(2S,3R,4S,5R,6S)-6-Benzyl­oxy­methyl-4-(methoxy­methyloxy)-9-oxo-8-oxa-1-aza­bi­cyclo­[4.3.0]­nonane-2,3,5-triyl tri­acetate

The relative configuration of the title compound, C₂₃H₂₉NO₁₁, prepared in a synthetic study on the natural product sphingofungin E, has been determined. The six-membered ring adopts a chair form and the five substituents are all axial.

S1. Comment

The title compound was synthesized in a synthetic study on sphingofungin E (Oishi et al., 2000). The stereochemistries at C-3, C-4 and C-5 (atom labels C2, C3 and C4, respectively) came from those at C-2, C-3 and C-4 of D-glucose, respectively.

S2. Experimental

The title compound was synthesized from D-glucose. The crystals were grown from a toluene solution.

S3. Refinement

There are two possible conformations of the methoxymethyloxy group. The site-occupation factors of O7—C12—O8—C13 and O7—C14—O8—C15 were assumed to be 65 and 35%, respectively. The C14 and C15 atoms were refined isotropically. The positional parameters of all the H atoms were calculated geometrically and fixed with U(H) = 1.2U_eq(parent atom). The absolute structure was assigned based on the known absolute configurations around the C2, C3 and C4 atoms, which came from D-glucose.

Computing details

Data collection: MSC/AFC Diffractometer Control Software (Molecular Structure Corporation, 1993); cell refinement: MSC/AFC Diffractometer Control Software; data reduction: TEXSAN (Molecular Structure Corporation, 1999); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: TEXSAN; software used to prepare material for publication: TEXSAN.

(I)

Crystal data

C23H29NO11	Dx = 1.297 Mg m^−3
Mr = 495.48	Mo Kα radiation, λ = 0.71073 Å
Tetragonal, P43	Cell parameters from 25 reflections
Hall symbol: P 43	θ = 10–15°
a = 14.381 (2) Å	µ = 0.10 mm^−1
c = 12.265 (2) Å	T = 296 K
V = 2536.4 (7) Å^3	Prism, colourless
Z = 4	0.5 × 0.5 × 0.5 mm

Data collection

Rigaku AFC-5S diffractometer	θmax = 26°
θ–2θ scans	h = 0→18
2844 measured reflections	k = 0→18
2621 independent reflections	l = 0→15
1656 reflections with I > 2σ(I)	3 standard reflections every 100 reflections
Rint = 0.010	intensity decay: none

Refinement

Refinement on F^2	H-atom parameters not refined
R[F^2 > 2σ(F^2)] = 0.047	w = 1/[σ^2(Fo^2) + {0.05(Fo^2 + 2Fc^2)/3}^2]
wR(F^2) = 0.116	(Δ/σ)max = 0.026
S = 1.19	Δρmax = 0.16 e Å^−3
2621 reflections	Δρmin = −0.14 e Å^−3
324 parameters	Absolute structure: see text, no Friedel pair

