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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 65| Part 5| May 2009| Page o1114

Cyclo­hexane-1,2,3,4,5-pentol

aDepartment of Physics, SMK Fomra Institute of Technology, Thaiyur, Chennai 603 103, India, bCAS in Botany, University of Madras, Guindy Campus, Chennai 600 025, India, and cDepartment of Physics, Presidency College (Autonomous), Chennai 600 005, India
*Correspondence e-mail: a_spandian@yahoo.com

(Received 10 March 2009; accepted 15 April 2009; online 25 April 2009)

In the title compound, C6H12O5, the cyclo­hexane ring adopts a chair conformation. The absolute configuration is not defined. However, the relative configuration can be assigned as 1R*,3R*,4S*,S*. In the crystal structure, mol­ecules are linked by strong inter­molecular O—H⋯O hydrogen bonds, producing a three-dimensional network.

Related literature

For details of the biological activity and applications of cyclohexane derivatives, see: Eddington et al. (2000[Eddington, N. D., Cox, D. S., Roberts, R. R., Stables, J. P., Powell, C. B. & Scott, A. R. (2000). Curr. Med. Chem. 7, 417-436.]); Padmavathi et al. (2000[Padmavathi, V., Reddy, B. J. M., Balaiah, A., Reddy, K. V. & Reddy, D. B. (2000). Molecules, 5, 1281-1286.], 2001[Padmavathi, V., Sharmila, K., Reddy, A. S. & Reddy, D. B. (2001). Indian J. Chem. Sect. B, 40, 11-14.]); Li & Strobel (2001[Li, J. Y. & Strobel, G. A. (2001). Phytochemistry, 57, 261-265.]). For puckering parameters and displacement asymmetric parameters, see: Cremer & Pople (1975[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358.]); Nardelli (1983[Nardelli, M. (1983). Acta Cryst. C39, 1141-1142.]).

[Scheme 1]

Experimental

Crystal data
  • C6H12O5

  • Mr = 164.16

  • Monoclinic, P 21

  • a = 6.4727 (5) Å

  • b = 8.4851 (6) Å

  • c = 6.8249 (5) Å

  • β = 110.796 (2)°

  • V = 350.41 (5) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.14 mm−1

  • T = 293 K

  • 0.21 × 0.19 × 0.17 mm

Data collection
  • Bruker Kappa APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.972, Tmax = 0.977

  • 5019 measured reflections

  • 2418 independent reflections

  • 2314 reflections with I > 2σ(I)

  • Rint = 0.020

Refinement
  • R[F2 > 2σ(F2)] = 0.033

  • wR(F2) = 0.086

  • S = 1.06

  • 2418 reflections

  • 105 parameters

  • 1 restraint

  • H-atom parameters constrained

  • Δρmax = 0.39 e Å−3

  • Δρmin = −0.19 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 994 Friedel pairs

  • Flack parameter: 0.7 (6)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O1—H1A⋯O3i 0.82 1.94 2.7347 (11) 164
O2—H2A⋯O4ii 0.82 1.96 2.7761 (12) 170
O3—H3A⋯O1iii 0.82 2.02 2.8417 (11) 177
O4—H4A⋯O5iv 0.82 1.91 2.7067 (12) 165
O5—H5⋯O2v 0.82 2.00 2.8036 (12) 166
Symmetry codes: (i) x+1, y, z; (ii) [-x+1, y+{\script{1\over 2}}, -z+1]; (iii) [-x+1, y-{\script{1\over 2}}, -z+1]; (iv) [-x, y-{\script{1\over 2}}, -z]; (v) x, y, z-1.

Data collection: APEX2 (Bruker, 2004[Bruker (2004). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: APEX2; data reduction: SAINT (Bruker, 2004[Bruker (2004). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); 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: ORTEP-3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

Cyclohexanes are either prepared from natural sources or entirely via synthetic routes. The reason for their preparation is a variety of medical effects. The molecules provide anticonvulsant, antimalarial, antiinflamatory and cardiovascular effects (Eddington et al., 2000). Cyclohexanes are also important intermediates for many biologically active compounds (Padmavathi et al., 2001; Padmavathi et al., 2000). A number of their derivatives have fungicidal and antitumor activities (Li & Strobel, 2001). Taking into consideration of these aspects, and in order to obtain a detailed information on the molecular structure in the solid state, the X-ray study of the title compound has been carried out.

