Monitoring transient events in infrared spectra using local mode analysis

Abstract

Time-resolved Fourier transformed infrared (FTIR) spectroscopy of chemical reactions is highly sensitive to minimal spatiotemporal changes. Structural features are decoded and represented in a comprehensible manner by combining FTIR spectroscopy with biomolecular simulations. Local mode analysis (LMA) is a tool to connect molecular motion based on a quantum mechanics simulation with infrared (IR) spectral features and vice versa. Here, we present the python-based software tool of LMA and demonstrate the novel feature of LMA to extract transient structural details and identify the related IR spectra at the case example of malonaldehyde (MA). Deuterated MA exists in two almost equally populated tautomeric states separated by a low barrier for proton transfer so IR spectra represent a mixture of both states. By state-dependent LMA, we obtain pure spectra for each tautomeric state occurring within the quantum mechanics trajectory. By time-resolved LMA, we obtain a clear view of the transition between states in the spectrum. Through local mode decomposition and the band-pass filter, marker bands for each state are identified. Thus, LMA is beneficial to analyze the experimental spectra based on a mixture of states by determining the individual contributions to the spectrum and motion of each state.

Non-hessian method for normal coordinates calculation

“…Seismologists were able to solve lots of seismological problems by developing a theoretical framework for the calculation of theoretical seismograms based on NMA [3,4]. Biochemists and biologists could understand dynamic global characters of macromolecules, which play an essential role in explaining their functions [5][6][7][8]. Chemists might be familiar with the determination of infrared (IR) and Raman peaks obtained from spectroscopy instruments by using NMA [9][10][11].…”