(Z)-{[3-(Hydroxy­meth­yl)-1,3-thia­zolidin-2-yl­idene]amino}formonitrile

Liu, X.-L.; Li, Y.-M.

doi:10.1107/S1600536809023095

organic compounds

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doi:10.1107/S1600536809023095

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(Z)-{[3-(Hydroxymethyl)-1,3-thiazolidin-2-ylidene]amino}formonitrile

Xin-Lin Liu ^a and Yu-Ming Li ^a ^*

^aInstitute of Cardiovascular Disease, Pingjin Hospital, Medical College of Armed Police Force, Tianjin 300162, People's Republic of China
^*Correspondence e-mail: yuming_li2009@yahoo.cn

(Received 13 June 2009; accepted 16 June 2009; online 20 June 2009)

In the title molecule, C₅H₇N₃OS, all the non-hydrogen atoms except the O atom are almost planar [maximum least squares plane deviation = 0.035 (3) Å for the N atom]. The crystal packing is stabilized by intermolecular O—H⋯N hydrogen bonds, which link the molecules into inversion dimers.

Related literature

For a related structure, see: Xie (2008 ). For the biological activity of thiazolidine-containing compounds, see: Iwata et al. (1988 ). For bond-length data, see: Allen et al. (1987 ).

Experimental

Crystal data

C₅H₇N₃OS
M_r = 157.20
Triclinic, $[P \overline 1]$
a = 5.5321 (11) Å
b = 8.1790 (16) Å
c = 8.4978 (17) Å
α = 101.56 (3)°
β = 100.39 (3)°
γ = 105.47 (3)°
V = 351.75 (16) Å³
Z = 2
Mo Kα radiation
μ = 0.39 mm⁻¹
T = 293 K
0.22 × 0.17 × 0.13 mm

Data collection

Rigaku R-AXIS RAPID IP area-detector diffractometer
Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ) T_min = 0.919, T_max = 0.951
2778 measured reflections
1234 independent reflections
1027 reflections with I > 2σ(I)
R_int = 0.014

Refinement

R[F² > 2σ(F²)] = 0.032
wR(F²) = 0.119
S = 1.19
1234 reflections
96 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.33 e Å⁻³
Δρ_min = −0.25 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1A⋯N3ⁱ	0.80 (3)	2.04 (3)	2.839 (3)	174 (3)
Symmetry code: (i) -x, -y+1, -z+2.

Data collection: RAPID-AUTO (Rigaku, 2004 ); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809023095/hg2526sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809023095/hg2526Isup2.hkl

checkCIF report

Comment top

Thiazolidine is an important kind of group in organic chemistry. Many compounds containing Thiazolidine groups possess a broad spectrum of biological activities (Iwata et al., 1988). Here, we report the title crystal structure.

In (Z)-(3-(hydroxymethyl)thiazolidin-2-ylideneamino)formonitrile (Fig. 1), all bond lengths are normal (Allen et al., 1987) and in a good agreement with those reported previously (Xie, 2008). It is known that the imino tautomers can exist as two geometrical isomers, syn (Z) and anti (E), but in this crystal, only Z isomers have been observed. The atoms of whole molecule except O atom (C1-C5/N1-N3/S1) are almost planar [maximum least squares plane deviation for N1 0.035 (3) Å]. The crystal packing is stabilized by intermolecular O—H···N hydrogen bonds, which link the molecules into dimers.

Related literature top

For a related structure, see: Xie (2008). For the biological activity of thiazolidine-containing compounds, see: Iwata et al. (1988). For bond-length data, see: Allen et al. (1987).

Experimental top

A mixture of (Z)-(thiazolidin-2-ylideneamino)formonitrile 10 mmol (1.27 g), paraformaldehyde (0.36 g, 12 mmol) and 0.01 g triethylamine were refluxed in absolute EtOH (20 mL) for 3 h. On cooling, the product crystallizes and was filtered and then recrystallized from absolute ethanol. Yield 1.51 g (96%). Single crystals suitable for X-ray measurements were obtained by recrystallization from ethanol at room temperature.

Computing details top

Data collection: RAPID-AUTO (Rigaku, 2004); cell refinement: RAPID-AUTO (Rigaku, 2004); data reduction: RAPID-AUTO (Rigaku, 2004); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

Fig. 1. The molecular structure of (I), with atom labels and 40% probability displacement ellipsoids for non-H atoms.

