l-Iditol

Takashita, T.; Horii, Y.; Otabara, A.; Ishii, T.

doi:10.1107/S2414314626008011

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 11| Part 8| August 2026| x260801

https://doi.org/10.1107/S2414314626008011

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L-Iditol

Tomoko Takashita,^a ^* Yoji Horii,^a Akari Otabara ^a and Tomohiko Ishii ^a

^aGraduate School of Science for Creative Emergence, Kagawa University, 2217-20 Hayashi-cho, Takamatsu, Kagawa 761-0396, Japan
^*Correspondence e-mail: [email protected]

Edited by L. Van Meervelt, Katholieke Universiteit Leuven, Belgium (Received 31 July 2026; accepted 5 August 2026; online 7 August 2026)

L-Iditol, C₆H₁₄O₆, the sugar alcohol corresponding to L-idose, was crystallized from aqueous solution. Colourless block-shaped single crystals suitable for single-crystal X-ray diffraction analysis were obtained. The title compound crystallizes in the monoclinic space group P2₁, with one molecule in the asymmetric unit. In the crystal, all six hydroxy groups act as donors in O—H⋯O hydrogen bonds, forming a three-dimensional hydrogen-bonded network. The crystal structure of its enantiomer, D-iditol, has been reported previously [Azarnia et al. (1972 ). Acta Cryst. B28, 1007–1013].

Keywords: crystal structure; hydrogen bonding; rare sugar; sugar alcohol; L-iditol.

CCDC reference: 2577698

Structure description

L-Iditol is the sugar alcohol corresponding to the rare sugar L-idose. Systematic bioproduction strategies have expanded the availability of rare hexoses and their corresponding sugar alcohols (Izumori, 2002 ). Sugar alcohols possess multiple hydroxy groups and can therefore form extensive intermolecular hydrogen-bonding networks. Elucidation of their molecular conformations and crystal packing is important for understanding their solid-state properties.

The crystal structure of the enantiomer D-iditol was reported previously by Azarnia et al. (1972; CSD refcode IDITOL), and that of racemic D,L-iditol was reported by Kopf et al. (1992 ; CSD refcode VOMXEA). The present study provides a modern high-precision single-crystal X-ray determination of the corresponding L enantiomer. The refinement converged at R₁ = 0.0337, and the standard uncertainties of the C—C and C—O bond lengths are in the range 0.003–0.004 Å. Together with the deposited structure-factor data and detailed hydrogen-bond geometry, the present results provide an updated crystallographic description of iditol and specifically document the crystal structure of the L enantiomer.

L-iditol adopts a twisted, acyclic six-carbon chain conformation (Fig. 1). The C1—C2—C3—C4, C2—C3—C4—C5 and C3—C4—C5—C6 torsion angles are −179.9 (2), 62.2 (3) and −175.3 (2)°, respectively. Single-crystal X-ray diffraction analysis revealed that it crystallizes in the monoclinic space group P2₁. The asymmetric unit contains one molecule of L-iditol. The stereogenic carbon atoms C2, C3, C4 and C5 have S, R, R and S configurations, respectively.

Figure 1
The molecular structure of L-iditol showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 50% probability level, and hydrogen atoms are shown as spheres of arbitrary radii.

In the crystal, all six hydroxy groups act as hydrogen-bond donors, forming six intermolecular O—H⋯O hydrogen bonds (Table 1). The donor⋯acceptor distances range from 2.736 (3) to 2.848 (3) Å. These interactions connect the molecules into a three-dimensional hydrogen-bonded network. The crystal packing viewed along the a axis is shown in Fig. 2. The intermolecular hydrogen bonding contributes to the consolidation of the crystal packing.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯O3ⁱ	0.82	2.04	2.834 (3)	163
O2—H2⋯O6ⁱⁱ	0.82	1.95	2.764 (3)	171
O3—H3⋯O5ⁱⁱⁱ	0.82	2.01	2.736 (3)	147
O4—H4⋯O2^iv	0.82	1.98	2.755 (2)	158
O5—H5⋯O1ⁱⁱⁱ	0.90 (4)	1.88 (4)	2.766 (3)	170 (3)
O6—H6⋯O3^v	0.82	2.25	2.848 (3)	130
Symmetry codes: (i) $[-x+1, y+{\script{1\over 2}}, -z+1]$ ; (ii) ; (iii) $[-x+1, y-{\script{1\over 2}}, -z]$ ; (iv) $[-x, y-{\script{1\over 2}}, -z]$ ; (v) $[-x, y+{\script{1\over 2}}, -z]$ .

