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Analysis of 1D+1D→3D polycatenation in SEQMUW
Algorithm:
1. Go to the SEQMUW record and compute the adjacency matrix. It is a ladder coordination polymer.
2. Simplify the crystal structure in the standard representation (Choose as central atom the metal Cd and the ligand will be represented by its barycenter). Remove 0- and 1-coordinated atoms in the simplified structure (see figure above right). The 2-coordinated atoms should be retained because they often play an important role in forming catenation.
3. Open an ADS window for the simplified structure and check the following ADS options.
4. Run ADS. You will get the following output.
ADS informs you that there is a polycatenation 1D+1D between two chains [110] and [110] with the angle 85.0° between the chain directions. So the polycatenation is inclined, not parallel. Pay attention that ADS does not recognize polycatenation and low-dimensional interpenetration; in the former case the resulting extended array of entangled nets has a higher dimensionality than each of the nets, in the latter case the dimensionalities coincide. At the same time inclined entanglement is always a polycatenation. About other differences between polycatenation and interpenetration see “Polycatenation, polythreading and polyknotting in coordination network chemistry” Carlucci L., Ciani G. & Proserpio D. M. (2003). Coord Chem. Rev. 246, 247-289 and Appendix 8.
5. To ensure that the array has an increased dimensionality, run IsoCryst and find catenating ladders.
To ensure that the ladders form an infinite array use Select/Translation tool and enter *1,1,1 to generate the copies if the selected ladders by all translations in the range from 111 to 111 (i.e. 111, 110, 111, etc.). If you want to generate only one copy of selected atoms by a separate translation, omit asterisk, i.e. enter 1,1,1 to generate one copy by the 1,1,1 translation.
It is easy to see for the picture after some rotation that the final entanglement is a 3D array. We cannot find any plane that separates it in disjoint parts.
6. Try to simplify the structure more by contracting 2-coordinated atoms. Does the simplification influence the polycatenation in this case?
Algorithm:
1. Go to the SEQMUW record and compute the adjacency matrix. It is a ladder coordination polymer.
2. Simplify the crystal structure in the standard representation (Choose as central atom the metal Cd and the ligand will be represented by its barycenter). Remove 0- and 1-coordinated atoms in the simplified structure (see figure above right). The 2-coordinated atoms should be retained because they often play an important role in forming catenation.
3. Open an ADS window for the simplified structure and check the following ADS options.
4. Run ADS. You will get the following output.
ADS informs you that there is a polycatenation 1D+1D between two chains [110] and [110] with the angle 85.0° between the chain directions. So the polycatenation is inclined, not parallel. Pay attention that ADS does not recognize polycatenation and low-dimensional interpenetration; in the former case the resulting extended array of entangled nets has a higher dimensionality than each of the nets, in the latter case the dimensionalities coincide. At the same time inclined entanglement is always a polycatenation. About other differences between polycatenation and interpenetration see “Polycatenation, polythreading and polyknotting in coordination network chemistry” Carlucci L., Ciani G. & Proserpio D. M. (2003). Coord Chem. Rev. 246, 247-289 and Appendix 8.
5. To ensure that the array has an increased dimensionality, run IsoCryst and find catenating ladders.
To ensure that the ladders form an infinite array use Select/Translation tool and enter *1,1,1 to generate the copies if the selected ladders by all translations in the range from 111 to 111 (i.e. 111, 110, 111, etc.). If you want to generate only one copy of selected atoms by a separate translation, omit asterisk, i.e. enter 1,1,1 to generate one copy by the 1,1,1 translation.
It is easy to see for the picture after some rotation that the final entanglement is a 3D array. We cannot find any plane that separates it in disjoint parts.
6. Try to simplify the structure more by contracting 2-coordinated atoms. Does the simplification influence the polycatenation in this case?
