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ISSN: 2056-9890
Volume 71| Part 10| October 2015| Pages 1212-1215

Crystal structure of 3-C-(N-benzyl­­oxy­carbon­yl)amino­methyl-3-de­­oxy-1,2:5,6-di-O-iso­propyl­­idene-α-D-allo­furan­ose

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aInstitute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry, Riga Technical University, P. Valdena 3/7, Riga, LV-1048, Latvia, and bLatvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
*Correspondence e-mail: d_stepanovs@osi.lv, maris_turks@ktf.rtu.lv

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 10 September 2015; accepted 19 September 2015; online 26 September 2015)

The title compound, C21H29NO7 (1) [systematic name: benzyl ({(3aR,5S,6R,6aR)-5-[(R)-2,2-dimethyl-1,3-dioxolan-4-yl]-2,2-di­methyl­tetrahydro­furo[2,3-d][1,3]dioxol-6-yl}meth­yl)carbamate], consists of a substituted 2,2-di­methyl­tetra­hydro­furo[2,3-d][1,3]dioxolane skeleton. The furan­ose ring adopts an envelope conformation close to C3-exo, where the C atom substituted by the benzyl carbamate group is the flap. The fused dioxolane ring also adopts an envelope conformation, as does the terminal dioxolane ring, with in each case an O atom as the flap. In the crystal, mol­ecules are linked by N—H⋯O and C–H⋯O hydrogen bonds, forming chains propagating along the b-axis direction.

1. Chemical context

The title compound, 3-C-(N-benzyl­oxycarbon­yl)amino­methyl-3-de­oxy-1,2:5,6-di-O-iso­propyl­idene-α-D-allo­furan­ose (1), was obtained as an inter­mediate in the syntheses of carbohydrate-based non-natural amino acids, so called sugar amino acids (Rjabovs et al., 2015[Rjabovs, V., Ostrovskis, P., Posevins, D., Kiselovs, G., Kumpiņš, V., Mishnev, A. & Turks, M. (2015). Eur. J. Org. Chem. pp. 5572-5584.]), by hydrogenation and carbamate protection of either nitro (Lugiņina et al., 2013[Lugiņina, J., Rjabovs, V., Belyakov, S. & Turks, M. (2013). Tetrahedron Lett. 54, 5328-5331.]) or azido (Filichev & Pedersen, 2001[Filichev, V. V. & Pedersen, E. B. (2001). Tetrahedron, 57, 9163-9168.]; Rjabova et al., 2012[Rjabova, J., Rjabovs, V., Moreno Vargas, A. J., Clavijo, E. M. & Turks, M. (2012). Cent. Eur. J. Chem. 10, 386-394.]) precursors (Fig. 1[link]).

[Scheme 1]
[Figure 1]
Figure 1
Synthesis of the title compound.

The synthesis of sugar amino acids and their properties and applications have been reported on by Rjabovs et al. (2015[Rjabovs, V., Ostrovskis, P., Posevins, D., Kiselovs, G., Kumpiņš, V., Mishnev, A. & Turks, M. (2015). Eur. J. Org. Chem. pp. 5572-5584.]), and reviewed by Rjabovs & Turks (2013[Rjabovs, V. & Turks, M. (2013). Tetrahedron, 69, 10693-10710.]) and Risseeuw et al. (2013[Risseeuw, M., Overhand, M., Fleet, G. W. & Simone, M. I. (2013). Amino Acids, 45, 613-689.]). The title compound can be used as a precursor for the syntheses of imino sugars and 10-aza-C-nucleosides (Filichev & Pedersen, 2001[Filichev, V. V. & Pedersen, E. B. (2001). Tetrahedron, 57, 9163-9168.]). The syntheses and biological properties of imino sugars have been reviewed by López et al. (2012[López, O., Merino-Montiel, P., Martos, S. & González-Benjumea, A. (2012). Carbohydrate Chemistry, Vol. 38, Chemical and Biological Approaches, edited by A. P. Rauter & T. K. Lindhorst, pp. 215-262. Cambridge: The Royal Society of Chemistry.]), while the syntheses and biological properties of aza-nucleosides have been reported on by Romeo et al. (2010[Romeo, G., Chiacchio, U., Corsaro, A. & Merino, P. (2010). Chem. Rev. 110, 3337-3370.]) and Merino (2006[Merino, P. (2006). Curr. Med. Chem. 13, 539-545.]).

2. Structural commentary

The title compound, Fig. 2[link], consists of a tetra­hydro­furan core fused with a dioxolane ring and substituted with dioxolane and (N-benzyl­oxycarbon­yl)amino­methyl moieties. The furan­ose ring adopts a conformation close to C3-exo. On the other hand, the furan­ose ring may be viewed as an envelope, where atom C3 deviates from the mean plane through atoms O1/C1/C2/C4 by 0.567 (2) Å. The fused dioxolane ring also adopts an envelope conformation, where O14 deviates from the mean plane through the four near planar atoms (O12/C1/C2/C13) by 0.422 (2) Å. The dihedral angle between the planar fragments of these rings is 67.1 (1)°. The five-membered ring of the 2,2-dimethyl-1,3-dioxolan-4-yl group also adopts an envelope conformation, with atom O7 deviating from the mean plane through the four planar atoms (O9/C5/C6/C8) by 0.519 (1) Å.

