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The title molecule, C
2H
6OSe, has a trigonal–pyramidal structure analogous to that of its sulfur analog, dimethyl sulfoxide (DMSO). The Se—O distance in dimethyl selenoxide (DMSeO) is 1.6756 (16) Å [
versus S—O of 1.531 (5) Å in DMSO], consistent with a highly polar σ bond. In the solid state, the molecules of DMSeO are linked into centrosymmetric dimers formed by two C—H
O hydrogen bonds. These dimers further aggregate into a ladder-like supramolecular network
via two additional intermolecular C—H
O interactions. As a result, each O atom of DMSeO acts as an acceptor of three hydrogen bonds.
Supporting information
CCDC reference: 288627
Dimethyl selenoxide was synthesized as described previously by us (Dikarev, Petrukhina et al., 2003). The solid was dissolved in n-hexane; the solution was then filtered and kept at 258 K, affording colorless crystals after 2 d. DMSeO decomposes before reaching the melting point (m.p. 365–366 K, sealed capillary). Our attempts to sublime DMSeO at 333 K or higher temperatures resulted in the decomposition of the material. Sublimation at lower temperatures provided amorphous powder that was not suitable for the X-ray analysis. The thermal degradation reaction of DMSeO in the presence of rhodium(II) trifluoroacetate in the gas phase at 403–413 K led to entrapment of the dimethyl selenide fragment in the form of its metal complex (Dikarev, Petrukhina et al., 2003). [For a prior report of the gas phase decomposition of DMSeO, see Rael et al. (1996).]
The range of the refined C—H distances is 0.92 (3)–0.97 (3) Å for the methyl groups.
Data collection: SMART (Bruker, 1999); cell refinement: SMART; data reduction: SAINT (Bruker, 1999); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and SHELXTL (Bruker, 1997); software used to prepare material for publication: SHELXTL.
Crystal data top
C2H6OSe | Z = 2 |
Mr = 125.03 | F(000) = 120 |
Triclinic, P1 | Dx = 2.063 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 4.9794 (7) Å | Cell parameters from 1564 reflections |
b = 6.1470 (9) Å | θ = 3.1–28.1° |
c = 6.8905 (10) Å | µ = 9.11 mm−1 |
α = 106.850 (2)° | T = 173 K |
β = 90.177 (2)° | Plate, colorless |
γ = 94.213 (2)° | 0.26 × 0.17 × 0.05 mm |
V = 201.24 (5) Å3 | |
Data collection top
Bruker SMART APEX CCD area-detector diffractometer | 895 independent reflections |
Radiation source: fine-focus sealed tube | 849 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.012 |
0.3° wide ω exposures scans | θmax = 28.1°, θmin = 3.1° |
Absorption correction: multi-scan (SADABS; Bruker, 1999) | h = −6→6 |
Tmin = 0.182, Tmax = 0.632 | k = −7→7 |
1735 measured reflections | l = −8→9 |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.017 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.045 | All H-atom parameters refined |
S = 1.09 | w = 1/[σ2(Fo2) + (0.03P)2 + 0.026P] where P = (Fo2 + 2Fc2)/3 |
895 reflections | (Δ/σ)max < 0.001 |
61 parameters | Δρmax = 0.37 e Å−3 |
0 restraints | Δρmin = −0.52 e Å−3 |
Crystal data top
C2H6OSe | γ = 94.213 (2)° |
Mr = 125.03 | V = 201.24 (5) Å3 |
