2,2′-[Methyl­enebis(sulfanedi­yl)]bis­(pyridine 1-oxide)

Siegel, D.J.; Howarth, A.N.; Traver, J.R.; Hillesheim, P.C.; Zeller, M.; Mirjafari, A.

doi:10.1107/S2414314620001716

organic compounds

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ISSN: 2414-3146

Volume 5| Part 2| February 2020| x200171

https://doi.org/10.1107/S2414314620001716

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2,2′-[Methylenebis(sulfanediyl)]bis(pyridine 1-oxide)

David J. Siegel,^a Alexis N. Howarth,^b Joseph R. Traver,^b Patrick C. Hillesheim,^b Matthias Zeller ^c and Arsalan Mirjafari ^a ^*

^aDepartment of Chemistry and Physics, Florida Gulf Coast University, 10501 FGCU Blvd. South, Fort Myers, FL, 33965, USA, ^bAve Maria University, Department of Chemistry and Physics, 5050 Ave Maria Blvd, Ave Maria FL, 34142, USA, and ^cPurdue University, Department of Chemistry, 560 Oval Drive, West Lafayette, Indiana, 47907, USA
^*Correspondence e-mail: amirjafari@fgcu.edu

Edited by R. J. Butcher, Howard University, USA (Received 13 December 2019; accepted 5 February 2020; online 11 February 2020)

The title compound, C₁₁H₁₀N₂O₂S₂, crystallizes with one complete molecule in the asymmetric unit. In the crystal, weak hydrogen bonding is observed between the N-oxide moieties and several C—H units.

Keywords: crystal structure; N-oxide; hydrogen bonding.

CCDC reference: 1982242

Structure description

The title compound (Fig. 1) crystallizes in the P2₁ space group with a single molecule in the asymmetric unit. The two nitrogen–oxygen bonds in the N-oxide moiety exhibit similar lengths [1.307 (3) and 1.309 (3). The two pyridine N-oxide rings exist in a staggered conformation with respect to each other, forming a dihedral angle of 66.55 (9)° (Fig. 2).

Figure 1
The molecular structure of the title compound shown with 50% probability ellipsoids.

Figure 2
Depiction of the dihedral plane angle of the two pyridine N-oxide moieties visualized within Mercury (Macrae et al., 2020

In the extended network, molecules are arranged in a zigzag pattern when viewed along [101] (Fig. 3); this arrangement facilitates weak hydrogen-bonding interactions between adjacent molecules (Table 1). Both oxygen atoms participate in hydrogen bonding, interacting with hydrogen atoms bound to the aromatic rings of the N-oxide moieties. In addition to the interactions with aromatic H atoms, O1 is involved in hydrogen bonding with the methylene H atoms from the thioether moiety. As a result of the zigzag arrangement of molecules, no π–π stacking is observed.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C2—H2⋯O1ⁱ	0.95	2.37	3.292 (3)	165
C9—H9⋯O2ⁱⁱ	0.95	2.70	3.405 (4)	131
C11—H11A⋯O1ⁱⁱⁱ	0.99	2.33	3.159 (3)	141
Symmetry codes: (i) $[-x+1, y+{\script{1\over 2}}, -z+1]$ ; (ii) $[-x+1, y-{\script{1\over 2}}, -z+2]$ ; (iii) $[-x+2, y+{\script{1\over 2}}, -z+1]$ .

Figure 3
Packing diagram for the title compound as viewed from the [101] direction. Dotted red lines depict the weak hydrogen bonds.

For related N-oxide crystal structures, see: Rybarczyk-Pirek et al. (2018 ), Amoedo-Portela et al. (2002 ), and de Castro et al. (2002 )

Synthesis and crystallization

An oven-dried 100 ml, 24/40 single-necked, round-bottomed flask was charged with a 4 cm oval Teflon-coated stir bar and 2-mercaptopyridine N-oxide sodium salt (1.00 g, 1 equiv.). Dry CH₂Cl₂ (4.24 ml, 10 equiv.) was then added to the flask via syringe. The flask neck was equipped with a water-jacketed reflux condenser (30.0 cm height, 24/40 joint) with a constant flow of water. The reaction vessel was placed in a pre-heated oil bath and refluxed for an hour under stirring. After the allotted time, the reaction vessel was removed from the oil bath and cooled to room temperature and colorless plates of 2,2′-[methylenebis(sulfanediyl)]bis(pyridine-1-oxide) formed over 5 d. The crystals were vacuum filtered and the residual solvent was removed under vacuum (1.40 mm H g) for 12 h to afford 2,2′-[methylenebis(sulfanediyl)]bis(pyridine-1-oxide) in high yield (89%).

