Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270108000668/tr3035sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270108000668/tr3035Isup2.hkl |
CCDC reference: 681565
For the preparation of indole-3-N,N,N',N'-tetramethylthiouronium iodide, to a solution of indole (0.600 g, 5.12 mmol) and N,N,N',N'-tetramethylthiourea (0.677 g, 5.12 mmol) in a 4:1 (v/v) mixture of MeOH and H2O (20 ml) were added I2 (1.30 g, 5.12 mmol) and KI (0.850 g, 5.12 mmol). The mixture was stirred overnight and then evaporated to dryness. The residue was washed with water and ether, yielding a dark-yellow powder (yield 1.67 g, 4.45 mmol, 87%). Analysis calculated for C13H18IN3S: C 41.61, H 4.83, N 11.20, S 8.54%; found: C 41.53, H 4.78, N 11.15, S 8.65%. 1H NMR (DMSO-d6): δ 12.00 (s, br, 1H, NH), 7.99 (d, 3JH—H = 2.7 Hz, 1H, indolyl 2-H), 7.53 (d, 3JH—H = 7.9 Hz, 1H, indolyl H), 7.43 (d, 3JH—H = 7.9 Hz, 1H, indolyl H), 7.26 (td, 3JH—H = 7.6 Hz, 4JH—H = 1.2 Hz, 1H, indolyl H), 7.18 (t, 3JH—H = 7.4 Hz, 1H, indolyl H), 3.14 (s, 12H, CH3). 13C{1H} NMR (DMSO-d6): δ 174.76 [C(NMe2)2], 136.25, 132.65, 126.97, 122.77, 121.02, 117.28, 112.75, 94.54 (8 × indolyl C), 43.58 (CH3). FT–IR (ATR, ν, cm-1): 3136, 3099, 1600, 1498, 1455, 1413, 1380, 1340, 1256, 1235, 1166, 1100, 1006, 874, 758, 751, 691.
For the preparation of indole-3-N,N,N',N'-tetramethylthiouronium nitrate, to a solution of AgNO3 (0.0453 g, 0.266 mmol) in EtOH (10 ml) was added indole-3-N,N,N',N'-tetramethylthiouronium iodide (0.100 g, 0.266 mmol). The mixture was refluxed for 1 h and then filtered to remove AgCl. The resulting cream-colored solution was concentrated in vacuo. Ether was added overnight by vapor diffusion. Colorless crystals formed, which proved to be suitable for X-ray diffraction studies. The crystals remaining after X-ray analysis were filtered off, washed with ether and dried in vacuo (yield 0.0667 g, 2.15 mmol, 81%). Analysis calculated for C13H18N4O3S: C 50.31, H 5.85, N 18.05, S 10.33%; found: C 50.46, H 5.80, N 18.15, S 10.25%. The 1H NMR spectrum was identical to that of the starting compound. FT–IR (ATR, ν, cm-1): 3100, 2927, 1599, 1502, 1456, 1362, 1324, 1256, 1238, 1208, 1166, 1112, 1101, 1059, 1042, 1009, 876, 830, 784, 760, 748.
The initial refinement was performed with a spherical atom model using the program SHELXL97 (Sheldrick, 2008) on F2 of all reflections. H atoms were refined freely with isotropic displacement parameters.
The results of the SHELXL97 refinement were then transferred to the program XD (Koritsanszky et al., 2003). After a spherical atom refinement, the H atoms were fixed and a spherical atom refinement of the non-H atoms was performed on data with sinθ/λ larger than 0.7 Å-1. In the following step, the non-H atoms were fixed and the positions and isotropic displacement parameters of the H atoms were refined on data with sinθ/λ smaller than 0.7 Å-1. A polarized density function with a bond-directed dipole was used here for the H atoms. The polarized H atom was introduced by Stewart et al. (1975) and adapted to the XD package by Macchi (2000).
