Lipid membranes are composed of a diverse set of phospholipids, proteins, and sterols. These molecules organize themselves into heterogeneous structures adapted for numerous biological functions. For example, mammalian cell membranes contain a large fraction of cholesterol which changes the membrane’s mechanical properties. Many techniques, such as fluorescence microscopy, NMR spectroscopy, and x-ray scattering, and molecular dynamics, have probed cell membranes to understand how their structure relates to their functions. Raman spectroscopy is another promising technique used to study membrane models. Raman-scattered light can be studied directly or enhanced by nanometallic structures to obtain surface-enhanced Raman spectra (SERS). Raman spectra relate to the vibrational energy levels of the membrane molecules and contain information about molecular structure. However, interpreting spectra is limited by the difficulty of assigning spectral features to molecular features. This is particularly true for larger molecules of biological relevance such as phospholipids and sterols. Our group has had success in using time-dependent density functional theory (TDDFT) to produce theoretical Raman spectra. These TDDFT spectra have been used in conjunction with Raman and SERS experimental spectra to find the orientation of bilayer-forming surfactants DTAB and CTAB. Similarly, our group obtained the orientation in a phospholipid bilayer of the membrane dyes laurdan, prodan, and di-4-ANNEPS, the amino acid tryptophan, and the sterol cholesterol. In this work, we will show molecular orientation result for the common phospholipid DOPC in a bilayer which we find to agree with other experimental techniques with an average chain tilt of 34°. TDDFT also allows us to calculate experimental spectra for different conformations of the same molecule. The resulting spectra have small but revealing differences. Comparing these TDDFT spectra with experimental Raman spectra, we can select the conformations likely present in the sample under study. We applied this analysis to anthraquinones, a large class of biomolecules. We identified common “fingerprint” modes of dihydroxyanthraquinones, and our conformational analysis agreed with crystal structure studies. We applied a similar analysis to cholesterol comparing the spectra of 10 conformers with powder and DOPC vesicle measurements. We found that cholesterol adopts a more space-filling set of conformations in vesicles than in powder.