organic compounds
Ethyl 2-amino-4,5-dimethylthiophene-3-carboxylate
aMedicinal, Aromatic and Poisonous Plants Research Center (MAPPRC), College of Pharmacy, King Saud University, PO Box 2457, Riyadh 11451, Saudi Arabia, bDepartment of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, PO Box 2457, Riyadh 11451, Saudi Arabia, and cX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: hkfun@usm.my
In the title compound, C9H13NO2S, the mean planes of thiophene ring [maximum deviation = 0.0042 (10) Å] and ethoxycarbonyl group [0.0242 (15) Å] are almost coplanar [dihedral angle between them = 0.68 (11)°]. The H atoms of the two methyl groups attached to the thiophene ring are each disordered over two orientations with site-occupancy ratios of 0.77 (4):0.23 (4) and 0.84 (4):0.16 (4). An intramolecular N—H⋯O hydrogen bond generates an S(6) ring motif. In the crystal, molecules are linked by N—H⋯O hydrogen bonds into an infinite wave-like chain running parallel to the b-axis direction. The also features C—H⋯π interactions.
Related literature
For the synthesis, see: Gewald (1965). For background to biologically active compounds prepared from the title compound, see: Alqasoumi et al. (2009); Ghorab et al. (2006, 2012). For hydrogen-bond motifs, see: Bernstein et al. (1995).
Experimental
Crystal data
|
Refinement
|
Data collection: APEX2 (Bruker, 2009); cell SAINT (Bruker, 2009); data reduction: SAINT; 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 and PLATON (Spek, 2009).
Supporting information
https://doi.org/10.1107/S1600536812026268/hb6845sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812026268/hb6845Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S1600536812026268/hb6845Isup3.cml
Ethyl 2-amino-4,5-dimethylthiophene-3-carboxylate was prepared according to the reported method (Gewald, 1965). The obtained solid was recrystallized from ethanol to give the title compound. Brown plates were obtained by slow evaporation from ethanol solution at room temperature.
The atoms H1N1 and H2N1 were located in a difference fourier map and refined freely [N—H = 0.88 (3) and 0.87 (2) Å]. The major parts of disordered H atoms attached to atoms C5 and C6 [(H5A, H5B, H5C) and (H6A, H6B, H6C)] were positioned geometrically, whereas the corresponding minor parts, (H5D, H5E, H5F) and (H6D, H6E, H6F) were located in a difference fourier map. A rotating group model (AFIX 137) was used for both major and minor parts of disordered methyl groups and refined using a riding model with Uiso(H) = 1.5Ueq(C) [C—H distance = 0.96 Å]. The refined site-occupancy ratios are (H5A, H5B, H5C):(H5D, H5E, H5F) = 0.77 (4):0.23 (4) and (H6A, H6B, H6C):(H6D, H6E, H6F) = 0.84 (4):0.16 (4). The remaining H atoms were positioned geometrically [C—H = 0.96 and 0.97 Å] and refined with Uiso(H) = 1.2 or 1.5Ueq(C). A rotating group model was also applied to the other methyl group in the final refinement.
Ethyl 2-amino-4,5-dimethylthiophene-3-carboxylate (Gewald, 1965) is useful in the synthesis of
especially thienopyrimidine derivatives (Alqasoumi et al., 2009), some of which possess biological activities (Ghorab et al., 2006). In the light of this, and as a continuation of our efforts towards synthesizing biologically active (Ghorab et al., 2012), the title compound was prepared and its is now reported.The molecular structure of the title compound is shown in Fig. 1. The mean plane of thiophene ring [S1/C1–C4; maximum deviation = 0.0042 (10) Å at atom C4] is almost coplanar with the mean plane of ethoxycarbonyl group [O1/O2/C7–C9; maximum deviation = 0.0242 (15) Å at atom C8] as indicated by the dihedral angle of 0.68 (11)°. The H atoms attached to atoms C5 and C6 are each disordered over two orientations with site-occupancy ratios of 0.77 (4):0.23 (4) and 0.84 (4):0.16 (4), respectively. An intramolecular N1—H1N1···O2 hydrogen bond generates an S(6) ring motif (Bernstein et al., 1995) in the molecule.