[Figure 2]
Figure 2
The mol­ecular structure of compound (1), with atom labelling. Displacement ellipsoids are drawn at the 50% probability level.

3. Supra­molecular features

In the crystal, mol­ecules are linked by N—H⋯O and C–H⋯O hydrogen bonds, forming chains propagating along the b-axis direction (Fig. 3[link] and Table 1[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N4′—H4′⋯O6′i 0.80 (3) 2.51 (3) 3.295 (3) 167 (2)
C6—H6B⋯O9ii 0.97 2.32 3.184 (3) 141
Symmetry codes: (i) x, y+1, z; (ii) x, y-1, z.
[Figure 3]
Figure 3
The crystal packing of compound (1), viewed along the a axis. Hydrogen bonds are shown as dashed lines (see Table 1[link] for details). For clarity only H atoms involved in these inter­actions have been included.

4. Database survey

A search of the Cambridge Structural Database (Version 5.36; Groom & Allen, 2014[Groom, C. R. & Allen, F. H. (2014). Angew. Chem. Int. Ed. 53, 662-671.]) for substituted 3a,5,6,6a-tetra­hydro­furo[2,3-d][1,3]dioxoles gave 485 hits (excluding metal-org­anics). However, only two structures are 3a,5,6,6a-tetra­hydrofuro[2,3-d][1,3]dioxol-6-yl­methyl­carbamic acid derivatives, viz. (3R)-3′-ethyl-1,2:5,6-di-O-iso­propyl­idene-spiro­(3-de­oxy-a-D-allo­furan­ose-3,5′-oxazolidin)-2′-one (CIDVES; Turks et al., 2013[Turks, M., Rodins, V., Rolava, E., Ostrovskis, P. & Belyakov, S. (2013). Carbohydr. Res. 375, 5-15.]), and (3R)-3′-phenyl­acetyl-1,2:5,6-di-O-iso­propylidene­spiro­(3-de­oxy-a-D-allo­furan­ose-3,5′-oxazolidin)-2′-one (YIMBED; Turks et al., 2013[Turks, M., Rodins, V., Rolava, E., Ostrovskis, P. & Belyakov, S. (2013). Carbohydr. Res. 375, 5-15.]).

5. Synthesis and crystallization

The two methods for the synthesis of compound (1) are illus­trated in Fig. 1[link].

From compound (2): A mixture of nitro­methyl compound (2) (5.00 g, 16.5 mmol, 1 equiv.) and 10% Pd/C (1.00 g) in MeOH (200 ml) was hydrogenated under 40 atm pressure at 313 K overnight (TLC control). The resulting reaction mixture was filtered through celite and the filtrate was evaporated under reduced pressure. The residue was dissolved in THF (60 ml) and a solution of K2CO3 (2.50 g, 18.1 mmol, 1.1 equiv.) in water (35 ml) was added. The resulting mixture was cooled to 273 K and N-(benzyl­oxycarbon­yloxy)succinimide (4.50 g, 18.1 mmol, 1.1 equiv) was added portion-wise. The reaction mixture was stirred at 273 K for 4 h (TLC control). Solid K2CO3 (1 g) was added and the formed layers were separated. The organic phase was washed with saturated aqueous solution of NaHSO4 (50 ml) while the aqueous phase was extracted with a mixture of hexa­nes and CH2Cl2 (3 × 100 ml, 8:2 v/v). The combined organic phase was washed with brine (2 × 100 ml), dried over Na2SO4, filtered and evaporated under reduced pressure. Crude product (1) was obtained as a yellow oil (6.60 g, 98% crude) and used further without additional purification.

From compound (3): Through a mixture of azide (3) (14.86 g, 49.7 mmol, 1.0 equiv) and 10% Pd/C (1.45 g) in MeOH (150 ml) hydrogen flow was passed at ambient temperature and pressure for 1 h (TLC control). The reaction mixture was filtered through a celite pad and the filtrate was evaporated under reduced pressure. The residue was dissolved in anhydrous CH2Cl2 (200 ml) and tri­ethyl­amine (8.5 ml, 61.0 mmol, 1.0 equiv) was added. The resulting solution was cooled to 273 K and benzyl chloro­formate (7.0 ml, 60.5 mmol, 1.2 equiv) was added portion-wise. The reaction mixture was stirred under an argon atmosphere at ambient temperature overnight. The solvent was evaporated under reduced pressure and the residue was dissolved in EtOAc (100 ml). The resulting solution was washed with a saturated aqueous solution of NaHCO3 (3 × 20 ml) and brine (3 × 30 ml), dried over Na2SO4, filtered and evaporated. Column chromatography (hexa­nes/EtOAc 4:1 to 2:1 v/v) yielded product (1) (15.22 g, 75%) as a colourless oil that solidifies at low temperatures. Rf = 0.6 (hexa­nes/EtOAc 1:1). 1H NMR (CDCl3, 300 MHz): 1.30, 1.34, 1.41, 1.50 (4s, 12H, 2 (H3C)2C), 2.13 [dq, J = 9.6, 4.9 Hz, 1H, H-C(3)], 3.52 [m, 2H, H2C(3′)], 3.77 [m, 1H, H-C(5)], 3.95 [m, 2H, H2C(6)], 4.11 [m, 1H, H-C(4]), 4.68 [t, J = 4.3 Hz, 1H, H-C(2)], 5.11 (s, AB syst., 2H, H2C-Ph), 5.67 (t, J = 6.0 Hz, 1H, HN), 5.75 [d, J = 3.8 Hz, 1H, H-C(1)], 7.35 (m, 5H, Ph). 13C NMR (CDCl3, 75 MHz): 25.2, 26.3, 26.5, 26.7, 38.0, 48.6, 66.5, 67.8, 77.3, 81.4, 82.0, 104.8, 109.8, 112.2, 128.0, 128.0, 128.5, 136.8, 156.4. HRMS: Calculated for C21H29NO7Na, [M + Na]+ 430.1842. Found: 430.1795.

