Some years ago I wrote this post. Now I want to come at it from a different angle.
A closed system spontaneously goes towards the state with maximum multiplicity, W. For a system with N molecules with energies \varepsilon_1, \varepsilon_2, \ldots we therefore want to find the values of N_i that maximises W(N_1, N_2, \ldots).
This is easier to do for \ln W than W, which is fine because W is a maximum when \ln W is a maximum, and this happens when
\frac{N_i}{N}= p_i = \frac{e^{-\beta \varepsilon_i}}{q}
\beta can be found by comparison to experiment. For example, the energy of an ideal monatomic gas with N_A particles is
U^{\mathrm{Trans}} = N_A \langle \varepsilon^{\mathrm{Trans}} \rangle = N_A\sum_i p_i \varepsilon_i = \frac{3N_A}{2\beta} = \tfrac{3}{2}RT \implies \beta = \frac{1}{kT}
where R is determined by measuring the temperature increase due to adding a known amount of energy to the system.
So far we have used \ln W instead of W for convenience, but is there something special about \ln W? Yes, the change in \ln W has can be expressed quite simply
d \ln W = \beta \sum_i \varepsilon_i dN_i = N \beta \sum_i \varepsilon_i dp_i = \frac{dU}{kT}
So change in internal energy U due to a redistribution of molecules among energy levels is equal to the change in \ln W (as opposed to W) multiplied by kT
dU = Td\left( k \ln W \right) = TdS
The final question is whether there is something special about \ln = \log_e as opposed to say \log_a where a \ne e? Well, \log_a W is a maximum when
\frac{N_i}{N}= p_i = \frac{a^{-\beta \varepsilon_i}}{q}
There is an extra term in the derivation but that cancels out in the end. So no change there.
What about \beta? There are two changes. The previous derivation of U^{\mathrm{Trans}} relied on this relation (I'll drop the "Trans" label for the moment)
\varepsilon_i e^{-\beta \varepsilon_i} = - \frac{d }{d \beta} e^{-\beta \varepsilon_i} \implies \langle \varepsilon \rangle = - \frac{1}{q} \frac{dq}{d\beta}
which now becomes
\varepsilon_i a^{-\beta \varepsilon_i} = - \frac{1}{\ln(a)} \frac{d }{d \beta} a^{-\beta \varepsilon_i} \implies \langle \varepsilon \rangle = - \frac{1}{q \ln(a)} \frac{dq}{d\beta}
While q has an extra \ln (a) term, the derivative wrt \beta is still the same and
U^{\mathrm{Trans}} = N_A \langle \varepsilon^{\mathrm{Trans}} \rangle = N_A\sum_i p_i \varepsilon_i = \frac{3N_A}{2 \ln (a) \beta} = \tfrac{3}{2}RT \implies \beta = \frac{1}{\ln (a) kT}
So, S = k \log_e W is special in the sense that the proportionality constant k is the experimentally measured ideal gas constant divided by Avogadro's number. In any other base we have to write either S = k \ln (a) \log_a W where k = R/N_A or S = k^\prime \log_a W where k^\prime = \ln(a)R/N_A
Clearly, S = k \log_e W is the most natural choice, and this is because e is the (only) value of a for which
\frac{d}{dx} a^x = a^x
In fact that is one way to define what e actually is.

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