Five varieties of hydrogen bond in 1-formyl-3-thiosemicarbazide: an electron density study

In an attempt to investigate the putative S—H...N hydrogen bond, we have studied the title compound, 1-formyl-3-thiosemicarbazide, which was revealed in a CSD search as a crystal structure which might show such an interaction. However, a redetermination of the structure at room temperature and careful analysis showed that the earlier study [Saxena et al. (1991). Acta Cryst. C47, 2374–2376] on which the CSD search was based was in error and that the possibility of an S—H...N hydrogen bond is negated. The presence of five other varieties of hydrogen bond (N—H...O, N—H...S, N—H...N, C—H...O, C—H...S) in the crystal packing prompted us to redirect our efforts and to undertake a study of the charge-density distribution at 90 K. The topological analysis of these five varieties of hydrogen bond was carried out with Bader's quantum theory of `atoms in molecules' and by applying Koch–Popelier's criteria. The analysis reveals that the hydrogen-bond strength is highest for N—H...O and lowest for C—H...S with N—H...S, N—H...N and C—H...O forming the middle order.

Computing details

Data collection: SMART (Bruker, 2004) for 293K, (90K); Bruker SMART for WNT/2000 v5.629 for 100K. Cell refinement: SMART (Bruker, 2004) for 293K, (90K); Bruker SMART for WNT/2000 v5.629 for 100K. Data reduction: SMART (Bruker, 2004) for 293K, (90K); Bruker SAINT Version 6.45,1997-2003 for 100K. Program(s) used to solve structure: SHELXS97 (Sheldrick, 1997) for 293K, (90K); Bruker SHELXTL Version 6.14,2000-2003 for 100K. Program(s) used to refine structure: SHELXL97 (Sheldrick, 1997) for 293K; Bruker SHELXTL Version 6.14,2000-2003 for 100K; Koritsanszky et al., (2003) for (90K). Molecular graphics: CAMERON (Watkin et al., 1996) for 293K; Bruker SHELXTL Version 6.14,2000-2003 for 100K; Koritsanszky et al., (2003) for (90K). Software used to prepare material for publication: PLATON (Spek, 2001) for 293K, (90K); Bruker SHELXTL Version 6.14,2000-2003 for 100K.

Figures

(293K) 1-formyl-3-thiosemicarbazide

Crystal data

C2H5N3OS	F(000) = 248
Mr = 119.16	Dx = 1.548 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 3850 reflections
a = 7.2569 (17) Å	θ = 2.8–26.4°
b = 7.4263 (18) Å	µ = 0.51 mm^−1
c = 9.593 (2) Å	T = 293 K
β = 98.606 (4)°	Prism, colorless
V = 511.2 (2) Å^3	0.37 × 0.28 × 0.16 mm
Z = 4

Data collection

Bruker SMART APEX CCD area detector diffractometer	1012 independent reflections
Radiation source: fine-focus sealed tube	961 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.014
ϕ & ω scans	θmax = 26.4°, θmin = 2.8°
Absorption correction: multi-scan R.H. Blessing, Acta Cryst. (1995), A51, 33-38	h = −8→9
Tmin = 0.827, Tmax = 0.923	k = −8→9
3850 measured reflections	l = −11→11

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.029	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.076	H atoms treated by a mixture of independent and constrained refinement
S = 1.08	w = 1/[σ^2(Fo^2) + (0.0429P)^2 + 0.1699P] where P = (Fo^2 + 2Fc^2)/3
1012 reflections	(Δ/σ)max = 0.001
80 parameters	Δρmax = 0.24 e Å^−3
0 restraints	Δρmin = −0.27 e Å^−3

Special details

Experimental. Crystal to Detector distance was 6.07 cm, ω range is 0.3 ° and exposure time was 15 s.

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 (Ų)

