N-Methyl­benzimidazole N-methyl­benzimidazolium hexa­fluoro­phosphate

In the title compound, C₈H₈N₂·C₈H₉N₂⁺·PF₆⁻, 50% of the N-methyl­benzimidazole residues are protonated. An N—H...N⁺ hydrogen bond with a D...A distance of 2.641 (2) Å is formed. The organic mol­ecules are located on crystallographic mirror planes and the PF₆⁻ counter-ions are located on crystallographic 2/m sites.

Key indicators

• Single-crystal X-ray study
• T = 150 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.038
• wR factor = 0.106
• Data-to-parameter ratio = 12.9

checkCIF/PLATON results

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Alert level C
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......       0.97
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT076_ALERT_1_C Occupancy       0.50 less than 1.0 for Sp.pos  .         H3
PLAT244_ALERT_4_C Low   'Solvent' Ueq as Compared to Neighbors for         P1

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   4 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion

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S1. Comment

During our investigations of ruthenium–bipyridine complexes with DNA model bases (Velders et al., 1999, 2000), we obtained crystals of both cis-[Ru(bipyridine)₂(N-methylbenzimidazole)₂](PF₆)₂ (Velders et al., 2005) and the title compound, (I), which contains a partly protonated N-methylbenzimidazole. The Cambridge Structural Database (Version 5.26 of November 2004, Updates 1 and 2; Allen, 2002) reports no other protonated N-methylbenzimidazole structures.

The asymmetric unit of (I) contains an N-methylbenzimidazole molecule located on a crystallographic mirror plane and a hexafluorophosphate counter-ion positioned on a crystallographic 2/m site. At 2.641 (2) Å from atom N3, a symmetry-related N3 atom is located. The short N···N distance and the electron-density maps strongly suggest the presence of an [N—H···N]⁺ hydrogen bond, where the H atom displays symmetry-induced disorder (see refinement details and Fig. 2). Atom N3 turns out to be protonated in 50% of the N-methylbenzimidazole residues, meaning that the studied crystal is a co-crystal of neutral N-methylbenzimidazole and the hexafluorophosphate salt of protonated N-methylbenzimidazole.

The crystal packing of (I) displays layers of partly protonated N-methylbenzimidazole and PF₆⁻ counter-ions (Fig. 3). Due to their location on special positions, the centres of gravity of all residues are located exactly in the ac plane. Short C—H···F contacts (Table 2) further stabilize these layers.

S2. Experimental

In a concentrated solution of cis-[Ru(bipyridine)₂(N-methylbenzimidazole)₂](PF₆)₂, N-methylbenzimidazole and NH₄PF₆ [Quantities?] in a water–acetone mixture [Ratio?], transparent crystals of the title compound formed after a few weeks at 277 K. The crystalline material was isolated by filtration and washed with water.

S3. Refinement

The short N3···N3(1 − x,y,-z) distance strongly suggests the presence of a hydrogen bond, either a symmetric [N···H···N]⁺ bond or an asymmetric [N—H···N]⁺ hydrogen bond, where the H atom displays symmetry-induced disorder. A difference Fourier map calculated without the contribution of atom H3 displays an elongated area of residual electron density between the two symmetry-related N3 atoms (Fig. 2). This density cannot be resolved into two separate H-atom positions. Refinement of the coordinates of a disordered asymmetrically located H atom, rather then an ordered symmetrically located H atom, resulted in a stable position for the H atom, with an N—H bond length of 0.89 (5) Å. The methyl group of N-methylbenzimidazole was refined as a rigid group, allowing for rotation around the N—C bond and displaying disorder over the crystallographic mirror plane in which N—C is located. All other H atoms were introduced in calculated positions, riding on their carrier atoms, with C—H = 0.95–0.98 Å [Please check added text]. The constraint U_iso(H) = 1.2 U_eq(carrier) was applied for all H atoms.

Computing details

Data collection: COLLECT (Nonius, 1998); cell refinement: DENZO (Otwinowski & Minor, 1997); data reduction: DENZO; program(s) used to solve structure: SHELXS86 (Sheldrick, 1985); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: PLATON.

