Non-metal cation (NMC) pentaborate structures, in which some amino acids (valine, leucine, isoleucine, and threonine) were used as cations, were synthesized. The structural characterization of molecules was carried out by elemental analysis, FT-IR, mass, B-11-NMR, and thermal analysis (TGA/DTA) methods. The hydrogen storage capacity of molecules was also calculated by taking experimental results into consideration. The FT-IR spectra support the similarity of structures. The characteristic peaks attributable to pentaborate rings and amino acids were observed. When thermal analysis data were examined, it was observed that pentaborate salts gave similar degradation steps and degradation products. As a final degradation product of all thermal analysis experiments, a glassy form of B2O3 was observed. The valine pentaborate is the most thermally stable. Also, the amounts of hydrate water outside the coordination sphere of the compounds were determined by thermal analysis curves. The peaks of boric acid, triborate, and pentaborate structures were obtained in ppm with the B-11-NMR results of synthesized pentaborate compounds. With powder X-ray spectroscopy, all structures were found to be crystalline but not suitable for single-crystal X-ray analysis. The molecular cavities of the compounds detected by BET were found to be 3.286, 1.873, 2.309, and 1.860 g/cm(3), respectively. A low number of molecular cavities can be interpreted in several existing hydrogen bonds in structures. The hydrogen storage capacities of the molecules were found to be in the range of 0.04 to 0.07% by mass.