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Acta Crystallogr Sect E Struct Rep Online. 2009 January 1; 65(Pt 1): o28.
Published online 2008 December 6. doi:  10.1107/S1600536808040452
PMCID: PMC2967947

3-Amino-5-bromo-2-iodo­pyridine

Abstract

The reaction of 3-amino-5-bromo­pyridine with N-iodo­succinimide in the presence of acetic acid produces the title compound, C5H4BrIN, with an iodo substituent in position 2 of the pyridine ring. The crystal structure features rather weak inter­molecular N—H(...)N hydrogen bonds linking the mol­ecules into chains along the z axis of the crystal.

Related literature

For structures of ortho-iodo­anilines, see: McWilliam et al. (2001 [triangle]); Sandor & Foxman (2000 [triangle]); Parkin et al. (2005 [triangle]).

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Object name is e-65-00o28-scheme1.jpg

Experimental

Crystal data

  • C5H4BrIN2
  • M r = 298.90
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-00o28-efi1.jpg
  • a = 4.0983 (12) Å
  • b = 15.172 (4) Å
  • c = 12.038 (3) Å
  • β = 90.152 (5)°
  • V = 748.5 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 9.53 mm−1
  • T = 100 (2) K
  • 0.40 × 0.33 × 0.04 mm

Data collection

  • Bruker APEXII CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2001 [triangle]) T min = 0.234, T max = 0.557
  • 3783 measured reflections
  • 1251 independent reflections
  • 1086 reflections with I > 2σ(I)
  • R int = 0.037

Refinement

  • R[F 2 > 2σ(F 2)] = 0.032
  • wR(F 2) = 0.082
  • S = 1.05
  • 1251 reflections
  • 82 parameters
  • H-atom parameters constrained
  • Δρmax = 1.33 e Å−3
  • Δρmin = −0.92 e Å−3

Data collection: APEX2 (Bruker, 2007 [triangle]); cell refinement: SAINT (Bruker, 2007 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808040452/rz2275sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808040452/rz2275Isup2.hkl

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

supplementary crystallographic information

Comment

The reaction of 5-bromo-3-aminopyridine with N-iodosuccinimide in the presence of acetic acid leads to iodo-substitution at position 2 of the pyridine ring, as shown by the X-ray study of the title compound (Fig. 1). To the best of our knowledge, this is the first structure of ortho-iodoaminopyridine derivative. The N2···I1 distance 3.259 (5) Å is typical for ortho-iodoanilines (McWilliam et al., 2001; Sandor & Foxman, 2000; Parkin et al., 2005) and may suggest involvement of the H2B atom in weak intramolecular N2—H2B···I1 interaction (Table 1).

The second `active' H-atom, H2A, participates in the intermolecular H-bond N2—H2A···N1i (symmetry code (i): x, 1/2 - y, z - 1/2; Table 1), which links the molecules into the chains along the z-axis of the crystal (Fig. 2). There are no strong halogen···halogen interactions in the structure; the shortest intermolecular I···I distances are 4.091 (1) Å and 4.098 (1) Å.

Experimental

To a solution of 3-amino-5-bromopyridine (100 mg, 0.56 mmol) in acetic acid (0.1 M, 5.61 ml) was added N-iodosuccinimide (133 mg, 0.56 mmol) at rt. After 3 h, the reaction was quenched with sat. sodium bicarbonate and extracted 3 times with EtOAc. The organic layers were combined, dried, filtered, and concentrated. The crude residue was subjected to flash chromatography (silica gel, 0–50% EtOAc/heptane). Isolated 93 mg (55%) of 3-amino-5-bromo-2-iodopyridine, as a brown solid. X-ray quality crystals were obtained by slow evaporation of a concentrated chromatography fraction (approx. 30% EtOAc/heptane). 1H NMR (400 MHz, DMSO-d6) (δ p.p.m.) 5.65 (s, 2 H), 7.16 (d, J = 2.27 Hz, 1 H), 7.67 (d, J = 2.01 Hz, 1 H). 13C NMR (101 MHz, DMSO-d6) (δ p.p.m.) 106.10, 120.01, 120.92, 137.97, 147.68.

Refinement

All H atoms were treated as riding with the C—H and N—H distances of 0.95 Å and 0.88 Å respectively; the Uiso(H) were set to 1.2Ueq of the carrying atom.

Figures

Fig. 1.
Molecular structure of the title compound, showing 50% probability displacement ellipsoids and atom numbering scheme. H atoms are drawn as circles with arbitrary small radius.
Fig. 2.
The crystal packing diagram viewed down the x-axis.

