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

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); 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

Crystal data

• C₆H₁₃O₃PSe

• M_r = 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) ų

• 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), using a multifaceted crystal model based on expressions derived by Clark & Reid (1995)] T_min = 0.179, T_max = 0.372

• 3146 measured reflections

• 1238 independent reflections

• 1214 reflections with I > 2σ(I)

• R_int = 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

• Δρ_max = 0.69 e Å⁻³

• Δρ_min = −0.33 e Å⁻³

• Absolute structure: Flack (1983), 189 Friedel pairs

• Flack parameter: −0.009 (10)

Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell refinement: CrysAlis RED (Oxford Diffraction, 2009); data reduction: CrysAlis RED; 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).

Supporting information

S1. Comment

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 n_O → 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

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).

S2. Experimental

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, ¹J_PSe =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, ¹J_PSe = 457 Hz.

S3. Refinement

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 U_iso(H) were set to 1.5 and 1.2 U_eq(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

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

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

Crystal data

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) Å^3	Needless, colourless
Z = 4	0.59 × 0.41 × 0.28 mm

Data collection

Oxford Diffraction KM-4-CCD diffractometer	1238 independent reflections
Radiation source: Mo Ka radiation	1214 reflections with I > 2σ(I)
Graphite monochromator	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

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.026	H-atom parameters constrained
wR(F^2) = 0.065	w = 1/[σ^2(Fo^2) + (0.0472P)^2] where P = (Fo^2 + 2Fc^2)/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	Absolute structure parameter: −0.009 (10)

Special details

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 (Ų)

	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*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

Geometric parameters (Å, º)

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)