Universal QM/MM approaches for general nanoscale applications

KS Csizi, M Reiher - Wiley Interdisciplinary Reviews …, 2023 - Wiley Online Library
Quantum mechanics/molecular mechanics (QM/MM) hybrid models allow one to address
chemical phenomena in complex molecular environments. Whereas this modeling approach …

Water in protein hydration and ligand recognition

M Maurer, C Oostenbrink - Journal of Molecular Recognition, 2019 - Wiley Online Library
This review describes selected basics of water in biomolecular recognition. We focus on a
qualitative understanding of the most important physical aspects, how these change in …

Systematic optimization of water models using liquid/vapor surface tension data

Y Qiu, PS Nerenberg, T Head-Gordon… - The Journal of Physical …, 2019 - ACS Publications
In this work, we investigate whether experimental surface tension measurements, which are
less sensitive to quantum and self-polarization corrections, are able to replace the usual …

Deriving a polarizable force field for biomolecular building blocks with minimal empirical calibration

KM Visscher, DP Geerke - The Journal of Physical Chemistry B, 2020 - ACS Publications
Force field parametrization involves a complex set of linked optimization problems, with the
goal of describing complex molecular interactions by using simple classical potential-energy …

Polarizable Embedding with a Transferable H2O Potential Function I: Formulation and Tests on Dimer

EO Jonsson, AO Dohn, H Jonsson - Journal of Chemical Theory …, 2019 - ACS Publications
The incorporation of mutual polarization in multiscale simulations where different regions of
the system are treated at different level of theory is important in studies of, for example …

Transferable Potential Function for Flexible H2O Molecules Based on the Single-Center Multipole Expansion

EO Jónsson, S Rasti, M Galynska… - Journal of Chemical …, 2022 - ACS Publications
A potential function is presented for describing a system of flexible H2O molecules based on
the single-center multipole expansion (SCME) of the electrostatic interaction. The model …

Polarizable Embedding with a Transferable H2O Potential Function II: Application to (H2O)n Clusters and Liquid Water

AO Dohn, EO Jonsson, H Jónsson - Journal of Chemical Theory …, 2019 - ACS Publications
The incorporation of polarization in multiscale quantum-mechanics/molecular-mechanics
(QM/MM) simulations is important for a variety of applications, for example, charge-transfer …

Hybrid molecular dynamics for elucidating cooperativity between halogen bond and water molecules during the interaction of p53-Y220C and the PhiKan5196 …

T Dong, H Peng, X He, X Wang, J Gao - Frontiers in Chemistry, 2020 - frontiersin.org
The cooperativity between hydrogen and halogen bonds plays an important role in rational
drug design. However, mimicking the dynamic cooperation between these bonds is a …

[PDF][PDF] Autonomous Construction of Quantum Hybrid Models for Biochemical Applications

KS Csizi - 2023 - research-collection.ethz.ch
Quantum mechanics/molecular mechanics (QM/MM) hybrid models allow one to address
chemical phenomena in complex molecular environments at the nanometer scale. This is …

[PDF][PDF] Nuclear quantum effects in solid ater: ne insights from computational modeling

S Rasti - 2022 - scholarlypublications …
Solid water, commonly referred to as ice, is ubiquitous throughout the universe as a material
with many unique properties. Ice plays an important role for cloud formation on earth and …