organic compounds
2,9-Bis(5-sulfanylidene-4,5-dihydro-1,3,4-oxadiazol-2-yl)-1,10-phenanthroline dimethyl sulfoxide disolvate
aDepartment of Chemistry, Boswell Science Complex, Tennessee State University, Nashville, 3500 John A. Merritt Blvd, Nashville, TN 37209, USA, bDepartment of Chemistry, Iowa State University, Ames, IA 50011-3111, USA, and cAgilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, CA 95051, USA
*Correspondence e-mail: tsiddiqu@tnstate.edu
In the title compound, C16H8N6O2S2·2C2H6OS, the phenanthroline molecule resides on a twofold axis, and the also contains a slightly disordered [occupancy ratio for S atom of 0.95 (3):0.047 (3)] molecule of dimethyl sulfoxide. The O atoms of the solvent molecule accept hydrogen bonds from the N—H groups of the five-membered 2,3-dihydro-1,3,4-oxadiazole-2-thione ring. This ring is nearly coplanar with the phenanthroline ring, with a dihedral angle between their least-squares planes of 8.86 (6)°. In the crystal, the molecules are linked by C—H⋯O interactions.
CCDC reference: 950902
Related literature
For the biological activity of the oxadiazole unit, see: Chen et al. (2000); Sun et al. (2013); El-Emam et al. (2004). For their anticancer activity, see: Zhang et al. (2011); Gudipati et al. (2011); Abou-Seri (2010). For related structures, see: Saeed et al. (2010); Fun et al. (2011); El-Emam et al. (2012, 2013).
Experimental
Crystal data
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Data collection: CrystalClear (Pflugrath, 1999); cell CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: WinGX (Farrugia, 2012) and publCIF (Westrip, 2010).
Supporting information
CCDC reference: 950902
10.1107/S1600536814003304/fj2661sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536814003304/fj2661Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536814003304/fj2661Isup3.cml
1,10-Phenanthroline-2,9-Di-S-methylhydrazinecarbodithioate (0.100 g, 0.21 mmol) was dissolved in THF (30 mL) with heat until a clear solution was formed. Then a solution of ZnCl2 (0.015 g, 0.11 mmol) in THF (5 mL) was added drop-wise to the carbodithioate solution. The resulting mixture was refluxed for 2–4 hrs. After completion of the reaction, as indicated by TLC, the reaction mixture was allowed to cool to room temperature. The solvent was evaporated under reduced pressure. The product was washed with ether and dried under vacuum. Recrystallization from DMSO yielded white crystals suitable for diffraction (0.076 g, 95%Y). 1HNMR (DMSO-d6, p.p.m.): δH 8.8 (d, 2H), 8.4(d, 2H), 8.2 (s, 2H). 13CNMR (DMSO-d6, p.p.m.): δC 178, 159, 144, 141, 138, 130, 128, 122. IR ν (cm-1): 3230 (N—H), 1196 (C—O), 3100–3000(C—H), 1600–1500 (aromatic C=C), 1373 (C=S).
One large residual peak near the DMSO solvent molecule appears to indicate an alternate position of the S atom (an inversion of the DMSO pyramid). The disorder of the S atom was refined to an occupancy of less than 5% for the minor position; the minor occupancy of the lighter atoms of the solvent molecule were not included in the model.
Non-hydrogen atoms were refined with anisotropic thermal parameters, and hydrogen atoms were included in calculated positions (riding model) with Uiso set to 1.2 times the Ueq of the parent atom. σ (I).
