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Acta Crystallogr Sect E Struct Rep Online. 2008 January 1; 64(Pt 1): o194.
Published online 2007 December 6. doi:  10.1107/S1600536807064707
PMCID: PMC2915257

Indole-3-thio­uronium nitrate

Abstract

In the title compound, C9H10N3S+·NO3 , the indole ring system and the thiouronium group are nearly perpendicular, with a dihedral angle of 88.62 (6)°. Hydrogen bonding generates two-dimensional networks which are linked to each other via π stacking inter­actions of the indole groups [average inter-planar ring–ring distance of 3.449 (2) Å].

Related literature

For reviews of the supra­molecular chemistry of thio­urea derivatives, see: Takemoto (2005 [triangle]); Fitzmaurice et al. (2002 [triangle]); Schmidtchen & Berger (1997 [triangle]). For anion recognition of thio­uronium salts, see: Esteban Gómez et al. (2005 [triangle]). For the synthesis of the title compound, see: Harris (1969 [triangle]); van der Geer et al. (2007 [triangle]). For thermal motion analysis, see: Schomaker & Trueblood (1998 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0o194-scheme1.jpg

Experimental

Crystal data

  • C9H10N3S+·NO3
  • M r = 254.27
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o194-efi1.jpg
  • a = 12.0524 (2) Å
  • b = 8.7395 (1) Å
  • c = 21.1893 (3) Å
  • V = 2231.91 (5) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.29 mm−1
  • T = 150 (2) K
  • 0.30 × 0.24 × 0.06 mm

Data collection

  • Nonius KappaCCD diffractometer
  • Absorption correction: none
  • 32180 measured reflections
  • 2563 independent reflections
  • 2120 reflections with I > 2σ(I)
  • R int = 0.048

Refinement

  • R[F 2 > 2σ(F 2)] = 0.032
  • wR(F 2) = 0.089
  • S = 1.04
  • 2563 reflections
  • 194 parameters
  • All H-atom parameters refined
  • Δρmax = 0.26 e Å−3
  • Δρmin = −0.23 e Å−3

Data collection: COLLECT (Nonius, 1999 [triangle]); cell refinement: HKL-2000 (Otwinowski & Minor, 1997 [triangle]); data reduction: HKL-2000; 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/S1600536807064707/bt2657sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536807064707/bt2657Isup2.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

Thiourea derivatives have found widespread application in molecular recognition and supramolecular chemistry, largely due to their hydrogen-bonding complementarity with carboxylate groups (Takemoto, 2005; Fitzmaurice et al., 2002; Schmidtchen & Berger, 1997). Of all thiourea derivatives, positively-charged thiouronium salts may be among the strongest anion receptors due to their increased acidity and the electrostatic stabilization of the anion-receptor complex (Esteban Gómez et al., 2005). Recently, we have demonstrated that N-substituted indole-3-thiouronium salts are readily available from indole by nucleophilic substitution at the nitrogen atom followed by electrophilic aromatic substitution with thiourea (van der Geer et al., 2007). In order to gain more insight into the hydrogen-bonding properties of indole-3-thiouronium salts, we have obtained the crystal structure of the title compound indole-3-thiouronium nitrate (I).

Bond distances and angles are as expected. The thiouronium group itself is planar, with the C—N bond lengths of 1.3076 (19) and 1.3162 (19) Å indicating a significant degree of double-bond character. Reflecting the resulting hindered rotation about the C—N bonds, solution-phase 1H NMR shows separate signals for the thiouronium hydrogen atoms cis and trans to sulfur at room temperature. The least-squares plane of the thiouronium moiety forms an interplanar angle of 88.62 (6)° with respect to the least-squares plane of the indole group (Fig. 1).

A thermal motion analysis using the program THMA11 (Schomaker & Trueblood, 1998) results in a low weighted R value (R = SQRT[(Σ (wΔU)2) / (Σ (wUobs)2)]) of 0.084 indicating that the molecule behaves as a rigid body in the solid state.

