FULL ANISOTROPIC MODEL FOR SIMULATING THE INFRARED REFLECTION ABSORPTION SPECTRA (IRRAS) OF SELF-ASSEMBLED MONOLAYERS (SAMS) FROM ALL-ATOM MOLECULAR DYNAMICS SIMULATIONS

Abstract

It is important to understand the internal molecular structure of molecular monolayers because that determines the physical and chemical properties of their surface. Infrared spectroscopy is a powerful method to measure the molecular orientation, but to fully harness the information, the spectra need to be compared to structural models. A full anisotropic model is established for simulating the infrared reflection absorption spectra (IRRAS) of self-assembled monolayers (SAMs) based on the methods of Allara and Parikh. The primary focus is to bridge the molecular structures from molecular dynamics simulations with the experimental spectra. The methylene and methyl group orientation are used in the simulations to calculate the complex refractive index tensors in the mid infrared (MIR) using experimental data from a reference phase. The Kramers-Kronig relation is used to calculate the frequency dependent refractive index tensor in the MIR from the absorption of each mode. The high frequency part of the refractive index tensor is calculated from atomic bond vectors in the simulation based on the bond polarizabilities. Afterwards, the IRRAS spectra can be computed using the 4×4 transfer matrix method. Finally, the IRRAS spectra of MD simulation results based on proposed SAM structures are compared.