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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 72| Part 3| March 2016| Pages 343-346

Crystal structure of (+)-methyl (E)-3-[(2S,4S,5R)-2-amino-5-hy­dr­oxy­meth­yl-2-tri­chloro­methyl-1,3-dioxolan-4-yl]-2-methyl­prop-2-enoate

CROSSMARK_Color_square_no_text.svg

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 22 January 2016; accepted 10 February 2016; online 17 February 2016)

In the title compound, C10H14Cl3NO5, the five-membered dioxolane ring adopts an envelope conformation. The C atom at the flap, which is bonded to the hy­droxy­methyl substituent, deviates from the mean plane of other ring atoms by 0.357 (5) Å. There are two intra­molecular hydrogen bonds (O—H⋯N and N—H⋯O) between the hy­droxy and amino groups, so that O- and N-bound H atoms involved in these hydrogen bonds are each disordered with equal occupancies of 0.50. The methyl 2-methyl­prop-2-enoate substituent also shows a disordered structure over two sets of sites with refined occupancies of 0.482 (5) and 0.518 (5). In the crystal, mol­ecules are connected into a dimer by an O—H⋯O hydrogen bond. The dimers are further linked by N—H⋯O, C—H⋯N and C—H⋯O inter­actions, extending a sheet structure parallel to (-101).

1. Chemical context

The 3,3-sigmatropic rearrangement of an allylic tri­chloro­acetimidate (Overman rearrangement; Overman, 1974[Overman, L. E. (1974). J. Am. Chem. Soc. 96, 597-599.], 1976[Overman, L. E. (1976). J. Am. Chem. Soc. 98, 2901-2910.]) is one of the most important reactions in organic chemistry. It has been utilized as a quite powerful tool to introduce the nitro­gen functional group because this imidate is easily available from an allylic alcohol with tri­chloro­aceto­nitrile (Cl3CC≡N). In the case of a diol, a cyclic ortho­amide (2-amino-2-tri­chloro­methyl-1,3-dioxolane) may be afforded by controlling the reaction conditions though bis-imidates are usually produced. We have explored the rearrangement of the cyclic ortho­amide prepared from a contiguous diol or triol, and have developed a novel strategy for the total synthesis of certain natural products (Nakayama et al., 2013[Nakayama, Y., Sekiya, R., Oishi, H., Hama, N., Yamazaki, M., Sato, T. & Chida, N. (2013). Chem. Eur. J. 19, 12052-12058.]). As part of our ongoing studies in this area, we now describe the synthesis and structure of the title compound.

[Scheme 1]

2. Structural commentary

The mol­ecular structure of the title compound is shown in Fig. 1[link]. The dioxolane ring (C5/O7/C8/C9/O10) adopts an envelope form with puckering parameters of Q(2) = 0.223 (3) Å and φ(2) = 111.7 (8)°. Atom C9 deviates from the mean plane of the other four atoms by 0.357 (5) Å. The hy­droxy H atom has two possible positions and the amino H atoms have three possible positions, generating two types of intra­molecular hydrogen bonds with an S(7) graph-set motif between the hy­droxy and amino groups, N6—H6A⋯O12 and O12—H12B⋯N6 (Table 1[link] and Fig. 2[link]). The occupation factor of atoms H12A, H12B and H6A is 0.5, while that of atoms H6B and H6C is 0.75. The unsaturated ester substituent (C15/C14/C16/O17/O18/C19) is disordered over two orientations with refined occupancies of 0.482 (5) and 0.518 (5).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O12—H12B⋯N6 0.82 (3) 2.22 (4) 2.986 (4) 155 (7)
N6—H6A⋯O12 0.87 (3) 2.31 (5) 2.986 (4) 135 (6)
O12—H12A⋯O12i 0.84 (3) 1.98 (4) 2.750 (4) 151 (5)
N6—H6C⋯O17Bii 0.81 (2) 2.57 (2) 3.369 (7) 169 (3)
C19A—H19C⋯N6iii 0.98 2.59 3.555 (15) 167
N6—H6B⋯O17Aiv 0.85 (2) 2.61 (5) 3.286 (7) 137 (5)
C19B—H19E⋯O12v 0.98 2.62 3.573 (11) 164
Symmetry codes: (i) -x+1, y, -z+1; (ii) [x-{\script{1\over 2}}, y-{\script{1\over 2}}, z-{\script{1\over 2}}]; (iii) [x+{\script{1\over 2}}, y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (iv) [x-{\script{1\over 2}}, y+{\script{1\over 2}}, z-{\script{1\over 2}}]; (v) -x+1, y+1, -z+1.
[Figure 1]
Figure 1
The mol­ecular structure of the title compound, showing the atom labelling. Displacement ellipsoids are drawn at the 50% probability levels. Only H atoms connected to O, N and chiral C atoms are shown for clarity. Other possible positions of disordered atoms have been omitted.
[Figure 2]
Figure 2
Three possible combinations of the hy­droxy and amino H atoms, the probabilities being (a) 25%, (a′) 25% and (b) 50%. Purple dotted lines indicate the intra­molecular N—H⋯O and O—H⋯N hydrogen bonds. Other H atoms have been omitted for clarity.

3. Supra­molecular features

The crystal packing is stabilized by O—H⋯O hydrogen bonding (O12—H12A⋯O12i; Table 1[link]), connecting mol­ecules related by a twofold rotation axis into a dimer. As the result of this inter­molecular linkage, the intra­molecular hydrogen-bonding pattern is restricted, as shown in Fig. 3[link]. The dimers are further linked by weak N—H⋯O, C—H⋯N and C—H⋯O inter­actions (N6—H6C⋯O17Bii and N6—H6B⋯O17Aiv, C19A—H19C⋯N6iii and C19B—H19E⋯O12v; Table 1[link], Figs. 4[link] and 5[link]) to form a sheet structure parallel to ([\overline{1}]01).

[Figure 3]
Figure 3
A pair of mol­ecules showing a correlation between the intra- and inter­molecular hydrogen bonds. A yellow dashed line indicates the inter­molecular O—H⋯O hydrogen bond. Purple dotted lines indicate the intra­molecular N—H⋯O and O—H⋯N hydrogen bonds. Only the H atoms of the hy­droxy and amino groups are shown for clarity. The other possible position of N-bound H atoms due to the disorder are omitted. [Symmetry code: (i) −x + 1, y, −z + 1.]
[Figure 4]
Figure 4
A packing diagram viewed down to the b axis. Yellow lines indicate the inter­molecular O—H⋯O hydrogen bonds, generating the dimers. Black dashed lines indicate the inter­molecular N—H⋯O, C—H⋯N and C—H⋯O inter­actions. Only H atoms involved in hydrogen bonds are shown for clarity. [Symmetry codes: (i) −x + 1, y, −z + 1; (ii) x − [{1\over 2}], y − [{1\over 2}], z − [{1\over 2}]; (iii) x + [{1\over 2}], y + [{1\over 2}], z + [{1\over 2}]; (vi) −x + [{3\over 2}], y + [{1\over 2}], −z + [{3\over 2}]; (vii) −x + [{1\over 2}], y + [{1\over 2}], −z + [{1\over 2}].]
[Figure 5]
Figure 5
A partial packing diagram viewed along [[\overline{1}]01], showing hydrogen bonding in the sheet structure. Overlapped mol­ecules indicate the dimer. Black dashed lines indicate the inter­molecular N—H⋯O, C—H⋯N and C—H⋯O inter­actions. Only H atoms involved in hydrogen bonds are shown for clarity.

4. Database survey

In the Cambridge Structural Database (CSD, Version 5.36, November 2014; Groom & Allen, 2014[Groom, C. R. & Allen, F. H. (2014). Angew. Chem. Int. Ed. 53, 662-671.]), eight structures possessing a 1,3-dioxolane core with 4-(prop-2-enoate-3-yl) and 5-hy­droxy­methyl substituents, (a), are registered (Fig. 6[link]). These include its 2,2-dimethyl, (b), 2-oxo, (c) and 2-alk­oxy-2-alkyl (orthoester) derivative, (d), but its 2-amino-2-tri­chloro­methyl derivative, (e), which is related to the title compound, (h), has not been reported.

[Figure 6]
Figure 6
The core structures for database survey; (a) 5-hy­droxy­methyl-4-(prop-2-enoate-3-yl) substituted 1,3-dioxolane, and its (b) 2,2-dimethyl, (c) 2-oxo, (d) 2-alk­oxy-2-alkyl and (e) 2-amino-2-tri­chloro­methyl derivatives, (f) 2,2,2-tri­chloro­ethan-1-amine, and its derivatives (g) 2-amino-2-tri­chloro­methyl-1,3-dioxolane (n = 1) or -1,3-dioxane (n = 2); and (h) the structure of the title compound.

On the other hand, a search in CSD for a 2,2,2-tri­chloro­ethan-1-amine skeleton, (f), gave 12 entries. These include two structures (LIBHIO: Rondot et al., 2007[Rondot, C., Retailleau, P. & Zhu, J. (2007). Org. Lett. 9, 247-250.]; WEKWOY: Haeckel et al., 1994[Haeckel, R., Troll, C., Fischer, H. & Schmidt, R. R. (1994). Synlett, pp. 84-86.]) with a 2-amino-2-tri­chloro­methyl-1,3-dioxolane or -1,3-dioxane core, (g). N-bound hydrogen atoms in the structure of LIBHIO were refined as having an sp3 configuration and tilted towards chlorine atoms, whereas those in other 11 structures were refined assuming an sp2 configuration of the N atom.

5. Synthesis and crystallization

The title compound was derived from D-erythrose, which was prepared according to the reported procedure (Storz et al., 1999[Storz, T., Bernet, B. & Vasella, A. (1999). Helv. Chim. Acta, 82, 2380-2412.]) from D-glucose (Yasushima et al., 2016[Yasushima, D., Sato, T. & Chida, N. (2016). In preparation.]). Purification was carried out by silica gel column chromatography, and colourless crystals were obtained from a toluene solution by slow evaporation at ambient temperature. M.p. 365–366 K. [α]20D + 33.8 (c 0.32, CHCl3).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. The unsaturated ester group is disordered; the atoms C15/C16/O17/O18/C19 were split into two sets of positions A and B with their geometries restrained, and the refined occupancies being 0.482 (5) and 0.518 (5), respectively.

Table 2
Experimental details

Crystal data
Chemical formula C10H14Cl3NO5
Mr 334.57
Crystal system, space group Monoclinic, I2
Temperature (K) 90
a, b, c (Å) 14.8821 (9), 5.5847 (3), 17.2971 (14)
β (°) 105.847 (2)
V3) 1382.96 (16)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.68
Crystal size (mm) 0.26 × 0.22 × 0.16
 
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 0.84, 0.90
No. of measured, independent and observed [I > 2σ(I)] reflections 11488, 2420, 2272
Rint 0.030
(sin θ/λ)max−1) 0.595
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.023, 0.052, 1.03
No. of reflections 2420
No. of parameters 207
No. of restraints 36
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.29, −0.21
Absolute structure Flack x determined using 959 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 −0.02 (2)
Computer programs: APEX2 (Bruker, 2014[Bruker (2014). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), 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.]).

