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ISSN: 2056-9890

Ethyl 2-amino-6-benzyl-4,5,6,7-tetra­hydro­thieno[2,3-c]pyridine-3-carboxyl­ate

aCollege of Chemistry and Chemical Engineering, Shanxi Datong University, Datong 037009, People's Republic of China
*Correspondence e-mail: ybsymsm@126.com

(Received 7 December 2010; accepted 11 December 2010; online 24 December 2010)

In the title compound, C17H20N2O2S, the tetra­hydro­pyridine ring adopts an envelope conformation with the N atom at the flap position; the phenyl ring makes a dihedral angle of 81.06 (10)° with the thio­phene ring. The amino group links with the carbonyl O atom via intra­molecular N—H⋯O hydrogen bonding, forming a six-membered ring. In the crystal, inter­molecular N—H⋯O hydrogen bonds link the mol­ecules into infinite chains running along the b axis.

Related literature

For the biological activity of thio­phene and its derivatives, see: Kidwai & Mishra (2003[Kidwai, M. & Mishra, A. D. (2003). Bull. Korean Chem.. Soc. 24, 1038-1040.]); Amr et al. (2006[Amr, A. G. E., Mohamed, A. M., Mohamed, S. F., Abdel-Hafez, N. A. & Hammam, A. E. F. G. (2006). Bioorg. Med. Chem. 14, 5481-5488.]); Sherif (1996[Sherif, S. M. (1996). Monatsh. Chem. 127, 955-962.]).

[Scheme 1]

Experimental

Crystal data
  • C17H20N2O2S

  • Mr = 316.41

  • Monoclinic, P 21 /n

  • a = 12.197 (3) Å

  • b = 9.936 (3) Å

  • c = 13.775 (4) Å

  • β = 103.430 (4)°

  • V = 1623.8 (8) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.21 mm−1

  • T = 293 K

  • 0.25 × 0.19 × 0.14 mm

Data collection
  • Bruker SMART APEX CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 1999[Bruker (1999). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.953, Tmax = 0.977

  • 8867 measured reflections

  • 2875 independent reflections

  • 2122 reflections with I > 2σ(I)

  • Rint = 0.030

Refinement
  • R[F2 > 2σ(F2)] = 0.042

  • wR(F2) = 0.107

  • S = 1.04

  • 2875 reflections

  • 205 parameters

  • 3 restraints

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

  • Δρmax = 0.20 e Å−3

  • Δρmin = −0.17 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H1N⋯O1i 0.81 (2) 2.17 (2) 2.972 (2) 171 (2)
N2—H2N⋯O1 0.81 (1) 2.17 (2) 2.777 (2) 132 (2)
Symmetry code: (i) [-x+{\script{3\over 2}}, y+{\script{1\over 2}}, -z+{\script{3\over 2}}].

Data collection: SMART (Bruker, 1999[Bruker (1999). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 1999[Bruker (1999). SMART, SAINT and SADABS. 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[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]; molecular graphics: SHELXTL[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]; software used to prepare material for publication: SHELXTL[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.].

Supporting information


Comment top

As part of an investigation of the thiophene and it's derivatives systems due to their diverse biological activities (Kidwai et al., 2003; Amr et al., 2006; Sherif et al., 1996), we present here the crystal structure of the title compound, (I).

In the crystal structure of title compound (Fig.1), all bond lengths and bond angles have standard dimensions.

The fragments (C8 to C12) of piperidine nearly planar (mean deviation from plane within 0.0632 (1) Å) while the the six-membered piperidine ring exhibits half-chair conformation. The amino group are hydrogen bonded to the carbonyl O atom of another molecule (Table 1), forming a one-dimensional supramolecular structure (Fig. 2). In addition, there are intramolecular N—H···O hydrogen-bonding interactions in the crystal.

Related literature top

For the biological activity of thiophene and its derivatives, see: Kidwai & Mishra (2003); Amr et al. (2006); Sherif (1996).

Experimental top

To the solution containing the ethyl 2-cyanoacetate (10 mmol, 1.06 ml), 1-benzylpiperidin-4-one (10 mmol, 1.80 ml) and powdered sulfur (12 mmol, 0.38 g) in DMF (6 ml), was under stirring triethylamine (1.20 ml) dropwise added. When the reaction was finished (TLC monitoring) the mixture was filtered with charcoal and poured into crushed ice. The formed crystals were filtered off and washed with water. The products were crystallized from ethanol.