In a final refinement, the positions and displacement parameters of the H atoms were fixed and non-H atoms were refined anisotropically. Multipole parameters were also refined in this step, for S atoms up to the hexadecapole level, and for C, N and O atoms up to the octopole level. For H atoms, a mononople and a dipole in bond direction was refined. The refinement was performed on F of reflections with F > 2σ(F). The weights in the least squares refinement were 1/σ2. 93.7% of the reflections were measured six or more times for useful merged σ values. Residual electron densities of the spherical atom refinement and the multipole refinement are given in Fig. 4.
The largest differences of mean-squares displacement amplitudes in the direction of the bonds (Hirshfeld, 1976) are 0.0014 (2) Å2 for N4—O2 in the anion and 0.0012 (2) Å2 for N2—C10 in the cation. The largest peaks and holes of the difference electron density map are close to atom O3 of the nitrate anion, with distances of 0.52 and 0.50 Å, respectively.
Data collection: COLLECT (Nonius, 1999); cell refinement: PEAKREF (Schreurs, 2005); data reduction: EVAL15 (Xian et al., 2006) and SADABS (Sheldrick, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: XD (Koritsanszky et al., 2003); molecular graphics: XD (Koritsanszky et al., 2003) and PLATON (Spek, 2003); software used to prepare material for publication: XD (Koritsanszky et al., 2003).
C13H18N3S+·NO3− | F(000) = 1312 |
Mr = 310.37 | Dx = 1.388 Mg m−3 |
Orthorhombic, Pbca | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ac 2ab | Cell parameters from 43746 reflections |
a = 12.46443 (1) Å | θ = 1.9–45.0° |
b = 11.02991 (7) Å | µ = 0.23 mm−1 |
c = 21.60929 (4) Å | T = 110 K |
V = 2970.88 (2) Å3 | Block, colourless |
Z = 8 | 0.36 × 0.24 × 0.24 mm |
Nonius KappaCCD diffractometer | 9924 reflections with I > 2σ(I) |
ϕ and ω scans | Rint = 0.034 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2006) | θmax = 45.0° |
Tmin = 0.744, Tmax = 0.943 | h = −24→24 |
247693 measured reflections | k = −21→21 |
12242 independent reflections | l = −42→42 |
Refinement on F | 0 restraints |
Least-squares matrix: full | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.020 | w1 = 1/[s2(Fo)] |
wR(F2) = 0.011 | (Δ/σ)max < 0.001 |
S = 2.03 | Δρmax = 0.34 e Å−3 |
9926 reflections | Δρmin = −0.29 e Å−3 |
570 parameters |
C13H18N3S+·NO3− | V = 2970.88 (2) Å3 |
Mr = 310.37 | Z = 8 |
Orthorhombic, Pbca | Mo Kα radiation |
