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The title compound, C26H38O16S, crystallizes with two unique half molecules in the asymmetric unit, where the central S atom in each of the unique molecules is positioned on a twofold rotation axis. The only major conformational difference between the two molecules concerns one of the acetyl groups. Except for that acetyl group, the atoms of the two different molecules, in an overlay of one molecule on the other, differ on average by only 0.06 (6) Å from each other.
Supporting information
CCDC reference: 667263
Key indicators
- Single-crystal X-ray study
- T = 293 K
- Mean (C-C) = 0.005 Å
- R factor = 0.039
- wR factor = 0.110
- Data-to-parameter ratio = 11.3
checkCIF/PLATON results
No syntax errors found
Alert level A
PLAT220_ALERT_2_A Large Non-Solvent O Ueq(max)/Ueq(min) ... 4.95 Ratio
| Author Response: This is a dynamic disorder of the carbonyl oxygen quite normal
for a protected saccharide without strong intermolecular hydrogen
bonds. Most probably the whole acetate group is involved in the
dynamic disorder but it is most clearly visible at this carbonyl
oxygen atom. The movement is perpendicular to the C=O bond direction
which is also physically sound.
|
PLAT220_ALERT_2_A Large Non-Solvent O Ueq(max)/Ueq(min) ... 4.87 Ratio
| Author Response: This is a dynamic disorder of the carbonyl oxygen quite normal
for a protected saccharide without strong intermolecular hydrogen
bonds. Most probably the whole acetate group is involved in the
dynamic disorder but it is most clearly visible at this carbonyl
oxygen atom. The movement is perpendicular to the C=O bond direction
which is also physically sound.
|
PLAT242_ALERT_2_A Check Low Ueq as Compared to Neighbors for C16A
| Author Response: This is also related to the dynamic disorder of the acetate groups
when intermolecular bonding is weak, as it is in this protected
saccharide. The C16A is the carbonyl carbon where the oxygen is
exhibiting a large movement.
|
PLAT242_ALERT_2_A Check Low Ueq as Compared to Neighbors for C24A
| Author Response: This is also related to the dynamic disorder of the acetate groups
when intermolecular bonding is weak, as it is in this protected
saccharide. The C16A is the carbonyl carbon where the oxygen is
exhibiting a large movement.
|
Alert level B
PLAT242_ALERT_2_B Check Low Ueq as Compared to Neighbors for C14A
| Author Response: This is also related to the dynamic disorder of the acetate groups
when intermolecular bonding is weak, as it is in this protected
saccharide. The C16A is the carbonyl carbon where the oxygen is
exhibiting a large movement.
|
Alert level C
PLAT213_ALERT_2_C Atom O24B has ADP max/min Ratio ............. 3.60 prola
PLAT220_ALERT_2_C Large Non-Solvent C Ueq(max)/Ueq(min) ... 2.88 Ratio
| Author Response: This is a dynamic disorder of the carbonyl oxygen quite normal
for a protected saccharide without strong intermolecular hydrogen
bonds. Most probably the whole acetate group is involved in the
dynamic disorder but it is most clearly visible at this carbonyl
oxygen atom. The movement is perpendicular to the C=O bond direction
which is also physically sound.
|
PLAT220_ALERT_2_C Large Non-Solvent C Ueq(max)/Ueq(min) ... 2.56 Ratio
| Author Response: This is a dynamic disorder of the carbonyl oxygen quite normal
for a protected saccharide without strong intermolecular hydrogen
bonds. Most probably the whole acetate group is involved in the
dynamic disorder but it is most clearly visible at this carbonyl
oxygen atom. The movement is perpendicular to the C=O bond direction
which is also physically sound.
|
PLAT222_ALERT_3_C Large Non-Solvent H Ueq(max)/Ueq(min) ... 3.60 Ratio
PLAT222_ALERT_3_C Large Non-Solvent H Ueq(max)/Ueq(min) ... 3.21 Ratio
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C12A
| Author Response: This is also related to the dynamic disorder of the acetate groups
when intermolecular bonding is weak, as it is in this protected
saccharide. The C16A is the carbonyl carbon where the oxygen is
exhibiting a large movement.
|
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for O21
| Author Response: This is also related to the dynamic disorder of the acetate groups
when intermolecular bonding is weak, as it is in this protected
saccharide. The C16A is the carbonyl carbon where the oxygen is
exhibiting a large movement.
|
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C22A
| Author Response: This is also related to the dynamic disorder of the acetate groups
when intermolecular bonding is weak, as it is in this protected
saccharide. The C16A is the carbonyl carbon where the oxygen is
exhibiting a large movement.
|
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C26A
| Author Response: This is also related to the dynamic disorder of the acetate groups
when intermolecular bonding is weak, as it is in this protected
saccharide. The C16A is the carbonyl carbon where the oxygen is
exhibiting a large movement.
