An Organic Zeolite With 10 ? Diameter Pores Assembles From a Soluble and Flexible Building Block by Non-Covalent Interactions

Article abstract of DOI:10.1002/open.201900006

Two similar molecular building blocks, which both contain a hydrogen-bonded nitro group, have been prepared and crystallised. One structure has more flexibility with a butyl side chain which allows an open framework organic zeolite to form with large 10 ?

Full text of DOI:10.1002/open.201900006

DOI: 10.1002/open.201900006
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An Organic Zeolite With 10 Å Diameter Pores Assembles
From a Soluble and Flexible Building Block by
Non-Covalent Interactions
[a]
M. John Plater* and William T. A. Harrison
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Two similar molecular building blocks, which both contain a
hydrogen-bonded nitro group, have been prepared and crystal-
lised. One structure has more flexibility with a butyl side chain
which allows an open framework organic zeolite to form with
large 10 Å diameter pores, whereas the other structure has less
flexibility with an aryl side chain and is close packed. The pore
size is comparable with those of the aluminophosphate VPI-5
(12 Å). It is concluded that some flexibility in the design of the
building block for porous organic molecular materials was
beneficial.
1. Introduction
channels were filled with solvent that could be evacuated by
[23–24]
heating.
Cyclic host 5 forms cylindrical channels 5–8 Å in
Recently we reported the crystal structures of cyclic hexameric
motifs formed from 2,4-bis(phenylamino) nitrobenzene 1 or 2,4-
bis(butylamino)nitrobenzene 2 in which adjacent molecules are
diameter stabilised by urea-urea hydrogen bonding and
[25–26]
aromatic stacking.
The material was able to absorb carbon
dioxide. 1,2-Dimethoxy-p-tert-butylcalix[4]dihydroquinone
6
[1–2]
linked by NÀ HÀ O hydrogen bonds (Figure 1).
The hexamers
crystallises in a tubular fashion to form two types of void space
filled with water molecules. One void space is a 3D network of
channels with diameters of 3.9 and 8.5 Å and the other void
space consists of spherical cages of 11.2 Å in diameter
formed from 2,4-bis(phenylamino)nitrobenzene 1 are stacked
on top of each other so that large channels arise but the
hexamers formed from 2,4-bis(butylamino)nitrobenzene 2 have
a staggered stacking arrangement so that channels do not
occur in the crystal. The open framework formed from
compound 1 is an example of a nanoporous material comprised
of discrete organic molecules between which there are only
weak non-covalent interactions. This is quite rare as most
[27–28]
connected by narrow channels.
The host retained its
structural integrity upon removal of the water molecules. 3,3’-
4,4’-Tetra(trimethylsilylethynyl)biphenyl 7 crystallises forming
narrow channels in three dimensions that interconnect large
[29]
internal voids of diameter 11 Å.
The porosity of the
[3]
organic molecules pack to minimise the void volume. In
contrast there are many examples of metal-organic frameworks
desolvated crystals was shown by nitrogen and hydrogen
absorption.
[
4–13]
(
MOF’s) which have porosity.
Organic crystals which form channels have been referred to
as ‘organic zeolites’ owing to their structural similarity to 2. Results and Discussion
[14]
inorganic ones.
Inorganic zeolites have many applications
such as molecular separation, heterogeneous catalysis, hydro-
Owing to the crystallisation of novel hydrogen bonded macro-
cyles from 2,4-bis(phenylamino)nitrobenzene 1 and from 2,4-bis
(butylamino)nitrobenzene 2 (Figure 1) we wanted to synthesise
more complex oligomeric scaffolds to investigate their molec-
ular frameworks with a view to discovering organic zeolites that
possess large channels with tailored pore sizes because of the
diverse derivatization chemistry that is possible. Two com-
pounds were made for comparison, Figures 3 and 4. The first
step involves coupling a primary amine, butylamine or aniline,
to give intermediates 9 and 12 respectively. These can be
isolated but it was found convenient to generate them in situ
and react them with 1,4-diaminobutane 10 to give compounds
11 and 13 respectively. Both compounds were successfully
crystallised and the structures were solved by X-ray single
crystal structure determinations.
[15–20]
gen storage and carbon dioxide capture.
The soluble
precursors required for organic zeolites may include and extend
the range of these applications because of solution processing,
[3]
the choice of components and their functionality (Figure 2)
Tris-(o-phenylenedioxy)cyclotriphosphazene 3 forms crystals
with empty 1D channels, 5 Å in diameter, that can clathrate
[21–22]
solvent and organic guest molecules.
Dipeptides such as
compound 4 crystallise with hydrogen bonded tubular assem-
blies forming 1D channels with diameters of 3–5.4 Å. These
[
a] Dr. M. J. Plater, Prof. W. T. A. Harrison
Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen,
AB24 3UE
E-mail: m.j.plater@abdn.ac.uk
©
2019 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.
This is an open access article under the terms of the Creative Commons
Attribution Non-Commercial NoDerivs License, which permits use and dis-
tribution in any medium, provided the original work is properly cited, the
use is non-commercial and no modifications or adaptations are made.
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Figure 1. Two examples of hydrogen-bonded hexamers crystallised from 2,4-bis(phenylamino)nitrobenzene 1 and 2,4-bis(butylamino)nitrobenzene 2
Figure 2. Some examples of ‘organic zeolites’ that crystallise possessing open channels.
2
.1. The Crystal Structure of Compound 11
nitro groups are almost coplanar with their attached rings
[
dihedral angle for N5/O1/O2+C1À C6=2.2 (4)°; N6/O3/O4+
Compound 11 crystallises with one molecule in the asymmetric
unit (Figure 5) in which the dihedral angle between the C1À C6
and C11À C16 aromatic rings is 37.91 (6)°. The chain linking these
rings is characterised by torsion angle of C4À N1À C7À C8=À 167.0
C11À C16=3.0 (3)°]. These geometries are consolidated by intra-
molecular N2À H2···O1 and N3À H3a···O3 hydrogen bonds. The N2-
bonded butyl side chain has an extended geometry whereas the
N3-bonded chain features disorder of the final methylene group
and methyl group over two sets of sites in a 0.509 (7):0.491 (7)
(
2), N1À C7À C8À C9=53.6 (3), C7À C8À C9À C10=166.5 (2),
C8À C9À C10À N4=61.8 (3) and C9À C10À N4À C11=86.8 (3)°. The
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Figure 3. The synthesis of building block 11. The molecular structure was shown, by an X-Ray single crystal structure determination, to be a porous organic
zeolite.
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Figure 4. The synthesis of building block 13 which was crystallised and the molecular structure determined to be close packed by an X-Ray single crystal
structure determination.
nanoporous one-dimensional [001] channel system (Figure 7). The
channel walls, 10 Å in diameter, consists of the methylene and
methyl groups of the C17À C20 butyl side chains and are
[30]
presumably strongly hydrophobic. A PLATON analysis of the
3
structure showed that some 2660 Å per unit cell, 20% of the unit-
cell volume, is solvent accessible ‘empty space.’ This may be
compared to the volume of a molecule of H in the liquid state of
2
3
about 50 Å . The pore size is comparable to that of the
[20]
aluminophosphate VPI-5 (12 Å)
Figure 5. The molecular structure of compound 11 from an X-Ray single
crystal structure determination showing 50% displacement ellipsoids with
hydrogen bonds indicated by double-dashed lines.
2
.2. The Crystal Structure of Compound 13
Compound 13 crystallises with two molecules (containing C1 and
C29) in the asymmetric unit with generally similar conformations,
which approximate overall to S shapes: the C1 molecule is
illustrated in Figure 8. The dihedral angles between the nitro-
benzene rings in the C1 and C29 molecules are 18.26 (19)° and
14.2 (2)° respectively. The linking chains in each molecule feature
gauche conformations for both the C À NÀ C À C (ar=aromatic,
ratio. Otherwise, the bond lengths and angles in structure 11 are
unexceptional.
In the crystal structure of compound 11, the para NH groups
in the linking chain are key to constructing the supramolecular
network. The N1À H1 group links to O4 (H···O=2.26 Å) in an
ar
m
m
m=methylene) groupings and near anti conformations for the
others. Each molecule features two intramolecular NÀ H···O hydro-
gen bonds from the ortho-NH group to one of the nitro O atoms,
as also seen in compound 11. Further similarities are seen in terms
of the dihedral angles between the nitrobenzene rings and their
pendant phenyl groups: 49.56 (15)° and 47.19 (14)° for the C1
molecule and 44.78 (14)° and 49.65 (13)° for the C29 molecule.
