organic compounds H23B S22iii bonds) and twofold symmetry axes (with tenmembered rings in a saddle shape using the N1ÐH1 S22i bonds); the rings share the C21ÐS22 bonds. The ribbons are
Acta Crystallographica Section C
Crystal Structure Communications ISSN 0108-2701
1H-Pyrrole-2-carbothioamide Matt C. Smith, Sian C. Davies, David L. Hughes and David J. Evans* Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, England Correspondence e-mail:
[email protected] Received 7 February 2001 Accepted 18 May 2001
The reaction of ethoxycarbonylpyrrole-2-thiocarboxamide with sodium hydroxide affords the known title compound, C5H6N2S, whose structure shows a three-dimensional hydrogen-bonded lattice.
Comment The title compound, (I), also known as pyrrole-2-thiocarboxamide, has been reported as a bidentate ligand to nickel(II) 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 Ni±Fe enzymes.
The molecule of (I) (Fig. 1) is essentially planar (r.m.s. Ê ), with a rotation deviation of the eight non-H atoms is 0.009 A about the C2ÐC21 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, viz. N1ÐH1 S22. Because the positions of the H and S atoms are determined principally by the geometry of the rigid pyrrole ring, the H S Ê is not as short as those in the ®vedistance of 2.79 (2) A membered hydrogen-bonded CÐCÐNÐH S rings generally found in dithiocarboxamides [e.g. N,N0 -bis(1-carboxyethyl)dithiooxamide; Vidal et al., 1999], where the range is 2.4± Ê . Similarly, our NÐH S angle of 101 (2) is at the acute 2.7 A 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 NÐH 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 N23Ð Acta Cryst. (2001). C57, 987±988
Figure 1
A 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: (i)±(iii) are as de®ned in Table 1; (iv) ÿx, y ÿ 12, 1 2 ÿ z].
crosslinked by single N23ÐH23A S22ii hydrogen bonds, (Fig. 1), which spiral along the twofold screw axes and complete a three-dimensional lattice of hydrogen bonds [symmetry codes: (i) 12 ÿ x; y; 1 ÿ z; (ii) ÿx; 12 y; 12 ÿ z; (iii) 1 1 1 2 ÿ x; 2 ÿ y; 2 ÿ z].
Figure 2
One layer of molecules in the unit cell of (I), showing the linking of molecules into chains parallel to the c axis. Symmetry codes are as in Table 1.
# 2001 International Union of Crystallography
Printed in Great Britain ± all rights reserved
987
organic compounds This hydrogen-bond scheme shows similarities with that in dithiooxamide (Wheatley, 1965), where eight- and tenmembered rings are also linked in chains. However, the tenmembered 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 hydrogenbonded rings in N,N0 -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,N0 -dicyclohexyldithiooxamide (Perec et al., 1995). Ê, The H S distances in these crystals are 2.85 and 3.11 A respectively. All the ten-membered ring systems reported here incorporate ®ve-membered intramolecular ring bonds. The H atoms are thus involved in bifurcated systems forming both intra- and intermolecular hydrogen bonds.
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. Crystal data ÿ3
C5H6N2S Mr = 126.18 Monoclinic, I2/a Ê a = 9.7411 (9) A Ê b = 7.5931 (7) A Ê c = 17.444 (2) A = 112.682 (8) Ê3 V = 1190.5 (2) A Z=8
Dx = 1.408 Mg m Mo K radiation Cell parameters from 24 re¯ections = 10±11 = 0.43 mmÿ1 T = 293 (1) K Block, pale brown 0.48 0.10 0.05 mm
Data collection Enraf±Nonius CAD-4 diffractometer Scintillation counter; !/ scans Absorption correction: scan (EMPABS; Sheldrick et al., 1977) Tmin = 0.044, Tmax = 0.078 2049 measured re¯ections 1734 independent re¯ections 1323 re¯ections with I > 2(I)
Rint = 0.036 max = 30 h = ÿ1 ! 12 k = ÿ1 ! 10 l = ÿ24 ! 24 3 standard re¯ections frequency: 167 min intensity decay: none
Re®nement w = 1/[ 2(Fo2) + (0.0479P)2 + 0.2968P] where P = (Fo2 + 2Fc2)/3 (/)max = ÿ0.001 Ê ÿ3 max = 0.24 e A Ê ÿ3 min = ÿ0.24 e A Extinction correction: SHELXL93 (Sheldrick, 1993) Extinction coef®cient: 0.0097 (18)
Re®nement on F 2 R[F 2 > 2(F 2)] = 0.035 wR(F 2) = 0.102 S = 1.05 1734 re¯ections 98 parameters All H-atom parameters re®ned
988
Matt C. Smith et al.
C5H6N2S
Table 1
Ê , ). Hydrogen-bonding geometry (A DÐH A
DÐH
H A
D A
DÐH A
N1ÐH1 S22 N1ÐH1 S22i N23ÐH23A S22ii N23ÐH23B S22iii
0.83 (2) 0.83 (2) 0.84 (2) 0.85 (2)
2.79 (2) 2.71 (2) 2.68 (2) 2.70 (2)
3.057 (1) 3.394 (1) 3.479 (2) 3.504 (2)
101 (2) 141 (2) 161 (2) 159 (2)
Symmetry codes: (i) 12 ÿ x; y; 1 ÿ z; (ii) ÿx; 12 y; 12 ÿ z; (iii) 12 ÿ x; 12 ÿ y; 12 ÿ z.
