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

Rjabovs, V.; Stepanovs, D.; Turks, M.

doi:10.1107/S2056989015017582

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ISSN: 2056-9890

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

doi:10.1107/S2056989015017582

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

Vitalijs Rjabovs,^a Dmitrijs Stepanovs ^b,^a ^* and Maris Turks ^a ^*

^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.

Keywords: crystal structure; 3-aminomethyl diacetone-D-allose; imino sugar precursor; sugar amino acid precursor; hydrogen bonding..

CCDC reference: 1425954

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 ), by hydrogenation and carbamate protection of either nitro (Lugiņina et al., 2013 ) or azido (Filichev & Pedersen, 2001 ; Rjabova et al., 2012 ) precursors (Fig. 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), and reviewed by Rjabovs & Turks (2013 ) and Risseeuw et al. (2013 ). The title compound can be used as a precursor 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 ).

2. Structural commentary

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 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
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 and Table 1).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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
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.

4. Database survey

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 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 ), 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).

5. Synthesis and crystallization

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): 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. R_f = 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. 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 U_iso(H) = 1.5U_eq(C) for methyl H atoms and 1.2U_eq(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
M_r	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)
V (Å³)	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
R_int	0.034
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	0.23, −0.21
Computer programs: KappaCCD Server Software (Nonius, 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 ).

Supporting information

CCDC reference: 1425954

Crystal structure: contains datablock I. DOI: 10.1107/S2056989015017582/su5210sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989015017582/su5210Isup2.hkl

checkCIF report

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 (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. R_f = 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

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

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

C₂₁H₂₉NO₇	F(000) = 436
M_r = 407.45	D_x = 1.321 Mg m⁻³
Monoclinic, P2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 11906 reflections
a = 9.3235 (3) Å	θ = 1.0–30.0°
b = 5.4118 (1) Å	µ = 0.10 mm⁻¹
c = 20.4381 (7) Å	T = 173 K
β = 96.748 (1)°	Block, colourless
V = 1024.10 (5) Å³	0.32 × 0.31 × 0.20 mm
Z = 2

Data collection top

Nonius KappaCCD diffractometer	2597 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.034
Graphite monochromator	θ_max = 30.1°, θ_min = 2.3°
CCD scans	h = −13→13
5535 measured reflections	k = −7→6
3279 independent reflections	l = −28→28

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.045	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.100	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ²(F_o²) + (0.044P)² + 0.1203P] where P = (F_o² + 2F_c²)/3
3279 reflections	(Δ/σ)_max < 0.001
270 parameters	Δρ_max = 0.23 e Å⁻³
1 restraint	Δρ_min = −0.21 e Å⁻³

Crystal data top

C₂₁H₂₉NO₇	V = 1024.10 (5) Å³
M_r = 407.45	Z = 2
Monoclinic, P2₁	Mo Kα radiation
a = 9.3235 (3) Å	µ = 0.10 mm⁻¹
b = 5.4118 (1) Å	T = 173 K
c = 20.4381 (7) Å	0.32 × 0.31 × 0.20 mm
β = 96.748 (1)°

Data collection top

Nonius KappaCCD diffractometer	2597 reflections with I > 2σ(I)
5535 measured reflections	R_int = 0.034
3279 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.045	1 restraint
wR(F²) = 0.100	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	Δρ_max = 0.23 e Å⁻³
3279 reflections	Δρ_min = −0.21 e Å⁻³
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

