Neutral, unprotected phenylalanyl-glycyl-glycine (FGG) has been found to adopt four distinct rotational conformers under jet-cooling conditions. These conformers include one dispersion-stabilized folded conformer and three extended conformers with little interaction between termini. Conformer-specific ionization followed by photodissociation via visible radiation results in photofragmentation ratios that differ according to the type of neutral conformer from which the ion was formed. The folded structure of FGG yields a fragment-to-parent ion ratio of 1.4; the extended structures yield fragment-to-parent ion ratios around 0.3. The reverse peptide sequence, Glycyl-glycyl-phenylalanine (GGF), which has been found to adopt one folded and one extended conformer under the experimental conditions, acts similarly to FGG in that its folded structure exhibits a greater fragmentation ratio. The folded conformer of GGF fragments with a fragment-to-parent ratio of 3, and the extended conformer fragments with a 0.5 ratio. These results suggest that these peptides do not have time to photoisomerize under the experimental conditions, as the extent of fragmentation depends on the starting neutral structure. Photofragmentation in this experiment is controlled by the distribution of charge in the peptide - positive charge on the phenyl chromophore shifts its absorption spectrum to the visible range and thus allows absorption of sufficient energy for dissociation via visible radiation of the molecule. The possible mechanism by which secondary structure influences charge flow in these peptides was explored using quantum chemical calculations. It is proposed that, based on calculated neutral-to-cation geometry changes and charge distributions, differences in charge delocalization propensities among conformer types may cause the differences in charge flow.