How to build methylene blue molecules in gaussview?
Answers
It would be of help if you tell us which dye are you dealing with. If the dye is plane or has a plane region holding part of the chromophore, you can just place two optimized monomers, on in front each other at 2.6-3.2 Angstroms of distance, holding the two pi systems planes parallel; then you can start an ordinary geometry optimization. You can try some different orientation and evaluate which is the most stable final structure.
You can further improve the geometry of encounter by considering this:
Make a graph of the electrostatic potential (I don't know what are you using for visualization, maybe gaussview, if not you can generate the electrostatic potential cube with cubegen utility and then use it with gabedit, VMD, molden or other visualization software, capable of opening gaussian cubes). Now take a look to the asymmetry in the charge distribution. You can orient the two monomers by ensuring that the most positive part of on monomer lies in front of the most negative of the other.
Another possibility is to follow Bartosz's suggestion, in case you were able to find X-ray evidence for very closely related molecules
Answer:
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