on F2 by full-matrix least-squares resulted in R1 = 0.0727 and wR2 = 0.1729 for 2742 reflections with I > 2Data collection: CrystalClear (Pflugrath, 1999); cell
CrystalClear (Pflugrath, 1999); data reduction: CrystalClear (Pflugrath, 1999); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: WinGX (Farrugia, 2012) and publCIF (Westrip, 2010).Fig. 1. Molecular structure showing 50% probability displacement ellipsoids. DMSO molecules are not shown | |
Fig. 2. Hydrogen bonding interaction with a DMSO solvent molecule | |
Fig. 3. Packing diagram viewed along the normal to (101). Note the solvent molecules are positioned between two compounds making hydrogen bonding feasible |
C16H8N6O2S2·2C2H6OS | F(000) = 1112 |
Mr = 536.66 | Dx = 1.47 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71075 Å |
Hall symbol: -C 2yc | Cell parameters from 2562 reflections |
a = 14.113 (11) Å | θ = 3–27.7° |
b = 11.161 (8) Å | µ = 0.43 mm−1 |
c = 16.708 (12) Å | T = 277 K |
β = 112.837 (14)° | Prism, white |
V = 2425 (3) Å3 | 0.42 × 0.26 × 0.15 mm |
Z = 4 |
Rigaku XtaLAB mini diffractometer | 1691 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.039 |
profile data from ω–scans | θmax = 27.5°, θmin = 3.0° |
Absorption correction: multi-scan (CrystalClear; Pflugrath, 1999) | h = −18→16 |
Tmin = 0.840, Tmax = 0.938 | k = −10→14 |
5592 measured reflections | l = −21→17 |
2741 independent reflections |
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)] = 0.067 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.171 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.03 | w = 1/[σ2(Fo2) + (0.0524P)2 + 6.1166P] where P = (Fo2 + 2Fc2)/3 |
2741 reflections | (Δ/σ)max = 0.001 |
164 parameters | Δρmax = 0.30 e Å−3 |
0 restraints | Δρmin = −0.59 e Å−3 |
C16H8N6O2S2·2C2H6OS | V = 2425 (3) Å3 |
Mr = 536.66 | Z = 4 |
Monoclinic, C2/c | Mo Kα radiation |
a = 14.113 (11) Å | µ = 0.43 mm−1 |
b = 11.161 (8) Å | T = 277 K |
c = 16.708 (12) Å | 0.42 × 0.26 × 0.15 mm |
β = 112.837 (14)° |
Rigaku XtaLAB mini diffractometer | 2741 independent reflections |
Absorption correction: multi-scan (CrystalClear; Pflugrath, 1999) | 1691 reflections with I > 2σ(I) |
Tmin = 0.840, Tmax = 0.938 | Rint = 0.039 |
5592 measured reflections |
R[F2 > 2σ(F2)] = 0.067 | 0 restraints |
wR(F2) = 0.171 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.03 | Δρmax = 0.30 e Å−3 |
2741 reflections | Δρmin = −0.59 e Å−3 |
164 parameters |
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
S2 | 0.26830 (13) | 1.33767 (13) | 0.77108 (7) | 0.0922 (6) | 0.953 (3) |
S2B | 0.265 (2) | 1.355 (3) | 0.695 (2) | 0.092* | 0.047 (3) |
O2 | 0.1971 (2) | 1.2428 (2) | 0.72136 (16) | 0.0647 (8) | |
C9 | 0.3844 (4) | 1.3093 (7) | 0.7638 (4) | 0.140 (3) | |
H9A | 0.4190 | 1.2459 | 0.8031 | 0.211* | |
H9B | 0.4260 | 1.3803 | 0.7787 | 0.211* | |
H9C | 0.3730 | 1.2858 | 0.7055 | 0.211* | |
C10 | 0.2382 (6) | 1.4660 (5) | 0.7056 (4) | 0.130 (2) | |
H10A | 0.2309 | 1.4449 | 0.6478 | 0.195* | |
H10B | 0.2922 | 1.5238 | 0.7291 | 0.195* | |
H10C | 0.1748 | 1.4994 | 0.7041 | 0.195* | |
S1 | 0.10833 (14) | 1.36039 (10) | 0.46674 (8) | 0.1039 (6) | |
O1 | 0.0925 (2) | 1.1303 (2) | 0.42720 (15) | 0.0574 (7) | |