In the crystal (Fig. 2), molecules are linked by N1—H2N1···O2 hydrogen bond into an infinite wave-like chain, propagating along the b axis. The crystal packing also features C—H···π interactions (Table 1), involving Cg1 which is the centroid of S1/C1–C4 ring.
For the synthesis, see: Gewald (1965). For background to biologically active compounds prepared from the title compound, see: Alqasoumi et al. (2009); Ghorab et al. (2006, 2012). For hydrogen-bond motifs, see: Bernstein et al. (1995).
Data collection: APEX2 (Bruker, 2009); cell
SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); 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) and PLATON (Spek, 2009).C9H13NO2S | F(000) = 424 |
Mr = 199.26 | Dx = 1.304 Mg m−3 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54178 Å |
Hall symbol: -P 2ybc | Cell parameters from 1386 reflections |
a = 7.9487 (2) Å | θ = 3.4–70.2° |
b = 9.8939 (3) Å | µ = 2.59 mm−1 |
c = 13.4348 (4) Å | T = 296 K |
β = 106.143 (2)° | Plate, brown |
V = 1014.90 (5) Å3 | 0.92 × 0.26 × 0.08 mm |
Z = 4 |
Bruker SMART APEXII CCD diffractometer | 1671 independent reflections |
Radiation source: fine-focus sealed tube | 1504 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.029 |
φ and ω scans | θmax = 65.0°, θmin = 5.6° |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | h = −6→8 |
Tmin = 0.199, Tmax = 0.820 | k = −11→11 |
6429 measured reflections | l = −15→15 |
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)] = 0.037 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.104 | w = 1/[σ2(Fo2) + (0.0573P)2 + 0.1221P] where P = (Fo2 + 2Fc2)/3 |
S = 1.07 | (Δ/σ)max = 0.001 |
1671 reflections | Δρmax = 0.19 e Å−3 |
132 parameters | Δρmin = −0.17 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: 0.0041 (9) |
C9H13NO2S | V = 1014.90 (5) Å3 |
Mr = 199.26 | Z = 4 |
Monoclinic, P21/c | Cu Kα radiation |
a = 7.9487 (2) Å | µ = 2.59 mm−1 |
b = 9.8939 (3) Å | T = 296 K |
c = 13.4348 (4) Å | 0.92 × 0.26 × 0.08 mm |
β = 106.143 (2)° |
Bruker SMART APEXII CCD diffractometer | 1671 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | 1504 reflections with I > 2σ(I) |
Tmin = 0.199, Tmax = 0.820 | Rint = 0.029 |
6429 measured reflections |
R[F2 > 2σ(F2)] = 0.037 | 0 restraints |
wR(F2) = 0.104 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.07 | Δρmax = 0.19 e Å−3 |
1671 reflections | Δρmin = −0.17 e Å−3 |
132 parameters |
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. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
S1 | 0.19746 (6) | 0.19752 (4) | 0.58473 (4) | 0.0611 (2) | |
O1 | 0.31318 (16) | 0.65860 (11) | 0.49116 (9) | 0.0545 (3) | |
O2 | 0.44541 (19) | 0.61171 (12) | 0.65701 (9) | 0.0667 (4) | |
N1 | 0.3976 (3) | 0.35938 (18) | 0.72936 (12) | 0.0726 (5) | |
