yes, because of the conjugated backbone, but also because of 3-dimensional interaction of the electron-rich system (you don't just have isolated chains, you have a complicated 3-dimensional structure which in case of the salt is (if well done) metallic; when neutralizing, you have a different backbone structure (different conjugation) and also 3-D interactions, but no conductivity, hence the bandgap has widened.

You can find something about the PAni structure here:

https://www.researchgate.net/publication/49593603_New_Insight_into_Organic_Metal_Polyaniline_Morphology_and_Structure?ev=srch_pub&_sg=sMQtv5a3YgJQIlCF%2BK039M%2FsQYEXL6clityGjDWRmCy%2F1FZ0UGc8CPxC3FhsfYyo_loiRoDD86g%2FzPumkCDoXZM2g6Y1eiKeYZo%2Fofm5i2vmBCC3nryLX4%2Feq369iaQBB_6oblhdUgVxaJn7KGT482yUua29u%2FvkYnnarLRkXMq4B5Sj1Fo%2BftIAausS4GXnoJ

Article New Insight into Organic Metal Polyaniline Morphology and Structure

My understanding is that conjugate backbone does not play any role in the color, its just the change in protonation that gives color.

CONDUCTING POLYMERS PREPARED BY

OXIDATIVE POLYMERIZATION: POLYANILINE

N. GOSPODINOVA, L. TERLEMEZYAN

Prog. Polym. Sci., Vol. 23, 1443–1484, 1998

sorry, that is not the correct description. The neutral (not at all protonated) Emeraldine base is blue which is determined by conjugated backbone and by the particle size. With protonation, the conjugated backbone (and the 3D intrachain!) conjugation is changed which leads to another colour, it happens to be green. Depending on how well the 3D conjugation is established, the green colour has a blueish or a yellowish shade (tone), the more metallic - the more yellowish (and the absorption extends into the near IR showing metallic properties).

https://www.researchgate.net/publication/49593603_New_Insight_into_Organic_Metal_Polyaniline_Morphology_and_Structure (and references cited therein, most of them accessible on my RG page as much as I am the author)

For the other oxidation states which are not protonated, like

- Leucoemeraldine (the fully reduced form): it is colourless transparent - no conjugation

- and the oxidized forms (purple / violett, partially conjugated)

you find different colours.

Article New Insight into Organic Metal Polyaniline Morphology and Structure

Thanks Dr Wessling for explanation. 3 dimensional structure means, intra/inter molecular H bonding interactions between polyaniline chains, and pi-pi interactions forms such 3D assembly ? Or crosslinking between the chains afford 3D assembly of polyaniline? Or all these three occurs for 3D assembly? 

Did you read this publication?

https://www.researchgate.net/publication/49593603_New_Insight_into_Organic_Metal_Polyaniline_Morphology_and_Structure

after protonation (and after further dispersion as you can learn in this paper), the PAni gets metallic. This means, that the electrons (those electrons which are responsible for conductivity) are not fixed to a certain location of the chain, but together in a cloud which fills the whole metallic space which is about 8 nm in size, look for the references in the a.m. paper, also available here on my RG site.

Whether or not H bonding is also between chains is a) not kown b) irrelevant for your question because we are dealing with a metallic space (also much more than just pi-pi interaction / conjugation), it is a metal!

Article New Insight into Organic Metal Polyaniline Morphology and Structure