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

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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. 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].

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[Furusho, Y., Matsuyama, T., Takata, T., Moriuchi, T. & Hirao, T. (2004). Tetrahedron Lett. 45, 9593-9597.]) and polymers (Miyagawa et al., 2010[Miyagawa, N., Watanabe, M., Matsuyama, T., Koyama, Y., Moriuchi, T., Hirao, T., Furusho, Y. & Takata, T. (2010). Chem. Commun. 46, 1920-1922.], 2011[Miyagawa, N., Kawasaki, A., Watanabe, M., Ogawa, M., Koyama, Y. & Takata, T. (2011). Kobunshi Ronbunshu, 68, 702-709.]), as starting materials of helical polymers (Inouye et al., 2004[Inouye, M., Waki, M. & Abe, H. (2004). J. Am. Chem. Soc. 126, 2022-2027.]; Waki et al., 2006[Waki, M., Abe, H. & Inouye, M. (2006). Chem. Eur. J. 12, 7839-7847.]; Abe, Machiguchi et al., 2008[Abe, H., Machiguchi, H., Matsumoto, S. & Inouye, M. (2008). J. Org. Chem. 73, 4650-4661.]; Abe, Murayama et al., 2008[Abe, H., Murayama, D., Kayamori, F. & Inouye, M. (2008). Macromolecules, 41, 6903-6909.]), and as ligands for transition-metal complexes (Hung et al., 2009[Hung, W.-C., Wang, L.-Y., Lai, C.-C., Liu, Y.-H., Peng, S.-M. & Chiu, S.-H. (2009). Tetrahedron Lett. 50, 267-270.]). 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[Holmes, B. T., Padgett, C. W., Krawiec, M. & Pennington, W. T. (2002). Cryst. Growth Des. 2, 619-624.]). 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.

[Scheme 1]

2. Structural commentary

The mol­ecular structure of the title compound is depicted in Fig. 1[link]. 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.

[Figure 1]
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[link] 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[link]), resulting in a ribbon-like structure along [011] (Fig. 3[link]). The pyridine ring forms ππ stacking inter­actions with that in a neighboring ribbon in an anti-parallel mode, resulting in a ππ network along the c axis (Fig. 4[link]). The centroid–centroid distance between the pyridine rings [CgCgiv; 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[Holmes, B. T., Padgett, C. W., Krawiec, M. & Pennington, W. T. (2002). Cryst. Growth Des. 2, 619-624.]), such ππ stacking inter­actions between the pyridine rings are not found.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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]
Figure 2
Packing diagram of the title compound, viewed down the c axis.
[Figure 3]
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]
Figure 4
Partial packing diagram of the title compound, showing the chain formation along the c axis by ππ 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[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) 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[Holmes, B. T., Padgett, C. W., Krawiec, M. & Pennington, W. T. (2002). Cryst. Growth Des. 2, 619-624.]). 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[Potts, K. T., Horwitz, C. P., Fessak, A., Keshavarz-K, M., Nash, K. E. & Toscano, P. J. (1993). J. Am. Chem. Soc. 115, 10444-10445.]). 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[link]. 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).

Table 2
Experimental details

Crystal data
Chemical formula C15H17NO2·H2O
Mr 261.31
Crystal system, space group Orthorhombic, Fdd2
Temperature (K) 113
a, b, c (Å) 31.9834 (14), 27.7358 (13), 6.6610 (4)
V3) 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.])
Tmin, Tmax 0.817, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 4676, 2071, 2045
Rint 0.015
(sin θ/λ)max−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
Δρmax, Δρmin (e Å−3) 0.18, −0.20
Absolute structure Flack x determined using 495 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 (11)
Computer programs: CrysAlis PRO (Rigaku OD, 2019[Rigaku OD (2019). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]), Olex2.solve (Bourhis et al., 2015[Bourhis, L. J., Dolomanov, O. V., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2015). Acta Cryst. A71, 59-75.]), Olex2.refine (Bourhis et al., 2015[Bourhis, L. J., Dolomanov, O. V., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2015). Acta Cryst. A71, 59-75.]) and OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]).

