5-Nitro-2-trifluoro­methyl-1H-benzimidazole monohydrate

Liu, M.-L.

doi:10.1107/S1600536812017060

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 68| Part 5| May 2012| Page o1487

doi:10.1107/S1600536812017060

Open

access

5-Nitro-2-trifluoromethyl-1H-benzimidazole monohydrate

Ming-Liang Liu ^a ^*

^aCollege of Chemistry and Chemical Engineering, Southeast University, Nanjing 210096, People's Republic of China
^*Correspondence e-mail: jgsdxlml@163.com

(Received 16 March 2012; accepted 18 April 2012; online 21 April 2012)

In the crystal structure of the title compound, C₈H₄F₃N₃O₂·H₂O, the main molecule and the water molecule are linked by an N—H⋯O hydrogen bond. O—H⋯N, O—H⋯O and C—H⋯O hydrogen bonds further link the molecules into sheets.

Related literature

The title compound was studied as part of a search for ferroelectric complexes. For background to ferroelectric complexes, see: Zhang et al. (2009 , 2010 ); Ye et al. (2009 ). For related structures, see: Liu (2011a ,b ).

Experimental

Crystal data

C₈H₄F₃N₃O₂·H₂O
M_r = 249.16
Monoclinic, P 2₁ /n
a = 7.6209 (15) Å
b = 10.393 (2) Å
c = 13.093 (3) Å
β = 97.63 (3)°
V = 1027.9 (4) Å³
Z = 4
Mo Kα radiation
μ = 0.16 mm⁻¹
T = 293 K
0.36 × 0.32 × 0.28 mm

Data collection

Rigaku Mercury2 diffractometer
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 ) T_min = 0.903, T_max = 0.921
10402 measured reflections
2344 independent reflections
1451 reflections with I > 2σ(I)
R_int = 0.051

Refinement

R[F² > 2σ(F²)] = 0.071
wR(F²) = 0.221
S = 1.05
2344 reflections
154 parameters
H-atom parameters constrained
Δρ_max = 0.59 e Å⁻³
Δρ_min = −0.32 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯O3	0.86	1.90	2.740 (3)	166
O3—H3A⋯N2ⁱ	0.92	1.96	2.872 (3)	169
O3—H3B⋯O2ⁱⁱ	0.76	2.30	3.050 (4)	170
C6—H6⋯O1ⁱⁱ	0.93	2.55	3.380 (4)	148
Symmetry codes: (i) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]$ ; (ii) $[x-{\script{1\over 2}}, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536812017060/go2048sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812017060/go2048Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812017060/go2048Isup3.cml

checkCIF report

Comment top

Recently much attention has been devoted to finding ferroelectric complexes. Ferroelectric materials that exhibit reversible electric polarization in response to an external electric field have found many applications such as nonvolatile memory storage, electronics and optics. The freezing of a certain functional group at low temperature forces significant orientational motions of the guest molecules and thus induces the formation of the ferroelectric phase. (Zhang et al. 2009; Ye et al. 2009; Zhang et al. 2010.). The title compound has been synthesized to investigate these properties.

The asymmetric unit of the title compound consists of one 5-nitro-2-trifluoromethylbenzimidazole molecule and one water molecule, (Figure 1), linked by the N1···H1A···O3 hydrogen bond, Table 1. The O3—H3A···.N2(x-1/2, -y+3/2, z-1/2), O3—H3B···O2(x-1/2, -y+1/2, z-1/2) and C6—H6···O1(x-1/2, -y+1/2, z-1/2), Table 1, intermolecular hydrogen bonds link the molecules to form sheets.

Related literature top

The title compound was studied as part of a search for ferroelectric complexes. For background to ferroelectric complexes, see: Zhang et al. (2009, 2010); Ye et al. (2009). For related structures, see: Liu (2011a,b).

Experimental top

5-nitro-2-trifluoromethylbenzimidazole was dissolved in ethanol to give a solution without any precipitate while stirring at the ambient temperature. Single crystals suitable for X-ray structure analysis were obtained by the slow evaporation of the above solution after 5 days in air.

Computing details top

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of the title compound, showing the atomic numbering scheme with 30% probability displacement ellipsoids.
	Fig. 2. View of the sheet formed by the hydrogen bonding. Hydrogen atoms not involved in the hydrogen bonding are omitted for clarity. The labelled C, N and O atoms lie in the asymmetric unit.

5-Nitro-2-trifluoromethyl-1H-benzimidazole monohydrate top

Crystal data top

C₈H₄F₃N₃O₂·H₂O	Z = 4
M_r = 249.16	F(000) = 504
Monoclinic, P2₁/n	D_x = 1.610 Mg m⁻³
Hall symbol: -P 2yn	Mo Kα radiation, λ = 0.71073 Å
a = 7.6209 (15) Å	θ = 3.4–27.5°
b = 10.393 (2) Å	µ = 0.16 mm⁻¹
c = 13.093 (3) Å	T = 293 K
β = 97.63 (3)°	Block, colourless
V = 1027.9 (4) Å³	0.36 × 0.32 × 0.28 mm

Data collection top

Rigaku Mercury2 diffractometer	2344 independent reflections
Radiation source: fine-focus sealed tube	1451 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.051
CCD_Profile_fitting scans	θ_max = 27.5°, θ_min = 3.1°
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	h = −9→9
T_min = 0.903, T_max = 0.921	k = −13→13
10402 measured reflections	l = −16→16

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)] = 0.071	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.221	H-atom parameters constrained
S = 1.05	w = 1/[σ²(F_o²) + (0.1019P)² + 0.6421P] where P = (F_o² + 2F_c²)/3
2344 reflections	(Δ/σ)_max < 0.001
154 parameters	Δρ_max = 0.59 e Å⁻³
0 restraints	Δρ_min = −0.32 e Å⁻³

Crystal data top

C₈H₄F₃N₃O₂·H₂O	V = 1027.9 (4) Å³
M_r = 249.16	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 7.6209 (15) Å	µ = 0.16 mm⁻¹
b = 10.393 (2) Å	T = 293 K
c = 13.093 (3) Å	0.36 × 0.32 × 0.28 mm
β = 97.63 (3)°

Data collection top

Rigaku Mercury2 diffractometer	2344 independent reflections
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	1451 reflections with I > 2σ(I)
T_min = 0.903, T_max = 0.921	R_int = 0.051
10402 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.071	0 restraints
wR(F²) = 0.221	H-atom parameters constrained
S = 1.05	Δρ_max = 0.59 e Å⁻³
2344 reflections	Δρ_min = −0.32 e Å⁻³
154 parameters

Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
F1	0.7199 (4)	0.8890 (3)	0.31003 (18)	0.1071 (10)
F2	0.7951 (5)	0.9620 (2)	0.4602 (3)	0.1403 (15)
F3	0.5316 (4)	0.9177 (3)	0.4078 (3)	0.1320 (13)
O1	0.9829 (5)	0.3172 (3)	0.7630 (3)	0.0971 (11)
O2	0.8506 (5)	0.1639 (3)	0.6747 (3)	0.1086 (12)
N1	0.6638 (3)	0.6404 (2)	0.38970 (18)	0.0471 (6)
H1A	0.6092	0.6413	0.3279	0.057*
N2	0.8035 (3)	0.7156 (2)	0.53963 (18)	0.0469 (6)
N3	0.8922 (4)	0.2768 (3)	0.6865 (3)	0.0687 (9)
C1	0.7950 (4)	0.5815 (3)	0.5434 (2)	0.0414 (7)
C2	0.8576 (4)	0.4973 (3)	0.6230 (2)	0.0493 (7)
H2	0.9157	0.5264	0.6857	0.059*
C3	0.7071 (4)	0.5333 (3)	0.4496 (2)	0.0426 (7)
C4	0.8283 (4)	0.3683 (3)	0.6032 (2)	0.0507 (8)
C5	0.7237 (4)	0.7440 (3)	0.4469 (2)	0.0449 (7)
C6	0.6781 (4)	0.4023 (3)	0.4317 (2)	0.0517 (8)
H6	0.6194	0.3722	0.3695	0.062*
C7	0.7404 (4)	0.3194 (3)	0.5103 (3)	0.0566 (8)
H7	0.7242	0.2311	0.5018	0.068*
C8	0.6956 (5)	0.8789 (3)	0.4077 (3)	0.0575 (8)
O3	0.4481 (4)	0.6193 (2)	0.20564 (17)	0.0755 (9)
H3A	0.4159	0.6728	0.1499	0.113*
H3B	0.4169	0.5518	0.1909	0.113*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
F1	0.182 (3)	0.0760 (16)	0.0689 (15)	0.0252 (17)	0.0363 (17)	0.0271 (13)
F2	0.216 (4)	0.0534 (15)	0.126 (2)	−0.0328 (19)	−0.072 (2)	0.0178 (15)
F3	0.113 (2)	0.090 (2)	0.203 (3)	0.0460 (17)	0.059 (2)	0.063 (2)
O1	0.115 (3)	0.081 (2)	0.084 (2)	0.0147 (18)	−0.0250 (19)	0.0302 (17)
O2	0.141 (3)	0.0490 (17)	0.131 (3)	0.0068 (18)	−0.002 (2)	0.0273 (17)
N1	0.0566 (15)	0.0497 (15)	0.0322 (12)	−0.0006 (12)	−0.0049 (10)	−0.0002 (10)
N2	0.0561 (15)	0.0411 (13)	0.0406 (13)	−0.0014 (11)	−0.0048 (11)	−0.0018 (10)
N3	0.075 (2)	0.0540 (19)	0.077 (2)	0.0149 (16)	0.0096 (17)	0.0202 (16)
C1	0.0439 (15)	0.0405 (15)	0.0387 (14)	−0.0014 (12)	0.0009 (12)	−0.0026 (12)
C2	0.0520 (17)	0.0517 (18)	0.0412 (15)	−0.0007 (14)	−0.0047 (13)	0.0020 (13)
C3	0.0439 (15)	0.0479 (17)	0.0355 (14)	−0.0031 (12)	0.0030 (11)	−0.0035 (12)
C4	0.0540 (17)	0.0450 (17)	0.0532 (18)	0.0084 (14)	0.0077 (14)	0.0076 (14)
C5	0.0513 (16)	0.0460 (16)	0.0363 (14)	0.0009 (13)	0.0015 (12)	−0.0007 (12)
C6	0.0626 (19)	0.0472 (18)	0.0448 (16)	−0.0064 (14)	0.0050 (14)	−0.0128 (13)
C7	0.066 (2)	0.0400 (17)	0.065 (2)	−0.0043 (15)	0.0136 (16)	−0.0068 (15)
C8	0.067 (2)	0.0504 (19)	0.0530 (19)	0.0026 (16)	0.0013 (16)	0.0036 (16)
O3	0.115 (2)	0.0493 (13)	0.0507 (14)	0.0082 (13)	−0.0307 (14)	−0.0022 (11)