N2 | 0.1421 (3) | 1.1611 (3) | 0.56291 (19) | 0.0557 (8) | |
N1 | 0.1384 (2) | 1.0401 (2) | 0.55250 (17) | 0.0506 (7) | |
N3 | 0.0448 (2) | 0.9170 (2) | 0.33922 (16) | 0.0397 (6) | |
C1 | 0.1091 (3) | 1.0258 (3) | 0.4711 (2) | 0.0444 (8) | |
C6 | 0.0494 (3) | 0.7019 (3) | 0.3399 (2) | 0.0520 (9) | |
C4 | 0.1181 (3) | 0.8082 (3) | 0.4726 (2) | 0.0548 (9) | |
H4 | 0.1506 | 0.8106 | 0.5328 | 0.066* | |
C7 | 0.0238 (4) | 0.5931 (3) | 0.2927 (2) | 0.0690 (12) | |
H7 | 0.0409 | 0.5206 | 0.3223 | 0.083* | |
C5 | 0.0973 (3) | 0.7028 (3) | 0.4299 (2) | 0.0614 (11) | |
H5 | 0.1148 | 0.6311 | 0.4606 | 0.074* | |
C2 | 0.1163 (3) | 1.2176 (3) | 0.4891 (2) | 0.0598 (10) | |
C8 | 0.0250 (3) | 0.8122 (3) | 0.2969 (2) | 0.0425 (7) | |
C3 | 0.0899 (3) | 0.9131 (3) | 0.4245 (2) | 0.0439 (8) | |
H2 | 0.164 (3) | 1.195 (3) | 0.616 (3) | 0.062 (11)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S2 | 0.1324 (13) | 0.1011 (10) | 0.0456 (6) | −0.0709 (9) | 0.0373 (7) | −0.0308 (6) |
O2 | 0.0782 (19) | 0.0651 (16) | 0.0492 (14) | −0.0269 (14) | 0.0228 (13) | −0.0169 (12) |
C9 | 0.090 (4) | 0.188 (7) | 0.113 (5) | −0.065 (5) | 0.007 (4) | 0.027 (5) |
C10 | 0.185 (7) | 0.066 (3) | 0.157 (6) | −0.052 (4) | 0.085 (5) | −0.023 (4) |
S1 | 0.1906 (17) | 0.0392 (6) | 0.0635 (7) | −0.0070 (7) | 0.0292 (9) | 0.0048 (5) |
O1 | 0.0884 (19) | 0.0388 (13) | 0.0382 (13) | −0.0047 (12) | 0.0170 (13) | 0.0007 (10) |
N2 | 0.081 (2) | 0.0418 (16) | 0.0369 (16) | −0.0088 (15) | 0.0144 (15) | −0.0045 (13) |
N1 | 0.069 (2) | 0.0379 (14) | 0.0381 (15) | −0.0046 (14) | 0.0135 (14) | 0.0010 (11) |
N3 | 0.0452 (16) | 0.0351 (14) | 0.0379 (14) | 0.0002 (11) | 0.0151 (12) | 0.0014 (10) |
C1 | 0.052 (2) | 0.0377 (17) | 0.0382 (18) | −0.0035 (15) | 0.0123 (15) | 0.0050 (13) |
C6 | 0.069 (2) | 0.0350 (17) | 0.0465 (19) | 0.0037 (16) | 0.0168 (17) | 0.0037 (14) |
C4 | 0.069 (3) | 0.050 (2) | 0.0354 (18) | 0.0045 (18) | 0.0087 (17) | 0.0039 (15) |
C7 | 0.109 (4) | 0.0306 (17) | 0.058 (2) | 0.004 (2) | 0.022 (2) | 0.0056 (15) |
C5 | 0.088 (3) | 0.0379 (19) | 0.047 (2) | 0.0087 (19) | 0.014 (2) | 0.0112 (15) |
C2 | 0.085 (3) | 0.044 (2) | 0.044 (2) | −0.0051 (19) | 0.0176 (19) | −0.0021 (15) |
C8 | 0.051 (2) | 0.0338 (16) | 0.0416 (17) | 0.0002 (14) | 0.0163 (15) | 0.0008 (13) |
C3 | 0.053 (2) | 0.0374 (17) | 0.0399 (17) | −0.0011 (15) | 0.0162 (16) | 0.0014 (13) |
S2—O2 | 1.474 (3) | N1—C1 | 1.269 (4) |
S2—C9 | 1.719 (7) | N3—C3 | 1.317 (4) |
S2—C10 | 1.751 (6) | N3—C8 | 1.338 (4) |
C9—H9A | 0.9600 | C1—C3 | 1.449 (4) |
C9—H9B | 0.9600 | C6—C5 | 1.389 (5) |
C9—H9C | 0.9600 | C6—C8 | 1.400 (4) |
C10—H10A | 0.9600 | C6—C7 | 1.416 (5) |
C10—H10B | 0.9600 | C4—C5 | 1.348 (5) |
C10—H10C | 0.9600 | C4—C3 | 1.387 (5) |
S1—C2 | 1.631 (4) | C4—H4 | 0.9300 |
O1—C1 | 1.348 (4) | C7—C7i | 1.321 (8) |
O1—C2 | 1.365 (4) | C7—H7 | 0.9300 |
N2—C2 | 1.305 (5) | C5—H5 | 0.9300 |
N2—N1 | 1.360 (4) | C8—C8i | 1.448 (6) |
N2—H2 | 0.89 (4) | ||
O2—S2—C9 | 106.7 (3) | O1—C1—C3 | 120.2 (3) |
O2—S2—C10 | 106.7 (3) | C5—C6—C8 | 118.0 (3) |
C9—S2—C10 | 96.5 (3) | C5—C6—C7 | 121.4 (3) |
S2—C9—H9A | 109.5 | C8—C6—C7 | 120.6 (3) |
S2—C9—H9B | 109.5 | C5—C4—C3 | 118.4 (3) |
