research communications
N-[(1R,5S,6S,9S)-5-hydroxymethyl-3,3,9-trimethyl-8-oxo-2,4,7-trioxabicyclo[4.3.0]nonan-9-yl]acetamide
of (+)-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
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.
Keywords: crystal structure; bicyclic compound; 1,3-dioxane; oxolane; hydrogen bond; hydroxy group.
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 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 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).
2. Structural commentary
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.
3. Supramolecular features
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).
4. Database survey
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.
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). Purification was carried out by silica gel 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 . 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).
details are summarized in Table 2
|
Supporting information
CCDC reference: 1475848
10.1107/S2056989016006800/is5451sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S2056989016006800/is5451Isup2.hkl
Supporting information file. DOI: 10.1107/S2056989016006800/is5451Isup3.cml
\ 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 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).
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 hydrophilicThe 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 -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
-fused oxolane rings adopt envelope forms with bridgehead C-1 position at the flap.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 α]28D + 157.7 (c 1.04, CHCl3). HRMS (ESI) m/z calculated for C12H19NO6Na+ [M + Na]+: 296.1110; found: 296.1104.
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. [Crystal data, data collection and structure
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).\ 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 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).
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 hydrophilicThe 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 -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
-fused oxolane rings adopt envelope forms with bridgehead C-1 position at the flap.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 α]28D + 157.7 (c 1.04, CHCl3). HRMS (ESI) m/z calculated for C12H19NO6Na+ [M + Na]+: 296.1110; found: 296.1104.
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. [ detailsCrystal data, data collection and structure
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).Data collection: APEX2 (Bruker, 2014); cell
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).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. | |
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.] | |
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.] | |
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. | |
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. |
C12H19NO6 | Dx = 1.336 Mg m−3 |
Mr = 273.28 | Melting point = 497–498 K |
Monoclinic, P21 | Cu Kα radiation, λ = 1.54178 Å |