X-Ray analysis confirms the molecular structure and atom connectivity for (I) (Fig. 1).The cyclohexane ring adopts the chair conformation with the puckering parameters q2 and ϕ (Cremer & Pople, 1975) and the smallest displacement asymmetric parameters, Δ, (Nardelli, 1983) as follows: q2=0.0673 (11) Å, ϕ=111.3 (9)°, Δs(C1)= 1.27 (8).

The atom O1 acts as a donor to the atom O3 of the neighbouring molecule. This hydrogen bond is involved in a motif C(6) forming an infinite chain along a axis, and also the atom O5 acts as a donor to the atom O2. This hydrogen bond is involved in a motif C(7) forming an infinite chain along c axis. The crystal packing is defined by O–H···O hydrogen bonds (Table 1, Fig. 2)

Related literature top

For biological activities, see: Eddington et al. (2000); Padmavathi et al. (2000, 2001); Li & Strobel (2001). For puckering parameters and displacement asymmetric parameters, see: Cremer & Pople (1975); Nardelli (1983)

Experimental top

The compound was isolated from Manilkara zapota(L) Van Royan leaves of ethyl acetate fraction by column chromatography. Single crystals of the title compound suitable for X-ray diffraction were obtained from a mixture of ethyl acetate and methanol (3:1) by slow evaporation.

Refinement top

All the H atoms were positioned geometrically, with O—H = 0.82 Å and C—H = 0.93 - 0.98 Å and constrained to ride on their parent atom, with UisoH=1.2Ueq(C).

