organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

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

(Received 19 July 2012; accepted 26 July 2012; online 1 August 2012)

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[Liu, K.-C. & Chen, H.-H. (1984). J. Heterocycl. Chem. 21, 911-912.]); Herbert et al. (1987[Herbert, J. M., Woodgate, P. D. & Denny, W. A. (1987). J. Med. Chem. 30, 2081-2086.]). For the NMR spectra, see Woodgate et al. (1988[Woodgate, P. D., Herbert, J. M. & Denny, W. A. (1988). Mag. Res. Chem. 26, 191-196.]). For related structures, see: Molčanov et al. (2012[Molčanov, K., Stolić, I., Kojić-Prodić, B., Kovačević, G. & Bajić, M. (2012). Acta Cryst. E68, o1360.]); Wang (2012[Wang, Y. (2012). Acta Cryst. E68, o1619.]); Tiritiris & Kantlehner (2012[Tiritiris, I. & Kantlehner, W. (2012). Acta Cryst. E68, o1812.]).

[Scheme 1]

Experimental

Crystal data
  • C12H11N2S+·I

  • Mr = 342.19

  • Monoclinic, P 21 /c

  • a = 7.0107 (14) Å

  • b = 8.8968 (18) Å

  • c = 19.520 (4) Å

  • β = 95.90 (3)°

  • V = 1211.1 (4) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 2.79 mm−1

  • T = 298 K

  • 0.20 × 0.17 × 0.10 mm

Data collection
  • Stoe IPDS 2T diffractometer

  • Absorption correction: numerical (X-RED32; Stoe & Cie, 2005[Stoe & Cie (2005). X-AREA and X-RED32. Stoe & Cie, Darmstadt, Germany.]) Tmin = 0.605, Tmax = 0.768

  • 8695 measured reflections

  • 3266 independent reflections

  • 2151 reflections with I > 2σ(I)

  • Rint = 0.053

Refinement
  • R[F2 > 2σ(F2)] = 0.044

  • wR(F2) = 0.094

  • S = 1.11

  • 3266 reflections

  • 152 parameters

  • 1 restraint

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.98 e Å−3

  • Δρmin = −0.47 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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.

Data collection: X-AREA (Stoe & Cie, 2005[Stoe & Cie (2005). X-AREA and X-RED32. Stoe & Cie, Darmstadt, Germany.]); cell refinement: X-AREA; data reduction: X-RED32 (Stoe & Cie, 2005[Stoe & Cie (2005). X-AREA and X-RED32. Stoe & Cie, Darmstadt, Germany.]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]).

Supporting information


Comment top

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.

Related literature top

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 top

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.

Refinement top

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.

Computing details top

Data collection: X-AREA (Stoe & Cie, 2005); cell refinement: 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).