Geometric parameters (Å, º) top

F1—C8	1.320 (4)	C1—C3	1.410 (4)
F2—C8	1.287 (4)	C2—C4	1.378 (5)
F3—C8	1.313 (4)	C2—H2	0.9300
O1—N3	1.214 (4)	C3—C6	1.394 (4)
O2—N3	1.219 (4)	C4—C7	1.403 (5)
N1—C5	1.355 (4)	C5—C8	1.499 (4)
N1—C3	1.377 (4)	C6—C7	1.377 (5)
N1—H1A	0.8596	C6—H6	0.9300
N2—C5	1.317 (4)	C7—H7	0.9300
N2—C1	1.397 (4)	O3—H3A	0.9240
N3—C4	1.481 (4)	O3—H3B	0.7573
C1—C2	1.396 (4)

C5—N1—C3	106.8 (2)	C7—C4—N3	118.6 (3)
C5—N1—H1A	126.6	N2—C5—N1	114.3 (3)
C3—N1—H1A	126.5	N2—C5—C8	123.5 (3)
C5—N2—C1	103.8 (2)	N1—C5—C8	122.1 (3)
O1—N3—O2	123.2 (3)	C7—C6—C3	117.0 (3)
O1—N3—C4	118.7 (3)	C7—C6—H6	121.5
O2—N3—C4	118.0 (4)	C3—C6—H6	121.5
C2—C1—N2	129.8 (3)	C6—C7—C4	119.9 (3)
C2—C1—C3	120.2 (3)	C6—C7—H7	120.1
N2—C1—C3	110.0 (2)	C4—C7—H7	120.1
C4—C2—C1	116.0 (3)	F2—C8—F3	106.7 (4)
C4—C2—H2	122.0	F2—C8—F1	108.4 (3)
C1—C2—H2	122.0	F3—C8—F1	103.5 (3)
N1—C3—C6	132.3 (3)	F2—C8—C5	113.4 (3)
N1—C3—C1	105.0 (2)	F3—C8—C5	112.3 (3)
C6—C3—C1	122.7 (3)	F1—C8—C5	111.9 (3)
C2—C4—C7	124.3 (3)	H3A—O3—H3B	108.4
C2—C4—N3	117.2 (3)

C5—N2—C1—C2	−179.8 (3)	C1—N2—C5—N1	0.0 (3)
C5—N2—C1—C3	−0.1 (3)	C1—N2—C5—C8	178.3 (3)
N2—C1—C2—C4	179.8 (3)	C3—N1—C5—N2	0.1 (3)
C3—C1—C2—C4	0.2 (4)	C3—N1—C5—C8	−178.2 (3)
C5—N1—C3—C6	179.5 (3)	N1—C3—C6—C7	−180.0 (3)
C5—N1—C3—C1	−0.2 (3)	C1—C3—C6—C7	−0.3 (5)
C2—C1—C3—N1	179.9 (3)	C3—C6—C7—C4	0.1 (5)
N2—C1—C3—N1	0.2 (3)	C2—C4—C7—C6	0.3 (5)
C2—C1—C3—C6	0.1 (4)	N3—C4—C7—C6	179.4 (3)
N2—C1—C3—C6	−179.5 (3)	N2—C5—C8—F2	17.5 (5)
C1—C2—C4—C7	−0.5 (5)	N1—C5—C8—F2	−164.4 (3)
C1—C2—C4—N3	−179.6 (3)	N2—C5—C8—F3	−103.5 (4)
O1—N3—C4—C2	−7.8 (5)	N1—C5—C8—F3	74.6 (4)
O2—N3—C4—C2	172.1 (3)	N2—C5—C8—F1	140.6 (3)
O1—N3—C4—C7	173.0 (3)	N1—C5—C8—F1	−41.3 (4)
O2—N3—C4—C7	−7.0 (5)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O3	0.86	1.90	2.740 (3)	166
O3—H3A···N2ⁱ	0.92	1.96	2.872 (3)	169
O3—H3B···O2ⁱⁱ	0.76	2.30	3.050 (4)	170
C6—H6···O1ⁱⁱ	0.93	2.55	3.380 (4)	148

Symmetry codes: (i) x−1/2, −y+3/2, z−1/2; (ii) x−1/2, −y+1/2, z−1/2.

Experimental details

Crystal data
Chemical formula	C₈H₄F₃N₃O₂·H₂O
M_r	249.16
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	293
a, b, c (Å)	7.6209 (15), 10.393 (2), 13.093 (3)
β (°)	97.63 (3)
V (Å³)	1027.9 (4)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.16
Crystal size (mm)	0.36 × 0.32 × 0.28

Data collection
Diffractometer	Rigaku Mercury2 diffractometer
Absorption correction	Multi-scan (CrystalClear; Rigaku, 2005)
T_min, T_max	0.903, 0.921
No. of measured, independent and observed [I > 2σ(I)] reflections	10402, 2344, 1451
R_int	0.051
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.071, 0.221, 1.05
No. of reflections	2344
No. of parameters	154
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.59, −0.32

Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O3	0.86	1.90	2.740 (3)	166
O3—H3A···N2ⁱ	0.92	1.96	2.872 (3)	169
O3—H3B···O2ⁱⁱ	0.76	2.30	3.050 (4)	170
C6—H6···O1ⁱⁱ	0.93	2.55	3.380 (4)	148

Symmetry codes: (i) x−1/2, −y+3/2, z−1/2; (ii) x−1/2, −y+1/2, z−1/2.

Acknowledgements

The author thanks an anonymous advisor from the Ordered Matter Science Research Centre, Southeast University, for great help in the revision of this paper.

References

Liu, M.-L. (2011a). Acta Cryst. E67, o2821. Web of Science CSD CrossRef IUCr Journals Google Scholar
Liu, M.-L. (2011b). Acta Cryst. E67, o3473. Web of Science CSD CrossRef IUCr Journals Google Scholar
Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar
Ye, H. Y., Fu, D. W., Zhang, Y., Zhang, W., Xiong, R. G. & Huang, S. P. (2009). J. Am. Chem. Soc. 131, 42–43. Web of Science CSD CrossRef PubMed CAS Google Scholar
Zhang, W., Chen, L. Z., Xiong, R. G., Nakamura, T. & Huang, S. P. (2009). J. Am. Chem. Soc. 131, 12544–12545. Web of Science CSD CrossRef PubMed CAS Google Scholar
Zhang, W., Ye, H. Y., Cai, H. L., Ge, J. Z., Xiong, R. G. & Huang, S. P. (2010). J. Am. Chem. Soc. 132, 7300–7302. Web of Science CSD CrossRef CAS PubMed Google Scholar