a = 12.46443 (1) Å | µ = 0.23 mm−1 |
b = 11.02991 (7) Å | T = 110 K |
c = 21.60929 (4) Å | 0.36 × 0.24 × 0.24 mm |
Nonius KappaCCD diffractometer | 12242 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2006) | 9924 reflections with I > 2σ(I) |
Tmin = 0.744, Tmax = 0.943 | Rint = 0.034 |
247693 measured reflections |
R[F2 > 2σ(F2)] = 0.020 | 0 restraints |
wR(F2) = 0.011 | H-atom parameters constrained |
S = 2.03 | Δρmax = 0.34 e Å−3 |
9926 reflections | Δρmin = −0.29 e Å−3 |
570 parameters |
Experimental. All frames were collected with a rotation angle of 1°. 364 (ϕ) and 453 frames (ω) had an exposure time of 20 s. 364 frames (ϕ) had an exposure time of 4 s. 220 frames (ω) had an exposure time of 100 s. 935 frames (ω) had an exposure time of 150 s. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.585023 (5) | 0.513021 (6) | 0.597567 (3) | 0.015 | |
O1 | 0.85945 (5) | 0.42997 (7) | 0.34113 (2) | 0.033 | |
O2 | 0.85897 (6) | 0.41030 (6) | 0.24132 (2) | 0.032 | |
O3 | 0.76206 (6) | 0.29172 (7) | 0.29729 (3) | 0.035 | |
N1 | 0.71393 (3) | 0.39633 (4) | 0.442256 (16) | 0.016 | |
N2 | 0.50667 (3) | 0.39070 (3) | 0.692843 (15) | 0.015 | |
N3 | 0.65585 (3) | 0.30190 (3) | 0.647822 (15) | 0.015 | |
N4 | 0.82637 (3) | 0.37762 (4) | 0.293055 (18) | 0.017 | |
C1 | 0.70568 (3) | 0.47639 (3) | 0.490549 (15) | 0.016 | |
C2 | 0.62468 (3) | 0.43963 (3) | 0.529776 (13) | 0.014 | |
C3 | 0.49521 (3) | 0.25383 (3) | 0.521848 (15) | 0.016 | |
C4 | 0.47373 (3) | 0.15363 (4) | 0.485154 (17) | 0.019 | |
C5 | 0.53437 (3) | 0.12892 (4) | 0.431485 (16) | 0.019 | |
C6 | 0.61733 (3) | 0.20431 (3) | 0.412873 (14) | 0.016 | |
C7 | 0.63867 (2) | 0.30598 (3) | 0.449793 (13) | 0.013 | |
C8 | 0.57935 (2) | 0.33104 (3) | 0.504170 (13) | 0.013 | |
C9 | 0.58384 (2) | 0.39142 (3) | 0.650401 (12) | 0.012 | |
C10 | 0.41015 (3) | 0.46528 (4) | 0.688203 (18) | 0.023 | |
C11 | 0.52470 (3) | 0.33796 (4) | 0.754327 (15) | 0.020 | |
C12 | 0.62720 (3) | 0.17585 (3) | 0.661155 (18) | 0.020 | |
C13 | 0.76534 (3) | 0.31836 (4) | 0.625531 (18) | 0.020 | |
H1 | 0.76532 | 0.40375 | 0.40739 | 0.037 | |
H2 | 0.75506 | 0.55465 | 0.49407 | 0.021 | |
H3 | 0.44749 | 0.27122 | 0.56193 | 0.023 | |
H4 | 0.41180 | 0.09438 | 0.49740 | 0.024 | |
H5 | 0.51699 | 0.05015 | 0.40479 | 0.026 | |
H6 | 0.66461 | 0.18822 | 0.37209 | 0.022 | |
H7 | 0.34429 | 0.41892 | 0.71186 | 0.034 | |
H8 | 0.42107 | 0.55355 | 0.70884 | 0.040 | |
H9 | 0.38462 | 0.47455 | 0.64026 | 0.035 | |
H10 | 0.47086 | 0.26235 | 0.76208 | 0.024 | |