X-ray quality single crystals were obtained by spontaneous crystallization of the title compound from the neat oily material at 277 K.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. The H atom on the amino group was located in a difference Fourier map and freely refined. The C-bound H atoms were positioned geometrically and refined as riding on their parent atoms: C—H = 0.93–0.98Å with Uiso(H) = 1.5Ueq(C) for methyl H atoms and 1.2Ueq(C) for other H atoms. Reflections (1,0,0) and (0,0,2), whose intensities were affected by the beam-stop, were removed from the final refinement.

Table 2
Experimental details

Crystal data
Chemical formula C21H29NO7
Mr 407.45
Crystal system, space group Monoclinic, P21
Temperature (K) 173
a, b, c (Å) 9.3235 (3), 5.4118 (1), 20.4381 (7)
β (°) 96.748 (1)
V3) 1024.10 (5)
Z 2
Radiation type Mo Kα
μ (mm−1) 0.10
Crystal size (mm) 0.32 × 0.31 × 0.20
 
Data collection
Diffractometer Nonius KappaCCD
No. of measured, independent and observed [I > 2σ(I)] reflections 5535, 3279, 2597
Rint 0.034
(sin θ/λ)max−1) 0.705
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.045, 0.100, 1.03
No. of reflections 3279
No. of parameters 270
No. of restraints 1
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.23, −0.21
Computer programs: KappaCCD Server Software (Nonius, 1997[Nonius (1997). KappaCCD Server Software. Nonius BV, Delft, The Netherlands.]), HKL DENZO and SCALEPACK (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]), SIR2011 (Burla et al., 2012[Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Mallamo, M., Mazzone, A., Polidori, G. & Spagna, R. (2012). J. Appl. Cryst. 45, 357-361.]), Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]), SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Chemical context top

\ The title compound, 3-C-(N-benzyl­oxycarbonyl)­amino­methyl-3-de­oxy-1,2:5,6-di-\ O-iso­propyl­idene-α-D-allo­furan­ose (1), was obtained as an inter­mediate in the syntheses of carbohydrate-based non-natural amino acids, so called sugar amino acids (Rjabovs et al., 2015), by hydrogenation and carbamate protection of either nitro (Lugiņina et al., 2013) or azido (Filichev & Pedersen, 2001; Rjabova et al., 2012) precursors (Fig. 1).

The synthesis of sugar amino acids and their properties and applications have been reported on by Rjabovs et al. (2015), and reviewed by Rjabovs & Turks (2013) and Risseeuw et al. (2013). They can be used as precursors for the syntheses of imino sugars and 10-aza-C-nucleosides (Filichev & Pedersen, 2001). The syntheses and biological properties of imino sugars have been reviewed by López et al. (2012), while the syntheses and biological properties of aza-nucleosides have been reported on by Romeo et al. (2010) and Merino (2006).

Structural commentary top

The title compound, Fig. 2, consists of a tetra­hydro­furan core fused with a dioxolane ring and substituted with dioxolane and (N-benzyl­oxycarbonyl)­amino­methyl moieties. The furan­ose ring adopts a conformation close to C3-exo. On the other hand, the furan­ose ring may be viewed as an envelope, where atom C3 deviates from the mean plane through atoms O1/C1/C2/C4 by 0.567 (2) Å. The fused dioxolane ring also adopts an envelope conformation, where O14 deviates from the mean plane through the four planar atoms (O12/C1/C2/C13) by 0.422 (2) Å. The dihedral angle between the planar fragments of these rings is 67.1 (1)°. The five-membered ring of the 2,2-di­methyl-1,3-dioxolan-4-yl group also adopts an envelope conformation, with atom O7 deviating from the mean plane through the four planar atoms (O9/C5/C6/C8) by 0.519 (1) Å.

Supra­molecular features top

In the crystal, molecules are linked by N—H···O and C–H···O hydrogen bonds, forming chains propagating along the b-axis direction (Fig. 3 and Table 1).

