International audienc

A persistent challenge in using the metadynamics method is deciding which degrees of freedom, or collective variables, should be biased because these selections are not obvious and require intuition about the system being studied. There are, however, collective variables, which can be constructed with only basic knowledge about the system studied, that provide an opportunity to alleviate this issue. We simulated two different reacting systems where two types of such collective variables (SPRINT coordinates and the collective variable-driven hyperdynamics method) were biased following the infrequent metadynamics method in order to recover the rates of reactions. We demonstrate that both generic collective variables are capable of reproducing the reaction rates of both systems and can enhance the efficiency of the simulation when compared to typical collective variables.

Estimating the transition rates and selectivity of multi-pathway systems with molecular dynamics simulations is expensive and often requires arduous sampling of many individual pathways. Developing a way to efficiently sample and characterize multi-pathway systems creates an opportunity to apply these tools to study systems that, previously, would have had a prohibitive computational cost. We present an approach that places quartic boundaries at the saddle points to isolate individual pathways without changing their observed rates, reducing the required number of events sampled and estimated rate uncertainty. In addition to rates, the selectivity between pathways is also accurately predicted as well. To further reduce the computational cost of the analysis, we have paired this approach with the infrequent metadynamics method. The method is demonstrated on model systems and stiffened alanine dipeptide. Furthermore, we present an appropriate method for recovering the energy barriers of specific transition paths by taking the slope of an Arrhenius plot generated from the infrequent metadynamics results at various temperatures. We also compare this method against another previously published literature to demonstrate its superior performance. In the future, these methods can be used in a variety of contexts where competing escape pathways with different barriers are relevant.

We investigate thermodynamic properties of small water clusters adsorbed on polycyclic aromatic hydrocarbons (PAHs), which are relevant systems in the context of astrophysical and atmospheric chemistry. We present heat capacity curves computed from parallel-tempering molecular dynamics and Monte Carlo simulations that were performed using the self-consistent-charge density-functional based tight-binding method. These curves are characteristic of the phase changes occurring in the aggregates and provide useful information on the evolution of the interaction between the water molecules and the PAHs as a function of temperature. After benchmarking our approach on the water hexamer and octamer in the gas phase, we present some results for these same clusters adsorbed on coronene and circumcoronene. When compared to the curves obtained for the isolated water clusters, the phase change temperature significantly decreases for the (H2O)8-PAH clusters whereas it depends on the nature of the PAH in the case of the hexamer. We analyse these differences as connected to the relative energies of the optimized characteristic isomers and to their dynamical behavior. We also evidence the population changes of the various cluster isomers as a function of temperature.