Figure 2
Crystal packing of L-iditol viewed along the a axis, showing the three-dimensional hydrogen-bonded network formed by O—H⋯O hydrogen bonds. Hydrogen bonds are shown as dashed lines, and the crystallographic b- and c-axis directions are indicated.

Synthesis and crystallization

Commercially available L-iditol (Sigma–Aldrich) was used as received without further purification. The sample was dissolved in water, and the solution was allowed to evaporate slowly at room temperature. Colorless block-shaped single crystals suitable for single-crystal X-ray diffraction analysis were obtained. The absolute configuration was assigned on the basis of the known configuration of the commercially available L-iditol sample.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. Although the refined value of the Flack parameter is slightly negative, it is within approximately 1.5 standard uncertainties of zero and is consistent with the absolute configuration assigned from the known configuration of the commercially available L-iditol sample.

Table 2
Experimental details

Crystal data
Chemical formula	C₆H₁₄O₆
M_r	182.17
Crystal system, space group	Monoclinic, P2₁
Temperature (K)	296
a, b, c (Å)	5.8678 (2), 8.3869 (3), 8.1213 (3)
β (°)	93.182 (2)
V (Å³)	399.05 (2)
Z	2
Radiation type	Cu Kα
μ (mm⁻¹)	1.19
Crystal size (mm)	0.10 × 0.10 × 0.10

Data collection
Diffractometer	Rigaku R-AXIS RAPID
Absorption correction	Multi-scan (ABSCOR; Rigaku, 1995 )
T_min, T_max	0.822, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	4219, 1377, 1329
R_int	0.057
(sin θ/λ)_max (Å⁻¹)	0.602

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.034, 0.083, 1.12
No. of reflections	1377
No. of parameters	114
No. of restraints	1
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.20, −0.20
Absolute structure	Flack x determined using 538 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter	−0.24 (16)
Computer programs: RAPID-AUTO (Rigaku, 2009 ), SHELXT2018/2 (Sheldrick, 2015a ), SHELXL2018/3 (Sheldrick, 2015b ) and OLEX2 (Dolomanov et al., 2009 ).

Structural data

CCDC reference: 2577698

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314626008011/vm4079sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314626008011/vm4079Isup2.hkl

Point-by-point response to the Co-editor's comments on manuscript vm4079 (L-iditol). DOI: https://doi.org/10.1107/S2414314626008011/vm4079sup3.docx

Supporting information file. DOI: https://doi.org/10.1107/S2414314626008011/vm4079Isup4.cml

checkCIF report

Computing details top

(2S,3R,4R,5S)-Hexane-1,2,3,4,5,6-hexol top

Crystal data top

C₆H₁₄O₆	F(000) = 196
M_r = 182.17	D_x = 1.516 Mg m⁻³
Monoclinic, P2₁	Cu Kα radiation, λ = 1.54187 Å
a = 5.8678 (2) Å	Cell parameters from 3800 reflections
b = 8.3869 (3) Å	θ = 5.3–68.3°
c = 8.1213 (3) Å	µ = 1.19 mm⁻¹
β = 93.182 (2)°	T = 296 K
V = 399.05 (2) Å³	Block, clear light colourless
Z = 2	0.1 × 0.1 × 0.1 mm

Data collection top

Rigaku R-AXIS RAPID diffractometer	1329 reflections with I > 2σ(I)
Detector resolution: 10.000 pixels mm^-1	R_int = 0.057
ω scans	θ_max = 68.2°, θ_min = 5.5°
Absorption correction: multi-scan (ABSCOR; Rigaku, 1995)	h = −6→7
T_min = 0.822, T_max = 1.000	k = −10→10
4219 measured reflections	l = −9→9
1377 independent reflections

Refinement top

Refinement on F²	H atoms treated by a mixture of independent and constrained refinement
Least-squares matrix: full	w = 1/[σ²(F_o²) + (0.032P)² + 0.0743P] where P = (F_o² + 2F_c²)/3
R[F² > 2σ(F²)] = 0.034	(Δ/σ)_max < 0.001
wR(F²) = 0.083	Δρ_max = 0.20 e Å⁻³
S = 1.12	Δρ_min = −0.20 e Å⁻³
1377 reflections	Extinction correction: SHELXL 2018/3 (Sheldrick, 2015b), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
114 parameters	Extinction coefficient: 0.165 (10)
1 restraint	Absolute structure: Flack x determined using 538 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
Primary atom site location: dual	Absolute structure parameter: −0.24 (16)
Hydrogen site location: mixed

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. The structure was solved using SHELXT (Sheldrick, 2015a) and refined on F² by full-matrix least-squares methods using SHELXL (Sheldrick, 2015b). All non-hydrogen atoms were refined anisotropically. The hydroxy hydrogen atom H5 was located in a difference-Fourier map and refined freely. All other hydrogen atoms were placed in geometrically calculated positions and refined using constrained models. The final refinement gave R₁ = 0.0337 for reflections with I > 2σ(I) and wR₂ = 0.0829 for all data. The maximum and minimum residual electron densities were 0.20 and -0.20 e Å^-3, respectively. The Flack parameter was -0.24 (16), determined using 538 quotients of the type [(I⁺) - (I^-)]/[(I⁺) + (I^-)] (Parsons et al., 2013). Although the refined value is slightly negative, it is within approximately 1.5 standard uncertainties of zero and is consistent with the absolute configuration assigned from the known configuration of the commercially available L-iditol sample.

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

	x	y	z	U_iso*/U_eq
O1	0.4782 (4)	0.8448 (2)	0.4118 (2)	0.0308 (6)
H1	0.503187	0.855873	0.511527	0.037*
O2	0.0813 (3)	0.6622 (2)	0.2718 (2)	0.0251 (5)
H2	0.078439	0.670204	0.372303	0.030*
O3	0.3411 (3)	0.3703 (2)	0.2584 (2)	0.0198 (5)
H3	0.365277	0.284701	0.213852	0.024*
O4	0.2410 (3)	0.3107 (2)	−0.0653 (2)	0.0230 (5)
H4	0.152240	0.286824	−0.142921	0.028*
O5	0.4315 (3)	0.5928 (2)	−0.2005 (2)	0.0216 (5)
H5	0.466 (6)	0.505 (5)	−0.258 (4)	0.044 (11)*
O6	0.0239 (4)	0.7005 (3)	−0.3950 (2)	0.0334 (6)
H6	−0.004973	0.782453	−0.345233	0.040*
C1	0.4802 (5)	0.6794 (3)	0.3717 (3)	0.0194 (6)
H1A	0.436997	0.616425	0.465156	0.023*
H1B	0.631996	0.647182	0.343478	0.023*
C2	0.3120 (4)	0.6535 (3)	0.2265 (3)	0.0168 (6)
H2A	0.335094	0.739105	0.146973	0.020*
C3	0.3538 (4)	0.4961 (3)	0.1405 (3)	0.0158 (6)
H3A	0.508825	0.497853	0.101329	0.019*
C4	0.1871 (4)	0.4652 (3)	−0.0076 (3)	0.0159 (6)
H4A	0.030915	0.464981	0.029349	0.019*
C5	0.2062 (5)	0.5907 (3)	−0.1429 (3)	0.0176 (6)
H5A	0.179351	0.694965	−0.093078	0.021*
C6	0.0294 (5)	0.5697 (4)	−0.2842 (3)	0.0257 (7)
H6A	0.062713	0.473021	−0.343878	0.031*
H6B	−0.119857	0.557352	−0.240093	0.031*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0586 (14)	0.0176 (11)	0.0153 (9)	−0.0104 (10)	−0.0058 (9)	−0.0010 (8)
O2	0.0237 (10)	0.0349 (12)	0.0161 (8)	0.0088 (9)	−0.0028 (7)	−0.0053 (8)
O3	0.0318 (10)	0.0126 (9)	0.0150 (9)	0.0036 (7)	0.0005 (7)	0.0004 (7)
O4	0.0313 (11)	0.0153 (9)	0.0214 (9)	0.0014 (8)	−0.0066 (7)	−0.0058 (8)
O5	0.0233 (10)	0.0194 (9)	0.0224 (10)	−0.0052 (8)	0.0047 (8)	−0.0020 (8)
O6	0.0435 (13)	0.0402 (13)	0.0168 (10)	0.0142 (10)	0.0035 (9)	0.0063 (10)
C1	0.0285 (14)	0.0152 (15)	0.0141 (12)	−0.0017 (11)	−0.0026 (11)	0.0000 (10)
C2	0.0239 (13)	0.0149 (13)	0.0114 (11)	−0.0002 (11)	0.0003 (10)	0.0018 (10)
C3	0.0193 (12)	0.0150 (13)	0.0130 (11)	0.0000 (10)	0.0014 (9)	−0.0001 (9)
C4	0.0190 (12)	0.0142 (13)	0.0148 (12)	−0.0012 (10)	0.0015 (10)	−0.0017 (9)
C5	0.0223 (13)	0.0169 (12)	0.0136 (12)	0.0024 (11)	0.0019 (10)	−0.0018 (10)
C6	0.0276 (15)	0.0305 (17)	0.0188 (13)	0.0007 (13)	−0.0015 (11)	0.0027 (12)

Geometric parameters (Å, º) top

O1—H1	0.8200	C1—H1B	0.9700
O1—C1	1.425 (3)	C1—C2	1.511 (3)
O2—H2	0.8200	C2—H2A	0.9800
O2—C2	1.424 (3)	C2—C3	1.521 (3)
O3—H3	0.8200	C3—H3A	0.9800
O3—C3	1.430 (3)	C3—C4	1.529 (3)
O4—H4	0.8200	C4—H4A	0.9800
O4—C4	1.420 (3)	C4—C5	1.530 (4)
O5—H5	0.90 (4)	C5—H5A	0.9800
O5—C5	1.427 (3)	C5—C6	1.514 (4)
O6—H6	0.8200	C6—H6A	0.9700
O6—C6	1.418 (4)	C6—H6B	0.9700
C1—H1A	0.9700

C1—O1—H1	109.5	C2—C3—H3A	108.2
C2—O2—H2	109.5	C2—C3—C4	113.3 (2)
C3—O3—H3	109.5	C4—C3—H3A	108.2
C4—O4—H4	109.5	O4—C4—C3	105.6 (2)
C5—O5—H5	114 (2)	O4—C4—H4A	109.2
C6—O6—H6	109.5	O4—C4—C5	111.3 (2)
O1—C1—H1A	110.2	C3—C4—H4A	109.2
O1—C1—H1B	110.2	C3—C4—C5	112.3 (2)
O1—C1—C2	107.7 (2)	C5—C4—H4A	109.2
H1A—C1—H1B	108.5	O5—C5—C4	110.5 (2)
C2—C1—H1A	110.2	O5—C5—H5A	107.3
C2—C1—H1B	110.2	O5—C5—C6	111.2 (2)
O2—C2—C1	112.4 (2)	C4—C5—H5A	107.3
O2—C2—H2A	107.5	C6—C5—C4	112.9 (2)
O2—C2—C3	110.1 (2)	C6—C5—H5A	107.3
C1—C2—H2A	107.5	O6—C6—C5	112.4 (2)
C1—C2—C3	111.6 (2)	O6—C6—H6A	109.1
C3—C2—H2A	107.5	O6—C6—H6B	109.1
O3—C3—C2	108.48 (18)	C5—C6—H6A	109.1
O3—C3—H3A	108.2	C5—C6—H6B	109.1
O3—C3—C4	110.3 (2)	H6A—C6—H6B	107.8

O1—C1—C2—O2	−73.8 (3)	O5—C5—C6—O6	−64.8 (3)
O1—C1—C2—C3	162.0 (2)	C1—C2—C3—O3	57.2 (3)
O2—C2—C3—O3	−68.3 (2)	C1—C2—C3—C4	−179.9 (2)
O2—C2—C3—C4	54.6 (2)	C2—C3—C4—O4	−176.3 (2)
O3—C3—C4—O4	−54.5 (2)	C2—C3—C4—C5	62.2 (3)
O3—C3—C4—C5	−176.0 (2)	C3—C4—C5—O5	59.4 (3)
O4—C4—C5—O5	−58.8 (3)	C3—C4—C5—C6	−175.3 (2)
O4—C4—C5—C6	66.5 (3)	C4—C5—C6—O6	170.3 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O3ⁱ	0.82	2.04	2.834 (3)	163
O2—H2···O6ⁱⁱ	0.82	1.95	2.764 (3)	171
O3—H3···O5ⁱⁱⁱ	0.82	2.01	2.736 (3)	147
O4—H4···O2^iv	0.82	1.98	2.755 (2)	158
O5—H5···O1ⁱⁱⁱ	0.90 (4)	1.88 (4)	2.766 (3)	170 (3)
O6—H6···O3^v	0.82	2.25	2.848 (3)	130

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

Acknowledgements

The authors thank Professor Genta Sakane (Okayama University of Science) for insightful discussions and technical suggestions, and Kei Takeshita (FUSHIMI Pharmaceutical Co., Ltd.) for valuable advice. This work received support from the JST Support for Pioneering Research Initiated by the Next Generation (SPRING) program, Japan.

References

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