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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 72| Part 5| May 2016| Pages 756-759
doi:10.1107/S2056989016006800

Crystal structure of (+)-N-[(1R,5S,6S,9S)-5-hy­droxy­methyl-3,3,9-tri­methyl-8-oxo-2,4,7-trioxabi­cyclo­[4.3.0]nonan-9-yl]acetamide

CROSSMARK_Color_square_no_text.svg
Takeshi Oishi,a* Shun Tsuzaki,b Tomoya Sugai,b Takaaki Satob and Noritaka Chidab

aSchool of Medicine, Keio University, Hiyoshi 4-1-1, Kohoku-ku, Yokohama 223-8521, Japan, and bDepartment of Applied Chemistry, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Kohoku-ku, Yokohama 223-8522, Japan
*Correspondence e-mail: oec@keio.jp

Edited by H. Ishida, Okayama University, Japan (Received 18 April 2016; accepted 22 April 2016; online 29 April 2016)

In the title compound, C12H19NO6, the six-membered 1,3-dioxane ring adopts a chair-like conformation. The seat of this chair, containing two O atoms, is essentially planar, with a maximum deviation of 0.0021 (12) Å. The five-membered oxolane ring cis-fused to the 1,3-dioxane ring adopts an envelope form. The bridgehead C atom at the flap, which is bonded to the tetra­substituted C atom of the oxolane ring, deviates from the mean plane of other ring atoms by 0.539 (4) Å. In the crystal, classical O—H⋯O and N—H⋯O hydrogen bonds link the mol­ecules into a sheet structure enclosing an R44(24) graph-set motif. Weak inter­molecular C—H⋯O inter­actions support the sheet formation.

CCDC reference: 1475848

1. Chemical context

Sphingofungin F [systematic name: (2S,3R,4R,5S,E)-2-amino-3,4,5-trihy­droxy-2-methyl-14-oxoicos-6-enoic acid] was isolated from the fermentation broth of Paecilomyces variotii by Horn et al. (1992[Horn, W. A., Smith, J. L., Bills, G. F., Raghoobar, S. L., Helms, G. L., Kurtz, M. B., Marrinan, J. A., Frommer, B. R., Thornton, R. A. & Mandala, S. M. (1992). J. Antibiot. 45, 1692-1696.]). It shows anti­fungal activity by inhibition of the serine palmitoyltransferase to suppress the early step of biosynthesis of the sphingosines (Zweerink et al., 1992[Zweerink, M. M., Edison, A. M., Wells, G. B., Pinto, W. & Lester, R. L. (1992). J. Biol. Chem. 267, 25032-25038.]). The structure of sphingofungin F features a hydro­philic α,α-disubstituted α-amino acid moiety possessing four contiguous stereocenters, connected to a hydro­phobic carbon chain by E-olefin. The title compound, which is equivalent to the hydro­philic part with correct stereochemistry, was provided in the total synthesis of sphingofungin F (Tsuzaki et al., 2015[Tsuzaki, S., Usui, S., Oishi, H., Yasushima, D., Fukuyasu, T., Oishi, T., Sato, T. & Chida, N. (2015). Org. Lett. 17, 1704-1707.]).

[Scheme 1]

2. Structural commentary

The mol­ecular structure of the title compound is shown in Fig. 1[link]. The 1,3-dioxane ring (C1/O2/C3/O4/C5/C6) is in a chair-like conformation with puckering parameters of Q = 0.497 (3) Å, θ = 169.6 (3)°, φ = 116.8 (16)°, Q(2) = 0.090 (3) Å and Q(3) = −0.489 (3) Å. The seat of this chair (C1/O2/O4/C5) is essentially planar with a maximum deviation of 0.0021 (12) Å for O4, and atoms C6 and C3, positioned at the headrest and the footrest, respectively, deviate from the mean plane of the seat by 0.524 (4) and −0.646 (3) Å. The equatorially oriented C5—C15 and C3—C17 bonds make angles with the normal of the Cremer & Pople plane being 63.41 (18) and 63.35 (18)°, respectively, while the C1—C9 bond is a little tilted from the ideal equatorial position with an angle of 50.50 (17)° due to the ring-fusion system. The oxolane ring (C1/C6/O7/C8/C9), which is cis-fused to the 1,3-dioxane ring, adopts an envelope form with puckering parameters of Q(2) = 0.345 (3) Å and φ(2) = 254.7 (4)°. The bridgehead atom C1 deviates from the mean plane of the other four ring atoms by 0.539 (4) Å.

[Figure 1]
Figure 1
The mol­ecular structure of the title compound, showing the atom labeling. Displacement ellipsoids are drawn at the 50% probability level. Only H atoms connected to N, O and chiral C atoms are shown for clarity.

