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ISSN: 2056-9890
Volume 72| Part 3| March 2016| Pages 314-317
doi:10.1107/S2056989016001845

Crystal structure of 3-de­­oxy-3-nitro­methyl-1,2;5,6-di-O-iso­propyl­­idene-α-D-allo­furan­ose

CROSSMARK_Color_square_no_text.svg
Jevgeņija Lugiņina,a Vitālijs Rjabovsa* and Dmitrijs Stepanovsb*

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, Str. Aizkraukles 21, Riga, LV 1006, Latvia
*Correspondence e-mail: vitalijs.rjabovs@rtu.lv, d_stepanovs@osi.lv

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 5 January 2016; accepted 31 January 2016; online 10 February 2016)

The title compound, C13H21NO7 {systematic name: (3aR,5S,6R,6aR)-5-[(R)-2,2-dimethyl-1,3-dioxolan-4-yl]-2,2-dimethyl-6-(nitro­meth­yl)tetra­hydro­furo[2,3-d][1,3]dioxole}, consists of a substituted 2,2-di­methyl­tetra­hydro­furo[2,3-d][1,3]dioxolane skeleton. The furan­ose ring A adopts a oT4 conformation. The fused dioxolane ring B and the substituent dioxolane ring C also have twisted conformations. There are no strong hydrogen bonds in the crystal structure: only weak C—H⋯O contacts are present, which link the mol­ecules to form a three-dimensional structure.

CCDC reference: 1451051

1. Chemical context

The title compound 1, has been used for the syntheses of isoxazoles (Lugiņina et al., 2013[Lugiņina, J., Rjabovs, V., Belyakov, S. & Turks, M. (2013). Tetrahedron Lett. 54, 5328-5331.]) and carbohydrate-based amines and amino acids (Rjabovs et al., 2015a[Rjabovs, V., Ostrovskis, P., Posevins, D., Kiselovs, G., Kumpiņš, V., Mishnev, A. & Turks, M. (2015a). Eur. J. Org. Chem. pp. 5572-5584.]). Carbohydrates with amino groups are valuable synthetic precursors and are easily converted to spiro­cyclic carbohydrate derivatives (Turks et al., 2013[Turks, M., Rodins, V., Rolava, E., Ostrovskis, P. & Belyakov, S. (2013). Carbohydr. Res. 375, 5-15.]), imino sugars (Filichev & Pedersen, 2001[Filichev, V. V. & Pedersen, E. B. (2001). Tetrahedron, 57, 9163-9168.]), nucleic acid mimetics (Rozners et al., 2003[Rozners, E., Katkevica, D., Bizdena, E. & Strömberg, R. (2003). J. Am. Chem. Soc. 125, 12125-12136.]), and azido sugars (Mackeviča et al., 2014[Mackeviča, J., Ostrovskis, P., Leffler, H., Nilsson, U. J., Rudovica, V., Viksna, A., Belyakov, S. & Turks, M. (2014). ARKIVOC, (iii), 90-112.]; 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.]). The latter are widely used for the syntheses of triazoles (Uzuleņa et al., 2015[Uzuleņa, J., Rjabovs, V., Moreno-Vargas, A. J. & Turks, M. (2015). Chem. Heterocycl. Compd, 51, 664-671.]; Grigorjeva et al., 2015[Grigorjeva, J., Uzuleņa, J., Rjabovs, V. & Turks, M. (2015). Chem. Heterocycl. Compd. 51, 883-890.]) and THF-amino acids (sugar amino acids) (Rjabovs & Turks, 2013[Rjabovs, V. & Turks, M. (2013). Tetrahedron, 69, 10693-10710.]).

[Scheme 1]

2. Structural commentary

The title compound 1, consists of a tetra­hydro­furan core (ring A) fused with a dioxolane ring (B) and substituted with a dioxolane (ring C) and a nitro­methyl group (Fig. 1[link]). The conformational analysis of the furan­ose ring (A) based on the inter­nal dihedral angles of the ring shows that its pseudo­rotational phase angle P = 70° (Altona & Sundaralingam, 1972[Altona, C. & Sundaralingam, M. (1972). J. Am. Chem. Soc. 94, 8205-8212.]; Taha et al., 2013[Taha, H. A., Richards, M. R. & Lowary, T. L. (2013). Chem. Rev. 113, 1851-1876.]). Thus, this ring adopts a conformation close to oT4, where O1 and C4 deviate by 0.214 (2) and −0.340 (3) Å, respectively, from the plane through atoms C1/C2/C3. Such a conformation of the furan­ose ring is rather unusual for 3-C-monosubstituted 3-de­oxy-1,2-O-iso­propyl­idene-α-D-allo­furan­oses. For example, previously reported structures (Rjabovs et al., 2014[Rjabovs, V., Mishnev, A., Kiselovs, G. & Turks, M. (2014). Acta Cryst. E70, o524-o525.], 2015a[Rjabovs, V., Ostrovskis, P., Posevins, D., Kiselovs, G., Kumpiņš, V., Mishnev, A. & Turks, M. (2015a). Eur. J. Org. Chem. pp. 5572-5584.],b[Rjabovs, V., Stepanovs, D. & Turks, M. (2015b). Acta Cryst. E71, 1212-1215.]) had conformations between 3E and 3T4. The fused dioxolane ring B also adopts a twisted conformation on bond C13—O12; these atoms deviate by −0.324 (4) and 0.224 (3) Å, respectively, from plane C1/C2/O14. The dihedral angle subtended by the mean planes of rings A and B is 63.7 (2)°. The five-membered ring of the 2,2-dimethyl-1,3-dioxolan-4-yl group, ring C, also adopts a twisted conformation, on bond C6—O7; these atoms deviate by 0.143 (4) and −0.381 (2) Å, respectively from plane C5/O9/C8.

