The lowest-energy structure, distribution of isomers, and their molecular properties depend significantly on the geometry and temperature. The total energy computations under DFT methodology are typically carried out at zero temperature; thereby, entropic contributions to total energy are neglected, even though functional materials work at finite temperature. In the present study, the probability of occurrence of one particular Be$_4$B$_8$ isomer at temperature T is estimated within the framework of quantum statistical mechanics and nanothermodynamics. To locate a list of all possible low-energy chiral and achiral structures, an exhaustive and efficient exploration of the potential/free energy surface is done by employing a multilevel multistep global genetic algorithm search coupled to DFT. Moreover, we discuss the energetic ordering of structures computed at the DFT level against single-point energy calculations at the CCSD(T) level of theory. The computed VCD/IR spectrum of each isomer is multiplied by their corresponding Boltzmann weight at temperature T; then, they are summed together to produce a final Boltzmann weighted spectrum. Additionally, we present chemical bonding analysis using the Adaptive Natural Density Partitioning method in the chiral putative global minimum. The transition state structures and the enantiomer-enantiomer and enantiomer-achiral activation energies as a function of temperature, evidence that a change from an endergonic to an exergonic type of reaction occurs at a temperature of 739 K.