My molecule that I am trying to reduce has an aryl nitro group and a tertiary amine on it. I am looking to make the HCl salt of the amine to additionally purify the molecule. My next step in my synthesis is to reduce the nitro group to an amine with Pd/C. Will the HCl react/effect the reduction reaction?
Most probably it has no influence, but why dont yot try the use of zinc or iron under acidic conditions or tin(II) chloride?
http://commonorganicchemistry.com/Rxn_Pages/Nitro_Reduction/Nitro_Reduction_Index.htm
Amalgamated zinc granules in hydrochloric acid would work, I think. Do a test run with a small sample see if other substituents remain intact.
HCl salt should not hurt, may even help. Hydrogenation in ethanol* or ethyl acetate should be straightforward, except you may want an additional equivalent of HCl to aid purification of product. Zn works well, but has to be removed from the mixture after reduction and can give some pretty unpleasant rag layers during extraction following neutralization. Unless you already plan to distill or run a column, hydrogenation will just be easier.
(*Every general reference on hydrogenation seems to give examples of Pd/C catalyzed hydrogenations in methanol, but that has a little flammability problem - spontaneous fires in Büchner funnels are common even if you degas well after the reaction. If your nitro compound requires methanol to dissolve, keep a dry beaker nearby that you can place upside-down over the filter funnel. Also if you're not that familiar with catalytic reduction, be sure to use glass fiber paper: Whatman GF/A GF/C or similar, because paper filters always leak the finer catalyst particles.)
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