In the structure re®nement, H atoms were included in idealized positions, apart from the 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 ®nally all were re®ned freely Ê ]. In the ®nal difference map, the highest [CÐH = 0.92 (2)±0.95 (2) A ÿ3 Ê peaks (to ca 0.24 e A ) were close to the midpoints of bonds. Data collection: CAD-4 EXPRESS (Enraf±Nonius, 1992); cell re®nement: CAD-4 EXPRESS; data reduction: CAD-4 processing program (Hursthouse, 1976); program(s) used to solve structure: SHELXS86 (Sheldrick, 1990); program(s) used to re®ne structure: SHELXL93 (Sheldrick, 1993); molecular graphics: ORTEPII (Johnson, 1971); software used to prepare material for publication: SHELXL93.
The authors would like to thank the Biotechnology and Biological Sciences Research Council for ®nancial support.
Supplementary data for this paper are available from the IUCr electronic archives (Reference: BM1450). Services for accessing these data are described at the back of the journal.
References Drew, M. G. B., Kisenyi, J. M. & Willey, G. R. (1982). J. Chem. Soc. Dalton Trans. pp. 1729±1732. Enraf±Nonius (1992). CAD-4 EXPRESS. Enraf±Nonius, Delft, The Netherlands. Hursthouse, M. B. (1976). CAD-4 processing program. Queen Mary College, London. Johnson, C. K. (1971). ORTEPII. Report ORNL-3794, revised. Oak Ridge National Laboratory, Tennessee, USA. Papadopoulos, E. P. (1973). J. Org. Chem. 38, 667±674. Perec, M., Baggio, R. & Garland, M. T. (1995). Acta Cryst. C51, 2182±2184. Sheldrick, G. M. (1990). Acta Cryst. A46, 467±473. Sheldrick, G. M. (1993). SHELXL93. University of GoÈttingen, Germany. Sheldrick, G. M., Orpen, A. G., Reichert, B. E. & Raithby, P. R. (1977). 4th European Crystallographic Meeting, Oxford. Abstracts, p. 147. Singh, B., Srivastava, P. & Srivastav, A. K. (1992). Synth. React. Inorg. Met. Org. Chem. 22, 299±310. Vidal, M. C. F., Lens, I., Castineiras, A., Matilla Hernandez, A., Tercero Moreno, J. M. & Niclos-Guiterrez, J. (1999). Polyhedron, 18, 3313±3319. Wheatley, P. J. (1965). J. Chem. Soc. pp. 396±400.
Acta Cryst. (2001). C57, 987±988
supporting information
supporting information Acta Cryst. (2001). C57, 987-988
[doi:10.1107/S0108270101008423]
1H-Pyrrole-2-carbothioamide Matt C. Smith, Sian C. Davies, David L. Hughes and David J. Evans 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. 1H-pyrrole-2-carbothioamide Crystal data C5H6N2S Mr = 126.18 Monoclinic, I2/a a = 9.7411 (9) Å b = 7.5931 (7) Å c = 17.444 (2) Å β = 112.682 (8)° V = 1190.5 (2) Å3 Z=8
F(000) = 528 Dx = 1.408 Mg m−3 Mo Kα radiation, λ = 0.71069 Å Cell parameters from 24 reflections θ = 10–11° µ = 0.43 mm−1 T = 293 K Block, pale brown 0.48 × 0.10 × 0.05 mm
Data collection Enraf-Nonius CAD-4 diffractometer Radiation source: fine-focus sealed tube Graphite monochromator scintillation counter; ω/θ scans Absorption correction: ψ-scan (EMPABS; Sheldrick et al., 1977) Tmin = 0.044, Tmax = 0.078 2049 measured reflections
1734 independent reflections 1323 reflections with I > 2σ(I) Rint = 0.036 θmax = 30.0°, θmin = 1.5° h = −1→12 k = −1→10 l = −24→24 3 standard reflections every 167 min intensity decay: none
Refinement Refinement on F2 Least-squares matrix: full R[F2 > 2σ(F2)] = 0.035 wR(F2) = 0.102 S = 1.05 1734 reflections 98 parameters 0 restraints Primary atom site location: structure-invariant direct methods
Acta Cryst. (2001). C57, 987-988
