organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890
Volume 68| Part 5| May 2012| Page o1487

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

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[Zhang, W., Chen, L. Z., Xiong, R. G., Nakamura, T. & Huang, S. P. (2009). J. Am. Chem. Soc. 131, 12544-12545.], 2010[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.]); Ye et al. (2009[Ye, H. Y., Fu, D. W., Zhang, Y., Zhang, W., Xiong, R. G. & Huang, S. P. (2009). J. Am. Chem. Soc. 131, 42-43.]). For related structures, see: Liu (2011a[Liu, M.-L. (2011a). Acta Cryst. E67, o2821.],b[Liu, M.-L. (2011b). Acta Cryst. E67, o3473.]).

[Scheme 1]

Experimental

Crystal data
  • C8H4F3N3O2·H2O

  • Mr = 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[Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.903, Tmax = 0.921

  • 10402 measured reflections

  • 2344 independent reflections

  • 1451 reflections with I > 2σ(I)

  • Rint = 0.051

Refinement
  • R[F2 > 2σ(F2)] = 0.071

  • wR(F2) = 0.221

  • S = 1.05

  • 2344 reflections

  • 154 parameters

  • H-atom parameters constrained

  • Δρmax = 0.59 e Å−3

  • Δρmin = −0.32 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: PLATON (Spek, 2009)[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]; software used to prepare material for publication: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]).

Supporting information


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.

Refinement top

H atoms were placed in calculated positions (N—H = 0.86 Å; C—H = 0.93 Å and were assigned fixed [Uiso = 1.2Ueq and allowed to ride. The H atoms bonding to the water O atom were found in difference Fourier map and fixed in the positions and allowed to ride with a fixed [Uiso = 1.5Ueq. The final positions of the hydrogen atoms were checked on a difference Fourier map.

