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

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

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[Catalano, V. J. & Etogo, A. O. (2007). Inorg. Chem. 46, 5608-5615.]); Feng et al. (2012[Feng, X., Wang, Y. F., Shi, Z. Q., Shang, J. J. & Wang, L. Y. (2012). Inorg. Chem. Commun. 22, 131-136.]); Keppler et al. (1987[Keppler, B. K., Wehe, D., Endres, H. & Rupp, W. (1987). Inorg. Chem. 26, 844-846.]); Poul et al. (2007[Poul, N. L., Campion, M., Douziech, B., Rondelez, Y., Clainche, L. L., Reinaud, O. & Mest, Y. L. (2007). J. Am. Chem. Soc. 129, 8801-8810.]); Saha et al. (2012[Saha, D., Das, S., Mardanya, S. & Baitalik, S. (2012). Dalton Trans. 41, 8886-8898.]); Samantaray et al. (2007[Samantaray, M. K., Katiyar, V., Pang, K., Nanavati, H. & Ghosh, P. (2007). J. Organomet. Chem. 692, 1672-1682.]); Takagaki et al. (2012[Takagaki, T., Bando, T. & Sugiyama, H. (2012). J. Am. Chem. Soc. 134, 13074-13081.]).

[Scheme 1]

Experimental

Crystal data
  • C9H9N2O2+·Cl

  • Mr = 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[Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.913, Tmax = 0.957

  • 7948 measured reflections

  • 1689 independent reflections

  • 1417 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.19 e Å−3

  • Δρmin = −0.20 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]); cell refinement: CrystalClear; data reduction: CrystalClear; 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/PC (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL/PC and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


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.

Refinement top

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 Uiso(H) = 1.2Ueq(C) for imidazole group and phenyl group. H atoms bound to O and N atoms were located in a difference Fourier map.

