1H-Pyrrole-2-carbothioamide

The reaction of ethoxy­carbonyl­pyrrole-2-thio­carbox­amide with sodium hydro­xide affords the known title compound, C₅H₆N₂S, whose structure shows a three-dimensional hydrogen-bonded lattice.

S1. Comment

The title compound, (I), also known as pyrrole-2-thiocarboxamide, has been reported as a bidentate ligand to nickel(II) ##AUTHOR: change OK ? by Singh et al. (1992). It has now been synthesized with the aim of producing novel nickel complexes for use as synthons in the preparation of analogues of the active sites of NiFe-enzymes. \sch

The molecule of (I) (Fig. 1) is essentially planar (r.m.s. deviation of the eight non-H atoms is 0.009 Å), with a rotation about the C2—C21 bond of 0.7 (1)° (calculated from the angles normal to the mean-planes of the N1/C2/C3/C21 and C2/C21/N23/S22 groups). The coplanarity of the thiocarboxamide group with the ring may be assisted by the formation of an intramolecular hydrogen bond, N1—H1···S22. Because the positions of the H and S atoms are determined principally by the geometry of the rigid pyrrole ring, the H···S distance of 2.79 (2) Å is not as short as those in the five-membered hydrogen-bonded C—C—N—H···S rings generally found in dithiocarboxamides [e.g. N,N'-bis(1-carboxyethyl)dithiooxamide; Vidal et al., 1999], where the range is 2.4–2.7 Å. Similarly, our N—H···S angle of 101 (2)° is at the acute end of the range of values found in such groups, viz. 103–124°, the lower values being found in bifurcated hydrogen bond cases (see below).

Molecules of (I) are linked by paired N—H···S hydrogen bonds into ribbons parallel to the c axis (Fig. 2). The pairs are arranged alternately about centres of symmetry (with shallow chair-shaped eight-membered rings involving the N23—H23B···S22ⁱⁱⁱ bonds) and twofold symmetry axes (with ten-membered rings in a saddle shape using the N1—H1···S22ⁱ bonds); the rings share the C21—S22 bonds. The ribbons are cross-linked by single N23—H23A···S22ⁱⁱ hydrogen bonds, (Fig. 1), which spiral along the twofold screw axes and complete a three-dimensional lattice of hydrogen bonds [symmetry codes: (i) 1/2 - x, y, 1 - z; (ii) -x, 1/2 + y, 1/2 - z; (iii) 1/2 - x, 1/2 - y, 1/2 - z].

This hydrogen-bond scheme shows similarities with that in dithiooxamide (Wheatley, 1965), where eight- and ten-membered rings are also linked in chains. However, the ten-membered ring there is without symmetry and has a different conformation, of two planes which are hinged sharply at the S···N vector of one dithiooxamide molecule. The ribbons are further linked into sheets and there are weaker hydrogen bonds between the sheets.

There are similar ten-membered intermolecular hydrogen-bonded rings in N,N'-diethyldithiooxamide (Drew et al., 1982), paired about inversion centres and linking the molecules into chains. Rather weaker links are found in chains of similar shape in N,N'-dicyclohexyldithiooxamide (Perec et al., 1995). The H···S distances in these crystals are 2.85 and 3.11 Å, respectively.

All the ten-membered ring systems reported here incorporate the five-membered intramolecular ring bonds. The H atoms are thus involved in bifurcated systems forming both intra- and inter-molecular hydrogen bonds.

Related literature

For related literature, see: Drew et al. (1982); Papadopoulos (1973); Perec et al. (1995); Singh et al. (1992); Vidal et al. (1999); Wheatley (1965).

S2. Experimental

Compound (I) was synthesized according to the method described by Papadopoulos (1973). Crystals of (I) were grown by solvent evaporation from an ethanol solution.

S3. Refinement

In the structure refinement, H atoms were included in idealized positions, apart from amide H atoms, which were located from difference Fourier maps. Initially, all H-atom parameters were set to ride on those of the parent atoms, but finally all were refined freely. In the final difference map, the highest peaks (to ca 0.24 e Å^-3) were close to the mid-points of bonds.

Computing details

Data collection: CAD-4 EXPRESS (Enraf-Nonius, 1992); cell refinement: CAD-4 EXPRESS; data reduction: CAD-4 processing program (Hursthouse, 1976); program(s) used to solve structure: SHELXS86 (Sheldrick, 1990); program(s) used to refine structure: SHELXL93 (Sheldrick, 1993); molecular graphics: ORTEPII (Johnson, 1971); software used to prepare material for publication: SHELXL93.

Figures

	Fig. 1. The molecular view of (I) showing the proposed intra- and intermolecular hydrogen bonds. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii; symmetry codes are as defined in Table 1.
	Fig. 2. One layer of molecules in the unit cell of (I), showing the linking of molecules into chains parallel to the c axis.

