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Analysis of self-catenation in coesite, SiO2
Algorithm:
1. Go to the SiO2/Coesite (the database entangle) record and compute the adjacency matrix.
2. Open an ADS window and check the option Write Data to .tnt to store the information on rings in the file entangle_r.tnt and the option Entanglement to find entanglements.
3. Run ADS and select all atoms as central. You will get the output with the following fragments:
...
The first part of the output indicates that 16a-circuit is crossed by two Si1–O1 bonds; each bond belongs to two other 16a-circuits, and each 16a-circuit is connected with the crossed 16a-circuit by a shortest chain of 6 bonds. The asterisk * at the beginning of each line means that the crossing circuits/rings are linked together (belong to the same structure group). Pay attention that in this session Max. Ring = 0, i.e. we consider entanglements between circuits, not rings.
The last part contains the summary table on all types of circuits/rings crossings. We see that there is only one type of crossing: between 16a-circuits; the circuits are interconnected by a shortest chain of 6 bonds; each circuit crosses another circuit one time forming one link (knot) of Hopf type; each circuit is crossed by two other circuits (Mult = 2).
4. Draw the knots in IsoCryst. For this purpose, click Image/Rings (on the top of the ADS window), expand the tree and grow the structure several (seven) times to get all records bold in the Tint file data window. Select 16a-ring and one of the Hopf links and click the Apply button. You will get two interweaved rings (Hopf link) in the picture.
Select both Hopf links in the list and click Apply again. You will plot both circuits/rings crossing a given one.
Use the Magic Wand tool to paint the atoms in red. Unselect magenta circuits (Ctrl-right-click) and paint the central circuit in green. Grow the structure one time. Select the central circuit and repeat growth. Repeat selecting and growing until the crossing rings are united by chains of bonds. Be sure that the shortest chain between crossing circuits contains 6 bonds.
Select the crossing rings again using the Tint file data window. Pay attention that if you have accidentally closed the window you may open it again using Select/Load Tint File command.
Use Select/Complement Selection to toggle the selection.
Apply Sphere and Wire model to the selected atoms. Now you see more clearly the entangled part of the structure.
Exercise: Analyze the self-catenation in XASDUQ, bis(μ2-2-ethylpyrazine-N,N')-Ag(I) hexafluoroantimonate in database entangle. The structure is already simplified.
Answer: Ring links are formed with 8c circles (that are also rings); the shortest chain between them contain 3 bonds; each circuit crosses another circuit one time forming one link of Hopf type; each circuit is crossed by two other circuits… so you recognize that this net is again coe.
Algorithm:
1. Go to the SiO2/Coesite (the database entangle) record and compute the adjacency matrix.
2. Open an ADS window and check the option Write Data to .tnt to store the information on rings in the file entangle_r.tnt and the option Entanglement to find entanglements.
3. Run ADS and select all atoms as central. You will get the output with the following fragments:
...
The first part of the output indicates that 16a-circuit is crossed by two Si1–O1 bonds; each bond belongs to two other 16a-circuits, and each 16a-circuit is connected with the crossed 16a-circuit by a shortest chain of 6 bonds. The asterisk * at the beginning of each line means that the crossing circuits/rings are linked together (belong to the same structure group). Pay attention that in this session Max. Ring = 0, i.e. we consider entanglements between circuits, not rings.
The last part contains the summary table on all types of circuits/rings crossings. We see that there is only one type of crossing: between 16a-circuits; the circuits are interconnected by a shortest chain of 6 bonds; each circuit crosses another circuit one time forming one link (knot) of Hopf type; each circuit is crossed by two other circuits (Mult = 2).
4. Draw the knots in IsoCryst. For this purpose, click Image/Rings (on the top of the ADS window), expand the tree and grow the structure several (seven) times to get all records bold in the Tint file data window. Select 16a-ring and one of the Hopf links and click the Apply button. You will get two interweaved rings (Hopf link) in the picture.
Select both Hopf links in the list and click Apply again. You will plot both circuits/rings crossing a given one.
Use the Magic Wand tool to paint the atoms in red. Unselect magenta circuits (Ctrl-right-click) and paint the central circuit in green. Grow the structure one time. Select the central circuit and repeat growth. Repeat selecting and growing until the crossing rings are united by chains of bonds. Be sure that the shortest chain between crossing circuits contains 6 bonds.
Select the crossing rings again using the Tint file data window. Pay attention that if you have accidentally closed the window you may open it again using Select/Load Tint File command.
Use Select/Complement Selection to toggle the selection.
Apply Sphere and Wire model to the selected atoms. Now you see more clearly the entangled part of the structure.
Exercise: Analyze the self-catenation in XASDUQ, bis(μ2-2-ethylpyrazine-N,N')-Ag(I) hexafluoroantimonate in database entangle. The structure is already simplified.
Answer: Ring links are formed with 8c circles (that are also rings); the shortest chain between them contain 3 bonds; each circuit crosses another circuit one time forming one link of Hopf type; each circuit is crossed by two other circuits… so you recognize that this net is again coe.
