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The title compound, C16H16N5+·Cl (nbbH+·Cl), displays N—H...N, N—H...Cl and π–π inter­actions in the crystal packing. The Cl anion is chelated by the nbbH+ cation via two N—H...Cl hydrogen bonds. Inter-ion N—H...N and N—H...Cl hydrogen bonds link ions related by 21 screw axes into chains along the c axis. These chains are further linked by glide-plane operations to generate a three-dimensional network, which is additionally stabilized by inter­chain π–π inter­actions.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270105021992/hj1062sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270105021992/hj1062Isup2.hkl
Contains datablock I

CCDC reference: 290572

Comment top

Bis(benzimidazol-2-ylmethyl)amine (nbb) has been utilized extensively to synthesize various transition metal complexes (Wahnon et al., 1994; Berends & Stephan, 1984). Each benzimidazol arm of nbb possesses one imine N atom and one amine NH group. The two imine N atoms can act as coordination donors to chelate a metal ion, while the two amine NH groups are potential hydrogen-bond donors. Without metal coordination, the two imine N atoms can also behave as hydrogen-bond acceptors. Therefore, nbb is a good candidate for formation of hydrogen-bonded adducts via intermolecular interactions. We have been interested in assembly of supramolecular aggregates with benzimidazole-related compounds (Su et al., 1998, 2000; Zhang, et al., 2005) and report here the structure of the title compound, nbbH+·Cl, (I). The single-crystal structure of nbb has been reported previously at room temperature (Calderazzo et al., 2003) and at 150 K (Tarazon Navarro & McKee, 2003); in both reports, the nbb molecule is disordered about an inversion centre

Our analysis establishes that the title compound has partial protonation of the two imine N atoms, as shown in Fig. 1. The nbbH+ cation adopts an almost planar conformation, the two benzimidazole rings forming a dihedral angle of 5.36 (9)°. Occupancy refinement showed that the H atom involved in ring protonation is equally disordered over the N2 and N3 sites, and each five-membered ring possesses a half-positive-charge, giving rise to the overrall nbbH+ cation (see scheme). The dimensions of the five-membered rings are fully consistent with this assignment. As listed in Table 1, the geometry of each benzimidazole ring is the same; in particular, the N2—C2 bond distance is identical to the N3—C10 distance [mean 1.315 (3) Å], while the N1—C2 and N4—C10 distances are also not significantly different [mean 1.335 (3) Å]. These findings are consistent with the N2—C2 and N3—C10 bonds possessing more double-bond character than the N1—C2 and N3—C10 bonds. In the disordered non-protonated nbb parent molecule at low temperature, the NC distance is 1.3183 (17) Å and the C—N(H) distance is 1.3573 (17) Å (Tarazon Navarro & McKee, 2003).

All five N atoms of the nbbH+ ion are involved in hydrogen bonds, as shown in Table 2. The Cl anion is chelated by atoms N1 and N4 via N—H···Cl hydrogen bonds. Atoms N2 and N3 form mutual inter-ion N2—H···N3 and N3—H···N2 hydrogen bonds, as shown in Fig. 2, each H atom having an occupancy of 0.5. Since the nbbH+ cation is bent, with two methylene (CH2) groups protruding between the two planar benzimidazole rings, the ions are not assembled into a dimer by formation of two complementary N—H···N hydrogen bonds. Instead, groups related by a 21 screw axis are connected in a head-to-tail fashion into an undulating one-dimensional chain, which extends along the c axis (Fig. 2). The N5/H5 moiety is also involved in a further N5—H5···Cl hydrogen bond (weaker compared with those of the chelating N—H···Cl hydrogen bonds), which links ions related by an a glide into columnar one-dimensional chains extending along the a axis, as shown in Fig. 3. This chain can also be considered to consist of oppositely overlapped nbbH+ cations. These cations are stacked along the a direction with overlap between five- and six-membered rings in the sequence (−1/2 + x, 3/2 − y, z), (x, y, z), (1/2 + x, 3/2 − y, z), (1 + x, y, z) etc. There exist ππ interactions between neighbouring cations. The shortest centroid-to-centroid distance is 3.554 (2) Å. The N—H···Cl hydrogen-bonded chain along the a axis is thus further stabilized by ππ stacking interactions. These chains along the a and c axial directions are also linked by N—H···N hydrogen bonds by operation of the space group n glide to generate a three-dimensional network. Thus, the crystal packing is ordered via synergetic contributions from N—H···N and N—H···Cl hydrogen bonds and ππ interactions, which together assemble the cations and anions into a three-dimensional framework.