Figures

	Fig. 1. A view of the title compound, showing 50% probability displacement ellipsoids. Atom H3 and the disordered methyl H atoms have site-occupancy factors of 0.5. [Symmetry codes: (i) −x,y,1 − z (ii) −x,-y,1 − z (iii) x,-y,z.]
	Fig. 2. Difference Fourier map of the ac plane, calculated without the contribution of atom H3. Green countours represent positive residual density, red contours represent negative residual density and the blue contours represent the zero level. Contour increment is 0.10 e Å^−3.
	Fig. 3. The crystal packing of (I) in the ac plane. Due to their location at special positions, the centres of gravity of all displayed residues are located in the ac plane. The H atom in the [N—H···N]^+ hydrogen bond is disordered over positions H3 and H3^i, as indicated in the plot. [Symmetry code: (i) 1 − x,y,-z.]

N-Methylbenzimidazole N-methylbenzimidazolium hexafluorophosphate (1/1/1)

Crystal data

C8H8N2·C8H9N2^+·PF6^−	F(000) = 420
Mr = 410.31	Quoted _cell_measurement_* data items refer to the initial cell determination. The cell parameters as reported in _cell_* are based on the complete data set.
Monoclinic, C2/m	Dx = 1.520 Mg m^−3
Hall symbol: -C 2y	Mo Kα radiation, λ = 0.71073 Å
a = 14.930 (4) Å	Cell parameters from 263 reflections
b = 6.6524 (12) Å	θ = 2.0–25.0°
c = 9.0261 (12) Å	µ = 0.22 mm^−1
β = 90.214 (17)°	T = 150 K
V = 896.5 (3) Å^3	Block, colourless
Z = 2	0.3 × 0.2 × 0.2 mm

Data collection

Nonius KappaCCD area-detector diffractometer	986 reflections with I > 2σ(I)
Radiation source: rotating anode	Rint = 0.051
Graphite monochromator	θmax = 27.4°, θmin = 2.3°
Detector resolution: 18.4 pixels mm^-1	h = −19→17
ϕ scans and ω scans with κ offset	k = −7→8
3017 measured reflections	l = −11→10
1072 independent reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.039	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.106	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ^2(Fo^2) + (0.0501P)^2 + 0.93P] where P = (Fo^2 + 2Fc^2)/3
1072 reflections	(Δ/σ)max < 0.001
83 parameters	Δρmax = 0.29 e Å^−3
0 restraints	Δρmin = −0.32 e Å^−3

Special details

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement on F² for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The observed criterion of F² > 2σ(F²) is used only for calculating -R-factor-obs 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 (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
N1	0.30928 (10)	0.00000	0.21975 (16)	0.0204 (4)
N3	0.41813 (10)	0.00000	0.05483 (17)	0.0230 (4)
C2	0.39788 (12)	0.00000	0.1972 (2)	0.0230 (5)
C4	0.33722 (12)	0.00000	−0.0219 (2)	0.0202 (5)
C5	0.26800 (12)	0.00000	0.08267 (19)	0.0189 (5)
C6	0.17781 (12)	0.00000	0.0414 (2)	0.0228 (5)
C7	0.16001 (13)	0.00000	−0.1091 (2)	0.0265 (5)
C8	0.22926 (14)	0.00000	−0.2142 (2)	0.0270 (5)
C9	0.31843 (14)	0.00000	−0.1734 (2)	0.0252 (5)
C10	0.26431 (14)	0.00000	0.3633 (2)	0.0272 (6)
P1	0.00000	0.00000	0.50000	0.0324 (3)
F1	0.07400 (7)	0.1669 (2)	0.53162 (15)	0.0677 (5)
F2	0.02662 (11)	0.00000	0.33144 (16)	0.0824 (11)
H2	0.44120	0.00000	0.27460	0.0280*
H3	0.474 (3)	0.00000	0.022 (6)	0.0280*	0.500
H6	0.13120	0.00000	0.11280	0.0270*
H7	0.09950	0.00000	−0.14220	0.0320*
H8	0.21420	0.00000	−0.31660	0.0320*
H9	0.36480	0.00000	−0.24510	0.0300*
H10A	0.24000	−0.13410	0.38310	0.0330*	0.500
H10B	0.21540	0.09830	0.36200	0.0330*	0.500
H10C	0.30740	0.03580	0.44120	0.0330*	0.500

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0195 (7)	0.0266 (8)	0.0151 (7)	0.0000	0.0008 (6)	0.0000
N3	0.0175 (7)	0.0310 (8)	0.0204 (8)	0.0000	0.0016 (6)	0.0000
C2	0.0194 (8)	0.0297 (9)	0.0199 (9)	0.0000	−0.0009 (7)	0.0000
C4	0.0194 (8)	0.0220 (8)	0.0191 (9)	0.0000	0.0007 (7)	0.0000
C5	0.0195 (8)	0.0194 (8)	0.0179 (8)	0.0000	0.0010 (7)	0.0000
C6	0.0189 (8)	0.0233 (9)	0.0263 (9)	0.0000	0.0005 (7)	0.0000
C7	0.0234 (9)	0.0249 (9)	0.0310 (10)	0.0000	−0.0079 (8)	0.0000
C8	0.0363 (10)	0.0269 (9)	0.0177 (9)	0.0000	−0.0069 (8)	0.0000
C9	0.0301 (10)	0.0277 (9)	0.0178 (9)	0.0000	0.0018 (7)	0.0000
C10	0.0292 (10)	0.0374 (11)	0.0149 (9)	0.0000	0.0050 (7)	0.0000
P1	0.0165 (3)	0.0606 (6)	0.0200 (4)	0.0000	−0.0012 (3)	0.0000
F1	0.0342 (6)	0.0805 (10)	0.0883 (9)	−0.0148 (6)	−0.0028 (5)	−0.0147 (7)
F2	0.0374 (8)	0.187 (3)	0.0229 (8)	0.0000	0.0042 (6)	0.0000

Geometric parameters (Å, º)

P1—F1^i	1.5914 (13)	C6—C7	1.383 (3)
P1—F1	1.5914 (13)	C7—C8	1.406 (3)
P1—F2	1.5739 (15)	C8—C9	1.380 (3)
P1—F1^ii	1.5914 (13)	C2—H2	0.9500
P1—F2^i	1.5739 (15)	C6—H6	0.9500
P1—F1^iii	1.5914 (13)	C7—H7	0.9500
N1—C2	1.339 (2)	C8—H8	0.9500
N1—C5	1.380 (2)	C9—H9	0.9500
N1—C10	1.462 (2)	C10—H10C^ii	0.9800
N3—C2	1.321 (2)	C10—H10A	0.9800
N3—C4	1.390 (2)	C10—H10B	0.9800
N3—H3	0.89 (5)	C10—H10C	0.9800
C4—C9	1.395 (3)	C10—H10A^ii	0.9800
C4—C5	1.402 (3)	C10—H10B^ii	0.9800
C5—C6	1.396 (3)
F1···C2^iv	3.327 (2)	C7···C5^x	3.5034 (13)
F1···C2^v	3.327 (2)	C8···C5^xiii	3.5319 (13)
F1···H8^vi	2.7300	C8···N1^xiii	3.3759 (10)
F1···H2^iv	2.8300	C8···C5^x	3.5319 (13)
F1···H8^vii	2.7300	C8···C10^xii	3.5896 (14)
F1···H10A^ii	2.8300	C8···C10^xi	3.5896 (14)
F1···H10B	2.6500	C8···C10^x	3.5896 (14)
F1···H10C^v	2.6700	C8···C5^xii	3.5319 (13)
F1···H2^v	2.8300	C8···N1^xi	3.3759 (10)
F2···H6	2.5200	C8···N1^xii	3.3759 (10)
F2···H6	2.5200	C8···C5^xi	3.5319 (13)
F2···H7^viii	2.5400	C8···C10^xiii	3.5896 (14)
F2···H7^ix	2.5400	C8···N1^x	3.3759 (10)
N1···C8^x	3.3759 (10)	C9···C6^xiii	3.5335 (13)
N1···C8^xi	3.3759 (10)	C9···C6^x	3.5335 (13)
N1···C8^xii	3.3759 (10)	C9···C6^xi	3.5335 (13)
N1···C8^xiii	3.3759 (10)	C9···C6^xii	3.5335 (13)
N3···N3^xiv	2.641 (2)	C10···C8^xi	3.5896 (14)
N3···N3^xv	2.641 (2)	C10···C8^xii	3.5896 (14)
N3···H3^xiv	1.76 (5)	C10···C8^xiii	3.5896 (14)
N3···H3^xv	1.76 (5)	C10···C8^x	3.5896 (14)
C2···C7^xii	3.5267 (13)	C2···H3^xv	2.76 (5)
C2···F1^xvi	3.327 (2)	C2···H3^xiv	2.76 (5)
C2···C7^xi	3.5267 (13)	C4···H3^xiv	2.82 (4)
C2···C7^x	3.5267 (13)	C4···H3^xv	2.82 (4)
C2···F1^v	3.327 (2)	C6···H10B	3.0200
C2···C7^xiii	3.5267 (13)	C6···H10B^ii	3.0200
C4···C6^xii	3.3384 (9)	C8···H10A^xiii	2.9100
C4···C6^xiii	3.3384 (9)	C8···H10A^x	2.9100
C4···C7^x	3.5303 (13)	C10···H8^vi	2.9900
C4···C7^xiii	3.5303 (13)	C10···H8^vii	2.9900
C4···C6^xi	3.3384 (9)	C10···H6	3.0000
C4···C6^x	3.3384 (9)	H2···H10C	2.5200
C4···C7^xi	3.5303 (13)	H2···H10C^ii	2.5200
C4···C7^xii	3.5303 (13)	H2···F1^v	2.8300
C5···C8^x	3.5319 (13)	H2···F1^xvi	2.8300
C5···C7^xii	3.5034 (13)	H3···N3^xiv	1.76 (5)
C5···C7^xiii	3.5034 (13)	H3···C2^xiv	2.76 (5)
C5···C8^xiii	3.5319 (13)	H3···C4^xiv	2.82 (4)
C5···C7^xi	3.5034 (13)	H3···N3^xv	1.76 (5)
C5···C8^xii	3.5319 (13)	H3···C2^xv	2.76 (5)
C5···C8^xi	3.5319 (13)	H3···C4^xv	2.82 (4)
C5···C7^x	3.5034 (13)	H6···C10	3.0000
C6···C4^xiii	3.3384 (9)	H6···F2	2.5200
C6···C9^x	3.5335 (13)	H6···F2	2.5200
C6···C4^x	3.3384 (9)	H7···F2^ix	2.5400
C6···C9^xi	3.5335 (13)	H7···F2^viii	2.5400
C6···C9^xiii	3.5335 (13)	H8···H10A^xiii	2.6000
C6···C4^xi	3.3384 (9)	H8···F1^xvii	2.7300
C6···C4^xii	3.3384 (9)	H8···F1^xviii	2.7300
C6···C9^xii	3.5335 (13)	H8···C10^xviii	2.9900
