The results of computational modeling for Hydroxyapatite (HAP) nanostructures and surface interactions properties are presented in this work. HAP were studied from first principles approaches using Local Density Approximation (LDA) method in combination with various quantum-chemical (QM), including Density Functional Theory (DFT) methods, and molecular mechanical (MM, BIO CHARM) methods from HypemChem 7.5/8.0 package. Obtained data then were used for studies of interactions of HAP clusters with various species (citrates, carbon nanotubes, living cells - osteoblasts, etc.).