Picking the lock of coordination cage catalysis

TK Piskorz, V Martí-Centelles, RL Spicer, F Duarte… - Chemical …, 2023 - pubs.rsc.org
The design principles of metallo-organic assembly reactions have facilitated access to
hundreds of coordination cages of varying size and shape. Many of these assemblies …

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 …

Low-temperature plasma for biology, hygiene, and medicine: Perspective and roadmap

M Laroussi, S Bekeschus, M Keidar… - … on Radiation and …, 2021 - ieeexplore.ieee.org
Plasma, the fourth and most pervasive state of matter in the visible universe, is a fascinating
medium that is connected to the beginning of our universe itself. Man-made plasmas are at …

Nanoscale chemical reaction exploration with a quantum magnifying glass

KS Csizi, M Steiner, M Reiher - Nature Communications, 2024 - nature.com
Nanoscopic systems exhibit diverse molecular substructures by which they facilitate specific
functions. Theoretical models of them, which aim at describing, understanding, and …

Strategies for the construction of machine-learning potentials for accurate and efficient atomic-scale simulations

AM Miksch, T Morawietz, J Kästner… - Machine Learning …, 2021 - iopscience.iop.org
Recent advances in machine-learning interatomic potentials have enabled the efficient
modeling of complex atomistic systems with an accuracy that is comparable to that of …

CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

S Feng, S Park, YK Choi, W Im - Journal of chemical theory and …, 2023 - ACS Publications
Molecular dynamics simulations of membranes and membrane proteins serve as
computational microscopes, revealing coordinated events at the membrane interface. As G …

Perspectives on the Role of Enzymatic Biocatalysis for the Degradation of Plastic PET

RP Magalhães, JM Cunha, SF Sousa - International Journal of Molecular …, 2021 - mdpi.com
Plastics are highly durable and widely used materials. Current methodologies of plastic
degradation, elimination, and recycling are flawed. In recent years, biodegradation (the …

H-Bonding Networks Dictate the Molecular Mechanism of H2O2 Activation by P450

X Zhang, Y Jiang, Q Chen, S Dong, Y Feng… - ACS …, 2021 - ACS Publications
Understanding the molecular basis for controlled H2O2 activation is of fundamental
importance for peroxide-driven catalysis by metalloenzymes. In addition to O2 activation in …

Systematic QM region construction in QM/MM calculations based on uncertainty quantification

F Brandt, CR Jacob - Journal of Chemical Theory and …, 2022 - ACS Publications
While QM/MM studies of enzymatic reactions are widely used in computational chemistry,
the results of such studies are subject to numerous sources of uncertainty, and the effect of …

Computer-aided understanding and engineering of enzymatic selectivity

L Wu, L Qin, Y Nie, Y Xu, YL Zhao - Biotechnology Advances, 2022 - Elsevier
Abstract Enzymes offering chemo-, regio-, and stereoselectivity enable the asymmetric
synthesis of high-value chiral molecules. Unfortunately, the drawback that naturally …