C7···C4^xiii	3.5303 (13)	H8···C10^xvii	2.9900
C7···C4^xii	3.5303 (13)	H8···H10A^x	2.6000
C7···C4^xi	3.5303 (13)	H10A···F1^ii	2.8300
C7···C2^xii	3.5267 (13)	H10A···H8^xi	2.6000
C7···C4^x	3.5303 (13)	H10A···C8^xiii	2.9100
C7···C2^xi	3.5267 (13)	H10A···C8^xi	2.9100
C7···C5^xi	3.5034 (13)	H10A···H8^xiii	2.6000
C7···C5^xiii	3.5034 (13)	H10B···C6	3.0200
C7···C5^xii	3.5034 (13)	H10B···F1	2.6500
C7···C2^x	3.5267 (13)	H10C···F1^v	2.6700
C7···C2^xiii	3.5267 (13)	H10C···H2	2.5200
F1^iii—P1—F1^ii	91.52 (6)	N1—C5—C6	131.79 (16)
F2—P1—F2^i	180.00	C5—C6—C7	116.34 (17)
F1—P1—F2	89.76 (7)	C6—C7—C8	121.58 (18)
F1—P1—F1^i	91.52 (6)	C7—C8—C9	122.08 (17)
F1—P1—F2^i	90.25 (7)	C4—C9—C8	116.87 (17)
F1—P1—F1^iii	180.00	N1—C2—H2	124.00
F1—P1—F1^ii	88.48 (6)	N3—C2—H2	124.00
F1^i—P1—F2	90.25 (7)	C5—C6—H6	122.00
F1^ii—P1—F2^i	90.25 (7)	C7—C6—H6	122.00
F1^iii—P1—F2	90.25 (7)	C8—C7—H7	119.00
F1^ii—P1—F2	89.76 (7)	C6—C7—H7	119.00
F1^i—P1—F2^i	89.76 (7)	C7—C8—H8	119.00
F1^i—P1—F1^iii	88.48 (6)	C9—C8—H8	119.00
F1^i—P1—F1^ii	180.00	C8—C9—H9	122.00
F1^iii—P1—F2^i	89.76 (7)	C4—C9—H9	122.00
C2—N1—C10	126.30 (15)	N1—C10—H10A	109.00
C2—N1—C5	107.56 (15)	N1—C10—H10B	110.00
C5—N1—C10	126.13 (15)	N1—C10—H10C	109.00
C2—N3—C4	106.44 (15)	H10A—C10—H10B	109.00
C2—N3—H3	123 (3)	H10A—C10—H10C	109.00
C4—N3—H3	131 (3)	H10B—C10—H10C	109.00
N1—C2—N3	112.18 (16)	N1—C10—H10A^ii	109.00
C5—C4—C9	120.92 (17)	N1—C10—H10B^ii	110.00
N3—C4—C5	107.81 (15)	N1—C10—H10C^ii	109.00
N3—C4—C9	131.27 (17)	H10A^ii—C10—H10B^ii	109.00
C4—C5—C6	122.21 (16)	H10A^ii—C10—H10C^ii	109.00
N1—C5—C4	106.00 (15)	H10B^ii—C10—H10C^ii	109.00
C5—N1—C2—N3	0.00 (2)	C9—C4—C5—N1	−180.00 (2)
C10—N1—C2—N3	180.00 (2)	N3—C4—C5—N1	0.00 (2)
C2—N1—C5—C4	0.00 (2)	N3—C4—C9—C8	−180.00 (2)
C2—N1—C5—C6	−180.00 (2)	C5—C4—C9—C8	0.00 (2)
C10—N1—C5—C4	−180.00 (2)	C9—C4—C5—C6	0.00 (2)
C10—N1—C5—C6	0.00 (2)	C4—C5—C6—C7	0.00 (2)
C4—N3—C2—N1	0.00 (2)	N1—C5—C6—C7	−180.00 (2)
C2—N3—C4—C5	0.00 (2)	C5—C6—C7—C8	0.00 (2)
C2—N3—C4—C9	180.00 (2)	C6—C7—C8—C9	0.00 (2)
N3—C4—C5—C6	−180.00 (2)	C7—C8—C9—C4	0.00 (2)

Symmetry codes: (i) −x, y, −z+1; (ii) x, −y, z; (iii) −x, −y, −z+1; (iv) −x+1/2, y+1/2, −z+1; (v) −x+1/2, −y+1/2, −z+1; (vi) x, y, z+1; (vii) x, −y, z+1; (viii) −x, y, −z; (ix) −x, −y, −z; (x) −x+1/2, y+1/2, −z; (xi) −x+1/2, y−1/2, −z; (xii) −x+1/2, −y+1/2, −z; (xiii) −x+1/2, −y−1/2, −z; (xiv) −x+1, y, −z; (xv) −x+1, −y, −z; (xvi) −x+1/2, y−1/2, −z+1; (xvii) x, −y, z−1; (xviii) x, y, z−1.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3···N3^xiv	0.89 (5)	1.76 (5)	2.641 (2)	176 (5)
C6—H6···F2	0.95	2.52	3.463 (3)	171
C7—H7···F2^viii	0.95	2.54	3.428 (3)	156

Symmetry codes: (viii) −x, y, −z; (xiv) −x+1, y, −z.