Literature DB >> 21577989

(1R,2S,3R,5S)-5-(1H-Benzimidazol-2-yl)cyclo-hexane-1,2,3,5-tetraol mono-hydrate.

Ying Cai1.   

Abstract

In the crystal structure of the title compound, C(13)H(16)N(2)O(4)·H(2)O, inter-molecular N-H⋯O, O-H⋯O and O-H⋯N hydrogen bonds form an extensive three-dimensional network, consolidating the crystal packing. The cyclo-hexane ring adopts a chair conformation.

Entities:  

Year:  2009        PMID： 21577989      PMCID： PMC2970496          DOI： 10.1107/S1600536809037957

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN： 1600-5368


Related literature

For the crystal structures of related compounds, see: Li et al. (1998 ▶); Gallagher et al. (2001 ▶); Howarth & Hanlon (2001 ▶); Huang et al. (2003 ▶); Kazak et al. (2006 ▶). For ring-puckering parameters, see: Cremer & Pople (1975 ▶).

Experimental

Crystal data

C13H16N2O4·H2O M = 282.29 Orthorhombic, a = 8.9684 (14) Å b = 9.4809 (15) Å c = 15.278 (4) Å V = 1299.0 (4) Å3 Z = 4 Mo Kα radiation μ = 0.11 mm−1 T = 293 K 0.30 × 0.30 × 0.30 mm

Data collection

Rigaku Mercury CCD diffractometer Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 ▶) T min = 0.817, T max = 0.906 12121 measured reflections 1716 independent reflections 1646 reflections with I > 2σ(I) R int = 0.030

