organic compounds
tert-Butyl N-(5-bromo-1H-imidazo[4,5-b]pyridin-2-ylmethyl)carbamate
aSchool of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, People's Republic of China, and bThe Pharmaceutical Research Institute of Tianjin, Tianjin 300193, People's Republic of China
*Correspondence e-mail: jwwang@sdu.edu.cn
In the molecule of the title compound, C12H15BrN4O2, the imidazole and pyridine rings are strictly coplanar [maximum deviation 0.006 (3) Å]. In the molecules are linked into chains running parallel to the a axis by intermolecular N—H⋯O hydrogen bonds. Centrosymmetrically related chains are further connected by N—H⋯N hydrogen-bonding interactions to form a two-dimensional layer structure parallel to the ab plane.
Related literature
For general background on the properties of imidazole derivatives, see: Dai et al. (2004); Durant et al. (1973); Wang et al. (2007). For the crystal structures of related compounds, see: Lorenc et al. (2008).
Experimental
Crystal data
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Refinement
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Data collection: SMART (Bruker, 2002); cell SAINT (Bruker, 2002); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: SHELXL97.
Supporting information
10.1107/S1600536808035393/rz2259sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536808035393/rz2259Isup2.hkl
5-Bromopyridine-2,3-diamine(3.7 g, 20 mmol) and N-(tert-butoxycarbonyl)glycine (3.5 g, 20 mmol) were dissolved in THF (40 ml) and cooled to 273 K. N,N'-Dicyclohexylcarbodiimide (4.94 g, 24 mmol) was then added in batches and the mixture was stirred at 273 K for half an hour and at room temperature overnight. The filtrate was evaporated to afford a green solid, which was dissolved in acetic acid (20 ml) and the solution was stirred at 353 K for 8 h. The acetic acid was removed under reduced pressure and the crude title compound was separated as a pale green solid. Crystals of the title compound suitable for X-ray analysis were obtained by slow evaporation at room temperature if a dichloromethane-methanol (6:1, v/v) solution (yield; 70%, m.p. 475–476 K).
H atoms bound to N atoms were located from a difference Fourier map and refined freely. All other H atoms were placed at calculated positions and included in the
in the riding-model approximation, with C—H = 0.93-0.98 Å and Uiso(H) = 1.2 Ueq(C) or 1.5 Ueq(C) for methylene and methyl H atoms.Data collection: SMART (Bruker, 2002); cell
SAINT (Bruker, 2002); data reduction: SAINT (Bruker, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).C12H15BrN4O2 | F(000) = 1328 |
Mr = 327.19 | Dx = 1.483 Mg m−3 |
Orthorhombic, Pbca | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ac 2ab | Cell parameters from 4297 reflections |
