X-ray and neutron diffraction studies of 2-amino-5-chloropyridine, C
5H
5ClN
2, were previously carried out at room temperature [Kvick & Backéus (1974).
Acta Cryst. B
30, 474–480; Kvick, Thomas & Koetzle (1976).
Acta Cryst. B
32, 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.
Supporting information
CCDC reference: 658008
Key indicators
- Single-crystal X-ray study
- T = 100 K
- Mean
(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
Single crystal of the title compound was grown in CHCl3 at room temperature.
All hydrogen atoms were found in difference Fourier synthesis and refined with
isotropic displacement parameters.
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).
2-amino-5-chloropyridine
top
Crystal data top
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) Å3 | 0.45 × 0.30 × 0.28 mm |
Z = 4 | |
Data collection top
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 top
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)] = 0.027 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.071 | All H-atom parameters refined |
S = 0.99 | w = 1/[σ2(Fo2) + (0.0369P)2 + 0.2721P] where P = (Fo2 + 2Fc2)/3 |
1285 reflections | (Δ/σ)max < 0.001 |
93 parameters | Δρmax = 0.35 e Å−3 |
0 restraints | Δρmin = −0.26 e Å−3 |
Crystal data top
C5H5ClN2 | V = 540.1 (3) Å3 |
Mr = 128.56 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 13.352 (4) Å | µ = 0.58 mm−1 |
b = 5.7576 (16) Å | T = 100 K |
c = 7.266 (2) Å | 0.45 × 0.30 × 0.28 mm |
β = 104.787 (6)° | |
Data collection top
Bruker APEXII CCD area-detector diffractometer | 1120 reflections with I > 2σ(I) |
4557 measured reflections | Rint = 0.027 |
1285 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.027 | 0 restraints |
wR(F2) = 0.071 | All H-atom parameters refined |
S = 0.99 | Δρmax = 0.35 e Å−3 |
1285 reflections | Δρmin = −0.26 e Å−3 |
93 parameters | |
Special details top
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 | 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 (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
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) top
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) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H5···N1i | 0.84 (2) | 2.19 (3) | 3.031 (2) | 175 |
C2—H3···Cgii | 0.95 (2) | 2.71 | 3.414 | 134 |
C5—H1···Cgiii | 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. |
Experimental details
Crystal data |
Chemical formula | C5H5ClN2 |
Mr | 128.56 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 100 |
a, b, c (Å) | 13.352 (4), 5.7576 (16), 7.266 (2) |
β (°) | 104.787 (6) |
V (Å3) | 540.1 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.58 |
Crystal size (mm) | 0.45 × 0.30 × 0.28 |
|
Data collection |
Diffractometer | Bruker APEXII CCD area-detector diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4557, 1285, 1120 |
Rint | 0.027 |
(sin θ/λ)max (Å−1) | 0.661 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.027, 0.071, 0.99 |
No. of reflections | 1285 |
No. of parameters | 93 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.35, −0.26 |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H5···N1i | 0.84 (2) | 2.19 (3) | 3.031 (2) | 175 |
C2—H3···Cgii | 0.95 (2) | 2.71 | 3.414 | 134 |
C5—H1···Cgiii | 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. |
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) Å3 compared to 13.4370 (6) Å, 5.7963 (5) Å, 7.5123 (6) Å and 563.78 Å3 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.