with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. details, including instrument design factors.Thanks are due to Robert Swinson for providing much of the new artwork, and to Scott Lowell for his keen-eyed proofreading. Two of us (M.A.T and M.T.) express our sincerest appreciation to our spouses and families for their patient endurance during the preparation of this book.

We review several methods for the calculation of vibrational spectra from ab initio molecular dynamics (AIMD) simulations and we present a new implementation in the trajectory analyzer TRAVIS. In particular, we show mass-weighted power spectra, infrared spectra, and Raman spectra with corresponding depolarization ratios, which are based on time-correlation functions of velocities, dipole moments, and polarizabilities, respectively. Using the four organic molecules methanol, acetone, nitromethane, and pinacol as test systems, we compare the spectra from AIMD simulations of the isolated molecules in gas phase to static calculations relying on the harmonic approximation and to experimental spectra recorded in a nonpolar solvent. The AIMD approach turns out to give superior results when anharmonicity effects are of particular importance. Using the example of methanol, we demonstrate the application to bulk phase systems, which are not directly accessible by static calculations, but for which the AIMD spectra also provide a very good approximation to experimental data. Finally, we investigate the influence of simulation time and temperature in the AIMD on the resulting spectra.

TRAVIS (“Trajectory Analyzer and Visualizer”) is a program package for post-processing and analyzing trajectories from molecular dynamics and Monte Carlo simulations, mostly focused on molecular condensed phase systems. It is an open source free software licensed under the GNU GPL, is platform independent, and does not require any external libraries. Nine years after the original publication of TRAVIS, we highlight some of the recent new functions and features in this article. At the same time, we shortly present some of the underlying algorithms in TRAVIS, which contribute to make trajectory analysis more efficient. Some modern visualization techniques such as Sankey diagrams are also demonstrated. Many analysis functions are implemented, covering structural analyses, dynamical analyses, and functions for predicting vibrational spectra from molecular dynamics simulations. While some of the analyses are known since several decades, others are very recent. For example, TRAVIS has been used to compute the first ab initio predictions in the literature of bulk phase vibrational circular dichroism spectra, bulk phase Raman optical activity spectra, and bulk phase resonance Raman spectra within the last few years.

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We present the Voronoi tessellation of electron density data to obtain molecular dipole moments in bulk phase ab initio molecular dynamics simulations for the calculation of vibrational spectra. Opposed to the established scheme of maximally localized Wannier functions, this approach does not rely on computationally demanding localization procedures. Nevertheless, we show at the examples of methanol, benzene, and phenol that it provides infrared and Raman spectra of similar quality and is even superior in specific cases like the Raman spectra of benzene and phenol. We have also applied the Voronoi method to a mixture of the ionic liquid 1-ethyl-3-methylimidazolium acetate with water, and show that it is advantageous in systems with significant charge transfer.