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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2016 Nov 30;72(Pt 12):1864–1866. doi: 10.1107/S2056989016018946

The synthesis and crystal structure of 2-(chloro­selan­yl)pyridine 1-oxide: the first monomeric organoselenenyl chloride stabilized by an intra­molecular secondary Se⋯O inter­action

Rizvan K Askerov a, Zhanna V Matsulevich b, Galina N Borisova b, Svetlana A Zalepkina c, Vasiliy F Smirnov c, Maria M Grishina d, Pavel V Dorovatovskii e, Alexander V Borisov b, Victor N Khrustalev d,f,*
PMCID: PMC5137629  PMID: 27980851

2-(Chloro­selan­yl)pyridine 1-oxide represents the first monomeric organoselenenyl chloride stabilized by an intra­molecular secondary Se⋯O inter­action.

Keywords: crystal structure, synchrotron radiation, organoselenenyl chloride, intra­molecular stabilization, secondary inter­actions

Abstract

The title compound, C5H4ClNOSe, is the product of the reaction of sulfuryl chloride and 2-selanyl-1-pyridine 1-oxide in di­chloro­methane. The mol­ecule has an almost planar geometry (r.m.s. deviation = 0.012 Å), and its mol­ecular structure is stabilized by an intra­molecular secondary Se⋯O inter­action of 2.353 (3) Å, closing a four-membered N—C—Se⋯O ring. The title compound represents the first monomeric organoselenenyl chloride stabilized intra­molecularly by an inter­action of this type. The non-valent attractive Se⋯O inter­action results in a substantial distortion of the geometry of the ipso-carbon atom. The endo-cyclic N—C—Se [102.1 (3)°] and exo-cyclic C—C—Se [136.9 (3)°] bond angles deviate significantly from the ideal value of 120° for an sp 2-hybridized carbon atom, the former bond angle being much smaller than the latter. In the crystal, mol­ecules are linked by C—H⋯O hydrogen bonds, forming zigzag chains propagating along [010]. The chains, which stack along the a-axis direction, are linked by offset π–π inter­actions [inter­centroid distance = 3.960 (3) Å], forming corrugated sheets parallel to the ab plane.

Chemical context  

Organoselenenyl halides RSeX (X = Cl, Br) play an important role in modern organic synthesis and are used as reagents for the functionalization of many classes of compounds, including organoselenium compounds with a broad spectrum of biologi­cal activities (Ranganathan et al., 2004 ▸; Selvakumar et al., 2010 ▸, 2011 ▸; Ninomiya et al., 2011 ▸; Singh & Wirth, 2011 ▸; Zade & Singh, 2014 ▸; Elsherbini et al., 2016 ▸). An essential aspect of the chemistry of selenenyl halides is the factors responsible for the stability of these reagents (Coles, 2006 ▸; Mukherjee et al., 2010 ▸; Nakanishi et al., 2013 ▸; Takaluoma et al., 2015 ▸). Recently, we have developed a new effective method for the stabilization of heteroarenselenenyl and -tellurenyl chlorides by the transformation of them to T-shaped zwitterionic adducts with hydro­chloric acid (Khrustalev et al., 2012 ▸, 2014 ▸, 2016 ▸). Moreover, we have established another stabilization method of heteroarenselenenyl and -tellurenyl chlorides by inter­molecular secondary Ch⋯N (Ch = Se, Te) inter­actions with the formation of dimers (Borisov et al., 2010a ▸,b ▸,c ▸; Khrustalev et al., 2016 ▸). Herein, we report on the synthesis and structural characterization of the first monomeric 2-(chloro­selan­yl)pyridine 1-oxide stabilized by an intra­molecular secondary Se⋯O inter­action.graphic file with name e-72-01864-scheme1.jpg

