Acta Cryst. (2009). E65, o97 [ doi:10.1107/S1600536808041366 ]
In the title compound, C6H6Cl2N2, intramolecular N-H
Cl and C-HCl contacts generate five-membered rings, producing S(5) ring motifs. Pairs of intermolecular N-HN hydrogen bonds link neighbouring molecules into dimers with R22(8) ring motifs. In the crystal structure, these dimers are connected by N-HCl interactions and are packed into columns.
Phosphorus oxychloride (POCl3) (15 ml) was added to 2-amino-6-methylpyridine (2 g, 0.019 mmol) and the mixture was refluxed at 383 K for 16 h. Excess POCl3 was distilled off. The solid residue was neutralized using KOH solution in an ice bath and a saturated NaHCO3 solution was added. The solid residue was filtered off, extracted with CHCl3, the solution was dried over anhydrous Na2SO4 and then concentrated under vacuum. The crude product was purified by column chromatography using silica gel with 20% ethyl acetate in petroleum ether as eluant to afford (I) (2.14 g, 65%) as a colourless crystalline solid, mp. 404–407 K.
All hydrogen atoms were located from a difference Fourier map and refined freely; range of C-H distances: 0.924 (7) to 1.02 (2) Å. See Table 1 for N-H distances.
Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); 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, 2003).
![[Figure 1]](./tk2343fig1thm.gif)
| Fig. 1. The molecular structure of (I), showing 50% probability displacement ellipsoids and the atomic numbering. Dashed lines show intramolecular hydrogen bonds. |
![[Figure 2]](./tk2343fig2thm.gif)
| Fig. 2. The crystal packing for (I), showing dimers with R22(8) motifs and stacking of the dimers into columns along the b-axis. Intermolecular interactions are drawn as dashed lines. |
| C6H6Cl2N2 | F(000) = 360 |
| Mr = 177.03 | Dx = 1.626 Mg m−3 |
| Monoclinic, P21/n | Melting point: 404 K |
| Hall symbol: -P 2yn | Mo Kα radiation, λ = 0.71073 Å |
| a = 12.7670 (3) Å | Cell parameters from 9896 reflections |
| b = 3.8037 (1) Å | θ = 2.4–40.3° |
| c = 15.4129 (3) Å | µ = 0.81 mm−1 |
| β = 104.990 (1)° | T = 100 K |
| V = 723.01 (3) Å3 | Block, colourless |
| Z = 4 | 0.45 × 0.31 × 0.28 mm |
| Bruker SMART APEXII CCD area-detector diffractometer | 3795 independent reflections |
| Radiation source: fine-focus sealed tube | 3485 reflections with I > 2˘I) |
| graphite | Rint = 0.026 |
| φ and ω scans | θmax = 37.5°, θmin = 2.4° |
| Absorption correction: multi-scan (SADABS; Bruker, 2005) | h = −21→21 |
| Tmin = 0.711, Tmax = 0.803 | k = −6→6 |
| 26531 measured reflections | l = −26→26 |
| Refinement on F2 | Primary atom site location: structure-invariant direct methods |
| Least-squares matrix: full | Secondary atom site location: difference Fourier map |
| R[F2 > 2σ(F2)] = 0.024 | Hydrogen site location: inferred from neighbouring sites |
| wR(F2) = 0.071 | All H-atom parameters refined |
| S = 1.11 | w = 1/[σ2(Fo2) + (0.037P)2 + 0.1631P] where P = (Fo2 + 2Fc2)/3 |
| 3795 reflections | (Δ/σ)max = 0.001 |
| 115 parameters | Δρmax = 0.61 e Å−3 |
| 0 restraints | Δρmin = −0.42 e Å−3 |
| C6H6Cl2N2 | V = 723.01 (3) Å3 |
| Mr = 177.03 | Z = 4 |
| Monoclinic, P21/n | Mo Kα radiation |
| a = 12.7670 (3) Å | µ = 0.81 mm−1 |
