Question

The generic structure of a cyanine dye is:
R^'? - N -C=C- (C=C)_k? -C=N^?+

R R^'

a. (1 pts) For the cyanine dyes “Cy3”, “Cy5” and “Cy7” (used in many nanoscience journal articles) what is the value of “k” in the generic structure above.

b. (3) For these 3 dyes, calculate the energy gap between the highest occupied (HOMO) and lowest unoccupied (LUMO) energy levels. State clearly any and all assumptions you made for this model to generate these energy gap values in Joules. (Assume that both terminal “C-N” groups together add 0.55 nm to the delocalization length. This number includes some “delocalization” into the “R” group as well as the C-N bond length – see class notes). Hint: Set up the formulae for the wavelength of light as a function of k using Excel or Matlab for Q1, parts b, c, and d.

c. (2) Calculate the wavelength of a photon that would correspond with that gap for each of the molecules in Q1a. Compare these values to those of the experimental absorption wavelength maxima you find online.

d. (3) Can you find a better estimate for these particular dyes in Part a (I suggested 0.55nm for both CN bonds + “delocalization” into the chemical group R, so try some other values) that would fit the experimental data more accurately?

e. (1) Explain why different types of cyanine dyes may have different values for this C-N “delocalization length”