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
[Figure 1] Fig. 1. The molecular structure of the title compound, showing the atomic numbering scheme with 30% probability displacement ellipsoids.
[Figure 2] 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·H2OZ = 4
Mr = 249.16F(000) = 504
Monoclinic, P21/nDx = 1.610 Mg m3
Hall symbol: -P 2ynMo Kα radiation, λ = 0.71073 Å
a = 7.6209 (15) Åθ = 3.4–27.5°
b = 10.393 (2) ŵ = 0.16 mm1
c = 13.093 (3) ÅT = 293 K
β = 97.63 (3)°Block, colourless
V = 1027.9 (4) Å30.36 × 0.32 × 0.28 mm
Data collection top
Rigaku Mercury2
diffractometer
2344 independent reflections
Radiation source: fine-focus sealed tube1451 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.051
CCD_Profile_fitting scansθmax = 27.5°, θmin = 3.1°
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)
h = 99
Tmin = 0.903, Tmax = 0.921k = 1313
10402 measured reflectionsl = 1616
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.071Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.221H-atom parameters constrained
S = 1.05 w = 1/[σ2(Fo2) + (0.1019P)2 + 0.6421P]
where P = (Fo2 + 2Fc2)/3
2344 reflections(Δ/σ)max < 0.001
154 parametersΔρmax = 0.59 e Å3
0 restraintsΔρmin = 0.32 e Å3
Crystal data top
C8H4F3N3O2·H2OV = 1027.9 (4) Å3
Mr = 249.16Z = 4
Monoclinic, P21/nMo Kα radiation
a = 7.6209 (15) ŵ = 0.16 mm1
b = 10.393 (2) ÅT = 293 K
c = 13.093 (3) Å0.36 × 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)
Tmin = 0.903, Tmax = 0.921Rint = 0.051
10402 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0710 restraints
wR(F2) = 0.221H-atom parameters constrained
S = 1.05Δρmax = 0.59 e Å3
2344 reflectionsΔρmin = 0.32 e Å3
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
xyzUiso*/Ueq
F10.7199 (4)0.8890 (3)0.31003 (18)0.1071 (10)
F20.7951 (5)0.9620 (2)0.4602 (3)0.1403 (15)
F30.5316 (4)0.9177 (3)0.4078 (3)0.1320 (13)
O10.9829 (5)0.3172 (3)0.7630 (3)0.0971 (11)
O20.8506 (5)0.1639 (3)0.6747 (3)0.1086 (12)
N10.6638 (3)0.6404 (2)0.38970 (18)0.0471 (6)
H1A0.60920.64130.32790.057*
N20.8035 (3)0.7156 (2)0.53963 (18)0.0469 (6)
N30.8922 (4)0.2768 (3)0.6865 (3)0.0687 (9)
C10.7950 (4)0.5815 (3)0.5434 (2)0.0414 (7)
C20.8576 (4)0.4973 (3)0.6230 (2)0.0493 (7)
H20.91570.52640.68570.059*
C30.7071 (4)0.5333 (3)0.4496 (2)0.0426 (7)
C40.8283 (4)0.3683 (3)0.6032 (2)0.0507 (8)
C50.7237 (4)0.7440 (3)0.4469 (2)0.0449 (7)
C60.6781 (4)0.4023 (3)0.4317 (2)0.0517 (8)
H60.61940.37220.36950.062*
C70.7404 (4)0.3194 (3)0.5103 (3)0.0566 (8)
H70.72420.23110.50180.068*
C80.6956 (5)0.8789 (3)0.4077 (3)0.0575 (8)
O30.4481 (4)0.6193 (2)0.20564 (17)0.0755 (9)
H3A0.41590.67280.14990.113*
H3B0.41690.55180.19090.113*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
F10.182 (3)0.0760 (16)0.0689 (15)0.0252 (17)0.0363 (17)0.0271 (13)
F20.216 (4)0.0534 (15)0.126 (2)0.0328 (19)0.072 (2)0.0178 (15)
F30.113 (2)0.090 (2)0.203 (3)0.0460 (17)0.059 (2)0.063 (2)
O10.115 (3)0.081 (2)0.084 (2)0.0147 (18)0.0250 (19)0.0302 (17)
O20.141 (3)0.0490 (17)0.131 (3)0.0068 (18)0.002 (2)0.0273 (17)
N10.0566 (15)0.0497 (15)0.0322 (12)0.0006 (12)0.0049 (10)0.0002 (10)
N20.0561 (15)0.0411 (13)0.0406 (13)0.0014 (11)0.0048 (11)0.0018 (10)
N30.075 (2)0.0540 (19)0.077 (2)0.0149 (16)0.0096 (17)0.0202 (16)
C10.0439 (15)0.0405 (15)0.0387 (14)0.0014 (12)0.0009 (12)0.0026 (12)
C20.0520 (17)0.0517 (18)0.0412 (15)0.0007 (14)0.0047 (13)0.0020 (13)
C30.0439 (15)0.0479 (17)0.0355 (14)0.0031 (12)0.0030 (11)0.0035 (12)
C40.0540 (17)0.0450 (17)0.0532 (18)0.0084 (14)0.0077 (14)0.0076 (14)
C50.0513 (16)0.0460 (16)0.0363 (14)0.0009 (13)0.0015 (12)0.0007 (12)
C60.0626 (19)0.0472 (18)0.0448 (16)0.0064 (14)0.0050 (14)0.0128 (13)
C70.066 (2)0.0400 (17)0.065 (2)0.0043 (15)0.0136 (16)0.0068 (15)
C80.067 (2)0.0504 (19)0.0530 (19)0.0026 (16)0.0013 (16)0.0036 (16)
O30.115 (2)0.0493 (13)0.0507 (14)0.0082 (13)0.0307 (14)0.0022 (11)
Geometric parameters (Å, º) top
F1—C81.320 (4)C1—C31.410 (4)
F2—C81.287 (4)C2—C41.378 (5)
F3—C81.313 (4)C2—H20.9300
O1—N31.214 (4)C3—C61.394 (4)
O2—N31.219 (4)C4—C71.403 (5)
N1—C51.355 (4)C5—C81.499 (4)
N1—C31.377 (4)C6—C71.377 (5)
N1—H1A0.8596C6—H60.9300
N2—C51.317 (4)C7—H70.9300
N2—C11.397 (4)O3—H3A0.9240
N3—C41.481 (4)O3—H3B0.7573
C1—C21.396 (4)
C5—N1—C3106.8 (2)C7—C4—N3118.6 (3)
C5—N1—H1A126.6N2—C5—N1114.3 (3)
C3—N1—H1A126.5N2—C5—C8123.5 (3)
C5—N2—C1103.8 (2)N1—C5—C8122.1 (3)
O1—N3—O2123.2 (3)C7—C6—C3117.0 (3)
O1—N3—C4118.7 (3)C7—C6—H6121.5
O2—N3—C4118.0 (4)C3—C6—H6121.5
C2—C1—N2129.8 (3)C6—C7—C4119.9 (3)
C2—C1—C3120.2 (3)C6—C7—H7120.1
N2—C1—C3110.0 (2)C4—C7—H7120.1
C4—C2—C1116.0 (3)F2—C8—F3106.7 (4)
C4—C2—H2122.0F2—C8—F1108.4 (3)
C1—C2—H2122.0F3—C8—F1103.5 (3)
N1—C3—C6132.3 (3)F2—C8—C5113.4 (3)
N1—C3—C1105.0 (2)F3—C8—C5112.3 (3)
C6—C3—C1122.7 (3)F1—C8—C5111.9 (3)
C2—C4—C7124.3 (3)H3A—O3—H3B108.4
C2—C4—N3117.2 (3)
C5—N2—C1—C2179.8 (3)C1—N2—C5—N10.0 (3)
C5—N2—C1—C30.1 (3)C1—N2—C5—C8178.3 (3)
N2—C1—C2—C4179.8 (3)C3—N1—C5—N20.1 (3)
C3—C1—C2—C40.2 (4)C3—N1—C5—C8178.2 (3)
C5—N1—C3—C6179.5 (3)N1—C3—C6—C7180.0 (3)
C5—N1—C3—C10.2 (3)C1—C3—C6—C70.3 (5)
C2—C1—C3—N1179.9 (3)C3—C6—C7—C40.1 (5)
N2—C1—C3—N10.2 (3)C2—C4—C7—C60.3 (5)
C2—C1—C3—C60.1 (4)N3—C4—C7—C6179.4 (3)
N2—C1—C3—C6179.5 (3)N2—C5—C8—F217.5 (5)
C1—C2—C4—C70.5 (5)N1—C5—C8—F2164.4 (3)
C1—C2—C4—N3179.6 (3)N2—C5—C8—F3103.5 (4)
O1—N3—C4—C27.8 (5)N1—C5—C8—F374.6 (4)
O2—N3—C4—C2172.1 (3)N2—C5—C8—F1140.6 (3)
O1—N3—C4—C7173.0 (3)N1—C5—C8—F141.3 (4)
O2—N3—C4—C77.0 (5)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···O30.861.902.740 (3)166
O3—H3A···N2i0.921.962.872 (3)169
O3—H3B···O2ii0.762.303.050 (4)170
C6—H6···O1ii0.932.553.380 (4)148
Symmetry codes: (i) x1/2, y+3/2, z1/2; (ii) x1/2, y+1/2, z1/2.

