[HTML][HTML] The ONIOM method and its applications

LW Chung, WMC Sameera, R Ramozzi… - Chemical …, 2015 - ACS Publications
The fields of theoretical and computational chemistry have come a long way since their
inception in the mid-20th century. Fifty years ago, only rudimentary approximations for very …

Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings

D Loco, L Lagardere, GA Cisneros, G Scalmani… - Chemical …, 2019 - pubs.rsc.org
In this work, we present a general route to hybrid Quantum Mechanics/Molecular Mechanics
(QM/MM) Molecular Dynamics for complex systems using a polarizable embedding. We …

Avoiding electron spill-out in QM/MM calculations on excited states with simple pseudopotentials

A Marefat Khah, P Reinholdt, JMH Olsen… - Journal of Chemical …, 2020 - ACS Publications
QM/MM calculations of electronic excitations with diffuse basis sets often have large errors
due to spill-out of electrons from the quantum subsystem. The Pauli repulsion of the …

Impact of an Ionic Liquid Solution on Horseradish Peroxidase Activity

S Chatterjee, J Nochebuena… - Journal of the American …, 2024 - ACS Publications
Horseradish peroxidase (HRP) is an enzyme that oxidizes pollutants from wastewater. A
previous report indicated that peroxidases can have an enhancement in initial enzymatic …

Analytic Gradients for the Electrostatic Embedding QM/MM Model in Periodic Boundary Conditions Using Particle-Mesh Ewald Sums and Electrostatic Potential Fitted …

S Bonfrate, N Ferré, M Huix-Rotllant - Journal of Chemical Theory …, 2024 - ACS Publications
Long-range electrostatic effects are fundamental for describing chemical reactivity in the
condensed phase. Here, we present the methodology of an efficient quantum …

Ion Mobility–Mass Spectrometry of Nucleic Acids

D Fabris - 2021 - books.rsc.org
The word “sequence” is perhaps the most likely to be named next to “nucleic acids” in any
word-association game related to science. However, there are many examples of natural …

Analytic gradients for the electrostatic embedding QM/MM in periodic boundary conditions using particle-mesh Ewald sums and electrostatic potential fitted charge …

S Bonfrate, N Ferré, M Huix-Rotllant - 2024 - chemrxiv.org
Long-range electrostatic effects are fundamental for describing chemical reactivity in the
condensed phase. Here, we present the methodology of an efficient quantum …

CCS for Modelling 3D Structures

EG Marklund, MT Degiacomi, A Politis, M Landreh - 2021 - books.rsc.org
Ion mobility–mass spectrometry (IM-MS) is fundamentally a separation technique that can be
used in the same manner as solution-phase chromatography (LC), with numerous analytical …

Divalent pseudoatoms for modeling Si (100) surfaces

BC Gamoke, U Das, HP Hratchian… - The Journal of Chemical …, 2013 - pubs.aip.org
An accurate first-principles treatment of complex systems, such as surfaces, continues to be
a major challenge in computational chemistry. A popular approach to treat such systems is …

The development and validation of a pseudoatoms approach for combined quantum mechanics and molecular mechanics calculations of polypeptide

Z Zhang, L Xu, G Wang, C Shao, L Jiang - Computational and Theoretical …, 2014 - Elsevier
A pseudoatoms approach was proposed for combined quantum mechanics and molecular
mechanics (QM/MM) calculations of polypeptide to ensure that each amino acid residue was …