	x	y	z	U_iso*/U_eq
O1	0.34514 (16)	0.3163 (3)	0.37758 (7)	0.0315 (4)
C1	0.2837 (2)	0.3609 (4)	0.31216 (10)	0.0257 (4)
H1	0.2922	0.5356	0.3006	0.031*
C2	0.3645 (2)	0.1973 (4)	0.26790 (10)	0.0236 (4)
H2	0.3840	0.2807	0.2273	0.028*
C3	0.5014 (2)	0.1255 (4)	0.31153 (9)	0.0216 (4)
H3	0.5695	0.2635	0.3118	0.026*
C4	0.4468 (2)	0.1149 (4)	0.37946 (9)	0.0219 (4)
H4	0.3965	−0.0419	0.3842	0.026*
C5	0.5571 (2)	0.1572 (4)	0.43934 (10)	0.0221 (4)
H5	0.5063	0.1803	0.4782	0.027*
C6	0.6694 (2)	−0.0473 (4)	0.45328 (10)	0.0239 (4)
H6A	0.6898	−0.0777	0.5002	0.029*
H6B	0.6366	−0.1997	0.4314	0.029*
O7	0.79329 (15)	0.0472 (3)	0.42712 (7)	0.0251 (3)
C8	0.7920 (2)	0.3060 (4)	0.43977 (10)	0.0234 (4)
O9	0.64107 (15)	0.3721 (3)	0.43018 (7)	0.0251 (3)
C10	0.8696 (3)	0.4342 (4)	0.38914 (12)	0.0326 (5)
H10A	0.8217	0.3997	0.3459	0.049*
H10B	0.9674	0.3758	0.3923	0.049*
H10C	0.8695	0.6092	0.3968	0.049*
C11	0.8532 (2)	0.3653 (4)	0.51018 (11)	0.0313 (5)
H11A	0.9549	0.3308	0.5161	0.047*
H11B	0.8057	0.2657	0.5400	0.047*
H11C	0.8376	0.5369	0.5190	0.047*
O12	0.13924 (16)	0.2825 (3)	0.30147 (9)	0.0356 (4)
C13	0.1257 (2)	0.0752 (4)	0.25826 (11)	0.0277 (5)
O14	0.27047 (15)	−0.0114 (3)	0.25586 (7)	0.0282 (3)
C15	0.0589 (3)	0.1589 (6)	0.19055 (13)	0.0490 (7)
H15A	0.1160	0.2897	0.1752	0.074*
H15B	−0.0375	0.2176	0.1932	0.074*
H15C	0.0558	0.0225	0.1604	0.074*
C16	0.0396 (3)	−0.1209 (5)	0.28758 (14)	0.0411 (6)
H16A	−0.0564	−0.0612	0.2904	0.062*
H16B	0.0849	−0.1617	0.3309	0.062*
H16C	0.0352	−0.2656	0.2602	0.062*
C3'	0.5763 (2)	−0.1049 (4)	0.29004 (10)	0.0240 (4)
H3'1	0.6569	−0.1470	0.3226	0.029*
H3'2	0.5093	−0.2427	0.2863	0.029*
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)
H8'1	0.7087	−0.4682	0.0856	0.050*
H8'2	0.8662	−0.3584	0.0979	0.050*
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''	0.8968	0.0708	0.0409	0.053*
C3''	0.7954 (3)	0.1460 (6)	−0.04903 (14)	0.0525 (7)
H3''	0.8502	0.2845	−0.0565	0.063*
C4''	0.6868 (3)	0.0694 (6)	−0.09655 (13)	0.0520 (8)
H4''	0.6679	0.1563	−0.1359	0.062*
C5''	0.6074 (3)	−0.1351 (7)	−0.08519 (13)	0.0523 (8)
H5''	0.5349	−0.1882	−0.1173	0.063*
C6''	0.6334 (3)	−0.2644 (6)	−0.02641 (13)	0.0454 (7)
H6''	0.5783	−0.4028	−0.0191	0.055*
H4'	0.647 (3)	0.080 (5)	0.2161 (12)	0.028 (7)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0247 (8)	0.0388 (9)	0.0308 (8)	0.0114 (7)	0.0028 (6)	−0.0044 (7)
