organic compounds
1,10-Phenanthroline–dithiooxamide (2/1)
aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and bDepartment of Chemistry, Bengal Engineering and Science University, Shibpur, Howrah 711 103, India
*Correspondence e-mail: hkfun@usm.my
The 12H8N2·0.5C2H4N2S2, contains one 1,10-phenanthroline molecule and a half-molecule of dithiooxamide, which lies across a crystallographic inversion center. The 1,10-phenanthroline unit is not strictly planar, with dihedral angles between the central benzene ring and the pyridine rings of 1.42 (10) and 1.40 (10)°. In the two 1,10-phenanthroline molecules are linked together by one dithiooxamide via intermolecular N—H⋯N hydrogen bonds.
of the title compound, CRelated literature
For background to the chemistry of 1,10-phenanthroline, see: Goswami et al. (2005); Han et al. (2009); Ishida et al. (2010). For a related structure, see: Fun et al. (2010). For standard bond-length data, see: Allen et al. (1987). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986).
Experimental
Crystal data
|
Refinement
|
Data collection: APEX2 (Bruker, 2009); cell SAINT (Bruker, 2009); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009).
Supporting information
https://doi.org/10.1107/S1600536810016405/lh5039sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810016405/lh5039Isup2.hkl
A mixture of commercially available 1,10-phenanthroline and dithiooxamide (1:1) was dissolved in methanol-chloroform (v/v 2:1). Single crystals were grown by slow evaporation of the solvent.
H3B and H3C were located in a difference Fourier map and refined freely [N–H = 0.82 (2) and 0.85 (2) Å]. The remaining H atoms were positioned geometrically and refined using a riding model with Uiso(H) = 1.2 Ueq(C) [C–H = 0.93 Å]. In the final difference Fourier map, the highest peak and the deepest hole are 0.77 and 0.60 Å, respectively, from atom S1.
1,10-Phenanthroline plays a very important role in the field of molecular recognition and supramolecular chemistry (Goswami et al., 2005). We have used 1,10-phenanthroline in the recognition of urea by designed synthetic receptors (Goswami et al., 2005). The title compound is also used in supramolecular co-ordination chemistry (Ishida et al., 2010; Han et al., 2009). Here we report the
of the 1,10-phenanthroline and guest molecule dithiooxamide.The
(Fig. 1), consists of one 1,10-phenanthroline and a half dithiooxamide. The dithiooxamide lies across a crystallographic inversion center [symmetry code = -x+2, -y+2, -z+1]. The 1,10-phenanthroline unit is not strictly planar, with dihedral angles between the central ring and the C1–C4/C12/N1 and C7–C10/N2/C11 rings of 1.42 (10) and 1.40 (10)°, respectively. The bond lengths are within normal ranges (Allen et al., 1987) and are comparable to those observed for closely related structure (Fun et al., 2010).In the
(Fig. 2), two 1,10-phenanthroline molecules are linked together by one dithiooxamide via intermolecular N3—H3C···N1(-x+1, y+1/2, -z+1/2) hydrogen bonds (Table 1).For background to the chemistry of 1,10-phenanthroline, see: Goswami et al. (2005); Han et al. (2009); Ishida et al. (2010). For a related structure, see: Fun et al. (2010). For standard bond-length data, see: Allen et al. (1987). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986).
Data collection: APEX2 (Bruker, 2009); cell
SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).C12H8N2·0.5C2H4N2S2 | F(000) = 500 |
Mr = 240.30 | Dx = 1.407 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 5115 reflections |
a = 10.5481 (3) Å | θ = 2.5–30.1° |
b = 10.0544 (3) Å | µ = 0.26 mm−1 |
c = 13.9960 (4) Å | T = 100 K |
β = 130.145 (2)° | Block, orange |
V = 1134.65 (6) Å3 | 0.28 × 0.26 × 0.10 mm |
Z = 4 |
Bruker SMART APEXII CCD area-detector diffractometer | 3374 independent reflections |
Radiation source: fine-focus sealed tube | 2307 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.074 |
φ and ω scans | θmax = 30.3°, θmin = 2.5° |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | h = −14→14 |
Tmin = 0.931, Tmax = 0.974 | k = −14→13 |
22512 measured reflections | l = −19→19 |
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)] = 0.062 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.160 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.07 | w = 1/[σ2(Fo2) + (0.0764P)2 + 0.8154P] where P = (Fo2 + 2Fc2)/3 |
3374 reflections | (Δ/σ)max < 0.001 |
162 parameters | Δρmax = 1.24 e Å−3 |
0 restraints | Δρmin = −0.40 e Å−3 |
C12H8N2·0.5C2H4N2S2 | V = 1134.65 (6) Å3 |
Mr = 240.30 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 10.5481 (3) Å | µ = 0.26 mm−1 |
b = 10.0544 (3) Å | T = 100 K |
c = 13.9960 (4) Å | 0.28 × 0.26 × 0.10 mm |
β = 130.145 (2)° |
Bruker SMART APEXII CCD area-detector diffractometer | 3374 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | 2307 reflections with I > 2σ(I) |
Tmin = 0.931, Tmax = 0.974 | Rint = 0.074 |
22512 measured reflections |
R[F2 > 2σ(F2)] = 0.062 | 0 restraints |
wR(F2) = 0.160 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.07 | Δρmax = 1.24 e Å−3 |
3374 reflections | Δρmin = −0.40 e Å−3 |
162 parameters |
Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K. |
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. 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. |
x | y | z | Uiso*/Ueq | ||
N1 | 0.3548 (2) | 0.2611 (2) | 0.34019 (17) | 0.0185 (4) | |
N2 | 0.5551 (2) | 0.4592 (2) | 0.36522 (18) | 0.0217 (4) | |
N3 | 0.8022 (2) | 0.9404 (2) | 0.36819 (19) | 0.0201 (4) | |
C1 | 0.2582 (3) | 0.1675 (2) | 0.3304 (2) | 0.0217 (5) | |
H1A | 0.1591 | 0.1482 | 0.2512 | 0.026* | |
C2 | 0.2959 (3) | 0.0962 (2) | 0.4317 (2) | 0.0234 (5) | |
H2A | 0.2241 | 0.0313 | 0.4198 | 0.028* | |
C3 | 0.4421 (3) | 0.1243 (3) | 0.5494 (2) | 0.0247 (5) | |
H3A | 0.4698 | 0.0791 | 0.6186 | 0.030* | |
C4 | 0.5493 (3) | 0.2219 (2) | 0.5643 (2) | 0.0193 (5) | |
C5 | 0.7051 (3) | 0.2534 (3) | 0.6845 (2) | 0.0240 (5) | |
H5A | 0.7382 | 0.2072 | 0.7549 | 0.029* | |
C6 | 0.8035 (3) | 0.3489 (3) | 0.6961 (2) | 0.0236 (5) | |
H6A | 0.9044 | 0.3670 | 0.7746 | 0.028* | |
C7 | 0.7561 (3) | 0.4235 (2) | 0.5902 (2) | 0.0193 (5) | |
C8 | 0.8544 (3) | 0.5272 (3) | 0.6009 (2) | 0.0248 (5) | |
H8A | 0.9528 | 0.5508 | 0.6790 | 0.030* | |
C9 | 0.8045 (3) | 0.5928 (3) | 0.4964 (3) | 0.0277 (6) | |
H9A | 0.8688 | 0.6604 | 0.5015 | 0.033* | |
C10 | 0.6528 (3) | 0.5553 (3) | 0.3803 (2) | 0.0267 (5) | |
H10A | 0.6190 | 0.6011 | 0.3095 | 0.032* | |
C11 | 0.6054 (3) | 0.3938 (2) | 0.4689 (2) | 0.0182 (5) | |
C12 | 0.4998 (3) | 0.2896 (2) | 0.4565 (2) | 0.0170 (4) | |
C13 | 0.9644 (3) | 0.9392 (2) | 0.4567 (2) | 0.0196 (5) | |
S1 | 1.08871 (7) | 0.81821 (6) | 0.47638 (6) | 0.02354 (18) | |
