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

Yin, W.-Y.

doi:10.1107/S1600536812051549

organic compounds

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ISSN: 2056-9890

Volume 69| Part 2| February 2013| Page o211

doi:10.1107/S1600536812051549

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

Wen-Yu Yin ^a ^*

^aDepartment of Chemistry & Materials Engineering, Jiangsu Laboratory of Advanced Functional Materials, Changshu Institute of Technology, Changshu 215500, Jiangsu, People's Republic of China
^*Correspondence e-mail: ywy21wz@sina.com

(Received 26 November 2012; accepted 21 December 2012; online 9 January 2013)

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, P 2₁ /c
a = 5.4032 (8) Å
b = 14.722 (2) Å
c = 12.1055 (18) Å
β = 96.182 (4)°
V = 957.3 (2) Å³
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[F² > 2σ(F²)] = 0.047
wR(F²) = 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

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) -x+2, -y+1, -z+1; (ii) $[-x+1, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

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 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536812051549/hp2052sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812051549/hp2052Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812051549/hp2052Isup3.cml

checkCIF report

Comment top

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).

Related literature top

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 top

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.

Computing details top

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); 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 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top

	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.

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

Crystal data top

C₉H₉N₂O₂⁺·Cl⁻	F(000) = 440
M_r = 212.63	D_x = 1.475 Mg m⁻³ D_m = 1.475 Mg m⁻³ D_m 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 top

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

Refinement top

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(F_o²) + (0.0102P)² + 1.0216P] where P = (F_o² + 2F_c²)/3
1689 reflections	(Δ/σ)_max < 0.001
134 parameters	Δρ_max = 0.19 e Å⁻³
0 restraints	Δρ_min = −0.20 e Å⁻³

Crystal data top

C₉H₉N₂O₂⁺·Cl⁻	V = 957.3 (2) Å³
M_r = 212.63	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 5.4032 (8) Å	µ = 0.37 mm⁻¹
b = 14.722 (2) Å	T = 293 K
c = 12.1055 (18) Å	0.25 × 0.15 × 0.12 mm
β = 96.182 (4)°

Data collection top

Rigaku Mercury diffractometer	1689 independent reflections
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	1417 reflections with I > 2σ(I)
T_min = 0.913, T_max = 0.957	R_int = 0.044
7948 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.047	0 restraints
wR(F²) = 0.083	H atoms treated by a mixture of independent and constrained refinement
S = 1.02	Δρ_max = 0.19 e Å⁻³
1689 reflections	Δρ_min = −0.20 e Å⁻³
134 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

	x	y	z	U_iso*/U_eq
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 (Å²) top

	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) top

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) top

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.

Experimental details

Crystal data
Chemical formula	C₉H₉N₂O₂⁺·Cl⁻
M_r	212.63
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	5.4032 (8), 14.722 (2), 12.1055 (18)
β (°)	96.182 (4)
V (Å³)	957.3 (2)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.37
Crystal size (mm)	0.25 × 0.15 × 0.12

Data collection
Diffractometer	Rigaku Mercury diffractometer
Absorption correction	Multi-scan (CrystalClear; Rigaku, 2005)
T_min, T_max	0.913, 0.957
No. of measured, independent and observed [I > 2σ(I)] reflections	7948, 1689, 1417
R_int	0.044
(sin θ/λ)_max (Å⁻¹)	0.594

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.047, 0.083, 1.02
No. of reflections	1689
No. of parameters	134
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.19, −0.20

Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL/PC (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···Cl1ⁱ	0.82	2.19	2.984 (2)	163.2
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.

Acknowledgements

This work was supported by the Natural Science Fund of Jiangsu Province, China (No. 08KJB150001).

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