Indole-3-thio­uronium iodide

Lutz, M.; Spek, A.L.; Geer, E.P.L. van der; Koten, G. van; Klein Gebbink, R.J.M.

doi:10.1107/S1600536807064719

organic compounds

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ISSN: 2056-9890

Volume 64| Part 1| January 2008| Page o195

https://doi.org/10.1107/S1600536807064719

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Indole-3-thiouronium iodide

Martin Lutz,^a Anthony L. Spek,^a ^* Erwin P. L. van der Geer,^b Gerard van Koten ^b and Robertus J. M. Klein Gebbink ^b

^aCrystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and ^bChemical Biology & Organic Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
^*Correspondence e-mail: a.l.spek@chem.uu.nl

(Received 29 November 2007; accepted 30 November 2007; online 6 December 2007)

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

Experimental

Crystal data

C₉H₁₀N₃S⁺·I⁻
M_r = 319.16
Monoclinic, P 2₁ /c
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 ) 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[F² > 2σ(F²)] = 0.018
wR(F²) = 0.045
S = 1.09
2668 reflections
167 parameters
All H-atom parameters refined
Δρ_max = 0.50 e Å⁻³
Δρ_min = −0.53 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1N⋯I1ⁱ	0.76 (2)	2.91 (2)	3.6295 (17)	158 (2)
N2—H2N⋯I1	0.86 (3)	2.76 (3)	3.5736 (18)	158 (2)
N2—H3N⋯I1ⁱⁱ	0.80 (2)	2.97 (2)	3.6269 (17)	141 (2)
N3—H4N⋯I1ⁱⁱⁱ	0.75 (3)	2.86 (3)	3.5990 (19)	165 (2)
N3—H5N⋯I1	0.88 (3)	2.95 (3)	3.7258 (19)	149 (2)
C1—H1⋯Cg1^iv	0.91 (2)	2.91 (2)	3.794 (2)	162.8 (18)
Symmetry codes: (i) x-1, y, z; (ii) -x+1, -y+1, -z; (iii) $[x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ ; (iv) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ . Cg1 is the centroid of the six-membered ring.

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

Supporting information

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

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536807064719/bt2659Isup2.hkl

checkCIF report

Comment top

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.

Related literature top

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

Experimental top

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.

Structure description top

Computing details top

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

Figures top

	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.

Indole-3-thiouronium iodide top

Crystal data top

C₉H₁₀N₃S⁺·I⁻	F(000) = 616
M_r = 319.16	D_x = 1.819 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 11915 reflections
a = 10.5098 (2) Å	θ = 2.0–27.5°
b = 10.6264 (3) Å	µ = 2.89 mm⁻¹
c = 10.6951 (4) Å	T = 150 K
β = 102.648 (2)°	Block, colourless
V = 1165.46 (6) Å³	0.30 × 0.30 × 0.30 mm
Z = 4

Data collection top

Nonius KappaCCD diffractometer	2668 independent reflections
Radiation source: rotating anode	2470 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.033
φ and ω scans	θ_max = 27.5°, θ_min = 2.0°
Absorption correction: multi-scan (SADABS; Sheldrick, 2002)	h = −13→13
T_min = 0.24, T_max = 0.42	k = −13→13
15531 measured reflections	l = −13→13

Refinement top

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)] = 0.018	Hydrogen site location: difference Fourier map
wR(F²) = 0.045	All H-atom parameters refined
S = 1.09	w = 1/[σ²(F_o²) + (0.0216P)² + 0.5241P] where P = (F_o² + 2F_c²)/3
2668 reflections	(Δ/σ)_max = 0.003
167 parameters	Δρ_max = 0.50 e Å⁻³
0 restraints	Δρ_min = −0.53 e Å⁻³

