2-(Carb­oxy­meth­yl)imidazo[1,2-a]pyridin-1-ium chloride

Abstract

In the crystal structure of the title salt, C₉H₉N₂O₂ ⁺·Cl⁻, the cations and anions are linked into chains parallel to [021] by O—H⋯Cl and N—H⋯Cl hydrogen bonds.

Related literature  

For the diversity of structures and the applications of compounds with an imidazole moiety, see: Catalano & Etogo (2007 ▶); Feng et al. (2012 ▶); Keppler et al. (1987 ▶); Poul et al. (2007 ▶); Saha et al. (2012 ▶); Samantaray et al. (2007 ▶); Takagaki et al. (2012 ▶).

Experimental  

Crystal data  

• C₉H₉N₂O₂ ⁺·Cl⁻

• M _r = 212.63

• Monoclinic,

• a = 5.4032 (8) Å

• b = 14.722 (2) Å

• c = 12.1055 (18) Å

• β = 96.182 (4)°

• V = 957.3 (2) ų

• Z = 4

• Mo Kα radiation

• μ = 0.37 mm⁻¹

• T = 293 K

• 0.25 × 0.15 × 0.12 mm

Data collection  

• Rigaku Mercury diffractometer

• Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 ▶) T _min = 0.913, T _max = 0.957

• 7948 measured reflections

• 1689 independent reflections

• 1417 reflections with I > 2σ(I)

• R _int = 0.044

Refinement  

• R[F ² > 2σ(F ²)] = 0.047

• wR(F ²) = 0.083

• S = 1.02

• 1689 reflections

• 134 parameters

• H atoms treated by a mixture of independent and constrained refinement

• Δρ_max = 0.19 e Å⁻³

• Δρ_min = −0.20 e Å⁻³

Data collection: CrystalClear (Rigaku, 2005 ▶); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: SHELXTL/PC (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXTL/PC and PLATON (Spek, 2009 ▶).

Supplementary Material

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

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯Cl1i	0.82	2.19	2.984 (2)	163
N2—H2A⋯Cl1ii	0.89 (3)	2.18 (3)	3.074 (2)	175 (3)

Symmetry codes: (i) ; (ii) .

supplementary crystallographic information

Comment

Derivatives of imidazole have received great attention for their applications in the field of biology (Catalano et al., 2007; Poul et al., 2007; Takagaki et al., 2012;). The most pervasive is the amino acid histidine, which has an imidazole side-chain (Feng et al., 2012; Samantaray et al., 2007;). In recent years, many derivatives have been used as antifungal agents and bone resorption inhibitors (Keppler et al., 1987; Saha et al., 2012;). As illustrated in Fig. 1, the title compound is composed of one imidazo[1,2-a]pyridin-2-acetic acid cation and a Cl^- anion. The acetic acid group is nearly coplanar with the heterocyele ring with the dihedral angle of 4°. The N2 atom is protonated with N2···H distance of 0.89 (3) Å. The ions are linked into one chain through intermolecular hydrogen bonds [O1—H1···Cl1ⁱ and N2—H2A···Cl1ⁱⁱ; symmetry code: i = 2 - x,1 - y,1 - z; ii = -x + 1, y + 1/2, -z + 3/2.] (shown in Fig. 2). The crystal structure is stabilized by van der waals forces (shown in Fig. 3).

Experimental

To a ethanol solution of 2-aminopyridine (7.21 g, 0.0766 mol) under nitrogen was added ethyl 4-chloroacetoacetate (6 g, 0.0365 mol). The mixture was refluxed for 2 h before concentrated to dryness. The residue was dissolved in 80 ml of purified water and extracted with ethyl acetate. The organic phase was concentrated to give a black oily consistency. 30% KOH (153 ml) was added and stirred for 3 h at 40 ^oC. The crystals will form after adding concentrated HCl.

Refinement

Carbon-bond H atoms were positioned geometrically (C—H = 0.93 Å for phenyl group, C—H = 0.93 Å for imidazole group), and were included in the refinement in the riding mode approximation, with U_iso(H) = 1.2U_eq(C) for imidazole group and phenyl group. H atoms bound to O and N atoms were located in a difference Fourier map.

