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The solid-state conformation of the title compound, C20H32N2O9, has been determined at 150 K. The pyran­ose ring has a distorted chair conformation. Among the possible conformations of the C-N glycosidic bond, that of the E rotamer is observed and a short intramolecular Cmethyl...O contact may partly stabilize this conformation. Crystal cohesion is stabilized by an extensive network of weak C-H...O hydrogen bonds and close contacts.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270101011465/sx1111sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270101011465/sx1111Isup2.hkl
Contains datablock I

CCDC reference: 175079

Comment top

The chemical and biological properties of organic compounds depend on their structure and conformation and, as many natural products and their derivatives have an N-acyl group joined to a sugar moiety, correct determination of their structure is sometimes challenging. Crystals of the title compound, (I), were obtained by Avalos et al. (1995) from the reaction of 2,3,4,6,-tetra-O-acetyl-N-thioacetyl-β-D-glucopyranosylamine, mercury oxide and diethylamine in dichloromethane. The same authors studied several glycoamidines by NMR spectroscopy, including the title compound, and confirmed the β-configuration of the prepared glycoamidine. The absolute configuration was assigned from the absolute stereochemistry of the starting material used in the synthesis. We therefore undertook the crystal structure determination of (I). The structural analysis shows that only one rotamer along the C—N bond (E) is present in the crystal. \sch

The structure of compound (I) was determined first at room temperature and then at 150 K, to reduce the dynamic disorder affecting the terminal groups. The isotropic displacement parameters at 150 K are almost three times smaller than those determined at room temperature.

Fig. 1 shows an ORTEPII view (Johnson, 1976) of the molecule of (I) along the c axis, together with the atomic numbering scheme. Bond lengths and angles (Table 1) agree with those of analogous compounds (Vega et al., 1986; Diánez et al., 1997), although the pyranose endocyclic bond lengths [O—C1 1.445 (3) and O—C5 1.436 (3) Å] do not show the anomeric effect characteristic of this system. The acetoxy and methylacetoxy groups are essentially planar.

The geometry observed for the pyranose ring is a distorted chair, with ring substitutents O2, O4, C6, O3 and N1 all in equatorial positions. The ring puckering parameters (Cremer & Pople, 1975) are Q = 0.591 (3) Å, ϕ = 42 (2)° and θ = 10 (1)°. The asymmetry parameters (Nardelli, 1983a) are ΔCs(C1) = 0.028 and ΔC2(C1—O) = 0.011. The glycosidic O—C1—N1—C11 torsion angle is -80.0 (3)°, which is within the range of the E rotamer of the glycosidic linkage; the O—C5—C6—O6 torsion angle is -67.4 (3)°. This conformation may be partly stalibized by a close intramolecular C—H···O interaction between C12 and the O atom in the pyranose ring, with C12···O 3.174 (1) and H···O 2.525 Å, and C12—H···O 123.6 (1)°.

In the absence of standard hydrogen-bonding donor or acceptor groups, the crystal packing is stabilized by a series of nine weak C—H···O interactions, many of which have the near-linear molecular geometries expected for close C—H···O contacts (Table 2).

Related literature top

For related literature, see: Avalos et al. (1995); Cremer & Pople (1975); Diánez et al. (1997); Johnson (1976); Nardelli (1983a); Vega et al. (1986).

Experimental top

Compound (I) was synthesized in the Organic Chemistry Department of Extremadura University, using the method of Avalos et al. (1995), from the reaction of 2,3,4,6,-tetra-O-acetyl-N-thioacetyl-β-D-glucopyranosylamine, mercury oxide and diethylamine in dichloromethane. Crystals of (I) were grown from ethyl ether.

Refinement top

No Friedel pairs were collected. The absolute configuration was known from the stereochemistry of the compound, established from the starting materials. All H atoms were placed at idealized positions using a riding model and were not refined.

Computing details top

Data collection: CAD-4 Software (Enraf-Nonius, 1989); cell refinement: SET4 (de Boer & Duisenberg, 1984) and CELDIM in CAD-4 Software; data reduction: XRAY76 (Stewart et al., 1976); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXL93 (Sheldrick, 1993); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: PARST (Nardelli, 1983b).

Figures top
[Figure 1] Fig. 1. The molecular view of (I) with the atom-numbering scheme. Displacement ellipsoids are drawn at the ?% probability level and H atoms have been omitted for clarity.
N1,N1-Diethyl-N2-(2,3,4,6-tetra-O-acetyl-β-D-glucopyranosyl)acetamidine top
Crystal data top
C20H32N2O9Dx = 1.277 Mg m3
Dm = 1.28 Mg m3
Dm measured by flotation in nitrobenzene and acetone
Mr = 444.48Melting point = 403–404 K
Orthorhombic, P212121Mo Kα radiation, λ = 0.71069 Å
a = 10.440 (2) ÅCell parameters from 25 reflections
b = 27.647 (5) Åθ = 2–30°
c = 8.012 (2) ŵ = 0.10 mm1
V = 2312.5 (8) Å3T = 150 K
Z = 4Prism, colourless
F(000) = 9520.60 × 0.49 × 0.40 mm
Data collection top
Enraf-Nonius CAD4
diffractometer
Rint = 0.000
Radiation source: fine-focus sealed tubeθmax = 35.0°, θmin = 2.1°
Graphite monochromatorh = 016
ω/2θ scansk = 044
5663 measured reflectionsl = 012
5663 independent reflections3 standard reflections every 120 min
4270 reflections with I > 2σ(I) intensity decay: none
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.069Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.182H-atom parameters constrained
S = 1.12 w = 1/[σ2(Fo2) + (0.0904P)2 + 1.8423P]
where P = (Fo2 + 2Fc2)/3
5663 reflections(Δ/σ)max = 0.001
280 parametersΔρmax = 0.57 e Å3
0 restraintsΔρmin = 0.50 e Å3
Crystal data top
C20H32N2O9V = 2312.5 (8) Å3
Mr = 444.48Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 10.440 (2) ŵ = 0.10 mm1
b = 27.647 (5) ÅT = 150 K
c = 8.012 (2) Å0.60 × 0.49 × 0.40 mm
Data collection top
Enraf-Nonius CAD4
diffractometer
Rint = 0.000
5663 measured reflections3 standard reflections every 120 min
5663 independent reflections intensity decay: none
4270 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.0690 restraints
wR(F2) = 0.182H-atom parameters constrained
S = 1.12Δρmax = 0.57 e Å3
5663 reflectionsΔρmin = 0.50 e Å3
280 parameters
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. Weighted R_factors wR and all goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. 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
xyzUiso*/Ueq
O0.0285 (2)0.86088 (7)0.1618 (3)0.0219 (4)
O20.2423 (2)0.90379 (8)0.1643 (3)0.0224 (4)
O30.0328 (2)0.97278 (7)0.1706 (3)0.0216 (4)
O40.0623 (2)0.98870 (7)0.1707 (3)0.0212 (4)
O60.2342 (2)0.88107 (9)0.2046 (3)0.0332 (5)
O220.1422 (3)0.88606 (13)0.4058 (3)0.0422 (7)
O320.2159 (2)1.01538 (10)0.1951 (3)0.0383 (6)
O420.2426 (3)0.99939 (14)0.0230 (5)0.0548 (9)
O620.3660 (4)0.8575 (2)0.4087 (5)0.084 (2)
N10.2007 (2)0.82122 (9)0.0262 (3)0.0237 (4)
N20.3183 (3)0.75345 (10)0.0750 (4)0.0301 (5)
C10.1510 (2)0.86660 (10)0.0802 (3)0.0209 (5)
H10.21320.88300.15650.025*
C20.1254 (2)0.89797 (10)0.0728 (3)0.0190 (4)
H20.06040.88180.14540.023*
C30.0766 (2)0.94764 (10)0.0224 (3)0.0190 (4)
H30.14580.96650.03420.023*
C40.0393 (2)0.94264 (9)0.0915 (3)0.0194 (4)
H40.11600.93290.02470.023*
C50.0159 (2)0.90583 (10)0.2306 (3)0.0210 (5)
H50.05000.91880.30930.025*
C60.1375 (3)0.89502 (11)0.3259 (4)0.0278 (5)
H6A0.12290.86840.40640.033*
H6B0.16580.92400.38840.033*
C110.2568 (3)0.79340 (11)0.1332 (4)0.0252 (5)
C120.2587 (4)0.80145 (13)0.3197 (4)0.0349 (7)
H12A0.34690.80730.35640.052*
H12B0.22500.77270.37620.052*
H12C0.20550.82950.34740.052*
C130.3209 (4)0.74392 (12)0.1046 (4)0.0333 (7)
