Crystal structure of 3-de-oxy-3-nitro-methyl-1,2;5,6-di-O-iso-propyl-idene-α-d-allo-furan-ose.

The title compound, C13H21NO7 {systematic name: (3aR,5S,6R,6aR)-5-[(R)-2,2-dimethyl-1,3-dioxolan-4-yl]-2,2-dimethyl-6-(nitro-meth-yl)tetra-hydro-furo[2,3-d][1,3]dioxole}, consists of a substituted 2,2-di-methyl-tetra-hydro-furo[2,3-d][1,3]dioxolane skeleton. The furan-ose ring A adopts a (o)T 4 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 mol-ecules to form a three-dimensional structure.

Chemical context

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

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 o T 4, 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 3 E and 3 T 4. 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

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

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 ▸ and Fig. 2 ▸).

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) ; (ii) ; (iii) .

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 ▸) and H atoms not involved in these inter­actions have been omitted for clarity.

Database survey

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 structures with a hydroxyl and a nitro­methyl group attached to atom C3 (BOGFOU: Turks et al., 2014 ▸; BOGFUA: Turks et al., 2014 ▸; CIDVO: Turks et al., 2013 ▸; USODEM: Zhang et al., 2011 ▸). They are diastereomers crystallizing in space groups P212121, P32, C2 and P61, respectively. In the fifth compound (KATWIN; Lugiņina et al., 2012 ▸), the extra substituent at atom C3 is a methylthio group; it crystallizes in space group C2.

Figure 3

Substructures used for the database survey.

Synthesis and crystallization

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). R = 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

Synthesis of the title compound.

Refinement

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 U iso(H) = 1.5U eq(C-meth­yl) and 1.2U eq(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
M r	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[F 2 > 2σ(F 2)], wR(F 2), 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 ▸), 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 ▸).

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

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

CCDC reference: 1451051

Additional supporting information: crystallographic information; 3D view; checkCIF report

C13H21NO7	Dx = 1.341 Mg m−3
Mr = 303.31	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121	Cell parameters from 26214 reflections
a = 5.5044 (2) Å	θ = 1.0–30.0°
b = 12.6144 (4) Å	µ = 0.11 mm−1
c = 21.6348 (9) Å	T = 173 K
V = 1502.21 (10) Å3	Needle, colourless
Z = 4	0.26 × 0.08 × 0.06 mm
F(000) = 648

Nonius KappaCCD diffractometer	2316 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	θmax = 30.1°, θmin = 3.2°
φ and ω scan	h = −7→7
4225 measured reflections	k = −17→17
4225 independent reflections	l = −30→30

Refinement on F2	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.065	H-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 reflections	Δρmax = 0.20 e Å−3
194 parameters	Δρmin = −0.25 e Å−3

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.

	x	y	z	Uiso*/Ueq
O1	0.1756 (4)	0.94348 (18)	0.03395 (11)	0.0372 (6)
C1	0.2580 (7)	0.8418 (3)	0.04912 (17)	0.0368 (9)
H1	0.3478	0.8095	0.0148	0.044*
C2	0.4157 (6)	0.8508 (3)	0.10747 (17)	0.0339 (8)
H2	0.5873	0.8361	0.0990	0.041*
C3	0.3744 (6)	0.9665 (2)	0.12881 (17)	0.0306 (8)
H3	0.5155	1.0090	0.1166	0.037*
C4	0.1536 (6)	1.0022 (2)	0.09017 (16)	0.0309 (8)
H4	0.0025	0.9832	0.1114	0.037*
C5	0.1502 (6)	1.1182 (3)	0.07239 (18)	0.0360 (9)
H5	0.3020	1.1371	0.0514	0.043*
C6	−0.0661 (6)	1.1468 (3)	0.03179 (19)	0.0392 (9)
H6A	−0.0244	1.2023	0.0026	0.047*
H6B	−0.1248	1.0854	0.0093	0.047*
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)
O9	0.1197 (4)	1.18174 (19)	0.12615 (13)	0.0470 (7)
C10	−0.0637 (8)	1.3514 (3)	0.1055 (2)	0.0489 (11)
H10A	−0.2159	1.3882	0.1027	0.073*
H10B	0.0184	1.3548	0.0664	0.073*
H10C	0.0354	1.3840	0.1367	0.073*
C11	−0.2428 (8)	1.2243 (3)	0.18262 (19)	0.0554 (11)
H11A	−0.2530	1.1505	0.1930	0.083*
H11B	−0.4035	1.2530	0.1786	0.083*
H11C	−0.1572	1.2614	0.2147	0.083*
O12	0.0607 (5)	0.77711 (19)	0.06819 (12)	0.0397 (6)
C13	0.1517 (6)	0.7096 (3)	0.11560 (17)	0.0346 (9)
O14	0.3131 (4)	0.77660 (18)	0.14980 (11)	0.0362 (6)
C15	0.2887 (8)	0.6163 (3)	0.08712 (19)	0.0489 (11)
H15A	0.3527	0.5723	0.1194	0.073*
H15B	0.4198	0.6425	0.0621	0.073*
H15C	0.1798	0.5756	0.0619	0.073*
C16	−0.0501 (7)	0.6743 (3)	0.1567 (2)	0.0484 (11)
H16A	−0.1272	0.7352	0.1748	0.073*
H16B	0.0138	0.6299	0.1889	0.073*
H16C	−0.1670	0.6352	0.1330	0.073*
C3'	0.3314 (6)	0.9814 (3)	0.19700 (17)	0.0339 (8)
H3'1	0.2859	1.0546	0.2044	0.041*
H3'2	0.1959	0.9372	0.2095	0.041*
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)