H3C | 0.752 (4) | 0.884 (3) | 0.314 (3) | 0.030 (8)* | |
H3B | 0.754 (4) | 1.004 (3) | 0.366 (3) | 0.032 (8)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0163 (8) | 0.0198 (10) | 0.0163 (9) | −0.0001 (7) | 0.0091 (7) | −0.0012 (7) |
N2 | 0.0213 (9) | 0.0205 (10) | 0.0208 (9) | −0.0015 (8) | 0.0125 (8) | 0.0007 (8) |
N3 | 0.0170 (9) | 0.0203 (11) | 0.0173 (9) | −0.0006 (8) | 0.0085 (8) | −0.0037 (8) |
C1 | 0.0182 (9) | 0.0207 (12) | 0.0216 (11) | −0.0002 (9) | 0.0108 (9) | −0.0009 (9) |
C2 | 0.0224 (10) | 0.0200 (12) | 0.0290 (12) | −0.0002 (9) | 0.0171 (10) | 0.0038 (10) |
C3 | 0.0234 (11) | 0.0260 (13) | 0.0237 (12) | 0.0047 (9) | 0.0148 (10) | 0.0081 (10) |
C4 | 0.0183 (9) | 0.0211 (12) | 0.0172 (10) | 0.0025 (8) | 0.0108 (8) | 0.0014 (9) |
C5 | 0.0203 (10) | 0.0314 (14) | 0.0149 (10) | 0.0062 (9) | 0.0090 (9) | 0.0033 (10) |
C6 | 0.0184 (10) | 0.0304 (14) | 0.0152 (10) | 0.0028 (9) | 0.0078 (9) | −0.0042 (9) |
C7 | 0.0154 (9) | 0.0196 (12) | 0.0200 (11) | 0.0023 (8) | 0.0101 (8) | −0.0039 (9) |
C8 | 0.0147 (9) | 0.0235 (13) | 0.0285 (12) | −0.0012 (8) | 0.0104 (9) | −0.0049 (10) |
C9 | 0.0230 (11) | 0.0205 (13) | 0.0401 (15) | −0.0037 (9) | 0.0206 (11) | −0.0027 (11) |
C10 | 0.0255 (11) | 0.0250 (13) | 0.0280 (12) | −0.0015 (10) | 0.0166 (10) | 0.0028 (10) |
C11 | 0.0165 (9) | 0.0186 (12) | 0.0177 (10) | 0.0012 (8) | 0.0103 (8) | −0.0010 (9) |
C12 | 0.0172 (9) | 0.0160 (11) | 0.0164 (10) | 0.0021 (8) | 0.0102 (8) | −0.0007 (8) |
C13 | 0.0205 (10) | 0.0239 (13) | 0.0157 (10) | −0.0008 (9) | 0.0122 (9) | 0.0015 (9) |
S1 | 0.0235 (3) | 0.0213 (3) | 0.0248 (3) | 0.0033 (2) | 0.0151 (2) | −0.0009 (2) |
N1—C1 | 1.328 (3) | C5—C6 | 1.344 (4) |
N1—C12 | 1.364 (3) | C5—H5A | 0.9300 |
N2—C10 | 1.326 (3) | C6—C7 | 1.433 (3) |
N2—C11 | 1.352 (3) | C6—H6A | 0.9300 |
N3—C13 | 1.315 (3) | C7—C8 | 1.408 (3) |
N3—H3C | 0.81 (3) | C7—C11 | 1.420 (3) |
N3—H3B | 0.81 (3) | C8—C9 | 1.364 (4) |
C1—C2 | 1.398 (3) | C8—H8A | 0.9300 |
C1—H1A | 0.9300 | C9—C10 | 1.411 (3) |
C2—C3 | 1.377 (3) | C9—H9A | 0.9300 |
C2—H2A | 0.9300 | C10—H10A | 0.9300 |
C3—C4 | 1.407 (3) | C11—C12 | 1.456 (3) |
C3—H3A | 0.9300 | C13—C13i | 1.535 (5) |
C4—C12 | 1.412 (3) | C13—S1 | 1.676 (2) |
C4—C5 | 1.438 (3) | ||
C1—N1—C12 | 117.8 (2) | C7—C6—H6A | 119.3 |
C10—N2—C11 | 117.2 (2) | C8—C7—C11 | 117.5 (2) |
C13—N3—H3C | 123 (2) | C8—C7—C6 | 122.4 (2) |
C13—N3—H3B | 117 (2) | C11—C7—C6 | 120.1 (2) |
H3C—N3—H3B | 120 (3) | C9—C8—C7 | 119.7 (2) |
N1—C1—C2 | 124.2 (2) | C9—C8—H8A | 120.1 |
N1—C1—H1A | 117.9 | C7—C8—H8A | 120.1 |
C2—C1—H1A | 117.9 | C8—C9—C10 | 118.2 (2) |
C3—C2—C1 | 118.3 (2) | C8—C9—H9A | 120.9 |
C3—C2—H2A | 120.8 | C10—C9—H9A | 120.9 |
C1—C2—H2A | 120.8 | N2—C10—C9 | 124.5 (2) |
C2—C3—C4 | 119.6 (2) | N2—C10—H10A | 117.8 |
C2—C3—H3A | 120.2 | C9—C10—H10A | 117.8 |
C4—C3—H3A | 120.2 | N2—C11—C7 | 122.9 (2) |
C3—C4—C12 | 118.0 (2) | N2—C11—C12 | 118.79 (19) |
C3—C4—C5 | 122.0 (2) | C7—C11—C12 | 118.3 (2) |
C12—C4—C5 | 120.0 (2) | N1—C12—C4 | 122.1 (2) |
C6—C5—C4 | 120.7 (2) | N1—C12—C11 | 118.4 (2) |
C6—C5—H5A | 119.7 | C4—C12—C11 | 119.46 (19) |
C4—C5—H5A | 119.7 | N3—C13—C13i | 114.4 (3) |
C5—C6—C7 | 121.4 (2) | N3—C13—S1 | 124.50 (19) |
C5—C6—H6A | 119.3 | C13i—C13—S1 | 121.1 (2) |
C12—N1—C1—C2 | −0.2 (3) | C10—N2—C11—C12 | 178.7 (2) |
N1—C1—C2—C3 | 0.2 (4) | C8—C7—C11—N2 | 0.9 (3) |