Special details

Refinement. Refinement using reflections with F² > 0.0 σ(F²). The weighted R-factor (wR) and goodness of fit (S) are based on F². R-factor (gt) are based on F. The threshold expression of F² > 2.0 σ(F²) is used only for calculating R-factor (gt).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
O1	0.8376 (2)	0.0426 (2)	0.1522 (9)	0.0708 (8)
O2	0.6961 (2)	−0.0126 (2)	0.1098 (9)	0.095 (1)
O3	0.6033 (2)	0.0822 (2)	0.3845 (9)	0.0616 (8)
O4	0.5143 (5)	−0.0318 (4)	0.3257 (10)	0.176 (2)
O5	0.5844 (2)	0.2293 (2)	0.1511 (9)	0.0685 (8)
O6	0.4895 (3)	0.3465 (3)	0.1936 (9)	0.139 (2)
O7	0.6760 (2)	0.2902 (2)	0.4182 (9)	0.0676 (8)
O8	0.6565 (4)	0.4513 (2)	0.4194 (9)	0.126 (2)
O9	0.7898 (2)	0.2565 (2)	0.1565 (9)	0.0544 (6)
O10	0.8245 (3)	0.4067 (2)	0.1749 (9)	0.095 (1)
O11	0.8208 (2)	0.0282 (2)	0.4279 (9)	0.0715 (8)
N1	0.7183 (2)	0.0905 (2)	0.2499 (9)	0.0481 (7)
C1	0.6233 (2)	0.1108 (2)	0.2744 (9)	0.0521 (8)
C2	0.6025 (3)	0.2138 (3)	0.2661 (9)	0.0565 (9)
C3	0.6802 (3)	0.2800 (2)	0.3030 (9)	0.0519 (8)
C4	0.7780 (2)	0.2474 (2)	0.2730 (9)	0.0485 (8)
C5	0.7948 (2)	0.1443 (2)	0.2961 (9)	0.0467 (8)
C6	0.8773 (3)	0.1035 (3)	0.2323 (9)	0.058 (1)
C7	0.7445 (3)	0.0357 (3)	0.1654 (9)	0.0625 (10)
C8	0.5483 (3)	0.0086 (3)	0.3992 (10)	0.087 (1)
C9	0.5325 (4)	−0.0080 (4)	0.518 (1)	0.108 (2)
C10	0.5245 (4)	0.2988 (4)	0.126 (1)	0.099 (2)
C11	0.5122 (6)	0.3063 (5)	0.006 (1)	0.148 (3)
C12	0.6184 (6)	0.3661 (5)	0.452 (1)	0.094 (2)	0.65
C13	0.746 (1)	0.4666 (9)	0.459 (2)	0.179 (5)	0.65
C14	0.716 (1)	0.383 (1)	0.456 (2)	0.091 (4)*	0.35
C15	0.569 (2)	0.439 (2)	0.472 (2)	0.160 (8)*	0.35
C16	0.8177 (3)	0.3398 (3)	0.1179 (9)	0.066 (1)
C17	0.8383 (4)	0.3356 (3)	−0.0004 (10)	0.098 (2)
C18	0.8061 (3)	0.1253 (2)	0.4178 (9)	0.0544 (9)
C19	0.8250 (3)	−0.0041 (3)	0.5345 (9)	0.069 (1)
C20	0.8342 (3)	−0.1084 (3)	0.5332 (9)	0.062 (1)
C21	0.7859 (3)	−0.1620 (3)	0.4599 (9)	0.072 (1)
C22	0.7954 (4)	−0.2575 (3)	0.4611 (10)	0.094 (2)
C23	0.8545 (4)	−0.2981 (3)	0.537 (1)	0.100 (2)
C24	0.9010 (4)	−0.2459 (4)	0.6098 (10)	0.104 (2)
C25	0.8917 (3)	−0.1516 (3)	0.6072 (10)	0.080 (1)
H1	0.5837	0.0773	0.2250	0.0626*
H2	0.5472	0.2273	0.3069	0.0678*
H3	0.6698	0.3397	0.2702	0.0623*
H4	0.8234	0.2844	0.3105	0.0582*
H5	0.9119	0.1523	0.1975	0.0691*
H6	0.9176	0.0695	0.2803	0.0691*
H7	0.5909	−0.0195	0.5534	0.1290*
H8	0.4927	−0.0611	0.5273	0.1290*
H9	0.5036	0.0456	0.5499	0.1290*
H10	0.5713	0.3188	−0.0278	0.1792*
H11	0.4879	0.2487	−0.0221	0.1792*
H12	0.4698	0.3558	−0.0106	0.1792*
H13	0.6136	0.3653	0.5306	0.1132*	0.65
H14	0.5578	0.3591	0.4210	0.1132*	0.65
H15	0.7455	0.4651	0.5379	0.2150*	0.65
H16	0.7687	0.5259	0.4353	0.2150*	0.65
H17	0.7873	0.4185	0.4332	0.2150*	0.65
H18	0.7768	0.3908	0.4254	0.1094*	0.35
H19	0.7197	0.3834	0.5339	0.1094*	0.35
H20	0.5773	0.4444	0.5488	0.1899*	0.35
