Potential building blocks for porous organic materials

Abstract

2,4-Difluoronitrobenzene has been reacted with a linker diamine (ethylenediamine or propylenediamine) and butylamine, in either order, to give new molecular building blocks for porous supramolecular networks. Two structures were established by X-ray single crystal structure determinations. The propylenediamine structure displays small pores, which may be due to the longer and more flexible linker in the structure.

Keywords

channel hydrogen bond hydrophobic packing porous supramolecular

Introduction

The sequential reaction of 2,4-difluoronitrobenzene, 1, with amines gave compounds 2 and 3 (Figure 1).^1–4 Butylamine reacts initially in the ortho (2) position of compound 1. The linker diamine 1,4-diaminobutane then couples two units together by reacting in the para (4) position to give compound 2.¹ Compound 3 was made en route to a building block for mauveine. 2,4-Difluoronitrobenzene 1 was reacted twice with aniline to give compound 3.³ This was a difficult reaction because the substrate is not reactive enough and aniline is less nucleophilic. The structures of compounds 2 and 3 were unambiguously established by X-ray single crystal structure determinations.

Figure 1.

2,4-Difluoronitrobenzene, 1, and two organic molecular building blocks, N¹, N¹′-(butane-1,4-diyl)bis(N³-butyl-4-nitrobenzene-1,3-diamine) (C₂₄H₃₆N₆O₄) 2 and 2,4-bis(phenylamino) nitrobenzene (C₁₈H₁₄N₃O₂) 3.

Figure 2 shows that compound 2 forms cyclic hexamers that are linked by bifurcated N–H^{. . .}(O, O) hydrogen bonds arising from the NH group of the linker diamine. An O atom of the nitro group also accepts an intramolecular N–H^{. . .}O hydrogen bond from its ortho amino group. The butyl groups are arranged on the inside of the ring to result in a hydrophobic channel or pore of about 10 Å in diameter (Figure 3). Figure 2 shows that compound 3 also forms cyclic hexamers, which are held together by double acceptor N–H^{. . .}O hydrogen bonds involving one oxygen atom of each nitro group and two amino groups (one intramolecular and one intermolecular bond). The other oxygen atom of each nitro group forms a close contact with the C–H bond opposite.^5–9 This supramolecular packing leaves a channel running through the crystal of about 10 Å in diameter (Figure 3).

Figure 2.

Two examples of hydrogen-bonded hexamers. Left: compound 2; right: compound 3.

Figure 3.

Left: hydrogen-bonded channels formed from compound 2; right: hydrogen-bonded channels formed from compound 3.

Figure 3 shows the packing diagrams from the X-ray single crystal structure determinations of compounds 2 (Left) and 3 (Right). In each case, the diagram shows the large one-dimensional channels or pores of the open framework structures. Compound 2 crystallises in space group R3 with approximately 2660 Å³ of free space per unit cell (~19.7% of the unit-cell volume). Compound 3 (space group P6cc) encapsulates some 762 Å³ of free space per unit cell (~14.5% of the unit-cell volume).

These pores are empty apart from disordered solvent molecules. Unlike many clathrates, the existence of an open framework does not depend upon the inclusion of guest molecules. There are, however, a number of organic zeolites^10–20 with potential for novel properties as well as metal-organic frameworks (MOFs)^21–25 and materials which form 1D channels.^26–35 These materials, known as nanoporous materials, with molecular-sized pores are of potential importance in molecular separation, heterogeneous catalysis, gas storage and carbon dioxide capture.

Discussion

Owing to the serendipitous discovery of porous structures formed from derivatives of 2,4-diaminonitrobenzene, such as compounds 2 and 3, we continued a research programme that involved making further diamino derivatives of 2,4-difluoronitrobenzene, 1, and their characterisation by X-ray single crystal structure determination where possible. Figures 4 –6 show the synthetic pathways. In each case compounds 4, 5 or 6 were synthesised in a one-pot reaction to simplify the procedure involved.

