Stereo-structures of protonated L-phenylalanine (L-Phe), L-tyrosine (L-Tyr) and L-tryptophan (L-Trp) containing homodipeptides (L-Tyr-L-Tyr, L-Phe-L-Phe, L-Trp-L-Trp) are carried out by ab initio calculations. The obtained data in gas phase are compared with experimental ones, received by linear-dichroic infrared (IR-LD) spectroscopy of solids, oriented as suspension in nematic mesophase. An observation of a good correlation between theoretical and spectroscopic geometry parameters established and illustrated the possibilities of this complex study approach for the prediction of the stereostructures in compounds in solid state. The protonation leads to little variance in the bond lengths and angles, expecting the COO- fragment, where a distortion of equalized COO- bond lengths, stabilizing a C=O double bond and C-O(H) one is established. Significant deviations of the dihedral angles as a result of the protonation are obtained in the skeletal aliphatic and amide- fragments. In L-Tyr-L-Tyr and L-Phe-L-Phe, a deviation of O=C-N-H torsion angle about 10-140 is predicted. The calculations show a trans-amide configuration in L-Trp-L-Trp and a cis-one after its protonation.