We report orientation angles for the alkyl chain, amide group, and oligo(ethylene glycol) (OEG) portion within self-assembled monolayers (SAMs) of OEG-terminated and amide containing alkanethiolates which, depending on the OEG length and substrate temperature, display unique conformations - all-trans or helical. Optimized geometries of the molecular constituents, characteristic vibration frequencies and transition dipole moments are obtained by using DFT methods with gradient corrections. These ab initio data are subsequently used to simulate infrared reflection-absorption (RA) spectra associated with different conformations and orientations. The obtained results have generated a deeper knowledge of the internal SAM structure, which is crucial for understanding phase and folding characteristics, interaction with water and ultimately the protein repellent properties of OEG-containing SAMs.