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Analysis of a H-bonded net for XEMZUK, 4,4′-Bipyridinium pentachloro-iron
Algorithm:
1. Go to XEMZUK record. Run AutoCN with the default options to compute the adjacency matrix. From the output you see that there are Hb (hydrogen bonds) involving Cl1 and H1, H2.
2. Plot the structure with IsoCryst.
At first look the structure appears complicated, so it will be very useful to proceed with the Simplify Adjacency Matrix procedure eliminating all the 0 and 1 connected atoms, keeping the H-bonds. Store the simplified structure in a new database XEMZUK and rename/add comments in the Formula field, to keep track of all the operations.
3. Display the simplified structure with IsoCryst. Grow the network (type few times Ctrl+W) then select the subnets after activate the button
“select polimeric chain”. Three different selections are possible: yellow just clicking on one atom, green with Shift+click, magenta with Ctrl+click (If you need more that 3 colours you will learn later how to get them, at the present just select all the subnets repeating the 3 colours). For XEMZUK we see that 3 colours are enough to select all the subnets. A possible entanglement (interpenetration or polycatenation) is present.
4. Close IsoCryst and open an ADS window. In the Common tab of ADS options check Save Simplified Net (Simplification method = Standard). In our example the H-bonds are connecting isolated molecules, so the node of the network will be the barycenter of the molecule. Therefore we must select for Bond types Valence = At. and H bonds = Mol. (all the others are None).
5. Now run ADS and click Whole Molecule in the window Choose Central Atoms, so the whole molecule is represented by its barycenter. XEMZUK is formed by two molecules/ions [FeCl5]2- and [bipyH2]2+ 1:1. The ADS simplification will describe the net with two nodes, one is called Sc for the centroid of [bipyH2]2+ and the other is Ti for the centroid of [FeCl5]2-. Both nodes are 4-connected. Classify the underlying net with ADS program. Open an ADS window/ADS options and set the Classification in Topology tab. Pay attention that you cannot use the Save Simplified Net and Classification options into one step (at the same time), answer Yes in appearing window Confirm. Now run ADS and select all atoms in the window Choose Central Atoms.
From the output is already possible to see that the structure is interpenetrated. What symmetry operations relate the three interpenetrating pts nets?
6. Display the new fully simplified network from the XEMZUK_c database and select the subnets to show that they are just 3.
Exercise: Analyze the interpenetration in SAYMUB01, bis(benzene-1,3,5-tricarboxylic acid) tris(1,2-bis(4-pyridyl)ethane). What bonds provide the three-periodic array? Determine the interpenetration parameters and topological type of nets. Simplify the structure and plot it in IsoCryst drawing different nets by different colors as shown below.
Answer: Molecules are connected with H-bonds to construct 18 interpenetrated frameworks. The two step simplification for H-bonded net is needed. Resulting 18-fold underling nets srs are related by translational (4 partial interpenetration vectors) and non-translational (“-1”) symmetry operations according to class of interpenetration IIIb.
To paint a net with a non-standard color, select it, toggle to the Magic Wand tool
and click on any atom of the selected net. In the Magic Wand window toggle to Selected mode to apply the action to selected atoms only, then open the Change Color window and select a color. Click Ok and unselect all the atoms.
This net array is a rare example when some nets of the array have no atom in a given unit cell. Therefore, starting from a single unit cell and growing the structure you will not get all nets in the picture. To show all of them, start from a set of unit cells specifying non-zero values for the IsoCryst Translations parameters.
Algorithm:
1. Go to XEMZUK record. Run AutoCN with the default options to compute the adjacency matrix. From the output you see that there are Hb (hydrogen bonds) involving Cl1 and H1, H2.
2. Plot the structure with IsoCryst.At first look the structure appears complicated, so it will be very useful to proceed with the Simplify Adjacency Matrix procedure eliminating all the 0 and 1 connected atoms, keeping the H-bonds. Store the simplified structure in a new database XEMZUK and rename/add comments in the Formula field, to keep track of all the operations.
3. Display the simplified structure with IsoCryst. Grow the network (type few times Ctrl+W) then select the subnets after activate the button
“select polimeric chain”. Three different selections are possible: yellow just clicking on one atom, green with Shift+click, magenta with Ctrl+click (If you need more that 3 colours you will learn later how to get them, at the present just select all the subnets repeating the 3 colours). For XEMZUK we see that 3 colours are enough to select all the subnets. A possible entanglement (interpenetration or polycatenation) is present.4. Close IsoCryst and open an ADS window. In the Common tab of ADS options check Save Simplified Net (Simplification method = Standard). In our example the H-bonds are connecting isolated molecules, so the node of the network will be the barycenter of the molecule. Therefore we must select for Bond types Valence = At. and H bonds = Mol. (all the others are None).
5. Now run ADS and click Whole Molecule in the window Choose Central Atoms, so the whole molecule is represented by its barycenter. XEMZUK is formed by two molecules/ions [FeCl5]2- and [bipyH2]2+ 1:1. The ADS simplification will describe the net with two nodes, one is called Sc for the centroid of [bipyH2]2+ and the other is Ti for the centroid of [FeCl5]2-. Both nodes are 4-connected. Classify the underlying net with ADS program. Open an ADS window/ADS options and set the Classification in Topology tab. Pay attention that you cannot use the Save Simplified Net and Classification options into one step (at the same time), answer Yes in appearing window Confirm. Now run ADS and select all atoms in the window Choose Central Atoms.
From the output is already possible to see that the structure is interpenetrated. What symmetry operations relate the three interpenetrating pts nets?
6. Display the new fully simplified network from the XEMZUK_c database and select the subnets to show that they are just 3.
Exercise: Analyze the interpenetration in SAYMUB01, bis(benzene-1,3,5-tricarboxylic acid) tris(1,2-bis(4-pyridyl)ethane). What bonds provide the three-periodic array? Determine the interpenetration parameters and topological type of nets. Simplify the structure and plot it in IsoCryst drawing different nets by different colors as shown below.
Answer: Molecules are connected with H-bonds to construct 18 interpenetrated frameworks. The two step simplification for H-bonded net is needed. Resulting 18-fold underling nets srs are related by translational (4 partial interpenetration vectors) and non-translational (“-1”) symmetry operations according to class of interpenetration IIIb.
To paint a net with a non-standard color, select it, toggle to the Magic Wand tool
and click on any atom of the selected net. In the Magic Wand window toggle to Selected mode to apply the action to selected atoms only, then open the Change Color window and select a color. Click Ok and unselect all the atoms.This net array is a rare example when some nets of the array have no atom in a given unit cell. Therefore, starting from a single unit cell and growing the structure you will not get all nets in the picture. To show all of them, start from a set of unit cells specifying non-zero values for the IsoCryst Translations parameters.