|
PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ... 5
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 0.992
Tmax scaled 0.992 Tmin scaled 0.942
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 25.68
From the CIF: _reflns_number_total 4492
Count of symmetry unique reflns 3391
Completeness (_total/calc) 132.47%
TEST3: Check Friedels for noncentro structure
Estimate of Friedel pairs measured 1101
Fraction of Friedel pairs measured 0.325
Are heavy atom types Z>Si present yes
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature 293 K
PLAT200_ALERT_1_G Check the Reported _diffrn_ambient_temperature . 293 K
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C12 = . S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C13 = . R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C14 = . R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C15 = . R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C22 = . S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C23 = . R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C24 = . R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C25 = . R
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints ....... 1
4 ALERT level A = In general: serious problem
1 ALERT level B = Potentially serious problem
10 ALERT level C = Check and explain
13 ALERT level G = General alerts; check
10 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
12 ALERT type 2 Indicator that the structure model may be wrong or deficient
5 ALERT type 3 Indicator that the structure quality may be low
1 ALERT type 4 Improvement, methodology, query or suggestion
0 ALERT type 5 Informative message, check
The title compound (I) was prepared from the trifluoromethanesulfonate
derivative (III) (Grandjean & Lukacs, 1996) as follows: sodium sulfide
nonahydrate (475 mg, 2.0 mmol) was dried by heating under vacuum and then
allowed to cool to RT. Molecular sieves 4Å (ca 500 mg) and
acetonitrile (6 ml) were added, followed by trifluoromethanesulfonate (III)
(500 mg, 1.0 mmol). The mixture was stirred at 50°C for 3 h, after which time
it was diluted with dichloromethane (50 ml) and filtered through Celite. The
filtrate was washed with HCl (1M, 50 ml) then NaHCO3 (sat. 50 ml),
then dried (Na2SO4), filtered and concentrated. The residue was purified
by flash column chromatography (3:1 pentane:ethyl acetate) to give the
thioether (II) (331 mg, 90%). Thioether (II) (214 mg) was dissolved in THF (3 ml) and cooled to -78 C, while ammonia (ca 20 ml) was condensed in.
Sodium (ca 140 mg) was added to give a deep blue solution, followed by
MeOH (0.04 ml). After 2 min, NH4Cl was added until the blue colour
disappeared and the solvents were allowed to evaporate. The crude material was
then acetylated with acetic anhydride (3 + 1.6 ml) and pyridine (3 + 1.6 ml)
overnight. Methanol (8 ml) and ethyl acetate (40 ml) were then added and the
mixture was washed with HCl (1M, 30 ml) then NaHCO3 (sat. 30 ml),
then dried (Na2SO4), filtered and concentrated. The residue was purified
by flash column chromatography (2:1 toluene:ethyl acetate) to give the title
compound (I) (131 mg, 71%). Crystals were grown from methanol solution by slow
evaporation of the solvent.
Several of the O-acyl groups showed substantial disorder most clearly
shown by the elongated ellipsoids especially of O14B, O16B and O24B. This
disorder most probably occurs due to the absence of strong intermolecular
hydrogen bonding interactions. Attempts to model the disorder did not improve
the fit, thus it is represented only by the elongated ellipsoids. All hydrogen
atoms were geometrically positioned and refined with riding motion,
d(C—H)=0.96, 0.97,0.98 Å for CH3, CH2 and CH respectivly. The
Uiso(H) = 1.5Ueq(C) for CH3 and 1.2Ueq(C) for
CH2 and CH. The transformation for the overlay (Fig. 3) was calculated with
the program ROTERA (Norrestam, 1991).
Structure description
top
The title compound (I) was synthesized as part of a program towards the
synthesis of thioether-linked disaccharides as new glycomimetics (Cumpstey,
2006). The title compound crystallizes with two unique half molecules in the
asymmetric unit. Both molecules are shown in Fig. 1. Both of the sulfur atoms
are positioned on a two fold axis whereby the second half of each molecule is
generated through the two fold rotation. A packing view of the structure is
shown in Fig 2. The conformations of the sugar rings in the two molecules are
very similar as can be seen from corresponding geometrical parameters for the
two rings. The Cremer Pople parameters (Cremer & Pople, 1975) for the ring
O15→ C11→ C12→ C13→
C14→ C15 are: Q=0.587 (3) Å, θ=0.0 (3)° and φ=159 (9)° while for
the ring O25→ C21→ C22→ C23→
C24→ C25 they are: Q=0.597 (3) Å, θ=1.3 (3)° and φ=244 (7)°.
Both rings are on C-form. The major conformational difference between the
molecules is shown in an overlay of the two unique half molecules (Fig. 3),
the acetyl group starting at O16 in one of the molecules deviates
significantly from the corresponding acetyl group, beginning with O26 in the
other molecule. The rest of the atoms, except for these two acetyl groups,
have an average deviation of 0.06 (6)Å between the atoms of one residue and
the overlaid residue.
For general background, see: Cumpstey (2006). For synthesis of the
trifluoromethanesulfonate precursor to the title compound, see: Grandjean &
Lukacs (1996). For geometrical calculations, see: Cremer & Pople (1975);
Norrestam (1991).
Data collection: CrysAlis CCD (Oxford Diffraction, 2007); cell refinement: CrysAlis RED (Oxford Diffraction, 2007); data reduction: CrysAlis RED (Oxford Diffraction, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: DIAMOND (Bergerhoff, 1996); software used to prepare material for publication: PLATON (Spek, 2003).