H9A—C9—H9B | 109.5 | C5—C4—H4 | 120.8 |
S2—C9—H9C | 109.5 | C3—C4—H4 | 120.8 |
H9A—C9—H9C | 109.5 | C7i—C7—C6 | 121.0 (2) |
H9B—C9—H9C | 109.5 | C7i—C7—H7 | 119.5 |
S2—C10—H10A | 109.5 | C6—C7—H7 | 119.5 |
S2—C10—H10B | 109.5 | C4—C5—C6 | 119.6 (3) |
H10A—C10—H10B | 109.5 | C4—C5—H5 | 120.2 |
S2—C10—H10C | 109.5 | C6—C5—H5 | 120.2 |
H10A—C10—H10C | 109.5 | N2—C2—O1 | 105.5 (3) |
H10B—C10—H10C | 109.5 | N2—C2—S1 | 131.2 (3) |
C1—O1—C2 | 105.4 (3) | O1—C2—S1 | 123.3 (3) |
C2—N2—N1 | 112.1 (3) | N3—C8—C6 | 122.5 (3) |
C2—N2—H2 | 126 (2) | N3—C8—C8i | 119.07 (17) |
N1—N2—H2 | 122 (2) | C6—C8—C8i | 118.39 (19) |
C1—N1—N2 | 104.0 (3) | N3—C3—C4 | 124.3 (3) |
C3—N3—C8 | 117.2 (3) | N3—C3—C1 | 117.6 (3) |
N1—C1—O1 | 112.9 (3) | C4—C3—C1 | 118.1 (3) |
N1—C1—C3 | 126.8 (3) | ||
C2—N2—N1—C1 | −0.5 (5) | C3—N3—C8—C6 | 0.7 (5) |
N2—N1—C1—O1 | −0.5 (4) | C3—N3—C8—C8i | 179.7 (4) |
N2—N1—C1—C3 | −178.3 (3) | C5—C6—C8—N3 | −0.9 (6) |
C2—O1—C1—N1 | 1.3 (4) | C7—C6—C8—N3 | 177.8 (4) |
C2—O1—C1—C3 | 179.2 (3) | C5—C6—C8—C8i | −180.0 (4) |
C5—C6—C7—C7i | 178.4 (6) | C7—C6—C8—C8i | −1.3 (6) |
C8—C6—C7—C7i | −0.2 (8) | C8—N3—C3—C4 | 0.2 (5) |
C3—C4—C5—C6 | 0.5 (6) | C8—N3—C3—C1 | −178.3 (3) |
C8—C6—C5—C4 | 0.3 (6) | C5—C4—C3—N3 | −0.8 (6) |
C7—C6—C5—C4 | −178.4 (4) | C5—C4—C3—C1 | 177.7 (4) |
N1—N2—C2—O1 | 1.2 (5) | N1—C1—C3—N3 | 169.7 (4) |
N1—N2—C2—S1 | 179.8 (4) | O1—C1—C3—N3 | −7.9 (5) |
C1—O1—C2—N2 | −1.5 (4) | N1—C1—C3—C4 | −9.0 (6) |
C1—O1—C2—S1 | 179.8 (3) | O1—C1—C3—C4 | 173.4 (3) |
Symmetry code: (i) −x, y, −z+1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O2 | 0.89 (4) | 1.73 (4) | 2.617 (4) | 172 (4) |
C9—H9C···O1ii | 0.96 | 2.62 | 3.399 (7) | 138 |
C10—H10B···O2iii | 0.96 | 2.57 | 3.317 (6) | 135 |
N2—H2···S2B | 0.89 (4) | 2.36 (5) | 3.10 (3) | 140 (3) |
Symmetry codes: (ii) −x+1/2, −y+5/2, −z+1; (iii) −x+1/2, y+1/2, −z+3/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O2 | 0.89 (4) | 1.73 (4) | 2.617 (4) | 172 (4) |
C9—H9C···O1i | 0.96 | 2.62 | 3.399 (7) | 138.4 |
C10—H10B···O2ii | 0.96 | 2.57 | 3.317 (6) | 135.3 |
N2—H2···S2B | 0.89 (4) | 2.36 (5) | 3.10 (3) | 140 (3) |
Symmetry codes: (i) −x+1/2, −y+5/2, −z+1; (ii) −x+1/2, y+1/2, −z+3/2. |
Acknowledgements
MK and TS acknowledge the US Department of Education for the purchase of a diffractometer.
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
Compounds containing the oxadiazol moieties are known for their antimicrobial and anticancer activities. The title compound was prepared and characterized with the aim of synthesizing a series of compounds that are potentially active. These compounds were synthesized by a new process.
The title compound crystallized as a dimethyl sulfoxide (DMSO) solvate. The O atoms of the solvent form strong hydrogen bonds with the N—H centers of the diazole moiety.
The molecules are essentially planar, although the plane of the oxadiazolic five membered thionyl groups are slightly rotated from the phenanthrolene plane (the two least-squares planes form an angle of 8.86 (5)°). The molecules are arranged in planar sheets, with each pair of thiol S atoms pointing at the two apical hydrogen atoms on the adjacent phenanthroline groups.