C1 | 0.3045 (2) | 0.34698 (16) | 0.62875 (12) | 0.0520 (4) | |
C2 | 0.2743 (2) | 0.44243 (15) | 0.55082 (11) | 0.0458 (4) | |
C3 | 0.1625 (2) | 0.39154 (16) | 0.45331 (12) | 0.0481 (4) | |
C4 | 0.1130 (2) | 0.26238 (18) | 0.46019 (14) | 0.0554 (4) | |
C5 | 0.0030 (3) | 0.1727 (2) | 0.37724 (19) | 0.0763 (6) | |
H5A | 0.0682 | 0.1482 | 0.3296 | 0.114* | 0.77 (4) |
H5B | −0.1014 | 0.2200 | 0.3408 | 0.114* | 0.77 (4) |
H5C | −0.0282 | 0.0926 | 0.4083 | 0.114* | 0.77 (4) |
H5D | −0.0262 | 0.2197 | 0.3122 | 0.114* | 0.23 (4) |
H5E | −0.1025 | 0.1489 | 0.3945 | 0.114* | 0.23 (4) |
H5F | 0.0673 | 0.0922 | 0.3720 | 0.114* | 0.23 (4) |
C6 | 0.1078 (2) | 0.46993 (19) | 0.35388 (13) | 0.0622 (5) | |
H6A | 0.0388 | 0.4131 | 0.2999 | 0.093* | 0.84 (4) |
H6B | 0.2100 | 0.5001 | 0.3355 | 0.093* | 0.84 (4) |
H6C | 0.0396 | 0.5468 | 0.3627 | 0.093* | 0.84 (4) |
H6D | −0.0103 | 0.4465 | 0.3171 | 0.093* | 0.16 (4) |
H6E | 0.1843 | 0.4485 | 0.3120 | 0.093* | 0.16 (4) |
H6F | 0.1145 | 0.5650 | 0.3689 | 0.093* | 0.16 (4) |
C7 | 0.3521 (2) | 0.57551 (15) | 0.57265 (11) | 0.0469 (4) | |
C8 | 0.3871 (3) | 0.79279 (16) | 0.50551 (15) | 0.0568 (4) | |
H8A | 0.5139 | 0.7884 | 0.5241 | 0.068* | |
H8B | 0.3524 | 0.8395 | 0.5602 | 0.068* | |
C9 | 0.3179 (3) | 0.8652 (2) | 0.40444 (17) | 0.0718 (6) | |
H9A | 0.3617 | 0.9561 | 0.4109 | 0.108* | |
H9B | 0.1923 | 0.8668 | 0.3862 | 0.108* | |
H9C | 0.3554 | 0.8190 | 0.3515 | 0.108* | |
H1N1 | 0.453 (3) | 0.438 (3) | 0.7431 (19) | 0.084 (7)* | |
H2N1 | 0.435 (3) | 0.291 (2) | 0.7699 (19) | 0.068 (6)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0783 (4) | 0.0381 (3) | 0.0662 (3) | −0.00222 (17) | 0.0189 (2) | 0.00472 (17) |
O1 | 0.0677 (7) | 0.0409 (6) | 0.0480 (6) | −0.0061 (5) | 0.0046 (5) | 0.0053 (5) |
O2 | 0.0971 (10) | 0.0438 (6) | 0.0460 (7) | −0.0060 (6) | −0.0019 (6) | −0.0041 (5) |
N1 | 0.1166 (14) | 0.0449 (9) | 0.0439 (8) | 0.0066 (9) | 0.0018 (8) | 0.0056 (7) |
C1 | 0.0693 (10) | 0.0379 (8) | 0.0470 (9) | 0.0063 (7) | 0.0132 (7) | 0.0005 (6) |
C2 | 0.0556 (9) | 0.0371 (8) | 0.0422 (8) | 0.0051 (6) | 0.0094 (6) | 0.0001 (6) |
C3 | 0.0503 (9) | 0.0433 (8) | 0.0470 (8) | 0.0018 (6) | 0.0075 (6) | −0.0021 (6) |
C4 | 0.0558 (10) | 0.0467 (9) | 0.0603 (10) | −0.0014 (7) | 0.0106 (7) | −0.0046 (7) |
C5 | 0.0745 (13) | 0.0581 (11) | 0.0847 (15) | −0.0130 (9) | 0.0031 (10) | −0.0155 (10) |
C6 | 0.0696 (11) | 0.0604 (11) | 0.0455 (9) | −0.0006 (8) | −0.0024 (7) | 0.0013 (7) |
C7 | 0.0578 (9) | 0.0382 (8) | 0.0414 (8) | 0.0048 (6) | 0.0081 (6) | 0.0001 (6) |
C8 | 0.0671 (11) | 0.0406 (9) | 0.0592 (10) | −0.0047 (7) | 0.0121 (8) | 0.0038 (7) |
C9 | 0.0820 (14) | 0.0516 (11) | 0.0755 (13) | −0.0027 (9) | 0.0114 (10) | 0.0196 (9) |
S1—C1 | 1.7264 (17) | C5—H5C | 0.9600 |
S1—C4 | 1.7429 (18) | C5—H5D | 0.9600 |
O1—C7 | 1.3348 (19) | C5—H5E | 0.9600 |
O1—C8 | 1.4429 (19) | C5—H5F | 0.9600 |
O2—C7 | 1.2228 (19) | C6—H6A | 0.9600 |
N1—C1 | 1.354 (2) | C6—H6B | 0.9600 |
N1—H1N1 | 0.88 (3) | C6—H6C | 0.9600 |
N1—H2N1 | 0.87 (2) | C6—H6D | 0.9600 |
C1—C2 | 1.381 (2) | C6—H6E | 0.9600 |
C2—C7 | 1.450 (2) | C6—H6F | 0.9600 |
C2—C3 | 1.453 (2) | C8—C9 | 1.498 (3) |
C3—C4 | 1.348 (2) | C8—H8A | 0.9700 |
C3—C6 | 1.501 (2) | C8—H8B | 0.9700 |
C4—C5 | 1.501 (3) | C9—H9A | 0.9600 |
C5—H5A | 0.9600 | C9—H9B | 0.9600 |
C5—H5B | 0.9600 | C9—H9C | 0.9600 |
C1—S1—C4 | 92.01 (8) | H5E—C5—H5F | 109.5 |
C7—O1—C8 | 117.66 (13) | C3—C6—H6A | 109.5 |
C1—N1—H1N1 | 112.9 (16) | C3—C6—H6B | 109.5 |
C1—N1—H2N1 | 123.7 (15) | C3—C6—H6C | 109.5 |
H1N1—N1—H2N1 | 119 (2) | C3—C6—H6D | 109.5 |
N1—C1—C2 | 128.80 (17) | C3—C6—H6E | 109.5 |
N1—C1—S1 | 120.01 (14) | H6D—C6—H6E | 109.5 |
C2—C1—S1 | 111.16 (12) | C3—C6—H6F | 109.5 |
C1—C2—C7 | 119.57 (14) | H6D—C6—H6F | 109.5 |
C1—C2—C3 | 112.36 (14) | H6E—C6—H6F | 109.5 |
C7—C2—C3 | 128.07 (13) | O2—C7—O1 | 121.49 (14) |
C4—C3—C2 | 112.56 (14) | O2—C7—C2 | 124.63 (14) |
C4—C3—C6 | 122.22 (15) | O1—C7—C2 | 113.88 (13) |
C2—C3—C6 | 125.21 (15) | O1—C8—C9 | 106.59 (15) |
C3—C4—C5 | 129.10 (18) | O1—C8—H8A | 110.4 |
C3—C4—S1 | 111.91 (12) | C9—C8—H8A | 110.4 |
C5—C4—S1 | 118.99 (15) | O1—C8—H8B | 110.4 |
C4—C5—H5A | 109.5 | C9—C8—H8B | 110.4 |
C4—C5—H5B | 109.5 | H8A—C8—H8B | 108.6 |
C4—C5—H5C | 109.5 | C8—C9—H9A | 109.5 |
C4—C5—H5D | 109.5 | C8—C9—H9B | 109.5 |
C4—C5—H5E | 109.5 | H9A—C9—H9B | 109.5 |
H5D—C5—H5E | 109.5 | C8—C9—H9C | 109.5 |
C4—C5—H5F | 109.5 | H9A—C9—H9C | 109.5 |
H5D—C5—H5F | 109.5 | H9B—C9—H9C | 109.5 |
C4—S1—C1—N1 | 178.55 (17) | C2—C3—C4—S1 | 0.56 (19) |
C4—S1—C1—C2 | 0.60 (14) | C6—C3—C4—S1 | 179.60 (14) |
N1—C1—C2—C7 | 1.8 (3) | C1—S1—C4—C3 | −0.67 (15) |
S1—C1—C2—C7 | 179.54 (12) | C1—S1—C4—C5 | 178.19 (17) |
N1—C1—C2—C3 | −178.12 (19) | C8—O1—C7—O2 | 0.8 (2) |
S1—C1—C2—C3 | −0.40 (18) | C8—O1—C7—C2 | −179.18 (15) |
C1—C2—C3—C4 | −0.1 (2) | C1—C2—C7—O2 | 0.0 (3) |
C7—C2—C3—C4 | 179.95 (16) | C3—C2—C7—O2 | 179.97 (16) |
C1—C2—C3—C6 | −179.12 (16) | C1—C2—C7—O1 | −179.94 (14) |
C7—C2—C3—C6 | 0.9 (3) | C3—C2—C7—O1 | 0.0 (2) |
C2—C3—C4—C5 | −178.16 (19) | C7—O1—C8—C9 | −177.97 (15) |
C6—C3—C4—C5 | 0.9 (3) |
Cg1 is the centroid of S1/C1–C4 ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N1···O2 | 0.89 (3) | 2.06 (3) | 2.744 (2) | 133 (2) |
N1—H2N1···O2i | 0.87 (2) | 2.12 (2) | 2.972 (2) | 167 (2) |
C8—H8A···Cg1ii | 0.97 | 2.78 | 3.600 (2) | 142 |
Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) −x+1, −y+1, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C9H13NO2S |
Mr | 199.26 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 296 |
a, b, c (Å) | 7.9487 (2), 9.8939 (3), 13.4348 (4) |
β (°) | 106.143 (2) |
V (Å3) | 1014.90 (5) |
