Related papers: Polyhalogenated Molecules in the Polarizable Ellip…
To contribute to the understanding of noncovalent binding of halogenated molecules with a biological activity, electrostatic potential (ESP) maps of more than 2,500 compounds were thoroughly analysed. A peculiar region of positive ESP,…
Positron binding energies in halogenated hydrocarbons are calculated \emph{ab initio} using many-body theory. For chlorinated molecules, including planars for which the interaction is highly anisotropic, very good to excellent agreement…
Halogen bonding has emerged as an important noncovalent interaction in a myriad of applications, including drug design, supramolecular assembly, and catalysis. Current understanding of the halogen bond is informed by electronic structure…
Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing…
We develop coarse-grained force fields for poly (vinyl alcohol) and poly (acrylic acid) oligomers. In both cases, one monomer is mapped onto a coarse-grained bead. The new force fields are designed to match structural properties such as…
Hybrid particle-field methods are computationally efficient approaches for modelling soft matter systems. So far applications of these methodologies have been limited to constant volume conditions. Here, we reformulate particle-field…
Long-range interactions are essential determinants of chemical system behaviour across diverse environments. We present a foundation framework that integrates explicit polarizable long-range physics with an equivariant graph neural network…
The possibility of an inhomogeneous charge density wave phase is investigated in a system of two coupled electron and hole monolayers separated by a hexagonal boron nitride insulating layer. The charge density wave state is induced through…
A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field is based upon the model electron density of a hydrogen-like…
Halogen bond (X-bond) is a noncovalent interaction between a halogen atom and an electron donor. It is often rationalized by a region of the positive electrostatic potential on the halogen atom, so-called $\sigma$-hole. The X-bond strength…
The electrostatic potential of a highly charged disc (clay platelet) in an electrolyte is investigated in detail. The corresponding non-linear Poisson-Boltzmann (PB) equation is solved numerically, and we show that the far-field behaviour…
We introduce a novel coarse-grained bead-spring model for flexible polymers to systematically examine the effects of an adjusted bonded potential on the formation and stability of structural macrostates in a thermal environment. The density…
Stretching dynamics of polymers in microfluidics is of particular interest for polymer scientists. As a charged polymer, a polyelectrolyte can be deformed from its coiled equilibrium configuration to an extended chain by applying uniform or…
Polarizable particle systems, including charged colloids, polarizable ions, biomolecular assemblies, and soft nanomaterials, can exhibit contact electrostatic interactions that depart strongly from Coulomb behavior when dielectric mismatch…
The hybrid particle-field molecular dynamics method is an efficient alternative to standard particle-based coarse grained approaches. In this work, we propose an automated protocol for optimisation of the effective parameters that define…
We present a new simple self-consistent field theory of the polarizable flexible polymer chain under the external constant electric field with account for the many-body electrostatic dipole correlations. We show the effect of electrostatic…
We demonstrate how an iterative method for potential inversion from distribution functions developed for simple liquid systems can be generalized to polymer systems. It uses the differences in the potentials of mean force between the…
Methodologies for creating reactive potential energy surfaces from molecular mechanics force-fields are becoming increasingly popular. To date, molecular mechanics force-fields use harmonic expressions to treat bonding stretches, which is a…
The interplay between shape anisotropy and directed long-range interactions enables the self-assembly of complex colloidal structures. As a recent highlight, ellipsoidal particles polarized in an external electric field were observed to…
The quality of biomolecular simulations critically depends on the accuracy of the force field used to calculate the potential energy of the molecular configurations. Currently, most simulations employ non-polarisable force fields, which…