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 O-bound hydrogen atom has two possible positions. They were refined isotropically with Uiso(H) = 1.5Ueq(O) and the O—H distances restrained. The N-bound hydrogen atoms have three possible positions. They were refined isotropically with Uiso(H) = 1.2Ueq(N) and the N—H and H⋯H distances restrained. The site-occupation factors of the disordered H atoms of the hy­droxy group (H12A and H12B) and one of the amino group (H6A) were uniquely assigned to 0.5 each based on the two possible patterns of the hydrogen-bonding linkages related by the twofold axis. The occupation factors of the other N-bound H6B and H6C atoms were assumed to be 0.75 each from a difference map.

Supporting information


Chemical context top

The 3,3-sigmatropic rearrangement of an allylic tri­chloro­acetimidate (Overman rearrangement; Overman, 1974, 1976) is one of the most important reactions in organic chemistry. It has been utilized as a quite powerful tool to introduce the nitro­gen functional group because this imidate is easily available from an allylic alcohol with tri­chloro­aceto­nitrile (Cl3CCN). In the case of a diol, a cyclic ortho­amide (2-amino-2-tri­chloro­methyl-1,3-dioxolane) may be afforded by controlling the reaction conditions though bis-imidates are usually produced. We have explored the rearrangement of the cyclic ortho­amide prepared from a contiguous diol or triol, and have developed a novel strategy for the total synthesis of certain natural products (Nakayama et al., 2013).

Structural commentary top

The molecular structure of the title compound is shown in Fig. 1. The dioxolane ring (C5/O7/C8/C9/O10) adopts an envelope form with puckering parameters of Q(2) = 0.223 (3) Å and φ(2) = 111.7 (8)°. Atom C9 deviates from the mean plane of the other four atoms by 0.357 (5) Å. The hy­droxy H atom has two possible positions and the amino H atoms have three possible positions, generating two types of intra­molecular hydrogen bonds with an S(7) graph-set motif between the hy­droxy and amino groups, N6—H6A···O12 and O12—H12B···N6 (Table 1and Fig. 2). The occupation factor of atoms H12A, H12B and H6A is 0.5, while that of atoms H6B and H6C is 0.75. The unsaturated ester substituent (C15/C14/C16/O17/O18/C19) is disordered over two orientations with refined occupancies of 0.482 (5) and 0.518 (5).

Supra­molecular features top

The crystal packing is stabilized by O—H···O hydrogen bonding (O12—H12A···O12i; Table 1), connecting molecules related by a twofold rotation axis into a dimer. As the result of this inter­molecular linkage, the intra­molecular hydrogen-bonding pattern is restricted, as shown in Fig. 3. The dimers are further linked by weak N—H···O, C—H···N and C—H···O inter­actions (N6—H6C···O17Bii and N6—H6B···O17Aiv, C19A—H19C···N6iii and C19B—H19E···O12v; Table 1, Figs. 4 and 5) to form a sheet structure parallel to (101).

Database survey top

In the Cambridge Structural Database (CSD, Version 5.36, November 2014; Groom & Allen, 2014), eight structures possessing a 1,3-dioxolane core with 4-(prop-2-enoate-3-yl) and 5-hy­droxy­methyl substituents, (a), are registered (Fig. 6). These include its 2,2-di­methyl, (b), 2-oxo, (c) and 2-alk­oxy-2-alkyl (orthoester) derivative, (d), but its 2-amino-2-tri­chloro­methyl derivative, (e), which is related to the title compound, (h), has not been reported.

On the other hand, a search in CSD for a 2,2,2-tri­chloro­ethan-1-amine skeleton, (f), gave 12 entries. These include two structures (LIBHIO: Rondot et al., 2007; WEKWOY: Haeckel et al., 1994) with a 2-amino-2-tri­chloro­methyl-1,3-dioxolane or -1,3-dioxane core, (g). N-bound hydrogen atoms in the structure of LIBHIO were refined as having an sp3 configuration and tilted towards chlorine atoms, whereas those in other 11 structures were refined assuming an sp2 configuration of the N atom.

Synthesis and crystallization top

The title compound was derived from D-erythrose, which was prepared according to the reported procedure (Storz et al., 1999) from D-glucose (Yasushima et al., 2016). Purification was carried out by silica gel column chromatography, and colourless crystals were obtained from a toluene solution by slow evaporation at ambient temperature. M.p. 365–366 K. [α]20D + 33.8 (c 0.32, CHCl3).

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 2. The unsaturated ester group is disordered; the atoms C15/C16/O17/O18/C19 were split into two sets of positions A and B with their geometries restrained, and the refined occupancies being 0.482 (5) and 0.518 (5), respectively.

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 O-bound hydrogen atom has two possible positions. They were refined isotropically with Uiso(H) = 1.5Ueq(O) and the O—H distances restrained. The N-bound hydrogen atoms have three possible positions. They were refined isotropically with Uiso(H) = 1.2Ueq(N) and the N—H and H···H distances restrained. The site-occupation factors of the disordered H atoms of the hy­droxy group (H12A and H12B) and one of the amino group (H6A) were uniquely assigned to 0.5 each based on the two possible patterns of the hydrogen-bonding linkages related by the twofold axis. The occupation factors of the other N-bound H6B and H6C atoms were assumed to be 0.75 each from a difference map.

Structure description top

The 3,3-sigmatropic rearrangement of an allylic tri­chloro­acetimidate (Overman rearrangement; Overman, 1974, 1976) is one of the most important reactions in organic chemistry. It has been utilized as a quite powerful tool to introduce the nitro­gen functional group because this imidate is easily available from an allylic alcohol with tri­chloro­aceto­nitrile (Cl3CCN). In the case of a diol, a cyclic ortho­amide (2-amino-2-tri­chloro­methyl-1,3-dioxolane) may be afforded by controlling the reaction conditions though bis-imidates are usually produced. We have explored the rearrangement of the cyclic ortho­amide prepared from a contiguous diol or triol, and have developed a novel strategy for the total synthesis of certain natural products (Nakayama et al., 2013).

The molecular structure of the title compound is shown in Fig. 1. The dioxolane ring (C5/O7/C8/C9/O10) adopts an envelope form with puckering parameters of Q(2) = 0.223 (3) Å and φ(2) = 111.7 (8)°. Atom C9 deviates from the mean plane of the other four atoms by 0.357 (5) Å. The hy­droxy H atom has two possible positions and the amino H atoms have three possible positions, generating two types of intra­molecular hydrogen bonds with an S(7) graph-set motif between the hy­droxy and amino groups, N6—H6A···O12 and O12—H12B···N6 (Table 1and Fig. 2). The occupation factor of atoms H12A, H12B and H6A is 0.5, while that of atoms H6B and H6C is 0.75. The unsaturated ester substituent (C15/C14/C16/O17/O18/C19) is disordered over two orientations with refined occupancies of 0.482 (5) and 0.518 (5).

The crystal packing is stabilized by O—H···O hydrogen bonding (O12—H12A···O12i; Table 1), connecting molecules related by a twofold rotation axis into a dimer. As the result of this inter­molecular linkage, the intra­molecular hydrogen-bonding pattern is restricted, as shown in Fig. 3. The dimers are further linked by weak N—H···O, C—H···N and C—H···O inter­actions (N6—H6C···O17Bii and N6—H6B···O17Aiv, C19A—H19C···N6iii and C19B—H19E···O12v; Table 1, Figs. 4 and 5) to form a sheet structure parallel to (101).

In the Cambridge Structural Database (CSD, Version 5.36, November 2014; Groom & Allen, 2014), eight structures possessing a 1,3-dioxolane core with 4-(prop-2-enoate-3-yl) and 5-hy­droxy­methyl substituents, (a), are registered (Fig. 6). These include its 2,2-di­methyl, (b), 2-oxo, (c) and 2-alk­oxy-2-alkyl (orthoester) derivative, (d), but its 2-amino-2-tri­chloro­methyl derivative, (e), which is related to the title compound, (h), has not been reported.

On the other hand, a search in CSD for a 2,2,2-tri­chloro­ethan-1-amine skeleton, (f), gave 12 entries. These include two structures (LIBHIO: Rondot et al., 2007; WEKWOY: Haeckel et al., 1994) with a 2-amino-2-tri­chloro­methyl-1,3-dioxolane or -1,3-dioxane core, (g). N-bound hydrogen atoms in the structure of LIBHIO were refined as having an sp3 configuration and tilted towards chlorine atoms, whereas those in other 11 structures were refined assuming an sp2 configuration of the N atom.

Synthesis and crystallization top

The title compound was derived from D-erythrose, which was prepared according to the reported procedure (Storz et al., 1999) from D-glucose (Yasushima et al., 2016). Purification was carried out by silica gel column chromatography, and colourless crystals were obtained from a toluene solution by slow evaporation at ambient temperature. M.p. 365–366 K. [α]20D + 33.8 (c 0.32, CHCl3).

Refinement details top

Crystal data, data collection and structure refinement details are summarized in Table 2. The unsaturated ester group is disordered; the atoms C15/C16/O17/O18/C19 were split into two sets of positions A and B with their geometries restrained, and the refined occupancies being 0.482 (5) and 0.518 (5), respectively.

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 O-bound hydrogen atom has two possible positions. They were refined isotropically with Uiso(H) = 1.5Ueq(O) and the O—H distances restrained. The N-bound hydrogen atoms have three possible positions. They were refined isotropically with Uiso(H) = 1.2Ueq(N) and the N—H and H···H distances restrained. The site-occupation factors of the disordered H atoms of the hy­droxy group (H12A and H12B) and one of the amino group (H6A) were uniquely assigned to 0.5 each based on the two possible patterns of the hydrogen-bonding linkages related by the twofold axis. The occupation factors of the other N-bound H6B and H6C atoms were assumed to be 0.75 each from a difference map.

