Hydroxyapatite (HAP, Ca10(PO4)6(OH)2) was studied from first principles approaches using the local density approximation (LDA) method in combination with various quantum-chemical (QM) and molecular mechanical (MM) methods from HypemChem 7.5/8.0. The data then were used for studies of HAP structures, and the interactions of HAP clusters with ionic species such as citrates. Computed data show that HAP can co-exist in different phases at room temperature, as both hexagonal and monoclinic. Special interest is connected with the ordered monoclinic structure, which could reveal piezoelectric properties. Obtained data on HAP interactions with citrates show the formation of differing HAP nanostructure forms, depending upon the concentration of citrate present