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The contrast between Pauling electronegativity and Mulliken electronegativity becomes clearer by following the measurements into the formulas. A Pauling bond-energy excess compares three compatible bond-dissociation energies; Mulliken electronegativity takes the arithmetic mean of an ionization energy and an electron affinity. The former asks how much stronger an unlike-atom chemical bond is than a stipulated baseline; the latter combines two different isolated-species energy gaps.

Actual readouts precede those model choices. In the nitrogen dissociation threshold from fragment images, fitted squared image radii versus assigned excitation energies reveal a threshold after accounting for the product quantum states. In the chlorine photodetachment threshold experiment, mass-selected anions overlap a tunable laser, and neutral-atom counts reveal the onset of Electron detachment. Opposite laser directions control the Doppler shift. That second threshold supplies an electron affinity, not an electronegativity; the Mulliken scale still needs an independent ionization energy.^[ref][ref]

For an original arithmetic comparison, stipulate isolated-species $I=(8,7,6)\mathrm{eV}$ and positive attachment-release $A_{\mathrm{ea}}=(0.5,3,3)\mathrm{eV}$ for fictitious species $A,B,C$. Their Mulliken electronegativities are $(4.25,5,4.5)\mathrm{eV}$. The largest ionization energy belongs to $A$, while the largest Mulliken electronegativity belongs to $B$: accepting an Electron matters as well as retaining one. Using signed attachment energies $(-0.5,-3,-3)\mathrm{eV}$ in $(I-\Delta E_{\mathrm{attach}})/2$ gives exactly the same results.

Independently stipulate $D_{RR}=300$ and $D_{XX}=(200,300,450)\mathrm{kJ}\mathrm{mo}{\mathrm{l}}^{-1}$ for $X=A,B,C$, with unlike-atom valuesThus $D_{RX}=(274.12125,396.485,592.09125)\mathrm{kJ}\mathrm{mo}{\mathrm{l}}^{-1}$, and the Pauling scale differences from $R$ are $(0.5,1,1.5)$. If all three fictitious species are placed above $R$ on that scale, their ordering is $A<B<C$, whereas the stipulated Mulliken scale gives $A<C<B$. The bond-dissociation energies and isolated-species energies were invented independently: this demonstrates what the formulas do, not a measured disagreement for actual chemical elements. A unit conversion cannot force these two input models to agree.

A Pauling bond-energy excess subtracts a chosen like-atom baseline from the unlike-atom bond-dissociation energy. For an unequal-input arithmetic example, stipulate $D_{AA}=200$, $D_{BB}=450$ and $D_{AB}=421.485\mathrm{kJ}\mathrm{mo}{\mathrm{l}}^{-1}$, all with one dissociation convention. The arithmetic mean baseline and excess areThe arithmetic-baseline Pauling scale model therefore gives $|{\chi }_{\mathrm{P}}(A)-{\chi }_{\mathrm{P}}(B)|=\sqrt{96.485/96.485}=1$. The bond-dissociation energy $421.485$ is not itself the excess: subtracting the baseline is essential. All three numbers are stipulated, not experimental values for named chemical elements.

Changing the baseline changes the model. For the same stipulated inputs, a geometric mean baseline would be $\sqrt{200\times 450}=300\mathrm{kJ}\mathrm{mo}{\mathrm{l}}^{-1}$, yielding an excess of $121.485\mathrm{kJ}\mathrm{mo}{\mathrm{l}}^{-1}$ and a difference of approximately $1.122$. It is a different construction, even though both start from the same bond-dissociation energies. State which baseline is used before comparing electronegativity differences.

The arithmetic-baseline Pauling scale also has a useful inverse: a difference of $0.5$ corresponds to an excess of $24.12125\mathrm{kJ}\mathrm{mo}{\mathrm{l}}^{-1}$, and a difference of $2$ corresponds to $385.94\mathrm{kJ}\mathrm{mo}{\mathrm{l}}^{-1}$. Doubling the electronegativity difference quadruples the modeled excess. Interchanging the endpoint labels changes neither quantity; the square root alone cannot choose the direction of bond polarization.

In The Nature of the Chemical Bond. IV. The Energy of Single Bonds and the Relative Electronegativity of Atoms (printed pp. 3576–3578, Table II and equation (1)), Linus Pauling organized excess energies for chemical bonds into an approximately additive map of their square roots. He also identified a limitation: his H–F map separation of $2$ predicted an excess of $4.00\mathrm{eV}$, exceeding his table's value by $1.23\mathrm{eV}$. Those are historical values and a historical model discrepancy, not modern recommended inputs.^[ref]