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Acta Crystallogr Sect E Struct Rep Online. 2009 November 1; 65(Pt 11): o2765.
Published online 2009 October 17. doi:  10.1107/S1600536809041737
PMCID: PMC2970977

2-Morpholino-4-oxo-4,5-dihydro­thio­phene-3-carbonitrile

Abstract

The title compound, C9H10N2O2S, was obtained from the treatment of ethyl 4-cyano-3-hydr­oxy-5-morpholinothio­phene-2-carboxyl­ate with concentrated HCl. The mean plane of the essentially planar dihydro­thio­phene ring is almost orthogonal to the mirror plane of the N-morpholine substituent, making a dihedral angle of 87.2 (2)°.

Related literature

For the structure of a similar compound with the morpholine substituent attached to dihydro­thio­phene ring, see: Moghaddam et al. (2005 [triangle]).

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Object name is e-65-o2765-scheme1.jpg

Experimental

Crystal data

  • C9H10N2O2S
  • M r = 210.25
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2765-efi1.jpg
  • a = 7.1931 (3) Å
  • b = 17.3275 (8) Å
  • c = 7.2793 (3) Å
  • β = 94.506 (2)°
  • V = 904.48 (7) Å3
  • Z = 4
  • Cu Kα radiation
  • μ = 2.98 mm−1
  • T = 100 K
  • 0.41 × 0.20 × 0.08 mm

Data collection

  • Bruker Kappa APEXII diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2001 [triangle]) T min = 0.765, T max = 0.919
  • 7337 measured reflections
  • 1607 independent reflections
  • 1531 reflections with I > 2σ(I)
  • R int = 0.027

Refinement

  • R[F 2 > 2σ(F 2)] = 0.026
  • wR(F 2) = 0.068
  • S = 1.08
  • 1607 reflections
  • 128 parameters
  • H-atom parameters constrained
  • Δρmax = 0.29 e Å−3
  • Δρmin = −0.20 e Å−3

Data collection: APEX2 (Bruker, 2007 [triangle]); cell refinement: SAINT (Bruker, 2007 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Supplementary Material

Crystal structure: contains datablocks pflj124, I. DOI: 10.1107/S1600536809041737/dn2498sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809041737/dn2498Isup2.hkl

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

supplementary crystallographic information

Comment

The title compound was obtained via the treatment of ethyl 4-cyano-3-hydroxy-5-morpholinothiophene-2-carboxylate with concentrated HCl, and its structural formula was confirmed by the present study (Fig. 1).

Dihydrothiophene ring C5/C6/C7/C8/S1 is planar within 0.02 Å. Its least squares plane is almost orthogonal to the mirror plane of the N-morpholine substituent passing through C5, N1 and O1 atoms: the corresponding dihedral angle being 92.8 (2)°. Similar conformation is observed in the related structure with morpholine substituent attached to dihydrothiophene ring (Moghaddam et al., 2005).

Experimental

Into a suspension of ethyl 4-cyano-3-hydroxy-5-morpholinothiophene-2-carboxylate (100 mg, 0.35 mmol) in MeOH (1.2 ml), was added concentrated HCl (0.2 ml) with stirring. The reaction mixture was heated in an oil bath at 60°C for 48 h to form a clear solution. The reaction solution was cooled to room temperature and the solvent was removed under reduced pressure. The resulting residue was neutralized with 2 N NaOH to pH 4. The precipitate was collected by filtration and rinsed with a solution of water/MeOH. The sample was dried under high vacuum to afford the desired compound as a white solid (52.1 mg, 58% yield). LC—MS (APCI, M+1) 211.2; 1H NMR (300 MHz, DMSO-d6) δ p.p.m. 3.87 (s, 3 H), 3.84 (dd, J=5.84, 2.07 Hz, 2 H), 3.68 - 3.79 (m, 5 H). The product was recrystallized from EtOAc/hexane/dichloromethane to yield single crystals suitable for X-ray diffraction studies.