H21	0.5441	0.3802	0.4531	0.1899*	0.35
H22	0.5276	0.4878	0.4471	0.1899*	0.35
H23	0.8577	0.3958	−0.0253	0.1175*
H24	0.8872	0.2914	−0.0131	0.1175*
H25	0.7835	0.3167	−0.0392	0.1175*
H26	0.7510	0.1434	0.4566	0.0652*
H27	0.8585	0.1589	0.4461	0.0652*
H28	0.7692	0.0130	0.5725	0.0830*
H29	0.8778	0.0227	0.5707	0.0830*
H30	0.7454	−0.1330	0.4077	0.0864*
H31	0.7619	−0.2954	0.4102	0.1132*
H32	0.8622	−0.3644	0.5379	0.1207*
H33	0.9403	−0.2748	0.6633	0.1243*
H34	0.9261	−0.1145	0.6582	0.0955*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.072 (1)	0.069 (2)	0.071 (2)	0.013 (1)	0.009 (1)	−0.022 (1)
O2	0.101 (2)	0.080 (2)	0.105 (3)	−0.004 (2)	−0.019 (2)	−0.054 (2)
O3	0.053 (1)	0.071 (2)	0.061 (1)	−0.010 (1)	0.006 (1)	0.010 (1)
O4	0.235 (6)	0.170 (5)	0.125 (4)	−0.156 (4)	0.023 (4)	−0.023 (3)
O5	0.068 (2)	0.072 (2)	0.066 (2)	−0.005 (1)	−0.012 (1)	0.010 (1)
O6	0.133 (4)	0.113 (3)	0.171 (5)	0.066 (3)	−0.024 (3)	0.016 (3)
O7	0.094 (2)	0.057 (2)	0.051 (1)	0.006 (1)	0.006 (2)	−0.008 (1)
O8	0.199 (5)	0.063 (2)	0.116 (3)	0.018 (2)	0.016 (3)	−0.016 (2)
O9	0.070 (2)	0.042 (1)	0.051 (1)	−0.008 (1)	0.009 (1)	0.000 (1)
O10	0.157 (3)	0.047 (2)	0.082 (2)	−0.029 (2)	0.004 (2)	0.006 (1)
O11	0.105 (2)	0.053 (1)	0.057 (1)	0.011 (1)	0.001 (2)	0.008 (1)
N1	0.050 (1)	0.042 (2)	0.052 (2)	−0.003 (1)	0.002 (1)	−0.003 (1)
C1	0.045 (1)	0.056 (2)	0.055 (2)	−0.010 (1)	−0.003 (2)	0.000 (2)
C2	0.048 (2)	0.059 (2)	0.062 (2)	0.005 (1)	0.004 (2)	0.003 (2)
C3	0.065 (2)	0.043 (2)	0.048 (2)	0.006 (1)	0.004 (2)	0.000 (2)
C4	0.057 (2)	0.040 (1)	0.048 (1)	−0.006 (1)	0.000 (2)	−0.004 (2)
C5	0.048 (2)	0.039 (1)	0.053 (2)	−0.005 (1)	0.001 (1)	0.001 (2)
C6	0.053 (2)	0.052 (2)	0.068 (2)	0.003 (2)	0.011 (2)	0.004 (2)
C7	0.074 (2)	0.047 (2)	0.066 (2)	0.009 (2)	0.006 (2)	−0.010 (2)
C8	0.072 (3)	0.077 (3)	0.112 (3)	−0.018 (2)	0.030 (3)	0.030 (3)
C9	0.096 (4)	0.111 (4)	0.115 (4)	−0.006 (3)	0.032 (3)	0.049 (4)
C10	0.083 (3)	0.076 (3)	0.138 (4)	−0.008 (2)	−0.040 (3)	0.047 (3)
C11	0.167 (6)	0.136 (5)	0.142 (4)	−0.040 (5)	−0.085 (6)	0.067 (5)
C12	0.112 (6)	0.080 (3)	0.091 (6)	0.035 (3)	0.032 (5)	−0.021 (4)
C13	0.222 (9)	0.15 (1)	0.16 (1)	−0.09 (1)	−0.013 (10)	−0.056 (9)
C16	0.081 (3)	0.045 (2)	0.074 (2)	−0.003 (2)	0.009 (2)	0.010 (1)
C17	0.147 (5)	0.072 (3)	0.075 (2)	0.005 (3)	0.027 (3)	0.014 (3)
C18	0.057 (2)	0.052 (1)	0.055 (2)	−0.003 (2)	−0.004 (2)	0.002 (2)
C19	0.084 (3)	0.067 (2)	0.056 (2)	0.007 (2)	−0.008 (2)	0.009 (2)
C20	0.056 (2)	0.067 (2)	0.062 (2)	0.003 (2)	0.005 (2)	0.014 (2)
C21	0.082 (3)	0.068 (2)	0.066 (3)	0.002 (2)	−0.005 (2)	0.012 (2)
C22	0.118 (4)	0.068 (2)	0.097 (4)	−0.009 (3)	0.004 (3)	0.004 (3)
C23	0.120 (4)	0.065 (3)	0.116 (4)	0.013 (3)	0.015 (3)	0.030 (3)
C24	0.108 (4)	0.092 (2)	0.111 (5)	0.025 (3)	−0.012 (3)	0.034 (3)
C25	0.068 (3)	0.087 (2)	0.084 (3)	0.013 (2)	−0.018 (2)	0.020 (3)

