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Acta Cryst. (2009). E65, o1013    [ doi:10.1107/S1600536809012574 ]

2,6-Bis(1H-benzimidazol-2-yl)pyridine methanol trisolvate

Y. Chen, J. Guo, X. Huang, R. Yun and H. Wu

Abstract top

In the title compound, C19H13N5·3CH4O, the 2,6-bis(2-benzimidazolyl)pyridine molecule is essentially planar with an r.m.s. deviation for all non-H atoms of 0.185 Å. The crystal structure is stabilized by intermolecular O-H...O, O-H...N and N-H...O hydrogen bonds and weak [pi]...[pi] stacking interactions with centroid-centroid distances of 3.6675 (16) and 3.6891 (15) Å. The atoms of one of the methanol solvent molecules are disordered over two sites with refined occupancies of 0.606(8) and 0.394(8).

Comment top

The synthesis of 2,6-bis(2-benzimidazolyl)pyridine has been reported in the literature (Addison & Burke 1981) and the crystal structures of the mono and sesqihydrates of this compound have been determined (Freire et al., 2003). During our studies of benzimidazole complexes involving a recrystallization of 2,6-bis(2-benzimidazolyl)pyridine from methanol we unexpectedly form the trimethanol solvate (I).

The molecular structure of the 2,6-bis(2-benzimidazolyl)pyridine molecule is shown in Fig. 1. The molecule is essentially planar with a rms deviation of all non-hydrogen fitted atoms = 0.185. The crystal structure is stabilized by intermolecular hydrogen bonds (see Table 1) and weak π···π stacking interactions (Fig. 2) with, centroid to centroid distances of 3.6675 (16) and 3.6891 (15)Å, between pryridine rings and benzimidazole rings of inversion related molecules.

Related literature top

For the crystal structures of the mono- and sesquihydrate analogs of 2,6-bis(2-benzimidazolyl)pyridine, see: Freire et al. (2003). For the synthesis of 2,6-bis(2-benzimidazolyl)pyridine, see: Addison & Burke (1981).

Experimental top

2,6-bis(2-benzimidazolyl)pyridine was prepared by the method of Addison & Burke (1981). After recrystallization from methanol, fine white needles were formed. The mother liquor was set aside for several days leading to the formation of crystals that were suitable for X-ray diffraction analysis.

Refinement top

All H atoms were found in difference electron maps and were subsequently refined in a riding-model approximation with C—H distances ranging from 0.95 to 0.98 Å and with Uiso(H) = 1.2 Ueq(C) for CH and Uiso(H) = 1.2 Ueq(O) for OH. H atoms bonded to N atoms were refined independently with isotropic displacement parameters. The atoms of one methanol solvent molecule is disordered over two sites with refined occupancies of 0.606 (8) and 0.394 (8).