Crystal data top

C₉H₁₀N₃S⁺·I⁻	V = 1165.46 (6) Å³
M_r = 319.16	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 10.5098 (2) Å	µ = 2.89 mm⁻¹
b = 10.6264 (3) Å	T = 150 K
c = 10.6951 (4) Å	0.30 × 0.30 × 0.30 mm
β = 102.648 (2)°

Data collection top

Nonius KappaCCD diffractometer	2668 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 2002)	2470 reflections with I > 2σ(I)
T_min = 0.24, T_max = 0.42	R_int = 0.033
15531 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.018	0 restraints
wR(F²) = 0.045	All H-atom parameters refined
S = 1.09	Δρ_max = 0.50 e Å⁻³
2668 reflections	Δρ_min = −0.53 e Å⁻³
167 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

	x	y	z	U_iso*/U_eq
S1	0.43028 (5)	0.17217 (4)	0.29661 (4)	0.02089 (10)
N1	0.08974 (16)	0.33441 (15)	0.18625 (17)	0.0243 (3)
H1N	0.024 (2)	0.343 (2)	0.140 (2)	0.017 (5)*
N2	0.49115 (18)	0.34694 (16)	0.13906 (16)	0.0237 (3)
H2N	0.541 (3)	0.384 (3)	0.097 (2)	0.039 (7)*
H3N	0.415 (2)	0.365 (2)	0.123 (2)	0.025 (6)*
N3	0.65635 (17)	0.21727 (17)	0.23827 (18)	0.0247 (3)
H4N	0.680 (2)	0.170 (2)	0.291 (2)	0.025 (6)*
H5N	0.711 (2)	0.251 (2)	0.196 (3)	0.040 (7)*
C1	0.18173 (18)	0.24948 (18)	0.17078 (18)	0.0220 (4)
H1	0.168 (2)	0.198 (2)	0.101 (2)	0.032 (6)*
C2	0.29152 (17)	0.26651 (17)	0.26602 (17)	0.0193 (3)
C3	0.3378 (2)	0.42952 (18)	0.45307 (19)	0.0238 (4)
H3	0.422 (2)	0.402 (2)	0.491 (2)	0.022 (5)*
C4	0.2801 (2)	0.52789 (19)	0.5048 (2)	0.0287 (4)
H4	0.325 (3)	0.574 (3)	0.577 (3)	0.047 (8)*
C5	0.1524 (2)	0.5675 (2)	0.4494 (2)	0.0312 (5)
H5	0.117 (2)	0.635 (2)	0.487 (2)	0.027 (6)*
C6	0.0801 (2)	0.5097 (2)	0.3418 (2)	0.0277 (4)
H6	−0.004 (3)	0.536 (2)	0.304 (3)	0.034 (7)*
C7	0.13841 (18)	0.40987 (18)	0.29061 (18)	0.0218 (4)
C8	0.26581 (17)	0.36941 (16)	0.34426 (17)	0.0189 (3)
C9	0.53403 (17)	0.25457 (16)	0.21755 (16)	0.0183 (3)
I1	0.770943 (11)	0.454617 (11)	0.031246 (11)	0.02163 (5)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0194 (2)	0.0196 (2)	0.0242 (2)	0.00360 (16)	0.00591 (17)	0.00584 (17)
N1	0.0146 (8)	0.0273 (8)	0.0288 (9)	0.0010 (6)	−0.0001 (7)	−0.0015 (7)
N2	0.0188 (8)	0.0262 (8)	0.0259 (8)	0.0001 (7)	0.0045 (7)	0.0077 (6)
N3	0.0202 (8)	0.0272 (9)	0.0278 (9)	0.0059 (7)	0.0076 (7)	0.0069 (7)
C1	0.0210 (9)	0.0227 (9)	0.0222 (9)	−0.0008 (7)	0.0047 (7)	−0.0001 (7)
C2	0.0160 (8)	0.0200 (8)	0.0227 (9)	0.0001 (7)	0.0058 (7)	0.0032 (7)
C3	0.0238 (10)	0.0234 (9)	0.0232 (9)	−0.0020 (7)	0.0032 (8)	0.0034 (7)
C4	0.0367 (13)	0.0238 (10)	0.0251 (10)	−0.0043 (8)	0.0059 (9)	−0.0023 (8)
C5	0.0365 (13)	0.0231 (10)	0.0378 (12)	0.0020 (8)	0.0165 (10)	−0.0032 (8)
C6	0.0219 (10)	0.0273 (10)	0.0354 (11)	0.0049 (8)	0.0094 (9)	0.0003 (8)
C7	0.0180 (9)	0.0211 (8)	0.0266 (9)	0.0004 (7)	0.0058 (7)	0.0023 (7)
C8	0.0185 (9)	0.0184 (8)	0.0210 (8)	−0.0006 (7)	0.0067 (7)	0.0042 (7)
C9	0.0198 (9)	0.0175 (8)	0.0173 (8)	−0.0007 (7)	0.0031 (6)	−0.0014 (6)
I1	0.01614 (8)	0.02314 (8)	0.02444 (8)	0.00029 (4)	0.00192 (5)	0.00236 (4)

