Organic Lego's

As mentioned in the previous posts there are a number of factors that effect the properties of a chromophore, such as pi-conjugation and electron withdrawing groups. The third objective of the Organic section of this course is to understand how molecular structure and intracellular targeting of the flurophore are related.

Chromophores that absorb light in the visible region usually have pi-conjugated systems as seen in the last post. There are mainly three different types of pi-systems that chromophore can exhibit: Linear Conjugation, Cross Conjugation, and Meta aromatic conjugation:


When looking at the development or construction of chrmophores a general set of rules can be applied. A chromphore is similar to that of a Lego house - each piece of the Lego house plays a vital role in the structure. If one Lego piece is overlooked you may not end up with a house.

A Chromophore is constructed with 5 types of molecules or "Chem-Lego" building blocks
1) Individual Pi-Units (conjugated double bonds or Pi-systems)
2) Individual Pi-Unit (non continuous)
3) Terminus Auxochrome (Base Donor)
4) Terminus Auxochrome (Acid-Acceptor)
5) Internal Secondary Unit

A Chromophore with all of these unit can be seen below, taken from Dr. Twieg's 2009 PowerPoint Presentation.