Ligand-binding affinity estimates supported by quantum-mechanical methods
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 …
energies for the binding of a small molecule to a biological macromolecule, which has …
Ab initio characterization of protein molecular dynamics with AI2BMD
Biomolecular dynamics simulation is a fundamental technology for life sciences research,
and its usefulness depends on its accuracy and efficiency,–. Classical molecular dynamics …
and its usefulness depends on its accuracy and efficiency,–. Classical molecular dynamics …
Response properties of embedded molecules through the polarizable embedding model
The polarizable embedding (PE) model is a fragment‐based quantum‐classical approach
aimed at accurate inclusion of environment effects in quantum‐mechanical response …
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
Molecular dynamics (MD) simulations have revolutionized the modeling of biomolecular
conformations and provided unprecedented insight into molecular interactions. Due to the …
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
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 …
size and magnitude. The electrostatic potential maps at the CAM-B3LYP-D3 (bj)/def2-QZVP …
Excited states in large molecular systems through polarizable embedding
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 …
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
We analyze the performance of the polarizable density embedding (PDE) model a new
multiscale computational approach designed for prediction and rationalization of general …
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 …
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
Multiple experiments on the electron transport through solid-state junctions based on
different proteins have suggested that the dominant transport mechanism is quantum …
different proteins have suggested that the dominant transport mechanism is quantum …
A projector-embedding approach for multiscale coupled-cluster calculations applied to citrate synthase
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 …
calculation of various electronic molecular properties. We present the coupling of projector …