Literature DB >> 21754563

2-[2-(1H-Imidazol-3-ium-5-yl)eth-yl]-3-(pyridin-2-yl)-2H-imidazo[1,5-a]pyridin-4-ium bis-(perchlorate).

Murat Türkyılmaz, Yakup Baran, Namık Ozdemir.   

Abstract

In the title mol-ecular salt, C(17)H(17)N(5) (+)·2ClO(4) (-), the dihedral angles between the fused-ring system and the pendant five- and six-membered heterocyclic rings are 6.4 (2) and 41.29 (19)°, respectively. The O atoms of both perchlorate anions are disordered over two sets of sites with occupancy ratios of 0.614 (8):0.386 (8) and 0.591 (7):0.409 (7). An intra-molecular C-H⋯N contact occurs in the cation. In the crystal, the components are linked by N-H⋯O and C-H⋯O hydrogen bonds and π-π stacking inter-actions [centroid-centroid separation = 3.642 (3) Å].

Entities:  

Year:  2011        PMID: 21754563      PMCID: PMC3089310          DOI: 10.1107/S1600536811015625

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For background to the biological properties of imidazopyridine compounds, see: Kaminski & Doweyko (1997 ▶); Sanfillipo et al. (1988 ▶); Lhassani et al. (1999 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

C17H17N5 2+·2ClO4 M = 490.26 Monoclinic, a = 15.044 (6) Å b = 11.303 (4) Å c = 12.783 (5) Å β = 108.009 (15)° V = 2067.1 (13) Å3 Z = 4 Mo Kα radiation μ = 0.37 mm−1 T = 273 K 0.35 × 0.20 × 0.20 mm

Data collection

Rigaku R-AXIS RAPID diffractometer 19199 measured reflections 4507 independent reflections 2540 reflections with I > 2σ(I) R int = 0.083

