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Synthesis, characterization and intermolecular interactions in crystals of two p-tert-butylthiacalix[4]arene diisocyanide and diamine derivatives
Accepted Manuscript Synthesis, characterization and intermolecular interactions in crystals of two p-tertbutylthiacalix[4]arene diisocyanide and diamine derivatives Sheng-Jie Shi, Xue-Xin Lv, Mei Zhao, Jian-Ping Ma, Dian-Shun Guo PII:
S0022-2860(16)30774-8
DOI:
10.1016/j.molstruc.2016.07.090
Reference:
MOLSTR 22793
To appear in:
Journal of Molecular Structure
Received Date: 29 March 2016 Revised Date:
31 May 2016
Accepted Date: 20 July 2016
Please cite this article as: S.-J. Shi, X.-X. Lv, M. Zhao, J.-P. Ma, D.-S. Guo, Synthesis, characterization and intermolecular interactions in crystals of two p-tert-butylthiacalix[4]arene diisocyanide and diamine derivatives, Journal of Molecular Structure (2016), doi: 10.1016/j.molstruc.2016.07.090. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
ACCEPTED MANUSCRIPT
Synthesis, characterization and intermolecular interactions in crystals of two p-tert-butylthiacalix[4]arene diisocyanide and diamine derivatives
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Sheng-Jie Shi, Xue-Xin Lv, Mei Zhao, Jian-Ping Ma, Dian-Shun Guo*
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Synthesis, characterization and intermolecular interactions in crystals of two p-tert-butylthiacalix[4]arene diisocyanide and diamine derivatives
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Sheng-Jie Shi, Xue-Xin Lv, Mei Zhao, Jian-Ping Ma, Dian-Shun Guo* College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan 250014, People's Republic of China
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ABSTRACT
The synthesis, the spectral characterization and the crystal structure of 25,27-bis(2-isocyanoethoxy)-
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5,11,17,23-tetra-tert-butyl-26,28-dihydroxythiacalix[4]arene and of the reaction intermediate 25,27-bis(2aminoethoxy)-5,11,17,23-tetra-tert-butyl-26,28-dihydroxythiacalix[4]arene are here described. The target diisonitrile compound crystallizes in the triclinic system with space group P-1 while the diamine intermediate is trigonal with space group R-3. In both structures, the thiacalix[4]arene units adopt a broadly similar pinched cone conformation, where two aromatic rings bearing an ethereal group are
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almost parallel while two phenolic rings lie near-vertically. In the supramolecular structure of both molecules, various intermolecular interactions involving C―H···O, C―H···C, C―H···π and weak C―H···S interactions were found. Moreover, the Hirshfeld surface analysis of the target compound was
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made to further confirm the crystal packing driving forces. Keywords: isocyanide, thiacalix[4]arene, crystal structure, hydrogen bonding, Hirshfeld surface analysis
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1. Introduction
Isocyanides are a unique building block widely applied in combinatorial chemistry for constructing nitrogen-containing heterocycle and dipeptide-like molecule libraries via multi-component Passerini and Ugi reactions [1, 2]. Thiacalix[4]arene, as one of the most fascinating scaffolds in supramolecular chemistry, has attracted much interest in the fields involving ion recognition and molecular switch [3-8]. Through selective modification of the lower rim of thiacalix[4]arene, a variety of thiacalix[4]arene derivatives could be obtained. In particular, thiacalix[4]arene diamine and diisocyanide derivatives are the key intermediates for synthesis of novel optical- and redox-active receptors easily linked by amide [9],
ACCEPTED MANUSCRIPT Schiff base [10], thiocarbamide [11] and peptide [12]. To our knowledge, thiacalix[4]arene isocyanide derivatives are not described so far. In this article, we report the synthesis and the structural determination of a novel thiacalix[4]arene diisonitrile derivative, 25,27-bis(2-isocyanoethoxy)-5,11,17,23-tetra-tert-butyl-26,28-dihydroxythiacalix-
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[4]arene (3) (Scheme 1), together with the crystal structure of its precursor, 25,27-bis(2-aminoethoxy)5,11,17,23-tetra-tert-butyl-26,28-dihydroxythiacalix[4]arene (1) [13]. Moreover, the Hirshfeld surface analysis of compound (3) was also made to further confirm the crystal packing driving forces compared with that of the similar thiacalix[4]arene nitrile derivative, 25,27-bis(cyanomethoxy)-5,11,17,23-tetra-
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tert-butyl-26,28-dihydroxythiacalix[4]arene (4) (Scheme 1) [13].
Scheme 1. Sythesis route of (3) and chemical structure of (4).
2. Experimental
2.1. Reagents and instruments
All the chemicals except p-tert-butylthiacalix[4]arene were purchased from Sigma Aldrich and used without further purification. Melting points were determined on a Yamaco apparatus without correction. Infrared spectra (using KBr in pellets) were recorded on a BIO-RAD FTS-40 IR spectrometer. 1H NMR and
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C NMR spectra were measured on a Brucker Advance 300 spectrometer. HR-MS spectra were
acquired on a maXis UHR-TOF spectrometer.
ACCEPTED MANUSCRIPT 2.2. Synthesis and crystallization 2.2.1. 25,27-Bis(2-aminoethoxy)-5,11,17,23-tetra-tert-butyl-26,28-dihydroxythiacalix[4]arene (1) A literature method [13] was used to synthesize (1) as a white solid (yield 81%; m.p. 294-296 oC). 1
H NMR (300 MHz, CDCl3): δ 7.65 (s, 4H, Ar-H), 7.15 (s, 4H, Ar-H), 4.52 (t, 4H, J = 4.5 Hz,
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OCH2), 3.33 (t, 4H, J = 4.5 Hz, NCH2), 2.63 (br, 6H, NH2, OH), 1.31 (s, 18H, t-Bu), 0.90 (s, 18H, t-Bu). HR-MS (ESI): calcd. for C46H54N2O4S4: [M]+ 806.3279, found: [M+H]+ 807.3358.
Single crystals of (1) suitable for X-ray diffraction analysis were developed as its two fifths hydrate by slow evaporation of a solution of (1) in C2H5OH/CH2Cl2 (1/1 v/v) at 0 oC.
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2.2.2. 25,27-Bis(2-formamidoethoxy)-5,11,17,23-tetra-tert-butyl-26,28-dihydroxythiacalix[4]arene (2) HCO2H (1.5 mL, 40.0 mmol) was added to a mixture of (1) (0.806 g, 1.0 mmol) and ZnO (1.040 g,
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13.0 mmol) in toluene (14.0 mL). The resulting mixture was stirred at 80 oC for 24 h and diluted with dichloromethane. After removal of the ZnO by filtration, the filtrate was washed with saturated NaHCO3 solution and brine, dried over anhydrous MgSO4. The organic layer was evaporated in vacuo and the residue was purified by flash column chromatography (CH3OH/CH2Cl2 = 1/80, RF = 0.3) to give (2) as a white solid (yield 72%; m.p. 210-212 oC).
1
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IR (cm–1): v 3369 (OH, NH), 2955, 2863, 1666 (C=O), 1443, 1385, 1241 (Ar-O-R), 879. H NMR (300 MHz, CDCl3): δ 8.57 (s, 2H, HC=O), 8.37 (s, 2H, OH), 7.95 (s, 2H, NH), 7.68 (s, 4H,
Ar-H), 7.35 (s, 4H, Ar-H), 4.49 (t, 4H, J = 4.5 Hz, OCH2), 3.93 (t, 4H, J = 4.5 Hz, NCH2), 1.30 (s, 18H,
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t-Bu), 1.02 (s, 18H, t-Bu).
