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Acta Crystallogr Sect E Struct Rep Online. 2010 April 1; 66(Pt 4): o949.
Published online 2010 March 27. doi:  10.1107/S1600536810010895
PMCID: PMC2983870

Methyl 2,3-di-O-acetyl-4-O-levulinoyl-1-O-(2,2,2-trichloro-2-imino­ethyl)-l-ido­pyran­osiduronate

Abstract

In the title compound, C18H22Cl3NO11, a novel derivative of l-idopyran­osiduronic acid, the six-membered ring adopts a chair conformation.

Related literature

For background to l-iduronic acids, see: Capila & Linhardt (2002 [triangle]); Jobron & Jacquinet (1998 [triangle]); Lee et al. (2004 [triangle]). For the synthesis of iduronic acid derivatives, see: Yu et al. (2004 [triangle]); Sanjoy et al. (2001 [triangle]); Lubineau et al. (2000 [triangle]); Lohman et al. (2003 [triangle]).

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Object name is e-66-0o949-scheme1.jpg

Experimental

Crystal data

  • C18H22Cl3NO11
  • M r = 534.72
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o949-efi1.jpg
  • a = 9.0498 (10) Å
  • b = 9.7560 (11) Å
  • c = 26.570 (3) Å
  • V = 2345.8 (4) Å3
  • Z = 4
  • Cu Kα radiation
  • μ = 4.07 mm−1
  • T = 173 K
  • 0.41 × 0.30 × 0.28 mm

Data collection

  • Rigaku R-AXIS RAPID IP area-detector diffractometer
  • Absorption correction: numerical (ABSCOR; Higashi, 1995 [triangle]) T min = 0.286, T max = 0.395
  • 16340 measured reflections
  • 4259 independent reflections
  • 3893 reflections with I > 2σ(I)
  • R int = 0.047

Refinement

  • R[F 2 > 2σ(F 2)] = 0.046
  • wR(F 2) = 0.100
  • S = 1.09
  • 4259 reflections
  • 302 parameters
  • H-atom parameters constrained
  • Δρmax = 0.45 e Å−3
  • Δρmin = −0.48 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1804 Friedel pairs
  • Flack parameter: 0.023 (18)

Data collection: RAPID-AUTO (Rigaku, 2001 [triangle]); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: XP (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXL97.

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810010895/bt5207sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810010895/bt5207Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors thank the NSFC for financial support.

supplementary crystallographic information

Comment

L-iduronic acids are key components of numerous biologically potent oligosaccharides and glycopeptides (Capila & Linhardt, 2002). For example, heparin, heparan sulfate (Jobron & Jacquinet, 1998), dermatan sulfate (Lee et al., 2004). This series of glycosaminoglycans plays an important role in a diverse set of biological processes which all contain L-idopyranosiduronic acids. To study the structure-activity relationship of such polymers, there is a need for chemically pure oligosaccharide sequences which can be prepared by organic syntheses.

Since iduronic acid itself is not commercially available, syntheses of iduronic acid derivatives (Yu et al., 2004) from a variety of starting materials, including idose, glucose, glycals,and glucuronic acid have been developed (Lubineau et al., 2000 & Lohman et al., 2003). Herein, we have explored a novel and efficient route toward the synthesis of L-idopyranosiduronate trichloroacetimidate which will be used as a key building block to synthesize dermatan sulfate.

Experimental

The title compound was prepared in 76.8% yield by treatment with trichloroaceonitrile and DBU at 0 °C. The reaction was stirred for 30 min then allowed to warm to room temperature. Solvent was evaporated and the residue purified by Flash silica gel column chromatography (silica quenched with 1% NEt3) afford the title compound as syrupy.

Refinement

H atoms were positioned geometrically and allowed to ride on their parent atoms, with C—H = 0.95—1.00 Å and Uiso(H) = 1.2—1.5Ueq(C).

Figures

Fig. 1.
The molecular structure of the title compound, displacement ellipsoids are at the 50% level.
Fig. 2.
A packing diagram of the title compound.

Crystal data

C18H22Cl3NO11Dx = 1.514 Mg m3
Mr = 534.72Cu Kα radiation, λ = 1.54186 Å
Orthorhombic, P212121Cell parameters from 1098 reflections
a = 9.0498 (10) Åθ = 2.2–27.5°
b = 9.7560 (11) ŵ = 4.07 mm1
c = 26.570 (3) ÅT = 173 K
V = 2345.8 (4) Å3Block, colorless
Z = 40.41 × 0.30 × 0.28 mm
F(000) = 1104

Data collection

Rigaku R-AXIS RAPID IP area-detector diffractometer4259 independent reflections
Radiation source: rotating anode3893 reflections with I > 2σ(I)
graphiteRint = 0.047
ω scans at fixed χ = 45°θmax = 68.2°, θmin = 3.3°
Absorption correction: numerical (ABSCOR; Higashi, 1995)h = −10→10
Tmin = 0.286, Tmax = 0.395k = −11→11
16340 measured reflectionsl = −32→31

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.046H-atom parameters constrained
wR(F2) = 0.100w = 1/[σ2(Fo2) + (0.0268P)2 + 1.8534P] where P = (Fo2 + 2Fc2)/3
S = 1.09(Δ/σ)max < 0.001
4259 reflectionsΔρmax = 0.45 e Å3
302 parametersΔρmin = −0.48 e Å3
0 restraintsAbsolute structure: Flack (1983), 1804 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.023 (18)

Special details

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 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)

xyzUiso*/Ueq
Cl10.43622 (11)0.42769 (10)−0.00915 (3)0.0470 (2)
Cl20.44529 (14)0.72085 (10)−0.00601 (4)0.0578 (3)
Cl30.62102 (10)0.56765 (16)0.06361 (4)0.0664 (3)
O10.2587 (2)0.4459 (2)0.17647 (7)0.0275 (5)
O20.3250 (2)0.4443 (2)0.09152 (8)0.0329 (5)
O30.0181 (2)0.2548 (2)0.14357 (8)0.0332 (5)
O4−0.0977 (3)0.3313 (3)0.07477 (9)0.0527 (7)
O50.3933 (2)0.1578 (2)0.10987 (8)0.0320 (5)
O60.2917 (3)−0.0176 (3)0.06774 (10)0.0488 (7)
O70.1922 (2)0.1967 (2)0.22751 (8)0.0285 (5)
O80.2316 (3)−0.0295 (2)0.23558 (11)0.0493 (7)
O90.1750 (4)0.1508 (4)0.35252 (12)0.0780 (11)
O100.3492 (3)0.4899 (3)0.27135 (9)0.0462 (7)
O110.4850 (3)0.2966 (3)0.26989 (8)0.0402 (6)
N10.2424 (3)0.6658 (3)0.08223 (11)0.0411 (7)
H1A0.27610.73510.06300.049*
C10.2099 (3)0.4196 (4)0.12743 (10)0.0284 (7)
H1C0.12570.48270.11980.034*
C20.1588 (3)0.2725 (3)0.11851 (12)0.0280 (7)
H2A0.14700.25580.08160.034*
C30.2619 (3)0.1663 (3)0.14075 (11)0.0269 (7)
H3A0.21170.07510.14190.032*
C40.3162 (4)0.2048 (3)0.19295 (11)0.0260 (7)
H4A0.39710.14160.20380.031*
C50.3679 (4)0.3526 (3)0.19531 (11)0.0271 (7)
H5A0.46090.36280.17540.033*
C60.3286 (4)0.5705 (4)0.06991 (11)0.0315 (7)
C70.4526 (4)0.5722 (4)0.03110 (11)0.0352 (7)
C8−0.1037 (4)0.2905 (4)0.11727 (13)0.0366 (8)
C9−0.2403 (4)0.2721 (4)0.14798 (15)0.0458 (10)
H9A−0.32710.29310.12730.069*
H9B−0.23730.33410.17700.069*
H9C−0.24610.17710.15980.069*
C100.3914 (4)0.0610 (4)0.07321 (11)0.0343 (7)
C110.5308 (4)0.0652 (4)0.04323 (13)0.0471 (9)
H11A0.50750.05430.00740.071*
H11B0.5962−0.00920.05400.071*
H11C0.58020.15350.04850.071*
C120.1578 (4)0.0694 (4)0.24437 (11)0.0323 (7)
C130.0114 (4)0.0687 (4)0.27120 (12)0.0350 (7)
H13A0.0108−0.00840.29540.042*
H13B−0.06740.05110.24620.042*
C14−0.0258 (4)0.1992 (4)0.29934 (12)0.0349 (8)
H14A−0.02910.27620.27510.042*
H14B−0.12540.18980.31430.042*
C150.0820 (4)0.2329 (4)0.34006 (13)0.0434 (9)
C160.0726 (6)0.3724 (4)0.36322 (14)0.0572 (12)
H16A0.15190.38320.38810.086*
H16B−0.02330.38320.37990.086*
H16C0.08320.44220.33690.086*
C170.3974 (4)0.3918 (3)0.24983 (12)0.0308 (7)
C180.5206 (4)0.3098 (4)0.32281 (13)0.0481 (10)
H18A0.58600.23460.33290.072*
H18B0.42950.30620.34270.072*
H18C0.57050.39750.32860.072*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0627 (6)0.0425 (5)0.0358 (4)−0.0035 (5)0.0135 (4)−0.0068 (4)