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 labelling. Displacement ellipsoids are drawn at the 50% probability levels. Only H atoms connected to O, N and chiral C atoms are shown for clarity. Other possible positions of disordered atoms have been omitted.
[Figure 2] Fig. 2. Three possible combinations of the hydroxy and amino H atoms, the probabilities being (a) 25%, (a') 25% and (b) 50%. Purple dotted lines indicate the intramolecular N—H···O and O—H···N hydrogen bonds. Other H atoms have been omitted for clarity.
[Figure 3] Fig. 3. A pair of molecules showing a correlation between the intra- and intermolecular hydrogen bonds. A yellow dashed line indicates the intermolecular O—H···O hydrogen bond. Purple dotted lines indicate the intramolecular N—H···O and O—H···N hydrogen bonds. Only the H atoms of the hydroxy and amino groups are shown for clarity. The other possible position of N-bound H atoms due to the disorder are omitted. [Symmetry code: (i) -x + 1, y, -z + 1.]
[Figure 4] Fig. 4. A packing diagram viewed down to the b axis. Yellow lines indicate the intermolecular O—H···O hydrogen bonds, generating the dimers. Black dashed lines indicate the intermolecular N—H···O, C—H···N and C—H···O interactions. Only H atoms involved in hydrogen bonds are shown for clarity. [Symmetry codes: (i) -x + 1, y, -z + 1; (ii) x - 1/2, y - 1/2, z - 1/2; (iii) x + 1/2, y + 1/2, z + 1/2; (vi) -x + 3/2, y + 1/2, -z + 3/2; (vii) -x + 1/2, y + 1/2, -z + 1/2.]
[Figure 5] Fig. 5. A partial packing diagram viewed along [101], showing hydrogen bonding in the sheet structure. Overlapped molecules indicate the dimer. Black dashed lines indicate the intermolecular N—H···O, C—H···N and C—H···O interactions. Only H atoms involved in hydrogen bonds are shown for clarity.
[Figure 6] Fig. 6. The core structures for database survey; (a) 5-hydroxymethyl-4-(prop-2-enoate-3-yl) substituted 1,3-dioxolane, and its (b) 2,2-dimethyl, (c) 2-oxo, (d) 2-alkoxy-2-alkyl and (e) 2-amino-2-trichloromethyl derivatives, (f) 2,2,2-trichloroethan-1-amine, and its derivatives (g) 2-amino-2-trichloromethyl-1,3-dioxolane (n = 1) or -1,3-dioxane (n = 2); and (h) the structure of the title compound.
(+)-Methyl (E)-3-[(2S,4S,5R)-2-amino-5-(hydroxymethyl)-2-trichloromethyl-1,3-dioxolan-4-yl]-2-methylprop-2-enoate top
Crystal data top
C10H14Cl3NO5Dx = 1.607 Mg m3
Mr = 334.57Melting point = 366–365 K
Monoclinic, I2Mo Kα radiation, λ = 0.71073 Å
a = 14.8821 (9) ÅCell parameters from 6489 reflections
b = 5.5847 (3) Åθ = 2.5–24.9°
c = 17.2971 (14) ŵ = 0.68 mm1
β = 105.847 (2)°T = 90 K
V = 1382.96 (16) Å3Prism, colourless
Z = 40.26 × 0.22 × 0.16 mm
F(000) = 688
Data collection top
Bruker D8 Venture
diffractometer
2420 independent reflections
Radiation source: fine-focus sealed tube2272 reflections with I > 2σ(I)
Multilayered confocal mirror monochromatorRint = 0.030
Detector resolution: 10.4167 pixels mm-1θmax = 25.0°, θmin = 2.5°
φ and ω scansh = 1717
Absorption correction: multi-scan
(SADABS; Bruker, 2014)
k = 66
Tmin = 0.84, Tmax = 0.90l = 2020
11488 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.023H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.052 w = 1/[σ2(Fo2) + (0.0137P)2 + 1.951P]
where P = (Fo2 + 2Fc2)/3
S = 1.03(Δ/σ)max = 0.001
2420 reflectionsΔρmax = 0.29 e Å3
207 parametersΔρmin = 0.21 e Å3
36 restraintsAbsolute structure: Flack x determined using 959 quotients [(I+)–(I)]/[(I+)+(I)] (Parsons et al., 2013)
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.02 (2)
Crystal data top
C10H14Cl3NO5V = 1382.96 (16) Å3
Mr = 334.57Z = 4
Monoclinic, I2Mo Kα radiation
a = 14.8821 (9) ŵ = 0.68 mm1
b = 5.5847 (3) ÅT = 90 K
c = 17.2971 (14) Å0.26 × 0.22 × 0.16 mm
β = 105.847 (2)°
Data collection top
Bruker D8 Venture
diffractometer
2420 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2014)
2272 reflections with I > 2σ(I)
Tmin = 0.84, Tmax = 0.90Rint = 0.030
11488 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.023H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.052Δρmax = 0.29 e Å3
S = 1.03Δρmin = 0.21 e Å3
2420 reflectionsAbsolute structure: Flack x determined using 959 quotients [(I+)–(I)]/[(I+)+(I)] (Parsons et al., 2013)
207 parametersAbsolute structure parameter: 0.02 (2)
36 restraints
Special details top

Experimental. M.p. 365–366 K (not corrected); [α]20D + 33.8 (c 0.32, CHCl3); IR (KBr): 3450, 3393, 3371, 3295, 3020, 2947, 2921, 2873, 1715, 1656, 1613, 1579, 1438, 1376, 1336, 1313, 1251, 1220, 1121, 1098, 1080, 1037, 1003, 977, 933, 909, 826, 803, 740, 585 cm-1; 1H NMR (500 MHz, CDCl3): δ (p.p.m.) 7.12 (dq, J = 7.5, 1.4 Hz, 1H; H13), 5.49 (t, J = 7.5 Hz, 1H; H8), 4.74 (dt, J = 7.5, 2.3 Hz, 1H; H9), 4.63 (bs, 1H; H12), 3.90 (dd, J = 12.9, 2.3 Hz, 1H; H11A), 3.77 (s, 3H; H19A–F), 3.57 (bd, J = 12.9 Hz, 1H; H11B), 3.06 (bs, 2H; H6), 1.90 (d, J = 1.4 Hz, 3H; H15A–F); 13C NMR (125 MHz, CDCl3): δ (p.p.m.) 167.6 (C), 135.6 (CH), 131.7 (C), 115.3 (C), 103.8 (C), 83.6 (CH), 79.8 (CH), 62.1 (CH2), 52.4 (CH3), 13.5 (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.

