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

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3,5-Di­chloro-6-methyl­pyridin-2-amine

aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and bDepartment of Chemistry, Bengal Engineering and Science University, Shibpur, Howrah 711 103, India
*Correspondence e-mail: hkfun@usm.my

(Received 5 December 2008; accepted 7 December 2008; online 13 December 2008)

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 R22(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[Bernstein, J., Davis, R. E., Shimoni, L. & Chamg, N.-L. (1995). Angew. Chem. Int. Ed. Eng1. 34, 1555-1573.]). For related literature and applications see, for example: Goswami & Maity (2007[Goswami, S. P. & Maity, A. C. (2007). Chem. Lett. 36, 552-555.]); Taylor et al. (1989[Taylor, E. C., Ray, P. S., Darwish, I. S., Johnson, J. L. & Rajagopalan, K. V. (1989). J. Am. Chem. Soc. 111, 7664-7665.]); Taylor & Ray (1988[Taylor, E. C. & Ray, P. S. (1988). J. Am. Chem. Soc. 53, 35-41.]); Beer et al. (1993[Beer, R. H., Jimenez, J. & Drago, R. S. (1993). J. Org. Chem. 58, 1746-1747.]); Goswami et al. (2000[Goswami, S. P., Ghosh, K. & Dasgupta, S. J. (2000). J. Org. Chem. 65, 1907-1914.], 2005[Goswami, S. P., Dey, S., Fun, H. K., Anjum, S. & Rahman, A. (2005). Tetrahedron Lett. 46, 7187-7191.]); Fun et al. (2008[Fun, H.-K., Chantrapromma, S., Jana, S., Chakrabarty, R. & Goswami, S. (2008). Acta Cryst. E64, o1659-o1660.]).

[Scheme 1]

Experimental

Crystal data
  • C6H6Cl2N2

  • Mr = 177.03

  • Monoclinic, P 21 /n

  • 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[Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.711, Tmax = 0.803

  • 26531 measured reflections

  • 3795 independent reflections

  • 3485 reflections with I > 2˘I)

  • Rint = 0.026

Refinement
  • R[F2 > 2σ(F2)] = 0.024

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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 code: (i) -x+1, -y+1, -z.

Data collection: APEX2 (Bruker, 2005[Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2005[Bruker (2005). APEX2, 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; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2003[Spek, A. L. (2003). J. Appl. Cryst. 36, 7-13.]).

Supporting information


Comment top

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.

Related literature top

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

Experimental top

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 top

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.

Computing details top

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).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I), showing 50% probability displacement ellipsoids and the atomic numbering. Dashed lines show intramolecular hydrogen bonds.
[Figure 2] 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.
3,5-Dichloro-6-methylpyridin-2-amine top
Crystal data top
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 top
Bruker SMART APEXII CCD area-detector
diffractometer
3795 independent reflections
Radiation source: fine-focus sealed tube3485 reflections with I > 2˘I)
Graphite monochromatorRint = 0.026
ϕ and ω scansθmax = 37.5°, θmin = 2.4°
Absorption correction: multi-scan
(SADABS; Bruker, 2005)
h = 2121
Tmin = 0.711, Tmax = 0.803k = 66
26531 measured reflectionsl = 2626
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)] = 0.024Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.071All 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 parametersΔρmax = 0.61 e Å3
0 restraintsΔρmin = 0.42 e Å3
Crystal data top
C6H6Cl2N2V = 723.01 (3) Å3
Mr = 177.03Z = 4
Monoclinic, P21/nMo Kα radiation
a = 12.7670 (3) ŵ = 0.81 mm1
b = 3.8037 (1) ÅT = 100 K
c = 15.4129 (3) Å0.45 × 0.31 × 0.28 mm
β = 104.990 (1)°
Data collection top
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 = 0.803Rint = 0.026
26531 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0240 restraints
wR(F2) = 0.071All H-atom parameters refined
S = 1.11Δρmax = 0.61 e Å3
3795 reflectionsΔρmin = 0.42 e Å3
115 parameters
Special details top

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) top
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) top
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, º) top
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—Cl1179.37 (5)
N1—C1—C2—C30.61 (10)C1—N1—C5—C40.64 (10)
N2—C1—C2—C3178.66 (7)C1—N1—C5—C6179.98 (6)
N1—C1—C2—Cl2179.63 (5)C3—C4—C5—N10.94 (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—C4179.95 (5)Cl1—C4—C5—C60.40 (10)
Hydrogen-bond geometry (Å, º) top
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, y1/2, z1/2.

Experimental details

Crystal data
Chemical formulaC6H6Cl2N2
Mr177.03
Crystal system, space groupMonoclinic, P21/n
Temperature (K)100
a, b, c (Å)12.7670 (3), 3.8037 (1), 15.4129 (3)
β (°) 104.990 (1)
V3)723.01 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.81
Crystal size (mm)0.45 × 0.31 × 0.28
Data collection
DiffractometerBruker SMART APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2005)
Tmin, Tmax0.711, 0.803
No. of measured, independent and
observed [I > 2˘I)] reflections
26531, 3795, 3485
Rint0.026
(sin θ/λ)max1)0.857
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.024, 0.071, 1.11
No. of reflections3795
No. of parameters115
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å3)0.61, 0.42

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2003).

Hydrogen-bond geometry (Å, º) top
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, y1/2, z1/2.
 

Acknowledgements

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.

References

First citationBeer, R. H., Jimenez, J. & Drago, R. S. (1993). J. Org. Chem. 58, 1746–1747.  CrossRef CAS Web of Science Google Scholar
First citationBernstein, J., Davis, R. E., Shimoni, L. & Chamg, N.-L. (1995). Angew. Chem. Int. Ed. Eng1. 34, 1555–1573.  CrossRef CAS Web of Science Google Scholar
First citationBruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationFun, H.-K., Chantrapromma, S., Jana, S., Chakrabarty, R. & Goswami, S. (2008). Acta Cryst. E64, o1659–o1660.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationGoswami, S. P., Dey, S., Fun, H. K., Anjum, S. & Rahman, A. (2005). Tetrahedron Lett. 46, 7187–7191.  Web of Science CSD CrossRef CAS Google Scholar
First citationGoswami, S. P., Ghosh, K. & Dasgupta, S. J. (2000). J. Org. Chem. 65, 1907–1914.  Web of Science CrossRef PubMed CAS Google Scholar
First citationGoswami, S. P. & Maity, A. C. (2007). Chem. Lett. 36, 552–555.  Web of Science CSD CrossRef CAS Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSpek, A. L. (2003). J. Appl. Cryst. 36, 7–13.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationTaylor, E. C. & Ray, P. S. (1988). J. Am. Chem. Soc. 53, 35–41.  CAS Google Scholar
First citationTaylor, E. C., Ray, P. S., Darwish, I. S., Johnson, J. L. & Rajagopalan, K. V. (1989). J. Am. Chem. Soc. 111, 7664–7665.  CrossRef CAS Web of Science Google Scholar

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