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Acta Cryst. (2008). E64, o1927    [ doi:10.1107/S1600536808028699 ]

Methyl 5-[N,N-bis(methoxycarbonylmethyl)amino]-4-cyano-2-methoxycarbonyl-3-thiopheneethanoate

Q. Wang, Z.-S. Li and B.-W. Sun

Abstract top

In the title compound, C16H18N2O8S, derived from ranelic acid, there is a highly substituted thiophene ring. The crystal structure involves intermolecular C-H...O and C-H...S hydrogen bonds.

Comment top

The title compound, (I), C16H18O8N2S, is an important intermediate in the synthesis of strontium ranelate, a medicine for the treatment of osteoporosis (Bonnelye et al., 2008; Fonseca, 2008). Strontium ranelate is composed of two stable strontium ions combined with the anion of organic ranelic acid. The ranelic acid is a carrier that makes the treatment palatable, and the strontium is the active component with regard to the bone. We report here the crystal structure of the title compound. The molecular structure of (I) is shown in Fig. 1 and geometric parameters are given in Table 1. In the crystal (Fig. 2 and Table 2), there are intermolecular C—H···O and C—H···S hydrogen bonds leading to a one-dimensional structure.

Related literature top

For related literature, see: Bonnelye et al. (2008); Fonseca (2008).

Experimental top

All chemicals used (reagent grade) were commercially available. Methyl 5-[bis(methoxycarbonylmethyl)amino]-4-cyano-3-(methoxycarbonyl)-2-thiophene- carboxylate (0.426 g, 0.1 mmol) was added to a solution containing ethanol (8 ml) and acetone (4 ml). The mixture was stirred at room temperature for 10 min and then filtered off. Colorless crystals suitable for X-ray analysis were obtained by slow evaporation at room temperature over several days.

Refinement top

All H atoms attached to C and N atom were fixed geometrically and treated as riding with C—H = 0.97 Å with Uiso(H) =1.2Ueq(C).

Computing details top

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick,2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title molecule, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level.
[Figure 2] Fig. 2. Crystal packing of the compound (I) viewed along the b axis. Hydrogen bonds are shown as dashed lines.
methyl 5-[N,N-bis(methoxycarbonylmethyl)amino]-4-cyano-2- methoxycarbonyl-3-thiophene-ethanoate top
Crystal data top
C16H18N2O8SZ = 2
Mr = 398.38F(000) = 416
Triclinic, P1Dx = 1.401 Mg m−3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 9.7164 (19) ÅCell parameters from 6733 reflections
b = 9.790 (2) Åθ = 3.3–27.3°
c = 10.170 (2) ŵ = 0.22 mm−1
α = 98.05 (3)°T = 293 K
β = 96.71 (3)°Prism, colorless
γ = 95.81 (3)°0.25 × 0.20 × 0.18 mm
V = 944.5 (3) Å3
Data collection top
Rigaku SCXmini
diffractometer		4313 independent reflections
Radiation source: fine-focus sealed tube3561 reflections with I > 2σ(I)
graphiteRint = 0.027
Detector resolution: 8.192 pixels mm-1θmax = 27.5°, θmin = 3.1°
ω scansh = −12→12
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)		k = −12→12
Tmin = 0.942, Tmax = 0.988l = −13→13
9976 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.048Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.130H atoms treated by a mixture of independent and constrained refinement
S = 1.03 w = 1/[σ2(Fo2) + (0.062P)2 + 0.411P]
where P = (Fo2 + 2Fc2)/3
4313 reflections(Δ/σ)max < 0.001
246 parametersΔρmax = 0.33 e Å−3
0 restraintsΔρmin = −0.38 e Å−3
Crystal data top
C16H18N2O8Sγ = 95.81 (3)°
Mr = 398.38V = 944.5 (3) Å3
Triclinic, P1Z = 2
a = 9.7164 (19) ÅMo Kα radiation
b = 9.790 (2) ŵ = 0.22 mm−1
c = 10.170 (2) ÅT = 293 K
α = 98.05 (3)°0.25 × 0.20 × 0.18 mm
β = 96.71 (3)°
Data collection top
Rigaku SCXmini
diffractometer		4313 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)		3561 reflections with I > 2σ(I)
Tmin = 0.942, Tmax = 0.988Rint = 0.027
9976 measured reflectionsθmax = 27.5°
Refinement top
R[F2 > 2σ(F2)] = 0.048H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.130Δρmax = 0.33 e Å−3
S = 1.03Δρmin = −0.38 e Å−3
4313 reflectionsAbsolute structure: ?
246 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

