organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

2,3,4-Tri-O-acetyl-β-L-arabino­pyranosyl tri­chloro­acetimidate

aScience and Engineering College of Chemistry and Biology, Yantai University, Yantai 264005, People's Republic of China
*Correspondence e-mail: zulisun10@126.com

(Received 9 January 2011; accepted 13 January 2011; online 22 January 2011)

In the title compound, C13H16Cl3NO8, the trichloro­acetimidate group is located in an axial postion on the anomeric carbon of the sugar ring.

Related literature

For applications of glycosyl trichloro­acetimidate in glycosyl bond formation, see: Schmidt & Zhu (2008[Schmidt, R. R. & Zhu, X. (2008). Glycoscience, edited by B. Fraser-Reid, K. Tatsuta & J. Thiem, pp. 451-524. Berlin, Heidelberg: Springer-Verlag.]). For the preparation of the title compound, see: Schmidt & Stumpp (1983[Schmidt, R. R. & Stumpp, M. (1983). Justus Liebigs Ann. Chem. pp. 1249-1256.]).

[Scheme 1]

Experimental

Crystal data
  • C13H16Cl3NO8

  • Mr = 420.62

  • Monoclinic, C 2

  • a = 21.384 (5) Å

  • b = 6.7994 (16) Å

  • c = 13.096 (3) Å

  • β = 96.796 (3)°

  • V = 1890.7 (8) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.52 mm−1

  • T = 298 K

  • 0.49 × 0.24 × 0.08 mm

Data collection
  • Bruker SMART CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2003[Bruker (2003). SADABS, SAINT and SMART. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.784, Tmax = 0.959

  • 4972 measured reflections

  • 3239 independent reflections

  • 2933 reflections with I > 2σ(I)

  • Rint = 0.021

Refinement
  • R[F2 > 2σ(F2)] = 0.037

  • wR(F2) = 0.087

  • S = 1.06

  • 3239 reflections

  • 226 parameters

  • 1 restraint

  • H-atom parameters constrained

  • Δρmax = 0.23 e Å−3

  • Δρmin = −0.17 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1334 Friedel pairs

  • Flack parameter: 0.04 (6)

Data collection: SMART (Bruker, 2003[Bruker (2003). SADABS, SAINT and SMART. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2003[Bruker (2003). SADABS, SAINT and SMART. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

The title compound, a very useful glycosyl intermediate in glycosyl bond formation, was prepared from L-arabinose according to literature (Schmidt et al., 1983) and its structure was further characterized by X-ray crystallographic techniques. The structure of 2,3,4-tri-O-acetyl-β-L-arabinopyranosyl trichloroacetimidate has monoclinic (C2) symmetry. The structure reveals that the trichloroacetimidate group is located at axial postion on anomeric carbon of sugar ring, as shown in Fig. 1. There is hydrogen bond interaction between N (1) and Cl (2) on the trichloroacetimidate group [N(1)···Cl(2) 3.009 (3) Å and N(1)—H(1)···Cl(2) 113.5 °].

Related literature top

For applications of glycosyl trichloroacetimidate in glycosyl bond formation, see: Schmidt et al. (2008). For the preparation of the title compound, see: Schmidt et al. (1983).

Experimental top

The title compound was prepared from L-arabinose by the following three steps: i) acetylation with Ac2O in pyridine; ii) selective removal of acetyl group on anomeric carbon by ammonia methanol solution; iii) trichloroacetimidate formation with Cl3CN/DBU in dichloromethane. Colorless single crystals were grown from a solution of petroleum ether/ethyl acetate (2:1).

Refinement top

All non-hydrogen atoms were refined with anisotropic displacement parameters. Hydrogen atoms attached to anisotropically refined atoms were placed in geometrically idealized positions and included as riding atoms with C—H = 0.98Å and Uiso(H) = 1.2*Ueq(C) (–CH); C—H = 0.96Å and Uiso(H) = 1.5*Ueq(C) (methyl); C—H = 0.97Å and Uiso(H) = 1.2*Ueq(C) (methylene); N—H = 0.88Å and Uiso(H) = 1.2*Ueq(N). The H atoms of one methyl is disordered over two closely spaced positions in 0.5/0.5 ratio.

Computing details top

Data collection: SMART (Bruker, 2003); cell refinement: SAINT (Bruker, 2003); data reduction: SAINT (Bruker, 2003); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. Elipsoid plot.
2,3,4-tri-O-acetyl-β-L-arabinopyranosyl trichloroacetimidate top
Crystal data top
C13H16Cl3NO8F(000) = 864
Mr = 420.62Dx = 1.478 Mg m3
Monoclinic, C2Mo Kα radiation, λ = 0.71073 Å
a = 21.384 (5) ÅCell parameters from 2245 reflections
b = 6.7994 (16) Åθ = 2.6–23.4°
c = 13.096 (3) ŵ = 0.52 mm1
β = 96.796 (3)°T = 298 K
V = 1890.7 (8) Å3Plan, colourless
Z = 40.49 × 0.24 × 0.08 mm
Data collection top
Bruker SMART CCD area-detector
diffractometer
3239 independent reflections
Radiation source: fine-focus sealed tube2933 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.021
ϕ and ω scansθmax = 25.5°, θmin = 1.9°
Absorption correction: multi-scan
(SADABS; Bruker, 2003)
h = 2521
Tmin = 0.784, Tmax = 0.959k = 86
4972 measured reflectionsl = 1215
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.037H-atom parameters constrained
wR(F2) = 0.087 w = 1/[σ2(Fo2) + (0.0276P)2 + 0.9525P]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max = 0.006
3239 reflectionsΔρmax = 0.23 e Å3
226 parametersΔρmin = 0.17 e Å3
1 restraintAbsolute structure: Flack (1983), 1334 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.04 (6)
Crystal data top
C13H16Cl3NO8V = 1890.7 (8) Å3
Mr = 420.62Z = 4
Monoclinic, C2Mo Kα radiation
a = 21.384 (5) ŵ = 0.52 mm1
b = 6.7994 (16) ÅT = 298 K
c = 13.096 (3) Å0.49 × 0.24 × 0.08 mm
β = 96.796 (3)°
Data collection top
Bruker SMART CCD area-detector
diffractometer
3239 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2003)
2933 reflections with I > 2σ(I)
Tmin = 0.784, Tmax = 0.959Rint = 0.021
4972 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.037H-atom parameters constrained
wR(F2) = 0.087Δρmax = 0.23 e Å3
S = 1.06Δρmin = 0.17 e Å3
3239 reflectionsAbsolute structure: Flack (1983), 1334 Friedel pairs
226 parametersAbsolute structure parameter: 0.04 (6)
1 restraint
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
C20.61191 (15)0.4264 (8)0.4040 (2)0.0721 (11)
C30.71252 (13)0.5071 (4)0.3556 (2)0.0431 (7)
H3A0.69370.63800.34480.052*
C40.77597 (14)0.5222 (4)0.4187 (2)0.0479 (7)
H4A0.80170.61540.38620.057*
H4B0.77040.57290.48630.057*
C50.81676 (12)0.2479 (4)0.33786 (19)0.0385 (6)
H5A0.83690.11970.35190.046*
C60.75450 (12)0.2193 (4)0.27061 (18)0.0354 (6)
H6A0.72850.12660.30440.042*
C70.71942 (11)0.4112 (4)0.25338 (17)0.0354 (5)
H7A0.74230.49910.21150.042*
C80.91695 (12)0.3220 (4)0.2839 (2)0.0449 (7)
C90.94598 (13)0.4576 (5)0.2087 (2)0.0518 (7)
C100.77615 (13)0.0517 (4)0.1675 (2)0.0453 (7)
C110.62909 (13)0.5066 (5)0.1420 (2)0.0461 (7)
C120.56681 (14)0.4375 (7)0.0926 (3)0.0725 (10)
H12A0.54640.54180.05190.109*
H12B0.54120.39950.14470.109*
H12C0.57260.32670.04930.109*
