research communications
R,E)-4-[(2R,4R)-2-amino-2-trichloromethyl-1,3-dioxolan-4-yl]-4-hydroxy-2-methylbut-2-enoate
of (–)-methyl (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, C10H14Cl3NO5, the five-membered dioxolane ring adopts an with the C atom bonded to the butenoate side chain as the flap. It deviates from the mean plane of the other atoms in the ring by 0.446 (6) Å. In the crystal, molecules are connected by O—H⋯O hydrogen bonds into helical chains running along the b-axis direction. The chains are linked into a sheet structure parallel to (001) by an N—H⋯O hydrogen bond. These classical hydrogen bonds enclose an R44(24) graph-set motif in the sheet structure. Furthermore, a weak intermolecular C—H⋯Cl interaction expands the sheet structures into a three-dimensional network.
Keywords: crystal structure; 1,3-dioxolane; hydroxy group; amino group; hydrogen bonding.
CCDC reference: 1554119
1. Chemical context
Cyclic compounds often play a significant role, not only in controlling stereochemistry due to their conformational rigidity, but also as protecting groups in organic synthesis. On the basis of this concept, we have explored the utilization of cyclic orthoamides, prepared from allylic diol and triol with known conditions (Overman, 1974; 1976), and have developed a new strategy for the total synthesis of a certain natural product (Nakayama, et al., 2013). The title compound is a structural isomer of a recently reported compound (Oishi et al., 2016).
2. Structural commentary
The molecular structure of the title compound is shown in Fig. 1. The 1,3-dioxolane ring (C5/O7/C8/C9/O10) adopts an with the flap atom C9 deviating by 0.446 (6) Å from the mean plane of the other four atoms [puckering parameters are Q(2) = 0.285 (4) Å and φ(2) = 296.7 (8)°]. The C=C and C=O double bonds of the unsaturated ester are slightly skewed with torsion angle C13=C14—C16=O18 being of 8.4 (6)°. There is a weak intramolecular N6—H6A⋯Cl1 interaction present (Table 1).
3. Supramolecular features
In the crystal, a classical O—H⋯O hydrogen bond (O12—H12⋯O17i; Table 1) connects the molecules into a helical-chain running along the b-axis direction, with a C(7) graph-set motif (Fig. 2). A classical N—H⋯O hydrogen bond (N6—H6B⋯O12ii; Table 1), which is formed between one of N-bound H atoms and hydroxy O group, links the chains into a sheet structure parallel to (001), also generating a C(7) graph-set motif (Fig. 3). In the sheet structure, the classical O—H⋯O and N—H⋯O hydrogen bonds enclose an R44(24) graph-set motif (Fig. 4). Furthermore, a weak C—H⋯Cl interaction (C8—H8B⋯Cl2iii; Table 1) supports the crystal packing to construct a three-dimensional architecture (Fig. 2). An intermolecular Cl1⋯O17 (x, y − 1, z) short contact of 3.076 (3) Å is also observed.
4. Database survey
In the Cambridge Structural Database (CSD, Version 5.38, Feb. 2017; Groom et al., 2016), there are two structures containing the 4-alkoxy-2-methyl-4-(2-methyl-1,3-dioxolan-4-yl)but-2-enoate skeleton, (a), related to the title compound (Fig. 5), but its 4-hydroxy free derivative (R = H) has not yet been reported.
For the cyclic orthoamide core with a trichloromethyl group on the central carbon atom, four structures are registered in the CSD. These are two derivatives (WEKWOY: Haeckel et al., 1994; and LAGMAK: Oishi et al., 2016) of 1,3-dioxolane (b), one derivative (WAXBEE: Metwally, 2011) of 1,3-oxathiolane (c), and one derivative (LIBHIO: Rondot et al., 2007) of 1,3-dioxane (d). The amino H atoms were refined as adopting an sp2 configuration for WEKWOY and WAXBEE, while they were refined assuming an sp3 configuration of the N atom for LIBHIO and LAGMAK, as in the present study. Each N—H bond of the amino group in LIBHIO is mostly eclipsed by the neighbouring C—Cl bonds of the trichloromethyl group, whereas those in the title compound are slightly tilted (Fig. 6). There is an intramolecular N—H⋯Cl interaction [H6A⋯Cl1 = 2.66 (4) Å; N6—H6A⋯Cl1 = 115 (3)°] in the title compound (Table 1), while the corresponding geometries are 2.76 Å and 109° in LIBHIO. These amino groups may be oriented to avoid intramolecular non-bonding short contacts as well as to form classical intermolecular hydrogen bonds. The amino H atoms in LAGMAK are disordered according to the possible intramolecular N—H⋯O and N⋯H—O hydrogen bonds with the hydroxy group (Oishi et al., 2016).
