organic compounds
2-Methylsulfanyl-1H-perimidin-3-ium iodide
aFalavarjan Branch, Islamic Azad University, Falavarjan, Isfahan, Iran
*Correspondence e-mail: ghorbani@iaufala.ac.ir, moha_ghorbani@yahoo.com
In the structure of the title salt C12H11N2S+·I−, the methylsulfanyl group of the cation is nearly coplanar with the perimidine rings, as indicated by the C—S—C—N torsion angles of 2.9 (5) and −177.2 (3)°, respectively. The (S)C—N bond lengths in the heterocyclic ring are approximately equal [1.325 (5) and 1.326 (6) Å] suggesting a degree of delocalization. In the crystal, cations and anions are linked via two discrete N—H⋯I hydrogen bonds, forming chains along the b axis.
Related literature
For synthetic details and applications, see: Liu & Chen (1984); Herbert et al. (1987). For the NMR spectra, see Woodgate et al. (1988). For related structures, see: Molčanov et al. (2012); Wang (2012); Tiritiris & Kantlehner (2012).
Experimental
Crystal data
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Refinement
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Data collection: X-AREA (Stoe & Cie, 2005); cell X-AREA; data reduction: X-RED32 (Stoe & Cie, 2005); 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, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).
Supporting information
10.1107/S1600536812033697/sj5260sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812033697/sj5260Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812033697/sj5260Isup3.cml
The title salt was prepared by a literature method (Liu & Chen, 1984; Herbert et al., 1987). Suitable single crystals for X-ray analysis were obtained from ethanol solution at room temperature.
All hydrogen atoms bound to carbon were positioned geometrically with C—H distances = 0.93–0.96 Å and included in a riding model approximation with Uiso(H) = 1.2 or 1.5Ueq(C). The N–H hydrogen atoms were located in a difference Fourier map and refined freely.
Data collection: X-AREA (Stoe & Cie, 2005); cell
X-AREA (Stoe & Cie, 2005); data reduction: X-RED32 (Stoe & Cie, 2005); 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, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).C12H11N2S+·I− | F(000) = 664 |
Mr = 342.19 | Dx = 1.877 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 3266 reflections |
a = 7.0107 (14) Å | θ = 2.1–29.2° |
b = 8.8968 (18) Å | µ = 2.79 mm−1 |
c = 19.520 (4) Å | T = 298 K |
β = 95.90 (3)° | Plate, green |
V = 1211.1 (4) Å3 | 0.20 × 0.17 × 0.10 mm |
Z = 4 |
Stoe IPDS 2T diffractometer | 3266 independent reflections |
Radiation source: fine-focus sealed tube | 2151 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.053 |
Detector resolution: 0.15 pixels mm-1 | θmax = 29.2°, θmin = 2.1° |
rotation method scans | h = −9→9 |
Absorption correction: numerical (X-RED32; Stoe & Cie, 2005) | k = −12→10 |
Tmin = 0.605, Tmax = 0.768 | l = −26→23 |
8695 measured 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)] = 0.044 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.094 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.11 | w = 1/[σ2(Fo2) + (0.0351P)2 + 0.0203P] where P = (Fo2 + 2Fc2)/3 |