Problematic three reflections (1 –5 10, –13 0 15 and –12 0 16) with |IobsIcalc|/σW(I) greater than 10 have been omitted in the final refinement.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
Cl10.49607 (5)0.41064 (14)0.10141 (4)0.02169 (18)
Cl20.69020 (5)0.44496 (13)0.18886 (5)0.02292 (19)
Cl30.57725 (5)0.87077 (13)0.15202 (5)0.0279 (2)
C40.5774 (2)0.5655 (5)0.17849 (19)0.0165 (7)
C50.5517 (2)0.5446 (6)0.25983 (19)0.0192 (7)
N60.4607 (2)0.6381 (8)0.25371 (19)0.0432 (10)
H6A0.453 (6)0.657 (12)0.301 (2)0.052*0.5
H6B0.453 (4)0.781 (5)0.236 (3)0.052*0.75
H6C0.433 (2)0.523 (6)0.230 (3)0.052*0.75
O70.61956 (15)0.6675 (4)0.31855 (13)0.0202 (5)
C80.6707 (2)0.5008 (6)0.37781 (19)0.0190 (7)
H80.73220.46560.36730.023*
C90.6103 (2)0.2743 (6)0.36247 (19)0.0206 (7)
H90.65190.13180.36590.025*
O100.55577 (18)0.3032 (4)0.28050 (13)0.0267 (6)
C110.5478 (2)0.2341 (6)0.4164 (2)0.0227 (7)
H11A0.50780.09280.39710.027*
H11B0.58670.19920.47150.027*
O120.49006 (15)0.4361 (5)0.41859 (12)0.0263 (5)
H12A0.496 (4)0.488 (9)0.4653 (18)0.039*0.5
H12B0.465 (5)0.491 (14)0.374 (2)0.039*0.5
C130.6872 (2)0.6143 (6)0.45876 (19)0.0230 (7)
H130.6470.74230.46360.028*
C140.7528 (2)0.5524 (7)0.5242 (2)0.0294 (9)
C15A0.818 (3)0.343 (6)0.5238 (16)0.044 (3)0.482 (5)
H15A0.82020.3110.46860.066*0.482 (5)
H15B0.79580.20070.54580.066*0.482 (5)
H15C0.88130.38330.55680.066*0.482 (5)
C16A0.767 (4)0.651 (8)0.6034 (12)0.033 (4)0.482 (5)
O17A0.8138 (4)0.5539 (12)0.6617 (3)0.0250 (10)0.482 (5)
O18A0.7178 (8)0.851 (4)0.5940 (10)0.028 (2)0.482 (5)
C19A0.7246 (9)0.960 (3)0.6710 (10)0.032 (2)0.482 (5)
H19A0.69830.85120.70370.047*0.482 (5)
H19B0.68991.11080.66310.047*0.482 (5)
H19C0.79040.99080.69850.047*0.482 (5)
C15B0.825 (2)0.365 (6)0.5320 (16)0.044 (3)0.518 (5)
H15D0.80450.25070.48760.066*0.518 (5)
H15E0.83310.28130.58320.066*0.518 (5)
H15F0.88370.4390.53020.066*0.518 (5)
C16B0.757 (3)0.706 (7)0.5989 (12)0.033 (4)0.518 (5)
O17B0.8182 (4)0.6902 (11)0.6645 (3)0.0250 (10)0.518 (5)
O18B0.6889 (7)0.875 (3)0.5956 (10)0.028 (2)0.518 (5)
C19B0.6959 (9)1.028 (2)0.6652 (9)0.032 (2)0.518 (5)
H19D0.69420.92860.71150.047*0.518 (5)
H19E0.64331.14020.65350.047*0.518 (5)
H19F0.75471.11710.67730.047*0.518 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0302 (4)0.0189 (4)0.0146 (3)0.0018 (4)0.0037 (3)0.0028 (3)
Cl20.0207 (4)0.0251 (5)0.0273 (4)0.0083 (3)0.0141 (3)0.0056 (4)
Cl30.0237 (4)0.0137 (4)0.0420 (5)0.0004 (3)0.0018 (4)0.0047 (4)
C40.0155 (16)0.0148 (16)0.0214 (16)0.0008 (12)0.0086 (13)0.0014 (13)
C50.0131 (17)0.0287 (18)0.0165 (17)0.0020 (13)0.0051 (13)0.0073 (14)
N60.0131 (15)0.089 (3)0.0263 (18)0.0115 (18)0.0024 (13)0.0247 (19)
O70.0208 (12)0.0169 (12)0.0172 (11)0.0036 (9)0.0047 (9)0.0012 (9)
C80.0137 (15)0.0210 (18)0.0223 (17)0.0045 (13)0.0048 (13)0.0037 (13)
C90.0240 (18)0.0197 (17)0.0206 (16)0.0036 (14)0.0104 (14)0.0002 (14)
O100.0369 (15)0.0285 (14)0.0170 (12)0.0178 (11)0.0112 (11)0.0035 (10)
C110.0295 (19)0.0227 (19)0.0208 (17)0.0012 (15)0.0150 (15)0.0007 (14)
O120.0254 (12)0.0362 (15)0.0209 (11)0.0051 (12)0.0123 (10)0.0023 (12)
C130.0171 (16)0.0258 (19)0.0244 (18)0.0025 (14)0.0027 (14)0.0030 (15)
C140.0161 (18)0.042 (2)0.0273 (19)0.0112 (15)0.0012 (15)0.0131 (17)
C15A0.021 (4)0.066 (5)0.039 (4)0.007 (4)0.000 (4)0.030 (4)
C16A0.014 (8)0.065 (16)0.018 (3)0.015 (6)0.000 (2)0.014 (5)
O17A0.0230 (16)0.033 (3)0.0179 (15)0.003 (3)0.0029 (13)0.002 (3)
O18A0.022 (6)0.039 (4)0.0231 (14)0.011 (5)0.006 (4)0.0089 (19)
C19A0.031 (7)0.034 (7)0.031 (3)0.005 (4)0.012 (5)0.017 (4)
C15B0.021 (4)0.066 (5)0.039 (4)0.007 (4)0.000 (4)0.030 (4)
C16B0.014 (8)0.065 (16)0.018 (3)0.015 (6)0.000 (2)0.014 (5)
O17B0.0230 (16)0.033 (3)0.0179 (15)0.003 (3)0.0029 (13)0.002 (3)
O18B0.022 (6)0.039 (4)0.0231 (14)0.011 (5)0.006 (4)0.0089 (19)
C19B0.031 (7)0.034 (7)0.031 (3)0.005 (4)0.012 (5)0.017 (4)
Geometric parameters (Å, º) top
Cl1—C41.763 (3)C13—H130.95
Cl2—C41.772 (3)C14—C16A1.439 (17)
Cl3—C41.765 (3)C14—C15B1.475 (17)
C4—C51.560 (4)C14—C15A1.524 (18)
C5—O101.392 (4)C14—C16B1.538 (16)
C5—O71.401 (4)C15A—H15A0.98
C5—N61.428 (5)C15A—H15B0.98
N6—H6A0.87 (3)C15A—H15C0.98
N6—H6B0.85 (2)C16A—O17A1.19 (2)
N6—H6C0.81 (2)C16A—O18A1.318 (19)
O7—C81.439 (4)O18A—C19A1.442 (17)
C8—C131.495 (4)C19A—H19A0.98
C8—C91.532 (4)C19A—H19B0.98
C8—H81.0C19A—H19C0.98
C9—O101.437 (4)C15B—H15D0.98
C9—C111.502 (5)C15B—H15E0.98
C9—H91.0C15B—H15F0.98
C11—O121.425 (4)C16B—O17B1.252 (19)
C11—H11A0.99C16B—O18B1.370 (18)
C11—H11B0.99O18B—C19B1.455 (16)
O12—H12A0.84 (3)C19B—H19D0.98
O12—H12B0.82 (3)C19B—H19E0.98
C13—C141.323 (5)C19B—H19F0.98
C5—C4—Cl1111.0 (2)C14—C13—C8125.8 (3)
C5—C4—Cl3108.9 (2)C14—C13—H13117.1
Cl1—C4—Cl3109.02 (17)C8—C13—H13117.1
C5—C4—Cl2109.8 (2)C13—C14—C16A126.6 (9)
Cl1—C4—Cl2109.01 (16)C13—C14—C15B127.6 (11)
Cl3—C4—Cl2109.09 (16)C13—C14—C15A121.4 (11)
O10—C5—O7108.4 (3)C16A—C14—C15A111.8 (12)
O10—C5—N6110.3 (3)C13—C14—C16B115.0 (7)
O7—C5—N6110.8 (3)C15B—C14—C16B117.3 (13)
O10—C5—C4107.5 (3)C14—C15A—H15A109.5
O7—C5—C4108.2 (3)C14—C15A—H15B109.5
N6—C5—C4111.5 (3)H15A—C15A—H15B109.5
C5—N6—H6A110 (5)C14—C15A—H15C109.5
C5—N6—H6B113 (4)H15A—C15A—H15C109.5
H6A—N6—H6B101 (5)H15B—C15A—H15C109.5
C5—N6—H6C95 (2)O17A—C16A—O18A132.0 (16)
H6A—N6—H6C113 (5)O17A—C16A—C14122.1 (15)
H6B—N6—H6C124 (5)O18A—C16A—C14106.0 (14)
C5—O7—C8109.6 (2)C16A—O18A—C19A110.2 (15)
O7—C8—C13108.2 (2)O18A—C19A—H19A109.5
O7—C8—C9103.9 (2)O18A—C19A—H19B109.5
C13—C8—C9116.8 (3)H19A—C19A—H19B109.5
O7—C8—H8109.2O18A—C19A—H19C109.5
C13—C8—H8109.2H19A—C19A—H19C109.5
C9—C8—H8109.2H19B—C19A—H19C109.5
O10—C9—C11110.5 (3)C14—C15B—H15D109.5
O10—C9—C8103.0 (2)C14—C15B—H15E109.5
C11—C9—C8116.7 (3)H15D—C15B—H15E109.5
O10—C9—H9108.8C14—C15B—H15F109.5
C11—C9—H9108.8H15D—C15B—H15F109.5
C8—C9—H9108.8H15E—C15B—H15F109.5
C5—O10—C9109.6 (2)O17B—C16B—O18B115.7 (13)
O12—C11—C9112.2 (3)O17B—C16B—C14124.9 (15)
O12—C11—H11A109.2O18B—C16B—C14119.4 (15)
C9—C11—H11A109.2C16B—O18B—C19B119.0 (13)
O12—C11—H11B109.2O18B—C19B—H19D109.5
C9—C11—H11B109.2O18B—C19B—H19E109.5
H11A—C11—H11B107.9H19D—C19B—H19E109.5
C11—O12—H12A113 (2)O18B—C19B—H19F109.5
C11—O12—H12B113 (6)H19D—C19B—H19F109.5
H12A—O12—H12B133 (6)H19E—C19B—H19F109.5
Cl1—C4—C5—O1062.2 (3)C8—C9—O10—C522.5 (3)
Cl3—C4—C5—O10177.8 (2)O10—C9—C11—O1264.2 (3)
Cl2—C4—C5—O1058.5 (3)C8—C9—C11—O1252.9 (4)
Cl1—C4—C5—O7179.0 (2)O7—C8—C13—C14158.9 (3)
Cl3—C4—C5—O761.0 (3)C9—C8—C13—C1484.4 (4)
Cl2—C4—C5—O758.4 (3)C8—C13—C14—C16A177 (4)
Cl1—C4—C5—N658.9 (4)C8—C13—C14—C15B2 (2)
Cl3—C4—C5—N661.2 (3)C8—C13—C14—C15A2 (2)
Cl2—C4—C5—N6179.5 (3)C8—C13—C14—C16B178 (3)
O10—C5—O7—C81.5 (4)C13—C14—C16A—O17A164 (4)
N6—C5—O7—C8122.7 (3)C15A—C14—C16A—O17A11 (7)
C4—C5—O7—C8114.7 (3)C13—C14—C16A—O18A15 (6)
C5—O7—C8—C13139.8 (3)C15A—C14—C16A—O18A170 (4)
C5—O7—C8—C915.0 (3)O17A—C16A—O18A—C19A1 (8)
O7—C8—C9—O1022.3 (3)C14—C16A—O18A—C19A178 (3)
C13—C8—C9—O10141.3 (3)C13—C14—C16B—O17B174 (4)
O7—C8—C9—C1198.9 (3)C15B—C14—C16B—O17B3 (7)
C13—C8—C9—C1120.1 (4)C13—C14—C16B—O18B6 (6)
O7—C5—O10—C914.0 (4)C15B—C14—C16B—O18B177 (4)
N6—C5—O10—C9107.5 (3)O17B—C16B—O18B—C19B3 (6)
C4—C5—O10—C9130.7 (2)C14—C16B—O18B—C19B177 (3)
C11—C9—O10—C5102.8 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O12—H12B···N60.82 (3)2.22 (4)2.986 (4)155 (7)
N6—H6A···O120.87 (3)2.31 (5)2.986 (4)135 (6)
O12—H12A···O12i0.84 (3)1.98 (4)2.750 (4)151 (5)
N6—H6C···O17Bii0.81 (2)2.57 (2)3.369 (7)169 (3)
C19A—H19C···N6iii0.982.593.555 (15)167
N6—H6B···O17Aiv0.85 (2)2.61 (5)3.286 (7)137 (5)
C19B—H19E···O12v0.982.623.573 (11)164
Symmetry codes: (i) x+1, y, z+1; (ii) x1/2, y1/2, z1/2; (iii) x+1/2, y+1/2, z+1/2; (iv) x1/2, y+1/2, z1/2; (v) x+1, y+1, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O12—H12B···N60.82 (3)2.22 (4)2.986 (4)155 (7)
N6—H6A···O120.87 (3)2.31 (5)2.986 (4)135 (6)
O12—H12A···O12i0.84 (3)1.98 (4)2.750 (4)151 (5)
N6—H6C···O17Bii0.81 (2)2.57 (2)3.369 (7)169 (3)
C19A—H19C···N6iii0.982.593.555 (15)167
N6—H6B···O17Aiv0.85 (2)2.61 (5)3.286 (7)137 (5)
C19B—H19E···O12v0.982.623.573 (11)164
Symmetry codes: (i) x+1, y, z+1; (ii) x1/2, y1/2, z1/2; (iii) x+1/2, y+1/2, z+1/2; (iv) x1/2, y+1/2, z1/2; (v) x+1, y+1, z+1.

Experimental details

Crystal data
Chemical formulaC10H14Cl3NO5
Mr334.57
Crystal system, space groupMonoclinic, I2
Temperature (K)90
a, b, c (Å)14.8821 (9), 5.5847 (3), 17.2971 (14)
β (°) 105.847 (2)
V3)1382.96 (16)
Z4
Radiation typeMo Kα
µ (mm1)0.68
Crystal size (mm)0.26 × 0.22 × 0.16
Data collection
DiffractometerBruker D8 Venture
Absorption correctionMulti-scan
(SADABS; Bruker, 2014)
Tmin, Tmax0.84, 0.90
No. of measured, independent and
observed [I > 2σ(I)] reflections
11488, 2420, 2272
Rint0.030
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.023, 0.052, 1.03
No. of reflections2420
No. of parameters207
No. of restraints36
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.29, 0.21
Absolute structureFlack x determined using 959 quotients [(I+)–(I)]/[(I+)+(I)] (Parsons et al., 2013)
Absolute structure parameter0.02 (2)

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 3| March 2016| Pages 343-346
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