Figure 4.

One-pot synthesis of compound 4.

Figure 5.

One-pot synthesis of compound 5.

Figure 6.

One-pot synthesis of compound 6.

For reasons that are not clear, the ortho fluorine atom is more reactive to nucleophilic displacement than the para fluorine atom (Figure 4). The inductive and mesomeric activation of the ortho position must be stronger. Ethylenediamine first links two halves together followed by capping with butylamine at both ends. The first fluorine atom can be displaced under milder conditions but the second deactivated fluorine atom is best displaced in a pressure vessel at a higher temperature so both reactions were done together. These products are poorly soluble, which presented some problems with the acquisition of ¹³C NMR data in D₆DMSO. Most peaks were observed but two weak, aromatic, signals were absent owing to poor solubility. The structure was confirmed with an X-ray single crystal structure determination (see below).

The synthesis of compound 5 is similar to that of compound 4 except that ethylenediamine has been replaced with 1,3-propylenediamine. This will introduce more flexibility into the linker but still less than that of the link formed using 1,4-butylenediamine in compound 2. These studies have shown that flexibility is important in allowing the molecule to pack with channels. The butyl chains are also an optimum length to reduce the polarity of the molecule making it easier to purify and isolate. If the linkers become too long, the crystal structures show disorder. The structure of 5 was confirmed by an X-ray single crystal structure determination.

Compound 6 is an isomer of compound 5 so the two can be compared. The order of addition of the two amines has been reversed. For compound 5, the linker diamine (1,3-propylenediamine) was added first then butylamine in the second step. For compound 6, butylamine was added first followed by the linker diamine. The compounds have similar polarity. Unfortunately, the structure of compound 6 could not be established by an X-ray single crystal structure determination as the crystals were of poor quality.

The molecular structure of compound 5, which crystallises with half a molecule in the asymmetric unit in the monoclinic space group I2/a (No. 15), is shown in Figure 7. The complete molecule is generated by crystallographic inversion symmetry (at ½, 1, ½ for the asymmetric unit). The dihedral angle between the C1–C6 benzene ring and its attached N3/O1/O2 nitro group is 2.03 (8)°, with the near-coplanarity being reinforced by an intramolecular N1–H^{. . .}O1 hydrogen bond with H^{. . .}O = 1.974 (14) Å and N–H^{. . .}O = 130.7 (12)°. The C8–C11 butyl side chain adopts an anti–gauche–anti (aga) conformation as indicated by the C4–N2–C8–C9, N2–C8–C9–C10 and C8–C9–C10–C11 torsion angles of −169.01 (10), 62.87 (12) and 172.99 (10)°, respectively.

Figure 7.

The molecular structure of compound 4 showing 50% displacement ellipsoids; the hydrogen bonds are shown as double-dashed lines. Symmetry code: (i) 1–x, 2–y, 1–z.

The extended structure of compound 4 features (100) sheets of molecules linked by N–H^{. . .}O hydrogen bonds. A PLATON³⁶ analysis of the structure did not reveal any free space and the packing may be regarded as ‘dense’.

The molecular structure of compound 5 (space group P1, No 2) consists of two molecules: molecule A containing C1 and molecule B containing C24 (Figure 8). For molecule A, the dihedral angles between the C1–C6 and C10–C15 benzene rings and their attached nitro groups are 7.1 (9) and 1.6 (7)°, respectively, and the dihedral angle between the rings themselves is 12.7 (3)°. Equivalent data for the C24–C29 and C33–C38 rings and their nitro groups in molecule B are 3.1 (7), 5.8 (7) and 23.9 (3)°, respectively. In every case, an intramolecular N–H^{. . .}O hydrogen bond arising from atom N1, N3, N7 or N9 helps to establish the conformation of the nitro groups. The diamino propyl linkers in both molecules adopt all anti conformations, with no torsion angle modulus smaller than 168.3°. The conformations of the N2, N8 and N10 side chains are all anti (minimum torsion angle modulus = 173.1°) but the N4 side chain is contorted with the N4–C20–C21–C22 torsion angle of −66.2 (14)° indicating a gauche conformation.