Refinement

R[F 2 > 2σ(F 2)] = 0.033 wR(F 2) = 0.079 S = 1.08 1716 reflections 253 parameters All H-atom parameters refined Δρmax = 0.14 e Å−3 Δρmin = −0.18 e Å−3 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: SHELXTL/PC (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXL97. Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809037957/bx2237sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536809037957/bx2237Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C13H16N2O4·H2OF(000) = 600
Mr = 282.29Dx = 1.443 Mg m−3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 3450 reflections
a = 8.9684 (14) Åθ = 2.6–27.4°
b = 9.4809 (15) ŵ = 0.11 mm−1
c = 15.278 (4) ÅT = 293 K
V = 1299.0 (4) Å3Prism, pink
Z = 40.30 × 0.30 × 0.30 mm
Rigaku Mercury CCD diffractometer1716 independent reflections
Radiation source: fine-focus sealed tube1646 reflections with I > 2σ(I)
graphiteRint = 0.030
Detector resolution: 13.6612 pixels mm-1θmax = 27.5°, θmin = 2.6°
ω scansh = −11→11
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)k = −12→12
Tmin = 0.817, Tmax = 0.906l = −18→19
12121 measured reflections
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.033All H-atom parameters refined
wR(F2) = 0.079w = 1/[σ2(Fo2) + (0.0412P)2 + 0.2437P] where P = (Fo2 + 2Fc2)/3
S = 1.08(Δ/σ)max < 0.001
1716 reflectionsΔρmax = 0.14 e Å−3
253 parametersΔρmin = −0.18 e Å−3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008)
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0476 (15)
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.
xyzUiso*/Ueq
O50.72771 (16)0.24370 (18)0.64625 (9)0.0354 (3)
C110.6615 (2)0.3526 (2)0.86815 (13)0.0301 (4)
O30.07767 (15)0.25080 (16)0.51676 (10)0.0348 (3)
O10.31588 (16)0.45480 (17)0.50248 (9)0.0356 (3)
N10.57765 (19)0.33374 (19)0.79210 (11)0.0348 (4)
N20.43215 (18)0.42648 (18)0.89530 (10)0.0292 (3)
O20.01088 (17)0.3204 (2)0.69454 (10)0.0435 (4)
C10.1920 (2)0.2640 (2)0.58171 (12)0.0276 (4)
C20.4434 (2)0.3787 (2)0.81175 (12)0.0286 (4)
C30.3703 (2)0.4282 (2)0.65804 (12)0.0280 (4)
C40.5722 (2)0.41153 (19)0.93338 (12)0.0264 (4)
C50.2540 (2)0.4136 (2)0.58515 (11)0.0258 (4)
C60.3142 (2)0.3786 (2)0.74770 (12)0.0266 (4)
C70.2462 (3)0.2298 (2)0.74082 (13)0.0347 (4)
C80.6284 (2)0.4454 (2)1.01561 (13)0.0332 (4)
C90.8684 (2)0.3580 (2)0.96474 (15)0.0368 (5)
C100.7779 (2)0.4184 (2)1.02923 (14)0.0351 (4)
C120.8121 (2)0.3239 (2)0.88366 (15)0.0371 (5)
C130.1264 (2)0.2240 (2)0.66954 (13)0.0340 (4)
O40.20679 (15)0.47505 (16)0.78330 (10)0.0363 (3)
H10.272 (2)0.196 (2)0.5665 (14)0.029 (5)*
H20.328 (3)0.161 (3)0.7259 (17)0.045 (7)*
H30.456 (3)0.376 (2)0.6402 (15)0.033 (6)*
H40.976 (3)0.341 (2)0.9775 (15)0.038 (6)*
H50.173 (3)0.477 (2)0.5973 (13)0.026 (5)*
H60.347 (3)0.459 (3)0.9186 (16)0.042 (7)*
H70.824 (3)0.440 (3)1.0846 (16)0.041 (6)*
H80.875 (3)0.290 (3)0.8364 (19)0.061 (8)*
H90.198 (3)0.206 (3)0.8007 (16)0.042 (6)*
H100.401 (3)0.527 (3)0.6663 (15)0.043 (7)*
H110.567 (3)0.488 (3)1.0588 (18)0.045 (7)*
H120.126 (3)0.252 (3)0.4704 (19)0.058 (9)*
H130.119 (3)0.445 (3)0.7643 (18)0.054 (8)*
H14−0.069 (3)0.299 (3)0.6691 (18)0.055 (8)*
H150.393 (3)0.403 (3)0.4937 (18)0.055 (8)*
H160.088 (3)0.123 (2)0.6650 (14)0.029 (6)*
H170.745 (4)0.156 (4)0.661 (2)0.074 (10)*
H180.673 (4)0.272 (4)0.695 (2)0.077 (10)*
U11U22U33U12U13U23
O50.0314 (7)0.0459 (9)0.0290 (7)0.0014 (7)0.0037 (6)−0.0055 (6)
C110.0283 (9)0.0381 (10)0.0239 (9)0.0032 (8)−0.0024 (7)−0.0007 (7)
O30.0279 (7)0.0504 (8)0.0260 (7)−0.0044 (7)−0.0035 (6)−0.0059 (7)
O10.0302 (7)0.0533 (9)0.0235 (7)−0.0023 (7)−0.0003 (6)0.0087 (6)
N10.0289 (8)0.0517 (10)0.0238 (8)0.0084 (8)−0.0033 (7)−0.0078 (7)
N20.0233 (7)0.0420 (9)0.0224 (8)0.0030 (7)−0.0015 (6)−0.0036 (7)
O20.0236 (7)0.0740 (11)0.0330 (8)−0.0094 (7)0.0042 (6)−0.0140 (8)
C10.0251 (8)0.0350 (9)0.0226 (8)0.0022 (8)−0.0019 (7)−0.0036 (7)
C20.0266 (9)0.0364 (9)0.0228 (9)0.0013 (8)0.0000 (7)−0.0028 (7)
C30.0236 (8)0.0362 (10)0.0240 (9)−0.0015 (8)−0.0020 (7)−0.0011 (7)
C40.0247 (8)0.0320 (8)0.0224 (9)−0.0004 (7)−0.0013 (7)0.0006 (7)
C50.0223 (8)0.0359 (9)0.0192 (8)0.0004 (8)0.0002 (7)0.0010 (7)
C60.0239 (8)0.0362 (9)0.0197 (8)0.0016 (7)−0.0004 (7)−0.0047 (7)
C70.0413 (11)0.0391 (10)0.0239 (9)−0.0045 (10)−0.0038 (8)0.0038 (8)
C80.0332 (9)0.0429 (10)0.0235 (9)0.0001 (9)−0.0019 (8)−0.0028 (8)
C90.0264 (9)0.0447 (11)0.0394 (11)0.0008 (9)−0.0063 (8)0.0066 (9)
C100.0341 (10)0.0412 (10)0.0300 (10)−0.0045 (9)−0.0109 (8)0.0034 (8)
C120.0273 (9)0.0486 (12)0.0355 (11)0.0068 (9)0.0003 (8)−0.0015 (9)
C130.0353 (10)0.0387 (11)0.0281 (10)−0.0111 (9)−0.0022 (8)−0.0012 (8)
O40.0248 (7)0.0507 (8)0.0335 (8)0.0058 (7)−0.0027 (6)−0.0141 (6)
O5—H170.88 (3)C3—C61.533 (3)
O5—H180.93 (4)C3—H30.95 (2)
C11—C41.395 (3)C3—H100.98 (3)
C11—N11.395 (2)C4—C81.391 (3)
C11—C121.398 (3)C5—H50.96 (2)
O3—C11.432 (2)C6—O41.435 (2)
O3—H120.83 (3)C6—C71.540 (3)
O1—C51.434 (2)C7—C131.531 (3)
O1—H150.86 (3)C7—H21.01 (3)
N1—C21.312 (2)C7—H91.04 (2)
N2—C21.358 (2)C8—C101.381 (3)
N2—C41.392 (2)C8—H110.95 (3)
N2—H60.90 (3)C9—C121.376 (3)
O2—C131.434 (3)C9—C101.399 (3)
O2—H140.84 (3)C9—H41.00 (2)
C1—C131.514 (3)C10—H70.96 (2)
C1—C51.524 (3)C12—H80.97 (3)
C1—H10.99 (2)C13—H161.02 (2)
C2—C61.517 (3)O4—H130.89 (3)
C3—C51.532 (2)
H17—O5—H1899 (3)C1—C5—H5108.0 (13)
C4—C11—N1109.71 (16)C3—C5—H5108.7 (12)
C4—C11—C12120.72 (19)O4—C6—C2105.52 (14)
N1—C11—C12129.55 (19)O4—C6—C3111.29 (16)
C1—O3—H12102.6 (19)C2—C6—C3109.00 (15)
C5—O1—H15107.0 (19)O4—C6—C7110.09 (16)
C2—N1—C11105.19 (16)C2—C6—C7110.33 (15)
C2—N2—C4106.96 (16)C3—C6—C7110.49 (15)
C2—N2—H6123.3 (16)C13—C7—C6111.08 (16)
C4—N2—H6129.7 (16)C13—C7—H2109.1 (15)
C13—O2—H14110 (2)C6—C7—H2108.6 (15)
O3—C1—C13108.30 (15)C13—C7—H9109.1 (15)
O3—C1—C5111.52 (15)C6—C7—H9107.7 (13)
C13—C1—C5110.17 (15)H2—C7—H9111 (2)
O3—C1—H1107.5 (12)C10—C8—C4116.39 (19)
C13—C1—H1109.1 (12)C10—C8—H11122.5 (16)
C5—C1—H1110.2 (12)C4—C8—H11121.1 (16)
N1—C2—N2113.06 (17)C12—C9—C10121.11 (19)
N1—C2—C6123.58 (17)C12—C9—H4119.5 (14)
N2—C2—C6123.37 (16)C10—C9—H4119.4 (14)
C5—C3—C6113.48 (15)C8—C10—C9122.24 (19)
C5—C3—H3107.0 (14)C8—C10—H7120.5 (16)
C6—C3—H3111.0 (14)C9—C10—H7117.3 (16)
C5—C3—H10111.7 (14)C9—C12—C11117.5 (2)
C6—C3—H10105.6 (14)C9—C12—H8122.3 (17)
H3—C3—H10107.9 (19)C11—C12—H8120.0 (17)
C8—C4—N2132.89 (18)O2—C13—C1110.91 (17)
C8—C4—C11122.02 (17)O2—C13—C7107.13 (16)
N2—C4—C11105.07 (16)C1—C13—C7110.40 (16)
O1—C5—C1111.36 (15)O2—C13—H16111.8 (13)
O1—C5—C3110.63 (14)C1—C13—H16107.9 (13)
C1—C5—C3110.96 (15)C7—C13—H16108.7 (13)
O1—C5—H5107.1 (12)C6—O4—H13105.7 (18)
C4—C11—N1—C2−0.5 (2)N1—C2—C6—C779.5 (2)
C12—C11—N1—C2−179.1 (2)N2—C2—C6—C7−101.0 (2)
C11—N1—C2—N20.2 (2)C5—C3—C6—O4−71.7 (2)
C11—N1—C2—C6179.75 (17)C5—C3—C6—C2172.34 (15)
C4—N2—C2—N10.2 (2)C5—C3—C6—C750.9 (2)
C4—N2—C2—C6−179.36 (17)O4—C6—C7—C1369.8 (2)
C2—N2—C4—C8178.1 (2)C2—C6—C7—C13−174.09 (16)
C2—N2—C4—C11−0.5 (2)C3—C6—C7—C13−53.5 (2)
N1—C11—C4—C8−178.15 (18)N2—C4—C8—C10−178.0 (2)
C12—C11—C4—C80.6 (3)C11—C4—C8—C100.4 (3)
N1—C11—C4—N20.6 (2)C4—C8—C10—C9−1.0 (3)
C12—C11—C4—N2179.4 (2)C12—C9—C10—C80.7 (3)
O3—C1—C5—O1−59.24 (19)C10—C9—C12—C110.3 (3)
C13—C1—C5—O1−179.53 (15)C4—C11—C12—C9−0.9 (3)
O3—C1—C5—C3177.05 (15)N1—C11—C12—C9177.6 (2)
C13—C1—C5—C356.76 (19)O3—C1—C13—O2−64.01 (19)
C6—C3—C5—O1−177.00 (16)C5—C1—C13—O258.20 (19)
C6—C3—C5—C1−52.9 (2)O3—C1—C13—C7177.41 (16)
N1—C2—C6—O4−161.58 (19)C5—C1—C13—C7−60.4 (2)
N2—C2—C6—O417.9 (2)C6—C7—C13—O2−61.7 (2)
N1—C2—C6—C3−42.0 (3)C6—C7—C13—C159.1 (2)
N2—C2—C6—C3137.55 (19)
D—H···AD—HH···AD···AD—H···A
N2—H6···O1i0.90 (3)2.11 (3)2.983 (2)164 (2)
O3—H12···O5ii0.83 (3)2.00 (3)2.831 (2)176 (3)
O4—H13···O20.89 (3)1.87 (3)2.660 (2)148 (3)
O2—H14···O5iii0.84 (3)1.93 (3)2.743 (2)163 (3)
O1—H15···O3iv0.86 (3)2.21 (3)3.066 (2)172 (3)
O5—H17···O4v0.88 (3)1.96 (4)2.827 (2)169 (3)
O5—H18···N10.93 (4)1.81 (4)2.740 (2)176 (3)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯AD⋯AD—H⋯A
N2—H6⋯O1i0.90 (3)2.11 (3)2.983 (2)164 (2)
O3—H12⋯O5ii0.83 (3)2.00 (3)2.831 (2)176 (3)
O4—H13⋯O20.89 (3)1.87 (3)2.660 (2)148 (3)
O2—H14⋯O5iii0.84 (3)1.93 (3)2.743 (2)163 (3)
O1—H15⋯O3iv0.86 (3)2.21 (3)3.066 (2)172 (3)
O5—H17⋯O4v0.88 (3)1.96 (4)2.827 (2)169 (3)
O5—H18⋯N10.93 (4)1.81 (4)2.740 (2)176 (3)

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .

  2 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  Intermolecular interactions in two (ferrocenylmethyl)benzimidazoles incorporating the 4-MeOC6H4 and 3,4-(MeO)2C6H3 groups: analysis of MeO-C-C distortions from ideal 120 degrees geometry.

Authors:  J F Gallagher; K Hanlon; J Howarth
Journal:  Acta Crystallogr C       Date:  2001-12-06       Impact factor: 1.172
  2 in total

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