Refinement

All H atoms were placed in geometrically calculated positions (C—H 0.99 Å) and included in the refinement in riding motion approximation. The Uiso(H) were set to 1.2Ueq of the carrying atom.

Figures

Fig. 1.
Molecular structure of the title compound, showing 50% probability displacement ellipsoids and atom numbering scheme. H atoms are drawn as circles with arbitrary small radius.

Crystal data

C9H10N2O2SF(000) = 440
Mr = 210.25Dx = 1.544 Mg m3
Monoclinic, P21/cCu Kα radiation, λ = 1.54178 Å
Hall symbol: -P 2ybcCell parameters from 2017 reflections
a = 7.1931 (3) Åθ = 8.0–49.4°
b = 17.3275 (8) ŵ = 2.98 mm1
c = 7.2793 (3) ÅT = 100 K
β = 94.506 (2)°Blade, colorless
V = 904.48 (7) Å30.41 × 0.20 × 0.08 mm
Z = 4

Data collection

Bruker Kappa APEXII diffractometer1607 independent reflections
Radiation source: fine-focus sealed tube1531 reflections with I > 2σ(I)
graphiteRint = 0.027
phi and ω scansθmax = 68.3°, θmin = 5.1°
Absorption correction: multi-scan (SADABS; Bruker, 2001)h = −7→8
Tmin = 0.765, Tmax = 0.919k = −20→20
7337 measured reflectionsl = −6→8

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.026H-atom parameters constrained
wR(F2) = 0.068w = 1/[σ2(Fo2) + (0.0333P)2 + 0.4P] where P = (Fo2 + 2Fc2)/3
S = 1.08(Δ/σ)max = 0.005
1607 reflectionsΔρmax = 0.29 e Å3
128 parametersΔρmin = −0.20 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0051 (4)

Special details

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 (Å2)

xyzUiso*/Ueq
S10.41531 (4)0.190051 (19)0.14477 (4)0.01446 (13)
O10.93155 (14)−0.01397 (6)0.25143 (14)0.0203 (2)
O20.60927 (14)0.39685 (6)0.22161 (14)0.0206 (2)
N21.03469 (17)0.30903 (7)0.41842 (18)0.0206 (3)
N10.72767 (15)0.12491 (7)0.28592 (16)0.0153 (3)
C30.7576 (2)−0.00224 (8)0.1488 (2)0.0202 (3)
H3A0.6948−0.05260.12610.024*
H3B0.77890.02100.02810.024*
C40.63342 (19)0.05034 (8)0.2519 (2)0.0186 (3)
H4A0.51330.05830.17830.022*
H4B0.60720.02630.37060.022*
C50.64590 (18)0.19201 (8)0.24689 (18)0.0127 (3)
C60.71300 (18)0.26741 (8)0.27408 (17)0.0132 (3)
C70.58227 (19)0.32720 (8)0.21546 (17)0.0143 (3)
C90.89130 (19)0.28941 (8)0.35321 (18)0.0147 (3)
C80.39555 (18)0.29364 (8)0.14293 (18)0.0163 (3)
H8A0.36220.31210.01590.020*
H8B0.29680.31010.22180.020*
C21.0259 (2)0.05782 (8)0.2777 (2)0.0204 (3)
H2A1.04900.07990.15620.025*
H2B1.14820.04910.34680.025*
C10.91428 (19)0.11467 (8)0.3821 (2)0.0191 (3)
H1A0.90190.09540.50860.023*
H1B0.97990.16490.39120.023*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.01039 (19)0.0182 (2)0.0144 (2)−0.00046 (11)−0.00152 (13)−0.00068 (11)
O10.0208 (5)0.0133 (5)0.0264 (5)0.0025 (4)−0.0004 (4)0.0007 (4)
O20.0198 (5)0.0151 (5)0.0270 (5)0.0026 (4)0.0030 (4)0.0025 (4)
N20.0156 (6)0.0184 (6)0.0273 (7)−0.0014 (5)−0.0015 (5)−0.0033 (5)
N10.0123 (5)0.0139 (6)0.0191 (6)−0.0009 (4)−0.0025 (5)−0.0008 (4)
C30.0230 (8)0.0154 (7)0.0216 (7)−0.0006 (5)−0.0021 (6)−0.0011 (5)
C40.0162 (7)0.0139 (7)0.0253 (7)−0.0039 (5)−0.0008 (6)−0.0010 (5)
C50.0111 (6)0.0169 (7)0.0102 (6)0.0006 (5)0.0018 (5)−0.0011 (5)
C60.0118 (6)0.0149 (7)0.0129 (6)0.0007 (5)0.0014 (5)−0.0003 (5)
C70.0142 (6)0.0174 (7)0.0118 (6)0.0011 (5)0.0040 (5)0.0008 (5)
C90.0167 (7)0.0116 (6)0.0161 (6)0.0015 (5)0.0036 (5)−0.0006 (5)
C80.0135 (7)0.0193 (7)0.0159 (7)0.0031 (5)−0.0001 (5)0.0011 (5)
C20.0158 (7)0.0160 (7)0.0293 (8)0.0006 (5)0.0008 (6)0.0049 (6)
C10.0147 (7)0.0145 (7)0.0267 (7)0.0004 (5)−0.0071 (6)0.0005 (5)

