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ISSN: 2056-9890

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

(Received 10 June 2012; accepted 10 June 2012; online 16 June 2012)

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 crystal structure also features C—H⋯π inter­actions.

Related literature

For the synthesis, see: Gewald (1965)[Gewald, K. (1965). Chem. Ber. 98, 3571-3577.]. For background to biologically active compounds prepared from the title compound, see: Alqasoumi et al. (2009[Alqasoumi, S. I., Ragab, F. A., Alafeefy, A. M., Galal, M. & Ghorab, M. M. (2009). Phosphorus Sulfur Silicon Relat. Elem. 184, 3241-3257.]); Ghorab et al. (2006,[Ghorab, M. M., Osman, A. N., Noaman, E., Heiba, H. I. & Zaher, N. H. (2006). Phosphorus Sulfur Silicon Relat. Elem. 181, 1935-1950.] 2012[Ghorab, M. M., Ragab, F. A., Heiba, H. I., Agha, H. M. & Nissan, Y. M. (2012). Arch. Pharm. Res. 35, 59-68.]). For hydrogen-bond motifs, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C9H13NO2S

  • Mr = 199.26

  • Monoclinic, P 21 /c

  • a = 7.9487 (2) Å

  • b = 9.8939 (3) Å

  • c = 13.4348 (4) Å

  • β = 106.143 (2)°

  • V = 1014.90 (5) Å3

  • Z = 4

  • Cu Kα radiation

  • μ = 2.59 mm−1

  • T = 296 K

  • 0.92 × 0.26 × 0.08 mm

Data collection
  • Bruker SMART APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.199, Tmax = 0.820

  • 6429 measured reflections

  • 1671 independent reflections

  • 1504 reflections with I > 2σ(I)

  • Rint = 0.029

Refinement
  • R[F2 > 2σ(F2)] = 0.037

  • wR(F2) = 0.104

  • S = 1.07

  • 1671 reflections

  • 132 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.19 e Å−3

  • Δρmin = −0.17 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of S1/C1–C4 ring.

D—H⋯A D—H H⋯A DA 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—H8ACg1ii 0.97 2.78 3.600 (2) 142
Symmetry codes: (i) [-x+1, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]; (ii) -x+1, -y+1, -z+1.

Data collection: APEX2 (Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; 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 and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

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.

Related literature top

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 top

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.

Refinement top

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.

Structure description top

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.

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).

