Ligand-binding affinity estimates supported by quantum-mechanical methods

U Ryde, P Soderhjelm - Chemical Reviews, 2016 - ACS Publications
One of the largest challenges of computational chemistry is calculation of accurate free
energies for the binding of a small molecule to a biological macromolecule, which has …

Ab initio characterization of protein molecular dynamics with AI2BMD

T Wang, X He, M Li, Y Li, R Bi, Y Wang, C Cheng… - Nature, 2024 - nature.com
Biomolecular dynamics simulation is a fundamental technology for life sciences research,
and its usefulness depends on its accuracy and efficiency,–. Classical molecular dynamics …

Response properties of embedded molecules through the polarizable embedding model

C Steinmann, P Reinholdt, MS Nørby… - … Journal of Quantum …, 2019 - Wiley Online Library
The polarizable embedding (PE) model is a fragment‐based quantum‐classical approach
aimed at accurate inclusion of environment effects in quantum‐mechanical response …

AIMD-Chig: Exploring the conformational space of a 166-atom protein Chignolin with ab initio molecular dynamics

T Wang, X He, M Li, B Shao, TY Liu - Scientific Data, 2023 - nature.com
Molecular dynamics (MD) simulations have revolutionized the modeling of biomolecular
conformations and provided unprecedented insight into molecular interactions. Due to the …

The strength and directionality of a halogen bond are co-determined by the magnitude and size of the σ-hole

M Kolář, J Hostaš, P Hobza - Physical Chemistry Chemical Physics, 2014 - pubs.rsc.org
The σ-holes of halogen atoms on various aromatic scaffolds were described in terms of their
size and magnitude. The electrostatic potential maps at the CAM-B3LYP-D3 (bj)/def2-QZVP …

Excited states in large molecular systems through polarizable embedding

NH List, JMH Olsen, J Kongsted - Physical Chemistry Chemical …, 2016 - pubs.rsc.org
In this perspective, we provide an overview of recent work within the polarizable embedding
scheme to describe properties of molecules in realistic environments of increasing …

Polarizable density embedding: A solution to the electron spill-out problem in multiscale modeling

P Reinholdt, J Kongsted, JMH Olsen - The Journal of Physical …, 2017 - ACS Publications
We analyze the performance of the polarizable density embedding (PDE) model a new
multiscale computational approach designed for prediction and rationalization of general …

Revisiting artifacts of Kohn–Sham density functionals for biosimulation

SA Slattery, JC Yon, EF Valeev - Journal of Chemical Theory and …, 2024 - ACS Publications
We revisit the problem of unphysical charge density delocalization/fractionalization induced
by the self-interaction error of common approximate Kohn–Sham (KS) density functional …

Can electron transport through a blue-copper azurin be coherent? An ab initio study

C Romero-Muniz, M Ortega, JG Vilhena… - The Journal of …, 2021 - ACS Publications
Multiple experiments on the electron transport through solid-state junctions based on
different proteins have suggested that the dominant transport mechanism is quantum …

A projector-embedding approach for multiscale coupled-cluster calculations applied to citrate synthase

SJ Bennie, MW van der Kamp… - Journal of chemical …, 2016 - ACS Publications
Projector-based embedding has recently emerged as a robust multiscale method for the
calculation of various electronic molecular properties. We present the coupling of projector …