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ISSN: 2056-9890

2-(Phenyl­selenon­yl)pyridine

aDepartment of Chemistry, D. A. V. College, Sector-10, Chandigarh, India, bDepartment of Chemistry & Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh 160 014, India, cA.E. Favorsky Irkutsk Institute of Chemistry, 1 Favorsky Street, Irkutsk, RUS-664033, Russian Federation, and dDepartment of Chemistry, Howard University, 525 College Street NW, Washington, DC 20059, USA
*Correspondence e-mail: rbutcher99@yahoo.com

(Received 12 June 2013; accepted 1 November 2013; online 20 November 2013)

In the title compound, C11H9NO2Se, the pyridine and phenyl rings are almost perpendicular, with the dihedral angle between their mean planes being 79.16 (7)°. In the crystal, the mol­ecules pack so as to form ruffled sheets in the (110) plane connected by weak C—H⋯O inter­actions. In addition, there are weak ππ inter­actions between the mean planes of both the phenyl [centroid–centroid perpendicular distance of 3.591 (2) Å and slippage of 1.854 (2) Å] and pyridine rings [centroid–centroid perpendicular distance of 3.348 (2) Å and slippage of 1.854 (2) Å].

Related literature

For the pharmacological activity of selenone derivatives, see: Abdel-Hafez & Hussein (2008[Abdel-Hafez, S. H. & Hussein, M. A. (2008). Arch. Pharm. 341, 240-246.]); Zhao et al. (2012[Zhao, L., Li, J., Li, Y., Liu, J., Wirth, T. & Li, Z. (2012). Bioorg. Med. Chem. 20, 2558-2563.]); Hassan et al. (2011[Hassan, W., Narayanaperumal, S., Santos, M. M., Gul, K., Mohammadzai, I. U., Braga, A. L., Rodrigues, O. D. & Rocha, J. B. T. (2011). Pharm. Anal. Acta. doi:10.4172/2153-2435.S3-002.]); Bhabak et al. (2011[Bhabak, K. P., Vernekar, A. A., Jakka, S. R., Roy, G. & Mugesh, G. (2011). Org. Biomol. Chem. 9, 5193-5200.]). For the chemistry of selenium compounds bonded directly to pyridine, see: Bhasin et al. (2013[Bhasin K. K., Arora E., Grover A. S., Jyoti, Singh. H., Mehta S. K, Bhasin, A. K. K. & Jacob C. (2013). J. Organomet. Chem. 732, 137-141.]). For the synthesis of pharmaceuticals, see: Nogueira & Rocha (2011[Nogueira, C. W. & Rocha, J. B. (2011). Arch. Toxicol. 85, 1313-1359.]). For the synthesis of perfumes, fine chemicals and polymers, see: Zeng et al. (2013[Zeng, J., Zhu, J., Pan, X., Zhang, Z., Zhou, N., Cheng, Z., Zhang, W. & Zhu, X. (2013). Polym. Chem. Advance Article.]).

[Scheme 1]

Experimental

Crystal data
  • C11H9NO2Se

  • Mr = 266.15

  • Triclinic, [P \overline 1]

  • a = 6.1598 (5) Å

  • b = 7.7223 (6) Å

  • c = 11.4952 (7) Å

  • α = 80.683 (6)°

  • β = 83.494 (6)°

  • γ = 74.614 (7)°

  • V = 518.83 (7) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 3.60 mm−1

  • T = 123 K

  • 0.50 × 0.26 × 0.16 mm

Data collection
  • Agilent Xcalibur (Ruby, Gemini) diffractometer

  • Absorption correction: analytical (CrysAlis PRO and CrysAlis RED; Agilent, 2012[Agilent (2012). CrysAlis PRO and CrysAlis RED. Agilent Technologies, Yarnton, England.]) Tmin = 0.383, Tmax = 0.613

  • 8688 measured reflections

  • 5196 independent reflections

  • 3965 reflections with I > 2σ(I)

  • Rint = 0.041

Refinement
  • R[F2 > 2σ(F2)] = 0.047

  • wR(F2) = 0.090

  • S = 1.01

  • 5196 reflections

  • 136 parameters

  • H-atom parameters constrained

  • Δρmax = 0.64 e Å−3

  • Δρmin = −0.76 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C2A—H2AA⋯O1i 0.95 2.50 3.331 (3) 146
C4A—H4AA⋯O1ii 0.95 2.53 3.341 (3) 143
C5A—H5AA⋯O2iii 0.95 2.35 3.188 (3) 146
Symmetry codes: (i) x-1, y, z; (ii) x-1, y+1, z; (iii) x, y+1, z.