Cl20.0917 (8)0.0412 (5)0.0405 (5)−0.0004 (5)0.0219 (5)0.0099 (4)
Cl30.0339 (5)0.1146 (10)0.0507 (5)−0.0158 (6)−0.0041 (4)0.0145 (7)
O10.0301 (11)0.0272 (12)0.0252 (10)0.0002 (10)0.0028 (9)−0.0002 (9)
O20.0336 (12)0.0322 (13)0.0330 (11)0.0029 (11)0.0122 (10)0.0045 (10)
O30.0228 (12)0.0440 (14)0.0328 (11)−0.0007 (11)0.0049 (10)−0.0025 (10)
O40.0407 (15)0.079 (2)0.0381 (15)0.0149 (15)−0.0022 (12)−0.0001 (14)
O50.0287 (12)0.0353 (13)0.0321 (11)−0.0007 (10)0.0113 (10)−0.0070 (10)
O60.0489 (16)0.0484 (16)0.0492 (15)−0.0084 (14)0.0079 (13)−0.0188 (13)
O70.0303 (12)0.0276 (12)0.0276 (11)−0.0022 (10)0.0105 (10)0.0035 (9)
O80.0546 (17)0.0269 (14)0.0664 (18)0.0040 (13)0.0261 (15)0.0048 (12)
O90.079 (2)0.089 (3)0.067 (2)0.029 (2)−0.0329 (19)−0.0091 (19)
O100.0583 (17)0.0445 (16)0.0359 (13)0.0033 (14)−0.0002 (13)−0.0117 (12)
O110.0410 (14)0.0437 (14)0.0358 (12)0.0008 (12)−0.0087 (11)0.0005 (11)
N10.052 (2)0.0306 (16)0.0402 (16)0.0008 (16)0.0072 (15)0.0049 (13)
C10.0252 (15)0.0342 (17)0.0259 (14)−0.0011 (15)0.0053 (12)0.0028 (15)
C20.0214 (15)0.0346 (18)0.0281 (16)−0.0045 (15)0.0052 (13)−0.0032 (14)
C30.0249 (16)0.0300 (17)0.0258 (15)−0.0021 (14)0.0094 (13)−0.0001 (13)
C40.0266 (16)0.0278 (17)0.0236 (15)−0.0022 (14)0.0063 (13)−0.0010 (13)
C50.0237 (16)0.0273 (16)0.0304 (16)−0.0014 (14)0.0025 (14)0.0014 (13)
C60.0374 (17)0.0334 (18)0.0237 (15)0.0014 (17)−0.0004 (13)0.0029 (15)
C70.0366 (18)0.0417 (19)0.0273 (15)−0.0030 (18)−0.0002 (14)0.0004 (15)
C80.0291 (18)0.043 (2)0.0373 (19)−0.0020 (17)0.0018 (15)−0.0103 (16)
C90.0248 (19)0.055 (2)0.058 (2)−0.0024 (18)0.0058 (17)−0.006 (2)
C100.0381 (18)0.0355 (18)0.0295 (16)0.0043 (18)0.0005 (14)−0.0050 (15)
C110.050 (2)0.050 (2)0.0415 (19)0.002 (2)0.0182 (17)−0.0085 (19)
C120.0360 (18)0.0289 (17)0.0319 (16)−0.0055 (17)0.0062 (14)0.0035 (15)
C130.0318 (17)0.0350 (18)0.0383 (17)−0.0042 (17)0.0068 (14)0.0049 (16)
C140.0305 (18)0.0380 (19)0.0363 (17)0.0014 (16)0.0072 (15)0.0054 (15)
C150.048 (2)0.055 (2)0.0276 (17)0.002 (2)0.0040 (17)0.0029 (17)
C160.075 (3)0.058 (3)0.039 (2)−0.008 (2)0.007 (2)−0.0088 (18)
C170.0275 (16)0.0347 (19)0.0301 (16)−0.0089 (15)0.0022 (14)−0.0008 (14)
C180.047 (2)0.065 (3)0.0320 (18)−0.011 (2)−0.0091 (17)0.0113 (18)