H13A0.23730.75320.15350.040*
H13B0.33280.70880.12310.040*
C140.4268 (5)0.7713 (2)0.1935 (6)0.0485 (10)
H14A0.42670.76260.31210.073*
H14B0.50960.76270.14420.073*
H14C0.41240.80610.18170.073*
C150.3984 (3)0.72173 (13)0.1776 (5)0.0350 (7)
H15A0.42580.73950.27880.042*
H15B0.47640.71300.11400.042*
C160.3297 (4)0.67590 (14)0.2297 (6)0.0468 (10)
H16A0.38550.65680.30270.070*
H16B0.30810.65690.13040.070*
H16C0.25110.68430.28980.070*
C210.2380 (3)0.89647 (11)0.3314 (4)0.0261 (5)
C220.3677 (4)0.90339 (14)0.4068 (5)0.0385 (8)
H22A0.42400.87680.37220.058*
H22B0.40370.93420.36870.058*
H22C0.36040.90360.52870.058*
C310.1130 (3)1.00352 (11)0.2473 (4)0.0255 (5)
C320.0555 (4)1.0209 (2)0.4090 (5)0.0391 (8)
H32A0.03811.02090.39990.059*
H32B0.08170.99940.49990.059*
H32C0.08541.05380.43230.059*
C410.1694 (3)1.01353 (12)0.1261 (4)0.0275 (6)
C420.1830 (4)1.06008 (12)0.2177 (4)0.0326 (7)
H42A0.14711.08640.15030.049*
H42B0.13691.05810.32400.049*
H42C0.27391.06640.23910.049*
C610.3446 (3)0.86356 (15)0.2624 (6)0.0431 (9)
C620.4338 (4)0.8507 (2)0.1236 (8)0.0574 (13)
H62A0.39860.86240.01760.086*
H62B0.51730.86590.14340.086*
H62C0.44410.81550.11880.086*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O0.0208 (8)0.0197 (8)0.0251 (9)0.0007 (7)0.0045 (7)0.0000 (7)
O20.0173 (7)0.0268 (9)0.0231 (8)0.0005 (7)0.0043 (7)0.0044 (7)
O30.0184 (7)0.0240 (9)0.0225 (8)0.0006 (7)0.0013 (7)0.0028 (7)
O40.0214 (8)0.0190 (8)0.0234 (8)0.0046 (7)0.0022 (7)0.0025 (7)
O60.0240 (9)0.0349 (12)0.0408 (13)0.0082 (9)0.0060 (9)0.0026 (10)
O220.0332 (12)0.069 (2)0.0241 (11)0.0016 (13)0.0021 (10)0.0090 (12)
O320.0303 (11)0.0449 (14)0.0396 (13)0.0158 (10)0.0015 (10)0.0102 (12)
O420.0375 (13)0.057 (2)0.070 (2)0.0243 (12)0.0260 (15)0.027 (2)
O620.066 (2)0.121 (4)0.064 (2)0.050 (2)0.042 (2)0.029 (2)
N10.0228 (10)0.0201 (10)0.0283 (11)0.0033 (8)0.0005 (9)0.0038 (9)
N20.0352 (13)0.0227 (11)0.0323 (13)0.0093 (10)0.0018 (11)0.0023 (10)
C10.0169 (10)0.0241 (12)0.0216 (11)0.0008 (8)0.0022 (9)0.0022 (9)
C20.0148 (9)0.0212 (11)0.0209 (10)0.0010 (8)0.0028 (8)0.0027 (9)
C30.0156 (9)0.0211 (11)0.0205 (10)0.0008 (8)0.0014 (8)0.0018 (9)
C40.0171 (9)0.0211 (11)0.0201 (10)0.0009 (8)0.0009 (9)0.0024 (9)
C50.0198 (10)0.0220 (11)0.0214 (11)0.0005 (9)0.0022 (9)0.0012 (9)
C60.0270 (12)0.0292 (13)0.0273 (12)0.0010 (11)0.0084 (11)0.0009 (11)
C110.0247 (11)0.0247 (12)0.0262 (12)0.0013 (10)0.0003 (10)0.0041 (10)
C120.047 (2)0.0318 (15)0.0254 (13)0.0095 (14)0.0000 (14)0.0005 (12)
C130.041 (2)0.0274 (14)0.0316 (15)0.0099 (13)0.0019 (14)0.0106 (12)
C140.054 (2)0.049 (2)0.042 (2)0.013 (2)0.009 (2)0.002 (2)
C150.035 (2)0.0283 (14)0.041 (2)0.0108 (12)0.0005 (15)0.0003 (14)
C160.052 (2)0.032 (2)0.057 (2)0.008 (2)0.010 (2)0.015 (2)
C210.0287 (12)0.0247 (12)0.0249 (11)0.0009 (10)0.0062 (11)0.0052 (10)
C220.034 (2)0.042 (2)0.040 (2)0.0007 (14)0.0194 (15)0.001 (2)
C310.0259 (12)0.0246 (12)0.0261 (12)0.0004 (10)0.0050 (11)0.0020 (10)
C320.037 (2)0.049 (2)0.032 (2)0.000 (2)0.0016 (14)0.013 (2)
C410.0244 (11)0.0302 (14)0.0279 (13)0.0089 (11)0.0004 (11)0.0010 (11)
C420.039 (2)0.0263 (14)0.0321 (14)0.0122 (12)0.0047 (13)0.0011 (12)
C610.0284 (14)0.039 (2)0.062 (2)0.0085 (13)0.021 (2)0.013 (2)
C620.0252 (15)0.060 (3)0.087 (4)0.013 (2)0.001 (2)0.005 (3)
Geometric parameters (Å, º) top
O—C51.436 (3)C12—H12A0.98
O—C11.445 (3)C12—H12B0.98
O2—C211.355 (4)C12—H12C0.98
O2—C21.433 (3)C13—C141.517 (6)
O3—C311.342 (3)C13—H13A0.99
O3—C31.450 (3)C13—H13B0.99
O4—C411.360 (3)C14—H14A0.98
O4—C41.443 (3)C14—H14B0.98
O6—C611.333 (4)C14—H14C0.98
O6—C61.453 (4)C15—C161.515 (6)
O22—C211.199 (4)C15—H15A0.99
O32—C311.199 (4)C15—H15B0.99
O42—C411.192 (4)C16—H16A0.98
O62—C611.205 (6)C16—H16B0.98
N1—C111.292 (4)C16—H16C0.98
N1—C11.425 (4)C21—C221.494 (5)
N2—C111.360 (4)C22—H22A0.98
N2—C131.463 (4)C22—H22B0.98
N2—C151.465 (4)C22—H22C0.98
C1—C21.525 (4)C31—C321.506 (5)
C1—H11.00C32—H32A0.98
C2—C31.519 (4)C32—H32B0.98
C2—H21.00C32—H32C0.98
C3—C41.522 (4)C41—C421.488 (5)
C3—H31.00C42—H42A0.98
C4—C51.529 (4)C42—H42B0.98
C4—H41.00C42—H42C0.98
C5—C61.512 (4)C61—C621.493 (7)
C5—H51.00C62—H62A0.98
C6—H6A0.99C62—H62B0.98
C6—H6B0.99C62—H62C0.98
C11—C121.511 (5)
C5—O—C1111.4 (2)N2—C13—H13B109
C21—O2—C2117.4 (2)C14—C13—H13B109
C31—O3—C3118.8 (2)H13A—C13—H13B108
C41—O4—C4117.8 (2)C13—C14—H14A110
C61—O6—C6117.7 (3)C13—C14—H14B110
C11—N1—C1119.2 (3)H14A—C14—H14B110
C11—N2—C13119.5 (3)C13—C14—H14C110
C11—N2—C15124.3 (3)H14A—C14—H14C110
C13—N2—C15115.7 (3)H14B—C14—H14C110
N1—C1—O111.3 (2)N2—C15—C16112.6 (3)
N1—C1—C2108.7 (2)N2—C15—H15A109
O—C1—C2105.7 (2)C16—C15—H15A109
N1—C1—H1110N2—C15—H15B109
O—C1—H1110C16—C15—H15B109
C2—C1—H1110H15A—C15—H15B108
O2—C2—C3108.7 (2)C15—C16—H16A110
O2—C2—C1109.0 (2)C15—C16—H16B110
C3—C2—C1111.1 (2)H16A—C16—H16B110
O2—C2—H2109C15—C16—H16C110
C3—C2—H2109H16A—C16—H16C110
C1—C2—H2109H16B—C16—H16C110
O3—C3—C2108.8 (2)O22—C21—O2123.7 (3)
O3—C3—C4106.5 (2)O22—C21—C22125.8 (3)
C2—C3—C4110.1 (2)O2—C21—C22110.5 (3)
O3—C3—H3111C21—C22—H22A110
C2—C3—H3111C21—C22—H22B110
C4—C3—H3111H22A—C22—H22B110
O4—C4—C3108.4 (2)C21—C22—H22C110
O4—C4—C5107.1 (2)H22A—C22—H22C110
C3—C4—C5111.8 (2)H22B—C22—H22C110
O4—C4—H4110O32—C31—O3124.9 (3)
C3—C4—H4110O32—C31—C32124.8 (3)
C5—C4—H4110O3—C31—C32110.3 (3)
O—C5—C6107.1 (2)C31—C32—H32A110
O—C5—C4110.4 (2)C31—C32—H32B110
C6—C5—C4111.4 (2)H32A—C32—H32B110
O—C5—H5109C31—C32—H32C110
C6—C5—H5109H32A—C32—H32C110
C4—C5—H5109H32B—C32—H32C110
O6—C6—C5107.4 (2)O42—C41—O4123.0 (3)
O6—C6—H6A110O42—C41—C42124.4 (3)
C5—C6—H6A110O4—C41—C42112.7 (3)
O6—C6—H6B110C41—C42—H42A110
C5—C6—H6B110C41—C42—H42B110
H6A—C6—H6B109H42A—C42—H42B110
N1—C11—N2118.1 (3)C41—C42—H42C110
N1—C11—C12125.0 (3)H42A—C42—H42C110
N2—C11—C12116.9 (3)H42B—C42—H42C110
C11—C12—H12A110O62—C61—O6123.3 (4)
C11—C12—H12B110O62—C61—C62125.1 (4)
H12A—C12—H12B110O6—C61—C62111.5 (4)
C11—C12—H12C110C61—C62—H62A110
H12A—C12—H12C110C61—C62—H62B110
H12B—C12—H12C110H62A—C62—H62B110
N2—C13—C14112.7 (3)C61—C62—H62C110
N2—C13—H13A109H62A—C62—H62C110
C14—C13—H13A109H62B—C62—H62C110
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C3—H3···O32i1.002.6533.552 (4)150
C5—H5···O22ii1.002.6383.393 (4)132
C12—H12C···O22ii0.982.6063.434 (5)142
C6—H6B···O42iii0.992.5623.547 (5)173
C22—H22C···O32iv0.982.7263.338 (5)121
C32—H32B···O32iv0.982.6633.458 (5)138
C22—H22A···O62v0.982.8603.395 (6)115
C32—H32A···O42vi0.982.4383.359 (5)156
C42—H42A···O62vi0.982.4833.403 (6)156
Symmetry codes: (i) x+1/2, y+2, z+1/2; (ii) x, y, z+1; (iii) x1/2, y+2, z+1/2; (iv) x+1/2, y+2, z1/2; (v) x+1, y, z1; (vi) x1/2, y+2, z1/2.

Experimental details

Crystal data
Chemical formulaC20H32N2O9
Mr444.48
Crystal system, space groupOrthorhombic, P212121
Temperature (K)150
a, b, c (Å)10.440 (2), 27.647 (5), 8.012 (2)
V3)2312.5 (8)
Z4
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.60 × 0.49 × 0.40
Data collection
DiffractometerEnraf-Nonius CAD4
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
5663, 5663, 4270
Rint0.000
(sin θ/λ)max1)0.806
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.069, 0.182, 1.12
No. of reflections5663
No. of parameters280
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.57, 0.50

Computer programs: CAD-4 Software (Enraf-Nonius, 1989), SET4 (de Boer & Duisenberg, 1984) and CELDIM in CAD-4 Software, XRAY76 (Stewart et al., 1976), SIR92 (Altomare et al., 1994), SHELXL93 (Sheldrick, 1993), ORTEPII (Johnson, 1976), PARST (Nardelli, 1983b).

Selected geometric parameters (Å, º) top
O—C51.436 (3)N2—C111.360 (4)
O—C11.445 (3)N2—C131.463 (4)
N1—C111.292 (4)N2—C151.465 (4)
N1—C11.425 (4)C11—C121.511 (5)
C5—O—C1111.4 (2)N1—C1—C2108.7 (2)
C11—N1—C1119.2 (3)O—C1—C2105.7 (2)
C11—N2—C13119.5 (3)N1—C11—N2118.1 (3)
C11—N2—C15124.3 (3)N1—C11—C12125.0 (3)
C13—N2—C15115.7 (3)N2—C11—C12116.9 (3)
N1—C1—O111.3 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C3—H3···O32i1.002.6533.552 (4)150
C5—H5···O22ii1.002.6383.393 (4)132
C12—H12C···O22ii0.982.6063.434 (5)142
C6—H6B···O42iii0.992.5623.547 (5)173
C22—H22C···O32iv0.982.7263.338 (5)121
C32—H32B···O32iv0.982.6633.458 (5)138
C22—H22A···O62v0.982.8603.395 (6)115
C32—H32A···O42vi0.982.4383.359 (5)156
C42—H42A···O62vi0.982.4833.403 (6)156
Symmetry codes: (i) x+1/2, y+2, z+1/2; (ii) x, y, z+1; (iii) x1/2, y+2, z+1/2; (iv) x+1/2, y+2, z1/2; (v) x+1, y, z1; (vi) x1/2, y+2, z1/2.
 

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