research communications
Crystallographic and spectroscopic characterization of 5-chloropyridine-2,3-diamine
aDepartment of Chemistry, Vassar College, Poughkeepsie, NY 12604, USA
*Correspondence e-mail: jotanski@vassar.edu
The two ortho-amino groups of the title compound, C5H6ClN3, twist out of the plane of the molecule to minimize intramolecular interaction between the amino hydrogen atoms. In the crystal, the amino groups and the pyridine N atom engage in intermolecular hydrogen bonding. The molecules pack into spiral hydrogen-bonded columns with offset face-to-face π-stacking.
Keywords: crystal structure; hydrogen bonding; π-stacking.
CCDC reference: 1562267
1. Chemical context
The title compound, 5-chloropyridine-2,3-diamine, is a trisubstituted pyridine featuring ortho-amino groups and a chlorine atom. While all of the sixteen isomers of 5-chloropyridine-2,3-diamine are commercially available, none of their crystal structures have been reported in the literature. 5-Chloropyridine-2,3-diamine may be produced by nitrating 2-amino-5-chloropyridine with nitric acid to give 2-amino-3-nitro-5-chloropyridine, which is then reduced with sodium dithionite (Israel & Day, 1959). The reduction may also be accomplished with hydrogen gas and Pd/C (Xie et al., 2016). 5-Chloropyridine-2,3-diamine has proven useful as a reagent in complex syntheses, such as in the synthesis of aldose reductase inhibitors with antioxidant activity (Han et al., 2016), the regioselective functionalization of imidazopyridines via alkenylation catalyzed by a Pd/Cu catalyst (Baladi et al., 2016), the preparation of amino acid oxidase inhibitors (Xie et al., 2016), the preparation of β-glucuronidase inhibitors (Taha et al., 2016), the preparation of imidazopyridine derivatives with activity against MCF-7 breast adenocarcinoma (Püsküllü et al., 2015) and the preparation of dihydroxyarene-substituted benzimidazoles, quinazolines and larger rings via cyclocondensation of diamines (Los et al., 2012).
2. Structural commentary
The molecular structure of the title compound 5-chloropyridine-2,3-diamine (Fig. 1) shows that the molecule is nearly planar with r.m.s deviation from the mean plane of all non-hydrogen atoms of 0.013 (3) Å. The amino groups ortho and meta to the pyridine nitrogen atom twist out of the plane of the molecule in such a way as to minimize contact with one another, with NH2 plane to molecular plane angles of 45 (3) and 34 (3)° for N2 and N3, respectively. It is notable that the achiral title compound crystallizes in a non-enantiogenic (Söhncke) although not a polar space group.
3. Supramolecular features
Notable intermolecular interactions observed in the structure of 5-chloropyridine-2,3-diamine (I) include Namine—H⋯Npyr and Namine—H⋯Namine hydrogen bonding interactions and offset face-to-face π-stacking. The molecules connect into a one-dimensional strip running parallel to the crystallographic b axis (Fig. 2) with long N3amine—H21⋯N2iiamine [symmetry code (ii) −x + 2, y − , −z + ] and N3amine—H22⋯N1iiipyr [symmetry code (iii) −x + 2, y + , −z + ] hydrogen bonding interactions with donor–acceptor distances of 3.250 (4) and 3.075 (4) Å, respectively (Table 1). A third Namine—H⋯Npyr hydrogen-bonding contact and offset face-to-face π-stacking can be seen to extend along the crystallographic a axis (Fig. 3), acting to link the one-dimensional strips into two-dimensional sheets. The N2amine—H12⋯N1pyri [symmetry code (i) −x + 1, y + , −z + ] contact exhibits a donor–acceptor distance 3.264 (3) Å. The π-stacking is characterized by a centroid-to-centroid distance of 3.756 (1) Å, plane-to-plane distances of 3.414 (2) Å and a ring offset of 1.568 (3) Å (Hunter & Saunders, 1990; Lueckheide et al., 2013). Alternatively, the three hydrogen-bonding contacts and the π-stacking taken together can be seen to form a spiral of 5-chloropyridine-2,3-diamine (I) molecules extending along the a-axis direction (Fig. 4).