Data collection: CrysAlis PRO (Agilent, 2012[Agilent (2012). CrysAlis PRO and CrysAlis RED. Agilent Technologies, Yarnton, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; 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: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

Organochalcogen compounds, especially containing selenium have continued to attract attention of researchers in academia as anti-cancer (Zhao et al., 2012), anti-oxidant (Hassan et al., 2011; Bhabak et al., 2011), anti-inflammatory and anti-allergic agents (Abdel-Hafez, & Hussein, 2008), and in industry because of their wide involvement as key intermediates for the synthesis of pharmaceuticals (Nogueira, & Rocha, 2011), perfumes, fine chemicals and polymers (Zeng et al., 2013). Curiously, compared to alkyl, aryl and mixed alkyl aryl selenium compounds, the chemistry of selenium compounds bonded directly to pyridine has not yet been exploited extensively (Bhasin et al. 2013). In continuation of our ongoing program directed at the synthesis of novel organoselenium derivatives, we report here the synthesis and crystal structure of 2-(phenylselenonyl)pyridine.

In the title compound, C11H9NO2Se, (I), the pyridine and phenyl rings are almost perpendicular with the dihedral angle between the mean planes being 79.16 (7)° (Fig. 1). The molecules pack so as to form ruffled sheets in the (1 1 0) plane connected by weak C—H···O intermolecular interactions (Fig. 2). In addition there are weak ππ interactions between both the phenyl groups (Cg···Cg perpendicular distance of 3.591 (2) Å with slippage of 1.854 (2) Å [2 -x, -y, 1 - z]) and pyridine rings (Cg···Cg perpendicular distance of 3.348 (2) Å with slippage of 1.854 (2) Å [1 -x, 1 - y, -z]) (Fig. 3).

Related literature top

For the pharmacological activity of selenone derivatives, see: Abdel-Hafez & Hussein (2008); Zhao et al. (2012); Hassan et al. (2011); Bhabak et al. (2011). For the chemistry of selenium compounds bonded directly to pyridine, see: Bhasin et al. (2013). For the synthesis of pharmaceuticals, see: Nogueira & Rocha (2011). For the synthesis of perfumes, fine chemicals and polymers, see: Zeng et al. (2013).

Experimental top

A stirred solution of 2-(phenylseleninyl)pyridine (0.235 g, 1 mmol) in glacial acetic acid (10 ml) was treated with (0.550 g, 3.5 mmol) potassium permanganate in small amounts. The reaction mixture was allowed to stir for 3 h at room temperature. The progress of the reaction mixture was monitored by thin layer chromatography. After completion of the reaction, the reaction mixture was neutralized with excess of saturated solution of sodium bicarbonate and extracted with dichloromethane (4 x 25 ml). The combined organic extracts were washed with water and dried over anhydrous MgSO4. Dichloromethane was removed on a rota-evaporator that yielded a white powder. Single crystals of the compound suitable for XRD were prepared by dissolving the obtained white powder in a (1:1) mixture of CHCl3 and CCl4 followed by slow evaporation. Yield = 85%. M.p.= 453–455°K.

Refinement top

All H atoms were placed in geometrically idealized positions and constrained to ride on their parent atoms with a C—H distance of 0.95 and Uiso (H) = 1.2Ueq(C).