All N—H groups act as hydrogen bond donors with the oxygen atoms of the nitrate anion as acceptors. O1 and O2 accept two hydrogen bonds, respectively, while O3 accepts only one. By this hydrogen bonding scheme a two-dimensional network in the a,b-plane is formed (Fig. 2).

Via π stacking interactions the indole ring systems form parallel, centrosymmetric dimers with an average ring···ring distance of 3.449 (2) Å (Fig. 3). These π stacking interactions occur between the two-dimensional hydrogen bonded layers.

Experimental

Indole-3-thiouronium iodide was prepared as described in literature (Harris, 1969). To a solution of indole-3-thiouronium iodide (0.100 g, 0.313 mmol) in EtOH (10 ml) was added AgNO3 (0.0532 g, 0.313 mmol). The solution was stirred for 1 h, filtered to remove AgCl, and concentrated to approximately 3 ml. Ether (60 ml) was added, and after 48 h, white needles were collected by centrifugation, washed with ether, and dried in vacuo. Yield: 0.0738 g (0.290 mmol, 93%). Anal. Calcd for C9H10N4O3S: C, 42.51; H, 3.96; N, 22.03; S, 12.61. Found: C, 42.32; H, 4.08; N, 21.92; S, 12.73. The 1H NMR spectrum was identical to that of indole-3-thiouronium iodide. FT—IR (ATR, ν, cm-1): 3335, 3264, 3122, 1662, 1640, 1498, 1423, 1388, 1308, 1237, 1218, 1128, 1104, 1065, 1049, 1006, 816, 744. Crystals suitable for X-ray diffraction studies were obtained by ether vapor diffusion into an EtOH solution of the product.

Refinement

364 frames were collected as [var phi] scans and 397 frames as ω scans with a rotation angle of 1° and an exposure time of 60 s, respectively.

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 bonding scheme in compound (I). View along the crystallographic b axis. C—H hydrogen atoms are omitted for clarity. Symmetry operations i: 1 - x, 1/2 + y, 0.5 - z; ii: 1/2 + x, y, 0.5 - z; iii: 2 - x, 1/2 + y, 0.5 - z.
Fig. 3.
π stacking interactions between the indole ring systems in (I). View along the crystallographic a axis. Symmetry operation i: 1 - x, 1 - y, -z.

Crystal data

C9H10N3S+·NO3F000 = 1056
Mr = 254.27Dx = 1.513 Mg m3
Orthorhombic, PbcaMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 44477 reflections
a = 12.0524 (2) Åθ = 1.0–27.5º
b = 8.7395 (1) ŵ = 0.29 mm1
c = 21.1893 (3) ÅT = 150 (2) K
V = 2231.91 (5) Å3Plate, colourless
Z = 80.30 × 0.24 × 0.06 mm