C130.78124 (19)0.1138 (5)0.0615 (3)0.0723 (10)
H13A0.79030.25200.06040.109*
H13B0.81450.04190.03530.109*
H13C0.74220.08810.01950.109*
Cl10.93304 (4)0.70622 (13)0.24083 (7)0.0688 (3)
Cl21.02723 (4)0.41909 (16)0.21284 (8)0.0838 (3)
Cl30.90994 (5)0.40977 (19)0.08308 (6)0.0833 (3)
O10.58775 (12)0.5583 (6)0.3561 (2)0.0997 (11)
O20.76398 (9)0.1433 (2)0.17167 (13)0.0429 (4)
O30.78190 (11)0.1520 (3)0.24214 (18)0.0617 (6)
O40.85537 (8)0.3662 (3)0.27922 (14)0.0441 (4)
O50.67371 (8)0.3848 (3)0.41230 (13)0.0521 (5)
O60.65015 (10)0.6661 (3)0.13335 (17)0.0622 (6)
O70.65915 (8)0.3634 (3)0.19901 (13)0.0436 (5)
O80.80828 (8)0.3379 (3)0.43005 (13)0.0445 (5)
N10.94316 (12)0.1918 (5)0.3390 (2)0.0720 (9)
H10.98340.17360.33290.108*
C10.57884 (18)0.2786 (11)0.4638 (3)0.125 (2)
H1A0.59750.27860.53420.187*0.50
H1B0.58280.15020.43490.187*0.50
H1C0.53510.31260.46070.187*0.50
H1'10.56380.34210.52170.187*0.50
H1'20.60770.17570.48770.187*0.50
H1'30.54390.22360.42040.187*0.50
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C20.0401 (16)0.130 (4)0.0470 (16)0.021 (2)0.0094 (13)0.009 (2)
C30.0419 (15)0.0449 (17)0.0431 (14)0.0097 (12)0.0079 (11)0.0031 (12)
C40.0467 (17)0.0527 (19)0.0437 (15)0.0000 (14)0.0027 (12)0.0069 (13)
C50.0312 (13)0.0394 (16)0.0447 (15)0.0055 (11)0.0040 (11)0.0105 (12)
C60.0375 (13)0.0336 (14)0.0359 (13)0.0016 (11)0.0078 (10)0.0053 (11)
C70.0317 (12)0.0351 (14)0.0394 (12)0.0002 (12)0.0043 (10)0.0052 (12)
C80.0304 (13)0.0492 (18)0.0543 (16)0.0029 (13)0.0022 (12)0.0009 (14)
C90.0375 (15)0.0553 (19)0.0639 (17)0.0045 (14)0.0122 (13)0.0024 (15)
C100.0404 (14)0.0346 (16)0.0615 (17)0.0002 (12)0.0087 (13)0.0024 (14)
C110.0378 (15)0.062 (2)0.0380 (14)0.0087 (14)0.0025 (11)0.0069 (13)
C120.0437 (17)0.095 (3)0.074 (2)0.0004 (19)0.0150 (15)0.017 (2)
C130.096 (3)0.048 (2)0.076 (2)0.0055 (19)0.0225 (19)0.0130 (18)
Cl10.0594 (5)0.0493 (5)0.1014 (7)0.0004 (4)0.0246 (4)0.0029 (5)
Cl20.0401 (4)0.0873 (7)0.1296 (8)0.0112 (4)0.0332 (5)0.0213 (6)
Cl30.0909 (7)0.1090 (8)0.0525 (4)0.0057 (6)0.0185 (4)0.0003 (5)
O10.0543 (15)0.161 (3)0.0849 (18)0.0531 (18)0.0137 (13)0.026 (2)
O20.0549 (12)0.0344 (11)0.0407 (10)0.0050 (8)0.0117 (8)0.0045 (8)
O30.0771 (15)0.0365 (12)0.0708 (14)0.0036 (11)0.0056 (11)0.0099 (11)
O40.0290 (9)0.0485 (12)0.0558 (10)0.0062 (8)0.0093 (7)0.0142 (9)
O50.0339 (9)0.0780 (15)0.0454 (10)0.0122 (10)0.0086 (8)0.0120 (11)
O60.0526 (13)0.0589 (16)0.0721 (14)0.0066 (11)0.0053 (10)0.0246 (12)
O70.0336 (9)0.0472 (12)0.0479 (10)0.0013 (9)0.0038 (7)0.0051 (9)
O80.0382 (10)0.0553 (12)0.0389 (9)0.0044 (9)0.0000 (8)0.0068 (9)
N10.0384 (14)0.083 (2)0.095 (2)0.0141 (15)0.0109 (13)0.0363 (19)
C10.045 (2)0.251 (7)0.080 (3)0.011 (3)0.0175 (19)0.045 (4)
Geometric parameters (Å, º) top
C2—O11.178 (5)C9—Cl21.752 (3)
C2—O51.343 (4)C9—Cl31.763 (3)
C2—C11.502 (6)C9—Cl11.771 (3)
C3—O51.442 (3)C10—O31.187 (3)
