Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations
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Classical molecular dynamics is more and more often coupled to quantum mechanical based techniques as a statistical tool to sample configurations of molecular systems embedded in complex environments. Nonetheless, the classical potentials describing the mo ...
Quantum-mechanical embedding methods have in recent years gained significant interest and may now be applied to predict a wide range of molecular properties calculated at different levels of theory. To reach a high level of accuracy in embedding methods, b ...
Polarizable quantum mechanical (QM)/molecular mechanics (MM)-embedding methods are currently among the most promising methods for computationally feasible, yet reliable, production calculations of localized excitations and molecular response properties of ...
We derive and validate averaged solvent parameters for embedding potentials to be used in polarizable embedding quantum mechanics/molecular mechanics (QM/MM) molecular property calculations of solutes in organic solvents. The parameters are solvent-specifi ...
We present a new generation of coarse-grained (CG) potentials that account for a simplified electrostatic description of soluble proteins. The treatment of permanent electrostatic dipoles of the backbone and polar side-chains allows to simulate proteins, p ...
This thesis addresses advances in the field of computational Nuclear Magnetic Resonance (NMR) with two specific objectives: 1) developing an approach enabling the direct probing of intramolecular electronic effects on molecular properties; 2) assessing and ...
The overarching objective of this thesis is extending and adapting the set of computational tools available for describing molecular precursors of organic semiconductors. The research presented within develops adhering to three principle goals: (1) provide ...
We investigate the structural properties of liquid water at near ambient conditions using first-principles molecular dynamics simulations based on a semilocal density functional augmented with nonlocal van der Waals interactions. The adopted scheme offers ...
The treatment of dispersion interactions is ubiquitous but computationally demanding for seamless ab initio approaches. A highly popular and simple remedy consists in correcting for the missing interactions a posteriori by adding an attractive energy term ...
Characteristic timescales associated with the function of biomolecules, like proteins, range from femtoseconds up to minutes, whereas their corresponding spatial extent ranges from few ̊A to μm when associating in large macromolecular complexes. Moreover, ...