Figures

Fig. 1.

The molecular structure of the title compound, with atom labels and anisotropic displacement ellipsoids (drawn at 30% probability level).

Fig. 2.

The packing of the title compound. Hydrogen bonds are shown as dashed lines. All H attached to carbon atoms were omitted for clarity.

Fig. 3.

Three dimensional strucure viewed along the a axis.

Crystal data

C9H9N2O2+·Cl−	F(000) = 440
Mr = 212.63	Dx = 1.475 Mg m−3Dm = 1.475 Mg m−3Dm measured by not measured
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 9784 reflections
a = 5.4032 (8) Å	θ = 3.2–25.0°
b = 14.722 (2) Å	µ = 0.37 mm−1
c = 12.1055 (18) Å	T = 293 K
β = 96.182 (4)°	Block, yellow
V = 957.3 (2) Å3	0.25 × 0.15 × 0.12 mm
Z = 4

Data collection

Rigaku Mercury diffractometer	1689 independent reflections
Radiation source: fine-focus sealed tube	1417 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.044
/w scans	θmax = 25.0°, θmin = 3.2°
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	h = −6→6
Tmin = 0.913, Tmax = 0.957	k = −17→17
7948 measured reflections	l = −14→14

Refinement

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)] = 0.047	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.083	H atoms treated by a mixture of independent and constrained refinement
S = 1.02	w = 1/[σ2(Fo2) + (0.0102P)2 + 1.0216P] where P = (Fo2 + 2Fc2)/3
1689 reflections	(Δ/σ)max < 0.001
134 parameters	Δρmax = 0.19 e Å−3
0 restraints	Δρmin = −0.20 e Å−3

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 (Ų)

	x	y	z	Uiso*/Ueq
Cl1	0.99075 (13)	0.33311 (5)	0.93211 (6)	0.0507 (2)
C1	0.3725 (4)	0.61391 (17)	0.6832 (2)	0.0372 (6)
C6	0.6807 (5)	0.57805 (17)	0.5799 (2)	0.0396 (6)
H6	0.8196	0.5503	0.5556	0.048*
O1	0.7448 (4)	0.72008 (14)	0.26206 (16)	0.0559 (6)
H1	0.8352	0.6986	0.2184	0.084*
O2	0.9053 (3)	0.60844 (14)	0.37360 (15)	0.0540 (5)
N1	0.5729 (4)	0.55760 (14)	0.67658 (17)	0.0363 (5)
C5	0.6379 (5)	0.49364 (18)	0.7568 (2)	0.0431 (7)
H2	0.7747	0.4561	0.7521	0.052*
C4	0.4994 (5)	0.48630 (19)	0.8428 (2)	0.0482 (7)
H3	0.5406	0.4428	0.8974	0.058*
C3	0.2926 (5)	0.5438 (2)	0.8513 (2)	0.0496 (7)
H4	0.1992	0.5377	0.9110	0.060*
C2	0.2295 (5)	0.60797 (19)	0.7725 (2)	0.0451 (7)
H5	0.0954	0.6467	0.7779	0.054*
N2	0.3549 (4)	0.66686 (16)	0.59268 (18)	0.0402 (5)
C7	0.5447 (5)	0.64601 (17)	0.5281 (2)	0.0374 (6)
C8	0.5594 (5)	0.69786 (18)	0.4237 (2)	0.0451 (7)
H8A	0.5862	0.7613	0.4428	0.054*
H8B	0.3994	0.6935	0.3792	0.054*
C9	0.7576 (5)	0.66897 (19)	0.3528 (2)	0.0419 (6)
H2A	0.251 (6)	0.714 (2)	0.581 (2)	0.067 (10)*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
Cl1	0.0547 (4)	0.0434 (4)	0.0564 (4)	−0.0043 (3)	0.0173 (3)	0.0008 (3)
C1	0.0329 (14)	0.0375 (15)	0.0410 (15)	−0.0032 (11)	0.0026 (12)	−0.0069 (12)
C6	0.0347 (14)	0.0426 (16)	0.0429 (15)	0.0031 (12)	0.0099 (12)	−0.0034 (12)
O1	0.0640 (14)	0.0566 (13)	0.0500 (12)	0.0101 (10)	0.0193 (10)	0.0099 (11)
O2	0.0505 (12)	0.0654 (14)	0.0475 (11)	0.0186 (11)	0.0110 (10)	0.0049 (10)
N1	0.0337 (11)	0.0358 (12)	0.0393 (12)	−0.0016 (10)	0.0035 (10)	−0.0030 (10)
C5	0.0395 (15)	0.0441 (16)	0.0448 (16)	0.0022 (12)	0.0002 (13)	0.0016 (13)
C4	0.0530 (18)	0.0477 (17)	0.0430 (16)	−0.0026 (14)	0.0010 (14)	0.0028 (13)
C3	0.0514 (17)	0.0566 (19)	0.0422 (16)	−0.0097 (15)	0.0113 (14)	−0.0047 (14)
C2	0.0400 (15)	0.0484 (17)	0.0484 (16)	0.0007 (13)	0.0115 (13)	−0.0100 (14)
N2	0.0363 (12)	0.0401 (13)	0.0446 (13)	0.0055 (11)	0.0066 (10)	−0.0019 (11)
C7	0.0346 (13)	0.0371 (15)	0.0408 (14)	−0.0023 (11)	0.0064 (12)	−0.0061 (12)
C8	0.0454 (16)	0.0442 (16)	0.0459 (16)	0.0053 (13)	0.0064 (13)	0.0007 (13)
C9	0.0410 (15)	0.0432 (16)	0.0412 (15)	−0.0040 (13)	0.0033 (12)	−0.0036 (13)