C NMR (75 MHz, CDCl3): δ 164.82, 161.95, 156.25, 149.10, 143.58, 135.39, 135.08, 128.55,
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121.28, 75.86, 38.44, 34.30, 34.17, 31.38, 30.84. HR-MS (ESI): calcd. for C46H58N2O6S4: [M]+ 862.3178, found: [M+Na]+ 885.3082. 2.2.3. 25,27-Bis(2-isocyanoethoxy)-5,11,17,23-tetra-tert-butyl-26,28-dihydroxythiacalix[4]arene (3) A solution of POCl3 (0.5 mL, 5.5 mmol) in dichloromethane (5.0 mL) was added dropwise to a solution of (2) (0.862 g, 1.0 mmol) and triethylamine (1.5 mL, 11.0 mmol) in dichloromethane (20.0 mL) at 0 oC. The resulting mixture was stirred for 2 h and then washed with saturated NaHCO3 solution and brine, dried over anhydrous MgSO4. The organic layer was evaporated in vacuo and the residue was purified by flash column chromatography (ethyl acetate/hexane = 1/5, RF = 0.4) to afford (3) as a white solid (yield 70%; m.p. 217-219 oC).
ACCEPTED MANUSCRIPT IR (cm–1): vmax 3399 (OH), 2955, 2921, 2857, 2151 (N≡C), 1444, 1385, 1242 (Ar-O-R), 874. 1
H NMR (300 MHz, CDCl3): δ 7.69 (s, 4H, Ar-H), 7.60 (s, 2H, OH), 6.97 (s, 4H, Ar-H), 4.81 (t, 4H,
J = 4.5 Hz, OCH2), 4.10 (t, 4H, J = 4.5 Hz, NCH2), 1.35 (s, 18H, t-Bu), 0.81 (s, 18H, t-Bu). 13
C NMR (75 MHz, CDCl3): δ 158.78, 155.46, 155.39, 148.73, 143.15, 134.49, 132.93, 128.84,
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121.94, 71.44, 42.14, 34.21, 34.07, 31.44, 30.72. HR-MS (ESI): calcd. for C46H54N2O4S4: [M]+ 826.2966, found: [M + Na]+ 849.2876.
Single crystals of (3) suitable for X-ray diffraction analysis were developed as its dichloromethane
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quartersolvate by slow evaporation of a solution of (3) in CH3OH/CH2Cl2 (1/1 v/v) at 0 oC. 2.3. Crystal structure determination
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Colorless single crystals of (1) and (3) were selected and mounted on glass fibers, respectively. The intensity data were measured at 100 K on an Agilent SuperNova CCD-based diffractometer (CuKα radiation, λ = 1.54184 Å) [14]. Empirical absorption corrections were applied using SCALE3 ABSPACK. The structures were solved by direct methods and difference Fourier syntheses, and refined by full-matrix least-squares technique on F2 using SHELXS-97 [15] and SHELXL-97 [16]. All non-hydrogen atoms
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were refined with anisotropic displacement parameters. Hydrogen atoms attached to refined atoms were placed in geometrically idealized positions and refined using a riding model with C–H = 0.93, 0.97 and 0.96 Å for aromatic, methylene and methyl H, respectively, Uiso(H) = 1.5Ueq(C) for methyl H, and Uiso(H) = 1.2Ueq(C) for all other H atoms. For (1), the aquo hydrogen atoms were located by Fourier difference
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synthesis and refined with isotropic displacement parameters subject to an O–H = 0.85(2) Å distance restraint. One aminoethyl of the molecule was disordered over two orientations with two fifths of a water
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molecule, and was refined with site occupation factors of 0.60(2):0.40(2). Its C–N bond lengths were refined in 1.435(10)–1.462(9) Å distance restraint, and C–C bond lengths were refined in 1.522(14)–1.580(20) Å distance restraint. The ADPs of C(21), C(22), N(2) and C(22') were restrained to be isotropic within a standard deviation of 0.005 Å2, and the atom N(2') was constrained to have the same ADPs as atom N(2). In total 30 geometric restraints were used in modeling the disorders. For (3), quarter of a CH2Cl2 molecule was disordered over two orientations, with refined site-occupation factors of 0.50(2):0.50(2). The C–Cl bond lengths were refined in 1.735(8)–1.771(8) Å distance restraint, and the ADPs of C(41), C(42) and C(40) were restrained to be isotropic within a standard deviation of 0.005 Å2.
ACCEPTED MANUSCRIPT In total 22 geometric restraints were used in modeling the disorders. Crystal data experimental details and H-bonds for (1) and (3) (their bond lengths and angles are reported in Tables S1 and S2 in the supplementary information file) are given in Tables 1 and 2, respectively.
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Table 1 Crystal and structure refinement data for (1) and (3).
(3)
Empirical formula
C44H58N2O4S4·2/5H2O
C46H54N2O4S4·1/4CH2Cl2
Formula weight
814.41
848.38
Temperature (K)
100
100
Crystal system
Trigonal
Triclinic
Space group
R-3
a (Å)
41.7716(11)
b (Å)
41.7716(11)
c (Å)
13.2598(3)
20.9525(9)
α (°)
90
77.325(3)
β (°)
90 120 3
P-1
12.4140(4) 18.6808(5)
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γ (°)
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(1)
76.818(3)
79.942(3)
Volume (Å )
20036.8(9)
4575.8(3)
Z
18
4
Dc (g/cm )
1.232
2.296
2.514
7848
1802
0.48 × 0.08 × 0.07
0.31 × 0.24 × 0.04
3.55 to 67.08
2.97 to 67.07
14119
32361
Independent reflections
7853
16306
Observed reflections (I > 2σ(I))
6430
11794
2
1.035
1.023
Final R indices (I > 2σ(I))
R = 0.0691, wR = 0.1881
R = 0.0630, wR = 0.1620
R indices (all data)
R = 0.0825, wR = 0.1976
R = 0.0894, wR = 0.1879
0.944, –0.930
1.617, –1.018
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1.215
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µ (mm ) F(000) Crystal size (mm) θ range (°)
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Collected reflections
Goodness-of-fit on F
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(∆ρ)max, (∆ρ)min (e·Å )
2.4. Hirshfeld surface analysis The Hirshfeld surfaces and 2D fingerprint plots for the conformers A and B of compound (3) together with compound (4) were generated using the program CrystalExplorer 3.1 [17]. All bond lengths to hydrogen atoms were normalized to standard neutron values (C–H = 1.083 Å, O–H = 0.983 Å, N–H = 1.009 Å) [18].
