Final answer:
To prevent the formation of covalent bonds between sodium and carboxylate oxygens in computational simulations, ensure the software models them as ions with ionic interactions, not as covalently bonded, and check that the input file is set up correctly with the proper charges and constraints.
Step-by-step explanation:
When conducting computational chemistry simulations using B3LYP/6-31g to determine the Gibbs free energy of solvation for a sodium salt of an alkylcarboxylate, the appearance of covalent bonds between sodium and carboxylate oxygens in the minimized structure indicates an issue with the way the simulation is modeling the ionic interactions. To prevent the formation of these unrealistic covalent bonds, ensure that the simulation software recognizes sodium as a cation and the carboxylate as an anion, and that their interactions are modeled as ionic rather than covalent.
This can typically be achieved through correct setup in the initial input file, specifying charges and potentially using constraints or restraints to maintain the ionic character of the sodium alkylcarboxylate complex. Additionally, reviewing the pseudopotentials or effective core potentials for sodium may help in appropriately representing the cation without the emergence of unwanted covalent interactions.