The interest to amino acid amides arises from their biological important role. Some C-n£\- amidated amino acids Ile, Val, Thr, Ser, Met, Trp, Gln and Arg have been studied by single crystal X-ray diffraction and their bioactivity have been compared with the corresponding amino acids due to most of mammalian peptide hormones as calcitonin, gastrin, neurokinins or neuropeptides possess a C-£\-terminal-amides. The most C-£\- amides are much more biologically active, comparing with the corresponding C-£\- terminal free acids. For example the "potency ratio" of peptide amide towards the corresponding peptide free acid in neurocinin is more than 40 000. Since the protonated forms of amino acid amides and C-£\-amidated peptides exists in the living cell their investigation could provide an understanding of their biological role. The choice of the acidity agent for the in vitro investigations are based manly of its own biological activity as for example squaric acid (H2Sq). Its application for synthesis of optically active amino acid derivatives with potential non-linear optical and electro-optical properties is well known, but its important biological role is intensively studied in last five years. A large number of medications based on H2Sq derivatives are effective inhibitors of protein tyrosine phosphatases or DNA polymerases from several viruses. H2Sq diamides replaced a phosphate diester linkage in oligodeoxynucleotide. Selective antagonist of ionotropic glutamate receptors is obtained by replacing of £^-carboxylic acid of a glutamate residue within a polyamine toxin with squaric acid derivatives. Some H2Sq-based peptides are inhibitors of matrix metalloprotease V1. These facts provoked the systematic investigations of hydrochlorides, hydrogensquarates and ester amides of squaric acid of amino acid amides of Ala, Arg, Tyr, Ser, Met, Ile, Lys, Tyr, Val, Leu, Pro and Phe. Some of them have been structurally characterized by single crystal X-ray diffraction. Their spectroscopic properties have been obtained using solid-state conventional and linearpolarised IR- and Raman spectroscopy and 1H- and 13C-NMR. However, the complicated spectroscopic data difficult in significant level their interpretation. Moreover, in the cases of hydrogensquarates and ester amides of squaric acid various intermolecular hydrogen bonds in solid-state with participation of H2Sq have been established. Having in mind that physical and chemical properties of above mentioned compounds can be precise calculated by means of ab initio and DFT methods at Hartee-Fock, MP2 and B3LYP level of theory, varying basis sets (6-31G*, 6-31G**, 6-31++G, 6-31++G*, 6-31++G**, 6-311G, 6-311G*, 6-311G** and 6-31++G**) have been employed. The results obtained allow a precise assignment of many vibrational bands to the corresponding normal modes as well as the electronic structure and conformational analysis have been carried out.
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