ACCEPTED MANUSCRIPT 3. Results and discussion 3.1. Synthesis and characterization of compound (3) Isocyanides are commonly synthesized via dehydration of a formamide compound with phosphorus oxychloride. We found that a solution of thiacalix[4]arene diformamide derivative (2) and triethylamine
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in dichloromethane was treated with phosphorus oxychloride at 0 oC for 2 h to afford thiacalix[4]arene diisocyanide derivative (3) in 70% yield. The reaction intermediate (2) was obtained in 72% yield by reacting (1), prepared by a literature method [13], with formic acid in the presence of zinc oxide.
by IR, 1H NMR, 13C NMR and HR-MS spectra. 3.2. Crystal structural description
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The structures of compound (3) together with its intermediates (1) and (2) were fully characterized
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Compound (1) with two fifths of water molecule crystallizes in the space group R-3 and its asymmetric unit contains one p-tert-butylthiacalix[4]arene molecule bearing two –OCH2CH2NH2 arms (Fig. 1). The thiacalix[4]arene unit shows a pinched cone conformation, where two opposite aromatic rings attaching –OCH2CH2NH2 group are almost parallel to each other forming an interplanar angle of 5.9(2)°, while two phenolic rings are tilted outwards and nearly perpendicular to each other creating an
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interplanar angle of 77.8(2)°. Such a conformation can be ascribed to the intramolecular O―H···O hydrogen bonds (Table 2) formed by both –OH groups with the same ethereal O(4) atom. A few of similar molecular conformations were observed in the crystal structures of thiacalix[4]arene derivatives [19, 20],
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whereas in the cases of some 1,3-disubstituted calix[4]arene derivatives, their calix[4]arene units usually present a perfect cone conformation owing to the intramolecular O―H···O hydrogen bonds produced by
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two –OH groups with the different ethereal O atoms [21]. The dihedral angles between the virtual plane (R) defined by the four bridging S atoms and C(1)–C(6), C(11)–C(16), C(23)–C(28) and C(33)–C(38) rings are 55.9(2), 77.0(2), 46.6(2) and 71.2(2)°, respectively. Both –OCH2CH2NH2 arms adopt a gauche conformation and point to one side close to the same –OH group, with N(1)···O(3) and N(2)···O(3) distances of 2.806(10) and 2.912(14) Å. One aminoethyl group was disordered over two orientations, showing the site-occupation factors of 0.60(2):0.40(2). Interestingly, three fifths of an intramolecular N(2)―H(2A)···O(3) hydrogen bond further stabilizes the pinched cone conformation, while two fifths of an intermolecular O(1W)―H(1D)···O(3) hydrogen bond occupies the site of N(2)―H(2A)···O(3) when the aminoethyl unit was disordered over the other position.
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Fig. 1. The molecular structures of (1) and (3), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level. The disordered atoms (dashed spheres) are shown for (1). The dashed lines represent O―H···O, N―H···O and C―H···C hydrogen bonds. H atoms not involved in the hydrogen bonds and
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disordered dichloromethane molecules have been omitted for clarity.
Compound (3) with one quarter of a dichloromethane molecule crystallizes in the space group P-1
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and its asymmetric unit consists of two crystallographically independent p-tert-butylthiacalix[4]arene molecules each bearing two isocyanoethyl moieties, A and B (Fig. 1). Similar to (1), the thiacalix[4]arene units of A and B also show a pinched cone conformation. The two opposite aromatic rings linking –OCH2CH2N≡C group are almost parallel but the two phenolic rings are nearly perpendicular mutually, with interplanar angles of 1.0(2), 84.0(2)° in A and 6.7(2), 86.7(2)° in B. All –OCH2CH2N≡C moieties in
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A and B also give a gauche conformation, with similar torsion angles, ranging from 59.0(4) to 69.8(5)°. In molecule A, both –OCH2CH2N≡C arms point vertically to two sides, whereas in B, both –OCH2CH2N≡C arms point parallel to one side owing to the formation of an intramolecular C(68)―H(68A)···C(92)
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hydrogen bond (Table 2) between the two arms. This is inconsistent with that of the similar nitrile compound (4), where both –OCH2C≡N arms oppositely point to two sides. The lengths of N(1)≡C(45),
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N(2)≡C(46), N(3)≡C(92) and N(4)≡C(91) bonds are 1.150(6), 1.157(7), 1.158(7) and 1.121(6) Å, respectively. Compared to the averaged length of the N≡C bonds (1.151 Å) [22], the N(4)≡C(91) length is slightly shorter, but also included in the length range of the N≡C bonds [1.092(15)–1.167(2) Å] [23, 24]. Half a dichoromethane molecule was disordered over two positions, giving refined site-occupation factors of 0.50(2):0.50(2). In the packing, six molecules of (1) combine in a sequential manner to construct a circular hexamer, showing a cyclohexane-like chair conformation, by co-operative intermolecular C(43)―H(43B)···Cg1i [Cg1 is the centroid of C(1)–C(6) ring] contacts [25] (Fig. 2a). Moreover, an S···S contact [26] occurs between the vicinal molecules, with an S(2)···S(1)i separation of 3.527(2) Å (S = 1.80 Å) [27], and
ACCEPTED MANUSCRIPT further stabilizes the hexamer. Next, such hexamers are stacked into a hexagonal channel by offset-face-to-face π-π interactions [28] between the C(11)–C(16) and C(23)–C(28) aromatic rings (Fig. 2b). The distance between the centroids of C(11)–C(16) and C(23)–C(28)(y – 1/3, –x + y + 1/3, –z + 4/3) rings is 3.808 Å. Interestingly, the inside of this hexagonal channel is hydrophilic, whereas the outside is
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hydrophobic.
Fig. 2. The supramolecular structure of (1): (a) An annular hexamer assembled by C–H···π interactions (dashed lines). H atoms not involved in C―H···π interactions, tert-butyl and disordered moieties have been omitted for
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clarity. (b) A hexagonal channel built with the annular hexamers by π⋅⋅⋅π interactions. All H atoms and disordered moieties have been omitted for clarity.
In the supramolecular structure, an asymmetric dimer of (3) is formed through an intermolecular
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C(90)―H(90B)···C(46) hydrogen bond between neighbouring molecules A and B, where C(90)―H(90B) acts as a hydrogen-bond donor and the acceptor is C(46) atom of the isocyano group. The H(90B)···C(46)
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distance (2.57 Å) is shorter than that reported previously (2.75 Å) [29]. Then, each dimer is connected in turn to produce a one-dimensional ABAB type of chain by C(22)―H(22A)···O(8)i hydrogen bond (Fig. 3). Moreover, this one-dimensional chain is further stabilized by intermolecular O(4)···S(5) [the distance O(4)···S(5) is 3.280(3) Å (O = 1.52 Å; S = 1.80 Å)] [26, 27] and C(21)―H(21A)···Cg2i [Cg2 is the centroid of C(57)–C(62) ring] contacts, as well as C(90)―H(90B)···C(46) and C(22)―H(22A)···O(8)i hydrogen bonds. In the packing of (4), however, a one-dimensional chain is formed between the same molecules by a combination of intermolecular C(3)―H(1)···N(1) hydrogen bonds. Next, these one-dimensional ABAB type of chains are head-to-tail linked to produce a two-dimensional network by weak interchain C(12)―H(12)···C(91)ii and C(10)―H(10A)···C(91)ii hydrogen bonds, locally creating
ACCEPTED MANUSCRIPT an R21(11) motif [30]. In such a two-dimensional network, all neighbours of A are molecule B and vice versa. Finally, these two-dimensional networks are alternately stacked into a three-dimensional framework stabilized by weak interlayer C―H···S hydrogen bonds. In addition, the disordered
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dichloromethane solvent molecules fill in the cavity of the three-dimensional framework.
Fig. 3. The hydrogen-bonded two-dimensional plane of (3), showing the C―H···C, C―H···O, C―H···π and O···S interactions (dashed lines), and the R21(11) motif. H atoms and tert-butyl groups not involved in the motif and disordered dichloromethane molecules have been omitted for clarity.
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Table 2
Hydrogen bond lengths (Å) and bond angles (°) for (1) and (3) d(D–H)
d(H⋅⋅⋅A)
d(D⋅⋅⋅A)
∠ D–H⋅⋅⋅A
O(1)–H(1)⋅⋅⋅O(4)
0.82
2.04
2.805(4)
154.9
O(3)–H(3)⋅⋅⋅O(4)
0.82
2.42
3.220(5)
166.3
0.86
2.13
2.911(14)
150.5
0.86
2.23
2.697(14)
113.8
0.97
2.54
3.389(5)
146.4
D–H⋅⋅⋅A
N(2)–H(2A)⋅⋅⋅O(3) O(1W)–H(1D)⋅⋅⋅O(3) (3)
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C(43)–H(43B)⋅⋅⋅Cg1
i
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(1)
O(1)–H(1)⋅⋅⋅O(2)
0.82
2.15
2.866(3)
146.5
O(3)–H(3)⋅⋅⋅O(2)
0.82
2.11
2.900(4)
160.5
O(5)–H(5)⋅⋅⋅O(6)
0.82
2.05
2.834(3)
160.2
O(7)–H(7)⋅⋅⋅O(6)
0.82
2.16
2.885(4)
146.9
C(68)–H(68A)⋅⋅⋅C(92)
0.97
2.66
3.454(8)
139.0
C(90)–H(90B)⋅⋅⋅C(46)
0.97
2.57
3.257(7)
127.4
0.97
2.54
3.444(5)
155.6
0.93
2.73
3.660(6)
173.0
0.96
2.81
3.749(7)
167.7
0.97
2.74
3.603(4)
148.0
C(22)–H(22A)⋅⋅⋅O(8) C(12)–H(12)⋅⋅⋅C(91)
i
ii
C(10)–H(10A)⋅⋅⋅C(91) C(21)–H(21A)⋅⋅⋅Cg2
i
ii
Symmetry codes: (i) x − y + 2/3, x + 1/3, −z + 7/3 for (1). (i) x, y − 1, z; (ii) x + 1, y − 1, z for (3), Cg1 is the centroid
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of C(1)–C(6) ring for (1). Cg2 is the centroid of C(57)–C(62) ring for (3).
ACCEPTED MANUSCRIPT 3.3. Hirshfeld surface analysis of (3) and (4) Hirshfeld surface analysis is a useful tool to confirm the crystal packing driving forces, so the Hirshfeld surfaces were made for the conformers A and B of isonitrile compound (3) together with nitrile compound (4) (Fig. 4). The Hirshfeld surfaces of (3) clearly show the different interactions between A
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and B, indicating that the formation of conformers A and B results from its varied molecular environment. The interactions of C···H and O···H in (3), and N···H and O···H in (4) can be seen in the Hirshfeld surfaces as the bright red spots, while the S···H contacts in (3) and (4) are the light red spots, showing weaker C―H···S hydrogen bonds. The unique relevant interactions are the C―H···C hydrogen bonds in
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(3), but the C―H···N hydrogen bonds in (4). The 2D fingerprint plots (Fig. 5, while their decomposition is reported in Fig. S1 in the supplementary information file) reveal significant differences between (3) and
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(4) due to their different interactions and percentages ascribed to the total Hirshfeld surface. The quantitative analysis shows that the contribution of H···H and C···H/H···C contacts in (3) is 56% and 20.2% for A, and 52.1% and 22.5% for B, respectively. Compared to (3), the contribution of C···H/H···C contacts in (4) is only 8.3%, which can be ascribed to the C―H···N hydrogen bonds replacing the C―H···C hydrogen bonds in the latter. A summary of the decomposed fingerprint plots (Fig. 6) confirms
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that the major intermolecular contacts are weak H···H, S···H/H···S and C···H/H···C interactions, which contribute 86.2% in conformer A but 85% in B. However, those are weak H···H, S···H/H···S and
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N···H/H···N contacts, which contribute only 79.8% in (4).
Fig. 4. Hirshfeld surface for conformers A (a) and B (b) of (3), and (4) (c). Neighbouring molecules associated with
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close contacts are shown along with distances between the atoms involved.
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Fig. 5. Fingerprint plots of conformers A (a) and B (b) of (3), and (4) (c).
Fig. 6. Distribution of intermolecular contacts from Hirshfeld surface analysis (%) for conformers A (a) and B (b) of (3), and (4) (c).
4. Conclusion
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In summary, the synthesis and the intermolecular interactions in crystal structures of the first thiacalix[4]arene diisocyanide derivative and its diamine precursor were described. In the solid states, the thiacalix[4]arene cores of both molecules show a broadly similar pinched cone conformation. While
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various intermolecular interactions involving C―H···O, C―H···C, C―H···π and weak C―H···S were found in the packing. Moreover, the crystal packing driving forces of the target diisocyanide compound
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were further confirmed by the Hirshfeld surface analysis.
Acknowledgment
Financial support of this work from the National Natural Science Foundation of China (grant No. 21372147) and the Undergraduate Innovative Research Training Program of China (grant No. 201510445114) is gratefully acknowledged.
Supplementary data Crystallographic data have been deposited with the Cambridge Crystallographic Data Centre (CCDC) as supplementary publications Nos. 1454590-1454591. Supplementary data related to this article can be
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[10] M. Kumar, A. Dhir, V. Bhalla, Regulation of metal ion recognition by allosteric effects in thiacalix[4]crown
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derivatives, Tetrahedron Lett. 54 (2013) 1524–1527. [12] G.-K. Shao, M. Zhao, Z. Wei, J.-P. Ma, D.-S. Guo, Two novel ferrocenyl dipeptide-like compounds generated via the Ugi four-component reaction, Acta Cryst. C71 (2015) 667–672. [13] V. Bhalla, M. Kumar, T. Hattori, S. Miyano, Stereoselective synthesis of all stereoisomers of vicinal and distal bis(O-2-aminoethyl)-p-tert-butylthiacalix[4]arene, Tetrahedron 60 (2004) 5881–5887. [14] Agilent, CrysAlis PRO. Aglient Technologies, Yarnton, Oxfordshire, England 2012. [15] G.M. Sheldrick, SHELXS-97, Program for Crystal Structure Solution, University of Göttingen, Germany 1997. [16] G.M. Sheldrick, SHELXL-97, Program for Crystal Structure Refinement, University of Göttingen, Germany 1997.
ACCEPTED MANUSCRIPT [17] S.K. Wolff, D.J. Grimwood, J.J. McKinnon, D. Jayatilaka, M.A. Spackman, CrystalExplorer, 2007. [18] F.H. Allen, O. Kennard, D.G. Watson, L. Brammer, A.G. Orpen, R. Taylor, Tables of bond lengths determined by X-ray and neutron diffraction. Part 1. Bond lengths in organic compounds, J. Chem. Soc., Perkin Trans. 2 (1987) S1–S19. [19] O.
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1,3-dialkoxythiacalix[4]arenes in the solid state, Acta Cryst. C62 (2006) o289–o294. [20] L.-L. Liu, L.-S. Chen, J.-P. Ma, D.-S. Guo, 5,17-Dibromo-26,28-dihydroxy-25,27-dipropoxy-2,8,14,20tetrathiacalix[4]arene, Acta Cryst. E67 (2011) o1110–o1111.
