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I'm doing some research about the dyes found in photography, and found Organic Chemistry of Photography by Shinsaku Fujita, which shows the dyes used. I'm looking at doing an excited states and UV-VIS calculation, of course optimized before with a geometry optimization, with some of the dyes presented in the book. Right now, I'm trying to build number one in the image below, but have come upon a bit of a stumbling block.

Blue dyes

The problem is the $\ce{(CH2)3SO2O-}$ and $\ce{(C2H5)3NH+}$ part on the rightmost nitrogen, as I'm not sure how to model the interaction between $\ce{(CH2)3SO2O-}$ and $\ce{(C2H5)3NH+}$ (triethylamine), as both have no more covalent bonds available.

To visualize the problem, I built out two molecules (everything but triethylamine as one, then triethylamine below). As you can see, both are connected with as many covalent bonds as possible.

allBut trie

How can I model the interaction between the two molecules (pictured above) in Gaussian, for UV/Vis calculations?

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    $\begingroup$ Ah, I think you are essentially asking - "how can these two molecules be covalently connected?". The answer is : presumably they are not! It seems likely that they form a mixture with some kind of non-covalent interaction. In other words, when you say 'occupied' you mean "each atom is as connected as possible", or similar? $\endgroup$ – gilleain Jan 4 '17 at 14:50
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    $\begingroup$ I've no idea, sadly! There may be many ways to model mixtures like this - that seems like a good question, so I could suggest that you alter your question to be something like "how do I create a model for a mixture of charged dyes", mentioning the tools you are using. $\endgroup$ – gilleain Jan 4 '17 at 14:59
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    $\begingroup$ what's the property you want to know? For some things it might be fine to omit the counter ion. $\endgroup$ – DSVA Jan 4 '17 at 15:11
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    $\begingroup$ The quaternary amine appears to be the counterion to the negatively charged dye species. $\endgroup$ – hBy2Py Jan 4 '17 at 15:11
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    $\begingroup$ This would be a very involved problem to solve and very difficult to specifically answer in full (sampling the potential energy surface in various configurations, benchmarking results, choice of model, etc.). As for computing non-covalent interactions, please see chemistry.stackexchange.com/questions/31/… and chemistry.stackexchange.com/questions/32714/…. $\endgroup$ – LordStryker Jan 5 '17 at 4:15
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As hBy2Py, Greg, and others have pointed out in their comments, the cation is just a counter ion for your benzothiazole-based cyanine dyes.

I suggest to be reasonably lazy and perform the calculations on the cyanine dye only.

Even for calculations in solvents of sufficient polarity (from an experimental photochemical perspective, acetonitrile seems to be a good choice), I would just ignore the cations.

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    $\begingroup$ Sorry for the long delay in response. Unfortunately, I am unable to perform the job with the time allotted, but it seems reasonable that it would work $\endgroup$ – DavisDude Jan 12 '17 at 14:24

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