Crystals suitable for diffraction formed slowly from a CD₂Cl₂ solution in an NMR tube.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₁H₁₀N₂O₂S₂
M_r	266.33
Crystal system, space group	Monoclinic, P2₁
Temperature (K)	150
a, b, c (Å)	4.1658 (2), 10.4706 (6), 12.7624 (7)
β (°)	95.958 (2)
V (Å³)	553.67 (5)
Z	2
Radiation type	Mo Kα
μ (mm⁻¹)	0.47
Crystal size (mm)	0.55 × 0.16 × 0.04

Data collection
Diffractometer	Bruker AXS D8 Quest CMOS
Absorption correction	Multi-scan (SADABS; Krause et al., 2015 )
T_min, T_max	0.528, 0.747
No. of measured, independent and observed [I > 2σ(I)] reflections	17033, 4262, 3794
R_int	0.070
(sin θ/λ)_max (Å⁻¹)	0.772

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.041, 0.100, 1.06
No. of reflections	4262
No. of parameters	154
No. of restraints	1
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.56, −0.48
Absolute structure	Flack x determined using 1650 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter	0.05 (4)
Computer programs: APEX3 and SAINT (Bruker, 2018 ), SHELXS97 (Sheldrick, 2008 ), SHELXL2018 (Sheldrick, 2015 , 2018 ), SHELXLE (Hübschle et al., 2011 ), PLATON (Spek, 2020 ), OLEX2 (Dolomanov et al., 2009 ), Mercury (Macrae et al., 2008), publCIF (Westrip, 2010 ) and enCIFer (Allen et al., 2004 ).

Structural data

CCDC reference: 1982242

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S2414314620001716/bv4026sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314620001716/bv4026Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314620001716/bv4026Isup3.cml

checkCIF report

Computing details top

Data collection: APEX3 (Bruker, 2018); cell refinement: SAINT (Bruker, 2018); data reduction: SAINT (Bruker, 2018); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2018 (Sheldrick, 2015, 2018), SHELXLE (Hübschle et al., 2011) and PLATON (Spek, 2020); molecular graphics: OLEX2 (Dolomanov et al., 2009) and Mercury (Macrae et al., 2008); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009), publCIF (Westrip, 2010) and enCIFer (Allen et al., 2004).

2,2'-[Methylenebis(sulfanediyl)]bis(pyridine 1-oxide) top

Crystal data top

C₁₁H₁₀N₂O₂S₂	F(000) = 276
M_r = 266.33	D_x = 1.598 Mg m⁻³
Monoclinic, P2₁	Mo Kα radiation, λ = 0.71073 Å
a = 4.1658 (2) Å	Cell parameters from 9929 reflections
b = 10.4706 (6) Å	θ = 2.5–33.3°
c = 12.7624 (7) Å	µ = 0.47 mm⁻¹
β = 95.958 (2)°	T = 150 K
V = 553.67 (5) Å³	Plate, colourless
Z = 2	0.55 × 0.16 × 0.04 mm

Data collection top

Bruker AXS D8 Quest CMOS diffractometer	4262 independent reflections
Radiation source: fine focus sealed tube X-ray source	3794 reflections with I > 2σ(I)
Triumph curved graphite crystal monochromator	R_int = 0.070
Detector resolution: 10.4167 pixels mm^-1	θ_max = 33.3°, θ_min = 2.5°
ω and phi scans	h = −6→5
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	k = −16→16
T_min = 0.528, T_max = 0.747	l = −19→19
17033 measured reflections

Refinement top

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)] = 0.041	H-atom parameters constrained
wR(F²) = 0.100	w = 1/[σ²(F_o²) + (0.0424P)² + 0.1658P] where P = (F_o² + 2F_c²)/3
S = 1.06	(Δ/σ)_max = 0.001
4262 reflections	Δρ_max = 0.56 e Å⁻³
154 parameters	Δρ_min = −0.48 e Å⁻³
1 restraint	Absolute structure: Flack x determined using 1650 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.05 (4)

Special details top

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.