Computing details top

Data collection: CrysAlis PRO (Agilent, 2012); cell refinement: CrysAlis PRO (Agilent, 2012); data reduction: CrysAlis PRO (Agilent, 2012); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. Molecular diagram of (I) illustrating the atom numbering scheme used. Thermal ellipsoids are at the 30% probability level.
[Figure 2] Fig. 2. Fig, 2. Molecular packing for (I) viewed along the c axis. Dashed lines indicate the weak C—H···O intermolecular interactions forming ruffled sheets in the (1 1 0) plane.
[Figure 3] Fig. 3. Molecular packing for (I) showing the ππ interactions between the mean planes of both the phenyl and pyridine rings.
2-(Phenylselenonyl)pyridine top
Crystal data top
C11H9NO2SeZ = 2
Mr = 266.15F(000) = 264
Triclinic, P1Dx = 1.704 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.1598 (5) ÅCell parameters from 2941 reflections
b = 7.7223 (6) Åθ = 3.1–37.5°
c = 11.4952 (7) ŵ = 3.60 mm1
α = 80.683 (6)°T = 123 K
β = 83.494 (6)°Triangular plate, colorless
γ = 74.614 (7)°0.50 × 0.26 × 0.16 mm
V = 518.83 (7) Å3
Data collection top
Agilent Xcalibur (Ruby, Gemini)
diffractometer
5196 independent reflections
Radiation source: Enhance (Mo) X-ray Source3965 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.041
Detector resolution: 10.5081 pixels mm-1θmax = 37.6°, θmin = 3.1°
ω scansh = 1010
Absorption correction: analytical
(CrysAlis PRO and CrysAlis RED; Agilent, 2012)
k = 1213
Tmin = 0.383, Tmax = 0.613l = 1819
8688 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.090H-atom parameters constrained
S = 1.01 w = 1/[σ2(Fo2) + (0.0241P)2]
where P = (Fo2 + 2Fc2)/3
5196 reflections(Δ/σ)max < 0.001
136 parametersΔρmax = 0.64 e Å3
0 restraintsΔρmin = 0.76 e Å3
Crystal data top
C11H9NO2Seγ = 74.614 (7)°
Mr = 266.15V = 518.83 (7) Å3
Triclinic, P1Z = 2
a = 6.1598 (5) ÅMo Kα radiation
b = 7.7223 (6) ŵ = 3.60 mm1
c = 11.4952 (7) ÅT = 123 K
α = 80.683 (6)°0.50 × 0.26 × 0.16 mm
β = 83.494 (6)°
Data collection top
Agilent Xcalibur (Ruby, Gemini)
diffractometer
5196 independent reflections
Absorption correction: analytical
(CrysAlis PRO and CrysAlis RED; Agilent, 2012)
3965 reflections with I > 2σ(I)
Tmin = 0.383, Tmax = 0.613Rint = 0.041
8688 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0470 restraints
wR(F2) = 0.090H-atom parameters constrained
S = 1.01Δρmax = 0.64 e Å3
5196 reflectionsΔρmin = 0.76 e Å3
136 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.