[Figure 1]
Figure 1
The mol­ecular structure of the title compound 1, showing the atom labelling. Displacement ellipsoids are drawn at the 50% probability level.

3. Supra­molecular features

In the crystal, mol­ecules are linked via C—H⋯O hydrogen bonds, forming chains along [100]. The chains are linked via further C—H⋯O hydrogen bonds, forming a three-dimensional structure (Table 1[link] and Fig. 2[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C3′—H3′2⋯O5′i 0.97 2.53 3.355 (4) 143
C1—H1⋯O12ii 0.98 2.41 3.386 (5) 178
C15—H15A⋯O6′iii 0.96 2.48 3.433 (5) 174
Symmetry codes: (i) x-1, y, z; (ii) [x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z]; (iii) [-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}].
[Figure 2]
Figure 2
A view along the b axis of the crystal packing of the title compound 1. Hydrogen bonds are shown as dashed lines (see Table 1[link]) and H atoms not involved in these inter­actions have been omitted for clarity.

4. Database survey

A search of the Cambridge Structural Database (Version 5.37; Groom & Allen, 2014[Groom, C. R. & Allen, F. H. (2014). Angew. Chem. Int. Ed. 53, 662-671.]) for substructure S1 (Fig. 3[link]) gave 137 hits, while a search for substructure S2 (Fig. 3[link]) gave only five hits. Amongst the latter compounds, four concern the structures with a hydroxyl and a nitro­methyl group attached to atom C3 (BOGFOU: Turks et al., 2014[Turks, M., Vēze, K., Kiselovs, G., Mackeviča, J., Lugiņina, J., Mishnev, A. & Marković, D. (2014). Carbohydr. Res. 391, 82-88.]; BOGFUA: Turks et al., 2014[Turks, M., Vēze, K., Kiselovs, G., Mackeviča, J., Lugiņina, J., Mishnev, A. & Marković, D. (2014). Carbohydr. Res. 391, 82-88.]; CIDVO: Turks et al., 2013[Turks, M., Rodins, V., Rolava, E., Ostrovskis, P. & Belyakov, S. (2013). Carbohydr. Res. 375, 5-15.]; USODEM: Zhang et al., 2011[Zhang, Q., Ke, Y., Cheng, W., Li, P. & Liu, H. (2011). Acta Cryst. E67, o1402.]). They are diastereomers crystallizing in space groups P212121, P32, C2 and P61, respectively. In the fifth compound (KATWIN; Lugiņina et al., 2012[Lugiņina, J., Rjabovs, V., Belyakov, S. & Turks, M. (2012). Carbohydr. Res. 350, 86-89.]), the extra substituent at atom C3 is a methylthio group; it crystallizes in space group C2.

[Figure 3]
Figure 3
Substructures used for the database survey.

5. Synthesis and crystallization

The title compound 1, was synthesized by reduction of the nitro olefin 2 (Albrecht & Moffatt, 1970[Albrecht, H. P. & Moffatt, J. G. (1970). Tetrahedron Lett. 11, 1063-1066.]; Filichev et al., 2001[Filichev, V. V., Brandt, M. & Pedersen, E. B. (2001). Carbohydr. Res. 333, 115-122.]; Lugiņina et al., 2012[Lugiņina, J., Rjabovs, V., Belyakov, S. & Turks, M. (2012). Carbohydr. Res. 350, 86-89.]) with sodium borohydride in methanol solution, as illustrated in Fig. 4[link]. NaBH4 (6.2 g, 163.9 mmol, 5.5 eq.) was added portion wise to a solution of 2 (9.1 g, 30.0 mmol, 1.0 eq.) in MeOH (200 ml) over 30 min at 273 K. After completion (monitored by TLC) the reaction mixture was acidified using 10% aqueous solution of AcOH to pH 6–7 and then evaporated to dryness. The residue was dissolved in EtOAc (90 ml), washed with brine (3 × 10 ml), dried over NaSO4, and evaporated. The product 1 was purified by column chromatography on silica gel (Hexanes/EtOAc 3:1 → 2:1) giving a white crystalline solid (yield: 6.5 g, 72%; m.p. 355–356 K). Rf = 0.9 (hexa­nes/EtOAc 1:1). 1H NMR (CDCl3, 300 MHz): δ 5.84 (d, J = 3.7 Hz, 1H), 4.88–4.82 (m, 21H), 4.68 (dd, AB syst., J = 14.9 Hz, J = 10.4 Hz, 1H), 4.14 (dd, J = 8.0 Hz, J = 5.5 Hz, 1H), 4.02–3.92 (m, 2H), 3.65 (dd, J = 9.9 Hz, J = 8.4 Hz, 1H), 2.74 (tt, J = 10.1 Hz, J = 4.4 Hz, 1H), 1.52 (s, 3H), 1.40, (s, 3H), 1.33 (s, 3H), 1.32 (s, 3H). 13C-NMR (75 MHz, CDCl3): δ 112.6, 110.1, 105.4, 80.5, 79.0, 77.8, 70.8, 68.2, 46.6, 26.8, 26.7, 26.4, 25.1. X-ray quality single crystals were obtained by slow evaporation of a di­chloro­methane solution at ambient temperature.

[Figure 4]
Figure 4
Synthesis of the title compound.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. The H atoms were included in calculated positions and refined as riding atoms: C—H = 0.96–0.98 Å with Uiso(H) = 1.5Ueq(C-meth­yl) and 1.2Ueq(C) for other H atoms. The absolute configuration is based on that of the starting material.

Table 2
Experimental details

Crystal data
Chemical formula C13H21NO7
Mr 303.31
Crystal system, space group Orthorhombic, P212121
Temperature (K) 173
a, b, c (Å) 5.5044 (2), 12.6144 (4), 21.6348 (9)
V (Å3) 1502.21 (10)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.11
Crystal size (mm) 0.26 × 0.08 × 0.06
 
Data collection
Diffractometer Nonius KappaCCD
No. of measured, independent and observed [I > 2σ(I)] reflections 4225, 4225, 2316
(sin θ/λ)max (Å−1) 0.705
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.065, 0.127, 1.01
No. of reflections 4225
No. of parameters 194
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.20, −0.26
Computer programs: KappaCCD Server Software (Nonius, 1997[Nonius (1997). KappaCCD Server Software. Nonius BV, Delft, The Netherlands.]), 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.]), SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]), 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

CCDC reference: 1451051

Crystal structure: contains datablock I. DOI: 10.1107/S2056989016001845/su5270sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989016001845/su5270Isup2.hkl

checkCIF report


Chemical context top

The title compound 1, has been used for the syntheses of isoxazoles (Lugiņina et al., 2013) and carbohydrate-based amines and amino acids (Rjabovs et al., 2015a). Carbohydrates with amino groups are valuable synthetic precursors and are easily converted to spiro­cyclic carbohydrate derivatives (Turks et al., 2013), imino sugars (Filichev & Pedersen, 2001), nucleic acid mimetics (Rozners et al., 2003), and azido sugars (Mackeviča et al., 2014; Rjabova et al., 2012). The latter are widely used for the syntheses of triazoles (Uzuleņa et al., 2015; Grigorjeva et al., 2015) and THF-amino acids (sugar amino acids) (Rjabovs & Turks, 2013).

Structural commentary top

The title compound 1, consists of a tetra­hydro­furan core (ring A) fused with a dioxolane ring (B) and substituted with a dioxolane (ring C) and a nitro­methyl group (Fig. 1). The conformational analysis of the furan­ose ring (A) based on the inter­nal dihedral angles of the ring shows that its pseudorotational phase angle P = 70° (Altona & Sundaralingam, 1972; Taha et al., 2013). Thus, this ring adopts a conformation close to oT4, where O1 and C4 deviate by 0.214 (2) and −0.340 (3) Å, respectively, from the plane through atoms C1/C2/C3. Such a conformation of the furan­ose ring is rather unusual for 3-C-monosubstituted 3-de­oxy-1,2-O-iso­propyl­idene-α-D-allo­furan­oses. For example, previously reported structures (Rjabovs et al., 2014, 2015a,b) had conformations between 3E and 3T4. The fused dioxolane ring B also adopts a twisted conformation on bond C13—O12; these atoms deviate by −0.324 (4) and 0.224 (3) Å, respectively, from plane C1/C2/O14. The dihedral angle subtended by the mean planes of rings A and B is 63.7 (2)°. The five-membered ring of the 2,2-di­methyl-1,3-dioxolan-4-yl group, ring C, also adopts a twisted conformation, on bond C6—O7; these atoms deviate by 0.143 (4) and −0.381 (2) Å, respectively from plane C5/O9/C8.

Supra­molecular features top

In the crystal, molecules are linked via C—H···O hydrogen bonds, forming chains along [100]. The chains are linked via further C—H···O hydrogen bonds, forming a three-dimensional structure (Table 1 and Fig. 2).

