The carboxylic acid and its conjugate base will definitely not elute at the same time, because one is a charged species and the other is neutral. The ratio of acid and conjugate base depends on the solution pH and the pKa of the acid, according to the Henderson-Hasselbach equation. At pH = pKa, the ratio is 1:1, at pH  = pKa - 1, the ratio would be 10:1 in favour of the acid.

When choosing an elution buffer for RP-HPLC of carboxylic acids on a C18 column, it is important to use a pH at least 2 units lower than the strongest acid among the analytes.

Unless the carboxylic acids contain benzene rings or conjugated double bonds, they will absorb at 210nm - only just within the useful region for HPLC.

Indeed, dissociation of weak acids depends on the pH of your solution, as Sally said.

If the pH of your mobile phase is basic, most of your acid will be dissociated in basic form (negative form, acetate for example). If the pH of your mobile phase is neutral or slightly acid, you will have neutral and basic species; that is, your acid will be partially dissociated. Under pH strongly acid, most of your acid will be as neutral form. At the same time, the pH of your solution will depend on the pKa of your acid.

On the other hand, positive species elute before neutral species and negative species later than neutral species from HPLC columns. Of course the UV absorbances and spectral profiles of negative, positive and neutral species are different.

Best,

Áurea.

Dear Mohammed, 

I work with Aristolochic Acids, some kind of natural organica acids in aristolochia genre. The elution system I was using is about acetic acid in water 0,5% and acetic acid en acetonitrile 0,5%... in HPLC-DAD only was detected the peaks corresponding at protonated species.

I Hope my experience can help you.

http://www.scielo.cl/pdf/jcchems/v58n4/art41.pdf

https://www.google.cl/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0CB8QFjAA&url=http%3A%2F%2Fwww.mdpi.com%2F2075-4450%2F4%2F4%2F533%2Fpdf&ei=DHgIVbuQGaTasAStsYDQBw&usg=AFQjCNEDu5Ax6p8TQsV4dLvvzvxJavZkUg&sig2=hN805bRXJy0KsTQC7n4qTw

This is a very good question. The carboxylate and carboxylic acid are unique species but the interconversion equilibrium is so fast that a chromatographic column cannot retard them differently. The UV detector detects the "chromophore" - it is oblivious of the molecule or its ionization state. For example, if we have benzoic acid, the benzoate and benzoic acid will be the same for the UV detector (or as long as the chromophore is not affected by pH like phenolphthalein). Their actual distribution percentage is determined by the pH of the mobile phase. In RPLC, in the presence of organic solvents the pKa are not the same as found in the tables.

Dear Farooq:

I agree with you as regards pKa in organic solvents is not the same as those found in tables. In fact there is no sense in talking about pKa in non aqueous solutions and organic solvents like acetonitrile, acids are almost non ionized.

But I disagree with you concerning UV/Visible spectra of a neutral molecule and its ionized form. For example, the UV/Vis spectrum of phenolate is very different from that of phenol, and the same for other organic acids. 

https://books.google.es/books?id=0pVQgwt5ODoC&pg=PA497&lpg=PA497&dq=phenol+and+phenolate+UV+spectra&source=bl&ots=U-n3gBpQMm&sig=6vwvIWWBcNQHIkthBj51f4Nw3-A&hl=es&sa=X&ei=jL0JVbuAGYSs7AbpxYCoDA&ved=0CEkQ6AEwBw#v=onepage&q=phenol%20and%20phenolate%20UV%20spectra&f=false

Thanks Aurea. I totally agree with your remark that's why I mentioned phenolphthalein as an example where the protonated and ionized forms are visually different.

Ok, Farooq.

Best,