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Journal logoSTRUCTURAL
CHEMISTRY
ISSN: 2053-2296

Methyl 2-acetamido-2-de­­oxy-β-D-gluco­pyran­oside dihydrate and methyl 2-formamido-2-de­­oxy-β-D-gluco­pyran­oside

aUniversity of Notre Dame, Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, Notre Dame, IN 46556-5670, USA
*Correspondence e-mail: aseriann@nd.edu

(Received 11 January 2011; accepted 9 March 2011; online 22 March 2011)

Methyl 2-acetamido-2-de­oxy-β-D-glucopyran­oside (β-GlcNAcOCH3), (I)[link], crystallizes from water as a dihydrate, C9H17NO6·H2O, containing two independent mol­ecules [denoted (IA) and (IB)] in the asymmetric unit, whereas the crystal structure of methyl 2-formamido-2-de­oxy-β-D-glucopyran­oside (β-GlcNFmOCH3), (II)[link], C8H15NO6, also obtained from water, is devoid of solvent water mol­ecules. The two mol­ecules of (I)[link] assume distorted 4C1 chair conformations. Values of φ for (IA) and (IB) indicate ring distortions towards BC2,C5 and C3,O5B, respectively. By comparison, (II)[link] shows considerably more ring distortion than mol­ecules (IA) and (IB), despite the less bulky N-acyl side chain. Distortion towards BC2,C5 was observed for (II)[link], similar to the findings for (IA). The amide bond conformation in each of (IA), (IB) and (II)[link] is trans, and the conformation about the C—N bond is anti (C—H is approximately anti to N—H), although the conformation about the latter bond within this group varies by ∼16°. The conformation of the exocyclic hy­droxy­methyl group was found to be gt in each of (IA), (IB) and (II)[link]. Comparison of the X-ray structures of (I)[link] and (II)[link] with those of other GlcNAc mono- and disaccharides shows that GlcNAc aldohexopyranosyl rings can be distorted over a wide range of geometries in the solid state.

Comment

Acyl­ation is an important covalent modification that affects the biological functions of saccharides and other biomolecules. Two types of saccharide acyl­ation are common in biological systems, N- and O-acyl­ation, and recent work has shown that different O-acylation patterns affect biological function. For example, this type of covalent control has been described recently for glycopeptidolipids involved in signaling through Toll-like receptors (Sweet et al., 2008[Sweet, L., Zhang, W., Torres-Fewell, H., Serianni, A. S., Boggess, W. & Schorey, J. (2008). J. Biol. Chem. 283, 33221-33231.]). N-Acyl­ation is found in biologically relevant monosaccharides, such as N-acetyl-D-glucosamine, N-acetyl-D-galactosamine and N-acetyl­neur­aminic acid. It has been shown recently that cistrans isomerization (CTI) of the amide bond in N-acyl­ated sugars can be detected in aqueous solution, with the cis/trans ratio dependent on, among other factors, the anomeric configuration of the saccharide (Hu, Zhang et al., 2010[Hu, X., Zhang, W., Carmichael, I. & Serianni, A. S. (2010). J. Am. Chem. Soc. 132, 4641-4652.]). For example, Ktrans/cis is ∼60 for methyl N-acetyl-α-D-glucosaminide and ∼38 for methyl N-acetyl-β-D-glucosaminide at 326 K. In support of NMR studies of saccharide CTI and of the param­eterization of NMR J couplings within saccharide exocyclic N-acyl fragments (Hu, Carmichael & Serianni, 2010[Hu, X., Carmichael, I. & Serianni, A. S. (2010). J. Org. Chem. 75, 4899-4910.]), we undertook the crystallization of methyl 2-acetamido-2-de­oxy-β-D-glucopyran­oside dihydrate, (I)[link], and methyl 2-formamido-2-de­oxy-β-D-glucopyran­oside, (II)[link]. Their crystal structures, reported here, are compared with the structurally related compounds N-acetyl-α-D-glucosamine (2-acetamido-2-de­oxy-α-D-glucopyran­ose), (III)[link] (α-GlcNAcOH; Mo & Jensen, 1975[Mo, F. & Jensen, L. H. (1975). Acta Cryst. B31, 2867-2873.]), β-chitobiose [2-acetamido-2-de­oxy-β-D-glucopy­ran­osyl-(1→4)-2-acetamido-2-de­oxy-β-D-glucopyran­ose], (IV)[link] (β-GlcNAcOH and β-GlcNAcOR; Mo, 1979[Mo, F. (1979). Acta Chem. Scand. Ser. A, 33, 207-218.]), α-chitobiose [2-acetamido-2-de­oxy-β-D-glucopyranosyl-(1→4)-2-acetamido-2-de­oxy-α-D-glucopyran­ose], (V)[link] (α-GlcNAcOH and β-GlcNAcOR; Mo & Jensen, 1978[Mo, F. & Jensen, L. H. (1978). Acta Cryst. B34, 1562-1569.]) and methyl β-D-glucopyran­oside, (VI)[link] (β-GlcOCH3; Jeffrey & Takagi, 1977[Jeffrey, G. A. & Takagi, S. (1977). Acta Cryst. B33, 738-742.]).

[Scheme 1]

Crystals of (I)[link] and (II)[link] were obtained from aqueous solutions by slow evaporation at room temperature. Compound (I)[link] crystallizes with two independent mol­ecules in the asymmetric unit [denoted (IA) and (IB)] and two solvent water mol­ecules (Fig. 1[link]a and 1b), whereas the unit cell of (II)[link] contains only one mol­ecule of the saccharide and no solvent water mol­ecules (Fig. 2[link]).

A comparison of selected structural parameters in compounds (I)[link]–(VI)[link] is shown in Table 1[link]. The average C1—C2 and C2—C3 bond lengths in (IA), (IB) and (II)[link] are 1.532 (1) and 1.534 (4) Å, respectively. These values are 0.01–0.02 Å greater than corresponding values in (VI)[link], which are 1.522 (4) and 1.515 (2) Å, respectively, presumably reflecting the different substitutions at C2. All other corresponding C—C bonds in (IA), (IB) and (VI)[link] have very similar lengths. Within the same three structures, the exocyclic C5—C6 bond appears to be the shortest C—C bond [1.516 (3) Å]. Similar inspections of the C1—O1 and C1—O5 bonds suggest a slight lengthening of the former and a slight shortening of the latter in N-acyl sugars (IA) and (IB) compared with the related bonds in the simple glycoside (VI)[link].

In all structures in Table 1[link] bearing an N-acyl group, the average C2—N1 bond length is 1.453 (5) Å. This bond is ∼0.03 Å longer than the average exocyclic (non-anomeric) C—OH bond length in a pyranosyl ring, which is 1.427 (4) Å in the same data set.

Within the N-acyl exocyclic fragment, the C8—O8 bond averages 1.236 (5) Å, with no discernible difference between N-acetyl and N-formyl groups. The C8—C9 bond averages 1.502 (8) Å, which is 0.02–0.03 Å shorter than the endocyclic C—C bonds found in the pyranosyl rings.

The N-acyl side chains in (IA), (IB) and (II)[link] contain the amide bond N1—C8 in a trans conformation, i.e. with C2—N1—C8—C9 torsion angles of ±179.1 (2)° in both (IA) and (IB), and an average C2—N1—C8—O8 torsion angle of 0.77 (2)° in (IA), (IB) and (II)[link]. These torsion angles also demonstrate that the amide group is planar. In all three structures, the conformation about the C2—N1 bond is anti, i.e. atom N1H is roughly anti to H2, which is consistent with the behavior reported in solution (Zhu et al., 2006[Zhu, Y., Pan, Q., Thibaudeau, C., Zhao, S., Carmichael, I. & Serianni, A. S. (2006). J. Org. Chem. 71, 466-479.]). However, inspection of the C1—C2—N1—C8 and C3—C2—N1—C8 torsion angles in (IA), (IB) and (II)[link] reveals a range of 91–108° in the former and −128 to −144° in the latter, indicating some flexibility about the C2—N1 bond in the solid state.

The C5—O5—C1 bond angles in (I)[link]–(VI)[link] appear to depend on anomeric configuration, with β-anomers yielding an average value of 112.0 (6)° and α-anomers an average of 114.7 (3)°. Within the full data set, the largest C—C—C bond angle within any given structure (β-anomers only) is C4—C5—C6, which averages 113.8 (11)°. The two bond angles that incorporate the carbonyl O atom, O8—C8—C9 and O8—C8—N1, are very similar in each structure and average 122.5 (14)° in the full data set. These results contrast with the remaining angle, N1—C8—C9, which is uniformly smaller than the others in any given structure and averages 116.0 (4)° in the full data set.

Within (IA), (IB) and (II)[link], the endocyclic ring torsion angles vary from 41 to 72° (absolute values), indicating that aldopyranosyl rings containing N-acyl substiutents at C2 are distorted. It is noteworthy that the extreme angles within this group are observed in (II)[link], where the C1—C2—C3—C4 and C1—O5—C5—C4 torsion angles are −41.09 (15) and 71.61 (13)°, respectively. Within (III)[link]–(VI)[link], these torsion angles range from 48 to 68° (absolute values). A more quantitative treatment of these torsion angles is provided by the Cremer–Pople parameters calculated for (I)[link]–(VI)[link] (Table 2[link]; Cremer & Pople, 1975[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358.]). The most distorted ring within (I)[link]–(VI)[link] is that of (II)[link], which yields a θ value of 16.59 (14)°. The least distorted ring is found in (Va), where θ = 0.9 (3)°, and the ring is almost an ideal 4C1 chair. The direction of distortion varies widely within this series of compounds. For (IA) and (II)[link], φ = 302.0 (12) and 314.4 (5)°, respectively, suggesting distortion towards BC2,C5. In contrast, φ for (IB) is 0 (2)°, or a C3,O5B distortion. These data show that not only can aldopyranosyl rings be substantially distorted when bearing an N-acyl functionality at C2, but the direction of distortion can also vary widely, with various boat (BC2,C5, C3,O5B and BC1,C4) and twist-boat (C1TBC5, C3TBC1, O5TBC2 and C5TBC1) conformations represented.

The exocyclic hy­droxy­methyl conformation in each of (IA), (IB) and (II)[link] is gt (C4 anti to O6), but the gg conformation (H5 anti to O6) is observed in each of (III)[link], (IVa), (Va) and (Vb). These data show that gg and gt conformations are favored in GlcNAc/NFm aldopyranosyl rings in the solid state, a behavior which is expected to mimic that in solution, based on related studies of the simpler Glcp anomers (Thibaudeau et al., 2004[Thibaudeau, C., Stenutz, R., Hertz, B., Klepach, T., Zhao, S., Wu, Q., Carmichael, I. & Serianni, A. S. (2004). J. Am. Chem. Soc. 126, 15668-15685.]).

