Crystal structure of 2,6-bis­(3-hy­droxy-3-methyl­but-1-yn-1-yl)pyridine monohydrate

Koizumi, T.; Takata, T.

doi:10.1107/S2056989020013304

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ISSN: 2056-9890

Volume 76| Part 11| November 2020| Pages 1737-1740

https://doi.org/10.1107/S2056989020013304

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Crystal structure of 2,6-bis(3-hydroxy-3-methylbut-1-yn-1-yl)pyridine monohydrate

Take-aki Koizumi ^a ^* and Toshikazu Takata ^a

^aSchool of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
^*Correspondence e-mail: koizumi.t.aa@m.titech.ac.jp

Edited by H. Ishida, Okayama University, Japan (Received 13 August 2020; accepted 5 October 2020; online 9 October 2020)

In the title pyridine derivative, C₁₅H₁₇NO₂·H₂O, the two OH groups are oriented in directions opposite to each other with respect to the plane of the pyridine ring. In the crystal, hydrogen bonds between the pyridine molecule and the water molecule, viz. O_hydroxy—H⋯O_water, O_hydroxy—H⋯O_hydroxy, O_water—H⋯O_hydroxy and O_water—H···N_pyridine, result in the formation of a ribbon-like structure running along [011].

Keywords: crystal structure; pyridine; hydrogen bonding; π–π stacking.

CCDC references: 2035321; 2035321

1. Chemical context

Pyridine derivatives with propargyl alcohol groups as substituents in the 2,6-positions are interesting compounds that have been used as synthons of many reactive compounds (Furusho et al., 2004 ) and polymers (Miyagawa et al., 2010 , 2011 ), as starting materials of helical polymers (Inouye et al., 2004 ; Waki et al., 2006 ; Abe, Machiguchi et al., 2008 ; Abe, Murayama et al., 2008 ), and as ligands for transition-metal complexes (Hung et al., 2009 ). Since such compounds have rigid structures containing one pyridine nitrogen and two alcoholic OH groups, they can be used to construct a higher order structure by coordination with metals and/or hydrogen-bond formation at multiple points. The crystal structures of 2,6-bis(3-methylbutyn-3-ol)pyridine, 1, and its complex with triphenylphosphine oxide (1-OPPh₃) were reported by Holmes et al. (2002 ). In the crystal of 1, the molecules form intermolecular hydrogen bonds with the pyridine ring and the two OH groups; the O—H⋯O hydrogen bonds from a 2₁ helical chain along the b-axis direction. The chains are linked by intermolecular N⋯H—O hydrogen bonds, forming a layer structure, and then form a stacking structure via C—H⋯O interactions between the layers. In contrast, in the case of 1-OPPh₃, each of the two OH groups forms a hydrogen bond with the O atom of OPPh₃ without forming a network structure. Hence, it is expected that the crystal packing of 1 strongly depends on the presence or absence of hydrogen bonding. However, to our knowledge, the present examples have only been structurally analysed with 2,6-bis(propargyl alcohol)-substituted pyridines. In this paper, we report the crystal structure of 2,6-bis(3-methylbutyn-3-ol)pyridine monohydrate, 1·H₂O.

2. Structural commentary

The molecular structure of the title compound is depicted in Fig. 1. The bond lengths of two C≡C triple bonds (C6≡C7 and C11≡C12) are 1.199 (2) and 1.191 (2) Å, respectively, consistent with the triple-bond character. The C_ipso—C≡C (C1—C6≡C7 and C5—C11≡C12) and C≡C–C(OH) (C6≡C7—C8 and C11≡C12—C13) bond angles are 176.0 (2), 176.4 (2), 174.6 (2) and 178.5 (2)°, respectively. C6≡C7—C8 is slightly distorted from a linear structure compared to the other bonds. The two OH groups are oriented in directions opposite to each other with respect to the plane of the pyridine ring, and the pyridine ring makes dihedral angles of 50.50 (17) and 57.58 (15)°, respectively, with the C7/C8/O1 and C12/C13/O2 planes.

Figure 1
The molecular structure of the title compound with the atom labelling. Displacement ellipsoids are drawn at the 50% probability level. A dashed line indicates the O—H⋯O hydrogen bond.