Refinement

R[F 2 > 2σ(F 2)] = 0.074 wR(F 2) = 0.214 S = 1.07 4507 reflections 363 parameters 198 restraints H-atom parameters constrained Δρmax = 0.45 e Å−3 Δρmin = −0.52 e Å−3 Data collection: PROCESS-AUTO (Rigaku, 1998 ▶); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2004) ▶; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 (Farrugia, 1997 ▶); software used to prepare material for publication: WinGX (Farrugia, 1999 ▶) and PLATON (Spek, 2009 ▶). Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811015625/hb5862sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536811015625/hb5862Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811015625/hb5862Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C17H17N52+·2ClO4F(000) = 1008
Mr = 490.26Dx = 1.575 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 11579 reflections
a = 15.044 (6) Åθ = 3.1–29.6°
b = 11.303 (4) ŵ = 0.37 mm1
c = 12.783 (5) ÅT = 273 K
β = 108.009 (15)°Block, brown
V = 2067.1 (13) Å30.35 × 0.20 × 0.20 mm
Z = 4
Rigaku R-AXIS RAPID diffractometer2540 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.083
graphiteθmax = 27.0°, θmin = 3.1°
Detector resolution: 10.00 pixels mm-1h = −19→19
ω scansk = −14→14
19199 measured reflectionsl = −16→16
4507 independent reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.074Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.214H-atom parameters constrained
S = 1.07w = 1/[σ2(Fo2) + (0.0979P)2 + 0.8991P] where P = (Fo2 + 2Fc2)/3
4507 reflections(Δ/σ)max < 0.001
363 parametersΔρmax = 0.45 e Å3
198 restraintsΔρmin = −0.52 e Å3
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.
xyzUiso*/UeqOcc. (<1)
Cl10.04647 (8)−0.10009 (10)0.30270 (8)0.0598 (4)
Cl20.38314 (10)0.18832 (12)0.36810 (11)0.0791 (4)
O1A0.1400 (4)−0.0618 (7)0.3141 (7)0.0894 (19)0.614 (8)
O2A−0.0092 (7)−0.0565 (8)0.2027 (5)0.115 (2)0.614 (8)
O3A0.0469 (7)−0.2260 (4)0.3022 (9)0.091 (2)0.614 (8)
O4A0.0210 (9)−0.0453 (14)0.3907 (6)0.069 (2)0.614 (8)
O1B0.0926 (10)−0.0210 (9)0.2511 (10)0.096 (2)0.386 (8)
O2B−0.0448 (5)−0.1148 (12)0.2321 (8)0.088 (3)0.386 (8)
O3B0.0868 (11)−0.2140 (7)0.3301 (15)0.092 (3)0.386 (8)
O4B0.0434 (15)−0.064 (2)0.4091 (8)0.064 (3)0.386 (8)
O5A0.4484 (9)0.1176 (9)0.4445 (8)0.114 (3)0.591 (7)
O6A0.3768 (6)0.2058 (7)0.2528 (5)0.113 (2)0.591 (7)
O7A0.3632 (7)0.2974 (6)0.4153 (7)0.089 (2)0.591 (7)
O8A0.2969 (5)0.1162 (7)0.3466 (6)0.0921 (19)0.591 (7)
O5B0.4416 (12)0.0902 (12)0.4024 (12)0.105 (3)0.409 (7)
O6B0.4497 (7)0.2597 (8)0.3319 (10)0.108 (3)0.409 (7)
O7B0.3793 (11)0.2623 (10)0.4594 (8)0.089 (3)0.409 (7)
O8B0.2861 (6)0.1717 (13)0.3009 (12)0.123 (3)0.409 (7)
N10.2084 (2)0.6878 (3)0.5373 (3)0.0568 (9)
N20.2744 (2)0.8592 (3)0.5682 (3)0.0525 (8)
N30.3643 (3)0.6138 (3)0.4591 (3)0.0678 (10)
N40.1981 (3)0.2840 (3)0.4732 (3)0.0602 (9)
H4N0.24310.29660.44650.072*
N50.0837 (3)0.2016 (3)0.5074 (3)0.0703 (11)
H5N0.04060.15150.50700.084*
C10.1678 (3)0.7453 (4)0.6032 (3)0.0633 (12)
H10.12150.71530.62990.076*
C20.2065 (3)0.8542 (4)0.6235 (3)0.0586 (11)
C30.1957 (4)0.9540 (5)0.6846 (4)0.0705 (13)
H30.15150.95330.72180.085*
C40.2487 (4)1.0493 (5)0.6890 (4)0.0786 (15)
H40.23981.11610.72700.094*
C50.3187 (4)1.0491 (4)0.6361 (4)0.0753 (14)
H50.35711.11510.64290.090*
C60.3313 (3)0.9565 (4)0.5763 (3)0.0616 (11)
H60.37710.95800.54140.074*
C70.2737 (3)0.7553 (3)0.5146 (3)0.0519 (10)
C80.3311 (3)0.7255 (4)0.4459 (3)0.0527 (10)
C90.3495 (3)0.8053 (4)0.3742 (4)0.0624 (11)
H90.32230.88000.36510.075*
C100.4094 (4)0.7724 (5)0.3157 (4)0.0763 (14)
H100.42560.82540.26910.092*