| b = 3.8037 (1) Å | T = 100 K |
| c = 15.4129 (3) Å | 0.45 × 0.31 × 0.28 mm |
| β = 104.990 (1)° |
| Bruker SMART APEXII CCD area-detector diffractometer | 3795 independent reflections |
| Absorption correction: multi-scan (SADABS; Bruker, 2005) | 3485 reflections with I > 2˘I) |
| Tmin = 0.711, Tmax = 0.803 | Rint = 0.026 |
| 26531 measured reflections | θmax = 37.5° |
| R[F2 > 2σ(F2)] = 0.024 | All H-atom parameters refined |
| wR(F2) = 0.071 | Δρmax = 0.61 e Å−3 |
| S = 1.11 | Δρmin = −0.42 e Å−3 |
| 3795 reflections | Absolute structure: ? |
| 115 parameters | Flack parameter: ? |
| 0 restraints | Rogers parameter: ? |
Experimental. The low-temperature data was collected with the Oxford Cyrosystem Cobra low-temperature attachment. |
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 | ||
| Cl1 | 0.116608 (15) | 0.89761 (5) | 0.117299 (12) | 0.01973 (5) | |
| Cl2 | 0.150078 (13) | 0.32687 (5) | −0.194719 (10) | 0.01603 (4) | |
| N1 | 0.36956 (5) | 0.65340 (16) | 0.02268 (4) | 0.01455 (9) | |
| N2 | 0.38950 (5) | 0.41291 (19) | −0.10983 (4) | 0.01738 (11) | |
| H2N1 | 0.4571 (12) | 0.379 (4) | −0.0819 (9) | 0.027 (3)* | |
| H1N1 | 0.3607 (11) | 0.284 (4) | −0.1526 (9) | 0.025 (3)* | |
| C1 | 0.32310 (5) | 0.51854 (18) | −0.05855 (4) | 0.01322 (10) | |
| C2 | 0.20904 (5) | 0.49965 (17) | −0.08923 (4) | 0.01321 (10) | |
| C3 | 0.14544 (5) | 0.61633 (18) | −0.03563 (4) | 0.01465 (10) | |
| H3 | 0.0672 (10) | 0.605 (3) | −0.0583 (8) | 0.022 (3)* | |
| C4 | 0.19660 (5) | 0.75331 (18) | 0.04856 (4) | 0.01450 (10) | |
| C5 | 0.30903 (5) | 0.77194 (18) | 0.07629 (4) | 0.01437 (10) | |
| C6 | 0.37037 (7) | 0.9165 (2) | 0.16549 (5) | 0.02130 (13) | |
| H6C | 0.4268 (13) | 1.055 (5) | 0.1579 (11) | 0.041 (4)* | |
| H6B | 0.4079 (16) | 0.744 (5) | 0.2083 (12) | 0.061 (5)* | |
| H6A | 0.3222 (16) | 1.071 (6) | 0.1929 (13) | 0.065 (6)* |
| U11 | U22 | U33 | U12 | U13 | U23 | |
| Cl1 | 0.02170 (8) | 0.02155 (8) | 0.01862 (8) | 0.00364 (6) | 0.01006 (6) | −0.00108 (5) |
| Cl2 | 0.01665 (7) | 0.01786 (7) | 0.01167 (7) | −0.00132 (5) | 0.00022 (5) | −0.00081 (5) |
| N1 | 0.0143 (2) | 0.0174 (2) | 0.0113 (2) | −0.00002 (17) | 0.00219 (17) | −0.00112 (17) |
| N2 | 0.0146 (2) | 0.0247 (3) | 0.0127 (2) | 0.00163 (19) | 0.00317 (18) | −0.00292 (19) |
| C1 | 0.0136 (2) | 0.0146 (2) | 0.0110 (2) | 0.00045 (18) | 0.00251 (18) | 0.00056 (18) |
| C2 | 0.0140 (2) | 0.0139 (2) | 0.0108 (2) | −0.00021 (18) | 0.00163 (17) | 0.00039 (18) |
| C3 | 0.0143 (2) | 0.0153 (2) | 0.0142 (2) | 0.00085 (19) | 0.00352 (19) | 0.0011 (2) |
| C4 | 0.0168 (2) | 0.0140 (2) | 0.0137 (2) | 0.0020 (2) | 0.00586 (19) | 0.00056 (19) |
| C5 | 0.0172 (2) | 0.0141 (2) | 0.0117 (2) | 0.00022 (19) | 0.00350 (19) | −0.00028 (19) |
| C6 | 0.0264 (3) | 0.0224 (3) | 0.0135 (3) | −0.0011 (3) | 0.0023 (2) | −0.0044 (2) |
| Cl1—C4 | 1.7396 (7) | C2—C3 | 1.3733 (9) |
| Cl2—C2 | 1.7346 (6) | C3—C4 | 1.3941 (9) |
| N1—C1 | 1.3409 (8) | C3—H3 | 0.970 (13) |
| N1—C5 | 1.3468 (9) | C4—C5 | 1.3894 (10) |
| N2—C1 | 1.3607 (9) | C5—C6 | 1.4996 (10) |
| N2—H2N1 | 0.869 (14) | C6—H6C | 0.924 (17) |
| N2—H1N1 | 0.828 (14) | C6—H6B | 0.96 (2) |
| C1—C2 | 1.4118 (9) | C6—H6A | 1.02 (2) |
