Literature DB >> 21579212

1-{2-[2-(1H-Benzimidazol-1-yl)eth-oxy]eth-yl}-1H-benzimidazol-3-ium hexa-fluoro-phosphate.

Sheng-Fu Sun1, Jin Xu, Da-Bin Qin.   

Abstract

In the title salt, C(18)H(19)N(4)O(+)·PF(6) (-), the dihedral angle between the benzimidazolium and benzimidazole ring systems is 16.24 (2)°. In the cation, a π-π inter-action is observed between the imidazolium ring and the benzene ring of the benzimidazole ring system [centroid-centroid distance = 3.5713 (11) Å]. The PF(6) (-) ion is disordered over two sites, with occupancies of 0.895 (2) and 0.105 (2). In the crystal structure, pairs of N-H⋯N hydrogen bonds link the cations, forming centrosymmetric dimers. The dimers are linked via π-π inter-actions [centroid-centroid distance = 3.5606 (11) Å]. In addition, C-H⋯F hydrogen bonds are observed.

Entities:  

Year:  2010        PMID: 21579212      PMCID: PMC2979123          DOI: 10.1107/S1600536810014534

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


Related literature

For the synthesis, see: Zeng et al. (2008 ▶). For general background to benzimidazole derivatives, see: Pal et al. (2007 ▶); Murru et al. (2009 ▶).

Experimental

Crystal data

C18H19N4OPF6 M = 452.34 Monoclinic, a = 10.5347 (18) Å b = 13.771 (2) Å c = 13.353 (2) Å β = 92.507 (2)° V = 1935.3 (6) Å3 Z = 4 Mo Kα radiation μ = 0.22 mm−1 T = 93 K 0.37 × 0.33 × 0.27 mm

Data collection

Rigaku SPIDER diffractometer Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ▶) T min = 0.923, T max = 0.943 11885 measured reflections 3959 independent reflections 3445 reflections with I > 2σ(I) R int = 0.026 Standard reflections: 0