Computing details top

Data collection: RAPID-AUTO (Rigaku/MSC 2004); cell refinement: RAPID-AUTO (Rigaku/MSC 2004); data reduction: RAPID-AUTO (Rigaku/MSC 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound. Displacement ellipsoids are drawn at the 30% probability level. H atoms and solvent molecules have been omitted for clarity.
[Figure 2] Fig. 2. Part of the crystal structure showing weak π···π stacking interactions. The solvent molecules are not shown
2,6-Bis(1H-benzimidazol-2-yl)pyridine methanol trisolvate top
Crystal data top
C19H13N5·3CH4OF(000) = 864
Mr = 407.47Dx = 1.276 Mg m−3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 3945 reflections
a = 11.2686 (9) Åθ = 3.2–25.5°
b = 15.0928 (13) ŵ = 0.09 mm−1
c = 13.0679 (11) ÅT = 153 K
β = 107.391 (2)°Block, colorless
V = 2120.9 (3) Å30.18 × 0.14 × 0.11 mm
Z = 4
Data collection top
Rigaku R-AXIS Spider
diffractometer		3945 independent reflections
Radiation source: fine-focus sealed tube2527 reflections with I > 2σ(I)
graphiteRint = 0.071
φ and ω scansθmax = 25.5°, θmin = 3.2°
Absorption correction: multi-scan
(Higashi, 1995)		h = −13→11
Tmin = 0.984, Tmax = 0.990k = −18→18
17035 measured reflectionsl = −15→15
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.077H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.236 w = 1/[σ2(Fo2) + (0.1505P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max = 0.002
3945 reflectionsΔρmax = 0.39 e Å−3
307 parametersΔρmin = −0.40 e Å−3
2 restraintsExtinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.040 (6)
Crystal data top
C19H13N5·3CH4OV = 2120.9 (3) Å3
Mr = 407.47Z = 4
Monoclinic, P21/nMo Kα radiation
a = 11.2686 (9) ŵ = 0.09 mm−1
b = 15.0928 (13) ÅT = 153 K
c = 13.0679 (11) Å0.18 × 0.14 × 0.11 mm
β = 107.391 (2)°
Data collection top
Rigaku R-AXIS Spider
diffractometer		2527 reflections with I > 2σ(I)
Absorption correction: multi-scan
(Higashi, 1995)		Rint = 0.071
Tmin = 0.984, Tmax = 0.990θmax = 25.5°
17035 measured reflectionsStandard reflections: 0
3945 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.077H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.236Δρmax = 0.39 e Å−3
S = 1.04Δρmin = −0.40 e Å−3
3945 reflectionsAbsolute structure: ?
307 parametersFlack parameter: ?
2 restraintsRogers parameter: ?
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*/UeqOcc. (<1)
O10.20534 (18)0.61337 (13)0.36351 (15)0.0631 (6)
H10.25090.65820.38160.076*
O20.65988 (19)0.23950 (14)0.57774 (17)0.0704 (6)
H20.60090.26260.52990.084*
N10.11042 (19)0.58598 (15)0.54657 (17)0.0477 (6)
N20.0754 (2)0.53929 (15)0.69788 (17)0.0517 (6)
N30.3694 (2)0.46017 (15)0.38227 (18)0.0510 (6)
N40.4825 (2)0.33787 (15)0.43304 (18)0.0536 (6)
N50.27120 (19)0.45211 (14)0.54781 (16)0.0492 (6)
C10.0280 (2)0.64631 (18)0.5671 (2)0.0498 (7)
C2−0.0274 (2)0.72243 (19)0.5148 (2)0.0558 (7)
H2A−0.01090.74320.45180.067*
C3−0.1076 (3)0.7667 (2)0.5589 (2)0.0609 (8)
H3−0.14760.81910.52540.073*
C4−0.1313 (3)0.7359 (2)0.6519 (2)0.0615 (8)
