Acetyl α-d-2,3,4-tri­acetyl­lyxo­pyran­oside

Culver, S.; Rhoad, J.S.

doi:10.1107/S2414314625000161

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 10| Part 1| January 2025| x250016

https://doi.org/10.1107/S2414314625000161

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Acetyl α-D-2,3,4-triacetyllyxopyranoside

Shawn Culver ^a and Jonathan S. Rhoad ^a ^*

^aMissouri Western State University, 4525 Downs Dr, Saint Joseph, MO 64507, USA
^*Correspondence e-mail: jrhoad1@missouriwestern.edu

Edited by W. T. A. Harrison, University of Aberdeen, United Kingdom (Received 6 January 2025; accepted 8 January 2025; online 10 January 2025)

The structure of the title compound, C₁₃H₁₈O₉, has monoclinic (P2₁) symmetry. It is of interest with respect to stereochemistry and the anomeric effect. Two acetyl subsituents adopt equatorial orientations and two are axial. The extended structure displays C—H⋯O hydrogen bonding.

Keywords: crystal structure; carbohydrate; anomeric effect; chair conformation.

CCDC reference: 2415464

Structure description

The anomeric effect is of interest to aid our understanding of conformational preferences and stereocontrol of reaction of carbohydrates and carbohydrate-like molecules (Juaristi, 2024 ; Alabugin et al., 2021 ). Our interest is in carbohydrate and carbohydrate analog ring conformations, leading to the synthesis of common carbohydrate derivatives. Recent methods have been used to try to evaluate the energy of the anomeric and related effects (Custodio Castro et al. 2024 ; Matamoros et al., 2024 ) using complex techniques to deconvolute steric effects from electronic effects.

The crystal structure of the title compound, C₁₃H₁₈O₉ (aLyx) (Fig. 1), is of interest because the two chair conformations each have two acetate groups in axial orientations and two acetate groups equatorial, with the acetate groups at positions 2 and 3 cis, so that in the chair conformations, they are always gauche. This means that the total energy of the steric interactions for each chair conformation is equal, so any difference in energy is due to the electronic interaction at the acetal group. In the solid state, aLyx is in the ⁴C₁ conformation, with Cremer & Pople (1975 ) puckering parameters of φ = 263 (3)°, θ = 4.3 (2)° and Q = 0.543 (2) Å. Since θ is close to 0°, it is in a nearly perfect chair conformation, while the Q parameter is lower than average, so the chair is a little flattened. The flattening is to be expected with two acetate groups in the axial position, as flattening the ring decreases gauche interactions of axial groups with the ring. The acetate substituent at the anomeric (C1) position is axial, indicating the influence of the anomeric effect. The key torsion angles are O1—C1—C2—O2 = 169.73 (14)° and O3—C3—C4—O4 = −71.1 (2)°. The configurations of the stereogenic centers are C1 R, C2 S, C3 R and C4 R, as expected for the lyxose starting material. This structure will be the starting point for calculations to quantify the anomeric effect in this sterically balanced molecule. In the crystal, weak C—H⋯O interactions (Table 1) link the molecules.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C1—H1⋯O8ⁱ	0.97 (3)	2.47 (3)	3.198 (3)	132 (2)
C5—H5B⋯O7ⁱ	0.94 (3)	2.63 (3)	3.528 (3)	160 (2)
C9—H9C⋯O5ⁱⁱ	0.97 (3)	2.57 (3)	3.434 (3)	149 (3)
C11—H11C⋯O6ⁱⁱⁱ	1.07 (4)	2.39 (4)	3.331 (3)	145 (3)
C13—H13C⋯O6ⁱⁱⁱ	0.92 (5)	2.66 (5)	3.554 (4)	162 (4)
Symmetry codes: (i) $[-x, y-{\script{1\over 2}}, -z+1]$ ; (ii) ; (iii) .

Figure 1
The molecular structure of aLyx showing 50% displacement ellipsoids.

Synthesis and crystallization

100 mg (6.7 mmol) of lyxose and 10 mg of sodium acetate were dissolved in approximately 2 ml of acetic anhydride. The solution was heated to reflux for 2 h. After cooling the reaction mixture to room temperature, the solution was poured over crushed ice. After the ice melted, the resulting oil was separated from the water and dissolved in minimal boiling ethanol. A few grains of activated charcoal were added to the ethanol and the solution was boiled as before. This was then passed through a cotton filter and eluted through a silica gel column with a 80:20 hexane-to-dichloromethane mobile phase. Upon evaporation, fine crystals were formed. The crystals were dissolved in a minimal amount of ether and allowed to evaporate overnight to form rectangular parallelepipeds of aLyx.

Refinement

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

Table 2
Experimental details

Crystal data
Chemical formula	C₁₃H₁₈O₉
M_r	318.27
Crystal system, space group	Monoclinic, P2₁
Temperature (K)	200
a, b, c (Å)	8.1174 (3), 9.5597 (4), 10.2580 (4)
β (°)	109.7341 (14)
V (Å³)	749.27 (5)
Z	2
Radiation type	Cu Kα
μ (mm⁻¹)	1.05
Crystal size (mm)	0.20 × 0.08 × 0.05

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Krause et al., 2015 )
T_min, T_max	0.650, 0.753
No. of measured, independent and observed [I > 2σ(I)] reflections	5524, 2107, 2081
R_int	0.025
(sin θ/λ)_max (Å⁻¹)	0.610

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.032, 0.076, 1.11
No. of reflections	2107
No. of parameters	270
No. of restraints	1
H-atom treatment	Only H-atom displacement parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.30, −0.25
Absolute structure	Flack x determined using 630 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013 )
Absolute structure parameter	0.08 (7)
Computer programs: APEX2 (Bruker, 2017 ), SAINT (Bruker, 2014 ), SHELXS97 and SHELXTL (Sheldrick 2008 ) and SHELXL2019/1 (Sheldrick, 2015 ).

Structural data

CCDC reference: 2415464

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314625000161/hb4504sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314625000161/hb4504Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314625000161/hb4504Isup3.cdx

checkCIF report

Computing details top

Acetyl α-D-2,3,4-triacetyllyxopyranoside top

Crystal data top

C₁₃H₁₈O₉	F(000) = 336
M_r = 318.27	D_x = 1.411 Mg m⁻³
Monoclinic, P2₁	Cu Kα radiation, λ = 1.54178 Å
a = 8.1174 (3) Å	Cell parameters from 5073 reflections
b = 9.5597 (4) Å	θ = 6.5–70.0°
c = 10.2580 (4) Å	µ = 1.05 mm⁻¹
β = 109.7341 (14)°	T = 200 K
V = 749.27 (5) Å³	Rectangular parallelepiped, colourless
Z = 2	0.20 × 0.08 × 0.05 mm

Data collection top

Bruker APEXII CCD diffractometer	2081 reflections with I > 2σ(I)
φ and ω scans	R_int = 0.025
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	θ_max = 70.1°, θ_min = 6.5°
T_min = 0.650, T_max = 0.753	h = −9→8
5524 measured reflections	k = −11→8
2107 independent reflections	l = −12→12

Refinement top

Refinement on F²	Only H-atom displacement parameters refined
Least-squares matrix: full	w = 1/[σ²(F_o²) + (0.0444P)² + 0.0979P] where P = (F_o² + 2F_c²)/3
R[F² > 2σ(F²)] = 0.032	(Δ/σ)_max < 0.001
wR(F²) = 0.076	Δρ_max = 0.30 e Å⁻³
S = 1.11	Δρ_min = −0.24 e Å⁻³
2107 reflections	Extinction correction: SHELXL2019/1 (Sheldrick, 2015), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
270 parameters	Extinction coefficient: 0.028 (3)
1 restraint	Absolute structure: Flack x determined using 630 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
Hydrogen site location: difference Fourier map	Absolute structure parameter: 0.08 (7)

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 ring and methyl hydrogen atoms were initially located in difference-Fourier maps and refined as individual isotropic atoms.

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

	x	y	z	U_iso*/U_eq
O1	−0.12797 (18)	0.61079 (17)	0.65441 (14)	0.0265 (4)
O2	0.18123 (17)	0.40848 (17)	0.55297 (15)	0.0261 (4)
O3	0.05956 (18)	0.56065 (17)	0.31122 (15)	0.0278 (4)
O4	−0.2996 (2)	0.45517 (19)	0.21466 (16)	0.0335 (4)
O5	−0.14941 (18)	0.37458 (16)	0.58585 (15)	0.0267 (4)
O6	−0.1547 (2)	0.5135 (2)	0.84634 (17)	0.0396 (4)
O7	0.4179 (2)	0.5469 (2)	0.5983 (2)	0.0458 (5)
O8	−0.1219 (2)	0.7203 (2)	0.17276 (16)	0.0374 (4)
O9	−0.2878 (4)	0.2352 (3)	0.1434 (2)	0.0698 (7)
C1	−0.0355 (3)	0.4874 (2)	0.6386 (2)	0.0249 (5)
H1	0.038 (3)	0.457 (3)	0.730 (3)	0.025 (6)*
C2	0.0676 (2)	0.5270 (2)	0.5439 (2)	0.0237 (4)
H2	0.138 (3)	0.606 (3)	0.571 (3)	0.020 (5)*
C3	−0.0509 (3)	0.5479 (2)	0.3942 (2)	0.0244 (4)
H3	−0.117 (3)	0.631 (3)	0.386 (2)	0.018 (5)*
C4	−0.1710 (3)	0.4228 (3)	0.3476 (2)	0.0260 (5)
H4	−0.103 (3)	0.344 (3)	0.343 (2)	0.020 (6)*
C5	−0.2688 (3)	0.3961 (3)	0.4481 (2)	0.0273 (5)
H5A	−0.342 (3)	0.470 (3)	0.446 (2)	0.017 (6)*
H5B	−0.336 (3)	0.315 (3)	0.427 (3)	0.021 (6)*
C6	−0.1753 (3)	0.6122 (3)	0.7703 (2)	0.0285 (5)
C7	−0.2522 (4)	0.7496 (3)	0.7883 (3)	0.0381 (6)
H7A	−0.211 (2)	0.7748 (15)	0.880 (5)	0.075 (12)*
H7B	−0.232 (7)	0.826 (6)	0.730 (6)	0.093 (15)*
H7C	−0.369 (8)	0.738 (7)	0.761 (6)	0.104 (18)*
C8	0.3551 (3)	0.4327 (3)	0.5903 (2)	0.0267 (5)
C9	0.4529 (3)	0.2978 (3)	0.6181 (2)	0.0305 (5)
H9A	0.414 (4)	0.237 (4)	0.535 (4)	0.050 (9)*
H9B	0.428 (4)	0.251 (4)	0.691 (3)	0.034 (7)*
H9C	0.579 (4)	0.312 (4)	0.648 (3)	0.045 (8)*
C10	0.0097 (3)	0.6518 (3)	0.2030 (2)	0.0301 (5)
C11	0.1387 (4)	0.6508 (4)	0.1280 (3)	0.0423 (6)
H11A	0.246 (5)	0.623 (5)	0.185 (4)	0.051 (9)*
H11B	0.141 (7)	0.742 (7)	0.088 (6)	0.092 (15)*
H11C	0.090 (5)	0.577 (5)	0.045 (4)	0.060 (10)*
C12	−0.3453 (3)	0.3515 (3)	0.1204 (2)	0.0394 (6)
C13	−0.4761 (4)	0.4017 (5)	−0.0120 (3)	0.0540 (9)
H13A	−0.544 (7)	0.482 (7)	0.009 (5)	0.092 (16)*
H13B	−0.546 (6)	0.333 (6)	−0.055 (5)	0.074 (13)*
H13C	−0.410 (6)	0.421 (6)	−0.067 (5)	0.074 (12)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0271 (7)	0.0251 (8)	0.0268 (6)	0.0027 (6)	0.0085 (5)	−0.0005 (6)
O2	0.0187 (7)	0.0230 (8)	0.0344 (7)	0.0007 (6)	0.0060 (5)	−0.0024 (6)
O3	0.0275 (7)	0.0268 (8)	0.0305 (7)	0.0011 (6)	0.0117 (6)	0.0024 (6)
O4	0.0309 (7)	0.0349 (10)	0.0273 (7)	−0.0029 (7)	0.0000 (6)	−0.0030 (7)
O5	0.0260 (7)	0.0231 (8)	0.0294 (7)	−0.0025 (6)	0.0073 (6)	0.0005 (6)
O6	0.0494 (9)	0.0388 (11)	0.0336 (8)	0.0015 (8)	0.0179 (7)	0.0031 (8)
O7	0.0252 (8)	0.0303 (10)	0.0781 (12)	−0.0055 (7)	0.0126 (8)	−0.0029 (10)
O8	0.0374 (9)	0.0336 (10)	0.0333 (8)	0.0012 (8)	0.0015 (6)	0.0044 (7)
O9	0.0903 (17)	0.0519 (16)	0.0528 (12)	0.0004 (14)	0.0051 (11)	−0.0247 (12)
C1	0.0236 (9)	0.0231 (11)	0.0262 (9)	0.0010 (8)	0.0061 (7)	−0.0016 (8)
C2	0.0208 (9)	0.0187 (11)	0.0306 (10)	0.0001 (8)	0.0071 (7)	−0.0019 (9)
C3	0.0228 (9)	0.0224 (11)	0.0282 (9)	0.0017 (9)	0.0090 (8)	−0.0006 (9)
C4	0.0227 (9)	0.0254 (11)	0.0265 (10)	0.0005 (9)	0.0038 (7)	−0.0025 (9)
C5	0.0222 (10)	0.0260 (12)	0.0310 (10)	−0.0018 (10)	0.0056 (8)	−0.0024 (9)
C6	0.0267 (10)	0.0316 (13)	0.0263 (9)	−0.0029 (9)	0.0075 (7)	−0.0049 (9)
C7	0.0417 (14)	0.0378 (15)	0.0361 (12)	0.0055 (11)	0.0146 (10)	−0.0067 (11)
C8	0.0212 (9)	0.0320 (12)	0.0262 (9)	−0.0009 (9)	0.0071 (7)	−0.0011 (9)
C9	0.0234 (10)	0.0325 (14)	0.0334 (11)	0.0029 (9)	0.0067 (8)	0.0030 (10)
C10	0.0326 (11)	0.0274 (12)	0.0259 (10)	−0.0081 (10)	0.0042 (8)	−0.0036 (9)
C11	0.0424 (14)	0.0515 (17)	0.0327 (12)	−0.0114 (12)	0.0124 (10)	0.0015 (12)
C12	0.0392 (12)	0.0507 (18)	0.0303 (11)	−0.0095 (12)	0.0144 (9)	−0.0103 (11)
C13	0.0473 (15)	0.084 (3)	0.0263 (11)	−0.0197 (18)	0.0065 (10)	−0.0040 (15)

Geometric parameters (Å, º) top

O1—C6	1.367 (3)	C4—C5	1.520 (3)
O1—C1	1.437 (3)	C4—H4	0.95 (3)
O2—C8	1.352 (3)	C5—H5A	0.92 (3)
O2—C2	1.444 (2)	C5—H5B	0.94 (3)
O3—C10	1.361 (3)	C6—C7	1.493 (4)
O3—C3	1.435 (2)	C7—H7A	0.91 (5)
O4—C12	1.346 (3)	C7—H7B	0.99 (6)
O4—C4	1.443 (2)	C7—H7C	0.90 (6)
O5—C1	1.405 (3)	C8—C9	1.491 (3)
O5—C5	1.433 (2)	C9—H9A	0.99 (4)
O6—C6	1.199 (3)	C9—H9B	0.95 (3)
O7—C8	1.196 (3)	C9—H9C	0.97 (3)
O8—C10	1.201 (3)	C10—C11	1.494 (3)
O9—C12	1.198 (4)	C11—H11A	0.91 (4)
C1—C2	1.528 (3)	C11—H11B	0.96 (7)
C1—H1	0.97 (3)	C11—H11C	1.07 (4)
C2—C3	1.525 (3)	C12—C13	1.493 (4)
C2—H2	0.94 (3)	C13—H13A	1.01 (6)
C3—C4	1.515 (3)	C13—H13B	0.89 (6)
C3—H3	0.94 (3)	C13—H13C	0.92 (5)

C6—O1—C1	114.64 (16)	O6—C6—C7	125.7 (2)
C8—O2—C2	117.83 (18)	O1—C6—C7	111.6 (2)
C10—O3—C3	117.73 (17)	C6—C7—H7A	109.7
C12—O4—C4	117.2 (2)	C6—C7—H7B	114 (3)
C1—O5—C5	114.06 (16)	H7A—C7—H7B	110.1
O5—C1—O1	111.88 (15)	C6—C7—H7C	107 (4)
O5—C1—C2	112.09 (17)	H7A—C7—H7C	109.4
O1—C1—C2	106.69 (17)	H7B—C7—H7C	106 (5)
O5—C1—H1	104.6 (17)	O7—C8—O2	123.8 (2)
O1—C1—H1	108.5 (16)	O7—C8—C9	126.10 (19)
C2—C1—H1	113.1 (15)	O2—C8—C9	110.1 (2)
O2—C2—C3	109.81 (16)	C8—C9—H9A	110 (2)
O2—C2—C1	103.86 (16)	C8—C9—H9B	109 (2)
C3—C2—C1	112.22 (16)	H9A—C9—H9B	108 (3)
O2—C2—H2	107.6 (16)	C8—C9—H9C	112 (2)
C3—C2—H2	108.1 (15)	H9A—C9—H9C	110 (3)
C1—C2—H2	115.0 (15)	H9B—C9—H9C	107 (3)
O3—C3—C4	110.17 (17)	O8—C10—O3	123.6 (2)
O3—C3—C2	107.51 (15)	O8—C10—C11	126.0 (2)
C4—C3—C2	109.53 (17)	O3—C10—C11	110.4 (2)
O3—C3—H3	109.2 (15)	C10—C11—H11A	111 (2)
C4—C3—H3	110.3 (15)	C10—C11—H11B	109 (3)
C2—C3—H3	110.1 (14)	H11A—C11—H11B	113 (4)
O4—C4—C3	108.18 (18)	C10—C11—H11C	106 (2)
O4—C4—C5	107.47 (16)	H11A—C11—H11C	109 (3)
C3—C4—C5	110.29 (17)	H11B—C11—H11C	108 (4)
O4—C4—H4	111.8 (15)	O9—C12—O4	123.2 (2)
C3—C4—H4	108.6 (15)	O9—C12—C13	126.0 (3)
C5—C4—H4	110.5 (15)	O4—C12—C13	110.8 (3)
O5—C5—C4	111.03 (16)	C12—C13—H13A	109 (3)
O5—C5—H5A	110.3 (15)	C12—C13—H13B	111 (3)
C4—C5—H5A	109.7 (15)	H13A—C13—H13B	112 (4)
O5—C5—H5B	105.0 (15)	C12—C13—H13C	104 (3)
C4—C5—H5B	112.4 (15)	H13A—C13—H13C	117 (5)
H5A—C5—H5B	108 (2)	H13B—C13—H13C	104 (4)
O6—C6—O1	122.7 (2)

C5—O5—C1—O1	64.6 (2)	C12—O4—C4—C5	−99.9 (2)
C5—O5—C1—C2	−55.2 (2)	O3—C3—C4—O4	−71.1 (2)
C6—O1—C1—O5	79.4 (2)	C2—C3—C4—O4	170.86 (16)
C6—O1—C1—C2	−157.64 (16)	O3—C3—C4—C5	171.64 (17)
C8—O2—C2—C3	114.69 (18)	C2—C3—C4—C5	53.6 (2)
C8—O2—C2—C1	−125.12 (17)	C1—O5—C5—C4	58.9 (2)
O5—C1—C2—O2	−67.48 (19)	O4—C4—C5—O5	−175.16 (18)
O1—C1—C2—O2	169.73 (14)	C3—C4—C5—O5	−57.5 (2)
O5—C1—C2—C3	51.1 (2)	C1—O1—C6—O6	−6.1 (3)
O1—C1—C2—C3	−71.7 (2)	C1—O1—C6—C7	173.50 (18)
C10—O3—C3—C4	97.3 (2)	C2—O2—C8—O7	−10.3 (3)
C10—O3—C3—C2	−143.44 (18)	C2—O2—C8—C9	170.07 (16)
O2—C2—C3—O3	−55.3 (2)	C3—O3—C10—O8	−0.8 (3)
C1—C2—C3—O3	−170.28 (18)	C3—O3—C10—C11	−179.63 (19)
O2—C2—C3—C4	64.4 (2)	C4—O4—C12—O9	1.9 (4)
C1—C2—C3—C4	−50.6 (2)	C4—O4—C12—C13	−178.94 (19)
C12—O4—C4—C3	141.0 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1···O8ⁱ	0.97 (3)	2.47 (3)	3.198 (3)	132 (2)
C5—H5B···O7ⁱ	0.94 (3)	2.63 (3)	3.528 (3)	160 (2)
C9—H9C···O5ⁱⁱ	0.97 (3)	2.57 (3)	3.434 (3)	149 (3)
C11—H11C···O6ⁱⁱⁱ	1.07 (4)	2.39 (4)	3.331 (3)	145 (3)
C13—H13C···O6ⁱⁱⁱ	0.92 (5)	2.66 (5)	3.554 (4)	162 (4)

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

Acknowledgements

The authors would like to thank Dr Victor Day and acknowledge the NSF-MRI grant (CHE-0923449) that was used to purchase the X-ray diffractometer and software used in this study.

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