Figures top
[Figure 1] Fig. 1. Preparation of the title compound from the reaction of perimidine-2-thione with methyl iodide under reflux conditions.
[Figure 2] Fig. 2. The molecular structure of the title compound, showing 50% probability displacement ellipsoids.
[Figure 3] Fig. 3. Chains of molecules along the b axis.
2-Methylsulfanyl-1H-perimidin-3-ium iodide top
Crystal data top
C12H11N2S+·IF(000) = 664
Mr = 342.19Dx = 1.877 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3266 reflections
a = 7.0107 (14) Åθ = 2.1–29.2°
b = 8.8968 (18) ŵ = 2.79 mm1
c = 19.520 (4) ÅT = 298 K
β = 95.90 (3)°Plate, green
V = 1211.1 (4) Å30.20 × 0.17 × 0.10 mm
Z = 4
Data collection top
Stoe IPDS 2T
diffractometer
3266 independent reflections
Radiation source: fine-focus sealed tube2151 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.053
Detector resolution: 0.15 pixels mm-1θmax = 29.2°, θmin = 2.1°
rotation method scansh = 99
Absorption correction: numerical
(X-RED32; Stoe & Cie, 2005)
k = 1210
Tmin = 0.605, Tmax = 0.768l = 2623
8695 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.044Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.094H 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 parametersΔρmax = 0.98 e Å3
1 restraintΔρmin = 0.47 e Å3
Crystal data top
C12H11N2S+·IV = 1211.1 (4) Å3
Mr = 342.19Z = 4
Monoclinic, P21/cMo Kα radiation
a = 7.0107 (14) ŵ = 2.79 mm1
b = 8.8968 (18) ÅT = 298 K
c = 19.520 (4) Å0.20 × 0.17 × 0.10 mm
β = 95.90 (3)°
Data collection top
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 = 0.768Rint = 0.053
8695 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0441 restraint
wR(F2) = 0.094H atoms treated by a mixture of independent and constrained refinement
S = 1.11Δρmax = 0.98 e Å3
3266 reflectionsΔρmin = 0.47 e Å3
152 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
I10.23717 (5)0.01191 (3)0.335840 (18)0.04724 (12)
S10.3337 (2)0.57350 (14)0.29413 (7)0.0475 (3)
N10.2710 (5)0.4113 (4)0.4069 (2)0.0308 (8)
N20.3149 (6)0.6660 (4)0.4194 (2)0.0341 (9)
C10.2992 (8)0.3909 (6)0.2564 (3)0.0481 (13)
H1A0.38610.32110.28060.072*
H1B0.32320.39500.20890.072*
H1C0.16960.35880.25950.072*
C20.3031 (6)0.5445 (5)0.3799 (2)0.0304 (9)
C30.2384 (6)0.3919 (5)0.4769 (2)0.0295 (9)
C40.1976 (7)0.2561 (5)0.5032 (3)0.0376 (11)
H40.19100.17070.47560.045*
C50.1651 (7)0.2459 (6)0.5733 (3)0.0432 (12)
H50.13630.15310.59160.052*
C60.1753 (7)0.3702 (6)0.6146 (3)0.0414 (12)
H60.15350.36070.66060.050*
C70.2184 (6)0.5129 (5)0.5885 (2)0.0344 (9)
C80.2492 (5)0.5236 (5)0.5181 (2)0.0295 (8)
C90.2892 (6)0.6642 (5)0.4898 (2)0.0299 (9)
C100.3011 (7)0.7923 (5)0.5285 (3)0.0406 (11)
H100.32950.88440.50950.049*
C110.2689 (7)0.7801 (6)0.5986 (3)0.0451 (13)
H110.27560.86640.62570.054*
C120.2284 (7)0.6463 (6)0.6281 (3)0.0434 (12)
H120.20740.64270.67440.052*
H10.274 (8)0.328 (7)0.387 (3)0.052*
H20.327 (8)0.746 (4)0.401 (3)0.052*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
I10.0704 (2)0.02971 (16)0.04296 (19)0.00194 (17)0.01260 (14)0.00215 (16)
S10.0825 (10)0.0347 (6)0.0260 (6)0.0092 (6)0.0095 (6)0.0024 (5)
N10.036 (2)0.0292 (18)0.029 (2)0.0009 (15)0.0099 (16)0.0010 (16)
N20.046 (2)0.0261 (18)0.031 (2)0.0010 (16)0.0056 (18)0.0030 (15)
C10.074 (4)0.037 (3)0.034 (3)0.008 (2)0.011 (3)0.008 (2)
C20.031 (2)0.032 (2)0.028 (2)0.0019 (17)0.0010 (18)0.0031 (17)
C30.025 (2)0.035 (2)0.030 (2)0.0053 (17)0.0057 (18)0.0056 (18)
C40.038 (3)0.036 (2)0.039 (3)0.000 (2)0.007 (2)0.004 (2)
C50.047 (3)0.044 (3)0.040 (3)0.001 (2)0.011 (2)0.011 (2)
C60.038 (3)0.056 (3)0.030 (3)0.005 (2)0.006 (2)0.009 (2)
C70.0287 (19)0.047 (3)0.027 (2)0.006 (2)0.0014 (16)0.002 (2)
C80.0248 (18)0.034 (2)0.029 (2)0.0038 (17)0.0010 (16)0.0004 (19)
C90.027 (2)0.033 (2)0.029 (2)0.0021 (17)0.0024 (18)0.0025 (18)
C100.047 (3)0.033 (2)0.040 (3)0.003 (2)0.003 (2)0.005 (2)
C110.046 (3)0.048 (3)0.040 (3)0.003 (2)0.002 (2)0.019 (2)
C120.041 (3)0.062 (3)0.026 (3)0.004 (2)0.001 (2)0.007 (2)
Geometric parameters (Å, º) top
S1—C21.730 (5)C4—H40.9300
S1—C11.789 (5)C5—C61.366 (7)
N1—C21.325 (5)C5—H50.9300
N1—C31.418 (6)C6—C71.413 (7)
N1—H10.85 (6)C6—H60.9300
N2—C21.325 (6)C7—C121.415 (7)
N2—C91.404 (6)C7—C81.415 (6)
N2—H20.811 (19)C8—C91.408 (6)
C1—H1A0.9600C9—C101.366 (6)
C1—H1B0.9600C10—C111.414 (7)
C1—H1C0.9600C10—H100.9300
C3—C41.356 (6)C11—C121.365 (8)
C3—C81.419 (6)C11—H110.9300
C4—C51.412 (7)C12—H120.9300
C2—S1—C1103.8 (2)C6—C5—H5119.5
C2—N1—C3122.9 (4)C4—C5—H5119.5
C2—N1—H1126 (4)C5—C6—C7121.0 (4)
C3—N1—H1111 (4)C5—C6—H6119.5
C2—N2—C9123.6 (4)C7—C6—H6119.5
C2—N2—H2118 (4)C6—C7—C12123.8 (4)
C9—N2—H2119 (4)C6—C7—C8118.0 (4)
S1—C1—H1A109.5C12—C7—C8118.1 (4)
S1—C1—H1B109.5C9—C8—C7119.8 (4)
H1A—C1—H1B109.5C9—C8—C3120.8 (4)
S1—C1—H1C109.5C7—C8—C3119.4 (4)
H1A—C1—H1C109.5C10—C9—N2121.7 (4)
H1B—C1—H1C109.5C10—C9—C8121.8 (4)
N1—C2—N2120.1 (4)N2—C9—C8116.5 (4)
N1—C2—S1124.2 (3)C9—C10—C11117.7 (5)
N2—C2—S1115.8 (3)C9—C10—H10121.1
C4—C3—N1122.4 (4)C11—C10—H10121.1
C4—C3—C8121.4 (4)C12—C11—C10122.4 (5)
N1—C3—C8116.2 (4)C12—C11—H11118.8
C3—C4—C5119.1 (5)C10—C11—H11118.8
C3—C4—H4120.4C11—C12—C7120.1 (5)
C5—C4—H4120.4C11—C12—H12119.9
C6—C5—C4121.0 (5)C7—C12—H12119.9
C3—N1—C2—N23.3 (7)C12—C7—C8—C3179.5 (4)
C3—N1—C2—S1177.2 (3)C4—C3—C8—C9179.2 (4)
C9—N2—C2—N12.1 (7)N1—C3—C8—C90.3 (6)
C9—N2—C2—S1178.4 (3)C4—C3—C8—C70.6 (6)
C1—S1—C2—N12.9 (5)N1—C3—C8—C7179.9 (4)
C1—S1—C2—N2177.7 (4)C2—N2—C9—C10179.5 (4)
C2—N1—C3—C4177.1 (4)C2—N2—C9—C80.0 (6)
C2—N1—C3—C82.4 (6)C7—C8—C9—C100.5 (6)
N1—C3—C4—C5179.4 (4)C3—C8—C9—C10179.7 (4)
C8—C3—C4—C50.0 (7)C7—C8—C9—N2179.0 (4)
C3—C4—C5—C60.4 (8)C3—C8—C9—N20.8 (6)
C4—C5—C6—C70.1 (8)N2—C9—C10—C11178.6 (5)
C5—C6—C7—C12179.1 (5)C8—C9—C10—C110.9 (7)
C5—C6—C7—C80.5 (7)C9—C10—C11—C120.5 (8)
C6—C7—C8—C9178.9 (4)C10—C11—C12—C70.3 (8)
C12—C7—C8—C90.3 (6)C6—C7—C12—C11179.3 (5)
C6—C7—C8—C30.8 (6)C8—C7—C12—C110.7 (7)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···I1i0.81 (2)2.72 (3)3.500 (4)161 (5)
N1—H1···I10.85 (6)2.98 (6)3.813 (4)169 (5)
Symmetry code: (i) x, y+1, z.