H11 | 0.51027 | 0.40979 | 0.78716 | 0.024 | |
H12 | 0.60488 | 0.30861 | 0.75941 | 0.022 | |
H13 | 0.66836 | 0.14199 | 0.70063 | 0.028 | |
H14 | 0.65067 | 0.12131 | 0.62037 | 0.025 | |
H15 | 0.54109 | 0.16620 | 0.66814 | 0.022 | |
H16 | 0.78630 | 0.41398 | 0.62487 | 0.021 | |
H17 | 0.77566 | 0.28143 | 0.57986 | 0.028 | |
H18 | 0.81991 | 0.27195 | 0.65651 | 0.030 |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.02199 (3) | 0.01192 (2) | 0.01145 (2) | 0.00257 (2) | 0.00118 (2) | 0.00074 (2) |
O1 | 0.0324 (2) | 0.0494 (3) | 0.01675 (19) | −0.0197 (2) | 0.00656 (17) | −0.0094 (2) |
O2 | 0.0455 (3) | 0.0338 (3) | 0.01623 (18) | −0.0166 (2) | 0.00793 (19) | −0.00173 (17) |
O3 | 0.0413 (3) | 0.0386 (3) | 0.0239 (2) | −0.0227 (3) | 0.0010 (2) | 0.0026 (2) |
N1 | 0.01562 (12) | 0.02088 (15) | 0.01103 (11) | −0.00073 (12) | 0.00253 (10) | 0.00176 (11) |
N2 | 0.01591 (12) | 0.01737 (13) | 0.01071 (11) | 0.00155 (11) | 0.00046 (10) | 0.00056 (10) |
N3 | 0.01528 (12) | 0.01361 (12) | 0.01461 (12) | 0.00191 (11) | 0.00017 (10) | 0.00201 (10) |
N4 | 0.01674 (13) | 0.02013 (16) | 0.01341 (14) | −0.00248 (12) | 0.00301 (11) | −0.00085 (12) |
C1 | 0.01722 (12) | 0.01748 (13) | 0.01277 (11) | −0.00200 (11) | 0.00122 (10) | 0.00249 (10) |
C2 | 0.01617 (11) | 0.01470 (12) | 0.01016 (10) | 0.00044 (10) | 0.00110 (9) | 0.00082 (9) |
C3 | 0.01553 (12) | 0.01940 (14) | 0.01297 (11) | −0.00184 (11) | 0.00258 (10) | −0.00065 (10) |
C4 | 0.01854 (13) | 0.02116 (15) | 0.01693 (13) | −0.00443 (12) | 0.00150 (11) | −0.00208 (12) |
C5 | 0.02045 (14) | 0.02076 (15) | 0.01530 (13) | −0.00163 (12) | −0.00010 (11) | −0.00359 (11) |
C6 | 0.01798 (12) | 0.02045 (14) | 0.01098 (11) | 0.00144 (12) | 0.00079 (10) | −0.00213 (10) |
C7 | 0.01369 (11) | 0.01694 (12) | 0.00974 (10) | 0.00122 (10) | 0.00067 (9) | 0.00068 (9) |
C8 | 0.01333 (10) | 0.01529 (11) | 0.00973 (10) | 0.00060 (10) | 0.00099 (9) | 0.00071 (9) |
C9 | 0.01469 (10) | 0.01278 (11) | 0.00995 (10) | 0.00095 (10) | −0.00028 (9) | 0.00033 (8) |
C10 | 0.01995 (14) | 0.02767 (18) | 0.02065 (15) | 0.00707 (14) | 0.00415 (12) | 0.00228 (13) |
C11 | 0.02355 (15) | 0.02321 (15) | 0.01176 (12) | −0.00103 (13) | 0.00113 (10) | 0.00261 (11) |
C12 | 0.02417 (15) | 0.01417 (13) | 0.02154 (14) | 0.00154 (12) | −0.00081 (12) | 0.00264 (11) |
C13 | 0.01565 (12) | 0.02285 (16) | 0.02275 (15) | 0.00335 (12) | 0.00078 (11) | 0.00424 (12) |
S1—C2 | 1.7452 (3) | C4—C5 | 1.4109 (5) |
S1—C9 | 1.7614 (3) | C4—H4 | 1.05 |