Geometric parameters (Å, º)

C1—N2	1.340 (3)	C4—C3	1.414 (4)
C1—N1	1.373 (3)	C4—H3	0.9300
C1—C2	1.398 (4)	C3—C2	1.359 (4)
C6—C7	1.354 (3)	C3—H4	0.9300
C6—N1	1.395 (3)	C2—H5	0.9300
C6—H6	0.9300	N2—C7	1.389 (3)
O1—C9	1.327 (3)	N2—H2A	0.89 (3)
O1—H1	0.8200	C7—C8	1.487 (4)
O2—C9	1.205 (3)	C8—C9	1.503 (4)
N1—C5	1.371 (3)	C8—H8A	0.9700
C5—C4	1.351 (4)	C8—H8B	0.9700
C5—H2	0.9300
N2—C1—N1	106.9 (2)	C3—C2—C1	117.9 (3)
N2—C1—C2	132.3 (2)	C3—C2—H5	121.0
N1—C1—C2	120.8 (2)	C1—C2—H5	121.0
C7—C6—N1	107.0 (2)	C1—N2—C7	109.9 (2)
C7—C6—H6	126.5	C1—N2—H2A	124 (2)
N1—C6—H6	126.5	C7—N2—H2A	125 (2)
C9—O1—H1	109.5	C6—C7—N2	107.4 (2)
C5—N1—C1	121.1 (2)	C6—C7—C8	134.2 (2)
C5—N1—C6	130.1 (2)	N2—C7—C8	118.4 (2)
C1—N1—C6	108.8 (2)	C7—C8—C9	116.5 (2)
C4—C5—N1	118.7 (3)	C7—C8—H8A	108.2
C4—C5—H2	120.7	C9—C8—H8A	108.2
N1—C5—H2	120.7	C7—C8—H8B	108.2
C5—C4—C3	121.0 (3)	C9—C8—H8B	108.2
C5—C4—H3	119.5	H8A—C8—H8B	107.3
C3—C4—H3	119.5	O2—C9—O1	124.5 (2)
C2—C3—C4	120.4 (3)	O2—C9—C8	125.9 (3)
C2—C3—H4	119.8	O1—C9—C8	109.6 (2)
C4—C3—H4	119.8

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···Cl1i	0.82	2.19	2.984 (2)	163
N2—H2A···Cl1ii	0.89 (3)	2.18 (3)	3.074 (2)	175 (3)

Symmetry codes: (i) −x+2, −y+1, −z+1; (ii) −x+1, y+1/2, −z+3/2.