5. Synthesis and crystallization
The title compound was afforded from L-threose, which can be prepared according to the reported procedure (Smith et al., 1992) from D-galactose (Kidena et al., 2017). Purification was carried out by silica gel and colourless crystals were obtained from a benzene solution under a hexane-saturated atmosphere, by slow evaporation at ambient temperature (m.p. 358–359 K). [α]D24 – 32.7 (c 1.01, CHCl3). HRMS (ESI) m/z calculated for C10H15Cl3NO5+ [M + H]+: 334.0016; found: 334.0016.
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) = 1.5Ueq(methyl C) and 1.2Ueq(C) for other C-bound H atoms. The hydroxy H atom was placed, guided by difference-Fourier maps, with O—H = 0.84 Å and refined with Uiso(H) = 1.5Ueq(O). The amino H atoms were placed, guided by difference-Fourier maps, and were refined with distance restraints of N—H = 0.86 (2) Å and H⋯H = 1.40 (2) Å, with Uiso(H) = 1.2Ueq(N).
details are summarized in Table 2Supporting information
CCDC reference: 1554119
https://doi.org/10.1107/S2056989017008283/su5377sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017008283/su5377Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989017008283/su5377Isup3.cml
Data collection: APEX3 (Bruker, 2016); cell
SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT2014/5 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014/7 (Sheldrick, 2015b); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: publCIF (Westrip, 2010) and PLATON (Spek, 2009).C10H14Cl3NO5 | Dx = 1.624 Mg m−3 |
Mr = 334.57 | Melting point = 358–359 K |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
a = 5.8494 (4) Å | Cell parameters from 8568 reflections |
b = 12.6458 (8) Å | θ = 2.7–25.4° |
c = 9.5658 (6) Å | µ = 0.68 mm−1 |
β = 104.763 (2)° | T = 90 K |
V = 684.23 (8) Å3 | Plate, colorless |
Z = 2 | 0.28 × 0.22 × 0.08 mm |
F(000) = 344 |
Bruker D8 Venture diffractometer | 2376 independent reflections |
Radiation source: fine-focus sealed tube | 2268 reflections with I > 2σ(I) |
Multilayered confocal mirror monochromator | Rint = 0.042 |
Detector resolution: 7.4074 pixels mm-1 | θmax = 25.0°, θmin = 2.2° |
φ and ω scans | h = −6→6 |
Absorption correction: multi-scan (SADABS; Bruker, 2016) | k = −15→15 |
Tmin = 0.83, Tmax = 0.95 | l = −11→11 |
10686 measured reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.030 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.060 | w = 1/[σ2(Fo2) + 0.7994P] where P = (Fo2 + 2Fc2)/3 |
S = 1.06 | (Δ/σ)max < 0.001 |
2376 reflections | Δρmax = 0.28 e Å−3 |
181 parameters | Δρmin = −0.29 e Å−3 |