C1	0.0195 (10)	0.0230 (9)	0.0345 (11)	0.0010 (8)	0.0020 (8)	0.0002 (9)
C2	0.0211 (10)	0.0238 (10)	0.0262 (10)	−0.0003 (8)	0.0038 (8)	0.0025 (8)
C3	0.0170 (9)	0.0232 (9)	0.0249 (10)	−0.0002 (8)	0.0032 (7)	−0.0002 (8)
C4	0.0189 (9)	0.0221 (10)	0.0255 (10)	0.0005 (7)	0.0065 (8)	−0.0007 (8)
C5	0.0225 (10)	0.0197 (9)	0.0250 (10)	−0.0009 (9)	0.0062 (8)	−0.0007 (8)
C6	0.0250 (11)	0.0190 (9)	0.0272 (10)	−0.0019 (8)	0.0016 (8)	0.0025 (8)
O7	0.0232 (7)	0.0175 (6)	0.0356 (8)	0.0016 (6)	0.0072 (6)	0.0001 (6)
C8	0.0191 (10)	0.0202 (9)	0.0309 (11)	−0.0007 (8)	0.0035 (8)	−0.0022 (8)
O9	0.0209 (7)	0.0162 (6)	0.0373 (8)	0.0016 (6)	−0.0002 (6)	−0.0009 (6)
C10	0.0311 (12)	0.0280 (11)	0.0403 (13)	−0.0024 (10)	0.0107 (9)	−0.0010 (10)
C11	0.0267 (11)	0.0284 (10)	0.0373 (12)	0.0007 (9)	−0.0031 (9)	−0.0035 (10)
O12	0.0190 (7)	0.0322 (9)	0.0553 (10)	0.0009 (7)	0.0031 (7)	−0.0107 (8)
C13	0.0202 (10)	0.0256 (10)	0.0361 (12)	0.0009 (8)	−0.0015 (8)	−0.0003 (9)
O14	0.0206 (7)	0.0272 (8)	0.0361 (8)	0.0014 (6)	0.0002 (6)	−0.0051 (6)
C15	0.0341 (13)	0.0673 (18)	0.0430 (15)	0.0070 (15)	−0.0067 (11)	0.0092 (14)
C16	0.0270 (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—C1	1.412 (2)	C13—C16	1.498 (3)
O1—C4	1.442 (2)	C13—C15	1.519 (3)
C1—O12	1.404 (2)	C15—H15A	0.9600
C1—C2	1.526 (3)	C15—H15B	0.9600
C1—H1	0.9800	C15—H15C	0.9600
C2—O14	1.433 (2)	C16—H16A	0.9600
C2—C3	1.519 (3)	C16—H16B	0.9600
C2—H2	0.9800	C16—H16C	0.9600
C3—C3'	1.519 (3)	C3'—N4'	1.457 (3)
C3—C4	1.535 (3)	C3'—H3'1	0.9700
C3—H3	0.9800	C3'—H3'2	0.9700
C4—C5	1.520 (3)	N4'—C5'	1.346 (3)
C4—H4	0.9800	N4'—H4'	0.80 (3)
C5—O9	1.427 (2)	C5'—O6'	1.209 (3)
C5—C6	1.527 (3)	C5'—O7'	1.355 (3)
C5—H5	0.9800	O7'—C8'	1.450 (3)
C6—O7	1.424 (3)	C8'—C1''	1.502 (3)
C6—H6A	0.9700	C8'—H8'1	0.9700
C6—H6B	0.9700	C8'—H8'2	0.9700
O7—C8	1.424 (2)	C1''—C2''	1.384 (4)
C8—O9	1.443 (2)	C1''—C6''	1.387 (4)
C8—C10	1.501 (3)	C2''—C3''	1.376 (4)
C8—C11	1.519 (3)	C2''—H2''	0.9300
C10—H10A	0.9600	C3''—C4''	1.382 (4)
C10—H10B	0.9600	C3''—H3''	0.9300
C10—H10C	0.9600	C4''—C5''	1.367 (5)
C11—H11A	0.9600	C4''—H4''	0.9300
C11—H11B	0.9600	C5''—C6''	1.387 (4)
C11—H11C	0.9600	C5''—H5''	0.9300
O12—C13	1.424 (3)	C6''—H6''	0.9300
C13—O14	1.435 (3)

