Literature DB >> 22719592

2,6-Bis(1H-benzimidazol-2-yl)pyridine butyric acid monosolvate dihydrate.

Songzhu Lin1, Ruokun Jia, Aimin He.   

Abstract

In the title compound, C(19)H(13)N(5)·C(4)H(8)O(2)·2H(2)O, the mol-ecular skeleton of the 2,6-bis-(benzimidazol-2-yl)pyridine (bbip) mol-ecule is essentially planar (r.m.s. deviation = 0.023 Å). An extensive three-dimensional network of inter-molecular N-H⋯O, O-H⋯O and O-H⋯N hydrogen bonds consolidates the crystal packing, which also exhibits π-π inter-actions between the five- and six-membered rings from neighbouring bbip mol-ecules.

Entities:  

Year:  2012        PMID: 22719592      PMCID: PMC3379394          DOI: 10.1107/S1600536812021915

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


Related literature

For background to supra­molecular inter­actions, see: Dale et al. (2004 ▶); Braga et al. (2005 ▶); Ring et al. (2006 ▶). For related structures, see: Freire et al. (2003 ▶); Xiao et al. (2010 ▶).

Experimental

Crystal data

C19H13N5·C4H8O2·2H2O M = 435.48 Triclinic, a = 9.3950 (19) Å b = 9.5611 (19) Å c = 13.805 (3) Å α = 103.27 (2)° β = 99.91 (3)° γ = 104.76 (3)° V = 1131.5 (4) Å3 Z = 2 Mo Kα radiation μ = 0.09 mm−1 T = 295 K 0.20 × 0.18 × 0.15 mm

Data collection

Enraf–Nonius CAD-4 diffractometer Absorption correction: ψ scan (North et al., 1968 ▶) T min = 0.982, T max = 0.987 8683 measured reflections 3981 independent reflections 3195 reflections with I > 2σ(I) R int = 0.019 3 standard reflections every 100 reflections intensity decay: none

Refinement

R[F 2 > 2σ(F 2)] = 0.045 wR(F 2) = 0.144 S = 1.10 3981 reflections 318 parameters 6 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.22 e Å−3 Δρmin = −0.25 e Å−3 Data collection: CAD-4 Software (Enraf–Nonius, 1989 ▶); cell refinement: CAD-4 Software; data reduction: NRCVAX (Gabe et al., 1989 ▶); 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: WinGX (Farrugia, 1999 ▶). Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812021915/cv5296sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812021915/cv5296Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536812021915/cv5296Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C19H13N5·C4H8O2·2H2OZ = 2
Mr = 435.48F(000) = 460
Triclinic, P1Dx = 1.278 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 9.3950 (19) ÅCell parameters from 25 reflections
b = 9.5611 (19) Åθ = 4–14°
c = 13.805 (3) ŵ = 0.09 mm1
α = 103.27 (2)°T = 295 K
β = 99.91 (3)°Block, colourless
γ = 104.76 (3)°0.20 × 0.18 × 0.15 mm
V = 1131.5 (4) Å3
Enraf–Nonius CAD-4 diffractometer3195 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.019
Graphite monochromatorθmax = 25.0°, θmin = 3.1°
ω scansh = −11→11
Absorption correction: ψ scan (North et al., 1968)k = −11→10
Tmin = 0.982, Tmax = 0.987l = −16→16
8683 measured reflections3 standard reflections every 100 reflections
3981 independent reflections intensity decay: none
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.045H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.144w = 1/[σ2(Fo2) + (0.0925P)2 + 0.059P] where P = (Fo2 + 2Fc2)/3
S = 1.10(Δ/σ)max < 0.001
3981 reflectionsΔρmax = 0.22 e Å3
318 parametersΔρmin = −0.25 e Å3
6 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.007 (3)
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*/Ueq
N10.12979 (14)0.51453 (15)−0.18153 (10)0.0466 (3)
N2−0.05854 (14)0.30191 (14)−0.26517 (10)0.0482 (3)
N3−0.04327 (13)0.62903 (14)−0.06414 (9)0.0407 (3)
N4−0.10826 (15)0.91520 (15)0.12949 (10)0.0473 (3)
N50.10055 (14)0.91107 (14)0.07405 (10)0.0423 (3)
C10.06996 (18)0.29713 (18)−0.30066 (12)0.0491 (4)
C20.0931 (2)0.1845 (2)−0.37465 (15)0.0685 (5)
H2B0.01510.0957−0.41000.082*
C30.2354 (2)0.2091 (2)−0.39367 (18)0.0796 (6)
H3B0.25280.1363−0.44370.095*
C40.3535 (2)0.3401 (3)−0.33982 (19)0.0801 (7)
H4B0.44850.3517−0.35380.096*
C50.3335 (2)0.4530 (2)−0.26625 (15)0.0652 (5)
H5B0.41260.5406−0.23030.078*
C60.18948 (18)0.42972 (18)−0.24846 (12)0.0479 (4)
C7−0.01687 (16)0.43359 (16)−0.19367 (11)0.0424 (4)
C8−0.11129 (17)0.49146 (16)−0.13058 (11)0.0422 (4)
C9−0.25971 (18)0.40738 (18)−0.13928 (13)0.0526 (4)
H9A−0.30280.3116−0.18570.063*
C10−0.34091 (19)0.46967 (19)−0.07748 (14)0.0575 (5)
H10A−0.44050.4162−0.08160.069*
C11−0.27421 (18)0.61135 (18)−0.00955 (13)0.0511 (4)
H11A−0.32770.65550.03260.061*
C12−0.12534 (16)0.68670 (16)−0.00542 (11)0.0408 (4)
C13−0.04638 (16)0.83768 (16)0.06640 (11)0.0409 (3)
C140.00703 (18)1.04751 (17)0.18249 (11)0.0464 (4)
C150.0069 (2)1.1702 (2)0.25982 (14)0.0621 (5)
H15A−0.07941.17160.28390.075*
C160.1385 (2)1.2887 (2)0.29928 (15)0.0689 (5)
H16A0.14121.37160.35110.083*
C170.2687 (2)1.2877 (2)0.26338 (14)0.0633 (5)
H17A0.35561.37050.29180.076*
C180.27226 (19)1.16824 (18)0.18751 (13)0.0536 (4)
H18A0.35891.16820.16360.064*
C190.13926 (17)1.04728 (17)0.14830 (11)0.0438 (4)
O1−0.44196 (15)0.06635 (14)−0.27630 (11)0.0743 (4)
O2−0.28356 (15)0.04486 (15)−0.37563 (10)0.0657 (4)
C20−0.7674 (3)−0.3547 (3)−0.4697 (2)0.1110 (10)
H20A−0.8595−0.3850−0.44810.167*
H20B−0.7183−0.4317−0.47250.167*
H20C−0.7909−0.3404−0.53660.167*
C21−0.6624 (2)−0.2079 (2)−0.39388 (18)0.0824 (7)
H21A−0.7139−0.1315−0.39020.099*
H21B−0.6411−0.2228−0.32630.099*
C22−0.5148 (2)−0.1512 (2)−0.42169 (14)0.0611 (5)
H22A−0.4618−0.2261−0.42270.073*
H22B−0.5366−0.1408−0.49050.073*
C23−0.41213 (18)−0.00337 (18)−0.35032 (13)0.0500 (4)
O1W−0.40511 (15)0.92334 (16)0.11934 (11)0.0647 (4)
O2W0.32779 (16)0.81969 (16)−0.04472 (12)0.0690 (4)
H20.1745 (19)0.6070 (13)−0.1365 (11)0.057 (5)*
H10.156 (2)0.873 (2)0.0390 (14)0.056 (5)*
H2W1−0.3168 (14)0.920 (3)0.1236 (19)0.100 (8)*
H2W20.350 (3)0.885 (2)−0.0747 (19)0.116 (10)*
H1W20.407 (2)0.839 (3)−0.0027 (17)0.129 (12)*
H1W1−0.435 (3)0.928 (3)0.1717 (13)0.106 (9)*
H3−0.228 (2)0.1309 (16)−0.3376 (16)0.096 (8)*
U11U22U33U12U13U23
N10.0350 (7)0.0439 (7)0.0510 (7)0.0049 (5)0.0084 (6)0.0045 (6)
N20.0399 (7)0.0449 (7)0.0514 (7)0.0072 (6)0.0116 (6)0.0037 (6)
N30.0329 (6)0.0430 (7)0.0420 (6)0.0082 (5)0.0075 (5)0.0094 (5)
N40.0398 (7)0.0497 (7)0.0466 (7)0.0087 (6)0.0125 (6)0.0070 (6)
N50.0336 (7)0.0437 (7)0.0456 (7)0.0076 (5)0.0109 (5)0.0089 (6)
C10.0409 (9)0.0491 (9)0.0513 (9)0.0088 (7)0.0121 (7)0.0078 (7)
C20.0587 (11)0.0579 (11)0.0726 (12)0.0080 (9)0.0231 (9)−0.0063 (9)
C30.0684 (13)0.0722 (13)0.0897 (14)0.0193 (10)0.0379 (11)−0.0039 (11)
C40.0530 (12)0.0789 (13)0.1034 (16)0.0164 (10)0.0377 (11)0.0069 (12)
C50.0414 (9)0.0656 (11)0.0781 (12)0.0069 (8)0.0204 (9)0.0071 (10)
C60.0401 (8)0.0490 (8)0.0510 (9)0.0116 (7)0.0120 (7)0.0094 (7)
C70.0351 (8)0.0431 (8)0.0445 (8)0.0082 (6)0.0065 (6)0.0106 (6)
C80.0364 (8)0.0405 (7)0.0456 (8)0.0082 (6)0.0073 (6)0.0104 (6)
C90.0399 (9)0.0417 (8)0.0638 (10)0.0011 (7)0.0123 (8)0.0048 (7)
C100.0368 (8)0.0498 (9)0.0759 (12)−0.0013 (7)0.0209 (8)0.0102 (8)
C110.0403 (9)0.0485 (9)0.0615 (10)0.0072 (7)0.0215 (7)0.0104 (7)
C120.0337 (8)0.0426 (8)0.0441 (8)0.0075 (6)0.0092 (6)0.0138 (6)
C130.0340 (8)0.0431 (8)0.0415 (8)0.0064 (6)0.0079 (6)0.0114 (6)
C140.0438 (9)0.0447 (8)0.0432 (8)0.0073 (7)0.0080 (7)0.0076 (7)
C150.0603 (11)0.0585 (10)0.0579 (10)0.0134 (9)0.0179 (8)0.0011 (8)
C160.0769 (14)0.0522 (10)0.0569 (10)0.0108 (9)0.0056 (9)−0.0058 (8)
C170.0569 (11)0.0499 (9)0.0618 (11)−0.0010 (8)−0.0030 (9)0.0077 (8)
C180.0413 (9)0.0513 (9)0.0569 (10)0.0023 (7)0.0027 (7)0.0138 (8)
C190.0387 (8)0.0453 (8)0.0416 (8)0.0073 (6)0.0041 (6)0.0118 (7)
O10.0559 (8)0.0539 (7)0.0927 (10)0.0011 (6)0.0302 (7)−0.0089 (7)
O20.0543 (8)0.0667 (8)0.0587 (7)0.0007 (6)0.0171 (6)0.0021 (6)
C200.103 (2)0.0735 (15)0.1010 (18)−0.0274 (14)−0.0127 (15)0.0078 (13)
C210.0645 (13)0.0620 (12)0.0910 (15)−0.0090 (10)0.0110 (11)0.0033 (11)
C220.0641 (12)0.0533 (9)0.0529 (9)0.0096 (9)0.0011 (8)0.0096 (8)
C230.0453 (9)0.0477 (9)0.0533 (9)0.0119 (7)0.0087 (7)0.0123 (7)
O1W0.0420 (7)0.0799 (9)0.0668 (8)0.0146 (6)0.0135 (6)0.0150 (7)
O2W0.0487 (8)0.0607 (8)0.0793 (9)−0.0024 (6)0.0019 (7)0.0172 (7)
N1—C71.358 (2)C11—H11A0.9300
N1—C61.375 (2)C12—C131.470 (2)
N1—H20.90 (2)C14—C151.393 (2)
N2—C71.3259 (19)C14—C191.403 (2)
N2—C11.386 (2)C15—C161.371 (3)
N3—C121.3350 (19)C15—H15A0.9300
N3—C81.3401 (19)C16—C171.398 (3)
N4—C131.3203 (19)C16—H16A0.9300
N4—C141.383 (2)C17—C181.373 (3)
N5—C131.3533 (19)C17—H17A0.9300
N5—C191.377 (2)C18—C191.391 (2)
N5—H10.86 (2)C18—H18A0.9300
C1—C21.393 (2)O1—C231.203 (2)
C1—C61.401 (2)O2—C231.315 (2)
C2—C31.379 (3)O2—H30.85 (2)
C2—H2B0.9300C20—C211.518 (3)
C3—C41.391 (3)C20—H20A0.9600
C3—H3B0.9300C20—H20B0.9600
C4—C51.378 (3)C20—H20C0.9600
C4—H4B0.9300C21—C221.504 (3)
C5—C61.388 (2)C21—H21A0.9700
C5—H5B0.9300C21—H21B0.9700
C7—C81.465 (2)C22—C231.496 (2)
C8—C91.390 (2)C22—H22A0.9700
C9—C101.374 (2)C22—H22B0.9700
C9—H9A0.9300O1W—H2W10.83 (2)
C10—C111.374 (2)O1W—H1W10.82 (2)
C10—H10A0.9300O2W—H2W20.82 (2)
C11—C121.385 (2)O2W—H1W20.81 (2)
C7—N1—C6107.54 (13)N4—C13—N5113.13 (13)
C7—N1—H2123.1 (12)N4—C13—C12124.76 (13)
C6—N1—H2129.3 (12)N5—C13—C12122.12 (13)
C7—N2—C1104.86 (13)N4—C14—C15129.84 (16)
C12—N3—C8117.15 (13)N4—C14—C19110.09 (13)
C13—N4—C14104.64 (13)C15—C14—C19120.07 (16)
C13—N5—C19107.30 (13)C16—C15—C14117.73 (18)
C13—N5—H1123.4 (13)C16—C15—H15A121.1
C19—N5—H1129.3 (13)C14—C15—H15A121.1
N2—C1—C2130.11 (16)C15—C16—C17121.52 (17)
N2—C1—C6109.96 (14)C15—C16—H16A119.2
C2—C1—C6119.92 (16)C17—C16—H16A119.2
C3—C2—C1117.73 (18)C18—C17—C16122.03 (17)
C3—C2—H2B121.1C18—C17—H17A119.0
C1—C2—H2B121.1C16—C17—H17A119.0
C2—C3—C4121.61 (18)C17—C18—C19116.43 (17)
C2—C3—H3B119.2C17—C18—H18A121.8
C4—C3—H3B119.2C19—C18—H18A121.8
C5—C4—C3121.71 (18)N5—C19—C18132.95 (15)
C5—C4—H4B119.1N5—C19—C14104.84 (14)
C3—C4—H4B119.1C18—C19—C14122.20 (15)
C4—C5—C6116.72 (18)C23—O2—H3113.9 (17)
C4—C5—H5B121.6C21—C20—H20A109.5
C6—C5—H5B121.6C21—C20—H20B109.5
N1—C6—C5132.63 (16)H20A—C20—H20B109.5
N1—C6—C1105.07 (14)C21—C20—H20C109.5
C5—C6—C1122.27 (16)H20A—C20—H20C109.5
N2—C7—N1112.57 (13)H20B—C20—H20C109.5
N2—C7—C8126.42 (14)C22—C21—C20113.3 (2)
N1—C7—C8121.00 (13)C22—C21—H21A108.9
N3—C8—C9123.26 (14)C20—C21—H21A108.9
N3—C8—C7115.06 (13)C22—C21—H21B108.9
C9—C8—C7121.67 (14)C20—C21—H21B108.9
C10—C9—C8118.15 (15)H21A—C21—H21B107.7
C10—C9—H9A120.9C23—C22—C21114.24 (16)
C8—C9—H9A120.9C23—C22—H22A108.7
C9—C10—C11119.67 (15)C21—C22—H22A108.7
C9—C10—H10A120.2C23—C22—H22B108.7
C11—C10—H10A120.2C21—C22—H22B108.7
C10—C11—C12118.33 (15)H22A—C22—H22B107.6
C10—C11—H11A120.8O1—C23—O2122.25 (16)
C12—C11—H11A120.8O1—C23—C22124.19 (16)
N3—C12—C11123.43 (14)O2—C23—C22113.56 (15)
N3—C12—C13115.37 (13)H2W1—O1W—H1W1117 (3)
C11—C12—C13121.19 (14)H2W2—O2W—H1W2102 (3)
C7—N2—C1—C2178.8 (2)C8—N3—C12—C13179.95 (13)
C7—N2—C1—C6−0.07 (19)C10—C11—C12—N30.1 (3)
N2—C1—C2—C3−178.9 (2)C10—C11—C12—C13−179.18 (15)
C6—C1—C2—C3−0.1 (3)C14—N4—C13—N5−0.62 (17)
C1—C2—C3—C41.3 (4)C14—N4—C13—C12179.13 (14)
C2—C3—C4—C5−1.3 (4)C19—N5—C13—N40.37 (18)
C3—C4—C5—C60.0 (4)C19—N5—C13—C12−179.38 (13)
C7—N1—C6—C5−177.18 (19)N3—C12—C13—N4178.66 (14)
C7—N1—C6—C10.76 (18)C11—C12—C13—N4−2.0 (2)
C4—C5—C6—N1178.9 (2)N3—C12—C13—N5−1.6 (2)
C4—C5—C6—C11.2 (3)C11—C12—C13—N5177.75 (14)
N2—C1—C6—N1−0.43 (19)C13—N4—C14—C15−178.98 (18)
C2—C1—C6—N1−179.43 (17)C13—N4—C14—C190.63 (17)
N2—C1—C6—C5177.78 (16)N4—C14—C15—C16−179.71 (17)
C2—C1—C6—C5−1.2 (3)C19—C14—C15—C160.7 (3)
C1—N2—C7—N10.58 (18)C14—C15—C16—C170.2 (3)
C1—N2—C7—C8−178.33 (15)C15—C16—C17—C18−0.4 (3)
C6—N1—C7—N2−0.87 (19)C16—C17—C18—C19−0.3 (3)
C6—N1—C7—C8178.11 (14)C13—N5—C19—C18−179.13 (17)
C12—N3—C8—C9−1.1 (2)C13—N5—C19—C140.05 (17)
C12—N3—C8—C7179.62 (13)C17—C18—C19—N5−179.70 (17)
N2—C7—C8—N3−179.30 (14)C17—C18—C19—C141.2 (2)
N1—C7—C8—N31.9 (2)N4—C14—C19—N5−0.42 (17)
N2—C7—C8—C91.4 (3)C15—C14—C19—N5179.24 (15)
N1—C7—C8—C9−177.42 (15)N4—C14—C19—C18178.87 (14)
N3—C8—C9—C100.9 (3)C15—C14—C19—C18−1.5 (3)
C7—C8—C9—C10−179.91 (15)C20—C21—C22—C23177.6 (2)
C8—C9—C10—C11−0.1 (3)C21—C22—C23—O10.2 (3)
C9—C10—C11—C12−0.4 (3)C21—C22—C23—O2−179.94 (17)
C8—N3—C12—C110.6 (2)
D—H···AD—HH···AD···AD—H···A
N1—H2···O2W0.90 (2)2.12 (1)3.006 (2)166 (2)
N5—H1···O2W0.86 (2)2.234 (19)3.083 (2)169.1 (17)
O1W—H2W1···N40.83 (2)1.96 (1)2.7901 (19)178 (3)
O2W—H2W2···O1Wi0.82 (2)2.04 (1)2.852 (2)168 (3)
O2W—H1W2···O1Wii0.81 (2)2.06 (1)2.856 (2)168 (3)
O1W—H1W1···O1iii0.82 (2)2.00 (1)2.795 (2)166 (3)
O2—H3···N20.85 (2)1.89 (1)2.712 (2)164 (2)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N1—H2⋯O2W0.90 (2)2.12 (1)3.006 (2)166 (2)
N5—H1⋯O2W0.86 (2)2.234 (19)3.083 (2)169.1 (17)
O1W—H2W1⋯N40.83 (2)1.96 (1)2.7901 (19)178 (3)
O2W—H2W2⋯O1Wi0.82 (2)2.04 (1)2.852 (2)168 (3)
O2W—H1W2⋯O1Wii0.81 (2)2.06 (1)2.856 (2)168 (3)
O1W—H1W1⋯O1iii0.82 (2)2.00 (1)2.795 (2)166 (3)
O2—H3⋯N20.85 (2)1.89 (1)2.712 (2)164 (2)

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

  3 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.  Supramolecular interactions in the 2,6-bis(benzimidazol-2-yl)pyridine-terephthalic acid-water (2/1/4) cocrystal.

Authors:  Hailian Xiao; Guixue Wang; Fangfang Jian
Journal:  Acta Crystallogr C       Date:  2010-08-04       Impact factor: 1.172

3.  Two hydrates of 2,6-bis(1H-benzimidazol-2-yl)pyridine.

Authors:  Eleonora Freire; Sergio Baggio; Juan Carlos Muñoz; Ricardo Baggio
Journal:  Acta Crystallogr C       Date:  2003-04-18       Impact factor: 1.172

  3 in total
  1 in total

1.  Adipic acid-2,6-bis-(1H-benzimidazol-2-yl)pyridine-water (1/2/4).

Authors:  Songzhu Lin; Ruokun Jia; Feng Gao; Xiaoqing Zhou
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-11-28
  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.