4 restraints | Absolute structure: Flack x determined using 993 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013). |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.04 (3) |
Experimental. IR (film): 3393, 3325, 2953, 1714, 1438, 1239, 1093, 1035, 825, 803, 749 cm-1; 1H NMR (500 MHz, CDCl3): δ (p.p.m.) 6.78 (dq, J = 8.7, 1.4 Hz, 1H; H13), 4.69–4.62 (m, 1H; H12), 4.65 (ddd, J = 7.0, 4.3, 2.9 Hz, 1H; H9), 4.43–4.39 (m, 3H; H8AB & H11), 3.75 (s, 3H; H19ABC), 2.95 (bs, 2H; H6AB), 1.92 (d, J = 1.4 Hz, 3H; H14ABC); 13C NMR (125 MHz, CDCl3): δ (p.p.m.) 168.2 (C; C16), 138.9 (CH; C13), 130.2 (C; C14), 116.0 (C; C5), 103.3 (C; C4), 82.9 (CH; C9), 70.1 (CH2; C8), 69.2 (CH; C11), 52.2 (CH3; C19), 13.2 (CH3; C14). |
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 | ||
Cl1 | 0.49362 (19) | 0.09132 (8) | 0.28126 (12) | 0.0182 (2) | |
Cl2 | 0.63815 (19) | 0.22438 (8) | 0.53302 (11) | 0.0188 (3) | |
Cl3 | 0.14274 (19) | 0.19083 (8) | 0.40183 (12) | 0.0218 (3) | |
C4 | 0.4229 (7) | 0.2071 (3) | 0.3659 (4) | 0.0158 (9) | |
C5 | 0.4173 (7) | 0.3050 (3) | 0.2656 (5) | 0.0136 (9) | |
N6 | 0.2535 (7) | 0.2954 (3) | 0.1287 (4) | 0.0173 (8) | |
H6A | 0.236 (7) | 0.230 (2) | 0.099 (5) | 0.021* | |
H6B | 0.121 (6) | 0.321 (3) | 0.128 (5) | 0.021* | |
O7 | 0.3602 (5) | 0.3953 (2) | 0.3345 (3) | 0.0151 (7) | |
C8 | 0.5670 (8) | 0.4608 (3) | 0.3782 (5) | 0.0163 (10) | |
H8A | 0.6482 | 0.4492 | 0.4812 | 0.02* | |
H8B | 0.5255 | 0.5366 | 0.3633 | 0.02* | |
C9 | 0.7202 (8) | 0.4255 (3) | 0.2809 (4) | 0.0149 (9) | |
H9 | 0.8909 | 0.4302 | 0.334 | 0.018* | |
O10 | 0.6524 (5) | 0.3163 (2) | 0.2537 (3) | 0.0136 (6) | |
C11 | 0.6763 (8) | 0.4863 (3) | 0.1386 (5) | 0.0146 (10) | |
H11 | 0.508 | 0.4774 | 0.0826 | 0.018* | |
O12 | 0.8311 (5) | 0.4449 (2) | 0.0574 (3) | 0.0162 (7) | |
H12 | 0.7506 | 0.417 | −0.019 | 0.024* | |
C13 | 0.7305 (7) | 0.6008 (3) | 0.1666 (4) | 0.0142 (9) | |
H13 | 0.8909 | 0.6187 | 0.2091 | 0.017* | |
C14 | 0.5772 (7) | 0.6801 (4) | 0.1381 (4) | 0.0137 (9) | |
C15 | 0.3168 (7) | 0.6713 (4) | 0.0683 (5) | 0.0198 (10) | |
H15A | 0.282 | 0.7022 | −0.0288 | 0.03* | |
H15B | 0.2282 | 0.7093 | 0.1268 | 0.03* | |
H15C | 0.2704 | 0.5966 | 0.0615 | 0.03* | |
C16 | 0.6582 (8) | 0.7912 (3) | 0.1764 (5) | 0.0146 (10) | |
O17 | 0.5238 (5) | 0.8654 (2) | 0.1682 (3) | 0.0165 (7) | |
O18 | 0.8922 (5) | 0.8021 (2) | 0.2209 (3) | 0.0151 (7) | |
C19 | 0.9749 (8) | 0.9094 (3) | 0.2504 (5) | 0.0209 (11) | |
H19A | 1.1481 | 0.9103 | 0.2763 | 0.031* | |
H19B | 0.918 | 0.9378 | 0.3307 | 0.031* | |
H19C | 0.9147 | 0.953 | 0.1641 | 0.031* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cl1 | 0.0221 (6) | 0.0107 (5) | 0.0232 (6) | 0.0009 (5) | 0.0080 (5) | −0.0014 (5) |
