Short-chain fatty acids (SCFAs), produced by microbes when dietary fiber ferments in the colon, are one of the most studied microbial products despite their volatility and complex matrices, which make analysis challenging. In the current study, we sought to address research gaps by exploring the commonalities and differences between the retention time changes for SCFAs in polar solvents. In one such solvent, dimethyl sulfoxide (DMSO), the retention time of the SCFA acetic acid shows a linear positive correlation with the equal volume increase in the DMSO solvent. We used gas chromatography–mass spectrometry to analyze the retention times of mixed solutions of formic acid, acetic acid, butyric acid, valeric acid, and toluene in the solvents DMSO and water and found that only the retention times of formic acid and acetic acid changed. We further compared the effect of three solvents with similar polarities, DMSO, N-methylpyrrolidone (NMP), and dimethylformamide (DMF), on the retention time of acetic acid and found that it increased in the DMSO–water solution more than in the NMP–water solution and remained unchanged in the DMF–water solution. This finding is consistent with quantum chemical calculations showing that the strength of the hydrogen bond between DMSO and acetic acid is greater than between NMP and acetic acid. Taken together, the chromatographic results and quantum chemical calculations indicate that, in all three solvents, the portion of the molecule with the smallest negative electrostatic potential (red) has high electron density and can easily donate electrons, forming a hydrogen bond with acetic acid. However, the portion with the largest positive electrostatic potential (blue) forms a bond with polyethylene glycol, a column stationary solution with a strong dipole moment, and is adsorbed on the stationary solution in the direction of the dipole moment. Therefore, the retention times of formic acid and acetic acid change under the combined influence of a series of complex intermolecular forces. In the chromatographic column, the outflow rate of DMF is higher than that of acetic acid, and the force of the hydrogen bond between DMF and acetic acid cannot overcome the outflow resistance of acetic acid, so the retention time of the acetic acid in the DMF–water solution does not change. The retention times of butyric acid and valeric acid are unchanged in aprotic polar solvents for the same reason.
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