Structural commentary  

The title compound, Fig. 1 ▸, is the product of the reaction of sulfuryl chloride and 2-selanyl-1-pyridine 1-oxide in di­chloro­methane. It has an almost planar geometry (r.m.s. deviation = 0.012 Å), and its mol­ecular structure is stabilized by an intra­molecular secondary Se1⋯O1 inter­action of 2.353 (3) Å, closing the four-membered N1—C2—Se1⋯O1 ring (Fig. 1 ▸). The non-valent attractive Se1⋯O1 inter­action results in the substantial distortion of the geometry of the ipso-C2 carbon atom. The endo-cyclic N1—C2—Se1 [102.1 (3)°] and exo-cyclic C3—C2—Se1 [136.9 (3)°] bond angles deviate significantly from the ideal value of 120° for an sp 2-hybridized carbon atom, the former angle being much smaller than the latter. The title compound represents the first monomeric organoselenenyl chloride stabilized intra­molecularly by an inter­action of this type. Previously, the analogous stabilization of monomeric organoselenenyl chlorides by intra­molecular secondary Se⋯S (Tiecco et al., 2006 ▸) and Se⋯N (Panda et al., 1999 ▸; Klapötke et al., 2004 ▸; Kulcsar et al., 2007 ▸; Pöllnitz et al., 2011 ▸) inter­actions have been reported.

Figure 1.

Figure 1

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The mol­ecular structure of the title compound, with atom labelling and displacement ellipsoids drawn at the 50% probability level. The dashed line indicates the intra­molecular secondary attractive Se1⋯O1 inter­action.

Supra­molecular features  

In the crystal, mol­ecules are linked by C—H⋯O hydrogen bonds (Table 1 ▸ and Fig. 2 ▸), forming zigzag chains propagating along the b-axis direction. The chains stack along the a-axis direction and are linked by offset π–π inter­actions, forming corrugated sheets parallel to the ab plane [Cg⋯Cg i,ii = 3.960 (3) Å, Cg is the centroid of the N1/C2–C6 ring, inter­planar distances = 3.590 (2) Å, slippages = 1.671 Å, symmetry codes: (i) x − 1, y, z; (ii) x + 1, y, z].

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C6—H6⋯O1i 0.95 2.34 3.101 (6) 137
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Symmetry code: (i) Inline graphic.

Figure 2.

Figure 2

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The crystal packing of the title compound viewed along the a axis. The intra­molecular secondary Se⋯O inter­actions and the inter­molecular C—H⋯O hydrogen bonds are shown as dashed lines (see Table 1 ▸).

Synthesis and crystallization  

The synthesis of the title compound is illustrated in Fig. 3 ▸. It was synthesized according to the procedure described previously by Borisov et al. (2010a ▸,b ▸,c ▸). A solution of sulfuryl chloride (0.27 g, 2 mmol) in di­chloro­methane (15 ml) was added to a solution of 2-selanyl-1-pyridine 1-oxide (0.35 g, 2 mmol) in di­chloro­methane (20 ml) at 293 K. After one h it was filtered to give the title compound (yield 0.33 g, 80%). The filtrate was evaporated in vacuo and recrystallization of the residue from di­chloro­methane solution gave an additional 0.06 g (15%) of the title compound. Colourless prismatic crystals of the title compound were obtained after recrystallization of the crude product from di­chloro­methane (m.p. 433–435 K). IR (KBr, cm−1), ν 1617, 1462, 1423, 1254, 1151, 836, 748, 621. 1H NMR (DMSO-d 6, 300 MHz, 300 K): δ = 8.28 (d, 1H, 3 J = 5.9, H6); 7.52 (d, 1H, 3 J = 7.3, H3); 7.43 (dd, 1H, 3 J = 7.8, 3 J = 7.3, H4); 7.30 (dd, 1H, 3 J = 7.8, 3 J = 5.9, H5). Analysis calculated for C5H4ClNOSe: C 24.81; H 1.93; N 6.72. Found: 24.43; H 1.83; N 6.65.

Figure 3.

Figure 3

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The synthesis of the title compound; the reaction of 2-selanyl-1-pyridine 1-oxide with sulfuryl chloride in di­chloro­methane.

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. The C-bound H atoms were placed in calculated positions and refined as riding: C—H = 0.95 Å with U iso(H) = 1.2U eq(C).