Database survey top

A search of the Cambridge Structural Database (Version 5.37; Groom & Allen, 2014) for substructure S1 (Fig. 3) gave 137 hits, while a search for substructure S2 (Fig. 3) gave only five hits. Amongst the latter compounds, four concern the same structure with both a hydroxyl and a nitro­methyl group on atom C3 (BOGFOU: Turks et al., 2014; BOGFUA: Turks et al., 2014; CIDVO: Turks et al., 2013; USODEM: Zhang et al., 2011). They are polymorphs crystallizing in space groups P212121, P32, C2 and P61, respectively. In the fifth compound (KATWIN; Lugiņina et al., 2012), the extra substituent on atom C3 is a methyl sulfanyl group; it crystallizes in space group C2.

Synthesis and crystallization top

The title compound 1, was synthesized by reduction of the nitro olefin 2 (Albrecht & Moffatt, 1970; Filichev et al., 2001; Lugiņina et al., 2012) with sodium borohydride in methanol solution, as illustrated in Fig. 4. NaBH4 (6.2 g, 163.9 mmol, 5.5 eq.) was added portion wise to a solution of 2 (9.1 g, 30.0 mmol, 1.0 eq.) in MeOH (200 ml) over 30 min at 273 K. After completion (monitored by TLC) the reaction mixture was acidified using 10% aqueous solution of AcOH to pH 6–7 and then evaporated to dryness. The residue was dissolved in EtOAc (90 ml), washed with brine (3 × 10 ml), dried over NaSO4, and evaporated. The product 1 was purified by column chromatography on silica gel (Hexanes/EtOAc 3:1 → 2:1) giving a white crystalline solid (yield: 6.5 g, 72%; m.p. 355–356 K). Rf = 0.9 (hexanes/EtOAc 1:1). 1H NMR (CDCl3, 300 MHz): δ 5.84 (d, J = 3.7 Hz, 1H), 4.88–4.82 (m, 21H), 4.68 (dd, AB syst., J = 14.9 Hz, J = 10.4 Hz, 1H), 4.14 (dd, J = 8.0 Hz, J = 5.5 Hz, 1H), 4.02–3.92 (m, 2H), 3.65 (dd, J = 9.9 Hz, J = 8.4 Hz, 1H), 2.74 (tt, J = 10.1 Hz, J = 4.4 Hz, 1H), 1.52 (s, 3H), 1.40, (s, 3H), 1.33 (s, 3H), 1.32 (s, 3H). 13C-NMR (75 MHz, CDCl3): δ 112.6, 110.1, 105.4, 80.5, 79.0, 77.8, 70.8, 68.2, 46.6, 26.8, 26.7, 26.4, 25.1. X-ray quality single crystals were obtained by slow evaporation of a di­chloro­methane solution at ambient temperature.

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 2. The H atoms were included in calculated positions and refined as riding atoms: C—H = 0.96–0.98 Å with Uiso(H) = 1.5Ueq(C-methyl) and 1.2Ueq(C) for other H atoms. The absolute configuration is based on that of the starting material.

Structure description top

The title compound 1, has been used for the syntheses of isoxazoles (Lugiņina et al., 2013) and carbohydrate-based amines and amino acids (Rjabovs et al., 2015a). Carbohydrates with amino groups are valuable synthetic precursors and are easily converted to spiro­cyclic carbohydrate derivatives (Turks et al., 2013), imino sugars (Filichev & Pedersen, 2001), nucleic acid mimetics (Rozners et al., 2003), and azido sugars (Mackeviča et al., 2014; Rjabova et al., 2012). The latter are widely used for the syntheses of triazoles (Uzuleņa et al., 2015; Grigorjeva et al., 2015) and THF-amino acids (sugar amino acids) (Rjabovs & Turks, 2013).

The title compound 1, consists of a tetra­hydro­furan core (ring A) fused with a dioxolane ring (B) and substituted with a dioxolane (ring C) and a nitro­methyl group (Fig. 1). The conformational analysis of the furan­ose ring (A) based on the inter­nal dihedral angles of the ring shows that its pseudorotational phase angle P = 70° (Altona & Sundaralingam, 1972; Taha et al., 2013). Thus, this ring adopts a conformation close to oT4, where O1 and C4 deviate by 0.214 (2) and −0.340 (3) Å, respectively, from the plane through atoms C1/C2/C3. Such a conformation of the furan­ose ring is rather unusual for 3-C-monosubstituted 3-de­oxy-1,2-O-iso­propyl­idene-α-D-allo­furan­oses. For example, previously reported structures (Rjabovs et al., 2014, 2015a,b) had conformations between 3E and 3T4. The fused dioxolane ring B also adopts a twisted conformation on bond C13—O12; these atoms deviate by −0.324 (4) and 0.224 (3) Å, respectively, from plane C1/C2/O14. The dihedral angle subtended by the mean planes of rings A and B is 63.7 (2)°. The five-membered ring of the 2,2-di­methyl-1,3-dioxolan-4-yl group, ring C, also adopts a twisted conformation, on bond C6—O7; these atoms deviate by 0.143 (4) and −0.381 (2) Å, respectively from plane C5/O9/C8.

In the crystal, molecules are linked via C—H···O hydrogen bonds, forming chains along [100]. The chains are linked via further C—H···O hydrogen bonds, forming a three-dimensional structure (Table 1 and Fig. 2).

A search of the Cambridge Structural Database (Version 5.37; Groom & Allen, 2014) for substructure S1 (Fig. 3) gave 137 hits, while a search for substructure S2 (Fig. 3) gave only five hits. Amongst the latter compounds, four concern the same structure with both a hydroxyl and a nitro­methyl group on atom C3 (BOGFOU: Turks et al., 2014; BOGFUA: Turks et al., 2014; CIDVO: Turks et al., 2013; USODEM: Zhang et al., 2011). They are polymorphs crystallizing in space groups P212121, P32, C2 and P61, respectively. In the fifth compound (KATWIN; Lugiņina et al., 2012), the extra substituent on atom C3 is a methyl sulfanyl group; it crystallizes in space group C2.

Synthesis and crystallization top

The title compound 1, was synthesized by reduction of the nitro olefin 2 (Albrecht & Moffatt, 1970; Filichev et al., 2001; Lugiņina et al., 2012) with sodium borohydride in methanol solution, as illustrated in Fig. 4. NaBH4 (6.2 g, 163.9 mmol, 5.5 eq.) was added portion wise to a solution of 2 (9.1 g, 30.0 mmol, 1.0 eq.) in MeOH (200 ml) over 30 min at 273 K. After completion (monitored by TLC) the reaction mixture was acidified using 10% aqueous solution of AcOH to pH 6–7 and then evaporated to dryness. The residue was dissolved in EtOAc (90 ml), washed with brine (3 × 10 ml), dried over NaSO4, and evaporated. The product 1 was purified by column chromatography on silica gel (Hexanes/EtOAc 3:1 → 2:1) giving a white crystalline solid (yield: 6.5 g, 72%; m.p. 355–356 K). Rf = 0.9 (hexanes/EtOAc 1:1). 1H NMR (CDCl3, 300 MHz): δ 5.84 (d, J = 3.7 Hz, 1H), 4.88–4.82 (m, 21H), 4.68 (dd, AB syst., J = 14.9 Hz, J = 10.4 Hz, 1H), 4.14 (dd, J = 8.0 Hz, J = 5.5 Hz, 1H), 4.02–3.92 (m, 2H), 3.65 (dd, J = 9.9 Hz, J = 8.4 Hz, 1H), 2.74 (tt, J = 10.1 Hz, J = 4.4 Hz, 1H), 1.52 (s, 3H), 1.40, (s, 3H), 1.33 (s, 3H), 1.32 (s, 3H). 13C-NMR (75 MHz, CDCl3): δ 112.6, 110.1, 105.4, 80.5, 79.0, 77.8, 70.8, 68.2, 46.6, 26.8, 26.7, 26.4, 25.1. X-ray quality single crystals were obtained by slow evaporation of a di­chloro­methane solution at ambient temperature.

Refinement details top

Crystal data, data collection and structure refinement details are summarized in Table 2. The H atoms were included in calculated positions and refined as riding atoms: C—H = 0.96–0.98 Å with Uiso(H) = 1.5Ueq(C-methyl) and 1.2Ueq(C) for other H atoms. The absolute configuration is based on that of the starting material.