Figure 8.

The molecular structure of compound 5 showing 50% displacement ellipsoids; the hydrogen bonds are shown as double-dashed lines.

The extended structure of compound 5 features (101) sheets of molecules linked by N–H. . .O hydrogen bonds arising from atoms N2, N4, N8 and N10, reinforced by C–H. . .O interactions to the same acceptor Oxygen atom arising from C5, C14, C28 and C35, respectively. There are small voids present when the structure is viewed down [100] (Figure 9) and a PLATON analysis of compound 5 revealed 353 Å3 per unit cell (~13% of the unit-cell volume) of free space. This presumably correlates with the fact that the calculated density of compound 5 (1.164 g cm^–3) is notably lower than that of compound 4 (1.335 g cm^–3) but these channels may be too small to accommodate other species and an alternative interpretation might be to regard this situation as a case of ‘inefficient packing’. The complementary N–H. . .O + C–H. . .O hydrogen-bond ‘synthon’ in compound 5 is very similar to that in compound 3 but the overall connectivity and packing is totally different to the hydrogen-bonded hexamers that occur in compound 3.

Figure 9.

Packing diagram of compound 5 in space-filling representation showing the small [100] channels or voids.

The supplementary section has NMR charts for compounds 4, 5 and 6.

Conclusion

Further studies on the synthesis of diamino-substituted derivatives made from 2,4-difluoronitrobenzene 1 and aliphatic amines are reported. These derivatives had precedent from previous studies that they might have porous properties and interesting structures.^1–4 The previous porous structures were discovered by chance by making an intermediate, 2,4-bis(phenylamino)nitrobenzene 3, for a novel mauveine synthesis. This compound is difficult to make, but it has provided ideas for making more accessible and related compounds with interesting properties based on 2,4-bis(alkylamino)nitrobenzene. Three different amines are reacted with 2,4-difluoronitrobenzene 1 in this paper. These are butylamine, ethylenediamine and propylenediamine. Previous studies showed that a flexible linker is necessary to crystallise a porous framework^1–2 and the extent of this is under investigation. The butyl groups help reduce the compound polarity making the products easier to isolate and purify. The ortho fluorine atoms are selectively displaced by the nucleophilic amines in preference to the para fluorine atoms. 2,4-Difluoronitrobenzene 1 is reactive but the mono-coupled product (not isolated) is much less reactive so the reactions were done in a pressure vessel at 150 °C. Two steps were combined in a one-pot reaction to simplify the procedure. The order of addition of the amines can be reversed, leading to isomers for comparison. Compound 4 was made by reacting 2,4-difluoronitrobenzene 1 with ethylenediamine followed by butylamine. Compound 5 was made by reacting 2,4-difluoronitrobenzene 1 with propylenediamine followed by butylamine. Compound 6 was made by reacting 2,4-difluoronitrobenzene 1 with butylamine first followed by propylenediamine. Compound 5 and 6 are isomers. Isomer 5 is easier to make because the first step requires 0.5eq of diamine linker with the more reactive 2,4-difluoronitrobenzene 1 followed by an excess of butylamine. The second step for making isomer 6 is difficult because it requires 0.5eq of the diamine linker with a less reactive unit. Data were collected on all three products. The structures of compounds 4 and 5 were established by X-ray single crystal structure determinations. Compound 6 is poorly crystalline which is unexpected since compound 2, which is more flexible and was reported previously, was crystalline. Currently the diamine linker, between two ortho or two para positions of the nitrobenzene derivative, needs to be formed with 1,4-diaminobutane or a longer chain. If the chains are too long then disorder is likely.⁴

