N¹,N¹-Diethyl-N²-(2,3,4,6-tetra-O-acetyl-[beta]-D-glucopyranosyl)acet­amidine

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 C_methyl...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.

S1. Comment

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 ΔC_s(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

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

S2. Experimental

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.

S3. Refinement

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

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

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

Crystal data

C20H32N2O9	Dx = 1.277 Mg m^−3 Dm = 1.28 Mg m^−3 Dm measured by flotation in nitrobenzene and acetone
Mr = 444.48	Melting point = 403–404 K
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71069 Å
a = 10.440 (2) Å	Cell parameters from 25 reflections
b = 27.647 (5) Å	θ = 2–30°
c = 8.012 (2) Å	µ = 0.10 mm^−1
V = 2312.5 (8) Å^3	T = 150 K
Z = 4	Prism, colourless
F(000) = 952	0.60 × 0.49 × 0.40 mm

Data collection

Enraf-Nonius CAD4 diffractometer	Rint = 0.000
Radiation source: fine-focus sealed tube	θmax = 35.0°, θmin = 2.1°
Graphite monochromator	h = 0→16
ω/2θ scans	k = 0→44
5663 measured reflections	l = 0→12
5663 independent reflections	3 standard reflections every 120 min
4270 reflections with I > 2σ(I)	intensity decay: none

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.069	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.182	H-atom parameters constrained
S = 1.12	w = 1/[σ^2(Fo^2) + (0.0904P)^2 + 1.8423P] where P = (Fo^2 + 2Fc^2)/3
5663 reflections	(Δ/σ)max = 0.001
280 parameters	Δρmax = 0.57 e Å^−3
0 restraints	Δρmin = −0.50 e Å^−3

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. 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 (Ų)