Refinement. C—H bond distances were constrained to 0.95 Å for aromatic C—H moieties. U_iso(H) values were set to 1.2 times U_eq(C).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
S1	0.81710 (15)	0.68956 (6)	0.58939 (4)	0.01584 (13)
S2	0.86177 (15)	0.83538 (6)	0.79102 (4)	0.01541 (13)
O1	0.8980 (5)	0.5371 (2)	0.42557 (17)	0.0230 (4)
O2	1.0430 (5)	0.7815 (2)	0.99221 (16)	0.0224 (4)
N1	0.7052 (5)	0.6307 (2)	0.39242 (17)	0.0162 (4)
N2	0.8365 (5)	0.6943 (2)	0.95562 (16)	0.0162 (4)
C1	0.6300 (6)	0.7213 (2)	0.46299 (19)	0.0152 (4)
C2	0.4276 (6)	0.8217 (3)	0.43009 (19)	0.0178 (5)
H2	0.373352	0.884463	0.479079	0.021*
C3	0.3049 (7)	0.8300 (3)	0.3252 (2)	0.0221 (5)
H3	0.167937	0.899069	0.301822	0.026*
C4	0.3825 (8)	0.7369 (3)	0.2540 (2)	0.0241 (6)
H4	0.299597	0.741896	0.181928	0.029*
C5	0.5806 (8)	0.6380 (3)	0.2897 (2)	0.0225 (5)
H5	0.631713	0.573381	0.241816	0.027*
C6	0.7073 (6)	0.7022 (3)	0.85309 (18)	0.0139 (4)
C7	0.4827 (6)	0.6128 (3)	0.8125 (2)	0.0169 (5)
H7	0.391355	0.618626	0.741250	0.020*
C8	0.3922 (7)	0.5152 (3)	0.8762 (2)	0.0197 (5)
H8	0.236511	0.454000	0.849241	0.024*
C9	0.5303 (7)	0.5072 (3)	0.9797 (2)	0.0223 (5)
H9	0.471354	0.440113	1.024029	0.027*
C10	0.7527 (7)	0.5969 (3)	1.0173 (2)	0.0209 (5)
H10	0.849794	0.590692	1.087870	0.025*
C11	0.6603 (6)	0.8234 (3)	0.65943 (18)	0.0150 (4)
H11A	0.692061	0.903548	0.620641	0.018*
H11B	0.425731	0.811823	0.662873	0.018*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0192 (3)	0.0155 (3)	0.0129 (2)	0.0026 (2)	0.00225 (19)	0.0004 (2)
S2	0.0194 (3)	0.0138 (3)	0.0131 (2)	−0.0019 (2)	0.00204 (19)	0.0002 (2)
O1	0.0299 (10)	0.0159 (9)	0.0243 (10)	0.0048 (8)	0.0075 (8)	−0.0012 (7)
O2	0.0259 (10)	0.0239 (10)	0.0165 (9)	−0.0057 (8)	−0.0023 (7)	−0.0028 (7)
N1	0.0205 (10)	0.0149 (10)	0.0141 (9)	−0.0027 (8)	0.0061 (8)	−0.0010 (7)
N2	0.0176 (9)	0.0173 (9)	0.0140 (8)	0.0023 (9)	0.0029 (7)	−0.0005 (8)
C1	0.0188 (11)	0.0143 (11)	0.0129 (9)	−0.0018 (9)	0.0038 (8)	−0.0002 (8)
C2	0.0214 (11)	0.0162 (11)	0.0159 (10)	−0.0005 (9)	0.0030 (8)	−0.0001 (9)
C3	0.0259 (12)	0.0223 (12)	0.0171 (10)	−0.0003 (11)	−0.0020 (9)	0.0022 (11)
C4	0.0302 (14)	0.0280 (14)	0.0135 (11)	−0.0070 (12)	−0.0004 (9)	0.0016 (10)
C5	0.0315 (14)	0.0230 (13)	0.0139 (11)	−0.0070 (11)	0.0060 (10)	−0.0028 (9)
C6	0.0151 (10)	0.0138 (10)	0.0131 (9)	0.0021 (9)	0.0035 (7)	0.0007 (8)
C7	0.0183 (11)	0.0168 (11)	0.0159 (11)	0.0004 (9)	0.0031 (9)	−0.0006 (8)
C8	0.0212 (12)	0.0148 (11)	0.0237 (12)	−0.0018 (10)	0.0053 (9)	0.0003 (9)
C9	0.0259 (13)	0.0190 (12)	0.0235 (13)	0.0030 (10)	0.0093 (10)	0.0070 (10)
C10	0.0248 (13)	0.0229 (12)	0.0154 (11)	0.0031 (11)	0.0044 (9)	0.0063 (9)
C11	0.0186 (11)	0.0148 (11)	0.0119 (9)	0.0012 (9)	0.0022 (8)	−0.0006 (9)