Refinement top

All H atoms bound to C atoms were positioned geometrically and refined as riding, with C—H = 0.93 Å (CH), C—H = 0.97 Å (CH2) and Uiso(H) = 1.2Ueq(C), C—H = 0.96 Å (CH3) and Uiso(H) = 1.5Ueq(C). The H atoms bound to N atoms were located in a difference Fourier map and refined with Uiso(H) = 1.2Ueq(N). The N—H distances were restrained.

Structure description top

As part of an investigation of the thiophene and it's derivatives systems due to their diverse biological activities (Kidwai et al., 2003; Amr et al., 2006; Sherif et al., 1996), we present here the crystal structure of the title compound, (I).

In the crystal structure of title compound (Fig.1), all bond lengths and bond angles have standard dimensions.

The fragments (C8 to C12) of piperidine nearly planar (mean deviation from plane within 0.0632 (1) Å) while the the six-membered piperidine ring exhibits half-chair conformation. The amino group are hydrogen bonded to the carbonyl O atom of another molecule (Table 1), forming a one-dimensional supramolecular structure (Fig. 2). In addition, there are intramolecular N—H···O hydrogen-bonding interactions in the crystal.

For the biological activity of thiophene and its derivatives, see: Kidwai & Mishra (2003); Amr et al. (2006); Sherif (1996).

Computing details top

Data collection: SMART (Bruker, 1999); cell refinement: SAINT (Bruker, 1999); data reduction: SAINT (Bruker, 1999); 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).