Otherwise, the bond lengths and angles in compound 13 may be
regarded as normal.
adjacent molecule generated by crystallographic inversion symme-
2
2
try to form an R (26) loop. The N4À H4 moiety forms an
asymmetric, bifurcated hydrogen bond to O1 (H···O=2.18 Å) and
O2 (H···O=2.52 Å) in an adjacent molecule to generate a
6
6
hexameric ring (Figure 6) with an R (78) graph-set motif. This
resembles the hydrogen-bonded hexamer in 2,4-bis(butylamino)
[1]
nitrobenzene 2 shown in Figure 1 above with the important
difference that the ortho N-butyl chain in compound 11 is oriented
towards the centre of the hexamer rather than pointing away
The packing for compound 13 is largely determined by
hydrogen bonds to nitro group oxygen atoms arising from the
para NH groups. Rather than inversion dimers and hexamers as
�
from it. The symmetry of the hexameric assembly is 3 about the
1
point (1, 0, = ) for the asymmetric molecule and its five clones.
2
Taken together, the N1 and N4 hydrogen bonds link the molecules
into ‘honeycomb’ (001) sheets. When the sheets are stacked in the
c-direction in space group R3, the pores overlap and generate a
seen in compound 11, the NÀ H···O hydrogen bonds in
4
4
compound 13 lead to tetrameric R (32) loops (Figure 9) as
�
components of two separate (for the C1 and C29 molecules)
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Figure 6. A hydrogen-bonded hexamer in the organic zeolite framework of compound 11 arising from cooperative N4À H4·· (O1,O2) links; symmetry code (i)
=1+y, 1À x+y, 1À z. The butyl side chains pack together forming channels which are 10 Å in diameter.
Figure 7. Space-filling representation of the packing in the organic zeolite framework of compound 11 showing the formation of 10 Å diameter [001] channels
centred at x=0, y=0 and equivalent locations according to rhombohedral crystal symmetry. The channels are of comparable size to those of the
[20]
aluminophosphate VPI-5 (12 Å)
infinite sheets, which both propagate in the (101) plane. No 3. Conclusions
pores or channels can be identified and PLATON did not reveal
any free space, so the packing may be described as ‘dense’,
An organic zeolite has been crystallised which possesses large
which is reflected in the much higher density in compound 13
channels 10 Å in diameter. These are large compared to those
which occur in typical organic zeolites described in the
À 3
À 3
(1.370 gcm ) compared to compound 11 (1.049 gcm ).
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Figure 8. The close packed structure of the C1 molecule in compound 13, from an X-Ray single crystal structure determination, showing 50% displacement
ellipsoids with hydrogen bonds indicated by double-dashed lines.
design may lead to tailored pores of increasing diameter and
[20]
stability with many applications.
Experimental
General: IR spectra were recorded on a diamond anvil spectropho-
tometer. UV spectra were recorded using a Perkin-Elmer Lambda 25
1
13
UV-VIS spectrometer with EtOH as the solvent. H and C NMR
spectra were recorded at 600 MHz and 150 MHz, respectively, using
a Varian 400 spectrometer. Chemical shifts, δ are given in ppm
relative to the residual solvent and coupling constants, J are given
in Hz. Low resolution and high resolution mass spectra were
obtained at the University of Wales, Swansea using electron impact
ionisation and chemical ionisation. Melting points were determined
on a Kofler hot-stage microscope. Compound 12 has been reported
[1]
Figure 9. The close packed structure of compound 13 showing the
formation of tetrameric assemblies as components of (101) infinite hydrogen
bonded sheets.
previously.
N-Butyl-5-fluoro-2-nitroaniline 9
2
,4-Difluoronitrobenzene
8
(500 mg, 3.14 mmol), butylamine
[3]
(230 mg, 3.15 mmol) and an excess of triethylamine (700 mg,
introduction and were formed using a flexible, rather than a
rigid, building block. They are similar in size to those of some
6.93 mmol) were mixed in EtOH (20 ml) and heated at 150°C for
1
2 h. After cooling the mixture was diluted with water (150 ml) and
[20]
inorganic zeolites such as the aluminophosphate VPI-5. The
pores are formed by the close packing of butyl side chains
which leaves a large hole in the center. In contrast replacement
of the butyl side chains with aryl rings changes the packing
mode into a close packed structure with no channels. This work
suggests that some flexibility in organic molecular building
blocks may allow packing which favours open channel
acidified with cHCl (2 ml). The mixture was then extracted with
CH Cl (100 ml×2) and the combined extracts were back extracted
2
2
with water (100 ml) followed by drying with MgSO and filtration.