1H-pyrrole-2-carbothioamide

Crystal data

C5H6N2S	F(000) = 528
Mr = 126.18	Dx = 1.408 Mg m^−3
Monoclinic, I2/a	Mo Kα radiation, λ = 0.71069 Å
a = 9.7411 (9) Å	Cell parameters from 24 reflections
b = 7.5931 (7) Å	θ = 10–11°
c = 17.444 (2) Å	µ = 0.43 mm^−1
β = 112.682 (8)°	T = 293 K
V = 1190.5 (2) Å^3	Block, pale brown
Z = 8	0.48 × 0.10 × 0.05 mm

Data collection

Enraf-Nonius CAD-4 diffractometer	1323 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.036
Graphite monochromator	θmax = 30.0°, θmin = 1.5°
scintillation counter; ω/θ scans	h = −1→12
Absorption correction: ψ-scan (EMPABS; Sheldrick et al., 1977)	k = −1→10
Tmin = 0.044, Tmax = 0.078	l = −24→24
2049 measured reflections	3 standard reflections every 167 min
1734 independent reflections	intensity decay: none

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: see text
R[F^2 > 2σ(F^2)] = 0.035	All H-atom parameters refined
wR(F^2) = 0.102	w = 1/[σ^2(Fo^2) + (0.0479P)^2 + 0.2968P] where P = (Fo^2 + 2Fc^2)/3
S = 1.05	(Δ/σ)max = −0.001
1734 reflections	Δρmax = 0.24 e Å^−3
98 parameters	Δρmin = −0.24 e Å^−3
0 restraints	Extinction correction: SHELXL93 (Sheldrick, 1993), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0097 (18)

Special details

Experimental. A pale brown rhomb crystal was cut to a block of size 0.48 x 0.10 x 0.05 mm, mounted on a glass fibre and coated with epoxy resin. After preliminary photographic examination, this was transferred to an Enraf–Nonius CAD4 diffractometer (with monochromated radiation) for determination of accurate cell parameters and measurement of diffraction intensities. During processing, corrections were applied for Lorentz-polarization effects, absorption (by semi-empirical ψ-scan methods; Sheldrick et al., 1977) and to eliminate negative net intensities (by Bayesian statistical methods). No deterioration correction was necessary. The structure was determined by the direct methods routines in the SHELXS86 program (Sheldrick, 1990) and refined by full-matrix least-squares methods, on F², in SHELXL93 (Sheldrick, 1993). The non-H atoms were refined with anisotropic thermal parameters. H atoms were included in idealized positions or, for the amide H atoms, as located from difference Fourier maps; initially, all H-atom parameters were set to ride on those of the parent atoms, but finally all were refined freely. An extinction correction was applied, using the EXTI function in SHELXL93. In the final difference map, the highest peaks (to ca 0.24 e Å^-3) were close to the mid-points of bonds. Scattering factors for neutral atoms were taken from International Tables (Vol. C, 1992). Computer programs used in this analysis have been noted above or in Table 4 of Anderson et al. (1986).

Additional reference:

Anderson, S. N., Richards, R. L. & Hughes, D. L. (1986). J. Chem. Soc. Dalton Trans. pp. 245–252.

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. Mean-plane data taken from final SHELXL listing: Least-squares planes (x,y,z in crystal coordinates) and deviations from them (* indicates atom used to define plane)

4.257 (0.008) x + 6.285 (0.004) y + 2.725 (0.017) z = 2.697 (0.007)

* -0.005 (0.001) N1 * 0.003 (0.001) C2 * 0.000 (0.001) C3 * -0.003 (0.001) C4 * 0.005 (0.001) C5 0.025 (0.003) C21 0.005 (0.003) S22 0.043 (0.004) N23

Rms deviation of fitted atoms = 0.004

4.170 (0.008) x + 6.292 (0.004) y + 2.926 (0.015) z = 2.781 (0.005)

Angle to previous plane (with approximate e.s.d.) = 0.72 (0.13)

* 0.001 (0.000) N1 * -0.004 (0.001) C2 * 0.001 (0.000) C3 * 0.001 (0.000) C21 0.015 (0.003) C4 0.026 (0.003) C5 - 0.025 (0.002) S22 0.008 (0.003) N23

Rms deviation of fitted atoms = 0.002

4.222 (0.005) x + 6.240 (0.003) y + 3.037 (0.017) z = 2.804 (0.005)

Angle to previous plane (with approximate e.s.d.) = 0.72 (0.12)

* -0.002 (0.000) C2 * 0.005 (0.001) C21 * -0.002 (0.000) S22 * -0.002 (0.000) N23 0.017 (0.003) N1 - 0.011 (0.002) C3 0.008 (0.003) C4 0.036 (0.004) C5

