Atomic force microscopy (AFM) and its many applications have opened up venues for probing the world at the nanometer scale. We have pursued the combination of non-ideal AFM (room temperature, open air or in solution) with molecular dynamics simulations to probe systems experimentally and describe their behavior on the atomic scale. We focused on the effect of electric fields both internal and external to nitrile probes. First, the influence of surface topography and plasmon resonances on Raman enhancements was explored using the Stark shift of a nitrile group. We observed that cyanide co-deposited with gold onto electrodes displays an overall DC field effect within large plasmonic fields. This DC field gives rise to surprisingly large vibrational Stark shifts, as high as 129 cm-1 with a gap mode tip enhanced Raman scattering configuration. Second, we explored electric field effects on a liquid crystal, 4-Cyano-4'-pentylbiphenyl, which has a known phase transition in response to external electric fields. Simulations of this molecule indicate an isotropic to nematic phase change with the application of an external field. These simulations currently predict spectral shifts in the IR and Raman spectra of the molecule. The simulations indicate these spectral shifts are due to local steric effects rather than external fields. These predictions as well as experimental Stark shifts of the nitrile group can then serve as local electric field reporters.