Experimental details

Crystal data
Chemical formulaC12H11N2S+·I
Mr342.19
Crystal system, space groupMonoclinic, P21/c
Temperature (K)298
a, b, c (Å)7.0107 (14), 8.8968 (18), 19.520 (4)
β (°) 95.90 (3)
V3)1211.1 (4)
Z4
Radiation typeMo Kα
µ (mm1)2.79
Crystal size (mm)0.20 × 0.17 × 0.10
Data collection
DiffractometerStoe IPDS 2T
diffractometer
Absorption correctionNumerical
(X-RED32; Stoe & Cie, 2005)
Tmin, Tmax0.605, 0.768
No. of measured, independent and
observed [I > 2σ(I)] reflections
8695, 3266, 2151
Rint0.053
(sin θ/λ)max1)0.687
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.044, 0.094, 1.11
No. of reflections3266
No. of parameters152
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)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).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···I1i0.811 (19)2.72 (3)3.500 (4)161 (5)
N1—H1···I10.85 (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

First citationFarrugia, L. J. (1997). J. Appl. Cryst. 30, 565.  CrossRef IUCr Journals
First citationFarrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838.  CrossRef CAS IUCr Journals
First citationHerbert, J. M., Woodgate, P. D. & Denny, W. A. (1987). J. Med. Chem. 30, 2081–2086.  CrossRef CAS PubMed Web of Science
First citationLiu, K.-C. & Chen, H.-H. (1984). J. Heterocycl. Chem. 21, 911–912.  CrossRef CAS
First citationMolčanov, K., Stolić, I., Kojić-Prodić, B., Kovačević, G. & Bajić, M. (2012). Acta Cryst. E68, o1360.  CSD CrossRef IUCr Journals
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationStoe & Cie (2005). X-AREA and X-RED32. Stoe & Cie, Darmstadt, Germany.
First citationTiritiris, I. & Kantlehner, W. (2012). Acta Cryst. E68, o1812.  CSD CrossRef IUCr Journals
First citationWang, Y. (2012). Acta Cryst. E68, o1619.  CSD CrossRef IUCr Journals
First citationWoodgate, P. D., Herbert, J. M. & Denny, W. A. (1988). Mag. Res. Chem. 26, 191–196.  CrossRef CAS Web of Science

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