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.
With the aid of molecular dynamics simulations, we study the structure and dynamics of different ionic liquid systems, with focus on hydrogen bond, ion pair and ion cage formation. To do so, we report radial distribution functions, their number integrals, and various time-correlation functions, from which we extract well-defined lifetimes by means of the reactive flux formalism. We explore the influence of polarizable force fields vs. non-polarizable ones with downscaled charges (±0.8) for the example of 1-butyl-3-methylimidazolium bromide. Furthermore, we use 1-butyl-3-methylimidazolium trifluoromethanesulfonate to investigate the impact of temperature and mixing with water as well as with the chloride ionic liquid. Smaller coordination numbers, larger distances, and tremendously accelerated dynamics are observed when the polarizable force field is applied. The same trends are found with increasing temperature. Adding water decreases the ion-ion coordination numbers whereas the water-ion and water-water coordination is enhanced. A domain analysis reveals that the nonpolar parts of the ions are dispersed and when more water is added the water clusters increase in size. The dynamics accelerate in general upon addition of water. In the ionic liquid mixture, the coordination number around the cation changes between the two anions, but the number integrals of the cation around the anions remain constant and the dynamics slow down with increasing content of the chloride ionic liquid.
Azolium cations are widely employed in organocatalysis to catalyse highly valuable synthetic processes in the presence of a base. These reactions are called "N-heterocyclic carbene catalysis", based on the assumption that they are initiated by the formation of a free carbene through deprotonation, which can then react with the substrates and thereby affect their reactivity to obtain the desired products. However, we herein provide evidence that an electrophilic aromatic substitution mechanism is energetically more favourable, in which the azolium cation reacts directly with the substrate, avoiding the formation of the free carbene in solution.
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