Computing details top

Data collection: KappaCCD Server Software (Nonius, 1997); cell refinement: SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR2011 (Burla et al., 2012); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound 1, showing the atom labelling. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. A view along the b axis of the crystal packing of the title compound 1. Hydrogen bonds are shown as dashed lines (see Table 1) and H atoms not involved in these interactions have been omitted for clarity.
[Figure 3] Fig. 3. Substructures used for the database survey.
[Figure 4] Fig. 4. Synthesis of the title compound.
(3aR,5S,6R,6aR)-5-[(R)-2,2-Dimethyl-1,3-\ dioxolan-4-yl]-2,2-dimethyl-6-(nitromethyl)tetrahydrofuro[2,3-d][1,3]\ dioxole top
Crystal data top
C13H21NO7Dx = 1.341 Mg m−3
Mr = 303.31Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121Cell parameters from 26214 reflections
a = 5.5044 (2) Åθ = 1.0–30.0°
b = 12.6144 (4) ŵ = 0.11 mm−1
c = 21.6348 (9) ÅT = 173 K
V = 1502.21 (10) Å3Needle, colourless
Z = 40.26 × 0.08 × 0.06 mm
F(000) = 648
Data collection top
Nonius KappaCCD
diffractometer		2316 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeθmax = 30.1°, θmin = 3.2°
φ and ω scanh = −7→7
4225 measured reflectionsk = −17→17
4225 independent reflectionsl = −30→30
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.065H-atom parameters constrained
wR(F2) = 0.127 w = 1/[σ2(Fo2) + (0.0367P)2 + 0.3523P]
where P = (Fo2 + 2Fc2)/3
S = 1.01(Δ/σ)max < 0.001
4225 reflectionsΔρmax = 0.20 e Å−3
194 parametersΔρmin = −0.25 e Å−3
Crystal data top
C13H21NO7V = 1502.21 (10) Å3
Mr = 303.31Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 5.5044 (2) ŵ = 0.11 mm−1
b = 12.6144 (4) ÅT = 173 K
c = 21.6348 (9) Å0.26 × 0.08 × 0.06 mm
Data collection top
Nonius KappaCCD
diffractometer		4225 independent reflections
4225 measured reflections2316 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.0650 restraints
wR(F2) = 0.127H-atom parameters constrained
S = 1.01Δρmax = 0.20 e Å−3
4225 reflectionsΔρmin = −0.25 e Å−3
194 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.1756 (4)0.94348 (18)0.03395 (11)0.0372 (6)
C10.2580 (7)0.8418 (3)0.04912 (17)0.0368 (9)
H10.34780.80950.01480.044*
C20.4157 (6)0.8508 (3)0.10747 (17)0.0339 (8)
H20.58730.83610.09900.041*
C30.3744 (6)0.9665 (2)0.12881 (17)0.0306 (8)
H30.51551.00900.11660.037*
C40.1536 (6)1.0022 (2)0.09017 (16)0.0309 (8)
H40.00250.98320.11140.037*
C50.1502 (6)1.1182 (3)0.07239 (18)0.0360 (9)
H50.30201.13710.05140.043*
C6−0.0661 (6)1.1468 (3)0.03179 (19)0.0392 (9)
H6A−0.02441.20230.00260.047*
H6B−0.12481.08540.00930.047*
O7−0.2414 (4)1.18276 (17)0.07540 (12)0.0391 (6)
C8−0.1090 (6)1.2369 (3)0.12245 (19)0.0393 (9)
O90.1197 (4)1.18174 (19)0.12615 (13)0.0470 (7)
C10−0.0637 (8)1.3514 (3)0.1055 (2)0.0489 (11)
H10A−0.21591.38820.10270.073*
H10B0.01841.35480.06640.073*
H10C0.03541.38400.13670.073*
C11−0.2428 (8)1.2243 (3)0.18262 (19)0.0554 (11)
H11A−0.25301.15050.19300.083*
H11B−0.40351.25300.17860.083*
H11C−0.15721.26140.21470.083*
O120.0607 (5)0.77711 (19)0.06819 (12)0.0397 (6)
C130.1517 (6)0.7096 (3)0.11560 (17)0.0346 (9)
O140.3131 (4)0.77660 (18)0.14980 (11)0.0362 (6)
C150.2887 (8)0.6163 (3)0.08712 (19)0.0489 (11)
H15A0.35270.57230.11940.073*
H15B0.41980.64250.06210.073*
H15C0.17980.57560.06190.073*