Geometric parameters (Å, º)

O1—C6	1.436 (5)	C9—H8	0.961
O1—C7	1.352 (5)	C9—H9	0.960
O2—C7	1.197 (6)	C10—C11	1.49 (1)
O3—C1	1.441 (5)	C11—H10	0.961
O3—C8	1.333 (6)	C11—H11	0.961
O4—C8	1.178 (8)	C11—H12	0.957
O5—C2	1.452 (5)	C12—H13	0.962
O5—C10	1.355 (6)	C12—H14	0.957
O6—C10	1.187 (9)	C13—H15	0.962
O7—C3	1.422 (5)	C13—H16	0.959
O7—C12	1.432 (8)	C13—H17	0.967
O7—C14	1.52 (2)	C14—H18	0.959
O8—C12	1.40 (1)	C14—H19	0.961
O8—C13	1.40 (2)	C15—H20	0.953
O8—C14	1.38 (2)	C15—H21	0.952
O8—C15	1.42 (3)	C15—H22	0.967
O9—C4	1.445 (5)	C16—C17	1.482 (7)
O9—C16	1.349 (5)	C17—H23	0.960
O10—C16	1.192 (5)	C17—H24	0.961
O11—C18	1.418 (5)	C17—H25	0.959
O11—C19	1.389 (5)	C18—H26	0.960
N1—C1	1.429 (5)	C18—H27	0.960
N1—C5	1.459 (5)	C19—C20	1.505 (6)
N1—C7	1.354 (5)	C19—H28	0.960
C1—C2	1.515 (6)	C19—H29	0.960
C1—H1	0.960	C20—C21	1.373 (7)
C2—C3	1.535 (6)	C20—C25	1.375 (6)
C2—H2	0.960	C21—C22	1.381 (7)
C3—C4	1.527 (5)	C21—H30	0.960
C3—H3	0.960	C22—C23	1.391 (9)
C4—C5	1.529 (5)	C22—H31	0.960
C4—H4	0.960	C23—C24	1.343 (9)
C5—C6	1.537 (6)	C23—H32	0.960
C5—C18	1.526 (6)	C24—C25	1.362 (7)
C6—H5	0.960	C24—H33	0.961
C6—H6	0.960	C25—H34	0.960
C8—C9	1.496 (9)	H14—H21	0.534
C9—H7	0.959	H17—H18	0.436
O1···C6^i	3.271 (5)	O6···C15^vi	3.38 (3)
O1···C18^i	3.447 (5)	O6···C11^iv	3.413 (9)
O2···C4^i	3.296 (5)	O6···C17^iv	3.526 (9)
O2···C9^ii	3.487 (7)	O8···C15^vi	3.26 (3)
O2···C24^iii	3.561 (8)	O10···C8^vi	3.163 (6)
O2···O10^i	3.580 (5)	O10···C9^vi	3.398 (7)
O3···O10^iv	3.169 (4)	O10···C2^vi	3.469 (5)
O4···C13^i	3.51 (2)	C15···C15^vi	3.59 (2)
O4···C23^v	3.545 (7)	C15···C15^iv	3.59 (2)
O4···O10^iv	3.572 (8)
C6—O1—C7	110.9 (3)	H10—C11—H11	109
C1—O3—C8	118.1 (4)	H10—C11—H12	109.6
C2—O5—C10	116.6 (4)	H11—C11—H12	109.6
C3—O7—C12	113.2 (5)	O7—C12—O8	110.8 (6)
C3—O7—C14	112.1 (7)	O7—C12—H13	109.0
C12—O8—C13	113.4 (9)	O7—C12—H14	109.2
C14—O8—C15	108 (1)	O8—C12—H13	109.0
C4—O9—C16	117.6 (3)	O8—C12—H14	109.3
C18—O11—C19	114.7 (3)	H13—C12—H14	109
C1—N1—C5	122.0 (3)	O8—C13—H15	109
C1—N1—C7	123.1 (3)	O8—C13—H16	110
C5—N1—C7	113.3 (3)	O8—C13—H17	109