Bis(methyl 2,4,6-tri-
O-acetyl-
β-
D-allofuranosid-3-yl)sulfane
top
Crystal data top
C26H38O16S | F(000) = 1352 |
Mr = 638.62 | Dx = 1.292 Mg m−3 |
Monoclinic, C2 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: C 2y | Cell parameters from 5794 reflections |
a = 22.6458 (13) Å | θ = 3.8–32.1° |
b = 7.2018 (3) Å | µ = 0.17 mm−1 |
c = 21.3260 (12) Å | T = 293 K |
β = 109.258 (7)° | Prism, colourless |
V = 3283.4 (3) Å3 | 0.30 × 0.05 × 0.05 mm |
Z = 4 | |
Data collection top
Oxford Diffraction Xcalibur-II with Sapphire-III CCD diffractometer | 4492 independent reflections |
Radiation source: Enhance (Mo) X-ray Source | 3486 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.021 |
Detector resolution: 16.5467 pixels mm-1 | θmax = 25.7°, θmin = 3.9° |
ω scans at different θ | h = −27→25 |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007) | k = −5→8 |
Tmin = 0.95, Tmax = 1.00 | l = −25→26 |
10820 measured reflections | |
Refinement top
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.039 | w = 1/[σ2(Fo2) + (0.0718P)2] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.110 | (Δ/σ)max < 0.001 |
S = 1.05 | Δρmax = 0.24 e Å−3 |
4492 reflections | Δρmin = −0.27 e Å−3 |
398 parameters | Extinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
1 restraint | Extinction coefficient: 0.0036 (7) |
Primary atom site location: structure-invariant direct methods | Absolute structure: Flack (1983), 1101 Friedel pairs |
Secondary atom site location: difference Fourier map | Absolute structure parameter: −0.03 (9) |
Crystal data top
C26H38O16S | V = 3283.4 (3) Å3 |
Mr = 638.62 | Z = 4 |
Monoclinic, C2 | Mo Kα radiation |
a = 22.6458 (13) Å | µ = 0.17 mm−1 |
b = 7.2018 (3) Å | T = 293 K |
c = 21.3260 (12) Å | 0.30 × 0.05 × 0.05 mm |
β = 109.258 (7)° | |
Data collection top
Oxford Diffraction Xcalibur-II with Sapphire-III CCD diffractometer | 4492 independent reflections |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007) | 3486 reflections with I > 2σ(I) |
Tmin = 0.95, Tmax = 1.00 | Rint = 0.021 |
10820 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.039 | H-atom parameters constrained |
wR(F2) = 0.110 | Δρmax = 0.24 e Å−3 |
S = 1.05 | Δρmin = −0.27 e Å−3 |
4492 reflections | Absolute structure: Flack (1983), 1101 Friedel pairs |
398 parameters | Absolute structure parameter: −0.03 (9) |
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 | Uiso*/Ueq | |
S1 | 0.0000 | 0.92953 (13) | 0.5000 | 0.0534 (3) | |
C13 | 0.06297 (12) | 0.7707 (4) | 0.49958 (13) | 0.0444 (6) | |
H13 | 0.0447 | 0.6545 | 0.4777 | 0.053* | |
C14 | 0.10871 (13) | 0.7272 (4) | 0.56881 (13) | 0.0473 (7) | |
H14 | 0.1396 | 0.6380 | 0.5639 | 0.057* | |
C15 | 0.14320 (13) | 0.8986 (5) | 0.60214 (13) | 0.0520 (7) | |
H15 | 0.1131 | 0.9893 | 0.6078 | 0.062* | |
O15 | 0.17528 (8) | 0.9763 (3) | 0.56093 (9) | 0.0549 (5) | |
C11 | 0.13600 (12) | 1.0308 (4) | 0.49624 (13) | 0.0479 (7) | |
H11 | 0.1064 | 1.1268 | 0.4992 | 0.057* | |
C12 | 0.10163 (12) | 0.8597 (4) | 0.46103 (13) | 0.0465 (7) | |
H12 | 0.1324 | 0.7692 | 0.4567 | 0.056* | |
O14 | 0.07742 (10) | 0.6447 (3) | 0.61058 (10) | 0.0607 (6) | |
C14A | 0.08051 (18) | 0.4616 (6) | 0.6179 (2) | 0.0791 (10) | |
O14B | 0.1048 (3) | 0.3678 (5) | 0.5886 (3) | 0.173 (2) | |
C14C | 0.0512 (3) | 0.3921 (8) | 0.6656 (3) | 0.127 (2) | |
H14A | 0.0396 | 0.2643 | 0.6561 | 0.191* | |
H14B | 0.0146 | 0.4643 | 0.6620 | 0.191* | |
H14C | 0.0804 | 0.4024 | 0.7099 | 0.191* | |
C16 | 0.19207 (16) | 0.8600 (6) | 0.66876 (16) | 0.0745 (10) | |
H16A | 0.2140 | 0.9738 | 0.6869 | 0.089* | |
H16B | 0.1722 | 0.8132 | 0.6995 | 0.089* | |
O16 | 0.23542 (11) | 0.7255 (5) | 0.66035 (11) | 0.0822 (8) | |
C16A | 0.2510 (2) | 0.5855 (8) | 0.6984 (2) | 0.1022 (15) | |
O16B | 0.2344 (4) | 0.5756 (11) | 0.7444 (3) | 0.272 (5) | |
C16C | 0.2925 (2) | 0.4510 (10) | 0.6811 (3) | 0.1246 (19) | |
H16C | 0.3351 | 0.4924 | 0.6992 | 0.187* | |
H16D | 0.2810 | 0.4416 | 0.6337 | 0.187* | |
H16E | 0.2885 | 0.3316 | 0.6993 | 0.187* | |
O11 | 0.17385 (10) | 1.0956 (4) | 0.46204 (11) | 0.0665 (6) | |
C11A | 0.1962 (3) | 1.2802 (7) | 0.4788 (3) | 0.1078 (17) | |
H11A | 0.1622 | 1.3661 | 0.4625 | 0.162* | |
H11B | 0.2276 | 1.3073 | 0.4589 | 0.162* | |
H11C | 0.2140 | 1.2914 | 0.5262 | 0.162* | |
O12 | 0.06299 (9) | 0.9156 (3) | 0.39597 (9) | 0.0605 (6) | |
C12A | 0.05499 (17) | 0.7933 (6) | 0.34735 (16) | 0.0647 (9) | |
O12B | 0.07856 (16) | 0.6436 (5) | 0.35551 (13) | 0.1047 (10) | |
C12C | 0.0102 (2) | 0.8648 (7) | 0.28403 (17) | 0.0952 (14) | |
H12A | 0.0015 | 0.7691 | 0.2509 | 0.143* | |
H12B | 0.0281 | 0.9701 | 0.2694 | 0.143* | |
H12C | −0.0280 | 0.9012 | 0.2910 | 0.143* | |
S2 | 0.5000 | 0.97527 (14) | 0.0000 | 0.0504 (3) | |
C23 | 0.46337 (14) | 0.8177 (4) | 0.04313 (13) | 0.0484 (7) | |
H23 | 0.4889 | 0.7050 | 0.0555 | 0.058* | |
C24 | 0.39672 (15) | 0.7633 (4) | 0.00179 (14) | 0.0545 (8) | |
H24 | 0.3807 | 0.6756 | 0.0274 | 0.065* | |
C25 | 0.35471 (13) | 0.9327 (5) | −0.01386 (14) | 0.0555 (7) | |
H25 | 0.3706 | 1.0234 | −0.0386 | 0.067* | |
O25 | 0.35581 (8) | 1.0108 (3) | 0.04826 (9) | 0.0588 (6) | |
C21 | 0.41579 (12) | 1.0751 (5) | 0.08979 (13) | 0.0510 (7) | |
H21 | 0.4316 | 1.1737 | 0.0679 | 0.061* | |
C22 | 0.45988 (13) | 0.9110 (5) | 0.10616 (13) | 0.0495 (7) | |
H22 | 0.4447 | 0.8204 | 0.1315 | 0.059* | |
O21 | 0.40895 (10) | 1.1376 (4) | 0.14776 (10) | 0.0702 (7) | |
C21A | 0.3779 (2) | 1.3135 (9) | 0.1412 (2) | 0.124 (2) | |
H21A | 0.4072 | 1.4111 | 0.1424 | 0.186* | |
H21B | 0.3616 | 1.3296 | 0.1771 | 0.186* | |
H21C | 0.3442 | 1.3177 | 0.0997 | 0.186* | |
O22 | 0.52012 (8) | 0.9780 (3) | 0.14720 (8) | 0.0509 (5) | |
C22A | 0.55538 (16) | 0.8637 (6) | 0.19447 (15) | 0.0627 (9) | |
O22B | 0.53879 (16) | 0.7114 (5) | 0.20135 (15) | 0.1117 (11) | |
C22C | 0.61622 (14) | 0.9470 (7) | 0.23186 (15) | 0.0776 (11) | |
H22A | 0.6287 | 0.9063 | 0.2772 | 0.116* | |
H22B | 0.6126 | 1.0798 | 0.2302 | 0.116* | |
H22C | 0.6470 | 0.9090 | 0.2125 | 0.116* | |
O24 | 0.39636 (12) | 0.6743 (3) | −0.05891 (11) | 0.0684 (6) | |
C24A | 0.3899 (2) | 0.4933 (6) | −0.06424 (18) | 0.0844 (11) | |
O24B | 0.3825 (4) | 0.4096 (5) | −0.0215 (2) | 0.248 (4) | |
C24C | 0.3930 (3) | 0.4115 (7) | −0.1262 (2) | 0.1039 (14) | |
H24A | 0.3988 | 0.2797 | −0.1208 | 0.156* | |
H24B | 0.4274 | 0.4647 | −0.1368 | 0.156* | |
H24C | 0.3547 | 0.4366 | −0.1616 | 0.156* | |
C26 | 0.28733 (15) | 0.8875 (6) | −0.05192 (17) | 0.0718 (10) | |
H26A | 0.2854 | 0.8141 | −0.0907 | 0.086* | |
H26B | 0.2701 | 0.8136 | −0.0241 | 0.086* | |
O26 | 0.25050 (9) | 1.0513 (4) | −0.07258 (10) | 0.0655 (6) | |
C26A | 0.24722 (15) | 1.1191 (6) | −0.13217 (16) | 0.0696 (10) | |
O26B | 0.27403 (14) | 1.0533 (6) | −0.16579 (13) | 0.1082 (11) | |
C26C | 0.2064 (2) | 1.2840 (9) | −0.1493 (2) | 0.1140 (19) | |
H26C | 0.2038 | 1.3269 | −0.1928 | 0.171* | |
H26D | 0.2236 | 1.3805 | −0.1174 | 0.171* | |
H26E | 0.1654 | 1.2520 | −0.1489 | 0.171* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
