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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

3-Amino-5-bromo-2-iodo­pyridine

aPfizer Global Research and Development, La Jolla Laboratories, 10614 Science Center Drive, San Diego, CA 92122, USA, and bDepartment of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
*Correspondence e-mail: alex.yanovsky@pfizer.com

(Received 27 November 2008; accepted 1 December 2008; online 6 December 2008)

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[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.]); Sandor & Foxman (2000[Sandor, R. B. & Foxman, B. M. (2000). Tetrahedron, 56, 6805-6812.]); Parkin et al. (2005[Parkin, A., Spanswick, C. K., Pulham, C. R. & Wilson, C. C. (2005). Acta Cryst. E61, o1087-o1089.]).

[Scheme 1]

Experimental

Crystal data
  • C5H4BrIN2

  • Mr = 298.90

  • Monoclinic, P 21 /c

  • 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[Bruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.234, Tmax = 0.557

  • 3783 measured reflections

  • 1251 independent reflections

  • 1086 reflections with I > 2σ(I)

  • Rint = 0.037

Refinement
  • R[F2 > 2σ(F2)] = 0.032

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2A⋯N1i 0.88 2.16 3.025 (8) 166
N2—H2B⋯I1 0.88 2.79 3.259 (5) 115
Symmetry code: (i) [x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

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.

Related literature top

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

Experimental top

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 top

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.

Computing details top

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

Figures top
[Figure 1] 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.
[Figure 2] Fig. 2. The crystal packing diagram viewed down the x-axis.
3-Amino-5-bromo-2-iodopyridine top
Crystal data top
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 top
Bruker APEXII CCD
diffractometer
1251 independent reflections
Radiation source: fine-focus sealed tube1086 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.037
ϕ and ω scansθmax = 25.3°, θmin = 2.2°
Absorption correction: analytical
(SADABS; Bruker, 2001)
h = 41
Tmin = 0.234, Tmax = 0.557k = 1718
3783 measured reflectionsl = 1014
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)] = 0.032Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.082H-atom parameters constrained
S = 1.05 w = 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
Crystal data top
C5H4BrIN2V = 748.5 (3) Å3
Mr = 298.90Z = 4
Monoclinic, P21/cMo Kα radiation
a = 4.0983 (12) ŵ = 9.53 mm1
b = 15.172 (4) ÅT = 100 K
c = 12.038 (3) Å0.40 × 0.33 × 0.04 mm
β = 90.152 (5)°
Data collection top
Bruker APEXII CCD
diffractometer
1251 independent reflections
Absorption correction: analytical
(SADABS; Bruker, 2001)
1086 reflections with I > 2σ(I)
Tmin = 0.234, Tmax = 0.557Rint = 0.037
3783 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0320 restraints
wR(F2) = 0.082H-atom parameters constrained
S = 1.05Δρmax = 1.33 e Å3
1251 reflectionsΔρmin = 0.92 e Å3
82 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
xyzUiso*/Ueq
I10.18405 (10)0.37509 (3)0.48761 (3)0.02516 (17)
Br10.56202 (16)0.01782 (4)0.28399 (5)0.0266 (2)
N20.0278 (15)0.3306 (4)0.2326 (4)0.0298 (13)
H2A0.08080.32820.16170.036*
H2B0.07600.37690.25890.036*
N10.1133 (14)0.1994 (4)0.4858 (4)0.0264 (13)
C20.2684 (18)0.1278 (4)0.4470 (6)0.0264 (15)
H20.32430.08150.49650.032*
C10.0390 (15)0.2637 (5)0.4165 (5)0.0242 (14)
C50.1071 (15)0.2622 (5)0.3019 (5)0.0227 (14)
C30.3480 (16)0.1208 (4)0.3350 (5)0.0221 (14)
C40.2713 (15)0.1878 (4)0.2636 (5)0.0213 (14)
H40.33030.18340.18740.026*
Atomic displacement parameters (Å2) top
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, º) top
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, º) top
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 code: (i) x, y+1/2, z1/2.

Experimental details

Crystal data
Chemical formulaC5H4BrIN2
Mr298.90
Crystal system, space groupMonoclinic, P21/c
Temperature (K)100
a, b, c (Å)4.0983 (12), 15.172 (4), 12.038 (3)
β (°) 90.152 (5)
V3)748.5 (3)
Z4
Radiation typeMo Kα
µ (mm1)9.53
Crystal size (mm)0.40 × 0.33 × 0.04
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correctionAnalytical
(SADABS; Bruker, 2001)
Tmin, Tmax0.234, 0.557
No. of measured, independent and
observed [I > 2σ(I)] reflections
3783, 1251, 1086
Rint0.037
(sin θ/λ)max1)0.601
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.032, 0.082, 1.05
No. of reflections1251
No. of parameters82
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)1.33, 0.92

Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2A···N1i0.882.163.025 (8)166.2
N2—H2B···I10.882.793.259 (5)115.0
Symmetry code: (i) x, y+1/2, z1/2.
 

References

First citationBruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationBruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationMcWilliam, 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.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
First citationParkin, A., Spanswick, C. K., Pulham, C. R. & Wilson, C. C. (2005). Acta Cryst. E61, o1087–o1089.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
First citationSandor, R. B. & Foxman, B. M. (2000). Tetrahedron, 56, 6805–6812.  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

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds