Of course the surface charge cannot be calculated from the formula of the neutral compound!
For hydroxyapatite I found zeta potential values in literature around -19 mV. this however changes with pH as phosphoric acid is a tribasic acid which will be protonated in acidic media.
the iron oxide or whatever the magnetic nanoparticles are will not change much, their surface charge will probably also be negative.
HAp has the brief formula as Ca10(PO4)6(OH)2, where you can observe that 10*2-3*6-2*2=-2. So, it should be negative without any magnetic cationic particles. If the cationic particles are present, then their composition should be considered for calculation for net charge of the overall unit.
"10*2-3*6-2*2=-2" - what did you count? Charge? Ca(2+), PO4(3-), OH(1-), so 10*(+2)+6*(-3)+2*(-1)=0.
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