Refinement

R[F 2 > 2σ(F 2)] = 0.040 wR(F 2) = 0.080 S = 1.00 3959 reflections 303 parameters 21 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.34 e Å−3 Δρmin = −0.28 e Å−3 Data collection: RAPID-AUTO (Rigaku/MSC, 2004 ▶); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: XP in SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXL97. Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810014534/ci5075sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536810014534/ci5075Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C18H19N4O+·PF6F(000) = 928
Mr = 452.34Dx = 1.553 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 5714 reflections
a = 10.5347 (18) Åθ = 3.1–27.5°
b = 13.771 (2) ŵ = 0.22 mm1
c = 13.353 (2) ÅT = 93 K
β = 92.507 (2)°Block, colourless
V = 1935.3 (6) Å30.37 × 0.33 × 0.27 mm
Z = 4
Rigaku SPIDER diffractometer3959 independent reflections
Radiation source: Rotating Anode3445 reflections with I > 2σ(I)
graphiteRint = 0.026
ω scansθmax = 26.4°, θmin = 3.1°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)h = −13→10
Tmin = 0.923, Tmax = 0.943k = −13→17
11885 measured reflectionsl = −15→16
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.040Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.080H atoms treated by a mixture of independent and constrained refinement
S = 1.00w = 1/[σ2(Fo2) + (0.0259P)2 + 0.968P] where P = (Fo2 + 2Fc2)/3
3959 reflections(Δ/σ)max = 0.001
303 parametersΔρmax = 0.34 e Å3
21 restraintsΔρmin = −0.28 e Å3
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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)
O10.20360 (11)0.51931 (8)0.18156 (8)0.0247 (3)
N10.53426 (13)0.40531 (10)0.31178 (10)0.0243 (3)
N20.41920 (13)0.39824 (9)0.17089 (10)0.0218 (3)
N30.26475 (13)0.62988 (10)0.35541 (10)0.0253 (3)
N40.39492 (14)0.60700 (10)0.48994 (10)0.0294 (3)
C10.61864 (16)0.39760 (11)0.23507 (12)0.0229 (3)
C20.75022 (16)0.39314 (12)0.23627 (13)0.0285 (4)
H20.80050.39640.29700.034*
C30.80419 (17)0.38372 (13)0.14435 (14)0.0319 (4)
H30.89410.38010.14200.038*
C40.73059 (17)0.37927 (13)0.05438 (13)0.0311 (4)
H40.77180.3730−0.00720.037*
C50.60018 (16)0.38377 (12)0.05330 (12)0.0262 (4)
H50.54990.3808−0.00750.031*
C60.54567 (15)0.39293 (11)0.14572 (12)0.0218 (3)
C70.41753 (16)0.40521 (11)0.27069 (12)0.0245 (4)
H70.34240.40950.30730.029*
C80.31129 (15)0.39532 (12)0.09736 (12)0.0242 (4)
H8A0.30300.32880.06980.029*
H8B0.32860.43970.04120.029*
C90.18818 (16)0.42403 (12)0.14171 (13)0.0262 (4)
H9A0.11850.42310.08950.031*
H9B0.16680.37800.19540.031*
C100.10406 (16)0.54786 (12)0.24439 (12)0.0272 (4)
H10A0.08900.49680.29470.033*
H10B0.02430.55840.20390.033*
C110.14574 (16)0.64079 (13)0.29557 (12)0.0277 (4)
H11A0.15680.69160.24420.033*
H11B0.07830.66270.33970.033*
C120.38716 (16)0.64002 (11)0.32253 (12)0.0231 (3)
C130.43309 (16)0.65920 (12)0.22830 (12)0.0262 (4)