	U11	U22	U33	U12	U13	U23
O1	0.0535 (15)	0.0301 (13)	0.0281 (14)	0.0051 (11)	−0.0038 (12)	−0.0004 (12)
C1	0.045 (2)	0.0324 (19)	0.033 (2)	0.0065 (17)	0.0013 (17)	−0.0011 (16)
C2	0.0328 (19)	0.0309 (18)	0.038 (2)	0.0052 (15)	0.0025 (17)	0.0038 (17)
C3	0.0258 (17)	0.0283 (19)	0.038 (2)	−0.0020 (13)	−0.0002 (15)	−0.0018 (16)
C4	0.0273 (17)	0.0285 (18)	0.037 (2)	−0.0028 (14)	−0.0016 (16)	−0.0007 (17)
C5	0.0299 (18)	0.0302 (19)	0.048 (2)	0.0000 (14)	−0.0025 (18)	0.0015 (18)
C6	0.038 (2)	0.0311 (19)	0.048 (2)	0.0058 (16)	−0.0062 (18)	0.0003 (19)
O7	0.0308 (13)	0.0349 (13)	0.0517 (17)	−0.0016 (11)	−0.0035 (12)	−0.0014 (13)
C8	0.038 (2)	0.0284 (19)	0.052 (3)	0.0024 (15)	−0.0039 (18)	−0.0024 (18)
O9	0.0418 (15)	0.0345 (14)	0.0646 (19)	0.0089 (11)	−0.0173 (13)	−0.0132 (14)
C10	0.055 (2)	0.030 (2)	0.062 (3)	−0.0002 (18)	0.003 (2)	0.003 (2)
C11	0.068 (3)	0.046 (2)	0.052 (3)	−0.004 (2)	0.002 (2)	0.003 (2)
O12	0.0432 (14)	0.0323 (13)	0.0436 (15)	−0.0020 (11)	−0.0114 (12)	0.0004 (13)
C13	0.040 (2)	0.0257 (18)	0.038 (2)	−0.0024 (15)	−0.0072 (17)	−0.0009 (16)
O14	0.0408 (14)	0.0327 (13)	0.0352 (15)	−0.0045 (11)	−0.0058 (12)	0.0045 (12)
C15	0.065 (3)	0.0281 (19)	0.053 (3)	0.0049 (18)	−0.004 (2)	−0.0008 (19)
C16	0.045 (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)