| C1—N1—C5 | 121.03 (6) | C5—C4—C3 | 120.23 (6) |
| C1—N2—H2N1 | 116.4 (9) | C5—C4—Cl1 | 121.27 (5) |
| C1—N2—H1N1 | 115.0 (9) | C3—C4—Cl1 | 118.50 (5) |
| H2N1—N2—H1N1 | 119.1 (13) | N1—C5—C4 | 120.35 (6) |
| N1—C1—N2 | 117.62 (6) | N1—C5—C6 | 116.03 (6) |
| N1—C1—C2 | 120.07 (6) | C4—C5—C6 | 123.62 (6) |
| N2—C1—C2 | 122.28 (6) | C5—C6—H6C | 109.4 (10) |
| C3—C2—C1 | 120.08 (6) | C5—C6—H6B | 115.3 (11) |
| C3—C2—Cl2 | 120.37 (5) | H6C—C6—H6B | 102.0 (15) |
| C1—C2—Cl2 | 119.55 (5) | C5—C6—H6A | 111.3 (11) |
| C2—C3—C4 | 118.24 (6) | H6C—C6—H6A | 107.2 (15) |
| C2—C3—H3 | 118.9 (7) | H6B—C6—H6A | 110.8 (14) |
| C4—C3—H3 | 122.8 (7) | ||
| C5—N1—C1—N2 | 178.27 (6) | C2—C3—C4—C5 | 0.46 (10) |
| C5—N1—C1—C2 | 0.13 (10) | C2—C3—C4—Cl1 | −179.37 (5) |
| N1—C1—C2—C3 | −0.61 (10) | C1—N1—C5—C4 | 0.64 (10) |
| N2—C1—C2—C3 | −178.66 (7) | C1—N1—C5—C6 | 179.98 (6) |
| N1—C1—C2—Cl2 | 179.63 (5) | C3—C4—C5—N1 | −0.94 (10) |
| N2—C1—C2—Cl2 | 1.58 (9) | Cl1—C4—C5—N1 | 178.89 (5) |
| C1—C2—C3—C4 | 0.29 (10) | C3—C4—C5—C6 | 179.77 (7) |
| Cl2—C2—C3—C4 | −179.95 (5) | Cl1—C4—C5—C6 | −0.40 (10) |
| D—H···A | D—H | H···A | D···A | D—H···A |
| N2—H2N1···N1i | 0.869 (15) | 2.168 (15) | 3.0320 (9) | 172.8 (13) |
| N2—H1N1···Cl2 | 0.828 (14) | 2.603 (14) | 3.0156 (7) | 112.3 (12) |
| C6—H6A···Cl1 | 1.02 (2) | 2.67 (2) | 3.1318 (9) | 108.0 (14) |
| N2—H1N1···Cl2ii | 0.828 (14) | 2.900 (14) | 3.6758 (7) | 156.9 (13) |
| Symmetry codes: (i) −x+1, −y+1, −z; (ii) −x+1/2, y−1/2, −z−1/2. |
| D—H···A | D—H | H···A | D···A | D—H···A |
| N2—H2N1···N1i | 0.869 (15) | 2.168 (15) | 3.0320 (9) | 172.8 (13) |
| N2—H1N1···Cl2 | 0.828 (14) | 2.603 (14) | 3.0156 (7) | 112.3 (12) |
| C6—H6A···Cl1 | 1.02 (2) | 2.67 (2) | 3.1318 (9) | 108.0 (14) |
| N2—H1N1···Cl2ii | 0.828 (14) | 2.900 (14) | 3.6758 (7) | 156.9 (13) |
| Symmetry codes: (i) −x+1, −y+1, −z; (ii) −x+1/2, y−1/2, −z−1/2. |
HKF and RK thank the Malaysian Government and Universiti Sains Malaysia for the Science Fund grant No. 305/PFIZIK/613312. RK thanks Universiti Sains Malaysia for a post-doctoral research fellowship. We thank the DST [SR/S1/OC-13/2005], Govt. of India, for financial support. ACM thanks the UGC, Govt. of India, for a fellowship. HKF also thanks Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012.
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The halogen substituted π-depleted heteroaromatics (e.g. pterin, quinoxaline, naphthyridine, or pyridine derivatives) are important intermediates in modern organic chemistry (Goswami & Maity 2007; Taylor et al. 1989; Taylor & Ray 1988; Beer et al. 1993), e.g. they are used as precursors for pharmacologically active compounds. These are also versatile compounds in manifold synthesis of artificial receptors for molecular recognition (Goswami et al. 2000, 2005; Fun et al. 2008).
In the title compound (I), Fig. 1, intramolecular N–H···Cl and C—H···Cl contacts generate five-membered rings, producing S(5) ring motifs (Bernstein et al., 1995). Pairs of intermolecular N—H···N hydrogen bonds link molecules into dimers with a R22(8) ring motif (Table 1). In the crystal structure, these dimers are connected by N—H···Cl interactions and are packed into columns along the b axis, Fig. 2.