H130.37750.66870.17120.031*
C140.56322 (17)0.66369 (12)0.22204 (13)0.0295 (4)
H140.59820.67640.15900.035*
C150.64530 (18)0.64993 (12)0.30653 (14)0.0314 (4)
H150.73450.65390.29940.038*
C160.59940 (17)0.63079 (12)0.39979 (13)0.0294 (4)
H160.65530.62140.45670.035*
C170.46803 (17)0.62576 (11)0.40726 (12)0.0249 (4)
C180.27606 (18)0.61067 (13)0.45479 (12)0.0299 (4)
H180.20530.60080.49530.036*
P1−0.07196 (5)0.71567 (4)0.57610 (4)0.02117 (17)0.8952 (16)
F1−0.10379 (15)0.71525 (12)0.45828 (8)0.0350 (3)0.8952 (16)
F2−0.03912 (12)0.71374 (11)0.69440 (8)0.0393 (4)0.8952 (16)
F30.05729 (13)0.77151 (12)0.55925 (10)0.0540 (4)0.8952 (16)
F4−0.19885 (12)0.65494 (12)0.59425 (9)0.0479 (4)0.8952 (16)
F5−0.14535 (18)0.81437 (11)0.58739 (10)0.0589 (5)0.8952 (16)
F60.00255 (14)0.61439 (10)0.56578 (10)0.0509 (4)0.8952 (16)
P1'−0.0834 (6)0.7250 (5)0.5725 (5)0.141 (8)0.1048 (16)
F1'−0.0918 (11)0.7157 (9)0.4533 (4)0.0350 (3)0.1048 (16)
F2'−0.0730 (10)0.7334 (8)0.6921 (5)0.0393 (4)0.1048 (16)
F3'−0.0180 (10)0.8283 (6)0.5636 (8)0.0540 (4)0.1048 (16)
F4'−0.1434 (9)0.6186 (6)0.5824 (8)0.0479 (4)0.1048 (16)
F5'−0.2196 (8)0.7721 (8)0.5714 (8)0.0589 (5)0.1048 (16)
F6'0.0549 (7)0.6755 (8)0.5745 (8)0.0509 (4)0.1048 (16)
H1N0.560 (2)0.4037 (15)0.3887 (16)0.052 (6)*
U11U22U33U12U13U23
O10.0252 (6)0.0252 (6)0.0238 (6)−0.0009 (5)0.0013 (5)−0.0021 (5)
N10.0294 (8)0.0246 (7)0.0183 (7)0.0024 (6)−0.0043 (6)−0.0007 (6)
N20.0255 (7)0.0219 (7)0.0177 (6)0.0001 (6)−0.0024 (5)−0.0005 (5)
N30.0272 (8)0.0310 (8)0.0175 (7)0.0061 (6)−0.0033 (6)−0.0007 (6)
N40.0360 (9)0.0325 (8)0.0192 (7)0.0027 (6)−0.0050 (6)0.0010 (6)
C10.0294 (9)0.0190 (8)0.0200 (8)0.0016 (6)−0.0023 (7)−0.0006 (6)
C20.0285 (9)0.0297 (9)0.0266 (9)0.0011 (7)−0.0083 (7)0.0012 (7)
C30.0248 (9)0.0350 (10)0.0357 (10)0.0030 (7)0.0004 (8)0.0041 (8)
C40.0323 (10)0.0361 (10)0.0252 (9)0.0054 (8)0.0048 (8)0.0035 (8)
C50.0319 (10)0.0281 (9)0.0184 (8)0.0021 (7)−0.0026 (7)0.0003 (7)
C60.0246 (9)0.0180 (8)0.0225 (8)0.0011 (6)−0.0026 (7)−0.0001 (6)
C70.0301 (9)0.0235 (8)0.0198 (8)0.0017 (7)0.0007 (7)−0.0002 (7)
C80.0261 (9)0.0254 (9)0.0204 (8)−0.0013 (7)−0.0059 (7)−0.0011 (7)
C90.0259 (9)0.0268 (9)0.0255 (9)−0.0024 (7)−0.0030 (7)−0.0015 (7)
C100.0230 (9)0.0346 (10)0.0240 (9)0.0024 (7)0.0012 (7)0.0020 (7)
C110.0249 (9)0.0357 (10)0.0222 (8)0.0076 (7)−0.0027 (7)−0.0003 (7)
C120.0281 (9)0.0199 (8)0.0207 (8)0.0022 (7)−0.0044 (7)−0.0031 (6)
C130.0329 (10)0.0262 (9)0.0189 (8)−0.0019 (7)−0.0055 (7)−0.0033 (7)
C140.0347 (10)0.0285 (9)0.0254 (9)−0.0061 (7)0.0015 (8)−0.0051 (7)
C150.0288 (10)0.0287 (9)0.0362 (10)−0.0045 (7)−0.0039 (8)−0.0048 (8)
C160.0332 (10)0.0246 (9)0.0294 (9)−0.0008 (7)−0.0120 (8)−0.0027 (7)
C170.0325 (9)0.0202 (8)0.0212 (8)0.0013 (7)−0.0056 (7)−0.0019 (6)
C180.0360 (10)0.0346 (10)0.0189 (8)0.0048 (8)−0.0004 (7)0.0013 (7)
P10.0156 (3)0.0302 (3)0.0175 (4)−0.0041 (2)−0.0011 (2)0.0053 (3)
