Cyclo­hexane-1,2,3,4,5-pentol

Ganesh, G.; Sivaraj, C.; Kannan, P.S.; Raaman, N.; SubbiahPandi, A.

doi:10.1107/S1600536809014135

organic compounds

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ISSN: 2056-9890

Volume 65| Part 5| May 2009| Page o1114

doi:10.1107/S1600536809014135

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Cyclohexane-1,2,3,4,5-pentol

G. Ganesh,^a C. Sivaraj,^b P. S. Kannan,^a N. Raaman ^b and A. SubbiahPandi ^c ^*

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

Experimental

Crystal data

C₆H₁₂O₅
M_r = 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 ) T_min = 0.972, T_max = 0.977
5019 measured reflections
2418 independent reflections
2314 reflections with I > 2σ(I)
R_int = 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
Δρ_max = 0.39 e Å⁻³
Δρ_min = −0.19 e Å⁻³
Absolute structure: Flack (1983 ), 994 Friedel pairs
Flack parameter: 0.7 (6)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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⋯O5^iv	0.82	1.91	2.7067 (12)	165
O5—H5⋯O2^v	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 ); cell refinement: APEX2; 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 and PLATON (Spek, 2009 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809014135/kp2211sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809014135/kp2211Isup2.hkl

checkCIF report

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)°, Δ_s(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.

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

	Fig. 1. The molecular structure of the title compound showing the 50% probability displacement ellipsoids.
	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

C₆H₁₂O₅	F(000) = 176
M_r = 164.16	D_x = 1.556 Mg m⁻³
Monoclinic, P2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 2418 reflections
a = 6.4727 (5) Å	θ = 3.2–33.3°
b = 8.4851 (6) Å	µ = 0.14 mm⁻¹
c = 6.8249 (5) Å	T = 293 K
β = 110.796 (2)°	Block, colourless
V = 350.41 (5) Å³	0.21 × 0.19 × 0.17 mm
Z = 2

Data collection top

Bruker Kappa APEXII CCD diffractometer	2418 independent reflections
Radiation source: fine-focus sealed tube	2314 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.020
ω scans	θ_max = 33.3°, θ_min = 3.2°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −9→9
T_min = 0.972, T_max = 0.977	k = −12→12
5019 measured reflections	l = −9→10

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.033	H-atom parameters constrained
wR(F²) = 0.086	w = 1/[σ²(F_o²) + (0.0548P)² + 0.0106P] where P = (F_o² + 2F_c²)/3
S = 1.06	(Δ/σ)_max < 0.001
2418 reflections	Δρ_max = 0.39 e Å⁻³
105 parameters	Δρ_min = −0.19 e Å⁻³
1 restraint	Absolute structure: Flack (1983), 994 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.7 (6)

Crystal data top

C₆H₁₂O₅	V = 350.41 (5) Å³
M_r = 164.16	Z = 2
Monoclinic, P2₁	Mo Kα radiation
a = 6.4727 (5) Å	µ = 0.14 mm⁻¹
b = 8.4851 (6) Å	T = 293 K
c = 6.8249 (5) Å	0.21 × 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)
T_min = 0.972, T_max = 0.977	R_int = 0.020
5019 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.033	H-atom parameters constrained
wR(F²) = 0.086	Δρ_max = 0.39 e Å⁻³
S = 1.06	Δρ_min = −0.19 e Å⁻³
2418 reflections	Absolute structure: Flack (1983), 994 Friedel pairs
105 parameters	Absolute 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

	x	y	z	U_iso*/U_eq
C1	0.39464 (15)	0.00491 (11)	0.41069 (16)	0.01595 (17)
H1	0.4688	−0.0926	0.4757	0.019*
C2	0.15563 (14)	−0.03135 (11)	0.27557 (15)	0.01522 (17)
H2	0.0821	0.0694	0.2247	0.018*
C3	0.13572 (14)	−0.13189 (11)	0.08297 (15)	0.01626 (17)
H3	−0.0198	−0.1352	−0.0093	0.020*
C4	0.27248 (16)	−0.06837 (11)	−0.04069 (15)	0.01663 (17)
H4	0.2741	−0.1468	−0.1456	0.020*
C5	0.51009 (15)	−0.03378 (11)	0.10101 (16)	0.01768 (18)
H5A	0.5837	−0.1318	0.1590	0.021*
H5B	0.5889	0.0137	0.0188	0.021*
C6	0.51703 (15)	0.07685 (11)	0.27875 (16)	0.01628 (17)
H6	0.4414	0.1747	0.2168	0.020*
O1	0.73862 (11)	0.11569 (9)	0.40896 (14)	0.02328 (17)
H1A	0.8190	0.0392	0.4180	0.035*
O2	0.38759 (13)	0.11155 (10)	0.57023 (13)	0.02410 (17)
H2A	0.5140	0.1337	0.6464	0.036*
O3	0.04224 (12)	−0.10449 (9)	0.39647 (13)	0.02046 (16)
H3A	0.1094	−0.1839	0.4529	0.031*
O4	0.20891 (12)	−0.28909 (9)	0.14488 (13)	0.02034 (16)
H4A	0.1094	−0.3390	0.1642	0.031*
O5	0.16705 (13)	0.07199 (9)	−0.14612 (13)	0.02343 (17)
H5	0.2119	0.0922	−0.2416	0.035*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0173 (4)	0.0179 (4)	0.0146 (4)	−0.0003 (3)	0.0080 (3)	−0.0012 (3)
C2	0.0156 (3)	0.0175 (4)	0.0152 (4)	0.0008 (3)	0.0088 (3)	0.0005 (3)
C3	0.0166 (3)	0.0182 (4)	0.0147 (4)	0.0003 (3)	0.0065 (3)	−0.0001 (3)
C4	0.0192 (4)	0.0187 (4)	0.0136 (4)	0.0020 (3)	0.0078 (3)	0.0000 (3)
C5	0.0179 (4)	0.0215 (4)	0.0167 (4)	0.0012 (3)	0.0099 (3)	−0.0006 (3)
C6	0.0159 (3)	0.0180 (4)	0.0173 (4)	−0.0007 (3)	0.0088 (3)	−0.0006 (3)
O1	0.0168 (3)	0.0249 (3)	0.0288 (4)	−0.0031 (3)	0.0089 (3)	−0.0074 (3)
O2	0.0253 (3)	0.0310 (4)	0.0205 (4)	−0.0075 (3)	0.0136 (3)	−0.0112 (3)
O3	0.0215 (3)	0.0226 (3)	0.0233 (4)	0.0010 (3)	0.0155 (3)	0.0027 (3)
O4	0.0231 (3)	0.0162 (3)	0.0237 (4)	−0.0008 (2)	0.0107 (3)	0.0000 (3)
O5	0.0265 (3)	0.0278 (4)	0.0195 (4)	0.0093 (3)	0.0125 (3)	0.0094 (3)

Geometric parameters (Å, º) top

C1—O2	1.4289 (13)	C4—H4	0.9800
C1—C6	1.5223 (14)	C5—C6	1.5218 (14)
C1—C2	1.5249 (12)	C5—H5A	0.9700
C1—H1	0.9800	C5—H5B	0.9700
C2—O3	1.4264 (12)	C6—O1	1.4319 (11)
C2—C3	1.5337 (14)	C6—H6	0.9800
C2—H2	0.9800	O1—H1A	0.8200
C3—O4	1.4282 (12)	O2—H2A	0.8200
C3—C4	1.5221 (14)	O3—H3A	0.8200
C3—H3	0.9800	O4—H4A	0.8200
C4—O5	1.4328 (12)	O5—H5	0.8200
C4—C5	1.5266 (13)

O2—C1—C6	111.16 (8)	O5—C4—H4	108.9
O2—C1—C2	106.77 (7)	C3—C4—H4	108.9
C6—C1—C2	110.64 (8)	C5—C4—H4	108.9
O2—C1—H1	109.4	C6—C5—C4	111.20 (8)
C6—C1—H1	109.4	C6—C5—H5A	109.4
C2—C1—H1	109.4	C4—C5—H5A	109.4
O3—C2—C1	110.97 (8)	C6—C5—H5B	109.4
O3—C2—C3	110.48 (7)	C4—C5—H5B	109.4
C1—C2—C3	112.89 (7)	H5A—C5—H5B	108.0
O3—C2—H2	107.4	O1—C6—C5	112.10 (8)
C1—C2—H2	107.4	O1—C6—C1	110.01 (8)
C3—C2—H2	107.4	C5—C6—C1	110.48 (8)
O4—C3—C4	107.32 (8)	O1—C6—H6	108.0
O4—C3—C2	110.35 (8)	C5—C6—H6	108.0
C4—C3—C2	112.94 (7)	C1—C6—H6	108.0
O4—C3—H3	108.7	C6—O1—H1A	109.5
C4—C3—H3	108.7	C1—O2—H2A	109.5
C2—C3—H3	108.7	C2—O3—H3A	109.5
O5—C4—C3	107.80 (8)	C3—O4—H4A	109.5
O5—C4—C5	110.57 (8)	C4—O5—H5	109.5
C3—C4—C5	111.73 (8)

O2—C1—C2—O3	−61.20 (10)	O4—C3—C4—C5	−72.15 (10)
C6—C1—C2—O3	177.71 (7)	C2—C3—C4—C5	49.69 (10)
O2—C1—C2—C3	174.15 (8)	O5—C4—C5—C6	65.25 (11)
C6—C1—C2—C3	53.07 (10)	C3—C4—C5—C6	−54.82 (11)
O3—C2—C3—O4	−54.15 (10)	C4—C5—C6—O1	−177.75 (8)
C1—C2—C3—O4	70.77 (10)	C4—C5—C6—C1	59.17 (10)
O3—C2—C3—C4	−174.27 (7)	O2—C1—C6—O1	59.39 (10)
C1—C2—C3—C4	−49.35 (10)	C2—C1—C6—O1	177.84 (8)
O4—C3—C4—O5	166.16 (7)	O2—C1—C6—C5	−176.32 (7)
C2—C3—C4—O5	−71.99 (10)	C2—C1—C6—C5	−57.87 (9)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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···O5^iv	0.82	1.91	2.7067 (12)	165
O5—H5···O2^v	0.82	2.00	2.8036 (12)	166

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

Experimental details

Crystal data
Chemical formula	C₆H₁₂O₅
M_r	164.16
Crystal system, space group	Monoclinic, P2₁
Temperature (K)	293
a, b, c (Å)	6.4727 (5), 8.4851 (6), 6.8249 (5)
β (°)	110.796 (2)
V (Å³)	350.41 (5)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.14
Crystal size (mm)	0.21 × 0.19 × 0.17

Data collection
Diffractometer	Bruker Kappa APEXII CCD diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.972, 0.977
No. of measured, independent and observed [I > 2σ(I)] reflections	5019, 2418, 2314
R_int	0.020
(sin θ/λ)_max (Å⁻¹)	0.771

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.033, 0.086, 1.06
No. of reflections	2418
No. of parameters	105
No. of restraints	1
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.39, −0.19
Absolute structure	Flack (1983), 994 Friedel pairs
Absolute structure parameter	0.7 (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···A	D—H	H···A	D···A	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···O5^iv	0.82	1.91	2.7067 (12)	165
O5—H5···O2^v	0.82	2.00	2.8036 (12)	166

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

Acknowledgements

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

References

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