H4−0.18750.76800.67950.074*
C5−0.0761 (2)0.6613 (2)0.7043 (2)0.0558 (7)
H5−0.09300.64110.76740.067*
C60.0060 (2)0.61602 (18)0.6613 (2)0.0500 (7)
C70.1350 (2)0.52423 (17)0.6263 (2)0.0479 (6)
C80.2211 (2)0.45155 (17)0.62863 (19)0.0467 (7)
C90.2477 (2)0.38735 (18)0.7084 (2)0.0513 (7)
H90.20960.38880.76410.062*
C100.3312 (2)0.32126 (18)0.7045 (2)0.0536 (7)
H100.35200.27670.75820.064*
C110.3837 (2)0.32049 (18)0.6221 (2)0.0529 (7)
H110.44110.27550.61810.063*
C120.3512 (2)0.38721 (17)0.5444 (2)0.0471 (7)
C130.4022 (2)0.39322 (17)0.4542 (2)0.0480 (7)
C140.5051 (2)0.37188 (19)0.3421 (2)0.0539 (7)
C150.5848 (3)0.3422 (2)0.2854 (2)0.0656 (8)
H150.63340.29010.30660.079*
C160.5905 (3)0.3906 (2)0.1981 (3)0.0695 (9)
H160.64420.37170.15840.083*
C170.5188 (3)0.4674 (2)0.1662 (2)0.0713 (9)
H170.52440.49900.10490.086*
C180.4406 (3)0.4980 (2)0.2211 (2)0.0616 (8)
H180.39300.55040.19990.074*
C190.4344 (2)0.44882 (18)0.3089 (2)0.0531 (7)
C200.1118 (3)0.6305 (3)0.2645 (3)0.0789 (10)
H20A0.04530.66610.27800.095*
H20B0.07730.57420.23120.095*
H20C0.14840.66280.21630.095*
C210.7174 (4)0.1739 (3)0.5314 (4)0.0958 (12)
H21A0.76390.20250.48790.115*
H21B0.65360.13500.48580.115*
H21C0.77450.13890.58830.115*
O30.1278 (5)0.5658 (3)0.9743 (4)0.094 (2)0.606 (8)
H3A0.14120.54251.03500.112*0.606 (8)
C220.2186 (8)0.5366 (7)0.9269 (9)0.0521 (19)0.606 (8)
H22A0.27300.58620.92270.062*0.606 (8)
H22B0.17740.51420.85470.062*0.606 (8)
H22C0.26810.48920.97070.062*0.606 (8)
O3'0.0859 (9)0.4916 (6)0.8986 (6)0.118 (4)0.394 (8)
H3'0.03250.50920.92720.141*0.394 (8)
C22'0.1816 (12)0.5468 (13)0.9232 (18)0.078 (5)0.394 (8)
H22D0.15220.60720.90220.094*0.394 (8)
H22E0.24050.52930.88480.094*0.394 (8)
H22F0.22300.54491.00060.094*0.394 (8)
H1N0.144 (3)0.589 (2)0.4954 (17)0.075 (10)*
H3N0.316 (3)0.5018 (17)0.380 (3)0.095 (12)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0689 (13)0.0565 (13)0.0638 (13)0.0040 (9)0.0197 (10)0.0078 (9)
O20.0655 (13)0.0665 (14)0.0811 (15)0.0113 (10)0.0249 (11)0.0109 (11)
N10.0473 (12)0.0518 (13)0.0463 (12)0.0027 (10)0.0175 (10)0.0002 (10)
N20.0524 (12)0.0558 (14)0.0479 (12)−0.0030 (10)0.0164 (10)−0.0030 (10)
N30.0535 (13)0.0505 (14)0.0516 (13)−0.0013 (10)0.0196 (10)−0.0001 (10)
N40.0559 (13)0.0514 (14)0.0553 (13)−0.0005 (10)0.0194 (10)−0.0041 (10)
N50.0515 (12)0.0491 (13)0.0443 (12)−0.0018 (10)0.0104 (10)−0.0040 (9)
C10.0490 (14)0.0486 (15)0.0505 (14)−0.0026 (12)0.0130 (11)−0.0065 (12)
C20.0579 (15)0.0553 (17)0.0534 (15)0.0034 (13)0.0154 (13)0.0005 (13)
C30.0564 (16)0.0600 (18)0.0634 (17)0.0060 (13)0.0134 (14)−0.0076 (14)
C40.0529 (15)0.067 (2)0.0655 (18)0.0034 (14)0.0188 (14)−0.0138 (15)
C50.0523 (15)0.0639 (19)0.0538 (15)−0.0056 (13)0.0195 (12)−0.0095 (13)
C60.0464 (13)0.0524 (16)0.0508 (14)−0.0025 (12)0.0140 (11)−0.0058 (12)
C70.0495 (14)0.0462 (15)0.0470 (14)−0.0030 (11)0.0130 (11)−0.0019 (11)
C80.0474 (14)0.0469 (15)0.0446 (13)−0.0029 (11)0.0119 (11)−0.0032 (11)
C90.0551 (15)0.0542 (17)0.0440 (14)−0.0031 (12)0.0136 (12)0.0031 (11)