Experimental top

The title compound was prepared by the condensation of iminodiacetic acid and 1,2-diaminobenzene in a 4 N HCl solution (yield 76%). Single crystals suitable for X-ray analysis were obtained by slow evaporation from ethanol solution at room temperature.

Refinement top

The systematic absences allow the space group to be either Pnma or Pna21, but a sensible solution and refinement were only possible with Pna21. All H atoms were located in a difference Fourier map. It was obvious from the difference maps that protonation had occurred equally at atoms N2 and N3, and the H atoms at these sites were assigned an occupancy of 0.5. Atom H5 (at N5) was clearly located such that N5 has pyramidal geometry. All H atoms were then allowed for as riding atoms (C—H = 0.93 and 0.97 Å, and N—H = 0.86 and 0.90 Å) with Uiso(H) values of 1.2 times Ueq(C,N). Friedel pairs were measured; however, the Flack (1983) parameter was indeterminate, indicating probable inversion twinning.

Computing details top

Data collection: SMART (Siemens, 1993); cell refinement: SAINT (Siemens, 1995); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 1997); software used to prepare material for publication: PLATON (Spek, 2003).

Figures top
[Figure 1] Fig. 1. A view of the title compound, showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are represented by circles of arbitrary size. Dashed lines indicate hydrogen bonds.
[Figure 2] Fig. 2. A view showing hydrogen-bonded chains along the c axis. Dashed lines indicate hydrogen bonds, and C-bound H atoms have been omitted. Symmetry operators are as in Table 2.
[Figure 3] Fig. 3. A view showing the hydrogen-bonded chain extending along the a axis. See Table 2 for details of the symmetry operator. Dashed lines indicate hydrogen bonds, and C-bound H atoms have been omitted. This plot also shows the ππ stacking between five- and six-membered rings in the sequence (bottom to top) (−1/2 + x, 3/2 − y, z), (x, y, z), (1/2 + x, 3/2 − y, z), (1 + x, y, z).
Bis(1H-benzimidazol-2-ylmethyl)aminium chloride top
Crystal data top
C16H16N5+·ClF(000) = 656
Mr = 313.79Dx = 1.384 Mg m3
Orthorhombic, Pna21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2nCell parameters from 1785 reflections
a = 7.607 (2) Åθ = 2.1–24.6°
b = 13.615 (3) ŵ = 0.26 mm1
c = 14.544 (3) ÅT = 293 K
V = 1506.3 (6) Å3Block, colorless
Z = 40.19 × 0.04 × 0.03 mm
Data collection top
Bruker SMART 1K CCD
diffractometer
2020 independent reflections
Radiation source: fine-focus sealed tube1771 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.024
ϕ and ω scansθmax = 25.0°, θmin = 2.1°
Absorption correction: multi-scan
(SADABS; Siemens, 1996)
h = 89
Tmin = 0.757, Tmax = 1.000k = 1416
6569 measured reflectionsl = 817
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)] = 0.027H-atom parameters constrained
wR(F2) = 0.067 w = 1/[σ2(Fo2) + (0.0419P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.01(Δ/σ)max = 0.001
2020 reflectionsΔρmax = 0.19 e Å3