C16−0.0501 (7)0.6743 (3)0.1567 (2)0.0484 (11)
H16A−0.12720.73520.17480.073*
H16B0.01380.62990.18890.073*
H16C−0.16700.63520.13300.073*
C3'0.3314 (6)0.9814 (3)0.19700 (17)0.0339 (8)
H3'10.28591.05460.20440.041*
H3'20.19590.93720.20950.041*
N4'0.5468 (6)0.9550 (2)0.23638 (16)0.0373 (7)
O5'0.7368 (4)0.9282 (2)0.21135 (13)0.0518 (8)
O6'0.5199 (5)0.9616 (3)0.29175 (14)0.0612 (9)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0535 (15)0.0301 (13)0.0281 (14)0.0051 (11)−0.0038 (12)−0.0004 (12)
C10.045 (2)0.0324 (19)0.033 (2)0.0065 (17)0.0013 (17)−0.0011 (16)
C20.0328 (19)0.0309 (18)0.038 (2)0.0052 (15)0.0025 (17)0.0038 (17)
C30.0258 (17)0.0283 (19)0.038 (2)−0.0020 (13)−0.0002 (15)−0.0018 (16)
C40.0273 (17)0.0285 (18)0.037 (2)−0.0028 (14)−0.0016 (16)−0.0007 (17)
C50.0299 (18)0.0302 (19)0.048 (2)0.0000 (14)−0.0025 (18)0.0015 (18)
C60.038 (2)0.0311 (19)0.048 (2)0.0058 (16)−0.0062 (18)0.0003 (19)
O70.0308 (13)0.0349 (13)0.0517 (17)−0.0016 (11)−0.0035 (12)−0.0014 (13)
C80.038 (2)0.0284 (19)0.052 (3)0.0024 (15)−0.0039 (18)−0.0024 (18)
O90.0418 (15)0.0345 (14)0.0646 (19)0.0089 (11)−0.0173 (13)−0.0132 (14)
C100.055 (2)0.030 (2)0.062 (3)−0.0002 (18)0.003 (2)0.003 (2)
C110.068 (3)0.046 (2)0.052 (3)−0.004 (2)0.002 (2)0.003 (2)
O120.0432 (14)0.0323 (13)0.0436 (15)−0.0020 (11)−0.0114 (12)0.0004 (13)
C130.040 (2)0.0257 (18)0.038 (2)−0.0024 (15)−0.0072 (17)−0.0009 (16)
O140.0408 (14)0.0327 (13)0.0352 (15)−0.0045 (11)−0.0058 (12)0.0045 (12)
C150.065 (3)0.0281 (19)0.053 (3)0.0049 (18)−0.004 (2)−0.0008 (19)
C160.045 (2)0.042 (2)0.059 (3)−0.0028 (18)0.000 (2)0.006 (2)
C3'0.0245 (17)0.038 (2)0.040 (2)−0.0017 (15)−0.0016 (16)−0.0010 (17)
N4'0.0387 (18)0.0316 (17)0.042 (2)−0.0026 (14)−0.0078 (16)0.0001 (16)
O5'0.0312 (14)0.0693 (19)0.0548 (19)0.0061 (14)−0.0057 (14)0.0012 (15)
O6'0.0627 (19)0.085 (2)0.0355 (18)0.0003 (16)−0.0099 (16)−0.0045 (17)
Geometric parameters (Å, º) top
O1—C11.399 (4)C8—C101.511 (5)
O1—C41.429 (4)C10—H10A0.9600
C1—O121.420 (4)C10—H10B0.9600
C1—C21.537 (5)C10—H10C0.9600
C1—H10.9800C11—H11A0.9600
C2—O141.427 (4)C11—H11B0.9600
C2—C31.547 (5)C11—H11C0.9600
C2—H20.9800O12—C131.424 (4)
C3—C3'1.506 (5)C13—O141.432 (4)
C3—C41.542 (5)C13—C161.491 (5)
C3—H30.9800C13—C151.527 (5)
C4—C51.514 (4)C15—H15A0.9600
C4—H40.9800C15—H15B0.9600
C5—O91.422 (4)C15—H15C0.9600
C5—C61.523 (5)C16—H16A0.9600
C5—H50.9800C16—H16B0.9600
C6—O71.424 (4)C16—H16C0.9600
C6—H6A0.9700C3'—N4'1.498 (4)
C6—H6B0.9700C3'—H3'10.9700
O7—C81.426 (4)C3'—H3'20.9700
C8—O91.441 (4)N4'—O6'1.210 (4)
C8—C111.504 (6)N4'—O5'1.225 (4)
C1—O1—C4107.6 (2)C11—C8—C10113.0 (3)
O1—C1—O12110.3 (3)C5—O9—C8109.2 (3)
O1—C1—C2107.9 (3)C8—C10—H10A109.5
O12—C1—C2103.7 (3)C8—C10—H10B109.5
O1—C1—H1111.5H10A—C10—H10B109.5
O12—C1—H1111.5C8—C10—H10C109.5
C2—C1—H1111.5H10A—C10—H10C109.5
O14—C2—C1104.8 (3)H10B—C10—H10C109.5
O14—C2—C3111.7 (3)C8—C11—H11A109.5
C1—C2—C3103.4 (3)C8—C11—H11B109.5
O14—C2—H2112.1H11A—C11—H11B109.5
C1—C2—H2112.1C8—C11—H11C109.5
C3—C2—H2112.1H11A—C11—H11C109.5
C3'—C3—C4111.8 (3)H11B—C11—H11C109.5
C3'—C3—C2115.7 (3)C1—O12—C13106.5 (3)
C4—C3—C2103.3 (3)O12—C13—O14103.8 (2)
C3'—C3—H3108.6O12—C13—C16110.2 (3)
C4—C3—H3108.6O14—C13—C16109.3 (3)
C2—C3—H3108.6O12—C13—C15110.1 (3)
O1—C4—C5106.6 (3)O14—C13—C15110.9 (3)
O1—C4—C3104.1 (3)C16—C13—C15112.2 (3)
C5—C4—C3115.5 (3)C2—O14—C13107.5 (2)
O1—C4—H4110.1C13—C15—H15A109.5