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
xyzUiso*/Ueq
Se0.80434 (4)0.23043 (3)0.224458 (18)0.02645 (6)
O11.0283 (3)0.2030 (2)0.13351 (14)0.0370 (4)
O20.6629 (3)0.0770 (2)0.24217 (15)0.0380 (4)
N1A0.6710 (4)0.6075 (3)0.17338 (18)0.0397 (5)
C1A0.5932 (3)0.4583 (3)0.17700 (17)0.0247 (4)
C2A0.3857 (3)0.4556 (3)0.14449 (17)0.0277 (4)
H2AA0.34260.34530.14870.033*
C3A0.2427 (4)0.6216 (4)0.10521 (19)0.0358 (5)
H3AA0.09780.62740.08160.043*
C4A0.3131 (5)0.7786 (3)0.1008 (2)0.0427 (6)
H4AA0.21660.89290.07410.051*
C5A0.5245 (5)0.7685 (3)0.1354 (2)0.0453 (7)
H5AA0.56960.87770.13270.054*
C1B0.8984 (4)0.2491 (3)0.37495 (17)0.0256 (4)
C2B0.7332 (4)0.3166 (3)0.45649 (18)0.0298 (4)
H2BA0.57990.35930.43820.036*
C3B0.7969 (4)0.3207 (4)0.5661 (2)0.0399 (6)
H3BA0.68530.36660.62510.048*
C4B1.0186 (4)0.2598 (3)0.5925 (2)0.0369 (5)
H4BA1.05870.26460.66910.044*
C5B1.1842 (4)0.1913 (3)0.50800 (19)0.0339 (5)
H5BA1.33730.14790.52670.041*
C6B1.1244 (4)0.1864 (3)0.39527 (18)0.0290 (4)
H6BA1.23440.14190.33510.035*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Se0.02928 (11)0.02457 (10)0.02608 (11)0.00452 (8)0.00550 (7)0.00652 (8)
O10.0355 (9)0.0416 (10)0.0296 (8)0.0001 (7)0.0011 (6)0.0110 (7)
O20.0452 (10)0.0285 (8)0.0461 (10)0.0152 (7)0.0171 (8)0.0027 (7)
N1A0.0512 (13)0.0364 (11)0.0364 (11)0.0169 (10)0.0067 (9)0.0069 (9)
C1A0.0273 (9)0.0254 (9)0.0207 (8)0.0040 (7)0.0021 (7)0.0053 (7)
C2A0.0274 (10)0.0341 (11)0.0219 (9)0.0085 (8)0.0002 (7)0.0044 (8)
C3A0.0293 (11)0.0469 (14)0.0254 (10)0.0010 (10)0.0005 (8)0.0044 (10)
C4A0.0578 (16)0.0332 (12)0.0253 (11)0.0083 (11)0.0003 (10)0.0052 (10)
C5A0.078 (2)0.0304 (12)0.0326 (12)0.0202 (13)0.0063 (12)0.0063 (10)
C1B0.0283 (10)0.0251 (9)0.0233 (9)0.0062 (8)0.0023 (7)0.0033 (8)
C2B0.0265 (10)0.0337 (11)0.0262 (10)0.0013 (8)0.0007 (7)0.0070 (9)
C3B0.0440 (14)0.0417 (14)0.0281 (11)0.0002 (11)0.0024 (9)0.0092 (10)
C4B0.0481 (14)0.0371 (12)0.0248 (10)0.0079 (11)0.0055 (9)0.0051 (9)
C5B0.0323 (11)0.0383 (12)0.0318 (11)0.0101 (10)0.0096 (9)0.0003 (10)
C6B0.0255 (10)0.0334 (11)0.0271 (10)0.0071 (8)0.0004 (7)0.0032 (9)
Geometric parameters (Å, º) top
Se—O11.6218 (16)C5A—H5AA0.9500
Se—O21.6234 (16)C1B—C2B1.359 (3)
Se—C1B1.9240 (19)C1B—C6B1.381 (3)
Se—C1A1.929 (2)C2B—C3B1.368 (3)
N1A—C1A1.354 (3)C2B—H2BA0.9500
N1A—C5A1.367 (3)C3B—C4B1.373 (3)
C1A—C2A1.378 (3)C3B—H3BA0.9500
C2A—C3A1.388 (3)C4B—C5B1.385 (3)
C2A—H2AA0.9500C4B—H4BA0.9500
C3A—C4A1.383 (4)C5B—C6B1.395 (3)
C3A—H3AA0.9500C5B—H5BA0.9500
C4A—C5A1.383 (4)C6B—H6BA0.9500
C4A—H4AA0.9500
O1—Se—O2117.59 (9)N1A—C5A—H5AA118.8
O1—Se—C1B106.80 (8)C4A—C5A—H5AA118.8
O2—Se—C1B109.14 (8)C2B—C1B—C6B124.39 (19)
O1—Se—C1A110.40 (9)C2B—C1B—Se116.78 (16)
O2—Se—C1A106.21 (9)C6B—C1B—Se118.75 (15)
C1B—Se—C1A106.17 (8)C1B—C2B—C3B117.2 (2)
C1A—N1A—C5A115.3 (2)C1B—C2B—H2BA121.4
N1A—C1A—C2A126.1 (2)C3B—C2B—H2BA121.4
N1A—C1A—Se115.30 (16)C2B—C3B—C4B121.4 (2)
C2A—C1A—Se118.53 (16)C2B—C3B—H3BA119.3
C1A—C2A—C3A116.9 (2)C4B—C3B—H3BA119.3
C1A—C2A—H2AA121.6C3B—C4B—C5B120.3 (2)
C3A—C2A—H2AA121.6C3B—C4B—H4BA119.8
C4A—C3A—C2A119.4 (2)C5B—C4B—H4BA119.8
C4A—C3A—H3AA120.3C4B—C5B—C6B119.5 (2)
C2A—C3A—H3AA120.3C4B—C5B—H5BA120.3
C3A—C4A—C5A119.8 (2)C6B—C5B—H5BA120.3
C3A—C4A—H4AA120.1C1B—C6B—C5B117.1 (2)
C5A—C4A—H4AA120.1C1B—C6B—H6BA121.4
N1A—C5A—C4A122.5 (2)C5B—C6B—H6BA121.4
C5A—N1A—C1A—C2A1.2 (3)O1—Se—C1B—C2B164.23 (17)
C5A—N1A—C1A—Se177.60 (16)O2—Se—C1B—C2B67.68 (19)
O1—Se—C1A—N1A60.19 (17)C1A—Se—C1B—C2B46.41 (19)
O2—Se—C1A—N1A171.30 (15)O1—Se—C1B—C6B18.7 (2)
C1B—Se—C1A—N1A55.21 (17)O2—Se—C1B—C6B109.38 (18)
O1—Se—C1A—C2A116.53 (16)C1A—Se—C1B—C6B136.53 (18)
O2—Se—C1A—C2A11.98 (18)C6B—C1B—C2B—C3B0.6 (4)
C1B—Se—C1A—C2A128.08 (16)Se—C1B—C2B—C3B176.31 (18)
N1A—C1A—C2A—C3A0.5 (3)C1B—C2B—C3B—C4B0.3 (4)
Se—C1A—C2A—C3A176.84 (14)C2B—C3B—C4B—C5B0.3 (4)
C1A—C2A—C3A—C4A0.1 (3)C3B—C4B—C5B—C6B0.7 (4)
C2A—C3A—C4A—C5A0.0 (3)C2B—C1B—C6B—C5B0.9 (3)
C1A—N1A—C5A—C4A1.2 (3)Se—C1B—C6B—C5B175.90 (16)
C3A—C4A—C5A—N1A0.7 (4)C4B—C5B—C6B—C1B0.9 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2A—H2AA···O1i0.952.503.331 (3)146
C4A—H4AA···O1ii0.952.533.341 (3)143
C5A—H5AA···O2iii0.952.353.188 (3)146
Symmetry codes: (i) x1, y, z; (ii) x1, y+1, z; (iii) x, y+1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2A—H2AA···O1i0.952.503.331 (3)145.9
C4A—H4AA···O1ii0.952.533.341 (3)142.8
C5A—H5AA···O2iii0.952.353.188 (3)146.3
Symmetry codes: (i) x1, y, z; (ii) x1, y+1, z; (iii) x, y+1, z.
 