S1 | 0.0376 (5) | 0.0389 (6) | 0.0859 (7) | 0.000 | 0.0233 (5) | 0.000 |
C13 | 0.0406 (14) | 0.0391 (15) | 0.0542 (15) | 0.0011 (12) | 0.0165 (13) | −0.0042 (13) |
C14 | 0.0430 (15) | 0.0508 (17) | 0.0515 (15) | 0.0151 (13) | 0.0202 (13) | 0.0019 (14) |
C15 | 0.0488 (15) | 0.061 (2) | 0.0486 (15) | 0.0013 (15) | 0.0193 (13) | −0.0055 (14) |
O15 | 0.0415 (9) | 0.0675 (14) | 0.0551 (11) | −0.0040 (10) | 0.0153 (8) | −0.0043 (11) |
C11 | 0.0423 (14) | 0.0547 (18) | 0.0510 (15) | −0.0002 (13) | 0.0211 (13) | −0.0010 (14) |
C12 | 0.0439 (15) | 0.0516 (17) | 0.0445 (14) | 0.0054 (13) | 0.0154 (12) | −0.0029 (13) |
O14 | 0.0732 (13) | 0.0534 (14) | 0.0690 (12) | 0.0163 (11) | 0.0415 (11) | 0.0114 (11) |
C14A | 0.097 (3) | 0.051 (2) | 0.107 (3) | 0.014 (2) | 0.059 (2) | 0.012 (2) |
O14B | 0.297 (6) | 0.0479 (18) | 0.278 (5) | 0.008 (3) | 0.233 (5) | −0.002 (3) |
C14C | 0.173 (5) | 0.080 (3) | 0.176 (5) | 0.033 (3) | 0.120 (4) | 0.059 (4) |
C16 | 0.070 (2) | 0.094 (3) | 0.0546 (19) | 0.008 (2) | 0.0140 (17) | −0.009 (2) |
O16 | 0.0631 (14) | 0.117 (2) | 0.0610 (13) | 0.0220 (15) | 0.0127 (12) | 0.0186 (16) |
C16A | 0.123 (4) | 0.104 (4) | 0.086 (3) | 0.003 (3) | 0.043 (3) | 0.030 (3) |
O16B | 0.424 (10) | 0.215 (7) | 0.290 (7) | 0.180 (7) | 0.271 (8) | 0.177 (6) |
C16C | 0.123 (4) | 0.121 (5) | 0.118 (3) | 0.048 (4) | 0.023 (3) | 0.018 (4) |
O11 | 0.0615 (13) | 0.0736 (16) | 0.0782 (13) | −0.0127 (12) | 0.0416 (11) | −0.0053 (13) |
C11A | 0.131 (4) | 0.090 (3) | 0.133 (4) | −0.048 (3) | 0.085 (3) | −0.014 (3) |
O12 | 0.0692 (12) | 0.0607 (14) | 0.0450 (11) | 0.0031 (11) | 0.0101 (9) | −0.0033 (11) |
C12A | 0.074 (2) | 0.073 (3) | 0.0491 (18) | −0.009 (2) | 0.0232 (17) | −0.0021 (18) |
O12B | 0.138 (3) | 0.097 (3) | 0.0672 (15) | 0.026 (2) | 0.0173 (16) | −0.0258 (17) |
C12C | 0.115 (3) | 0.100 (3) | 0.057 (2) | −0.021 (3) | 0.011 (2) | 0.004 (2) |
S2 | 0.0613 (6) | 0.0382 (5) | 0.0579 (6) | 0.000 | 0.0282 (5) | 0.000 |
C23 | 0.0598 (18) | 0.0373 (16) | 0.0488 (15) | −0.0016 (13) | 0.0190 (14) | 0.0019 (13) |
C24 | 0.071 (2) | 0.0448 (17) | 0.0457 (15) | −0.0159 (16) | 0.0166 (15) | 0.0003 (14) |
C25 | 0.0516 (15) | 0.061 (2) | 0.0480 (15) | −0.0126 (15) | 0.0085 (13) | −0.0003 (15) |
O25 | 0.0420 (10) | 0.0770 (16) | 0.0533 (11) | −0.0082 (10) | 0.0100 (9) | −0.0079 (11) |
C21 | 0.0415 (15) | 0.0599 (18) | 0.0476 (15) | 0.0003 (14) | 0.0093 (12) | −0.0031 (14) |
C22 | 0.0518 (15) | 0.0502 (17) | 0.0466 (14) | −0.0089 (14) | 0.0164 (12) | 0.0023 (14) |
O21 | 0.0554 (12) | 0.097 (2) | 0.0535 (11) | 0.0139 (13) | 0.0119 (10) | −0.0157 (12) |
C21A | 0.102 (3) | 0.154 (5) | 0.091 (3) | 0.076 (4) | −0.001 (3) | −0.036 (3) |
O22 | 0.0438 (9) | 0.0566 (12) | 0.0459 (9) | 0.0004 (10) | 0.0060 (8) | 0.0055 (10) |
C22A | 0.066 (2) | 0.076 (3) | 0.0431 (16) | 0.0171 (19) | 0.0140 (16) | 0.0132 (17) |
O22B | 0.119 (2) | 0.087 (2) | 0.100 (2) | −0.007 (2) | −0.0042 (18) | 0.044 (2) |
C22C | 0.0615 (19) | 0.111 (3) | 0.0533 (17) | 0.012 (2) | 0.0090 (15) | 0.004 (2) |
O24 | 0.1048 (17) | 0.0452 (13) | 0.0560 (11) | −0.0225 (12) | 0.0276 (12) | −0.0062 (10) |
C24A | 0.143 (3) | 0.047 (2) | 0.066 (2) | −0.011 (2) | 0.037 (2) | 0.0012 (19) |
O24B | 0.606 (13) | 0.048 (2) | 0.171 (4) | −0.011 (4) | 0.237 (6) | −0.003 (3) |
C24C | 0.156 (4) | 0.069 (3) | 0.088 (3) | −0.025 (3) | 0.042 (3) | −0.024 (2) |
C26 | 0.062 (2) | 0.074 (3) | 0.068 (2) | −0.0157 (19) | 0.0062 (17) | 0.0081 (19) |
O26 | 0.0550 (12) | 0.0881 (17) | 0.0511 (11) | −0.0059 (12) | 0.0145 (9) | 0.0006 (12) |
C26A | 0.062 (2) | 0.091 (3) | 0.0586 (19) | 0.0005 (19) | 0.0241 (17) | 0.0071 (19) |
O26B | 0.126 (2) | 0.138 (3) | 0.0759 (16) | 0.043 (2) | 0.0538 (17) | 0.0097 (18) |
C26C | 0.118 (4) | 0.132 (5) | 0.106 (3) | 0.047 (4) | 0.055 (3) | 0.041 (3) |
Geometric parameters (Å, º) top
S1—C13i | 1.831 (3) | S2—C23 | 1.824 (3) |
S1—C13 | 1.831 (3) | S2—C23ii | 1.824 (3) |
C13—C12 | 1.526 (4) | C23—C24 | 1.527 (4) |
C13—C14 | 1.530 (4) | C23—C22 | 1.528 (4) |
C13—H13 | 0.9800 | C23—H23 | 0.9800 |
C14—O14 | 1.437 (3) | C24—O24 | 1.442 (4) |
C14—C15 | 1.508 (5) | C24—C25 | 1.515 (5) |
C14—H14 | 0.9800 | C24—H24 | 0.9800 |
C15—O15 | 1.426 (3) | C25—O25 | 1.432 (4) |
C15—C16 | 1.511 (4) | C25—C26 | 1.509 (4) |
C15—H15 | 0.9800 | C25—H25 | 0.9800 |
O15—C11 | 1.428 (3) | O25—C21 | 1.432 (3) |
C11—O11 | 1.377 (3) | C21—O21 | 1.372 (3) |
C11—C12 | 1.517 (4) | C21—C22 | 1.511 (4) |
C11—H11 | 0.9800 | C21—H21 | 0.9800 |
C12—O12 | 1.432 (3) | C22—O22 | 1.439 (3) |
C12—H12 | 0.9800 | C22—H22 | 0.9800 |
O14—C14A | 1.327 (5) | O21—C21A | 1.432 (6) |
C14A—O14B | 1.173 (5) | C21A—H21A | 0.9600 |
C14A—C14C | 1.474 (5) | C21A—H21B | 0.9600 |
C14C—H14A | 0.9600 | C21A—H21C | 0.9600 |
C14C—H14B | 0.9600 | O22—C22A | 1.342 (4) |
C14C—H14C | 0.9600 | C22A—O22B | 1.184 (5) |
C16—O16 | 1.432 (5) | C22A—C22C | 1.473 (5) |
C16—H16A | 0.9700 | C22C—H22A | 0.9600 |
C16—H16B | 0.9700 | C22C—H22B | 0.9600 |
O16—C16A | 1.269 (6) | C22C—H22C | 0.9600 |
C16A—O16B | 1.163 (5) | O24—C24A | 1.313 (5) |
C16A—C16C | 1.478 (8) | C24A—O24B | 1.151 (5) |
C16C—H16C | 0.9600 | C24A—C24C | 1.470 (6) |
C16C—H16D | 0.9600 | C24C—H24A | 0.9600 |
C16C—H16E | 0.9600 | C24C—H24B | 0.9600 |
O11—C11A | 1.425 (6) | C24C—H24C | 0.9600 |
C11A—H11A | 0.9600 | C26—O26 | 1.428 (5) |
C11A—H11B | 0.9600 | C26—H26A | 0.9700 |
C11A—H11C | 0.9600 | C26—H26B | 0.9700 |
O12—C12A | 1.327 (4) | O26—C26A | 1.340 (4) |
C12A—O12B | 1.190 (5) | C26A—O26B | 1.181 (4) |
C12A—C12C | 1.488 (5) | C26A—C26C | 1.474 (7) |
C12C—H12A | 0.9600 | C26C—H26C | 0.9600 |
C12C—H12B | 0.9600 | C26C—H26D | 0.9600 |
C12C—H12C | 0.9600 | C26C—H26E | 0.9600 |
| | | |
C13i—S1—C13 | 102.64 (18) | C23—S2—C23ii | 103.03 (19) |
C12—C13—C14 | 106.2 (2) | C24—C23—C22 | 107.0 (2) |
C12—C13—S1 | 109.04 (19) | C24—C23—S2 | 113.33 (19) |
C14—C13—S1 | 113.80 (18) | C22—C23—S2 | 109.5 (2) |
C12—C13—H13 | 109.2 | C24—C23—H23 | 109.0 |
C14—C13—H13 | 109.2 | C22—C23—H23 | 109.0 |
S1—C13—H13 | 109.2 | S2—C23—H23 | 109.0 |
O14—C14—C15 | 109.3 (2) | O24—C24—C25 | 110.0 (2) |
O14—C14—C13 | 111.6 (2) | O24—C24—C23 | 110.1 (2) |
C15—C14—C13 | 111.6 (2) | C25—C24—C23 | 110.5 (2) |
O14—C14—H14 | 108.1 | O24—C24—H24 | 108.7 |
C15—C14—H14 | 108.1 | C25—C24—H24 | 108.7 |
C13—C14—H14 | 108.1 | C23—C24—H24 | 108.7 |
O15—C15—C14 | 108.7 (2) | O25—C25—C26 | 106.8 (2) |
O15—C15—C16 | 106.7 (2) | O25—C25—C24 | 107.1 (2) |
C14—C15—C16 | 113.4 (3) | C26—C25—C24 | 113.2 (3) |
O15—C15—H15 | 109.3 | O25—C25—H25 | 109.9 |
C14—C15—H15 | 109.3 | C26—C25—H25 | 109.9 |
C16—C15—H15 | 109.3 | C24—C25—H25 | 109.9 |
C15—O15—C11 | 114.94 (19) | C25—O25—C21 | 115.02 (19) |
O11—C11—O15 | 107.9 (2) | O21—C21—O25 | 107.3 (2) |
O11—C11—C12 | 108.7 (2) | O21—C21—C22 | 108.1 (2) |
O15—C11—C12 | 108.0 (2) | O25—C21—C22 | 108.0 (3) |
O11—C11—H11 | 110.7 | O21—C21—H21 | 111.1 |
O15—C11—H11 | 110.7 | O25—C21—H21 | 111.1 |
C12—C11—H11 | 110.7 | C22—C21—H21 | 111.1 |
O12—C12—C11 | 107.5 (2) | O22—C22—C21 | 107.4 (2) |
O12—C12—C13 | 111.4 (2) | O22—C22—C23 | 111.6 (2) |
C11—C12—C13 | 111.5 (2) | C21—C22—C23 | 111.3 (2) |
