The simulation of complex molecular systems requires vastly different time and length scales to be overcome. Multiscale modeling enables cost-effective investigations based on hierarchical multi-level descriptions, e.g., quantum mechanics/molecular mechanics (QM/MM), while advanced sampling eases the exploration of reaction paths in reasonable computing times. Care has to be taken, however, that the use of such schemes does not result in unphysical results. In this thesis, we study the behaviour of an interesting prototype reaction, proton transfer in water, under different simulation set-ups. The nature of an excess proton in water remains a topic of debate in the literature, with both the Zundel and Eigen ions being proposed as candidate structures. In this work, we initially proceed assuming a Zundel-to-Zundel mechanism, but are ultimately unable to confirm the stability of a Zundel ion within our simulation set-up. Methodologically, the diffusive liquid medium requires the multiscale scheme to be adaptive, i.e., it needs to allow for water molecules entering and leaving the QM zone. The majority of the presented work is thus concerned with the implementation of the so-called adaptive buffered-force QM/MM (AdBF-QM/MM) method, which has previously been shown to reproduce the structure of liquid water and been applied to calculate free energy profiles of proton transfer reactions in water. We use Python’s Atomic Simulation Environment to interface the FHI-aims package for density functional theory (DFT) with the LAMMPS code for molecular dynamics (MD). Taking advantage of the method’s flexibility, several simulations are run to test how the precise set-up influences the reaction. To monitor proton transfer, an energy based reaction coordinate is implemented, which takes solvent effects into account. This requires the parametrization of force fields, which is achieved using Bayesian strategies. Finally, umbrella sampling is used to calculate free energy profiles of the studied reaction. In the AdBF-QM/MM framework, we note the critical role of the QM region, as its size must be sufficient for quantum behaviour to emerge. Furthermore, the buffer size must balance the cost of the extended QM/MM calculations while preventing close interactions between the QM charge density and MM point charges. If the buffer is too small, the proton is attracted to the edge of the QM zone. We also observe the sensitivity of the reaction coordinate being severely exaggerated when the system drifts away from the intended range. Finally, our results suggest the respective stability of the Zundel and Eigen ions to be very sensitive to the precise QM/MM setup.     «

The simulation of complex molecular systems requires vastly different time and length scales to be overcome. Multiscale modeling enables cost-effective investigations based on hierarchical multi-level descriptions, e.g., quantum mechanics/molecular mechanics (QM/MM), while advanced sampling eases the exploration of reaction paths in reasonable computing times. Care has to be taken, however, that the use of such schemes does not result in unphysical results. In this thesis, we study the behavi...     »

The simulation of complex molecular systems requires vastly different time and length scales to be overcome. Multiscale modeling enables cost-effective investigations based on hierarchical multi-level descriptions, e.g., quantum mechanics/molecular mechanics (QM/MM), while advanced sampling eases the exploration of reaction paths in reasonable computing times. Care has to be taken, however, that the use of such schemes does not result in unphysical results. In this thesis, we study the behaviour of an interesting prototype reaction, proton transfer in water, under different simulation set-ups. The nature of an excess proton in water remains a topic of debate in the literature, with both the Zundel and Eigen ions being proposed as candidate structures. In this work, we initially proceed assuming a Zundel-to-Zundel mechanism, but are ultimately unable to confirm the stability of a Zundel ion within our simulation set-up. Methodologically, the diffusive liquid medium requires the multiscale scheme to be adaptive, i.e., it needs to allow for water molecules entering and leaving the QM zone. The majority of the presented work is thus concerned with the implementation of the so-called adaptive buffered-force QM/MM (AdBF-QM/MM) method, which has previously been shown to reproduce the structure of liquid water and been applied to calculate free energy profiles of proton transfer reactions in water. We use Python’s Atomic Simulation Environment to interface the FHI-aims package for density functional theory (DFT) with the LAMMPS code for molecular dynamics (MD). Taking advantage of the method’s flexibility, several simulations are run to test how the precise set-up influences the reaction. To monitor proton transfer, an energy based reaction coordinate is implemented, which takes solvent effects into account. This requires the parametrization of force fields, which is achieved using Bayesian strategies. Finally, umbrella sampling is used to calculate free energy profiles of the studied reaction. In the AdBF-QM/MM framework, we note the critical role of the QM region, as its size must be sufficient for quantum behaviour to emerge. Furthermore, the buffer size must balance the cost of the extended QM/MM calculations while preventing close interactions between the QM charge density and MM point charges. If the buffer is too small, the proton is attracted to the edge of the QM zone. We also observe the sensitivity of the reaction coordinate being severely exaggerated when the system drifts away from the intended range. Finally, our results suggest the respective stability of the Zundel and Eigen ions to be very sensitive to the precise QM/MM setup.     «

The simulation of complex molecular systems requires vastly different time and length scales to be overcome. Multiscale modeling enables cost-effective investigations based on hierarchical multi-level descriptions, e.g., quantum mechanics/molecular mechanics (QM/MM), while advanced sampling eases the exploration of reaction paths in reasonable computing times. Care has to be taken, however, that the use of such schemes does not result in unphysical results. In this thesis, we study the behavi...     »