相关论文: Ligand Discrimination in Myoglobin from Linear-Sca…

Normally, understanding the temperature dependent transport properties of strongly correlated electron systems remains challenging task due to complex electronic structure and its variations (around E$_{F}$) with temperature. Here, we…

We perform first-principles quantum mechanical studies of dioxygen ligand binding to the hemocyanin protein. Electronic correlation effects in the functional site of hemocyanin are investigated using a state-of-the-art approach, treating…

The accurate screening of candidate drug ligands against target proteins through computational approaches is of prime interest to drug development efforts. Such virtual screening depends in part on methods to predict the binding affinity…

We investigate the DFT+U approach as a viable solution to describe the low-lying states of ligated and unligated iron heme complexes. Besides their central role in organometallic chemistry, these compounds represent a paradigmatic case…

If a deuterated molecule containing strong intramolecular hydrogen bonds is placed in a hydrogenated solvent it may preferentially exchange deuterium for hydrogen. This preference is due to the difference between the vibrational zero-point…

Comparative molecular dynamics simulations of a hexamer cluster of the protic ionic liquid ethylammonium nitrate are performed using density functional theory (DFT) and density functional-based tight binding (DFTB) methods. The focus is on…

Y-doped BaZrO$_3$ is a promising proton conductor for intermediate temperature solid oxide fuel cells. In this work, a combination of static DFT calculations and DFT based molecular dynamics (DFT-MD) was used to study proton conduction in…

Predicting how protein mutations affect drug binding remains a major challenge, particularly when the mutations are distal from the binding site. In this study, we introduce a coupled simulation workflow that combines long-time-scale…

This work considers how the properties of hydrogen bonded complexes, D-H....A, are modified by the quantum motion of the shared proton. Using a simple two-diabatic state model Hamiltonian, the analysis of the symmetric case, where the donor…

Hydrogen embrittlement is a prime cause of several degradation effects in metals. Since grain boundaries (GBs) act efficiently as sinks for hydrogen atoms, H is thought to segregate in these regions, affecting the local formation of…

Intrinsically disordered proteins participate in many biological processes by folding upon binding with other proteins. However, coupled folding and binding processes are not well understood from an atomistic point of view. One of the main…

The Landau-Ginzburg-Wilson paradigm is applied to model the low-temperature crystallographic C$\alpha$ backbone structure of sperm whale myoglobin. The Glauber protocol is employed to simulate its response to an increase in ambient…

Molecular docking is a crucial step in the development of new drugs as it guides the positioning of a small molecule (ligand) within the pocket of a target protein. In the literature, a feasibility study explored the potential of D-Wave…

Predicting accurate protein-ligand binding affinity is important in drug discovery but remains a challenge even with computationally expensive biophysics-based energy scoring methods and state-of-the-art deep learning approaches. Despite…

We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics (MD) simulations are suggested by single-molecule studies of protein-DNA…

The contribution of a specific hydrogen bond in apoflavodoxin to protein stability is investigated by combining theory, experiment and simulation. Although hydrogen bonds are major determinants of protein structure and function, their…

A hydrophilic liquid, such as water, forms hydrogen bonds with a hydrophilic substrate. The strength and locality of the hydrogen bonding interactions prohibit slip of the liquid over the substrate. The question then arises how the contact…

We theoretically study the effect of a localized unpaired dangling bond (DB) on occupied molecular orbital conduction through a styrene molecule bonded to a n++ H:Si(001)-(2x1) surface. For molecules relatively far from the DB, we find good…

Rare-earth trihydrides ($R$H$_3$) exhibit intriguing coupled electronic and structural properties as a function of doping, hydrogen vacancies, and thermodynamic conditions. Theoretical studies of these materials typically rely on density…

The kinetics of hydrogen diffusion in C15 cubic and C14 hexagonal TiCr$_2$H$_x$ (0 < $x$ <= 4) Laves-phase hydrogen storage alloys is investigated with density functional theory (DFT) and machine learning interatomic potentials (MLIPs).…