C1—O1—C4	110.30 (15)	C1—O12—C13	110.36 (16)
O12—C1—O1	111.76 (17)	O12—C13—O14	105.28 (15)
O12—C1—C2	105.29 (17)	O12—C13—C16	108.82 (19)
O1—C1—C2	106.75 (16)	O14—C13—C16	109.43 (18)
O12—C1—H1	110.9	O12—C13—C15	109.1 (2)
O1—C1—H1	110.9	O14—C13—C15	110.69 (19)
C2—C1—H1	110.9	C16—C13—C15	113.2 (2)
O14—C2—C3	110.74 (16)	C2—O14—C13	107.18 (15)
O14—C2—C1	102.96 (16)	C13—C15—H15A	109.5
C3—C2—C1	103.87 (16)	C13—C15—H15B	109.5
O14—C2—H2	112.8	H15A—C15—H15B	109.5
C3—C2—H2	112.8	C13—C15—H15C	109.5
C1—C2—H2	112.8	H15A—C15—H15C	109.5
C2—C3—C3'	115.04 (17)	H15B—C15—H15C	109.5
C2—C3—C4	101.29 (16)	C13—C16—H16A	109.5
C3'—C3—C4	116.30 (17)	C13—C16—H16B	109.5
C2—C3—H3	107.9	H16A—C16—H16B	109.5
C3'—C3—H3	107.9	C13—C16—H16C	109.5
C4—C3—H3	107.9	H16A—C16—H16C	109.5
O1—C4—C5	106.73 (15)	H16B—C16—H16C	109.5
O1—C4—C3	103.54 (15)	N4'—C3'—C3	109.09 (17)
C5—C4—C3	117.26 (16)	N4'—C3'—H3'1	109.9
O1—C4—H4	109.7	C3—C3'—H3'1	109.9
C5—C4—H4	109.7	N4'—C3'—H3'2	109.9
C3—C4—H4	109.7	C3—C3'—H3'2	109.9
O9—C5—C4	110.29 (16)	H3'1—C3'—H3'2	108.3
O9—C5—C6	103.92 (14)	C5'—N4'—C3'	121.7 (2)
C4—C5—C6	115.15 (17)	C5'—N4'—H4'	116.9 (18)
O9—C5—H5	109.1	C3'—N4'—H4'	120.3 (18)
C4—C5—H5	109.1	O6'—C5'—N4'	125.9 (2)
C6—C5—H5	109.1	O6'—C5'—O7'	125.2 (2)
O7—C6—C5	103.79 (16)	N4'—C5'—O7'	108.9 (2)
O7—C6—H6A	111.0	C5'—O7'—C8'	117.5 (2)
C5—C6—H6A	111.0	O7'—C8'—C1''	106.1 (2)
O7—C6—H6B	111.0	O7'—C8'—H8'1	110.5
C5—C6—H6B	111.0	C1''—C8'—H8'1	110.5
H6A—C6—H6B	109.0	O7'—C8'—H8'2	110.5
C6—O7—C8	105.08 (16)	C1''—C8'—H8'2	110.5
O7—C8—O9	104.38 (16)	H8'1—C8'—H8'2	108.7
O7—C8—C10	108.31 (18)	C2''—C1''—C6''	118.9 (2)
O9—C8—C10	109.48 (17)	C2''—C1''—C8'	120.8 (2)
O7—C8—C11	111.69 (17)	C6''—C1''—C8'	120.2 (3)
O9—C8—C11	109.16 (17)	C3''—C2''—C1''	120.6 (3)
C10—C8—C11	113.42 (18)	C3''—C2''—H2''	119.7
C5—O9—C8	108.74 (14)	C1''—C2''—H2''	119.7
C8—C10—H10A	109.5	C2''—C3''—C4''	120.4 (3)
C8—C10—H10B	109.5	C2''—C3''—H3''	119.8
H10A—C10—H10B	109.5	C4''—C3''—H3''	119.8
C8—C10—H10C	109.5	C5''—C4''—C3''	119.4 (3)
H10A—C10—H10C	109.5	C5''—C4''—H4''	120.3
H10B—C10—H10C	109.5	C3''—C4''—H4''	120.3
C8—C11—H11A	109.5	C4''—C5''—C6''	120.8 (3)
C8—C11—H11B	109.5	C4''—C5''—H5''	119.6
H11A—C11—H11B	109.5	C6''—C5''—H5''	119.6
C8—C11—H11C	109.5	C5''—C6''—C1''	119.9 (3)
H11A—C11—H11C	109.5	C5''—C6''—H6''	120.1
H11B—C11—H11C	109.5	C1''—C6''—H6''	120.1