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) top
xyzUiso*/Ueq
C10.0925 (5)0.8277 (4)0.4871 (3)0.0967 (13)
H1A0.165 (3)0.894 (3)0.4933 (6)0.145*
H1B0.116 (3)0.7635 (17)0.5387 (14)0.145*
H1C0.018 (2)0.866 (3)0.5154 (12)0.145*
C20.0887 (2)0.8372 (2)0.2560 (2)0.0414 (5)
C30.03705 (19)0.7542 (2)0.11943 (19)0.0374 (4)
H3A0.06610.66200.11640.045*
H3B−0.06420.74410.10590.045*
C4−0.01502 (19)0.8243 (2)−0.1025 (2)0.0366 (4)
H4A0.02310.8874−0.15820.044*
H4B−0.09620.8606−0.07020.044*
C5−0.0589 (2)0.6829 (2)−0.1857 (2)0.0427 (5)
C6−0.2176 (5)0.5578 (4)−0.3673 (4)0.1086 (14)
H6A−0.28910.5740−0.43480.163*
H6B−0.25670.4957−0.31260.163*
H6C−0.14480.5171−0.40940.163*
C70.22416 (18)0.80692 (18)−0.00849 (18)0.0312 (4)
C80.30195 (18)0.86329 (19)−0.09923 (18)0.0321 (4)
C90.2567 (2)0.9617 (2)−0.18082 (19)0.0369 (4)
C100.43987 (18)0.82416 (19)−0.09451 (18)0.0335 (4)
C110.5374 (2)0.8694 (2)−0.18941 (19)0.0404 (4)
H11A0.54040.9690−0.18760.048*
H11B0.63070.8498−0.15920.048*
C120.4935 (2)0.7974 (2)−0.3310 (2)0.0446 (5)
C130.5241 (4)0.8027 (4)−0.5571 (3)0.0940 (11)
H13A0.57360.8606−0.60920.141*
H13B0.42570.7956−0.58640.141*
H13C0.55410.7119−0.56860.141*
C140.46807 (18)0.7442 (2)0.00257 (18)0.0335 (4)
C150.59750 (19)0.6869 (2)0.04245 (19)0.0360 (4)
C160.7100 (2)0.5700 (2)0.2060 (2)0.0501 (5)
H16A0.68910.52450.28020.075*
H16B0.78150.64660.23660.075*
H16C0.74180.50530.13960.075*
O10.0564 (2)0.76176 (18)0.34904 (16)0.0637 (5)
O20.1471 (2)0.95261 (18)0.27677 (18)0.0673 (5)
O3−0.0096 (2)0.57999 (18)−0.1647 (2)0.0719 (6)
O4−0.15997 (19)0.68911 (18)−0.28405 (17)0.0626 (5)
O50.4141 (3)0.6943 (2)−0.3638 (2)0.1020 (9)
O60.5525 (2)0.8633 (2)−0.41698 (17)0.0695 (5)
O70.70142 (14)0.69773 (18)−0.01103 (16)0.0520 (4)
O80.58547 (14)0.62078 (16)0.14789 (15)0.0438 (3)
N10.08891 (15)0.81812 (17)0.01103 (16)0.0346 (3)
N20.2253 (2)1.0438 (2)−0.2444 (2)0.0535 (5)
S0.32536 (5)0.71175 (5)0.08736 (5)0.03457 (14)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.151 (4)0.103 (3)0.0364 (14)0.029 (2)0.0078 (17)0.0058 (15)
C20.0371 (10)0.0491 (12)0.0399 (11)0.0130 (9)0.0055 (8)0.0071 (9)
C30.0266 (9)0.0471 (11)0.0394 (10)0.0020 (7)0.0078 (7)0.0087 (8)
C40.0280 (9)0.0392 (10)0.0447 (11)0.0078 (7)0.0016 (8)0.0136 (8)
C50.0412 (11)0.0444 (11)0.0418 (11)0.0083 (9)−0.0004 (8)0.0071 (9)
C60.132 (3)0.080 (2)0.088 (2)0.010 (2)−0.054 (2)−0.0192 (19)
C70.0275 (8)0.0346 (9)0.0308 (9)0.0026 (7)0.0019 (7)0.0052 (7)
C80.0301 (9)0.0364 (9)0.0297 (9)0.0015 (7)0.0031 (7)0.0069 (7)