Geometric parameters (Å, º) top

S1—C1	1.749 (3)	C3—H3	0.9500
S1—C11	1.820 (3)	C4—C5	1.373 (4)
S2—C6	1.759 (3)	C4—H4	0.9500
S2—C11	1.802 (2)	C5—H5	0.9500
O1—N1	1.309 (3)	C6—C7	1.385 (4)
O2—N2	1.307 (3)	C7—C8	1.383 (4)
N1—C5	1.361 (3)	C7—H7	0.9500
N1—C1	1.366 (3)	C8—C9	1.388 (4)
N2—C10	1.356 (3)	C8—H8	0.9500
N2—C6	1.365 (3)	C9—C10	1.371 (4)
C1—C2	1.386 (4)	C9—H9	0.9500
C2—C3	1.385 (3)	C10—H10	0.9500
C2—H2	0.9500	C11—H11A	0.9900
C3—C4	1.393 (4)	C11—H11B	0.9900

C1—S1—C11	99.12 (11)	C4—C5—H5	119.4
C6—S2—C11	102.00 (12)	N2—C6—C7	120.1 (2)
O1—N1—C5	120.8 (2)	N2—C6—S2	110.72 (19)
O1—N1—C1	118.8 (2)	C7—C6—S2	129.16 (18)
C5—N1—C1	120.4 (2)	C8—C7—C6	119.6 (2)
O2—N2—C10	121.2 (2)	C8—C7—H7	120.2
O2—N2—C6	118.6 (2)	C6—C7—H7	120.2
C10—N2—C6	120.2 (2)	C7—C8—C9	119.5 (3)
N1—C1—C2	120.1 (2)	C7—C8—H8	120.2
N1—C1—S1	111.44 (18)	C9—C8—H8	120.2
C2—C1—S1	128.50 (19)	C10—C9—C8	119.4 (3)
C3—C2—C1	119.5 (2)	C10—C9—H9	120.3
C3—C2—H2	120.3	C8—C9—H9	120.3
C1—C2—H2	120.3	N2—C10—C9	121.1 (2)
C2—C3—C4	120.0 (3)	N2—C10—H10	119.4
C2—C3—H3	120.0	C9—C10—H10	119.4
C4—C3—H3	120.0	S2—C11—S1	110.79 (14)
C5—C4—C3	119.0 (3)	S2—C11—H11A	109.5
C5—C4—H4	120.5	S1—C11—H11A	109.5
C3—C4—H4	120.5	S2—C11—H11B	109.5
N1—C5—C4	121.2 (3)	S1—C11—H11B	109.5
N1—C5—H5	119.4	H11A—C11—H11B	108.1