Supporting information


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·H2ODx = 1.175 Mg m3
Mr = 261.31Cu Kα radiation, λ = 1.54184 Å
Orthorhombic, Fdd2Cell parameters from 4276 reflections
a = 31.9834 (14) Åθ = 4.2–74.9°
b = 27.7358 (13) ŵ = 0.66 mm1
c = 6.6610 (4) ÅT = 113 K
V = 5908.9 (5) Å3Plate, white
Z = 160.34 × 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 Source2045 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.015
Detector resolution: 10.0000 pixels mm-1θmax = 75.0°, θmin = 4.2°
ω scansh = 4025
Absorption correction: multi-scan
(CrysAlisPro; Rigaku OD, 2019)
k = 2234
Tmin = 0.817, Tmax = 1.000l = 85
4676 measured reflections
Refinement top
Refinement on F2Hydrogen site location: mixed
Least-squares matrix: fullH 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 = 1.04Δρmax = 0.18 e Å3
2071 reflectionsΔρmin = 0.19 e Å3
192 parametersAbsolute structure: Flack x determined using 495 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
1 restraintAbsolute 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
xyzUiso*/Ueq
O10.35948 (3)0.32551 (4)0.6275 (2)0.0246 (3)
O20.34219 (3)0.65799 (4)0.3581 (2)0.0216 (3)
O30.38487 (4)0.74210 (5)0.3415 (3)0.0329 (4)
N10.27513 (4)0.49371 (5)0.5965 (3)0.0166 (3)
H10.3733 (8)0.3523 (9)0.623 (5)0.041 (7)*
H20.3550 (7)0.6863 (9)0.339 (5)0.037 (6)*
H2A0.1959640.4197640.6154140.022*
H30.1583470.4925230.6281270.023*
H3A0.4117 (8)0.7423 (8)0.345 (5)0.033 (6)*
H3B0.3782 (8)0.7679 (10)0.288 (5)0.042 (7)*
H40.1947720.5658820.6115130.022*
H9A0.3131940.2557730.5049560.037*
H9B0.2711460.2858490.4692270.037*
H9C0.2909320.2823730.6894250.037*
H10A0.3537620.3607670.2645770.041*
H10B0.3102430.3365770.2020180.041*
H10C0.3502050.3034100.2448220.041*
H14A0.3036490.7339240.5139510.036*
H14B0.2712510.7048030.6511370.036*
H14C0.2699060.6990270.4121770.036*
H15A0.3690170.6411980.7193810.043*
H15B0.3331120.6680960.8437020.043*
H15C0.3640360.6984830.7034670.043*
C10.25351 (4)0.45203 (5)0.6000 (3)0.0160 (3)
C20.21008 (5)0.44989 (5)0.6118 (3)0.0182 (3)
C30.18798 (5)0.49280 (6)0.6182 (3)0.0193 (4)
C40.20942 (4)0.53608 (5)0.6100 (3)0.0183 (3)
C50.25298 (4)0.53508 (5)0.5995 (3)0.0159 (3)
C60.27810 (5)0.40863 (6)0.5837 (3)0.0186 (4)
C70.29850 (5)0.37292 (5)0.5576 (3)0.0190 (4)
C80.32310 (5)0.32951 (6)0.5046 (3)0.0179 (4)
C90.29729 (5)0.28434 (6)0.5457 (3)0.0244 (4)
C100.33542 (6)0.33286 (6)0.2844 (3)0.0275 (4)
C110.27666 (4)0.57928 (5)0.5862 (3)0.0170 (3)
C120.29570 (4)0.61579 (6)0.5643 (3)0.0178 (3)
C130.31907 (5)0.66164 (5)0.5422 (3)0.0181 (4)
C140.28820 (5)0.70362 (6)0.5287 (3)0.0238 (4)
C150.34897 (6)0.66791 (7)0.7178 (4)0.0290 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0193 (5)0.0161 (5)0.0383 (9)0.0015 (4)0.0082 (6)0.0042 (6)
O20.0195 (5)0.0166 (5)0.0287 (7)0.0014 (4)0.0053 (6)0.0013 (6)
O30.0154 (5)0.0246 (6)0.0586 (11)0.0014 (4)0.0000 (7)0.0166 (7)
N10.0161 (5)0.0165 (6)0.0173 (8)0.0000 (4)0.0002 (6)0.0005 (6)
C10.0187 (7)0.0157 (7)0.0138 (8)0.0000 (5)0.0010 (7)0.0008 (7)
C20.0186 (6)0.0176 (7)0.0182 (9)0.0035 (5)0.0006 (7)0.0009 (7)
C30.0144 (6)0.0230 (8)0.0205 (9)0.0004 (6)0.0009 (7)0.0010 (8)
