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Acta Crystallogr Sect E Struct Rep Online. 2009 June 1; 65(Pt 6): o1249.
Published online 2009 May 14. doi:  10.1107/S1600536809016742
PMCID: PMC2969634

Methyl 3-[3-(ethoxy­carbon­yl)thio­ureido]-1H-pyrazole-5-carboxyl­ate

Abstract

The title compound, C9H12N4O4S, was proven to be the product of the reaction of methyl 5-amino-1H-pyrazole-3-carboxyl­ate with ethyl isothio­cyanato­carbonate. All non-H atoms of the mol­ecule are planar, the mean deviation from the least squares plane being 0.048 Å. The intra­molecular N—H(...)O bond involving the NH-group, which links the thio­urea and pyrazole fragments, closes a six-membered pseudo-heterocyclic ring, and two more hydrogen bonds (N—H(...)O with the participation of the pyrazole NH group and N—H(...)S involving the second thio­urea NH group) link the mol­ecules into infinite chains running along [1An external file that holds a picture, illustration, etc.
Object name is e-65-o1249-efi1.jpg0].

Related literature

For the structures of similar N-pyrazole-substituted thio­urea derivatives, see: Pask et al. (2006 [triangle]); Wen et al. (2006 [triangle]).

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Object name is e-65-o1249-scheme1.jpg

Experimental

Crystal data

  • C9H12N4O4S
  • M r = 272.29
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1249-efi2.jpg
  • a = 8.0855 (8) Å
  • b = 9.0035 (8) Å
  • c = 9.5959 (9) Å
  • α = 64.510 (1)°
  • β = 82.294 (1)°
  • γ = 78.716 (1)°
  • V = 617.39 (10) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.28 mm−1
  • T = 208 K
  • 0.20 × 0.15 × 0.10 mm

Data collection

  • Siemens P4 diffractometer with APEX CCD detector
  • Absorption correction: multi-scan (SADABS; Bruker, 2001 [triangle]) T min = 0.947, T max = 0.973
  • 5852 measured reflections
  • 2653 independent reflections
  • 2255 reflections with I > 2σ(I)
  • R int = 0.044

Refinement

  • R[F 2 > 2σ(F 2)] = 0.040
  • wR(F 2) = 0.113
  • S = 1.04
  • 2653 reflections
  • 166 parameters
  • H-atom parameters constrained
  • Δρmax = 0.39 e Å−3
  • Δρmin = −0.28 e Å−3

Data collection: SMART (Bruker, 1997 [triangle]); cell refinement: SAINT (Bruker, 1997 [triangle]); data reduction: SAINT; program(s) used to solve structure: SIR2004 (Burla et al., 2005 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-32 (Farrugia, 1997 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809016742/dn2451sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809016742/dn2451Isup2.hkl

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

supplementary crystallographic information

Comment

The reaction of methyl 5-amino-1H-pyrazole-3-carboxylate with ethyl isothiocyanatocarbonate produces the pyrazole-thiourea deivative; its structure was established by the present X-ray study (Fig.1).

All non-H atoms of the molecule are planar (mean deviation from its least squares plane is 0.048 Å), in contrast to previously studied pyrazole-thiourea derivative (Wen et al., 2006), where the pyrazole fragment has a nitrile substituent in position 4 and pyrazole/thiourea fragments form dihedral angle of 46.2°. Another similar compound, where pyrazole has no substituents in position 4 (Pask et al., 2006), is also essentially planar, just like the title compound.

There are three NH-groups in the molecule which are responsible for the formation of three independent H-bonds in the crystal (Table 2). The intramolecular N2—H2···O2 bond closes the 6-membered pseudo-cycle, whereas two intermolecular H-bonds each produce typical centrosymmmetric pairing motive, and their combination thus gives rise to infinite chains running along the [1,-2,0]. direction in the crystal (Fig. 2).

Experimental

A suspension of methyl 5-amino-1H-pyrazole-3-carboxylate (2.0 g, 14.2 mmol) in 10 ml of ethyl acetate and 40 ml of benzene was cooled to 0°C and stirred. To this solution, ethyl isothiocyanatocarbonate (2.04 g, 15.6 mmol) in 10 ml benzene was added dropwise. The resulting reaction mixture was allowed to warm up to room temperature, and stirring was continued for 5 h. The reaction mixture was filtered, and washed with plenty of ether to afford the desired product (3.32 g, 12.2 mmol, 86.0% yield). 1H NMR (400 MHz, DMSO-d6) δ p.p.m.: 13.99 (br. s., 1 H), 12.12 (br. s., 1 H), 11.48 (br. s., 1 H), 7.51 (s, 1 H), 4.22 (q, J=7.07 Hz, 2 H), 3.85 (s, 3 H), 1.26 (t, J=7.07 Hz, 3 H).

Refinement

All H atoms were placed in geometrically calculated positions (N—H 0.87 Å, C—H 0.94 Å, 0.97 Å, 0.98 Å, for aromatic, methyl and methylene H atoms respectively) and included in the refinement in riding motion approximation. The Uiso(H) were set to 1.2Ueq of the carrying atom for aromatic, methylene, methyne and amine groups, and 1.5Ueq for methyl H atoms.

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.
Fig. 2.
Packing diagram for the title compound viewed approximately along the a axis; H-bonds are shown as dashed lines.

Crystal data

C9H12N4O4SZ = 2
Mr = 272.29F(000) = 284
Triclinic, P1Dx = 1.465 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 8.0855 (8) ÅCell parameters from 3767 reflections
b = 9.0035 (8) Åθ = 2.5–27.8°
c = 9.5959 (9) ŵ = 0.28 mm1
α = 64.510 (1)°T = 208 K
β = 82.294 (1)°Block, colorless
γ = 78.716 (1)°0.20 × 0.15 × 0.10 mm
V = 617.39 (10) Å3

Data collection

Siemens P4 diffractometer with APEX CCD2653 independent reflections
Radiation source: fine-focus sealed tube2255 reflections with I > 2σ(I)
graphiteRint = 0.044
[var phi] and ω scansθmax = 28.2°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2001)h = −5→10
Tmin = 0.947, Tmax = 0.973k = −11→11
5852 measured reflectionsl = −11→12

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.040H-atom parameters constrained
wR(F2) = 0.113w = 1/[σ2(Fo2) + (0.0521P)2 + 0.1805P] where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max = 0.001
2653 reflectionsΔρmax = 0.39 e Å3
166 parametersΔρmin = −0.28 e Å3
0 restraintsExtinction correction: SHELXL (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.064 (8)

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
C10.7861 (3)0.9454 (2)−0.0198 (2)0.0539 (6)
H1A0.66530.9725−0.03200.081*
H1B0.84461.0106−0.11560.081*
H1C0.81250.97060.06260.081*
C20.8414 (3)0.7653 (2)0.0194 (2)0.0451 (5)
H2A0.81350.7375−0.06190.054*
H2B0.96380.73660.03010.054*
C30.7832 (2)0.5090 (2)0.22047 (19)0.0319 (4)
C40.6784 (2)0.27556 (19)0.44802 (18)0.0285 (4)
C50.7965 (2)−0.00499 (19)0.46055 (19)0.0300 (4)
C60.7316 (2)−0.1229 (2)0.5968 (2)0.0310 (4)
H60.6562−0.10480.67340.037*
C70.8050 (2)−0.2725 (2)0.59165 (19)0.0312 (4)
C80.7909 (2)−0.4462 (2)0.6958 (2)0.0328 (4)
C90.6497 (3)−0.6292 (2)0.9141 (2)0.0435 (5)
H9A0.6341−0.68940.85500.065*
H9B0.5509−0.62670.98310.065*
H9C0.7486−0.68440.97410.065*
N10.69023 (19)0.44206 (16)0.35749 (16)0.0322 (3)
H10.63160.51270.39170.039*
N20.77543 (19)0.16936 (16)0.39615 (16)0.0327 (3)
H20.83400.21520.30990.039*
N30.9003 (2)−0.07384 (17)0.37579 (17)0.0360 (4)
N40.9033 (2)−0.23814 (17)0.46052 (17)0.0344 (3)
H40.9626−0.31410.43330.041*
O10.75193 (17)0.67399 (14)0.16595 (14)0.0374 (3)
O20.87813 (18)0.43041 (15)0.15826 (15)0.0425 (3)
O30.87755 (18)−0.56425 (14)0.67884 (15)0.0407 (3)
O40.67259 (17)−0.46002 (15)0.80911 (15)0.0397 (3)
S10.54880 (6)0.22717 (5)0.60563 (5)0.03395 (17)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0681 (15)0.0334 (10)0.0449 (11)−0.0077 (10)0.0106 (10)−0.0060 (8)
C20.0512 (12)0.0338 (9)0.0352 (9)−0.0029 (8)0.0133 (8)−0.0061 (8)
C30.0347 (9)0.0267 (8)0.0311 (8)0.0000 (7)0.0010 (7)−0.0119 (6)
C40.0312 (9)0.0247 (7)0.0300 (8)0.0008 (6)−0.0025 (7)−0.0137 (6)
C50.0340 (9)0.0240 (8)0.0333 (8)0.0005 (6)−0.0013 (7)−0.0154 (7)
C60.0343 (9)0.0257 (8)0.0346 (8)0.0005 (6)0.0007 (7)−0.0171 (7)
C70.0346 (9)0.0259 (8)0.0359 (9)−0.0010 (7)−0.0003 (7)−0.0174 (7)
C80.0356 (9)0.0295 (8)0.0373 (9)−0.0036 (7)0.0003 (7)−0.0189 (7)
C90.0499 (12)0.0310 (9)0.0460 (11)−0.0095 (8)0.0089 (9)−0.0147 (8)
N10.0393 (8)0.0234 (7)0.0306 (7)−0.0001 (6)0.0074 (6)−0.0127 (6)
N20.0405 (8)0.0234 (7)0.0313 (7)−0.0012 (6)0.0061 (6)−0.0124 (6)
N30.0436 (9)0.0251 (7)0.0383 (8)−0.0008 (6)0.0038 (7)−0.0160 (6)
N40.0403 (9)0.0256 (7)0.0396 (8)−0.0003 (6)0.0042 (7)−0.0195 (6)
O10.0432 (7)0.0254 (6)0.0341 (6)−0.0013 (5)0.0113 (5)−0.0091 (5)
O20.0514 (8)0.0321 (7)0.0377 (7)0.0001 (6)0.0138 (6)−0.0160 (6)
O30.0490 (8)0.0263 (6)0.0472 (7)−0.0015 (6)0.0073 (6)−0.0204 (6)
O40.0455 (8)0.0274 (6)0.0448 (7)−0.0050 (5)0.0098 (6)−0.0174 (5)
S10.0400 (3)0.0257 (2)0.0328 (2)−0.00173 (17)0.00760 (18)−0.01324 (18)