The structure of (I)[link] forms hydrogen-bonded pairs of (IA) and (IB) molecules of through hy­droxy atom O6A to atom O6B. In turn, atom O6B forms a hydrogen bond to atom O6Aiii of the next pair related by translation along the a axis. In addition, the amide groups form hydrogen bonds, although this is to the same GlcNAc mol­ecule related by translation along the a axis (all symmetry codes as in Table 3[link]). Amide atom N1A of (IA) has a bifurcated hydrogen bond shared between the adjacent amide carbonyl atom O8Ai and meth­oxy atom O1Ai. Amide atom N1B of (IB) has a single hydrogen bond to amide atom O8Bi. This association results in chains of pairs of (IA) and (IB) that run through the lattice parallel to the a axis. These chains are hydrogen bonded to other chains via hy­droxy–hy­droxy (O4B⋯O4Aii) or hy­droxy–water inter­actions. The water mol­ecules are located in a hydro­philic channel lined with amide O atoms (O8B) and hy­droxy groups, again parallel to the a axis. One motif that is apparent is a hydrogen-bonded ring formed by four sets of these hydrogen-bonded chains. These rings are oriented around a hydro­phobic channel formed by the methyl groups of the meth­oxy moieties and the acetamide methyl group (Fig. 3[link]; see Table 3[link] for specific details). Overall, this structure forms a highly hydrogen-bonded three-dimensional network of water and amido­saccharide mol­ecules.

The structure of (II)[link] also forms a three-dimensional network of hydrogen-bonded mol­ecules. The network is formed from sheets of (II)[link] that have hydrogen bonds through atom O4 to atom O8iii running parallel to the b axis (related by the 21 screw axis) and from atom O6 to atom O4iv along the c axis, and thus these sheets lie in the bc plane of the lattice. Propagation of these sheets into the third dimension is via hydrogen bonds from atom O3 to atom O6ii and from atom N1 to atom O8i of sheets in the next layer along the a axis (Fig. 4; all symmetry codes as in Table 4[link][link]).

[Figure 1]
Figure 1
Labeling schemes for (a) mol­ecule (IA) with water mol­ecules and (b) mol­ecule (IB). Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2]
Figure 2
The atom-labeling scheme for compound (II)[link]. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 3]
Figure 3
Hydrogen-bonding scheme for mol­ecules (IA) and (IB), viewed along the a axis. Dashed lines (blue in the electronic version of the paper) represent hydrogen bonds.
[Figure 4]
Figure 4
Hydrogen-bonding scheme for (II)[link], viewed along the a axis. Dashed lines (blue in the electronic version of the paper) represent hydrogen bonds.

Experimental

Compounds (I)[link] and (II)[link] were prepared as described recently in the literature (Hu, Zhang et al., 2010[Hu, X., Zhang, W., Carmichael, I. & Serianni, A. S. (2010). J. Am. Chem. Soc. 132, 4641-4652.]). Both compounds were crystallized from water at room temperature, giving long colorless needle-like crystals that were harvested for X-ray analysis.

Compound (I)[link]

Crystal data
  • C9H17NO6·H2O

  • Mr = 253.25

  • Orthorhombic, P 21 21 21

  • a = 4.6886 (1) Å

  • b = 14.4501 (3) Å

  • c = 34.7880 (7) Å

  • V = 2356.91 (8) Å3

  • Z = 8

  • Cu Kα radiation

  • μ = 1.06 mm−1

  • T = 100 K

  • 0.25 × 0.03 × 0.02 mm

Data collection
  • Bruker APEX diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) Tmin = 0.760, Tmax = 0.977

  • 21482 measured reflections

  • 4311 independent reflections

  • 3722 reflections with I > 2σ(I)

  • Rint = 0.054

Refinement
  • R[F2 > 2σ(F2)] = 0.043

  • wR(F2) = 0.111

  • S = 1.06

  • 4311 reflections

  • 323 parameters

  • 6 restraints

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.20 e Å−3

  • Δρmin = −0.26 e Å−3

  • Absolute structure: the configuration was determined based on the known handedness of the chiral C atoms within the structure

  • Flack parameter: −0.4 (2); 1726 Friedel pairs

Table 1
Comparison of geometric parameters in compounds (I)[link]–(VI)[link]

gg denotes a gauchegauche conformation and gt gauchetrans.

Parameter β-GlcNAcOCH3 β-GlcNAcOCH3 β-GlcNFmOCH3 α-GlcNAcOH β-GlcNAcOH β-GlcNAcOR α-GlcNAcOH β-GlcNAcOR β-GlcOCH3
  (IA) (IB) (II)[link] (III)[link] (IVa) (IVb) (Va) (Vb) (VI)[link]
Bond lengths (Å)
C1—C2 1.533 (3) 1.531 (3) 1.5318 (19) 1.534 (2) 1.522 (5) 1.522 (3) 1.526 (5) 1.515 (4) 1.522 (4)
C2—C3 1.530 (3) 1.534 (3) 1.5383 (19) 1.531 (3) 1.521 (4) 1.531 (4) 1.527 (5) 1.517 (5) 1.515 (2)
C3—C4 1.527 (3) 1.525 (3) 1.5302 (19) 1.521 (3) 1.531 (3) 1.516 (5) 1.520 (4) 1.516 (4) 1.529 (3)
C4—C5 1.526 (3) 1.523 (3) 1.5284 (18) 1.528 (3) 1.536 (4) 1.507 (5) 1.519 (5) 1.537 (4) 1.527 (4)
C5—C6 1.519 (3) 1.514 (3) 1.5137 (19) 1.514 (2) 1.501 (4) 1.499 (5) 1.512 (5) 1.517 (4) 1.516 (2)
C1—O1 1.389 (3) 1.387 (3) 1.3899 (17) 1.390 (3) 1.389 (4) 1.389 (4) 1.361 (5) 1.395 (4) 1.379 (2)
C1—O5 1.418 (3) 1.423 (3) 1.4198 (17) 1.434 (2) 1.427 (3) 1.429 (3) 1.418 (4) 1.414 (4) 1.433 (2)
C2—N1 1.456 (3) 1.455 (3) 1.4615 (18) 1.457 (2) 1.450 (3) 1.446 (3) 1.450 (4) 1.460 (4)  
C2—O2                 1.426 (2)
C3—O3 1.430 (3) 1.424 (3) 1.4282 (16) 1.430 (2) 1.430 (4) 1.424 (4) 1.421 (5) 1.431 (4) 1.425 (4)
C4—O4/O1 1.424 (3) 1.425 (3) 1.4252 (17) 1.434 (2) 1.448 (3) 1.425 (3) 1.448 (3) 1.422 (4) 1.426 (2)
C5—O5 1.443 (3) 1.435 (3) 1.4349 (17) 1.448 (2) 1.429 (3) 1.436 (4) 1.438 (4) 1.427 (5) 1.440 (2)
C6—O6 1.430 (3) 1.430 (3) 1.4341 (17) 1.416 (3) 1.413 (4) 1.415 (5) 1.419 (5) 1.423 (5) 1.417 (4)
C7—O1 1.445 (3) 1.439 (3) 1.4391 (16)           1.430 (4)
C8—O8 1.237 (3) 1.235 (4) 1.2334 (18) 1.235 (2) 1.243 (4) 1.246 (4) 1.231 (4) 1.231 (4)  
C8—C9 1.508 (3) 1.510 (3)   1.508 (3) 1.497 (5) 1.496 (6) 1.490 (6) 1.506 (7)  
                   
Bond angles (°)
C1—C2—C3 111.22 (19) 109.71 (19) 112.42 (11) 110.11 (13) 111.5 (4) 110.9 (4) 110.0 (2) 109.3 (3) 108.4 (2)
C2—C3—C4 111.5 (2) 111.9 (2) 112.95 (11) 110.88 (15) 109.6 (4) 112.1 (4) 109.7 (3) 109.1 (2) 110.82 (13)
C3—C4—C5 107.7 (2) 110.12 (19) 108.46 (10) 108.77 (15) 111.2 (4) 110.0 (4) 110.7 (3) 110.3 (3) 111.15 (15)
C4—C5—O5 106.79 (19) 108.70 (19) 106.84 (10) 108.41 (13) 110.1 (4) 108.2 (4) 109.3 (2) 110.4 (3) 108.5 (3)
C5—O5—C1 111.9 (2) 111.8 (2) 111.09 (10) 114.97 (14) 112.6 (4) 112.1 (4) 114.5 (3) 112.9 (2) 111.55 (11)
O5—C1—C2 110.80 (19) 108.8 (2) 111.39 (11) 109.24 (15) 109.3 (4) 109.1 (4) 109.6 (3) 110.0 (2) 108.38 (18)
C4—C5—C6 113.9 (2) 112.3 (2) 114.51 (11) 114.77 (16) 113.3 (4) 115.5 (4) 114.3 (3) 113.1 (3) 112.33 (16)
C2—N1—C8 122.6 (2) 121.8 (2) 123.60 (12) 122.17 (18) 122.9 (4) 124.9 (4) 124.8 (3) 122.0 (3)  
N1—C8—C9 116.1 (2) 116.4 (2)   116.01 (18) 116.3 (4) 115.9 (5) 115.3 (3) 115.8 (4)  
O8—C8—C9 121.3 (2) 120.7 (2)   120.93 (16) 122.2 (4) 122.7 (5) 120.7 (3) 120.2 (4)  
O8—C8—N1 122.6 (2) 122.9 (2) 125.18 (13) 123.06 (16) 121.5 (4) 121.3 (4) 123.9 (3) 123.9 (3)  
                   
Torsion angles (°)
C1—C2—C3—C4 −47.9 (3) −50.1 (3) −41.09 (15) −54.6 (2) −52.1 (4) −48.2 (4) −54.4 (4) −56.7 (3) −54.3 (3)
C1—O5—C5—C4 69.3 (2) 66.5 (2) 71.61 (13) 62.5 (2) 61.8 (4) 67.4 (4) 60.4 (3) 59.1 (4) 63.4 (3)
C2—C3—C4—C5 55.1 (3) 50.3 (3) 49.70 (15) 56.8 (2) 50.4 (4) 50.9 (4) 54.5 (3) 54.2 (4) 51.7 (3)
C2—C1—O5—C5 −61.8 (3) −66.6 (3) −62.48 (14) −59.9 (2) −62.9 (4) −64.4 (4) −60.9 (3) −62.1 (3) −67.9 (3)
C2—C1—O1—C7/C4 175.5 (2) 169.5 (2) 170.83 (11)     151.7 (4)   161.5 (2) 169.19 (15)
C3—C4—C5—O5 −63.9 (3) −56.6 (3) −63.27 (13) −58.4 (2) −54.8 (4) −58.6 (4) −55.7 (3) −54.7 (4) −54.2 (2)
C3—C2—C1—O5 49.6 (3) 56.6 (3) 45.79 (15) 53.8 (4) 57.6 (4) 53.1 (4) 56.5 (4) 60.0 (3) 61.5 (2)
C3—C4—C5—C6 178.8 (2) −173.9 (2) 178.36 (13) −177.51 (17) −174.4 (4) −178.1 (4) −174.5 (3) −175.6 (3) −171.9 (2)
O5—C5—C6—O6 64.3 (3) 65.2 (3) 66.48 (14) −60.71 (18) −60.6 (4) 58.6 (4) −74.6 (4) −65.5 (3) 68.7 (3)
  gt gt gt gg gg gt gg gg gt
C1—C2—N1—C8 108.2 (3) 100.0 (3) 91.34 (14) 140.89 (17) 100.5 (4) 113.7 (4) 138.7 (3) 100.5 (4)  
C3—C2—N1—C8 −128.1 (2) −137.2 (2) −144.29 (13) −96.8 (2) −135.2 (4) −122.5 (4) −98.9 (4) −137.0 (3)  
C2—N1—C8—C9 179.1 (2) −179.1 (2)   169.86 (15) −173.7 (4) 178.4 (5) −179.6 (4) −173.9 (4)  
  trans trans   trans trans trans trans trans  
C2—N1—C8—O8 −1.2 (4) 0.8 (4) 2.7 (2) −9.7 (2) 5.2 (7) −5.3 (6) −2.1 (6) 2.9 (5)  

Table 2
Cremer–Pople puckering parameters in compounds (I)[link]–(VI)[link]

Compound θ (°) φ (°) Q (Å) q2 (Å) q3 (Å) Conformer
(IA) 11.4 (3) 302.0 (12) 0.595 (3) 0.118 (3) 0.583 (3) BC2,C5
(IB) 7.1 (2) 0 (2) 0.585 (3) 0.078 (2) 0.580 (3) C3,O5B
(II)[link] 16.59 (14) 314.4 (5) 0.5791 (14) 0.1654 (14) 0.5550 (14) BC2,C5
(III)[link] 3.8 (2) 274 (3) 0.582 (2) 0.031 (2) 0.581 (2) C1TBC5
(IVa) 4.8 (3) 19 (4) 0.568 (3) 0.044 (3) 0.566 (3) C3TBC1
(IVb) 8.7 (3) 338 (2) 0.577 (3) 0.089 (9) 0.570 (3) O5TBC2
(Va) 0.9 (3) 55 (3) 0.572 (3) 0.006 (3) 0.572 (3) BC1,C4
(Vb) 2.3 (3) 97 (6) 0.580 (3) 0.029 (3) 0.580 (3) C5TBC1
(VI)[link] 6.94 (19) 38 (2) 0.597 (2) 0.072 (2) 0.593 (2) C3TBC1
B denotes a boat conformation and TB a skew or twist-boat.

Table 3
Hydrogen-bond geometry (Å, °) for (I)[link]

D—H⋯A D—H H⋯A DA D—H⋯A
O3A—H3OA⋯O1Wi 0.84 1.85 2.672 (3) 166
O4A—H4OA⋯O2W 0.84 2.01 2.806 (3) 158
O6A—H6OA⋯O6B 0.84 2.01 2.837 (3) 170
N1A—H1NA⋯O8Ai 0.88 2.50 3.132 (3) 129
O3B—H3OB⋯O2Wii 0.84 1.85 2.658 (3) 160
O4B—H4OB⋯O4Aii 0.84 2.07 2.898 (2) 167
O6B—H6OB⋯O6Aiii 0.84 1.98 2.815 (3) 173
N1B—H1NB⋯O8Bi 0.88 2.02 2.838 (3) 154
O1W—H1WA⋯O3A 0.84 (1) 2.02 (1) 2.843 (3) 167 (3)
O1W—H1WB⋯O3Aiv 0.84 (1) 2.03 (1) 2.847 (2) 165 (3)
O2W—H2WA⋯O8Av 0.84 (1) 2.01 (1) 2.837 (2) 171 (3)
O2W—H2WB⋯O3Bvi 0.83 (1) 1.90 (1) 2.728 (3) 174 (3)
Symmetry codes: (i) x-1, y, z; (ii) [-x, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]; (iii) x+1, y, z; (iv) [x+{\script{1\over 2}}], [-y+{\script{3\over 2}}, -z]; (v) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z]; (vi) [-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}].

Compound (II)[link]

Crystal data
  • C8H15NO6

  • Mr = 221.21

  • Monoclinic, P 21

  • a = 4.5374 (5) Å

  • b = 15.8837 (16) Å

  • c = 6.8993 (7) Å

  • β = 100.185 (4)°

  • V = 489.40 (9) Å3

  • Z = 2

  • Cu Kα radiation

  • μ = 1.11 mm−1

  • T = 100 K

  • 0.34 × 0.07 × 0.06 mm

Data collection
  • Bruker APEX diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) Tmin = 0.703, Tmax = 0.940

  • 6422 measured reflections

  • 1744 independent reflections

  • 1744 reflections with I > 2σ(I)

  • Rint = 0.021

Refinement
  • R[F2 > 2σ(F2)] = 0.027

  • wR(F2) = 0.070

  • S = 1.06

  • 1744 reflections

  • 137 parameters

  • 1 restraint

  • H-atom parameters constrained

  • Δρmax = 0.16 e Å−3

  • Δρmin = −0.21 e Å−3

  • Absolute structure: the configuration was determined based on the known handedness of the chiral C atoms within the structure.

  • Flack parameter: 0.13 (14); 806 Friedel pairs

Table 4
Hydrogen-bond geometry (Å, °) for (II)[link]

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯O8i 0.88 2.29 3.0213 (16) 141
N1—H1⋯O1i 0.88 2.48 3.1621 (15) 134
O3—H3⋯O6ii 0.84 1.89 2.7271 (14) 173
O4—H4⋯O8iii 0.84 1.90 2.7438 (14) 177
O6—H6⋯O3iv 0.84 1.94 2.7749 (14) 171
Symmetry codes: (i) x-1, y, z; (ii) x-1, y, z-1; (iii) [-x, y-{\script{1\over 2}}, -z]; (iv) x, y, z+1.

The absolute configurations of (I)[link] and (II)[link] were determined both from the known configuration of the starting materials and by comparison of the intensities of Friedel pairs of reflections. However, the Flack parameters were inconclusive [x = −0.4 (2) for (I)[link] and 0.13 (14) for (II)[link]; Flack, 1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]]. Further confirmation of the configurations was sought by the Hooft analysis, yielding a Hooft y parameter of −0.13 (12) and P2(true) and P3(true) values of 1.000 and 1.000 for (I)[link], and a Hooft y parameter of 0.16 (4) and P2(true) and P3(true) values of 1.000 and 1.000 for (II)[link] (Hooft et al., 2008[Hooft, R. W. W., Straver, L. H. & Spek, A. L. (2008). J. Appl. Cryst. 41, 96-103.]).

For both structures, the hydroxy, amide and, where applicable, water H atoms were all located from a difference Fourier map and initially included in those positions. The hydroxy and amide H atoms were subsequently constrained to have reasonable geometric X—H bond distances and angles (N—H = 0.88 Å and O—H = 0.84 Å). Where applicable, mild restraints were applied to the water O—H bond distances [0.84 (1) Å]. All C—H bonds were constrained to distances of 0.98–1.00 Å. For all H atoms, Uiso(H) = 1.5Ueq(C) for methyl H atoms or 1.2Ueq(C) for all others.

Data collection: APEX2 (Bruker–Nonius, 2009[Bruker-Nonius (2009). APEX2 (Version 2009-9) and SAINT (Version 7.60A). Bruker-Nonius AXS Inc., Madison, Wisconsin, USA.]) for (I)[link]; APEX2 (Bruker–Nonius, 2008[Bruker-Nonius (2008). APEX2 (Version 2008-6) and SAINT (Version 7.53A). Bruker-Nonius AXS Inc., Madison, Wisconsin, USA.]) for (II)[link]. Cell refinement: SAINT (Bruker–Nonius, 2009[Bruker-Nonius (2009). APEX2 (Version 2009-9) and SAINT (Version 7.60A). Bruker-Nonius AXS Inc., Madison, Wisconsin, USA.]) for (I)[link]; SAINT (Bruker–Nonius, 2008[Bruker-Nonius (2008). APEX2 (Version 2008-6) and SAINT (Version 7.53A). Bruker-Nonius AXS Inc., Madison, Wisconsin, USA.]) for (II)[link]. Data reduction: SAINT (Bruker–Nonius, 2009[Bruker-Nonius (2009). APEX2 (Version 2009-9) and SAINT (Version 7.60A). Bruker-Nonius AXS Inc., Madison, Wisconsin, USA.]) for (I)[link]; SAINT (Bruker–Nonius, 2008[Bruker-Nonius (2008). APEX2 (Version 2008-6) and SAINT (Version 7.53A). Bruker-Nonius AXS Inc., Madison, Wisconsin, USA.]) for (II)[link]. For both compounds, 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: XP (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) and POV-Ray (Cason, 2003[Cason, C. J. (2003). POV-Ray. Version 3.6.2. Persistence of Vision Raytracer Pty. Ltd, Victoria, Australia.]); software used to prepare material for publication: XCIF (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Comment top

Acylation is an important covalent modification that affects the biological functions of saccharides and other biomolecules. Two types of saccharide acylation are common in biological systems, N- and O-acylation, and recent work has shown that different O-acetylation patterns affect biological function. For example, this type of covalent control has been described recently for glycopeptidolipids involved in signaling through Toll-like receptors (Sweet et al., 2008). N-Acetylation is found in biologically relevant monosaccharides, such as N-acetyl-D-glucosamine, N-acetyl D-galactosamine and N-acetylneuraminic acid. It has been shown recently that cistrans isomerization (CTI) of the amide bond in N-acetylated sugars can be detected in aqueous solution, with the cis/trans ratio dependent on, among other factors, the anomeric configuration of the saccharide (Hu, Zhang et al., 2010). For example, Ktrans/cis is ~60 for methyl N-acetyl-α-D-glucosaminide and ~38 for methyl N-acetyl-β-D-glucosaminide at 326 K. In support of NMR studies of saccharide CTI and of the parameterization of NMR J couplings within saccharide exocyclic N-acyl fragments (Hu, Carmichael & Serianni, 2010), we undertook the crystallization of methyl 2-acetamido-2-deoxy-β-D-glucopyranoside dihydrate, (I), and methyl 2-formamido-2-deoxy-β-D-glucopyranoside, (II). Their crystal structures, reported here, are compared with the structurally related compounds N-acetyl-α-D-glucosamine (2-acetamido-2-deoxy-α-D-glucopyranose), (III) (α-GlcNAcOH; Mo & Jensen, 1975), β-chitobiose [2-acetamido-2-deoxy-β-D-glucopyranosyl-(1 4)–2-acetamido-2-deoxy-β-D-glucopyranose], (IV) (β-GlcNAcOH and β-GlcNAcOR; Mo, 1979), α-chitobiose [2-acetamido-2-deoxy-β-D-glucopyranosyl-(1 4)–2-acetamido-2-deoxy-α-D-glucopyranose], (V) (α-GlcNAcOH and β-GlcNACOR; Mo & Jensen, 1978) and methyl β-D-glucopyranoside, (VI) (β-GlcOCH3; Jeffrey & Takagi, 1977).

Crystals of (I) and (II) were obtained from aqueous solutions by slow evaporation at room temperature. Compound (I) crystallizes with two independent molecules in the asymmetric unit [denoted (IA) and (IB)] and two solvent water molecules (Figs. 1a and 1b), whereas the unit cell of (II) contains only one molecule of the saccharide and no solvent water molecules (Fig. 2).

A comparison of selected structural parameters in compounds (I)–(VI) is shown in Table 1. The average C1—C2 and C2—C3 bond lengths in (IA), (IB) and (II) are 1.532 (1) and 1.534 (4) Å, respectively. These values are 0.01–0.02 Å greater than corresponding values in (VI), which are 1.522 and 1.515 Å, respectively, presumably reflecting the different substitutions at C2. All other corresponding C—C bonds in (IA), (IB) and (VI) have very similar lengths. Within the same three structures, the exocyclic C5—C6 bond appears to be the shortest C—C bond [1.516 (3) Å]. Similar inspections of the C1—O1 and C1—O5 bonds suggest a slight lengthening of the former and a slight shortening of the latter in N-acyl sugars (IA) and (IB) compared with the related bonds in the simple glycoside (VI).

In all structures in Table 1 bearing an N-acyl group, the average C2—N1 bond length is 1.453 (5) Å. This bond is ~0.03 Å longer than the average exocyclic (non-anomeric) C—OH bond length in a pyranosyl ring, which is 1.427 (4) Å in the same data set.

