Molecular Dynamics On Oligopeptides To Associate Vibrational Density Of States With Raman Spectra

Raman spectra provides unique information on the conformation, ionization, hydrogen bonding, and hydrophobic interactions of peptide main chains and amino-acid side chains of proteins. However, obtaining Raman spectra through experimentation presents a challenge due to irradiation. During irradiation, the spectrum of the scattered radiation is measured at a definite angle with a suitable spectrometer, causing the intensity of the Raman lines to be one-millionth the intensity of the source. In our study, we develop simple peptide models and perform molecular dynamics simulations to calculate Vibrational Density of States (VDOS), specifically focusing on mid-range frequencies between 600-1800 cm-1. VDOS calculations in the Groningen Machine for Chemical Simulations (GROMACS) molecular dynamics package are presented and compared with Raman spectra generated from experimental measurement. Characteristic peaks of VDOS and Raman spectra are confirmed using Density Functional Theory and then mathematically modelled for correlation. In this study, we present an analytic model for our approximation relating VDOS to Raman spectra. From the uniqueness of Raman spectra, we investigate a mathematical model to predict the Raman spectra of complex protein structures from VDOS, with the objective of developing new computational methods to expedite the measurement of Raman spectra for protein analysis