The iodo group appears to be intact on the basis of the presence of a signal at the expected chemical shift, by H-1 NMR. Also, the compound that we were trying to alkylate, BOC-ornithine-isonicotinate, seems to have alkylated on the pyridine nitrogen, on the basis of a triplet at about 4.65 ppm, which we assign to a R-CH2-N(pyridinium) on the basis of model compounds. In storage the ester would only have whatever impurities it picked up in silica gel chromatography. In other words, I don't think it was stored in the presence of an oxidant.
From a practical point of view, we would like to complete the synthesis by deprotecting the molecule, which means removing the BOC group and the alcohol which makes up the ester, assuming that there actually still is some alkyl group protecting the carboxylic acid. Without knowing the identity of this group, I really have no idea whether or not this is a fool's errand.
Here are the C-13 data in CDCl3: 178.9, 32.8, 32.6, 25.5, 5.9 ppm. There are some very small peaks in the aromatic region. The H-1 data are: 3.21 triplet, 2.41 triplet, 1.92 multiplet, 1.89 triplet. Based on the NMR data, it looks as if the whole 4-methoxybenzyl group is gone, and we now have the free acid. I don't understand how we (a) were able to move the free acid through silica (25% to 75% EtOAc in hexanes) or to see the free acid on TLC plates using only UV-active plates. These results don't make sense.