2-Acetamido-N-benzyl-1,4-imino-1,2,4-tride-oxy-l-xylitol (N-benzyl-l-XYLNAc).

X-ray crystallography defines the relative configuration at the three-stereogenic centres in the title compound N-benzyl-l-XYLNAc, C(14)H(20)N(2)O(3). The five-membered pyrrolidine ring adopts an envelope conformation with the N atom lying out of the plane of the other four atoms. In the crystal structure, inter-molecular O-H⋯O, N-H⋯O and O-H⋯N hydrogen bonds link the mol-ecules into chains along [100]. The carbonyl group O atom acts as an acceptor for a bifurcated hydrogen bond. The absolute configuration is determined by the use of l-glucuronolactone as the starting material for the synthesis.

Related literature

For imino­sugars see: Asano et al. (2000 ▶); Watson et al. (2001 ▶). For the inhibition of hexosaminidases, see: Liu, Numa et al. (2004 ▶); Reese et al. (2007 ▶); Liu, Iqbal et al. (2004 ▶); Woynarowska et al. (1992 ▶). For piperidine hexosaminidase inhibitors, see: Tatsuta et al. (1997 ▶); Fleet et al. (1986 ▶, 1987 ▶); Steiner et al. (2009 ▶); Ho et al. (2010 ▶); For furan­ose hexosaminidase inhibitors, see: Usuki et al. (2009 ▶); Rountree et al. (2007 ▶, 2009 ▶); Boomkamp et al. (2010 ▶). For strategies for cancer treatment, see: Kato et al. (2010 ▶); Greco et al. (2009 ▶). For the use of glucuronolactone as a starting material for the synthesis of imino­sugars, see: Best, Wang et al. (2010 ▶); Best, Chairatana et al. (2010 ▶).

Experimental

Crystal data

C14H20N2O3

M = 264.32

Orthorhombic,

a = 4.9731 (1) Å

b = 10.0145 (3) Å

c = 26.9297 (7) Å

V = 1341.18 (6) Å3

Z = 4

Mo Kα radiation

μ = 0.09 mm−1

T = 150 K

0.50 × 0.15 × 0.05 mm

Data collection

Nonius KappaCCD area-detector diffractometer

Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997 ▶) T min = 0.77, T max = 1.00

7494 measured reflections

1788 independent reflections

1471 reflections with I > 2σ(I)

R int = 0.040

Refinement

R[F 2 > 2σ(F 2)] = 0.051

wR(F 2) = 0.130

S = 0.95

1788 reflections

172 parameters

H-atom parameters constrained

Δρmax = 0.33 e Å−3

Δρmin = −0.46 e Å−3

Data collection: COLLECT (Nonius, 2001 ▶); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997 ▶); data reduction: DENZO/SCALEPACK and Görbitz (1999 ▶); 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.

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810014145/lh5029sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810014145/lh5029Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C14H20N2O3	F(000) = 568
Mr = 264.32	Dx = 1.309 Mg m−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 1650 reflections
a = 4.9731 (1) Å	θ = 5–27°
b = 10.0145 (3) Å	µ = 0.09 mm−1
c = 26.9297 (7) Å	T = 150 K
V = 1341.18 (6) Å3	Needle, colourless
Z = 4	0.50 × 0.15 × 0.05 mm

Nonius KappaCCD area-detector diffractometer	1471 reflections with I > 2σ(I)
graphite	Rint = 0.040
ω scans	θmax = 27.5°, θmin = 5.1°
Absorption correction: multi-scan (DENZO/SCALEPACK; Otwinowski & Minor, 1997)	h = −6→6
Tmin = 0.77, Tmax = 1.00	k = −12→12
7494 measured reflections	l = −34→34
1788 independent reflections

Refinement on F2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.051	H-atom parameters constrained
wR(F2) = 0.130	Method = Modified Sheldrick w = 1/[σ2(F2) + (0.07P)2 + 0.9P], where P = [max(Fo2,0) + 2Fc2]/3
S = 0.95	(Δ/σ)max = 0.0003
1788 reflections	Δρmax = 0.33 e Å−3
172 parameters	Δρmin = −0.46 e Å−3
0 restraints

	x	y	z	Uiso*/Ueq
O1	0.9783 (4)	0.43009 (19)	0.61171 (7)	0.0319
C2	0.7716 (7)	0.4811 (3)	0.58063 (10)	0.0297
C3	0.6606 (6)	0.6164 (3)	0.59663 (10)	0.0231
N4	0.4652 (5)	0.6138 (2)	0.63782 (8)	0.0240
C5	0.5868 (6)	0.5705 (3)	0.68516 (10)	0.0294
C6	0.3890 (6)	0.5636 (3)	0.72762 (9)	0.0260
C7	0.1951 (6)	0.4640 (3)	0.72916 (10)	0.0290
C8	0.0221 (7)	0.4529 (3)	0.76921 (11)	0.0382
C9	0.0372 (7)	0.5432 (4)	0.80805 (11)	0.0431
C10	0.2268 (8)	0.6428 (4)	0.80709 (11)	0.0441
C11	0.4029 (7)	0.6540 (3)	0.76700 (11)	0.0359
C12	0.3731 (6)	0.7532 (3)	0.64027 (10)	0.0262
C13	0.3392 (6)	0.7942 (3)	0.58540 (9)	0.0240
C14	0.5058 (6)	0.6899 (3)	0.55652 (9)	0.0259
O15	0.3165 (4)	0.6041 (2)	0.53220 (7)	0.0325
N16	0.4213 (5)	0.9324 (2)	0.57677 (8)	0.0258
C17	0.2483 (6)	1.0276 (3)	0.56297 (10)	0.0243
C18	0.3628 (7)	1.1653 (3)	0.55702 (12)	0.0344
O19	0.0046 (4)	1.0055 (2)	0.55648 (7)	0.0301
H22	0.8439	0.4905	0.5468	0.0376*
H21	0.6258	0.4171	0.5801	0.0378*
H31	0.8146	0.6719	0.6070	0.0290*
H51	0.6619	0.4808	0.6798	0.0390*
H52	0.7323	0.6330	0.6949	0.0386*
H71	0.1814	0.4027	0.7021	0.0362*
H81	−0.1097	0.3838	0.7705	0.0516*
H91	−0.0852	0.5371	0.8355	0.0554*
H101	0.2377	0.7039	0.8338	0.0523*
H111	0.5375	0.7242	0.7665	0.0449*
H122	0.2057	0.7596	0.6587	0.0343*
H121	0.5034	0.8116	0.6565	0.0343*
H131	0.1474	0.7860	0.5763	0.0293*
H141	0.6349	0.7323	0.5324	0.0339*
H181	0.2239	1.2282	0.5501	0.0525*
H183	0.4944	1.1658	0.5306	0.0528*
H182	0.4537	1.1924	0.5865	0.0527*
H151	0.3832	0.5671	0.5065	0.0524*
H161	0.5958	0.9521	0.5796	0.0324*
H11	1.0957	0.4903	0.6166	0.0526*

	U11	U22	U33	U12	U13	U23
O1	0.0291 (11)	0.0288 (11)	0.0377 (10)	0.0048 (10)	0.0042 (10)	0.0039 (9)
C2	0.0294 (15)	0.0284 (15)	0.0313 (13)	0.0024 (14)	0.0030 (13)	−0.0026 (12)
C3	0.0188 (12)	0.0250 (13)	0.0255 (12)	−0.0023 (12)	0.0046 (11)	−0.0004 (11)
N4	0.0245 (12)	0.0263 (12)	0.0212 (10)	0.0009 (11)	0.0047 (10)	0.0021 (9)
C5	0.0259 (14)	0.0339 (16)	0.0285 (13)	0.0004 (14)	−0.0001 (13)	0.0041 (12)
C6	0.0275 (13)	0.0278 (15)	0.0228 (12)	0.0025 (13)	−0.0014 (12)	0.0050 (11)
C7	0.0293 (15)	0.0328 (16)	0.0250 (12)	0.0011 (13)	−0.0034 (12)	0.0055 (12)
C8	0.0334 (16)	0.050 (2)	0.0309 (14)	−0.0051 (16)	0.0010 (14)	0.0136 (14)
C9	0.0385 (17)	0.063 (2)	0.0279 (14)	0.0076 (19)	0.0069 (14)	0.0106 (15)
C10	0.058 (2)	0.047 (2)	0.0277 (14)	0.007 (2)	0.0017 (17)	−0.0042 (14)
C11	0.0422 (18)	0.0360 (17)	0.0295 (14)	−0.0026 (15)	−0.0002 (15)	−0.0017 (13)
C12	0.0263 (14)	0.0271 (15)	0.0251 (12)	0.0021 (13)	0.0047 (12)	0.0014 (11)
C13	0.0213 (14)	0.0231 (14)	0.0275 (13)	−0.0009 (12)	0.0012 (12)	0.0019 (11)
C14	0.0265 (14)	0.0282 (14)	0.0230 (12)	−0.0031 (13)	0.0035 (13)	−0.0009 (11)
O15	0.0286 (11)	0.0400 (12)	0.0288 (9)	−0.0021 (10)	−0.0029 (9)	−0.0099 (9)
N16	0.0213 (11)	0.0238 (12)	0.0322 (12)	−0.0029 (11)	−0.0003 (10)	0.0021 (10)
C17	0.0248 (13)	0.0254 (14)	0.0228 (12)	−0.0001 (12)	−0.0009 (12)	−0.0023 (11)
C18	0.0349 (17)	0.0257 (15)	0.0427 (16)	−0.0007 (14)	−0.0017 (16)	0.0013 (13)
O19	0.0213 (9)	0.0343 (11)	0.0345 (10)	0.0027 (10)	−0.0024 (9)	−0.0056 (9)