F10.0370 (7)0.0499 (7)0.0182 (5)0.0021 (5)0.0012 (4)0.0020 (5)
F20.0360 (9)0.0587 (9)0.0220 (5)−0.0174 (6)−0.0105 (5)0.0105 (5)
F30.0427 (9)0.0789 (11)0.0405 (8)−0.0350 (8)0.0021 (6)0.0096 (7)
F40.0266 (8)0.0901 (11)0.0269 (6)−0.0273 (7)−0.0006 (6)0.0019 (7)
F50.0895 (13)0.0551 (10)0.0322 (8)0.0370 (9)0.0014 (8)−0.0026 (7)
F60.0558 (9)0.0451 (9)0.0519 (8)0.0174 (7)0.0044 (7)0.0118 (7)
P1'0.167 (16)0.22 (2)0.030 (7)−0.026 (15)−0.032 (8)0.006 (9)
F1'0.0370 (7)0.0499 (7)0.0182 (5)0.0021 (5)0.0012 (4)0.0020 (5)
F2'0.0360 (9)0.0587 (9)0.0220 (5)−0.0174 (6)−0.0105 (5)0.0105 (5)
F3'0.0427 (9)0.0789 (11)0.0405 (8)−0.0350 (8)0.0021 (6)0.0096 (7)
F4'0.0266 (8)0.0901 (11)0.0269 (6)−0.0273 (7)−0.0006 (6)0.0019 (7)
F5'0.0895 (13)0.0551 (10)0.0322 (8)0.0370 (9)0.0014 (8)−0.0026 (7)
F6'0.0558 (9)0.0451 (9)0.0519 (8)0.0174 (7)0.0044 (7)0.0118 (7)
O1—C91.4224 (19)C10—C111.507 (2)
O1—C101.4266 (19)C10—H10A0.99
N1—C71.325 (2)C10—H10B0.99
N1—C11.389 (2)C11—H11A0.99
N1—H1N1.05 (2)C11—H11B0.99
N2—C71.337 (2)C12—C131.393 (2)
N2—C61.390 (2)C12—C171.400 (2)
N2—C81.470 (2)C13—C141.378 (2)
N3—C181.353 (2)C13—H130.95
N3—C121.387 (2)C14—C151.404 (2)
N3—C111.465 (2)C14—H140.95
N4—C181.319 (2)C15—C161.381 (3)
N4—C171.398 (2)C15—H150.95
C1—C21.387 (2)C16—C171.394 (2)
C1—C61.392 (2)C16—H160.95
C2—C31.381 (2)C18—H180.95
C2—H20.95P1—F51.5742 (14)
C3—C41.402 (3)P1—F31.5883 (13)
C3—H30.95P1—F11.5942 (12)
C4—C51.375 (2)P1—F21.6025 (12)
C4—H40.95P1—F41.6041 (12)
C5—C61.389 (2)P1—F61.6092 (14)
C5—H50.95P1'—F5'1.574 (3)
C7—H70.95P1'—F3'1.588 (3)
C8—C91.502 (2)P1'—F1'1.595 (3)
C8—H8A0.99P1'—F2'1.601 (3)
C8—H8B0.99P1'—F4'1.603 (3)
C9—H9A0.99P1'—F6'1.608 (3)
C9—H9B0.99
C9—O1—C10113.54 (12)C10—C11—H11B109.1
C7—N1—C1107.87 (14)H11A—C11—H11B107.8
C7—N1—H1N126.9 (11)N3—C12—C13132.02 (15)
C1—N1—H1N125.0 (11)N3—C12—C17105.74 (14)
C7—N2—C6107.41 (13)C13—C12—C17122.24 (16)
C7—N2—C8128.63 (14)C14—C13—C12116.68 (16)
C6—N2—C8123.95 (13)C14—C13—H13121.7
C18—N3—C12106.67 (14)C12—C13—H13121.7
C18—N3—C11126.26 (15)C13—C14—C15121.63 (16)
C12—N3—C11127.04 (13)C13—C14—H14119.2
C18—N4—C17105.03 (14)C15—C14—H14119.2
C2—C1—N1131.78 (15)C16—C15—C14121.52 (17)
C2—C1—C6121.47 (15)C16—C15—H15119.2
N1—C1—C6106.75 (14)C14—C15—H15119.2
C3—C2—C1116.36 (16)C15—C16—C17117.52 (16)
C3—C2—H2121.8C15—C16—H16121.2
C1—C2—H2121.8C17—C16—H16121.2
C2—C3—C4122.12 (17)C16—C17—N4130.48 (16)
C2—C3—H3118.9C16—C17—C12120.41 (16)
C4—C3—H3118.9N4—C17—C12109.11 (15)
C5—C4—C3121.46 (16)N4—C18—N3113.45 (16)
C5—C4—H4119.3N4—C18—H18123.3
C3—C4—H4119.3N3—C18—H18123.3
C4—C5—C6116.52 (16)F5—P1—F391.33 (10)
C4—C5—H5121.7F5—P1—F190.84 (8)
C6—C5—H5121.7F3—P1—F190.37 (7)
C5—C6—N2131.09 (15)F5—P1—F290.33 (7)
C5—C6—C1122.08 (15)F3—P1—F289.90 (7)
N2—C6—C1106.83 (14)F1—P1—F2178.79 (8)
N1—C7—N2111.14 (15)F5—P1—F491.13 (10)
N1—C7—H7124.4F3—P1—F4177.42 (10)
N2—C7—H7124.4F1—P1—F490.37 (7)