Geometric parameters (Å, °)

S1—C51.7639 (13)C4—H4B0.9900
S1—C81.8004 (14)C5—C61.4014 (18)
O1—C31.4204 (17)C6—C91.4163 (18)
O1—C21.4227 (17)C6—C71.4410 (18)
O2—C71.2227 (17)C7—C81.5197 (18)
N2—C91.1523 (19)C8—H8A0.9900
N1—C51.3238 (17)C8—H8B0.9900
N1—C41.4710 (17)C2—C11.513 (2)
N1—C11.4751 (17)C2—H2A0.9900
C3—C41.515 (2)C2—H2B0.9900
C3—H3A0.9900C1—H1A0.9900
C3—H3B0.9900C1—H1B0.9900
C4—H4A0.9900
C5—S1—C893.15 (6)O2—C7—C6126.92 (13)
C3—O1—C2109.68 (10)O2—C7—C8121.60 (12)
C5—N1—C4122.97 (11)C6—C7—C8111.48 (12)
C5—N1—C1125.44 (11)N2—C9—C6178.37 (15)
C4—N1—C1111.37 (11)C7—C8—S1108.17 (9)
O1—C3—C4110.79 (11)C7—C8—H8A110.1
O1—C3—H3A109.5S1—C8—H8A110.1
C4—C3—H3A109.5C7—C8—H8B110.1
O1—C3—H3B109.5S1—C8—H8B110.1
C4—C3—H3B109.5H8A—C8—H8B108.4
H3A—C3—H3B108.1O1—C2—C1111.75 (11)
N1—C4—C3109.24 (11)O1—C2—H2A109.3
N1—C4—H4A109.8C1—C2—H2A109.3
C3—C4—H4A109.8O1—C2—H2B109.3
N1—C4—H4B109.8C1—C2—H2B109.3
C3—C4—H4B109.8H2A—C2—H2B107.9
H4A—C4—H4B108.3N1—C1—C2109.81 (11)
N1—C5—C6130.26 (12)N1—C1—H1A109.7
N1—C5—S1117.43 (10)C2—C1—H1A109.7
C6—C5—S1112.30 (10)N1—C1—H1B109.7
C5—C6—C9126.81 (12)C2—C1—H1B109.7
C5—C6—C7114.77 (12)H1A—C1—H1B108.2
C9—C6—C7118.42 (12)

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: DN2498).

References

  • Bruker (2001). SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Bruker (2007). APEX2 and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Moghaddam, F. M., Boeini, H. Z., Bagheri, M., Ruëdi, P. & Linden, A. (2005). Sulfur Chem.26, 245–250.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography