1-(3-Carboxy­benz­yl)-1H-benzo[d]imidazol-3-ium nitrate monohydrate

Zhao, X.X.; Ma, J.P.; Huang, R.Q.; Dong, Y.B.

doi:10.1107/S1600536807025949

1-(3-Carboxybenzyl)-1H-benzo[d]imidazol-3-ium nitrate monohydrate

X. X. Zhao, J. P. Ma, R. Q. Huang and Y. B. Dong

In the crystal structure of the title compound, C₁₅H₁₃N₂O₂⁺·NO₃⁻·H₂O, O—H

O and N—H

O hydrogen bonds link the cations, the nitrate anions and the water molecules.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807025949/nc2033sup1.cif Contains datablocks I, global
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536807025949/nc2033Isup2.hkl Contains datablock I

CCDC reference: 657720

checkCIF report

Key indicators

Single-crystal X-ray study
T = 298 K
Mean (C-C) = 0.005 Å
R factor = 0.066
wR factor = 0.166
Data-to-parameter ratio = 12.2

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT154_ALERT_1_C The su's on the Cell Angles are Equal  (x 10000)        400 Deg.
PLAT244_ALERT_4_C Low   'Solvent' Ueq as Compared to Neighbors for         N3
PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ...          5
PLAT480_ALERT_4_C Long H...A H-Bond Reported H6A    ..  N3      ..       2.68 Ang.

Alert level G
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          3

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

   1 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
   2 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Comment top

The title compound was obtained by accident in the reaction of 2,5-bis(benzo[d]imidazol methylphenyl)-1,3,4-oxadiazol with nitric acid and its crystal structure was confirmed by X-ray diffraction. In the crystal structure the organic cations are connected via O—H···O hydrogen bonding between the carboxyl hydrogen atoms and the water molecules. The water molecules act also as donor for O—H···O hydrogen bonds to the carbonyl oxygen atoms and to the nitrate anions (Fig. 1 and Table 1). The N—H H atoms forms weak bifurcated hydrogen bond to the nitrate anions.

Experimental top

2,5-bis(benzo[d]imidazol methylphenyl)-1,3,4-oxadiazol (48.2 mg, 0.10 mmol), 0.04 ml of concentrated nitric acid and 5 ml of water were seeled in a teflon-lined stainless steel autoclave, heated at 150 degree for 40 h and cooled down to room

Structure description top

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SMART; data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 2000); software used to prepare material for publication: SHELXTL.

Figures top

Fig. 1. Crystal structure of I with labelling and displacement ellipsoids drawn at the 30% probability level. Intermolecular hydrogen bonding is shown as dashed lines. Symmetry codes: (i):1 - x,-y,2 - z; (ii): -x,1 - y,1 - z)

1-(3-Carboxybenzyl)-1H-benzo[d]imidazol-3-ium nitrate monohydrate top

Crystal data top

C₁₅H₁₃N₂O₂⁺·NO₃⁻·H₂O	Z = 2
M_r = 333.30	F(000) = 348
Triclinic, P1	D_x = 1.442 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 7.473 (2) Å	Cell parameters from 884 reflections
b = 7.974 (2) Å	θ = 2.6–23.5°
c = 13.092 (4) Å	µ = 0.11 mm⁻¹
α = 80.201 (4)°	T = 298 K
β = 87.226 (4)°	Block, yellow
γ = 89.146 (4)°	0.39 × 0.17 × 0.16 mm
V = 767.8 (4) Å³

Data collection top

Bruker SMART CCD area-detector diffractometer	1892 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.016
Graphite monochromator	θ_max = 25.0°, θ_min = 2.6°
φ and ω scans	h = −6→8
3255 measured reflections	k = −9→9
2669 independent reflections	l = −14→15

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.066	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.166	H-atom parameters constrained
S = 1.07	w = 1/[σ²(F_o²) + (0.072P)² + 0.234P] where P = (F_o² + 2F_c²)/3
2669 reflections	(Δ/σ)_max < 0.001
218 parameters	Δρ_max = 0.29 e Å⁻³
3 restraints	Δρ_min = −0.16 e Å⁻³

Crystal data top

C₁₅H₁₃N₂O₂⁺·NO₃⁻·H₂O	γ = 89.146 (4)°
M_r = 333.30	V = 767.8 (4) Å³
Triclinic, P1	Z = 2
a = 7.473 (2) Å	Mo Kα radiation
b = 7.974 (2) Å	µ = 0.11 mm⁻¹
c = 13.092 (4) Å	T = 298 K
α = 80.201 (4)°	0.39 × 0.17 × 0.16 mm
β = 87.226 (4)°

Data collection top

Bruker SMART CCD area-detector diffractometer	1892 reflections with I > 2σ(I)
3255 measured reflections	R_int = 0.016
2669 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.066	3 restraints
wR(F²) = 0.166	H-atom parameters constrained
S = 1.07	Δρ_max = 0.29 e Å⁻³
2669 reflections	Δρ_min = −0.16 e Å⁻³
218 parameters

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

	x	y	z	U_iso*/U_eq
O5	0.0870 (4)	0.2889 (4)	0.7702 (2)	0.0833 (8)
O3	−0.0372 (4)	0.5364 (3)	0.7297 (2)	0.0791 (8)
C1	0.2502 (4)	0.2061 (4)	0.5525 (2)	0.0478 (8)
C2	0.3531 (4)	0.0568 (4)	0.6032 (2)	0.0418 (7)
C3	0.2819 (4)	−0.1032 (4)	0.6114 (2)	0.0489 (8)
H3	0.1680	−0.1158	0.5881	0.059*
C4	0.3772 (5)	−0.2447 (4)	0.6537 (3)	0.0571 (9)
H4	0.3288	−0.3528	0.6591	0.068*
C5	0.5468 (4)	−0.2241 (4)	0.6883 (2)	0.0511 (8)
H5	0.6122	−0.3194	0.7166	0.061*
C6	0.6202 (4)	−0.0643 (4)	0.6816 (2)	0.0415 (7)
C7	0.5228 (4)	0.0756 (4)	0.6377 (2)	0.0428 (7)
H7	0.5716	0.1837	0.6313	0.051*
C8	0.8047 (4)	−0.0442 (4)	0.7193 (2)	0.0495 (8)
H8A	0.8845	−0.1291	0.6966	0.059*
H8B	0.8506	0.0673	0.6889	0.059*
C9	0.8492 (4)	−0.2011 (4)	0.8964 (3)	0.0602 (9)
H9	0.8939	−0.2998	0.8753	0.072*
C10	0.7576 (4)	−0.0185 (5)	0.9952 (3)	0.0560 (9)
C11	0.7128 (5)	0.0675 (6)	1.0765 (3)	0.0736 (11)
H11	0.7212	0.0165	1.1455	0.088*
C12	0.6555 (5)	0.2319 (6)	1.0489 (3)	0.0853 (13)
H12	0.6264	0.2951	1.1010	0.102*
C13	0.6389 (5)	0.3082 (5)	0.9462 (3)	0.0795 (12)
H13	0.5981	0.4201	0.9313	0.095*
C14	0.6818 (5)	0.2214 (4)	0.8661 (3)	0.0613 (9)
H14	0.6705	0.2710	0.7971	0.074*
C15	0.7422 (4)	0.0575 (4)	0.8936 (2)	0.0461 (7)
N1	0.8026 (3)	−0.0630 (3)	0.83307 (19)	0.0473 (6)
N2	0.8239 (4)	−0.1808 (4)	0.9934 (2)	0.0656 (8)
H2A	0.8451	−0.2559	1.0469	0.079*
O1	0.1054 (3)	0.1933 (3)	0.51702 (19)	0.0648 (7)
O2	0.3318 (3)	0.3517 (3)	0.54908 (18)	0.0615 (6)
H2	0.2747	0.4280	0.5147	0.092*
O6	0.1746 (3)	0.6002 (3)	0.43115 (18)	0.0626 (6)
H6A	0.1330	0.5518	0.3831	0.094*
H6B	0.0926	0.6570	0.4572	0.094*
N3	0.0482 (4)	0.4312 (4)	0.7898 (2)	0.0619 (8)
O4	0.0916 (4)	0.4709 (3)	0.8734 (2)	0.0901 (9)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O5	0.099 (2)	0.0782 (18)	0.0726 (19)	0.0321 (16)	−0.0032 (14)	−0.0163 (14)
O3	0.106 (2)	0.0669 (16)	0.0624 (17)	0.0138 (15)	−0.0301 (15)	−0.0006 (13)
C1	0.0491 (19)	0.058 (2)	0.0396 (18)	0.0042 (16)	−0.0025 (14)	−0.0176 (14)
C2	0.0449 (17)	0.0519 (18)	0.0310 (16)	0.0026 (14)	0.0022 (12)	−0.0153 (13)
C3	0.0479 (18)	0.059 (2)	0.0425 (18)	−0.0013 (16)	0.0006 (13)	−0.0169 (15)
C4	0.066 (2)	0.053 (2)	0.053 (2)	−0.0115 (17)	0.0020 (16)	−0.0144 (16)
C5	0.061 (2)	0.0510 (19)	0.0411 (18)	0.0056 (16)	−0.0007 (14)	−0.0087 (14)
C6	0.0446 (17)	0.0498 (17)	0.0298 (16)	0.0023 (14)	0.0020 (12)	−0.0075 (13)
C7	0.0450 (17)	0.0503 (17)	0.0342 (16)	−0.0015 (14)	0.0015 (12)	−0.0111 (13)
C8	0.0470 (18)	0.0559 (18)	0.0448 (19)	0.0058 (15)	0.0006 (13)	−0.0080 (14)
C9	0.056 (2)	0.061 (2)	0.061 (2)	0.0052 (17)	−0.0157 (16)	0.0001 (18)
C10	0.0477 (19)	0.075 (2)	0.045 (2)	−0.0176 (17)	−0.0078 (14)	−0.0072 (17)
C11	0.063 (2)	0.110 (3)	0.048 (2)	−0.026 (2)	−0.0002 (17)	−0.013 (2)
C12	0.080 (3)	0.114 (4)	0.071 (3)	−0.028 (3)	0.021 (2)	−0.047 (3)
C13	0.086 (3)	0.076 (3)	0.080 (3)	−0.008 (2)	0.020 (2)	−0.031 (2)
C14	0.066 (2)	0.061 (2)	0.056 (2)	−0.0068 (18)	0.0057 (16)	−0.0129 (17)
C15	0.0408 (17)	0.0532 (19)	0.0440 (18)	−0.0103 (14)	−0.0014 (13)	−0.0065 (14)
N1	0.0440 (15)	0.0502 (15)	0.0466 (16)	0.0010 (12)	−0.0090 (11)	−0.0031 (12)
N2	0.0603 (18)	0.074 (2)	0.056 (2)	−0.0014 (16)	−0.0205 (14)	0.0121 (15)
O1	0.0537 (14)	0.0676 (15)	0.0794 (17)	0.0101 (12)	−0.0249 (12)	−0.0254 (12)
O2	0.0622 (15)	0.0528 (14)	0.0696 (17)	0.0026 (12)	−0.0157 (11)	−0.0076 (12)
O6	0.0566 (13)	0.0565 (13)	0.0749 (17)	0.0027 (11)	−0.0119 (11)	−0.0098 (11)
N3	0.0667 (19)	0.065 (2)	0.0504 (19)	0.0015 (16)	−0.0042 (14)	−0.0002 (15)
O4	0.133 (2)	0.0772 (18)	0.0630 (18)	0.0008 (17)	−0.0435 (16)	−0.0091 (14)