O1—C2	1.420 (4)	C9—H91	0.960
O1—H11	0.850	C10—C11	1.394 (5)
C2—C3	1.525 (4)	C10—H101	0.946
C2—H22	0.984	C11—H111	0.971
C2—H21	0.967	C12—C13	1.543 (4)
C3—N4	1.475 (3)	C12—H122	0.971
C3—C14	1.517 (4)	C12—H121	0.976
C3—H31	0.987	C13—C14	1.543 (4)
N4—C5	1.476 (3)	C13—N16	1.462 (3)
N4—C12	1.471 (4)	C13—H131	0.988
C5—C6	1.510 (4)	C14—O15	1.434 (3)
C5—H51	0.984	C14—H141	1.007
C5—H52	0.992	O15—H151	0.852
C6—C7	1.388 (4)	N16—C17	1.337 (4)
C6—C11	1.396 (4)	N16—H161	0.893
C7—C8	1.384 (4)	C17—C18	1.500 (4)
C7—H71	0.954	C17—O19	1.245 (4)
C8—C9	1.385 (5)	C18—H181	0.954
C8—H81	0.954	C18—H183	0.966
C9—C10	1.373 (5)	C18—H182	0.953
C2—O1—H11	109.5	C11—C10—H101	120.1
O1—C2—C3	114.5 (2)	C6—C11—C10	120.3 (3)
O1—C2—H22	108.4	C6—C11—H111	119.5
C3—C2—H22	108.0	C10—C11—H111	120.2
O1—C2—H21	108.3	N4—C12—C13	104.1 (2)
C3—C2—H21	108.7	N4—C12—H122	110.6
H22—C2—H21	108.9	C13—C12—H122	112.3
C2—C3—N4	115.8 (2)	N4—C12—H121	112.4
C2—C3—C14	114.5 (2)	C13—C12—H121	110.0
N4—C3—C14	102.1 (2)	H122—C12—H121	107.5
C2—C3—H31	107.5	C12—C13—C14	104.1 (2)
N4—C3—H31	107.9	C12—C13—N16	111.9 (2)
C14—C3—H31	108.8	C14—C13—N16	114.2 (2)
C3—N4—C5	112.6 (2)	C12—C13—H131	108.7
C3—N4—C12	102.8 (2)	C14—C13—H131	109.7
C5—N4—C12	111.6 (2)	N16—C13—H131	108.0
N4—C5—C6	113.6 (2)	C13—C14—C3	104.0 (2)
N4—C5—H51	107.2	C13—C14—O15	106.5 (2)
C6—C5—H51	108.5	C3—C14—O15	111.5 (2)
N4—C5—H52	110.0	C13—C14—H141	112.5
C6—C5—H52	107.7	C3—C14—H141	109.9
H51—C5—H52	109.8	O15—C14—H141	112.1
C5—C6—C7	120.5 (3)	C14—O15—H151	112.1
C5—C6—C11	120.9 (3)	C13—N16—C17	122.7 (2)
C7—C6—C11	118.5 (3)	C13—N16—H161	117.8
C6—C7—C8	120.8 (3)	C17—N16—H161	119.4
C6—C7—H71	119.3	N16—C17—C18	116.2 (3)
C8—C7—H71	119.9	N16—C17—O19	122.6 (3)
C7—C8—C9	120.2 (3)	C18—C17—O19	121.2 (3)
C7—C8—H81	120.9	C17—C18—H181	110.7
C9—C8—H81	119.0	C17—C18—H183	109.9
C8—C9—C10	119.9 (3)	H181—C18—H183	110.0
C8—C9—H91	120.4	C17—C18—H182	110.7
C10—C9—H91	119.7	H181—C18—H182	108.6
C9—C10—C11	120.3 (3)	H183—C18—H182	106.8
C9—C10—H101	119.6

D—H···A	D—H	H···A	D···A	D—H···A
C5—H51···O1	0.98	2.47	3.111 (4)	123
C14—H141···O15i	1.01	2.56	3.514 (4)	159
O15—H151···O19i	0.85	1.94	2.790 (4)	173
N16—H161···O19ii	0.89	2.19	3.041 (4)	159
O1—H11···N4ii	0.85	2.29	3.121 (4)	167

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O15—H151⋯O19i	0.85	1.94	2.790 (4)	173
N16—H161⋯O19ii	0.89	2.19	3.041 (4)	159
O1—H11⋯N4ii	0.85	2.29	3.121 (4)	167

Symmetry codes: (i) ; (ii) .