O1—N4 | 1.2580 (6) | C5—C6 | 1.3866 (5) |
O2—N4 | 1.2429 (5) | C5—H5 | 1.07 |
O3—N4 | 1.2444 (6) | C6—C7 | 1.4017 (5) |
N1—C1 | 1.3709 (5) | C6—H6 | 1.08 |
N1—C7 | 1.3783 (5) | C7—C8 | 1.4156 (4) |
N1—H1 | 0.99 | C10—H7 | 1.09 |
N2—C9 | 1.3291 (4) | C10—H8 | 1.08 |
N2—C10 | 1.4608 (5) | C10—H9 | 1.09 |
N2—C11 | 1.4677 (4) | C11—H10 | 1.08 |
N3—C9 | 1.3355 (4) | C11—H11 | 1.08 |
N3—C12 | 1.4641 (5) | C11—H12 | 1.06 |
N3—C13 | 1.4586 (5) | C12—H13 | 1.06 |
C1—C2 | 1.3792 (4) | C12—H14 | 1.11 |
C1—H2 | 1.06 | C12—H15 | 1.09 |
C2—C8 | 1.4353 (4) | C13—H16 | 1.09 |
C3—C4 | 1.3863 (5) | C13—H17 | 1.08 |
C3—C8 | 1.4039 (4) | C13—H18 | 1.08 |
C3—H3 | 1.07 | ||
C2—S1—C9 | 101.142 (14) | N1—C7—C8 | 108.20 (3) |
C1—N1—C7 | 108.95 (3) | C6—C7—C8 | 121.98 (3) |
C1—N1—H1 | 125.0 | C2—C8—C3 | 134.06 (3) |
C7—N1—H1 | 126.1 | C2—C8—C7 | 106.10 (3) |
C9—N2—C10 | 123.05 (3) | C3—C8—C7 | 119.84 (3) |
C9—N2—C11 | 121.08 (3) | S1—C9—N2 | 117.25 (3) |
C10—N2—C11 | 114.29 (3) | S1—C9—N3 | 122.03 (2) |
C9—N3—C12 | 122.00 (3) | N2—C9—N3 | 120.72 (3) |
C9—N3—C13 | 123.41 (3) | N2—C10—H7 | 108.8 |
C12—N3—C13 | 114.29 (3) | N2—C10—H8 | 112.1 |
O1—N4—O2 | 120.17 (5) | N2—C10—H9 | 111.0 |
O1—N4—O3 | 119.99 (5) | H7—C10—H8 | 108.9 |
O2—N4—O3 | 119.83 (5) | H7—C10—H9 | 105.6 |
N1—C1—C2 | 109.48 (3) | H8—C10—H9 | 110.2 |
N1—C1—H2 | 122.3 | N2—C11—H10 | 110.5 |
C2—C1—H2 | 128.2 | N2—C11—H11 | 106.2 |
S1—C2—C1 | 125.94 (3) | N2—C11—H12 | 111.1 |
S1—C2—C8 | 126.81 (2) | H10—C11—H11 | 111.1 |
C1—C2—C8 | 107.25 (3) | H10—C11—H12 | 109.5 |
C4—C3—C8 | 118.18 (3) | H11—C11—H12 | 108.3 |
C4—C3—H3 | 120.0 | N3—C12—H13 | 112.0 |
C8—C3—H3 | 121.9 | N3—C12—H14 | 107.2 |
C3—C4—C5 | 121.38 (3) | N3—C12—H15 | 111.1 |
C3—C4—H4 | 119.7 | H13—C12—H14 | 108.7 |
C5—C4—H4 | 118.9 | H13—C12—H15 | 109.3 |
C4—C5—C6 | 121.48 (3) | H14—C12—H15 | 108.5 |
C4—C5—H5 | 119.6 | N3—C13—H16 | 110.5 |
C6—C5—H5 | 118.9 | N3—C13—H17 | 111.6 |
C5—C6—C7 | 117.14 (3) | N3—C13—H18 | 109.0 |
C5—C6—H6 | 123.2 | H16—C13—H17 | 109.1 |
C7—C6—H6 | 119.7 | H16—C13—H18 | 108.4 |
N1—C7—C6 | 129.82 (3) | H17—C13—H18 | 108.3 |
C9—S1—C2—C1 | −130.40 (3) | N1—C1—C2—C8 | −0.49 (4) |
C9—S1—C2—C8 | 50.03 (3) | S1—C2—C8—C3 | 0.90 (5) |
C2—S1—C9—N2 | −142.61 (3) | S1—C2—C8—C7 | −179.21 (2) |
C2—S1—C9—N3 | 36.25 (3) | C1—C2—C8—C3 | −178.74 (4) |
C7—N1—C1—C2 | −0.40 (4) | C1—C2—C8—C7 | 1.15 (4) |
C1—N1—C7—C6 | −179.36 (3) | C8—C3—C4—C5 | 0.12 (5) |
C1—N1—C7—C8 | 1.13 (4) | C4—C3—C8—C2 | −179.46 (4) |