4
The filtrate was evaporated in vacuo and purified by chromatog-
raphy on silica gel. Elution with dichloromethane gave the title
compound (147 mg, 22%) as a yellow oil which crystallised on
scratching, m.p. 37–38°C (from ether/light petroleum ether 40–60);
1
3
H NMR (600 MHz; CDCl , 25°C): δ=7.92 (t, J(H,H)=12 and 6 Hz,
3
[12]
3
frameworks and that a wider range of functional groups, such
as the nitro group, can be used. In this work building blocks
with steric bulk can favour crystallisation of a cyclic hexameric
motif, rather than an extended array, that leads to a porous
solid. An anology is provided in solution assembly where steric
bulk favours cyclic ‘rosettes’ rather than extended ‘crinkled
1H), 7.89 (s, 1H), 6.21 (d, J(H,H)=12 Hz, 1H), 6.07 (t, J(H,H)=12 and
6
0
Hz, 1H), 2.96-3.02 (m, 2H), 1.43–1.50 (m, 2H), 1.19–1.27 (m, 2H),
.73 (t, J(H,H)=6 Hz, 3H); C NMR (150 MHz, CDCl , 25 C): δ=
3
13
°
3
168.3, 166.8, 147.5, 129.9, 103.8, 99.4, 99.0, 43.0, 30.7, 20.2, 13.7; IR
(Diamond): 526, 576, 748, 827, 993, 1056, 1214, 1249, 1509, 1572,
À 1
1
627, 2863, 2937, 2963, 3380 cm ; UV/Vis (EtOH): λ
(ɛ)=409
max
À 1
3
À 1
(50,118), 229 (50,118 mol dm cm ); HRMS (Orbitrap ASAP): m/z
[31]
+
tape’ motifs.
Also, in a broader context for the future,
calcd for C10H13FN O : 213.1039 [M + H]; found: 213.1038.
2 2
oligomeric building blocks may be designed and extended by
iterative synthesis to cell membrane dimensions and molecular
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1
N ,N ’-(Butane-1,4-diyl)bis
(
highly-disordered solvent molecules but these could not be
modelled and the crystal data below only refer to the main
molecule. The crystal of compound 13 chosen for data collection
was found to be a non-merohedral twin with the components
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3
N -butyl-4-nitrobenzene-1,3-diamine) 11
2
,4-Difluoronitrobenzene (500 mg, 3.14 mmol), butylamine
230 mg, 3.15 mmol) and an excess of triethylamine (700 mg,
8
(
6
1
related by a rotation of 180
fractions refined to 0.5339 (8): 0.4661 (8).
°
about [001] in real space; the domain
.93 mmol) were mixed in EtOH (20 ml) and heated at 150°C for
2 h. The mixture was allowed to cool and 1,4-diaminobutane 10
(
138 mg, 1.57 mmol) was added. The mixture was heated for a
11 C H N O , M =472.59, light-orange needle, 0.30×0.03×
24 36
6
4
r
�
further 12 h at 150°C. After cooling the mixture was diluted with
water (150 ml) and acidified with cHCl (2 ml). The mixture was then
extracted with CH Cl (100 ml×2) and the combined extracts were
0.03 mm, trigonal, space group R3 (No. 148), a=32.1022 (10) Å, c=
3
À 1
15.0899 (5) Å, V=13467.5 (10) Å , Z=18, μ=0.073 mm , 1calc
=
À 3
1.049 gcm , 30466 data scanned (2θmax =51
°
), RInt =0.035, R(F)=
0.080 [4414 merged reflections with I>2σ(I)], wR(F )=0.263 (5569
2
2
2
back extracted with water (100 ml) followed by drying with MgSO4
and filtration. The filtrate was evaporated in vacuo and purified by
chromatography on silica gel. Dichloromethane elutes by-products
then elution with an ether/dichloromethane mixture (20:80) gave
1
1
1
1
1
1
1
1
1
1
2
2
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5
5
5
merged reflections), CCDC deposition number 1887584.
1
3 C H N O , M =512.56, yellow slab, 0.20×0.04×0.02 mm,
28 28 6 4 r
monoclinic, space group P2 (No. 4), a=8.1538 (4) Å, b=15.5507
1
the title compound (105 mg, 13%) as a yellow solid, m.p. 124–
3
(
6) Å, c=19.6185 (8) Å, β=92.247 (4)°, V=2485.66 (18) Å , Z=4,
1
1
25°C (from ether/light petroleum ether 40–60); H NMR (600 MHz;
À 1
À 3
μ=0.094 mm , 1 =1.370 gcm , 12320 data scanned from two
calc
CDCl , 25°C): δ=8.52 (s, 2H), 7.98 (d, J(H,H)=12 Hz, 2H), 5.92 (d, J
3
twin components (2θ =52°), R(F)=0.064 [9234 reflections with
max
(
H,H)=12 Hz, 2H), ), 5.63 (s, 2H), 3.19–3.29 (m, 8H), 1.81–1.83 (m,
2
I>2σ(I)], wR(F )=0.134 (12320 reflections), absolute structure
3
4
1
H), 1.68–1.74 (m 4H), 1.43–1.52 (m, 4H), 0.95–0.99 (t, J(H,H)=
indeterminate, CCDC deposition number 1887585.