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: 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).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound with 30% probability displacement ellipsoids. The dashed line represents the intramolecular N—H···O hydrogen bond.
[Figure 2] Fig. 2. The crystal packing of the title compound. The dashed lines represent the hydrogen bonds. For clarity sake, hydrogen atoms not involved in hydrogen bonding have been omitted.
Ethyl 2-amino-4,5-dimethylthiophene-3-carboxylate top
Crystal data top
C9H13NO2SF(000) = 424
Mr = 199.26Dx = 1.304 Mg m3
Monoclinic, P21/cCu Kα radiation, λ = 1.54178 Å
Hall symbol: -P 2ybcCell parameters from 1386 reflections
a = 7.9487 (2) Åθ = 3.4–70.2°
b = 9.8939 (3) ŵ = 2.59 mm1
c = 13.4348 (4) ÅT = 296 K
β = 106.143 (2)°Plate, brown
V = 1014.90 (5) Å30.92 × 0.26 × 0.08 mm
Z = 4
Data collection top
Bruker SMART APEXII CCD
diffractometer
1671 independent reflections
Radiation source: fine-focus sealed tube1504 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.029
φ and ω scansθmax = 65.0°, θmin = 5.6°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 68
Tmin = 0.199, Tmax = 0.820k = 1111
6429 measured reflectionsl = 1515
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)] = 0.037H 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 reflectionsΔρmax = 0.19 e Å3
132 parametersΔρmin = 0.17 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: 0.0041 (9)
Crystal data top
C9H13NO2SV = 1014.90 (5) Å3
Mr = 199.26Z = 4
Monoclinic, P21/cCu Kα radiation
a = 7.9487 (2) ŵ = 2.59 mm1
b = 9.8939 (3) ÅT = 296 K
c = 13.4348 (4) Å0.92 × 0.26 × 0.08 mm
β = 106.143 (2)°
Data collection top
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 = 0.820Rint = 0.029
6429 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0370 restraints
wR(F2) = 0.104H atoms treated by a mixture of independent and constrained refinement
S = 1.07Δρmax = 0.19 e Å3
1671 reflectionsΔρmin = 0.17 e Å3
132 parameters
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*/UeqOcc. (<1)
S10.19746 (6)0.19752 (4)0.58473 (4)0.0611 (2)
O10.31318 (16)0.65860 (11)0.49116 (9)0.0545 (3)
O20.44541 (19)0.61171 (12)0.65701 (9)0.0667 (4)
N10.3976 (3)0.35938 (18)0.72936 (12)0.0726 (5)
C10.3045 (2)0.34698 (16)0.62875 (12)0.0520 (4)
C20.2743 (2)0.44243 (15)0.55082 (11)0.0458 (4)
C30.1625 (2)0.39154 (16)0.45331 (12)0.0481 (4)
C40.1130 (2)0.26238 (18)0.46019 (14)0.0554 (4)
C50.0030 (3)0.1727 (2)0.37724 (19)0.0763 (6)
H5A0.06820.14820.32960.114*0.77 (4)
H5B0.10140.22000.34080.114*0.77 (4)
H5C0.02820.09260.40830.114*0.77 (4)
H5D0.02620.21970.31220.114*0.23 (4)
H5E0.10250.14890.39450.114*0.23 (4)
H5F0.06730.09220.37200.114*0.23 (4)
C60.1078 (2)0.46993 (19)0.35388 (13)0.0622 (5)
H6A0.03880.41310.29990.093*0.84 (4)
H6B0.21000.50010.33550.093*0.84 (4)
H6C0.03960.54680.36270.093*0.84 (4)
H6D0.01030.44650.31710.093*0.16 (4)
H6E0.18430.44850.31200.093*0.16 (4)
H6F0.11450.56500.36890.093*0.16 (4)
C70.3521 (2)0.57551 (15)0.57265 (11)0.0469 (4)
C80.3871 (3)0.79279 (16)0.50551 (15)0.0568 (4)
H8A0.51390.78840.52410.068*
H8B0.35240.83950.56020.068*
C90.3179 (3)0.8652 (2)0.40444 (17)0.0718 (6)
H9A0.36170.95610.41090.108*
H9B0.19230.86680.38620.108*
H9C0.35540.81900.35150.108*
H1N10.453 (3)0.438 (3)0.7431 (19)0.084 (7)*
H2N10.435 (3)0.291 (2)0.7699 (19)0.068 (6)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0783 (4)0.0381 (3)0.0662 (3)0.00222 (17)0.0189 (2)0.00472 (17)
O10.0677 (7)0.0409 (6)0.0480 (6)0.0061 (5)0.0046 (5)0.0053 (5)
O20.0971 (10)0.0438 (6)0.0460 (7)0.0060 (6)0.0019 (6)0.0041 (5)
N10.1166 (14)0.0449 (9)0.0439 (8)0.0066 (9)0.0018 (8)0.0056 (7)
C10.0693 (10)0.0379 (8)0.0470 (9)0.0063 (7)0.0132 (7)0.0005 (6)
C20.0556 (9)0.0371 (8)0.0422 (8)0.0051 (6)0.0094 (6)0.0001 (6)
C30.0503 (9)0.0433 (8)0.0470 (8)0.0018 (6)0.0075 (6)0.0021 (6)
C40.0558 (10)0.0467 (9)0.0603 (10)0.0014 (7)0.0106 (7)0.0046 (7)
C50.0745 (13)0.0581 (11)0.0847 (15)0.0130 (9)0.0031 (10)0.0155 (10)
C60.0696 (11)0.0604 (11)0.0455 (9)0.0006 (8)0.0024 (7)0.0013 (7)
C70.0578 (9)0.0382 (8)0.0414 (8)0.0048 (6)0.0081 (6)0.0001 (6)
C80.0671 (11)0.0406 (9)0.0592 (10)0.0047 (7)0.0121 (8)0.0038 (7)
C90.0820 (14)0.0516 (11)0.0755 (13)0.0027 (9)0.0114 (10)0.0196 (9)
Geometric parameters (Å, º) top
S1—C11.7264 (17)C5—H5C0.9600
S1—C41.7429 (18)C5—H5D0.9600
O1—C71.3348 (19)C5—H5E0.9600
O1—C81.4429 (19)C5—H5F0.9600
O2—C71.2228 (19)C6—H6A0.9600
N1—C11.354 (2)C6—H6B0.9600
N1—H1N10.88 (3)C6—H6C0.9600
N1—H2N10.87 (2)C6—H6D0.9600
C1—C21.381 (2)C6—H6E0.9600
C2—C71.450 (2)C6—H6F0.9600
C2—C31.453 (2)C8—C91.498 (3)
C3—C41.348 (2)C8—H8A0.9700
C3—C61.501 (2)C8—H8B0.9700
C4—C51.501 (3)C9—H9A0.9600
C5—H5A0.9600C9—H9B0.9600
C5—H5B0.9600C9—H9C0.9600
C1—S1—C492.01 (8)H5E—C5—H5F109.5
C7—O1—C8117.66 (13)C3—C6—H6A109.5
C1—N1—H1N1112.9 (16)C3—C6—H6B109.5
C1—N1—H2N1123.7 (15)C3—C6—H6C109.5
H1N1—N1—H2N1119 (2)C3—C6—H6D109.5
N1—C1—C2128.80 (17)C3—C6—H6E109.5
N1—C1—S1120.01 (14)H6D—C6—H6E109.5
C2—C1—S1111.16 (12)C3—C6—H6F109.5
C1—C2—C7119.57 (14)H6D—C6—H6F109.5
C1—C2—C3112.36 (14)H6E—C6—H6F109.5
C7—C2—C3128.07 (13)O2—C7—O1121.49 (14)
C4—C3—C2112.56 (14)O2—C7—C2124.63 (14)
C4—C3—C6122.22 (15)O1—C7—C2113.88 (13)
C2—C3—C6125.21 (15)O1—C8—C9106.59 (15)
C3—C4—C5129.10 (18)O1—C8—H8A110.4
C3—C4—S1111.91 (12)C9—C8—H8A110.4
C5—C4—S1118.99 (15)O1—C8—H8B110.4
C4—C5—H5A109.5C9—C8—H8B110.4
C4—C5—H5B109.5H8A—C8—H8B108.6
C4—C5—H5C109.5C8—C9—H9A109.5
C4—C5—H5D109.5C8—C9—H9B109.5
C4—C5—H5E109.5H9A—C9—H9B109.5
H5D—C5—H5E109.5C8—C9—H9C109.5
C4—C5—H5F109.5H9A—C9—H9C109.5
H5D—C5—H5F109.5H9B—C9—H9C109.5
C4—S1—C1—N1178.55 (17)C2—C3—C4—S10.56 (19)
C4—S1—C1—C20.60 (14)C6—C3—C4—S1179.60 (14)
N1—C1—C2—C71.8 (3)C1—S1—C4—C30.67 (15)
S1—C1—C2—C7179.54 (12)C1—S1—C4—C5178.19 (17)
N1—C1—C2—C3178.12 (19)C8—O1—C7—O20.8 (2)
S1—C1—C2—C30.40 (18)C8—O1—C7—C2179.18 (15)
C1—C2—C3—C40.1 (2)C1—C2—C7—O20.0 (3)
C7—C2—C3—C4179.95 (16)C3—C2—C7—O2179.97 (16)
C1—C2—C3—C6179.12 (16)C1—C2—C7—O1179.94 (14)
C7—C2—C3—C60.9 (3)C3—C2—C7—O10.0 (2)
C2—C3—C4—C5178.16 (19)C7—O1—C8—C9177.97 (15)
C6—C3—C4—C50.9 (3)
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of S1/C1–C4 ring.
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O20.89 (3)2.06 (3)2.744 (2)133 (2)
N1—H2N1···O2i0.87 (2)2.12 (2)2.972 (2)167 (2)
C8—H8A···Cg1ii0.972.783.600 (2)142
Symmetry codes: (i) x+1, y1/2, z+3/2; (ii) x+1, y+1, z+1.

Experimental details

Crystal data
Chemical formulaC9H13NO2S
Mr199.26
Crystal system, space groupMonoclinic, P21/c
Temperature (K)296
a, b, c (Å)7.9487 (2), 9.8939 (3), 13.4348 (4)
β (°) 106.143 (2)
V3)1014.90 (5)
Z4
Radiation typeCu Kα
µ (mm1)2.59
Crystal size (mm)0.92 × 0.26 × 0.08
Data collection
DiffractometerBruker SMART APEXII CCD
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.199, 0.820
No. of measured, independent and
observed [I > 2σ(I)] reflections
6429, 1671, 1504
Rint0.029
(sin θ/λ)max1)0.588
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.037, 0.104, 1.07
No. of reflections1671
No. of parameters132
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.19, 0.17

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of S1/C1–C4 ring.
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O20.89 (3)2.06 (3)2.744 (2)133 (2)
N1—H2N1···O2i0.87 (2)2.12 (2)2.972 (2)167 (2)
C8—H8A···Cg1ii0.972.783.600 (2)142
Symmetry codes: (i) x+1, y1/2, 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

First citationAlqasoumi, S. I., Ragab, F. A., Alafeefy, A. M., Galal, M. & Ghorab, M. M. (2009). Phosphorus Sulfur Silicon Relat. Elem. 184, 3241–3257.  Web of Science CrossRef CAS Google Scholar
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