N2—C8—C9112.67 (13)F2—P1—F489.30 (6)
N2—C8—H8A109.1F5—P1—F6179.35 (8)
C9—C8—H8A109.1F3—P1—F689.03 (8)
N2—C8—H8B109.1F1—P1—F689.69 (8)
C9—C8—H8B109.1F2—P1—F689.14 (8)
H8A—C8—H8B107.8F4—P1—F688.51 (9)
O1—C9—C8107.68 (13)F5'—P1'—F3'91.6 (3)
O1—C9—H9A110.2F5'—P1'—F1'90.8 (3)
C8—C9—H9A110.2F3'—P1'—F1'90.2 (3)
O1—C9—H9B110.2F5'—P1'—F2'90.1 (3)
C8—C9—H9B110.2F3'—P1'—F2'89.9 (3)
H9A—C9—H9B108.5F1'—P1'—F2'179.1 (4)
O1—C10—C11107.08 (13)F5'—P1'—F4'90.8 (3)
O1—C10—H10A110.3F3'—P1'—F4'177.5 (4)
C11—C10—H10A110.3F1'—P1'—F4'90.2 (3)
O1—C10—H10B110.3F2'—P1'—F4'89.6 (3)
C11—C10—H10B110.3F5'—P1'—F6'179.1 (4)
H10A—C10—H10B108.6F3'—P1'—F6'89.2 (3)
N3—C11—C10112.69 (14)F1'—P1'—F6'89.7 (3)
N3—C11—H11A109.1F2'—P1'—F6'89.5 (3)
C10—C11—H11A109.1F4'—P1'—F6'88.4 (3)
N3—C11—H11B109.1
C7—N1—C1—C2−179.03 (17)C9—O1—C10—C11169.54 (13)
C7—N1—C1—C60.03 (17)C18—N3—C11—C10−94.78 (19)
N1—C1—C2—C3178.85 (16)C12—N3—C11—C1087.35 (19)
C6—C1—C2—C3−0.1 (2)O1—C10—C11—N3−58.98 (17)
C1—C2—C3—C40.3 (3)C18—N3—C12—C13179.45 (17)
C2—C3—C4—C5−0.2 (3)C11—N3—C12—C13−2.3 (3)
C3—C4—C5—C60.0 (2)C18—N3—C12—C170.01 (17)
C4—C5—C6—N2−179.17 (16)C11—N3—C12—C17178.22 (15)
C4—C5—C6—C10.2 (2)N3—C12—C13—C14−179.43 (16)
C7—N2—C6—C5179.09 (16)C17—C12—C13—C14−0.1 (2)
C8—N2—C6—C5−0.4 (3)C12—C13—C14—C15−0.2 (2)
C7—N2—C6—C1−0.31 (17)C13—C14—C15—C160.3 (3)
C8—N2—C6—C1−179.76 (13)C14—C15—C16—C17−0.1 (2)
C2—C1—C6—C5−0.1 (2)C15—C16—C17—N4179.34 (16)
N1—C1—C6—C5−179.29 (14)C15—C16—C17—C12−0.2 (2)
C2—C1—C6—N2179.35 (14)C18—N4—C17—C16−179.82 (17)
N1—C1—C6—N20.17 (17)C18—N4—C17—C12−0.29 (18)
C1—N1—C7—N2−0.23 (18)N3—C12—C17—C16179.76 (14)
C6—N2—C7—N10.34 (18)C13—C12—C17—C160.3 (2)
C8—N2—C7—N1179.76 (14)N3—C12—C17—N40.17 (17)
C7—N2—C8—C913.2 (2)C13—C12—C17—N4−179.34 (14)
C6—N2—C8—C9−167.43 (14)C17—N4—C18—N30.31 (19)
C10—O1—C9—C8−167.47 (13)C12—N3—C18—N4−0.21 (19)
N2—C8—C9—O158.10 (17)C11—N3—C18—N4−178.43 (15)
D—H···AD—HH···AD···AD—H···A
N1—H1N···N4i1.05 (2)1.68 (2)2.724 (2)176 (2)
C4—H4···F3ii0.952.413.130 (2)133
C7—H7···F4iii0.952.233.100 (2)152
C9—H9B···F2iii0.992.403.340 (2)159
C11—H11A···F2iv0.992.513.066 (2)116
C16—H16···F4v0.952.393.300 (2)161
C18—H18···F60.952.383.298 (2)163
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N1—H1N⋯N4i1.05 (2)1.68 (2)2.724 (2)176 (2)
C4—H4⋯F3ii0.952.413.130 (2)133
C7—H7⋯F4iii0.952.233.100 (2)152
C9—H9B⋯F2iii0.992.403.340 (2)159
C11—H11A⋯F2iv0.992.513.066 (2)116
C16—H16⋯F4v0.952.393.300 (2)161
C18—H18⋯F60.952.383.298 (2)163

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

  2 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.  Copper(I)-catalyzed synthesis of substituted 2-mercapto benzimidazoles.

Authors:  Siva Murru; Bhisma K Patel; Jean Le Bras; Jacques Muzart
Journal:  J Org Chem       Date:  2009-03-06       Impact factor: 4.354

  2 in total

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