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Acta Crystallogr Sect E Struct Rep Online. 2009 January 1; 65(Pt 1): o97.
Published online 2008 December 13. doi:  10.1107/S1600536808041366
PMCID: PMC2968004

3,5-Dichloro-6-methyl­pyridin-2-amine

Abstract

In the title compound, C6H6Cl2N2, intra­molecular N–H(...)Cl and C—H(...)Cl contacts generate five-membered rings, producing S(5) ring motifs. Pairs of inter­molecular N—H(...)N hydrogen bonds link neighbouring mol­ecules into dimers with R 2 2(8) ring motifs. In the crystal structure, these dimers are connected by N—H(...)Cl inter­actions and are packed into columns.

Related literature

For details of hydrogen-bond motifs, see: Bernstein et al. (1995 [triangle]). For related literature and applications see, for example: Goswami & Maity (2007 [triangle]); Taylor et al. (1989 [triangle]); Taylor & Ray (1988 [triangle]); Beer et al. (1993 [triangle]); Goswami et al. (2000 [triangle], 2005 [triangle]); Fun et al. (2008 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-00o97-scheme1.jpg

Experimental

Crystal data

  • C6H6Cl2N2
  • M r = 177.03
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-00o97-efi1.jpg
  • a = 12.7670 (3) Å
  • b = 3.8037 (1) Å
  • c = 15.4129 (3) Å
  • β = 104.990 (1)°
  • V = 723.01 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.81 mm−1
  • T = 100.0 (1) K
  • 0.45 × 0.31 × 0.28 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.711, T max = 0.803
  • 26531 measured reflections
  • 3795 independent reflections
  • 3485 reflections with I > 2˘I)
  • R int = 0.026

Refinement

  • R[F 2 > 2σ(F 2)] = 0.024
  • wR(F 2) = 0.071
  • S = 1.11
  • 3795 reflections
  • 115 parameters
  • All H-atom parameters refined
  • Δρmax = 0.61 e Å−3
  • Δρmin = −0.42 e Å−3

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2003 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808041366/tk2343sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808041366/tk2343Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

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.

supplementary crystallographic information

Comment

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.

Experimental

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.

Refinement

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.

Figures

Fig. 1.
The molecular structure of (I), showing 50% probability displacement ellipsoids and the atomic numbering. Dashed lines show intramolecular hydrogen bonds.
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.

Crystal data

C6H6Cl2N2F(000) = 360
Mr = 177.03Dx = 1.626 Mg m3
Monoclinic, P21/nMelting point: 404 K
Hall symbol: -P 2ynMo Kα radiation, λ = 0.71073 Å
a = 12.7670 (3) ÅCell parameters from 9896 reflections
b = 3.8037 (1) Åθ = 2.4–40.3°
c = 15.4129 (3) ŵ = 0.81 mm1
β = 104.990 (1)°T = 100 K
V = 723.01 (3) Å3Block, colourless
Z = 40.45 × 0.31 × 0.28 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer3795 independent reflections
Radiation source: fine-focus sealed tube3485 reflections with I > 2˘I)
graphiteRint = 0.026
[var phi] and ω scansθmax = 37.5°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −21→21
Tmin = 0.711, Tmax = 0.803k = −6→6
26531 measured reflectionsl = −26→26

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.024Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.071All H-atom parameters refined
S = 1.11w = 1/[σ2(Fo2) + (0.037P)2 + 0.1631P] where P = (Fo2 + 2Fc2)/3
3795 reflections(Δ/σ)max = 0.001
115 parametersΔρmax = 0.61 e Å3
0 restraintsΔρmin = −0.42 e Å3