Geometric parameters (Å, º) top

S1—C2	1.7406 (18)	C1—H1	0.91 (2)
S1—C9	1.7533 (19)	C2—C8	1.438 (2)
N1—C1	1.359 (2)	C3—C4	1.383 (3)
N1—C7	1.379 (3)	C3—C8	1.396 (3)
N1—H1N	0.76 (2)	C3—H3	0.94 (2)
N2—C9	1.306 (2)	C4—C5	1.407 (4)
N2—H2N	0.86 (3)	C4—H4	0.95 (3)
N2—H3N	0.80 (2)	C5—C6	1.377 (3)
N3—C9	1.317 (2)	C5—H5	0.94 (2)
N3—H4N	0.75 (3)	C6—C7	1.396 (3)
N3—H5N	0.88 (3)	C6—H6	0.93 (3)
C1—C2	1.374 (3)	C7—C8	1.404 (3)

C2—S1—C9	101.87 (9)	C3—C4—C5	121.3 (2)
C1—N1—C7	109.70 (16)	C3—C4—H4	122.2 (18)
C1—N1—H1N	124.2 (16)	C5—C4—H4	116.5 (18)
C7—N1—H1N	125.7 (16)	C6—C5—C4	121.3 (2)
C9—N2—H2N	121.1 (18)	C6—C5—H5	119.9 (14)
C9—N2—H3N	120.1 (17)	C4—C5—H5	118.8 (14)
H2N—N2—H3N	118 (2)	C5—C6—C7	117.18 (19)
C9—N3—H4N	118.3 (18)	C5—C6—H6	121.6 (15)
C9—N3—H5N	120.9 (17)	C7—C6—H6	121.2 (15)
H4N—N3—H5N	121 (2)	N1—C7—C6	129.98 (18)
N1—C1—C2	109.07 (17)	N1—C7—C8	107.73 (16)
N1—C1—H1	120.7 (15)	C6—C7—C8	122.29 (18)
C2—C1—H1	130.0 (15)	C3—C8—C7	119.67 (17)
C1—C2—C8	107.29 (17)	C3—C8—C2	134.13 (18)
C1—C2—S1	126.63 (15)	C7—C8—C2	106.20 (16)
C8—C2—S1	125.81 (14)	N2—C9—N3	121.41 (18)
C4—C3—C8	118.29 (19)	N2—C9—S1	121.45 (15)
C4—C3—H3	121.6 (14)	N3—C9—S1	117.12 (14)
C8—C3—H3	120.1 (14)

