organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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

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[Xie, B. (2008). Acta Cryst. E64, o1237.]). For the biological activity of thia­zolidine-containing compounds, see: Iwata et al. (1988[Iwata, C., Watanabe, M., Okamoto, S., Fujimoto, M., Sakae, M., Katsurada, M. & Imanishi, T. (1988). Synthesis, 3, 261-262.]). For bond-length data, see: Allen et al. (1987[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.]).

[Scheme 1]

Experimental

Crystal data
  • C5H7N3OS

  • Mr = 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[Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.919, Tmax = 0.951

  • 2778 measured reflections

  • 1234 independent reflections

  • 1027 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.33 e Å−3

  • Δρmin = −0.25 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Rigaku (2004). RAPID-AUTO. Rigaku Corporation, Takyo, Japan.]); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information


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.

Refinement top

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 Uiso(H) = 1.2 times Ueq(C).

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
[Figure 1] 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
C5H7N3OSZ = 2
Mr = 157.20F(000) = 164
Triclinic, P1Dx = 1.484 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 5.5321 (11) ÅCell parameters from 2501 reflections
b = 8.1790 (16) Åθ = 2.3–25.1°
c = 8.4978 (17) ŵ = 0.39 mm1
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 Anode1027 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.014
ω oscillation scansθmax = 25.0°, θmin = 3.2°
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
h = 66
Tmin = 0.919, Tmax = 0.951k = 99
2778 measured reflectionsl = 1010
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.032H 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 reflectionsΔρmax = 0.33 e Å3
96 parametersΔρmin = 0.25 e Å3
0 restraintsExtinction correction: SHELXTL (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.052 (16)
Crystal data top
C5H7N3OSγ = 105.47 (3)°
Mr = 157.20V = 351.75 (16) Å3
Triclinic, P1Z = 2
a = 5.5321 (11) ÅMo Kα radiation
b = 8.1790 (16) ŵ = 0.39 mm1
c = 8.4978 (17) ÅT = 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)
Tmin = 0.919, Tmax = 0.951Rint = 0.014
2778 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0320 restraints
wR(F2) = 0.119H atoms treated by a mixture of independent and constrained refinement
S = 1.19Δρmax = 0.33 e Å3
1234 reflectionsΔρmin = 0.25 e Å3
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
xyzUiso*/Ueq
S10.15141 (12)0.91511 (8)0.84635 (8)0.0509 (3)
O10.3210 (4)0.3944 (2)0.6397 (3)0.0640 (6)
N10.3875 (3)0.6968 (2)0.7503 (2)0.0450 (5)
N20.2714 (4)0.6719 (2)0.9942 (2)0.0490 (5)
N30.0736 (5)0.7702 (3)1.2185 (3)0.0640 (6)
C10.3729 (7)0.7839 (5)0.6182 (4)0.0724 (9)
H1B0.27830.69800.51380.087*
H1C0.54600.84000.60900.087*
C20.2400 (6)0.9180 (4)0.6529 (3)0.0592 (7)
H2B0.08660.89160.56420.071*
H2C0.35451.03350.66000.071*
C30.4959 (5)0.5525 (3)0.7414 (3)0.0529 (6)
H3A0.64950.58090.69930.063*
H3B0.54770.53890.85210.063*
C40.2782 (4)0.7467 (3)0.8711 (3)0.0395 (5)
C50.1620 (5)0.7289 (3)1.1096 (3)0.0482 (6)
H1A0.216 (6)0.353 (4)0.686 (4)0.080 (10)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0639 (4)0.0564 (4)0.0506 (4)0.0356 (3)0.0251 (3)0.0217 (3)
O10.0818 (13)0.0500 (10)0.0697 (13)0.0227 (9)0.0443 (11)0.0109 (9)
N10.0543 (11)0.0508 (10)0.0416 (11)0.0272 (9)0.0206 (9)0.0158 (8)
N20.0661 (12)0.0492 (11)0.0457 (12)0.0278 (9)0.0249 (9)0.0202 (9)
N30.0854 (16)0.0641 (13)0.0531 (14)0.0263 (12)0.0342 (12)0.0195 (11)
C10.101 (2)0.102 (2)0.0584 (17)0.0688 (19)0.0462 (16)0.0452 (16)
C20.0827 (17)0.0620 (15)0.0481 (15)0.0335 (14)0.0262 (13)0.0240 (12)
C30.0601 (14)0.0561 (14)0.0562 (15)0.0318 (12)0.0255 (12)0.0166 (12)
C40.0416 (11)0.0386 (10)0.0389 (12)0.0140 (9)0.0111 (9)0.0087 (9)
C50.0622 (14)0.0462 (12)0.0421 (14)0.0191 (11)0.0171 (11)0.0179 (10)
Geometric parameters (Å, º) top
S1—C41.735 (2)N3—C51.156 (3)
S1—C21.801 (3)C1—C21.486 (4)
O1—C31.392 (3)C1—H1B0.9700
O1—H1A0.80 (3)C1—H1C0.9700
N1—C41.331 (3)C2—H2B0.9700
N1—C11.447 (3)C2—H2C0.9700
N1—C31.455 (3)C3—H3A0.9700
N2—C51.314 (3)C3—H3B0.9700
N2—C41.315 (3)
C4—S1—C292.28 (11)S1—C2—H2B110.0
C3—O1—H1A111 (2)C1—C2—H2C110.0
C4—N1—C1116.2 (2)S1—C2—H2C110.0
C4—N1—C3122.77 (19)H2B—C2—H2C108.4
C1—N1—C3120.8 (2)O1—C3—N1112.3 (2)
C5—N2—C4118.1 (2)O1—C3—H3A109.1
N1—C1—C2110.0 (2)N1—C3—H3A109.1
N1—C1—H1B109.7O1—C3—H3B109.1
C2—C1—H1B109.7N1—C3—H3B109.1
N1—C1—H1C109.7H3A—C3—H3B107.9
C2—C1—H1C109.7N2—C4—N1121.5 (2)
H1B—C1—H1C108.2N2—C4—S1125.35 (17)
C1—C2—S1108.30 (18)N1—C4—S1113.20 (17)
C1—C2—H2B110.0N3—C5—N2174.2 (3)
C4—N1—C1—C21.7 (4)C1—N1—C4—N2177.4 (2)
C3—N1—C1—C2176.5 (2)C3—N1—C4—N22.8 (3)
N1—C1—C2—S10.2 (3)C1—N1—C4—S12.5 (3)
C4—S1—C2—C10.9 (2)C3—N1—C4—S1177.14 (17)
C4—N1—C3—O195.2 (3)C2—S1—C4—N2178.0 (2)
C1—N1—C3—O179.2 (3)C2—S1—C4—N11.95 (18)
C5—N2—C4—N1179.5 (2)C4—N2—C5—N3171 (3)
C5—N2—C4—S10.6 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···N3i0.80 (3)2.04 (3)2.839 (3)174 (3)
Symmetry code: (i) x, y+1, z+2.

Experimental details

Crystal data
Chemical formulaC5H7N3OS
Mr157.20
Crystal system, space groupTriclinic, 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)
V3)351.75 (16)
Z2
Radiation typeMo Kα
µ (mm1)0.39
Crystal size (mm)0.22 × 0.17 × 0.13
Data collection
DiffractometerRigaku R-AXIS RAPID IP area-detector
diffractometer
Absorption correctionMulti-scan
(ABSCOR; Higashi, 1995)
Tmin, Tmax0.919, 0.951
No. of measured, independent and
observed [I > 2σ(I)] reflections
2778, 1234, 1027
Rint0.014
(sin θ/λ)max1)0.594
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.032, 0.119, 1.19
No. of reflections1234
No. of parameters96
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.33, 0.25

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

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···N3i0.80 (3)2.04 (3)2.839 (3)174 (3)
Symmetry code: (i) x, y+1, z+2.
 

References

First citationAllen, 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
First citationHigashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.  Google Scholar
First citationIwata, C., Watanabe, M., Okamoto, S., Fujimoto, M., Sakae, M., Katsurada, M. & Imanishi, T. (1988). Synthesis, 3, 261–262.  Google Scholar
First citationRigaku (2004). RAPID-AUTO. Rigaku Corporation, Takyo, Japan.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationXie, B. (2008). Acta Cryst. E64, o1237.  Web of Science CSD CrossRef IUCr Journals Google Scholar

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