	x	y	z	Uiso*/Ueq
S1	0.78081 (5)	0.18924 (5)	0.54094 (4)	0.03944 (17)
C2	0.9854 (2)	0.29268 (18)	0.60197 (14)	0.0286 (3)
N3	0.9916 (2)	0.44516 (19)	0.67164 (15)	0.0395 (3)
N4	1.14576 (17)	0.21758 (18)	0.57826 (14)	0.0340 (3)
N5	1.31717 (17)	0.29497 (17)	0.62762 (13)	0.0347 (3)
H5	1.3606	0.3785	0.5796	0.042*
C6	1.4154 (2)	0.2403 (2)	0.74972 (16)	0.0340 (3)
O7	1.35930 (16)	0.13404 (17)	0.82965 (12)	0.0465 (3)
H3A	0.888 (3)	0.498 (3)	0.6861 (19)	0.052 (5)*
H3B	1.091 (3)	0.492 (3)	0.702 (2)	0.052 (6)*
H4	1.149 (3)	0.116 (3)	0.5415 (19)	0.039 (5)*
H6	1.537 (3)	0.297 (2)	0.763 (2)	0.046 (5)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0244 (2)	0.0430 (3)	0.0486 (3)	0.00265 (14)	−0.00218 (16)	−0.01180 (16)
C2	0.0283 (7)	0.0320 (7)	0.0249 (6)	0.0028 (5)	0.0024 (5)	0.0014 (5)
N3	0.0311 (7)	0.0377 (7)	0.0490 (8)	0.0015 (6)	0.0035 (6)	−0.0126 (6)
N4	0.0245 (6)	0.0357 (7)	0.0408 (7)	0.0004 (5)	0.0016 (5)	−0.0086 (6)
N5	0.0250 (6)	0.0412 (7)	0.0380 (7)	−0.0058 (5)	0.0055 (5)	0.0043 (5)
C6	0.0247 (7)	0.0398 (8)	0.0375 (8)	−0.0035 (6)	0.0052 (6)	−0.0039 (7)
O7	0.0417 (6)	0.0565 (7)	0.0401 (6)	−0.0130 (6)	0.0026 (5)	0.0082 (5)

Geometric parameters (Å, º)

S1—C2	1.6959 (15)	N4—H4	0.83 (2)
C2—N3	1.312 (2)	N5—C6	1.340 (2)
C2—N4	1.3405 (19)	N5—H5	0.8600
N3—H3A	0.88 (2)	C6—O7	1.212 (2)
N3—H3B	0.82 (2)	C6—H6	0.97 (2)
N4—N5	1.3876 (17)
N3—C2—N4	118.74 (14)	N5—N4—H4	116.2 (13)
N3—C2—S1	121.89 (12)	C6—N5—N4	120.36 (13)
N4—C2—S1	119.37 (11)	C6—N5—H5	119.8
C2—N3—H3A	120.0 (13)	N4—N5—H5	119.8
C2—N3—H3B	121.0 (14)	O7—C6—N5	124.40 (14)
H3A—N3—H3B	119 (2)	O7—C6—H6	125.5 (12)
C2—N4—N5	121.78 (13)	N5—C6—H6	110.1 (12)
C2—N4—H4	121.7 (13)

(100K) 1-formyl-3-thiosemicarbazide

Crystal data

C2H5N3OS	F(000) = 248
Mr = 119.15	Dx = 1.583 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 4707 reflections
a = 7.2339 (5) Å	θ = 2.8–26.0°
b = 7.3703 (5) Å	µ = 0.52 mm^−1
c = 9.4771 (7) Å	T = 100 K
β = 98.426 (1)°	Block, colorless
V = 499.83 (6) Å^3	0.28 × 0.25 × 0.16 mm
Z = 4

Data collection

CCD area detector diffractometer	982 independent reflections
Radiation source: fine-focus sealed tube	953 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.017
phi and ω scans	θmax = 26.0°, θmin = 2.9°
Absorption correction: multi-scan SADABS	h = −8→8
Tmin = 0.868, Tmax = 0.922	k = −9→9
6106 measured reflections	l = −11→11

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.025	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.065	H atoms treated by a mixture of independent and constrained refinement
S = 1.08	w = 1/[σ^2(Fo^2) + (0.0381P)^2 + 0.2485P] where P = (Fo^2 + 2Fc^2)/3
982 reflections	(Δ/σ)max < 0.001
80 parameters	Δρmax = 0.20 e Å^−3
0 restraints	Δρmin = −0.26 e Å^−3

Special details

Experimental. X-ray data were collected at 100 K with phi and omega scan. stratigy of the data collection was done using COSMO supplied by BRUKER AXS.

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 (Ų)

	x	y	z	Uiso*/Ueq
C2	0.51400 (18)	0.29455 (17)	0.39851 (13)	0.0128 (3)
C6	0.08200 (17)	0.23961 (18)	0.24985 (14)	0.0145 (3)
N4	0.35312 (15)	0.21776 (16)	0.42325 (12)	0.0145 (3)
N5	0.18118 (16)	0.29668 (15)	0.37321 (12)	0.0146 (3)
N3	0.50740 (17)	0.44900 (16)	0.32790 (12)	0.0161 (3)
O7	0.13925 (13)	0.13081 (13)	0.16897 (10)	0.0187 (2)
S1	0.72032 (4)	0.19016 (4)	0.45953 (3)	0.01576 (14)
H3A	0.612 (3)	0.499 (2)	0.3145 (17)	0.024*
H3B	0.404 (3)	0.498 (2)	0.2971 (18)	0.024*
H4	0.350 (2)	0.115 (3)	0.4623 (19)	0.024*
H5	0.134 (3)	0.349 (2)	0.427 (2)	0.024*
H6	−0.041 (3)	0.297 (2)	0.2348 (19)	0.021 (4)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C2	0.0146 (6)	0.0141 (6)	0.0095 (6)	−0.0009 (4)	0.0010 (5)	−0.0025 (5)
C6	0.0121 (6)	0.0154 (6)	0.0164 (6)	0.0002 (5)	0.0028 (5)	0.0034 (5)
N4	0.0111 (5)	0.0148 (5)	0.0172 (6)	0.0006 (4)	0.0004 (4)	0.0037 (4)
N5	0.0116 (6)	0.0169 (6)	0.0154 (6)	0.0035 (4)	0.0029 (4)	−0.0019 (4)
N3	0.0130 (5)	0.0158 (6)	0.0194 (6)	−0.0001 (4)	0.0016 (4)	0.0043 (4)
O7	0.0189 (5)	0.0212 (5)	0.0160 (5)	0.0038 (4)	0.0028 (4)	−0.0023 (4)
S1	0.0112 (2)	0.0163 (2)	0.0190 (2)	−0.00057 (11)	−0.00037 (13)	0.00372 (11)

Geometric parameters (Å, º)

C2—N3	1.3178 (17)	N4—N5	1.3919 (16)
C2—N4	1.3452 (18)	N4—H4	0.84 (2)
C2—S1	1.7032 (13)	N5—H5	0.764 (19)
C6—O7	1.2228 (17)	N3—H3A	0.869 (19)
C6—N5	1.3464 (17)	N3—H3B	0.843 (18)
C6—H6	0.974 (18)
N3—C2—N4	118.95 (12)	N5—N4—H4	116.4 (12)
N3—C2—S1	121.83 (10)	C6—N5—N4	120.08 (11)
N4—C2—S1	119.22 (10)	C6—N5—H5	120.6 (14)
O7—C6—N5	124.25 (12)	N4—N5—H5	116.7 (14)
O7—C6—H6	125.2 (10)	C2—N3—H3A	118.4 (12)
N5—C6—H6	110.5 (10)	C2—N3—H3B	120.9 (12)
C2—N4—N5	121.17 (11)	H3A—N3—H3B	120.7 (17)
C2—N4—H4	122.2 (12)

(90K) 1-formyl-3-thiosemicarbazide

Crystal data

C2H5N3OS	F(000) = 248
Mr = 119.16	Dx = 1.583 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 24842 reflections
a = 7.2359 (3) Å	θ = 2.8–50.3°
b = 7.3713 (3) Å	µ = 0.52 mm^−1
c = 9.4768 (4) Å	T = 90 K
β = 98.403 (2)°	Prism, colorless
V = 500.05 (4) Å^3	0.37 × 0.28 × 0.16 mm
Z = 4

Data collection

Bruker SMART APEX CCD area detector diffractometer	5136 independent reflections
Radiation source: fine-focus sealed tube	4514 reflections with > 3σ(I)
Graphite monochromator	Rint = 0.025
ϕ & ω scans	θmax = 50.3°, θmin = 2.8°
Absorption correction: multi-scan R.H. Blessing, Acta Cryst. (1995), A51, 33-38	h = −15→15
Tmin = 0.826, Tmax = 0.920	k = −15→15
24842 measured reflections	l = −19→20

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.014	All H-atom parameters refined
wR(F^2) = 0.015	w2 = 1/[s^2(Fo^2)]
S = 1.56	(Δ/σ)max < 0.001
4518 reflections	Δρmax = 0.30 e Å^−3
207 parameters	Δρmin = −0.25 e Å^−3
0 restraints	Absolute structure: unk
Primary atom site location: structure-invariant direct methods

Special details

Experimental. Crystal to Detector distance was 6.07 cm, ω range is 0.3 ° and exposure time was 20 s, 40 s and 60 s in three batches respectively.

