Related papers: Predicting binding free energies in solution
Equations of state for hydrogen bonding fluids are typically described by two energy scales. A short range highly directional hydrogen bond energy scale, as well as a reference energy scale which accounts for dispersion and orientationally…
Ab initio calculations including electron correlation are still extremely costly except for the smallest atoms and molecules. Therefore, our purpose in the present study is to employ a bond-order correlation approach to obtain, via…
We discuss the energy distribution of free-electron Fermi-gas, a problem with a textbook solution of Gaussian energy fluctuations in the limit of a large system. We find that for a small system, characterized solely by its heat capacity…
Sets of free energy differences are useful for finding the equilibria of chemical reactions, while absolute free energies have little physical meaning. However finding the relative free energy between two macrostates by subtraction of their…
The behaviour of molecules in space is to a large extent governed by where they freeze out or sublimate. The molecular binding energy is thus an important parameter for many astrochemical studies. This parameter is usually determined with…
Common force fields overestimate the hydration free energies of hydrophobic solutes, leading to an exaggerated hydrophobic effect. We compute the hydration free energies of linear alkanes from methane to eicosane (C${20}$H${42}$) using free…
While the exact total energy of a separated open system varies linearly as a function of average electron number between adjacent integers, the energy predicted by semi-local density functional approximations curves upward and the…
Theories of solvation free energies often involve electrostatic potentials at the position of a solute charge. Simulation calculations that apply cutoffs and periodic boundary conditions based on molecular centers result in center-dependent…
The accurate prediction of solvation free energies is critical for understanding various phenomena in the liquid phase, including reaction rates, equilibrium constants, activity coefficients, and partition coefficients. Despite extensive…
One may impose to a system with spontaneous broken symmetry, boundary conditions which correspond to different pure states at two ends of a sample. For a discrete Ising-like broken symmetry, boundary conditions with opposite spins in two…
Heating of trapped ion clouds by interactions with free electrons crossing the trapping potential was observed. A model describing such process was proposed and discussed. The presented approach predicts two effects: pushing and heating of…
We report a computational study of the structural and energetic properties of water clustersand singly-charged water cluster anions containing from 20 to 573 water molecules. We have used both a classical and a quantum description of the…
We describe a model of electron transfer reactions affected by local binding to the donor or acceptor sites of a particle in equilibrium with the solution. The statistics of fluctuations of the donor-acceptor energy gap caused by…
A non-perturbative theory is presented which allows to calculate the solvation free energy of polarizable ions near a water-vapor and water-oil interfaces. The theory predicts that larger halogen anions are adsorbed at the interface, while…
Accurate absolute binding free energy (ABFE) calculations can reduce the time and cost of identifying drug candidates from a diverse pool of molecules that may have been overlooked experimentally. These calculations typically employ…
Continuum solvation models enable efficient first principles calculations of chemical reactions in solution, but require extensive parametrization and fitting for each solvent and class of solute systems. Here, we examine the assumptions of…
Liquid states theories have emerged as a numerically efficient alternative to costly molecular dynamics simulations of electron transfer reactions in solution. In a recent paper [Chem. Sci., 2019, 10, 2130], we introduced the framework to…
Our atomistic molecular dynamics simulations reveal the existence of bound and free water molecules in the hydration layer of an aqueous micelle. The bound water molecules can be either singly or doubly hydrogen bonded to the polar head…
We present a new method to evaluate vibrational free energies of atomic systems without a priori specification of an interatomic potential. Our model-agnostic approach leverages descriptors, high-dimensional feature vectors of atomic…
A recent tight-binding scheme provides a method for extending the results of first principles calculations to regimes involving $10^2 - 10^3$ atoms in a unit cell. The method uses an analytic set of two-center, non-orthogonal tight-binding…