For a specific experiment, I'm looking for a dye which would emit around 680 nm. Preferably one I could buy easily commercially. Are there any databases which might give the emission spectra of specific dyes? Or any other methods to find dyes at around $\ce{680 nm}$.

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    $\begingroup$ I suggest searching for “laser dyes” online. There should be lots of them and they are listed by emission wavelength. Cresyl violet 670 perchlorate emits around 670 nm and nile blue 690 perchlorate around 690 nm. Several companies sell quality laser dyes and dyes for other fluorescence applications. $\endgroup$ – Ed V Jun 30 '19 at 23:13
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    $\begingroup$ Note that many laser dyes have toxicity issues, so check the MSDS (SDS). $\endgroup$ – Jon Custer Jun 30 '19 at 23:45

There are two dyes commonly used in biochemistry research with $\lambda_\mathrm{Ex}$ of around $\pu{650 nm}$. They are Alexa Fluor 647 from ThermoFisher and Cyanine5 (Cy5) from Lumiprobe. Two example of these two categories are illustrated in the following figure. Either probe can be ordered according to the way you want to conjugate to your substrate (azide and alkyne groups are shown here). For example, IgG conjugate of Alexa Fluor 647 with amide linkage is shown in the insert.

AF647 & Cy5

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    $\begingroup$ I believe there is an Alexa Fluor 680 available. $\endgroup$ – evildemonic Jul 1 '19 at 13:30
  • $\begingroup$ @evildemonic: Yes, it is. Actually, Alexa Fluor 660 has the requested $\lambda_\mathrm{ex}$. However, I realized that after I made the slide so I thought it wouldn't heart $\pu{15 nm}$ difference by my experience. :-) $\endgroup$ – Mathew Mahindaratne Jul 1 '19 at 16:53

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