Within the N-acyl exocyclic fragment, the C8—O8 bond averages 1.236 (5) Å, with no discernible difference between N-acetyl and N-formyl groups. The C8—C9 bond averages 1.502 (8) Å, which is 0.02–0.03 Å shorter than the endocyclic C—C bonds found in the pyranosyl rings.

The N-acyl side-chains in (IA), (IB) and (II) contain the amide bond N1—C8 in a trans conformation, i.e. with C2—N1—C8—C9 torsion angles of ±179.1 (2)° in both (IA) and (IB), and an average C2—N1—C8—O8 torsion angle of 0.77 (2)° in (IA), (IB) and (II). These torsion angles also demonstrate that the amide group is planar. In all three structures, the conformation about the C2—N1 bond is anti, i.e. atom N1H is roughly anti to H2, which is consistent with the behavior reported in solution (Zhu et al., 2006). However, inspection of the C1—C2—N1—C8 and C3—C2—N1—C8 torsion angles in (IA), (IB) and (II) reveals ranges of 91–108° in the former and -128 to -144° in the latter, indicating some flexibility about the C2—N1 bond in the solid state.

The C5—O5—C1 bond angles in (I)–(VI) appear to depend on anomeric configuration, with β-anomers yielding an average value of 112.0 (6)° and α-anomers an average of 114.7 (3)°. Within the full data set, the largest C—C—C bond angle within any given structure (β-anomers only) is C4—C5—C6, which averages 113.8 (11)°. The two bond angles that incorporate the carbonyl O atom, O8—C8—C9 and O8—C8—N1, are very similar in each structure and average 122.5 (14)° in the full data set. These results contrast with the remaining angle, N1—C8—C9, which is uniformly smaller than the others in any given structure and averages 116.0 (4)° in the full data set.

Within (IA), (IB) and (II), the endocyclic ring torsions vary from 41 to 72° (absolute values), indicating that aldopyranosyl rings containing N-acyl substiutents at C2 are distorted. It is noteworthy that the extreme angles within this group are observed in (II), where the C1—C2—C3—C4 and C1—O5—C5—C4 torsion angles are -41.09 (15) and 71.61 (13)°, respectively. Within (III)–(VI), these torsions range from 48 to 68° (absolute values). A more quantitative treatment of these torsions is provided by the Cremer–Pople parameters calculated for (I)–(VI) (Table 2; Cremer & Pople, 1975). The most distorted ring within (I)–(VI) is that of (II), which yields a θ value of 16.59 (14)°. The least distorted ring is found in (Va), where θ = 0.9 (3)°, and the ring is almost an ideal 4C1 chair. The direction of distortion varies widely within this series of compounds. For (IA) and (II), ϕ = 302.0 (12) and 314.4 (5)°, respectively, suggesting distortion towards BC2,C5. In contrast, ϕ for (IB) is 0(2)°, or a C3,O5B distortion. These data show that not only can aldopyranosyl rings be substantially distorted when bearing an N-acyl functionality at C2, but the direction of distortion can also vary widely, with various boat (BC2,C5, C3,O5B and BC1,C4) and twist-boat (C1TBC5, C3TBC1, O5TBC2 and C5TBC1) conformations represented.

Exocyclic hydroxymethyl conformation in (IA), (IB) and (II) is gt (C4 anti to O6), but the gg conformation (H5 anti to O6) is observed in (III), (IVa), (Va) and (Vb). These data show that gg and gt conformations are favored in GlcNAc/NFm aldopyranosyl rings in the solid state, behavior which is expected to mimic that in solution based on related studies of the simpler Glcp anomers (Thibaudeau et al., 2004).

The structure of (I) forms hydrogen-bonded pairs through hydroxy atom O6A to atom O6B. In turn, atom O6B forms a hydrogen bond to atom O6A of the next pair related by translation along the a axis. In addition, the amide groups form hydrogen bonds, although this is to the same GlcNAc molecule related by translation along the a axis. The (IA) amide atom N1A has a bifurcated hydrogen bond shared between the adjacent amide carbonyl atom O8A and methoxy atom O1A. The (IB) amide atom N1B has a single hydrogen bond to amide atom O8B. This association results in chains of pairs of (IA) and (IB) that run through the lattice parallel to the a axis. These chains are hydrogen-bonded to other chains via hydroxy–hydroxy interactions (O4B···O4A) or hydroxy–water interactions. The water molecules are located in a hydrophilic channel lined with amide O atoms (O8B) and hydroxy groups, again parallel to the a axis. One motif that is apparent is a hydrogen-bonded ring formed by four sets of these hydrogen-bonded chains. These rings are oriented around a hydrophobic channel formed by the methyl groups of the methoxy moieties and the acetamide methyl group (Fig. 3; see Table 3 for specific details). Overall, this structure forms a highly hydrogen-bonded three-dimensional network of water and amidosaccharide molecules.

The structure of (II) also forms a three-dimensional network of hydrogen-bonded molecules. The network is formed from sheets of (II) that have hydrogen bonds through atom O4 to atom O8 running parallel to the b axis (related by the 21 screw axis) and from atom O6 to atom O3 along the c axis, and thus these sheets lie in the bc plane of the lattice. Propagation of these sheets into the third dimension is via hydrogen bonds from atom O3 to atom O6 and from atom N1 to atom O8 of sheets in the next layer along the a axis (Fig. 4).

Related literature top

For related literature, see: Cremer & Pople (1975); Flack (1983); Hooft et al. (2008); Hu, Carmichael & Serianni (2010); Hu, Zhang, Carmichael & Serianni (2010); Jeffrey & Takagi (1977); Mo (1979); Mo & Jensen (1975, 1978); Sweet et al. (2008); Thibaudeau et al. (2004); Zhu et al. (2006).

Experimental top

Compounds (I) and (II) were prepared as described recently in the literature (Hu, Zhang et al., 2010). Both compounds were crystallized from water at room temperature, giving long colorless needle-like crystals that were harvested for X-ray analysis.

Refinement top

The absolute configurations of (I) and (II) were determined both from the known configuration of the starting materials and by comparison of the intensities of Friedel pairs of reflections. However, the Flack parameters were inconclusive [x = -0.4 (2) for (I) and x = 0.16 (14) for (II) [0.13 (14) in CIF - please check]; Flack, 1983]. Further confirmation of the configurations was sought by the Hooft analysis, yielding a Hooft y parameter of -0.13 (12) and P2(true) and P3(true) values of 1.000 and 1.000 for (I), and a Hooft y parameter of 0.16 (4) and P2(true) and P3(true) values of 1.000 and 1.000 for (II) (Hooft et al., 2008). [Please confirm added text]

For both structures, the hydroxy, amide and, where applicable, water H atoms were all located from a difference Fourier map and initially included in those positions. The hydroxy and amide H atoms were subsequently constrained to have reasonable geometric X—H bond distances and angles (N—H = 0.88 and O—H = 0.84 Å). Where applicable, mild restraints to the water O—H bond distances were applied [0.84 (1) Å]. All C—H bonds were constrained to distances of 0.98–1.00 Å. For all H atoms, Uiso(H) = 1.5Ueq(C) for methyl H atoms or 1.2Ueq(C) for all others.

Computing details top

Data collection: APEX2 (Bruker Nonius, 2009) for (I); APEX2 (Bruker Nonius, 2008) for (II). Cell refinement: SAINT (Bruker Nonius, 2009) for (I); SAINT (Bruker Nonius, 2008) for (II). Data reduction: SAINT (Bruker Nonius, 2009) for (I); SAINT (Bruker Nonius, 2008) for (II). For both compounds, program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP (Sheldrick, 2008) and POV-RAY (Cason, 2003); software used to prepare material for publication: XCIF (Sheldrick, 2008) and publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. Labeling schemes for (a) molecule (IA) with water molecules and (b) molecule (IB). Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. The atom-labeling scheme for compound (II). Displacement ellipsoids are drawn at the 50% probability level.
[Figure 3] Fig. 3. Hydrogen-bonding scheme for molecules (IA) and (IB), viewed along the a axis. Dashed lines (blue in the electronic version of the paper) represent hydrogen bonds.
[Figure 4] Fig. 4. Hydrogen-bonding scheme for (II), viewed along the a axis. Dashed lines (blue in the electronic version of the paper) represent hydrogen bonds.
(I) Methyl 2-acetamido-2-deoxy-β-D-glucopyranoside dihydrate top
Crystal data top
C9H17NO6·H2OF(000) = 1088
Mr = 253.25Dx = 1.427 Mg m3
Orthorhombic, P212121Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2ac 2abCell parameters from 3464 reflections
a = 4.6886 (1) Åθ = 2.5–69.3°
b = 14.4501 (3) ŵ = 1.06 mm1
c = 34.7880 (7) ÅT = 100 K
V = 2356.91 (8) Å3Rod, colourless
Z = 80.25 × 0.03 × 0.02 mm
Data collection top
Bruker APEX
diffractometer
4311 independent reflections
Radiation source: fine-focus sealed tube3722 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.054
Detector resolution: 8.33 pixels mm-1θmax = 69.7°, θmin = 2.5°
ω and ϕ scansh = 55
Absorption correction: multi-scan
(SADABS; Sheldrick, 2008)
k = 1715
Tmin = 0.760, Tmax = 0.977l = 4242
21482 measured reflections
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)] = 0.043H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.111 w = 1/[σ2(Fo2) + (0.0611P)2 + 0.2362P]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
4311 reflectionsΔρmax = 0.20 e Å3
323 parametersΔρmin = 0.26 e Å3
6 restraintsAbsolute structure: The configuration was determined based on the known handedness of the chiral C atoms within the structure
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.4 (2)
Crystal data top
C9H17NO6·H2OV = 2356.91 (8) Å3
Mr = 253.25Z = 8
Orthorhombic, P212121Cu Kα radiation
a = 4.6886 (1) ŵ = 1.06 mm1
b = 14.4501 (3) ÅT = 100 K
c = 34.7880 (7) Å0.25 × 0.03 × 0.02 mm
Data collection top
Bruker APEX
diffractometer
4311 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2008)
3722 reflections with I > 2σ(I)
Tmin = 0.760, Tmax = 0.977Rint = 0.054
21482 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.043H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.111Δρmax = 0.20 e Å3
S = 1.06Δρmin = 0.26 e Å3
4311 reflectionsAbsolute structure: The configuration was determined based on the known handedness of the chiral C atoms within the structure
323 parametersAbsolute structure parameter: 0.4 (2)
6 restraints
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.

The absolute configuration of (IA) and (IB) was determined both by the known configuration and by the comparison of intensities of Friedel pairs of refelctoins. However, the "Flack Parameter" is inconclusive (-0.4 (2), Flack, 1983). Further confirmation of the configuration was sought by the Hooft analysis, yielding a Hooft y parameter of -0.13 (12) and P2(true) and P3(true) values of 1.000 and 1.000 (Hooft et al., 2008).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O1A0.5019 (4)1.01643 (12)0.10252 (5)0.0249 (4)
O3A0.0147 (4)0.77214 (12)0.04674 (4)0.0239 (4)
H3OA0.16640.74120.04620.029*
O4A0.1213 (4)0.70071 (12)0.12345 (5)0.0261 (4)
H4OA0.12070.66060.10600.031*
O5A0.3512 (4)0.89756 (12)0.13984 (5)0.0236 (4)
O6A0.2345 (5)0.85070 (13)0.21745 (4)0.0269 (4)
H6OA0.39060.87900.21610.032*
O8A0.4770 (4)0.96829 (13)0.00669 (5)0.0289 (4)
N1A0.0838 (5)0.96940 (14)0.04438 (5)0.0230 (5)
H1NA0.08960.99140.04770.028*
C1A0.2700 (6)0.95948 (17)0.11017 (7)0.0224 (5)
H1AA0.10240.99740.11850.027*
C2A0.1996 (6)0.90667 (17)0.07315 (6)0.0214 (5)
H2AA0.38090.88000.06280.026*
C3A0.0065 (6)0.82680 (17)0.08098 (6)0.0223 (5)
H3AA0.20100.85240.08620.027*
C4A0.0894 (6)0.76899 (17)0.11538 (7)0.0233 (5)
H4AA0.27560.73830.10950.028*
C5A0.1244 (6)0.83421 (17)0.14954 (7)0.0227 (5)
H5AA0.05670.86930.15390.027*
C6A0.2140 (6)0.78608 (17)0.18643 (7)0.0249 (6)
H6AA0.07280.73760.19300.030*
H6AB0.40100.75570.18250.030*
C7A0.5551 (7)1.08176 (17)0.13314 (7)0.0303 (6)
H7AA0.70921.12380.12560.045*
H7AB0.61051.04830.15650.045*
H7AC0.38161.11760.13820.045*
C8A0.2308 (6)0.99501 (17)0.01305 (7)0.0241 (5)
C9A0.0792 (6)1.05925 (18)0.01432 (7)0.0259 (6)
H9AA0.21511.10450.02450.039*
H9AB0.07401.09160.00070.039*
H9AC0.00211.02330.03560.039*
O1B0.9086 (4)0.76022 (12)0.32909 (5)0.0271 (4)
O3B0.4687 (4)1.01843 (12)0.39090 (4)0.0242 (4)
H3OB0.30921.01560.40180.029*
O4B0.3359 (4)1.08765 (12)0.31410 (5)0.0262 (4)
H4OB0.30111.12010.33360.031*
O5B0.8057 (4)0.89217 (12)0.29652 (5)0.0239 (4)
O6B0.7373 (4)0.95967 (13)0.22034 (4)0.0268 (4)
H6OB0.88700.92780.22150.032*
O8B0.9940 (5)0.79804 (15)0.42041 (5)0.0344 (5)
N1B0.5606 (5)0.81929 (14)0.39308 (5)0.0231 (5)
H1NB0.37720.80650.39400.028*
C1B0.7037 (6)0.82856 (17)0.32456 (7)0.0233 (5)
H1BA0.51860.80080.31610.028*
C2B0.6663 (6)0.87963 (17)0.36277 (7)0.0213 (5)
H2BA0.85690.90390.37090.026*
C3B0.4651 (6)0.96231 (17)0.35726 (6)0.0224 (5)
H3BA0.26700.93890.35300.027*
C4B0.5527 (6)1.02200 (17)0.32311 (7)0.0225 (5)
H4BA0.73391.05530.32930.027*
C5B0.5973 (6)0.96175 (17)0.28769 (6)0.0232 (5)
H5BA0.41320.93170.28020.028*
C6B0.7151 (6)1.01601 (18)0.25401 (7)0.0256 (6)
H6BA0.58861.06930.24860.031*
H6BB0.90591.04040.26080.031*
C7B0.9410 (7)0.70406 (18)0.29520 (7)0.0311 (7)
H7BA1.06010.65020.30120.047*
H7BB1.03190.74060.27490.047*
H7BC0.75310.68310.28650.047*
C8B0.7351 (6)0.78257 (18)0.41962 (7)0.0247 (5)
C9B0.5983 (6)0.71994 (18)0.44908 (7)0.0276 (6)
H9BA0.67640.73370.47460.041*
H9BB0.63790.65520.44250.041*
H9BC0.39170.73020.44930.041*
O1W0.5067 (5)0.67786 (13)0.03237 (5)0.0262 (4)
H1WA0.347 (4)0.698 (2)0.0390 (7)0.031*
H1WB0.525 (6)0.6853 (19)0.0085 (3)0.031*
O2W0.0227 (4)0.55444 (13)0.07407 (5)0.0267 (4)
H2WA0.027 (6)0.550 (2)0.0501 (3)0.032*
H2WB0.182 (4)0.542 (2)0.0832 (7)0.032*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O1A0.0290 (10)0.0251 (9)0.0205 (8)0.0013 (8)0.0014 (8)0.0022 (6)
O3A0.0291 (10)0.0260 (9)0.0166 (7)0.0030 (8)0.0013 (8)0.0007 (7)
O4A0.0345 (11)0.0255 (9)0.0184 (8)0.0046 (8)0.0019 (8)0.0007 (7)
O5A0.0271 (10)0.0270 (9)0.0168 (7)0.0012 (8)0.0028 (8)0.0008 (7)
O6A0.0320 (10)0.0335 (10)0.0152 (8)0.0025 (8)0.0002 (8)0.0034 (7)
O8A0.0291 (10)0.0362 (10)0.0213 (8)0.0019 (9)0.0032 (8)0.0031 (7)
N1A0.0262 (12)0.0256 (11)0.0172 (9)0.0001 (9)0.0005 (9)0.0008 (8)
C1A0.0239 (13)0.0246 (12)0.0188 (11)0.0002 (10)0.0004 (11)0.0002 (9)
C2A0.0229 (13)0.0242 (12)0.0170 (11)0.0019 (10)0.0014 (10)0.0024 (9)
C3A0.0227 (12)0.0279 (12)0.0165 (11)0.0015 (11)0.0003 (11)0.0012 (9)
C4A0.0280 (14)0.0233 (12)0.0188 (11)0.0017 (10)0.0011 (11)0.0001 (9)
C5A0.0272 (14)0.0234 (12)0.0176 (11)0.0011 (11)0.0024 (11)0.0013 (9)
C6A0.0338 (15)0.0233 (13)0.0176 (11)0.0010 (11)0.0003 (11)0.0005 (9)
C7A0.0392 (17)0.0251 (13)0.0266 (12)0.0019 (12)0.0036 (12)0.0040 (10)
C8A0.0322 (15)0.0243 (12)0.0159 (11)0.0058 (11)0.0032 (11)0.0026 (9)
C9A0.0315 (14)0.0275 (13)0.0188 (11)0.0037 (11)0.0003 (11)0.0005 (10)
O1B0.0352 (11)0.0263 (9)0.0199 (8)0.0056 (8)0.0031 (8)0.0013 (7)
O3B0.0259 (9)0.0297 (9)0.0169 (8)0.0025 (8)0.0022 (8)0.0025 (6)
O4B0.0340 (11)0.0270 (10)0.0175 (8)0.0043 (8)0.0004 (8)0.0021 (7)
O5B0.0279 (10)0.0257 (9)0.0181 (8)0.0020 (8)0.0041 (8)0.0020 (7)
O6B0.0312 (10)0.0336 (10)0.0156 (8)0.0036 (8)0.0005 (8)0.0013 (7)
O8B0.0276 (11)0.0501 (12)0.0255 (9)0.0002 (10)0.0015 (9)0.0069 (8)
N1B0.0253 (12)0.0256 (11)0.0183 (9)0.0002 (9)0.0017 (9)0.0008 (8)
C1B0.0266 (14)0.0244 (13)0.0191 (11)0.0015 (10)0.0015 (11)0.0018 (10)
C2B0.0237 (13)0.0230 (12)0.0172 (11)0.0019 (10)0.0006 (10)0.0023 (9)
C3B0.0255 (13)0.0253 (12)0.0166 (10)0.0003 (11)0.0012 (11)0.0019 (9)
C4B0.0249 (14)0.0220 (12)0.0207 (11)0.0020 (10)0.0001 (10)0.0005 (9)
C5B0.0282 (14)0.0248 (13)0.0167 (11)0.0002 (11)0.0002 (11)0.0018 (9)
C6B0.0328 (15)0.0271 (13)0.0169 (11)0.0018 (11)0.0015 (11)0.0008 (10)
C7B0.0472 (19)0.0247 (13)0.0214 (12)0.0064 (13)0.0034 (13)0.0046 (10)
C8B0.0290 (14)0.0263 (13)0.0187 (11)0.0027 (11)0.0007 (11)0.0016 (9)
C9B0.0337 (15)0.0275 (13)0.0216 (11)0.0031 (11)0.0014 (12)0.0032 (10)
O1W0.0298 (10)0.0325 (10)0.0162 (7)0.0007 (8)0.0011 (8)0.0004 (7)
O2W0.0275 (10)0.0354 (10)0.0174 (8)0.0012 (9)0.0003 (8)0.0010 (7)
Geometric parameters (Å, º) top
O1A—C1A1.389 (3)N1A—H1NA0.8800
O1A—C7A1.445 (3)C1A—H1AA1.0000
O3A—C3A1.430 (3)C2A—H2AA1.0000
O4A—C4A1.424 (3)C3A—H3AA1.0000
O5A—C1A1.418 (3)C4A—H4AA1.0000
O5A—C5A1.443 (3)C5A—H5AA1.0000
O6A—C6A1.430 (3)C6A—H6AA0.9900
O8A—C8A1.237 (3)C6A—H6AB0.9900
N1A—C8A1.342 (3)C7A—H7AA0.9800
N1A—C2A1.456 (3)C7A—H7AB0.9800
C1A—C2A1.533 (3)C7A—H7AC0.9800
C2A—C3A1.530 (3)C9A—H9AA0.9800
C3A—C4A1.527 (3)C9A—H9AB0.9800
C4A—C5A1.526 (3)C9A—H9AC0.9800
C5A—C6A1.519 (3)O3B—H3OB0.8400
C8A—C9A1.508 (3)O4B—H4OB0.8400
O1B—C1B1.387 (3)O6B—H6OB0.8400
O1B—C7B1.439 (3)N1B—H1NB0.8800
O3B—C3B1.424 (3)C1B—H1BA1.0000
O4B—C4B1.425 (3)C2B—H2BA1.0000
O5B—C1B1.423 (3)C3B—H3BA1.0000
O5B—C5B1.435 (3)C4B—H4BA1.0000
O6B—C6B1.430 (3)C5B—H5BA1.0000
O8B—C8B1.235 (4)C6B—H6BA0.9900
N1B—C8B1.343 (3)C6B—H6BB0.9900
N1B—C2B1.455 (3)C7B—H7BA0.9800
C1B—C2B1.531 (3)C7B—H7BB0.9800
C2B—C3B1.534 (3)C7B—H7BC0.9800
C3B—C4B1.525 (3)C9B—H9BA0.9800
C4B—C5B1.523 (3)C9B—H9BB0.9800
C5B—C6B1.514 (3)C9B—H9BC0.9800
C8B—C9B1.510 (3)O1W—H1WA0.839 (10)
O3A—H3OA0.8400O1W—H1WB0.840 (10)
O4A—H4OA0.8400O2W—H2WA0.837 (10)
O6A—H6OA0.8400O2W—H2WB0.833 (10)
C1A—O1A—C7A112.4 (2)C1B—O5B—C5B111.8 (2)
C1A—O5A—C5A111.9 (2)C8B—N1B—C2B121.8 (2)
C8A—N1A—C2A122.6 (2)O1B—C1B—O5B107.8 (2)
O1A—C1A—O5A107.6 (2)O1B—C1B—C2B108.9 (2)
O1A—C1A—C2A107.60 (19)O5B—C1B—C2B108.8 (2)
O5A—C1A—C2A110.80 (19)N1B—C2B—C1B112.3 (2)
N1A—C2A—C3A110.9 (2)N1B—C2B—C3B110.3 (2)
N1A—C2A—C1A110.37 (19)C1B—C2B—C3B109.71 (19)
C3A—C2A—C1A111.22 (19)O3B—C3B—C4B108.37 (19)
O3A—C3A—C4A111.01 (19)O3B—C3B—C2B109.47 (19)
O3A—C3A—C2A106.58 (19)C4B—C3B—C2B111.9 (2)
C4A—C3A—C2A111.5 (2)O4B—C4B—C5B107.49 (19)
O4A—C4A—C5A110.42 (19)O4B—C4B—C3B110.8 (2)
O4A—C4A—C3A109.2 (2)C5B—C4B—C3B110.12 (19)
C5A—C4A—C3A107.7 (2)O5B—C5B—C6B106.3 (2)
O5A—C5A—C6A106.5 (2)O5B—C5B—C4B108.70 (19)
O5A—C5A—C4A106.79 (19)C6B—C5B—C4B112.3 (2)
C6A—C5A—C4A113.9 (2)O6B—C6B—C5B111.4 (2)
O6A—C6A—C5A110.9 (2)O8B—C8B—N1B122.9 (2)
O8A—C8A—N1A122.6 (2)O8B—C8B—C9B120.7 (2)
O8A—C8A—C9A121.3 (2)N1B—C8B—C9B116.4 (2)
N1A—C8A—C9A116.1 (2)C3B—O3B—H3OB109.5
C3A—O3A—H3OA109.5C4B—O4B—H4OB109.5
C4A—O4A—H4OA109.5C6B—O6B—H6OB109.5
C6A—O6A—H6OA109.5C8B—N1B—H1NB119.1
C8A—N1A—H1NA118.7C2B—N1B—H1NB119.1
C2A—N1A—H1NA118.7O1B—C1B—H1BA110.4
O1A—C1A—H1AA110.2O5B—C1B—H1BA110.4
O5A—C1A—H1AA110.2C2B—C1B—H1BA110.4
C2A—C1A—H1AA110.2N1B—C2B—H2BA108.1
N1A—C2A—H2AA108.1C1B—C2B—H2BA108.1
C3A—C2A—H2AA108.1C3B—C2B—H2BA108.1
C1A—C2A—H2AA108.1O3B—C3B—H3BA109.0
O3A—C3A—H3AA109.2C4B—C3B—H3BA109.0
C4A—C3A—H3AA109.2C2B—C3B—H3BA109.0
C2A—C3A—H3AA109.2O4B—C4B—H4BA109.5
O4A—C4A—H4AA109.8C5B—C4B—H4BA109.5
C5A—C4A—H4AA109.8C3B—C4B—H4BA109.5
C3A—C4A—H4AA109.8O5B—C5B—H5BA109.8
O5A—C5A—H5AA109.8C6B—C5B—H5BA109.8
C6A—C5A—H5AA109.8C4B—C5B—H5BA109.8
C4A—C5A—H5AA109.8O6B—C6B—H6BA109.3
O6A—C6A—H6AA109.5C5B—C6B—H6BA109.3
C5A—C6A—H6AA109.5O6B—C6B—H6BB109.3
O6A—C6A—H6AB109.5C5B—C6B—H6BB109.3
C5A—C6A—H6AB109.5H6BA—C6B—H6BB108.0
H6AA—C6A—H6AB108.0O1B—C7B—H7BA109.5
O1A—C7A—H7AA109.5O1B—C7B—H7BB109.5
O1A—C7A—H7AB109.5H7BA—C7B—H7BB109.5
H7AA—C7A—H7AB109.5O1B—C7B—H7BC109.5
O1A—C7A—H7AC109.5H7BA—C7B—H7BC109.5
H7AA—C7A—H7AC109.5H7BB—C7B—H7BC109.5
H7AB—C7A—H7AC109.5C8B—C9B—H9BA109.5
C8A—C9A—H9AA109.5C8B—C9B—H9BB109.5
C8A—C9A—H9AB109.5H9BA—C9B—H9BB109.5
H9AA—C9A—H9AB109.5C8B—C9B—H9BC109.5
C8A—C9A—H9AC109.5H9BA—C9B—H9BC109.5
H9AA—C9A—H9AC109.5H9BB—C9B—H9BC109.5
H9AB—C9A—H9AC109.5H1WA—O1W—H1WB108 (2)
C1B—O1B—C7B112.4 (2)H2WA—O2W—H2WB110 (2)
C7A—O1A—C1A—O5A71.1 (2)C7B—O1B—C1B—O5B66.6 (3)
C7A—O1A—C1A—C2A169.5 (2)C7B—O1B—C1B—C2B175.5 (2)
C5A—O5A—C1A—O1A179.18 (18)C5B—O5B—C1B—O1B175.46 (19)
C5A—O5A—C1A—C2A61.8 (3)C5B—O5B—C1B—C2B66.6 (3)
C8A—N1A—C2A—C3A128.1 (2)C8B—N1B—C2B—C1B100.0 (3)
C8A—N1A—C2A—C1A108.2 (3)C8B—N1B—C2B—C3B137.2 (2)
O1A—C1A—C2A—N1A69.5 (3)O1B—C1B—C2B—N1B63.1 (3)
O5A—C1A—C2A—N1A173.1 (2)O5B—C1B—C2B—N1B179.7 (2)
O1A—C1A—C2A—C3A167.0 (2)O1B—C1B—C2B—C3B173.8 (2)
O5A—C1A—C2A—C3A49.6 (3)O5B—C1B—C2B—C3B56.6 (3)
N1A—C2A—C3A—O3A67.6 (2)N1B—C2B—C3B—O3B65.5 (3)
C1A—C2A—C3A—O3A169.1 (2)C1B—C2B—C3B—O3B170.2 (2)
N1A—C2A—C3A—C4A171.08 (19)N1B—C2B—C3B—C4B174.33 (19)
C1A—C2A—C3A—C4A47.9 (3)C1B—C2B—C3B—C4B50.1 (3)
O3A—C3A—C4A—O4A66.2 (3)O3B—C3B—C4B—O4B70.1 (3)
C2A—C3A—C4A—O4A175.10 (19)C2B—C3B—C4B—O4B169.13 (19)
O3A—C3A—C4A—C5A173.8 (2)O3B—C3B—C4B—C5B171.1 (2)
C2A—C3A—C4A—C5A55.1 (3)C2B—C3B—C4B—C5B50.3 (3)
C1A—O5A—C5A—C6A168.62 (19)C1B—O5B—C5B—C6B172.4 (2)
C1A—O5A—C5A—C4A69.3 (2)C1B—O5B—C5B—C4B66.5 (2)
O4A—C4A—C5A—O5A176.89 (19)O4B—C4B—C5B—O5B177.39 (19)
C3A—C4A—C5A—O5A63.9 (3)C3B—C4B—C5B—O5B56.6 (3)
O4A—C4A—C5A—C6A59.6 (3)O4B—C4B—C5B—C6B65.3 (3)
C3A—C4A—C5A—C6A178.8 (2)C3B—C4B—C5B—C6B173.9 (2)
O5A—C5A—C6A—O6A64.3 (3)O5B—C5B—C6B—O6B65.2 (3)
C4A—C5A—C6A—O6A178.3 (2)C4B—C5B—C6B—O6B176.1 (2)
C2A—N1A—C8A—O8A1.2 (4)C2B—N1B—C8B—O8B0.8 (4)
C2A—N1A—C8A—C9A179.1 (2)C2B—N1B—C8B—C9B179.1 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3A—H3OA···O1Wi0.841.852.672 (3)166
O4A—H4OA···O2W0.842.012.806 (3)158
O6A—H6OA···O6B0.842.012.837 (3)170
N1A—H1NA···O8Ai0.882.503.132 (3)129
O3B—H3OB···O2Wii0.841.852.658 (3)160
O4B—H4OB···O4Aii0.842.072.898 (2)167
O6B—H6OB···O6Aiii0.841.982.815 (3)173
N1B—H1NB···O8Bi0.882.022.838 (3)154
O1W—H1WA···O3A0.84 (1)2.02 (1)2.843 (3)167 (3)
O1W—H1WB···O3Aiv0.84 (1)2.03 (1)2.847 (2)165 (3)
O2W—H2WA···O8Av0.84 (1)2.01 (1)2.837 (2)171 (3)
O2W—H2WB···O3Bvi0.83 (1)1.90 (1)2.728 (3)174 (3)
Symmetry codes: (i) x1, y, z; (ii) x, y+1/2, z+1/2; (iii) x+1, y, z; (iv) x+1/2, y+3/2, z; (v) x1/2, y+3/2, z; (vi) x+1, y1/2, z+1/2.
(II) methyl 2-formamido-2-deoxy-β-D-glucopyranoside top
Crystal data top
C8H15NO6F(000) = 236
Mr = 221.21Dx = 1.501 Mg m3
Monoclinic, P21Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2ybCell parameters from 6827 reflections
a = 4.5374 (5) Åθ = 2.8–68.8°
b = 15.8837 (16) ŵ = 1.11 mm1
c = 6.8993 (7) ÅT = 100 K
β = 100.185 (4)°Rod, colourless
V = 489.40 (9) Å30.34 × 0.07 × 0.06 mm
Z = 2
Data collection top
Bruker APEX
diffractometer
1744 independent reflections
Radiation source: fine-focus sealed tube1744 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.021
Detector resolution: 8.33 pixels mm-1θmax = 69.2°, θmin = 5.6°
ω and ϕ scansh = 54
Absorption correction: multi-scan
(SADABS; Sheldrick, 2008)
k = 1918
Tmin = 0.703, Tmax = 0.940l = 88
6422 measured reflections
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)] = 0.027H-atom parameters constrained
wR(F2) = 0.070 w = 1/[σ2(Fo2) + (0.0474P)2 + 0.0947P]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max = 0.001
1744 reflectionsΔρmax = 0.16 e Å3
137 parametersΔρmin = 0.21 e Å3
1 restraintAbsolute structure: The configuration was determined based on the known handedness of the chiral C atoms within the structure.
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.13 (14)
Crystal data top
C8H15NO6V = 489.40 (9) Å3
Mr = 221.21Z = 2
Monoclinic, P21Cu Kα radiation
a = 4.5374 (5) ŵ = 1.11 mm1
b = 15.8837 (16) ÅT = 100 K
c = 6.8993 (7) Å0.34 × 0.07 × 0.06 mm
β = 100.185 (4)°
Data collection top
Bruker APEX
diffractometer
1744 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2008)
1744 reflections with I > 2σ(I)
Tmin = 0.703, Tmax = 0.940Rint = 0.021
6422 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.027H-atom parameters constrained
wR(F2) = 0.070Δρmax = 0.16 e Å3
S = 1.06Δρmin = 0.21 e Å3
1744 reflectionsAbsolute structure: The configuration was determined based on the known handedness of the chiral C atoms within the structure.
137 parametersAbsolute structure parameter: 0.13 (14)
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.