C10—N2—C9—S1 | 16.08 (5) | C4—C3—C8—C7 | 0.67 (5) |
C10—N2—C9—N3 | −162.79 (3) | C3—C4—C5—C6 | −0.58 (6) |
C11—N2—C9—S1 | −148.75 (3) | C4—C5—C6—C7 | 0.22 (5) |
C11—N2—C9—N3 | 32.38 (5) | C5—C6—C7—N1 | −178.87 (4) |
C12—N3—C9—S1 | −142.67 (3) | C5—C6—C7—C8 | 0.58 (5) |
C12—N3—C9—N2 | 36.16 (5) | N1—C7—C8—C2 | −1.40 (3) |
C13—N3—C9—S1 | 30.69 (5) | N1—C7—C8—C3 | 178.51 (3) |
C13—N3—C9—N2 | −150.49 (3) | C6—C7—C8—C2 | 179.05 (3) |
N1—C1—C2—S1 | 179.87 (3) | C6—C7—C8—C3 | −1.04 (5) |
Experimental details
Crystal data | |
Chemical formula | C13H18N3S+·NO3− |
Mr | 310.37 |
Crystal system, space group | Orthorhombic, Pbca |
Temperature (K) | 110 |
a, b, c (Å) | 12.46443 (1), 11.02991 (7), 21.60929 (4) |
V (Å3) | 2970.88 (2) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.23 |
Crystal size (mm) | 0.36 × 0.24 × 0.24 |
Data collection | |
Diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2006) |
Tmin, Tmax | 0.744, 0.943 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 247693, 12242, 9924 |
Rint | 0.034 |
(sin θ/λ)max (Å−1) | 0.995 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.020, 0.011, 2.03 |
No. of reflections | 9926 |
No. of parameters | 570 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.34, −0.29 |
Computer programs: COLLECT (Nonius, 1999), PEAKREF (Schreurs, 2005), EVAL15 (Xian et al., 2006) and SADABS (Sheldrick, 2006), SHELXS97 (Sheldrick, 2008), XD (Koritsanszky et al., 2003) and PLATON (Spek, 2003).
S1—C2 | 1.7452 (3) | N2—C9 | 1.3291 (4) |
S1—C9 | 1.7614 (3) | N3—C9 | 1.3355 (4) |
C2—S1—C9 | 101.142 (14) | S1—C9—N3 | 122.03 (2) |
S1—C9—N2 | 117.25 (3) | N2—C9—N3 | 120.72 (3) |
C2—S1—C9—N2 | −142.61 (3) | C11—N2—C9—S1 | −148.75 (3) |
C2—S1—C9—N3 | 36.25 (3) | C12—N3—C9—S1 | −142.67 (3) |
C10—N2—C9—S1 | 16.08 (5) | C13—N3—C9—S1 | 30.69 (5) |
Bond | d(Å) | d1(Å) | d2(Å) | ρ(eÅ-3) | ellipticity | del2f(eÅ-5) |
S1-C2 | 1.7455 | 0.8861 | 0.8593 | 1.334 (8) | 0.13 | -4.202 (14) |
S1-C9 | 1.7618 | 0.8748 | 0.8870 | 1.320 (8) | 0.24 | -3.818 (14) |
N1-C1 | 1.3708 | 0.8162 | 0.5547 | 2.17 (2) | 0.16 | -21.15 (9) |
N1-C7 | 1.3789 | 0.7892 | 0.5897 | 2.193 (18) | 0.20 | -19.76 (7) |
N2-C9 | 1.3291 | 0.7685 | 0.5606 | 2.490 (18) | 0.25 | -26.93 (8) |
N2-C10 | 1.4609 | 0.8630 | 0.5979 | 1.738 (19) | 0.07 | -11.60 (6) |
N2-C11 | 1.4684 | 0.8551 | 0.6133 | 1.662 (16) | 0.03 | -8.87 (5) |
N3-C9 | 1.3355 | 0.7738 | 0.5617 | 2.442 (18) | 0.22 | -26.12 (8) |
N3-C12 | 1.4646 | 0.8524 | 0.6122 | 1.694 (18) | 0.10 | -9.74 (6) |
