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Acta Crystallogr Sect E Struct Rep Online. 2008 January 1; 64(Pt 1): o195.
Published online 2007 December 6. doi:  10.1107/S1600536807064719
PMCID: PMC2915258

Indole-3-thio­uronium iodide

Abstract

In the title compound, C9H10N3S+·I, the indole ring system and the thiouronium group are essentially perpendicular, with a dihedral angle of 89.87 (8)°. By inter­molecular hydrogen bonding, a three-dimensional network is formed, which is additionally supported by inter­molecular C—H(...)π inter­actions.

Related literature

For the synthesis of the title compound, see: Harris (1969 [triangle]); van der Geer et al. (2007 [triangle]). For the crystal structures of similar compounds, see: Lutz et al. (2008 [triangle]); Ng (1995 [triangle]). For the characterization of C—H(...)π inter­actions, see: Malone et al. (1997 [triangle]). For thermal-motion analysis, see: Schomaker & Trueblood (1998 [triangle]). For the Cambridge Structural Database (update of August 2007), see: Allen (2002 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0o195-scheme1.jpg

Experimental

Crystal data

  • C9H10N3S+·I
  • M r = 319.16
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o195-efi1.jpg
  • a = 10.5098 (2) Å
  • b = 10.6264 (3) Å
  • c = 10.6951 (4) Å
  • β = 102.648 (2)°
  • V = 1165.46 (6) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 2.89 mm−1
  • T = 150 (2) K
  • 0.30 × 0.30 × 0.30 mm

Data collection

  • Nonius KappaCCD diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 2002 [triangle]) T min = 0.24, T max = 0.42
  • 15531 measured reflections
  • 2668 independent reflections
  • 2470 reflections with I > 2σ(I)
  • R int = 0.033

Refinement

  • R[F 2 > 2σ(F 2)] = 0.018
  • wR(F 2) = 0.045
  • S = 1.09
  • 2668 reflections
  • 167 parameters
  • All H-atom parameters refined
  • Δρmax = 0.50 e Å−3
  • Δρmin = −0.53 e Å−3

Data collection: COLLECT (Nonius, 1999 [triangle]); cell refinement: PEAKREF (Schreurs, 2005 [triangle]); data reduction: EVAL14 (Duisenberg et al., 2003 [triangle]) and SADABS (Sheldrick, 2002 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997 [triangle]); molecular graphics: PLATON (Spek, 2003 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536807064719/bt2659sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536807064719/bt2659Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

This work was supported by the Council for Chemical Sciences of the Netherlands Organization for Scientific Research (CW–NWO).

supplementary crystallographic information

Comment

Uronium and thiouronium ions are positively charged with the charge delocalized over the N—C—N group. In crystal engineering this group is therefore complementary to the negatively charged carboxylate group, not only in charge distribution but also in hydrogen-bonding ability.

The molecular geometry of the cation of title compound indole-3-thiouronium iodide (I) (Fig. 1) is very similar to the corresponding nitrate salt (Lutz et al., 2007). The C—N bond lengths of 1.306 (2) and 1.317 (2) Å show significant double bond character while the C—S bond of 1.7533 (19) Å is in the expected range for a single bond. Similar distances and angles have also been found in the benzylthiouronium cation (Ng, 1995).

As in the nitrate salt, the cation consists of two planar subunits, i.e. the indole and the thiouronium moieties, which are perpendicular to each other with an angle of 89.87 (8)° between the corresponding least squares planes. The weighted R value of a thermal motion analysis using the program THMA11 (Schomaker & Trueblood, 1998) results in a low weighted R value of 0.106, which is slightly higher than in the nitrate salt (0.084).

The iodide anion is surrounded by five N—H groups which act as hydrogen bond donors (Fig. 2). This results in a three dimensional hydrogen bonded network. The H···I distances of 2.76 (3) to 2.97 (2) Å are in the same range as found for other N—H···I hydrogen bonds in the Cambridge Structural Database (update August 2007; Allen, 2002), where we calculate an average H···I distance of 2.80 Å. In general, N—H···I hydrogen bonds are relatively weak; the average hydrogen bonded intermolecular N···I distance is 3.65 Å in the Cambridge Structural Database, which is not shorter than the sum of van der Waals radii of 1.55 (nitrogen) plus 1.98 Å (iodine).

