Tom FRÖMBGEN1, Vahideh ALIZADEH1, Jan BLASIUS1, Leonard DICK1, Luke WYLIE1, Barbara KIRCHNER1
1Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn, Germany
Ionic liquids (IL) have gained enormous importance in chemical research during the last two decades as they are potential candidates for a wide range of applications, e.g. including electrochemistry, catalysis, and carbon dioxide capture. To fully understand the interactions in ILs and the resulting properties, experimental and theoretical insights are required. In the field of computational chemistry, atomistic simulations have become an invaluable tool, as these enable the investigation of structural and dynamic properties of liquid systems. In this work, we summarize our expertise in the field of simulating and analyzing molecular dynamics (MD) trajectories, and present a set of best practices and common pitfalls for analyzing the trajectories of ILs.
As a role model system, we chose the well-known IL [C2C1Im][NTf2]. From the simulation point of view, we will highlight the importance of the choice of force field and discuss size effects, the inclusion of polarizable force fields and charge-scaling. Furthermore, we will show different analysis methods as implemented in our open-source code TRAVIS. This includes static properties such as the radial and spatial distribution functions or cluster analysis. Moreover, we will discuss the analysis of dynamic properties such as diffusion coefficients, hydrogen bond life times, velocity autocorrelation functions and vibrational spectra.