N3-C13 | 1.4587 | 0.8690 | 0.5897 | 1.693 (18) | 0.04 | -10.84 (6) |
C1-C2 | 1.3799 | 0.7189 | 0.6610 | 2.214 (14) | 0.31 | -19.60 (4) |
C2-C8 | 1.4372 | 0.7176 | 0.7196 | 1.966 (13) | 0.18 | -14.80 (3) |
C3-C4 | 1.3862 | 0.7034 | 0.6829 | 2.198 (15) | 0.22 | -19.98 (4) |
C3-C8 | 1.4042 | 0.6769 | 0.7273 | 2.109 (14) | 0.21 | -18.67 (4) |
C4-C5 | 1.4111 | 0.7036 | 0.7075 | 2.078 (14) | 0.21 | -17.75 (4) |
C5-C6 | 1.3867 | 0.7230 | 0.6636 | 2.171 (16) | 0.21 | -19.25 (4) |
C6-C7 | 1.4025 | 0.6665 | 0.7360 | 2.114 (15) | 0.23 | -18.74 (4) |
C7-C8 | 1.4158 | 0.7206 | 0.6952 | 2.106 (13) | 0.21 | -18.32 (3) |
S1 | -0.123 |
O1 | -0.214 |
O2 | -0.142 |
O3 | -0.174 |
N1 | -0.097 |
N2 | -0.128 |
N3 | -0.136 |
N4 | +0.025 |
C1 | -0.149 |
C2 | -0.173 |
C3 | -0.143 |
C4 | -0.127 |
C5 | -0.160 |
C6 | -0.112 |
C7 | -0.109 |
C8 | -0.102 |
C9 | -0.112 |
C10 | -0.300 |
C11 | -0.389 |
C12 | -0.251 |
C13 | -0.244 |
H1 | +0.241 |
H2 | +0.224 |
H3 | +0.177 |
H4 | +0.161 |
H5 | +0.147 |
H6 | +0.192 |
H7 | +0.181 |
H8 | +0.153 |
H9 | +0.166 |
H10 | +0.169 |
H11 | +0.171 |
H12 | +0.189 |
H13 | +0.206 |
H14 | +0.203 |
H15 | +0.214 |
H16 | +0.238 |
H17 | +0.167 |
H18 | +0.162 |
Urea and thiourea derivatives can be efficient metal-free organocatalysts (Takemoto, 2005). In this context, their hydrogen-bonding abilities play a central role in molecular recognitition. We therefore performed crystal structure determinations of the title compound, (I), indole-3-thiouronium nitrate, (II) (Lutz et al., 2008a), and indole-3-thiouronium iodide, (III) (Lutz et al., 2008b). In order to investigate the bonding situation of the tetramethylthiouronium group, a multipole refinement and topological analysis of (I) were performed.
The molecular structure of (I) consist of two parts, viz. a planar indole moiety and a nonplanar thiouronium moiety (Fig. 1). The short C9—N bonds (Table 1) indicate a significant double-bond character, but they are slightly longer than those in the corresponding NH2 compounds (II) and (III) [1.306 (2)–1.317 (2) Å]. The corresponding C—N bond lengths in urea (Zavodnik et al., 1999) and N,N,N',N'-tetramethylurea (Frampton & Parkes, 1996) are 1.343 and 1.3706 (13) Å, respectively. A comparison with the corresponding thiourea derivatives cannnot be considered here, because free thiourea undergoes ferroelectric phase transitions (Takahashi et al., 1990) and the crystal structure of N,N,N',N'-tetramethylthiourea is not available in the literature.
As a result of the tetramethyl substitution of the thiouronium group, the molecule has only one NH hydrogen-bond donor. Atom O1 of the nitrate anion accepts this hydrogen bond to form an isolated cation–anion pair with graph-set descriptor D (Etter, 1990). The NH2 derivatives (II) and (III) have five hydrogen-bond donors and form polymeric two- and three-dimensional networks, respectively. The density of 1.388 Mg m-3 in (I) is consequently lower than the 1.513 Mg m-3 in (II).
The indole ring systems form centrosymmetric, parallel dimers. The intermolecular distance between atom S1(1 - x, 1 - y, 1 - z) and the least-squares plane of the indole ring is 3.43323 (6) Å. Despite this relatively short distance we do not assume π-stacking interactions, because the indole systems are not on top of each other (Fig. 2). The intermolecular distance between the centers of gravity of the five-membered rings is consequently very long [4.5681 (2) Å].
A search of the Cambridge Structural Database (update of August 2007; Allen, 2002) revealed 38 entries containing thiouronium and four entries for N,N,N',N'-tetramethylthiouronium compounds, of which 12 are drawn with an S═C9 double bond (e.g. Abashev et al., 1987). 20 entries have a C9═N double bond and consequently a positive charge on an N atom (e.g. Garner et al., 1998). Nine entries have the positive charge delocalized over the N—C—N group (e.g. Ishii et al., 2000) and one entry has no indication about the bond order. To investigate the bonding situation of the thiouronium group, we performed a high-resolution diffraction experiment on (I), followed by a multipole refinement of the structure. Deformation densities of the indole system and the environment of atom C9 are shown in Fig. 3.
A topological analysis of the cation shows that the Laplacians at the bond critical points of the C9—N bonds have the highest magnitudes, of -26.33 (7) and -26.02 (7) e Å-5, respectively (Table 3). Because the Laplacian at the bond critical point is a measure of the bond strength (Bader, 1990), this analysis clearly shows that these are the strongest bonds in the cations. The negative sign of the values indicates covalent bonding. A quantum-chemical study of urea (Gatti et al., 1994) gives a value of -1.15 a.u. (corresponding to -27.71 e Å-5) for the Laplacian at the bond critical point of the C—N single bond. In an experimental study of urea (Zavodnik et al., 1999), a value of -27.34 e Å-5 was determined. We can therefore conclude that the bond strengths of the C—N bonds in (I) and in urea are very similar.
The Laplacians at the bond critical points of the C—S bonds of -4.918 (19) and -5.008 (19) e Å-5 are very similar to the C—S single bonds of the dipeptide DL-alanylmethionine, with values of -4.9 and -4.7 e Å-5 (Guillot et al., 2001). The bond order of the C—S bonds in (I) is thus best described as a single bond.
The net charges of the atoms (Table 4) derived from the monopole populations indicate a negative charge concentration on the C atoms of the four methyl groups. As expected, the positive charges are distributed over the H atoms. Adding these charges gives a negative charge of -0.51 for the nitrate anion and, because of the applied electroneutrality constraint, +0.51 for the cation.
A thermal motion analysis using the program THMA11 (Schomaker & Trueblood, 1998) results in a low weighted R value {R = [Σ(wΔU)2/Σ(wUobs)2]1/2} of 0.093, indicating that the molecule behaves as a rigid body in the solid state at 110 K. This value can be decreased if the thiouronium moiety is treated as an independent rigid body with the S1—C9 bond as rotation axis, resulting in R = 0.065. This analysis additionally supports the description of S1—C9 as a single bond allowing free rotation.