Triclinic, P1 | Z = 2 |
a = 4.9794 (7) Å | Mo Kα radiation |
b = 6.1470 (9) Å | µ = 9.11 mm−1 |
c = 6.8905 (10) Å | T = 173 K |
α = 106.850 (2)° | 0.26 × 0.17 × 0.05 mm |
β = 90.177 (2)° | |
Data collection top
Bruker SMART APEX CCD area-detector diffractometer | 895 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 1999) | 849 reflections with I > 2σ(I) |
Tmin = 0.182, Tmax = 0.632 | Rint = 0.012 |
1735 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.017 | 0 restraints |
wR(F2) = 0.045 | All H-atom parameters refined |
S = 1.09 | Δρmax = 0.37 e Å−3 |
895 reflections | Δρmin = −0.52 e Å−3 |
61 parameters | |
Special details top
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. Least-squares planes (x,y,z in crystal coordinates) and deviations from them (* indicates atom used to define plane) 2.0101 (0.0047) x + 4.8194 (0.0044) y + 1.0854 (0.0079) z = 2.3375 (0.0048) * 0.0000 (0.0000) C1 * 0.0000 (0.0000) C2 * 0.0000 (0.0000) O1 0.8383 (0.0012) Se1 Rms deviation of fitted atoms = 0.0000 |
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 | x | y | z | Uiso*/Ueq | |
Se1 | 0.20890 (4) | 0.39901 (3) | 0.76732 (3) | 0.02254 (9) | |
O1 | −0.1284 (3) | 0.3691 (3) | 0.7526 (3) | 0.0334 (4) | |
C1 | 0.3086 (4) | 0.2451 (4) | 0.4938 (3) | 0.0252 (4) | |
C2 | 0.2988 (5) | 0.1617 (4) | 0.8825 (4) | 0.0289 (4) | |
H2C | 0.217 (5) | 0.027 (5) | 0.803 (4) | 0.032 (7)* | |
H1A | 0.500 (5) | 0.242 (4) | 0.492 (4) | 0.025 (6)* | |
H1B | 0.242 (6) | 0.333 (5) | 0.417 (4) | 0.035 (7)* | |
H1C | 0.214 (6) | 0.098 (5) | 0.457 (4) | 0.033 (7)* | |
H2B | 0.237 (6) | 0.208 (6) | 1.021 (5) | 0.049 (8)* | |
H2A | 0.486 (7) | 0.147 (5) | 0.867 (5) | 0.046 (8)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
Se1 | 0.02083 (13) | 0.02192 (13) | 0.02400 (13) | 0.00146 (8) | 0.00169 (8) | 0.00536 (9) |
O1 | 0.0183 (7) | 0.0435 (10) | 0.0399 (9) | 0.0067 (6) | 0.0025 (6) | 0.0134 (7) |
C1 | 0.0260 (11) | 0.0275 (11) | 0.0221 (9) | 0.0021 (9) | 0.0002 (8) | 0.0070 (9) |
C2 | 0.0290 (11) | 0.0315 (12) | 0.0286 (11) | 0.0047 (9) | −0.0009 (9) | 0.0117 (10) |
Geometric parameters (Å, º) top
Se1—O1 | 1.6756 (16) | C1—H1C | 0.95 (3) |
Se1—C2 | 1.930 (2) | C2—H2C | 0.92 (3) |
Se1—C1 | 1.932 (2) | C2—H2B | 0.97 (3) |
C1—H1A | 0.95 (3) | C2—H2A | 0.95 (3) |
C1—H1B | 0.93 (3) | | |
| | | |
O1—Se1—C2 | 103.11 (9) | H1B—C1—H1C | 110 (2) |
O1—Se1—C1 | 102.79 (9) | Se1—C2—H2C | 107.5 (17) |
C2—Se1—C1 | 95.95 (10) | Se1—C2—H2B | 105 (2) |
Se1—C1—H1A | 108.0 (15) | H2C—C2—H2B | 115 (2) |
Se1—C1—H1B | 103.6 (18) | Se1—C2—H2A | 107.1 (19) |
H1A—C1—H1B | 114 (2) | H2C—C2—H2A | 106 (2) |
Se1—C1—H1C | 106.9 (16) | H2B—C2—H2A | 116 (2) |
H1A—C1—H1C | 114 (2) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
C1—H1A···O1i | 0.95 (3) | 2.49 (3) | 3.238 (3) | 135.2 (19) |
C1—H1B···O1ii | 0.93 (3) | 2.54 (3) | 3.457 (3) | 169 (2) |
C2—H2A···O1i | 0.95 (3) | 2.53 (3) | 3.272 (3) | 135 (3) |
Symmetry codes: (i) x+1, y, z; (ii) −x, −y+1, −z+1. |
Experimental details
Crystal data |
Chemical formula | C2H6OSe |
Mr | 125.03 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 173 |
a, b, c (Å) | 4.9794 (7), 6.1470 (9), 6.8905 (10) |
α, β, γ (°) | 106.850 (2), 90.177 (2), 94.213 (2) |
V (Å3) | 201.24 (5) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 9.11 |
Crystal size (mm) | 0.26 × 0.17 × 0.05 |
|
Data collection |
Diffractometer | Bruker SMART APEX CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 1999) |
Tmin, Tmax | 0.182, 0.632 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 1735, 895, 849 |
Rint | 0.012 |
(sin θ/λ)max (Å−1) | 0.664 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.017, 0.045, 1.09 |
No. of reflections | 895 |
No. of parameters | 61 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.37, −0.52 |
Selected geometric parameters (Å, º) topSe1—O1 | 1.6756 (16) | Se1—C1 | 1.932 (2) |
Se1—C2 | 1.930 (2) | | |
| | | |
O1—Se1—C2 | 103.11 (9) | C2—Se1—C1 | 95.95 (10) |
O1—Se1—C1 | 102.79 (9) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
C1—H1A···O1i | 0.95 (3) | 2.49 (3) | 3.238 (3) | 135.2 (19) |
C1—H1B···O1ii | 0.93 (3) | 2.54 (3) | 3.457 (3) | 169 (2) |
C2—H2A···O1i | 0.95 (3) | 2.53 (3) | 3.272 (3) | 135 (3) |
Symmetry codes: (i) x+1, y, z; (ii) −x, −y+1, −z+1. |
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Dimethyl selenoxide (DMSeO) is of interest because of its biological activity and redox cycling (Lanfear et al., 1994; Goeger & Ganter, 1994; Bray et al., 2001) and role in the global selenium cycle (Rael et al., 1996; Zhang et al., 1999; Zhang & Frankenberger, 2000), as well as its excellent hydrogen-bond acceptor properties, which are superior to those of dimethyl sulfoxide (DMSO; Renault & Le Questel, 2004). Also of interest is the proper description of the chalcogen–oxygen bonds in DMSeO and DMSO, which can be treated as single polar bonds or as double bonds involving d orbitals (Bartell et al., 1970; Mezey & Haas, 1982; Dobado et al., 1999; Chesnut & Quin, 2004). We present here the first X-ray structural characterization of dimethyl selenoxide, (I), revealing its geometry and solid-state packing. The latter is notable for involving aggregates held together by three C—H hydrogen bonds to each O atom, which is consistent with a highly polar Se+–O− bond with three lone pairs on the O atom.
Similar to DMSO, the molecule of DMSeO exhibits a trigonal–pyramidal shape (Fig. 1) with an Se—Caverage distance of 1.931 (3) Å, an Se—O distance of 1.6756 (16) Å, a C—Se—Oaverage angle of 103.0 (3)° and an C—Se—C angle of 95.95 (10)° (Table 1). The sum of the angles about the Se atom, ΣX—Se—Y, (ca 302°) is less than the expected value for pyramidal trisubstituted selenium with one lone pair (ca 328.5°) and less than the analogous value for DMSO (ca 311°) (Thomas et al., 1966). Consequently, the pyramid formed with the O atom and two C atoms as a base and the S-atom as an apex in the DMSO molecule is considerably flatter than that in DMSeO. The perpendicular distance from the apical chalcogen atom to the base plane is 0.8383 (12) Å in DMSeO versus only 0.706 Å in the DMSO molecule. This difference can mostly be attributed to the influence of the chalcogen lone pair size (4d versus 3d) on the final shape of the molecule.