The absolute configuration of (II) was determined both by the known configuration and by the comparison of intensities of Friedel pairs of reflections. However, the "Flack parameter" is inconclusive (0.16 (14), Flack, 1983). Further confirmation of the configuration was determined by the Hooft analysis, yielding a Hooft y parameter of 0.16 (4) and P2(true) and P3(true) values of 1.000 and 1.000 (Hooft et al., 2008).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
N10.2017 (3)0.71728 (7)0.10020 (16)0.0144 (3)
H10.39090.71960.11320.017*
O10.3423 (2)0.70731 (6)0.39700 (14)0.0153 (2)
O30.2868 (2)0.54758 (6)0.08114 (14)0.0165 (2)
H30.44380.51900.11200.020*
O40.3240 (2)0.42177 (6)0.22397 (15)0.0157 (2)
H40.27650.38180.15590.019*
O50.2267 (2)0.57256 (6)0.46455 (14)0.0143 (2)
O60.1860 (2)0.46548 (6)0.79389 (15)0.0181 (2)
H60.03920.49270.81990.022*
O80.1723 (2)0.78734 (7)0.01196 (15)0.0189 (2)
C10.1075 (3)0.65022 (9)0.3842 (2)0.0141 (3)
H1A0.04550.67150.46020.017*
C20.0322 (3)0.64118 (9)0.1663 (2)0.0142 (3)
H2A0.13380.63570.08920.017*
C30.2326 (3)0.56275 (9)0.1262 (2)0.0139 (3)
H3A0.42880.57570.16660.017*
C40.0992 (3)0.48537 (9)0.2417 (2)0.0134 (3)
H4A0.07780.46450.18770.016*
C50.0042 (3)0.51034 (9)0.4576 (2)0.0140 (3)
H5A0.17890.53540.50720.017*
C60.1248 (3)0.43908 (9)0.5920 (2)0.0165 (3)
H6A0.01880.39160.57750.020*
H6B0.31230.41900.55280.020*
C70.4591 (4)0.73055 (9)0.5975 (2)0.0190 (3)
H7A0.29600.75160.66020.029*
H7B0.61060.77470.59920.029*
H7C0.55030.68120.66960.029*
C80.0855 (3)0.78315 (9)0.0214 (2)0.0150 (3)
H8A0.21110.83080.01180.018*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0146 (6)0.0138 (6)0.0144 (5)0.0016 (5)0.0016 (4)0.0006 (5)
O10.0172 (5)0.0149 (5)0.0132 (5)0.0046 (4)0.0014 (4)0.0014 (4)
O30.0184 (5)0.0186 (5)0.0114 (5)0.0031 (4)0.0004 (4)0.0007 (4)
O40.0174 (6)0.0136 (5)0.0167 (5)0.0035 (4)0.0048 (4)0.0037 (4)
O50.0146 (5)0.0126 (5)0.0149 (4)0.0009 (4)0.0007 (3)0.0004 (4)
O60.0219 (5)0.0192 (5)0.0125 (5)0.0009 (4)0.0007 (4)0.0014 (4)
O80.0201 (5)0.0180 (5)0.0197 (5)0.0011 (4)0.0069 (4)0.0042 (4)
C10.0150 (7)0.0122 (7)0.0153 (7)0.0012 (5)0.0033 (5)0.0002 (5)
C20.0158 (7)0.0130 (6)0.0142 (7)0.0004 (5)0.0033 (5)0.0003 (5)
C30.0128 (6)0.0153 (7)0.0133 (6)0.0010 (6)0.0019 (5)0.0012 (6)
C40.0151 (7)0.0125 (7)0.0130 (7)0.0019 (5)0.0033 (6)0.0017 (5)
C50.0147 (7)0.0134 (7)0.0140 (7)0.0010 (5)0.0030 (5)0.0008 (5)
C60.0184 (7)0.0159 (7)0.0144 (7)0.0016 (5)0.0010 (6)0.0003 (5)
C70.0212 (8)0.0187 (7)0.0164 (7)0.0031 (6)0.0015 (6)0.0034 (6)
C80.0195 (8)0.0130 (6)0.0119 (6)0.0009 (6)0.0013 (5)0.0016 (6)
Geometric parameters (Å, º) top
N1—C81.3302 (19)N1—H10.8800
N1—C21.4615 (18)O3—H30.8400
O1—C11.3899 (17)O4—H40.8400
O1—C71.4391 (16)O6—H60.8400
O3—C31.4282 (16)C1—H1A1.0000
O4—C41.4252 (17)C2—H2A1.0000
O5—C11.4198 (17)C3—H3A1.0000
O5—C51.4349 (17)C4—H4A1.0000
O6—C61.4341 (17)C5—H5A1.0000
O8—C81.2334 (18)C6—H6A0.9900
C1—C21.5318 (19)C6—H6B0.9900
C2—C31.5383 (19)C7—H7A0.9800
C3—C41.5302 (19)C7—H7B0.9800
C4—C51.5284 (18)C7—H7C0.9800
C5—C61.5137 (19)C8—H8A0.9500
C8—N1—C2123.60 (12)C2—C1—H1A110.0
C1—O1—C7112.10 (10)N1—C2—H2A108.1
C1—O5—C5111.09 (10)C1—C2—H2A108.1
O1—C1—O5107.89 (11)C3—C2—H2A108.1
O1—C1—C2107.63 (11)O3—C3—H3A108.1
O5—C1—C2111.39 (11)C4—C3—H3A108.1
N1—C2—C1109.40 (11)C2—C3—H3A108.1
N1—C2—C3110.61 (11)O4—C4—H4A110.0
C1—C2—C3112.42 (11)C5—C4—H4A110.0
O3—C3—C4111.60 (11)C3—C4—H4A110.0
O3—C3—C2107.96 (11)O5—C5—H5A109.4
C4—C3—C2112.95 (11)C6—C5—H5A109.4
O4—C4—C5109.98 (11)C4—C5—H5A109.4
O4—C4—C3108.27 (11)O6—C6—H6A109.4
C5—C4—C3108.46 (11)C5—C6—H6A109.4
O5—C5—C6107.07 (12)O6—C6—H6B109.4
O5—C5—C4106.84 (10)C5—C6—H6B109.4
C6—C5—C4114.51 (11)H6A—C6—H6B108.0
O6—C6—C5111.33 (11)O1—C7—H7A109.5
O8—C8—N1125.18 (13)O1—C7—H7B109.5
C8—N1—H1118.2H7A—C7—H7B109.5
C2—N1—H1118.2O1—C7—H7C109.5
C3—O3—H3109.5H7A—C7—H7C109.5
C4—O4—H4109.5H7B—C7—H7C109.5
C6—O6—H6109.5O8—C8—H8A117.4
O1—C1—H1A110.0N1—C8—H8A117.4
O5—C1—H1A110.0
C7—O1—C1—O568.85 (14)O3—C3—C4—O469.13 (14)
C7—O1—C1—C2170.83 (11)C2—C3—C4—O4169.02 (10)
C5—O5—C1—O1179.60 (10)O3—C3—C4—C5171.55 (10)
C5—O5—C1—C262.48 (14)C2—C3—C4—C549.70 (15)
C8—N1—C2—C191.34 (15)C1—O5—C5—C6165.27 (11)
C8—N1—C2—C3144.29 (13)C1—O5—C5—C471.61 (13)
O1—C1—C2—N172.83 (13)O4—C4—C5—O5178.49 (11)
O5—C1—C2—N1169.10 (11)C3—C4—C5—O563.27 (13)
O1—C1—C2—C3163.87 (11)O4—C4—C5—C660.12 (15)
O5—C1—C2—C345.79 (15)C3—C4—C5—C6178.36 (13)
N1—C2—C3—O372.40 (13)O5—C5—C6—O666.48 (14)
C1—C2—C3—O3164.98 (11)C4—C5—C6—O6175.29 (11)
N1—C2—C3—C4163.71 (11)C2—N1—C8—O82.7 (2)
C1—C2—C3—C441.09 (15)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O8i0.882.293.0213 (16)141
N1—H1···O1i0.882.483.1621 (15)134
O3—H3···O6ii0.841.892.7271 (14)173
O4—H4···O8iii0.841.902.7438 (14)177
O6—H6···O3iv0.841.942.7749 (14)171
Symmetry codes: (i) x1, y, z; (ii) x1, y, z1; (iii) x, y1/2, z; (iv) x, y, z+1.

Experimental details

(I)(II)
Crystal data
Chemical formulaC9H17NO6·H2OC8H15NO6
Mr253.25221.21
Crystal system, space groupOrthorhombic, P212121Monoclinic, P21
Temperature (K)100100
a, b, c (Å)4.6886 (1), 14.4501 (3), 34.7880 (7)4.5374 (5), 15.8837 (16), 6.8993 (7)
α, β, γ (°)90, 90, 9090, 100.185 (4), 90
V3)2356.91 (8)489.40 (9)
Z82
Radiation typeCu KαCu Kα
µ (mm1)1.061.11
Crystal size (mm)0.25 × 0.03 × 0.020.34 × 0.07 × 0.06
Data collection
DiffractometerBruker APEX
diffractometer
Bruker APEX
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2008)
Multi-scan
(SADABS; Sheldrick, 2008)
Tmin, Tmax0.760, 0.9770.703, 0.940
No. of measured, independent and
observed [I > 2σ(I)] reflections
21482, 4311, 3722 6422, 1744, 1744
Rint0.0540.021
(sin θ/λ)max1)0.6080.606
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.043, 0.111, 1.06 0.027, 0.070, 1.06
No. of reflections43111744
No. of parameters323137
No. of restraints61
H-atom treatmentH atoms treated by a mixture of independent and constrained refinementH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.20, 0.260.16, 0.21
Absolute structureThe configuration was determined based on the known handedness of the chiral C atoms within the structureThe configuration was determined based on the known handedness of the chiral C atoms within the structure.
Absolute structure parameter0.4 (2)0.13 (14)

