If a biodiesel contains cis and trans isomers ,how we can identify that ,it will come as a different peak near the original peak or does it have an entirely different retention time peak. ?
If possible, I would buy the cis- or trans-isomers, derivatize them and inject them individually into the GC. This is the easiest way to solve your separation problem.
Two separate questions!
Usually, the cis-trans isomers are close to one another in retention time.
The esterification reaction (making FAMEs) opens the bond, which can rotate, and then close. This can produce equal amounts of each isomer unless that bond is sterically hindered.
FAMEs are only a 'fingerprint' procedure though many oils react differently and thus have a different profile. Examples are given in the USP for corn, soybean, and canola oils.
I think you should inject standard solution or you know the required temperature for cis and trans and make comparison
if you used long column 60m you can easily separate them if you don't have one you may modify the rate method or the temperature program to be isotherm for one min in cis and rising again to reach your method.
useful link
https://www.researchgate.net/post/How_do_I_calculate_the_retention_indices_for_my_FAME_calibration_compounds
Do literature search for fats and oils in foods; cis - trans isomerism is a major issue with adulteration and hydrogenation.
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