Cl2 | 0.0220 (6) | 0.0165 (6) | 0.0159 (5) | −0.0020 (5) | 0.0014 (4) | 0.0028 (5) |
Cl3 | 0.0160 (6) | 0.0218 (6) | 0.0312 (6) | −0.0003 (5) | 0.0124 (5) | 0.0039 (5) |
C4 | 0.015 (2) | 0.017 (3) | 0.017 (2) | −0.0005 (19) | 0.0063 (18) | −0.001 (2) |
C5 | 0.012 (2) | 0.012 (2) | 0.016 (2) | −0.0005 (19) | 0.0046 (19) | −0.0001 (19) |
N6 | 0.0160 (19) | 0.017 (2) | 0.018 (2) | 0.0019 (17) | 0.0027 (17) | −0.0012 (17) |
O7 | 0.0155 (16) | 0.0100 (16) | 0.0208 (16) | 0.0031 (13) | 0.0068 (13) | −0.0037 (13) |
C8 | 0.022 (2) | 0.011 (2) | 0.016 (2) | −0.002 (2) | 0.0044 (19) | −0.0007 (19) |
C9 | 0.016 (2) | 0.012 (2) | 0.016 (2) | −0.0047 (18) | 0.0028 (18) | −0.0050 (19) |
O10 | 0.0141 (15) | 0.0077 (15) | 0.0204 (16) | 0.0000 (12) | 0.0068 (13) | 0.0006 (12) |
C11 | 0.014 (2) | 0.013 (2) | 0.016 (2) | 0.0026 (18) | 0.0025 (19) | 0.0009 (19) |
O12 | 0.0160 (16) | 0.0174 (17) | 0.0154 (16) | −0.0006 (13) | 0.0042 (13) | −0.0033 (14) |
C13 | 0.014 (2) | 0.014 (2) | 0.015 (2) | −0.0002 (19) | 0.0040 (18) | −0.002 (2) |
C14 | 0.018 (2) | 0.011 (2) | 0.013 (2) | −0.003 (2) | 0.0053 (18) | 0.0030 (19) |
C15 | 0.014 (2) | 0.016 (2) | 0.030 (3) | 0.0027 (19) | 0.006 (2) | 0.000 (2) |
C16 | 0.018 (2) | 0.017 (2) | 0.010 (2) | 0.001 (2) | 0.0072 (18) | 0.002 (2) |
O17 | 0.0167 (16) | 0.0138 (16) | 0.0186 (16) | 0.0034 (14) | 0.0034 (13) | 0.0005 (14) |
O18 | 0.0124 (16) | 0.0105 (15) | 0.0208 (16) | −0.0026 (13) | 0.0016 (13) | −0.0004 (13) |
C19 | 0.020 (3) | 0.009 (2) | 0.030 (3) | −0.0012 (19) | 0.000 (2) | −0.003 (2) |
Cl1—C4 | 1.773 (4) | C11—C13 | 1.492 (6) |
Cl2—C4 | 1.778 (4) | C11—H11 | 1.0 |
Cl3—C4 | 1.770 (4) | O12—H12 | 0.84 |
C4—C5 | 1.561 (6) | C13—C14 | 1.327 (6) |
C5—O7 | 1.401 (5) | C13—H13 | 0.95 |
C5—O10 | 1.416 (5) | C14—C16 | 1.498 (6) |
C5—N6 | 1.417 (6) | C14—C15 | 1.503 (6) |
N6—H6A | 0.87 (2) | C15—H15A | 0.98 |
N6—H6B | 0.84 (2) | C15—H15B | 0.98 |
O7—C8 | 1.438 (5) | C15—H15C | 0.98 |
C8—C9 | 1.514 (6) | C16—O17 | 1.213 (5) |
C8—H8A | 0.99 | C16—O18 | 1.333 (5) |
C8—H8B | 0.99 | O18—C19 | 1.444 (5) |
C9—O10 | 1.442 (5) | C19—H19A | 0.98 |
C9—C11 | 1.527 (6) | C19—H19B | 0.98 |
C9—H9 | 1.0 | C19—H19C | 0.98 |
C11—O12 | 1.433 (5) | ||
C5—C4—Cl3 | 109.6 (3) | O12—C11—C13 | 108.4 (3) |
C5—C4—Cl1 | 110.2 (3) | O12—C11—C9 | 108.3 (3) |
Cl3—C4—Cl1 | 109.1 (2) | C13—C11—C9 | 110.4 (3) |
C5—C4—Cl2 | 110.8 (3) | O12—C11—H11 | 109.9 |
Cl3—C4—Cl2 | 108.6 (2) | C13—C11—H11 | 109.9 |
Cl1—C4—Cl2 | 108.5 (2) | C9—C11—H11 | 109.9 |
O7—C5—O10 | 108.0 (3) | C11—O12—H12 | 109.5 |
O7—C5—N6 | 108.5 (3) | C14—C13—C11 | 126.5 (4) |
O10—C5—N6 | 112.1 (3) | C14—C13—H13 | 116.7 |
O7—C5—C4 | 109.1 (3) | C11—C13—H13 | 116.7 |
O10—C5—C4 | 105.1 (3) | C13—C14—C16 | 120.2 (4) |
N6—C5—C4 | 113.8 (4) | C13—C14—C15 | 126.2 (4) |
C5—N6—H6A | 112 (3) | C16—C14—C15 | 113.6 (4) |
C5—N6—H6B | 112 (3) | C14—C15—H15A | 109.5 |
H6A—N6—H6B | 109 (4) | C14—C15—H15B | 109.5 |
C5—O7—C8 | 108.8 (3) | H15A—C15—H15B | 109.5 |
O7—C8—C9 | 103.7 (3) | C14—C15—H15C | 109.5 |
O7—C8—H8A | 111.0 | H15A—C15—H15C | 109.5 |
C9—C8—H8A | 111.0 | H15B—C15—H15C | 109.5 |
O7—C8—H8B | 111.0 | O17—C16—O18 | 122.5 (4) |
C9—C8—H8B | 111.0 | O17—C16—C14 | 123.3 (4) |
H8A—C8—H8B | 109.0 | O18—C16—C14 | 114.2 (4) |
O10—C9—C8 | 102.4 (3) | C16—O18—C19 | 115.2 (3) |
O10—C9—C11 | 110.2 (3) | O18—C19—H19A | 109.5 |
C8—C9—C11 | 114.1 (4) | O18—C19—H19B | 109.5 |
O10—C9—H9 | 110.0 | H19A—C19—H19B | 109.5 |
C8—C9—H9 | 110.0 | O18—C19—H19C | 109.5 |
C11—C9—H9 | 110.0 | H19A—C19—H19C | 109.5 |
C5—O10—C9 | 108.0 (3) | H19B—C19—H19C | 109.5 |
Cl3—C4—C5—O7 | 59.6 (4) | C4—C5—O10—C9 | −131.3 (3) |
Cl1—C4—C5—O7 | 179.7 (3) | C8—C9—O10—C5 | 27.3 (4) |
Cl2—C4—C5—O7 | −60.2 (4) | C11—C9—O10—C5 | −94.5 (4) |
Cl3—C4—C5—O10 | 175.2 (3) | O10—C9—C11—O12 | −65.3 (4) |
Cl1—C4—C5—O10 | −64.7 (3) | C8—C9—C11—O12 | −179.8 (3) |
Cl2—C4—C5—O10 | 55.5 (4) | O10—C9—C11—C13 | 176.1 (3) |
Cl3—C4—C5—N6 | −61.8 (4) | C8—C9—C11—C13 | 61.6 (5) |
Cl1—C4—C5—N6 | 58.4 (4) | O12—C11—C13—C14 | 127.4 (4) |
Cl2—C4—C5—N6 | 178.5 (3) | C9—C11—C13—C14 | −114.1 (5) |
O10—C5—O7—C8 | −4.9 (4) | C11—C13—C14—C16 | 178.3 (4) |
N6—C5—O7—C8 | −126.7 (4) | C11—C13—C14—C15 | −1.5 (7) |
C4—C5—O7—C8 | 108.8 (3) | C13—C14—C16—O17 | −171.5 (4) |
C5—O7—C8—C9 | 21.5 (4) | C15—C14—C16—O17 | 8.3 (6) |
O7—C8—C9—O10 | −29.3 (4) | C13—C14—C16—O18 | 8.4 (6) |
O7—C8—C9—C11 | 89.7 (4) | C15—C14—C16—O18 | −171.7 (3) |
O7—C5—O10—C9 | −14.9 (4) | O17—C16—O18—C19 | −3.5 (6) |
N6—C5—O10—C9 | 104.6 (4) | C14—C16—O18—C19 | 176.6 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N6—H6A···Cl1 | 0.87 (2) | 2.66 (4) | 3.118 (4) | 115 (3) |
O12—H12···O17i | 0.84 | 1.97 | 2.774 (4) | 161 |
N6—H6B···O12ii | 0.84 (2) | 2.28 (3) | 3.047 (5) | 152 (4) |
C8—H8B···Cl2iii | 0.99 | 2.83 | 3.713 (5) | 149 |
Symmetry codes: (i) −x+1, y−1/2, −z; (ii) x−1, y, z; (iii) −x+1, y+1/2, −z+1. |
Acknowledgements
We thank Professor S. Ohba (Keio University, Japan) for his valuable advice.
Funding information
Funding for this research was provided by: Keio Gijuku Fukuzawa Memorial Fund for the Advancement of Education and Research.
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