Database survey top

\ A search of the Cambridge Structural Database (Version 5.36; Groom & Allen, 2014) for substituted 3a,5,6,6a-tetra­hydro­furo[2,3-d][1,3]dioxoles gave 485 hits (excluding metalorganics). However, only two structures are 3a,5,6,6a-tetra­hydro­furo[2,3-d][1,3]dioxol-6-yl­methyl­carbamic acid derivatives, viz. (3R)-3'-ethyl-1,2:5,6-di-O-iso­propyl­idene-spiro­(3-de­oxy-\ a-D-allo­furan­ose-3,5'-oxazolidin)-2'-one (CIDVES; Turks et al., 2013), and (3R)-3'-phenyl­acetyl-1,2:5,6-di-O-iso­propyl­idene­spiro­(3-de­oxy-\ a-D-allo­furan­ose-3,5'-oxazolidin)-2'-one (YIMBED; Turks et al., 2013).

Synthesis and crystallization top

The two methods for the synthesis of compound (1) are illustrated in Fig. 1.

From compound (2): A mixture of nitro­methyl compound (2) (5.00 g, 16.5 mmol, 1 equiv.) and 10% Pd/C (1.00 g) in MeOH (200 ml) was hydrogenated under 40 atm pressure at 313 K overnight (TLC control). The resulting reaction mixture was filtered through celite and the filtrate was evaporated under reduced pressure. The residue was dissolved in THF (60 ml) and a solution of K2CO3 (2.50 g, 18.1 mmol, 1.1 equiv.) in water (35 ml) was added. The resulting mixture was cooled to 273 K and N-(benzyl­oxycarbonyl­oxy)succinimide (4.50 g, 18.1 mmol, 1.1 equiv) was added portion-wise. The reaction mixture was stirred at 273 K for 4 h (TLC control). Solid K2CO3 (1 g) was added and the formed layers were separated. The organic phase was washed with saturated aqueous solution of NaHSO4 (50 ml) while the aqueous phase was extracted with a mixture of hexanes and CH2Cl2 (3 × 100 ml, 8:2 v/v). The combined organic phase was washed with brine (2 × 100 ml), dried over Na2SO4, filtered and evaporated under reduced pressure. Crude product (1) was obtained as a yellow oil (6.60 g, 98% crude) and used further without additional purification.

From compound (3): A mixture of azide (3) (14.86 g, 49.7 mmol, 1.0 equiv) and 10% Pd/C (1.45 g) in MeOH (150 ml) hydrogen flow was passed at ambient temperature and pressure for 1 h (TLC control). The reaction mixture was filtered through a celite pad and the filtrate was evaporated under reduced pressure. The residue was dissolved in anhydrous CH2Cl2 (200 ml) and tri­ethyl­amine (8.5 ml, 61.0 mmol, 1.0 equiv) was added. The resulting solution was cooled to 273 K and benzyl chloro­formate (7.0 ml, 60.5 mmol, 1.2 equiv) was added portion-wise. The reaction mixture was stirred under an argon atmosphere at ambient temperature overnight. The solvent was evaporated under reduced pressure and the residue was dissolved in EtOAc (100 ml). The resulting solution was washed with a saturated aqueous solution of NaHCO3 (3 × 20 ml and brine (3 × 30 ml), dried over Na2SO4, filtered and evaporated. Column chromatography (hexanes/EtOAc 4:1 to 2:1 v/v) yielded product (1) (15.22 g, 75%) as a colourless oil that solidifies at low temperatures. Rf = 0.6 (hexanes/EtOAc 1:1). 1H NMR (CDCl3, 300 MHz): 1.30, 1.34, 1.41, 1.50 (4s, 12H, 2 (H3C)2C), 2.13 [dq, J = 9.6, 4.9 Hz, 1H, H—C(3)], 3.52 [m, 2H, H2C(3')], 3.77 [m, 1H, H—C(5)], 3.95 [m, 2H, H2C(6)], 4.11 [m, 1H, H—C(4]), 4.68 [t, J = 4.3 Hz, 1H, H—C(2)], 5.11 (s, AB syst., 2H, H2C—Ph), 5.67 (t, J = 6.0 Hz, 1H, HN), 5.75 [d, J = 3.8 Hz, 1H, H—C(1)], 7.35 (m, 5H, Ph). 13C NMR (CDCl3, 75 MHz): 25.2, 26.3, 26.5, 26.7, 38.0, 48.6, 66.5, 67.8, 77.3, 81.4, 82.0, 104.8, 109.8, 112.2, 128.0, 128.0, 128.5, 136.8, 156.4. HRMS: Calculated for C21H29NO7Na, [M + Na]+ 430.1842. Found: 430.1795.

X-ray quality single crystals were obtained by spontaneous crystallization of the title compound from the neat oily material at 277 K.

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 2. The H atom on the amino group was located in a difference Fourier map and freely refined. The C-bound H atoms were positioned geometrically and refined as riding on their parent atoms: C—H = 0.93–0.98Å with Uiso(H) = 1.5Ueq(C) for methyl H atoms and 1.2Ueq(C) for other H atoms. Reflections (1,0,0) and (0,0,2), whose intensities were affected by the beam-stop, were removed from the final refinement.

Related literature top

For related literature, see: Filichev & Pedersen (2001); Groom & Allen (2014); López et al. (2012); Lugiņina et al. (2013); Merino (2006); Risseeuw et al. (2013); Rjabova et al. (2012); Rjabovs & Turks (2013); Rjabovs et al. (2015); Romeo et al. (2010); Turks et al. (2013).

