Net-Clipping: An Approach to Deduce the Topology of Metal-Organic Frameworks Built with Zigzag Ligands

Article abstract of DOI:10.1021/jacs.0c03404

Herein we propose a new approach for deducing the topology of metal-organic frameworks (MOFs) assembled from organic ligands of low symmetry, which we call net-clipping. It is based on the construction of nets by rational deconstruction of edge-transitive

Full text of DOI:10.1021/jacs.0c03404

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Communication
Net-Clipping: An Approach to Deduce the Topology of
Metal-Organic Frameworks Built with Zigzag Ligands
Borja Ortín-Rubio, Hosein Ghasempour, Vincent Guillerm, Ali
Morsali, Judith Juanhuix, Inhar Imaz, and Daniel Maspoch
J. Am. Chem. Soc., Just Accepted Manuscript • Publication Date (Web): 01 May 2020
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Net-Clipping: An Approach to Deduce the Topology of Metal-
Organic Frameworks Built with Zigzag Ligands
Borja Ortín-Rubio,† Hosein Ghasempour,‡ Vincent Guillerm,*† Ali Morsali,‡ Judith Juanhuix,§ Inhar
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Imaz,*† and Daniel Maspoch*†⊥
†Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and Barcelona Institute of Science and
Technology, Campus UAB, Bellaterra, 08193 Barcelona, Spain.
‡Department of Chemistry, Faculty of Sciences, Tarbiat Modares University, P. O. Box 14115-175, Tehran, Iran.
§Alba Synchrotron Light Facility, 08290 Cerdanyola del Vallès, Barcelona, Spain.
⊥ICREA, Pg. Lluís Companys 23, Barcelona, 08010, Spain.
Supporting information for this article is given via a link at the end of the document
KEYWORDS. metal-organic framework • reticular chemistry • topology • zigzag ligand
ABSTRACT: Herein we propose a new approach for deducing the topology of metal-organic frameworks (MOFs) assembled
from organic ligands of low symmetry, which we call net-clipping. It is based on the construction of nets by rational
deconstruction of edge-transitive nets comprising higher-connected molecular building blocks (MBBs). We have applied net-
clipping to predict the topologies of MOFs containing zigzag ligands. To this end, we derived 2-connected (2-c) zigzag ligands
from 4-c square-like MBBs by first splitting the 4-c nodes into two 3-c nodes and then, clipping their two diagonally connecting
groups. We demonstrate that, when this approach is applied to the 17 edge-transitive nets containing square-like 4-c MBBs,
net-clipping deduces generation of ten nets with different underlying topologies. Moreover, we report that literature and
experimental research corroborate successful implementation of our approach. As proof-of-concept, we employed net-
clipping to form three new MOFs built with zigzag ligands, each of which exhibits the deduced topology.
Reticular chemistry, defined as the “process of
assembling judiciously designed rigid molecular building
blocks (MBBs) into predetermined ordered structures
(networks), which are held together by strong bonding”,1,2
has become essential in the design and synthesis of porous
metal-organic frameworks (MOFs). Its success lies in
precise analysis of the geometry and connectivity of the
MBBs as well as in classification of their assemblies into
different topologies.3 Thus, over the past two decades,
application of the mathematic discipline of topology to
MBBs4,5 [or secondary building units (SBUs)]2,6 has enabled
synthesis of myriad MOFs based on reticulation of edge-
transitive nets or their derived nets. Complementarily to
these approaches, researchers have recently devised new
design strategies to further expand rational design of MOFs,
including supermolecular building blocks (SBBs)7–9 and
supermolecular building layers (SBLs).9,10 These strategies
also include the merged-net approach, which is based on
merging two edge-transitive nets into one minimal edge-
transitive net, a useful strategy for rational design of mixed-
linker MOFs.11
(known as geometry mismatch)12 that complicates rational
design of MOFs, as has been observed with use of less-
symmetric, 2-connected (2-c) groups such as bent,13 twisted
14
or zigzag ligands/MBBs.15 In addition, the various
possibilities of orientation of non-linear ligands around
inorganic MBBs lead to a high number of theoretical
possibilities for polymorphism and therefore, a low
structural predictability (Figure S1).16,17 However, as high
symmetry would likely be mostly favored, we reasoned that
less-symmetric ligands could be derived from more-
symmetric MBBs of higher connectivity by simply reducing
the connectivity of the latter. For example, a zigzag ligand
can be formed by removing the two diagonally connecting
groups of the two 3-c nodes derived from a 4-c MBB (Figure
1a). Accordingly, we reasoned that MOF structures made of
less-symmetric ligands could be anticipated via rational
clipping of the connecting groups of more-symmetric MBBs
in edge-transitive nets. This new approach, which we have
called net-clipping, provides further insights to our recent
works on transversal reticular chemistry15 and geometry
mismatch12 and can facilitate rational design of MOFs built
up from less-symmetric MBBs.
Herein we report a new design approach that, unlike the
rational, bottom-up construction of edge-transitive nets, is
based on the top-down deconstruction of edge-transitive
nets. Our group recently reported that the combination of
certain building blocks can induce structural irregularity
We propose use of net-clipping to rationalize/anticipate
the MOFs that could be built from zigzag ligands. To this
end, among the 54 edge-transitive nets (with D-symbol size
≤ 32) reported by O’Keeffe et al.,18 we first selected the
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Table 1. Net-clipping of all the derived nets from 4-c
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square nodes in the 17 selected edge-transitive nets.
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4
Clipped
Net
MBB
Main Topology
Derived Net
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tbd
xaa
ptd
tbo
pto
srs
sql
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fof
fog
nbo
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tfb
ucp
sqc12288*
lil
rhr
lvt
sql
lim
sty
Initial
ssa
structure;
Bond sets:
1,3:bbp**
stu
stw
stj
sql
lvt
Figure 1. a) Schematic of the deconstruction of a 4-c square
MBB in a zigzag building block by splitting the node into two
3-c triangles in different axes (node splitting), and then
removing two diagonally connections (net-clipping). b)
Schematic showing an example of our approach (node
splitting + net clipping) applied to an edge-transitive net
built from 4-c and 6-c triangular prism MBBs.
ssb
pts
stx
dmd
dmg
dmh
tfi
dia
hst
3,4T45***
seventeen nets assembled from 4-c square-like MBBs.
These nets are formed by combining a 4-c MBB with other
polygonal and polyhedral MBBs (Table 1). Next, we derived
these nets by splitting the 4-c nodes into two 3-c nodes
(Figure 1).19 This node splitting step is important to reduce
the symmetry of the 4-c MBBs and convert them into
rectangular shapes, from which the two zigzag ligands can
be originated by clipping the two diagonally connecting
groups (Figure 1).20 Notably, this process led to 39 derived
nets.21 Importantly, reducing the symmetry of some of the
initial edge-transitive nets (nbo, ssb, pts, scu and ftw) leads
to two-symmetrically different 4-c planar nodes. In these
cases, as the two types of nodes can be split distinctly, more
than two derived nets can be formed.
pth
she
soc
stp
qtz
hxg
crs
acs
sqc12215*
cdj
edq
ttp
ttx
tty
cut
scu
bcu
3,3,8T132***
sqc3520*
sqc
csq
sqc3782*
xly
xlz
kle
kxe
ttv
We then applied net-clipping to the derived nets by
erasing the two diagonally connecting groups to mimic the
presence of a zigzag-shaped MBBs (Figure 1b; Figures S4-
S20). The ten resultant nets are summarized in Table 1. We
concluded that most 3D nets (pto, ssb, pts, pth, she, soc,
stp, scu and ftw) are clipped into other 3D nets (srs, lvt, dia,
qtz, hxg, crs, acs, bcu and fcu, respectively); that some 3D
nets (nbo, lvt and ssb) are clipped into the 2D sql net; and
that the remaining nets (tbo, rhr, ssa, sqc, csq and shp)
cannot be clipped into other nets. Interestingly, we found a
common feature among all these latter edge-transitive nets:
the presence of a 6-cycle22 that comprises three 3-c nodes
(derived from three 4-c nodes) and three other MBBs and
that frustrates the net clipping in a fully zigzag fashion
(Figures S21,S22).
ftw
fcu
ced
cec
shp
* Topologies corresponding to the Systre code in the
Epinet database.
