N-Benzyl-1,3-dide­oxy-1,3-imino-l-xylitol

Jenkinson, S.F.; Lenagh-Snow, G.M.J.; Fleet, G.W.J.; Thompson, A.L.

doi:10.1107/S160053681103399X

organic compounds

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Volume 67| Part 9| September 2011| Page o2452

doi:10.1107/S160053681103399X

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N-Benzyl-1,3-dideoxy-1,3-imino-L-xylitol

Sarah F. Jenkinson,^a ^* Gabriel M. J. Lenagh-Snow,^a George W. J. Fleet ^a and Amber L. Thompson ^b

^aDepartment of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, England, and ^bDepartment of Chemical Crystallography, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, England
^*Correspondence e-mail: sarah.jenkinson@chem.ox.ac.uk

(Received 16 August 2011; accepted 19 August 2011; online 27 August 2011)

The structure determination confirms the stereochemistry of the title compound, C₁₂H₁₇NO₃, which contains a four-membered azetidine ring system. The absolute configuration was determined by the use of D-glucose as the starting material. In the crystal, O—H⋯O and O—H⋯N hydrogen bonds link the molecules into layers in the ab plane.

Related literature

For related literature on azetidines, see: Krämer et al. (1997 ); Michaud et al. (1997a ,b ); Dekaris & Reissig (2010 ); Soengas et al. (2011 ). For related literature on iminosugars, see: Asano et al. (2000 ); Watson et al. (2001 ). For details of the cryostat, see: Cosier & Glazer (1986 ).

Experimental

Crystal data

C₁₂H₁₇NO₃
M_r = 223.27
Orthorhombic, P 2₁ 2₁ 2₁
a = 6.2309 (2) Å
b = 9.3918 (4) Å
c = 19.9175 (9) Å
V = 1165.56 (8) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 150 K
0.20 × 0.10 × 0.07 mm

Data collection

Nonius KappaCCD diffractometer
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997 ) T_min = 0.97, T_max = 0.99
6149 measured reflections
1541 independent reflections
1098 reflections with I > 2σ(I)
R_int = 0.065

Refinement

R[F² > 2σ(F²)] = 0.045
wR(F²) = 0.102
S = 0.95
1541 reflections
146 parameters
H-atom parameters constrained
Δρ_max = 0.49 e Å⁻³
Δρ_min = −0.49 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O4—H41⋯O16ⁱ	0.84	2.18	2.825 (4)	134
O16—H161⋯O1ⁱⁱ	0.84	1.90	2.735 (4)	171
O1—H11⋯N6ⁱ	0.86	1.86	2.719 (4)	171
Symmetry codes: (i) $[-x+2, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (ii) $[-x+1, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

Data collection: COLLECT (Nonius, 2001 ); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1994 ); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003 ); molecular graphics: CAMERON (Watkin et al., 1996 ); software used to prepare material for publication: CRYSTALS.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053681103399X/lh5318sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S160053681103399X/lh5318Isup2.hkl

checkCIF report

Comment top

Azetidines (Michaud et al., 1997a,b; Dekaris & Reissig, 2010; Soengas et al., 2011) are a relatively unstudied class of iminosugars (Asano et al., 2000; Watson et al., 2001) but initial results (Krämer et al., 1997) have shown that they can exhibit interesting biological activity. The title compound was formed from a protected ribofuranose derived from D-glucose (Fig. 1).

The molecular structure of the title compound is shown in Fig. 2. The four-membered ring system adopts a puckered conformation. The structure consists of hydrogen bonded layers of molecules in the ab plane (Fig. 3, Fig. 4). Each molecule is a hydrgen-bond donor and acceptor for three hydrogen bonds. Only classical hydrogen bonding was considered.

Related literature top

For related literature on azetidines, see: Krämer et al. (1997); Michaud et al. (1997a,b); Dekaris & Reissig (2010); Soengas et al. (2011). For related literature on iminosugars, see: Asano et al. (2000); Watson et al. (2001). For details of the cryostat, see: Cosier & Glazer (1986).

Experimental top

The title compound was recrystallized from methanol: [α]_D²⁵ -103.0 (c 0.23 in MeOH); m.p. 452–453 K.