3. Supra­molecular features

In the crystal, an O—H⋯O hydrogen bond (O16—H16⋯O14i; Table 1[link]) connects the mol­ecules into a chain structure running along the c axis, with a C(10) graph-set motif (Fig. 2[link]). A weak C—H⋯O inter­action (C13—H13B⋯O7iv; Table 1[link]) supports formation of the chain. The chains are linked into a sheet structure parallel to (100) by an N—H⋯O hydrogen bond (N11—H11⋯O16ii; Table 1[link]) which generates a C(8) graph-set motif (Fig. 3[link]). Weak C—H⋯O inter­actions (C5—H5⋯O10iii, C19—H19A⋯O4iii and C13—H13C⋯O14v; Table 1[link]) are also observed between the chains. In this sheet structure, the classical O—H⋯O and N—H⋯O hydrogen bonds enclose an R44(24) graph-set motif, and the other weak C—H⋯O inter­actions add to the stability of the network (Fig. 4[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O16—H16⋯O14i 0.84 1.91 2.742 (2) 168
N11—H11⋯O16ii 0.88 2.28 2.928 (3) 131
C5—H5⋯O10iii 1.00 2.42 3.289 (3) 145
C19—H19A⋯O4iii 0.98 2.52 3.386 (3) 147
C13—H13B⋯O7iv 0.98 2.55 3.433 (3) 150
C13—H13C⋯O14v 0.98 2.62 3.424 (3) 140
Symmetry codes: (i) x, y, z+1; (ii) [-x+2, y-{\script{1\over 2}}, -z+1]; (iii) [-x+2, y+{\script{1\over 2}}, -z+1]; (iv) x, y, z-1; (v) [-x+2, y-{\script{1\over 2}}, -z].
[Figure 2]
Figure 2
A partial packing diagram, viewed down the b axis, showing the chain structure running along the c axis. Yellow lines indicate the inter­molecular O—H⋯O hydrogen bonds. Black dashed lines indicate weak inter­molecular C—H⋯O inter­actions. Only H atoms involved in the hydrogen bonds are shown for clarity. [Symmetry codes: (i) x, y, z + 1; (iv) x, y, z − 1.]
[Figure 3]
Figure 3
Another partial packing diagram, viewed down the c axis, showing the sheet structure parallel to (100). Yellow lines indicate the inter­molecular N—H⋯O hydrogen bonds. Black dashed lines indicate weak inter­molecular C—H⋯O inter­actions. Only H atoms involved in the hydrogen bonds are shown for clarity. [Symmetry codes: (ii) −x + 2, y − [{1\over 2}], −z + 1; (iii) −x + 2, y + [{1\over 2}], −z + 1; (vi) x, y + 1, z + 1.]
[Figure 4]
Figure 4
A packing diagram, viewed down the a axis, showing the hydrogen bonds in the sheet structure parallel to (100). Yellow lines indicate inter­molecular O—H⋯O and N—H⋯O hydrogen bonds. Black dashed lines indicate weak inter­molecular C—H⋯O inter­actions. Only H atoms involved in the hydrogen bonds are shown for clarity.

4. Database survey

In the Cambridge Structural Database (CSD, Version 5.37, November 2015; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]), 18 structures containing a 2,4,7-trioxabi­cyclo­[4.3.0]nonan-8-one skeleton, (a), are registered (Fig. 5[link]). These include five compounds (YISHIR and YISHUD: Han et al., 1994[Han, S.-Y., Joullié, M. M., Fokin, V. V. & Petasis, N. A. (1994). Tetrahedron Asymmetry, 5, 2535-2562.]; LAVVIO: Watkin et al., 2005[Watkin, D. J., Parry, L. L., Hotchkiss, D. J., Eastwick-Field, V. & Fleet, G. W. J. (2005). Acta Cryst. E61, o3302-o3303.]; ZINDEH and ZINDIL: Glawar et al., 2013[Glawar, A. F. G., Jenkinson, S. F., Newberry, S. J., Thompson, A. L., Nakagawa, S., Yoshihara, A., Akimitsu, K., Izumori, K., Butters, T. D., Kato, A. & Fleet, G. W. J. (2013). Org. Biomol. Chem. 11, 6886-6899.]) with 3,3-dimethyl substituents, (b); one compound (NUIJAS: Henkel et al., 1998[Henkel, S., Frey, W., Remen, L., Gracza, T. & Jäger, V. (1998). Z. Kristallogr. New Cryst. Struct. 213, 71-72.]) with 5-hy­droxy­methyl substituent, (c); and one compound (QIFFUH: Hotchkiss et al., 2007[Hotchkiss, D. J., Jenkinson, S. F., Booth, K. V., Fleet, G. W. J. & Watkin, D. J. (2007). Acta Cryst. E63, o2168-o2170.]) possessing a tetra­substituted carbon with nitro­gen at the C-9 position, (d). The conformations of the bicyclic systems in these seven structures are similar to those in the title compound: the 1,3-dioxane rings adopt chair-like forms, and the cis-fused oxolane rings adopt envelope forms with bridgehead C-1 position at the flap.

[Figure 5]
Figure 5
The core structures for database survey: (a) 2,4,7-trioxabi­cyclo­[4.3.0]nonan-8-one, and its derivatives with (b) 3,3-dimethyl, (c) 5-hy­droxy­methyl and (d) 9-methyl-9-N-substituents.

5. Synthesis and crystallization

The title compound was afforded in the total synthesis of sphingofungin F from a D-ribose derivative (Tsuzaki et al., 2015[Tsuzaki, S., Usui, S., Oishi, H., Yasushima, D., Fukuyasu, T., Oishi, T., Sato, T. & Chida, N. (2015). Org. Lett. 17, 1704-1707.]). Purification was carried out by silica gel column chromatography, and colorless crystals were obtained from an ethyl acetate solution under a hexane-saturated atmosphere, by slow evaporation at ambient temperature. M.p. 497–498 K. [α]28D + 157.7 (c 1.04, CHCl3). HRMS (ESI) m/z calculated for C12H19NO6Na+ [M + Na]+: 296.1110; found: 296.1104.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. C-bound H atoms were positioned geometrically with C—H = 0.95–1.00 Å, and constrained to ride on their parent atoms with Uiso(H) = 1.2Ueq(C) or 1.5Ueq(methyl C). The hy­droxy H atom was placed guided by difference maps, with O—H = 0.84 Å and with Uiso(H) = 1.5Ueq(O). The amide H atom was also placed guided by difference maps, with N—H = 0.88 Å and with Uiso(H) = 1.2Ueq(N).

Table 2
Experimental details

Crystal data
Chemical formula C12H19NO6
Mr 273.28
Crystal system, space group Monoclinic, P21
Temperature (K) 90
a, b, c (Å) 8.2102 (3), 9.9513 (3), 8.7480 (3)
β (°) 108.142 (2)
V (Å3) 679.20 (4)
Z 2
Radiation type Cu Kα
μ (mm−1) 0.91
Crystal size (mm) 0.14 × 0.14 × 0.07
 
Data collection
Diffractometer Bruker D8 Venture
Absorption correction Multi-scan (SADABS; Bruker, 2014[Bruker (2014). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.88, 0.94
No. of measured, independent and observed [I > 2σ(I)] reflections 8304, 2386, 2235
Rint 0.039
(sin θ/λ)max (Å−1) 0.596
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.032, 0.068, 1.00
No. of reflections 2386
No. of parameters 177
No. of restraints 1
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.20, −0.18
Absolute structure Flack x determined using 941 quotients [(I+)−(I−)]/[(I+)+(I−)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.])
Absolute structure parameter 0.13 (11)
Computer programs: APEX2 and SAINT (Bruker, 2014[Bruker (2014). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXS2013 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), Mercury (Macrae et al., 2006[Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453-457.]), publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information

CCDC reference: 1475848

Crystal structure: contains datablocks global, I. DOI: 10.1107/S2056989016006800/is5451sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989016006800/is5451Isup2.hkl

Supporting information file. DOI: 10.1107/S2056989016006800/is5451Isup3.cml

checkCIF report


Chemical context top

\ Sphingofungin F [systematic name: (2S,3R,4R,5S,E)-2-amino-3,4,5-tri­hydroxy-\ 2-methyl-14-oxoicos-6-enoic acid] was isolated from the fermentation broth of Paecilomyces variotii by Horn et al. (1992). It shows anti­fungal activity by inhibition of the serine palmitoyltransferase to suppress the early step of biosynthesis of the sphingosines (Zweerink et al., 1992). The structure of sphingofungin F features a hydro­philic α,α-disubstituted α-amino acid moiety possessing four contiguous stereocenters, connected to a hydro­philic carbon chain by E-olefin. The title compound, which is equivalent to the hydro­philic part with correct stereochemistry, was provided in the total synthesis of sphingofungin F (Tsuzaki et al., 2015).

Structural commentary top

The molecular structure of the title compound is shown in Fig. 1. The 1,3-dioxane ring (C1/O2/C3/O4/C5/C6) is in a chair-like conformation with puckering parameters of Q = 0.497 (3) Å, θ = 169.6 (3)°, φ = 116.8 (16)°, Q(2) = 0.090 (3) Å and Q(3) = –0.489 (3) Å. The seat of this chair (C1/O2/O4/C5) is essentially planar with a maximum deviation of 0.0021 (12) Å for O4, and atoms C6 and C3, positioned at the headrest and the footrest, respectively, deviate from the mean plane of the seat by 0.524 (4) and –0.646 (3) Å. The equatorially oriented C5—C15 and C3—C17 bonds make angles with the normal of the Cremer & Pople plane being 63.41 (18) and 63.35 (18)°, respectively, while the C1—C9 bond is a little tilted from the ideal equatorial position with an angle of 50.50 (17)° due to the ring-fusion system. The oxolane ring (C1/C6/O7/C8/C9), which is cis-fused to the 1,3-dioxane ring, adopts an envelope form with puckering parameters of Q(2) = 0.345 (3) Å and φ(2) = 254.7 (4)°. The bridgehead atom C1 deviates from the mean plane of the other four ring atoms by 0.539 (4) Å.

Supra­molecular features top

In the crystal, an O—H···O hydrogen bond (O16—H16···O14i; Table 1) connects the molecules into a chain structure running along the c axis, with a C(10) graph-set motif (Fig. 2). A weak C—H···O inter­action (C13—H13B···O7iv; Table 1) supports formation of the chain. The chains are linked into a sheet structure parallel to (100) by an N—H···O hydrogen bond (N11—H11···O16ii; Table 1) which generates a C(8) graph-set motif (Fig. 3). Weak C—H···O inter­actions (C5—H5···O10iii, C19—H19A···O4iii and C13—H13C···O14v; Table 1) are also observed between the chains. In this sheet structure, the classical O—H···O and N—H···O hydrogen bonds enclose an R44(24) graph-set motif, and the other weak C—H···O inter­actions add to the stability of the network (Fig. 4).

Database survey top

In the Cambridge Structural Database (CSD, Version 5.37, November 2015; Groom et al., 2016), 18 structures containing a 2,4,7-trioxabi­cyclo­[4.3.0]nonan-8-one skeleton, (a), are registered (Fig. 5). These include five compounds (YISHIR and YISHUD: Han et al., 1994; LAVVIO: Watkin et al., 2005; ZINDEH and ZINDIL: Glawar et al., 2013) with 3,3-di­methyl substituents, (b); one compound (NUIJAS: Henkel et al., 1998) with 5-hy­droxy­methyl substituent, (c); and one compound (QIFFUH: Hotchkiss et al., 2007) possessing a tetra­substituted carbon with nitro­gen at the C-9 position, (d). The conformations of the bicyclic systems in these seven structures are similar to those in the title compound: the 1,3-dioxane rings adopt chair-like forms, and the cis-fused oxolane rings adopt envelope forms with bridgehead C-1 position at the flap.

Synthesis and crystallization top

The title compound was afforded in the total synthesis of sphingofungin F from a D-ribose derivative (Tsuzaki et al., 2015). Purification was carried out by silica gel column chromatography, and colorless crystals were obtained from an ethyl acetate solution under a hexane-saturated atmosphere, by slow evaporation at ambient temperature. M.p. 497–498 K. [α]28D + 157.7 (c 1.04, CHCl3). HRMS (ESI) m/z calculated for C12H19NO6Na+ [M + Na]+: 296.1110; found: 296.1104.

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 2. C-bound H atoms were positioned geometrically with C—H = 0.95–1.00 Å, and constrained to ride on their parent atoms with Uiso(H) = 1.2Ueq(C) or 1.5Ueq(methyl C). The hy­droxy H atom was placed guided by difference maps, with O—H = 0.84 Å and with Uiso(H) = 1.5Ueq(O). The amide H atom was also placed guided by difference maps, with N—H = 0.88 Å and with Uiso(H) = 1.2Ueq(N).

Structure description top

\ Sphingofungin F [systematic name: (2S,3R,4R,5S,E)-2-amino-3,4,5-tri­hydroxy-\ 2-methyl-14-oxoicos-6-enoic acid] was isolated from the fermentation broth of Paecilomyces variotii by Horn et al. (1992). It shows anti­fungal activity by inhibition of the serine palmitoyltransferase to suppress the early step of biosynthesis of the sphingosines (Zweerink et al., 1992). The structure of sphingofungin F features a hydro­philic α,α-disubstituted α-amino acid moiety possessing four contiguous stereocenters, connected to a hydro­philic carbon chain by E-olefin. The title compound, which is equivalent to the hydro­philic part with correct stereochemistry, was provided in the total synthesis of sphingofungin F (Tsuzaki et al., 2015).

The molecular structure of the title compound is shown in Fig. 1. The 1,3-dioxane ring (C1/O2/C3/O4/C5/C6) is in a chair-like conformation with puckering parameters of Q = 0.497 (3) Å, θ = 169.6 (3)°, φ = 116.8 (16)°, Q(2) = 0.090 (3) Å and Q(3) = –0.489 (3) Å. The seat of this chair (C1/O2/O4/C5) is essentially planar with a maximum deviation of 0.0021 (12) Å for O4, and atoms C6 and C3, positioned at the headrest and the footrest, respectively, deviate from the mean plane of the seat by 0.524 (4) and –0.646 (3) Å. The equatorially oriented C5—C15 and C3—C17 bonds make angles with the normal of the Cremer & Pople plane being 63.41 (18) and 63.35 (18)°, respectively, while the C1—C9 bond is a little tilted from the ideal equatorial position with an angle of 50.50 (17)° due to the ring-fusion system. The oxolane ring (C1/C6/O7/C8/C9), which is cis-fused to the 1,3-dioxane ring, adopts an envelope form with puckering parameters of Q(2) = 0.345 (3) Å and φ(2) = 254.7 (4)°. The bridgehead atom C1 deviates from the mean plane of the other four ring atoms by 0.539 (4) Å.

In the crystal, an O—H···O hydrogen bond (O16—H16···O14i; Table 1) connects the molecules into a chain structure running along the c axis, with a C(10) graph-set motif (Fig. 2). A weak C—H···O inter­action (C13—H13B···O7iv; Table 1) supports formation of the chain. The chains are linked into a sheet structure parallel to (100) by an N—H···O hydrogen bond (N11—H11···O16ii; Table 1) which generates a C(8) graph-set motif (Fig. 3). Weak C—H···O inter­actions (C5—H5···O10iii, C19—H19A···O4iii and C13—H13C···O14v; Table 1) are also observed between the chains. In this sheet structure, the classical O—H···O and N—H···O hydrogen bonds enclose an R44(24) graph-set motif, and the other weak C—H···O inter­actions add to the stability of the network (Fig. 4).

In the Cambridge Structural Database (CSD, Version 5.37, November 2015; Groom et al., 2016), 18 structures containing a 2,4,7-trioxabi­cyclo­[4.3.0]nonan-8-one skeleton, (a), are registered (Fig. 5). These include five compounds (YISHIR and YISHUD: Han et al., 1994; LAVVIO: Watkin et al., 2005; ZINDEH and ZINDIL: Glawar et al., 2013) with 3,3-di­methyl substituents, (b); one compound (NUIJAS: Henkel et al., 1998) with 5-hy­droxy­methyl substituent, (c); and one compound (QIFFUH: Hotchkiss et al., 2007) possessing a tetra­substituted carbon with nitro­gen at the C-9 position, (d). The conformations of the bicyclic systems in these seven structures are similar to those in the title compound: the 1,3-dioxane rings adopt chair-like forms, and the cis-fused oxolane rings adopt envelope forms with bridgehead C-1 position at the flap.

Synthesis and crystallization top

The title compound was afforded in the total synthesis of sphingofungin F from a D-ribose derivative (Tsuzaki et al., 2015). Purification was carried out by silica gel column chromatography, and colorless crystals were obtained from an ethyl acetate solution under a hexane-saturated atmosphere, by slow evaporation at ambient temperature. M.p. 497–498 K. [α]28D + 157.7 (c 1.04, CHCl3). HRMS (ESI) m/z calculated for C12H19NO6Na+ [M + Na]+: 296.1110; found: 296.1104.

Refinement details top

Crystal data, data collection and structure refinement details are summarized in Table 2. C-bound H atoms were positioned geometrically with C—H = 0.95–1.00 Å, and constrained to ride on their parent atoms with Uiso(H) = 1.2Ueq(C) or 1.5Ueq(methyl C). The hy­droxy H atom was placed guided by difference maps, with O—H = 0.84 Å and with Uiso(H) = 1.5Ueq(O). The amide H atom was also placed guided by difference maps, with N—H = 0.88 Å and with Uiso(H) = 1.2Ueq(N).

Computing details top

Data collection: APEX2 (Bruker, 2014); cell refinement: SAINT (Bruker, 2014); data reduction: SAINT (Bruker, 2014); program(s) used to solve structure: SHELXS2013 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: Mercury (Macrae et al., 2006); software used to prepare material for publication: publCIF (Westrip, 2010) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, showing the atom labeling. Displacement ellipsoids are drawn at the 50% probability level. Only H atoms connected to N, O and chiral C atoms are shown for clarity.
[Figure 2] Fig. 2. A partial packing diagram, viewed down the b axis, showing the chain structure running along the c axis. Yellow lines indicate the intermolecular O—H···O hydrogen bonds. Black dashed lines indicate weak intermolecular C—H···O interactions. Only H atoms involved in the hydrogen bonds are shown for clarity. [Symmetry codes: (i) x, y, z + 1; (iv) x, y, z - 1.]
[Figure 3] Fig. 3. Another partial packing diagram, viewed down the c axis, showing the sheet structure parallel to (100). Yellow lines indicate the intermolecular N—H···O hydrogen bonds. Black dashed lines indicate weak intramolecular C—H···O interactions. Only H atoms involved in the hydrogen bonds are shown for clarity. [Symmetry codes: (ii) -x + 2, y - 1/2, -z + 1; (iii) -x + 2, y + 1/2, -z + 1; (vi) x, y + 1, z + 1.]
[Figure 4] Fig. 4. A packing diagram, viewed down the a axis, showing the hydrogen bonds in the sheet structure parallel to (100). Yellow lines indicate intermolecular O—H···O and N—H···O hydrogen bonds. Black dashed lines indicate weak intermolecular C—H···O interactions. Only H atoms involved in the hydrogen bonds are shown for clarity.
[Figure 5] Fig. 5. The core structures for database survey: (a) 2,4,7-trioxabicyclo[4.3.0]nonan-8-one, and its derivatives with (b) 3,3-dimethyl, (c) 5-hydroxymethyl and (d) 9-methyl-9-N-substituents.
(+)-N-[(1R,5S,6S,9S)-5-Hydroxymethyl-3,3,9-trimethyl-8-oxo-2,4,7-trioxabicyclo[4.3.0]nonan-9-yl]acetamide top
Crystal data top
C12H19NO6Dx = 1.336 Mg m−3
Mr = 273.28Melting point = 497–498 K
Monoclinic, P21Cu Kα radiation, λ = 1.54178 Å
a = 8.2102 (3) ÅCell parameters from 5609 reflections
b = 9.9513 (3) Åθ = 5.3–66.5°
c = 8.7480 (3) ŵ = 0.91 mm−1
β = 108.142 (2)°T = 90 K
V = 679.20 (4) Å3Prism, colorless
Z = 20.14 × 0.14 × 0.07 mm
F(000) = 292
Data collection top
Bruker D8 Venture
diffractometer		2386 independent reflections
Radiation source: fine-focus sealed tube2235 reflections with I > 2σ(I)
Multilayered confocal mirror monochromatorRint = 0.039
Detector resolution: 10.4167 pixels mm-1θmax = 66.8°, θmin = 5.3°
φ and ω scansh = −9→9
Absorption correction: multi-scan
(SADABS; Bruker, 2014)		k = −11→11
Tmin = 0.88, Tmax = 0.94l = −10→10
8304 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.032H-atom parameters constrained
wR(F2) = 0.068 w = 1/[σ2(Fo2) + 0.324P]
where P = (Fo2 + 2Fc2)/3
S = 1.00(Δ/σ)max < 0.001
2386 reflectionsΔρmax = 0.20 e Å−3
177 parametersΔρmin = −0.18 e Å−3
1 restraintAbsolute structure: Flack x determined using 941 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.13 (11)
Crystal data top
C12H19NO6V = 679.20 (4) Å3
Mr = 273.28Z = 2
Monoclinic, P21Cu Kα radiation
a = 8.2102 (3) ŵ = 0.91 mm−1
b = 9.9513 (3) ÅT = 90 K
c = 8.7480 (3) Å0.14 × 0.14 × 0.07 mm
β = 108.142 (2)°
Data collection top
Bruker D8 Venture
diffractometer		2386 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2014)		2235 reflections with I > 2σ(I)
Tmin = 0.88, Tmax = 0.94Rint = 0.039
8304 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.032H-atom parameters constrained
wR(F2) = 0.068Δρmax = 0.20 e Å−3
S = 1.00Δρmin = −0.18 e Å−3
2386 reflectionsAbsolute structure: Flack x determined using 941 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
177 parametersAbsolute structure parameter: 0.13 (11)
1 restraint
Special details top