C3—C41.506 (4)C10—O21.353 (3)
C3—C71.512 (4)C10—C131.467 (4)
C3—H3A0.9800C11—O61.185 (4)
C4—O81.430 (3)C11—O71.344 (3)
C4—H4A0.9700C11—C121.486 (4)
C4—H4B0.9700C12—H12A0.9600
C5—O81.385 (3)C12—H12B0.9600
C5—O41.438 (3)C12—H12C0.9600
C5—C61.519 (3)C13—H13A0.9600
C5—H5A0.9800C13—H13B0.9600
C6—O21.432 (3)C13—H13C0.9600
C6—C71.508 (4)N1—H10.8820
C6—H6A0.9800C1—H1A0.9600
C7—O71.434 (3)C1—H1B0.9600
C7—H7A0.9800C1—H1C0.9600
C8—N11.234 (4)C1—H1'10.9600
C8—O41.345 (3)C1—H1'20.9600
C8—C91.533 (4)C1—H1'30.9600
O1—C2—O5124.7 (4)O2—C10—C13110.9 (3)
O1—C2—C1125.7 (3)O6—C11—O7123.6 (3)
O5—C2—C1109.6 (4)O6—C11—C12125.4 (3)
O5—C3—C4107.0 (2)O7—C11—C12111.0 (3)
O5—C3—C7109.2 (2)C11—C12—H12A109.5
C4—C3—C7109.8 (2)C11—C12—H12B109.5
O5—C3—H3A110.2H12A—C12—H12B109.5
C4—C3—H3A110.2C11—C12—H12C109.5
C7—C3—H3A110.2H12A—C12—H12C109.5
O8—C4—C3113.0 (2)H12B—C12—H12C109.5
O8—C4—H4A109.0C10—C13—H13A109.5
C3—C4—H4A109.0C10—C13—H13B109.5
O8—C4—H4B109.0H13A—C13—H13B109.5
C3—C4—H4B109.0C10—C13—H13C109.5
H4A—C4—H4B107.8H13A—C13—H13C109.5
O8—C5—O4111.1 (2)H13B—C13—H13C109.5
O8—C5—C6111.5 (2)C10—O2—C6116.1 (2)
O4—C5—C6106.32 (19)C8—O4—C5118.1 (2)
O8—C5—H5A109.3C2—O5—C3117.2 (3)
O4—C5—H5A109.3C11—O7—C7117.0 (2)
C6—C5—H5A109.3C5—O8—C4114.1 (2)
O2—C6—C7107.34 (19)C8—N1—H1115.3
O2—C6—C5111.3 (2)C2—C1—H1A109.5
C7—C6—C5111.2 (2)C2—C1—H1B109.5
O2—C6—H6A109.0H1A—C1—H1B109.5
C7—C6—H6A109.0C2—C1—H1C109.5
C5—C6—H6A109.0H1A—C1—H1C109.5
O7—C7—C6106.3 (2)H1B—C1—H1C109.5
O7—C7—C3111.17 (19)C2—C1—H1'1109.5
C6—C7—C3109.9 (2)H1A—C1—H1'151.8
O7—C7—H7A109.8H1B—C1—H1'1140.8
C6—C7—H7A109.8H1C—C1—H1'160.7
C3—C7—H7A109.8C2—C1—H1'2109.5
N1—C8—O4124.2 (3)H1A—C1—H1'260.7
N1—C8—C9128.1 (3)H1B—C1—H1'251.8
O4—C8—C9107.8 (2)H1C—C1—H1'2140.8
C8—C9—Cl2111.5 (2)H1'1—C1—H1'2109.5
C8—C9—Cl3108.8 (2)C2—C1—H1'3109.5
Cl2—C9—Cl3108.89 (17)H1A—C1—H1'3140.8
C8—C9—Cl1109.6 (2)H1B—C1—H1'360.7
Cl2—C9—Cl1108.52 (17)H1C—C1—H1'351.8
Cl3—C9—Cl1109.53 (17)H1'1—C1—H1'3109.5
O3—C10—O2122.1 (3)H1'2—C1—H1'3109.5
O3—C10—C13127.0 (3)
O5—C3—C4—O864.9 (3)O3—C10—O2—C63.8 (4)
C7—C3—C4—O853.5 (3)C13—C10—O2—C6176.7 (2)
O8—C5—C6—O2174.5 (2)C7—C6—O2—C10159.8 (2)
O4—C5—C6—O253.3 (3)C5—C6—O2—C1078.3 (3)
O8—C5—C6—C754.9 (3)N1—C8—O4—C53.4 (4)
O4—C5—C6—C766.4 (2)C9—C8—O4—C5175.5 (2)
O2—C6—C7—O764.1 (2)O8—C5—O4—C898.2 (3)
C5—C6—C7—O7173.92 (18)C6—C5—O4—C8140.3 (2)
O2—C6—C7—C3175.5 (2)O1—C2—O5—C32.1 (5)
C5—C6—C7—C353.6 (3)C1—C2—O5—C3177.3 (3)
O5—C3—C7—O752.8 (3)C4—C3—O5—C2146.6 (3)
C4—C3—C7—O7169.9 (2)C7—C3—O5—C294.6 (3)
O5—C3—C7—C664.5 (3)O6—C11—O7—C71.3 (4)
C4—C3—C7—C652.5 (3)C12—C11—O7—C7178.5 (2)
N1—C8—C9—Cl23.6 (4)C6—C7—O7—C11155.7 (2)
O4—C8—C9—Cl2177.5 (2)C3—C7—O7—C1184.8 (3)
N1—C8—C9—Cl3116.5 (3)O4—C5—O8—C462.6 (3)
O4—C8—C9—Cl362.4 (3)C6—C5—O8—C455.8 (3)
N1—C8—C9—Cl1123.8 (3)C3—C4—O8—C556.4 (3)
O4—C8—C9—Cl157.3 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···Cl20.882.553.009 (3)114