** Topology corresponding to the subnet transformation
symbols nomenclature.
*** Topologies corresponding to the TOPOS symbols
nomenclature.
end, we chose two types of MOFs assembled from
combining a 4-c MBB with a 4-c square-like MBB or a 12-c
cuboctahedral MBB. Then, we combined the zigzag ligand
analogs (derived from the 4-c MBB) with the corresponding
Once we had theoretically deduced the MOF structures
that could be formed using zigzag ligands, we
experimentally assessed our net-clipping approach. To this
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polyhedral MBBs to synthesize two new MOFs, whose
tetracarboxylate (3,3’,5,5’-ABTC) ligands.23 In this case, net-
clipping deduced the formation of a 2D sql MOF (Table 1).
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topologies we compared with those that we had deduced by
net-clipping. Note that, in two other cases, to further
support the net-clipping approach, we used MOF structures
already reported in the literature (MOFs made by
combining a 4-c MBB with 4-c tetrahedral or 8-c cubic
MBBs).
Remarkably,
replacing
3,3’,5,5’-ABTC
with
the
corresponding zigzag 3,3’-azobenzene-dicarboxylate (3,3’-
ABDC) ligand, afforded the expected 2D sql MOF (Figure
2a,top). This entailed reaction of copper(II) nitrate salt and
H2(3,3’-ABDC) in N,N-dimethylformamide (DMF) under
solvothermal conditions, which yielded green needle-
shaped crystals of Cu-sql-3,3’-ABDC. Single-crystal X-ray
diffraction (SCXRD) revealed formation of a ABCD packing
We began with the nbo MOF PCN-10 (derived net: fof),
which is built by connecting 4-c square-like Cu(II) paddle-
wheel
MBBs
through
4-c
3,3’,5,5’-azobenzene-
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Figure 2. Schematic of the net-clipping approach applied to formation of MOFs from (a) 3,3’,5,5’-ABTC ligand to zigzag 3,3’-
ABDC combined with (top) 4-c paddle-wheel Cu(II) MBBs and (bottom) 8-c cubic Zr(IV)-based MBBs; and from (b) 3,3’,5,5’-
BPTC to 3,3’-BPDC ligand combined with (top) 4-c tetrahedral In(III)-based MBBs and (bottom) 12-c cuboctahedral Tb(III)-
based MBBs.
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of a 2D-network of formula Cu2(3,3’-ABDC)2 (H2O)2, which
crystallizes in the C2/m space group (Figure 2). As expected,
the building unit in Cu-sql-3,3’-ABDC is the Cu(II) paddle-
wheel unit. In this framework, each of these units is
connected to four others through four bridging zigzag 3,3’-
ABDC ligands, adopting a 4-c sql underlying topology
(Figure 2a,top).
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predicts formation of a MOF with the fcu underlying
topology. To investigate this, we used the zigzag 3,3’-BPDC
ligand as a substitute for the 4-c 3,3’,5,5’-BPTC ligand.
Reaction of terbium(III) nitrate salt and H2(3,3’-BPDC) in
the presence of 2-fluorobenzoic acid in DMF under
solvothermal conditions yielded transparent octahedral
crystals of Tb-fcu-3,3’-BPDC. SCXRD revealed formation of
a 3D net with formula [(CH3)2NH2]2[Tb6(μ3-OH)8(3,3’-
BPDC)6(H2O)4], which crystallizes in the P21/n space group.
As we had expected, the presence of 2-fluorobenzoic acid as
modulator29 enabled formation of the hexanuclear RE MBB
in Tb-fcu-3,3’-BPDC. In this framework, each of these MBBs
is connected to twelve others, through twelve bridging
zigzag 3,3’-BPDC groups, adopting overall a 12-c fcu
topology (Figure 2b, bottom). Note that, compared to the
archetypical 12-c Zr-fcu-4,4’-BPDC (known as UiO-67),30
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Interestingly, our net-clipping approach is further
corroborated by the fact that an isostructural sql MOF made
by linking Zn(II) paddle-wheel units by 3,3’-ABDC ligands
had previously been described by Liang et al.24 Similarly,
two other independently, previously reported structures
reinforce our approach: NOTT-204,25 a pts MOF (derived
net: tfi) built by linking the 4-c 3,3’,5,5’-biphenyl-
tetracarboxylate (3,3’,5,5’-BPTC) ligand and the 4-c
tetrahedral In(III)-based MBB; and InOF-4,26 a dia-MOF
made of connecting the same 4-c tetrahedral In(III)-based
MBBs through the zigzag 3,3’-biphenyl-dicarboxylate (3,3’-
BPDC) ligand. Interestingly, both of these MOF structures
are related by net-clipping, which deduced formation of a
clipped dia topology from a pts topology (Table 1 and
Figure 2b,top).
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Tb-fcu-3,3’-BPDC shows
a less-symmetric, distorted
structure. We attributed this feature to the transversal
parameter of the zigzag ligand as well as to the different
metal-based MBBs, in which Zr(IV) ions had been replaced
with Tb(III) ions, thereby a slightly different coordination
environment (Figures S30,S31).
Once we had confirmed the feasibility of our net-clipping
approach, we applied it to synthesize a new acs-MOF built
with a zigzag ligand. To this end, we synthesized a rigid
zigzag 1,5-naphtalenedicarboxate (1,5-NDC) ligand and
selected the well-known [Fe(III)]3O trimeric unit as the
trigonal prism MBB.31 We synthesized this zigzag ligand
because, to our knowledge, a stp MOF assembled from the
corresponding 4-c 1,4,5,8-naphtalenetetracarboxylate
ligand and a 6-c trigonal prism MBB - for which net-clipping
deduced formation of an acs topology - have never
previously been reported. First, H2(1,5-NDC) was
synthesized from the corresponding diamine-derivative via
several functional group interconversions (see SI). Then,
the Fe(III) trimeric unit was synthesized in an acetic acid
solution, according to a literature protocol.32 Finally, the
pre-formed Fe(III) unit was reacted with H2(1,5-NDC) and
acetic acid in DMF under solvothermal conditions for 48 h.
After this period, orange hexagonal crystals suitable for
SCXRD were collected. SCXRD revealed formation of a 3D
structure with formula Fe3(μ3-O)(1,5-NDC)3(H2O)2(OH),
which crystallizes in the P-63m space group. In Fe-acs-1,5-
NDC, each trimer is connected to six others through six
zigzag 1,5-NDC ligands, adopting the 6-c acs underlying
topology (Figure 3). Note that the structure of Fe-acs-1,5-
NDC, although slightly distorted, is similar to that of MOF-
235/MIL-88B,33,34 which also exhibits an underlying acs
topology.
Next, we shifted our attention to another MOF assembled
from the 4-c 3,3’,5,5’-ABTC ligand and a higher-connected
MBB, the 8-c cubic Zr6O4(OH)4(OOC-R)8(H2O)4(OH)4
hexanuclear MBB.27 This MOF shows the scu topology, in
which we reasoned that replacement of 3,3’,5,5’-ABTC with
3,3’-ABDC would generate a clipped bcu MOF (Table 1).
Interestingly, our group recently reported that combination
of this 8-c MBB with a series of zigzag ligands, including 3,3’-
ABDC, leads to formation of MOFs with the bcu topology
(Figure 2a,bottom), which further supports net-clipping.15
Recently, Eddaoudi et al. reported that combining 4-c
ligands (e.g. 3,3’,5,5’-ABTC or 3,3’,5,5’-BPTC) with 12-c
cuboctahedral rare earth metal (RE) MBBs affords RE-ftw-
MOFs (derived net: kle).28 From this topology, net-clipping
a)
b)
c)
In summary, we have proposed and validated a new
approach, net-clipping, for rational design of MOFs made of
zigzag ligands. First, we demonstrated the relationship
between these ligands and more symmetric 4-c ligands.
Next, we studied the edge-transitive nets with 4-c nodes
with associated square vertex figure, and their derived nets,
to identify the possible outcomes. Then, we applied our net-
clipping approach to deduce the different topologies that
should be accessible upon assembly of zigzag ligands with
different polyhedral MBBs. Finally, we demonstrated the
feasibility of net-clipping through the successful design and
assembly of three novel MOFs based on MBBs with different
Figure 3. Crystal structure of Fe-acs-1,5-NDC, showing a)
the zigzag connection between the Fe-trimers; b) the
trigonal bipyramid cage; and c) the channels formed
through the c axis.
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SGR 238), and the ERC under the EU-FP7 (ERC-Co 615954). It
connectivities: Cu-sql-3,3’-ABDC (4-c, paddle wheel), Fe-
acs-1,5-NDC (6-c, trimer) and Tb-fcu-3,3’-BPDC (12-c,
hexamer). Our approach enriches the repertoire for
topological predictions, and we anticipate the application of
net-clipping to bent ligands, via clipping of 4-c MBBs in
other ways, as well as its eventual use with MBBs of other
connectivity.
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was also funded by the CERCA Program/Generalitat de
Catalunya. ICN2 is supported by the Severo Ochoa program
from the Spanish MINECO (Grant No. SEV-2017-0706).
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ASSOCIATED CONTENT
The Supporting Information is available free of charge via the
Internet at http://pubs.acs.org.
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Chemicals, instrumentation, net-clipping approach
and synthetic procedures, schemes of the topologies
resulting
from
the
net-clipping,
PXRD,
crystallographic data, structural details and 1H NMR.
AUTHOR INFORMATION
Corresponding Author
Vincent Guillerm - Catalan Institute of Nanoscience and
Nanotechnology (ICN2), CSIC and Barcelona Institute of
Science and Technology, Campus UAB, Bellaterra, 08193
Barcelona, Spain; E-mail: vguillerm@protonmail.com
Present address: Functional Materials Design, Discovery &
Development Research Group (FMD3), Advanced
Membranes & Porous Materials Center, Division of
Physical Sciences and Engineering, King Abdullah
University of Science and Technology (KAUST), Thuwal
23955-6900, Kingdom of Saudi Arabia.
Inhar Imaz - Catalan Institute of Nanoscience and
Nanotechnology (ICN2), CSIC and Barcelona Institute of
Science and Technology, Campus UAB, Bellaterra, 08193
Barcelona, Spain; E-mail: inhar.imaz@icn2.cat
Daniel Maspoch - Catalan Institute of Nanoscience and
Nanotechnology (ICN2), CSIC and Barcelona Institute of
Science and Technology, Campus UAB, Bellaterra, 08193
Barcelona, Spain; ICREA, Pg. Lluís Companys 23,
Barcelona, 08010, Spain; E-mail:
daniel.maspoch@icn2.cat
Authors
Borja Ortín-Rubio - Catalan Institute of Nanoscience and
Nanotechnology (ICN2), CSIC and Barcelona Institute of
Science and Technology, Campus UAB, Bellaterra, 08193
Barcelona, Spain.
(12) Guillerm, V.; Maspoch, D. Geometry Mismatch and Reticular
Chemistry: Strategies to Assemble Metal-Organic Frameworks
with Non-Default Topologies. J. Am. Chem. Soc. 2019, 141, 16517–
16538.
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Hosein Ghasempour - Department of Chemistry, Faculty of
Sciences, Tarbiat Modares University, P. O. Box 14115-175,
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Ali Morsali - Department of Chemistry, Faculty of Sciences,
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ACKNOWLEDGMENT
This work was supported by the Spanish MINECO (project
RTI2018-095622-B-I00), the Catalan AGAUR (project 2017
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