In addition to the N—H···I hydrogen bonds there are weak intermolecular C—H···π interactions between H1 and the six-membered ring of the indole moiety (Fig. 3). The distance of H1 to the least squares plane of the six-membered ring is 2.83 (2) Å and the distance to the center of gravity of this ring is 2.91 (2) Å (Table 2). According to the classification of Malone et al. (1997) this is a "Type I" C—H···π interaction.

Experimental

Indole-3-thiouronium iodide was prepared as described in literature (Harris, 1969; van der Geer et al., 2007) and crystallized by diethyl ether vapor diffusion into an acetone solution.

Refinement

All H atoms were freely refined.

Figures

Fig. 1.
: The molecular structure of (I). Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
Fig. 2.
: Hydrogen bonded environment of the iodide in (I). C—H hydrogen atoms are omitted for clarity. Symmetry operations i: 1 + x, y, z; ii: 1 - x, 1 - y, -z; iii: x, 0.5 - y, z - 1/2.
Fig. 3.
: C—H···π interaction in (I). View along the crystallographic b axis. Symmetry operation i: x, 0.5 - y, z - 1/2.

Crystal data

C9H10N3S+·IF000 = 616
Mr = 319.16Dx = 1.819 Mg m3
Monoclinic, P21/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 11915 reflections
a = 10.5098 (2) Åθ = 2.0–27.5º
b = 10.6264 (3) ŵ = 2.89 mm1
c = 10.6951 (4) ÅT = 150 (2) K
β = 102.648 (2)ºBlock, colourless
V = 1165.46 (6) Å30.30 × 0.30 × 0.30 mm
Z = 4

Data collection

Nonius KappaCCD diffractometer2668 independent reflections
Radiation source: rotating anode2470 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.033
T = 150(2) Kθmax = 27.5º
[var phi] and ω scansθmin = 2.0º
Absorption correction: multi-scan(SADABS; Sheldrick, 2002)h = −13→13
Tmin = 0.24, Tmax = 0.42k = −13→13
15531 measured reflectionsl = −13→13

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.018All H-atom parameters refined
wR(F2) = 0.045  w = 1/[σ2(Fo2) + (0.0216P)2 + 0.5241P] where P = (Fo2 + 2Fc2)/3
S = 1.09(Δ/σ)max = 0.003
2668 reflectionsΔρmax = 0.50 e Å3
167 parametersΔρmin = −0.53 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

Special details

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)

