Ethyl α-l-sorboside

Nagayama, N.; Taniguchi, N.; Matsumoto, M.; Takeshita, K.; Ishii, T.

doi:10.1107/S2414314620016259

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 5| Part 12| December 2020| x201625

https://doi.org/10.1107/S2414314620016259

Open

access

Ethyl α-L-sorboside

Natsumi Nagayama,^a Norito Taniguchi,^a Mao Matsumoto,^a Kei Takeshita ^b and Tomohiko Ishii ^a ^*

^aDepartment of Advanced Materials Science, Faculty of Engineering, Kagawa University, 2217-20 Hayashi-cho, Takamatsu, Kagawa 761-0396, Japan, and ^bFushimi Pharmaceutical Co Ltd, 307 Minatomachi, Marugame, Kagawa 763-8605, Japan
^*Correspondence e-mail: ishii.tomohiko@kagawa-u.ac.jp

Edited by R. J. Butcher, Howard University, USA (Received 30 November 2020; accepted 15 December 2020; online 18 December 2020)

Ethyl L-sorboside, C₈H₁₆O₆, was prepared from the rare sugar L-sorbose, C₆H₁₂O₆, and crystallized. It was confirmed that ethyl L-sorboside formed α-pyranose with a ²C₅ conformation. In the crystal, molecules are linked by O—H⋯O hydrogen bonds, forming a three-dimensional network. The unit-cell volume of the title ethyl α-L-sorboside is 940.63 Å³ (Z = 4), which is about 194.69 Å³ (26.1%) bigger than that of L-sorbose [745.94 Å³ (Z = 4)].

Keywords: crystal structure; hydrogen bonding; rare sugar; alkyl sorboside.

CCDC reference: 2046786

Structure description

The rare sugar L-sorbose is the first L-form hexose found in nature (Itoh et al., 1995 ; Khan et al., 1992 ; Nordenson et al., 1979 ). Ethyl L-sorboside (Fig. 1) is an α-pyranose form in which the OH group located on the C-2 position in the rare sugar L-sorbose is converted into the ethoxy group OC₂H₅. The molecular weight of C₈H₁₆O₆ is 208. On the other hand, the molecular weight of C₆H₁₂O₆ is 180. So, the increase in molecular weight is about 16%. In contrast, the volume has increased by 26%. This point is characteristic. In other words, sorbose is highly crystalline and has a high density. On the other hand, the addition of the ethoxy group, which is hydrophobic, weakens inter-molecular interactions between sugar molecules, resulting in a decrease in density and an increase in volume.

Figure 1
An ORTEP view of the title compound with the atom-labelling scheme. The displacement ellipsoids of all non-hydrogen atoms are drawn at the 50% probability level. H atoms are shown as small spheres of arbitrary radii.

In this study, we aimed to create a single crystal of ethyl L-sorboside. The space group is non-centrosymmetric, P2₁2₁2₁, and there are total of four sorboside molecules in the unit cell (Z = 4). The crystal structure of ethyl L-sorboside features a three-dimensional hydrogen-bonded network (Table 1), with each molecule interacting with six neighbours. There are four intermolecular hydrogen bonds and an additional intramolecular hydrogen bond (Fig. 2).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯O3ⁱ	0.82	2.00	2.811 (3)	169
O3—H3⋯O4ⁱⁱ	0.82	1.94	2.750 (3)	167
O4—H4⋯O3	0.82	2.52	2.879 (2)	108
O4—H4⋯O5ⁱⁱ	0.82	2.00	2.791 (2)	163
O5—H5⋯O6ⁱⁱⁱ	0.82	2.35	2.988 (2)	136
Symmetry codes: (i) $[-x, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (ii) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]$ ; (iii) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]$ .

Figure 2
A packing diagram of the title compound, showing the hydrogen-bonding network (dotted lines).

Synthesis and crystallization

Ethyl L-sorboside, α-sorbopyranoside form, was prepared by Fischer glycosidation from L-sorbose and ethanol (Taguchi et al., 2018 ). The Fisher method produces isomers such as α-, β-, and furanose. Therefore, chromatographic separation using an ion-exchange resin was performed. After the separation step, the solution was evaporated to syrup. Small single crystals were obtained by keeping the flask at room temperature. It is obvious that the synthesized ethyl α-L-sorbose is still in the L-form after dehydrative condensation, because L-sorbose is used as the starting material. The absolute structure were also confirmed by the Flack (1983 ) parameter.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₈H₁₆O₆
M_r	208.21
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	296
a, b, c (Å)	6.8203 (8), 8.6934 (10), 15.865 (2)
V (Å³)	940.63 (19)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	1.09
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	0.462, 0.897
No. of measured, independent and observed [F² > 2.0σ(F²)] reflections	10373, 1721, 1602
R_int	0.091
(sin θ/λ)_max (Å⁻¹)	0.602

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.037, 0.090, 1.07
No. of reflections	1721
No. of parameters	127
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.20, −0.27
Absolute structure	Flack x determined using 581 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter	0.06 (12)
Computer programs: RAPID-AUTO (Rigaku, 2009 ), SIR2014 (Burla et al., 2015 ), SHELXL2018/3 (Sheldrick, 2015 ) and CrystalStructure (Rigaku, 2019 ).

Structural data

CCDC reference: 2046786

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314620016259/bv4033sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314620016259/bv4033Isup2.hkl

checkCIF report

Computing details top

Data collection: RAPID-AUTO (Rigaku, 2009); cell refinement: RAPID-AUTO (Rigaku, 2009); data reduction: RAPID-AUTO (Rigaku, 2009); program(s) used to solve structure: SIR2014 (Burla et al., 2015); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015); molecular graphics: CrystalStructure (Rigaku, 2019); software used to prepare material for publication: CrystalStructure (Rigaku, 2019).

Ethyl α-L-sorboside top

Crystal data top

C₈H₁₆O₆	D_x = 1.470 Mg m⁻³
M_r = 208.21	Cu Kα radiation, λ = 1.54187 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 9046 reflections
a = 6.8203 (8) Å	θ = 5.1–68.6°
b = 8.6934 (10) Å	µ = 1.09 mm⁻¹
c = 15.865 (2) Å	T = 296 K
V = 940.63 (19) Å³	Block, colorless
Z = 4	0.10 × 0.10 × 0.10 mm
F(000) = 448.00

Data collection top

Rigaku R-AXIS RAPID diffractometer	1602 reflections with F² > 2.0σ(F²)
Detector resolution: 10.000 pixels mm^-1	R_int = 0.091
ω scans	θ_max = 68.3°, θ_min = 5.6°
Absorption correction: multi-scan (ABSCOR; Rigaku, 1995)	h = −7→8
T_min = 0.462, T_max = 0.897	k = −10→10
10373 measured reflections	l = −19→18
1721 independent reflections

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.037	H-atom parameters constrained
wR(F²) = 0.090	w = 1/[σ²(F_o²) + (0.0379P)² + 0.0827P] where P = (F_o² + 2F_c²)/3
S = 1.07	(Δ/σ)_max < 0.001
1721 reflections	Δρ_max = 0.20 e Å⁻³
127 parameters	Δρ_min = −0.27 e Å⁻³
0 restraints	Absolute structure: Flack x determined using 581 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.06 (12)
Secondary atom site location: difference Fourier map

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 was performed using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F². R-factor (gt) are based on F. The threshold expression of F² > 2.0 sigma(F²) is used only for calculating R-factor (gt).

H atoms were positioned geometrically (C—H = 0.98, 0.97 or 0.96 Å, and O—H = 0.82 Å) and refined using as riding with U_iso(H) = 1.2U_eq(C or O), allowing for free rotation of the OH groups.

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

	x	y	z	U_iso*/U_eq
O1	0.0029 (3)	0.18389 (19)	0.69407 (12)	0.0427 (6)
H1	−0.027589	0.171200	0.743583	0.051*
O2	0.3056 (3)	0.46513 (18)	0.70305 (10)	0.0272 (4)
O3	0.0535 (3)	0.66379 (18)	0.63075 (10)	0.0309 (5)
H3	−0.023262	0.711551	0.600806	0.037*
O4	0.2892 (3)	0.71889 (18)	0.48325 (11)	0.0313 (5)
H4	0.222838	0.785460	0.506192	0.038*
O5	0.6053 (3)	0.51250 (18)	0.46175 (12)	0.0393 (6)
H5	0.633778	0.456529	0.421987	0.047*
O6	0.2702 (3)	0.28944 (17)	0.59356 (11)	0.0257 (4)
C1	−0.0118 (4)	0.3405 (3)	0.67368 (18)	0.0331 (6)
H1A	−0.052757	0.397130	0.723326	0.040*
H1B	−0.111982	0.353631	0.630877	0.040*
C2	0.1802 (4)	0.4074 (3)	0.64149 (16)	0.0238 (6)
C3	0.1421 (4)	0.5445 (3)	0.58310 (15)	0.0225 (5)
H3A	0.050371	0.512312	0.538941	0.027*
C4	0.3292 (4)	0.5991 (2)	0.54174 (16)	0.0242 (6)
H4A	0.420080	0.636598	0.584961	0.029*
C5	0.4209 (4)	0.4673 (3)	0.49524 (16)	0.0251 (6)
H5A	0.334371	0.435115	0.449203	0.030*
C6	0.4498 (4)	0.3347 (3)	0.55571 (16)	0.0283 (6)
H6A	0.505486	0.248021	0.525599	0.034*
H6B	0.541691	0.364895	0.599347	0.034*
C7	0.3484 (6)	0.3705 (3)	0.77397 (18)	0.0434 (8)
H7A	0.392720	0.269868	0.755600	0.052*
H7B	0.232444	0.357408	0.808608	0.052*
C8	0.5050 (5)	0.4492 (4)	0.8224 (2)	0.0500 (9)
H8A	0.538256	0.388699	0.870993	0.060*
H8B	0.618825	0.461344	0.787445	0.060*
H8C	0.459315	0.548465	0.840200	0.060*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0666 (16)	0.0315 (10)	0.0301 (10)	−0.0161 (9)	0.0115 (10)	0.0011 (8)
O2	0.0373 (11)	0.0233 (9)	0.0210 (9)	−0.0029 (8)	−0.0068 (8)	0.0021 (7)
O3	0.0390 (12)	0.0297 (9)	0.0241 (9)	0.0174 (8)	0.0028 (9)	0.0013 (7)
O4	0.0418 (12)	0.0220 (8)	0.0299 (10)	0.0040 (8)	0.0069 (9)	0.0058 (7)
O5	0.0410 (12)	0.0257 (9)	0.0512 (13)	−0.0061 (8)	0.0240 (10)	−0.0085 (9)
O6	0.0287 (10)	0.0190 (8)	0.0292 (10)	−0.0008 (7)	0.0060 (8)	−0.0011 (6)
C1	0.0334 (16)	0.0325 (14)	0.0335 (15)	−0.0032 (12)	0.0054 (13)	0.0051 (11)
C2	0.0277 (14)	0.0217 (12)	0.0221 (13)	0.0013 (10)	0.0001 (11)	−0.0003 (9)
C3	0.0250 (14)	0.0213 (11)	0.0213 (12)	0.0031 (10)	0.0019 (10)	−0.0016 (10)
C4	0.0292 (15)	0.0196 (11)	0.0239 (13)	−0.0014 (10)	0.0021 (11)	−0.0001 (9)
C5	0.0260 (14)	0.0215 (12)	0.0279 (14)	−0.0037 (10)	0.0088 (11)	−0.0035 (9)
C6	0.0268 (16)	0.0236 (12)	0.0344 (15)	0.0044 (11)	0.0057 (12)	−0.0015 (10)
C7	0.066 (2)	0.0321 (14)	0.0324 (16)	−0.0072 (14)	−0.0163 (16)	0.0080 (12)
C8	0.057 (2)	0.0532 (18)	0.0398 (18)	−0.0050 (16)	−0.0183 (17)	0.0121 (14)

Geometric parameters (Å, º) top

O1—C1	1.403 (3)	C2—C3	1.532 (3)
O1—H1	0.8200	C3—C4	1.512 (3)
O2—C2	1.392 (3)	C3—H3A	0.9800
O2—C7	1.424 (3)	C4—C5	1.499 (3)
O3—C3	1.418 (3)	C4—H4A	0.9800
O3—H3	0.8200	C5—C6	1.512 (3)
O4—C4	1.421 (3)	C5—H5A	0.9800
O4—H4	0.8200	C6—H6A	0.9700
O5—C5	1.420 (3)	C6—H6B	0.9700
O5—H5	0.8200	C7—C8	1.483 (4)
O6—C2	1.416 (3)	C7—H7A	0.9700
O6—C6	1.419 (3)	C7—H7B	0.9700
C1—C2	1.521 (4)	C8—H8A	0.9600
C1—H1A	0.9700	C8—H8B	0.9600
C1—H1B	0.9700	C8—H8C	0.9600

C1—O1—H1	109.5	O4—C4—H4A	109.5
C2—O2—C7	118.2 (2)	C5—C4—H4A	109.5
C3—O3—H3	109.5	C3—C4—H4A	109.5
C4—O4—H4	109.5	O5—C5—C4	109.99 (19)
C5—O5—H5	109.5	O5—C5—C6	109.5 (2)
C2—O6—C6	113.59 (17)	C4—C5—C6	108.94 (19)
O1—C1—C2	112.8 (2)	O5—C5—H5A	109.5
O1—C1—H1A	109.0	C4—C5—H5A	109.5
C2—C1—H1A	109.0	C6—C5—H5A	109.5
O1—C1—H1B	109.0	O6—C6—C5	111.6 (2)
C2—C1—H1B	109.0	O6—C6—H6A	109.3
H1A—C1—H1B	107.8	C5—C6—H6A	109.3
O2—C2—O6	111.8 (2)	O6—C6—H6B	109.3
O2—C2—C1	115.5 (2)	C5—C6—H6B	109.3
O6—C2—C1	106.1 (2)	H6A—C6—H6B	108.0
O2—C2—C3	104.35 (19)	O2—C7—C8	106.9 (2)
O6—C2—C3	108.20 (18)	O2—C7—H7A	110.3
C1—C2—C3	110.8 (2)	C8—C7—H7A	110.3
O3—C3—C4	111.19 (19)	O2—C7—H7B	110.3
O3—C3—C2	108.60 (18)	C8—C7—H7B	110.3
C4—C3—C2	111.3 (2)	H7A—C7—H7B	108.6
O3—C3—H3A	108.6	C7—C8—H8A	109.5
C4—C3—H3A	108.6	C7—C8—H8B	109.5
C2—C3—H3A	108.6	H8A—C8—H8B	109.5
O4—C4—C5	108.6 (2)	C7—C8—H8C	109.5
O4—C4—C3	110.6 (2)	H8A—C8—H8C	109.5
C5—C4—C3	109.02 (19)	H8B—C8—H8C	109.5

C7—O2—C2—O6	−71.6 (3)	C1—C2—C3—C4	−172.6 (2)
C7—O2—C2—C1	49.9 (3)	O3—C3—C4—O4	−63.0 (2)
C7—O2—C2—C3	171.7 (2)	C2—C3—C4—O4	175.78 (17)
C6—O6—C2—O2	−55.5 (2)	O3—C3—C4—C5	177.69 (19)
C6—O6—C2—C1	177.7 (2)	C2—C3—C4—C5	56.5 (3)
C6—O6—C2—C3	58.9 (3)	O4—C4—C5—O5	64.3 (3)
O1—C1—C2—O2	−88.5 (3)	C3—C4—C5—O5	−175.1 (2)
O1—C1—C2—O6	36.0 (3)	O4—C4—C5—C6	−175.7 (2)
O1—C1—C2—C3	153.2 (2)	C3—C4—C5—C6	−55.2 (3)
O2—C2—C3—O3	−60.3 (2)	C2—O6—C6—C5	−60.9 (3)
O6—C2—C3—O3	−179.47 (19)	O5—C5—C6—O6	177.60 (19)
C1—C2—C3—O3	64.7 (3)	C4—C5—C6—O6	57.3 (3)
O2—C2—C3—C4	62.5 (2)	C2—O2—C7—C8	172.0 (2)
O6—C2—C3—C4	−56.7 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O3ⁱ	0.82	2.00	2.811 (3)	169
O3—H3···O4ⁱⁱ	0.82	1.94	2.750 (3)	167
O4—H4···O3	0.82	2.52	2.879 (2)	108
O4—H4···O5ⁱⁱ	0.82	2.00	2.791 (2)	163
O5—H5···O6ⁱⁱⁱ	0.82	2.35	2.988 (2)	136

Symmetry codes: (i) −x, y−1/2, −z+3/2; (ii) x−1/2, −y+3/2, −z+1; (iii) x+1/2, −y+1/2, −z+1.

Acknowledgements

The authors are sincerely grateful to Professor Genta Sakane (Okayama University of Science) for excellent discussion and useful technical advice.

Funding information

The authors are grateful to Grants-in-Aid for Rare Sugar Research of Kagawa University and the Strategic Foundational Technology Improvement Support Operation (Supporting Industry Program) for financial support.

References

Burla, M. C., Caliandro, R., Carrozzini, B., Cascarano, G. L., Cuocci, C., Giacovazzo, C., Mallamo, M., Mazzone, A. & Polidori, G. (2015). J. Appl. Cryst. 48, 306–309. Web of Science CrossRef CAS IUCr Journals Google Scholar
Flack, H. D. (1983). Acta Cryst. A39, 876–881. CrossRef CAS Web of Science IUCr Journals Google Scholar
Itoh, H., Sato, T., Takeuchi, T., Khan, A. R. & Izumori, K. (1995). J. Ferment. Bioeng. 79, 184–185. CrossRef CAS Web of Science Google Scholar
Khan, A. R., Takahata, S., Okaya, H., Tsumura, T. & Izumori, K. (1992). J. Ferment. Bioeng. 74, 149–152. CrossRef CAS Web of Science Google Scholar
Nordenson, S., Takagi, S. & Jeffrey, G. A. (1979). Acta Cryst. B35, 1005–1007. CSD CrossRef CAS IUCr Journals Web of Science Google Scholar
Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249–259. Web of Science CrossRef CAS IUCr Journals Google Scholar
Rigaku (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan. Google Scholar
Rigaku (2009). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan. Google Scholar
Rigaku (2019). CrystalStructure. Rigaku Corporation, Tokyo, Japan. Google Scholar
Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Taguchi, H., Sogo, K., Ishii, T., Yoshihara, A. & Fukada, K. (2018). IUCrData, 3, x180114. 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.