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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 66| Part 8| August 2010| Page o1999
https://doi.org/10.1107/S1600536810026577

Ethyl 5-methyl­imidazo[1,2-a]pyridine-2-carboxyl­ate

Jin-hua Yao,a Lan-fang Wang,a Bing Guo,a Kang Ana and Jian-ning Guana*

aDepartment of Applied Chemistry, College of Science, Nanjing University of Technology, No.5 Xinmofan Road, Nanjing, Nanjing 210009, People's Republic of China
*Correspondence e-mail: guanjn@sina.com

(Received 18 June 2010; accepted 5 July 2010; online 14 July 2010)

The title compound, C11H12N2O2, was synthesized from the reaction of 6-methyl­pyridin-2-amine and ethyl 3-bromo-2-oxopropionate. In the mol­ecular structure, the six- and five-membered rings are individually almost planar with r.m.s. deviations of 0.003 and 0.002 Å, respectively. The two rings are almost coplanar, the dihedral angle between their planes being 1.4 (3)°. Inter­molecular C—H⋯O and C—H⋯N hydrogen bonds are present in the crystal structure.

Related literature

For the biological properties of related compounds, see: Xia et al. (2005[Xia, G., Li, J., Peng, A., Lai, S., Zhang, S., Shen, J., Liu, Z., Chen, X. & Ji, R. (2005). Bioorg. Med. Chem. Lett. 15, 2790-2794.]); Warshakoon et al. (2006[Warshakoon, N. C., Wu, S., Boyer, A., Kawamoto, R., Sheville, J., Renock, S., Xu, K., Pokross, M., Evdokimov, A. G., Walter, R. & Mekel, M. (2006). Bioorg. Med. Chem. Lett. 16, 5598-5601.]); Imaeda et al. (2008[Imaeda, Y., Kawasamoto, T., Tobisu, M., Konishi, N., Hiroe, K., Kawamura, M., Tanaka, T. & Kubo, K. (2008). Bioorg. Med. Chem. 16, 3125-3140.]). For the synthetic procedure, see: Xia et al. (2005[Xia, G., Li, J., Peng, A., Lai, S., Zhang, S., Shen, J., Liu, Z., Chen, X. & Ji, R. (2005). Bioorg. Med. Chem. Lett. 15, 2790-2794.]). For bond-length data, see: Allen et al. (1987[Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1-19.]).

[Scheme 1]

Experimental

Crystal data

  • C11H12N2O2

  • Mr = 204.23

  • Monoclinic, C 2/c

  • a = 17.164 (3) Å

  • b = 10.521 (2) Å

  • c = 13.759 (3) Å

  • β = 124.77 (3)°

  • V = 2041 (1) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 293 K

  • 0.30 × 0.20 × 0.10 mm
Data collection

  • Enraf–Nonius CAD-4 diffractometer

  • Absorption correction: ψ scan (North et al., 1968[North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351-359.]) Tmin = 0.973, Tmax = 0.991

  • 1923 measured reflections

  • 1859 independent reflections

  • 1360 reflections with I > 2σ(I)

  • Rint = 0.028

  • 3 standard reflections every 200 reflections intensity decay: 1%
Refinement

  • R[F2 > 2σ(F2)] = 0.051

  • wR(F2) = 0.152

  • S = 1.00

  • 1859 reflections

  • 137 parameters

  • H-atom parameters constrained

  • Δρmax = 0.24 e Å−3

  • Δρmin = −0.20 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C2—H2A⋯N1i 0.93 2.59 3.461 (4) 155
C3—H3A⋯O1i 0.93 2.58 3.456 (4) 157
Symmetry code: (i) [-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994[Enraf-Nonius (1989). CAD-4 EXPRESS. Enraf-Nonius, Delft, The Netherlands.]); cell refinement: CAD-4 EXPRESS; data reduction: XCAD4 (Harms & Wocadlo, 1995[Harms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.]); 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: SHELXL97.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536810026577/im2214sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810026577/im2214Isup2.hkl