Data collection

Nonius KappaCCD diffractometer2120 reflections with I > 2σ(I)
Radiation source: rotating anodeRint = 0.048
Monochromator: graphiteθmax = 27.5º
T = 150(2) Kθmin = 1.9º
[var phi] and ω scansh = −15→15
Absorption correction: nonek = −11→11
32180 measured reflectionsl = −27→27
2563 independent reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.032All H-atom parameters refined
wR(F2) = 0.089  w = 1/[σ2(Fo2) + (0.0479P)2 + 0.7806P] where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max < 0.001
2563 reflectionsΔρmax = 0.26 e Å3
194 parametersΔρmin = −0.23 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
S10.69778 (3)0.42394 (4)0.119223 (18)0.02623 (13)
N10.37464 (10)0.47136 (15)0.12180 (6)0.0261 (3)
H1N0.3086 (14)0.448 (2)0.1367 (9)0.034 (5)*
N20.67908 (11)0.63413 (15)0.21093 (6)0.0247 (3)
H2N0.7073 (14)0.693 (2)0.2402 (9)0.036 (5)*
H3N0.6067 (17)0.642 (2)0.2016 (8)0.037 (5)*
N30.85228 (11)0.53570 (16)0.19399 (7)0.0281 (3)
H4N0.8814 (17)0.598 (2)0.2236 (10)0.049 (6)*
H5N0.9029 (17)0.481 (2)0.1728 (10)0.048 (6)*
C10.47062 (12)0.40523 (18)0.14151 (7)0.0263 (3)
H10.4724 (13)0.320 (2)0.1715 (8)0.030 (4)*
C20.55884 (11)0.47801 (17)0.11306 (6)0.0224 (3)
C30.56104 (12)0.70408 (16)0.03254 (7)0.0241 (3)
H30.6404 (14)0.7099 (18)0.0278 (7)0.025 (4)*
C40.49126 (14)0.80176 (18)0.00043 (7)0.0283 (3)
H40.5191 (15)0.876 (2)−0.0291 (9)0.037 (5)*
C50.37534 (13)0.79541 (18)0.00913 (7)0.0296 (3)
H50.3302 (14)0.868 (2)−0.0129 (9)0.040 (5)*
C60.32737 (12)0.68900 (18)0.04876 (7)0.0267 (3)
H60.2499 (15)0.6822 (18)0.0556 (7)0.028 (4)*
C70.39845 (11)0.58860 (16)0.08036 (6)0.0222 (3)
C80.51463 (11)0.59550 (15)0.07326 (6)0.0203 (3)
C90.74591 (11)0.54277 (16)0.18022 (6)0.0219 (3)
O10.78687 (8)0.82212 (13)0.30339 (5)0.0302 (3)
O20.95458 (8)0.75180 (13)0.27976 (5)0.0308 (3)
O30.92651 (9)0.94570 (13)0.34188 (5)0.0351 (3)
N40.88984 (10)0.84099 (14)0.30879 (6)0.0240 (3)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.0208 (2)0.0269 (2)0.0309 (2)0.00496 (14)−0.00216 (14)−0.00352 (15)
N10.0191 (6)0.0331 (7)0.0262 (6)−0.0050 (5)0.0008 (5)0.0028 (5)
N20.0174 (6)0.0284 (7)0.0284 (7)0.0015 (5)−0.0012 (5)−0.0036 (6)
N30.0179 (6)0.0306 (7)0.0357 (7)0.0028 (5)−0.0010 (5)−0.0007 (6)
C10.0244 (7)0.0292 (8)0.0253 (7)−0.0031 (6)−0.0015 (6)0.0024 (6)
C20.0186 (6)0.0248 (7)0.0239 (7)0.0001 (5)−0.0017 (5)−0.0015 (6)
C30.0212 (7)0.0245 (7)0.0265 (7)−0.0034 (6)0.0018 (6)−0.0024 (6)
C40.0323 (8)0.0253 (8)0.0273 (8)−0.0035 (6)−0.0004 (6)0.0022 (6)
C50.0311 (8)0.0286 (8)0.0291 (8)0.0039 (6)−0.0066 (6)−0.0009 (6)
C60.0190 (7)0.0326 (8)0.0287 (8)0.0008 (6)−0.0038 (6)−0.0048 (6)
C70.0198 (7)0.0260 (7)0.0207 (6)−0.0029 (6)−0.0005 (5)−0.0030 (5)
C80.0178 (6)0.0222 (7)0.0209 (7)−0.0010 (5)−0.0001 (5)−0.0029 (5)
C90.0175 (6)0.0228 (7)0.0255 (7)−0.0004 (5)−0.0009 (5)0.0059 (6)
O10.0145 (5)0.0416 (6)0.0345 (6)0.0011 (4)0.0000 (4)−0.0075 (5)
O20.0186 (5)0.0431 (7)0.0308 (6)0.0075 (5)0.0033 (4)0.0002 (5)
O30.0293 (6)0.0403 (7)0.0358 (6)−0.0102 (5)0.0002 (5)−0.0051 (5)
N40.0177 (6)0.0309 (7)0.0235 (6)0.0003 (5)0.0013 (5)0.0042 (5)

Geometric parameters (Å, °)

