organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 71| Part 7| July 2015| Pages o444-o445

Crystal structure of ethyl 4-(2-meth­­oxy­phen­yl)-6-methyl-2-sulfanyl­­idene-1,2,3,4-tetra­hydro­pyrimidine-5-carboxyl­ate

aChemistry and Environmental Division, Manchester Metropolitan University, Manchester M1 5GD, England, bChemistry Department, Faculty of Science, Minia University, 61519 El-Minia, Egypt, cDepartment of Chemistry, Tulane University, New Orleans, LA 70118, USA, dDepartment of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Turkey, and eChemistry Department, Faculty of Science, Sohag University, 82524 Sohag, Egypt
*Correspondence e-mail: abdala_15@yahoo.com

Edited by H. Ishida, Okayama University, Japan (Received 13 May 2015; accepted 23 May 2015; online 3 June 2015)

In the title compound, C15H18N2O3S, the hydro­pyrimidine ring adopts a sofa conformation with the methine C atom as the flap. The benzene ring is almost perpendicular to the mean plane of the hydro­pyrimidine ring, making a dihedral angle of 85.51 (8)°, and the meth­oxy O atom lies over the centre of the pyrimidine ring. In the crystal, weak N—H⋯S inter­actions form a zigzag chain running along the b-axis direction.

1. Related literature

For syntheses of di­hydro­pyrimidino­nes and their analogous, see: Biginelli (1893[Biginelli, P. (1893). Gazz. Chim. Ital. 23, 360-416.]); Varala et al. (2003[Varala, R., Alam, M. M. & Adapa, S. R. (2003). Synlett, pp. 67-70.]); Gohain et al. (2004[Gohain, M., Prajapati, D. & Sandhu, J. S. (2004). Synlett, pp. 0235-0238.]); Ahmed et al. (2009[Ahmed, B., Khan, R. A., Habibullah & Keshari, M. (2009). Tetrahedron Lett. 50, 2889-2892.]). For biological activities of hydro­pyrimidino­nes, see: Salehi et al. (2006[Salehi, P., Dabiri, M., Khosropour, A. R. & Roozbehniya, P. (2006). J. Iran. Chem. Soc. 3, 98-104.]); Singh et al. (2010[Singh, O. M., Devi, N. S., Devi, L. R. & Khumanthem, N. (2010). Int. J. Drug Des. Discov. 1, 258-264.]); Hed et al. (2009[Hed, L. C., Sharma, R., Pareek, C. & Chaudhari, P. B. (2009). Eur. J. Chem. 6, 770-774.]); Russowsky et al. (2007[Russowsky, D., Benvenutti, E. V., Roxo, G. S. & Grasel, F. (2007). Lett. Org. Chem. 4, 39-42.]); Shah et al. (2009[Shah, T. B., Gupte, A., Patel, M. R., Chaudhari, V. S., Patel, H. & Patel, V. C. (2009). Indian J. Chem. Sect. B, 48, 88-96.]). For the synthesis of the title compound, see: Ahmed et al. (2012[Ahmed, E. A., Mohamed, M. A. A. & El-Saghier, A. M. M. (2012). J. Am. Sci. 8, 815-818.]).

[Scheme 1]

2. Experimental

2.1. Crystal data

  • C15H18N2O3S

  • Mr = 306.37

  • Triclinic, [P \overline 1]

  • a = 7.9791 (2) Å

  • b = 8.2031 (2) Å

  • c = 11.8405 (3) Å

  • α = 81.987 (1)°

  • β = 87.975 (1)°

  • γ = 80.850 (1)°

  • V = 757.60 (3) Å3

  • Z = 2

  • Cu Kα radiation

  • μ = 2.00 mm−1

  • T = 150 K

  • 0.25 × 0.21 × 0.12 mm

2.2. Data collection

  • Bruker D8 VENTURE PHOTON 100 CMOS diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2014[Bruker (2014). APEX2, SAINT and SADABS. Bruker AXS, Inc., Madison, Wisconsin, USA.]) Tmin = 0.73, Tmax = 0.79

  • 9145 measured reflections

  • 2929 independent reflections

  • 2773 reflections with I > 2σ(I)

  • Rint = 0.021

2.3. Refinement

  • R[F2 > 2σ(F2)] = 0.039

  • wR(F2) = 0.101

  • S = 1.08

  • 2929 reflections

  • 193 parameters

  • H-atom parameters constrained

  • Δρmax = 0.43 e Å−3

  • Δρmin = −0.26 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1A⋯S1i 0.91 2.46 3.3539 (13) 167
N2—H2A⋯S1ii 0.91 2.58 3.4327 (14) 157
Symmetry codes: (i) -x+2, -y+1, -z+2; (ii) -x+2, -y, -z+2.