checkCIF report


Comment top

Imidazo[1,2a]pyridine derivatives are of great interest because of their chemical and pharmaceutical properties. Some derivatives play a key role in preparing hypoxia inducible factor 1α prolyl hydroxylase inhibitors. And HIF-1α is of great potential value for treating ischemic diseases (Warshakoon et al.,2006). Some can be used as a material for preparing a series of FXa inhibitors, which can be used to cure various kinds of thromboembolic diseases (Imaeda et al.,2008). Herein we report the crystal structure of the title compound, (I). The molecular structure of (I) is shown in Fig.1. In this structure ring A (C1/C2/C3/C4/N2/C7) is a planar six-mermbered ring and the mean deviation from plane is 0.0027 Å, ring B(C4/N1/C5/C6/N2) is a planar five-mermbered ring with a mean deviation from planarity of 0.0018 Å. The dihedral angle between A and B ring is 1.4 (3)°. In the crystal structure, intermolecular C—H···O and C—H···N hydrogen bonds (Table 1) link the molecules to form a trimeric unit (Fig. 2).

Related literature top

For the biological properties of related compounds, see: Xia et al. (2005); Warshakoon et al. (2006); Imaeda et al. (2008). For the synthetic procedure, see: Xia et al. (2005). For bond-length data, see: Allen et al. (1987).

Experimental top

6-Methyl-pyridin-2-ylamine (8 mmol) and 3-bromo-2-oxo-propionic acid ethyl ester (12 mmol) were added to 50 mL ethanol. The mixture was refluxed for 6 h and then the solvent was totally evaporated. Solid anhydrous KHCO3 was added until pH=8 had been reached. Set aside for 3 h led to the observation of a white, flocculent precipitate, which was filtered and dried (yield ca. 52.6%, Xia et al. (2005)). Crystals suitable for X-ray analysis were obtained by dissolving (I) (0.5 g) in ethyl acetate (20 ml) and evaporating the solvent slowly at room temperature for about 10 d.

Refinement top

All H atoms were positioned geometrically, with C—H= 0.97, 0.96 and 0.93 Å for methylene, methyl and aromatic H atoms, respectively, and constrained to ride on their parent atoms, with Uiso(H)=xUeq(C), where x=1.5 for methyl H atoms and x=1.2 for all other H atoms.

Structure description top

Imidazo[1,2a]pyridine derivatives are of great interest because of their chemical and pharmaceutical properties. Some derivatives play a key role in preparing hypoxia inducible factor 1α prolyl hydroxylase inhibitors. And HIF-1α is of great potential value for treating ischemic diseases (Warshakoon et al.,2006). Some can be used as a material for preparing a series of FXa inhibitors, which can be used to cure various kinds of thromboembolic diseases (Imaeda et al.,2008). Herein we report the crystal structure of the title compound, (I). The molecular structure of (I) is shown in Fig.1. In this structure ring A (C1/C2/C3/C4/N2/C7) is a planar six-mermbered ring and the mean deviation from plane is 0.0027 Å, ring B(C4/N1/C5/C6/N2) is a planar five-mermbered ring with a mean deviation from planarity of 0.0018 Å. The dihedral angle between A and B ring is 1.4 (3)°. In the crystal structure, intermolecular C—H···O and C—H···N hydrogen bonds (Table 1) link the molecules to form a trimeric unit (Fig. 2).

For the biological properties of related compounds, see: Xia et al. (2005); Warshakoon et al. (2006); Imaeda et al. (2008). For the synthetic procedure, see: Xia et al. (2005). For bond-length data, see: Allen et al. (1987).