Experimental

IR spectra were recorded on a diamond-attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectrometer. Ultraviolet (UV) spectra were recorded using a Perkin Elmer Lambda 25 UV-Vis spectrometer with EtOH as the solvent. The term sh means shoulder. ¹H and ¹³C nuclear magnetic resonance (NMR) spectra were recorded at 400 and 100.5 MHz, respectively, using a Bruker 400 spectrometer. Chemical shifts, δ, are given in ppm and measured by comparison with the residual solvent. Coupling constants, J, are given in Hz. High-resolution mass spectra were obtained at the University of Wales, Swansea, using an Atmospheric Solids Analysis Probe (ASAP) (positive mode) instrument: Xevo G2-S ASAP. Melting points were determined on a Cole-Palmer Stuart microscope.

Compound 4

2,4-Difluoronitrobenzene (250 mg, 1.57 mmol) in EtOH (10 ml) was mixed with ethylenediamine (47 mg, 0.79 mmol) and Et₃N (159 mg, 1.57 mmol) in a Teflon-lined Parr pressure vessel. The vessel was heated at 150 °C for 12 h and then left to cool. An excess of BuNH₂ (230 mg, 3.14 mmol) and EtOH (1 mL) were added. The vessel was heated for a further 12 h at 150 °C. After cooling, the contents of the vessel were diluted with DCM (100 mL) and extracted with water (150 mL) using a separating funnel. The DCM layer was collected, dried with MgSO₄, filtered under gravity, then concentrated in vacuo. DCM, petroleum ether and EtOAc were investigated in various ratios and mixtures by TLC to find a good separation of the product from the other by-products. The product was purified by column chromatography on flash silica, using neat DCM to remove impurities then changing solvent to DCM/EtOAc (98:2) once the impurities were removed. Fractions 52–58 were collected. The crystals were then recrystallised in a large beaker by adding DCM and a small amount of petroleum ether and leaving the solvent to slowly evaporate. This produced the title compound (101 mg, 14 %) as orange blocks, mp 237–238 °C (from dichloromethane:light petroleum ether). λ_max (EtOH)/nm 399 (log ε 4.1); ν_max (diamond)(cm^–1) 3335w, 1613s, 1546s, 1510s, 1469s, 1427s, 1409s, 1266s, 1220s, 1163s, 134s, 824s, 749s, 606s, 559s and 449s; δ_H (400 MHz; CDCl₃) 0.91 (6H, t, J = 7.0), 1.36 (4H, s, J = 8.0), 1.53 (4H, q, J = 8.0), 3.08 (4H, q, J = 5.0), 3.62 (4H, s), 5.76 (2H, NH), 6.07 (2H, dd, J = 2.0 and 9.0), 7.09 (2H, t, J = 4.0 and 9.0), 7.81 (2H, d, J = 9.0 Hz) and 8.66 (2H, s, NH); δ_C (100.1 MHz; CDCl₃) 14.2, 20.1, 30.9, 41.6, 42.2, 122.2, 128.6, 148.5 and 155.4) Two aromatic resonances are missing owing to poor solubility; m/z (Orbitrap ASAP) 445.2568 (M⁺ + H, 100%) C₂₂H₃₂N₆O₄H requires 445.2563.

Compound 5

2,4-Difluoronitrobenzene (250 mg, 1.57 mmol) in EtOH (10 mL) was mixed with 1,3- diaminopropane (58 mg, 0.79 mmol) and Et₃N (159 mg, 1.57 mmol) in a Teflon-lined Parr pressure vessel. The vessel was heated at 150 °C for 12 h and then left to cool. An excess of BuNH₂ (230 mg, 3.14 mmol) and EtOH (1 mL) were added. The vessel was heated for a further 12 h at 150 °C. After cooling, the contents of the vessel were diluted with DCM (100 mL), EtOAc (15 mL), and extracted with water (150 mL) using a separating funnel. The DCM layer was collected, dried with MgSO₄, filtered under gravity and then concentrated in vacuo. The product was purified by column chromatography on flash silica using neat petroleum ether to remove impurities then changing solvent to petroleum ether/EtOAc (60:40) once the impurities were removed. Fractions 14–17 were collected and then recrystallised in a large beaker by adding DCM and a small amount of light petroleum ether. The solvent was left to slowly evaporate which yielded the title compound (73 mg, 10%) as yellow crystals, mp 149–150 °C (from dichloromethane:light petroleum ether). λ_max (EtOH)/nm 401 (log ε 4.2); ν_max (diamond)(cm^–1) 3328w, 1614s, 1517s, 1544s, 1510s, 1456s, 1394s, 1312s, 1255s, 807s and 784s; δ_H (400 MHz; CDCl₃)1.01 (6H, t, J = 8.0), 1.44 (4H, s, J = 8.0), 1.63 (4H, q, J = 8.0), 2.13 (2H, q, J = 6.0), 3.17 (4H, q, J = 6.0), 3.43 (4H, q, J = 6.0), 4.55 (2H, s, NH), 5.67 (2H, d, J = 2.0), 5.93 (2H, dd, J = 2.0 and 9.0), 8.03 (2H, d, J = 9.0) and 8.61 (2H, s, NH); δ_C (100.1 MHz; CDCl₃) 13.8, 20.1, 28.4, 31.4, 39.9, 42.9, 90.0, 104.6, 123.6, 129.3, 148.1 and 154.7; m/z (Orbitrap ASAP) 459.2711 (M⁺ + H, 100%) C₂₃H₃₄N₆O₄H requires 459.2720.

Compound 6

2,4-Difluoronitrobenzene (250 mg, 1.57 mmol) in EtOH (10 mL) was added to a Teflon-lined Parr pressure vessel along with BuNH₂ (115 mg, 1.57 mmol) and an excess of Et₃N (318 mg, 3.14 mmol). The vessel was heated at 150 °C for 12 h and then left to cool. 1,3-Diaminopropane (58.2 mg, 0.79 mmol) and EtOH (1 mL) were then added. The vessel was heated at 150 °C for a further 12 h. Once cooled, the contents of the vessel were diluted with DCM (100 mL) and extracted with water (150 mL) using a separating funnel. The DCM layer was collected, dried with MgSO₄, filtered under gravity, and then concentrated in vacuo. The product was purified by column chromatography on flash silica using DCM/EtOAc (95:5) and fractions 21–24 were collected. The crystals were then recrystallised in a large beaker by adding DCM and a small amount of light petroleum ether leaving the solvent to slowly evaporate. This gave the title compound (89 mg, 12 %) as orange-yellow crystals, mp 139– 140 °C (from dichloromethane:light petroleum ether). λ_max (EtOH)/nm 404 (log ε 3.8); ν_max (diamond)(cm^–1) 3311s, 1616s, 1578s, 1540s, 1459s, 1396s, 1322s, 1252s, 1189s, 1160s, 808s, 751s, 652s and 544s; δ_H (400 MHz; D₆DMSO) 0.91 (6H, t, J = 8.0), 1.36 (4H, s, J = 8.0), 1.59 (4H, q, J = 8.0), 1.87 (2H, q, J = 6.0), 3.19 (4H, q, J = 6.0), 3.25 (4H, q, J = 5.0), 5.67 (2H, s, NH), 6.08 (2H, dd, J = 2.0 and 9.0), 7.22 (2H, t, J = 4.0), 7.82 (2H, d, J = 9.0) and 8.47 (2H, NH); δ_C (100.1 MHz; D₆DMSO) 14.0, 20.3, 27.8, 30.5, 42.0, 88.8, 106.5, 122.2, 128.8, 148.5 and 155.6 (one alkyl resonance is missing); m/z (Orbitrap ASAP) 459.2728 (M⁺ + H, 100%) C₂₃H₃₄N₆O₄H requires 459.2720.

Crystal-structure determinations

The crystal structures of 4 and 5 were established using intensity data collected on a Rigaku CCD diffractometer at T = 100 K. The structures were routinely solved by dual-space methods using SHELXT³⁷ and the structural models were completed and optimised by refinement against |F|2 with SHELXL-2018.³⁸ For 4, the N-bound hydrogen atoms were located in difference maps and their positions were freely refined; for 5, the N-bound H atoms were geometrically placed (N–H = 0.88 Å) and refined as riding atoms. The C-bound hydrogen atoms in both structures were placed in idealised locations (C–H = 0.95–0.99 Å depending on hybridisation) and refined as riding atoms. The methyl groups were allowed to rotate, but not to tip, to best fit the electron density. The constraint U_iso(H) = 1.2U_eq(carrier) or 1.5U_eq(methyl carrier) was applied in all cases. Full details of the structures and refinements are available in the deposited cifs. The crystal quality of 5 is poor, which presumably correlates with the high R-factors, but the molecular conformation and packing have been unambiguously established.

Crystal data for 4: C₂₂H₃₂N₆O₄ (dark orange block 0.18 × 0.10 × 0.07 mm), Mr = 444.53, monoclinic, space group I2/a (No. 15), a = 17.6468 (2) Å, b = 8.48036 (11) Å, c = 14.80948 (17) Å, β = 93.6182 (11)°, V = 2211.84 (5) Å³, Z = 4, T = 100 K, Cu Kα radiation, λ = 1.54178 Å, μ = 0.769 mm^–1, ρ_calc = 1.335 g cm^–3, 17553 reflections measured (10.0 ⩽ 2θ ⩽ 140.5°), 2107 unique (R_Int = 0.028), R(F) = 0.033 [1956 reflections with I > 2σ(I)], wR(F²) = 0.093 (all data), Δρ_min,max (e Å–3) = −0.19, +0.20, CCDC deposition number 2356107.

Crystal data for 5: C₂₃H₃₄N₆O₄ (yellow plate 0.16 × 0.06 × 0.02 mm), Mr = 458.56, triclinic, space group P1 (No. 2), a = 7.7776 (8) Å, b = 18.1074 (13) Å, c = 20.2744 (15) Å, α = 108.814 (7)°, β = 95.134 (8)°, γ = 101.146 (8)°, V = 2616.1 (4) Å³, Z = 4, T = 100 K, Cu Kα radiation, λ = 1.54178 Å, μ = 0.664 mm^–1, ρcalc = 1.164 g cm^–3, 41156 reflections measured (5.72 ⩽ 2θ ⩽ 147.2°), 9675 unique (R_Int = 0.113), R(F) = 0.201 [6745 reflections with I > 2σ(I)], wR(F²) = 0.505 (all data), Δρ_min,max (e Å^–3) = −0.43, +1.34, CCDC deposition number 2356108.

Supplemental Material

sj-docx-1-chl-10.1177_17475198241293518 – Supplemental material for Potential building blocks for porous organic materials

Supplemental material, sj-docx-1-chl-10.1177_17475198241293518 for Potential building blocks for porous organic materials by Michael John Plater, Maisie A Cowie and William TA Harrison in Journal of Chemical Research

Footnotes

Acknowledgements

We thank the UK EPSRC National Mass Spectrometry Service Centre for mass spectrometric data and the UK National Crystallography Centre (University of Southampton) for the X-ray data collections. Maisie Cowie performed all synthesis and obtained the characterisation data and WTA Harrison solved the crystallographic data sets. Data sets were obtained free of charge from the National Crystallography Center, Southampton University.

Declaration of conflicting interests

The author(s) declared no potential conflicts of interest with respect to the research, authorship and/or publication of this article.

Funding

The author(s) received no financial support for the research, authorship and/or publication of this article.

ORCID iD

Michael John Plater

Supplemental material

Supplemental material for this article is available online.

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