200 parametersΔρmin = 0.16 e Å3
1 restraintAbsolute structure: Flack (1983), 637 Friedel pairs?
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.36 (7)
Crystal data top
C16H16N5+·ClV = 1506.3 (6) Å3
Mr = 313.79Z = 4
Orthorhombic, Pna21Mo Kα radiation
a = 7.607 (2) ŵ = 0.26 mm1
b = 13.615 (3) ÅT = 293 K
c = 14.544 (3) Å0.19 × 0.04 × 0.03 mm
Data collection top
Bruker SMART 1K CCD
diffractometer
2020 independent reflections
Absorption correction: multi-scan
(SADABS; Siemens, 1996)
1771 reflections with I > 2σ(I)
Tmin = 0.757, Tmax = 1.000Rint = 0.024
6569 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.027H-atom parameters constrained
wR(F2) = 0.067Δρmax = 0.19 e Å3
S = 1.01Δρmin = 0.16 e Å3
2020 reflectionsAbsolute structure: Flack (1983), 637 Friedel pairs?
200 parametersAbsolute structure parameter: 0.36 (7)
1 restraint
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)
N10.0512 (2)0.74555 (12)0.66884 (14)0.0374 (4)
H10.00090.77230.71550.045*
N20.1621 (2)0.63180 (12)0.57910 (13)0.0361 (4)
H20.19420.57520.55890.043*0.50
N30.2418 (2)0.55635 (13)1.02709 (13)0.0371 (4)
H30.23970.49441.03850.044*0.50
N40.2066 (2)0.69743 (13)0.95583 (14)0.0385 (5)
H40.17870.73870.91350.046*
N50.0272 (3)0.61128 (13)0.80927 (14)0.0501 (6)
H50.07580.62420.83710.060*
C10.0079 (3)0.57179 (15)0.71900 (15)0.0393 (5)
H1A0.09320.51910.72390.047*
H1B0.09950.54460.69360.047*
C20.0771 (3)0.64963 (15)0.65605 (16)0.0349 (5)
C30.1904 (3)0.72231 (16)0.53660 (16)0.0346 (5)
C40.2672 (3)0.74615 (19)0.45354 (17)0.0444 (6)
H4A0.31660.69840.41590.053*
C50.2673 (3)0.8434 (2)0.4290 (2)0.0549 (7)
H5A0.31770.86180.37330.066*
C60.1941 (4)0.9153 (2)0.4851 (2)0.0562 (8)
H60.19510.98030.46540.067*
C70.1206 (3)0.89294 (16)0.5687 (2)0.0469 (6)
H70.07370.94120.60670.056*
C80.1198 (3)0.79431 (14)0.59359 (17)0.0351 (5)
C90.1284 (3)0.54739 (17)0.86727 (18)0.0437 (6)
H9A0.22920.52300.83340.052*
H9B0.05710.49150.88510.052*
C100.1896 (3)0.59992 (15)0.95112 (17)0.0364 (5)
C110.3012 (3)0.63025 (15)1.08526 (17)0.0361 (5)
C120.3706 (3)0.62602 (17)1.17369 (18)0.0448 (6)
H120.38650.56641.20380.054*
C130.4146 (3)0.71369 (19)1.21459 (19)0.0505 (7)
H130.46300.71341.27330.061*
C140.3881 (3)0.80322 (19)1.1696 (2)0.0549 (7)
H140.41870.86111.19950.066*
C150.3187 (3)0.80842 (17)1.0828 (2)0.0479 (6)
H150.30040.86821.05340.058*
C160.2773 (3)0.72020 (16)1.04122 (17)0.0387 (5)
Cl10.09411 (8)0.88137 (4)0.82646 (5)0.04764 (17)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0437 (11)0.0317 (9)0.0369 (11)0.0029 (8)0.0012 (9)0.0032 (9)
N20.0440 (11)0.0311 (9)0.0332 (11)0.0004 (7)0.0020 (9)0.0010 (9)
N30.0464 (11)0.0297 (9)0.0351 (11)0.0028 (8)0.0018 (9)0.0023 (9)
N40.0447 (11)0.0339 (10)0.0368 (12)0.0003 (8)0.0014 (10)0.0077 (9)
N50.0635 (13)0.0457 (11)0.0410 (14)0.0082 (9)0.0083 (11)0.0036 (10)
C10.0512 (14)0.0330 (11)0.0337 (13)0.0025 (11)0.0030 (11)0.0003 (10)
C20.0382 (12)0.0331 (11)0.0334 (13)0.0009 (9)0.0030 (11)0.0020 (10)
C30.0360 (12)0.0339 (11)0.0340 (13)0.0005 (9)0.0057 (11)0.0030 (10)
C40.0468 (14)0.0514 (14)0.0350 (14)0.0055 (11)0.0009 (12)0.0035 (12)
C50.0610 (16)0.0626 (17)0.0409 (14)0.0171 (13)0.0032 (13)0.0131 (15)
C60.0682 (19)0.0403 (14)0.0602 (19)0.0114 (13)0.0172 (15)0.0177 (13)
C70.0489 (15)0.0341 (12)0.0577 (18)0.0002 (10)0.0111 (13)0.0021 (12)
C80.0367 (12)0.0327 (11)0.0360 (13)0.0014 (9)0.0061 (10)0.0045 (10)
C90.0543 (14)0.0380 (12)0.0387 (13)0.0003 (11)0.0059 (11)0.0038 (11)
C100.0391 (12)0.0323 (12)0.0380 (14)0.0007 (10)0.0025 (11)0.0036 (11)
C110.0358 (13)0.0343 (12)0.0380 (13)0.0008 (9)0.0030 (11)0.0028 (11)
C120.0450 (14)0.0478 (14)0.0414 (15)0.0006 (11)0.0043 (12)0.0033 (12)
C130.0506 (15)0.0619 (17)0.0391 (14)0.0081 (13)0.0011 (12)0.0073 (13)
C140.0578 (17)0.0493 (15)0.0575 (19)0.0147 (13)0.0063 (14)0.0120 (14)
C150.0557 (16)0.0345 (13)0.0536 (17)0.0052 (10)0.0076 (13)0.0008 (13)
C160.0377 (12)0.0380 (12)0.0405 (14)0.0029 (10)0.0041 (11)0.0008 (11)
Cl10.0574 (3)0.0379 (3)0.0476 (3)0.0062 (2)0.0003 (3)0.0040 (3)
Geometric parameters (Å, º) top
N1—C21.334 (3)C4—H4A0.93
N1—C81.382 (3)C5—C61.390 (4)
N1—H10.86C5—H5A0.93
N2—C21.315 (3)C6—C71.373 (4)
N2—C31.395 (3)C6—H60.93
N2—H20.86C7—C81.391 (3)
N3—C101.315 (3)C7—H70.93
N3—C111.390 (3)C9—C101.489 (3)
N3—H30.86C9—H9A0.97
N4—C101.336 (3)C9—H9B0.97
N4—C161.388 (3)C11—C121.391 (3)
N4—H40.86C11—C161.394 (3)
N5—C91.436 (3)C12—C131.375 (3)
N5—C11.444 (3)C12—H120.93
N5—H50.90C13—C141.398 (4)
C1—C21.496 (3)C13—H130.93
C1—H1A0.97C14—C151.370 (4)
C1—H1B0.97C14—H140.93
C3—C41.381 (3)C15—C161.381 (3)
C3—C81.392 (3)C15—H150.93
C4—C51.372 (4)
C2—N1—C8107.71 (19)C5—C6—H6119.1
C2—N1—H1126.1C6—C7—C8116.5 (2)
C8—N1—H1126.1C6—C7—H7121.7
C2—N2—C3106.84 (18)C8—C7—H7121.7
C2—N2—H2126.6N1—C8—C7132.2 (2)
C3—N2—H2126.6N1—C8—C3106.20 (17)
C10—N3—C11106.43 (18)C7—C8—C3121.6 (2)
C10—N3—H3126.8N5—C9—C10110.98 (18)
C11—N3—H3126.8N5—C9—H9A109.4
C10—N4—C16107.78 (19)C10—C9—H9A109.4
C10—N4—H4126.1N5—C9—H9B109.4
C16—N4—H4126.1C10—C9—H9B109.4
C9—N5—C1114.08 (18)H9A—C9—H9B108.0
C9—N5—H5108.7N3—C10—N4112.1 (2)
C1—N5—H5108.7N3—C10—C9124.46 (19)
N5—C1—C2110.96 (17)N4—C10—C9123.4 (2)
N5—C1—H1A109.4N3—C11—C12131.0 (2)
C2—C1—H1A109.4N3—C11—C16108.3 (2)
N5—C1—H1B109.4C12—C11—C16120.7 (2)
C2—C1—H1B109.4C13—C12—C11117.2 (2)
H1A—C1—H1B108.0C13—C12—H12121.4
N2—C2—N1111.83 (19)C11—C12—H12121.4
N2—C2—C1124.26 (19)C12—C13—C14121.3 (3)
N1—C2—C1123.8 (2)C12—C13—H13119.4
C4—C3—C8121.3 (2)C14—C13—H13119.4
C4—C3—N2131.3 (2)C15—C14—C13122.1 (3)
C8—C3—N2107.4 (2)C15—C14—H14118.9
C5—C4—C3117.1 (2)C13—C14—H14118.9
C5—C4—H4A121.5C14—C15—C16116.5 (2)
C3—C4—H4A121.5C14—C15—H15121.7
C4—C5—C6121.8 (3)C16—C15—H15121.7
C4—C5—H5A119.1C15—C16—N4132.4 (2)
C6—C5—H5A119.1C15—C16—C11122.2 (2)
C7—C6—C5121.8 (2)N4—C16—C11105.38 (19)
C7—C6—H6119.1
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···Cl10.862.313.146 (2)164
N2—H2···N3i0.861.892.739 (2)172
N3—H3···N2ii0.861.912.739 (2)161
N4—H4···Cl10.862.413.247 (2)166
N5—H5···Cl1iii0.902.523.306 (3)147
Symmetry codes: (i) x, y+1, z1/2; (ii) x, y+1, z+1/2; (iii) x1/2, y+3/2, z.