Experimental details

Crystal data
Chemical formulaC13H16Cl3NO8
Mr420.62
Crystal system, space groupMonoclinic, C2
Temperature (K)298
a, b, c (Å)21.384 (5), 6.7994 (16), 13.096 (3)
β (°) 96.796 (3)
V3)1890.7 (8)
Z4
Radiation typeMo Kα
µ (mm1)0.52
Crystal size (mm)0.49 × 0.24 × 0.08
Data collection
DiffractometerBruker SMART CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2003)
Tmin, Tmax0.784, 0.959
No. of measured, independent and
observed [I > 2σ(I)] reflections
4972, 3239, 2933
Rint0.021
(sin θ/λ)max1)0.606
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.037, 0.087, 1.06
No. of reflections3239
No. of parameters226
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.23, 0.17
Absolute structureFlack (1983), 1334 Friedel pairs
Absolute structure parameter0.04 (6)

Computer programs: SMART (Bruker, 2003), SAINT (Bruker, 2003), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···Cl20.882.553.009 (3)114
 

Acknowledgements

This work was supported by a grant from the National High Technology Research and Development Program of China (863 Program) (No. 2007AA03A229)

References

First citationBruker (2003). SADABS, SAINT and SMART. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationSchmidt, R. R. & Stumpp, M. (1983). Justus Liebigs Ann. Chem. pp. 1249–1256.  CrossRef Google Scholar
First citationSchmidt, R. R. & Zhu, X. (2008). Glycoscience, edited by B. Fraser-Reid, K. Tatsuta & J. Thiem, pp. 451–524. Berlin, Heidelberg: Springer-Verlag.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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