Computing details top

Data collection: CAD-4 EXPRESS (Enraf-Nonius, 1994); cell refinement: CAD-4 EXPRESS (Enraf-Nonius, 1994); data reduction: XCAD4 (Harms & Wocadlo, 1995); 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: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. A view of the molecular structure of (I). Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. A packing diagram for (I). Dashed lines indicate an intermolecular C—H···N hydrogen bond and an intermolecular C—H···O hydrogen bond.
Ethyl 5-methylimidazo[1,2-a]pyridine-2-carboxylate top
Crystal data top
C11H12N2O2F(000) = 864
Mr = 204.23Dx = 1.329 Mg m−3
Monoclinic, C2/cMelting point = 425–426 K
Hall symbol: -C 2ycMo Kα radiation, λ = 0.71073 Å
a = 17.164 (3) ÅCell parameters from 25 reflections
b = 10.521 (2) Åθ = 9–13°
c = 13.759 (3) ŵ = 0.09 mm−1
β = 124.77 (3)°T = 293 K
V = 2041 (1) Å3Block, colorless
Z = 80.30 × 0.20 × 0.10 mm
Data collection top
Enraf–Nonius CAD-4
diffractometer		1360 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.028
Graphite monochromatorθmax = 25.3°, θmin = 2.4°
ω/2θ scansh = −20→0
Absorption correction: ψ scan
(North et al., 1968)		k = −12→0
Tmin = 0.973, Tmax = 0.991l = −13→16
1923 measured reflections3 standard reflections every 200 reflections
1859 independent reflections intensity decay: 1%
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.051H-atom parameters constrained
wR(F2) = 0.152 w = 1/[σ2(Fo2) + (0.1P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.00(Δ/σ)max < 0.001
1859 reflectionsΔρmax = 0.24 e Å−3
137 parametersΔρmin = −0.20 e Å−3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0117 (17)
Crystal data top
C11H12N2O2V = 2041 (1) Å3
Mr = 204.23Z = 8
Monoclinic, C2/cMo Kα radiation
a = 17.164 (3) ŵ = 0.09 mm−1
b = 10.521 (2) ÅT = 293 K
c = 13.759 (3) Å0.30 × 0.20 × 0.10 mm
β = 124.77 (3)°
Data collection top
Enraf–Nonius CAD-4
diffractometer		1360 reflections with I > 2σ(I)
Absorption correction: ψ scan
(North et al., 1968)		Rint = 0.028
Tmin = 0.973, Tmax = 0.9913 standard reflections every 200 reflections
1923 measured reflections intensity decay: 1%
1859 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0510 restraints
wR(F2) = 0.152H-atom parameters constrained
S = 1.00Δρmax = 0.24 e Å−3
1859 reflectionsΔρmin = −0.20 e Å−3
137 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
N10.12866 (11)0.40243 (18)0.19751 (15)0.0466 (5)
O10.07064 (11)0.13738 (15)0.15389 (15)0.0602 (5)
C10.06679 (17)0.7803 (2)0.15626 (19)0.0523 (6)
H1B0.05020.86580.14520.063*
N20.02673 (11)0.56505 (15)0.13920 (13)0.0376 (4)
O2−0.07427 (10)0.20448 (14)0.09371 (13)0.0512 (5)
C20.16246 (17)0.7466 (3)0.2109 (2)0.0582 (6)
H2A0.20750.81020.23460.070*
C30.19016 (14)0.6232 (2)0.22978 (18)0.0527 (6)
H3A0.25370.60200.26650.063*
C40.12108 (13)0.5273 (2)0.19286 (17)0.0422 (5)
C50.03813 (14)0.3590 (2)0.14702 (17)0.0408 (5)
C6−0.02457 (13)0.45553 (19)0.11134 (16)0.0387 (5)
H6A−0.08960.44870.07510.046*
C7−0.00174 (15)0.6916 (2)0.11927 (17)0.0432 (5)
C8−0.10473 (15)0.7154 (2)0.05724 (19)0.0509 (6)
H8A−0.11640.80530.04800.076*
H8B−0.12600.68070.10280.076*
H8C−0.13850.6757−0.01920.076*
C90.01645 (14)0.2218 (2)0.13352 (17)0.0432 (5)
C10−0.10735 (16)0.0748 (2)0.0699 (2)0.0560 (6)
H10A−0.07010.02410.14120.067*
H10B−0.10110.03860.00980.067*
C11−0.20816 (17)0.0755 (3)0.0283 (2)0.0727 (8)
H11A−0.2321−0.00990.01140.109*
H11B−0.24430.1261−0.04210.109*
H11C−0.21340.11090.08870.109*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0347 (9)0.0568 (12)0.0450 (10)0.0026 (8)0.0208 (8)0.0007 (8)
O10.0514 (10)0.0524 (10)0.0734 (11)0.0127 (8)0.0335 (9)0.0054 (8)
C10.0589 (14)0.0472 (13)0.0525 (13)−0.0098 (11)0.0328 (11)−0.0024 (10)
N20.0335 (9)0.0460 (10)0.0347 (9)−0.0019 (7)0.0202 (7)−0.0025 (7)
O20.0443 (9)0.0417 (9)0.0654 (10)−0.0026 (6)0.0301 (8)−0.0048 (7)
C20.0540 (14)0.0666 (16)0.0554 (13)−0.0196 (12)0.0320 (11)−0.0058 (12)
C30.0362 (11)0.0717 (17)0.0488 (13)−0.0106 (10)0.0234 (10)−0.0027 (11)
C40.0330 (10)0.0564 (14)0.0360 (10)−0.0003 (9)0.0188 (8)−0.0004 (9)
C50.0365 (10)0.0492 (12)0.0365 (10)0.0012 (9)0.0207 (9)0.0003 (9)
C60.0327 (10)0.0457 (12)0.0372 (10)−0.0037 (9)0.0196 (8)−0.0020 (9)
C70.0474 (12)0.0466 (13)0.0387 (11)−0.0031 (10)0.0264 (9)−0.0024 (9)
C80.0498 (13)0.0447 (13)0.0588 (13)0.0022 (10)0.0313 (11)−0.0019 (10)
C90.0397 (11)0.0491 (13)0.0401 (11)0.0056 (9)0.0223 (9)0.0022 (9)
C100.0557 (14)0.0427 (13)0.0662 (15)−0.0034 (10)0.0327 (12)−0.0038 (11)
C110.0557 (15)0.0608 (17)0.092 (2)−0.0087 (12)0.0369 (15)−0.0109 (14)
Geometric parameters (Å, º) top
N1—C41.318 (3)C3—H3A0.9300
N1—C51.369 (2)C5—C61.352 (3)
O1—C91.198 (2)C5—C91.475 (3)
C1—C71.353 (3)C6—H6A0.9300
C1—C21.407 (3)C7—C81.482 (3)
C1—H1B0.9300C8—H8A0.9600
N2—C61.366 (2)C8—H8B0.9600
N2—C71.391 (3)C8—H8C0.9600
N2—C41.401 (2)C10—C111.480 (3)
O2—C91.336 (2)C10—H10A0.9700
O2—C101.442 (3)C10—H10B0.9700
C2—C31.357 (4)C11—H11A0.9600
C2—H2A0.9300C11—H11B0.9600
C3—C41.412 (3)C11—H11C0.9600
C4—N1—C5104.84 (16)C1—C7—C8126.6 (2)
C7—C1—C2121.8 (2)N2—C7—C8116.43 (18)
C7—C1—H1B119.1C7—C8—H8A109.5
C2—C1—H1B119.1C7—C8—H8B109.5
C6—N2—C7130.90 (17)H8A—C8—H8B109.5
C6—N2—C4105.97 (16)C7—C8—H8C109.5
C7—N2—C4123.11 (16)H8A—C8—H8C109.5
C9—O2—C10116.01 (17)H8B—C8—H8C109.5
C3—C2—C1121.2 (2)O1—C9—O2124.2 (2)
C3—C2—H2A119.4O1—C9—C5126.1 (2)
C1—C2—H2A119.4O2—C9—C5109.67 (17)
C2—C3—C4119.0 (2)O2—C10—C11107.8 (2)
C2—C3—H3A120.5O2—C10—H10A110.2
C4—C3—H3A120.5C11—C10—H10A110.2
N1—C4—N2111.15 (17)O2—C10—H10B110.2
N1—C4—C3130.93 (19)C11—C10—H10B110.2
N2—C4—C3117.91 (19)H10A—C10—H10B108.5
C6—C5—N1111.79 (19)C10—C11—H11A109.5
C6—C5—C9126.71 (19)C10—C11—H11B109.5
N1—C5—C9121.48 (18)H11A—C11—H11B109.5
C5—C6—N2106.24 (17)C10—C11—H11C109.5
C5—C6—H6A126.9H11A—C11—H11C109.5
N2—C6—H6A126.9H11B—C11—H11C109.5
C1—C7—N2117.0 (2)
C7—C1—C2—C3−0.6 (3)C4—N2—C6—C5−0.42 (19)
C1—C2—C3—C40.4 (3)C2—C1—C7—N20.9 (3)
C5—N1—C4—N2−0.5 (2)C2—C1—C7—C8−177.8 (2)
C5—N1—C4—C3−179.0 (2)C6—N2—C7—C1−178.96 (19)
C6—N2—C4—N10.6 (2)C4—N2—C7—C1−1.2 (3)
C7—N2—C4—N1−177.71 (17)C6—N2—C7—C8−0.2 (3)
C6—N2—C4—C3179.30 (17)C4—N2—C7—C8177.64 (16)
C7—N2—C4—C31.0 (3)C10—O2—C9—O1−2.8 (3)
C2—C3—C4—N1177.8 (2)C10—O2—C9—C5176.75 (17)
C2—C3—C4—N2−0.6 (3)C6—C5—C9—O1171.5 (2)
C4—N1—C5—C60.2 (2)N1—C5—C9—O1−6.9 (3)
C4—N1—C5—C9178.87 (19)C6—C5—C9—O2−8.0 (3)
N1—C5—C6—N20.2 (2)N1—C5—C9—O2173.49 (16)
C9—C5—C6—N2−178.43 (18)C9—O2—C10—C11179.40 (18)
C7—N2—C6—C5177.67 (18)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2A···N1i0.932.593.461 (4)155
C3—H3A···O1i0.932.583.456 (4)157
Symmetry code: (i) −x+1/2, y+1/2, −z+1/2.