C90.0335 (9)0.0429 (10)0.0348 (10)0.0016 (8)0.0064 (7)0.0084 (8)
C100.0292 (9)0.0388 (10)0.0312 (9)−0.0010 (7)0.0047 (7)0.0039 (8)
C110.0329 (10)0.0530 (12)0.0366 (10)−0.0014 (8)0.0081 (8)0.0128 (9)
C120.0494 (12)0.0491 (12)0.0391 (11)0.0046 (10)0.0171 (9)0.0112 (9)
C130.137 (3)0.106 (3)0.0417 (15)−0.002 (2)0.0369 (17)0.0125 (16)
C140.0259 (8)0.0432 (10)0.0318 (9)0.0027 (7)0.0055 (7)0.0068 (8)
C150.0280 (9)0.0429 (10)0.0358 (10)0.0015 (7)0.0030 (7)0.0045 (8)
C160.0396 (11)0.0547 (13)0.0573 (13)0.0102 (9)−0.0046 (10)0.0188 (11)
O10.0920 (13)0.0632 (11)0.0376 (8)0.0077 (9)0.0124 (8)0.0119 (8)
O20.0858 (13)0.0538 (10)0.0547 (10)−0.0060 (9)−0.0015 (9)0.0011 (8)
O30.0808 (13)0.0454 (9)0.0806 (13)0.0218 (9)−0.0235 (10)−0.0024 (9)
O40.0680 (11)0.0608 (10)0.0513 (10)0.0112 (8)−0.0206 (8)0.0029 (8)
O50.161 (2)0.0805 (14)0.0505 (11)−0.0555 (15)0.0369 (13)−0.0065 (10)
O60.0858 (13)0.0810 (12)0.0413 (9)−0.0148 (10)0.0204 (9)0.0163 (9)
O70.0305 (7)0.0792 (11)0.0519 (9)0.0127 (7)0.0118 (6)0.0202 (8)
O80.0322 (7)0.0563 (9)0.0478 (8)0.0104 (6)0.0060 (6)0.0207 (7)
N10.0255 (7)0.0430 (9)0.0366 (8)0.0047 (6)0.0049 (6)0.0094 (7)
N20.0579 (12)0.0532 (11)0.0536 (11)0.0069 (9)0.0061 (9)0.0237 (9)
S0.0279 (2)0.0437 (3)0.0358 (3)0.00654 (18)0.00741 (17)0.0147 (2)
Geometric parameters (Å, °) top
C1—O11.448 (3)C8—C91.427 (3)
C1—H1A0.9033C8—C101.428 (3)
C1—H1B0.9033C9—N21.143 (3)
C1—H1C0.9033C10—C141.363 (3)
C2—O21.191 (3)C10—C111.508 (3)
C2—O11.325 (3)C11—C121.504 (3)
C2—C31.510 (3)C11—H11A0.9700
C3—N11.456 (2)C11—H11B0.9700
C3—H3A0.9700C12—O51.189 (3)
C3—H3B0.9700C12—O61.308 (3)
C4—N11.455 (2)C13—O61.448 (3)
C4—C51.511 (3)C13—H13A0.9600
C4—H4A0.9700C13—H13B0.9600
C4—H4B0.9700C13—H13C0.9600
C5—O31.193 (3)C14—C151.466 (3)
C5—O41.330 (2)C14—S1.7420 (18)
C6—O41.457 (3)C15—O71.204 (2)
C6—H6A0.9600C15—O81.338 (2)
C6—H6B0.9600C16—O81.448 (2)
C6—H6C0.9600C16—H16A0.9600
C7—N11.365 (2)C16—H16B0.9600
C7—C81.396 (2)C16—H16C0.9600
C7—S1.7323 (19)
O1—C1—H1A109.5C14—C10—C11126.48 (17)
O1—C1—H1B109.5C8—C10—C11121.39 (17)
H1A—C1—H1B109.5C12—C11—C10112.45 (16)
O1—C1—H1C109.5C12—C11—H11A109.1
H1A—C1—H1C109.5C10—C11—H11A109.1
H1B—C1—H1C109.5C12—C11—H11B109.1
O2—C2—O1125.5 (2)C10—C11—H11B109.1
O2—C2—C3125.5 (2)H11A—C11—H11B107.8
O1—C2—C3108.99 (18)O5—C12—O6122.9 (2)
N1—C3—C2112.93 (16)O5—C12—C11125.5 (2)
N1—C3—H3A109.0O6—C12—C11111.64 (19)
C2—C3—H3A109.0O6—C13—H13A109.5
N1—C3—H3B109.0O6—C13—H13B109.5
C2—C3—H3B109.0H13A—C13—H13B109.5
H3A—C3—H3B107.8O6—C13—H13C109.5