Z | 4 |
Radiation type | Cu Kα |
µ (mm−1) | 2.59 |
Crystal size (mm) | 0.92 × 0.26 × 0.08 |
Data collection | |
Diffractometer | Bruker SMART APEXII CCD |
Absorption correction | Multi-scan (SADABS; Bruker, 2009) |
Tmin, Tmax | 0.199, 0.820 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6429, 1671, 1504 |
Rint | 0.029 |
(sin θ/λ)max (Å−1) | 0.588 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.037, 0.104, 1.07 |
No. of reflections | 1671 |
No. of parameters | 132 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.19, −0.17 |
Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
Cg1 is the centroid of S1/C1–C4 ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N1···O2 | 0.89 (3) | 2.06 (3) | 2.744 (2) | 133 (2) |
N1—H2N1···O2i | 0.87 (2) | 2.12 (2) | 2.972 (2) | 167 (2) |
C8—H8A···Cg1ii | 0.97 | 2.78 | 3.600 (2) | 142 |
Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) −x+1, −y+1, −z+1. |
Footnotes
‡Thomson Reuters ResearcherID: A-3561-2009.
Acknowledgements
The authors are grateful for the sponsorship of the Research Center, College of Pharmacy, and the Deanship of Scientific Research, King Saud University, Riyadh, Saudi Arabia. HKF and TSC thank Universiti Sains Malaysia (USM) for the Research University Grant (1001/PFIZIK/811160). TSC also thanks the Malaysian Government and USM for the award of a research fellowship.
References
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Ethyl 2-amino-4,5-dimethylthiophene-3-carboxylate (Gewald, 1965) is useful in the synthesis of heterocyclic compounds, especially thienopyrimidine derivatives (Alqasoumi et al., 2009), some of which possess biological activities (Ghorab et al., 2006). In the light of this, and as a continuation of our efforts towards synthesizing biologically active heterocyclic compounds (Ghorab et al., 2012), the title compound was prepared and its crystal structure is now reported.
The molecular structure of the title compound is shown in Fig. 1. The mean plane of thiophene ring [S1/C1–C4; maximum deviation = 0.0042 (10) Å at atom C4] is almost coplanar with the mean plane of ethoxycarbonyl group [O1/O2/C7–C9; maximum deviation = 0.0242 (15) Å at atom C8] as indicated by the dihedral angle of 0.68 (11)°. The H atoms attached to atoms C5 and C6 are each disordered over two orientations with site-occupancy ratios of 0.77 (4):0.23 (4) and 0.84 (4):0.16 (4), respectively. An intramolecular N1—H1N1···O2 hydrogen bond generates an S(6) ring motif (Bernstein et al., 1995) in the molecule.
In the crystal (Fig. 2), molecules are linked by N1—H2N1···O2 hydrogen bond into an infinite wave-like chain, propagating along the b axis. The crystal packing also features C—H···π interactions (Table 1), involving Cg1 which is the centroid of S1/C1–C4 ring.