Phenyl 2,3,4-tri-O-acetyl-1-thio-α-L-rhamnopyran­oside: a glycosyl donor

The title compound, C₁₈H₂₂O₇S, is the product of the per-O-acetyl­ation and thio­glycosyl­ation of the hexose L-(+)-rhamnopyran­ose. The structure has a chair conformation and the thio­phenyl group on the anomeric carbon (C-1) is in an axial position.

Key indicators

• Single-crystal X-ray study
• T = 295 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.035
• wR factor = 0.095
• Data-to-parameter ratio = 8.5

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT062_ALERT_4_C Rescale T(min) & T(max) by .....................       0.96
PLAT063_ALERT_3_C Crystal Probably too Large for Beam Size .......       0.80 mm
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for          S
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         C7
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         C9
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for        C11
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for        C13
PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ...          5
PLAT380_ALERT_4_C Check Incorrectly? Oriented X(sp2)-Methyl Moiety         C8
PLAT380_ALERT_4_C Check Incorrectly? Oriented X(sp2)-Methyl Moiety        C10
PLAT380_ALERT_4_C Check Incorrectly? Oriented X(sp2)-Methyl Moiety        C12

Alert level G
ABSTM02_ALERT_3_G  When printed, the submitted absorption T values will be
            replaced by the scaled T values. Since the ratio of scaled T's
            is identical to the ratio of reported T values, the scaling
            does not imply a change to the absorption corrections used in
            the study.
            Ratio of Tmax expected/reported      0.961
            Tmax scaled      0.961 Tmin scaled      0.871
REFLT03_ALERT_4_G  WARNING: Large fraction of Friedel related reflns may
                     be needed to determine absolute structure
           From the CIF: _diffrn_reflns_theta_max           25.00
           From the CIF: _reflns_number_total               2014
           Count of symmetry unique reflns         1846
           Completeness (_total/calc)            109.10%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured       168
           Fraction of Friedel pairs measured     0.091
           Are heavy atom types Z>Si present        yes
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C1     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C4     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C5     = .          S
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          1

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
  11 ALERT level C = Check and explain
   8 ALERT level G = General alerts; check

   5 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   5 ALERT type 2 Indicator that the structure model may be wrong or deficient
   4 ALERT type 3 Indicator that the structure quality may be low
   5 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

Rhamnolipids comprise one of the most important classes of biosurfactants (Lang et al., 1999) and exhibit diverse biological functions (Leisinger et al., 1979). For the above reasons, the total synthesis of rhamnolipids has attracted considerable attention recently (Bauer et al., 2006). Thioglycosides have been widely used as a glycosyl donor in synthetic carbohydrate chemistry (Garegg, 1997; Norberg, 1995). According to the literature (Agnihotri et al., 2005), the title compound, C₁₈H₂₂O₇S (I), was synthesized via one-pot two-step reaction of the commercially available optically pure L-(+)-rhamnopyranose as the starting material. As a part of our study on the total synthesis of rhamnolipids, the structure of (I) was investigated (Fig. 1). Notably, the thiophenyl group on anomeric carbon (C-1) is in an axial position.

Related literature

For related literature, see: Agnihotri et al. (2005); Bauer et al. (2006); Garegg (1997); Lang & Wullbrandt (1999); Leisinger & Margraff (1979); Norberg (1995).

S2. Experimental

To a stirred suspension of L-(+)-rhamnopyranose ([a]²⁰_D = + 8.2°) (0.846 g, 5.16 mmol) in acetic anhydride (Ac₂O) (2.0 ml, 21.29 mmol) was added BF₃.OEt₂ (3.9 ml, 30.96 mmol) in one portion at 0°C. The mixture was stirred for 5 min at 0°C, and then was continuously stirred at room temperature for 15 min. After completion of this reaction, thiophenol (0.8 ml, 7.74 mmol) was added to the mixture at 0°C. The reaction mixture was allowed to stir for additional 4 h at room temperature. Finally, the reaction mixture was diluted with CH₂Cl₂, and washed with aqueous NaHCO₃ and brine. The organic layer was dried over MgSO₄, and solvent was removed in vacuo to afford a crude thioglycoside product. The crude product was recrystalized from CH₂Cl₂ at room temperature, affording single crystals of (I).

S3. Refinement

All the H atoms were included in the riding-model approximation, with C—H = 0.93–0.98 Å, and with U_iso(H) = 1.2 or 1.5U_eq(C).

Computing details

Data collection: XSCANS (Siemens, 1995); cell refinement: XSCANS; data reduction: SHELXTL (Bruker, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Figures

Fig. 1. The molecular structure of the title compound, showing the atom numbering scheme. Displacement ellipsoids for non-H atoms are represented at the 30% probability level.

Phenyl 2,3,4-tri-O-acetyl-1-thio-α-L-rhamnopyranoside

Crystal data

C18H22O7S	F(000) = 404
Mr = 382.42	Dx = 1.275 Mg m^−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 29 reflections
a = 9.3919 (11) Å	θ = 6.0–12.4°
b = 11.6665 (13) Å	µ = 0.20 mm^−1
c = 9.5762 (9) Å	T = 295 K
β = 108.336 (8)°	Plate, colourless
V = 996.00 (19) Å^3	0.8 × 0.8 × 0.2 mm
Z = 2

Data collection

Bruker P4 diffractometer	1726 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.016
Graphite monochromator	θmax = 25.0°, θmin = 2.2°
ω scans	h = −11→1
Absorption correction: empirical (using intensity measurements) (North et al., 1968)	k = −13→1
Tmin = 0.906, Tmax = 1.000	l = −11→11
2399 measured reflections	3 standard reflections every 97 reflections
2014 independent reflections	intensity decay: none

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F^2 > 2σ(F^2)] = 0.035	w = 1/[σ^2(Fo^2) + (0.0528P)^2 + 0.0914P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.095	(Δ/σ)max < 0.001
S = 1.06	Δρmax = 0.15 e Å^−3
2014 reflections	Δρmin = −0.15 e Å^−3
236 parameters	Extinction correction: SHELXL97 (Sheldrick, 1997), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
1 restraint	Extinction coefficient: 0.071 (5)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), with how many Friedel pairs?
Secondary atom site location: difference Fourier map	Absolute structure parameter: 0.15 (11)

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
S	0.71622 (9)	0.58066 (11)	0.27509 (10)	0.0893 (4)
O1	0.9073 (2)	0.5858 (2)	0.1105 (2)	0.0684 (6)
O2	1.1033 (3)	0.3275 (2)	0.2803 (3)	0.0776 (6)
O3	1.3394 (4)	0.3395 (3)	0.2778 (5)	0.1269 (12)
O4	1.2028 (2)	0.4910 (2)	0.5112 (2)	0.0700 (6)
O5	1.0905 (4)	0.4401 (4)	0.6729 (3)	0.1258 (13)
O6	1.1337 (2)	0.6904 (2)	0.3493 (2)	0.0647 (6)
O7	1.1768 (3)	0.7723 (3)	0.5708 (3)	0.1008 (9)
C1	0.9412 (4)	0.4654 (4)	0.1286 (3)	0.0732 (9)
H1A	0.8576	0.4255	0.1481	0.088*
C2	1.0808 (4)	0.4495 (3)	0.2584 (3)	0.0651 (8)
H2A	1.1672	0.4845	0.2384	0.078*
C3	1.0615 (3)	0.4993 (3)	0.3959 (3)	0.0615 (8)
H3A	0.9853	0.4555	0.4234	0.074*
C4	1.0142 (3)	0.6235 (3)	0.3728 (3)	0.0607 (8)
H4A	0.9894	0.6525	0.4584	0.073*
C5	0.8789 (3)	0.6376 (3)	0.2326 (3)	0.0661 (8)
H5A	0.8627	0.7197	0.2123	0.079*
C6	0.9561 (5)	0.4222 (5)	−0.0152 (4)	0.1013 (14)
H6A	0.8632	0.4338	−0.0926	0.152*
H6B	0.9799	0.3420	−0.0068	0.152*
H6C	1.0347	0.4635	−0.0375	0.152*
C7	1.2363 (5)	0.2831 (4)	0.2874 (4)	0.0862 (11)
C8	1.2399 (7)	0.1577 (4)	0.3079 (6)	0.1234 (18)
H8A	1.3371	0.1291	0.3126	0.185*
H8B	1.1650	0.1228	0.2267	0.185*
H8C	1.2199	0.1397	0.3978	0.185*
C9	1.2027 (4)	0.4579 (4)	0.6445 (4)	0.0773 (9)
C10	1.3577 (5)	0.4463 (5)	0.7456 (4)	0.1005 (13)
H10A	1.3550	0.4221	0.8406	0.151*
H10B	1.4080	0.5189	0.7546	0.151*
H10C	1.4107	0.3904	0.7073	0.151*
C11	1.2070 (4)	0.7624 (3)	0.4583 (3)	0.0685 (8)
C12	1.3237 (5)	0.8277 (5)	0.4201 (5)	0.1000 (13)
H12A	1.3734	0.8781	0.4997	0.150*
H12B	1.2784	0.8719	0.3328	0.150*
H12C	1.3955	0.7756	0.4028	0.150*
C13	0.5623 (3)	0.6339 (3)	0.1330 (3)	0.0634 (8)
C14	0.4234 (3)	0.6131 (4)	0.1486 (4)	0.0804 (10)
H14A	0.4167	0.5725	0.2299	0.096*
C15	0.2955 (4)	0.6515 (4)	0.0456 (5)	0.0940 (13)
H15A	0.2029	0.6381	0.0588	0.113*
C16	0.3018 (4)	0.7092 (4)	−0.0761 (4)	0.0826 (10)
H16A	0.2141	0.7330	−0.1470	0.099*
C17	0.4385 (4)	0.7316 (3)	−0.0930 (4)	0.0762 (9)
H17A	0.4438	0.7725	−0.1746	0.091*
C18	0.5683 (3)	0.6936 (4)	0.0104 (3)	0.0752 (9)
H18A	0.6607	0.7084	−0.0025	0.090*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S	0.0608 (4)	0.1375 (10)	0.0750 (5)	0.0014 (6)	0.0291 (4)	0.0332 (6)
O1	0.0708 (11)	0.0835 (16)	0.0546 (11)	−0.0044 (12)	0.0251 (9)	0.0021 (11)
O2	0.0880 (15)	0.0677 (16)	0.0893 (15)	−0.0044 (13)	0.0454 (13)	−0.0008 (13)
O3	0.109 (2)	0.112 (3)	0.187 (3)	0.026 (2)	0.086 (2)	0.017 (3)
O4	0.0659 (12)	0.0861 (17)	0.0605 (12)	0.0013 (12)	0.0233 (10)	0.0060 (12)
O5	0.119 (2)	0.196 (4)	0.0671 (14)	−0.034 (3)	0.0365 (15)	0.014 (2)
O6	0.0648 (12)	0.0733 (14)	0.0601 (11)	−0.0079 (11)	0.0253 (10)	−0.0048 (11)
O7	0.1001 (18)	0.133 (3)	0.0669 (13)	−0.0129 (18)	0.0227 (13)	−0.0250 (16)
C1	0.079 (2)	0.078 (2)	0.0663 (18)	−0.0140 (18)	0.0280 (16)	−0.0045 (18)
C2	0.0703 (18)	0.066 (2)	0.0684 (17)	−0.0064 (16)	0.0353 (15)	−0.0024 (16)
C3	0.0561 (16)	0.075 (2)	0.0580 (15)	−0.0048 (16)	0.0242 (13)	0.0023 (15)
C4	0.0561 (15)	0.077 (2)	0.0561 (15)	−0.0040 (15)	0.0273 (13)	−0.0025 (14)
C5	0.0604 (15)	0.083 (2)	0.0590 (16)	0.0003 (17)	0.0252 (13)	0.0051 (16)
C6	0.131 (4)	0.107 (3)	0.0647 (19)	−0.003 (3)	0.028 (2)	−0.013 (2)
C7	0.114 (3)	0.077 (3)	0.084 (2)	0.009 (2)	0.055 (2)	−0.001 (2)
C8	0.185 (5)	0.084 (3)	0.126 (4)	0.026 (3)	0.084 (4)	0.008 (3)
C9	0.094 (2)	0.078 (2)	0.0596 (18)	−0.005 (2)	0.0231 (18)	0.0009 (17)
C10	0.116 (3)	0.094 (3)	0.076 (2)	0.013 (3)	0.009 (2)	0.004 (2)
C11	0.0626 (17)	0.072 (2)	0.0609 (17)	0.0046 (16)	0.0051 (14)	0.0010 (17)
C12	0.098 (3)	0.097 (3)	0.098 (3)	−0.032 (3)	0.020 (2)	−0.001 (3)
C13	0.0618 (15)	0.0681 (19)	0.0667 (17)	−0.0021 (16)	0.0294 (14)	0.0037 (16)
C14	0.0677 (18)	0.091 (3)	0.090 (2)	0.0028 (19)	0.0366 (17)	0.024 (2)
C15	0.0639 (19)	0.118 (4)	0.107 (3)	0.006 (2)	0.0362 (19)	0.027 (3)
C16	0.069 (2)	0.087 (3)	0.092 (2)	0.014 (2)	0.0260 (17)	0.011 (2)
C17	0.080 (2)	0.082 (2)	0.0682 (18)	0.0037 (19)	0.0257 (16)	0.0099 (18)
C18	0.0639 (17)	0.098 (3)	0.0676 (18)	−0.0056 (19)	0.0264 (15)	0.0052 (19)

Geometric parameters (Å, º)

S—C13	1.758 (3)	C6—H6C	0.9600
S—C5	1.826 (3)	C7—C8	1.475 (7)
O1—C5	1.414 (4)	C8—H8A	0.9600
O1—C1	1.439 (5)	C8—H8B	0.9600
O2—C7	1.333 (5)	C8—H8C	0.9600
O2—C2	1.445 (4)	C9—C10	1.479 (5)
O3—C7	1.198 (5)	C10—H10A	0.9600
O4—C9	1.334 (4)	C10—H10B	0.9600
O4—C3	1.439 (4)	C10—H10C	0.9600
O5—C9	1.186 (5)	C11—C12	1.473 (5)
O6—C11	1.348 (4)	C12—H12A	0.9600
O6—C4	1.442 (4)	C12—H12B	0.9600
O7—C11	1.202 (4)	C12—H12C	0.9600
C1—C2	1.508 (5)	C13—C18	1.381 (5)
C1—C6	1.513 (5)	C13—C14	1.381 (4)
C1—H1A	0.9800	C14—C15	1.368 (5)
C2—C3	1.502 (4)	C14—H14A	0.9300
C2—H2A	0.9800	C15—C16	1.363 (6)
C3—C4	1.511 (5)	C15—H15A	0.9300
C3—H3A	0.9800	C16—C17	1.369 (5)
C4—C5	1.540 (4)	C16—H16A	0.9300
C4—H4A	0.9800	C17—C18	1.380 (5)
C5—H5A	0.9800	C17—H17A	0.9300
C6—H6A	0.9600	C18—H18A	0.9300
C6—H6B	0.9600
C13—S—C5	103.93 (15)	O2—C7—C8	111.9 (4)
C5—O1—C1	114.2 (2)	C7—C8—H8A	109.5
C7—O2—C2	118.8 (3)	C7—C8—H8B	109.5
C9—O4—C3	118.4 (3)	H8A—C8—H8B	109.5
C11—O6—C4	116.7 (2)	C7—C8—H8C	109.5
O1—C1—C2	108.7 (3)	H8A—C8—H8C	109.5
O1—C1—C6	107.2 (3)	H8B—C8—H8C	109.5
C2—C1—C6	113.8 (3)	O5—C9—O4	122.5 (3)
O1—C1—H1A	109.0	O5—C9—C10	126.6 (4)
C2—C1—H1A	109.0	O4—C9—C10	110.8 (3)
C6—C1—H1A	109.0	C9—C10—H10A	109.5
O2—C2—C3	107.8 (3)	C9—C10—H10B	109.5
O2—C2—C1	106.9 (3)	H10A—C10—H10B	109.5
C3—C2—C1	111.2 (3)	C9—C10—H10C	109.5
O2—C2—H2A	110.3	H10A—C10—H10C	109.5
C3—C2—H2A	110.3	H10B—C10—H10C	109.5
C1—C2—H2A	110.3	O7—C11—O6	123.1 (3)
O4—C3—C2	108.1 (2)	O7—C11—C12	125.2 (4)
O4—C3—C4	109.6 (3)	O6—C11—C12	111.6 (3)
C2—C3—C4	110.7 (3)	C11—C12—H12A	109.5
O4—C3—H3A	109.5	C11—C12—H12B	109.5
C2—C3—H3A	109.5	H12A—C12—H12B	109.5
C4—C3—H3A	109.5	C11—C12—H12C	109.5
O6—C4—C3	109.5 (2)	H12A—C12—H12C	109.5
O6—C4—C5	106.0 (2)	H12B—C12—H12C	109.5
C3—C4—C5	110.7 (3)	C18—C13—C14	118.2 (3)
O6—C4—H4A	110.2	C18—C13—S	126.4 (2)
C3—C4—H4A	110.2	C14—C13—S	115.4 (2)
C5—C4—H4A	110.2	C15—C14—C13	120.6 (3)
O1—C5—C4	110.9 (2)	C15—C14—H14A	119.7
O1—C5—S	114.7 (2)	C13—C14—H14A	119.7
C4—C5—S	106.6 (2)	C16—C15—C14	120.9 (3)
O1—C5—H5A	108.1	C16—C15—H15A	119.5
C4—C5—H5A	108.1	C14—C15—H15A	119.5
S—C5—H5A	108.1	C15—C16—C17	119.4 (3)
C1—C6—H6A	109.5	C15—C16—H16A	120.3
C1—C6—H6B	109.5	C17—C16—H16A	120.3
H6A—C6—H6B	109.5	C16—C17—C18	120.2 (3)
C1—C6—H6C	109.5	C16—C17—H17A	119.9
H6A—C6—H6C	109.5	C18—C17—H17A	119.9
H6B—C6—H6C	109.5	C17—C18—C13	120.6 (3)
O3—C7—O2	123.4 (4)	C17—C18—H18A	119.7
O3—C7—C8	124.7 (5)	C13—C18—H18A	119.7