Refinement. Multipole Refinement

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
S(1)	0.279680 (6)	0.809654 (6)	0.540387 (5)	0.012
O(7)	0.86115 (3)	0.86953 (3)	0.83120 (2)	0.015
N(3)	0.49275 (3)	0.55014 (3)	0.67235 (2)	0.013
N(4)	0.64756 (3)	0.78212 (3)	0.57685 (2)	0.011
N(5)	0.81864 (3)	0.70289 (3)	0.62614 (2)	0.011
C(2)	0.48613 (3)	0.70517 (2)	0.60133 (2)	0.009
C(6)	0.91839 (3)	0.76004 (3)	0.75009 (2)	0.011
H(3A)	0.36982	0.48844	0.68842	0.017 (2)
H(3B)	0.61594	0.48849	0.71535	0.026 (2)
H(4)	0.65368	0.90756	0.52988	0.018 (2)
H(5)	0.88850	0.63714	0.55385	0.025 (2)
H(6)	1.05545	0.69726	0.76793	0.024 (3)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S(1)	0.00820 (2)	0.01222 (2)	0.01441 (2)	−0.00066 (1)	−0.00030 (1)	0.00314 (1)
O(7)	0.01408 (7)	0.01745 (7)	0.01231 (6)	0.00399 (5)	0.00115 (5)	−0.00283 (5)
N(3)	0.01117 (6)	0.01150 (6)	0.01571 (7)	−0.00060 (5)	0.00144 (5)	0.00438 (5)
N(4)	0.00825 (6)	0.01140 (6)	0.01393 (6)	−0.00068 (4)	0.00101 (5)	0.00284 (5)
N(5)	0.00880 (6)	0.01345 (6)	0.01193 (6)	0.00144 (5)	0.00142 (5)	−0.00153 (5)
C(2)	0.00872 (6)	0.00979 (5)	0.00950 (6)	−0.00057 (4)	0.00073 (4)	0.00077 (4)
C(6)	0.00924 (6)	0.01308 (6)	0.01119 (6)	0.00180 (5)	0.00138 (5)	−0.00013 (5)

Geometric parameters (Å, º)

S(1)—C(2)	1.7048 (2)	N(4)—C(2)	1.3487 (3)
O(7)—C(6)	1.2275 (3)	N(4)—H(4)	1.0300
N(3)—C(2)	1.3235 (3)	N(5)—C(6)	1.3529 (3)
N(3)—H(3A)	1.0300	N(5)—H(5)	1.0300
N(3)—H(3B)	1.0300	C(6)—H(6)	1.0850
N(4)—N(5)	1.3866 (3)
C(2)—N(3)—H(3A)	119.250	C(6)—N(5)—H(5)	118.201
C(2)—N(3)—H(3B)	123.161	S(1)—C(2)—N(3)	121.812 (15)
H(3A)—N(3)—H(3B)	117.570	S(1)—C(2)—N(4)	119.327 (14)
N(5)—N(4)—C(2)	121.194 (18)	N(3)—C(2)—N(4)	118.861 (18)
N(5)—N(4)—H(4)	115.534	O(7)—C(6)—N(5)	124.219 (19)
C(2)—N(4)—H(4)	123.015	O(7)—C(6)—H(6)	124.56
N(4)—N(5)—C(6)	119.873 (18)	N(5)—C(6)—H(6)	111.222
N(4)—N(5)—H(5)	118.352
H(3A)—N(3)—C(2)—S(1)	2.10	H(4)—N(4)—N(5)—C(6)	77.40
H(3A)—N(3)—C(2)—N(4)	−177.90	H(4)—N(4)—N(5)—H(5)	−80.90
H(3B)—N(3)—C(2)—S(1)	−176.20	H(4)—N(4)—C(2)—S(1)	5.20
H(3B)—N(3)—C(2)—N(4)	3.70	H(4)—N(4)—C(2)—N(3)	−174.70
N(5)—N(4)—C(2)—S(1)	179.17 (1)	N(4)—N(5)—C(6)—O(7)	6.50 (3)
N(5)—N(4)—C(2)—N(3)	−0.80 (2)	N(4)—N(5)—C(6)—H(6)	−173.10
C(2)—N(4)—N(5)—C(6)	−96.90 (2)	H(5)—N(5)—C(6)—O(7)	164.80
C(2)—N(4)—N(5)—H(5)	104.80	H(5)—N(5)—C(6)—H(6)	−14.80