A redetermination of 2-amino-5-chloro­pyridine at 100 K

X-ray and neutron diffraction studies of 2-amino-5-chloro­pyridine, C₅H₅ClN₂, were previously carried out at room temperature [Kvick & Backéus (1974). Acta Cryst. B30, 474–480; Kvick, Thomas & Koetzle (1976). Acta Cryst. B32, 224–231]. This report is a redetermination of the crystal structure at 100 K. As previously observed, mol­ecules form centrosymmetric dimers via two N—H...N hydrogen bonds. In addition, C—H...π inter­actions are generated from mol­ecules related by c-glide transformations, which form extended two-dimensional aggregation in the bc plane.

Key indicators

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.027
• wR factor = 0.071
• Data-to-parameter ratio = 13.8

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT222_ALERT_3_C Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       3.80 Ratio
PLAT420_ALERT_2_C D-H Without Acceptor       N2     -   H4     ...          ?

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   2 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

This work is a continuation of the previous studies on the influence of hydrogen bonds (Ravikumar et al. 2001; Zakaria et al. 2002; Zou et al. 2003) and other non-covalent forces (Pourayoubi & Mahjoub 2007) on crystal stabilization. Some investigations of crystal structures of organic molecules which can play a role as model substances for biologically systems have been reported (Simpson & Marsh 1966; Averbuch-Pouchot et al. 1988; Iitaka 1961; Barlow et al. 1989). The crystal structures of 6-chloro-2-hyroxypyridine, the addition compound 6-chloro-2-hydroxypyridine-2-pyridone and 5-chloro-2-pyridone have been reported by Kvick & Olovsson (1968), Almlöf et al. (1971) and Kvick & Booles (1972). Furthermore, the X-ray crystal structure and neutron diffraction study of 2-amino-5-chloropyridine was previously studied at room temperature (Kvick & Backéus 1974; Kvick et al. 1976). Here, we report the structure of 2-amino-5-chloropyridine (Fig. 1), C₅H₃N(NH₂)Cl, at 100 K. a, b, and c and the volume of the unit cell are 13.352 (4) Å, 5.7576 (16) Å, 7.266 (2) Å and 540.1 (3) ų compared to 13.4370 (6) Å, 5.7963 (5) Å, 7.5123 (6) Å and 563.78 ų at room temperature (Kvick & Backéus 1974)]. In the crystal structure, molecules exist as a centrosymmtric dimers produced via two N2—H1N···N1ⁱ hydrogen bonds, Table 1. The donor···acceptor distance at 100 K is similar to the one reported in the previous work at room temperature [N···N = 3.058 (2) Å with an almost linear bond angle, N2—H1···N1=179 (2)°, (Kvick & Backéus 1974)]. The C—H..π interactions (between hydrogen atoms of the C2 and C5 and the phenyl groups) are generated from molecules related by c-glide transformations which form extended 2-D aggregation along the bc plane (Table 1 and Fig. 2). An alternate view of part the crystal structure (along c crystal axes) is shown in Fig. 3.

Related literature

For related literature, see: Almlöf et al. (1971); Averbuch-Pouchot et al. (1988); Barlow et al. (1989); Iitaka (1961); Kvick & Backéus (1974); Kvick et al. (1976); Kvick & Booles (1972); Kvick & Olovsson (1968); Pourayoubi & Mahjoub (2007); Ravikumar et al. (2001); Zakaria et al. (2002); Zou et al. (2003); Simpson & Marsh (1966).

S2. Experimental

Single crystal of the title compound was grown in CHCl₃ at room temperature.

S3. Refinement

All hydrogen atoms were found in difference Fourier synthesis and refined with isotropic displacement parameters.

Computing details

Data collection: APEX2 (Bruker, 2005); cell refinement: APEX2 (Bruker, 2005); data reduction: APEX2 (Bruker, 2005); program(s) used to solve structure: SHELXTL (Sheldrick, 1998); program(s) used to refine structure: SHELXTL (Sheldrick, 1998); molecular graphics: SHELXTL (Sheldrick, 1998); software used to prepare material for publication: SHELXTL (Sheldrick, 1998).

Figures

	Fig. 1. Molecular structure (50% probability level) of the title compound.
	Fig. 2. The N—H···N hydrogen bonds and C—H···π interations (dotted lines) in the title compound [symmetry codes: (A) 1 - x, -y, 1 - z, (B) x, -y - 1/2, z + 1/2, (C) x, -y + 1/2, z - 1/2].
	Fig. 3. Crystal packing fragment (along c crystal axes). Hydrogen bonds are shown with dashed lines.

2-amino-5-chloropyridine

Crystal data

C5H5ClN2	F(000) = 264
Mr = 128.56	Dx = 1.581 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2192 reflections
a = 13.352 (4) Å	θ = 3.2–30.2°
b = 5.7576 (16) Å	µ = 0.58 mm^−1
c = 7.266 (2) Å	T = 100 K
β = 104.787 (6)°	Plate, colourless
V = 540.1 (3) Å^3	0.45 × 0.30 × 0.28 mm
Z = 4

Data collection

Bruker APEXII CCD area-detector diffractometer	1120 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.027
Graphite monochromator	θmax = 28.0°, θmin = 3.2°
phi and ω scans	h = −17→16
4557 measured reflections	k = −7→7
1285 independent reflections	l = −9→9

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.027	Hydrogen site location: difference Fourier map
wR(F^2) = 0.071	All H-atom parameters refined
S = 0.99	w = 1/[σ^2(Fo^2) + (0.0369P)^2 + 0.2721P] where P = (Fo^2 + 2Fc^2)/3
1285 reflections	(Δ/σ)max < 0.001
93 parameters	Δρmax = 0.35 e Å^−3
0 restraints	Δρmin = −0.26 e Å^−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
Cl1	0.07655 (3)	0.32409 (6)	0.36049 (5)	0.01544 (12)
N1	0.36278 (9)	0.0679 (2)	0.46525 (17)	0.0137 (3)
N2	0.43944 (11)	−0.2738 (2)	0.5964 (2)	0.0215 (3)
C1	0.35261 (11)	−0.1409 (2)	0.5433 (2)	0.0137 (3)
C2	0.25635 (11)	−0.2195 (2)	0.56561 (19)	0.0134 (3)
C3	0.17031 (11)	−0.0806 (2)	0.50649 (19)	0.0129 (3)
C4	0.18174 (11)	0.1365 (2)	0.42853 (19)	0.0120 (3)
C5	0.27789 (11)	0.2027 (2)	0.4098 (2)	0.0125 (3)
H1	0.2870 (14)	0.350 (3)	0.354 (2)	0.010 (4)*
H2	0.1058 (16)	−0.130 (3)	0.514 (3)	0.023 (5)*
H3	0.2503 (13)	−0.367 (3)	0.621 (2)	0.013 (4)*
H4	0.4369 (16)	−0.398 (4)	0.660 (3)	0.029 (5)*
H5	0.4960 (19)	−0.226 (4)	0.580 (3)	0.038 (6)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl1	0.01112 (18)	0.01549 (19)	0.01969 (19)	0.00267 (12)	0.00392 (13)	0.00262 (12)
N1	0.0130 (6)	0.0129 (6)	0.0151 (5)	−0.0003 (4)	0.0036 (5)	0.0008 (4)
N2	0.0162 (7)	0.0180 (7)	0.0317 (8)	0.0056 (5)	0.0089 (6)	0.0107 (6)
C1	0.0145 (7)	0.0134 (6)	0.0133 (6)	0.0011 (5)	0.0036 (5)	−0.0009 (5)
C2	0.0172 (7)	0.0109 (6)	0.0126 (6)	−0.0007 (5)	0.0050 (5)	0.0000 (5)
C3	0.0134 (7)	0.0140 (7)	0.0124 (6)	−0.0030 (5)	0.0052 (5)	−0.0019 (5)
C4	0.0109 (6)	0.0121 (6)	0.0122 (6)	0.0023 (5)	0.0016 (5)	−0.0013 (5)
C5	0.0137 (7)	0.0105 (6)	0.0131 (6)	−0.0009 (5)	0.0030 (5)	−0.0005 (5)

Geometric parameters (Å, º)

Cl1—C4	1.7404 (14)	C2—C3	1.375 (2)
N1—C5	1.3479 (19)	C2—H3	0.954 (17)
N1—C1	1.3506 (19)	C3—C4	1.3970 (19)
N2—C1	1.3602 (19)	C3—H2	0.92 (2)
N2—H4	0.86 (2)	C4—C5	1.379 (2)
N2—H5	0.84 (2)	C5—H1	0.961 (16)
C1—C2	1.410 (2)
C5—N1—C1	118.11 (12)	C2—C3—C4	118.55 (13)
C1—N2—H4	118.4 (14)	C2—C3—H2	121.5 (12)
C1—N2—H5	120.5 (16)	C4—C3—H2	119.9 (12)
H4—N2—H5	121 (2)	C5—C4—C3	119.23 (13)
N1—C1—N2	116.76 (13)	C5—C4—Cl1	120.31 (11)
N1—C1—C2	121.73 (13)	C3—C4—Cl1	120.45 (11)
N2—C1—C2	121.50 (13)	N1—C5—C4	122.98 (13)
C3—C2—C1	119.39 (13)	N1—C5—H1	116.5 (10)
C3—C2—H3	119.8 (10)	C4—C5—H1	120.5 (10)
C1—C2—H3	120.8 (10)
C5—N1—C1—N2	179.49 (13)	C2—C3—C4—C5	1.3 (2)
C5—N1—C1—C2	0.6 (2)	C2—C3—C4—Cl1	−177.34 (11)
N1—C1—C2—C3	0.0 (2)	C1—N1—C5—C4	−0.3 (2)
N2—C1—C2—C3	−178.79 (14)	C3—C4—C5—N1	−0.7 (2)
C1—C2—C3—C4	−1.0 (2)	Cl1—C4—C5—N1	177.96 (11)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H5···N1^i	0.84 (2)	2.19 (3)	3.031 (2)	175
C2—H3···Cg^ii	0.95 (2)	2.71	3.414	134
C5—H1···Cg^iii	0.96 (2)	2.76	3.506	131

Symmetry codes: (i) −x+1, −y, −z+1; (ii) x, −y−1/2, z+1/2; (iii) x, −y+1/2, z−1/2.