o-Methyl­seleno­benzoyl cyanide

In the crystal structure of the title compound, C₉H₇NOSe, a potential anti-oxidizing agent, the whole mol­ecule lies in the (0,y,z) plane except for two methyl H atoms, whose positions are symmetry-related across that plane. A close Se...Se contact [3.359 (2) Å] is observed. There are no hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.008 Å
• R factor = 0.041
• wR factor = 0.111
• Data-to-parameter ratio = 11.5

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


 Alert Level C:



PLAT_371  Alert C Long   C(sp2)-C(sp1) Bond  C(8)   -   C(9)   =       1.49 Ang.

General Notes



ABSTM_02  When printed, the submitted absorption T values will be replaced
          by the scaled T values. Since the ratio of scaled T's is
          identical to the ratio of reported T values, the scaling does
          not imply a change to the absorption corrections used in the
          study.
          Ratio of Tmax expected/reported      0.787
          Tmax scaled      0.295 Tmin scaled      0.110


 0 Alert Level A = Potentially serious problem

 0 Alert Level B = Potential problem

 1 Alert Level C = Please check

---

S1. Comment

Some modifications of the molecular structure of Ebselen (Natterman/RP, 1981; Dupont et al., 1990), an anti-inflammatory compound, have been attempted in order to obtain a more soluble derivative which retains the pharmacological properties. The crystal structure of the title compound, (I), was determined in order to identify without ambiguity a potential antioxidant derivative. All the atomic positions, except for two H atoms of the methyl group, were refined in the plane (0,y,z) of the unit cell. All the atoms have an occupation factor of 0.5. The crystal packing is governed by van der Waals interactions. There is an Se···Seⁱ close contact [symmetry code: (i) x, -y, 1 - z) of 3.359 (2) Å, rather less than the sum of Se atom radii (3.8 Å; Bondi, 1964). The distance is nevertheless larger than that of a covalent Se—Se bond [2.3229 (6) Å; Kumar & Nangia, 2000].

S2. Experimental

The synthesis of the title compound was carried out in two steps. o-Methylselenobenzoic acid was treated with α,α-dichloromethyl ether and then with KCN (Messali, 2001). A yellow single-crystal was obtained by slow evaporation of a toluene solution.

S3. Refinement

All H atoms were included in the refinement in the-riding model approximation, with isotropic displacement parameters fixed at 1.2U_eq of the parent atom (1.5 U_eq for methyl H atoms).

Computing details

Data collection: DIF4 (Stoe & Cie, 1987); cell refinement: DIF4; data reduction: REDU4 (Stoe & Cie, 1987); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPIII (Burnett & Johnson, 1996); software used to prepare material for publication: SHELXL97.

Figures

Fig. 1. The molecular structure of (I) with the atom-labelling scheme. Displacement ellipsoids are shown at the 50% probability level.

o-Methylselenobenzoyl cyanide

Crystal data

C9H7NOSe	F(000) = 880
Mr = 224.12	Dx = 1.677 Mg m^−3
Orthorhombic, Cmca	Cu Kα radiation, λ = 1.54180 Å
Hall symbol: -C 2bc 2	Cell parameters from 32 reflections
a = 6.8433 (19) Å	θ = 31.5–36.3°
b = 15.585 (9) Å	µ = 5.31 mm^−1
c = 16.6460 (12) Å	T = 293 K
V = 1775.4 (12) Å^3	Prism, yellow
Z = 8	0.61 × 0.38 × 0.23 mm

Data collection

Stoe–Siemens AED four-circle diffractometer	624 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.000
Graphite monochromator	θmax = 67.9°, θmin = 5.3°
ω scans	h = 0→8
Absorption correction: ψ scan (EMPIR; Stoe & Cie, 1987)	k = 0→18
Tmin = 0.140, Tmax = 0.375	l = 0→20
848 measured reflections	2 standard reflections every 60 min
848 independent reflections	intensity decay: 5%

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)] = 0.042	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.111	w = 1/[σ^2(Fo^2) + (0.0712P)^2 + 0.7549P] where P = (Fo^2 + 2Fc^2)/3
S = 1.01	(Δ/σ)max < 0.001
848 reflections	Δρmax = 0.41 e Å^−3
74 parameters	Δρmin = −0.34 e Å^−3
0 restraints	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0078 (6)

Special details

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
Se1	0.0000	0.09438 (4)	0.45132 (3)	0.0814 (4)
O1	0.0000	0.1952 (2)	0.5863 (2)	0.0840 (11)
N1	0.0000	0.3958 (3)	0.6510 (3)	0.0974 (16)
C1	0.0000	0.2081 (3)	0.4125 (3)	0.0691 (12)
C2	0.0000	0.2265 (4)	0.3304 (3)	0.0767 (14)
H2	0.0000	0.1816	0.2936	0.092*
C3	0.0000	0.3098 (4)	0.3028 (3)	0.0869 (17)
H3	0.0000	0.3205	0.2479	0.104*
C4	0.0000	0.3766 (4)	0.3554 (4)	0.0887 (16)
H4	0.0000	0.4327	0.3361	0.106*
C5	0.0000	0.3620 (4)	0.4361 (3)	0.0808 (15)
H5	0.0000	0.4082	0.4714	0.097*
C6	0.0000	0.2779 (3)	0.4665 (3)	0.0700 (13)
C7	0.0000	0.0321 (4)	0.3510 (3)	0.0968 (19)
H7A	0.0000	−0.0284	0.3617	0.145*
H7B	0.1145	0.0469	0.3207	0.145*	0.50
H7C	−0.1145	0.0469	0.3207	0.145*	0.50
C8	0.0000	0.2641 (4)	0.5529 (3)	0.0748 (14)
C9	0.0000	0.3414 (4)	0.6056 (3)	0.0804 (14)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Se1	0.1192 (6)	0.0709 (5)	0.0542 (4)	0.000	0.000	0.0010 (2)
O1	0.111 (3)	0.084 (2)	0.0572 (19)	0.000	0.000	0.0011 (17)
N1	0.134 (5)	0.093 (3)	0.066 (3)	0.000	0.000	−0.014 (2)
C1	0.081 (3)	0.072 (3)	0.055 (2)	0.000	0.000	0.003 (2)
C2	0.100 (4)	0.078 (3)	0.052 (2)	0.000	0.000	0.000 (2)
C3	0.119 (5)	0.087 (3)	0.054 (3)	0.000	0.000	0.007 (2)
C4	0.113 (5)	0.082 (3)	0.071 (3)	0.000	0.000	0.009 (3)
C5	0.109 (4)	0.067 (3)	0.066 (3)	0.000	0.000	0.002 (2)
C6	0.081 (3)	0.074 (3)	0.055 (3)	0.000	0.000	0.000 (2)
C7	0.150 (6)	0.079 (3)	0.062 (3)	0.000	0.000	−0.007 (3)
C8	0.092 (4)	0.080 (4)	0.052 (2)	0.000	0.000	−0.005 (2)
C9	0.097 (4)	0.089 (3)	0.056 (2)	0.000	0.000	−0.001 (3)

Geometric parameters (Å, º)

Se1—C1	1.887 (5)	C4—C5	1.362 (7)
Se1—C7	1.932 (5)	C4—H4	0.9300
O1—C8	1.210 (7)	C5—C6	1.405 (8)
N1—C9	1.135 (7)	C5—H5	0.9300
C1—C2	1.398 (6)	C6—C8	1.454 (5)
C1—C6	1.410 (7)	C7—H7A	0.9600
C2—C3	1.377 (8)	C7—H7B	0.9600
C2—H2	0.9300	C7—H7C	0.9600
C3—C4	1.360 (8)	C8—C9	1.491 (8)
C3—H3	0.9300
C1—Se1—C7	100.2 (2)	C6—C5—H5	119.6
C2—C1—C6	117.8 (5)	C5—C6—C1	119.3 (4)
C2—C1—Se1	121.8 (4)	C5—C6—C8	119.6 (5)
C6—C1—Se1	120.5 (4)	C1—C6—C8	121.1 (5)
C3—C2—C1	121.2 (5)	Se1—C7—H7A	109.5
C3—C2—H2	119.4	Se1—C7—H7B	109.5
C1—C2—H2	119.4	H7A—C7—H7B	109.5
C4—C3—C2	120.6 (5)	Se1—C7—H7C	109.5
C4—C3—H3	119.7	H7A—C7—H7C	109.5
C2—C3—H3	119.7	H7B—C7—H7C	109.5
C3—C4—C5	120.4 (5)	O1—C8—C6	125.9 (5)
C3—C4—H4	119.8	O1—C8—C9	116.5 (4)
C5—C4—H4	119.8	C6—C8—C9	117.6 (5)
C4—C5—C6	120.8 (5)	N1—C9—C8	174.4 (6)
C4—C5—H5	119.6