Experimental details

Crystal data
Chemical formulaC11H12N2O2
Mr204.23
Crystal system, space groupMonoclinic, C2/c
Temperature (K)293
a, b, c (Å)17.164 (3), 10.521 (2), 13.759 (3)
β (°) 124.77 (3)
V (Å3)2041 (1)
Z8
Radiation typeMo Kα
µ (mm−1)0.09
Crystal size (mm)0.30 × 0.20 × 0.10
Data collection
DiffractometerEnraf–Nonius CAD-4
Absorption correctionψ scan
(North et al., 1968)
Tmin, Tmax0.973, 0.991
No. of measured, independent and
observed [I > 2σ(I)] reflections		1923, 1859, 1360
Rint0.028
(sin θ/λ)max (Å−1)0.601
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.051, 0.152, 1.00
No. of reflections1859
No. of parameters137
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.24, −0.20

Computer programs: CAD-4 EXPRESS (Enraf-Nonius, 1994), XCAD4 (Harms & Wocadlo, 1995), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2A···N1i0.932.593.461 (4)155
C3—H3A···O1i0.932.583.456 (4)157
Symmetry code: (i) −x+1/2, y+1/2, −z+1/2.
 

Acknowledgements

The authors would like to thank Professor Hua-qin Wang of Nanjing University for the data collection.

References

First citationAllen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.  CSD CrossRef Web of Science Google Scholar
 First citationEnraf–Nonius (1989). CAD-4 EXPRESS. Enraf–Nonius, Delft, The Netherlands.  Google Scholar
 First citationHarms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.  Google Scholar
 First citationImaeda, Y., Kawasamoto, T., Tobisu, M., Konishi, N., Hiroe, K., Kawamura, M., Tanaka, T. & Kubo, K. (2008). Bioorg. Med. Chem. 16, 3125–3140.  Web of Science CrossRef PubMed CAS Google Scholar
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ISSN: 2056-9890
Volume 66| Part 8| August 2010| Page o1999
https://doi.org/10.1107/S1600536810026577
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