4. Database survey
The Cambridge Structural Database (Groom et al., 2016) contains about fifty structurally similar compounds to 5-chloropyridine-2,3-diamine (I), with 2-amino-5-chloropyridine (AMCLPY12) (Pourayoubi et al., 2007) and 2-amino-3-chloropyridine (URAXER) (Hu et al., 2011) being the most chemically and structurally similar. The C—Cl bond length in the title compound, with distance 1.748 (3) Å, is comparable to those in 2-amino-5-chloropyridine (AMCLPY12) and 2-amino-3-chloropyridine (URAXER), with distances 1.7404 (14) and 1.735 (3) Å, respectively. The C—Namine distances in the title compound, 1.406 (4) and 1.385 (4) Å, however, are somewhat longer than in 2-amino-5-chloropyridine (AMCLPY12) [1.3602 (19) Å] and 2-amino-3-chloropyridine (URAXER) [1.351 (4) Å]. 2-amino-5-chloropyridine (AMCLPY12), which does not have the meta-NH2 substitution of the title compound, packs in a herringbone formation featuring centrosymmetric head-to-tail Namine—H⋯Npyr hydrogen bonding dimers with donor–acceptor distance 3.031 (2) Å. 2-Amino-3-chloropyridine (URAXER), has a meta-Cl substitution in place of the meta-NH2 in the title compound. Like 2-amino-5-chloropyridine (AMCLPY12), 2-amino-3-chloropyridine (URAXER) features a herringbone packing with centrosymmetric head-to-tail Namine—H⋯Npyr hydrogen-bonded dimer with a similar donor–acceptor distance of 3.051 (5) Å. The similar hydrogen-bonding motif in these two related compounds differs from the title compound, which does not exhibit centrosymmetric hydrogen-bonding dimerization. 2-Amino-3-chloropyridine (URAXER) also has short intermolecular Cl⋯Cl interactions of 3.278 (3) Å, where no such short halogen–halogen contact was observed in 2-amino-5-chloropyridine (AMCLPY12) or the title compound.
5. Synthesis and crystallization
5-Chloropyridine-2,3-diamine (97%) was purchased from Aldrich Chemical Company, USA. A single crystal suitable for analysis was selected from the purchased sample and used as received.
6. Analytical data
1H NMR (Bruker Avance 400 MHz, DMSO d6): δ 4.99 (br s, 2 H, NH2), 5.55 (br s, 2 H, NH2), 6.69 (d, 1 H, J = 2.3 Hz, CarylH), 7.21 (d, 1 H, J = 2.3 Hz, CarylH). 13C NMR (13C{1H}, 100.6 MHz, DMSO d6): δ 116.58 (CarylH), 118.38 (Caryl), 131.32 (Caryl), 131.66 (CarylH), 147.10 (Caryl). IR (Thermo Nicolet iS50, ATR, cm−1): 3392 (m, N—H str), 3309 (m, N—H str), 3172 (m, aryl C—H str), 1637 (s, aryl C=C str), 1572 (m), 1472 (s), 1421 (m), 1347 (w), 1307 (w), 1280 (w), 1240 (m), 1068 (m), 939 (w), 887 (w), 861 (m), 792 (m), 770 (m), 680 (s), 630 (s), 568 (s), 490 (s), 449 (s). GC/MS (Hewlett-Packard MS 5975/GC 7890): M+ = 143 (calc. exact mass = 143.03).
7. Refinement
Crystal data, data collection and structure . All non-hydrogen atoms were refined anisotropically. Hydrogen atoms on carbon were included in calculated positions and refined using a riding model with C—H = 0.95 Å and Uiso(H) = 1.2Ueq(C) of the aryl C-atoms. The positions of the four amino hydrogen atoms were found in the difference map and they were refined semi-freely using a distance restraint d(N—H) = 0.91 Å, and Uiso(H) = 1.2Ueq(N).