Geometric parameters (Å, °)

Cl1—C71.776 (4)C4—C51.517 (4)
Cl2—C71.754 (4)C4—H4A1.0000
Cl3—C71.753 (3)C5—C171.522 (4)
O1—C11.399 (3)C5—H5A1.0000
O1—C51.433 (4)C6—C71.524 (4)
O2—C61.359 (4)C8—C91.492 (5)
O2—C11.433 (3)C9—H9A0.9800
O3—C81.351 (4)C9—H9B0.9800
O3—C21.447 (3)C9—H9C0.9800
O4—C81.199 (4)C10—C111.492 (4)
O5—C101.357 (4)C11—H11A0.9800
O5—C31.447 (3)C11—H11B0.9800
O6—C101.194 (4)C11—H11C0.9800
O7—C121.356 (4)C12—C131.504 (4)
O7—C41.452 (3)C13—C141.515 (5)
O8—C121.197 (4)C13—H13A0.9900
O9—C151.208 (5)C13—H13B0.9900
O10—C171.197 (4)C14—C151.493 (5)
O11—C171.333 (4)C14—H14A0.9900
O11—C181.448 (4)C14—H14B0.9900
N1—C61.256 (4)C15—C161.496 (5)
N1—H1A0.9001C16—H16A0.9800
C1—C21.527 (4)C16—H16B0.9800
C1—H1C1.0000C16—H16C0.9800
C2—C31.514 (4)C18—H18A0.9800
C2—H2A1.0000C18—H18B0.9800
C3—C41.518 (4)C18—H18C0.9800
C3—H3A1.0000
C1—O1—C5115.3 (2)C8—C9—H9A109.5
C6—O2—C1116.8 (2)C8—C9—H9B109.5
C8—O3—C2116.7 (2)H9A—C9—H9B109.5
C10—O5—C3115.9 (2)C8—C9—H9C109.5
C12—O7—C4115.9 (2)H9A—C9—H9C109.5
C17—O11—C18117.3 (3)H9B—C9—H9C109.5
C6—N1—H1A101.4O6—C10—O5123.0 (3)
O1—C1—O2111.1 (2)O6—C10—C11126.3 (3)
O1—C1—C2114.3 (3)O5—C10—C11110.7 (3)
O2—C1—C2105.9 (2)C10—C11—H11A109.5
O1—C1—H1C108.4C10—C11—H11B109.5
O2—C1—H1C108.4H11A—C11—H11B109.5
C2—C1—H1C108.4C10—C11—H11C109.5
O3—C2—C3106.3 (2)H11A—C11—H11C109.5
O3—C2—C1107.9 (2)H11B—C11—H11C109.5
C3—C2—C1113.3 (3)O8—C12—O7123.1 (3)
O3—C2—H2A109.7O8—C12—C13125.5 (3)
C3—C2—H2A109.7O7—C12—C13111.3 (3)
C1—C2—H2A109.7C12—C13—C14115.2 (3)
O5—C3—C2108.9 (2)C12—C13—H13A108.5
O5—C3—C4105.4 (2)C14—C13—H13A108.5
C2—C3—C4112.8 (3)C12—C13—H13B108.5
O5—C3—H3A109.9C14—C13—H13B108.5
C2—C3—H3A109.9H13A—C13—H13B107.5
C4—C3—H3A109.9C15—C14—C13113.4 (3)
O7—C4—C5105.3 (2)C15—C14—H14A108.9
O7—C4—C3108.3 (2)C13—C14—H14A108.9
C5—C4—C3111.9 (3)C15—C14—H14B108.9
O7—C4—H4A110.4C13—C14—H14B108.9
C5—C4—H4A110.4H14A—C14—H14B107.7
C3—C4—H4A110.4O9—C15—C14120.5 (4)
O1—C5—C4112.1 (3)O9—C15—C16122.0 (4)
O1—C5—C17107.1 (3)C14—C15—C16117.5 (4)
C4—C5—C17109.4 (3)C15—C16—H16A109.5
O1—C5—H5A109.4C15—C16—H16B109.5
C4—C5—H5A109.4H16A—C16—H16B109.5
C17—C5—H5A109.4C15—C16—H16C109.5
N1—C6—O2123.1 (3)H16A—C16—H16C109.5
N1—C6—C7128.7 (3)H16B—C16—H16C109.5
O2—C6—C7108.2 (3)O10—C17—O11125.6 (3)
C6—C7—Cl3107.9 (2)O10—C17—C5126.3 (3)
C6—C7—Cl2111.2 (3)O11—C17—C5108.1 (3)
Cl3—C7—Cl2109.31 (19)O11—C18—H18A109.5
C6—C7—Cl1109.7 (2)O11—C18—H18B109.5
Cl3—C7—Cl1110.4 (2)H18A—C18—H18B109.5
Cl2—C7—Cl1108.34 (16)O11—C18—H18C109.5
O4—C8—O3122.4 (3)H18A—C18—H18C109.5
O4—C8—C9126.3 (4)H18B—C18—H18C109.5
O3—C8—C9111.2 (3)
C5—O1—C1—O2−68.1 (3)C3—C4—C5—C17171.0 (3)
C5—O1—C1—C251.8 (3)C1—O2—C6—N14.3 (5)
C6—O2—C1—O1−94.0 (3)C1—O2—C6—C7−176.8 (2)
C6—O2—C1—C2141.3 (3)N1—C6—C7—Cl3108.7 (4)
C8—O3—C2—C3−151.7 (3)O2—C6—C7—Cl3−70.2 (3)
C8—O3—C2—C186.4 (3)N1—C6—C7—Cl2−11.1 (5)
O1—C1—C2—O372.9 (3)O2—C6—C7—Cl2170.0 (2)
O2—C1—C2—O3−164.5 (2)N1—C6—C7—Cl1−131.0 (3)
O1—C1—C2—C3−44.6 (3)O2—C6—C7—Cl150.2 (3)
O2—C1—C2—C378.1 (3)C2—O3—C8—O42.0 (5)
C10—O5—C3—C2−93.1 (3)C2—O3—C8—C9−177.9 (3)
C10—O5—C3—C4145.6 (3)C3—O5—C10—O6−3.6 (5)
O3—C2—C3—O5167.4 (2)C3—O5—C10—C11178.4 (3)
C1—C2—C3—O5−74.3 (3)C4—O7—C12—O86.8 (5)
O3—C2—C3—C4−75.9 (3)C4—O7—C12—C13−168.6 (3)
C1—C2—C3—C442.4 (3)O8—C12—C13—C14152.1 (4)
C12—O7—C4—C5−159.4 (3)O7—C12—C13—C14−32.6 (4)
C12—O7—C4—C380.8 (3)C12—C13—C14—C15−61.0 (4)
O5—C3—C4—O7−172.2 (2)C13—C14—C15—O9−9.9 (5)
C2—C3—C4—O769.0 (3)C13—C14—C15—C16168.3 (3)
O5—C3—C4—C572.1 (3)C18—O11—C17—O102.6 (5)
C2—C3—C4—C5−46.6 (3)C18—O11—C17—C5−176.6 (3)
C1—O1—C5—C4−55.9 (3)O1—C5—C17—O10−6.6 (4)
C1—O1—C5—C17−175.8 (2)C4—C5—C17—O10−128.3 (4)
O7—C4—C5—O1−65.1 (3)O1—C5—C17—O11172.7 (2)
C3—C4—C5—O152.4 (3)C4—C5—C17—O1150.9 (3)
O7—C4—C5—C1753.6 (3)

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BT5207).

References

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