Data collection: APEX2 (Bruker, 2014[Bruker (2014). APEX2, SAINT and SADABS. Bruker AXS, Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2014[Bruker (2014). APEX2, SAINT and SADABS. Bruker AXS, Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]); molecular graphics: DIAMOND (Brandenburg & Putz, 2012[Brandenburg, K. & Putz, H. (2012). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: SHELXL2014.

Supporting information


Comment top

Dihydropyrimidin-2(1H)-one scaffold compounds are an important class of substances in organic and medicinal chemistry. Aryl-substituted 3, 4-dihydropyrimidin-2(1H)-ones and their sulfur analogue have been reported to possess diverse range of pharmacological activity (Salehi et al., 2006) such as anticancer, anti HIV, antibacterial, antimalarial, antihypertensive, sedative, hypnotics, anticonvulsant, antithyroid,antihistaminic agents and antibiotics (Singh et al., 2010; Hed et al., 2009; Russowsky et al., 2007; Shah et al., 2009). This stimulated the invention of a wide range of synthetic methods for their preparation and chemical transformations. In recent years, several modified procedures have been reported to improve the efficiency of the Biginelli dihydropyrimidine synthesis (Biginelli, 1893) by using different catalysts e.g. Lewis acids (Varala et al., 2003; Gohain et al., 2004) or by using basic condition via phase transfer catalysis (Ahmed et al., 2009). In this context, we report in this study the crystal structure of the title compound.

In the title compound (Fig. 1), the plane of the benzene ring is almost parallel to the C1···N2 vector with the methoxy oxygen atom (O1) lying over the centre of the pyrimidine ring. The pyrimidine ring has Cremer-Pople puckering parameters Q = 0.201 (2) Å, θ = 62.2 (5)° and ϕ = 42.9 (2)°. In the crystal, weak N—H···S interactions (Table 1) form a chain running parallel to the b axis (Figs. 2 & 3).

Related literature top

For syntheses of dihydropyrimidinones and their analogous, see: Biginelli (1893); Varala et al. (2003); Gohain et al. (2004); Ahmed et al. (2009). For biological activities of hydropyrimidinones, see: Salehi et al. (2006); Singh et al. (2010); Hed et al. (2009); Russowsky et al. (2007); Shah et al. (2009). For the synthesis of the title compound, see: Ahmed et al. (2012).

Experimental top

The title compound was prepared according to our reported method (Ahmed et al., 2012). Colourless crystals suitable for X-ray analysis were grown from ethanol (m.p. 473–475 K, yield 98%).

Refinement top

H-atoms attached to C were placed in calculated positions (C—H = 0.95–1.00 Å), while those attached to N were placed in a difference map and their parameters adjusted to give N—H = 0.91 Å. All were included as riding contributions with isotropic displacement parameters 1.2 or 1.5 times those of the attached atoms.