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound. Displacement ellipsoids are drawn at the 30% probabilitylevel.
[Figure 2] Fig. 2. View of the one-dimensional supra-molecular chain of the title compound formed by hydrogen bonding (dashed lines). H atoms of C omitted for clarity.
Ethyl 2-amino-6-benzyl-4,5,6,7-tetrahydrothieno[2,3-c]pyridine-3-carboxylate top
Crystal data top
C17H20N2O2SF(000) = 672
Mr = 316.41Dx = 1.294 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 2875 reflections
a = 12.197 (3) Åθ = 2.2–25.1°
b = 9.936 (3) ŵ = 0.21 mm1
c = 13.775 (4) ÅT = 293 K
β = 103.430 (4)°Block, yellow
V = 1623.8 (8) Å30.25 × 0.19 × 0.14 mm
Z = 4
Data collection top
Bruker SMART APEX CCD
diffractometer
2875 independent reflections
Radiation source: fine-focus sealed tube2122 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.030
ω scansθmax = 25.1°, θmin = 2.0°
Absorption correction: multi-scan
(SADABS; Bruker, 1999)
h = 1414
Tmin = 0.953, Tmax = 0.977k = 1011
8867 measured reflectionsl = 1614
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)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.107H atoms treated by a mixture of independent and constrained refinement
S = 1.04 w = 1/[σ2(Fo2) + (0.0533P)2 + 0.2035P]
where P = (Fo2 + 2Fc2)/3
2875 reflections(Δ/σ)max < 0.001
205 parametersΔρmax = 0.20 e Å3
3 restraintsΔρmin = 0.17 e Å3
Crystal data top
C17H20N2O2SV = 1623.8 (8) Å3
Mr = 316.41Z = 4
Monoclinic, P21/nMo Kα radiation
a = 12.197 (3) ŵ = 0.21 mm1
b = 9.936 (3) ÅT = 293 K
c = 13.775 (4) Å0.25 × 0.19 × 0.14 mm
β = 103.430 (4)°
Data collection top
Bruker SMART APEX CCD
diffractometer
2875 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 1999)
2122 reflections with I > 2σ(I)
Tmin = 0.953, Tmax = 0.977Rint = 0.030
8867 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0423 restraints
wR(F2) = 0.107H atoms treated by a mixture of independent and constrained refinement
S = 1.04Δρmax = 0.20 e Å3
2875 reflectionsΔρmin = 0.17 e Å3
205 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*/Ueq
C10.15299 (16)0.6448 (2)0.47716 (17)0.0480 (5)
H10.15930.63540.41150.058*
C20.14619 (18)0.7720 (2)0.51559 (19)0.0583 (6)
H20.14770.84720.47570.070*
C30.13735 (19)0.7877 (2)0.6113 (2)0.0610 (6)
H30.13250.87340.63700.073*
C40.1356 (2)0.6766 (3)0.67014 (19)0.0630 (6)
H40.13000.68730.73590.076*
C50.14210 (18)0.5487 (2)0.63200 (17)0.0539 (6)
H50.14080.47400.67240.065*
C60.15054 (15)0.5310 (2)0.53451 (16)0.0416 (5)
C70.15136 (17)0.3930 (2)0.48984 (17)0.0503 (6)
H7A0.08000.34940.48890.060*
H7B0.15770.40220.42120.060*
C80.23336 (17)0.17339 (19)0.49528 (17)0.0480 (5)
H8A0.24760.18220.42920.058*
H8B0.15710.14010.48780.058*
C90.31573 (15)0.07232 (19)0.55515 (16)0.0441 (5)
H9A0.28750.04120.61150.053*
H9B0.32160.00490.51360.053*
C100.43028 (15)0.13375 (19)0.59228 (14)0.0372 (5)
C110.44382 (15)0.26693 (19)0.58452 (15)0.0409 (5)
C120.35245 (15)0.36571 (19)0.54262 (17)0.0471 (5)
H12A0.36330.44730.58240.057*
H12B0.35520.38900.47480.057*
C130.53359 (15)0.06514 (18)0.64255 (14)0.0371 (4)
C140.62303 (15)0.15380 (19)0.66948 (15)0.0405 (5)
C150.54785 (16)0.07575 (19)0.66775 (14)0.0400 (5)
C160.45439 (19)0.28970 (19)0.65815 (19)0.0562 (6)
H16A0.52390.32510.64560.067*
H16B0.39210.33070.61060.067*
C170.4472 (2)0.3267 (2)0.7607 (2)0.0746 (8)
H17A0.44970.42290.76760.112*
H17B0.37770.29350.77300.112*
H17C0.50950.28770.80800.112*
O10.63729 (11)0.12830 (13)0.70893 (11)0.0503 (4)
O20.45118 (11)0.14512 (13)0.64303 (12)0.0540 (4)
S10.58197 (4)0.31782 (5)0.63602 (5)0.0502 (2)
N10.24303 (12)0.30618 (15)0.54336 (13)0.0417 (4)
N20.73186 (14)0.12651 (18)0.71338 (16)0.0544 (5)
H1N0.7738 (18)0.1883 (17)0.7340 (17)0.065*
H2N0.7441 (19)0.0488 (15)0.7300 (17)0.065*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0413 (11)0.0530 (14)0.0484 (13)0.0033 (10)0.0078 (10)0.0019 (10)
C20.0566 (14)0.0454 (14)0.0690 (17)0.0080 (11)0.0066 (12)0.0068 (12)
C30.0595 (15)0.0463 (14)0.0756 (19)0.0028 (11)0.0125 (13)0.0119 (12)
C40.0689 (16)0.0696 (17)0.0550 (15)0.0006 (13)0.0232 (12)0.0077 (13)
C50.0573 (14)0.0506 (14)0.0553 (15)0.0017 (11)0.0157 (11)0.0094 (11)
C60.0290 (10)0.0431 (12)0.0510 (13)0.0035 (8)0.0058 (9)0.0013 (10)
C70.0397 (11)0.0476 (13)0.0586 (14)0.0062 (10)0.0012 (10)0.0040 (10)
C80.0384 (11)0.0411 (12)0.0595 (14)0.0027 (9)0.0009 (10)0.0071 (10)
C90.0378 (11)0.0329 (11)0.0592 (14)0.0022 (8)0.0063 (10)0.0038 (9)
C100.0346 (10)0.0327 (10)0.0445 (12)0.0012 (8)0.0100 (9)0.0014 (8)
C110.0332 (10)0.0334 (11)0.0561 (13)0.0011 (8)0.0100 (9)0.0031 (9)
C120.0373 (11)0.0359 (11)0.0667 (15)0.0017 (9)0.0090 (10)0.0065 (10)
C130.0356 (10)0.0296 (10)0.0459 (12)0.0007 (8)0.0090 (9)0.0015 (8)
C140.0355 (10)0.0358 (11)0.0495 (13)0.0015 (8)0.0087 (9)0.0003 (9)
C150.0387 (11)0.0353 (11)0.0456 (12)0.0004 (9)0.0088 (9)0.0041 (9)
C160.0553 (14)0.0261 (11)0.0791 (18)0.0048 (9)0.0010 (12)0.0014 (10)
C170.0791 (18)0.0546 (15)0.083 (2)0.0141 (13)0.0051 (15)0.0115 (14)
O10.0399 (8)0.0375 (8)0.0689 (10)0.0062 (6)0.0032 (7)0.0037 (7)
O20.0413 (8)0.0291 (8)0.0841 (11)0.0039 (6)0.0006 (7)0.0050 (7)
S10.0357 (3)0.0324 (3)0.0794 (4)0.0055 (2)0.0068 (3)0.0047 (3)
N10.0319 (8)0.0328 (9)0.0576 (11)0.0020 (7)0.0048 (8)0.0008 (8)
N20.0363 (10)0.0392 (10)0.0810 (15)0.0036 (8)0.0002 (9)0.0014 (10)
Geometric parameters (Å, º) top
C1—C21.380 (3)C10—C111.341 (3)
C1—C61.383 (3)C10—C131.458 (3)
C1—H10.9300C11—C121.497 (3)
C2—C31.357 (3)C11—S11.7445 (19)
C2—H20.9300C12—N11.462 (2)
C3—C41.372 (3)C12—H12A0.9700
C3—H30.9300C12—H12B0.9700
C4—C51.384 (3)C13—C141.384 (3)
C4—H40.9300C13—C151.443 (3)
C5—C61.382 (3)C14—N21.352 (2)
C5—H50.9300C14—S11.736 (2)
C6—C71.505 (3)C15—O11.224 (2)
C7—N11.468 (2)C15—O21.340 (2)
C7—H7A0.9700C16—O21.451 (2)
C7—H7B0.9700C16—C171.482 (3)
C8—N11.469 (2)C16—H16A0.9700
C8—C91.521 (3)C16—H16B0.9700
C8—H8A0.9700C17—H17A0.9600
C8—H8B0.9700C17—H17B0.9600
C9—C101.501 (3)C17—H17C0.9600
C9—H9A0.9700N2—H1N0.807 (15)
C9—H9B0.9700N2—H2N0.809 (14)
C2—C1—C6121.2 (2)C10—C11—C12125.70 (17)
C2—C1—H1119.4C10—C11—S1112.26 (14)
C6—C1—H1119.4C12—C11—S1121.95 (14)
C3—C2—C1120.2 (2)N1—C12—C11109.34 (16)
C3—C2—H2119.9N1—C12—H12A109.8
C1—C2—H2119.9C11—C12—H12A109.8
C2—C3—C4119.8 (2)N1—C12—H12B109.8
C2—C3—H3120.1C11—C12—H12B109.8
C4—C3—H3120.1H12A—C12—H12B108.3
C3—C4—C5120.3 (2)C14—C13—C15120.63 (17)
C3—C4—H4119.9C14—C13—C10111.72 (17)
C5—C4—H4119.9C15—C13—C10127.61 (17)
C6—C5—C4120.6 (2)N2—C14—C13128.54 (18)
C6—C5—H5119.7N2—C14—S1119.99 (15)
C4—C5—H5119.7C13—C14—S1111.45 (14)
C5—C6—C1117.87 (19)O1—C15—O2122.38 (18)
C5—C6—C7121.5 (2)O1—C15—C13124.76 (18)
C1—C6—C7120.6 (2)O2—C15—C13112.84 (16)
N1—C7—C6114.01 (16)O2—C16—C17112.14 (19)
N1—C7—H7A108.8O2—C16—H16A109.2
C6—C7—H7A108.8C17—C16—H16A109.2
N1—C7—H7B108.8O2—C16—H16B109.2
C6—C7—H7B108.8C17—C16—H16B109.2
H7A—C7—H7B107.6H16A—C16—H16B107.9
N1—C8—C9112.02 (16)C16—C17—H17A109.5
N1—C8—H8A109.2C16—C17—H17B109.5
C9—C8—H8A109.2H17A—C17—H17B109.5
N1—C8—H8B109.2C16—C17—H17C109.5
C9—C8—H8B109.2H17A—C17—H17C109.5
H8A—C8—H8B107.9H17B—C17—H17C109.5
C10—C9—C8111.19 (16)C15—O2—C16118.70 (15)
C10—C9—H9A109.4C14—S1—C1191.59 (9)
C8—C9—H9A109.4C12—N1—C7110.42 (15)
C10—C9—H9B109.4C12—N1—C8109.76 (16)
C8—C9—H9B109.4C7—N1—C8109.22 (15)
H9A—C9—H9B108.0C14—N2—H1N118.7 (16)
C11—C10—C13112.98 (16)C14—N2—H2N114.6 (16)
C11—C10—C9119.74 (17)H1N—N2—H2N124 (2)
C13—C10—C9127.21 (17)
C6—C1—C2—C30.3 (3)C9—C10—C13—C150.3 (3)
C1—C2—C3—C40.2 (4)C15—C13—C14—N25.0 (3)
C2—C3—C4—C50.4 (4)C10—C13—C14—N2177.1 (2)
C3—C4—C5—C60.1 (4)C15—C13—C14—S1176.97 (15)
C4—C5—C6—C10.4 (3)C10—C13—C14—S10.9 (2)
C4—C5—C6—C7176.62 (19)C14—C13—C15—O13.6 (3)
C2—C1—C6—C50.6 (3)C10—C13—C15—O1178.95 (19)
C2—C1—C6—C7176.49 (19)C14—C13—C15—O2175.16 (18)
C5—C6—C7—N158.6 (3)C10—C13—C15—O22.3 (3)
C1—C6—C7—N1124.5 (2)O1—C15—O2—C165.2 (3)
N1—C8—C9—C1043.7 (2)C13—C15—O2—C16176.01 (18)
C8—C9—C10—C1110.4 (3)C17—C16—O2—C1586.3 (2)
C8—C9—C10—C13172.76 (19)N2—C14—S1—C11177.73 (18)
C13—C10—C11—C12175.99 (19)C13—C14—S1—C110.45 (17)
C9—C10—C11—C121.2 (3)C10—C11—S1—C140.11 (17)
C13—C10—C11—S10.6 (2)C12—C11—S1—C14176.65 (18)
C9—C10—C11—S1177.86 (15)C11—C12—N1—C7171.98 (17)
C10—C11—C12—N119.4 (3)C11—C12—N1—C851.5 (2)
S1—C11—C12—N1156.87 (15)C6—C7—N1—C1261.0 (2)
C11—C10—C13—C141.0 (3)C6—C7—N1—C8178.23 (18)
C9—C10—C13—C14177.97 (19)C9—C8—N1—C1266.7 (2)
C11—C10—C13—C15176.68 (19)C9—C8—N1—C7172.09 (18)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H1N···O1i0.81 (2)2.17 (2)2.972 (2)171 (2)
N2—H2N···O10.81 (1)2.17 (2)2.777 (2)132 (2)
Symmetry code: (i) x+3/2, y+1/2, z+3/2.