Computing details top

Data collection: COLLECT (Nonius, 2001); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS (Betteridge et al., 2003).

Figures top

	Fig. 1. Synthetic Scheme.
	Fig. 2. The title compound with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitary radius.
	Fig. 3. Packing diagram of the compound projected along the a axis. Hydrogen bonding is denoted by dotted lines.
	Fig. 4. Packing diagram of the compound projected along the b axis. Hydrogen bonding is denoted by dotted lines.

N-Benzyl-1,3-dideoxy-1,3-imino-L-xylitol top

Crystal data top

C₁₂H₁₇NO₃	F(000) = 480
M_r = 223.27	D_x = 1.272 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 1467 reflections
a = 6.2309 (2) Å	θ = 5–27°
b = 9.3918 (4) Å	µ = 0.09 mm⁻¹
c = 19.9175 (9) Å	T = 150 K
V = 1165.56 (8) Å³	Prism, colourless
Z = 4	0.20 × 0.10 × 0.07 mm

Data collection top

Nonius KappaCCD diffractometer	1098 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.065
ω scans	θ_max = 27.5°, θ_min = 5.2°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −8→8
T_min = 0.97, T_max = 0.99	k = −12→12
6149 measured reflections	l = −25→25
1541 independent reflections

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.045	Method = modified Sheldrick, w = 1/[σ²(F²) + (0.05P)² + 0.13P], where P = [max(F_o²,0) + 2F_c²]/3
wR(F²) = 0.102	(Δ/σ)_max = 0.0002627
S = 0.95	Δρ_max = 0.49 e Å⁻³
1541 reflections	Δρ_min = −0.49 e Å⁻³
146 parameters	Extinction correction: Larson (1970), Equation 22
0 restraints	Extinction coefficient: 400 (70)
Primary atom site location: structure-invariant direct methods

Crystal data top

C₁₂H₁₇NO₃	V = 1165.56 (8) Å³
M_r = 223.27	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 6.2309 (2) Å	µ = 0.09 mm⁻¹
b = 9.3918 (4) Å	T = 150 K
c = 19.9175 (9) Å	0.20 × 0.10 × 0.07 mm

Data collection top

Nonius KappaCCD diffractometer	1541 independent reflections
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	1098 reflections with I > 2σ(I)
T_min = 0.97, T_max = 0.99	R_int = 0.065
6149 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.045	0 restraints
wR(F²) = 0.102	H-atom parameters constrained
S = 0.95	Δρ_max = 0.49 e Å⁻³
1541 reflections	Δρ_min = −0.49 e Å⁻³
146 parameters