Computing details top

Data collection: APEX2 (Bruker, 2014); cell refinement: SAINT (Bruker, 2014); data reduction: SAINT (Bruker, 2014); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015b).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound showing labeling scheme and 50% probability ellipsoids.
[Figure 2] Fig. 2. A section of the chain formed by N—H···S hydrogen bonds (dashed lines).
[Figure 3] Fig. 3. A packing diagram viewed along the b axis. N—H···S interactions are shown as dotted lines.
Ethyl 4-(2-methoxyphenyl)-6-methyl-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carboxylate top
Crystal data top
C15H18N2O3SZ = 2
Mr = 306.37F(000) = 324
Triclinic, P1Dx = 1.343 Mg m3
a = 7.9791 (2) ÅCu Kα radiation, λ = 1.54178 Å
b = 8.2031 (2) ÅCell parameters from 7936 reflections
c = 11.8405 (3) Åθ = 3.8–72.2°
α = 81.987 (1)°µ = 2.00 mm1
β = 87.975 (1)°T = 150 K
γ = 80.850 (1)°Thick plate, colourless
V = 757.60 (3) Å30.25 × 0.21 × 0.12 mm
Data collection top
Bruker D8 VENTURE PHOTON 100 CMOS
diffractometer
2929 independent reflections
Radiation source: INCOATEC IµS micro–focus source2773 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.021
Detector resolution: 10.4167 pixels mm-1θmax = 72.2°, θmin = 3.8°
ω scansh = 99
Absorption correction: multi-scan
(SADABS; Bruker, 2014)
k = 1010
Tmin = 0.73, Tmax = 0.79l = 1414
9145 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)] = 0.039Hydrogen site location: mixed
wR(F2) = 0.101H-atom parameters constrained
S = 1.08 w = 1/[σ2(Fo2) + (0.0487P)2 + 0.4254P]
where P = (Fo2 + 2Fc2)/3
2929 reflections(Δ/σ)max = 0.001
193 parametersΔρmax = 0.43 e Å3
0 restraintsΔρmin = 0.26 e Å3
Crystal data top
C15H18N2O3Sγ = 80.850 (1)°
Mr = 306.37V = 757.60 (3) Å3
Triclinic, P1Z = 2
a = 7.9791 (2) ÅCu Kα radiation
b = 8.2031 (2) ŵ = 2.00 mm1
c = 11.8405 (3) ÅT = 150 K
α = 81.987 (1)°0.25 × 0.21 × 0.12 mm
β = 87.975 (1)°
Data collection top
Bruker D8 VENTURE PHOTON 100 CMOS
diffractometer
2929 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2014)
2773 reflections with I > 2σ(I)
Tmin = 0.73, Tmax = 0.79Rint = 0.021
9145 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0390 restraints
wR(F2) = 0.101H-atom parameters constrained
S = 1.08Δρmax = 0.43 e Å3
2929 reflectionsΔρmin = 0.26 e Å3
193 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. H-atoms attached to carbon were placed in calculated positions (C—H = 0.95 - 0.98 Å) while those attached to nitrogen were placed in locations derived from a difference map and their parameters adjusted to give N—H = 0.91 Å. All were included as riding contributions with isotropic displacement parameters 1.2 - 1.5 times those of the attached atoms.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S11.08339 (5)0.22865 (4)1.02799 (3)0.02400 (13)
O10.64475 (15)0.28798 (15)0.86937 (10)0.0312 (3)
O20.8568 (2)0.26940 (18)0.47910 (11)0.0494 (4)
O30.75790 (16)0.52294 (15)0.52331 (9)0.0304 (3)
N10.96037 (16)0.42742 (15)0.84338 (11)0.0213 (3)
H1A0.96170.51090.88640.026*
N20.99441 (17)0.14788 (16)0.83198 (11)0.0240 (3)
H2A1.00800.04310.87100.029*
C10.85934 (19)0.47576 (19)0.73835 (13)0.0216 (3)
H10.90840.56850.69160.026*
C21.00503 (19)0.27318 (19)0.89394 (13)0.0209 (3)
C30.9414 (2)0.1739 (2)0.71936 (13)0.0247 (3)
C40.9585 (3)0.0158 (2)0.66684 (15)0.0351 (4)
H4A0.87220.02710.60820.053*
H4B0.94290.07700.72590.053*
H4C1.07170.00610.63200.053*
C50.88282 (19)0.3296 (2)0.66990 (13)0.0230 (3)
C60.8339 (2)0.3648 (2)0.54883 (14)0.0277 (3)
C70.6888 (2)0.5701 (2)0.40933 (14)0.0331 (4)
H7A0.60510.49800.39590.040*
H7B0.78060.55880.35120.040*
C80.6050 (3)0.7480 (3)0.40272 (18)0.0486 (5)
H8A0.51720.75800.46250.073*
H8B0.55290.78410.32780.073*
H8C0.69000.81830.41360.073*
C90.6761 (2)0.5437 (2)0.76670 (13)0.0255 (3)
C100.6100 (2)0.7098 (2)0.72635 (15)0.0304 (4)
H100.67970.77850.68170.036*
C110.4425 (3)0.7744 (2)0.75156 (17)0.0382 (4)
H110.39720.88610.72280.046*
C120.3434 (2)0.6753 (2)0.81827 (16)0.0370 (4)
H120.22980.72050.83570.044*
C130.4043 (2)0.5117 (2)0.86057 (15)0.0320 (4)
H130.33420.44520.90680.038*
C140.5720 (2)0.4459 (2)0.83384 (13)0.0269 (3)
C150.5435 (2)0.1762 (2)0.93170 (16)0.0361 (4)
H15A0.49880.22051.00130.054*
H15B0.61330.06710.95210.054*
H15C0.44890.16420.88450.054*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0304 (2)0.0195 (2)0.0222 (2)0.00308 (15)0.00427 (14)0.00340 (14)
O10.0296 (6)0.0277 (6)0.0355 (6)0.0073 (5)0.0044 (5)0.0011 (5)
O20.0744 (10)0.0443 (8)0.0274 (7)0.0095 (7)0.0101 (6)0.0165 (6)
O30.0391 (7)0.0314 (6)0.0209 (6)0.0055 (5)0.0058 (5)0.0026 (5)
N10.0255 (6)0.0180 (6)0.0217 (6)0.0048 (5)0.0032 (5)0.0046 (5)
N20.0309 (7)0.0181 (6)0.0238 (6)0.0034 (5)0.0014 (5)0.0056 (5)
C10.0237 (7)0.0218 (7)0.0202 (7)0.0052 (6)0.0020 (6)0.0033 (6)
C20.0202 (7)0.0206 (7)0.0227 (7)0.0045 (6)0.0013 (6)0.0044 (6)
C30.0261 (8)0.0261 (8)0.0241 (8)0.0069 (6)0.0019 (6)0.0084 (6)
C40.0497 (11)0.0273 (9)0.0309 (9)0.0059 (8)0.0026 (8)0.0121 (7)
C50.0235 (7)0.0256 (8)0.0217 (7)0.0063 (6)0.0014 (6)0.0067 (6)
C60.0278 (8)0.0332 (9)0.0233 (8)0.0059 (7)0.0010 (6)0.0066 (6)
C70.0370 (9)0.0430 (10)0.0199 (8)0.0104 (8)0.0046 (7)0.0000 (7)
C80.0683 (14)0.0410 (11)0.0346 (10)0.0088 (10)0.0160 (10)0.0062 (8)
C90.0268 (8)0.0292 (8)0.0222 (7)0.0048 (6)0.0031 (6)0.0081 (6)
C100.0335 (9)0.0276 (8)0.0289 (8)0.0007 (7)0.0053 (7)0.0055 (7)
C110.0398 (10)0.0284 (9)0.0436 (10)0.0035 (8)0.0066 (8)0.0041 (8)
C120.0352 (9)0.0377 (10)0.0367 (9)0.0019 (8)0.0000 (7)0.0094 (8)
C130.0320 (9)0.0368 (9)0.0278 (8)0.0069 (7)0.0017 (7)0.0049 (7)
C140.0294 (8)0.0286 (8)0.0233 (8)0.0044 (7)0.0036 (6)0.0049 (6)
C150.0366 (10)0.0323 (9)0.0386 (10)0.0106 (8)0.0047 (8)0.0033 (8)
Geometric parameters (Å, º) top
S1—C21.6969 (15)C5—C61.476 (2)
O1—C141.349 (2)C7—C81.498 (3)
O1—C151.430 (2)C7—H7A0.9900
O2—C61.205 (2)C7—H7B0.9900
O3—C61.340 (2)C8—H8A0.9800
O3—C71.4541 (19)C8—H8B0.9800
N1—C21.322 (2)C8—H8C0.9800
N1—C11.4783 (18)C9—C141.397 (2)
N1—H1A0.9098C9—C101.403 (2)
N2—C21.3580 (19)C10—C111.395 (3)
N2—C31.391 (2)C10—H100.9500
N2—H2A0.9098C11—C121.376 (3)