Table 2. Experimental details.

Crystal data
Chemical formula C5H4ClNOSe
M r 208.50
Crystal system, space group Monoclinic, P21/c
Temperature (K) 100
a, b, c (Å) 3.9601 (8), 7.5102 (15), 22.350 (5)
β (°) 94.32 (3)
V (Å3) 662.8 (2)
Z 4
Radiation type Synchrotron, λ = 0.96990 Å
μ (mm−1) 13.68
Crystal size (mm) 0.05 × 0.03 × 0.03
 
Data collection
Diffractometer Rayonix SX-165 CCD
Absorption correction Multi-scan (SCALA; Evans, 2006 ▸)
T min, T max 0.550, 0.660
No. of measured, independent and observed [I > 2σ(I)] reflections 5526, 1310, 1121
R int 0.083
(sin θ/λ)max (Å−1) 0.636
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S 0.074, 0.175, 1.01
No. of reflections 1310
No. of parameters 83
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 1.26, −1.58
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Computer programs: Automar (MarXperts, 2015 ▸), iMosflm (Battye et al., 2011 ▸), SHELXS97 and SHELXTL (Sheldrick, 2008 ▸) and SHELXL2014/6 (Sheldrick, 2015 ▸).

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989016018946/su5337sup1.cif

e-72-01864-sup1.cif (184.9KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989016018946/su5337Isup2.hkl

e-72-01864-Isup2.hkl (72.4KB, hkl)

CCDC reference: 1519449

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

The work was supported by the Ministry of Education of the Russian Federation (Agreement number 02.a03.21.0008 of June 24, 2016) and the Russian Foundation for Basic Research (Grant No. 14–03-00914).

supplementary crystallographic information

Crystal data

C5H4ClNOSe F(000) = 400
Mr = 208.50 Dx = 2.089 Mg m−3
Monoclinic, P21/c Synchrotron radiation, λ = 0.96990 Å
a = 3.9601 (8) Å Cell parameters from 600 reflections
b = 7.5102 (15) Å θ = 5.0–35.0°
c = 22.350 (5) Å µ = 13.68 mm−1
β = 94.32 (3)° T = 100 K
V = 662.8 (2) Å3 Prism, colourless
Z = 4 0.05 × 0.03 × 0.03 mm
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Data collection

Rayonix SX-165 CCD diffractometer 1121 reflections with I > 2σ(I)
/f scan Rint = 0.083
Absorption correction: multi-scan (SCALA; Evans, 2006) θmax = 38.1°, θmin = 5.0°
Tmin = 0.550, Tmax = 0.660 h = −4→4
5526 measured reflections k = −9→9
1310 independent reflections l = −28→28
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Refinement

Refinement on F2 Secondary atom site location: difference Fourier map
Least-squares matrix: full Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.074 H-atom parameters constrained
wR(F2) = 0.175 w = 1/[σ2(Fo2) + (0.06P)2 + 1.6P] where P = (Fo2 + 2Fc2)/3
S = 1.01 (Δ/σ)max = 0.001
1310 reflections Δρmax = 1.26 e Å−3
83 parameters Δρmin = −1.58 e Å−3
0 restraints Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: difference Fourier map Extinction coefficient: 0.054 (3)
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Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.
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Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