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
[Figure 1] Fig. 1. The molecular structure of the title compound, with atom labels and anisotropic displacement ellipsoids (drawn at 30% probability level).
[Figure 2] 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.
[Figure 3] 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+·ClF(000) = 440
Mr = 212.63Dx = 1.475 Mg m3
Dm = 1.475 Mg m3
Dm measured by not measured
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 9784 reflections
a = 5.4032 (8) Åθ = 3.2–25.0°
b = 14.722 (2) ŵ = 0.37 mm1
c = 12.1055 (18) ÅT = 293 K
β = 96.182 (4)°Block, yellow
V = 957.3 (2) Å30.25 × 0.15 × 0.12 mm
Z = 4
Data collection top
Rigaku Mercury
diffractometer
1689 independent reflections
Radiation source: fine-focus sealed tube1417 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.044
/w scansθmax = 25.0°, θmin = 3.2°
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)
h = 66
Tmin = 0.913, Tmax = 0.957k = 1717
7948 measured reflectionsl = 1414
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)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.083H 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 parametersΔρmax = 0.19 e Å3
0 restraintsΔρmin = 0.20 e Å3
Crystal data top
C9H9N2O2+·ClV = 957.3 (2) Å3
Mr = 212.63Z = 4
Monoclinic, P21/cMo Kα radiation
a = 5.4032 (8) ŵ = 0.37 mm1
b = 14.722 (2) ÅT = 293 K
c = 12.1055 (18) Å0.25 × 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)
Tmin = 0.913, Tmax = 0.957Rint = 0.044
7948 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0470 restraints
wR(F2) = 0.083H atoms treated by a mixture of independent and constrained refinement
S = 1.02Δρmax = 0.19 e Å3
1689 reflectionsΔρmin = 0.20 e Å3
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
xyzUiso*/Ueq
Cl10.99075 (13)0.33311 (5)0.93211 (6)0.0507 (2)
C10.3725 (4)0.61391 (17)0.6832 (2)0.0372 (6)
C60.6807 (5)0.57805 (17)0.5799 (2)0.0396 (6)
H60.81960.55030.55560.048*
O10.7448 (4)0.72008 (14)0.26206 (16)0.0559 (6)
H10.83520.69860.21840.084*
O20.9053 (3)0.60844 (14)0.37360 (15)0.0540 (5)
N10.5729 (4)0.55760 (14)0.67658 (17)0.0363 (5)
C50.6379 (5)0.49364 (18)0.7568 (2)0.0431 (7)
H20.77470.45610.75210.052*
C40.4994 (5)0.48630 (19)0.8428 (2)0.0482 (7)
H30.54060.44280.89740.058*
C30.2926 (5)0.5438 (2)0.8513 (2)0.0496 (7)
H40.19920.53770.91100.060*
C20.2295 (5)0.60797 (19)0.7725 (2)0.0451 (7)
H50.09540.64670.77790.054*
N20.3549 (4)0.66686 (16)0.59268 (18)0.0402 (5)
C70.5447 (5)0.64601 (17)0.5281 (2)0.0374 (6)
C80.5594 (5)0.69786 (18)0.4237 (2)0.0451 (7)
H8A0.58620.76130.44280.054*
H8B0.39940.69350.37920.054*
C90.7576 (5)0.66897 (19)0.3528 (2)0.0419 (6)
H2A0.251 (6)0.714 (2)0.581 (2)0.067 (10)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0547 (4)0.0434 (4)0.0564 (4)0.0043 (3)0.0173 (3)0.0008 (3)
C10.0329 (14)0.0375 (15)0.0410 (15)0.0032 (11)0.0026 (12)0.0069 (12)
C60.0347 (14)0.0426 (16)0.0429 (15)0.0031 (12)0.0099 (12)0.0034 (12)
O10.0640 (14)0.0566 (13)0.0500 (12)0.0101 (10)0.0193 (10)0.0099 (11)
O20.0505 (12)0.0654 (14)0.0475 (11)0.0186 (11)0.0110 (10)0.0049 (10)
N10.0337 (11)0.0358 (12)0.0393 (12)0.0016 (10)0.0035 (10)0.0030 (10)
C50.0395 (15)0.0441 (16)0.0448 (16)0.0022 (12)0.0002 (13)0.0016 (13)
C40.0530 (18)0.0477 (17)0.0430 (16)0.0026 (14)0.0010 (14)0.0028 (13)
C30.0514 (17)0.0566 (19)0.0422 (16)0.0097 (15)0.0113 (14)0.0047 (14)
C20.0400 (15)0.0484 (17)0.0484 (16)0.0007 (13)0.0115 (13)0.0100 (14)
N20.0363 (12)0.0401 (13)0.0446 (13)0.0055 (11)0.0066 (10)0.0019 (11)
C70.0346 (13)0.0371 (15)0.0408 (14)0.0023 (11)0.0064 (12)0.0061 (12)
C80.0454 (16)0.0442 (16)0.0459 (16)0.0053 (13)0.0064 (13)0.0007 (13)
C90.0410 (15)0.0432 (16)0.0412 (15)0.0040 (13)0.0033 (12)0.0036 (13)
Geometric parameters (Å, º) top
C1—N21.340 (3)C4—C31.414 (4)
C1—N11.373 (3)C4—H30.9300
C1—C21.398 (4)C3—C21.359 (4)
C6—C71.354 (3)C3—H40.9300
C6—N11.395 (3)C2—H50.9300
C6—H60.9300N2—C71.389 (3)
O1—C91.327 (3)N2—H2A0.89 (3)
O1—H10.8200C7—C81.487 (4)
O2—C91.205 (3)C8—C91.503 (4)
N1—C51.371 (3)C8—H8A0.9700
C5—C41.351 (4)C8—H8B0.9700
C5—H20.9300
N2—C1—N1106.9 (2)C3—C2—C1117.9 (3)
N2—C1—C2132.3 (2)C3—C2—H5121.0
N1—C1—C2120.8 (2)C1—C2—H5121.0
C7—C6—N1107.0 (2)C1—N2—C7109.9 (2)
C7—C6—H6126.5C1—N2—H2A124 (2)
N1—C6—H6126.5C7—N2—H2A125 (2)
C9—O1—H1109.5C6—C7—N2107.4 (2)
C5—N1—C1121.1 (2)C6—C7—C8134.2 (2)
C5—N1—C6130.1 (2)N2—C7—C8118.4 (2)
C1—N1—C6108.8 (2)C7—C8—C9116.5 (2)
C4—C5—N1118.7 (3)C7—C8—H8A108.2
C4—C5—H2120.7C9—C8—H8A108.2
N1—C5—H2120.7C7—C8—H8B108.2
C5—C4—C3121.0 (3)C9—C8—H8B108.2
C5—C4—H3119.5H8A—C8—H8B107.3
C3—C4—H3119.5O2—C9—O1124.5 (2)
C2—C3—C4120.4 (3)O2—C9—C8125.9 (3)
C2—C3—H4119.8O1—C9—C8109.6 (2)
C4—C3—H4119.8
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···Cl1i0.822.192.984 (2)163
N2—H2A···Cl1ii0.89 (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 formulaC9H9N2O2+·Cl
Mr212.63
Crystal system, space groupMonoclinic, P21/c
Temperature (K)293
a, b, c (Å)5.4032 (8), 14.722 (2), 12.1055 (18)
β (°) 96.182 (4)
V3)957.3 (2)
Z4
Radiation typeMo Kα
µ (mm1)0.37
Crystal size (mm)0.25 × 0.15 × 0.12
Data collection
DiffractometerRigaku Mercury
diffractometer
Absorption correctionMulti-scan
(CrystalClear; Rigaku, 2005)
Tmin, Tmax0.913, 0.957
No. of measured, independent and
observed [I > 2σ(I)] reflections
7948, 1689, 1417
Rint0.044
(sin θ/λ)max1)0.594
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.047, 0.083, 1.02
No. of reflections1689
No. of parameters134
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
O1—H1···Cl1i0.822.192.984 (2)163.2
N2—H2A···Cl1ii0.89 (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).

References

First citationCatalano, V. J. & Etogo, A. O. (2007). Inorg. Chem. 46, 5608–5615.  Web of Science CSD CrossRef PubMed CAS
First citationFeng, X., Wang, Y. F., Shi, Z. Q., Shang, J. J. & Wang, L. Y. (2012). Inorg. Chem. Commun. 22, 131–136.  Web of Science CrossRef CAS
First citationKeppler, B. K., Wehe, D., Endres, H. & Rupp, W. (1987). Inorg. Chem. 26, 844–846.  CSD CrossRef CAS Web of Science
First citationPoul, N. L., Campion, M., Douziech, B., Rondelez, Y., Clainche, L. L., Reinaud, O. & Mest, Y. L. (2007). J. Am. Chem. Soc. 129, 8801–8810.  PubMed
First citationRigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.
First citationSaha, D., Das, S., Mardanya, S. & Baitalik, S. (2012). Dalton Trans. 41, 8886–8898.  Web of Science CSD CrossRef CAS PubMed
First citationSamantaray, M. K., Katiyar, V., Pang, K., Nanavati, H. & Ghosh, P. (2007). J. Organomet. Chem. 692, 1672–1682.  Web of Science CSD CrossRef CAS
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals
First citationTakagaki, T., Bando, T. & Sugiyama, H. (2012). J. Am. Chem. Soc. 134, 13074–13081.  Web of Science CrossRef CAS PubMed

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