C100.0587 (16)0.0499 (16)0.0518 (15)0.0000 (12)0.0159 (13)0.0066 (12)
C110.0517 (15)0.0486 (16)0.0548 (15)0.0031 (12)0.0106 (12)0.0008 (12)
C120.0474 (14)0.0437 (15)0.0480 (14)−0.0022 (11)0.0108 (11)−0.0047 (11)
C130.0478 (14)0.0440 (15)0.0515 (14)−0.0022 (11)0.0140 (11)−0.0038 (11)
C140.0536 (15)0.0539 (17)0.0570 (16)−0.0096 (12)0.0211 (13)−0.0116 (13)
C150.0624 (17)0.068 (2)0.0706 (19)−0.0118 (15)0.0260 (15)−0.0182 (16)
C160.0716 (19)0.076 (2)0.070 (2)−0.0209 (17)0.0358 (16)−0.0247 (17)
C170.081 (2)0.082 (2)0.0552 (17)−0.0275 (18)0.0271 (16)−0.0105 (16)
C180.0663 (17)0.0607 (19)0.0588 (16)−0.0094 (14)0.0202 (14)−0.0025 (14)
C190.0548 (15)0.0552 (17)0.0486 (15)−0.0087 (12)0.0145 (12)−0.0072 (12)
C200.073 (2)0.091 (3)0.070 (2)−0.0099 (18)0.0166 (17)0.0182 (18)
C210.087 (2)0.073 (3)0.131 (3)0.0229 (19)0.037 (2)0.005 (2)
O30.106 (4)0.102 (4)0.070 (3)−0.012 (3)0.021 (3)0.001 (2)
C220.024 (4)0.086 (5)0.050 (3)0.011 (3)0.016 (4)0.010 (3)
O3'0.130 (8)0.127 (7)0.088 (5)−0.044 (6)0.020 (5)0.001 (5)
C22'0.021 (7)0.147 (13)0.070 (7)0.039 (7)0.019 (6)0.000 (6)
Geometric parameters (Å, °) top
O1—C201.427 (3)C10—H100.9500
O1—H10.8400C11—C121.399 (4)
O2—C211.415 (4)C11—H110.9500
O2—H20.8400C12—C131.460 (4)
N1—C71.363 (3)C14—C151.398 (4)
N1—C11.383 (3)C14—C191.402 (4)
N1—H1N0.866 (10)C15—C161.372 (5)
N2—C71.324 (3)C15—H150.9500
N2—C61.399 (3)C16—C171.404 (5)
N3—C131.354 (3)C16—H160.9500
N3—C191.381 (4)C17—C181.372 (4)
N3—H3N0.863 (10)C17—H170.9500
N4—C131.321 (3)C18—C191.385 (4)
N4—C141.386 (4)C18—H180.9500
N5—C81.338 (3)C20—H20A0.9800
N5—C121.341 (3)C20—H20B0.9800
C1—C21.386 (4)C20—H20C0.9800
C1—C61.402 (4)C21—H21A0.9800
C2—C31.381 (4)C21—H21B0.9800
C2—H2A0.9500C21—H21C0.9800
C3—C41.398 (4)O3—C221.414 (10)
C3—H30.9500O3—H3A0.8400
C4—C51.367 (4)C22—H22A0.9800
C4—H40.9500C22—H22B0.9800
C5—C61.397 (4)C22—H22C0.9800
C5—H50.9500O3'—C22'1.324 (19)
C7—C81.459 (4)O3'—H3'0.8400
C8—C91.389 (3)C22'—H22D0.9800
C9—C101.383 (4)C22'—H22E0.9800
C9—H90.9500C22'—H22F0.9800
C10—C111.374 (4)
C20—O1—H1109.5N5—C12—C11122.3 (3)
C21—O2—H2109.5N5—C12—C13114.4 (2)
C7—N1—C1107.3 (2)C11—C12—C13123.4 (2)
C7—N1—H1N126 (2)N4—C13—N3112.8 (2)
C1—N1—H1N126 (2)N4—C13—C12126.1 (2)
C7—N2—C6104.5 (2)N3—C13—C12121.0 (2)
C13—N3—C19107.4 (2)N4—C14—C15130.3 (3)
C13—N3—H3N128 (3)N4—C14—C19109.9 (2)
C19—N3—H3N125 (3)C15—C14—C19119.8 (3)
C13—N4—C14105.0 (2)C16—C15—C14117.8 (3)
C8—N5—C12117.9 (2)C16—C15—H15121.1
N1—C1—C2132.8 (3)C14—C15—H15121.1
N1—C1—C6105.1 (2)C15—C16—C17121.4 (3)
C2—C1—C6122.1 (3)C15—C16—H16119.3
C3—C2—C1116.7 (3)C17—C16—H16119.3
C3—C2—H2A121.6C18—C17—C16121.7 (3)
C1—C2—H2A121.6C18—C17—H17119.1
C2—C3—C4121.4 (3)C16—C17—H17119.1
C2—C3—H3119.3C17—C18—C19116.9 (3)
C4—C3—H3119.3C17—C18—H18121.6
C5—C4—C3122.2 (3)C19—C18—H18121.6
C5—C4—H4118.9N3—C19—C18132.6 (3)
C3—C4—H4118.9N3—C19—C14104.9 (2)
C4—C5—C6117.3 (3)C18—C19—C14122.4 (3)
C4—C5—H5121.4O1—C20—H20A109.5
C6—C5—H5121.4O1—C20—H20B109.5
C5—C6—N2129.6 (3)H20A—C20—H20B109.5
C5—C6—C1120.4 (3)O1—C20—H20C109.5
N2—C6—C1110.1 (2)H20A—C20—H20C109.5
N2—C7—N1113.1 (2)H20B—C20—H20C109.5
N2—C7—C8126.1 (2)O2—C21—H21A109.5
N1—C7—C8120.8 (2)O2—C21—H21B109.5
N5—C8—C9123.3 (2)H21A—C21—H21B109.5
N5—C8—C7114.4 (2)O2—C21—H21C109.5
C9—C8—C7122.2 (2)H21A—C21—H21C109.5
C10—C9—C8118.2 (3)H21B—C21—H21C109.5
C10—C9—H9120.9C22'—O3'—H3'109.5
C8—C9—H9120.9O3'—C22'—H22D109.5
C11—C10—C9119.5 (2)O3'—C22'—H22E109.5
C11—C10—H10120.3H22D—C22'—H22E109.5
C9—C10—H10120.3O3'—C22'—H22F109.5
C10—C11—C12118.8 (2)H22D—C22'—H22F109.5
C10—C11—H11120.6H22E—C22'—H22F109.5
C12—C11—H11120.6
C7—N1—C1—C2179.1 (3)C9—C10—C11—C120.2 (4)
C7—N1—C1—C6−0.4 (3)C8—N5—C12—C11−0.5 (3)
N1—C1—C2—C3179.4 (3)C8—N5—C12—C13−179.5 (2)
C6—C1—C2—C3−1.1 (4)C10—C11—C12—N50.4 (4)
C1—C2—C3—C40.1 (4)C10—C11—C12—C13179.4 (2)
C2—C3—C4—C50.4 (4)C14—N4—C13—N31.0 (3)
C3—C4—C5—C60.0 (4)C14—N4—C13—C12−178.6 (2)
C4—C5—C6—N2179.5 (2)C19—N3—C13—N4−0.9 (3)
C4—C5—C6—C1−1.0 (4)C19—N3—C13—C12178.7 (2)
C7—N2—C6—C5178.7 (3)N5—C12—C13—N4179.9 (2)
C7—N2—C6—C1−0.9 (3)C11—C12—C13—N40.8 (4)
N1—C1—C6—C5−178.8 (2)N5—C12—C13—N30.3 (3)
C2—C1—C6—C51.6 (4)C11—C12—C13—N3−178.7 (2)
N1—C1—C6—N20.8 (3)C13—N4—C14—C15178.1 (3)
C2—C1—C6—N2−178.8 (2)C13—N4—C14—C19−0.7 (3)
C6—N2—C7—N10.6 (3)N4—C14—C15—C16−178.7 (3)
C6—N2—C7—C8179.5 (2)C19—C14—C15—C160.1 (4)
C1—N1—C7—N2−0.1 (3)C14—C15—C16—C17−0.2 (4)
C1—N1—C7—C8−179.1 (2)C15—C16—C17—C180.6 (5)
C12—N5—C8—C9−0.1 (3)C16—C17—C18—C19−0.9 (4)
C12—N5—C8—C7−179.9 (2)C13—N3—C19—C18−177.7 (3)
N2—C7—C8—N5−178.7 (2)C13—N3—C19—C140.4 (3)
N1—C7—C8—N50.1 (3)C17—C18—C19—N3178.6 (3)
N2—C7—C8—C91.5 (4)C17—C18—C19—C140.8 (4)
N1—C7—C8—C9−179.7 (2)N4—C14—C19—N30.2 (3)
N5—C8—C9—C100.7 (4)C15—C14—C19—N3−178.7 (2)
C7—C8—C9—C10−179.6 (2)N4—C14—C19—C18178.6 (2)
C8—C9—C10—C11−0.7 (4)C15—C14—C19—C18−0.4 (4)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1—H1···O2i0.841.832.670 (3)176
O2—H2···N40.841.912.741 (3)168
N1—H1N···O10.87 (1)2.07 (1)2.927 (3)171 (3)
N3—H3N···O10.86 (1)2.07 (1)2.925 (3)171 (4)
Symmetry codes: (i) −x+1, −y+1, −z+1.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O1—H1···O2i0.841.832.670 (3)176
O2—H2···N40.841.912.741 (3)168
N1—H1N···O10.87 (1)2.07 (1)2.927 (3)171 (3)
N3—H3N···O10.86 (1)2.07 (1)2.925 (3)171 (4)
Symmetry codes: (i) −x+1, −y+1, −z+1.
Acknowledgements top

The authors acknowledge financial support and a grant from `Qing Lan' Talent Engineering Funds and Students' Science and Technology Innovation Funds (grant No. DXS2008–040,041) of Lanzhou Jiaotong University. A grant from the Middle-Young Age Science Foundation (grant No. 3YS061-A25–023) and Long Yuan `Qing Nian' of Gansu Province is also acknowledged.

references
References top

Addison, A. W. & Burke, P. J. (1981). J. Heterocycl. Chem. 18, 803–805.

Freire, E., Baggio, S., Munñoz, J. C. & Baggioc, R. (2003). Acta Cryst. C59, o259-o262.

Higashi, T. (1995). Rigaku Corporation, Tokyo, Japan.

Rigaku/MSC (2004). RAPID-AUTO. Rigaku/MSC, The Woodlans, Texas, USA.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Spek, A. L. (2009). Acta Cryst. D65, 148–155.