Geometric parameters (Å, °)

C1—C21.486 (3)C5—N21.401 (2)
C1—H1A0.9700C6—C71.380 (2)
C1—H1B0.9700C6—H60.9400
C1—H1C0.9700C7—N41.343 (2)
C2—O11.463 (2)C7—C81.466 (2)
C2—H2A0.9800C8—O31.214 (2)
C2—H2B0.9800C8—O41.329 (2)
C3—O21.214 (2)C9—O41.452 (2)
C3—O11.3278 (19)C9—H9A0.9700
C3—N11.374 (2)C9—H9B0.9700
C4—N21.338 (2)C9—H9C0.9700
C4—N11.387 (2)N1—H10.8700
C4—S11.6617 (16)N2—H20.8700
C5—N31.340 (2)N3—N41.344 (2)
C5—C61.397 (2)N4—H40.8700
C2—C1—H1A109.5N4—C7—C6107.60 (14)
C2—C1—H1B109.5N4—C7—C8119.72 (14)
H1A—C1—H1B109.5C6—C7—C8132.67 (16)
C2—C1—H1C109.5O3—C8—O4123.84 (16)
H1A—C1—H1C109.5O3—C8—C7123.32 (16)
H1B—C1—H1C109.5O4—C8—C7112.84 (14)
O1—C2—C1106.83 (15)O4—C9—H9A109.5
O1—C2—H2A110.4O4—C9—H9B109.5
C1—C2—H2A110.4H9A—C9—H9B109.5
O1—C2—H2B110.4O4—C9—H9C109.5
C1—C2—H2B110.4H9A—C9—H9C109.5
H2A—C2—H2B108.6H9B—C9—H9C109.5
O2—C3—O1125.25 (16)C3—N1—C4127.95 (13)
O2—C3—N1125.62 (15)C3—N1—H1116.0
O1—C3—N1109.13 (13)C4—N1—H1116.0
N2—C4—N1114.69 (14)C4—N2—C5129.41 (14)
N2—C4—S1126.73 (12)C4—N2—H2115.3
N1—C4—S1118.59 (11)C5—N2—H2115.3
N3—C5—C6112.89 (14)C5—N3—N4103.49 (14)
N3—C5—N2114.22 (15)C7—N4—N3112.76 (13)
C6—C5—N2132.89 (15)C7—N4—H4123.6
C7—C6—C5103.26 (14)N3—N4—H4123.6
C7—C6—H6128.4C3—O1—C2116.14 (14)
C5—C6—H6128.4C8—O4—C9115.46 (13)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···S1i0.872.513.347 (1)161
N2—H2···O20.871.922.657 (2)141
N4—H4···O3ii0.872.032.876 (2)164

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x+2, −y−1, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: DN2451).

References

  • Bruker (1997). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Bruker (2001). SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Polidori, G. & Spagna, R. (2005). J. Appl. Cryst.38, 381–388.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Farrugia, L. J. (1999). J. Appl. Cryst.32, 837–838.
  • Pask, C. M., Camm, K. D., Kilner, C. A. & Halcrow, M. A. (2006). Tetrahedron Lett. 2531–2534.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Wen, L.-R., Li, M., Zhou, J.-X. & Liu, P. (2006). Acta Cryst. E62, o940–o941.

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