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

Abstract

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,

• 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) ų

• 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[F ² > 2σ(F ²)] = 0.032

• wR(F ²) = 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

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.

Supplementary Material

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

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) .

supplementary crystallographic information

Comment

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.

Experimental

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.

Refinement

All H atoms were found on difference maps. The hydroxyl H atoms were refined freely, giving an O—H bond distance of 0.80 Å. The remaining H atoms were placed in calculated positions, with C—H = 0.97 Å with U_iso(H) = 1.2 times U_eq(C).

Figures

Fig. 1.

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

Crystal data

C5H7N3OS	Z = 2
Mr = 157.20	F(000) = 164
Triclinic, P1	Dx = 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

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

Refinement

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(Fo2) + (0.0703P)2 + 0.06P] where P = (Fo2 + 2Fc2)/3
S = 1.19	(Δ/σ)max < 0.001
1234 reflections	Δρmax = 0.33 e Å−3
96 parameters	Δρmin = −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)

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
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 (Ų)

	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, °)

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, °)

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 codes: (i) −x, −y+1, −z+2.