I know benzene rings in tryptophan at 280nm give the absorption so is this the only criterion for a molecule to possess a chromophore?. Or do the functional groups play a pivotal role along with symmetry of the molecule. Plus the polarity would dictate its absorption of light in either aqueous or organic dissolved solvents. If there are papers on pyocyanin/ phenazine methosulphate chromophore or other phenazine compounds please share them.
To rephrase slightly what part of pyo structure is chromophorous?. Acrydine dye is a similar structure along with ribitol Vitamin B3 with three aromatic rings. Anthraquinones, and hydroxyquinolones should absorb with a UV detector at 250nm. Aeruginosin compounds too should have similar structure.
If Carbon chain is longer then attraction of C1-C-C-C=C2 from C1 to C2 is less compared to the central atoms hence less electron delocalisation by the middle carbon chain.
I know extensive pie delocalisation across the molecule if lone pairs oxygen drawn towards the end of the molecule aswell as the middle so the para-attraction of atoms?. Alternating single and double bonds in benzene so resonate less because energy gap is smaller than wider benzene energy gap if no heteroatoms in benzene ring?!. some sort of sharing of lone electrons towards nearby and all atoms?.
A rapid search returned theses references. It seems that the imino nitrogen (the one close to the carbonyl oxygen) is protonated. The pKa is 4.9. Look in particular the EST paper (Environ. Sci. Technol. 2012, 46, 10605−10613, link below) which gives the references for the different protonation sites. Please ask if this is not clear enough.
http://ajplung.physiology.org/content/287/1/L94
http://pubs.acs.org/doi/pdfplus/10.1021/es302046h
http://onlinelibrary.wiley.com/doi/10.1002/mbo3.142/epdf
http://pubs.acs.org/doi/pdfplus/10.1021/es302046h
You may find this useful:
http://www.chem.ucla.edu/~bacher/UV-vis/uv_vis_tetracyclone.html.html
Hi Gibson,
Read the following paper:
Spectroscopic characteristics and some chemical properties of N-methylphenazinium methyl sulfate (phenazine methosulfate) and pyocyanine at the …
WS Zaugg - Journal of Biological Chemistry, Vol.239,(1964)3964. Good Luck
A chromophore is the part of the molecule bearing the "color", in fact the UV-Vis absorption. Even a carbonyl group is a chromophore. More generally any function absorbing in UV-Vis can be considered as a chromophore. Conjugated systems (pi electrons delocalized through conjugation) are the most common chromophores, and include aromatic systems. Phenazine is made of C & N atoms with sp2 hybrids that makes a completely conjugated structure and highly absorbing. Quaternization of N should reduce conjugation (shifts the absorption wavelength to shorter values, and absorption coefficient to lower value) but the aromatic (benzene) rings still present are also chromophoric. Solvent effects have also an effect on absorption, but this may be considered in general as a secondary effect. pH may have a larger effect on acido-basic chromophores.
i also want to know in pyocyanin's structure which nitrogen lone pair becomes protonated first in the two proton reduction reaction to completely reduce pyo!. Which nitrogen lone pair would destabilise the molecule the most would be bound but I am not organic chemist so dont know if its uppermost nitrogen thats protonated first or the downmost?!.
https://www.google.ie/imgres?imgurl=https://upload.wikimedia.org/wikipedia/commons/5/5f/Pyocyanin.png&imgrefurl=https://en.wikipedia.org/wiki/Pyocyanin&h=502&w=614&tbnid=5fg6wy_CFuLnGM:&tbnh=160&tbnw=195&usg=__Olm8A_bAEkylXx-Jd73F9bo_sBY=&vet=10ahUKEwjTrrqg3a_WAhWFaVAKHXL2BiMQ9QEIKTAA..i&docid=KsjnrEr5lpgQBM&sa=X&ved=0ahUKEwjTrrqg3a_WAhWFaVAKHXL2BiMQ9QEIKTAA
A rapid search returned theses references. It seems that the imino nitrogen (the one close to the carbonyl oxygen) is protonated. The pKa is 4.9. Look in particular the EST paper (Environ. Sci. Technol. 2012, 46, 10605−10613, link below) which gives the references for the different protonation sites. Please ask if this is not clear enough.
http://ajplung.physiology.org/content/287/1/L94
http://pubs.acs.org/doi/pdfplus/10.1021/es302046h
http://onlinelibrary.wiley.com/doi/10.1002/mbo3.142/epdf
http://pubs.acs.org/doi/pdfplus/10.1021/es302046h
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