In this work, the properties of hydroxyapatite (HAP) nanoparticles (NPs) have been studied both theoretically and experimentally focusing on computational analysis. HAP is widely used to fabricate implants, for drug delivery, etc. The physical properties of the nanosized HAP particles play an important role in the interaction with cells in the human body and are of great interest. Computer simulation was employed to understand the properties of HAP clusters (Ca(5)(PO(4))(3)OH) including formation energies, dipole moments and polarization (surface charges) by molecular mechanics (MM + , OPLS) and mostly by quantum semi-empirical Hartree-Fock (PM3) methods. The size of the simulated cluster is found to affect its dipole moment, polarization, and, finally, the electron work function- ϕ. These parameters depend on the concentration of hydrogen atoms H (or protons) at the surface. Values of ϕ were experimentally estimated via photoelectron emission measurements. The magnitude of ϕ was demonstrated to have a positive correlation on sizes. The NPs demonstrated a capability to be gathered within conglomerates. This property is confirmed by the calculated data for various sizes. Their sizes have a positive correlation on ϕ by the native particles. The main results show that the distributions of dipole moments have very different space orientations (along the OX, OY and OZ axes, the OZ axis is oriented along the OH column) and change with the addition of hydrogen atoms, which saturate the broken hydrogen bonds. This electrical property of NP leads to different behaviors and motions with consequent aggregation: (1) for the case of NPs having dipole moment oriented preferably perpendicular to the OZ axis (with more hydrogen bonds saturated by added H)-the HAP NP aggregates with hexagonal orientation and forms a wider and more spherical shape (sphere-like or bundle-like); (2) for the case of NPs having dipole moment oriented along the OZ axis (as is the case in the absence of added protons or non-saturated hydrogen bonds)-the NPs firstly rotated and oriented along this axis to form the most elongated cylindrical shape (rod-like).