Theoretical Methods for Vibrational Spectroscopy and Collision Induced Dissociation in the Gas Phase

Abstract

In this chapter we review recent advances in theoretical methods to understand and rationalize anharmonic vibrational spectroscopy (IR-MPD and IR-PD) and collision induced dissociations (CID) in the gas phase. We focused our attention on the application of molecular dynamics-based methods. DFT-based molecular dynamics was shown to be able to reproduce InfraRed Multi-Photon Dissociation (IR-MPD) and InfraRed Pre-Dissociation (IR-PD) action spectroscopy experiments, and help assign the vibrational bands, taking into account finite temperature, conformational dynamics, and various anharmonicities. Crucial examples of dynamical vibrational spectroscopy are given on the protonated Ala n H(+) series (related to IR-MPD in the 800-4,000 cm(-1) domain), ionic clusters (related to IR-PD in the 3,000-4,000 cm(-1) region), and neutral peptides (related to IR-MPD in the far-IR). We give examples from simple (e.g., cationized urea) to more complex (e.g., peptides and carbohydrates) molecular systems where molecular dynamics was particularly suited to understanding CID experiments.

Molecular dynamics simulation of the electron ionization mass spectrum of tabun

“…However, when employing static theoretical methods, some essential aspects of the fragmentation dynamics are ignored. Chemical dynamics simulations properly address these aspects, 14–16 even for molecules as large as peptides 17, 18 . This powerful and relatively novel approach named “theoretical MS” was pioneered by Hase and coworkers for modeling mass spectrometric behavior 19–21 .…”

Raman Optical Activity Spectra from Density Functional Perturbation Theory and Density-Functional-Theory-Based Molecular Dynamics

“…It is worth mentioning that it is in general difficult in the calculation of gas-phase spectra from DFT-based MD to fulfill the equipartition theorem, which leads to deviations in the band intensities. 48,50,105 Furthermore, DFT-based MD simulations at room temperature may be worth to be carried out as well as a more detailed study about the basis set and density functional dependence of the ROA DFT-based MD spectra in order to facilitate the comparison to experimental data. For condensed phase systems, taking into account periodic boundary conditions in the ROA calculations will be vital as well.…”

“…11 An alternative way for the calculation of vibrational spectra is based on DFT-based molecular dynamics (MD) where the conformational phase space, hydrogen-bonding dynamics, and other local geometry arrangements can be explored at ambient conditions, taking into account realistic thermodynamic conditions as employed in experiment. 48 Vibrational spectra can be obtained from DFT-based MD via Fourier transformation of certain time correlation functions. This ansatz has the advantage that band shapes are directly obtained from the calculation and no artificial broadening has to be applied.…”

IR Spectroscopic Techniques to Study Isolated Biomolecules

“…In the far-IR spectral range, such a comparison between experiment and theory is often complicated by the generally more substantial anharmonicity of the vibrations, thereby limiting the use of this range of the IR spectrum for conformational elucidation [97]. Recent developments showed that Born-Oppenheimer Molecular Dynamics (BOMD) techniques as presented in [98] are a promising tool for the detailed structural characterization of jet-cooled peptides [99]. BOMD simulations naturally include the effects of anharmonic vibrational potentials [100] and have been applied successfully to reveal the far-IR signatures of specific secondary motifs and hydrogen-bond stretching vibrations in capped peptides [99].…”