a = 10.7400 (11) Å | θ = 2.4–24.9° |
b = 9.6717 (9) Å | µ = 2.81 mm−1 |
c = 28.215 (3) Å | T = 298 K |
V = 2930.8 (5) Å3 | Plate, colourless |
Z = 8 | 0.20 × 0.10 × 0.05 mm |
Bruker SMART APEX area-detector diffractometer | 3374 independent reflections |
Radiation source: fine-focus sealed tube | 2285 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.031 |
ϕ and ω scans | θmax = 27.6°, θmin = 2.4° |
Absorption correction: multi-scan (SADABS; Bruker, 2002) | h = −13→13 |
Tmin = 0.604, Tmax = 0.872 | k = −12→8 |
16102 measured reflections | l = −36→29 |
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)] = 0.038 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.102 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.01 | w = 1/[σ2(Fo2) + (0.0412P)2 + 2.0629P] where P = (Fo2 + 2Fc2)/3 |
3374 reflections | (Δ/σ)max = 0.001 |
180 parameters | Δρmax = 0.72 e Å−3 |
0 restraints | Δρmin = −0.65 e Å−3 |
C12H15BrN4O2 | V = 2930.8 (5) Å3 |
Mr = 327.19 | Z = 8 |
Orthorhombic, Pbca | Mo Kα radiation |
a = 10.7400 (11) Å | µ = 2.81 mm−1 |
b = 9.6717 (9) Å | T = 298 K |
c = 28.215 (3) Å | 0.20 × 0.10 × 0.05 mm |
Bruker SMART APEX area-detector diffractometer | 3374 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2002) | 2285 reflections with I > 2σ(I) |
Tmin = 0.604, Tmax = 0.872 | Rint = 0.031 |
16102 measured reflections |
R[F2 > 2σ(F2)] = 0.038 | 0 restraints |
wR(F2) = 0.102 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.01 | Δρmax = 0.72 e Å−3 |
3374 reflections | Δρmin = −0.65 e Å−3 |
180 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
Br1 | 0.13230 (4) | 0.06577 (4) | 0.356022 (12) | 0.07448 (16) | |
O1 | 0.2545 (2) | 0.37496 (19) | 0.61523 (7) | 0.0588 (5) | |
O2 | 0.1723 (2) | 0.55519 (18) | 0.65633 (7) | 0.0532 (5) | |
N1 | 0.0365 (2) | 0.3710 (2) | 0.45039 (8) | 0.0492 (5) | |
N2 | 0.1726 (2) | 0.4846 (2) | 0.50653 (8) | 0.0425 (5) | |
N3 | 0.35221 (19) | 0.3775 (2) | 0.48963 (8) | 0.0481 (5) | |
N4 | 0.2808 (2) | 0.5942 (2) | 0.59153 (8) | 0.0441 (5) | |
C1 | 0.0386 (3) | 0.2736 (3) | 0.41650 (10) | 0.0508 (7) | |
H1 | −0.0350 | 0.2529 | 0.4006 | 0.061* | |
C2 | 0.1457 (3) | 0.2029 (3) | 0.40420 (9) | 0.0488 (6) | |
C3 | 0.2584 (3) | 0.2271 (3) | 0.42539 (9) | 0.0499 (6) | |
H3 | 0.3301 | 0.1795 | 0.4167 | 0.060* | |
C4 | 0.2590 (2) | 0.3268 (3) | 0.46047 (8) | 0.0426 (6) | |
C5 | 0.1455 (2) | 0.3930 (3) | 0.47101 (9) | 0.0395 (5) | |
C6 | 0.2964 (2) | 0.4704 (3) | 0.51590 (9) | 0.0414 (6) | |
C7 | 0.3610 (2) | 0.5565 (3) | 0.55229 (10) | 0.0463 (6) | |
H7A | 0.4320 | 0.5056 | 0.5644 | 0.056* | |
H7B | 0.3920 | 0.6400 | 0.5374 | 0.056* | |
C8 | 0.2370 (2) | 0.4976 (3) | 0.62088 (9) | 0.0411 (6) | |