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: APEX2 (Bruker, 2004); data reduction: SAINT (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound showing the 50% probability displacement ellipsoids.
[Figure 2] Fig. 2. The packing diagram of the title compound, view along the a axis forming a three dimensional network.
Cyclohexane-1,2,3,4,5-pentol top
Crystal data top
C6H12O5F(000) = 176
Mr = 164.16Dx = 1.556 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 2418 reflections
a = 6.4727 (5) Åθ = 3.2–33.3°
b = 8.4851 (6) ŵ = 0.14 mm1
c = 6.8249 (5) ÅT = 293 K
β = 110.796 (2)°Block, colourless
V = 350.41 (5) Å30.21 × 0.19 × 0.17 mm
Z = 2
Data collection top
Bruker Kappa APEXII CCD
diffractometer
2418 independent reflections
Radiation source: fine-focus sealed tube2314 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.020
ω scansθmax = 33.3°, θmin = 3.2°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 99
Tmin = 0.972, Tmax = 0.977k = 1212
5019 measured reflectionsl = 910
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.033H-atom parameters constrained
wR(F2) = 0.086 w = 1/[σ2(Fo2) + (0.0548P)2 + 0.0106P]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
2418 reflectionsΔρmax = 0.39 e Å3
105 parametersΔρmin = 0.19 e Å3
1 restraintAbsolute structure: Flack (1983), 994 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.7 (6)
Crystal data top
C6H12O5V = 350.41 (5) Å3
Mr = 164.16Z = 2
Monoclinic, P21Mo Kα radiation
a = 6.4727 (5) ŵ = 0.14 mm1
b = 8.4851 (6) ÅT = 293 K
c = 6.8249 (5) Å0.21 × 0.19 × 0.17 mm
β = 110.796 (2)°
Data collection top
Bruker Kappa APEXII CCD
diffractometer
2418 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
2314 reflections with I > 2σ(I)
Tmin = 0.972, Tmax = 0.977Rint = 0.020
5019 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.033H-atom parameters constrained
wR(F2) = 0.086Δρmax = 0.39 e Å3
S = 1.06Δρmin = 0.19 e Å3
2418 reflectionsAbsolute structure: Flack (1983), 994 Friedel pairs
105 parametersAbsolute structure parameter: 0.7 (6)
1 restraint
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
xyzUiso*/Ueq
C10.39464 (15)0.00491 (11)0.41069 (16)0.01595 (17)
H10.46880.09260.47570.019*
C20.15563 (14)0.03135 (11)0.27557 (15)0.01522 (17)
H20.08210.06940.22470.018*
C30.13572 (14)0.13189 (11)0.08297 (15)0.01626 (17)
H30.01980.13520.00930.020*
C40.27248 (16)0.06837 (11)0.04069 (15)0.01663 (17)
H40.27410.14680.14560.020*
C50.51009 (15)0.03378 (11)0.10101 (16)0.01768 (18)
H5A0.58370.13180.15900.021*
H5B0.58890.01370.01880.021*
C60.51703 (15)0.07685 (11)0.27875 (16)0.01628 (17)
H60.44140.17470.21680.020*
O10.73862 (11)0.11569 (9)0.40896 (14)0.02328 (17)
H1A0.81900.03920.41800.035*
O20.38759 (13)0.11155 (10)0.57023 (13)0.02410 (17)
H2A0.51400.13370.64640.036*
O30.04224 (12)0.10449 (9)0.39647 (13)0.02046 (16)
H3A0.10940.18390.45290.031*
O40.20891 (12)0.28909 (9)0.14488 (13)0.02034 (16)
H4A0.10940.33900.16420.031*
O50.16705 (13)0.07199 (9)0.14612 (13)0.02343 (17)
H50.21190.09220.24160.035*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0173 (4)0.0179 (4)0.0146 (4)0.0003 (3)0.0080 (3)0.0012 (3)
C20.0156 (3)0.0175 (4)0.0152 (4)0.0008 (3)0.0088 (3)0.0005 (3)
C30.0166 (3)0.0182 (4)0.0147 (4)0.0003 (3)0.0065 (3)0.0001 (3)
C40.0192 (4)0.0187 (4)0.0136 (4)0.0020 (3)0.0078 (3)0.0000 (3)
C50.0179 (4)0.0215 (4)0.0167 (4)0.0012 (3)0.0099 (3)0.0006 (3)
C60.0159 (3)0.0180 (4)0.0173 (4)0.0007 (3)0.0088 (3)0.0006 (3)
O10.0168 (3)0.0249 (3)0.0288 (4)0.0031 (3)0.0089 (3)0.0074 (3)
O20.0253 (3)0.0310 (4)0.0205 (4)0.0075 (3)0.0136 (3)0.0112 (3)
O30.0215 (3)0.0226 (3)0.0233 (4)0.0010 (3)0.0155 (3)0.0027 (3)
O40.0231 (3)0.0162 (3)0.0237 (4)0.0008 (2)0.0107 (3)0.0000 (3)
O50.0265 (3)0.0278 (4)0.0195 (4)0.0093 (3)0.0125 (3)0.0094 (3)
Geometric parameters (Å, º) top
C1—O21.4289 (13)C4—H40.9800
C1—C61.5223 (14)C5—C61.5218 (14)
C1—C21.5249 (12)C5—H5A0.9700
C1—H10.9800C5—H5B0.9700
C2—O31.4264 (12)C6—O11.4319 (11)
C2—C31.5337 (14)C6—H60.9800
C2—H20.9800O1—H1A0.8200
C3—O41.4282 (12)O2—H2A0.8200
C3—C41.5221 (14)O3—H3A0.8200
C3—H30.9800O4—H4A0.8200
C4—O51.4328 (12)O5—H50.8200
C4—C51.5266 (13)
O2—C1—C6111.16 (8)O5—C4—H4108.9
O2—C1—C2106.77 (7)C3—C4—H4108.9
C6—C1—C2110.64 (8)C5—C4—H4108.9
O2—C1—H1109.4C6—C5—C4111.20 (8)
C6—C1—H1109.4C6—C5—H5A109.4
C2—C1—H1109.4C4—C5—H5A109.4
O3—C2—C1110.97 (8)C6—C5—H5B109.4
O3—C2—C3110.48 (7)C4—C5—H5B109.4
C1—C2—C3112.89 (7)H5A—C5—H5B108.0
O3—C2—H2107.4O1—C6—C5112.10 (8)
C1—C2—H2107.4O1—C6—C1110.01 (8)
C3—C2—H2107.4C5—C6—C1110.48 (8)
O4—C3—C4107.32 (8)O1—C6—H6108.0
O4—C3—C2110.35 (8)C5—C6—H6108.0
C4—C3—C2112.94 (7)C1—C6—H6108.0
O4—C3—H3108.7C6—O1—H1A109.5
C4—C3—H3108.7C1—O2—H2A109.5
C2—C3—H3108.7C2—O3—H3A109.5
O5—C4—C3107.80 (8)C3—O4—H4A109.5
O5—C4—C5110.57 (8)C4—O5—H5109.5
C3—C4—C5111.73 (8)
O2—C1—C2—O361.20 (10)O4—C3—C4—C572.15 (10)
C6—C1—C2—O3177.71 (7)C2—C3—C4—C549.69 (10)
O2—C1—C2—C3174.15 (8)O5—C4—C5—C665.25 (11)
C6—C1—C2—C353.07 (10)C3—C4—C5—C654.82 (11)
O3—C2—C3—O454.15 (10)C4—C5—C6—O1177.75 (8)
C1—C2—C3—O470.77 (10)C4—C5—C6—C159.17 (10)
O3—C2—C3—C4174.27 (7)O2—C1—C6—O159.39 (10)
C1—C2—C3—C449.35 (10)C2—C1—C6—O1177.84 (8)
O4—C3—C4—O5166.16 (7)O2—C1—C6—C5176.32 (7)
C2—C3—C4—O571.99 (10)C2—C1—C6—C557.87 (9)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···O3i0.821.942.7347 (11)164
O2—H2A···O4ii0.821.962.7761 (12)170
O3—H3A···O1iii0.822.022.8417 (11)177
O4—H4A···O5iv0.821.912.7067 (12)165
O5—H5···O2v0.822.002.8036 (12)166
Symmetry codes: (i) x+1, y, z; (ii) x+1, y+1/2, z+1; (iii) x+1, y1/2, z+1; (iv) x, y1/2, z; (v) x, y, z1.

Experimental details

Crystal data
Chemical formulaC6H12O5
Mr164.16
Crystal system, space groupMonoclinic, P21
Temperature (K)293
a, b, c (Å)6.4727 (5), 8.4851 (6), 6.8249 (5)
β (°) 110.796 (2)
V3)350.41 (5)
Z2
Radiation typeMo Kα
µ (mm1)0.14
Crystal size (mm)0.21 × 0.19 × 0.17
Data collection
DiffractometerBruker Kappa APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.972, 0.977
No. of measured, independent and
observed [I > 2σ(I)] reflections
5019, 2418, 2314
Rint0.020
(sin θ/λ)max1)0.771
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.033, 0.086, 1.06
No. of reflections2418
No. of parameters105
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.39, 0.19
Absolute structureFlack (1983), 994 Friedel pairs
Absolute structure parameter0.7 (6)

Computer programs: APEX2 (Bruker, 2004), SAINT (Bruker, 2004), SHELXS97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···O3i0.821.942.7347 (11)164
O2—H2A···O4ii0.821.962.7761 (12)170
O3—H3A···O1iii0.822.022.8417 (11)177
O4—H4A···O5iv0.821.912.7067 (12)165
O5—H5···O2v0.822.002.8036 (12)166
Symmetry codes: (i) x+1, y, z; (ii) x+1, y+1/2, z+1; (iii) x+1, y1/2, z+1; (iv) x, y1/2, z; (v) x, y, z1.
 

Acknowledgements

GG and ASP thank Dr Babu Varghese, SAIF, IIT, Chennai, India, for the X-ray intensity data collection.

References

First citationBruker (2004). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationCremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354–1358.  CrossRef CAS Web of Science Google Scholar
First citationEddington, N. D., Cox, D. S., Roberts, R. R., Stables, J. P., Powell, C. B. & Scott, A. R. (2000). Curr. Med. Chem. 7, 417–436.  Web of Science CrossRef PubMed CAS Google Scholar
First citationFarrugia, L. J. (1997). J. Appl. Cryst. 30, 565.  CrossRef IUCr Journals Google Scholar
First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationLi, J. Y. & Strobel, G. A. (2001). Phytochemistry, 57, 261–265.  Web of Science CrossRef PubMed CAS Google Scholar
First citationNardelli, M. (1983). Acta Cryst. C39, 1141–1142.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationPadmavathi, V., Reddy, B. J. M., Balaiah, A., Reddy, K. V. & Reddy, D. B. (2000). Molecules, 5, 1281–1286.  Web of Science CrossRef CAS Google Scholar
First citationPadmavathi, V., Sharmila, K., Reddy, A. S. & Reddy, D. B. (2001). Indian J. Chem. Sect. B, 40, 11–14.  Google Scholar
First citationSheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.  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

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 65| Part 5| May 2009| Page o1114
Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds