Recently the oxygen-reconstructed tantalum surface Ta(001)-p(3$times$3)-O has experienced considerable attention due its use as a potential platform for Majorana physics in adatom chains. Experimental studies using scanning tunneling microscopy and spectroscopy found rich atomic and electronic structures already for the clean Ta(001)-O surface, which we combine here with $ab~initio$ methods. We discover two metastable superstructures at the root of the different topographic patterns, discuss its emergence during annealing, and identify the electronic properties. The latter is determined as the sole origin for the contrast reversal seen at positive bias. The observed effects are essentially connected to the two distinct oxygen states appearing on the surface in different geometries. The second superstructure was found in simulations by introducing oxygen vacancies, what was also observed in tantalum pentoxide systems. Additionally we study the charge distribution on the oxidized surface and underline its importance for the adsorption process of polarizable atoms and molecules.
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