I have designed a molecule using hydrocarbons A and B. I am getting the formation energy slightly positive (~0.04 eV). As per my experience, any positive formation energy means that the designed molecule will be not stable. Is there any way to synthesize a molecule for which the theoretical formation energy was predicted to be positive?
The theoretical formation energy is a little ambiguous here, depending on the way you calculate it. Is it a 0 K calculation (for example using DFT)? or have you already accounted for the entropic effects?
If it is a 0 K calculation then it is indeed difficult to synthesize this particular compound. However, it is not impossible since you are still taking into account only the thermodynamics of the system rather than the kinetics. So you have to figure out some kinetic parameters to lock in your metastable configurations. This can be done by quick annealing or changing your precursors.
However, if you are already accounting for entropy in your calculations. You can go check through lower temperatures if your formation energy becomes negative.
Furthermore, formation energies are usually calculated with reference to a certain precursor. So do check if the formation energies are properly calculated or consider changing the precursors.