In this work, the properties of hydroxyapatite (HAP) nanoparticles (NPs) havebeen studied both theoretically and experimentally focusing on computationalanalysis. HAP is widely used to fabricate implants, for drug delivery, etc. Thephysical properties of the nanosized HAP particles play an important rolein the interaction with cells in the human body and are of great interest.Computer simulation was employed to understand the properties of HAP clusters(Ca5(PO4)3OH) 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 simulatedcluster is found to affect its dipole moment, polarization, and, finally, the electron work function—φ. Theseparameters depend on the concentration of hydrogen atoms H (or protons) at the surface. Values ofφ were experimentally estimated via photoelectron emission measurements. The magnitude ofφ was demonstrated to have a positive correlation on sizes. The NPs demonstrated acapability to be gathered within conglomerates. This property is confirmed bythe calculated data for various sizes. Their sizes have a positive correlation onφ by the native particles. The main results show that the distributionsof dipole moments have very different space orientations (along theOX,OY andOZ axes,the OZ axis is oriented along the OH column) and change with the addition of hydrogenatoms, which saturate the broken hydrogen bonds. This electrical property ofNP leads to different behaviors and motions with consequent aggregation: (1) forthe case of NPs having dipole moment oriented preferably perpendicular to theOZ axis (with more hydrogen bonds saturated by added H)—the HAP NP aggregates withhexagonal orientation and forms a wider and more spherical shape (sphere-like orbundle-like); (2) for the case of NPs having dipole moment oriented along theOZ axis (as is the case in the absence of added protons or non-saturated hydrogen bonds)—theNPs firstly rotated and oriented along this axis to form the most elongated cylindricalshape (rod-like).