xyzUiso*/Ueq
S10.43028 (5)0.17217 (4)0.29661 (4)0.02089 (10)
N10.08974 (16)0.33441 (15)0.18625 (17)0.0243 (3)
H1N0.024 (2)0.343 (2)0.140 (2)0.017 (5)*
N20.49115 (18)0.34694 (16)0.13906 (16)0.0237 (3)
H2N0.541 (3)0.384 (3)0.097 (2)0.039 (7)*
H3N0.415 (2)0.365 (2)0.123 (2)0.025 (6)*
N30.65635 (17)0.21727 (17)0.23827 (18)0.0247 (3)
H4N0.680 (2)0.170 (2)0.291 (2)0.025 (6)*
H5N0.711 (2)0.251 (2)0.196 (3)0.040 (7)*
C10.18173 (18)0.24948 (18)0.17078 (18)0.0220 (4)
H10.168 (2)0.198 (2)0.101 (2)0.032 (6)*
C20.29152 (17)0.26651 (17)0.26602 (17)0.0193 (3)
C30.3378 (2)0.42952 (18)0.45307 (19)0.0238 (4)
H30.422 (2)0.402 (2)0.491 (2)0.022 (5)*
C40.2801 (2)0.52789 (19)0.5048 (2)0.0287 (4)
H40.325 (3)0.574 (3)0.577 (3)0.047 (8)*
C50.1524 (2)0.5675 (2)0.4494 (2)0.0312 (5)
H50.117 (2)0.635 (2)0.487 (2)0.027 (6)*
C60.0801 (2)0.5097 (2)0.3418 (2)0.0277 (4)
H6−0.004 (3)0.536 (2)0.304 (3)0.034 (7)*
C70.13841 (18)0.40987 (18)0.29061 (18)0.0218 (4)
C80.26581 (17)0.36941 (16)0.34426 (17)0.0189 (3)
C90.53403 (17)0.25457 (16)0.21755 (16)0.0183 (3)
I10.770943 (11)0.454617 (11)0.031246 (11)0.02163 (5)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.0194 (2)0.0196 (2)0.0242 (2)0.00360 (16)0.00591 (17)0.00584 (17)
N10.0146 (8)0.0273 (8)0.0288 (9)0.0010 (6)−0.0001 (7)−0.0015 (7)
N20.0188 (8)0.0262 (8)0.0259 (8)0.0001 (7)0.0045 (7)0.0077 (6)
N30.0202 (8)0.0272 (9)0.0278 (9)0.0059 (7)0.0076 (7)0.0069 (7)
C10.0210 (9)0.0227 (9)0.0222 (9)−0.0008 (7)0.0047 (7)−0.0001 (7)
C20.0160 (8)0.0200 (8)0.0227 (9)0.0001 (7)0.0058 (7)0.0032 (7)
C30.0238 (10)0.0234 (9)0.0232 (9)−0.0020 (7)0.0032 (8)0.0034 (7)
C40.0367 (13)0.0238 (10)0.0251 (10)−0.0043 (8)0.0059 (9)−0.0023 (8)
C50.0365 (13)0.0231 (10)0.0378 (12)0.0020 (8)0.0165 (10)−0.0032 (8)
C60.0219 (10)0.0273 (10)0.0354 (11)0.0049 (8)0.0094 (9)0.0003 (8)
C70.0180 (9)0.0211 (8)0.0266 (9)0.0004 (7)0.0058 (7)0.0023 (7)
C80.0185 (9)0.0184 (8)0.0210 (8)−0.0006 (7)0.0067 (7)0.0042 (7)
C90.0198 (9)0.0175 (8)0.0173 (8)−0.0007 (7)0.0031 (6)−0.0014 (6)
I10.01614 (8)0.02314 (8)0.02444 (8)0.00029 (4)0.00192 (5)0.00236 (4)

Geometric parameters (Å, °)

