Cluster simplification of the crystal structure of NAPFUG, a Metal-Organic Framework Zn4O(NBT)2, H3NBT= 4,4′,4′′-nitrilotrisbenzoic acid. 

  1. Open the database cluster_repr and compute the adjacency matrices for the crystal structures (default parameters for AutoCN, no Hydrogen Bonds are present).
  2. Duplicate the entry C42 H24 N2 O13 Zn4 (NAPFUG) so you can make any changes and save the original structure: right-click and choose Duplicate command (or also from the top menu bar: Compound/Duplicate).
  3. Following the Tips of the previous example, remove all the 1-connected atoms to get a simpler view of the content of the unit cell.
  4. Open the IsoCryst window and with the button on, select one atom to check if there are one or more nets. This will show that for NAPFUG there are more than one nets.
  5. Choose to display only the selected subnet clicking on (Show selection only).

    Pay attention that the standard representation will not be appropriate here, instead we need to simplify the whole polynuclear groups (clusters) as a single node using “cluster representation”: the nodes are the Zn4O(COO)4 clusters and the tri-benzoic ligands, hence the underlying net could be described as 6-c (cluster) and 3-c (ligand).

  6. The long way will be to change (one by one) selected bonds into H-bonds as to “isolate” the cluster by Hbonds, then do the standard representation as illustrated in the previous example 1 for SAYNAI. But there is a semiautomatic mode. Open a window of the program ADS, click Options, check the option Common/Save Simplified Net and Simplification Method = Cluster. Be sure that the Cluster Rings limits are set to zero (default values), otherwise only rings within the specified limits will be considered in the simplification procedure.

    Press Ok and run the program.

  7. Select All atoms (this is essential, because the program look for rings of all bonds, see Appendix 2 for details and definitions), and run. You will get a new entry in the cluster_repr_c database where the bonds that define the boundary of the cluster are changed into H-bonds (as in the figure below).

  8. Now we can apply the standard simplification for H-bonded molecules (the Whole molecule selection) and all the clusters and 6-rings will be changed into single points.

    The database cluster_repr_c_c of the next level of simplification will be created.

    The final net contains 5 pseudoatoms (nodes): a 6-c (Ti) pseudoatom represents the barycenter of Zn4O(COO)6 cluster, 2-c (Sc) pseudoatoms are the benzene rings centroids, and 3-c are the nitrogen atoms of the H3NBT ligand (These information are written in the Comment window under SIMPLIG: Sc=C6H4 Ti=C6O13Zn4).

Check with ADS and you will find that there are two interpenetrated underlying nets pyr (see Module 5).
A good exercise is to reproduce the representations of FOXRAM as illustrated here below from figure 2 and supplementary in “Underlying nets in three-periodic coordination polymers: topology, taxonomy and prediction from a computer-aided analysis of the Cambridge Structural Database” E. V. Alexandrov, V. A. Blatov, A. V. Kochetkov and D. M. Proserpio CrystEngComm, 2011, 13, 3947-3958.

The different possible methods of simplification of the coordination framework in FORXAM. (top)
Standard representation; (middle) cluster representation with intercluster bonds belonging to 24- and 39- cycles; (bottom) cluster representation with intercluster bonds belonging to only 39-cycles

In the next page is reported a fragment of the ToposPro output for the FORXAM crystal structure showing the table of symmetry independent bonds with the size (N) of the minimum (shortest) circuits to which each of them belong shown in the last column. The bonds of groups (i)-(iv) are selected by green, yellow, cyan, and grey, respectively.
(i) grey N=0 are dangling bonds: typically C-H, and here also Zn-O (water).
(ii) yellow N=3,4,6,8 are bonds belonging to small cycles.
(iii) cyan N=24 gives cluster representation 1 ubt.
(iv) green N=39 gives alternative cluster representation 2 fcu.

24-circuit for C1-C2
(C-H removed)
39-circuit for Zn2-N1
(C-H removed, one ligand is disordered)

Exercise: simplify the other structures from the database cluster_repr. They contains examples of MOFs from O. M. Yaghi & coworkers (Nature 1999, 402, 276-279; Science 2010, 329, 424-428), M. Schröder & coworkers (Chem. Commun. 2009, 1025-1027), I.D. Williams (Science 1999, 283, 1148-11509), J. Long & coworkers (Inorg. Chem. 2008, 47, 11-13),

On equivalent modes of simplification see also: “Deconstructing the Crystal Structures of Metal-Organic Frameworks and Related Materials into Their Underlying Nets” M. O’Keeffe and O. M. Yaghi Chem. Rev. 2012, 112, 675-702.


RefCode Types of bonds considered Shortest circuit defining cluster D* Underlying net Entanglement Comments
ACUHOV H-bonds, valence 8 0D 3-c hcb 2-fold interp. 3-c nodes - H-bonded dimers
BIWSIK valence 6 0D 3,8-c the 2-fold interp. 3-c nodes - central triazine-rings of ligands;
8-c nodes - clusters {Mn4ClO4(CN4)8};
valence 6 0D 3,6-с qom - 3-c nodes - central benzene-rings of ligands;
6-c nodes - clusters {Zn4O(CO2)6};
valence 6 0D 3,6-с toz
- 3-c nodes - central benzene-rings of ligands;
6-c node - clusters {Zn4O(CO2)6};
note that some {Zn4O(CO2)6} clusters are disordered, but cluster simplification works well
CUSYAR valence 46 1D - - There is a rod packing representation of the structure
valence 6 0D 3,4-с tbo - 3-c nodes - central benzene-rings of ligands;
4-c nodes - clusters {Cu2O2(CO2)4}
valence 6 0D 3,4-с ntt - 3-c nodes - central and some of peripheral benzene-rings of ligands;
4-c node - clusters {Cu2O2(CO2)4}
FOPFAS valence 24 0D 3,24-с rht - 3-c nodes - central and some of peripheral benzene-rings of the ligand;
24-c node - clusters {Cu24O24(C6H3(CO2))24}
valence 6 0D 3,6-c ith-d - 3-c nodes - central benzene-rings of one ligand;
6-c nodes – clusters {Zn4O(CO2)6};
note that naphthalene-groups are disordered, but cluster simplification works well
valence 6 0D 3,6-c qom - 3-c nodes - central benzene-rings of the ligand;
6-c nodes – {Zn4O(CO2)6};
note that the {Zn4O(CO2)6} clusters are disordered, but cluster simplification works well
valence 6 0D 6-c pcu - 6-c nodes – {Zn4O(CO2)6}

* Dimensionality of cluster

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