Computing details top

Data collection: KappaCCD Server Software (Nonius, 1997); cell refinement: HKL SCALEPACK (Otwinowski & Minor, 1997); data reduction: HKL DENZO and SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR2011 (Burla et al., 2012); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. Synthesis of the title compound.
[Figure 2] Fig. 2. The molecular structure of compound (1), with atom labelling. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 3] Fig. 3. The crystal packing of compound (1), viewed along the a axis. Hydrogen bonds are shown as dashed lines (see Table 1 for details). For clarity only H atoms involved in these interactions have been included.
3-C-(N-Benzyloxycarbonyl)aminomethyl-3-deoxy-1,2:5,6-di-\ O-isopropylidene-α-D-allofuranose top
Crystal data top
C21H29NO7F(000) = 436
Mr = 407.45Dx = 1.321 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 11906 reflections
a = 9.3235 (3) Åθ = 1.0–30.0°
b = 5.4118 (1) ŵ = 0.10 mm1
c = 20.4381 (7) ÅT = 173 K
β = 96.748 (1)°Block, colourless
V = 1024.10 (5) Å30.32 × 0.31 × 0.20 mm
Z = 2
Data collection top
Nonius KappaCCD
diffractometer
2597 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.034
Graphite monochromatorθmax = 30.1°, θmin = 2.3°
CCD scansh = 1313
5535 measured reflectionsk = 76
3279 independent reflectionsl = 2828
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)] = 0.045Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.100H atoms treated by a mixture of independent and constrained refinement
S = 1.03 w = 1/[σ2(Fo2) + (0.044P)2 + 0.1203P]
where P = (Fo2 + 2Fc2)/3
3279 reflections(Δ/σ)max < 0.001
270 parametersΔρmax = 0.23 e Å3
1 restraintΔρmin = 0.21 e Å3
Crystal data top
C21H29NO7V = 1024.10 (5) Å3
Mr = 407.45Z = 2
Monoclinic, P21Mo Kα radiation
a = 9.3235 (3) ŵ = 0.10 mm1
b = 5.4118 (1) ÅT = 173 K
c = 20.4381 (7) Å0.32 × 0.31 × 0.20 mm
β = 96.748 (1)°
Data collection top
Nonius KappaCCD
diffractometer
2597 reflections with I > 2σ(I)
5535 measured reflectionsRint = 0.034
3279 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0451 restraint
wR(F2) = 0.100H atoms treated by a mixture of independent and constrained refinement
S = 1.03Δρmax = 0.23 e Å3
3279 reflectionsΔρmin = 0.21 e Å3
270 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. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.34514 (16)0.3163 (3)0.37758 (7)0.0315 (4)
C10.2837 (2)0.3609 (4)0.31216 (10)0.0257 (4)
H10.29220.53560.30060.031*
C20.3645 (2)0.1973 (4)0.26790 (10)0.0236 (4)
H20.38400.28070.22730.028*
C30.5014 (2)0.1255 (4)0.31153 (9)0.0216 (4)
H30.56950.26350.31180.026*
C40.4468 (2)0.1149 (4)0.37946 (9)0.0219 (4)
H40.39650.04190.38420.026*
C50.5571 (2)0.1572 (4)0.43934 (10)0.0221 (4)
H50.50630.18030.47820.027*
C60.6694 (2)0.0473 (4)0.45328 (10)0.0239 (4)
H6A0.68980.07770.50020.029*
H6B0.63660.19970.43140.029*
O70.79329 (15)0.0472 (3)0.42712 (7)0.0251 (3)
C80.7920 (2)0.3060 (4)0.43977 (10)0.0234 (4)
O90.64107 (15)0.3721 (3)0.43018 (7)0.0251 (3)
C100.8696 (3)0.4342 (4)0.38914 (12)0.0326 (5)
H10A0.82170.39970.34590.049*
H10B0.96740.37580.39230.049*
H10C0.86950.60920.39680.049*