S1—C21.7406 (18)C1—H10.91 (2)
S1—C91.7533 (19)C2—C81.438 (2)
N1—C11.359 (2)C3—C41.383 (3)
N1—C71.379 (3)C3—C81.396 (3)
N1—H1N0.76 (2)C3—H30.94 (2)
N2—C91.306 (2)C4—C51.407 (4)
N2—H2N0.86 (3)C4—H40.95 (3)
N2—H3N0.80 (2)C5—C61.377 (3)
N3—C91.317 (2)C5—H50.94 (2)
N3—H4N0.75 (3)C6—C71.396 (3)
N3—H5N0.88 (3)C6—H60.93 (3)
C1—C21.374 (3)C7—C81.404 (3)
C2—S1—C9101.87 (9)C3—C4—C5121.3 (2)
C1—N1—C7109.70 (16)C3—C4—H4122.2 (18)
C1—N1—H1N124.2 (16)C5—C4—H4116.5 (18)
C7—N1—H1N125.7 (16)C6—C5—C4121.3 (2)
C9—N2—H2N121.1 (18)C6—C5—H5119.9 (14)
C9—N2—H3N120.1 (17)C4—C5—H5118.8 (14)
H2N—N2—H3N118 (2)C5—C6—C7117.18 (19)
C9—N3—H4N118.3 (18)C5—C6—H6121.6 (15)
C9—N3—H5N120.9 (17)C7—C6—H6121.2 (15)
H4N—N3—H5N121 (2)N1—C7—C6129.98 (18)
N1—C1—C2109.07 (17)N1—C7—C8107.73 (16)
N1—C1—H1120.7 (15)C6—C7—C8122.29 (18)
C2—C1—H1130.0 (15)C3—C8—C7119.67 (17)
C1—C2—C8107.29 (17)C3—C8—C2134.13 (18)
C1—C2—S1126.63 (15)C7—C8—C2106.20 (16)
C8—C2—S1125.81 (14)N2—C9—N3121.41 (18)
C4—C3—C8118.29 (19)N2—C9—S1121.45 (15)
C4—C3—H3121.6 (14)N3—C9—S1117.12 (14)
C8—C3—H3120.1 (14)
C7—N1—C1—C21.0 (2)C4—C3—C8—C70.1 (3)
N1—C1—C2—C8−0.6 (2)C4—C3—C8—C2−179.7 (2)
N1—C1—C2—S1173.64 (14)N1—C7—C8—C3−179.32 (17)
C9—S1—C2—C196.99 (19)C6—C7—C8—C30.4 (3)
C9—S1—C2—C8−89.75 (17)N1—C7—C8—C20.5 (2)
C8—C3—C4—C5−0.3 (3)C6—C7—C8—C2−179.74 (18)
C3—C4—C5—C60.1 (3)C1—C2—C8—C3179.9 (2)
C4—C5—C6—C70.4 (3)S1—C2—C8—C35.5 (3)
C1—N1—C7—C6179.4 (2)C1—C2—C8—C70.1 (2)
C1—N1—C7—C8−0.9 (2)S1—C2—C8—C7−174.27 (14)
C5—C6—C7—N1179.0 (2)C2—S1—C9—N2−11.53 (17)
C5—C6—C7—C8−0.7 (3)C2—S1—C9—N3170.10 (14)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N···I1i0.76 (2)2.91 (2)3.6295 (17)158 (2)
N2—H2N···I10.86 (3)2.76 (3)3.5736 (18)158 (2)
N2—H3N···I1ii0.80 (2)2.97 (2)3.6269 (17)141 (2)
N3—H4N···I1iii0.75 (3)2.86 (3)3.5990 (19)165 (2)
N3—H5N···I10.88 (3)2.95 (3)3.7258 (19)149 (2)
C1—H1···Cg1iv0.91 (2)2.91 (2)3.794 (2)162.8 (18)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BT2659).

References

  • Allen, F. H. (2002). Acta Cryst. B58, 380–388. [PubMed]
  • Duisenberg, A. J. M., Kroon-Batenburg, L. M. J. & Schreurs, A. M. M. (2003). J. Appl. Cryst.36, 220–229.
  • Geer, E. P. L. van der, Li, Q., van Koten, G., Klein Gebbink, R. J. M. & Hessen, B. (2007). Inorg. Chim. Acta, doi:10.1016/j.ica.2007.09.021.
  • Harris, R. L. N. (1969). Tetrahedron Lett. 4465–4466.
  • Lutz, M., Spek, A. L., van der Geer, E. P. L., van Koten, G. & Klein Gebbink, R. J. M. (2008). Acta Cryst. E64, o194.
  • Malone, J. F., Murray, C. M., Charlton, M. H., Docherty, R. & Lavery, A. J. (1997). J. Chem. Soc. Faraday Trans.93, 3429–3436.
  • Ng, S. W. (1995). Acta Cryst. C51, 1143–1144.
  • Nonius (1999). COLLECT Nonius BV, Delft, The Netherlands.
  • Schomaker, V. & Trueblood, K. N. (1998). Acta Cryst. B54, 507–514.
  • Schreurs, A. M. M. (2005). PEAKREF Utrecht University, The Netherlands.
  • Sheldrick, G. M. (1997). SHELXS97 and SHELXL97 University of Göttingen, Germany.
  • Sheldrick, G. M. (2002). SADABS University of Göttingen, Germany.
  • Spek, A. L. (2003). J. Appl. Cryst.36, 7–13.

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