Crystal data

C5H4BrIN2F(000) = 544
Mr = 298.90Dx = 2.652 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2536 reflections
a = 4.0983 (12) Åθ = 2.7–25.3°
b = 15.172 (4) ŵ = 9.53 mm1
c = 12.038 (3) ÅT = 100 K
β = 90.152 (5)°Plate, colourless
V = 748.5 (3) Å30.40 × 0.33 × 0.04 mm
Z = 4

Data collection

Bruker APEXII CCD diffractometer1251 independent reflections
Radiation source: fine-focus sealed tube1086 reflections with I > 2σ(I)
graphiteRint = 0.037
[var phi] and ω scansθmax = 25.3°, θmin = 2.2°
Absorption correction: analytical (SADABS; Bruker, 2001)h = −4→1
Tmin = 0.234, Tmax = 0.557k = −17→18
3783 measured reflectionsl = −10→14

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)] = 0.032Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.082H-atom parameters constrained
S = 1.05w = 1/[σ2(Fo2) + (0.037P)2 + 2.524P] where P = (Fo2 + 2Fc2)/3
1251 reflections(Δ/σ)max = 0.003
82 parametersΔρmax = 1.33 e Å3
0 restraintsΔρmin = −0.92 e Å3

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 (Å2)

xyzUiso*/Ueq
I10.18405 (10)0.37509 (3)0.48761 (3)0.02516 (17)
Br1−0.56202 (16)0.01782 (4)0.28399 (5)0.0266 (2)
N2−0.0278 (15)0.3306 (4)0.2326 (4)0.0298 (13)
H2A−0.08080.32820.16170.036*
H2B0.07600.37690.25890.036*
N1−0.1133 (14)0.1994 (4)0.4858 (4)0.0264 (13)
C2−0.2684 (18)0.1278 (4)0.4470 (6)0.0264 (15)
H2−0.32430.08150.49650.032*
C1−0.0390 (15)0.2637 (5)0.4165 (5)0.0242 (14)
C5−0.1071 (15)0.2622 (5)0.3019 (5)0.0227 (14)
C3−0.3480 (16)0.1208 (4)0.3350 (5)0.0221 (14)
C4−0.2713 (15)0.1878 (4)0.2636 (5)0.0213 (14)
H4−0.33030.18340.18740.026*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
I10.0244 (3)0.0324 (3)0.0187 (3)−0.00094 (16)−0.00522 (18)−0.00340 (17)
Br10.0285 (4)0.0274 (4)0.0238 (4)−0.0007 (3)−0.0039 (3)−0.0027 (3)
N20.044 (4)0.029 (3)0.016 (3)−0.002 (3)−0.008 (3)−0.001 (2)
N10.035 (3)0.030 (3)0.015 (3)0.002 (2)−0.005 (2)0.002 (2)
C20.035 (4)0.024 (4)0.020 (3)0.000 (3)−0.007 (3)0.002 (3)
C10.017 (3)0.036 (4)0.020 (3)0.004 (3)−0.006 (3)−0.008 (3)
C50.017 (3)0.035 (4)0.016 (3)0.006 (3)−0.001 (2)−0.002 (3)
C30.021 (4)0.027 (4)0.018 (3)0.005 (3)−0.001 (3)−0.001 (3)
C40.021 (3)0.033 (4)0.011 (3)0.007 (3)−0.005 (2)−0.006 (3)

Geometric parameters (Å, °)

I1—C12.102 (7)C2—C31.390 (9)
Br1—C31.894 (7)C2—H20.9500
N2—C51.371 (9)C1—C51.407 (9)
N2—H2A0.8800C5—C41.393 (9)
N2—H2B0.8800C3—C41.368 (9)
N1—C11.320 (9)C4—H40.9500
N1—C21.342 (9)
C5—N2—H2A120.0N2—C5—C4121.8 (5)
C5—N2—H2B120.0N2—C5—C1122.6 (6)
H2A—N2—H2B120.0C4—C5—C1115.6 (6)
C1—N1—C2119.3 (5)C4—C3—C2119.9 (6)
N1—C2—C3120.6 (6)C4—C3—Br1121.1 (5)
N1—C2—H2119.7C2—C3—Br1119.0 (5)
C3—C2—H2119.7C3—C4—C5120.4 (6)
N1—C1—C5124.2 (6)C3—C4—H4119.8
N1—C1—I1116.0 (4)C5—C4—H4119.8
C5—C1—I1119.8 (5)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2A···N1i0.882.163.025 (8)166
N2—H2B···I10.882.793.259 (5)115

Symmetry codes: (i) x, −y+1/2, z−1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: RZ2275).

References

  • Bruker (2001). SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Bruker (2007). APEX2 and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • McWilliam, S. A., Skakle, J. M. S., Low, J. N., Wardell, J. L., Garden, S. J., Pinto, A. C., Torres, J. C. & Glidewell, C. (2001). Acta Cryst. C57, 942–945. [PubMed]
  • Parkin, A., Spanswick, C. K., Pulham, C. R. & Wilson, C. C. (2005). Acta Cryst. E61, o1087–o1089.
  • Sandor, R. B. & Foxman, B. M. (2000). Tetrahedron, 56, 6805–6812.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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