Experimental details

Crystal data
Chemical formulaC16H16N5+·Cl
Mr313.79
Crystal system, space groupOrthorhombic, Pna21
Temperature (K)293
a, b, c (Å)7.607 (2), 13.615 (3), 14.544 (3)
V3)1506.3 (6)
Z4
Radiation typeMo Kα
µ (mm1)0.26
Crystal size (mm)0.19 × 0.04 × 0.03
Data collection
DiffractometerBruker SMART 1K CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Siemens, 1996)
Tmin, Tmax0.757, 1.000
No. of measured, independent and
observed [I > 2σ(I)] reflections
6569, 2020, 1771
Rint0.024
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.027, 0.067, 1.01
No. of reflections2020
No. of parameters200
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.19, 0.16
Absolute structureFlack (1983), 637 Friedel pairs?
Absolute structure parameter0.36 (7)

Computer programs: SMART (Siemens, 1993), SAINT (Siemens, 1995), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Bruker, 1997), PLATON (Spek, 2003).

Selected bond lengths (Å) top
N1—C21.334 (3)N3—C111.390 (3)
N1—C81.382 (3)N4—C101.336 (3)
N2—C21.315 (3)N4—C161.388 (3)
N2—C31.395 (3)N5—C91.436 (3)
N3—C101.315 (3)N5—C11.444 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···Cl10.862.313.146 (2)164
N2—H2···N3i0.861.892.739 (2)172
N3—H3···N2ii0.861.912.739 (2)161
N4—H4···Cl10.862.413.247 (2)166
N5—H5···Cl1iii0.902.523.306 (3)147
Symmetry codes: (i) x, y+1, z1/2; (ii) x, y+1, z+1/2; (iii) x1/2, y+3/2, z.
 

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