a = 8.2102 (3) Å | Cell parameters from 5609 reflections |
b = 9.9513 (3) Å | θ = 5.3–66.5° |
c = 8.7480 (3) Å | µ = 0.91 mm−1 |
β = 108.142 (2)° | T = 90 K |
V = 679.20 (4) Å3 | Prism, colorless |
Z = 2 | 0.14 × 0.14 × 0.07 mm |
F(000) = 292 |
Bruker D8 Venture diffractometer | 2386 independent reflections |
Radiation source: fine-focus sealed tube | 2235 reflections with I > 2σ(I) |
Multilayered confocal mirror monochromator | Rint = 0.039 |
Detector resolution: 10.4167 pixels mm-1 | θmax = 66.8°, θmin = 5.3° |
φ and ω scans | h = −9→9 |
Absorption correction: multi-scan (SADABS; Bruker, 2014) | k = −11→11 |
Tmin = 0.88, Tmax = 0.94 | l = −10→10 |
8304 measured reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.032 | H-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 reflections | Δρmax = 0.20 e Å−3 |
177 parameters | Δρmin = −0.18 e Å−3 |
1 restraint | Absolute structure: Flack x determined using 941 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.13 (11) |
C12H19NO6 | V = 679.20 (4) Å3 |
Mr = 273.28 | Z = 2 |
Monoclinic, P21 | Cu Kα radiation |
a = 8.2102 (3) Å | µ = 0.91 mm−1 |
b = 9.9513 (3) Å | T = 90 K |
c = 8.7480 (3) Å | 0.14 × 0.14 × 0.07 mm |
β = 108.142 (2)° |
Bruker D8 Venture diffractometer | 2386 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2014) | 2235 reflections with I > 2σ(I) |
Tmin = 0.88, Tmax = 0.94 | Rint = 0.039 |
8304 measured reflections |
R[F2 > 2σ(F2)] = 0.032 | H-atom parameters constrained |
wR(F2) = 0.068 | Δρmax = 0.20 e Å−3 |
S = 1.00 | Δρmin = −0.18 e Å−3 |
2386 reflections | Absolute structure: Flack x determined using 941 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
177 parameters | Absolute structure parameter: 0.13 (11) |
1 restraint |
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. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.9761 (3) | 0.3025 (3) | 0.3147 (3) | 0.0188 (6) | |
H1 | 0.9423 | 0.3845 | 0.2459 | 0.023* | |
O2 | 0.8860 (2) | 0.18536 (19) | 0.2398 (2) | 0.0201 (4) | |
C3 | 0.7125 (3) | 0.1762 (3) | 0.2378 (3) | 0.0206 (6) | |
O4 | 0.7068 (2) | 0.17674 (19) | 0.3987 (2) | 0.0210 (4) | |
C5 | 0.7792 (3) | 0.2941 (3) | 0.4887 (3) | 0.0204 (6) | |
H5 | 0.7051 | 0.3729 | 0.4412 | 0.024* | |
C6 | 0.9578 (3) | 0.3214 (3) | 0.4822 (3) | 0.0199 (6) | |
H6 | 0.9921 | 0.4151 | 0.5201 | 0.024* | |
O7 | 1.0816 (2) | 0.22653 (18) | 0.5827 (2) | 0.0209 (4) | |
C8 | 1.2000 (3) | 0.1928 (3) | 0.5118 (3) | 0.0197 (6) | |
C9 | 1.1663 (3) | 0.2685 (3) | 0.3525 (3) | 0.0188 (6) | |
O10 | 1.3137 (2) | 0.1152 (2) | 0.5716 (2) | 0.0250 (5) | |
N11 | 1.2014 (3) | 0.1803 (2) | 0.2341 (2) | 0.0189 (5) | |
H11 | 1.2597 | 0.1056 | 0.2656 | 0.023* | |
C12 | 1.1456 (3) | 0.2118 (3) | 0.0764 (3) | 0.0199 (6) | |
C13 | 1.1567 (4) | 0.1008 (3) | −0.0361 (3) | 0.0243 (6) | |
H13A | 1.2479 | 0.0382 | 0.0198 | 0.037* | |
H13B | 1.1822 | 0.139 | −0.1294 | 0.037* | |
H13C | 1.0471 | 0.0528 | −0.0722 | 0.037* | |
O14 | 1.0868 (2) | 0.32336 (19) | 0.0272 (2) | 0.0232 (4) | |
C15 | 0.7705 (4) | 0.2708 (3) | 0.6581 (3) | 0.0223 (6) | |
H15A | 0.6511 | 0.2505 | 0.6536 | 0.027* | |
H15B | 0.8432 | 0.1931 | 0.7074 | 0.027* | |
O16 | 0.8286 (2) | 0.3877 (2) | 0.7522 (2) | 0.0251 (4) | |
H16 | 0.9172 | 0.3693 | 0.8284 | 0.038* | |
C17 | 0.6531 (4) | 0.0385 (3) | 0.1716 (3) | 0.0265 (6) | |
H17A | 0.735 | −0.0292 | 0.2314 | 0.04* | |
H17B | 0.6455 | 0.035 | 0.0577 | 0.04* | |
H17C | 0.54 | 0.0202 | 0.1828 | 0.04* | |
C18 | 0.6035 (4) | 0.2878 (3) | 0.1367 (3) | 0.0248 (6) | |
H18A | 0.646 | 0.3752 | 0.1842 | 0.037* | |
H18B | 0.484 | 0.2765 | 0.1339 | 0.037* | |
H18C | 0.6104 | 0.2834 | 0.027 | 0.037* | |
C19 | 1.2807 (3) | 0.3934 (3) | 0.3836 (3) | 0.0225 (6) | |
H19A | 1.2492 | 0.4528 | 0.4593 | 0.034* | |
H19B | 1.2653 | 0.4411 | 0.2821 | 0.034* | |
H19C | 1.4009 | 0.3663 | 0.4295 | 0.034* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0219 (13) | 0.0169 (14) | 0.0158 (12) | −0.0014 (11) | 0.0034 (10) | 0.0009 (11) |
O2 | 0.0200 (9) | 0.0209 (10) | 0.0178 (8) | −0.0027 (8) | 0.0033 (7) | −0.0019 (8) |
C3 | 0.0201 (13) | 0.0240 (14) | 0.0163 (12) | −0.0004 (12) | 0.0036 (10) | 0.0020 (13) |
O4 | 0.0253 (10) | 0.0196 (10) | 0.0165 (9) | −0.0042 (8) | 0.0044 (7) | −0.0005 (8) |
C5 | 0.0235 (14) | 0.0174 (14) | 0.0190 (13) | 0.0008 (11) | 0.0049 (10) | −0.0018 (12) |
C6 | 0.0247 (15) | 0.0149 (14) | 0.0179 (13) | 0.0023 (11) | 0.0035 (11) | −0.0008 (11) |
O7 | 0.0227 (10) | 0.0232 (11) | 0.0155 (9) | 0.0015 (8) | 0.0038 (7) | 0.0010 (8) |
C8 | 0.0202 (13) | 0.0199 (14) | 0.0162 (12) | −0.0041 (11) | 0.0016 (10) | −0.0031 (12) |
C9 | 0.0217 (14) | 0.0185 (14) | 0.0150 (12) | 0.0001 (10) | 0.0039 (10) | −0.0021 (11) |
O10 | 0.0265 (11) | 0.0251 (11) | 0.0199 (10) | 0.0042 (9) | 0.0021 (8) | 0.0016 (9) |
N11 | 0.0204 (11) | 0.0182 (11) | 0.0168 (11) | 0.0034 (9) | 0.0040 (8) | −0.0010 (10) |
C12 | 0.0160 (12) | 0.0230 (15) | 0.0196 (13) | −0.0034 (11) | 0.0043 (10) | −0.0029 (12) |
C13 | 0.0298 (16) | 0.0242 (15) | 0.0185 (13) | 0.0026 (12) | 0.0069 (11) | −0.0003 (12) |
O14 | 0.0292 (10) | 0.0189 (11) | 0.0190 (9) | 0.0018 (8) | 0.0040 (8) | 0.0024 (8) |
C15 | 0.0244 (15) | 0.0226 (15) | 0.0191 (13) | −0.0023 (11) | 0.0057 (11) | −0.0022 (12) |
O16 | 0.0310 (11) | 0.0215 (10) | 0.0188 (10) | 0.0032 (9) | 0.0018 (8) | −0.0035 (9) |
C17 | 0.0260 (15) | 0.0288 (16) | 0.0223 (14) | −0.0040 (12) | 0.0040 (12) | −0.0041 (13) |
C18 | 0.0223 (14) | 0.0299 (17) | 0.0195 (13) | −0.0006 (12) | 0.0028 (11) | 0.0035 (13) |
C19 | 0.0229 (14) | 0.0216 (14) | 0.0219 (14) | −0.0021 (11) | 0.0053 (11) | −0.0020 (13) |
C1—O2 | 1.426 (3) | N11—H11 | 0.88 |
C1—C6 | 1.530 (4) | C12—O14 | 1.233 (3) |
C1—C9 | 1.530 (4) | C12—C13 | 1.501 (4) |
C1—H1 | 1.0 | C13—H13A | 0.98 |
O2—C3 | 1.422 (3) | C13—H13B | 0.98 |
C3—O4 | 1.423 (3) | C13—H13C | 0.98 |
C3—C17 | 1.509 (4) | C15—O16 | 1.419 (3) |
C3—C18 | 1.525 (4) | C15—H15A | 0.99 |
O4—C5 | 1.431 (3) | C15—H15B | 0.99 |
C5—C6 | 1.510 (4) | O16—H16 | 0.84 |
C5—C15 | 1.523 (4) | C17—H17A | 0.98 |
C5—H5 | 1.0 | C17—H17B | 0.98 |
C6—O7 | 1.463 (3) | C17—H17C | 0.98 |
C6—H6 | 1.0 | C18—H18A | 0.98 |
O7—C8 | 1.349 (3) | C18—H18B | 0.98 |
C8—O10 | 1.199 (3) | C18—H18C | 0.98 |
C8—C9 | 1.532 (4) | C19—H19A | 0.98 |
C9—N11 | 1.453 (3) | C19—H19B | 0.98 |
C9—C19 | 1.530 (4) | C19—H19C | 0.98 |
N11—C12 | 1.348 (3) | ||
O2—C1—C6 | 110.4 (2) | C12—N11—H11 | 119.7 |
O2—C1—C9 | 105.5 (2) | C9—N11—H11 | 119.7 |
C6—C1—C9 | 102.6 (2) | O14—C12—N11 | 122.6 (3) |
O2—C1—H1 | 112.6 | O14—C12—C13 | 122.0 (2) |
C6—C1—H1 | 112.6 | N11—C12—C13 | 115.4 (2) |
C9—C1—H1 | 112.6 | C12—C13—H13A | 109.5 |
C3—O2—C1 | 115.6 (2) | C12—C13—H13B | 109.5 |
O2—C3—O4 | 109.22 (18) | H13A—C13—H13B | 109.5 |
O2—C3—C17 | 105.4 (2) | C12—C13—H13C | 109.5 |
O4—C3—C17 | 106.1 (2) | H13A—C13—H13C | 109.5 |
O2—C3—C18 | 111.4 (2) | H13B—C13—H13C | 109.5 |
O4—C3—C18 | 112.1 (2) | O16—C15—C5 | 109.3 (2) |
C17—C3—C18 | 112.2 (2) | O16—C15—H15A | 109.8 |
C3—O4—C5 | 114.3 (2) | C5—C15—H15A | 109.8 |
O4—C5—C6 | 111.6 (2) | O16—C15—H15B | 109.8 |
O4—C5—C15 | 105.8 (2) | C5—C15—H15B | 109.8 |
C6—C5—C15 | 113.9 (2) | H15A—C15—H15B | 108.3 |
O4—C5—H5 | 108.5 | C15—O16—H16 | 109.5 |
C6—C5—H5 | 108.5 | C3—C17—H17A | 109.5 |
C15—C5—H5 | 108.5 | C3—C17—H17B | 109.5 |
O7—C6—C5 | 111.2 (2) | H17A—C17—H17B | 109.5 |
O7—C6—C1 | 103.9 (2) | C3—C17—H17C | 109.5 |
C5—C6—C1 | 113.6 (2) | H17A—C17—H17C | 109.5 |
O7—C6—H6 | 109.3 | H17B—C17—H17C | 109.5 |
C5—C6—H6 | 109.3 | C3—C18—H18A | 109.5 |
C1—C6—H6 | 109.3 | C3—C18—H18B | 109.5 |
C8—O7—C6 | 110.5 (2) | H18A—C18—H18B | 109.5 |
O10—C8—O7 | 122.3 (2) | C3—C18—H18C | 109.5 |
O10—C8—C9 | 127.5 (2) | H18A—C18—H18C | 109.5 |
O7—C8—C9 | 110.1 (2) | H18B—C18—H18C | 109.5 |
N11—C9—C19 | 111.8 (2) | C9—C19—H19A | 109.5 |
N11—C9—C1 | 113.3 (2) | C9—C19—H19B | 109.5 |
C19—C9—C1 | 112.8 (2) | H19A—C19—H19B | 109.5 |
N11—C9—C8 | 109.3 (2) | C9—C19—H19C | 109.5 |
C19—C9—C8 | 108.1 (2) | H19A—C19—H19C | 109.5 |
C1—C9—C8 | 100.9 (2) | H19B—C19—H19C | 109.5 |
C12—N11—C9 | 120.6 (2) | ||
C6—C1—O2—C3 | 51.4 (3) | C6—O7—C8—C9 | 1.5 (3) |
C9—C1—O2—C3 | 161.5 (2) | O2—C1—C9—N11 | 33.6 (3) |
C1—O2—C3—O4 | −59.9 (3) | C6—C1—C9—N11 | 149.3 (2) |
C1—O2—C3—C17 | −173.5 (2) | O2—C1—C9—C19 | 161.8 (2) |
C1—O2—C3—C18 | 64.6 (3) | C6—C1—C9—C19 | −82.5 (3) |
O2—C3—O4—C5 | 59.4 (3) | O2—C1—C9—C8 | −83.1 (2) |
C17—C3—O4—C5 | 172.6 (2) | C6—C1—C9—C8 | 32.6 (3) |
C18—C3—O4—C5 | −64.6 (3) | O10—C8—C9—N11 | 39.2 (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—C19 | 96.4 (2) |
C15—C5—C6—O7 | 45.7 (3) | O10—C8—C9—C1 | 158.7 (3) |
O4—C5—C6—C1 | 42.7 (3) | O7—C8—C9—C1 | −22.2 (3) |
C15—C5—C6—C1 | 162.4 (2) | C19—C9—N11—C12 | −75.4 (3) |
O2—C1—C6—O7 | 79.1 (2) | C1—C9—N11—C12 | 53.3 (3) |
C9—C1—C6—O7 | −32.9 (2) | C8—C9—N11—C12 | 164.9 (2) |
O2—C1—C6—C5 | −41.8 (3) | C9—N11—C12—O14 | 11.3 (4) |
C9—C1—C6—C5 | −153.9 (2) | C9—N11—C12—C13 | −167.6 (2) |
C5—C6—O7—C8 | 142.6 (2) | O4—C5—C15—O16 | −175.7 (2) |
C1—C6—O7—C8 | 20.1 (3) | C6—C5—C15—O16 | 61.4 (3) |
C6—O7—C8—O10 | −179.4 (2) |
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−1/2, −z+1; (iii) −x+2, y+1/2, −z+1; (iv) x, y, z−1; (v) −x+2, y−1/2, −z. |
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−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 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) |
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) |
Absolute structure parameter | 0.13 (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.
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