Secondary atom site location: difference Fourier map Hydrogen site location: see text All H-atom parameters refined w = 1/[σ2(Fo2) + (0.0479P)2 + 0.2968P] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max = −0.001 Δρmax = 0.24 e Å−3 Δρmin = −0.24 e Å−3
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supporting information Extinction correction: SHELXL93 (Sheldrick, 1993), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
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 semiempirical 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 (Å2)
N1 H1 C2 C3 H3
x
y
z
Uiso*/Ueq
0.0179 (2) 0.094 (2) −0.0157 (2) −0.1457 (2) −0.196 (2)
0.2233 (2) 0.170 (3) 0.2817 (2) 0.3788 (2) 0.434 (3)
0.44519 (8) 0.4748 (14) 0.36564 (9) 0.34391 (11) 0.2936 (14)
0.0474 (3) 0.060 (6)* 0.0384 (3) 0.0471 (4) 0.065 (6)*
Acta Cryst. (2001). C57, 987-988
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supporting information C4 H4 C5 H5 C21 S22 N23 H23A H23B
−0.1886 (2) −0.275 (2) −0.0849 (2) −0.079 (2) 0.0772 (2) 0.23141 (4) 0.0363 (2) −0.043 (3) 0.094 (2)
0.3781 (2) 0.433 (3) 0.2823 (3) 0.259 (3) 0.2418 (2) 0.11583 (5) 0.3054 (2) 0.363 (3) 0.293 (3)
0.41145 (12) 0.4141 (13) 0.47322 (11) 0.5259 (14) 0.32086 (9) 0.36306 (2) 0.24458 (9) 0.2218 (14) 0.2193 (13)
0.0522 (4) 0.056 (5)* 0.0547 (4) 0.068 (6)* 0.0389 (3) 0.0448 (2) 0.0531 (4) 0.061 (6)* 0.060 (6)*
Atomic displacement parameters (Å2)
N1 C2 C3 C4 C5 C21 S22 N23
U11
U22
U33
U12
U13
U23
0.0424 (7) 0.0357 (6) 0.0425 (8) 0.0474 (8) 0.0546 (9) 0.0361 (6) 0.0399 (2) 0.0467 (8)
0.0618 (8) 0.0415 (7) 0.0524 (9) 0.0571 (10) 0.0706 (11) 0.0422 (7) 0.0539 (3) 0.0731 (10)
0.0378 (6) 0.0366 (6) 0.0469 (8) 0.0591 (10) 0.0456 (9) 0.0356 (7) 0.0368 (2) 0.0412 (7)
0.0103 (6) 0.0004 (5) 0.0074 (7) 0.0095 (7) 0.0097 (8) −0.0021 (5) 0.0078 (2) 0.0142 (7)
0.0151 (5) 0.0123 (5) 0.0179 (6) 0.0284 (8) 0.0266 (8) 0.0108 (5) 0.01057 (15) 0.0190 (6)
0.0077 (6) 0.0019 (5) 0.0109 (7) 0.0079 (8) 0.0078 (8) −0.0031 (5) −0.00414 (15) 0.0116 (7)
Geometric parameters (Å, º) N1—C5 N1—C2 N1—H1 C2—C3 C2—C21 C3—C4 C3—H3
1.349 (2) 1.371 (2) 0.83 (2) 1.386 (2) 1.437 (2) 1.394 (2) 0.92 (2)
C4—C5 C4—H4 C5—H5 C21—N23 C21—S22 N23—H23A N23—H23B
1.368 (3) 0.95 (2) 0.92 (2) 1.324 (2) 1.6916 (15) 0.84 (2) 0.85 (2)
C5—N1—C2 C5—N1—H1 C2—N1—H1 N1—C2—C3 N1—C2—C21 C3—C2—C21 C2—C3—C4 C2—C3—H3 C4—C3—H3 C5—C4—C3 C5—C4—H4
109.80 (14) 123.2 (16) 126.7 (16) 106.57 (13) 121.83 (13) 131.60 (14) 107.88 (14) 126.4 (13) 125.7 (13) 107.26 (15) 126.2 (13)
C3—C4—H4 N1—C5—C4 N1—C5—H5 C4—C5—H5 N23—C21—C2 N23—C21—S22 C2—C21—S22 C21—N23—H23A C21—N23—H23B H23A—N23—H23B
126.6 (13) 108.5 (2) 122.1 (13) 129.5 (13) 117.44 (14) 121.06 (12) 121.49 (11) 122.1 (16) 118.7 (14) 119 (2)
C5—N1—C2—C3 C5—N1—C2—C21 N1—C2—C3—C4 C21—C2—C3—C4
−0.8 (2) 178.6 (2) 0.3 (2) −179.0 (2)
C3—C4—C5—N1 N1—C2—C21—N23 C3—C2—C21—N23 N1—C2—C21—S22
−0.8 (2) −179.42 (15) −0.2 (3) 1.5 (2)
Acta Cryst. (2001). C57, 987-988
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supporting information C2—C3—C4—C5 C2—N1—C5—C4
0.3 (2) 1.0 (2)
C3—C2—C21—S22
−179.30 (14)
Hydrogen-bond geometry (Å, º) D—H···A
D—H
H···A
D···A
D—H···A
N1—H1···S22 N1—H1···S22i N23—H23A···S22ii N23—H23B···S22iii
0.83 (2) 0.83 (2) 0.84 (2) 0.85 (2)
2.79 (2) 2.71 (2) 2.68 (2) 2.70 (2)
3.057 (1) 3.394 (1) 3.479 (2) 3.504 (2)
101 (2) 141 (2) 161 (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.
Acta Cryst. (2001). C57, 987-988
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