O3—C1—N1	109.2 (3)	H15—C13—H16	109
O3—C1—C2	107.6 (3)	H15—C13—H17	108
O3—C1—H1	109.3	H16—C13—H17	108
N1—C1—C2	112.0 (3)	O7—C14—O8	107 (1)
N1—C1—H1	109.3	O7—C14—H18	109
C2—C1—H1	109.4	O7—C14—H19	109
O5—C2—C1	104.5 (3)	O8—C14—H18	110
O5—C2—C3	108.8 (3)	O8—C14—H19	110
O5—C2—H2	109.0	H18—C14—H19	109
C1—C2—C3	116.3 (3)	O8—C15—H20	109
C1—C2—H2	109.0	O8—C15—H21	109
C3—C2—H2	109.0	O8—C15—H22	108
O7—C3—C2	109.0 (3)	H20—C15—H21	110
O7—C3—C4	108.1 (3)	H20—C15—H22	109
O7—C3—H3	108.5	H21—C15—H22	109
C2—C3—C4	114.1 (3)	O9—C16—O10	122.3 (4)
C2—C3—H3	108.5	O9—C16—C17	111.5 (4)
C4—C3—H3	108.5	O10—C16—C17	126.2 (4)
O9—C4—C3	108.6 (3)	C16—C17—H23	109.5
O9—C4—C5	104.6 (3)	C16—C17—H24	109.4
O9—C4—H4	110.0	C16—C17—H25	109.5
C3—C4—C5	113.5 (3)	H23—C17—H24	109.4
C3—C4—H4	110.0	H23—C17—H25	109.6
C5—C4—H4	110.0	H24—C17—H25	109.5
N1—C5—C4	108.9 (3)	O11—C18—C5	106.1 (3)
N1—C5—C6	100.5 (3)	O11—C18—H26	110.3
N1—C5—C18	111.4 (3)	O11—C18—H27	110.3
C4—C5—C6	113.4 (3)	C5—C18—H26	110.3
C4—C5—C18	111.8 (3)	C5—C18—H27	110.3
C6—C5—C18	110.3 (3)	H26—C18—H27	109.4
O1—C6—C5	105.9 (3)	O11—C19—C20	109.1 (4)
O1—C6—H5	110.4	O11—C19—H28	109.6
O1—C6—H6	110.4	O11—C19—H29	109.6
C5—C6—H5	110.4	C20—C19—H28	109.6
C5—C6—H6	110.3	C20—C19—H29	109.6
H5—C6—H6	109.5	H28—C19—H29	109
O1—C7—O2	123.3 (4)	C19—C20—C21	121.4 (4)
O1—C7—N1	109.0 (4)	C19—C20—C25	119.7 (4)
O2—C7—N1	127.7 (4)	C21—C20—C25	118.8 (4)
O3—C8—O4	122.3 (5)	C20—C21—C22	120.1 (5)
O3—C8—C9	110.4 (6)	C20—C21—H30	120.0
O4—C8—C9	127.1 (5)	C22—C21—H30	119.9
C8—C9—H7	109.5	C21—C22—C23	119.1 (6)
C8—C9—H8	109	C21—C22—H31	120.5
C8—C9—H9	109.5	C23—C22—H31	120.4
H7—C9—H8	109.5	C22—C23—C24	120.9 (5)
H7—C9—H9	109	C22—C23—H32	119.6
H8—C9—H9	109.4	C24—C23—H32	119.6
O5—C10—O6	122.5 (6)	C23—C24—C25	119.5 (5)
O5—C10—C11	110.7 (7)	C23—C24—H33	120.2
O6—C10—C11	126.8 (6)	C25—C24—H33	120.3
C10—C11—H10	109.4	C20—C25—C24	121.6 (5)
C10—C11—H11	109.4	C20—C25—H34	119.2
C10—C11—H12	109	C24—C25—H34	119.2

Symmetry codes: (i) −y+1, x−1, z−1/4; (ii) −x+1, −y, z−1/2; (iii) y+1, −x+1, z−3/4; (iv) y, −x+1, z+1/4; (v) −y, x−1, z−1/4; (vi) −y+1, x, z−1/4.