Experimental. IR (KBr): 3311, 2967, 2896, 1785, 1658, 1539, 1170, 1117, 1057 cm-1; 1H NMR (500 MHz, CDCl3): δ (p.p.m.) 5.91 (s, 1H; H11), 4.82 (d, J = 2.0 Hz, 1H; H1), 4.37 (dd, J = 2.0, 1.7 Hz, 1H; H6), 4.21 (ddd, J = 7.2, 5.5, 1.7 Hz, 1H; H5), 3.92–3.79 (m, 2H; H15AB), 2.05 (bs, 1H; H16), 2.00 (s, 3H; H14ABC), 1.60 (s, 3H; H19ABC), 1.46 (s, 3H; H18ABC), 1.35 (s, 3H; H17ABC); 13C NMR (125 MHz, CDCl3): δ (p.p.m.) 176.9 (C), 170.1 (C), 98.8 (CH), 71.6 (CH), 71.5 (CH), 68.9 (CH), 62.3 (CH2), 61.6 (C), 29.1 (CH3), 23.5 (CH3), 19.2 (CH3), 18.0 (CH3).

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2σ(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
xyzUiso*/Ueq
C10.9761 (3)0.3025 (3)0.3147 (3)0.0188 (6)
H10.94230.38450.24590.023*
O20.8860 (2)0.18536 (19)0.2398 (2)0.0201 (4)
C30.7125 (3)0.1762 (3)0.2378 (3)0.0206 (6)
O40.7068 (2)0.17674 (19)0.3987 (2)0.0210 (4)
C50.7792 (3)0.2941 (3)0.4887 (3)0.0204 (6)
H50.70510.37290.44120.024*
C60.9578 (3)0.3214 (3)0.4822 (3)0.0199 (6)
H60.99210.41510.52010.024*
O71.0816 (2)0.22653 (18)0.5827 (2)0.0209 (4)
C81.2000 (3)0.1928 (3)0.5118 (3)0.0197 (6)
C91.1663 (3)0.2685 (3)0.3525 (3)0.0188 (6)
O101.3137 (2)0.1152 (2)0.5716 (2)0.0250 (5)
N111.2014 (3)0.1803 (2)0.2341 (2)0.0189 (5)
H111.25970.10560.26560.023*
C121.1456 (3)0.2118 (3)0.0764 (3)0.0199 (6)
C131.1567 (4)0.1008 (3)−0.0361 (3)0.0243 (6)
H13A1.24790.03820.01980.037*
H13B1.18220.139−0.12940.037*
H13C1.04710.0528−0.07220.037*
O141.0868 (2)0.32336 (19)0.0272 (2)0.0232 (4)
C150.7705 (4)0.2708 (3)0.6581 (3)0.0223 (6)
H15A0.65110.25050.65360.027*
H15B0.84320.19310.70740.027*
O160.8286 (2)0.3877 (2)0.7522 (2)0.0251 (4)
H160.91720.36930.82840.038*
C170.6531 (4)0.0385 (3)0.1716 (3)0.0265 (6)
H17A0.735−0.02920.23140.04*
H17B0.64550.0350.05770.04*
H17C0.540.02020.18280.04*
C180.6035 (4)0.2878 (3)0.1367 (3)0.0248 (6)
H18A0.6460.37520.18420.037*
H18B0.4840.27650.13390.037*
H18C0.61040.28340.0270.037*
C191.2807 (3)0.3934 (3)0.3836 (3)0.0225 (6)
H19A1.24920.45280.45930.034*
H19B1.26530.44110.28210.034*
H19C1.40090.36630.42950.034*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0219 (13)0.0169 (14)0.0158 (12)−0.0014 (11)0.0034 (10)0.0009 (11)
O20.0200 (9)0.0209 (10)0.0178 (8)−0.0027 (8)0.0033 (7)−0.0019 (8)
C30.0201 (13)0.0240 (14)0.0163 (12)−0.0004 (12)0.0036 (10)0.0020 (13)
O40.0253 (10)0.0196 (10)0.0165 (9)−0.0042 (8)0.0044 (7)−0.0005 (8)
C50.0235 (14)0.0174 (14)0.0190 (13)0.0008 (11)0.0049 (10)−0.0018 (12)
C60.0247 (15)0.0149 (14)0.0179 (13)0.0023 (11)0.0035 (11)−0.0008 (11)
O70.0227 (10)0.0232 (11)0.0155 (9)0.0015 (8)0.0038 (7)0.0010 (8)
C80.0202 (13)0.0199 (14)0.0162 (12)−0.0041 (11)0.0016 (10)−0.0031 (12)
C90.0217 (14)0.0185 (14)0.0150 (12)0.0001 (10)0.0039 (10)−0.0021 (11)
O100.0265 (11)0.0251 (11)0.0199 (10)0.0042 (9)0.0021 (8)0.0016 (9)
N110.0204 (11)0.0182 (11)0.0168 (11)0.0034 (9)0.0040 (8)−0.0010 (10)
C120.0160 (12)0.0230 (15)0.0196 (13)−0.0034 (11)0.0043 (10)−0.0029 (12)
C130.0298 (16)0.0242 (15)0.0185 (13)0.0026 (12)0.0069 (11)−0.0003 (12)
O140.0292 (10)0.0189 (11)0.0190 (9)0.0018 (8)0.0040 (8)0.0024 (8)
C150.0244 (15)0.0226 (15)0.0191 (13)−0.0023 (11)0.0057 (11)−0.0022 (12)
O160.0310 (11)0.0215 (10)0.0188 (10)0.0032 (9)0.0018 (8)−0.0035 (9)
C170.0260 (15)0.0288 (16)0.0223 (14)−0.0040 (12)0.0040 (12)−0.0041 (13)
C180.0223 (14)0.0299 (17)0.0195 (13)−0.0006 (12)0.0028 (11)0.0035 (13)
C190.0229 (14)0.0216 (14)0.0219 (14)−0.0021 (11)0.0053 (11)−0.0020 (13)
Geometric parameters (Å, º) top
C1—O21.426 (3)N11—H110.88
C1—C61.530 (4)C12—O141.233 (3)
C1—C91.530 (4)C12—C131.501 (4)
C1—H11.0C13—H13A0.98
O2—C31.422 (3)C13—H13B0.98
C3—O41.423 (3)C13—H13C0.98
C3—C171.509 (4)C15—O161.419 (3)
C3—C181.525 (4)C15—H15A0.99
O4—C51.431 (3)C15—H15B0.99
C5—C61.510 (4)O16—H160.84
C5—C151.523 (4)C17—H17A0.98
C5—H51.0C17—H17B0.98
C6—O71.463 (3)C17—H17C0.98
C6—H61.0C18—H18A0.98
O7—C81.349 (3)C18—H18B0.98
C8—O101.199 (3)C18—H18C0.98
C8—C91.532 (4)C19—H19A0.98
C9—N111.453 (3)C19—H19B0.98
C9—C191.530 (4)C19—H19C0.98
N11—C121.348 (3)
O2—C1—C6110.4 (2)C12—N11—H11119.7
O2—C1—C9105.5 (2)C9—N11—H11119.7
C6—C1—C9102.6 (2)O14—C12—N11122.6 (3)
O2—C1—H1112.6O14—C12—C13122.0 (2)
C6—C1—H1112.6N11—C12—C13115.4 (2)
C9—C1—H1112.6C12—C13—H13A109.5
C3—O2—C1115.6 (2)C12—C13—H13B109.5
O2—C3—O4109.22 (18)H13A—C13—H13B109.5
O2—C3—C17105.4 (2)C12—C13—H13C109.5
O4—C3—C17106.1 (2)H13A—C13—H13C109.5
O2—C3—C18111.4 (2)H13B—C13—H13C109.5
O4—C3—C18112.1 (2)O16—C15—C5109.3 (2)
C17—C3—C18112.2 (2)O16—C15—H15A109.8
C3—O4—C5114.3 (2)C5—C15—H15A109.8
O4—C5—C6111.6 (2)O16—C15—H15B109.8
O4—C5—C15105.8 (2)C5—C15—H15B109.8
C6—C5—C15113.9 (2)H15A—C15—H15B108.3
O4—C5—H5108.5C15—O16—H16109.5
C6—C5—H5108.5C3—C17—H17A109.5
C15—C5—H5108.5C3—C17—H17B109.5
O7—C6—C5111.2 (2)H17A—C17—H17B109.5
O7—C6—C1103.9 (2)C3—C17—H17C109.5
C5—C6—C1113.6 (2)H17A—C17—H17C109.5
O7—C6—H6109.3H17B—C17—H17C109.5
C5—C6—H6109.3C3—C18—H18A109.5
C1—C6—H6109.3C3—C18—H18B109.5
C8—O7—C6110.5 (2)H18A—C18—H18B109.5
O10—C8—O7122.3 (2)C3—C18—H18C109.5
O10—C8—C9127.5 (2)H18A—C18—H18C109.5
O7—C8—C9110.1 (2)H18B—C18—H18C109.5
N11—C9—C19111.8 (2)C9—C19—H19A109.5
N11—C9—C1113.3 (2)C9—C19—H19B109.5
C19—C9—C1112.8 (2)H19A—C19—H19B109.5
N11—C9—C8109.3 (2)C9—C19—H19C109.5
C19—C9—C8108.1 (2)H19A—C19—H19C109.5
C1—C9—C8100.9 (2)H19B—C19—H19C109.5
C12—N11—C9120.6 (2)
C6—C1—O2—C351.4 (3)C6—O7—C8—C91.5 (3)
C9—C1—O2—C3161.5 (2)O2—C1—C9—N1133.6 (3)
C1—O2—C3—O4−59.9 (3)C6—C1—C9—N11149.3 (2)
C1—O2—C3—C17−173.5 (2)O2—C1—C9—C19161.8 (2)
C1—O2—C3—C1864.6 (3)C6—C1—C9—C19−82.5 (3)
O2—C3—O4—C559.4 (3)O2—C1—C9—C8−83.1 (2)
C17—C3—O4—C5172.6 (2)C6—C1—C9—C832.6 (3)
C18—C3—O4—C5−64.6 (3)O10—C8—C9—N1139.2 (4)
C3—O4—C5—C6−52.2 (3)O7—C8—C9—N11−141.7 (2)
C3—O4—C5—C15−176.5 (2)O10—C8—C9—C19−82.7 (3)
O4—C5—C6—O7−74.1 (3)O7—C8—C9—C1996.4 (2)
C15—C5—C6—O745.7 (3)O10—C8—C9—C1158.7 (3)
O4—C5—C6—C142.7 (3)O7—C8—C9—C1−22.2 (3)
C15—C5—C6—C1162.4 (2)C19—C9—N11—C12−75.4 (3)
O2—C1—C6—O779.1 (2)C1—C9—N11—C1253.3 (3)
C9—C1—C6—O7−32.9 (2)C8—C9—N11—C12164.9 (2)
O2—C1—C6—C5−41.8 (3)C9—N11—C12—O1411.3 (4)
C9—C1—C6—C5−153.9 (2)C9—N11—C12—C13−167.6 (2)
C5—C6—O7—C8142.6 (2)O4—C5—C15—O16−175.7 (2)
C1—C6—O7—C820.1 (3)C6—C5—C15—O1661.4 (3)
C6—O7—C8—O10−179.4 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O16—H16···O14i0.841.912.742 (2)168
N11—H11···O16ii0.882.282.928 (3)131
C5—H5···O10iii1.002.423.289 (3)145
C19—H19A···O4iii0.982.523.386 (3)147
C13—H13B···O7iv0.982.553.433 (3)150
C13—H13C···O14v0.982.623.424 (3)140
Symmetry codes: (i) x, y, z+1; (ii) −x+2, y−1/2, −z+1; (iii) −x+2, y+1/2, −z+1; (iv) x, y, z−1; (v) −x+2, y−1/2, −z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O16—H16···O14i0.841.912.742 (2)168
N11—H11···O16ii0.882.282.928 (3)131
C5—H5···O10iii1.002.423.289 (3)145
C19—H19A···O4iii0.982.523.386 (3)147
C13—H13B···O7iv0.982.553.433 (3)150
C13—H13C···O14v0.982.623.424 (3)140
Symmetry codes: (i) x, y, z+1; (ii) −x+2, y−1/2, −z+1; (iii) −x+2, y+1/2, −z+1; (iv) x, y, z−1; (v) −x+2, y−1/2, −z.

Experimental details

Crystal data
Chemical formulaC12H19NO6
Mr273.28
Crystal system, space groupMonoclinic, P21
Temperature (K)90
a, b, c (Å)8.2102 (3), 9.9513 (3), 8.7480 (3)
β (°) 108.142 (2)
V (Å3)679.20 (4)
Z2
Radiation typeCu Kα
µ (mm−1)0.91
Crystal size (mm)0.14 × 0.14 × 0.07
Data collection
DiffractometerBruker D8 Venture
Absorption correctionMulti-scan
(SADABS; Bruker, 2014)
Tmin, Tmax0.88, 0.94
No. of measured, independent and
observed [I > 2σ(I)] reflections		8304, 2386, 2235
Rint0.039
(sin θ/λ)max (Å−1)0.596
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.032, 0.068, 1.00
No. of reflections2386
No. of parameters177
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.20, −0.18
Absolute structureFlack x determined using 941 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
Absolute structure parameter0.13 (11)

Computer programs: APEX2 (Bruker, 2014), SAINT (Bruker, 2014), SHELXS2013 (Sheldrick, 2008), SHELXL2014 (Sheldrick, 2015), Mercury (Macrae et al., 2006), publCIF (Westrip, 2010) and PLATON (Spek, 2009).

 

Acknowledgements

This research was partially supported by the Keio Gijuku Fukuzawa Memorial Fund for the Advancement of Education and Research. We also thank Professor S. Ohba (Keio University, Japan) for his valuable advice.

References

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ISSN: 2056-9890
Volume 72| Part 5| May 2016| Pages 756-759
doi:10.1107/S2056989016006800
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