O1—N1—C1—C2	179.7 (2)	C10—N2—C6—C7	1.9 (3)
C5—N1—C1—C2	−0.4 (4)	O2—N2—C6—S2	0.4 (3)
O1—N1—C1—S1	−0.4 (3)	C10—N2—C6—S2	−179.0 (2)
C5—N1—C1—S1	179.46 (19)	C11—S2—C6—N2	179.53 (17)
C11—S1—C1—N1	−179.00 (19)	C11—S2—C6—C7	−1.5 (3)
C11—S1—C1—C2	0.9 (3)	N2—C6—C7—C8	−0.5 (4)
N1—C1—C2—C3	−0.5 (4)	S2—C6—C7—C8	−179.4 (2)
S1—C1—C2—C3	179.6 (2)	C6—C7—C8—C9	−0.7 (4)
C1—C2—C3—C4	0.7 (4)	C7—C8—C9—C10	0.5 (4)
C2—C3—C4—C5	0.1 (4)	O2—N2—C10—C9	178.4 (3)
O1—N1—C5—C4	−179.0 (3)	C6—N2—C10—C9	−2.2 (4)
C1—N1—C5—C4	1.2 (4)	C8—C9—C10—N2	0.9 (4)
C3—C4—C5—N1	−1.0 (4)	C6—S2—C11—S1	−71.09 (14)
O2—N2—C6—C7	−178.7 (2)	C1—S1—C11—S2	−170.31 (14)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···O1ⁱ	0.95	2.37	3.292 (3)	165
C9—H9···O2ⁱⁱ	0.95	2.70	3.405 (4)	131
C11—H11A···O1ⁱⁱⁱ	0.99	2.33	3.159 (3)	141

Symmetry codes: (i) −x+1, y+1/2, −z+1; (ii) −x+1, y−1/2, −z+2; (iii) −x+2, y+1/2, −z+1.

Funding information

This material is based upon work supported by the National Science Foundation through the Major Research Instrumentation Program under grant No. CHE 1625543 (funding for the single-crystal X-ray diffractometer). Acknowledgment is made to the Donors of the American Chemical Society Petroleum Research Fund for support of this research. The authors gratefully acknowledge the Communities in Transition Initiative for the generous support.

References

Allen, F. H., Johnson, O., Shields, G. P., Smith, B. R. & Towler, M. (2004). J. Appl. Cryst. 37, 335–338. Web of Science CrossRef CAS IUCr Journals Google Scholar
Amoedo-Portela, A., Carballo, R., Casas, J. S., García-Martínez, E., Gómez-Alonso, C., Sánchez-González, A., Sordo, J. & Vázquez-López, E. M. (2002). Z. Anorg. Allg. Chem. 628, 939–950. CAS Google Scholar
Bruker (2018). APEX3 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Castro, V. D. de, de Lima, G. M., Filgueiras, C. A. L. & Gambardella, M. T. P. (2002). J. Mol. Struct. 609, 199–203. Google Scholar
Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341. Web of Science CrossRef CAS IUCr Journals Google Scholar
Hübschle, C. B., Sheldrick, G. M. & Dittrich, B. (2011). J. Appl. Cryst. 44, 1281–1284. Web of Science CrossRef IUCr Journals Google Scholar
Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3–10. Web of Science CSD CrossRef ICSD CAS IUCr Journals Google Scholar
Macrae, C. F., Sovago, I., Cottrell, S. J., Galek, P. T. A., McCabe, P., Pidcock, E., Platings, M., Shields, G. P., Stevens, J. S., Towler, M. & Wood, P. A. (2020). J. Appl. Cryst. 53, 226–235. Web of Science CrossRef CAS IUCr Journals Google Scholar
Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249–259. Web of Science CrossRef CAS IUCr Journals Google Scholar
Rybarczyk-Pirek, A. J., Łukomska-Rogala, M., Wzgarda-Raj, K., Wojtulewski, S. & Palusiak, M. (2018). Cryst. Growth Des. 18, 7373–7382. CAS Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2018). University of Göttingen, Germany. Google Scholar
Spek, A. L. (2020). Acta Cryst. E76, 1–11. Web of Science CrossRef IUCr Journals Google Scholar
Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925. Web of Science CrossRef CAS IUCr Journals Google Scholar

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