C110.4437 (4)0.6597 (6)0.3288 (5)0.0821 (16)
H110.48390.63470.29070.099*
C120.4184 (4)0.5831 (5)0.3986 (4)0.0814 (15)
H120.44040.50570.40370.098*
C130.1788 (3)0.5677 (4)0.4936 (4)0.0613 (11)
H13A0.20000.55290.43040.074*
H13B0.11120.56290.46970.074*
C140.2189 (3)0.4744 (4)0.5806 (4)0.0643 (12)
H14A0.28560.46730.59320.077*
H14B0.20910.49790.64920.077*
C150.1729 (3)0.3587 (4)0.5444 (3)0.0554 (10)
C160.1433 (3)0.1910 (4)0.4521 (4)0.0674 (12)
H160.14630.12850.40600.081*
C170.1007 (3)0.3047 (4)0.5659 (4)0.0660 (12)
H170.06830.33250.61220.079*
U11U22U33U12U13U23
Cl10.0669 (7)0.0630 (7)0.0559 (6)0.0019 (5)0.0283 (5)−0.0003 (5)
Cl20.0943 (9)0.0704 (8)0.0883 (9)0.0208 (7)0.0509 (8)0.0218 (6)
O1A0.080 (3)0.106 (4)0.101 (4)−0.012 (3)0.056 (3)−0.012 (4)
O2A0.137 (5)0.124 (5)0.068 (3)0.020 (4)0.006 (3)0.017 (3)
O3A0.116 (6)0.064 (3)0.094 (5)−0.010 (3)0.036 (5)−0.007 (3)
O4A0.072 (6)0.074 (5)0.072 (3)−0.001 (4)0.040 (4)−0.005 (4)
O1B0.122 (5)0.102 (5)0.083 (5)−0.009 (4)0.059 (4)0.011 (4)
O2B0.090 (4)0.108 (6)0.057 (4)0.004 (4)0.010 (3)−0.016 (4)
O3B0.107 (7)0.069 (4)0.090 (6)0.020 (4)0.014 (6)−0.004 (4)
O4B0.071 (7)0.072 (6)0.050 (3)−0.007 (5)0.023 (4)−0.003 (4)
O5A0.106 (4)0.092 (5)0.122 (6)0.031 (4)0.005 (5)0.007 (4)
O6A0.149 (5)0.109 (5)0.102 (3)0.040 (4)0.071 (4)0.024 (3)
O7A0.098 (5)0.061 (3)0.117 (5)0.006 (3)0.047 (5)0.009 (3)
O8A0.098 (3)0.090 (4)0.084 (4)0.007 (3)0.022 (3)−0.004 (3)
O5B0.111 (5)0.082 (5)0.124 (7)0.034 (5)0.038 (6)0.013 (5)
O6B0.139 (5)0.098 (5)0.118 (6)0.011 (4)0.087 (4)0.020 (5)
O7B0.091 (5)0.083 (6)0.106 (5)−0.001 (5)0.050 (5)−0.003 (4)
O8B0.117 (4)0.115 (7)0.114 (6)0.018 (4)0.002 (5)−0.001 (5)
N10.060 (2)0.056 (2)0.054 (2)−0.0036 (17)0.0177 (18)0.0058 (16)
N20.061 (2)0.052 (2)0.0438 (18)0.0022 (16)0.0154 (16)0.0031 (15)
N30.073 (3)0.061 (2)0.066 (2)0.0037 (19)0.017 (2)−0.0068 (19)
N40.065 (2)0.058 (2)0.062 (2)−0.0012 (18)0.0260 (19)0.0045 (18)
N50.060 (2)0.057 (2)0.094 (3)−0.0071 (18)0.024 (2)0.015 (2)
C10.062 (3)0.077 (3)0.051 (2)0.002 (2)0.019 (2)0.011 (2)
C20.058 (3)0.073 (3)0.043 (2)0.012 (2)0.013 (2)0.011 (2)
C30.077 (3)0.086 (4)0.049 (2)0.019 (3)0.019 (2)0.000 (2)
C40.099 (4)0.071 (3)0.060 (3)0.018 (3)0.017 (3)−0.008 (2)
C50.098 (4)0.054 (3)0.063 (3)0.000 (3)0.009 (3)−0.005 (2)
C60.078 (3)0.050 (2)0.054 (2)−0.007 (2)0.017 (2)0.000 (2)
C70.057 (2)0.049 (2)0.048 (2)−0.0030 (19)0.0136 (19)0.0069 (18)
C80.054 (2)0.053 (2)0.049 (2)−0.0041 (19)0.0132 (19)−0.0070 (19)
C90.065 (3)0.071 (3)0.053 (2)−0.007 (2)0.022 (2)−0.008 (2)
C100.077 (3)0.092 (4)0.063 (3)−0.027 (3)0.025 (3)−0.010 (3)
C110.063 (3)0.105 (5)0.085 (4)−0.014 (3)0.033 (3)−0.031 (3)
C120.071 (3)0.084 (4)0.086 (4)0.007 (3)0.020 (3)−0.026 (3)
C130.067 (3)0.055 (3)0.059 (3)−0.014 (2)0.014 (2)0.007 (2)
C140.074 (3)0.056 (3)0.061 (3)−0.003 (2)0.017 (2)0.007 (2)
C150.058 (3)0.056 (2)0.054 (2)0.000 (2)0.020 (2)0.006 (2)
C160.072 (3)0.053 (3)0.073 (3)−0.002 (2)0.017 (3)0.001 (2)
C170.066 (3)0.065 (3)0.075 (3)0.004 (2)0.034 (3)0.008 (2)
Cl1—O2A1.385 (5)N5—H5N0.8600
Cl1—O2B1.401 (6)C1—C21.352 (6)
Cl1—O1B1.414 (6)C1—H10.9300
Cl1—O3B1.420 (6)C2—C31.410 (6)
Cl1—O3A1.423 (5)C3—C41.330 (7)
Cl1—O4A1.436 (4)C3—H30.9300
Cl1—O4B1.436 (5)C4—C51.417 (7)
Cl1—O1A1.435 (5)C4—H40.9300
Cl2—O5B1.400 (6)C5—C61.343 (6)
Cl2—O5A1.401 (5)C5—H50.9300
Cl2—O7A1.444 (5)C6—H60.9300
Cl2—O7B1.452 (6)C7—C81.448 (5)
Cl2—O8B1.459 (7)C8—C91.374 (6)
Cl2—O6A1.461 (5)C9—C101.388 (6)
Cl2—O6B1.468 (6)C9—H90.9300
Cl2—O8A1.484 (6)C10—C111.365 (8)
N1—C71.344 (5)C10—H100.9300
N1—C11.350 (5)C11—C121.379 (8)
N1—C131.483 (5)C11—H110.9300