N1—C4—C5111.64 (16)H13A—C13—H13C109.5
N1—C4—H4A109.3H13B—C13—H13C109.5
C5—C4—H4A109.3C10—C14—C15129.21 (17)
N1—C4—H4B109.3C10—C14—S112.01 (14)
C5—C4—H4B109.3C15—C14—S118.78 (14)
H4A—C4—H4B108.0O7—C15—O8124.03 (18)
O3—C5—O4125.0 (2)O7—C15—C14125.19 (18)
O3—C5—C4124.21 (19)O8—C15—C14110.78 (16)
O4—C5—C4110.76 (17)O8—C16—H16A109.5
O4—C6—H6A109.5O8—C16—H16B109.5
O4—C6—H6B109.5H16A—C16—H16B109.5
H6A—C6—H6B109.5O8—C16—H16C109.5
O4—C6—H6C109.5H16A—C16—H16C109.5
H6A—C6—H6C109.5H16B—C16—H16C109.5
H6B—C6—H6C109.5C2—O1—C1116.7 (2)
N1—C7—C8129.48 (17)C5—O4—C6116.3 (2)
N1—C7—S120.44 (14)C12—O6—C13117.7 (2)
C8—C7—S110.07 (13)C15—O8—C16116.74 (16)
C7—C8—C9124.59 (17)C7—N1—C4119.77 (16)
C7—C8—C10113.62 (16)C7—N1—C3117.45 (15)
C9—C8—C10121.51 (16)C4—N1—C3115.49 (15)
N2—C9—C8177.3 (2)C7—S—C1492.11 (9)
C14—C10—C8112.12 (16)
O2—C2—C3—N111.3 (3)S—C14—C15—O7177.27 (17)
O1—C2—C3—N1−169.76 (17)C10—C14—C15—O8176.21 (19)
N1—C4—C5—O3−3.4 (3)S—C14—C15—O8−3.1 (2)
N1—C4—C5—O4176.17 (17)O2—C2—O1—C11.7 (4)
N1—C7—C8—C98.5 (3)C3—C2—O1—C1−177.2 (2)
S—C7—C8—C9−171.41 (15)O3—C5—O4—C63.0 (4)
N1—C7—C8—C10−177.50 (17)C4—C5—O4—C6−176.6 (3)
S—C7—C8—C102.6 (2)O5—C12—O6—C13−3.2 (4)
C7—C8—C9—N2129 (5)C11—C12—O6—C13177.7 (2)
C10—C8—C9—N2−45 (5)O7—C15—O8—C165.2 (3)
C7—C8—C10—C14−2.7 (2)C14—C15—O8—C16−174.41 (17)
C9—C8—C10—C14171.57 (17)C8—C7—N1—C434.7 (3)
C7—C8—C10—C11177.14 (16)S—C7—N1—C4−145.47 (15)
C9—C8—C10—C11−8.6 (3)C8—C7—N1—C3−176.48 (18)
C14—C10—C11—C12109.2 (2)S—C7—N1—C33.4 (2)
C8—C10—C11—C12−70.6 (2)C5—C4—N1—C776.6 (2)
C10—C11—C12—O5−17.2 (4)C5—C4—N1—C3−72.8 (2)
C10—C11—C12—O6161.94 (19)C2—C3—N1—C776.1 (2)
C8—C10—C14—C15−177.92 (18)C2—C3—N1—C4−133.71 (17)
C11—C10—C14—C152.3 (3)N1—C7—S—C14178.60 (15)
C8—C10—C14—S1.4 (2)C8—C7—S—C14−1.50 (14)
C11—C10—C14—S−178.35 (15)C10—C14—S—C70.03 (15)
C10—C14—C15—O7−3.4 (3)C15—C14—S—C7179.46 (15)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
C3—H3A···O3i0.972.513.355 (3)146.
C16—H16A···O5ii0.962.573.421 (3)148.
C16—H16C···Sii0.962.873.727 (3)149.
Symmetry codes: (i) −x, −y+1, −z; (ii) −x+1, −y+1, −z.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
C3—H3A···O3i0.972.513.355 (3)146.
C16—H16A···O5ii0.962.573.421 (3)148.
C16—H16C···Sii0.962.873.727 (3)149.
Symmetry codes: (i) −x, −y+1, −z; (ii) −x+1, −y+1, −z.
references
References top

Bonnelye, E., Chabadel, A., Saltel, F. & Jurdic, P. (2008). Bone, 42, 129–138.

Fonseca, J. E. (2008). Rheumatology, 47, iv17–iv19.

Rigaku. (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.