O12—C12—H12 | 108.8 | O22—C22—H22 | 108.8 |
C11—C12—H12 | 108.8 | C21—C22—H22 | 108.8 |
C13—C12—H12 | 108.8 | C23—C22—H22 | 108.8 |
C14A—O14—C14 | 117.8 (2) | C21—O21—C21A | 113.5 (3) |
O14B—C14A—O14 | 121.7 (3) | O21—C21A—H21A | 109.5 |
O14B—C14A—C14C | 124.7 (4) | O21—C21A—H21B | 109.5 |
O14—C14A—C14C | 113.6 (3) | H21A—C21A—H21B | 109.5 |
C14A—C14C—H14A | 109.5 | O21—C21A—H21C | 109.5 |
C14A—C14C—H14B | 109.5 | H21A—C21A—H21C | 109.5 |
H14A—C14C—H14B | 109.5 | H21B—C21A—H21C | 109.5 |
C14A—C14C—H14C | 109.5 | C22A—O22—C22 | 117.4 (3) |
H14A—C14C—H14C | 109.5 | O22B—C22A—O22 | 121.8 (3) |
H14B—C14C—H14C | 109.5 | O22B—C22A—C22C | 126.1 (3) |
O16—C16—C15 | 109.1 (3) | O22—C22A—C22C | 112.0 (3) |
O16—C16—H16A | 109.9 | C22A—C22C—H22A | 109.5 |
C15—C16—H16A | 109.9 | C22A—C22C—H22B | 109.5 |
O16—C16—H16B | 109.9 | H22A—C22C—H22B | 109.5 |
C15—C16—H16B | 109.9 | C22A—C22C—H22C | 109.5 |
H16A—C16—H16B | 108.3 | H22A—C22C—H22C | 109.5 |
C16A—O16—C16 | 121.0 (3) | H22B—C22C—H22C | 109.5 |
O16B—C16A—O16 | 119.3 (6) | C24A—O24—C24 | 119.1 (3) |
O16B—C16A—C16C | 125.4 (5) | O24B—C24A—O24 | 119.5 (4) |
O16—C16A—C16C | 115.3 (4) | O24B—C24A—C24C | 124.4 (4) |
C16A—C16C—H16C | 109.5 | O24—C24A—C24C | 116.1 (3) |
C16A—C16C—H16D | 109.5 | C24A—C24C—H24A | 109.5 |
H16C—C16C—H16D | 109.5 | C24A—C24C—H24B | 109.5 |
C16A—C16C—H16E | 109.5 | H24A—C24C—H24B | 109.5 |
H16C—C16C—H16E | 109.5 | C24A—C24C—H24C | 109.5 |
H16D—C16C—H16E | 109.5 | H24A—C24C—H24C | 109.5 |
C11—O11—C11A | 114.5 (3) | H24B—C24C—H24C | 109.5 |
O11—C11A—H11A | 109.5 | O26—C26—C25 | 111.8 (3) |
O11—C11A—H11B | 109.5 | O26—C26—H26A | 109.2 |
H11A—C11A—H11B | 109.5 | C25—C26—H26A | 109.2 |
O11—C11A—H11C | 109.5 | O26—C26—H26B | 109.2 |
H11A—C11A—H11C | 109.5 | C25—C26—H26B | 109.2 |
H11B—C11A—H11C | 109.5 | H26A—C26—H26B | 107.9 |
C12A—O12—C12 | 116.9 (3) | C26A—O26—C26 | 116.0 (3) |
O12B—C12A—O12 | 123.2 (3) | O26B—C26A—O26 | 123.4 (4) |
O12B—C12A—C12C | 125.8 (4) | O26B—C26A—C26C | 125.3 (4) |
O12—C12A—C12C | 110.9 (4) | O26—C26A—C26C | 111.3 (3) |
C12A—C12C—H12A | 109.5 | C26A—C26C—H26C | 109.5 |
C12A—C12C—H12B | 109.5 | C26A—C26C—H26D | 109.5 |
H12A—C12C—H12B | 109.5 | H26C—C26C—H26D | 109.5 |
C12A—C12C—H12C | 109.5 | C26A—C26C—H26E | 109.5 |
H12A—C12C—H12C | 109.5 | H26C—C26C—H26E | 109.5 |
H12B—C12C—H12C | 109.5 | H26D—C26C—H26E | 109.5 |
| | | |
C13i—S1—C13—C12 | 147.8 (2) | C23ii—S2—C23—C22 | 151.4 (2) |
C13i—S1—C13—C14 | −93.8 (2) | C23ii—S2—C23—C24 | −89.2 (2) |
C12—C13—C14—O14 | 179.1 (2) | C22—C23—C24—O24 | 179.8 (2) |
S1—C13—C14—O14 | 59.1 (3) | S2—C23—C24—O24 | 59.0 (3) |
C12—C13—C14—C15 | 56.5 (3) | C22—C23—C24—C25 | 58.1 (3) |
S1—C13—C14—C15 | −63.5 (3) | S2—C23—C24—C25 | −62.8 (3) |
O14—C14—C15—O15 | 178.6 (2) | O24—C24—C25—O25 | 178.4 (2) |
C13—C14—C15—O15 | −57.6 (3) | C23—C24—C25—O25 | −59.8 (3) |
O14—C14—C15—C16 | 60.0 (3) | O24—C24—C25—C26 | 60.9 (3) |
C13—C14—C15—C16 | −176.1 (2) | C23—C24—C25—C26 | −177.2 (2) |
C14—C15—O15—C11 | 60.2 (3) | C26—C25—O25—C21 | −175.8 (3) |
C16—C15—O15—C11 | −177.1 (3) | C24—C25—O25—C21 | 62.6 (3) |
C15—O15—C11—O11 | −177.7 (3) | C25—O25—C21—O21 | −177.5 (3) |
C15—O15—C11—C12 | −60.4 (3) | C25—O25—C21—C22 | −61.2 (3) |
O11—C11—C12—O12 | −62.6 (3) | O21—C21—C22—O22 | −64.9 (3) |
O15—C11—C12—O12 | −179.32 (19) | O25—C21—C22—O22 | 179.29 (18) |
O11—C11—C12—C13 | 175.1 (2) | O21—C21—C22—C23 | 172.7 (2) |
O15—C11—C12—C13 | 58.4 (3) | O25—C21—C22—C23 | 56.8 (3) |
C14—C13—C12—O12 | −177.0 (2) | C24—C23—C22—O22 | −176.6 (2) |