Acknowledgements

This work was supported by the Department of Science and Technology, DST, New Delhi (Research Grant SR/S1/IC-37/2009). RJB wishes to acknowledge the NSF–MRI program (grant CHE-0619278) for funds to purchase the diffractometer as well as the Howard University Nanoscience Facility for access to liquid nitro­gen.

References

First citationAbdel-Hafez, S. H. & Hussein, M. A. (2008). Arch. Pharm. 341, 240–246.  CAS
First citationAgilent (2012). CrysAlis PRO and CrysAlis RED. Agilent Technologies, Yarnton, England.
First citationBhabak, K. P., Vernekar, A. A., Jakka, S. R., Roy, G. & Mugesh, G. (2011). Org. Biomol. Chem. 9, 5193–5200.  Web of Science CSD CrossRef CAS PubMed
First citationBhasin K. K., Arora E., Grover A. S., Jyoti, Singh. H., Mehta S. K, Bhasin, A. K. K. & Jacob C. (2013). J. Organomet. Chem. 732, 137–141.
First citationHassan, W., Narayanaperumal, S., Santos, M. M., Gul, K., Mohammadzai, I. U., Braga, A. L., Rodrigues, O. D. & Rocha, J. B. T. (2011). Pharm. Anal. Acta. doi:10.4172/2153-2435.S3-002.
First citationNogueira, C. W. & Rocha, J. B. (2011). Arch. Toxicol. 85, 1313–1359.  Web of Science CrossRef CAS PubMed
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationZeng, J., Zhu, J., Pan, X., Zhang, Z., Zhou, N., Cheng, Z., Zhang, W. & Zhu, X. (2013). Polym. Chem. Advance Article.
First citationZhao, L., Li, J., Li, Y., Liu, J., Wirth, T. & Li, Z. (2012). Bioorg. Med. Chem. 20, 2558–2563.  Web of Science CrossRef CAS PubMed

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