Special details

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
Cl10.116608 (15)0.89761 (5)0.117299 (12)0.01973 (5)
Cl20.150078 (13)0.32687 (5)−0.194719 (10)0.01603 (4)
N10.36956 (5)0.65340 (16)0.02268 (4)0.01455 (9)
N20.38950 (5)0.41291 (19)−0.10983 (4)0.01738 (11)
H2N10.4571 (12)0.379 (4)−0.0819 (9)0.027 (3)*
H1N10.3607 (11)0.284 (4)−0.1526 (9)0.025 (3)*
C10.32310 (5)0.51854 (18)−0.05855 (4)0.01322 (10)
C20.20904 (5)0.49965 (17)−0.08923 (4)0.01321 (10)
C30.14544 (5)0.61633 (18)−0.03563 (4)0.01465 (10)
H30.0672 (10)0.605 (3)−0.0583 (8)0.022 (3)*
C40.19660 (5)0.75331 (18)0.04856 (4)0.01450 (10)
C50.30903 (5)0.77194 (18)0.07629 (4)0.01437 (10)
C60.37037 (7)0.9165 (2)0.16549 (5)0.02130 (13)
H6C0.4268 (13)1.055 (5)0.1579 (11)0.041 (4)*
H6B0.4079 (16)0.744 (5)0.2083 (12)0.061 (5)*
H6A0.3222 (16)1.071 (6)0.1929 (13)0.065 (6)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.02170 (8)0.02155 (8)0.01862 (8)0.00364 (6)0.01006 (6)−0.00108 (5)
Cl20.01665 (7)0.01786 (7)0.01167 (7)−0.00132 (5)0.00022 (5)−0.00081 (5)
N10.0143 (2)0.0174 (2)0.0113 (2)−0.00002 (17)0.00219 (17)−0.00112 (17)
N20.0146 (2)0.0247 (3)0.0127 (2)0.00163 (19)0.00317 (18)−0.00292 (19)
C10.0136 (2)0.0146 (2)0.0110 (2)0.00045 (18)0.00251 (18)0.00056 (18)
C20.0140 (2)0.0139 (2)0.0108 (2)−0.00021 (18)0.00163 (17)0.00039 (18)
C30.0143 (2)0.0153 (2)0.0142 (2)0.00085 (19)0.00352 (19)0.0011 (2)
C40.0168 (2)0.0140 (2)0.0137 (2)0.0020 (2)0.00586 (19)0.00056 (19)
C50.0172 (2)0.0141 (2)0.0117 (2)0.00022 (19)0.00350 (19)−0.00028 (19)
C60.0264 (3)0.0224 (3)0.0135 (3)−0.0011 (3)0.0023 (2)−0.0044 (2)

Geometric parameters (Å, °)

Cl1—C41.7396 (7)C2—C31.3733 (9)
Cl2—C21.7346 (6)C3—C41.3941 (9)
N1—C11.3409 (8)C3—H30.970 (13)
N1—C51.3468 (9)C4—C51.3894 (10)
N2—C11.3607 (9)C5—C61.4996 (10)
N2—H2N10.869 (14)C6—H6C0.924 (17)
N2—H1N10.828 (14)C6—H6B0.96 (2)
C1—C21.4118 (9)C6—H6A1.02 (2)
C1—N1—C5121.03 (6)C5—C4—C3120.23 (6)
C1—N2—H2N1116.4 (9)C5—C4—Cl1121.27 (5)
C1—N2—H1N1115.0 (9)C3—C4—Cl1118.50 (5)
H2N1—N2—H1N1119.1 (13)N1—C5—C4120.35 (6)
N1—C1—N2117.62 (6)N1—C5—C6116.03 (6)
N1—C1—C2120.07 (6)C4—C5—C6123.62 (6)
N2—C1—C2122.28 (6)C5—C6—H6C109.4 (10)
C3—C2—C1120.08 (6)C5—C6—H6B115.3 (11)
C3—C2—Cl2120.37 (5)H6C—C6—H6B102.0 (15)
C1—C2—Cl2119.55 (5)C5—C6—H6A111.3 (11)
C2—C3—C4118.24 (6)H6C—C6—H6A107.2 (15)
C2—C3—H3118.9 (7)H6B—C6—H6A110.8 (14)
C4—C3—H3122.8 (7)
C5—N1—C1—N2178.27 (6)C2—C3—C4—C50.46 (10)
C5—N1—C1—C20.13 (10)C2—C3—C4—Cl1−179.37 (5)
N1—C1—C2—C3−0.61 (10)C1—N1—C5—C40.64 (10)
N2—C1—C2—C3−178.66 (7)C1—N1—C5—C6179.98 (6)
N1—C1—C2—Cl2179.63 (5)C3—C4—C5—N1−0.94 (10)
N2—C1—C2—Cl21.58 (9)Cl1—C4—C5—N1178.89 (5)
C1—C2—C3—C40.29 (10)C3—C4—C5—C6179.77 (7)
Cl2—C2—C3—C4−179.95 (5)Cl1—C4—C5—C6−0.40 (10)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2N1···N1i0.869 (15)2.168 (15)3.0320 (9)172.8 (13)
N2—H1N1···Cl20.828 (14)2.603 (14)3.0156 (7)112.3 (12)
C6—H6A···Cl11.02 (2)2.67 (2)3.1318 (9)108.0 (14)
N2—H1N1···Cl2ii0.828 (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.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: TK2343).

References

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Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography