As mentioned previously, due to the observed flexibility of the proposed nanologic molecule, means must be found to impose planarity on the molecule. One possible way of achieving this is by interconnecting more than one nanologic molecule together. This was achieved using Sybyl's molecular editing features, by attaching 6 carbon poly-acetylene strands to the four corners of the molecule, and attaching another nanologic molecule to these strands. This molecule, which we will refer to as the dimer from here on, was also geometry optimized to give the lowest energy conformation using the AM1 semiempirical parameter set under Sybyl. The minimized dimer molecule is shown in

Figure 9. The minimized dimer of the nanologic molecule.

Figure 9. As we did previously for the 'monomer' of the nanologic molecule, this molecule was also used in a MD simulation. The dimer molecule underwent the same treatment as was described for the monomer molecule concerning heating, equilibration, and

Figure 10. The dimer of the nanologic molecule at 25 picoseconds.

constant temperature runs. Again a 50 ps run was used for the production run. The results at 25 ps are shown in Figure 10, and at 50 ps in Figure 11. These two conformations are good representatives of most of the conformations of the dimer during

Figure 11. The dimer of the nanologic molecule at 50 picoseconds.

50ps of dynamics. The dimer showed that indeed the whole system had much less

Figure 12. The trimer of the nanologic molecule at 25 ps.

flexibility than the monomer.

The success of the dimer molecule in reducing flexibility prompted us to explore the issue further by creating a 'trimer' molecule in the same fashion as the dimer. That is by using the same points of attachment, and the same 6 carbon strands of polyacetylene to attach a third nanologic molecule to the other two. The trimer molecule received the same treatment as the other two molecules regarding minimization, and dynamics under Sybyl. We looked at the conformations during the 50 ps production run, and once again the conformations at 25 ps and at 50ps are good representatives of the other conformations. The 25 and 50 ps conformations are found in figures 12 and 13 respectively.

Figure 13. The trimer at 50 ps.

There is progressively less flexibility in the molecules when considering the progression from the monomer to the trimer. This suggests that the more nanologic molecules are assembled together, the less flexible the overall system, and as a result, the more planar each individual nanologic molecule is in the system. Planarity is essential for proper % orbital overlap, conjugation, and conductivity throughout each nanologic molecule.

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