Experimental details

Crystal data
Chemical formulaC8H4F3N3O2·H2O
Mr249.16
Crystal system, space groupMonoclinic, P21/n
Temperature (K)293
a, b, c (Å)7.6209 (15), 10.393 (2), 13.093 (3)
β (°) 97.63 (3)
V3)1027.9 (4)
Z4
Radiation typeMo Kα
µ (mm1)0.16
Crystal size (mm)0.36 × 0.32 × 0.28
Data collection
DiffractometerRigaku Mercury2
diffractometer
Absorption correctionMulti-scan
(CrystalClear; Rigaku, 2005)
Tmin, Tmax0.903, 0.921
No. of measured, independent and
observed [I > 2σ(I)] reflections
10402, 2344, 1451
Rint0.051
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.071, 0.221, 1.05
No. of reflections2344
No. of parameters154
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
N1—H1A···O30.861.902.740 (3)166
O3—H3A···N2i0.921.962.872 (3)169
O3—H3B···O2ii0.762.303.050 (4)170
C6—H6···O1ii0.932.553.380 (4)148
Symmetry codes: (i) x1/2, y+3/2, z1/2; (ii) x1/2, y+1/2, z1/2.
 

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

First citationLiu, M.-L. (2011a). Acta Cryst. E67, o2821.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationLiu, M.-L. (2011b). Acta Cryst. E67, o3473.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationRigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationYe, 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
First citationZhang, 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
First citationZhang, 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

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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 5| May 2012| Page o1487
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