HAP is one of the most widely used materials in contemporary nanobiomedicine and nanotechnology. The interaction between HAP based biomaterials and living cells is improved, if the HAP surface is charged electrically. The charge is inducible on HAP structures by the proton transport along the OH chains in columnar channels. These chains are formed by OH ions along c-axis and are surrounded by calcium triangles. The results of computing simulation and studying of hydroxyapatite (HAP) properties and its hydrogen bonds and proton transfer peculiarities, surface and polarization properties are presented. The reported data presents as ab initio quantum-chemical calculations (with Gaussian98 code, HF, 6-31G(d),), as well semi-empirical (PM3) and DFT by HyperChem 8.0, which clarify the double-well asymmetric potential energy profile and were held to investigate the energy barriers for proton transport along the columnar channel. The calculated values of barriers can explain long storage of polarization charge, which is observed in experiments, as electrets effect. A possibility to transfer proton via the barrier is supported due to the experiment. High pressure of hydrogen and followed electromagnetic stimulation induced transfer of the proton. In fact, the electron work function was altered for different kind of ceramics.