Hi.

I think that the chlorophyll pigments won't be affected in the transesterification reaction. I did carry out such an extraction, I used chloroform and methanol to extract lipids from microalgae.  Following the transesterification reaction, the pigment were still there but didn't mess the biodiesel production. There was no problem detecting it. I think that there would be no problem separating your biodiesel from the mixture either following the transesterification reaction.

Many thanks Keshini for your help. I will try to find such method.

Considering that the chlorophyll pigments are more polar than lipids you can extract them to a more polar solvent.

Although I have not tested the below procedure, I think that if you mix one volume of your hexane extract with an equal volume of an acetone:water (80:20 v/v) mixture and then vortex and centrifuge them, two layers will appear. The upper layer (hexane phase) will contain the lipids and the bottom one (acetone:water phase) will contain the chlorophylls. For better results, you may need to increase the water proportion against the acetone.

Many thanks for your suggestion George, I will try your proposed method in converting the lipid to oil.

Try out with methanol as  chlorophyll is soluble in it.

Thank you Rahul for your suggestion. If it is soluble in methanol, it would be soluble in water right?

 You may refer to the following paper:  Optimization of an Analytical

Procedure for Extraction of Lipids from Microalgae: http://s3.amazonaws.com/academia.edu.documents/35802505/57D27249.pdf?AWSAccessKeyId=AKIAJ56TQJRTWSMTNPEA&Expires=1472188610&Signature=3ckLdUwupPxPz8ww0dDItyWCBJA%3D&response-content-disposition=inline%3B%20filename%3DOptimization_of_an_Analytical_Procedure.pdf

Chlorophyll will always be on contamimant. Treat with chloroform MeOH and methylate that fraction. Look at Industrial Algae Measurements on the Algae Biomass Organisation web site for a valuable discussion of he subject.

you could filter the lipid extract using activated charcoal.