C1—C51.522 (2)C11—H110.9500
C1—C91.523 (2)C12—C131.382 (3)
C1—H11.0000C12—H120.9500
C3—C51.347 (2)C13—C141.403 (2)
C3—C41.501 (2)C13—H130.9500
C4—H4A0.9800C15—H15A0.9800
C4—H4B0.9800C15—H15B0.9800
C4—H4C0.9800C15—H15C0.9800
C14—O1—C15118.77 (14)C8—C7—H7A110.4
C6—O3—C7116.45 (13)O3—C7—H7B110.4
C2—N1—C1125.30 (12)C8—C7—H7B110.4
C2—N1—H1A117.1H7A—C7—H7B108.6
C1—N1—H1A114.7C7—C8—H8A109.5
C2—N2—C3123.59 (14)C7—C8—H8B109.5
C2—N2—H2A116.2H8A—C8—H8B109.5
C3—N2—H2A119.5C7—C8—H8C109.5
N1—C1—C5108.79 (12)H8A—C8—H8C109.5
N1—C1—C9110.68 (12)H8B—C8—H8C109.5
C5—C1—C9115.38 (12)C14—C9—C10118.77 (16)
N1—C1—H1107.2C14—C9—C1121.76 (15)
C5—C1—H1107.2C10—C9—C1119.46 (15)
C9—C1—H1107.2C11—C10—C9120.32 (17)
N1—C2—N2117.28 (14)C11—C10—H10119.8
N1—C2—S1122.70 (11)C9—C10—H10119.8
N2—C2—S1119.94 (12)C12—C11—C10119.55 (17)
C5—C3—N2119.62 (14)C12—C11—H11120.2
C5—C3—C4127.50 (15)C10—C11—H11120.2
N2—C3—C4112.89 (14)C11—C12—C13121.84 (17)
C3—C4—H4A109.5C11—C12—H12119.1
C3—C4—H4B109.5C13—C12—H12119.1
H4A—C4—H4B109.5C12—C13—C14118.62 (17)
C3—C4—H4C109.5C12—C13—H13120.7
H4A—C4—H4C109.5C14—C13—H13120.7
H4B—C4—H4C109.5O1—C14—C9115.19 (15)
C3—C5—C6121.63 (14)O1—C14—C13123.92 (15)
C3—C5—C1120.93 (14)C9—C14—C13120.89 (16)
C6—C5—C1117.42 (14)O1—C15—H15A109.5
O2—C6—O3122.34 (16)O1—C15—H15B109.5
O2—C6—C5126.96 (16)H15A—C15—H15B109.5
O3—C6—C5110.70 (13)O1—C15—H15C109.5
O3—C7—C8106.67 (14)H15A—C15—H15C109.5
O3—C7—H7A110.4H15B—C15—H15C109.5
C2—N1—C1—C525.4 (2)C3—C5—C6—O3171.37 (14)
C2—N1—C1—C9102.32 (16)C1—C5—C6—O36.8 (2)
C1—N1—C2—N216.9 (2)C6—O3—C7—C8177.69 (16)
C1—N1—C2—S1166.47 (11)N1—C1—C9—C1461.89 (18)
C3—N2—C2—N10.7 (2)C5—C1—C9—C1462.18 (19)
C3—N2—C2—S1176.02 (12)N1—C1—C9—C10116.92 (15)
C2—N2—C3—C56.0 (2)C5—C1—C9—C10119.01 (16)
C2—N2—C3—C4173.96 (15)C14—C9—C10—C111.1 (2)
N2—C3—C5—C6176.60 (14)C1—C9—C10—C11179.90 (15)
C4—C3—C5—C63.3 (3)C9—C10—C11—C121.3 (3)
N2—C3—C5—C15.3 (2)C10—C11—C12—C130.7 (3)
C4—C3—C5—C1174.72 (16)C11—C12—C13—C140.3 (3)
N1—C1—C5—C318.7 (2)C15—O1—C14—C9175.65 (14)
C9—C1—C5—C3106.35 (17)C15—O1—C14—C134.3 (2)
N1—C1—C5—C6163.15 (13)C10—C9—C14—O1179.93 (14)
C9—C1—C5—C671.79 (18)C1—C9—C14—O11.1 (2)
C7—O3—C6—O25.8 (2)C10—C9—C14—C130.1 (2)
C7—O3—C6—C5174.41 (13)C1—C9—C14—C13178.93 (14)
C3—C5—C6—O28.9 (3)C12—C13—C14—O1179.41 (16)
C1—C5—C6—O2172.98 (18)C12—C13—C14—C90.5 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···S1i0.912.463.3539 (13)167
N2—H2A···S1ii0.912.583.4327 (14)157
Symmetry codes: (i) x+2, y+1, z+2; (ii) x+2, y, z+2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···S1i0.912.463.3539 (13)167
N2—H2A···S1ii0.912.583.4327 (14)157
Symmetry codes: (i) x+2, y+1, z+2; (ii) x+2, y, z+2.
 

Acknowledgements

The support of NSF–MRI grant No. 1228232 for the purchase of the diffractometer and Tulane University for support of the Tulane Crystallography Laboratory are gratefully acknowledged.

References

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Volume 71| Part 7| July 2015| Pages o444-o445
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