A search of the Cambridge Structural Database (CSD; Version 5.26 of February 2005; Allen, 2002) revealed 15 crystal structures of different selenoxides. The Se—O and Se—C bond lengths are very similar within this class of compounds and lie in the ranges 1.621–1.690 and 1.907–1.958 Å, respectively. Introduction of electron-withdrawing perfluorinated substituents into the molecule provides shortening of the Se—O and Se—C bond lengths (Gockel et al., 2000; Klapotke et al., 2002). It is also informative to compare the selenium–oxygen distances in (CH3)2SeO with (CH3)2SeO2 (dimethyl selenone, DMSeO2), which is the oxidized form of (I). The distance in DMSeO2 [1.626 (1) Å; Dikarev, Becker et al., 2003] is 0.05 Å shorter than that in dimethyl selenoxide [1.6756 (16) Å; Table 1]. This observation is consistent with the fact that the Se—O bond in selenoxides is weaker than that in selenones.
Recent high-level calculations showed that the bonding to the central Se atom is consistent with a model of a highly polarized Se—O σ bond rather than an Se═O double bond, the bond strength depending mainly on electrostatic interactions (Dobado et al., 1999). These calculations on DMSeO at the B3LYP and at the MP2(full) (values in parentheses) levels, using the 6–311+G* basis set, predict Se—O = 1.672 (1.663) Å, C—Se = 1.983 (1.948) Å, C—Se—O = 104.0° (103.8°) and C—Se—C = 94.4° (93.8°), ΣX—Se—Y being approximately equal to 302° (301°). Our X-ray structural data show a very good agreement with the geometrical values obtained from calculations.
We have recently presented the first example of dimethyl selenoxide coordinated to the dirhodium(II,II) tetra(trifluoroacetate) complex (Dikarev, Petrukhina et al., 2003). The first approximation of the DMSeO geometry has been proposed based on the observed fact (Cotton et al., 2001) that the selected metal complex does not significantly alter structural parameters of coordinated ligands. Our predictions based on the X-ray study of the dimethyl selenoxide complex (Se—O = 1.70 Å, Se—C = 1.92 Å and Σ X—Se—Y = 301°) are in a good agreement with the data presented here for uncomplexed DMSeO. This result proves the great potential of the proposed adduct-formation technique for retrieving geometric information for compounds that are liquids or low-melting solids or for compounds that resist providing crystalline samples suitable for X-ray diffraction studies.
In the crystal structure of (I) (Fig. 2), the DMSeO molecules form centrosymmetric dimers by two pairs of C—H···O hydrogen bonds. These dimers are further linked through two additional intermolecular C—H···O hydrogen bonds to form ladder-like pseudo-two-dimensional layers that do not interpenetrate with each other. Atoms C1 and O1 in the title molecule at (x, y, z) act as hydrogen-bond donor and acceptor, respectively, to atoms O1 and C1 in the molecule at (−x, 1 − y, 1 − z), thus generating a centrosymmetric dimer centered at (0, 1/2, 1/2). Moreover, atoms C1 and C2 at (x, y, z) both act as hydrogen-bond donors to atom O1 in the molecule at (x + 1, y, z), thus producing a one-dimensional chain running parallel to the [100] direction and generated by translation. The DMSeO molecules that formed dimers lie in two different one-dimensional chains, related to each other by inversion.
It is worth stressing that the formation of three hydrogen bonds by one O atom in the solid-state structure of (I) supports the model of a strongly polarized σ Se—O bond; similar formation of multiple hydrogen bonds to an O atom was also seen in the solid-state structure of DMSO (Thomas et al., 1966). Alternatively, a selenium–oxygen double bond would be much less likely to lead to the observed intermolecular aggregation of the DMSeO molecules (Fig. 2), but would rather result in separate one-dimensional chains. Thus, our structural study provides additional verification of a larger contribution of the polarized σ Se—O bond to the resonance hybrid of DMSeO.