O1—C1	1.399 (4)	C8—C10	1.511 (5)
O1—C4	1.429 (4)	C10—H10A	0.9600
C1—O12	1.420 (4)	C10—H10B	0.9600
C1—C2	1.537 (5)	C10—H10C	0.9600
C1—H1	0.9800	C11—H11A	0.9600
C2—O14	1.427 (4)	C11—H11B	0.9600
C2—C3	1.547 (5)	C11—H11C	0.9600
C2—H2	0.9800	O12—C13	1.424 (4)
C3—C3'	1.506 (5)	C13—O14	1.432 (4)
C3—C4	1.542 (5)	C13—C16	1.491 (5)
C3—H3	0.9800	C13—C15	1.527 (5)
C4—C5	1.514 (4)	C15—H15A	0.9600
C4—H4	0.9800	C15—H15B	0.9600
C5—O9	1.422 (4)	C15—H15C	0.9600
C5—C6	1.523 (5)	C16—H16A	0.9600
C5—H5	0.9800	C16—H16B	0.9600
C6—O7	1.424 (4)	C16—H16C	0.9600
C6—H6A	0.9700	C3'—N4'	1.498 (4)
C6—H6B	0.9700	C3'—H3'1	0.9700
O7—C8	1.426 (4)	C3'—H3'2	0.9700
C8—O9	1.441 (4)	N4'—O6'	1.210 (4)
C8—C11	1.504 (6)	N4'—O5'	1.225 (4)
C1—O1—C4	107.6 (2)	C11—C8—C10	113.0 (3)
O1—C1—O12	110.3 (3)	C5—O9—C8	109.2 (3)
O1—C1—C2	107.9 (3)	C8—C10—H10A	109.5
O12—C1—C2	103.7 (3)	C8—C10—H10B	109.5
O1—C1—H1	111.5	H10A—C10—H10B	109.5
O12—C1—H1	111.5	C8—C10—H10C	109.5
C2—C1—H1	111.5	H10A—C10—H10C	109.5
O14—C2—C1	104.8 (3)	H10B—C10—H10C	109.5
O14—C2—C3	111.7 (3)	C8—C11—H11A	109.5
C1—C2—C3	103.4 (3)	C8—C11—H11B	109.5
O14—C2—H2	112.1	H11A—C11—H11B	109.5
C1—C2—H2	112.1	C8—C11—H11C	109.5
C3—C2—H2	112.1	H11A—C11—H11C	109.5
C3'—C3—C4	111.8 (3)	H11B—C11—H11C	109.5
C3'—C3—C2	115.7 (3)	C1—O12—C13	106.5 (3)
C4—C3—C2	103.3 (3)	O12—C13—O14	103.8 (2)
C3'—C3—H3	108.6	O12—C13—C16	110.2 (3)
C4—C3—H3	108.6	O14—C13—C16	109.3 (3)
C2—C3—H3	108.6	O12—C13—C15	110.1 (3)
O1—C4—C5	106.6 (3)	O14—C13—C15	110.9 (3)
O1—C4—C3	104.1 (3)	C16—C13—C15	112.2 (3)
C5—C4—C3	115.5 (3)	C2—O14—C13	107.5 (2)
O1—C4—H4	110.1	C13—C15—H15A	109.5
C5—C4—H4	110.1	C13—C15—H15B	109.5
C3—C4—H4	110.1	H15A—C15—H15B	109.5
O9—C5—C4	109.8 (3)	C13—C15—H15C	109.5
O9—C5—C6	104.2 (3)	H15A—C15—H15C	109.5
C4—C5—C6	112.7 (3)	H15B—C15—H15C	109.5
O9—C5—H5	110.0	C13—C16—H16A	109.5
C4—C5—H5	110.0	C13—C16—H16B	109.5
C6—C5—H5	110.0	H16A—C16—H16B	109.5
O7—C6—C5	102.9 (3)	C13—C16—H16C	109.5
O7—C6—H6A	111.2	H16A—C16—H16C	109.5
C5—C6—H6A	111.2	H16B—C16—H16C	109.5
O7—C6—H6B	111.2	N4'—C3'—C3	113.9 (3)
C5—C6—H6B	111.2	N4'—C3'—H3'1	108.8
H6A—C6—H6B	109.1	C3—C3'—H3'1	108.8
C6—O7—C8	106.2 (2)	N4'—C3'—H3'2	108.8
O7—C8—O9	104.8 (3)	C3—C3'—H3'2	108.8
O7—C8—C11	108.5 (3)	H3'1—C3'—H3'2	107.7
O9—C8—C11	109.2 (3)	O6'—N4'—O5'	124.1 (3)
O7—C8—C10	111.7 (3)	O6'—N4'—C3'	116.8 (3)
O9—C8—C10	109.3 (3)	O5'—N4'—C3'	119.1 (3)
C4—O1—C1—O12	82.3 (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—O14	126.3 (3)	C6—O7—C8—C10	85.4 (3)
O12—C1—C2—O14	9.3 (3)	C4—C5—O9—C8	−115.4 (3)
O1—C1—C2—C3	9.3 (4)	C6—C5—O9—C8	5.6 (4)
O12—C1—C2—C3	−107.7 (3)	O7—C8—O9—C5	16.0 (4)
O14—C2—C3—C3'	23.3 (4)	C11—C8—O9—C5	132.1 (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—C4	13.1 (3)	C2—C1—O12—C13	−29.2 (3)
C1—O1—C4—C5	161.0 (3)	C1—O12—C13—O14	38.3 (3)
C1—O1—C4—C3	38.5 (3)	C1—O12—C13—C16	155.2 (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—C13	13.7 (3)
C3'—C3—C4—C5	87.7 (4)	C3—C2—O14—C13	125.0 (3)
C2—C3—C4—C5	−147.3 (3)	O12—C13—O14—C2	−31.8 (3)
O1—C4—C5—O9	177.9 (3)	C16—C13—O14—C2	−149.4 (3)
C3—C4—C5—O9	−67.0 (4)	C15—C13—O14—C2	86.4 (3)
O1—C4—C5—C6	62.2 (4)	C4—C3—C3'—N4'	−176.0 (3)
C3—C4—C5—C6	177.3 (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—O7	94.0 (3)	C3—C3'—N4'—O5'	2.6 (4)
C5—C6—O7—C8	35.7 (3)

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