C9 | 0.1098 (3) | 0.4696 (3) | 0.69213 (10) | 0.0563 (7) | |
C10 | 0.2031 (4) | 0.3846 (5) | 0.71874 (13) | 0.0989 (13) | |
H10A | 0.2389 | 0.3172 | 0.6978 | 0.148* | |
H10B | 0.1625 | 0.3384 | 0.7446 | 0.148* | |
H10C | 0.2675 | 0.4436 | 0.7308 | 0.148* | |
C11 | 0.0119 (4) | 0.3815 (5) | 0.66859 (16) | 0.1005 (14) | |
H11A | 0.0515 | 0.3131 | 0.6491 | 0.151* | |
H11B | −0.0406 | 0.4389 | 0.6493 | 0.151* | |
H11C | −0.0375 | 0.3366 | 0.6924 | 0.151* | |
C12 | 0.0497 (4) | 0.5769 (4) | 0.72365 (14) | 0.0929 (13) | |
H12A | 0.1132 | 0.6315 | 0.7386 | 0.139* | |
H12B | 0.0005 | 0.5317 | 0.7474 | 0.139* | |
H12C | −0.0027 | 0.6358 | 0.7049 | 0.139* | |
H2 | 0.124 (3) | 0.537 (3) | 0.5189 (11) | 0.051 (9)* | |
H3A | 0.272 (2) | 0.678 (3) | 0.5990 (8) | 0.034 (7)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Br1 | 0.0908 (3) | 0.0764 (3) | 0.0563 (2) | 0.00984 (19) | 0.00153 (17) | −0.02719 (16) |
O1 | 0.0800 (14) | 0.0302 (10) | 0.0660 (12) | 0.0025 (9) | 0.0186 (11) | −0.0051 (9) |
O2 | 0.0700 (13) | 0.0381 (10) | 0.0516 (11) | 0.0002 (9) | 0.0197 (9) | −0.0059 (8) |
N1 | 0.0436 (12) | 0.0482 (13) | 0.0559 (14) | 0.0046 (10) | −0.0002 (10) | −0.0114 (11) |
N2 | 0.0382 (12) | 0.0406 (12) | 0.0488 (13) | 0.0050 (10) | 0.0065 (10) | −0.0055 (10) |
N3 | 0.0387 (11) | 0.0575 (14) | 0.0482 (12) | 0.0069 (10) | 0.0078 (10) | −0.0079 (11) |
N4 | 0.0540 (14) | 0.0259 (11) | 0.0524 (13) | −0.0004 (9) | 0.0092 (10) | −0.0055 (9) |
C1 | 0.0515 (16) | 0.0472 (16) | 0.0539 (16) | 0.0033 (13) | −0.0026 (13) | −0.0078 (13) |
C2 | 0.0593 (17) | 0.0493 (15) | 0.0379 (13) | 0.0037 (13) | 0.0066 (12) | −0.0044 (11) |
C3 | 0.0513 (16) | 0.0556 (16) | 0.0427 (14) | 0.0107 (13) | 0.0110 (12) | −0.0047 (12) |
C4 | 0.0414 (13) | 0.0478 (15) | 0.0385 (12) | 0.0051 (11) | 0.0104 (11) | 0.0005 (11) |
C5 | 0.0417 (13) | 0.0368 (13) | 0.0401 (13) | 0.0018 (11) | 0.0069 (11) | −0.0008 (10) |
C6 | 0.0391 (13) | 0.0430 (14) | 0.0420 (14) | −0.0003 (11) | 0.0083 (11) | 0.0012 (11) |
C7 | 0.0411 (13) | 0.0492 (15) | 0.0486 (15) | −0.0048 (12) | 0.0061 (12) | −0.0017 (12) |
C8 | 0.0457 (14) | 0.0332 (13) | 0.0445 (13) | −0.0005 (11) | 0.0024 (11) | −0.0051 (11) |
C9 | 0.0630 (18) | 0.0561 (17) | 0.0499 (16) | −0.0051 (14) | 0.0154 (14) | −0.0002 (13) |
C10 | 0.109 (3) | 0.124 (3) | 0.064 (2) | 0.021 (3) | 0.009 (2) | 0.025 (2) |
C11 | 0.085 (3) | 0.115 (3) | 0.101 (3) | −0.044 (3) | 0.024 (2) | −0.015 (3) |
C12 | 0.109 (3) | 0.093 (3) | 0.077 (2) | 0.001 (2) | 0.045 (2) | −0.012 (2) |
Br1—C2 | 1.904 (3) | C3—H3 | 0.9300 |
O1—C8 | 1.211 (3) | C4—C5 | 1.409 (3) |
O2—C8 | 1.339 (3) | C6—C7 | 1.493 (4) |
O2—C9 | 1.469 (3) | C7—H7A | 0.9700 |
N1—C5 | 1.325 (3) | C7—H7B | 0.9700 |
N1—C1 | 1.342 (3) | C9—C10 | 1.498 (5) |
N2—C6 | 1.362 (3) | C9—C11 | 1.507 (5) |
N2—C5 | 1.369 (3) | C9—C12 | 1.512 (4) |
N2—H2 | 0.81 (3) | C10—H10A | 0.9600 |
N3—C6 | 1.310 (3) | C10—H10B | 0.9600 |
N3—C4 | 1.385 (3) | C10—H10C | 0.9600 |
N4—C8 | 1.335 (3) | C11—H11A | 0.9600 |
N4—C7 | 1.449 (3) | C11—H11B | 0.9600 |
N4—H3A | 0.84 (3) | C11—H11C | 0.9600 |
C1—C2 | 1.383 (4) | C12—H12A | 0.9600 |
C1—H1 | 0.9300 | C12—H12B | 0.9600 |
C2—C3 | 1.370 (4) | C12—H12C | 0.9600 |
C3—C4 | 1.382 (3) | ||
C8—O2—C9 | 121.1 (2) | N4—C7—H7B | 109.0 |
C5—N1—C1 | 114.3 (2) | C6—C7—H7B | 109.0 |
C6—N2—C5 | 106.5 (2) | H7A—C7—H7B | 107.8 |
C6—N2—H2 | 128 (2) | O1—C8—N4 | 123.3 (2) |
C5—N2—H2 | 126 (2) | O1—C8—O2 | 125.9 (2) |
C6—N3—C4 | 104.4 (2) | N4—C8—O2 | 110.8 (2) |
C8—N4—C7 | 120.4 (2) | O2—C9—C10 | 110.4 (3) |
C8—N4—H3A | 118.5 (17) | O2—C9—C11 | 109.5 (3) |
C7—N4—H3A | 120.2 (17) | C10—C9—C11 | 112.1 (3) |
N1—C1—C2 | 122.6 (3) | O2—C9—C12 | 102.3 (2) |
N1—C1—H1 | 118.7 | C10—C9—C12 | 111.6 (3) |
C2—C1—H1 | 118.7 | C11—C9—C12 | 110.5 (3) |
C3—C2—C1 | 122.8 (2) | C9—C10—H10A | 109.5 |
C3—C2—Br1 | 119.8 (2) | C9—C10—H10B | 109.5 |
C1—C2—Br1 | 117.4 (2) | H10A—C10—H10B | 109.5 |
C2—C3—C4 | 115.9 (2) | C9—C10—H10C | 109.5 |
C2—C3—H3 | 122.1 | H10A—C10—H10C | 109.5 |
C4—C3—H3 | 122.1 | H10B—C10—H10C | 109.5 |
C3—C4—N3 | 132.5 (2) | C9—C11—H11A | 109.5 |
C3—C4—C5 | 117.7 (2) | C9—C11—H11B | 109.5 |
N3—C4—C5 | 109.8 (2) | H11A—C11—H11B | 109.5 |
N1—C5—N2 | 127.9 (2) | C9—C11—H11C | 109.5 |
N1—C5—C4 | 126.8 (2) | H11A—C11—H11C | 109.5 |
N2—C5—C4 | 105.4 (2) | H11B—C11—H11C | 109.5 |
N3—C6—N2 | 114.0 (2) | C9—C12—H12A | 109.5 |
N3—C6—C7 | 124.0 (2) | C9—C12—H12B | 109.5 |
N2—C6—C7 | 122.1 (2) | H12A—C12—H12B | 109.5 |
N4—C7—C6 | 113.0 (2) | C9—C12—H12C | 109.5 |
N4—C7—H7A | 109.0 | H12A—C12—H12C | 109.5 |
C6—C7—H7A | 109.0 | H12B—C12—H12C | 109.5 |
C5—N1—C1—C2 | −0.2 (4) | N3—C4—C5—N2 | 0.5 (3) |
N1—C1—C2—C3 | −0.4 (4) | C4—N3—C6—N2 | 0.4 (3) |
N1—C1—C2—Br1 | 179.1 (2) | C4—N3—C6—C7 | −178.3 (2) |
C1—C2—C3—C4 | 0.5 (4) | C5—N2—C6—N3 | −0.1 (3) |
Br1—C2—C3—C4 | −178.99 (19) | C5—N2—C6—C7 | 178.7 (2) |
C2—C3—C4—N3 | 179.1 (3) | C8—N4—C7—C6 | 65.8 (3) |
C2—C3—C4—C5 | 0.0 (4) | N3—C6—C7—N4 | −149.7 (2) |
C6—N3—C4—C3 | −179.6 (3) | N2—C6—C7—N4 | 31.7 (3) |
C6—N3—C4—C5 | −0.5 (3) | C7—N4—C8—O1 | −4.5 (4) |
C1—N1—C5—N2 | −179.8 (3) | C7—N4—C8—O2 | 175.7 (2) |
C1—N1—C5—C4 | 0.7 (4) | C9—O2—C8—O1 | −2.6 (4) |
C6—N2—C5—N1 | −179.8 (3) | C9—O2—C8—N4 | 177.2 (2) |
C6—N2—C5—C4 | −0.3 (3) | C8—O2—C9—C10 | 61.7 (4) |
C3—C4—C5—N1 | −0.7 (4) | C8—O2—C9—C11 | −62.3 (4) |
N3—C4—C5—N1 | −179.9 (2) | C8—O2—C9—C12 | −179.5 (3) |
C3—C4—C5—N2 | 179.8 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···N1i | 0.81 (3) | 2.12 (3) | 2.911 (3) | 165 (3) |
N4—H3A···O1ii | 0.84 (3) | 1.98 (3) | 2.822 (3) | 178 (2) |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x+1/2, y+1/2, z. |
Experimental details
Crystal data | |
Chemical formula | C12H15BrN4O2 |
Mr | 327.19 |
Crystal system, space group | Orthorhombic, Pbca |
Temperature (K) | 298 |
a, b, c (Å) | 10.7400 (11), 9.6717 (9), 28.215 (3) |
V (Å3) | 2930.8 (5) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 2.81 |
Crystal size (mm) | 0.20 × 0.10 × 0.05 |
Data collection | |
Diffractometer | Bruker SMART APEX area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2002) |
Tmin, Tmax | 0.604, 0.872 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 16102, 3374, 2285 |
Rint | 0.031 |
(sin θ/λ)max (Å−1) | 0.653 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.038, 0.102, 1.01 |
No. of reflections | 3374 |
No. of parameters | 180 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.72, −0.65 |
Computer programs: SMART (Bruker, 2002), SAINT (Bruker, 2002), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···N1i | 0.81 (3) | 2.12 (3) | 2.911 (3) | 165 (3) |
N4—H3A···O1ii | 0.84 (3) | 1.98 (3) | 2.822 (3) | 178 (2) |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x+1/2, y+1/2, z. |
Acknowledgements
The authors thank the National Basic Research Priority Program for the Science Fund grant No. 2003CCA027.
References
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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.
Nitrogen heterocyclic compounds and their derivatives are substances which show diverse biological activity (Dai et al., 2004). Among them, imidazo[4,5-b]pyridine compounds are an important class of imidazole derivatives, which are widely used in the field of medicine (Durant et al., 1973; Wang et al., 2007). As a continuation of our studies on this subject, the structure of the title compound is described herein.
In the molecule of the title compound (Fig. 1) the imidazole and pyridine rings are strictly coplanar, the maximum deviation from the mean plane of the two rings being 0.006 (3) Å for atom C4. The C6—N2 and C6—N3 bond lengths in the imidazole ring are 1.362 (3) and 1.310 (3) Å, respectively; the bond angles between non-hydrogen atoms of the pyridine ring are in the range 114.3 (2)–126.8 (2)°, which is in line with the values reported for similar compounds (Lorenc et al., 2008). In the crystal packing, intermolecular N—H···O hydrogen bonds involving the amide and carbonyl groups (Table 1) link adjacent molecules into chains parallel to the a axis. Centrosymmetrically related chains are further linked by intermolecular N—H···N hydrogen bonds to form a two-dimensional layer structure parallel to the ab plane (Fig. 2).