Computer programs: APEX2 (Bruker Nonius, 2009), APEX2 (Bruker Nonius, 2008), SAINT (Bruker Nonius, 2009), SAINT (Bruker Nonius, 2008), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), XP (Sheldrick, 2008) and POV-RAY (Cason, 2003), XCIF (Sheldrick, 2008) and publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) for (I) top
D—H···AD—HH···AD···AD—H···A
O3A—H3OA···O1Wi0.841.852.672 (3)166.0
O4A—H4OA···O2W0.842.012.806 (3)158.1
O6A—H6OA···O6B0.842.012.837 (3)170.1
N1A—H1NA···O8Ai0.882.503.132 (3)128.9
O3B—H3OB···O2Wii0.841.852.658 (3)159.5
O4B—H4OB···O4Aii0.842.072.898 (2)166.9
O6B—H6OB···O6Aiii0.841.982.815 (3)173.1
N1B—H1NB···O8Bi0.882.022.838 (3)154.0
O1W—H1WA···O3A0.839 (10)2.020 (12)2.843 (3)167 (3)
O1W—H1WB···O3Aiv0.840 (10)2.028 (13)2.847 (2)165 (3)
O2W—H2WA···O8Av0.837 (10)2.007 (10)2.837 (2)171 (3)
O2W—H2WB···O3Bvi0.833 (10)1.899 (10)2.728 (3)174 (3)
Symmetry codes: (i) x1, y, z; (ii) x, y+1/2, z+1/2; (iii) x+1, y, z; (iv) x+1/2, y+3/2, z; (v) x1/2, y+3/2, z; (vi) x+1, y1/2, z+1/2.
Hydrogen-bond geometry (Å, º) for (II) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O8i0.882.293.0213 (16)141.1
N1—H1···O1i0.882.483.1621 (15)134.2
O3—H3···O6ii0.841.892.7271 (14)172.6
O4—H4···O8iii0.841.902.7438 (14)177.1
O6—H6···O3iv0.841.942.7749 (14)171.3
Symmetry codes: (i) x1, y, z; (ii) x1, y, z1; (iii) x, y1/2, z; (iv) x, y, z+1.
Cremer–Pople puckering parameters in compounds (I)–(VII) top
Compoundθ (°)ϕ (°)Q (Å)q2 (Å)q3 (Å)Conformera
(IA)11.4 (3)302.0 (12)0.595 (3)0.118 (3)0.583 (3)BC2,C5
(IB)7.1 (2)0(2)0.585 (3)0.078 (2)0.580 (3)C3,O5B
(II)16.59 (14)314.4 (5)0.5791 (14)0.1654 (14)0.5550 (14)BC2,C5
(III)3.8 (2)274 (3)0.582 (2)0.031 (2)0.581 (2)C1TBC5
(IVa)4.8 (3)19 (4)0.568 (3)0.044 (3)0.566 (3)C3TBC1
(IVb)8.7 (3)338 (2)0.577 (3)0.089 (9)0.570 (3)O5TBC2
(Va)0.9 (3)55 (3)0.572 (3)0.006 (3)0.572 (3)BC1,C4
(Vb)2.3 (3)97 (6)0.580 (3)0.029 (3)0.580 (3)C5TBC1
(VI)6.94 (19)38 (2)0.597 (2)0.072 (2)0.593 (2)C3TBC1
Note: (a) B = boat and S = skew or twist-boat.
Comparison of structural parameters in compounds (I)–(VII) top
Parameterβ-GlcNAcOCH3β-GlcNAcOCH3β-GlcNFmOCH3α-GlcNAcOHβ-GlcNAcOHβ-GlcNAcORα-GlcNAcOHβ-GlcNAcORβ-GlcOCH3
(IA)(IB)(II)(III)(IVa)(IVb)(Va)(Vb)(VI)
Bond lengths (Å)
C1—C21.533 (3)1.531 (3)1.5318 (19)1.534 (2)1.522 (5)1.522 (3)1.526 (5)1.515 (4)1.522 (4)
C2—C31.530 (3)1.534 (3)1.5383 (19)1.531 (3)1.521 (4)1.531 (4)1.527 (5)1.517 (5)1.515 (2)
C3—C41.527 (3)1.525 (3)1.5302 (19)1.521 (3)1.531 (3)1.516 (5)1.520 (4)1.516 (4)1.529 (3)
C4—C51.526 (3)1.523 (3)1.5284 (18)1.528 (3)1.536 (4)1.507 (5)1.519 (5)1.537 (4)1.527 (4)
C5—C61.519 (3)1.514 (3)1.5137 (19)1.514 (2)1.501 (4)1.499 (5)1.512 (5)1.517 (4)1.516 (2)
C1—O11.389 (3)1.387 (3)1.3899 (17)1.390 (3)1.389 (4)1.389 (4)1.361 (5)1.395 (4)1.379 (2)
C1—O51.418 (3)1.423 (3)1.4198 (17)1.434 (2)1.427 (3)1.429 (3)1.418 (4)1.414 (4)1.433 (2)
C2—N11.456 (3)1.455 (3)1.4615 (18)1.457 (2)1.450 (3)1.446 (3)1.450 (4)1.460 (4)
C2—O21.426 (2)
C3—O31.430 (3)1.424 (3)1.4282 (16)1.430 (2)1.430 (4)1.424 (4)1.421 (5)1.431 (4)1.425 (4)
C4—O4/O11.424 (3)1.425 (3)1.4252 (17)1.434 (2)1.448 (3)1.425 (3)1.448 (3)1.422 (4)1.426 (2)
C5—O51.443 (3)1.435 (3)1.4349 (17)1.448 (2)1.429 (3)1.436 (4)1.438 (4)1.427 (5)1.440 (2)
C6—O61.430 (3)1.430 (3)1.4341 (17)1.416 (3)1.413 (4)1.415 (5)1.419 (5)1.423 (5)1.417 (4)
C7—O11.445 (3)1.439 (3)1.4391 (16)1.430 (4)
C8-O81.237 (3)1.235 (4)1.2334 (18)1.235 (2)1.243 (4)1.246 (4)1.231 (4)1.231 (4)
C8—C91.508 (3)1.510 (3)1.508 (3)1.497 (5)1.496 (6)1.490 (6)1.506 (7)
Bond angles (°)
C1—C2—C3111.22 (19)109.71 (19)112.42 (11)110.11 (13)111.5 (4)110.9 (4)110.0 (2)109.3 (3)108.4 (2)
C2—C3—C4111.5 (2)111.9 (2)112.95 (11)110.88 (15)109.6 (4)112.1 (4)109.7 (3)109.1 (2)110.82 (13)
C3—C4—C5107.7 (2)110.12 (19)108.46 (10)108.77 (15)111.2 (4)110.0 (4)110.7 (3)110.3 (3)111.15 (15)
C4—C5—O5106.79 (19)108.70 (19)106.84 (10)108.41 (13)110.1 (4)108.2 (4)109.3 (2)110.4 (3)108.5 (3)
C5—O5—C1111.9 (2)111.8 (2)111.09 (10)114.97 (14)112.6 (4)112.1 (4)114.5 (3)112.9 (2)111.55 (11)
O5—C1—C2110.80 (19)108.8 (2)111.39 (11)109.24 (15)109.3 (4)109.1 (4)109.6 (3)110.0 (2)108.38 (18)
C4—C5—C6113.9 (2)112.3 (2)114.51 (11)114.77 (16)113.3 (4)115.5 (4)114.3 (3)113.1 (3)112.33 (16)
C2—N1—C8122.6 (2)121.8 (2)123.60 (12)122.17 (18)122.9 (4)124.9 (4)124.8 (3)122.0 (3)
N1—C8—C9116.1 (2)116.4 (2)116.01 (18)116.3 (4)115.9 (5)115.3 (3)115.8 (4)
O8—C8—C9121.3 (2)120.7 (2)120.93 (16)122.2 (4)122.7 (5)120.7 (3)120.2 (4)
O8—C8—N1122.6 (2)122.9 (2)125.18 (13)123.06 (16)121.5 (4)121.3 (4)123.9 (3)123.9 (3)
Torsion angles (°)
C1—C2—C3—C4-47.9 (3)-50.1 (3)-41.09 (15)-54.6 (2)-52.1 (4)-48.2 (4)-54.4 (4)-56.7 (3)-54.3 (3)
C1—O5—C5—C469.3 (2)66.5 (2)71.61 (13)62.5 (2)61.8 (4)67.4 (4)60.4 (3)59.1 (4)63.4 (3)
C2—C3—C4—C555.1 (3)50.3 (3)49.70 (15)56.8 (2)50.4 (4)50.9 (4)54.5 (3)54.2 (4)51.7 (3)
C2—C1—O5—C5-61.8 (3)-66.6 (3)-62.48 (14)-59.9 (2)-62.9 (4)-64.4 (4)-60.9 (3)-62.1 (3)-67.9 (3)
C2—C1—O1—C7/C4175.5 (2)169.5 (2)170.83 (11)151.7 (4)161.5 (2)169.19 (15)
C3—C4—C5—O5-63.9 (3)-56.6 (3)-63.27 (13)-58.4 (2)-54.8 (4)-58.6 (4)-55.7 (3)-54.7 (4)-54.2 (2)
C3—C2—C1—O549.6 (3)56.6 (3)45.79 (15)53.8 (4)57.6 (4)53.1 (4)56.5 (4)60.0 (3)61.5 (2)
C3—C4—C5—C6178.8 (2)-173.9 (2)178.36 (13)-177.51 (17)-174.4 (4)-178.1 (4)-174.5 (3)-175.6 (3)-171.9 (2)
O5—C5—C6—O664.3 (3)65.2 (3)66.48 (14)-60.71 (18)-60.6 (4)58.6 (4)-74.6 (4)-65.5 (3)68.7 (3)
gtgtgtgggggtgggggt
C1—C2—N1—C8108.2 (3)100.0 (3)91.34 (14)140.89 (17)100.5 (4)113.7 (4)138.7 (3)100.5 (4)
C3—C2—N1—C8-128.1 (2)-137.2 (2)-144.29 (13)-96.8 (2)-135.2 (4)-122.5 (4)-98.9 (4)-137.0 (3)
C2—N1—C8—C9179.1 (2)-179.1 (2)169.86 (15)-173.7 (4)178.4 (5)-179.6 (4)-173.9 (4)
transtranstranstranstranstranstrans
C2—N1—C8—O8-1.2 (4)0.8 (4)2.7 (2)-9.7 (2)5.2 (7)-5.3 (6)-2.1 (6)2.9 (5)
Note: gg is gauchegauche and gt is gauchetrans.
 

References

First citationBruker–Nonius (2008). APEX2 (Version 2008-6) and SAINT (Version 7.53A). Bruker–Nonius AXS Inc., Madison, Wisconsin, USA.
First citationBruker–Nonius (2009). APEX2 (Version 2009-9) and SAINT (Version 7.60A). Bruker–Nonius AXS Inc., Madison, Wisconsin, USA.
First citationCason, C. J. (2003). POV-Ray. Version 3.6.2. Persistence of Vision Raytracer Pty. Ltd, Victoria, Australia.
First citationCremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354–1358.  CrossRef CAS Web of Science
First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals
First citationHooft, R. W. W., Straver, L. H. & Spek, A. L. (2008). J. Appl. Cryst. 41, 96–103.  Web of Science CrossRef CAS IUCr Journals
First citationHu, X., Carmichael, I. & Serianni, A. S. (2010). J. Org. Chem. 75, 4899–4910.  Web of Science CrossRef CAS PubMed
First citationHu, X., Zhang, W., Carmichael, I. & Serianni, A. S. (2010). J. Am. Chem. Soc. 132, 4641–4652.  Web of Science CrossRef CAS PubMed
First citationJeffrey, G. A. & Takagi, S. (1977). Acta Cryst. B33, 738–742.  CSD CrossRef CAS IUCr Journals Web of Science
First citationMo, F. (1979). Acta Chem. Scand. Ser. A, 33, 207–218.  CrossRef
First citationMo, F. & Jensen, L. H. (1975). Acta Cryst. B31, 2867–2873.  CSD CrossRef CAS IUCr Journals Web of Science
First citationMo, F. & Jensen, L. H. (1978). Acta Cryst. B34, 1562–1569.  CSD CrossRef CAS IUCr Journals Web of Science
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationSweet, L., Zhang, W., Torres-Fewell, H., Serianni, A. S., Boggess, W. & Schorey, J. (2008). J. Biol. Chem. 283, 33221–33231.  Web of Science CrossRef PubMed CAS
First citationThibaudeau, C., Stenutz, R., Hertz, B., Klepach, T., Zhao, S., Wu, Q., Carmichael, I. & Serianni, A. S. (2004). J. Am. Chem. Soc. 126, 15668–15685.  Web of Science CrossRef PubMed CAS
First citationWestrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.  Web of Science CrossRef CAS IUCr Journals
First citationZhu, Y., Pan, Q., Thibaudeau, C., Zhao, S., Carmichael, I. & Serianni, A. S. (2006). J. Org. Chem. 71, 466–479.  Web of Science CrossRef PubMed CAS

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