C110.8532 (2)0.3653 (4)0.51018 (11)0.0313 (5)
H11A0.95490.33080.51610.047*
H11B0.80570.26570.54000.047*
H11C0.83760.53690.51900.047*
O120.13924 (16)0.2825 (3)0.30147 (9)0.0356 (4)
C130.1257 (2)0.0752 (4)0.25826 (11)0.0277 (5)
O140.27047 (15)0.0114 (3)0.25586 (7)0.0282 (3)
C150.0589 (3)0.1589 (6)0.19055 (13)0.0490 (7)
H15A0.11600.28970.17520.074*
H15B0.03750.21760.19320.074*
H15C0.05580.02250.16040.074*
C160.0396 (3)0.1209 (5)0.28758 (14)0.0411 (6)
H16A0.05640.06120.29040.062*
H16B0.08490.16170.33090.062*
H16C0.03520.26560.26020.062*
C3'0.5763 (2)0.1049 (4)0.29004 (10)0.0240 (4)
H3'10.65690.14700.32260.029*
H3'20.50930.24270.28630.029*
N4'0.6281 (2)0.0585 (4)0.22661 (9)0.0279 (4)
C5'0.6706 (2)0.2436 (4)0.18935 (10)0.0279 (5)
O6'0.66529 (19)0.4616 (3)0.20170 (8)0.0363 (4)
O7'0.71820 (19)0.1464 (3)0.13471 (8)0.0403 (4)
C8'0.7650 (3)0.3172 (5)0.08682 (11)0.0418 (6)
H8'10.70870.46820.08560.050*
H8'20.86620.35840.09790.050*
C1''0.7418 (3)0.1870 (5)0.02154 (11)0.0355 (5)
C2''0.8230 (3)0.0185 (6)0.00934 (12)0.0444 (6)
H2''0.89680.07080.04090.053*
C3''0.7954 (3)0.1460 (6)0.04903 (14)0.0525 (7)
H3''0.85020.28450.05650.063*
C4''0.6868 (3)0.0694 (6)0.09655 (13)0.0520 (8)
H4''0.66790.15630.13590.062*
C5''0.6074 (3)0.1351 (7)0.08519 (13)0.0523 (8)
H5''0.53490.18820.11730.063*
C6''0.6334 (3)0.2644 (6)0.02641 (13)0.0454 (7)
H6''0.57830.40280.01910.055*
H4'0.647 (3)0.080 (5)0.2161 (12)0.028 (7)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0247 (8)0.0388 (9)0.0308 (8)0.0114 (7)0.0028 (6)0.0044 (7)
C10.0195 (10)0.0230 (9)0.0345 (11)0.0010 (8)0.0020 (8)0.0002 (9)
C20.0211 (10)0.0238 (10)0.0262 (10)0.0003 (8)0.0038 (8)0.0025 (8)
C30.0170 (9)0.0232 (9)0.0249 (10)0.0002 (8)0.0032 (7)0.0002 (8)
C40.0189 (9)0.0221 (10)0.0255 (10)0.0005 (7)0.0065 (8)0.0007 (8)
C50.0225 (10)0.0197 (9)0.0250 (10)0.0009 (9)0.0062 (8)0.0007 (8)
C60.0250 (11)0.0190 (9)0.0272 (10)0.0019 (8)0.0016 (8)0.0025 (8)
O70.0232 (7)0.0175 (6)0.0356 (8)0.0016 (6)0.0072 (6)0.0001 (6)
C80.0191 (10)0.0202 (9)0.0309 (11)0.0007 (8)0.0035 (8)0.0022 (8)
O90.0209 (7)0.0162 (6)0.0373 (8)0.0016 (6)0.0002 (6)0.0009 (6)
C100.0311 (12)0.0280 (11)0.0403 (13)0.0024 (10)0.0107 (9)0.0010 (10)
C110.0267 (11)0.0284 (10)0.0373 (12)0.0007 (9)0.0031 (9)0.0035 (10)
O120.0190 (7)0.0322 (9)0.0553 (10)0.0009 (7)0.0031 (7)0.0107 (8)
C130.0202 (10)0.0256 (10)0.0361 (12)0.0009 (8)0.0015 (8)0.0003 (9)
O140.0206 (7)0.0272 (8)0.0361 (8)0.0014 (6)0.0002 (6)0.0051 (6)
C150.0341 (13)0.0673 (18)0.0430 (15)0.0070 (15)0.0067 (11)0.0092 (14)
C160.0270 (12)0.0316 (12)0.0651 (17)0.0012 (10)0.0069 (11)0.0080 (12)
C3'0.0235 (10)0.0266 (10)0.0226 (10)0.0031 (8)0.0053 (8)0.0002 (8)
N4'0.0324 (10)0.0264 (9)0.0262 (9)0.0010 (8)0.0086 (7)0.0008 (8)
C5'0.0249 (11)0.0371 (12)0.0215 (10)0.0018 (9)0.0015 (8)0.0028 (9)
O6'0.0486 (11)0.0295 (8)0.0319 (9)0.0045 (8)0.0087 (7)0.0024 (7)
O7'0.0574 (11)0.0382 (9)0.0287 (8)0.0009 (9)0.0195 (7)0.0046 (7)
C8'0.0536 (15)0.0439 (14)0.0300 (12)0.0132 (13)0.0142 (11)0.0045 (11)
C1''0.0417 (13)0.0390 (13)0.0274 (11)0.0092 (11)0.0106 (9)0.0045 (10)
C2''0.0479 (15)0.0494 (15)0.0354 (14)0.0047 (13)0.0027 (11)0.0031 (12)