Rms deviation of fitted atoms = 0.003

Refinement. Refinement on F² for ALL reflections except for 0 with very negative F² or flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The observed criterion of F² > σ(F²) is used only for calculating R-factor-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 (Ų)

	x	y	z	Uiso*/Ueq
N1	0.0179 (2)	0.2233 (2)	0.44519 (8)	0.0474 (3)
H1	0.094 (2)	0.170 (3)	0.4748 (14)	0.060 (6)*
C2	−0.0157 (2)	0.2817 (2)	0.36564 (9)	0.0384 (3)
C3	−0.1457 (2)	0.3788 (2)	0.34391 (11)	0.0471 (4)
H3	−0.196 (2)	0.434 (3)	0.2936 (14)	0.065 (6)*
C4	−0.1886 (2)	0.3781 (2)	0.41145 (12)	0.0522 (4)
H4	−0.275 (2)	0.433 (3)	0.4141 (13)	0.056 (5)*
C5	−0.0849 (2)	0.2823 (3)	0.47322 (11)	0.0547 (4)
H5	−0.079 (2)	0.259 (3)	0.5259 (14)	0.068 (6)*
C21	0.0772 (2)	0.2418 (2)	0.32086 (9)	0.0389 (3)
S22	0.23141 (4)	0.11583 (5)	0.36306 (2)	0.0448 (2)
N23	0.0363 (2)	0.3054 (2)	0.24458 (9)	0.0531 (4)
H23A	−0.043 (3)	0.363 (3)	0.2218 (14)	0.061 (6)*
H23B	0.094 (2)	0.293 (3)	0.2193 (13)	0.060 (6)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0424 (7)	0.0618 (8)	0.0378 (6)	0.0103 (6)	0.0151 (5)	0.0077 (6)
C2	0.0357 (6)	0.0415 (7)	0.0366 (6)	0.0004 (5)	0.0123 (5)	0.0019 (5)
C3	0.0425 (8)	0.0524 (9)	0.0469 (8)	0.0074 (7)	0.0179 (6)	0.0109 (7)
C4	0.0474 (8)	0.0571 (10)	0.0591 (10)	0.0095 (7)	0.0284 (8)	0.0079 (8)
C5	0.0546 (9)	0.0706 (11)	0.0456 (9)	0.0097 (8)	0.0266 (8)	0.0078 (8)
C21	0.0361 (6)	0.0422 (7)	0.0356 (7)	−0.0021 (5)	0.0108 (5)	−0.0031 (5)
S22	0.0399 (2)	0.0539 (3)	0.0368 (2)	0.0078 (2)	0.01057 (15)	−0.00414 (15)
N23	0.0467 (8)	0.0731 (10)	0.0412 (7)	0.0142 (7)	0.0190 (6)	0.0116 (7)

Geometric parameters (Å, º)

N1—C5	1.349 (2)	C4—C5	1.368 (3)
N1—C2	1.371 (2)	C4—H4	0.95 (2)
N1—H1	0.83 (2)	C5—H5	0.92 (2)
C2—C3	1.386 (2)	C21—N23	1.324 (2)
C2—C21	1.437 (2)	C21—S22	1.6916 (15)
C3—C4	1.394 (2)	N23—H23A	0.84 (2)
C3—H3	0.92 (2)	N23—H23B	0.85 (2)
C5—N1—C2	109.80 (14)	C3—C4—H4	126.6 (13)
C5—N1—H1	123.2 (16)	N1—C5—C4	108.5 (2)
C2—N1—H1	126.7 (16)	N1—C5—H5	122.1 (13)
N1—C2—C3	106.57 (13)	C4—C5—H5	129.5 (13)
N1—C2—C21	121.83 (13)	N23—C21—C2	117.44 (14)
C3—C2—C21	131.60 (14)	N23—C21—S22	121.06 (12)
C2—C3—C4	107.88 (14)	C2—C21—S22	121.49 (11)
C2—C3—H3	126.4 (13)	C21—N23—H23A	122.1 (16)
C4—C3—H3	125.7 (13)	C21—N23—H23B	118.7 (14)
C5—C4—C3	107.26 (15)	H23A—N23—H23B	119 (2)
C5—C4—H4	126.2 (13)
C5—N1—C2—C3	−0.8 (2)	C3—C4—C5—N1	−0.8 (2)
C5—N1—C2—C21	178.6 (2)	N1—C2—C21—N23	−179.42 (15)
N1—C2—C3—C4	0.3 (2)	C3—C2—C21—N23	−0.2 (3)
C21—C2—C3—C4	−179.0 (2)	N1—C2—C21—S22	1.5 (2)
C2—C3—C4—C5	0.3 (2)	C3—C2—C21—S22	−179.30 (14)
C2—N1—C5—C4	1.0 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···S22	0.83 (2)	2.79 (2)	3.057 (1)	101 (2)
N1—H1···S22^i	0.83 (2)	2.71 (2)	3.394 (1)	141 (2)
N23—H23A···S22^ii	0.84 (2)	2.68 (2)	3.479 (2)	161 (2)
N23—H23B···S22^iii	0.85 (2)	2.70 (2)	3.504 (2)	159 (2)

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