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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 Imaz,* and Daniel Maspoch*


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 leads to generation of 10 nets with diff erent 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 diff erent topologies.3 Thus, over the past two decades, application of the mathematics 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, research- ers
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
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 (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 nonlinear 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.
We propose the 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’Keeff e et al.,18 we first selected the 17 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 diff erent 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.
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
diff erent 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.


We then applied net-clipping to the derived nets by erasing the two diagonally connecting groups to mimic the presence of
zigzag-shaped MBBs (Figure 1b; Figures S4−S20). The 10 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 and S22).

Once we had theoretically deduced the MOF structures that could be formed using zigzag ligands, we experimentally assessed
our net-clipping approach. To this 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 polyhedral MBBs to synthesize two new MOFs, whose 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).
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-tetracarboxylate (3,3′,5,5′-ABTC) ligands.23 In this case, net-clipping induced the
formation of a 2D sql MOF (Table 1). Remarkably, replacing 3,3′,5,5′-ABTC with the corresponding zigzag 3,3′- azobenzene-
dicarboxylate (3,3′-ABDC) ligand aff orded 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 diff raction (SCXRD) revealed formation of an
ABCD packing 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).
Table 1. Net-Clipping of All the Derived Nets from 4-c Square Nodes in the 17 Selected Edge-Transitive Netsa




a
 For the derived nets, asterisks indicate the following: *topologies corresponding to the Systre code in the Epinet database; **topology
corresponding to the subnet transformation symbols nomenclature; and ***topologies corresponding to the TOPOS symbols
nomenclature.

Interestingly, our net-clipping approach is further corrobo- rated 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 by 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 induced
formation of a clipped dia topology from a pts topology (Table 1 and Figure 2b, top).




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.

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 aff ords RE-ftw- MOFs (derived net: kle).28 From this topology, net-clipping 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 12 others, through 12 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 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 diff erent metal-based MBBs, in which Zr(IV) ions
had been replaced with Tb(III) ions, thereby providing a slightly diff erent coordination environment (Figures S30 and
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-naphthalenedicarboxylate (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, an stp MOF assembled from the corresponding 4-c 1,4,5,8-naphthalenetetracarboxylate ligand and a 6-c trigonal
prism MBB for which net-clipping induced formation of an acs topology has never previously been reported. First, H2(1,5-
NDC) was synthesized from the corresponding diamine derivative via several functional group interconver- sions (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 Fe 3 (μ 3 -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.




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.

 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 an associated square vertex figure, and their derived nets, to identify the possible
outcomes. Then, we applied our net-clipping approach to deduce the diff erent topologies that should be accessible upon
assembly of zigzag ligands with diff erent polyhedral MBBs. Finally, we demonstrated the feasibility of net-clipping through
the successful design and assembly of three novel MOFs based on MBBs with diff erent connectiv- ities: 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.

ASSOCIATED CONTENT
Supporting Information
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/jacs.0c03404.
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 spectra, including Figures S1−S31 (PDF)
X-ray crystallographic data for Cu-sql-3,3′-ABDC (CIF) X-ray crystallographic data for Fe-acs-1.5-NDC (CIF) X-ray
crystallographic data for Tb-fcu-3,3′-BPDC (CIF)
AUTHOR INFORMATION
      Corresponding Authors
Vincent Guillerm − Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and Barcelona Institute of Science and Technology,
Bellaterra 08193, Barcelona, Spain; orcid.org/0000-0003-3460-223X; Email: vguillerm@protonmail.com
Inhar Imaz − Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and Barcelona Institute of Science and Technology, Bellaterra
08193, Barcelona, Spain; orcid.org/0000-0002-0278-1141; Email: inhar.imaz@ icn2.cat
Daniel Maspoch − Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and Barcelona Institute of Science and Technology, Bellaterra
08193, Barcelona, Spain; ICREA, 08010 Barcelona, Spain; orcid.org/0000-0003- 1325-9161; Email: daniel.maspoch@icn2.cat
Authors
Borja Ortín-Rubio − Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and Barcelona Institute of Science and Technology, Bellaterra
08193, Barcelona, Spain
Hosein Ghasempour − Department of Chemistry, Faculty of Sciences, Tarbiat Modares University, Tehran, Iran
Ali Morsali − Department of Chemistry, Faculty of Sciences, Tarbiat Modares University, Tehran, Iran; orcid.org/0000- 0002-1828-7287
Judith Juanhuix − Alba Synchrotron Light Facility, Cerdanyola del Valles̀08290, Barcelona, Spain; orcid.org/0000-0003- 3728-8215
Complete contact information is available at: https://pubs.acs.org/10.1021/jacs.0c03404

Notes
The authors declare no competing financial interest.

ACKNOWLEDGMENTS
This work was supported by the Spanish MINECO (project RTI2018-095622-B-I00), the Catalan AGAUR (project 2017 SGR
238), and the ERC under the EU-FP7 (ERC-Co 615954). It 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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