3266 reflections | (Δ/σ)max = 0.001 |
152 parameters | Δρmax = 0.98 e Å−3 |
1 restraint | Δρmin = −0.47 e Å−3 |
C12H11N2S+·I− | V = 1211.1 (4) Å3 |
Mr = 342.19 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 7.0107 (14) Å | µ = 2.79 mm−1 |
b = 8.8968 (18) Å | T = 298 K |
c = 19.520 (4) Å | 0.20 × 0.17 × 0.10 mm |
β = 95.90 (3)° |
Stoe IPDS 2T diffractometer | 3266 independent reflections |
Absorption correction: numerical (X-RED32; Stoe & Cie, 2005) | 2151 reflections with I > 2σ(I) |
Tmin = 0.605, Tmax = 0.768 | Rint = 0.053 |
8695 measured reflections |
R[F2 > 2σ(F2)] = 0.044 | 1 restraint |
wR(F2) = 0.094 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.11 | Δρmax = 0.98 e Å−3 |
3266 reflections | Δρmin = −0.47 e Å−3 |
152 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
I1 | 0.23717 (5) | 0.01191 (3) | 0.335840 (18) | 0.04724 (12) | |
S1 | 0.3337 (2) | 0.57350 (14) | 0.29413 (7) | 0.0475 (3) | |
N1 | 0.2710 (5) | 0.4113 (4) | 0.4069 (2) | 0.0308 (8) | |
N2 | 0.3149 (6) | 0.6660 (4) | 0.4194 (2) | 0.0341 (9) | |
C1 | 0.2992 (8) | 0.3909 (6) | 0.2564 (3) | 0.0481 (13) | |
H1A | 0.3861 | 0.3211 | 0.2806 | 0.072* | |
H1B | 0.3232 | 0.3950 | 0.2089 | 0.072* | |
H1C | 0.1696 | 0.3588 | 0.2595 | 0.072* | |
C2 | 0.3031 (6) | 0.5445 (5) | 0.3799 (2) | 0.0304 (9) | |
C3 | 0.2384 (6) | 0.3919 (5) | 0.4769 (2) | 0.0295 (9) | |
C4 | 0.1976 (7) | 0.2561 (5) | 0.5032 (3) | 0.0376 (11) | |
H4 | 0.1910 | 0.1707 | 0.4756 | 0.045* | |
C5 | 0.1651 (7) | 0.2459 (6) | 0.5733 (3) | 0.0432 (12) | |
H5 | 0.1363 | 0.1531 | 0.5916 | 0.052* | |
C6 | 0.1753 (7) | 0.3702 (6) | 0.6146 (3) | 0.0414 (12) | |
H6 | 0.1535 | 0.3607 | 0.6606 | 0.050* | |
C7 | 0.2184 (6) | 0.5129 (5) | 0.5885 (2) | 0.0344 (9) | |
C8 | 0.2492 (5) | 0.5236 (5) | 0.5181 (2) | 0.0295 (8) | |
C9 | 0.2892 (6) | 0.6642 (5) | 0.4898 (2) | 0.0299 (9) | |
C10 | 0.3011 (7) | 0.7923 (5) | 0.5285 (3) | 0.0406 (11) | |
H10 | 0.3295 | 0.8844 | 0.5095 | 0.049* | |
C11 | 0.2689 (7) | 0.7801 (6) | 0.5986 (3) | 0.0451 (13) | |
H11 | 0.2756 | 0.8664 | 0.6257 | 0.054* | |
C12 | 0.2284 (7) | 0.6463 (6) | 0.6281 (3) | 0.0434 (12) | |
H12 | 0.2074 | 0.6427 | 0.6744 | 0.052* | |
H1 | 0.274 (8) | 0.328 (7) | 0.387 (3) | 0.052* | |
H2 | 0.327 (8) | 0.746 (4) | 0.401 (3) | 0.052* |
U11 | U22 | U33 | U12 | U13 | U23 | |
I1 | 0.0704 (2) | 0.02971 (16) | 0.04296 (19) | −0.00194 (17) | 0.01260 (14) | 0.00215 (16) |
S1 | 0.0825 (10) | 0.0347 (6) | 0.0260 (6) | −0.0092 (6) | 0.0095 (6) | 0.0024 (5) |
N1 | 0.036 (2) | 0.0292 (18) | 0.029 (2) | −0.0009 (15) | 0.0099 (16) | −0.0010 (16) |
N2 | 0.046 (2) | 0.0261 (18) | 0.031 (2) | −0.0010 (16) | 0.0056 (18) | 0.0030 (15) |
C1 | 0.074 (4) | 0.037 (3) | 0.034 (3) | −0.008 (2) | 0.011 (3) | −0.008 (2) |
C2 | 0.031 (2) | 0.032 (2) | 0.028 (2) | 0.0019 (17) | 0.0010 (18) | 0.0031 (17) |
C3 | 0.025 (2) | 0.035 (2) | 0.030 (2) | 0.0053 (17) | 0.0057 (18) | 0.0056 (18) |
C4 | 0.038 (3) | 0.036 (2) | 0.039 (3) | 0.000 (2) | 0.007 (2) | 0.004 (2) |
C5 | 0.047 (3) | 0.044 (3) | 0.040 (3) | −0.001 (2) | 0.011 (2) | 0.011 (2) |
C6 | 0.038 (3) | 0.056 (3) | 0.030 (3) | 0.005 (2) | 0.006 (2) | 0.009 (2) |
C7 | 0.0287 (19) | 0.047 (3) | 0.027 (2) | 0.006 (2) | 0.0014 (16) | 0.002 (2) |
C8 | 0.0248 (18) | 0.034 (2) | 0.029 (2) | 0.0038 (17) | 0.0010 (16) | −0.0004 (19) |
C9 | 0.027 (2) | 0.033 (2) | 0.029 (2) | 0.0021 (17) | 0.0024 (18) | −0.0025 (18) |
C10 | 0.047 (3) | 0.033 (2) | 0.040 (3) | 0.003 (2) | 0.003 (2) | −0.005 (2) |
C11 | 0.046 (3) | 0.048 (3) | 0.040 (3) | 0.003 (2) | −0.002 (2) | −0.019 (2) |
C12 | 0.041 (3) | 0.062 (3) | 0.026 (3) | 0.004 (2) | 0.001 (2) | −0.007 (2) |
S1—C2 | 1.730 (5) | C4—H4 | 0.9300 |
S1—C1 | 1.789 (5) | C5—C6 | 1.366 (7) |
N1—C2 | 1.325 (5) | C5—H5 | 0.9300 |
N1—C3 | 1.418 (6) | C6—C7 | 1.413 (7) |
N1—H1 | 0.85 (6) | C6—H6 | 0.9300 |
N2—C2 | 1.325 (6) | C7—C12 | 1.415 (7) |
N2—C9 | 1.404 (6) | C7—C8 | 1.415 (6) |
N2—H2 | 0.811 (19) | C8—C9 | 1.408 (6) |
C1—H1A | 0.9600 | C9—C10 | 1.366 (6) |
C1—H1B | 0.9600 | C10—C11 | 1.414 (7) |
C1—H1C | 0.9600 | C10—H10 | 0.9300 |
C3—C4 | 1.356 (6) | C11—C12 | 1.365 (8) |
C3—C8 | 1.419 (6) | C11—H11 | 0.9300 |
C4—C5 | 1.412 (7) | C12—H12 | 0.9300 |
C2—S1—C1 | 103.8 (2) | C6—C5—H5 | 119.5 |
C2—N1—C3 | 122.9 (4) | C4—C5—H5 | 119.5 |
C2—N1—H1 | 126 (4) | C5—C6—C7 | 121.0 (4) |
C3—N1—H1 | 111 (4) | C5—C6—H6 | 119.5 |
C2—N2—C9 | 123.6 (4) | C7—C6—H6 | 119.5 |
C2—N2—H2 | 118 (4) | C6—C7—C12 | 123.8 (4) |
C9—N2—H2 | 119 (4) | C6—C7—C8 | 118.0 (4) |
S1—C1—H1A | 109.5 | C12—C7—C8 | 118.1 (4) |
S1—C1—H1B | 109.5 | C9—C8—C7 | 119.8 (4) |
H1A—C1—H1B | 109.5 | C9—C8—C3 | 120.8 (4) |
S1—C1—H1C | 109.5 | C7—C8—C3 | 119.4 (4) |
H1A—C1—H1C | 109.5 | C10—C9—N2 | 121.7 (4) |
H1B—C1—H1C | 109.5 | C10—C9—C8 | 121.8 (4) |
N1—C2—N2 | 120.1 (4) | N2—C9—C8 | 116.5 (4) |
N1—C2—S1 | 124.2 (3) | C9—C10—C11 | 117.7 (5) |
N2—C2—S1 | 115.8 (3) | C9—C10—H10 | 121.1 |
C4—C3—N1 | 122.4 (4) | C11—C10—H10 | 121.1 |
C4—C3—C8 | 121.4 (4) | C12—C11—C10 | 122.4 (5) |
N1—C3—C8 | 116.2 (4) | C12—C11—H11 | 118.8 |
C3—C4—C5 | 119.1 (5) | C10—C11—H11 | 118.8 |
C3—C4—H4 | 120.4 | C11—C12—C7 | 120.1 (5) |
C5—C4—H4 | 120.4 | C11—C12—H12 | 119.9 |
C6—C5—C4 | 121.0 (5) | C7—C12—H12 | 119.9 |
C3—N1—C2—N2 | 3.3 (7) | C12—C7—C8—C3 | −179.5 (4) |
C3—N1—C2—S1 | −177.2 (3) | C4—C3—C8—C9 | −179.2 (4) |
C9—N2—C2—N1 | −2.1 (7) | N1—C3—C8—C9 | 0.3 (6) |
C9—N2—C2—S1 | 178.4 (3) | C4—C3—C8—C7 | 0.6 (6) |
C1—S1—C2—N1 | 2.9 (5) | N1—C3—C8—C7 | −179.9 (4) |
C1—S1—C2—N2 | −177.7 (4) | C2—N2—C9—C10 | −179.5 (4) |
C2—N1—C3—C4 | 177.1 (4) | C2—N2—C9—C8 | 0.0 (6) |
C2—N1—C3—C8 | −2.4 (6) | C7—C8—C9—C10 | 0.5 (6) |
N1—C3—C4—C5 | −179.4 (4) | C3—C8—C9—C10 | −179.7 (4) |
C8—C3—C4—C5 | 0.0 (7) | C7—C8—C9—N2 | −179.0 (4) |
C3—C4—C5—C6 | −0.4 (8) | C3—C8—C9—N2 | 0.8 (6) |
C4—C5—C6—C7 | 0.1 (8) | N2—C9—C10—C11 | 178.6 (5) |
C5—C6—C7—C12 | 179.1 (5) | C8—C9—C10—C11 | −0.9 (7) |
C5—C6—C7—C8 | 0.5 (7) | C9—C10—C11—C12 | 0.5 (8) |