Special details top

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems open-flow nitrogen cryostat (Cosier & Glazer, 1986) with a nominal stability of 0.1 K.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.7910 (3)	0.89266 (18)	0.79718 (9)	0.0257
C2	0.8327 (4)	0.7498 (3)	0.81847 (12)	0.0246
C3	0.9587 (4)	0.6675 (3)	0.76640 (12)	0.0212
O4	1.1771 (3)	0.71531 (19)	0.75988 (9)	0.0261
C5	0.8472 (4)	0.6736 (3)	0.69895 (12)	0.0206
N6	0.9436 (3)	0.5853 (2)	0.64366 (9)	0.0198
C7	1.0678 (4)	0.6647 (3)	0.59325 (12)	0.0248
C8	1.1061 (4)	0.5768 (3)	0.53082 (12)	0.0252
C9	1.2467 (4)	0.4615 (3)	0.53077 (13)	0.0286
C10	1.2791 (5)	0.3829 (3)	0.47302 (15)	0.0384
C11	1.1727 (5)	0.4177 (3)	0.41474 (14)	0.0366
C12	1.0312 (5)	0.5309 (3)	0.41392 (14)	0.0373
C13	0.9984 (5)	0.6088 (3)	0.47187 (13)	0.0313
C14	0.7214 (4)	0.5438 (3)	0.62186 (13)	0.0277
C15	0.6349 (4)	0.5921 (3)	0.69017 (12)	0.0245
O16	0.6117 (3)	0.48138 (19)	0.73784 (9)	0.0277
H22	0.9101	0.7535	0.8624	0.0291*
H21	0.6964	0.7000	0.8265	0.0280*
H31	0.9716	0.5645	0.7806	0.0250*
H51	0.8349	0.7719	0.6843	0.0251*
H72	1.2057	0.6871	0.6139	0.0252*
H71	0.9916	0.7537	0.5814	0.0268*
H91	1.3207	0.4363	0.5701	0.0319*
H101	1.3719	0.3075	0.4739	0.0480*
H111	1.1995	0.3646	0.3761	0.0436*
H121	0.9557	0.5547	0.3747	0.0440*
H131	0.9009	0.6860	0.4710	0.0365*
H141	0.7104	0.4397	0.6145	0.0348*
H142	0.6670	0.5939	0.5830	0.0324*
H151	0.5114	0.6524	0.6881	0.0289*
H41	1.1628	0.8040	0.7623	0.0399*
H161	0.4864	0.4499	0.7314	0.0409*
H11	0.8789	0.9468	0.8187	0.0398*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0245 (9)	0.0213 (9)	0.0312 (9)	0.0011 (8)	−0.0042 (8)	−0.0039 (9)
C2	0.0288 (15)	0.0219 (14)	0.0231 (13)	−0.0006 (12)	−0.0021 (11)	0.0021 (11)
C3	0.0174 (12)	0.0210 (13)	0.0251 (13)	−0.0022 (11)	−0.0003 (11)	0.0004 (12)
O4	0.0193 (9)	0.0254 (10)	0.0336 (10)	0.0013 (8)	−0.0012 (8)	−0.0025 (9)
C5	0.0242 (13)	0.0189 (12)	0.0187 (11)	−0.0011 (11)	0.0015 (11)	−0.0004 (11)
N6	0.0205 (10)	0.0233 (11)	0.0157 (10)	−0.0008 (10)	−0.0005 (9)	−0.0030 (10)
C7	0.0226 (13)	0.0283 (15)	0.0236 (13)	−0.0042 (13)	0.0003 (12)	−0.0009 (12)
C8	0.0246 (14)	0.0304 (15)	0.0206 (12)	−0.0055 (13)	0.0004 (11)	0.0012 (12)
C9	0.0224 (13)	0.0402 (17)	0.0232 (13)	0.0039 (13)	0.0016 (12)	0.0029 (13)
C10	0.0325 (16)	0.0423 (18)	0.0404 (16)	0.0075 (15)	0.0068 (15)	−0.0048 (16)
C11	0.0372 (16)	0.0458 (19)	0.0267 (14)	0.0000 (16)	0.0051 (14)	−0.0056 (15)
C12	0.0399 (17)	0.0489 (19)	0.0232 (14)	−0.0010 (17)	−0.0029 (14)	−0.0025 (14)
C13	0.0350 (16)	0.0333 (16)	0.0256 (13)	0.0041 (14)	−0.0033 (12)	0.0017 (14)
C14	0.0212 (13)	0.0347 (16)	0.0273 (14)	−0.0005 (13)	−0.0055 (12)	−0.0009 (13)
C15	0.0174 (12)	0.0286 (15)	0.0275 (12)	0.0059 (12)	−0.0002 (11)	0.0017 (13)
O16	0.0215 (9)	0.0282 (10)	0.0335 (10)	−0.0042 (8)	−0.0010 (9)	0.0070 (9)

Geometric parameters (Å, º) top

O1—C2	1.431 (3)	C8—C9	1.393 (4)
O1—H11	0.862	C8—C13	1.385 (4)
C2—C3	1.513 (3)	C9—C10	1.382 (4)
C2—H22	1.000	C9—H91	0.939
C2—H21	0.982	C10—C11	1.376 (4)
C3—O4	1.439 (3)	C10—H101	0.914
C3—C5	1.514 (3)	C11—C12	1.381 (4)
C3—H31	1.011	C11—H111	0.932
O4—H41	0.839	C12—C13	1.382 (4)
C5—N6	1.504 (3)	C12—H121	0.939
C5—C15	1.538 (3)	C13—H131	0.945
C5—H51	0.971	C14—C15	1.532 (3)
N6—C7	1.471 (3)	C14—H141	0.991
N6—C14	1.503 (3)	C14—H142	0.967
C7—C8	1.512 (3)	C15—O16	1.416 (3)
C7—H72	0.976	C15—H151	0.956
C7—H71	0.990	O16—H161	0.844