S1—C13—C12—O12 | −54.0 (3) | S2—C23—C22—O22 | −53.4 (3) |
C14—C13—C12—C11 | −56.9 (3) | C24—C23—C22—C21 | −56.6 (3) |
S1—C13—C12—C11 | 66.1 (3) | S2—C23—C22—C21 | 66.6 (3) |
C15—C14—O14—C14A | −136.4 (3) | O25—C21—O21—C21A | −74.9 (4) |
C13—C14—O14—C14A | 99.7 (3) | C22—C21—O21—C21A | 168.8 (3) |
C14—O14—C14A—O14B | −4.3 (7) | C21—C22—O22—C22A | 145.7 (2) |
C14—O14—C14A—C14C | 175.5 (4) | C23—C22—O22—C22A | −92.1 (3) |
O15—C15—C16—O16 | −62.7 (4) | C22—O22—C22A—O22B | 2.1 (5) |
C14—C15—C16—O16 | 57.0 (4) | C22—O22—C22A—C22C | 178.7 (2) |
C15—C16—O16—C16A | −132.0 (4) | C25—C24—O24—C24A | −134.0 (4) |
C16—O16—C16A—O16B | −7.2 (9) | C23—C24—O24—C24A | 104.0 (4) |
C16—O16—C16A—C16C | 175.8 (4) | C24—O24—C24A—O24B | 2.7 (8) |
O15—C11—O11—C11A | −78.7 (4) | C24—O24—C24A—C24C | −177.2 (3) |
C12—C11—O11—C11A | 164.4 (3) | O25—C25—C26—O26 | 69.2 (3) |
C11—C12—O12—C12A | 146.0 (3) | C24—C25—C26—O26 | −173.2 (3) |
C13—C12—O12—C12A | −91.5 (3) | C25—C26—O26—C26A | 89.9 (3) |
C12—O12—C12A—O12B | −0.7 (5) | C26—O26—C26A—O26B | −2.0 (5) |
C12—O12—C12A—C12C | 175.7 (3) | C26—O26—C26A—C26C | 178.1 (4) |
Symmetry codes: (i) −x, y, −z+1; (ii) −x+1, y, −z. |
Experimental details
Crystal data |
Chemical formula | C26H38O16S |
Mr | 638.62 |
Crystal system, space group | Monoclinic, C2 |
Temperature (K) | 293 |
a, b, c (Å) | 22.6458 (13), 7.2018 (3), 21.3260 (12) |
β (°) | 109.258 (7) |
V (Å3) | 3283.4 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.17 |
Crystal size (mm) | 0.30 × 0.05 × 0.05 |
|
Data collection |
Diffractometer | Oxford Diffraction Xcalibur-II with Sapphire-III CCD |
Absorption correction | Multi-scan (CrysAlis RED; Oxford Diffraction, 2007) |
Tmin, Tmax | 0.95, 1.00 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 10820, 4492, 3486 |
Rint | 0.021 |
(sin θ/λ)max (Å−1) | 0.610 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.039, 0.110, 1.05 |
No. of reflections | 4492 |
No. of parameters | 398 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.24, −0.27 |
Absolute structure | Flack (1983), 1101 Friedel pairs |
Absolute structure parameter | −0.03 (9) |
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The title compound (I) was synthesized as part of a program towards the synthesis of thioether-linked disaccharides as new glycomimetics (Cumpstey, 2006). The title compound crystallizes with two unique half molecules in the asymmetric unit. Both molecules are shown in Fig. 1. Both of the sulfur atoms are positioned on a two fold axis whereby the second half of each molecule is generated through the two fold rotation. A packing view of the structure is shown in Fig 2. The conformations of the sugar rings in the two molecules are very similar as can be seen from corresponding geometrical parameters for the two rings. The Cremer Pople parameters (Cremer & Pople, 1975) for the ring O15→ C11→ C12→ C13→ C14→ C15 are: Q=0.587 (3) Å, θ=0.0 (3)° and φ=159 (9)° while for the ring O25→ C21→ C22→ C23→ C24→ C25 they are: Q=0.597 (3) Å, θ=1.3 (3)° and φ=244 (7)°. Both rings are on C-form. The major conformational difference between the molecules is shown in an overlay of the two unique half molecules (Fig. 3), the acetyl group starting at O16 in one of the molecules deviates significantly from the corresponding acetyl group, beginning with O26 in the other molecule. The rest of the atoms, except for these two acetyl groups, have an average deviation of 0.06 (6)Å between the atoms of one residue and the overlaid residue.