C3''0.0637 (18)0.0468 (15)0.0491 (17)0.0009 (16)0.0156 (14)0.0045 (14)
C4''0.0669 (19)0.0580 (19)0.0323 (14)0.0206 (16)0.0110 (13)0.0033 (13)
C5''0.0498 (16)0.075 (2)0.0310 (13)0.0108 (17)0.0005 (11)0.0100 (14)
C6''0.0480 (15)0.0546 (16)0.0352 (13)0.0027 (13)0.0111 (11)0.0086 (12)
Geometric parameters (Å, º) top
O1—C11.412 (2)C13—C161.498 (3)
O1—C41.442 (2)C13—C151.519 (3)
C1—O121.404 (2)C15—H15A0.9600
C1—C21.526 (3)C15—H15B0.9600
C1—H10.9800C15—H15C0.9600
C2—O141.433 (2)C16—H16A0.9600
C2—C31.519 (3)C16—H16B0.9600
C2—H20.9800C16—H16C0.9600
C3—C3'1.519 (3)C3'—N4'1.457 (3)
C3—C41.535 (3)C3'—H3'10.9700
C3—H30.9800C3'—H3'20.9700
C4—C51.520 (3)N4'—C5'1.346 (3)
C4—H40.9800N4'—H4'0.80 (3)
C5—O91.427 (2)C5'—O6'1.209 (3)
C5—C61.527 (3)C5'—O7'1.355 (3)
C5—H50.9800O7'—C8'1.450 (3)
C6—O71.424 (3)C8'—C1''1.502 (3)
C6—H6A0.9700C8'—H8'10.9700
C6—H6B0.9700C8'—H8'20.9700
O7—C81.424 (2)C1''—C2''1.384 (4)
C8—O91.443 (2)C1''—C6''1.387 (4)
C8—C101.501 (3)C2''—C3''1.376 (4)
C8—C111.519 (3)C2''—H2''0.9300
C10—H10A0.9600C3''—C4''1.382 (4)
C10—H10B0.9600C3''—H3''0.9300
C10—H10C0.9600C4''—C5''1.367 (5)
C11—H11A0.9600C4''—H4''0.9300
C11—H11B0.9600C5''—C6''1.387 (4)
C11—H11C0.9600C5''—H5''0.9300
O12—C131.424 (3)C6''—H6''0.9300
C13—O141.435 (3)
C1—O1—C4110.30 (15)C1—O12—C13110.36 (16)
O12—C1—O1111.76 (17)O12—C13—O14105.28 (15)
O12—C1—C2105.29 (17)O12—C13—C16108.82 (19)
O1—C1—C2106.75 (16)O14—C13—C16109.43 (18)
O12—C1—H1110.9O12—C13—C15109.1 (2)
O1—C1—H1110.9O14—C13—C15110.69 (19)
C2—C1—H1110.9C16—C13—C15113.2 (2)
O14—C2—C3110.74 (16)C2—O14—C13107.18 (15)
O14—C2—C1102.96 (16)C13—C15—H15A109.5
C3—C2—C1103.87 (16)C13—C15—H15B109.5
O14—C2—H2112.8H15A—C15—H15B109.5
C3—C2—H2112.8C13—C15—H15C109.5
C1—C2—H2112.8H15A—C15—H15C109.5
C2—C3—C3'115.04 (17)H15B—C15—H15C109.5
C2—C3—C4101.29 (16)C13—C16—H16A109.5
C3'—C3—C4116.30 (17)C13—C16—H16B109.5
C2—C3—H3107.9H16A—C16—H16B109.5
C3'—C3—H3107.9C13—C16—H16C109.5
C4—C3—H3107.9H16A—C16—H16C109.5
O1—C4—C5106.73 (15)H16B—C16—H16C109.5
O1—C4—C3103.54 (15)N4'—C3'—C3109.09 (17)
C5—C4—C3117.26 (16)N4'—C3'—H3'1109.9
O1—C4—H4109.7C3—C3'—H3'1109.9
C5—C4—H4109.7N4'—C3'—H3'2109.9
C3—C4—H4109.7C3—C3'—H3'2109.9
O9—C5—C4110.29 (16)H3'1—C3'—H3'2108.3
O9—C5—C6103.92 (14)C5'—N4'—C3'121.7 (2)
C4—C5—C6115.15 (17)C5'—N4'—H4'116.9 (18)
O9—C5—H5109.1C3'—N4'—H4'120.3 (18)
C4—C5—H5109.1O6'—C5'—N4'125.9 (2)
C6—C5—H5109.1O6'—C5'—O7'125.2 (2)
O7—C6—C5103.79 (16)N4'—C5'—O7'108.9 (2)
O7—C6—H6A111.0C5'—O7'—C8'117.5 (2)
C5—C6—H6A111.0O7'—C8'—C1''106.1 (2)
O7—C6—H6B111.0O7'—C8'—H8'1110.5
C5—C6—H6B111.0C1''—C8'—H8'1110.5
H6A—C6—H6B109.0O7'—C8'—H8'2110.5
C6—O7—C8105.08 (16)C1''—C8'—H8'2110.5
O7—C8—O9104.38 (16)H8'1—C8'—H8'2108.7
O7—C8—C10108.31 (18)C2''—C1''—C6''118.9 (2)
O9—C8—C10109.48 (17)C2''—C1''—C8'120.8 (2)
O7—C8—C11111.69 (17)C6''—C1''—C8'120.2 (3)
O9—C8—C11109.16 (17)C3''—C2''—C1''120.6 (3)
C10—C8—C11113.42 (18)C3''—C2''—H2''119.7
C5—O9—C8108.74 (14)C1''—C2''—H2''119.7
C8—C10—H10A109.5C2''—C3''—C4''120.4 (3)
C8—C10—H10B109.5C2''—C3''—H3''119.8
H10A—C10—H10B109.5C4''—C3''—H3''119.8
C8—C10—H10C109.5C5''—C4''—C3''119.4 (3)
H10A—C10—H10C109.5C5''—C4''—H4''120.3
H10B—C10—H10C109.5C3''—C4''—H4''120.3
C8—C11—H11A109.5C4''—C5''—C6''120.8 (3)
C8—C11—H11B109.5C4''—C5''—H5''119.6
H11A—C11—H11B109.5C6''—C5''—H5''119.6
C8—C11—H11C109.5C5''—C6''—C1''119.9 (3)
H11A—C11—H11C109.5C5''—C6''—H6''120.1
H11B—C11—H11C109.5C1''—C6''—H6''120.1
C4—O1—C1—O12107.54 (18)C11—C8—O9—C595.99 (19)
C4—O1—C1—C27.1 (2)O1—C1—O12—C13111.56 (19)
O12—C1—C2—O1420.6 (2)C2—C1—O12—C134.0 (2)
O1—C1—C2—O1498.33 (18)C1—O12—C13—O1414.4 (2)
O12—C1—C2—C3136.12 (17)C1—O12—C13—C16131.58 (19)
O1—C1—C2—C317.2 (2)C1—O12—C13—C15104.5 (2)
O14—C2—C3—C3'49.2 (2)C3—C2—O14—C13140.31 (17)
C1—C2—C3—C3'159.10 (16)C1—C2—O14—C1329.82 (19)
O14—C2—C3—C477.1 (2)O12—C13—O14—C228.1 (2)
C1—C2—C3—C432.8 (2)C16—C13—O14—C2144.9 (2)
C1—O1—C4—C5152.58 (16)C15—C13—O14—C289.6 (2)
C1—O1—C4—C328.2 (2)C2—C3—C3'—N4'65.0 (2)
C2—C3—C4—O137.23 (19)C4—C3—C3'—N4'176.82 (16)
C3'—C3—C4—O1162.69 (16)C3—C3'—N4'—C5'165.57 (19)
C2—C3—C4—C5154.43 (17)C3'—N4'—C5'—O6'3.5 (4)
C3'—C3—C4—C580.1 (2)C3'—N4'—C5'—O7'177.68 (18)
O1—C4—C5—O967.04 (19)O6'—C5'—O7'—C8'0.7 (3)
C3—C4—C5—O948.4 (2)N4'—C5'—O7'—C8'178.11 (19)
O1—C4—C5—C6175.77 (16)C5'—O7'—C8'—C1''153.0 (2)
C3—C4—C5—C668.8 (2)O7'—C8'—C1''—C2''67.3 (3)
O9—C5—C6—O720.8 (2)O7'—C8'—C1''—C6''109.6 (3)
C4—C5—C6—O799.97 (19)C6''—C1''—C2''—C3''0.9 (4)
C5—C6—O7—C835.75 (19)C8'—C1''—C2''—C3''176.1 (2)
C6—O7—C8—O937.11 (19)C1''—C2''—C3''—C4''0.5 (4)
C6—O7—C8—C10153.69 (17)C2''—C3''—C4''—C5''0.3 (4)
C6—O7—C8—C1180.7 (2)C3''—C4''—C5''—C6''0.7 (4)
C4—C5—O9—C8125.60 (16)C4''—C5''—C6''—C1''0.3 (4)
C6—C5—O9—C81.7 (2)C2''—C1''—C6''—C5''0.5 (4)
O7—C8—O9—C523.5 (2)C8'—C1''—C6''—C5''176.5 (2)
C10—C8—O9—C5139.31 (17)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4···O6i0.80 (3)2.51 (3)3.295 (3)167 (2)
C6—H6B···O9ii0.972.323.184 (3)141
Symmetry codes: (i) x, y+1, z; (ii) x, y1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4'—H4'···O6'i0.80 (3)2.51 (3)3.295 (3)167 (2)
C6—H6B···O9ii0.972.323.184 (3)141
Symmetry codes: (i) x, y+1, z; (ii) x, y1, z.

Experimental details

Crystal data
Chemical formulaC21H29NO7
Mr407.45
Crystal system, space groupMonoclinic, P21
Temperature (K)173
a, b, c (Å)9.3235 (3), 5.4118 (1), 20.4381 (7)
β (°) 96.748 (1)
V3)1024.10 (5)
Z2
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.32 × 0.31 × 0.20
Data collection
DiffractometerNonius KappaCCD
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
5535, 3279, 2597
Rint0.034
(sin θ/λ)max1)0.705
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.045, 0.100, 1.03
No. of reflections3279
No. of parameters270
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.23, 0.21

Computer programs: KappaCCD Server Software (Nonius, 1997), HKL SCALEPACK (Otwinowski & Minor, 1997), HKL DENZO and SCALEPACK (Otwinowski & Minor, 1997), SIR2011 (Burla et al., 2012), Mercury (Macrae et al., 2008), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

 

Acknowledgements

JSC `Olainfarm' is acknowledged for the donation of diacetone—glucose. JSC `Grindeks' is acknowledged for the donation of organic solvents.

References

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Volume 71| Part 10| October 2015| Pages 1212-1215
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