Geometric parameters (Å, º) top

O5—N3	1.232 (4)	C9—N1	1.314 (4)
O3—N3	1.240 (3)	C9—H9	0.9300
C1—O1	1.211 (3)	C10—C15	1.374 (4)
C1—O2	1.313 (3)	C10—N2	1.382 (4)
C1—C2	1.484 (4)	C10—C11	1.386 (5)
C2—C3	1.375 (4)	C11—C12	1.367 (5)
C2—C7	1.386 (4)	C11—H11	0.9300
C3—C4	1.375 (4)	C12—C13	1.389 (6)
C3—H3	0.9300	C12—H12	0.9300
C4—C5	1.387 (4)	C13—C14	1.375 (5)
C4—H4	0.9300	C13—H13	0.9300
C5—C6	1.382 (4)	C14—C15	1.371 (4)
C5—H5	0.9300	C14—H14	0.9300
C6—C7	1.379 (4)	C15—N1	1.402 (4)
C6—C8	1.507 (4)	N2—H2A	0.8600
C7—H7	0.9300	O2—H2	0.8200
C8—N1	1.471 (4)	O6—H6A	0.8642
C8—H8A	0.9700	O6—H6B	0.8499
C8—H8B	0.9700	N3—O4	1.249 (4)
C9—N2	1.312 (4)

O1—C1—O2	123.6 (3)	C15—C10—N2	106.6 (3)
O1—C1—C2	122.7 (3)	C15—C10—C11	121.5 (4)
O2—C1—C2	113.7 (3)	N2—C10—C11	131.9 (3)
C3—C2—C7	119.7 (3)	C12—C11—C10	115.8 (4)
C3—C2—C1	119.2 (3)	C12—C11—H11	122.1
C7—C2—C1	121.0 (3)	C10—C11—H11	122.1
C4—C3—C2	120.6 (3)	C11—C12—C13	122.6 (4)
C4—C3—H3	119.7	C11—C12—H12	118.7
C2—C3—H3	119.7	C13—C12—H12	118.7
C3—C4—C5	119.1 (3)	C14—C13—C12	121.2 (4)
C3—C4—H4	120.5	C14—C13—H13	119.4
C5—C4—H4	120.5	C12—C13—H13	119.4
C6—C5—C4	121.2 (3)	C15—C14—C13	116.3 (4)
C6—C5—H5	119.4	C15—C14—H14	121.9
C4—C5—H5	119.4	C13—C14—H14	121.9
C7—C6—C5	118.7 (3)	C14—C15—C10	122.6 (3)
C7—C6—C8	120.8 (3)	C14—C15—N1	131.2 (3)
C5—C6—C8	120.5 (3)	C10—C15—N1	106.2 (3)
C6—C7—C2	120.7 (3)	C9—N1—C15	107.8 (3)
C6—C7—H7	119.6	C9—N1—C8	125.4 (3)
C2—C7—H7	119.6	C15—N1—C8	126.8 (2)
N1—C8—C6	111.5 (2)	C9—N2—C10	108.6 (3)
N1—C8—H8A	109.3	C9—N2—H2A	125.7
C6—C8—H8A	109.3	C10—N2—H2A	125.7
N1—C8—H8B	109.3	C1—O2—H2	109.5
C6—C8—H8B	109.3	H6A—O6—H6B	110.3
H8A—C8—H8B	108.0	O5—N3—O3	121.9 (3)
N2—C9—N1	110.8 (3)	O5—N3—O4	119.7 (3)
N2—C9—H9	124.6	O3—N3—O4	118.3 (3)
N1—C9—H9	124.6

O1—C1—C2—C3	−0.5 (4)	C11—C12—C13—C14	−0.7 (6)
O2—C1—C2—C3	−179.9 (2)	C12—C13—C14—C15	−0.4 (5)
O1—C1—C2—C7	176.4 (3)	C13—C14—C15—C10	0.8 (5)
O2—C1—C2—C7	−3.0 (4)	C13—C14—C15—N1	−177.4 (3)
C7—C2—C3—C4	0.1 (4)	N2—C10—C15—C14	−179.3 (3)
C1—C2—C3—C4	177.1 (3)	C11—C10—C15—C14	−0.1 (5)
C2—C3—C4—C5	0.1 (4)	N2—C10—C15—N1	−0.6 (3)
C3—C4—C5—C6	0.5 (5)	C11—C10—C15—N1	178.5 (3)
C4—C5—C6—C7	−1.2 (4)	N2—C9—N1—C15	0.1 (3)
C4—C5—C6—C8	−179.9 (3)	N2—C9—N1—C8	−176.8 (3)
C5—C6—C7—C2	1.4 (4)	C14—C15—N1—C9	178.8 (3)
C8—C6—C7—C2	−180.0 (2)	C10—C15—N1—C9	0.3 (3)
C3—C2—C7—C6	−0.8 (4)	C14—C15—N1—C8	−4.4 (5)
C1—C2—C7—C6	−177.8 (2)	C10—C15—N1—C8	177.1 (3)
C7—C6—C8—N1	103.7 (3)	C6—C8—N1—C9	100.1 (3)
C5—C6—C8—N1	−77.7 (3)	C6—C8—N1—C15	−76.1 (3)
C15—C10—C11—C12	−0.9 (5)	N1—C9—N2—C10	−0.5 (4)
N2—C10—C11—C12	177.9 (3)	C15—C10—N2—C9	0.7 (3)
C10—C11—C12—C13	1.3 (6)	C11—C10—N2—C9	−178.3 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···O4ⁱ	0.86	1.91	2.735 (4)	159
N2—H2A···O5ⁱ	0.86	2.44	3.168 (4)	143
N2—H2A···N3ⁱ	0.86	2.51	3.352 (4)	168
O2—H2···O6	0.82	1.78	2.599 (3)	173
O6—H6A···O3ⁱⁱ	0.86	1.91	2.775 (3)	175
O6—H6A···N3ⁱⁱ	0.86	2.68	3.454 (4)	150
O6—H6B···O1ⁱⁱ	0.85	1.94	2.773 (3)	167

Symmetry codes: (i) −x+1, −y, −z+2; (ii) −x, −y+1, −z+1.

Experimental details

Crystal data
Chemical formula	C₁₅H₁₃N₂O₂⁺·NO₃⁻·H₂O
M_r	333.30
Crystal system, space group	Triclinic, P1
Temperature (K)	298
a, b, c (Å)	7.473 (2), 7.974 (2), 13.092 (4)
α, β, γ (°)	80.201 (4), 87.226 (4), 89.146 (4)
V (Å³)	767.8 (4)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.39 × 0.17 × 0.16

Data collection
Diffractometer	Bruker SMART CCD area-detector
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	3255, 2669, 1892
R_int	0.016
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.066, 0.166, 1.07
No. of reflections	2669
No. of parameters	218
No. of restraints	3
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.29, −0.16

Computer programs: SMART (Bruker, 2000), SMART, SAINT (Bruker, 2000), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Bruker, 2000), SHELXTL.