6-Nitro­benzimidazolium dihydrogen phosphate 6-nitro­benzimidazole solvate dihydrate

In the crystal structure of the title compound, C₇H₆N₃O₂⁺·H₂PO₄⁻·C₇H₅N₃O₂·2H₂O, the components are connected through O—H...O, N—H...O and O—H...N hydrogen-bonding inter­actions, forming a sheet-like structure parallel to (101). Adjacent sheets are further linked together by strong O—H...O hydrogen-bonds involving the dihydrogenphosphate groups. π–π stacking inter­actions between neighbouring aromatic constituents [centroid–centroid distance 3.653 (3) Å] help to consolidate the crystal packing.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.041
• wR factor = 0.141
• Data-to-parameter ratio = 15.3

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT417_ALERT_2_B Short Inter D-H..H-D       H9B    ..  H10B    ..       2.04 Ang.

Alert level C
PLAT245_ALERT_2_C U(iso) H9A     Smaller than U(eq) O9      by ...       0.01 AngSq
PLAT245_ALERT_2_C U(iso) H9B     Smaller than U(eq) O9      by ...       0.01 AngSq
PLAT245_ALERT_2_C U(iso) H10A    Smaller than U(eq) O10     by ...       0.03 AngSq
PLAT245_ALERT_2_C U(iso) H10B    Smaller than U(eq) O10     by ...       0.03 AngSq
PLAT355_ALERT_3_C Long    O-H Bond (0.82A)   O6     -   H6A    ...       1.03 Ang.
PLAT910_ALERT_3_C Missing # of FCF Reflections Below Th(Min) .....          7
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.600          5
PLAT042_ALERT_1_C Calc. and Reported MoietyFormula Strings  Differ          ?
PLAT480_ALERT_4_C Long H...A H-Bond Reported H10B   ..  O3      ..       2.61 Ang.
PLAT737_ALERT_1_C D...A   Calc    3.107(5), Rep    3.106(2) ......       2.50 su-Ra
              O10  -O3      1.555   2.776
PLAT912_ALERT_4_C Missing # of FCF Reflections Above STh/L=  0.600         36

Alert level G
PLAT154_ALERT_1_G The su's on the Cell Angles are Equal  (x 10000)       3000 Deg.
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported   _diffrn_ambient_temperature        293 K

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

   5 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   5 ALERT type 2 Indicator that the structure model may be wrong or deficient
   3 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

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S1. Comment

Phosphates are of great interest because of their rich crystal chemistry and practical applications. Up to now, numerous inorganic metal phosphates have been reported (e.g. Benard et al., 1996; Jensen et al., 2000). Furthermore, various of these phosphates were synthesized by structure-orienting templates molecules, most ferquently amines (Sameski et al., 1993; Lii et al., 1998). Compared with these inorganic phosphates, the synthesis of non-metal phosphates was less well explored in the past decades (Dakhlaoui et al., 2007). Herein, we describe the synthesis and crystal structure of the title compound (I), a new non-metal phosphate with formula (C₇H₆N₃O₂)[H₂PO₄]^.(C₇H₅N₃O₂)^.2(H₂O)

As shown in Fig.1, the structure of (I) consists of one (C₇H₆N₃O₂)⁺ cation, one [H₂PO₄]^- anion, one (C₇H₅N₃O₂) solvent molecule and two H₂O molecules, viz. one imidazole molecule is protonated, one imidazole molecule acts as an unprotonated solvent and a dihydrogenphosphate group is present. The O—P—O angles are in the range 105.62 (11)—115.73 (13) °. The P—O bond lengths to the terminal O atoms are 1.500 (2) and 1.504 (2) Å while the P—OH bond lengths are considerably longer with 1.5591 (19) and 1.562 (2) Å.

As is well known, hydrogen bonding interactions play an important role in the formation and stability of low-dimensional structures. In the present structure, the [(C₇H₆N₃O₂)]⁺ cations, [H₂PO₄]^- anions, (C₇H₅N₃O₂) and H₂O molecules are linked together through hydrogen bonds: N1—H1A···O7, N5—H5B···O7; N2—H2A···O9, O6—H6A···N4, O9—H4A···O4, O9—H9B···O10, O10—H10B···O3 (Fig. 2), forming a two-dimensional sheetlike structure parallel to (101). Adjacent sheets are further linked together by strong H-bonding interactions [O5—H5A···O8, O10—H10A···O8, O10—H10B···O9]. π—π stacking interactions between neighboring 6-nitrobenzimidazole molecules with an interplanar distance of 3.653 (3) Å help to consolidate a three-dimensional supramolecular network structure (Fig. 3).

Related literature

For the preparation of inorganic metal phosphates, see: Benard et al. (1996); Jensen et al. (2000). For template synthesis of phosphates, see: Sameski et al. (1993); Lii et al. (1998). For phosphates with organic cations, see: Dakhlaoui et al. (2007).

S2. Experimental

The title compound was obtained by the reaction of phosphoric acid, 6-nitrobenzimidazole and methanol/distilled water under room temperature. Typically, a mixture of phosphoric acid (0.2 ml), analytically pure 6-nitrobenzimidazole (0.164 g) and methanol/distilled water (10 ml/10 ml) was stirred at room temperature before it was filtered. The final filtrate was allowed to evaporate slowly at room temperature for 7 days to obtain yellow crystals.

S3. Refinement

All H atoms associated with C atoms and N atoms were positioned geometrically and refined as riding model, with N–H = 0.86 Å, C–H_aromatic type = 0.93 Å, U_iso(H) = 1.2U_eq(N), U_iso(H) = 1.2U_eq(C). Hydrogen atoms attached to O5, O6, O9 and O10 were discernible from difference Fourier maps. Their U_iso(H) values were fixed at 0.05 Ų and their coordinates were not refined.

Computing details

Data collection: RAPID-AUTO (Rigaku, 1998); cell refinement: RAPID-AUTO (Rigaku, 1998); data reduction: Crystal Structure (Rigaku/MSC, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPII (Johnson, 1976) and DIAMOND (Brandenburg, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures

	Fig. 1. The molecular structure of the title compound, with the atomic numbering scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are shown as small spheres of arbitrary radius.
	Fig. 2. The layer structure of (C7H6N3O2)[H2PO4]^.(C7H5N3O2)^.2(H2O). Hydrogen bonds are indicated by dashed lines.
	Fig. 3. A packing diagram for the title compound, viewed along the a axis. Dashed lines indicate hydrogen bonds.

6-Nitrobenzimidazolium dihydrogen phosphate 6-nitrobenzimidazole solvate dihydrate

Crystal data

C7H6N3O2^+·H2PO4^−·C7H5N3O2·2H2O	Z = 2
Mr = 460.31	F(000) = 476
Triclinic, P1	Dx = 1.610 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 9.4683 (19) Å	Cell parameters from 6404 reflections
b = 9.990 (2) Å	θ = 3.1–27.5°
c = 11.407 (2) Å	µ = 0.22 mm^−1
α = 90.73 (3)°	T = 293 K
β = 107.10 (3)°	Platelet, yellow
γ = 111.66 (3)°	0.37 × 0.32 × 0.12 mm
V = 949.4 (3) Å^3

Data collection

Rigaku R-AXIS RAPID diffractometer	4286 independent reflections
Radiation source: fine-focus sealed tube	2827 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.021
ω scans	θmax = 27.5°, θmin = 3.1°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −12→12
Tmin = 0.924, Tmax = 0.975	k = −12→12
9332 measured reflections	l = −14→14

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)] = 0.041	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.141	H-atom parameters constrained
S = 1.14	w = 1/[σ^2(Fo^2) + (0.0532P)^2 + 0.7024P] where P = (Fo^2 + 2Fc^2)/3
4286 reflections	(Δ/σ)max = 0.005
280 parameters	Δρmax = 0.43 e Å^−3
0 restraints	Δρmin = −0.47 e Å^−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
P1	0.46015 (8)	0.77962 (7)	0.52850 (6)	0.03448 (19)
O1	1.0279 (3)	0.6110 (3)	0.1175 (3)	0.0759 (8)
N1	0.4441 (3)	0.4733 (2)	0.2701 (2)	0.0392 (5)
H1A	0.4368	0.4114	0.3221	0.047*
C1	0.6946 (3)	0.4893 (3)	0.2258 (2)	0.0336 (5)
H1B	0.7181	0.4226	0.2760	0.040*
O2	0.9605 (3)	0.4445 (3)	0.2308 (2)	0.0638 (6)
N2	0.3902 (3)	0.6274 (2)	0.1497 (2)	0.0385 (5)
H2A	0.3417	0.6800	0.1120	0.046*
C2	0.5632 (3)	0.5227 (3)	0.2149 (2)	0.0313 (5)
O3	1.1886 (3)	1.0612 (3)	0.1237 (3)	0.0771 (8)
N3	0.9352 (3)	0.5369 (3)	0.1686 (2)	0.0447 (6)
C3	0.5284 (3)	0.6217 (3)	0.1383 (2)	0.0317 (5)
O4	1.0632 (3)	1.1997 (3)	0.1303 (3)	0.0762 (8)
N4	1.0431 (3)	0.7285 (2)	0.4511 (2)	0.0379 (5)
C4	0.6251 (3)	0.6929 (3)	0.0684 (2)	0.0376 (6)
H4B	0.6011	0.7583	0.0168	0.045*
O5	0.4699 (3)	0.8359 (2)	0.40310 (18)	0.0489 (5)
H5A	0.4918	0.9324	0.4014	0.050*
N5	0.8298 (3)	0.7543 (2)	0.47608 (19)	0.0375 (5)
H5B	0.7499	0.7403	0.5024	0.045*
C5	0.7570 (3)	0.6616 (3)	0.0796 (2)	0.0376 (6)
H5C	0.8259	0.7070	0.0355	0.045*
O6	0.2931 (2)	0.6510 (2)	0.4983 (2)	0.0471 (5)
H6A	0.1868	0.6647	0.4826	0.050*
N6	1.0976 (3)	1.0955 (3)	0.1613 (2)	0.0492 (6)
C6	0.7888 (3)	0.5623 (3)	0.1566 (2)	0.0347 (6)
O7	0.5822 (2)	0.7132 (2)	0.57244 (19)	0.0456 (5)
C7	0.3444 (3)	0.5381 (3)	0.2287 (3)	0.0425 (6)
H7B	0.2539	0.5234	0.2518	0.051*
O8	0.4731 (3)	0.8988 (2)	0.61749 (16)	0.0435 (5)
C8	1.0885 (3)	0.9142 (3)	0.3032 (2)	0.0367 (6)
H8B	1.1769	0.9045	0.2902	0.044*
O9	0.2853 (3)	0.8166 (3)	0.0119 (2)	0.0625 (6)
H9A	0.2025	0.8421	0.0112	0.050*
H9B	0.3401	0.8590	−0.0339	0.050*
C9	1.0114 (3)	0.8331 (3)	0.3813 (2)	0.0320 (5)
O10	0.4652 (3)	0.9058 (3)	0.8556 (2)	0.0754 (8)
H10A	0.4652	0.8914	0.7771	0.050*
H10B	0.5564	0.9646	0.9008	0.050*
C10	0.8767 (3)	0.8494 (3)	0.3970 (2)	0.0322 (5)
C11	0.8168 (3)	0.9477 (3)	0.3391 (2)	0.0389 (6)
H11A	0.7279	0.9578	0.3508	0.047*
C12	0.8942 (3)	1.0293 (3)	0.2638 (2)	0.0401 (6)
H12A	0.8592	1.0976	0.2244	0.048*
C13	1.0254 (3)	1.0093 (3)	0.2469 (2)	0.0364 (6)
C14	0.9324 (3)	0.6863 (3)	0.5052 (2)	0.0387 (6)
H14A	0.9253	0.6161	0.5585	0.046*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
P1	0.0389 (4)	0.0324 (4)	0.0420 (4)	0.0175 (3)	0.0220 (3)	0.0148 (3)
O1	0.0584 (15)	0.097 (2)	0.104 (2)	0.0408 (15)	0.0564 (15)	0.0469 (16)
N1	0.0364 (12)	0.0418 (13)	0.0442 (13)	0.0156 (10)	0.0187 (10)	0.0156 (10)
C1	0.0338 (13)	0.0333 (13)	0.0338 (13)	0.0131 (11)	0.0109 (10)	0.0113 (10)
O2	0.0587 (14)	0.0820 (17)	0.0750 (16)	0.0482 (14)	0.0283 (12)	0.0319 (13)
N2	0.0416 (13)	0.0427 (13)	0.0403 (12)	0.0253 (11)	0.0146 (10)	0.0109 (10)
C2	0.0294 (12)	0.0323 (13)	0.0327 (13)	0.0109 (10)	0.0120 (10)	0.0063 (10)
O3	0.0843 (18)	0.103 (2)	0.0893 (18)	0.0559 (17)	0.0655 (16)	0.0499 (16)
N3	0.0375 (13)	0.0537 (15)	0.0484 (14)	0.0204 (12)	0.0182 (11)	0.0078 (11)
C3	0.0347 (13)	0.0311 (13)	0.0282 (12)	0.0131 (11)	0.0084 (10)	0.0037 (9)
O4	0.0911 (19)	0.0713 (16)	0.101 (2)	0.0464 (15)	0.0594 (16)	0.0566 (15)
N4	0.0334 (12)	0.0393 (12)	0.0444 (13)	0.0156 (10)	0.0151 (10)	0.0105 (10)
C4	0.0433 (15)	0.0337 (13)	0.0330 (13)	0.0130 (12)	0.0107 (11)	0.0087 (10)
O5	0.0798 (15)	0.0367 (10)	0.0441 (11)	0.0264 (11)	0.0341 (11)	0.0164 (8)
N5	0.0325 (12)	0.0453 (13)	0.0373 (12)	0.0135 (10)	0.0172 (9)	0.0084 (9)
C5	0.0366 (14)	0.0419 (15)	0.0325 (13)	0.0109 (12)	0.0144 (11)	0.0086 (11)
O6	0.0365 (11)	0.0321 (10)	0.0764 (14)	0.0126 (8)	0.0240 (10)	0.0171 (9)
N6	0.0469 (14)	0.0591 (16)	0.0500 (15)	0.0219 (13)	0.0252 (12)	0.0194 (12)
C6	0.0289 (13)	0.0423 (14)	0.0322 (13)	0.0149 (11)	0.0078 (10)	0.0036 (10)
O7	0.0405 (11)	0.0490 (11)	0.0649 (13)	0.0249 (9)	0.0316 (10)	0.0280 (10)
C7	0.0383 (15)	0.0491 (16)	0.0470 (16)	0.0212 (13)	0.0182 (12)	0.0106 (12)
O8	0.0659 (13)	0.0377 (10)	0.0380 (10)	0.0233 (10)	0.0281 (9)	0.0151 (8)
C8	0.0297 (13)	0.0420 (15)	0.0407 (14)	0.0125 (11)	0.0166 (11)	0.0042 (11)
O9	0.0635 (14)	0.0811 (16)	0.0725 (15)	0.0465 (13)	0.0389 (12)	0.0432 (12)
C9	0.0291 (12)	0.0320 (13)	0.0331 (13)	0.0088 (10)	0.0116 (10)	0.0031 (10)
O10	0.0840 (19)	0.100 (2)	0.0467 (13)	0.0308 (16)	0.0344 (13)	0.0136 (13)
C10	0.0298 (13)	0.0349 (13)	0.0319 (13)	0.0097 (11)	0.0133 (10)	0.0055 (10)
C11	0.0332 (14)	0.0465 (15)	0.0410 (15)	0.0189 (12)	0.0133 (11)	0.0054 (11)
C12	0.0376 (14)	0.0437 (15)	0.0426 (15)	0.0183 (12)	0.0148 (12)	0.0108 (11)
C13	0.0357 (14)	0.0355 (14)	0.0360 (14)	0.0090 (11)	0.0150 (11)	0.0075 (10)
C14	0.0367 (14)	0.0356 (14)	0.0417 (15)	0.0111 (12)	0.0132 (11)	0.0093 (11)

Geometric parameters (Å, º)

P1—O8	1.500 (2)	O5—H5A	0.9100
P1—O7	1.504 (2)	N5—C14	1.348 (4)
P1—O5	1.5591 (19)	N5—C10	1.364 (3)
P1—O6	1.562 (2)	N5—H5B	0.8600
O1—N3	1.221 (3)	C5—C6	1.391 (4)
N1—C7	1.315 (4)	C5—H5C	0.9300
N1—C2	1.388 (3)	O6—H6A	1.0287
N1—H1A	0.8600	N6—C13	1.463 (3)
C1—C2	1.376 (3)	C7—H7B	0.9300
C1—C6	1.378 (3)	C8—C13	1.371 (4)
C1—H1B	0.9300	C8—C9	1.396 (3)
O2—N3	1.221 (3)	C8—H8B	0.9300
N2—C7	1.328 (3)	O9—H9A	0.9074
N2—C3	1.374 (3)	O9—H9B	0.8512
N2—H2A	0.8600	C9—C10	1.405 (3)
C2—C3	1.393 (3)	O10—H10A	0.9048
O3—N6	1.215 (3)	O10—H10B	0.8438
N3—C6	1.467 (3)	C10—C11	1.389 (4)
C3—C4	1.394 (4)	C11—C12	1.373 (4)
O4—N6	1.228 (3)	C11—H11A	0.9300
N4—C14	1.310 (3)	C12—C13	1.395 (4)
N4—C9	1.388 (3)	C12—H12A	0.9300
C4—C5	1.367 (4)	C14—H14A	0.9300
C4—H4B	0.9300
O8—P1—O7	115.73 (13)	C6—C5—H5C	119.8
O8—P1—O5	109.95 (10)	P1—O6—H6A	123.8
O7—P1—O5	108.51 (11)	O3—N6—O4	122.7 (3)
O8—P1—O6	110.30 (12)	O3—N6—C13	118.9 (3)
O7—P1—O6	105.62 (11)	O4—N6—C13	118.4 (2)
O5—P1—O6	106.23 (13)	C1—C6—C5	124.3 (2)
C7—N1—C2	107.7 (2)	C1—C6—N3	117.6 (2)
C7—N1—H1A	126.2	C5—C6—N3	118.0 (2)
C2—N1—H1A	126.2	N1—C7—N2	110.9 (2)
C2—C1—C6	114.8 (2)	N1—C7—H7B	124.5
C2—C1—H1B	122.6	N2—C7—H7B	124.5
C6—C1—H1B	122.6	C13—C8—C9	115.7 (2)
C7—N2—C3	108.4 (2)	C13—C8—H8B	122.2
C7—N2—H2A	125.8	C9—C8—H8B	122.2
C3—N2—H2A	125.8	H9A—O9—H9B	116.1
C1—C2—N1	131.2 (2)	N4—C9—C8	130.5 (2)
C1—C2—C3	122.0 (2)	N4—C9—C10	109.0 (2)
N1—C2—C3	106.8 (2)	C8—C9—C10	120.4 (2)
O1—N3—O2	122.8 (3)	H10A—O10—H10B	110.3
O1—N3—C6	118.4 (2)	N5—C10—C11	132.1 (2)
O2—N3—C6	118.8 (2)	N5—C10—C9	105.6 (2)
N2—C3—C2	106.2 (2)	C11—C10—C9	122.3 (2)
N2—C3—C4	131.9 (2)	C12—C11—C10	117.3 (2)
C2—C3—C4	121.9 (2)	C12—C11—H11A	121.4
C14—N4—C9	104.8 (2)	C10—C11—H11A	121.4
C5—C4—C3	116.5 (2)	C11—C12—C13	119.7 (3)
C5—C4—H4B	121.8	C11—C12—H12A	120.1
C3—C4—H4B	121.8	C13—C12—H12A	120.1
P1—O5—H5A	115.9	C8—C13—C12	124.6 (2)
C14—N5—C10	107.1 (2)	C8—C13—N6	118.7 (2)
C14—N5—H5B	126.5	C12—C13—N6	116.7 (2)
C10—N5—H5B	126.5	N4—C14—N5	113.5 (2)
C4—C5—C6	120.4 (2)	N4—C14—H14A	123.3
C4—C5—H5C	119.8	N5—C14—H14A	123.3

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O7^i	0.86	1.74	2.600 (2)	179
N2—H2A···O9	0.86	1.92	2.752 (2)	164
O6—H6A···N4^ii	1.03	1.66	2.665 (2)	165
O5—H5A···O8^iii	0.91	1.62	2.531 (2)	174
N5—H5B···O7	0.86	1.91	2.773 (2)	176
O9—H9A···O3^ii	0.91	2.59	3.269 (2)	132
O9—H9A···O4^iv	0.91	2.43	3.161 (2)	137
O9—H9B···O10^v	0.85	1.92	2.754 (2)	165
O10—H10A···O8	0.91	1.85	2.740 (2)	169
O10—H10B···O9^iii	0.84	2.16	2.917 (2)	149
O10—H10B···O3^vi	0.84	2.61	3.106 (2)	119

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