3. Supramolecular features

Fig. 2 depicts the packing of 1·H₂O along the c axis. The water molecules present as the crystallization solvent form intermolecular O—H⋯O and O—H⋯N interactions with the hydroxyl groups and the N atoms of the pyridine unit of molecule 1 (Table 1), resulting in a ribbon-like structure along [011] (Fig. 3). The pyridine ring forms π–π stacking interactions with that in a neighboring ribbon in an anti-parallel mode, resulting in a π–π network along the c axis (Fig. 4). The centroid–centroid distance between the pyridine rings [Cg⋯Cg^iv; symmetry code: (iv) −x + $[{1\over 2}]$ , −y + 1, z + $[{1\over 2}]$ ] is 3.5538 (11) Å. In the crystal of non-solvated 1 (space group P2₁/c; Holmes et al., 2002), such π–π stacking interactions between the pyridine rings are not found.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯O2ⁱ	0.86 (3)	1.90 (3)	2.7640 (15)	175 (3)
O2—H2⋯O3	0.89 (3)	1.82 (2)	2.7052 (17)	170 (3)
O3—H3A⋯N1ⁱⁱ	0.86 (3)	2.02 (3)	2.8790 (18)	179 (3)
O3—H3B⋯O1ⁱⁱⁱ	0.83 (3)	2.01 (3)	2.8361 (19)	173 (3)
Symmetry codes: (i) $[-x+{\script{3\over 4}}, y-{\script{1\over 4}}, z+{\script{1\over 4}}]$ ; (ii) $[-x+{\script{3\over 4}}, y+{\script{1\over 4}}, z-{\script{1\over 4}}]$ ; (iii) $[x, y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

Figure 2
Packing diagram of the title compound, viewed down the c axis.

Figure 3
Partial packing diagram of the title compound, showing the O—H⋯O and O—H⋯N hydrogen bonds (dashed lines) between 1 and water molecules.

Figure 4
Partial packing diagram of the title compound, showing the chain formation along the c axis by π–π interactions (dashed lines). [Symmetry codes: (b) −x + $[{1\over 2}]$ , −y + 1, z + $[{1\over 2}]$ ; (c) −x + $[{1\over 2}]$ , −y + 1, z − $[{1\over 2}]$ .]

4. Database survey

The Cambridge Structural Database (CSD version 5.41, update of March 2020; Groom et al., 2016 ) has 138 entries for structures containing 2,6-diethynylpyridine scaffolds, and for 2,6-bis(1-propyn-3-ol) derivatives gave two hits. The non-solvated compound 2,6-bis(3-methylbutyn-3-ol)pyridine (refcode LUMYEX) and its complex with O=PPh₃ (LUMYIB) have been reported (Holmes et al., 2002). The benzene derivative containing two propargyl alcohol units at the 1,3-positions gives 34 hits; however, there is no report of a simple benzene derivative having a structure similar to that of 1.

5. Synthesis and crystallization

2,6-Bis(3-methylbutyn-3-ol)pyridine was prepared by using a modified Potts method (Potts et al., 1993 ). 2,6-Dibromopyridine (9.1 g, 38 mmol) was reacted with 2-methyl-3-butyn-2-ol (13 g, 151 mmol) using CuI (225 mg, 1.3 mmol)/PdCl₂(PPh₃)₂ (840 mg, 1.3 mmol) as a catalyst in a THF (50 mL)–NEt₃ (150 mL) solvent for 19 h at room temperature. The resulting dark-brown solution was quenched with an aqueous NH₄Cl solution and the obtained solid was eliminated by celite filtration. The solution was extracted by AcOEt, and the organic phase was dried over MgSO₄. After filtering off the desiccant, the filtrate was concentrated and subjected to silica-gel chromatography (eluent: AcOEt:hexane 3:2). Single crystals suitable for X-ray diffraction studies were obtained from an ethyl acetate solution via slow evaporation in air.

6. Refinement

Crystal data, data collection and refinement details are summarized in Table 2. Water H atoms and alcohol H atoms were located in a difference-Fourier map, and were refined freely. All of the C-bound H atoms were positioned geometrically (C—H = 0.93 or 0.98 Å), and were refined using a riding model, with U_iso(H) = 1.2U_eq (aromatic-C) or 1.5U_eq (methyl-C).

Table 2
Experimental details

Crystal data
Chemical formula	C₁₅H₁₇NO₂·H₂O
M_r	261.31
Crystal system, space group	Orthorhombic, Fdd2
Temperature (K)	113
a, b, c (Å)	31.9834 (14), 27.7358 (13), 6.6610 (4)
V (Å³)	5908.9 (5)
Z	16
Radiation type	Cu Kα
μ (mm⁻¹)	0.66
Crystal size (mm)	0.34 × 0.1 × 0.1

Data collection
Diffractometer	Rigaku XtaLAB Synergy R, DW system, HyPix
Absorption correction	Multi-scan (CrysAlis PRO; Rigaku OD, 2019 $[Rigaku OD (2019). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ )
T_min, T_max	0.817, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	4676, 2071, 2045
R_int	0.015
(sin θ/λ)_max (Å⁻¹)	0.626

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.029, 0.082, 1.04
No. of reflections	2071
No. of parameters	192
No. of restraints	1
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.18, −0.20
Absolute structure	Flack x determined using 495 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter	0.02 (11)
Computer programs: CrysAlis PRO (Rigaku OD, 2019 $[Rigaku OD (2019). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ ), Olex2.solve (Bourhis et al., 2015 ), Olex2.refine (Bourhis et al., 2015) and OLEX2 (Dolomanov et al., 2009 ).

Supporting information

CCDC references: 2035321; 2035321

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989020013304/is5553sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989020013304/is5553Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989020013304/is5553Isup3.cml

checkCIF report

Computing details top

Data collection: CrysAlis PRO (Rigaku OD, 2019); cell refinement: CrysAlis PRO (Rigaku OD, 2019); data reduction: CrysAlis PRO (Rigaku OD, 2019); program(s) used to solve structure: Olex2.solve (Bourhis et al., 2015); program(s) used to refine structure: Olex2.refine (Bourhis et al., 2015); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

4-[6-(3-Hydroxy-3-methylbut-1-yn-1-yl)pyridin-2-yl]-2-methylbut-3-yn-2-ol monohydrate top

Crystal data top

C₁₅H₁₇NO₂·H₂O	D_x = 1.175 Mg m⁻³
M_r = 261.31	Cu Kα radiation, λ = 1.54184 Å
Orthorhombic, Fdd2	Cell parameters from 4276 reflections
a = 31.9834 (14) Å	θ = 4.2–74.9°
b = 27.7358 (13) Å	µ = 0.66 mm⁻¹
c = 6.6610 (4) Å	T = 113 K
V = 5908.9 (5) Å³	Plate, white
Z = 16	0.34 × 0.1 × 0.1 mm
F(000) = 2240

Data collection top

Rigaku XtaLAB Synergy R, DW system, HyPix diffractometer	2071 independent reflections
Radiation source: Rotating-anode X-ray tube, Rigaku (Cu) X-ray Source	2045 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.015
Detector resolution: 10.0000 pixels mm^-1	θ_max = 75.0°, θ_min = 4.2°
ω scans	h = −40→25
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2019)	k = −22→34
T_min = 0.817, T_max = 1.000	l = −8→5
4676 measured reflections

Refinement top

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.029	w = 1/[σ²(F_o²) + (0.0555P)² + 3.7832P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.082	(Δ/σ)_max < 0.001
S = 1.04	Δρ_max = 0.18 e Å⁻³
2071 reflections	Δρ_min = −0.19 e Å⁻³
192 parameters	Absolute structure: Flack x determined using 495 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
1 restraint	Absolute structure parameter: 0.02 (11)
Primary atom site location: iterative

Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.35948 (3)	0.32551 (4)	0.6275 (2)	0.0246 (3)
O2	0.34219 (3)	0.65799 (4)	0.3581 (2)	0.0216 (3)
O3	0.38487 (4)	0.74210 (5)	0.3415 (3)	0.0329 (4)
N1	0.27513 (4)	0.49371 (5)	0.5965 (3)	0.0166 (3)
H1	0.3733 (8)	0.3523 (9)	0.623 (5)	0.041 (7)*
H2	0.3550 (7)	0.6863 (9)	0.339 (5)	0.037 (6)*
H2A	0.195964	0.419764	0.615414	0.022*
H3	0.158347	0.492523	0.628127	0.023*
H3A	0.4117 (8)	0.7423 (8)	0.345 (5)	0.033 (6)*
H3B	0.3782 (8)	0.7679 (10)	0.288 (5)	0.042 (7)*
H4	0.194772	0.565882	0.611513	0.022*
H9A	0.313194	0.255773	0.504956	0.037*
H9B	0.271146	0.285849	0.469227	0.037*
H9C	0.290932	0.282373	0.689425	0.037*
H10A	0.353762	0.360767	0.264577	0.041*
H10B	0.310243	0.336577	0.202018	0.041*
H10C	0.350205	0.303410	0.244822	0.041*
H14A	0.303649	0.733924	0.513951	0.036*
H14B	0.271251	0.704803	0.651137	0.036*
H14C	0.269906	0.699027	0.412177	0.036*
H15A	0.369017	0.641198	0.719381	0.043*
H15B	0.333112	0.668096	0.843702	0.043*
H15C	0.364036	0.698483	0.703467	0.043*
C1	0.25351 (4)	0.45203 (5)	0.6000 (3)	0.0160 (3)
C2	0.21008 (5)	0.44989 (5)	0.6118 (3)	0.0182 (3)
C3	0.18798 (5)	0.49280 (6)	0.6182 (3)	0.0193 (4)
C4	0.20942 (4)	0.53608 (5)	0.6100 (3)	0.0183 (3)
C5	0.25298 (4)	0.53508 (5)	0.5995 (3)	0.0159 (3)
C6	0.27810 (5)	0.40863 (6)	0.5837 (3)	0.0186 (4)
C7	0.29850 (5)	0.37292 (5)	0.5576 (3)	0.0190 (4)
C8	0.32310 (5)	0.32951 (6)	0.5046 (3)	0.0179 (4)
C9	0.29729 (5)	0.28434 (6)	0.5457 (3)	0.0244 (4)
C10	0.33542 (6)	0.33286 (6)	0.2844 (3)	0.0275 (4)
C11	0.27666 (4)	0.57928 (5)	0.5862 (3)	0.0170 (3)
C12	0.29570 (4)	0.61579 (6)	0.5643 (3)	0.0178 (3)
C13	0.31907 (5)	0.66164 (5)	0.5422 (3)	0.0181 (4)
C14	0.28820 (5)	0.70362 (6)	0.5287 (3)	0.0238 (4)
C15	0.34897 (6)	0.66791 (7)	0.7178 (4)	0.0290 (4)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0193 (5)	0.0161 (5)	0.0383 (9)	−0.0015 (4)	−0.0082 (6)	0.0042 (6)
O2	0.0195 (5)	0.0166 (5)	0.0287 (7)	−0.0014 (4)	0.0053 (6)	0.0013 (6)
O3	0.0154 (5)	0.0246 (6)	0.0586 (11)	−0.0014 (4)	0.0000 (7)	0.0166 (7)
N1	0.0161 (5)	0.0165 (6)	0.0173 (8)	0.0000 (4)	−0.0002 (6)	0.0005 (6)
C1	0.0187 (7)	0.0157 (7)	0.0138 (8)	0.0000 (5)	−0.0010 (7)	0.0008 (7)
C2	0.0186 (6)	0.0176 (7)	0.0182 (9)	−0.0035 (5)	−0.0006 (7)	0.0009 (7)
C3	0.0144 (6)	0.0230 (8)	0.0205 (9)	−0.0004 (6)	−0.0009 (7)	0.0010 (8)
C4	0.0175 (7)	0.0180 (7)	0.0195 (9)	0.0022 (5)	0.0000 (7)	0.0000 (7)
C5	0.0183 (7)	0.0157 (7)	0.0136 (9)	−0.0003 (5)	0.0001 (7)	0.0007 (7)
C6	0.0185 (7)	0.0174 (7)	0.0200 (9)	−0.0027 (5)	−0.0010 (7)	0.0019 (7)
C7	0.0178 (6)	0.0168 (7)	0.0225 (9)	−0.0029 (5)	0.0009 (7)	0.0029 (8)
C8	0.0163 (6)	0.0143 (7)	0.0232 (10)	0.0003 (5)	−0.0017 (7)	0.0024 (7)
C9	0.0228 (7)	0.0164 (7)	0.0339 (11)	−0.0046 (6)	−0.0014 (8)	0.0015 (8)
C10	0.0299 (8)	0.0245 (8)	0.0280 (11)	0.0067 (7)	0.0065 (8)	0.0042 (8)
C11	0.0174 (7)	0.0175 (7)	0.0161 (8)	0.0017 (5)	−0.0005 (7)	−0.0004 (7)
C12	0.0173 (6)	0.0172 (7)	0.0190 (9)	0.0025 (6)	−0.0001 (6)	−0.0009 (7)
C13	0.0179 (7)	0.0135 (7)	0.0229 (10)	0.0004 (5)	0.0002 (7)	0.0001 (7)
C14	0.0230 (7)	0.0161 (7)	0.0322 (11)	0.0031 (6)	0.0025 (8)	0.0023 (8)
C15	0.0340 (9)	0.0203 (8)	0.0327 (11)	−0.0043 (7)	−0.0129 (8)	0.0014 (8)

Geometric parameters (Å, º) top

O2—C13	1.436 (2)	C4—C3	1.384 (2)
O2—H2	0.89 (3)	C13—C14	1.529 (2)
O1—C8	1.427 (2)	C13—C15	1.521 (3)
O1—H1	0.86 (3)	C2—H2A	0.9500
O3—H3A	0.86 (3)	C2—C3	1.385 (2)
O3—H3B	0.83 (3)	C3—H3	0.9500
N1—C1	1.3473 (19)	C9—H9A	0.9800
N1—C5	1.3488 (19)	C9—H9B	0.9800
C1—C6	1.442 (2)	C9—H9C	0.9800
C1—C2	1.393 (2)	C10—H10A	0.9800
C8—C7	1.481 (2)	C10—H10B	0.9800
C8—C9	1.525 (2)	C10—H10C	0.9800
C8—C10	1.522 (3)	C14—H14A	0.9800
C5—C4	1.3952 (19)	C14—H14B	0.9800
C5—C11	1.444 (2)	C14—H14C	0.9800
C12—C11	1.191 (2)	C15—H15A	0.9800
C12—C13	1.482 (2)	C15—H15B	0.9800
C7—C6	1.199 (2)	C15—H15C	0.9800
C4—H4	0.9500

C13—O2—H2	107 (2)	C3—C2—C1	118.31 (13)
C8—O1—H1	109.4 (19)	C3—C2—H2A	120.8
H3A—O3—H3B	105 (2)	C4—C3—C2	119.44 (13)
C1—N1—C5	117.40 (12)	C4—C3—H3	120.3
N1—C1—C6	115.80 (12)	C2—C3—H3	120.3
N1—C1—C2	123.32 (13)	C8—C9—H9A	109.5
C2—C1—C6	120.85 (13)	C8—C9—H9B	109.5
O1—C8—C7	111.09 (14)	C8—C9—H9C	109.5
O1—C8—C9	105.94 (14)	H9A—C9—H9B	109.5
O1—C8—C10	110.27 (13)	H9A—C9—H9C	109.5
C7—C8—C9	109.73 (13)	H9B—C9—H9C	109.5
C7—C8—C10	108.51 (15)	C8—C10—H10A	109.5
C10—C8—C9	111.32 (16)	C8—C10—H10B	109.5
N1—C5—C4	122.83 (14)	C8—C10—H10C	109.5
N1—C5—C11	116.47 (12)	H10A—C10—H10B	109.5
C4—C5—C11	120.68 (14)	H10A—C10—H10C	109.5
C11—C12—C13	178.5 (2)	H10B—C10—H10C	109.5
C6—C7—C8	174.6 (2)	C13—C14—H14A	109.5
C5—C4—H4	120.7	C13—C14—H14B	109.5
C3—C4—C5	118.66 (14)	C13—C14—H14C	109.5
C3—C4—H4	120.7	H14A—C14—H14B	109.5
C12—C11—C5	176.4 (2)	H14A—C14—H14C	109.5
C7—C6—C1	176.0 (2)	H14B—C14—H14C	109.5
O2—C13—C12	106.48 (13)	C13—C15—H15A	109.5
O2—C13—C14	109.61 (14)	C13—C15—H15B	109.5
O2—C13—C15	109.95 (14)	C13—C15—H15C	109.5
C12—C13—C14	109.48 (12)	H15A—C15—H15B	109.5
C12—C13—C15	109.82 (15)	H15A—C15—H15C	109.5
C15—C13—C14	111.38 (14)	H15B—C15—H15C	109.5
C1—C2—H2A	120.8

N1—C1—C2—C3	0.7 (3)	C5—N1—C1—C6	176.16 (16)
N1—C5—C4—C3	0.1 (3)	C5—N1—C1—C2	−1.8 (3)
C1—N1—C5—C4	1.3 (3)	C5—C4—C3—C2	−1.3 (3)
C1—N1—C5—C11	−177.20 (15)	C11—C5—C4—C3	178.62 (17)
C1—C2—C3—C4	0.9 (3)	C6—C1—C2—C3	−177.14 (17)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O2ⁱ	0.86 (3)	1.90 (3)	2.7640 (15)	175 (3)
O2—H2···O3	0.89 (3)	1.82 (2)	2.7052 (17)	170 (3)
O3—H3A···N1ⁱⁱ	0.86 (3)	2.02 (3)	2.8790 (18)	179 (3)
O3—H3B···O1ⁱⁱⁱ	0.83 (3)	2.01 (3)	2.8361 (19)	173 (3)

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

Acknowledgements

The authors thank the CREST program (JST, JPMJCR1522) for financial support.

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