C1—C2—C3—C4 | −0.7 (4) | C6—C7—C11—N2 | −179.0 (2) |
C2—C3—C4—C12 | 1.3 (4) | C8—C7—C11—C12 | −178.2 (2) |
C2—C3—C4—C5 | −178.6 (2) | C6—C7—C11—C12 | 1.9 (3) |
C3—C4—C5—C6 | −178.7 (2) | C1—N1—C12—C4 | 0.8 (3) |
C12—C4—C5—C6 | 1.4 (4) | C1—N1—C12—C11 | −178.8 (2) |
C4—C5—C6—C7 | 0.8 (4) | C3—C4—C12—N1 | −1.3 (3) |
C5—C6—C7—C8 | 177.7 (2) | C5—C4—C12—N1 | 178.6 (2) |
C5—C6—C7—C11 | −2.4 (3) | C3—C4—C12—C11 | 178.2 (2) |
C11—C7—C8—C9 | −1.3 (3) | C5—C4—C12—C11 | −1.8 (3) |
C6—C7—C8—C9 | 178.6 (2) | N2—C11—C12—N1 | 0.7 (3) |
C7—C8—C9—C10 | 1.2 (4) | C7—C11—C12—N1 | 179.81 (19) |
C11—N2—C10—C9 | 0.3 (4) | N2—C11—C12—C4 | −178.9 (2) |
C8—C9—C10—N2 | −0.7 (4) | C7—C11—C12—C4 | 0.2 (3) |
C10—N2—C11—C7 | −0.4 (3) |
Symmetry code: (i) −x+2, −y+2, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3C···N1ii | 0.81 (3) | 2.08 (3) | 2.876 (3) | 167 (4) |
Symmetry code: (ii) −x+1, y+1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C12H8N2·0.5C2H4N2S2 |
Mr | 240.30 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 100 |
a, b, c (Å) | 10.5481 (3), 10.0544 (3), 13.9960 (4) |
β (°) | 130.145 (2) |
V (Å3) | 1134.65 (6) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.26 |
Crystal size (mm) | 0.28 × 0.26 × 0.10 |
Data collection | |
Diffractometer | Bruker SMART APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2009) |
Tmin, Tmax | 0.931, 0.974 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 22512, 3374, 2307 |
Rint | 0.074 |
(sin θ/λ)max (Å−1) | 0.709 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.062, 0.160, 1.07 |
No. of reflections | 3374 |
No. of parameters | 162 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 1.24, −0.40 |
Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3C···N1i | 0.81 (3) | 2.08 (3) | 2.876 (3) | 167 (4) |
Symmetry code: (i) −x+1, y+1/2, −z+1/2. |
Acknowledgements
The authors thank Universiti Sains Malaysia (USM) for the Research University Golden Goose Grant (1001/PFIZIK/811012). WSL thanks the Malaysian Government and USM for the award of Research Fellowship. SG and ACM thank the CSIR [No. 01 (2292)/09/ EMR-II], Government of India, for financial support.
References
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1,10-Phenanthroline plays a very important role in the field of molecular recognition and supramolecular chemistry (Goswami et al., 2005). We have used 1,10-phenanthroline in the recognition of urea by designed synthetic receptors (Goswami et al., 2005). The title compound is also used in supramolecular co-ordination chemistry (Ishida et al., 2010; Han et al., 2009). Here we report the co-crystal of the 1,10-phenanthroline and guest molecule dithiooxamide.
The asymmetric unit (Fig. 1), consists of one 1,10-phenanthroline and a half dithiooxamide. The dithiooxamide lies across a crystallographic inversion center [symmetry code = -x+2, -y+2, -z+1]. The 1,10-phenanthroline unit is not strictly planar, with dihedral angles between the central ring and the C1–C4/C12/N1 and C7–C10/N2/C11 rings of 1.42 (10) and 1.40 (10)°, respectively. The bond lengths are within normal ranges (Allen et al., 1987) and are comparable to those observed for closely related structure (Fun et al., 2010).
In the crystal structure (Fig. 2), two 1,10-phenanthroline molecules are linked together by one dithiooxamide via intermolecular N3—H3C···N1(-x+1, y+1/2, -z+1/2) hydrogen bonds (Table 1).