13
2 Hz, 6H); C NMR (150 MHz, CDCl , 25°C): δ=154.5, 148.8, 129.2,
3
123.6, 104.8, 89.9. 42.8, 42.5, 30.9, 26.6, 20.4, 13.9; IR (Diamond):
548, 749, 799, 1160, 1257, 1406, 1466, 1572, 1612, 2861, 2928, 2954,
À 1
3
331 cm ; UV/Vis (EtOH): λmax (ɛ)=406 (19,952), 234
À 1
3
À 1
(
50,118 mol dm cm ); HRMS (Orbitrap ASAP): m/z calcd for Acknowledgements
+
C H N O : 473.2876 [M +H]; found: 473.2880 .
2
4
36
6
4
We thank the Naional Mass Spectrometry Foundation, University
of Swansea for the high-resolution mass spectrometry data and
theNational Crystallography Centre, University of Southampton,
for the X-ray data collections.
1
1’
N ,N -(Butane-1,4-diyl)bis
(
3
4-nitro-N -phenylbenzene-1,3-diamine) 13
2
,4-Difluoronitrobenzene 8 (500 mg, 3.14 mmol), aniline (292 mg,
3.14 mmol) and an excess of triethylamine (700 mg, 6.93 mmol)
were mixed in EtOH (20 ml) and heated at 150
mixture was allowed to cool and 1,4-diaminobutane 10 (138 mg,
°
C for 12 h. The
Conflict of Interest
1
.57 mmol) was added. The mixture was heated for a further 12 h
at 150°C. After cooling the mixture was diluted with water (150 ml)
and acidified with cHCl (2 ml). The mixture was then extracted with
CH Cl (100 ml×2) and the combined extracts were back extracted
The authors declare no conflict of interest.
2
2
Keywords: supramolecular chemistry · hydrogen bonds · crystal
engineering · organic zeolites
with water (100 ml) followed by drying with MgSO and filtration.
The filtrate was evaporated in vacuo and purified by chromatog-
raphy on silica gel. Dichloromethane elutes by-products then the
4
title compound (115 mg, 14%) as a yellow solid, m.p. 176–178°C
1
(
2
from ether/light petroleum ether 40–60); H NMR (600 MHz; CDCl ,
3
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5°C): δ=9.95 (2H, s), 8.09 (2H, d, J=12.0), 7.39-7.43 (4H, m), 7.30–
[
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7.32 (4H, m), 7.21–7.24 (2H, m), 6.08 (2H, s), 6.00 (2H, d, J=12.0),
13
3.07–3.10 (4H, m), 1.60–1.63 (4H, m); C NMR (150 MHz, CDCl ,
3
[
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2
1
1
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5°C): δ=165.6, 154.0, 147.6, 138.9, 129.6, 129.3, 125.6, 124.7,
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À 1
323 cm ; UV/Vis (EtOH): λ
15,849 mol dm cm ); HRMS (Orbitrap ASAP): m/z calcd for
(ɛ)=408 (19,952), 276 (7,943), 225
max
À 1
3
À 1
(
+
C H N O : 513.2250 [M +H]; found: 513.2254.
2
8
28
6
4
[
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collected at T=100 K using a Rigaku AFC12 area-detector diffrac-
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solved by direct methods and completed and optimised by
[
[
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2
[32]
refinement against jFj with SHELXL-2014. The H atoms were
positioned geometrically (NÀ H=0.88 Å, CÀ H=0.95–0.99 Å) and
[
[
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refined as riding atoms with the constraint U (H)=1.2U (carrier)
iso
eq
or 1.5U (methyl carrier) applied in all cases. One of the butyl side
chains in compound 11 was modelled as being disordered over
two sets of sites. The [001] channels in compound 11 may contain
eq
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Manuscript received: January 8, 2019
Revised manuscript received: February 10, 2019
ChemistryOpen 2019, 8, 457–463
www.chemistryopen.org
463
© 2019 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA