053*
H4C1.07851.03611.20750.053*
C51.0866 (4)0.8934 (4)1.0014 (4)0.0317 (8)
H5A1.15870.95840.97830.048*
H5B1.04530.83320.93340.048*
H5C1.13530.83451.06790.048*
C60.4408 (6)1.0359 (5)0.7641 (5)0.0502 (13)
H6A0.42410.95730.70750.075*
H6B0.51841.09730.74490.075*
H6C0.34931.09010.75880.075*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Se10.02636 (18)0.0350 (2)0.0420 (2)0.00387 (16)0.01415 (14)0.0031 (2)
P10.0210 (4)0.0227 (4)0.0225 (4)0.0011 (3)0.0029 (3)0.0025 (4)
O10.0235 (13)0.0358 (15)0.0182 (11)0.0015 (9)0.0056 (10)0.0014 (10)
O20.0287 (12)0.0229 (11)0.0273 (12)0.0058 (9)0.0014 (10)0.0014 (11)
O30.0294 (13)0.0375 (13)0.0351 (14)0.0044 (12)0.0027 (11)0.0129 (13)
C10.0289 (18)0.0251 (15)0.0266 (17)0.0075 (14)0.0088 (15)0.0013 (15)
C20.0282 (16)0.0323 (17)0.0189 (14)0.0088 (13)0.0029 (13)0.0021 (14)
C30.0240 (17)0.0262 (17)0.0210 (15)0.0061 (13)0.0065 (14)0.0029 (14)
C40.039 (2)0.0370 (19)0.0292 (18)0.0188 (17)0.0060 (15)0.0077 (18)
C50.0253 (18)0.039 (2)0.0296 (18)0.0000 (14)0.0021 (14)0.0003 (18)
C60.044 (3)0.054 (3)0.050 (3)0.026 (2)0.003 (2)0.005 (2)
Geometric parameters (Å, º) top
Se1—C61.962 (6)C2—H2B0.99
Se1—P12.2094 (9)C3—C51.534 (5)
P1—O31.456 (3)C3—C41.537 (5)
P1—O21.574 (3)C4—H4A0.98
P1—O11.579 (3)C4—H4B0.98
O1—C11.460 (4)C4—H4C0.98
O2—C21.468 (4)C5—H5A0.98
C1—C31.523 (5)C5—H5B0.98
C1—H1A0.99C5—H5C0.98
C1—H1B0.99C6—H6A0.98
C2—C31.512 (5)C6—H6B0.98
C2—H2A0.99C6—H6C0.98
C6—Se1—P193.09 (15)C1—C3—C5110.1 (3)
O3—P1—O2112.74 (15)C2—C3—C4107.1 (3)
O3—P1—O1111.84 (16)C1—C3—C4108.2 (3)
O2—P1—O1105.49 (14)C5—C3—C4110.3 (3)
O3—P1—Se1114.08 (12)C3—C4—H4A109.5
O2—P1—Se1105.16 (11)C3—C4—H4B109.5
O1—P1—Se1106.89 (10)H4A—C4—H4B109.5
C1—O1—P1118.3 (2)C3—C4—H4C109.5
C2—O2—P1119.0 (2)H4A—C4—H4C109.5
O1—C1—C3111.1 (3)H4B—C4—H4C109.5
O1—C1—H1A109.4C3—C5—H5A109.5
C3—C1—H1A109.4C3—C5—H5B109.5
O1—C1—H1B109.4H5A—C5—H5B109.5
C3—C1—H1B109.4C3—C5—H5C109.5
H1A—C1—H1B108H5A—C5—H5C109.5
O2—C2—C3112.1 (3)H5B—C5—H5C109.5
O2—C2—H2A109.2Se1—C6—H6A109.5
C3—C2—H2A109.2Se1—C6—H6B109.5
O2—C2—H2B109.2H6A—C6—H6B109.5
C3—C2—H2B109.2Se1—C6—H6C109.5
H2A—C2—H2B107.9H6A—C6—H6C109.5
C2—C3—C1109.6 (3)H6B—C6—H6C109.5
C2—C3—C5111.5 (3)
C6—Se1—P1—O361.8 (2)P1—O1—C1—C354.9 (4)
C6—Se1—P1—O2174.2 (2)P1—O2—C2—C351.4 (4)
C6—Se1—P1—O162.4 (2)O2—C2—C3—C156.3 (4)
O3—P1—O1—C1166.5 (2)O2—C2—C3—C565.9 (4)
O2—P1—O1—C143.6 (3)O2—C2—C3—C4173.4 (3)
Se1—P1—O1—C168.0 (3)O1—C1—C3—C258.0 (4)
O3—P1—O2—C2163.9 (3)O1—C1—C3—C565.0 (4)
O1—P1—O2—C241.6 (3)O1—C1—C3—C4174.5 (3)
Se1—P1—O2—C271.2 (3)

Experimental details

Crystal data
Chemical formulaC6H13O3PSe
Mr243.09
Crystal system, space groupMonoclinic, Cc
Temperature (K)150
a, b, c (Å)9.2252 (4), 9.4842 (4), 11.4160 (6)
β (°) 101.078 (5)
V3)980.22 (8)
Z4
Radiation typeMo Kα
µ (mm1)3.96
Crystal size (mm)0.59 × 0.41 × 0.28
Data collection
DiffractometerOxford Diffraction KM-4-CCD
diffractometer
Absorption correctionAnalytical
[CrysAlis RED (Oxford Diffraction, 2009), using a multifaceted crystal model based on expressions derived by Clark & Reid (1995)]
Tmin, Tmax0.179, 0.372
No. of measured, independent and
observed [I > 2σ(I)] reflections
3146, 1238, 1214
Rint0.045
(sin θ/λ)max1)0.639
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.026, 0.065, 1.05
No. of reflections1238
No. of parameters103
No. of restraints2
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.69, 0.33
Absolute structureFlack (1983), 189 Friedel pairs
Absolute structure parameter0.009 (10)

Computer programs: CrysAlis CCD (Oxford Diffraction, 2009), CrysAlis RED (Oxford Diffraction, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997) and Mercury (Macrae et al., 2006), WinGX (Farrugia, 1999), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

 

References

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