(Z)-{[3-(Hydroxymethyl)-1,3-thiazolidin-2-ylidene]amino}formonitrile top

Crystal data top

C₅H₇N₃OS	Z = 2
M_r = 157.20	F(000) = 164
Triclinic, P1	D_x = 1.484 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 5.5321 (11) Å	Cell parameters from 2501 reflections
b = 8.1790 (16) Å	θ = 2.3–25.1°
c = 8.4978 (17) Å	µ = 0.39 mm⁻¹
α = 101.56 (3)°	T = 293 K
β = 100.39 (3)°	Needle, colorless
γ = 105.47 (3)°	0.22 × 0.17 × 0.13 mm
V = 351.75 (16) Å³

Data collection top

Rigaku R-AXIS RAPID IP area-detector diffractometer	1234 independent reflections
Radiation source: Rotating Anode	1027 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.014
ω oscillation scans	θ_max = 25.0°, θ_min = 3.2°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −6→6
T_min = 0.919, T_max = 0.951	k = −9→9
2778 measured reflections	l = −10→10

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.032	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.119	w = 1/[σ²(F_o²) + (0.0703P)² + 0.06P] where P = (F_o² + 2F_c²)/3
S = 1.19	(Δ/σ)_max < 0.001
1234 reflections	Δρ_max = 0.33 e Å⁻³
96 parameters	Δρ_min = −0.25 e Å⁻³
0 restraints	Extinction correction: SHELXTL (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.052 (16)

Crystal data top

C₅H₇N₃OS	γ = 105.47 (3)°
M_r = 157.20	V = 351.75 (16) Å³
Triclinic, P1	Z = 2
a = 5.5321 (11) Å	Mo Kα radiation
b = 8.1790 (16) Å	µ = 0.39 mm⁻¹
c = 8.4978 (17) Å	T = 293 K
α = 101.56 (3)°	0.22 × 0.17 × 0.13 mm
β = 100.39 (3)°

Data collection top

Rigaku R-AXIS RAPID IP area-detector diffractometer	1234 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	1027 reflections with I > 2σ(I)
T_min = 0.919, T_max = 0.951	R_int = 0.014
2778 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.032	0 restraints
wR(F²) = 0.119	H atoms treated by a mixture of independent and constrained refinement
S = 1.19	Δρ_max = 0.33 e Å⁻³
1234 reflections	Δρ_min = −0.25 e Å⁻³
96 parameters

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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	0.15141 (12)	0.91511 (8)	0.84635 (8)	0.0509 (3)
O1	0.3210 (4)	0.3944 (2)	0.6397 (3)	0.0640 (6)
N1	0.3875 (3)	0.6968 (2)	0.7503 (2)	0.0450 (5)
N2	0.2714 (4)	0.6719 (2)	0.9942 (2)	0.0490 (5)
N3	0.0736 (5)	0.7702 (3)	1.2185 (3)	0.0640 (6)
C1	0.3729 (7)	0.7839 (5)	0.6182 (4)	0.0724 (9)
H1B	0.2783	0.6980	0.5138	0.087*
H1C	0.5460	0.8400	0.6090	0.087*
C2	0.2400 (6)	0.9180 (4)	0.6529 (3)	0.0592 (7)
H2B	0.0866	0.8916	0.5642	0.071*
H2C	0.3545	1.0335	0.6600	0.071*
C3	0.4959 (5)	0.5525 (3)	0.7414 (3)	0.0529 (6)
H3A	0.6495	0.5809	0.6993	0.063*
H3B	0.5477	0.5389	0.8521	0.063*
C4	0.2782 (4)	0.7467 (3)	0.8711 (3)	0.0395 (5)
C5	0.1620 (5)	0.7289 (3)	1.1096 (3)	0.0482 (6)
H1A	0.216 (6)	0.353 (4)	0.686 (4)	0.080 (10)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0639 (4)	0.0564 (4)	0.0506 (4)	0.0356 (3)	0.0251 (3)	0.0217 (3)
O1	0.0818 (13)	0.0500 (10)	0.0697 (13)	0.0227 (9)	0.0443 (11)	0.0109 (9)
N1	0.0543 (11)	0.0508 (10)	0.0416 (11)	0.0272 (9)	0.0206 (9)	0.0158 (8)
N2	0.0661 (12)	0.0492 (11)	0.0457 (12)	0.0278 (9)	0.0249 (9)	0.0202 (9)
N3	0.0854 (16)	0.0641 (13)	0.0531 (14)	0.0263 (12)	0.0342 (12)	0.0195 (11)
C1	0.101 (2)	0.102 (2)	0.0584 (17)	0.0688 (19)	0.0462 (16)	0.0452 (16)
C2	0.0827 (17)	0.0620 (15)	0.0481 (15)	0.0335 (14)	0.0262 (13)	0.0240 (12)
C3	0.0601 (14)	0.0561 (14)	0.0562 (15)	0.0318 (12)	0.0255 (12)	0.0166 (12)
C4	0.0416 (11)	0.0386 (10)	0.0389 (12)	0.0140 (9)	0.0111 (9)	0.0087 (9)
C5	0.0622 (14)	0.0462 (12)	0.0421 (14)	0.0191 (11)	0.0171 (11)	0.0179 (10)

Geometric parameters (Å, º) top

S1—C4	1.735 (2)	N3—C5	1.156 (3)
S1—C2	1.801 (3)	C1—C2	1.486 (4)
O1—C3	1.392 (3)	C1—H1B	0.9700
O1—H1A	0.80 (3)	C1—H1C	0.9700
N1—C4	1.331 (3)	C2—H2B	0.9700
N1—C1	1.447 (3)	C2—H2C	0.9700
N1—C3	1.455 (3)	C3—H3A	0.9700
N2—C5	1.314 (3)	C3—H3B	0.9700
N2—C4	1.315 (3)

C4—S1—C2	92.28 (11)	S1—C2—H2B	110.0
C3—O1—H1A	111 (2)	C1—C2—H2C	110.0
C4—N1—C1	116.2 (2)	S1—C2—H2C	110.0
C4—N1—C3	122.77 (19)	H2B—C2—H2C	108.4
C1—N1—C3	120.8 (2)	O1—C3—N1	112.3 (2)
C5—N2—C4	118.1 (2)	O1—C3—H3A	109.1
N1—C1—C2	110.0 (2)	N1—C3—H3A	109.1
N1—C1—H1B	109.7	O1—C3—H3B	109.1
C2—C1—H1B	109.7	N1—C3—H3B	109.1
N1—C1—H1C	109.7	H3A—C3—H3B	107.9
C2—C1—H1C	109.7	N2—C4—N1	121.5 (2)
H1B—C1—H1C	108.2	N2—C4—S1	125.35 (17)
C1—C2—S1	108.30 (18)	N1—C4—S1	113.20 (17)
C1—C2—H2B	110.0	N3—C5—N2	174.2 (3)

C4—N1—C1—C2	1.7 (4)	C1—N1—C4—N2	177.4 (2)
C3—N1—C1—C2	176.5 (2)	C3—N1—C4—N2	2.8 (3)
N1—C1—C2—S1	−0.2 (3)	C1—N1—C4—S1	−2.5 (3)
C4—S1—C2—C1	−0.9 (2)	C3—N1—C4—S1	−177.14 (17)
C4—N1—C3—O1	95.2 (3)	C2—S1—C4—N2	−178.0 (2)
C1—N1—C3—O1	−79.2 (3)	C2—S1—C4—N1	1.95 (18)
C5—N2—C4—N1	179.5 (2)	C4—N2—C5—N3	−171 (3)
C5—N2—C4—S1	−0.6 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1A···N3ⁱ	0.80 (3)	2.04 (3)	2.839 (3)	174 (3)

Symmetry code: (i) −x, −y+1, −z+2.

Experimental details

Crystal data
Chemical formula	C₅H₇N₃OS
M_r	157.20
Crystal system, space group	Triclinic, P1
Temperature (K)	293
a, b, c (Å)	5.5321 (11), 8.1790 (16), 8.4978 (17)
α, β, γ (°)	101.56 (3), 100.39 (3), 105.47 (3)
V (Å³)	351.75 (16)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.39
Crystal size (mm)	0.22 × 0.17 × 0.13

Data collection
Diffractometer	Rigaku R-AXIS RAPID IP area-detector diffractometer
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995)
T_min, T_max	0.919, 0.951
No. of measured, independent and observed [I > 2σ(I)] reflections	2778, 1234, 1027
R_int	0.014
(sin θ/λ)_max (Å⁻¹)	0.594

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.032, 0.119, 1.19
No. of reflections	1234
No. of parameters	96
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.33, −0.25

Computer programs: RAPID-AUTO (Rigaku, 2004), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1A···N3ⁱ	0.80 (3)	2.04 (3)	2.839 (3)	174 (3)

Symmetry code: (i) −x, −y+1, −z+2.

References

Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19. CrossRef Web of Science Google Scholar
Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan. Google Scholar
Iwata, C., Watanabe, M., Okamoto, S., Fujimoto, M., Sakae, M., Katsurada, M. & Imanishi, T. (1988). Synthesis, 3, 261–262. Google Scholar
Rigaku (2004). RAPID-AUTO. Rigaku Corporation, Takyo, Japan. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Xie, B. (2008). Acta Cryst. E64, o1237. Web of Science CSD CrossRef IUCr Journals Google Scholar

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 65| Part 7| July 2009| Page o1645

doi:10.1107/S1600536809023095

Open

access