C40.0175 (7)0.0180 (7)0.0195 (9)0.0022 (5)0.0000 (7)0.0000 (7)
C50.0183 (7)0.0157 (7)0.0136 (9)0.0003 (5)0.0001 (7)0.0007 (7)
C60.0185 (7)0.0174 (7)0.0200 (9)0.0027 (5)0.0010 (7)0.0019 (7)
C70.0178 (6)0.0168 (7)0.0225 (9)0.0029 (5)0.0009 (7)0.0029 (8)
C80.0163 (6)0.0143 (7)0.0232 (10)0.0003 (5)0.0017 (7)0.0024 (7)
C90.0228 (7)0.0164 (7)0.0339 (11)0.0046 (6)0.0014 (8)0.0015 (8)
C100.0299 (8)0.0245 (8)0.0280 (11)0.0067 (7)0.0065 (8)0.0042 (8)
C110.0174 (7)0.0175 (7)0.0161 (8)0.0017 (5)0.0005 (7)0.0004 (7)
C120.0173 (6)0.0172 (7)0.0190 (9)0.0025 (6)0.0001 (6)0.0009 (7)
C130.0179 (7)0.0135 (7)0.0229 (10)0.0004 (5)0.0002 (7)0.0001 (7)
C140.0230 (7)0.0161 (7)0.0322 (11)0.0031 (6)0.0025 (8)0.0023 (8)
C150.0340 (9)0.0203 (8)0.0327 (11)0.0043 (7)0.0129 (8)0.0014 (8)
Geometric parameters (Å, º) top
O2—C131.436 (2)C4—C31.384 (2)
O2—H20.89 (3)C13—C141.529 (2)
O1—C81.427 (2)C13—C151.521 (3)
O1—H10.86 (3)C2—H2A0.9500
O3—H3A0.86 (3)C2—C31.385 (2)
O3—H3B0.83 (3)C3—H30.9500
N1—C11.3473 (19)C9—H9A0.9800
N1—C51.3488 (19)C9—H9B0.9800
C1—C61.442 (2)C9—H9C0.9800
C1—C21.393 (2)C10—H10A0.9800
C8—C71.481 (2)C10—H10B0.9800
C8—C91.525 (2)C10—H10C0.9800
C8—C101.522 (3)C14—H14A0.9800
C5—C41.3952 (19)C14—H14B0.9800
C5—C111.444 (2)C14—H14C0.9800
C12—C111.191 (2)C15—H15A0.9800
C12—C131.482 (2)C15—H15B0.9800
C7—C61.199 (2)C15—H15C0.9800
C4—H40.9500
C13—O2—H2107 (2)C3—C2—C1118.31 (13)
C8—O1—H1109.4 (19)C3—C2—H2A120.8
H3A—O3—H3B105 (2)C4—C3—C2119.44 (13)
C1—N1—C5117.40 (12)C4—C3—H3120.3
N1—C1—C6115.80 (12)C2—C3—H3120.3
N1—C1—C2123.32 (13)C8—C9—H9A109.5
C2—C1—C6120.85 (13)C8—C9—H9B109.5
O1—C8—C7111.09 (14)C8—C9—H9C109.5
O1—C8—C9105.94 (14)H9A—C9—H9B109.5
O1—C8—C10110.27 (13)H9A—C9—H9C109.5
C7—C8—C9109.73 (13)H9B—C9—H9C109.5
C7—C8—C10108.51 (15)C8—C10—H10A109.5
C10—C8—C9111.32 (16)C8—C10—H10B109.5
N1—C5—C4122.83 (14)C8—C10—H10C109.5
N1—C5—C11116.47 (12)H10A—C10—H10B109.5
C4—C5—C11120.68 (14)H10A—C10—H10C109.5
C11—C12—C13178.5 (2)H10B—C10—H10C109.5
C6—C7—C8174.6 (2)C13—C14—H14A109.5
C5—C4—H4120.7C13—C14—H14B109.5
C3—C4—C5118.66 (14)C13—C14—H14C109.5
C3—C4—H4120.7H14A—C14—H14B109.5
C12—C11—C5176.4 (2)H14A—C14—H14C109.5
C7—C6—C1176.0 (2)H14B—C14—H14C109.5
O2—C13—C12106.48 (13)C13—C15—H15A109.5
O2—C13—C14109.61 (14)C13—C15—H15B109.5
O2—C13—C15109.95 (14)C13—C15—H15C109.5
C12—C13—C14109.48 (12)H15A—C15—H15B109.5
C12—C13—C15109.82 (15)H15A—C15—H15C109.5
C15—C13—C14111.38 (14)H15B—C15—H15C109.5
C1—C2—H2A120.8
N1—C1—C2—C30.7 (3)C5—N1—C1—C6176.16 (16)
N1—C5—C4—C30.1 (3)C5—N1—C1—C21.8 (3)
C1—N1—C5—C41.3 (3)C5—C4—C3—C21.3 (3)
C1—N1—C5—C11177.20 (15)C11—C5—C4—C3178.62 (17)
C1—C2—C3—C40.9 (3)C6—C1—C2—C3177.14 (17)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···O2i0.86 (3)1.90 (3)2.7640 (15)175 (3)
O2—H2···O30.89 (3)1.82 (2)2.7052 (17)170 (3)
O3—H3A···N1ii0.86 (3)2.02 (3)2.8790 (18)179 (3)
O3—H3B···O1iii0.83 (3)2.01 (3)2.8361 (19)173 (3)
Symmetry codes: (i) x+3/4, y1/4, z+1/4; (ii) x+3/4, y+1/4, z1/4; (iii) x, y+1/2, z1/2.
 

Acknowledgements

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

References

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