C7—N1—C1—C2	1.0 (2)	C4—C3—C8—C7	0.1 (3)
N1—C1—C2—C8	−0.6 (2)	C4—C3—C8—C2	−179.7 (2)
N1—C1—C2—S1	173.64 (14)	N1—C7—C8—C3	−179.32 (17)
C9—S1—C2—C1	96.99 (19)	C6—C7—C8—C3	0.4 (3)
C9—S1—C2—C8	−89.75 (17)	N1—C7—C8—C2	0.5 (2)
C8—C3—C4—C5	−0.3 (3)	C6—C7—C8—C2	−179.74 (18)
C3—C4—C5—C6	0.1 (3)	C1—C2—C8—C3	179.9 (2)
C4—C5—C6—C7	0.4 (3)	S1—C2—C8—C3	5.5 (3)
C1—N1—C7—C6	179.4 (2)	C1—C2—C8—C7	0.1 (2)
C1—N1—C7—C8	−0.9 (2)	S1—C2—C8—C7	−174.27 (14)
C5—C6—C7—N1	179.0 (2)	C2—S1—C9—N2	−11.53 (17)
C5—C6—C7—C8	−0.7 (3)	C2—S1—C9—N3	170.10 (14)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···I1ⁱ	0.76 (2)	2.91 (2)	3.6295 (17)	158 (2)
N2—H2N···I1	0.86 (3)	2.76 (3)	3.5736 (18)	158 (2)
N2—H3N···I1ⁱⁱ	0.80 (2)	2.97 (2)	3.6269 (17)	141 (2)
N3—H4N···I1ⁱⁱⁱ	0.75 (3)	2.86 (3)	3.5990 (19)	165 (2)
N3—H5N···I1	0.88 (3)	2.95 (3)	3.7258 (19)	149 (2)
C1—H1···Cg1^iv	0.91 (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.

Experimental details

Crystal data
Chemical formula	C₉H₁₀N₃S⁺·I⁻
M_r	319.16
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	150
a, b, c (Å)	10.5098 (2), 10.6264 (3), 10.6951 (4)
β (°)	102.648 (2)
V (Å³)	1165.46 (6)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	2.89
Crystal size (mm)	0.30 × 0.30 × 0.30

Data collection
Diffractometer	Nonius KappaCCD
Absorption correction	Multi-scan (SADABS; Sheldrick, 2002)
T_min, T_max	0.24, 0.42
No. of measured, independent and observed [I > 2σ(I)] reflections	15531, 2668, 2470
R_int	0.033
(sin θ/λ)_max (Å⁻¹)	0.650

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.018, 0.045, 1.09
No. of reflections	2668
No. of parameters	167
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.50, −0.53

Computer programs: COLLECT (Nonius, 1999), PEAKREF (Schreurs, 2005), EVAL14 (Duisenberg et al., 2003) and SADABS (Sheldrick, 2002), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003).

Selected geometric parameters (Å, º) top

S1—C2	1.7406 (18)	N2—C9	1.306 (2)
S1—C9	1.7533 (19)	N3—C9	1.317 (2)

C2—S1—C9	101.87 (9)	N2—C9—S1	121.45 (15)
N2—C9—N3	121.41 (18)	N3—C9—S1	117.12 (14)

C9—S1—C2—C1	96.99 (19)	C2—S1—C9—N2	−11.53 (17)
C9—S1—C2—C8	−89.75 (17)	C2—S1—C9—N3	170.10 (14)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···I1ⁱ	0.76 (2)	2.91 (2)	3.6295 (17)	158 (2)
N2—H2N···I1	0.86 (3)	2.76 (3)	3.5736 (18)	158 (2)
N2—H3N···I1ⁱⁱ	0.80 (2)	2.97 (2)	3.6269 (17)	141 (2)
N3—H4N···I1ⁱⁱⁱ	0.75 (3)	2.86 (3)	3.5990 (19)	165 (2)
N3—H5N···I1	0.88 (3)	2.95 (3)	3.7258 (19)	149 (2)
C1—H1···Cg1^iv	0.91 (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.

Acknowledgements

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

References

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