C2—O1—H11	106.9	C7—C8—C13	120.2 (2)
O1—C2—C3	111.7 (2)	C9—C8—C13	118.2 (2)
O1—C2—H22	108.3	C8—C9—C10	120.5 (3)
C3—C2—H22	111.6	C8—C9—H91	120.3
O1—C2—H21	109.7	C10—C9—H91	119.2
C3—C2—H21	108.5	C9—C10—C11	120.3 (3)
H22—C2—H21	106.9	C9—C10—H101	119.4
C2—C3—O4	113.2 (2)	C11—C10—H101	120.3
C2—C3—C5	110.5 (2)	C10—C11—C12	120.0 (3)
O4—C3—C5	110.0 (2)	C10—C11—H111	118.9
C2—C3—H31	109.8	C12—C11—H111	121.1
O4—C3—H31	104.4	C11—C12—C13	119.5 (3)
C5—C3—H31	108.7	C11—C12—H121	120.9
C3—O4—H41	101.8	C13—C12—H121	119.6
C3—C5—N6	116.5 (2)	C8—C13—C12	121.4 (3)
C3—C5—C15	118.5 (2)	C8—C13—H131	119.5
N6—C5—C15	89.19 (17)	C12—C13—H131	119.1
C3—C5—H51	109.8	N6—C14—C15	89.48 (18)
N6—C5—H51	109.6	N6—C14—H141	111.2
C15—C5—H51	111.8	C15—C14—H141	113.5
C5—N6—C7	115.48 (19)	N6—C14—H142	115.3
C5—N6—C14	89.22 (17)	C15—C14—H142	116.3
C7—N6—C14	114.8 (2)	H141—C14—H142	109.7
N6—C7—C8	111.6 (2)	C5—C15—C14	86.89 (19)
N6—C7—H72	106.5	C5—C15—O16	112.1 (2)
C8—C7—H72	109.0	C14—C15—O16	114.5 (2)
N6—C7—H71	109.8	C5—C15—H151	113.7
C8—C7—H71	109.9	C14—C15—H151	114.9
H72—C7—H71	109.9	O16—C15—H151	112.5
C7—C8—C9	121.6 (2)	C15—O16—H161	104.4

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C11—H111···O4ⁱ	0.93	2.55	3.457 (4)	164
C15—H151···O4ⁱⁱ	0.96	2.59	3.377 (4)	139
O4—H41···O16ⁱⁱⁱ	0.84	2.18	2.825 (4)	134
O16—H161···O1^iv	0.84	1.90	2.735 (4)	171
O1—H11···N6ⁱⁱⁱ	0.86	1.86	2.719 (4)	171

Symmetry codes: (i) −x+5/2, −y+1, z−1/2; (ii) x−1, y, z; (iii) −x+2, y+1/2, −z+3/2; (iv) −x+1, y−1/2, −z+3/2.

Experimental details

Crystal data
Chemical formula	C₁₂H₁₇NO₃
M_r	223.27
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	150
a, b, c (Å)	6.2309 (2), 9.3918 (4), 19.9175 (9)
V (Å³)	1165.56 (8)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.20 × 0.10 × 0.07

Data collection
Diffractometer	Nonius KappaCCD diffractometer
Absorption correction	Multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)
T_min, T_max	0.97, 0.99
No. of measured, independent and observed [I > 2σ(I)] reflections	6149, 1541, 1098
R_int	0.065
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.045, 0.102, 0.95
No. of reflections	1541
No. of parameters	146
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.49, −0.49

Computer programs: COLLECT (Nonius, 2001), DENZO/SCALEPACK (Otwinowski & Minor, 1997), SIR92 (Altomare et al., 1994), CRYSTALS (Betteridge et al., 2003), CAMERON (Watkin et al., 1996).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O4—H41···O16ⁱ	0.84	2.18	2.825 (4)	134
O16—H161···O1ⁱⁱ	0.84	1.90	2.735 (4)	171
O1—H11···N6ⁱ	0.86	1.86	2.719 (4)	171

Symmetry codes: (i) −x+2, y+1/2, −z+3/2; (ii) −x+1, y−1/2, −z+3/2.

References

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