[21] Y. Liu, S. Li, X.-P. Bai, T. Wada, Y. Inoue, Complexation thermodynamics of p-tert-butylcalix[4]arene
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[22] K.M. Skodje, L.M. Hinkle, M.O. Miranda, K.R. Mann, D.E. Janzen, Nonisomorphous X-ray structures of tritylnitrile and tritylisonitrile, J. Chem. Crystallogr. 42 (2012) 972–980.
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[23] T.F. Molinski, D.J. Faulkner, Three new diterpene isonitriles from a Palauan sponge of the genus Halichondria, J. Org. Chem. 52 (1987) 3334–3337.
[24] J. Buschmann, S. Kleinhenz, D. Lentz, P. Luger, K.V. Madappat, D. Preugschat, J.S. Thrasher, Crystal and molecular structures of trifluoroacrylonitrile, F2C=CF-CN, and trifluorovinyl isocyanide, F2C=CF-NC, by low-temperature X-ray crystallography and ab initio calculations, Inorg. Chem. 39 (2000) 2807–2812. [25] S. Tsuzuki, K. Honda, T. Uchimaru, M. Mikami, K. Tanabe, The magnitude of the CH/π interaction between
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benzene and some model hydrocarbons, J. Am. Chem. Soc. 122 (2000) 3746–3753. [26] P. Nagy, D. Szabó, I. Kapovits, Á. Kucsman, G. Argay, A. Kálmán, Intramolecular S⋅⋅⋅S and S⋅⋅⋅O close contacts in 1,8-bis(phenylsulfanyl)naphthalene derivatives of different sulfur valence state: an X-ray study, J. Mol. Struct. 606 (2002) 61–76.
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interaction: model chemistry calculations of benzene dimer interaction, J. Am. Chem. Soc. 124 (2002) 104–112.
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ACCEPTED MANUSCRIPT Hihlights
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A novel thiacalix[4]arene diisocyanide derivative was firstly synthesized. A hexagonal channel assemblized in crystal of thiacalix[4]arene diamine derivative. Hirshfeld surface analysis of thiacalix[4]arene diisocyanide and dicyanide compounds.
S0022-2860(16)30774-8
DOI:
10.1016/j.molstruc.2016.07.090
Reference:
MOLSTR 22793
To appear in:
Journal of Molecular Structure
Received Date: 29 March 2016 Revised Date:
31 May 2016
Accepted Date: 20 July 2016
Please cite this article as: S.-J. Shi, X.-X. Lv, M. Zhao, J.-P. Ma, D.-S. Guo, Synthesis, characterization and intermolecular interactions in crystals of two p-tert-butylthiacalix[4]arene diisocyanide and diamine derivatives, Journal of Molecular Structure (2016), doi: 10.1016/j.molstruc.2016.07.090. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
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Synthesis, characterization and intermolecular interactions in crystals of two p-tert-butylthiacalix[4]arene diisocyanide and diamine derivatives
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Sheng-Jie Shi, Xue-Xin Lv, Mei Zhao, Jian-Ping Ma, Dian-Shun Guo*
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Synthesis, characterization and intermolecular interactions in crystals of two p-tert-butylthiacalix[4]arene diisocyanide and diamine derivatives
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Sheng-Jie Shi, Xue-Xin Lv, Mei Zhao, Jian-Ping Ma, Dian-Shun Guo* College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan 250014, People's Republic of China
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ABSTRACT
The synthesis, the spectral characterization and the crystal structure of 25,27-bis(2-isocyanoethoxy)-
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5,11,17,23-tetra-tert-butyl-26,28-dihydroxythiacalix[4]arene and of the reaction intermediate 25,27-bis(2aminoethoxy)-5,11,17,23-tetra-tert-butyl-26,28-dihydroxythiacalix[4]arene are here described. The target diisonitrile compound crystallizes in the triclinic system with space group P-1 while the diamine intermediate is trigonal with space group R-3. In both structures, the thiacalix[4]arene units adopt a broadly similar pinched cone conformation, where two aromatic rings bearing an ethereal group are
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almost parallel while two phenolic rings lie near-vertically. In the supramolecular structure of both molecules, various intermolecular interactions involving C―H···O, C―H···C, C―H···π and weak C―H···S interactions were found. Moreover, the Hirshfeld surface analysis of the target compound was
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made to further confirm the crystal packing driving forces. Keywords: isocyanide, thiacalix[4]arene, crystal structure, hydrogen bonding, Hirshfeld surface analysis
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1. Introduction
Isocyanides are a unique building block widely applied in combinatorial chemistry for constructing nitrogen-containing heterocycle and dipeptide-like molecule libraries via multi-component Passerini and Ugi reactions [1, 2]. Thiacalix[4]arene, as one of the most fascinating scaffolds in supramolecular chemistry, has attracted much interest in the fields involving ion recognition and molecular switch [3-8]. Through selective modification of the lower rim of thiacalix[4]arene, a variety of thiacalix[4]arene derivatives could be obtained. In particular, thiacalix[4]arene diamine and diisocyanide derivatives are the key intermediates for synthesis of novel optical- and redox-active receptors easily linked by amide [9],
ACCEPTED MANUSCRIPT Schiff base [10], thiocarbamide [11] and peptide [12]. To our knowledge, thiacalix[4]arene isocyanide derivatives are not described so far. In this article, we report the synthesis and the structural determination of a novel thiacalix[4]arene diisonitrile derivative, 25,27-bis(2-isocyanoethoxy)-5,11,17,23-tetra-tert-butyl-26,28-dihydroxythiacalix-
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[4]arene (3) (Scheme 1), together with the crystal structure of its precursor, 25,27-bis(2-aminoethoxy)5,11,17,23-tetra-tert-butyl-26,28-dihydroxythiacalix[4]arene (1) [13]. Moreover, the Hirshfeld surface analysis of compound (3) was also made to further confirm the crystal packing driving forces compared with that of the similar thiacalix[4]arene nitrile derivative, 25,27-bis(cyanomethoxy)-5,11,17,23-tetra-
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tert-butyl-26,28-dihydroxythiacalix[4]arene (4) (Scheme 1) [13].
Scheme 1. Sythesis route of (3) and chemical structure of (4).
2. Experimental
2.1. Reagents and instruments
All the chemicals except p-tert-butylthiacalix[4]arene were purchased from Sigma Aldrich and used without further purification. Melting points were determined on a Yamaco apparatus without correction. Infrared spectra (using KBr in pellets) were recorded on a BIO-RAD FTS-40 IR spectrometer. 1H NMR and
13
C NMR spectra were measured on a Brucker Advance 300 spectrometer. HR-MS spectra were
acquired on a maXis UHR-TOF spectrometer.
ACCEPTED MANUSCRIPT 2.2. Synthesis and crystallization 2.2.1. 25,27-Bis(2-aminoethoxy)-5,11,17,23-tetra-tert-butyl-26,28-dihydroxythiacalix[4]arene (1) A literature method [13] was used to synthesize (1) as a white solid (yield 81%; m.p. 294-296 oC). 1
H NMR (300 MHz, CDCl3): δ 7.65 (s, 4H, Ar-H), 7.15 (s, 4H, Ar-H), 4.52 (t, 4H, J = 4.5 Hz,
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OCH2), 3.33 (t, 4H, J = 4.5 Hz, NCH2), 2.63 (br, 6H, NH2, OH), 1.31 (s, 18H, t-Bu), 0.90 (s, 18H, t-Bu). HR-MS (ESI): calcd. for C46H54N2O4S4: [M]+ 806.3279, found: [M+H]+ 807.3358.
Single crystals of (1) suitable for X-ray diffraction analysis were developed as its two fifths hydrate by slow evaporation of a solution of (1) in C2H5OH/CH2Cl2 (1/1 v/v) at 0 oC.
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2.2.2. 25,27-Bis(2-formamidoethoxy)-5,11,17,23-tetra-tert-butyl-26,28-dihydroxythiacalix[4]arene (2) HCO2H (1.5 mL, 40.0 mmol) was added to a mixture of (1) (0.806 g, 1.0 mmol) and ZnO (1.040 g,
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13.0 mmol) in toluene (14.0 mL). The resulting mixture was stirred at 80 oC for 24 h and diluted with dichloromethane. After removal of the ZnO by filtration, the filtrate was washed with saturated NaHCO3 solution and brine, dried over anhydrous MgSO4. The organic layer was evaporated in vacuo and the residue was purified by flash column chromatography (CH3OH/CH2Cl2 = 1/80, RF = 0.3) to give (2) as a white solid (yield 72%; m.p. 210-212 oC).
1
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IR (cm–1): v 3369 (OH, NH), 2955, 2863, 1666 (C=O), 1443, 1385, 1241 (Ar-O-R), 879. H NMR (300 MHz, CDCl3): δ 8.57 (s, 2H, HC=O), 8.37 (s, 2H, OH), 7.95 (s, 2H, NH), 7.68 (s, 4H,
Ar-H), 7.35 (s, 4H, Ar-H), 4.49 (t, 4H, J = 4.5 Hz, OCH2), 3.93 (t, 4H, J = 4.5 Hz, NCH2), 1.30 (s, 18H,
13
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t-Bu), 1.02 (s, 18H, t-Bu).
C NMR (75 MHz, CDCl3): δ 164.82, 161.95, 156.25, 149.10, 143.58, 135.39, 135.08, 128.55,
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121.28, 75.86, 38.44, 34.30, 34.17, 31.38, 30.84. HR-MS (ESI): calcd. for C46H58N2O6S4: [M]+ 862.3178, found: [M+Na]+ 885.3082. 2.2.3. 25,27-Bis(2-isocyanoethoxy)-5,11,17,23-tetra-tert-butyl-26,28-dihydroxythiacalix[4]arene (3) A solution of POCl3 (0.5 mL, 5.5 mmol) in dichloromethane (5.0 mL) was added dropwise to a solution of (2) (0.862 g, 1.0 mmol) and triethylamine (1.5 mL, 11.0 mmol) in dichloromethane (20.0 mL) at 0 oC. The resulting mixture was stirred for 2 h and then washed with saturated NaHCO3 solution and brine, dried over anhydrous MgSO4. The organic layer was evaporated in vacuo and the residue was purified by flash column chromatography (ethyl acetate/hexane = 1/5, RF = 0.4) to afford (3) as a white solid (yield 70%; m.p. 217-219 oC).
ACCEPTED MANUSCRIPT IR (cm–1): vmax 3399 (OH), 2955, 2921, 2857, 2151 (N≡C), 1444, 1385, 1242 (Ar-O-R), 874. 1
H NMR (300 MHz, CDCl3): δ 7.69 (s, 4H, Ar-H), 7.60 (s, 2H, OH), 6.97 (s, 4H, Ar-H), 4.81 (t, 4H,
J = 4.5 Hz, OCH2), 4.10 (t, 4H, J = 4.5 Hz, NCH2), 1.35 (s, 18H, t-Bu), 0.81 (s, 18H, t-Bu). 13
C NMR (75 MHz, CDCl3): δ 158.78, 155.46, 155.39, 148.73, 143.15, 134.49, 132.93, 128.84,
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121.94, 71.44, 42.14, 34.21, 34.07, 31.44, 30.72. HR-MS (ESI): calcd. for C46H54N2O4S4: [M]+ 826.2966, found: [M + Na]+ 849.2876.
Single crystals of (3) suitable for X-ray diffraction analysis were developed as its dichloromethane
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quartersolvate by slow evaporation of a solution of (3) in CH3OH/CH2Cl2 (1/1 v/v) at 0 oC. 2.3. Crystal structure determination
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Colorless single crystals of (1) and (3) were selected and mounted on glass fibers, respectively. The intensity data were measured at 100 K on an Agilent SuperNova CCD-based diffractometer (CuKα radiation, λ = 1.54184 Å) [14]. Empirical absorption corrections were applied using SCALE3 ABSPACK. The structures were solved by direct methods and difference Fourier syntheses, and refined by full-matrix least-squares technique on F2 using SHELXS-97 [15] and SHELXL-97 [16]. All non-hydrogen atoms
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were refined with anisotropic displacement parameters. Hydrogen atoms attached to refined atoms were placed in geometrically idealized positions and refined using a riding model with C–H = 0.93, 0.97 and 0.96 Å for aromatic, methylene and methyl H, respectively, Uiso(H) = 1.5Ueq(C) for methyl H, and Uiso(H) = 1.2Ueq(C) for all other H atoms. For (1), the aquo hydrogen atoms were located by Fourier difference
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synthesis and refined with isotropic displacement parameters subject to an O–H = 0.85(2) Å distance restraint. One aminoethyl of the molecule was disordered over two orientations with two fifths of a water
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molecule, and was refined with site occupation factors of 0.60(2):0.40(2). Its C–N bond lengths were refined in 1.435(10)–1.462(9) Å distance restraint, and C–C bond lengths were refined in 1.522(14)–1.580(20) Å distance restraint. The ADPs of C(21), C(22), N(2) and C(22') were restrained to be isotropic within a standard deviation of 0.005 Å2, and the atom N(2') was constrained to have the same ADPs as atom N(2). In total 30 geometric restraints were used in modeling the disorders. For (3), quarter of a CH2Cl2 molecule was disordered over two orientations, with refined site-occupation factors of 0.50(2):0.50(2). The C–Cl bond lengths were refined in 1.735(8)–1.771(8) Å distance restraint, and the ADPs of C(41), C(42) and C(40) were restrained to be isotropic within a standard deviation of 0.005 Å2.
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Table 1 Crystal and structure refinement data for (1) and (3).
(3)
Empirical formula
C44H58N2O4S4·2/5H2O
C46H54N2O4S4·1/4CH2Cl2
Formula weight
814.41
848.38
Temperature (K)
100
100
Crystal system
Trigonal
Triclinic
Space group
R-3
a (Å)
41.7716(11)
b (Å)
41.7716(11)
c (Å)
13.2598(3)
20.9525(9)
α (°)
90
77.325(3)
β (°)
90 120 3
P-1
12.4140(4) 18.6808(5)
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γ (°)
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(1)
76.818(3)
79.942(3)
Volume (Å )
20036.8(9)
4575.8(3)
Z
18
4
Dc (g/cm )
1.232
2.296
2.514
7848
1802
0.48 × 0.08 × 0.07
0.31 × 0.24 × 0.04
3.55 to 67.08
2.97 to 67.07
14119
32361
Independent reflections
7853
16306
Observed reflections (I > 2σ(I))
6430
11794
2
1.035
1.023
Final R indices (I > 2σ(I))
R = 0.0691, wR = 0.1881
R = 0.0630, wR = 0.1620
R indices (all data)
R = 0.0825, wR = 0.1976
R = 0.0894, wR = 0.1879
0.944, –0.930
1.617, –1.018
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µ (mm ) F(000) Crystal size (mm) θ range (°)
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Collected reflections
Goodness-of-fit on F
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(∆ρ)max, (∆ρ)min (e·Å )
2.4. Hirshfeld surface analysis The Hirshfeld surfaces and 2D fingerprint plots for the conformers A and B of compound (3) together with compound (4) were generated using the program CrystalExplorer 3.1 [17]. All bond lengths to hydrogen atoms were normalized to standard neutron values (C–H = 1.083 Å, O–H = 0.983 Å, N–H = 1.009 Å) [18].
ACCEPTED MANUSCRIPT 3. Results and discussion 3.1. Synthesis and characterization of compound (3) Isocyanides are commonly synthesized via dehydration of a formamide compound with phosphorus oxychloride. We found that a solution of thiacalix[4]arene diformamide derivative (2) and triethylamine
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in dichloromethane was treated with phosphorus oxychloride at 0 oC for 2 h to afford thiacalix[4]arene diisocyanide derivative (3) in 70% yield. The reaction intermediate (2) was obtained in 72% yield by reacting (1), prepared by a literature method [13], with formic acid in the presence of zinc oxide.
by IR, 1H NMR, 13C NMR and HR-MS spectra. 3.2. Crystal structural description
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The structures of compound (3) together with its intermediates (1) and (2) were fully characterized
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Compound (1) with two fifths of water molecule crystallizes in the space group R-3 and its asymmetric unit contains one p-tert-butylthiacalix[4]arene molecule bearing two –OCH2CH2NH2 arms (Fig. 1). The thiacalix[4]arene unit shows a pinched cone conformation, where two opposite aromatic rings attaching –OCH2CH2NH2 group are almost parallel to each other forming an interplanar angle of 5.9(2)°, while two phenolic rings are tilted outwards and nearly perpendicular to each other creating an
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interplanar angle of 77.8(2)°. Such a conformation can be ascribed to the intramolecular O―H···O hydrogen bonds (Table 2) formed by both –OH groups with the same ethereal O(4) atom. A few of similar molecular conformations were observed in the crystal structures of thiacalix[4]arene derivatives [19, 20],
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whereas in the cases of some 1,3-disubstituted calix[4]arene derivatives, their calix[4]arene units usually present a perfect cone conformation owing to the intramolecular O―H···O hydrogen bonds produced by
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two –OH groups with the different ethereal O atoms [21]. The dihedral angles between the virtual plane (R) defined by the four bridging S atoms and C(1)–C(6), C(11)–C(16), C(23)–C(28) and C(33)–C(38) rings are 55.9(2), 77.0(2), 46.6(2) and 71.2(2)°, respectively. Both –OCH2CH2NH2 arms adopt a gauche conformation and point to one side close to the same –OH group, with N(1)···O(3) and N(2)···O(3) distances of 2.806(10) and 2.912(14) Å. One aminoethyl group was disordered over two orientations, showing the site-occupation factors of 0.60(2):0.40(2). Interestingly, three fifths of an intramolecular N(2)―H(2A)···O(3) hydrogen bond further stabilizes the pinched cone conformation, while two fifths of an intermolecular O(1W)―H(1D)···O(3) hydrogen bond occupies the site of N(2)―H(2A)···O(3) when the aminoethyl unit was disordered over the other position.
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Fig. 1. The molecular structures of (1) and (3), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level. The disordered atoms (dashed spheres) are shown for (1). The dashed lines represent O―H···O, N―H···O and C―H···C hydrogen bonds. H atoms not involved in the hydrogen bonds and
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disordered dichloromethane molecules have been omitted for clarity.
Compound (3) with one quarter of a dichloromethane molecule crystallizes in the space group P-1
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and its asymmetric unit consists of two crystallographically independent p-tert-butylthiacalix[4]arene molecules each bearing two isocyanoethyl moieties, A and B (Fig. 1). Similar to (1), the thiacalix[4]arene units of A and B also show a pinched cone conformation. The two opposite aromatic rings linking –OCH2CH2N≡C group are almost parallel but the two phenolic rings are nearly perpendicular mutually, with interplanar angles of 1.0(2), 84.0(2)° in A and 6.7(2), 86.7(2)° in B. All –OCH2CH2N≡C moieties in
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A and B also give a gauche conformation, with similar torsion angles, ranging from 59.0(4) to 69.8(5)°. In molecule A, both –OCH2CH2N≡C arms point vertically to two sides, whereas in B, both –OCH2CH2N≡C arms point parallel to one side owing to the formation of an intramolecular C(68)―H(68A)···C(92)
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hydrogen bond (Table 2) between the two arms. This is inconsistent with that of the similar nitrile compound (4), where both –OCH2C≡N arms oppositely point to two sides. The lengths of N(1)≡C(45),
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N(2)≡C(46), N(3)≡C(92) and N(4)≡C(91) bonds are 1.150(6), 1.157(7), 1.158(7) and 1.121(6) Å, respectively. Compared to the averaged length of the N≡C bonds (1.151 Å) [22], the N(4)≡C(91) length is slightly shorter, but also included in the length range of the N≡C bonds [1.092(15)–1.167(2) Å] [23, 24]. Half a dichoromethane molecule was disordered over two positions, giving refined site-occupation factors of 0.50(2):0.50(2). In the packing, six molecules of (1) combine in a sequential manner to construct a circular hexamer, showing a cyclohexane-like chair conformation, by co-operative intermolecular C(43)―H(43B)···Cg1i [Cg1 is the centroid of C(1)–C(6) ring] contacts [25] (Fig. 2a). Moreover, an S···S contact [26] occurs between the vicinal molecules, with an S(2)···S(1)i separation of 3.527(2) Å (S = 1.80 Å) [27], and
ACCEPTED MANUSCRIPT further stabilizes the hexamer. Next, such hexamers are stacked into a hexagonal channel by offset-face-to-face π-π interactions [28] between the C(11)–C(16) and C(23)–C(28) aromatic rings (Fig. 2b). The distance between the centroids of C(11)–C(16) and C(23)–C(28)(y – 1/3, –x + y + 1/3, –z + 4/3) rings is 3.808 Å. Interestingly, the inside of this hexagonal channel is hydrophilic, whereas the outside is
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hydrophobic.
Fig. 2. The supramolecular structure of (1): (a) An annular hexamer assembled by C–H···π interactions (dashed lines). H atoms not involved in C―H···π interactions, tert-butyl and disordered moieties have been omitted for
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clarity. (b) A hexagonal channel built with the annular hexamers by π⋅⋅⋅π interactions. All H atoms and disordered moieties have been omitted for clarity.
In the supramolecular structure, an asymmetric dimer of (3) is formed through an intermolecular
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C(90)―H(90B)···C(46) hydrogen bond between neighbouring molecules A and B, where C(90)―H(90B) acts as a hydrogen-bond donor and the acceptor is C(46) atom of the isocyano group. The H(90B)···C(46)
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distance (2.57 Å) is shorter than that reported previously (2.75 Å) [29]. Then, each dimer is connected in turn to produce a one-dimensional ABAB type of chain by C(22)―H(22A)···O(8)i hydrogen bond (Fig. 3). Moreover, this one-dimensional chain is further stabilized by intermolecular O(4)···S(5) [the distance O(4)···S(5) is 3.280(3) Å (O = 1.52 Å; S = 1.80 Å)] [26, 27] and C(21)―H(21A)···Cg2i [Cg2 is the centroid of C(57)–C(62) ring] contacts, as well as C(90)―H(90B)···C(46) and C(22)―H(22A)···O(8)i hydrogen bonds. In the packing of (4), however, a one-dimensional chain is formed between the same molecules by a combination of intermolecular C(3)―H(1)···N(1) hydrogen bonds. Next, these one-dimensional ABAB type of chains are head-to-tail linked to produce a two-dimensional network by weak interchain C(12)―H(12)···C(91)ii and C(10)―H(10A)···C(91)ii hydrogen bonds, locally creating
ACCEPTED MANUSCRIPT an R21(11) motif [30]. In such a two-dimensional network, all neighbours of A are molecule B and vice versa. Finally, these two-dimensional networks are alternately stacked into a three-dimensional framework stabilized by weak interlayer C―H···S hydrogen bonds. In addition, the disordered
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dichloromethane solvent molecules fill in the cavity of the three-dimensional framework.
Fig. 3. The hydrogen-bonded two-dimensional plane of (3), showing the C―H···C, C―H···O, C―H···π and O···S interactions (dashed lines), and the R21(11) motif. H atoms and tert-butyl groups not involved in the motif and disordered dichloromethane molecules have been omitted for clarity.
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Table 2
Hydrogen bond lengths (Å) and bond angles (°) for (1) and (3) d(D–H)
d(H⋅⋅⋅A)
d(D⋅⋅⋅A)
∠ D–H⋅⋅⋅A
O(1)–H(1)⋅⋅⋅O(4)
0.82
2.04
2.805(4)
154.9
O(3)–H(3)⋅⋅⋅O(4)
0.82
2.42
3.220(5)
166.3
0.86
2.13
2.911(14)
150.5
0.86
2.23
2.697(14)
113.8
0.97
2.54
3.389(5)
146.4
D–H⋅⋅⋅A
N(2)–H(2A)⋅⋅⋅O(3) O(1W)–H(1D)⋅⋅⋅O(3) (3)
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C(43)–H(43B)⋅⋅⋅Cg1
i
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(1)
O(1)–H(1)⋅⋅⋅O(2)
0.82
2.15
2.866(3)
146.5
O(3)–H(3)⋅⋅⋅O(2)
0.82
2.11
2.900(4)
160.5
O(5)–H(5)⋅⋅⋅O(6)
0.82
2.05
2.834(3)
160.2
O(7)–H(7)⋅⋅⋅O(6)
0.82
2.16
2.885(4)
146.9
C(68)–H(68A)⋅⋅⋅C(92)
0.97
2.66
3.454(8)
139.0
C(90)–H(90B)⋅⋅⋅C(46)
0.97
2.57
3.257(7)
127.4
0.97
2.54
3.444(5)
155.6
0.93
2.73
3.660(6)
173.0
0.96
2.81
3.749(7)
167.7
0.97
2.74
3.603(4)
148.0
C(22)–H(22A)⋅⋅⋅O(8) C(12)–H(12)⋅⋅⋅C(91)
i
ii
C(10)–H(10A)⋅⋅⋅C(91) C(21)–H(21A)⋅⋅⋅Cg2
i
ii
Symmetry codes: (i) x − y + 2/3, x + 1/3, −z + 7/3 for (1). (i) x, y − 1, z; (ii) x + 1, y − 1, z for (3), Cg1 is the centroid
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of C(1)–C(6) ring for (1). Cg2 is the centroid of C(57)–C(62) ring for (3).
ACCEPTED MANUSCRIPT 3.3. Hirshfeld surface analysis of (3) and (4) Hirshfeld surface analysis is a useful tool to confirm the crystal packing driving forces, so the Hirshfeld surfaces were made for the conformers A and B of isonitrile compound (3) together with nitrile compound (4) (Fig. 4). The Hirshfeld surfaces of (3) clearly show the different interactions between A
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and B, indicating that the formation of conformers A and B results from its varied molecular environment. The interactions of C···H and O···H in (3), and N···H and O···H in (4) can be seen in the Hirshfeld surfaces as the bright red spots, while the S···H contacts in (3) and (4) are the light red spots, showing weaker C―H···S hydrogen bonds. The unique relevant interactions are the C―H···C hydrogen bonds in
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(3), but the C―H···N hydrogen bonds in (4). The 2D fingerprint plots (Fig. 5, while their decomposition is reported in Fig. S1 in the supplementary information file) reveal significant differences between (3) and
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(4) due to their different interactions and percentages ascribed to the total Hirshfeld surface. The quantitative analysis shows that the contribution of H···H and C···H/H···C contacts in (3) is 56% and 20.2% for A, and 52.1% and 22.5% for B, respectively. Compared to (3), the contribution of C···H/H···C contacts in (4) is only 8.3%, which can be ascribed to the C―H···N hydrogen bonds replacing the C―H···C hydrogen bonds in the latter. A summary of the decomposed fingerprint plots (Fig. 6) confirms
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that the major intermolecular contacts are weak H···H, S···H/H···S and C···H/H···C interactions, which contribute 86.2% in conformer A but 85% in B. However, those are weak H···H, S···H/H···S and
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N···H/H···N contacts, which contribute only 79.8% in (4).
Fig. 4. Hirshfeld surface for conformers A (a) and B (b) of (3), and (4) (c). Neighbouring molecules associated with
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close contacts are shown along with distances between the atoms involved.
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Fig. 5. Fingerprint plots of conformers A (a) and B (b) of (3), and (4) (c).
Fig. 6. Distribution of intermolecular contacts from Hirshfeld surface analysis (%) for conformers A (a) and B (b) of (3), and (4) (c).
4. Conclusion
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In summary, the synthesis and the intermolecular interactions in crystal structures of the first thiacalix[4]arene diisocyanide derivative and its diamine precursor were described. In the solid states, the thiacalix[4]arene cores of both molecules show a broadly similar pinched cone conformation. While
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various intermolecular interactions involving C―H···O, C―H···C, C―H···π and weak C―H···S were found in the packing. Moreover, the crystal packing driving forces of the target diisocyanide compound
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were further confirmed by the Hirshfeld surface analysis.
Acknowledgment
Financial support of this work from the National Natural Science Foundation of China (grant No. 21372147) and the Undergraduate Innovative Research Training Program of China (grant No. 201510445114) is gratefully acknowledged.
Supplementary data Crystallographic data have been deposited with the Cambridge Crystallographic Data Centre (CCDC) as supplementary publications Nos. 1454590-1454591. Supplementary data related to this article can be
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ACCEPTED MANUSCRIPT Hihlights
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A novel thiacalix[4]arene diisocyanide derivative was firstly synthesized. A hexagonal channel assemblized in crystal of thiacalix[4]arene diamine derivative. Hirshfeld surface analysis of thiacalix[4]arene diisocyanide and dicyanide compounds.