C6—C7—C8—C9 | 178.9 (4) | C10—C11—C12—C7 | 0.3 (8) |
C12—C7—C8—C9 | 0.3 (6) | C6—C7—C12—C11 | −179.3 (5) |
C6—C7—C8—C3 | −0.8 (6) | C8—C7—C12—C11 | −0.7 (7) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···I1i | 0.81 (2) | 2.72 (3) | 3.500 (4) | 161 (5) |
N1—H1···I1 | 0.85 (6) | 2.98 (6) | 3.813 (4) | 169 (5) |
Symmetry code: (i) x, y+1, z. |
Experimental details
Crystal data | |
Chemical formula | C12H11N2S+·I− |
Mr | 342.19 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 298 |
a, b, c (Å) | 7.0107 (14), 8.8968 (18), 19.520 (4) |
β (°) | 95.90 (3) |
V (Å3) | 1211.1 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 2.79 |
Crystal size (mm) | 0.20 × 0.17 × 0.10 |
Data collection | |
Diffractometer | Stoe IPDS 2T diffractometer |
Absorption correction | Numerical (X-RED32; Stoe & Cie, 2005) |
Tmin, Tmax | 0.605, 0.768 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8695, 3266, 2151 |
Rint | 0.053 |
(sin θ/λ)max (Å−1) | 0.687 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.044, 0.094, 1.11 |
No. of reflections | 3266 |
No. of parameters | 152 |
No. of restraints | 1 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.98, −0.47 |
Computer programs: X-AREA (Stoe & Cie, 2005), X-RED32 (Stoe & Cie, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···I1i | 0.811 (19) | 2.72 (3) | 3.500 (4) | 161 (5) |
N1—H1···I1 | 0.85 (6) | 2.98 (6) | 3.813 (4) | 169 (5) |
Symmetry code: (i) x, y+1, z. |
Acknowledgements
The author thanks the Islamic Azad University-Falavarjan Branch for financial support. He also wishes to thank Professor Mehdi Bakavoli, Ferdowsi University of Mashhad, and Dr Behrouz Notash, Shahid Beheshti University, for their helpful assistance.
References
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The title compound is used in the synthesis of some potentially active antitumor agents (Herbert et al., 1987) and heterocyclic compounds (Liu & Chen, 1984). So far, the structure of this compound and its neutral form has been studied using 13C and 1H NMR spectroscopy (Woodgate et al., 1988). Herein, the crystal structure of this salt is investigated using X-ray crystallography.
In the structure of the 2-methylsulfanylperimidinium cation, the methylsulfanyl group is nearly coplanar with perimidine rings [the torsion angles N1—C2—S—C1 and N2—C2—S—C1 are 2.9 (5)° and -177.2 (3)°, respectively]. Because of conjugation between the lone pair electrons of the S atom and the amidinum moiety (HN—C=NH+) in the cation, the C2—S bond length [1.730 (5) Å] is shorter than C1—S [1.789 (5) Å]. Also, like other amidinium cations (Molčanov et al., 2012; Wang, 2012; Tiritiris & Kantlehner, 2012), the C—N bond lengths in the cation are approximately equal [the bond lengths of C2—N1 and C2—N2 are 1.325 (5) Å and 1.325 (6) Å, respectively].
In the crystal lattice, the cations and anions are linked together via two different N—H···I hydrogen bonds, in which every iodide anion act as a bridge between two 2-methylsulfanylperimidinium cations.