x y z Uiso*/Ueq
Se1 0.51523 (13) 0.26936 (7) 0.34782 (2) 0.02716 (17)
Cl1 0.4514 (3) 0.18592 (14) 0.44303 (4) 0.0331 (3)
O1 0.6571 (9) 0.4577 (4) 0.26942 (12) 0.0347 (8)
N1 0.7603 (10) 0.5643 (5) 0.31523 (14) 0.0290 (8)
C2 0.7093 (11) 0.4927 (5) 0.36941 (16) 0.0266 (9)
C3 0.7969 (12) 0.5838 (6) 0.42160 (17) 0.0301 (10)
H3 0.7578 0.5342 0.4596 0.036*
C4 0.9449 (14) 0.7515 (6) 0.4172 (2) 0.0334 (13)
H4 1.0115 0.8173 0.4524 0.040*
C5 0.9941 (12) 0.8213 (7) 0.36099 (19) 0.0343 (12)
H5 1.0906 0.9365 0.3579 0.041*
C6 0.9047 (14) 0.7257 (5) 0.3095 (2) 0.0317 (12)
H6 0.9436 0.7720 0.2710 0.038*
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Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
Se1 0.0427 (4) 0.0202 (3) 0.0200 (3) −0.00320 (19) 0.0117 (3) −0.00209 (16)
Cl1 0.0522 (7) 0.0277 (5) 0.0208 (4) −0.0077 (5) 0.0122 (4) 0.0037 (4)
O1 0.058 (2) 0.0284 (15) 0.0190 (12) −0.0061 (14) 0.0139 (13) −0.0045 (12)
N1 0.044 (2) 0.0265 (17) 0.0177 (14) 0.0022 (16) 0.0106 (13) −0.0035 (13)
C2 0.041 (2) 0.0217 (19) 0.0183 (16) 0.0003 (18) 0.0111 (15) −0.0008 (14)
C3 0.049 (3) 0.028 (2) 0.0144 (16) −0.0006 (19) 0.0089 (16) 0.0008 (15)
C4 0.049 (3) 0.027 (2) 0.024 (2) −0.0035 (19) 0.004 (2) −0.0028 (15)
C5 0.051 (3) 0.026 (2) 0.0267 (19) −0.002 (2) 0.0033 (19) −0.0008 (19)
C6 0.048 (3) 0.0180 (18) 0.030 (2) 0.0009 (18) 0.009 (2) 0.0062 (15)
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Geometric parameters (Å, º)

Se1—C2 1.892 (4) C3—H3 0.9500
Se1—Cl1 2.2506 (11) C4—C5 1.389 (7)
O1—N1 1.339 (4) C4—H4 0.9500
N1—C6 1.350 (6) C5—C6 1.381 (6)
N1—C2 1.354 (5) C5—H5 0.9500
C2—C3 1.374 (6) C6—H6 0.9500
C3—C4 1.395 (6)
C2—Se1—Cl1 94.48 (11) C5—C4—C3 119.6 (4)
O1—N1—C6 124.8 (3) C5—C4—H4 120.2
O1—N1—C2 112.9 (3) C3—C4—H4 120.2
C6—N1—C2 122.3 (4) C6—C5—C4 120.9 (4)
N1—C2—C3 121.0 (4) C6—C5—H5 119.6
N1—C2—Se1 102.1 (3) C4—C5—H5 119.6
C3—C2—Se1 136.9 (3) N1—C6—C5 118.1 (4)
C2—C3—C4 118.0 (4) N1—C6—H6 120.9
C2—C3—H3 121.0 C5—C6—H6 120.9
C4—C3—H3 121.0
O1—N1—C2—C3 −179.4 (4) Se1—C2—C3—C4 178.9 (4)
C6—N1—C2—C3 1.4 (7) C2—C3—C4—C5 0.9 (7)
O1—N1—C2—Se1 0.7 (4) C3—C4—C5—C6 −1.3 (8)
C6—N1—C2—Se1 −178.5 (4) O1—N1—C6—C5 179.2 (4)
Cl1—Se1—C2—N1 −179.0 (3) C2—N1—C6—C5 −1.7 (7)
Cl1—Se1—C2—C3 1.0 (5) C4—C5—C6—N1 1.6 (8)
N1—C2—C3—C4 −1.0 (7)
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Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
C6—H6···O1i 0.95 2.34 3.101 (6) 137
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Symmetry code: (i) −x+2, y+1/2, −z+1/2.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989016018946/su5337sup1.cif

e-72-01864-sup1.cif (184.9KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989016018946/su5337Isup2.hkl

e-72-01864-Isup2.hkl (72.4KB, hkl)

CCDC reference: 1519449

Additional supporting information: crystallographic information; 3D view; checkCIF report

Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

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