S1—C21.7448 (14)C3—C41.378 (2)
S1—C91.7566 (15)C3—C81.399 (2)
N1—C11.359 (2)C3—H30.963 (17)
N1—C71.3795 (19)C4—C51.410 (2)
N1—H1N0.880 (18)C4—H40.963 (18)
N2—C91.3076 (19)C5—C61.380 (2)
N2—H2N0.87 (2)C5—H50.955 (19)
N2—H3N0.90 (2)C6—C71.397 (2)
N3—C91.3162 (19)C6—H60.946 (18)
N3—H4N0.90 (2)C7—C81.4096 (19)
N3—H5N0.89 (2)O1—N41.2572 (15)
C1—C21.378 (2)O2—N41.2628 (16)
C1—H10.979 (18)O3—N41.2348 (16)
C2—C81.432 (2)
C2—S1—C9102.23 (7)C3—C4—H4121.7 (11)
C1—N1—C7109.54 (12)C5—C4—H4117.2 (11)
C1—N1—H1N124.0 (12)C6—C5—C4121.41 (14)
C7—N1—H1N126.1 (12)C6—C5—H5120.3 (11)
C9—N2—H2N118.1 (11)C4—C5—H5118.3 (11)
C9—N2—H3N122.4 (11)C5—C6—C7117.25 (14)
H2N—N2—H3N119.5 (16)C5—C6—H6123.3 (10)
C9—N3—H4N120.3 (13)C7—C6—H6119.5 (10)
C9—N3—H5N125.3 (13)N1—C7—C6130.09 (13)
H4N—N3—H5N113.9 (18)N1—C7—C8107.84 (12)
N1—C1—C2109.03 (13)C6—C7—C8122.07 (13)
N1—C1—H1122.8 (10)C3—C8—C7119.47 (13)
C2—C1—H1128.2 (10)C3—C8—C2134.50 (13)
C1—C2—C8107.55 (12)C7—C8—C2106.03 (12)
C1—C2—S1125.65 (12)N2—C9—N3121.22 (14)
C8—C2—S1126.55 (11)N2—C9—S1121.59 (11)
C4—C3—C8118.73 (14)N3—C9—S1117.19 (11)
C4—C3—H3121.4 (10)O3—N4—O1120.15 (12)
C8—C3—H3119.8 (10)O3—N4—O2120.86 (12)
C3—C4—C5121.04 (15)O1—N4—O2118.99 (12)
C7—N1—C1—C2−0.19 (17)C4—C3—C8—C70.1 (2)
N1—C1—C2—C8−0.26 (17)C4—C3—C8—C2179.62 (15)
N1—C1—C2—S1−174.86 (11)N1—C7—C8—C3178.96 (13)
C9—S1—C2—C1−95.95 (14)C6—C7—C8—C3−1.2 (2)
C9—S1—C2—C890.45 (13)N1—C7—C8—C2−0.71 (15)
C8—C3—C4—C51.3 (2)C6—C7—C8—C2179.17 (13)
C3—C4—C5—C6−1.7 (2)C1—C2—C8—C3−179.01 (16)
C4—C5—C6—C70.6 (2)S1—C2—C8—C3−4.5 (2)
C1—N1—C7—C6−179.29 (15)C1—C2—C8—C70.60 (16)
C1—N1—C7—C80.58 (16)S1—C2—C8—C7175.14 (11)
C5—C6—C7—N1−179.32 (14)C2—S1—C9—N24.19 (14)
C5—C6—C7—C80.8 (2)C2—S1—C9—N3−176.06 (11)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N···O1i0.880 (18)2.036 (19)2.8290 (16)149.4 (16)
N2—H2N···O10.87 (2)2.00 (2)2.8679 (17)174.2 (16)
N2—H3N···O2ii0.90 (2)2.108 (19)2.9013 (16)147.0 (16)
N3—H4N···O20.90 (2)2.00 (2)2.8966 (19)172.5 (19)
N3—H5N···O3iii0.89 (2)2.10 (2)2.8817 (17)145.0 (18)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BT2657).

References

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  • Nonius (1999). COLLECT Nonius BV, Delft, The Netherlands.
  • Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press.
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  • Spek, A. L. (2003). J. Appl. Cryst.36, 7–13.
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