The enhancement of the molecular Raman signal in plasmon-assisted surface-enhanced Raman scattering (SERS) results from electromagnetic and chemical mechanisms, the latter determined to a large extent by the chemical interaction between the molecules and the hosting plasmonic nanoparticles. A precise quantification of the chemical mechanism in SERS based on quantum chemistry calculations is often challenging due to the interplay between the chemical and electromagnetic effects. Based on an atomistic description of the SERS signal, which includes the effect of strong field inhomogeneities, we introduce a comprehensive approach to evaluate the chemical enhancement in SERS, which conveniently removes the electromagnetic contribution inherent to any quantum calculation of the Raman polarization. Our approach uses density functional theory (DFT) and time-dependent DFT to compute the total SERS signal, together with the electromagnetic and chemical enhancement factors. We apply this framework to study the chemical enhancement of biphenyl-4,4'-dithiol embedded between two gold clusters. Although we find that for small clusters the total SERS enhancement is mainly determined by the chemical mechanism, our procedure enables removal of the electromagnetic contribution and isolation of the contribution of the bare chemical effect. This approach can be applied to reproduce and understand Raman line activation and strength in practical and challenging SERS configurations such as in plasmonic nano- and pico-cavities.
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