N2—C71.358 (5)C12—H120.9300
N2—C61.377 (5)C13—C141.515 (6)
N2—C21.411 (5)C13—H13A0.9700
N3—C121.331 (6)C13—H13B0.9700
N3—C81.349 (5)C14—C151.486 (6)
N4—C161.312 (6)C14—H14A0.9700
N4—C151.377 (5)C14—H14B0.9700
N4—H4N0.8600C15—C171.347 (6)
N5—C161.307 (6)C16—H160.9300
N5—C171.366 (6)C17—H170.9300
O2B—Cl1—O1B107.4 (7)C3—C4—H4119.9
O2B—Cl1—O3B108.1 (7)C5—C4—H4119.9
O1B—Cl1—O3B117.0 (9)C6—C5—C4121.9 (5)
O2A—Cl1—O3A110.7 (5)C6—C5—H5119.1
O2A—Cl1—O4A109.8 (6)C4—C5—H5119.1
O3A—Cl1—O4A116.0 (8)C5—C6—N2118.2 (4)
O2B—Cl1—O4B109.4 (9)C5—C6—H6120.9
O1B—Cl1—O4B115.2 (12)N2—C6—H6120.9
O3B—Cl1—O4B99.4 (12)N1—C7—N2105.9 (4)
O2A—Cl1—O1A106.3 (5)N1—C7—C8127.7 (4)
O3A—Cl1—O1A107.2 (5)N2—C7—C8126.4 (4)
O4A—Cl1—O1A106.3 (7)N3—C8—C9123.7 (4)
O5A—Cl2—O7A112.8 (5)N3—C8—C7114.1 (4)
O5B—Cl2—O7B112.5 (8)C9—C8—C7122.1 (4)
O5B—Cl2—O8B120.0 (10)C8—C9—C10118.8 (5)
O7B—Cl2—O8B105.4 (9)C8—C9—H9120.6
O5A—Cl2—O6A126.4 (6)C10—C9—H9120.6
O7A—Cl2—O6A110.4 (4)C11—C10—C9117.9 (5)
O5B—Cl2—O6B96.3 (10)C11—C10—H10121.0
O7B—Cl2—O6B97.9 (7)C9—C10—H10121.0
O8B—Cl2—O6B122.8 (8)C10—C11—C12119.7 (5)
O5A—Cl2—O8A101.5 (7)C10—C11—H11120.2
O7A—Cl2—O8A105.3 (5)C12—C11—H11120.2
O6A—Cl2—O8A96.1 (5)N3—C12—C11123.6 (5)
C7—N1—C1111.3 (4)N3—C12—H12118.2
C7—N1—C13126.3 (4)C11—C12—H12118.2
C1—N1—C13122.3 (4)N1—C13—C14110.9 (3)
C7—N2—C6129.5 (4)N1—C13—H13A109.5
C7—N2—C2108.9 (4)C14—C13—H13A109.5
C6—N2—C2121.5 (4)N1—C13—H13B109.5
C12—N3—C8116.1 (4)C14—C13—H13B109.5
C16—N4—C15110.1 (4)H13A—C13—H13B108.1
C16—N4—H4N125.0C15—C14—C13110.1 (4)
C15—N4—H4N125.0C15—C14—H14A109.6
C16—N5—C17109.3 (4)C13—C14—H14A109.6
C16—N5—H5N125.3C15—C14—H14B109.6
C17—N5—H5N125.3C13—C14—H14B109.6
N1—C1—C2107.9 (4)H14A—C14—H14B108.2
N1—C1—H1126.1C17—C15—N4105.1 (4)
C2—C1—H1126.1C17—C15—C14131.5 (4)
C1—C2—C3135.9 (5)N4—C15—C14123.3 (4)
C1—C2—N2106.0 (4)N5—C16—N4107.9 (4)
C3—C2—N2118.1 (4)N5—C16—H16126.0
C4—C3—C2120.1 (5)N4—C16—H16126.0
C4—C3—H3120.0C15—C17—N5107.5 (4)
C2—C3—H3120.0C15—C17—H17126.2
C3—C4—C5120.2 (5)N5—C17—H17126.2
C7—N1—C1—C20.8 (5)C12—N3—C8—C7−179.2 (4)
C13—N1—C1—C2−176.6 (4)N1—C7—C8—N3−41.5 (6)
N1—C1—C2—C3−179.7 (5)N2—C7—C8—N3139.5 (4)
N1—C1—C2—N2−1.2 (4)N1—C7—C8—C9138.6 (4)
C7—N2—C2—C11.3 (4)N2—C7—C8—C9−40.4 (6)
C6—N2—C2—C1−176.5 (4)N3—C8—C9—C10−3.5 (7)
C7—N2—C2—C3−179.9 (4)C7—C8—C9—C10176.4 (4)
C6—N2—C2—C32.4 (6)C8—C9—C10—C113.0 (7)
C1—C2—C3—C4178.3 (5)C9—C10—C11—C12−0.1 (7)
N2—C2—C3—C4−0.1 (6)C8—N3—C12—C112.4 (7)
C2—C3—C4—C5−2.5 (7)C10—C11—C12—N3−2.8 (8)
C3—C4—C5—C63.0 (8)C7—N1—C13—C14104.7 (5)
C4—C5—C6—N2−0.7 (7)C1—N1—C13—C14−78.3 (5)
C7—N2—C6—C5−179.2 (4)N1—C13—C14—C15167.9 (4)
C2—N2—C6—C5−2.0 (6)C16—N4—C15—C170.7 (5)
C1—N1—C7—N20.1 (5)C16—N4—C15—C14−177.3 (4)
C13—N1—C7—N2177.3 (3)C13—C14—C15—C17−96.1 (6)
C1—N1—C7—C8−179.1 (4)C13—C14—C15—N481.3 (5)
C13—N1—C7—C8−1.9 (7)C17—N5—C16—N40.0 (5)
C6—N2—C7—N1176.7 (4)C15—N4—C16—N5−0.4 (5)
C2—N2—C7—N1−0.8 (4)N4—C15—C17—N5−0.7 (5)
C6—N2—C7—C8−4.1 (7)C14—C15—C17—N5177.1 (4)
C2—N2—C7—C8178.4 (4)C16—N5—C17—C150.5 (5)
C12—N3—C8—C90.8 (6)
D—H···AD—HH···AD···AD—H···A
C13—H13A···N30.972.483.001 (6)113
C16—H16···O1A0.932.443.351 (8)167
N4—H4N···O7A0.861.972.807 (10)165
N5—H5N···O4Ai0.862.182.927 (16)145
C11—H11···O6Aii0.932.463.224 (9)139
C6—H6···O5Aiii0.932.603.331 (17)136
C5—H5···O6Aiv0.932.433.139 (8)133
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
C13—H13A⋯N30.972.483.001 (6)113
C16—H16⋯O1A0.932.443.351 (8)167
N4—H4N⋯O7A0.861.972.807 (10)165
N5—H5N⋯O4Ai0.862.182.927 (16)145
C11—H11⋯O6Aii0.932.463.224 (9)139
C6—H6⋯O5Aiii0.932.603.331 (17)136
C5—H5⋯O6Aiv0.932.433.139 (8)133

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

  4 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  Antiulcer agents. 6. Analysis of the in vitro biochemical and in vivo gastric antisecretory activity of substituted imidazo[1,2-a]pyridines and related analogues using comparative molecular field analysis and hypothetical active site lattice methodologies.

Authors:  J J Kaminski; A M Doweyko
Journal:  J Med Chem       Date:  1997-02-14       Impact factor: 7.446

3.  Synthesis of (aryloxy)alkylamines. 2. Novel imidazo-fused heterocycles with calcium channel blocking and local anesthetic activity.

Authors:  P J Sanfilippo; M Urbanski; J B Press; B Dubinsky; J B Moore
Journal:  J Med Chem       Date:  1988-11       Impact factor: 7.446

4.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  4 in total
  2 in total

1.  Crystal structures of an imidazo[1,5-a]pyridinium-based ligand and its (C13H12N3)2[CdI4] hybrid salt.

Authors:  Olga Yu Vassilyeva; Elena A Buvaylo; Vladimir N Kokozay; Brian W Skelton; Alexandre N Sobolev
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2019-07-19

2.  Crystal structure of imidazo[1,5-a]pyridinium-based hybrid salt (C13H12N3)2[MnCl4].

Authors:  Olga Yu Vassilyeva; Elena A Buvaylo; Vladimir N Kokozay; Svitlana R Petrusenko; Andrii K Melnyk; Brian W Skelton
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2020-02-06
  2 in total

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