details are summarized in Table 2Supporting information
CCDC reference: 1562267
https://doi.org/10.1107/S2056989017010489/fy2122sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017010489/fy2122Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989017010489/fy2122Isup3.cml
Data collection: APEX2 (Bruker, 2013); cell
SAINT (Bruker, 2013); data reduction: SAINT (Bruker, 2013); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: SHELXTL2014 (Sheldrick, 2008); software used to prepare material for publication: SHELXTL2014 (Sheldrick, 2008), OLEX2 (Dolomanov et al., 2009) and Mercury (Macrae et al., 2008).C5H6ClN3 | Dx = 1.590 Mg m−3 |
Mr = 143.58 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, P212121 | Cell parameters from 4306 reflections |
a = 3.7565 (8) Å | θ = 2.6–29.7° |
b = 8.7002 (17) Å | µ = 0.53 mm−1 |
c = 18.350 (4) Å | T = 125 K |
V = 599.7 (2) Å3 | Plate, colourless |
Z = 4 | 0.10 × 0.05 × 0.04 mm |
F(000) = 296 |
Bruker APEXII CCD diffractometer | 1845 independent reflections |
Radiation source: fine-focus sealed tube | 1477 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.087 |
Detector resolution: 8.3333 pixels mm-1 | θmax = 30.5°, θmin = 2.2° |
φ and ω scans | h = −5→5 |
Absorption correction: multi-scan (SADABS; Bruker, 2013) | k = −12→12 |
Tmin = 0.75, Tmax = 0.98 | l = −26→26 |
14989 measured reflections |
Refinement on F2 | Hydrogen site location: mixed |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.041 | w = 1/[σ2(Fo2) + (0.0308P)2 + 0.2158P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.084 | (Δ/σ)max < 0.001 |
S = 1.07 | Δρmax = 0.37 e Å−3 |
1845 reflections | Δρmin = −0.38 e Å−3 |
94 parameters | Absolute structure: Flack x determined using 511 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
4 restraints | Absolute structure parameter: 0.01 (6) |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
x | y | z | Uiso*/Ueq | ||
Cl1 | 0.5035 (2) | 0.46707 (8) | 0.47194 (3) | 0.01872 (16) | |
N1 | 0.8538 (6) | 0.4647 (3) | 0.67658 (12) | 0.0148 (5) | |
N2 | 0.5894 (7) | 0.8717 (3) | 0.67694 (14) | 0.0153 (5) | |
H11 | 0.464 (9) | 0.928 (3) | 0.6466 (14) | 0.018* | |
H12 | 0.530 (10) | 0.872 (3) | 0.7224 (12) | 0.018* | |
N3 | 0.8976 (7) | 0.6490 (3) | 0.76777 (13) | 0.0154 (5) | |
H21 | 1.032 (9) | 0.580 (3) | 0.7905 (15) | 0.018* | |
H22 | 0.955 (10) | 0.748 (3) | 0.7772 (16) | 0.018* | |
C1 | 0.7608 (8) | 0.4231 (3) | 0.60820 (16) | 0.0157 (6) | |
H1 | 0.7977 | 0.3199 | 0.5931 | 0.019* | |
C2 | 0.6148 (7) | 0.5258 (4) | 0.56011 (14) | 0.0138 (5) | |
C3 | 0.5497 (7) | 0.6759 (3) | 0.58152 (14) | 0.0121 (6) | |
H3 | 0.445 | 0.747 | 0.5486 | 0.015* | |
C4 | 0.6388 (7) | 0.7209 (3) | 0.65122 (15) | 0.0122 (6) | |
C5 | 0.8035 (7) | 0.6100 (3) | 0.69716 (15) | 0.0125 (6) |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cl1 | 0.0204 (3) | 0.0220 (3) | 0.0138 (3) | −0.0021 (4) | −0.0034 (3) | −0.0035 (3) |
N1 | 0.0154 (11) | 0.0144 (11) | 0.0145 (11) | 0.0014 (11) | −0.0007 (9) | −0.0001 (11) |
N2 | 0.0182 (14) | 0.0137 (12) | 0.0140 (11) | 0.0036 (9) | −0.0003 (9) | 0.0000 (9) |
N3 | 0.0162 (14) | 0.0152 (12) | 0.0148 (11) | −0.0009 (10) | −0.0036 (9) | 0.0004 (10) |
C1 | 0.0176 (15) | 0.0126 (14) | 0.0171 (14) | 0.0008 (11) | 0.0014 (12) | −0.0019 (11) |
C2 | 0.0101 (12) | 0.0202 (13) | 0.0112 (11) | −0.0036 (12) | 0.0002 (9) | −0.0016 (12) |
C3 | 0.0061 (14) | 0.0157 (12) | 0.0146 (12) | −0.0022 (10) | 0.0009 (10) | 0.0040 (10) |
C4 | 0.0064 (12) | 0.0142 (14) | 0.0160 (14) | −0.0003 (10) | 0.0026 (11) | 0.0004 (11) |
C5 | 0.0066 (13) | 0.0184 (15) | 0.0125 (13) | −0.0017 (11) | 0.0021 (10) | 0.0011 (11) |
Cl1—C2 | 1.748 (3) | N3—H22 | 0.90 (2) |
N1—C5 | 1.333 (4) | C1—C2 | 1.371 (4) |
N1—C1 | 1.352 (4) | C1—H1 | 0.95 |
N2—C4 | 1.406 (4) | C2—C3 | 1.385 (4) |
N2—H11 | 0.88 (2) | C3—C4 | 1.379 (4) |
N2—H12 | 0.86 (2) | C3—H3 | 0.95 |
N3—C5 | 1.385 (4) | C4—C5 | 1.423 (4) |
N3—H21 | 0.89 (2) | ||
C5—N1—C1 | 118.7 (3) | C1—C2—Cl1 | 120.1 (2) |
C4—N2—H11 | 112 (2) | C3—C2—Cl1 | 119.7 (2) |
C4—N2—H12 | 111 (2) | C4—C3—C2 | 119.2 (3) |
H11—N2—H12 | 118 (3) | C4—C3—H3 | 120.4 |
C5—N3—H21 | 115 (2) | C2—C3—H3 | 120.4 |
C5—N3—H22 | 118 (2) | C3—C4—N2 | 123.0 (3) |
H21—N3—H22 | 114 (3) | C3—C4—C5 | 117.5 (3) |
N1—C1—C2 | 121.8 (3) | N2—C4—C5 | 119.4 (3) |
N1—C1—H1 | 119.1 | N1—C5—N3 | 117.5 (3) |
C2—C1—H1 | 119.1 | N1—C5—C4 | 122.5 (2) |
C1—C2—C3 | 120.2 (3) | N3—C5—C4 | 119.9 (3) |
C5—N1—C1—C2 | −0.5 (4) | C1—N1—C5—N3 | 179.3 (2) |
N1—C1—C2—C3 | −1.7 (4) | C1—N1—C5—C4 | 3.3 (4) |
N1—C1—C2—Cl1 | 179.3 (2) | C3—C4—C5—N1 | −4.0 (4) |
C1—C2—C3—C4 | 1.0 (4) | N2—C4—C5—N1 | 179.0 (3) |
Cl1—C2—C3—C4 | −180.0 (2) | C3—C4—C5—N3 | −179.8 (3) |
C2—C3—C4—N2 | 178.5 (3) | N2—C4—C5—N3 | 3.2 (4) |
C2—C3—C4—C5 | 1.7 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H12···N1i | 0.86 (2) | 2.48 (3) | 3.264 (3) | 151 (3) |
N3—H21···N2ii | 0.89 (2) | 2.38 (2) | 3.250 (4) | 166 (3) |
N3—H22···N1iii | 0.90 (2) | 2.19 (2) | 3.075 (4) | 167 (3) |
Symmetry codes: (i) −x+1, y+1/2, −z+3/2; (ii) −x+2, y−1/2, −z+3/2; (iii) −x+2, y+1/2, −z+3/2. |
Acknowledgements
This work was supported by Vassar College. X-ray facilities were provided by the US National Science Foundation (grants Nos. 0521237 and 0911324 to JMT). NMR facilities were provided by the US National Science Foundation (grant No. 1526982 to JMT and TG). We acknowledge the Salmon Fund of Vassar College for funding publication expenses.
Funding information
Funding for this research was provided by: National Science Foundation, Directorate for Mathematical and Physical Sciences (grant No. 0521237 to Joseph M. Tanski); National Science Foundation, Directorate for Mathematical and Physical Sciences (grant No. 0911324 to Joseph M. Tanski); National Science Foundation, Directorate for Mathematical and Physical Sciences (grant No. 1526982 to Joseph M. Tanski, Teresa A. Garrett).
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