Crystal structure of 2-chloro-3-(di­meth­oxy­meth­yl)-6-meth­oxy­quinoline

Nanjappa Chandrika; Tholappanavara H Suresha Kumara; Jerry P Jasinski; Sean P Millikan; Hemmige S Yathirajan; Christopher Glidewell

doi:10.1107/S205698901500804X

. 2015 Apr 30;71(Pt 5):o364–o365. doi: 10.1107/S205698901500804X

Crystal structure of 2-chloro-3-(dimethoxymethyl)-6-methoxyquinoline

Nanjappa Chandrika ^a, Tholappanavara H Suresha Kumara ^b, Jerry P Jasinski ^c,^*, Sean P Millikan ^c, Hemmige S Yathirajan ^d, Christopher Glidewell ^e

PMCID: PMC4420130 PMID: 25995951

Abstract

The title compound, C₁₃H₁₄ClNO₃, crystallizes with Z′ = 2 in the space group Pca2₁, but a search for possible additional crystallographic symmetry found none. However, the crystal structure exhibits pseudosymmetry as the two independent molecules are related by an approximate but non-crystallographic inversion located close to (0.38, 0.26, 1/2) in the selected asymmetric unit, and the structure exhibits partial inversion twinning. The approximate inversion relationship between the two molecules in the selected asymmetric unit is clearly shown by comparison of the relevant torsion angle in the two molecules; the corresponding torsion angles have similar, although not identical magnitudes but with opposite signs. The mean planes of the quinoline rings in the two independent molecules are almost parallel, with a dihedral angle of only 0.16 (3)° between them, and the mutual orientation of these rings permits significant π–π stacking interactions between them [centroid–centroid distances = 3.7579 (15) and 3.7923 (15) Å]. In addition, the bimolecular aggregates which are related by translation along [010] are linked by a further π–π stacking interaction [centroid–centroid distance = 3.7898 (15) Å], so forming a π-stacked chain running parallel to [010]. However, there are no C—H⋯N hydrogen bonds in the structure nor, despite the number of independent aromatic rings, are there any C—H⋯π hydrogen bonds; hence there are no direction-specific interactions between adjacent π-stacked chains.

Keywords: crystal structure, quinolone, pseudosymmetry, twinning, π–π stacking interactions

Related literature

For structures of substituted 2-chloroquinolines, see Insuasty et al. (2006 ▸); Hathwar et al. (2010 ▸); Anuradha et al. (2013a ▸,b ▸). graphic file with name e-71-0o364-scheme1.jpg

Experimental

Crystal data

C₁₃H₁₄ClNO₃
M _r = 267.70
Orthorhombic,
a = 27.1156 (9) Å
b = 7.1401 (3) Å
c = 13.0804 (5) Å
V = 2532.47 (17) Å³
Z = 8
Mo Kα radiation
μ = 0.30 mm⁻¹
T = 173 K
0.48 × 0.32 × 0.22 mm

Data collection

Agilent Eos Gemini diffractometer
Absorption correction: multi-scan (CrysAlis RED; Agilent, 2012 ▸) T _min = 0.808, T _max = 0.936
29727 measured reflections
5975 independent reflections
5204 reflections with I > 2σ(I)
R _int = 0.037

Refinement

R[F ² > 2σ(F ²)] = 0.040
wR(F ²) = 0.097
S = 1.08
5975 reflections
331 parameters
1 restraint
H-atom parameters constrained
Δρ_max = 0.25 e Å⁻³
Δρ_min = −0.22 e Å⁻³
Absolute structure: Flack (1983 ▸) x determined using 1610 quotients [(I ⁺)−(I ⁻)]/[(I ⁺)+(I ⁻)] (Parsons et al., 2013 ▸)
Absolute structure parameter: 0.43 (3)

Data collection: CrysAlis PRO (Agilent, 2012 ▸); cell refinement: CrysAlis PRO; data reduction: CrysAlis RED (Agilent, 2012 ▸); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▸); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015 ▸); molecular graphics: PLATON (Spek, 2009 ▸); software used to prepare material for publication: SHELXL2014 and PLATON.

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S205698901500804X/hg5440sup1.cif

e-71-0o364-sup1.cif^{(994.6KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S205698901500804X/hg5440Isup2.hkl

e-71-0o364-Isup2.hkl^{(327.5KB, hkl)}

Click here for additional data file.^{(5.1KB, cml)}

Supporting information file. DOI: 10.1107/S205698901500804X/hg5440Isup3.cml

Click here for additional data file.^{(1.3MB, tif)}

. DOI: 10.1107/S205698901500804X/hg5440fig1.tif

The two independent molecules in the title compound showing the atom-labelling scheme. Displacement ellipsoids are shown at the 30% probability level.

Click here for additional data file.^{(1.1MB, tif)}

. DOI: 10.1107/S205698901500804X/hg5440fig2.tif

The two molecules in the selected asymmetric unit, viewed normal to the planes of the quinolone units, showing the ring overlap which leads to a π..π sktacking interaction. For the sake of clarity, the H atoms have been omitted.

Click here for additional data file.^{(1.2MB, tif)}

. DOI: 10.1107/S205698901500804X/hg5440fig3.tif

A stereoview of part of the crystal structure of the title compound showing the formation of a π-stacked chain parallel to [010]. For the sake of clarity, the H atoms have been omitted.

CCDC reference: 1061227

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Selected torsion angles ().

C12C13C13AO131	69.4(3)
C12C13C13AO132	165.7(2)
C13C13AO131C131	57.4(3)
C13C13AO132C132	170.6(2)
C22C23C23AO231	73.3(3)
C22C23C23AO232	162.3(2)
C23C23AO231C231	58.2(3)
C23C23AO232C232	170.3(2)

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Acknowledgments

NC thanks Jain University for research facilities and JPJ acknowledges the NSF–MRI program (grant No. 1039027) for funds to purchase the X-ray diffractometer.

supplementary crystallographic information

S1. Structural commentary

It is convenient to refer to the molecules containing atoms N11 and N21 as molecules of types 1 and 2 respectively. Within the selected asymmetric unit (Fig. 1), the mean planes of the heterocyclic ring of the type 1 molecule and the carbocyclic ring of the type 2 molecule make a dihedral angle of 2.84 (12) °; the ring centroid separation is 3.7579 (15) Å, and the shortest perpendicular distance for the centroid of one ring to the plane of the other is 3.3998 (10) Å, with a ring-centroid offset of ca 1.60 Å (Fig. 2). For contact between the carbocylic ring in the type 1 molecule and the heterocyclic ring of the type 2 molecule, the corresponding values are 2.63 (12)°, 3.7923 (15) Å, 3.3993 (11) Å and ca 1.68 Å (Fig. 2). In addition, the mean planes of the carbocyclic ring in the type 1 molecule at (x, y, z) and the type 2 molecule at (x, -1 + y, z) make a dihedral angle of only 0.12 (12)°: the ring-centroid separation is 3.7898 (15) Å, the interplanar spacing is 3.5924 (10) Å, and the ring-centroid offset is ca 1.207 Å, leading to the formation of a π-stacked chain of alternating type 1 and type 2 molecules running parallel to the [010] direction (Fig. 3).

S2. Synthesis and crystallization

Sodium cyanotrohydridoborate (963.9 mg, 15.1 mmol was added in a single portion to a solution of (E)-1-((2-chloro-6-methoxyquinolin-3-yl)methylene)-2- (3-fluorophenyl)hydrazine (500 mg, 1.5 mmol) in methanol (20 cm³) and the mixture was then stirred for 30 min. The solution was cooled to 273 K and hydrogen chloride solution (16 mol dm^-3, 4 cm ³) was added dropwise during 10 min. Crushed ice was then added followed by the addition of ice-cold water, and the aqueous mixture was exhaustively extracted with ethyl acetate; the combined extracts were dried over anhydrous sodium sulfate, and the organic solvent was removed under educed pressure. The resulting crude product was purified by chromatography on silica gel using a mixture of hexane and ethyl acetate (19:1, v/v). Crystals of the title compound suitable for single-crystal X-ray diffraction were obtained by slow evaporation, at ambient temperature and in the presence of air, of a solution in hexane-ethyl acetate (1:1, v/v).

S3. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 1. All H atoms were located in difference maps and then treated as riding atoms in geometrically idealized positions with C—H distances 0.95 Å (aryl and heteroaryl) 0.98 Å (methyl) or 1.00 Å (aliphatic CH), and with U_iso(H) = kU_eq(C), where k = 1.5 for the methyl groups, which were permitted to rotate but not to tilt and 1.2 for all other H atoms. The value of the Flack x parameter (Flack, 1983) calculated using 1610 quotients of type [(I+)-(I–)]/[(I+)+(I–)] (Parsons et al., 2013), x = 0.0.43 (3), indicated partial inversion twinning: the conventional calculation using the TWIN and BASF commands in SHELXL gave a less precise value x = 0.49 (8).