C4—O1—C1—O12	107.54 (18)	C11—C8—O9—C5	−95.99 (19)
C4—O1—C1—C2	−7.1 (2)	O1—C1—O12—C13	−111.56 (19)
O12—C1—C2—O14	−20.6 (2)	C2—C1—O12—C13	4.0 (2)
O1—C1—C2—O14	98.33 (18)	C1—O12—C13—O14	14.4 (2)
O12—C1—C2—C3	−136.12 (17)	C1—O12—C13—C16	131.58 (19)
O1—C1—C2—C3	−17.2 (2)	C1—O12—C13—C15	−104.5 (2)
O14—C2—C3—C3'	49.2 (2)	C3—C2—O14—C13	140.31 (17)
C1—C2—C3—C3'	159.10 (16)	C1—C2—O14—C13	29.82 (19)
O14—C2—C3—C4	−77.1 (2)	O12—C13—O14—C2	−28.1 (2)
C1—C2—C3—C4	32.8 (2)	C16—C13—O14—C2	−144.9 (2)
C1—O1—C4—C5	152.58 (16)	C15—C13—O14—C2	89.6 (2)
C1—O1—C4—C3	28.2 (2)	C2—C3—C3'—N4'	65.0 (2)
C2—C3—C4—O1	−37.23 (19)	C4—C3—C3'—N4'	−176.82 (16)
C3'—C3—C4—O1	−162.69 (16)	C3—C3'—N4'—C5'	−165.57 (19)
C2—C3—C4—C5	−154.43 (17)	C3'—N4'—C5'—O6'	3.5 (4)
C3'—C3—C4—C5	80.1 (2)	C3'—N4'—C5'—O7'	−177.68 (18)
O1—C4—C5—O9	−67.04 (19)	O6'—C5'—O7'—C8'	0.7 (3)
C3—C4—C5—O9	48.4 (2)	N4'—C5'—O7'—C8'	−178.11 (19)
O1—C4—C5—C6	175.77 (16)	C5'—O7'—C8'—C1''	153.0 (2)
C3—C4—C5—C6	−68.8 (2)	O7'—C8'—C1''—C2''	67.3 (3)
O9—C5—C6—O7	−20.8 (2)	O7'—C8'—C1''—C6''	−109.6 (3)
C4—C5—C6—O7	99.97 (19)	C6''—C1''—C2''—C3''	0.9 (4)
C5—C6—O7—C8	35.75 (19)	C8'—C1''—C2''—C3''	−176.1 (2)
C6—O7—C8—O9	−37.11 (19)	C1''—C2''—C3''—C4''	−0.5 (4)
C6—O7—C8—C10	−153.69 (17)	C2''—C3''—C4''—C5''	−0.3 (4)
C6—O7—C8—C11	80.7 (2)	C3''—C4''—C5''—C6''	0.7 (4)
C4—C5—O9—C8	−125.60 (16)	C4''—C5''—C6''—C1''	−0.3 (4)
C6—C5—O9—C8	−1.7 (2)	C2''—C1''—C6''—C5''	−0.5 (4)
O7—C8—O9—C5	23.5 (2)	C8'—C1''—C6''—C5''	176.5 (2)
C10—C8—O9—C5	139.31 (17)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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.

Experimental details

Crystal data
Chemical formula	C₂₁H₂₉NO₇
M_r	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)
V (Å³)	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 diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	5535, 3279, 2597
R_int	0.034
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	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

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. Web of Science CrossRef CAS IUCr Journals Google Scholar
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Volume 71| Part 10| October 2015| Pages 1212-1215

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research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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

1. Chemical context

2. Structural commentary

3. Supra­molecular features

4. Database survey

5. Synthesis and crystallization

6. Refinement

Supporting information

Acknowledgements

References

research communications

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

3. Supramolecular features