research communications
of 2,6-bis(3-hydroxy-3-methylbut-1-yn-1-yl)pyridine monohydrate
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
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. Ohydroxy—H⋯Owater, Ohydroxy—H⋯Ohydroxy, Owater—H⋯Ohydroxy and Owater—H···Npyridine, result in the formation of a ribbon-like structure running along [011].
Keywords: crystal structure; pyridine; hydrogen bonding; π–π stacking.
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 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 Cipso—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.
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⋯Cgiv; symmetry code: (iv) −x + , −y + 1, z + ] 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.
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 (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 . 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 Uiso(H) = 1.2Ueq (aromatic-C) or 1.5Ueq (methyl-C).
details are summarized in Table 2Supporting information
https://doi.org/10.1107/S2056989020013304/is5553sup1.cif
contains datablock I. DOI: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
Data collection: CrysAlis PRO (Rigaku OD, 2019); cell
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).C15H17NO2·H2O | Dx = 1.175 Mg m−3 |
Mr = 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 |
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 | Rint = 0.015 |
Detector resolution: 10.0000 pixels mm-1 | θmax = 75.0°, θmin = 4.2° |
ω scans | h = −40→25 |
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2019) | k = −22→34 |
Tmin = 0.817, Tmax = 1.000 | l = −8→5 |
4676 measured reflections |
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(Fo2) + (0.0555P)2 + 3.7832P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.082 | (Δ/σ)max < 0.001 |
S = 1.04 | Δρmax = 0.18 e Å−3 |
2071 reflections | Δρmin = −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 |
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. |
x | y | z | Uiso*/Ueq | ||
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) |
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) |
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) |
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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