C5—C4—H4110.1C13—C15—H15B109.5
C3—C4—H4110.1H15A—C15—H15B109.5
O9—C5—C4109.8 (3)C13—C15—H15C109.5
O9—C5—C6104.2 (3)H15A—C15—H15C109.5
C4—C5—C6112.7 (3)H15B—C15—H15C109.5
O9—C5—H5110.0C13—C16—H16A109.5
C4—C5—H5110.0C13—C16—H16B109.5
C6—C5—H5110.0H16A—C16—H16B109.5
O7—C6—C5102.9 (3)C13—C16—H16C109.5
O7—C6—H6A111.2H16A—C16—H16C109.5
C5—C6—H6A111.2H16B—C16—H16C109.5
O7—C6—H6B111.2N4'—C3'—C3113.9 (3)
C5—C6—H6B111.2N4'—C3'—H3'1108.8
H6A—C6—H6B109.1C3—C3'—H3'1108.8
C6—O7—C8106.2 (2)N4'—C3'—H3'2108.8
O7—C8—O9104.8 (3)C3—C3'—H3'2108.8
O7—C8—C11108.5 (3)H3'1—C3'—H3'2107.7
O9—C8—C11109.2 (3)O6'—N4'—O5'124.1 (3)
O7—C8—C10111.7 (3)O6'—N4'—C3'116.8 (3)
O9—C8—C10109.3 (3)O5'—N4'—C3'119.1 (3)
C4—O1—C1—O1282.3 (3)C6—O7—C8—O9−32.8 (3)
C4—O1—C1—C2−30.3 (3)C6—O7—C8—C11−149.3 (3)
O1—C1—C2—O14126.3 (3)C6—O7—C8—C1085.4 (3)
O12—C1—C2—O149.3 (3)C4—C5—O9—C8−115.4 (3)
O1—C1—C2—C39.3 (4)C6—C5—O9—C85.6 (4)
O12—C1—C2—C3−107.7 (3)O7—C8—O9—C516.0 (4)
O14—C2—C3—C3'23.3 (4)C11—C8—O9—C5132.1 (3)
C1—C2—C3—C3'135.5 (3)C10—C8—O9—C5−103.8 (3)
O14—C2—C3—C4−99.1 (3)O1—C1—O12—C13−144.5 (3)
C1—C2—C3—C413.1 (3)C2—C1—O12—C13−29.2 (3)
C1—O1—C4—C5161.0 (3)C1—O12—C13—O1438.3 (3)
C1—O1—C4—C338.5 (3)C1—O12—C13—C16155.2 (3)
C3'—C3—C4—O1−155.8 (3)C1—O12—C13—C15−80.4 (3)
C2—C3—C4—O1−30.8 (3)C1—C2—O14—C1313.7 (3)
C3'—C3—C4—C587.7 (4)C3—C2—O14—C13125.0 (3)
C2—C3—C4—C5−147.3 (3)O12—C13—O14—C2−31.8 (3)
O1—C4—C5—O9177.9 (3)C16—C13—O14—C2−149.4 (3)
C3—C4—C5—O9−67.0 (4)C15—C13—O14—C286.4 (3)
O1—C4—C5—C662.2 (4)C4—C3—C3'—N4'−176.0 (3)
C3—C4—C5—C6177.3 (3)C2—C3—C3'—N4'66.2 (4)
O9—C5—C6—O7−25.0 (3)C3—C3'—N4'—O6'−177.3 (3)
C4—C5—C6—O794.0 (3)C3—C3'—N4'—O5'2.6 (4)
C5—C6—O7—C835.7 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C3′—H3′2···O5′i0.972.533.355 (4)143
C1—H1···O12ii0.982.413.386 (5)178
C15—H15A···O6′iii0.962.483.433 (5)174
Symmetry codes: (i) x−1, y, z; (ii) x+1/2, −y+3/2, −z; (iii) −x+1, y−1/2, −z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C3'—H3'2···O5'i0.972.533.355 (4)143
C1—H1···O12ii0.982.413.386 (5)178
C15—H15A···O6'iii0.962.483.433 (5)174
Symmetry codes: (i) x−1, y, z; (ii) x+1/2, −y+3/2, −z; (iii) −x+1, y−1/2, −z+1/2.

Experimental details

Crystal data
Chemical formulaC13H21NO7
Mr303.31
Crystal system, space groupOrthorhombic, P212121
Temperature (K)173
a, b, c (Å)5.5044 (2), 12.6144 (4), 21.6348 (9)
V (Å3)1502.21 (10)
Z4
Radiation typeMo Kα
µ (mm−1)0.11
Crystal size (mm)0.26 × 0.08 × 0.06
Data collection
DiffractometerNonius KappaCCD
Absorption correction–
No. of measured, independent and
observed [I > 2σ(I)] reflections		4225, 4225, 2316
Rint?
(sin θ/λ)max (Å−1)0.705
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.065, 0.127, 1.01
No. of reflections4225
No. of parameters194
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.20, −0.25

Computer programs: KappaCCD Server Software (Nonius, 1997), DENZO and SCALEPACK (Otwinowski & Minor, 1997), SIR2011 (Burla et al., 2012), SHELXL2014 (Sheldrick, 2015), ORTEP-3 for Windows (Farrugia, 2012), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

 

Acknowledgements

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

References

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ISSN: 2056-9890
Volume 72| Part 3| March 2016| Pages 314-317
doi:10.1107/S2056989016001845
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