Experimental details

Crystal data
Chemical formulaC17H20N2O2S
Mr316.41
Crystal system, space groupMonoclinic, P21/n
Temperature (K)293
a, b, c (Å)12.197 (3), 9.936 (3), 13.775 (4)
β (°) 103.430 (4)
V3)1623.8 (8)
Z4
Radiation typeMo Kα
µ (mm1)0.21
Crystal size (mm)0.25 × 0.19 × 0.14
Data collection
DiffractometerBruker SMART APEX CCD
Absorption correctionMulti-scan
(SADABS; Bruker, 1999)
Tmin, Tmax0.953, 0.977
No. of measured, independent and
observed [I > 2σ(I)] reflections
8867, 2875, 2122
Rint0.030
(sin θ/λ)max1)0.597
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.107, 1.04
No. of reflections2875
No. of parameters205
No. of restraints3
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.20, 0.17

Computer programs: SMART (Bruker, 1999), SAINT (Bruker, 1999), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H1N···O1i0.807 (15)2.172 (15)2.972 (2)171 (2)
N2—H2N···O10.809 (14)2.169 (18)2.777 (2)132 (2)
Symmetry code: (i) x+3/2, y+1/2, z+3/2.
 

Acknowledgements

We thank the Natural Science Foundation of Shanxi Province, China (No. 2010011018) for supporting this work.

References

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