[JenM]

I have used fluorescence to measure the quantum yield of the cleavage of a bond. My starting complex (a) does not fluoresce, however, once the bond is cleaved the product (b) is highly fluorescent.
The problem is that both complexes a and b absorb at very similar wavelengths and there is not possible excitation wavelength that would be selective for a. I was wondering if any one would know how to factor the inner filter effect, due to the formation of b, into my calculations.

Thank you in advance!

[Corribus]

As long as the concentration is sufficiently dilute, you don't need to worry about the inner filter effect. 

[Enthalpy]

Can you have a narrow beam of excitation light? Moving this beam and observing the fluorescence intensity would tell you the absorption.

[Corribus]

Do you mean spatially narrow or spectrally narrow (bandwidth)? Because I'm not sure I follow what you're saying.

[JenM]

Thank you for your replies.
I think I figured it out; by measuring a standard curve of conc. vs emission intensity using the fluorescent compound (b) I can calculate the number of molecules converted at each time point. From this and the extinction coefficient at the wavelength of excitation I can calculate the OD of b at each time point.
I know the concentration of my sample at the start (a), so I can minus the number of molecules converted from the starting amount and calculate the number of molecules of a left. I know the extinction coefficient of a so I can calculate the OD of my starting material at my time point also.
From these two ODs I can then calculate the percentage of incident light that is being absorbed by each species.