	x	y	z	Uiso*/Ueq
O	0.0285 (2)	0.86088 (7)	0.1618 (3)	0.0219 (4)
O2	0.2423 (2)	0.90379 (8)	−0.1643 (3)	0.0224 (4)
O3	0.0328 (2)	0.97278 (7)	−0.1706 (3)	0.0216 (4)
O4	−0.0623 (2)	0.98870 (7)	0.1707 (3)	0.0212 (4)
O6	−0.2342 (2)	0.88107 (9)	0.2046 (3)	0.0332 (5)
O22	0.1422 (3)	0.88606 (13)	−0.4058 (3)	0.0422 (7)
O32	0.2159 (2)	1.01538 (10)	−0.1951 (3)	0.0383 (6)
O42	−0.2426 (3)	0.99939 (14)	0.0230 (5)	0.0548 (9)
O62	−0.3660 (4)	0.8575 (2)	0.4087 (5)	0.084 (2)
N1	0.2007 (2)	0.82122 (9)	0.0262 (3)	0.0237 (4)
N2	0.3183 (3)	0.75345 (10)	0.0750 (4)	0.0301 (5)
C1	0.1510 (2)	0.86660 (10)	0.0802 (3)	0.0209 (5)
H1	0.2132	0.8830	0.1565	0.025*
C2	0.1254 (2)	0.89797 (10)	−0.0728 (3)	0.0190 (4)
H2	0.0604	0.8818	−0.1454	0.023*
C3	0.0766 (2)	0.94764 (10)	−0.0224 (3)	0.0190 (4)
H3	0.1458	0.9665	0.0342	0.023*
C4	−0.0393 (2)	0.94264 (9)	0.0915 (3)	0.0194 (4)
H4	−0.1160	0.9329	0.0247	0.023*
C5	−0.0159 (2)	0.90583 (10)	0.2306 (3)	0.0210 (5)
H5	0.0500	0.9188	0.3093	0.025*
C6	−0.1375 (3)	0.89502 (11)	0.3259 (4)	0.0278 (5)
H6A	−0.1229	0.8684	0.4064	0.033*
H6B	−0.1658	0.9240	0.3884	0.033*
C11	0.2568 (3)	0.79340 (11)	0.1332 (4)	0.0252 (5)
C12	0.2587 (4)	0.80145 (13)	0.3197 (4)	0.0349 (7)
H12A	0.3469	0.8073	0.3564	0.052*
H12B	0.2250	0.7727	0.3762	0.052*
H12C	0.2055	0.8295	0.3474	0.052*
C13	0.3209 (4)	0.74392 (12)	−0.1046 (4)	0.0333 (7)
H13A	0.2373	0.7532	−0.1535	0.040*
H13B	0.3328	0.7088	−0.1231	0.040*
C14	0.4268 (5)	0.7713 (2)	−0.1935 (6)	0.0485 (10)
H14A	0.4267	0.7626	−0.3121	0.073*
H14B	0.5096	0.7627	−0.1442	0.073*
H14C	0.4124	0.8061	−0.1817	0.073*
C15	0.3984 (3)	0.72173 (13)	0.1776 (5)	0.0350 (7)
H15A	0.4258	0.7395	0.2788	0.042*
H15B	0.4764	0.7130	0.1140	0.042*
C16	0.3297 (4)	0.67590 (14)	0.2297 (6)	0.0468 (10)
H16A	0.3855	0.6568	0.3027	0.070*
H16B	0.3081	0.6569	0.1304	0.070*
H16C	0.2511	0.6843	0.2898	0.070*
C21	0.2380 (3)	0.89647 (11)	−0.3314 (4)	0.0261 (5)
C22	0.3677 (4)	0.90339 (14)	−0.4068 (5)	0.0385 (8)
H22A	0.4240	0.8768	−0.3722	0.058*
H22B	0.4037	0.9342	−0.3687	0.058*
H22C	0.3604	0.9036	−0.5287	0.058*
C31	0.1130 (3)	1.00352 (11)	−0.2473 (4)	0.0255 (5)
C32	0.0555 (4)	1.0209 (2)	−0.4090 (5)	0.0391 (8)
H32A	−0.0381	1.0209	−0.3999	0.059*
H32B	0.0817	0.9994	−0.4999	0.059*
H32C	0.0854	1.0538	−0.4323	0.059*
C41	−0.1694 (3)	1.01353 (12)	0.1261 (4)	0.0275 (6)
C42	−0.1830 (4)	1.06008 (12)	0.2177 (4)	0.0326 (7)
H42A	−0.1471	1.0864	0.1503	0.049*
H42B	−0.1369	1.0581	0.3240	0.049*
H42C	−0.2739	1.0664	0.2391	0.049*
C61	−0.3446 (3)	0.86356 (15)	0.2624 (6)	0.0431 (9)
C62	−0.4338 (4)	0.8507 (2)	0.1236 (8)	0.0574 (13)
H62A	−0.3986	0.8624	0.0176	0.086*
H62B	−0.5173	0.8659	0.1434	0.086*
H62C	−0.4441	0.8155	0.1188	0.086*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O	0.0208 (8)	0.0197 (8)	0.0251 (9)	0.0007 (7)	0.0045 (7)	0.0000 (7)
O2	0.0173 (7)	0.0268 (9)	0.0231 (8)	0.0005 (7)	0.0043 (7)	−0.0044 (7)
O3	0.0184 (7)	0.0240 (9)	0.0225 (8)	0.0006 (7)	0.0013 (7)	0.0028 (7)
O4	0.0214 (8)	0.0190 (8)	0.0234 (8)	0.0046 (7)	−0.0022 (7)	−0.0025 (7)
O6	0.0240 (9)	0.0349 (12)	0.0408 (13)	−0.0082 (9)	0.0060 (9)	0.0026 (10)
O22	0.0332 (12)	0.069 (2)	0.0241 (11)	−0.0016 (13)	0.0021 (10)	−0.0090 (12)
O32	0.0303 (11)	0.0449 (14)	0.0396 (13)	−0.0158 (10)	−0.0015 (10)	0.0102 (12)
O42	0.0375 (13)	0.057 (2)	0.070 (2)	0.0243 (12)	−0.0260 (15)	−0.027 (2)
O62	0.066 (2)	0.121 (4)	0.064 (2)	−0.050 (2)	0.042 (2)	−0.029 (2)
N1	0.0228 (10)	0.0201 (10)	0.0283 (11)	0.0033 (8)	−0.0005 (9)	−0.0038 (9)
N2	0.0352 (13)	0.0227 (11)	0.0323 (13)	0.0093 (10)	−0.0018 (11)	−0.0023 (10)
C1	0.0169 (10)	0.0241 (12)	0.0216 (11)	0.0008 (8)	0.0022 (9)	−0.0022 (9)
C2	0.0148 (9)	0.0212 (11)	0.0209 (10)	−0.0010 (8)	0.0028 (8)	−0.0027 (9)
C3	0.0156 (9)	0.0211 (11)	0.0205 (10)	−0.0008 (8)	0.0014 (8)	0.0018 (9)
C4	0.0171 (9)	0.0211 (11)	0.0201 (10)	−0.0009 (8)	0.0009 (9)	−0.0024 (9)
C5	0.0198 (10)	0.0220 (11)	0.0214 (11)	0.0005 (9)	0.0022 (9)	−0.0012 (9)
C6	0.0270 (12)	0.0292 (13)	0.0273 (12)	0.0010 (11)	0.0084 (11)	−0.0009 (11)
C11	0.0247 (11)	0.0247 (12)	0.0262 (12)	0.0013 (10)	−0.0003 (10)	−0.0041 (10)
C12	0.047 (2)	0.0318 (15)	0.0254 (13)	0.0095 (14)	0.0000 (14)	−0.0005 (12)
C13	0.041 (2)	0.0274 (14)	0.0316 (15)	0.0099 (13)	−0.0019 (14)	−0.0106 (12)
C14	0.054 (2)	0.049 (2)	0.042 (2)	0.013 (2)	0.009 (2)	0.002 (2)
C15	0.035 (2)	0.0283 (14)	0.041 (2)	0.0108 (12)	−0.0005 (15)	−0.0003 (14)
C16	0.052 (2)	0.032 (2)	0.057 (2)	0.008 (2)	0.010 (2)	0.015 (2)
C21	0.0287 (12)	0.0247 (12)	0.0249 (11)	0.0009 (10)	0.0062 (11)	−0.0052 (10)
C22	0.034 (2)	0.042 (2)	0.040 (2)	0.0007 (14)	0.0194 (15)	0.001 (2)
C31	0.0259 (12)	0.0246 (12)	0.0261 (12)	0.0004 (10)	0.0050 (11)	0.0020 (10)
C32	0.037 (2)	0.049 (2)	0.032 (2)	0.000 (2)	0.0016 (14)	0.013 (2)
C41	0.0244 (11)	0.0302 (14)	0.0279 (13)	0.0089 (11)	0.0004 (11)	−0.0010 (11)
C42	0.039 (2)	0.0263 (14)	0.0321 (14)	0.0122 (12)	0.0047 (13)	0.0011 (12)
C61	0.0284 (14)	0.039 (2)	0.062 (2)	−0.0085 (13)	0.021 (2)	−0.013 (2)
C62	0.0252 (15)	0.060 (3)	0.087 (4)	−0.013 (2)	−0.001 (2)	0.005 (3)

Geometric parameters (Å, º)

O—C5	1.436 (3)	C12—H12A	0.98
O—C1	1.445 (3)	C12—H12B	0.98
O2—C21	1.355 (4)	C12—H12C	0.98
O2—C2	1.433 (3)	C13—C14	1.517 (6)
O3—C31	1.342 (3)	C13—H13A	0.99
O3—C3	1.450 (3)	C13—H13B	0.99
O4—C41	1.360 (3)	C14—H14A	0.98
O4—C4	1.443 (3)	C14—H14B	0.98
O6—C61	1.333 (4)	C14—H14C	0.98
O6—C6	1.453 (4)	C15—C16	1.515 (6)
O22—C21	1.199 (4)	C15—H15A	0.99
O32—C31	1.199 (4)	C15—H15B	0.99
O42—C41	1.192 (4)	C16—H16A	0.98
O62—C61	1.205 (6)	C16—H16B	0.98
N1—C11	1.292 (4)	C16—H16C	0.98
N1—C1	1.425 (4)	C21—C22	1.494 (5)
N2—C11	1.360 (4)	C22—H22A	0.98
N2—C13	1.463 (4)	C22—H22B	0.98
N2—C15	1.465 (4)	C22—H22C	0.98
C1—C2	1.525 (4)	C31—C32	1.506 (5)
C1—H1	1.00	C32—H32A	0.98
C2—C3	1.519 (4)	C32—H32B	0.98
C2—H2	1.00	C32—H32C	0.98
C3—C4	1.522 (4)	C41—C42	1.488 (5)
C3—H3	1.00	C42—H42A	0.98
C4—C5	1.529 (4)	C42—H42B	0.98
C4—H4	1.00	C42—H42C	0.98
C5—C6	1.512 (4)	C61—C62	1.493 (7)
C5—H5	1.00	C62—H62A	0.98
C6—H6A	0.99	C62—H62B	0.98
C6—H6B	0.99	C62—H62C	0.98
C11—C12	1.511 (5)
C5—O—C1	111.4 (2)	N2—C13—H13B	109
C21—O2—C2	117.4 (2)	C14—C13—H13B	109
C31—O3—C3	118.8 (2)	H13A—C13—H13B	108
C41—O4—C4	117.8 (2)	C13—C14—H14A	110
C61—O6—C6	117.7 (3)	C13—C14—H14B	110
C11—N1—C1	119.2 (3)	H14A—C14—H14B	110
C11—N2—C13	119.5 (3)	C13—C14—H14C	110
C11—N2—C15	124.3 (3)	H14A—C14—H14C	110
C13—N2—C15	115.7 (3)	H14B—C14—H14C	110
N1—C1—O	111.3 (2)	N2—C15—C16	112.6 (3)
N1—C1—C2	108.7 (2)	N2—C15—H15A	109
O—C1—C2	105.7 (2)	C16—C15—H15A	109
N1—C1—H1	110	N2—C15—H15B	109
O—C1—H1	110	C16—C15—H15B	109
C2—C1—H1	110	H15A—C15—H15B	108
O2—C2—C3	108.7 (2)	C15—C16—H16A	110
O2—C2—C1	109.0 (2)	C15—C16—H16B	110
C3—C2—C1	111.1 (2)	H16A—C16—H16B	110
O2—C2—H2	109	C15—C16—H16C	110
C3—C2—H2	109	H16A—C16—H16C	110
C1—C2—H2	109	H16B—C16—H16C	110
O3—C3—C2	108.8 (2)	O22—C21—O2	123.7 (3)
O3—C3—C4	106.5 (2)	O22—C21—C22	125.8 (3)
C2—C3—C4	110.1 (2)	O2—C21—C22	110.5 (3)
O3—C3—H3	111	C21—C22—H22A	110
C2—C3—H3	111	C21—C22—H22B	110
C4—C3—H3	111	H22A—C22—H22B	110
O4—C4—C3	108.4 (2)	C21—C22—H22C	110
O4—C4—C5	107.1 (2)	H22A—C22—H22C	110
C3—C4—C5	111.8 (2)	H22B—C22—H22C	110
O4—C4—H4	110	O32—C31—O3	124.9 (3)
C3—C4—H4	110	O32—C31—C32	124.8 (3)
C5—C4—H4	110	O3—C31—C32	110.3 (3)
O—C5—C6	107.1 (2)	C31—C32—H32A	110
O—C5—C4	110.4 (2)	C31—C32—H32B	110
C6—C5—C4	111.4 (2)	H32A—C32—H32B	110
O—C5—H5	109	C31—C32—H32C	110
C6—C5—H5	109	H32A—C32—H32C	110
C4—C5—H5	109	H32B—C32—H32C	110
O6—C6—C5	107.4 (2)	O42—C41—O4	123.0 (3)
O6—C6—H6A	110	O42—C41—C42	124.4 (3)
C5—C6—H6A	110	O4—C41—C42	112.7 (3)
O6—C6—H6B	110	C41—C42—H42A	110
C5—C6—H6B	110	C41—C42—H42B	110
H6A—C6—H6B	109	H42A—C42—H42B	110
N1—C11—N2	118.1 (3)	C41—C42—H42C	110
N1—C11—C12	125.0 (3)	H42A—C42—H42C	110
N2—C11—C12	116.9 (3)	H42B—C42—H42C	110
C11—C12—H12A	110	O62—C61—O6	123.3 (4)
C11—C12—H12B	110	O62—C61—C62	125.1 (4)
H12A—C12—H12B	110	O6—C61—C62	111.5 (4)
C11—C12—H12C	110	C61—C62—H62A	110
H12A—C12—H12C	110	C61—C62—H62B	110
H12B—C12—H12C	110	H62A—C62—H62B	110
N2—C13—C14	112.7 (3)	C61—C62—H62C	110
N2—C13—H13A	109	H62A—C62—H62C	110
C14—C13—H13A	109	H62B—C62—H62C	110

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3···O32^i	1.00	2.653	3.552 (4)	150
C5—H5···O22^ii	1.00	2.638	3.393 (4)	132
C12—H12C···O22^ii	0.98	2.606	3.434 (5)	142
C6—H6B···O42^iii	0.99	2.562	3.547 (5)	173
C22—H22C···O32^iv	0.98	2.726	3.338 (5)	121
C32—H32B···O32^iv	0.98	2.663	3.458 (5)	138
C22—H22A···O62^v	0.98	2.860	3.395 (6)	115
C32—H32A···O42^vi	0.98	2.438	3.359 (5)	156
C42—H42A···O62^vi	0.98	2.483	3.403 (6)	156

Symmetry codes: (i) −x+1/2, −y+2, z+1/2; (ii) x, y, z+1; (iii) −x−1/2, −y+2, z+1/2; (iv) −x+1/2, −y+2, z−1/2; (v) x+1, y, z−1; (vi) −x−1/2, −y+2, z−1/2.