In situ gap-mode Raman spectra were acquired in an electrochemical environment on a single-crystal gold electrode employing a Au(100)|4,4'-biphenyldithiol (BPDT)|Au-NP(55 nm) sandwich assembly. This geometry enabled an investigation of the influence of an applied electrochemical gate field on the conformational changes in nanojunctions, such as the torsion angle (phi) of molecules. A linear correlation between the intensity ratio I-C=C/ICring-S and cos(2) phi in 4,4'-BPDT-type molecular junctions was established and subsequently utilized to estimate the potential dependence of the torsion angle of the "flexible" molecule M1 at different potentials. The latter decreases as the potential (charge) becomes more negative, resulting in better pi-pi coupling, which correlates with enhanced junction conductance. The demonstrated spectroelectrochemical strategy and the direct correlation of the spectroscopic results with (single) molecular conductance studies may guide the selection and elucidation of functional molecules for potential applications in novel nanodevices.