Related papers: Predicting binding free energies in solution
The theory behind computation of absolute binding free energies using explicit-solvent molecular simulations is well-established, yet somewhat complex, with counter-intuitive aspects. This leads to frequent frustration, common…
The hydration free energies of ions exhibit an approximately quadratic dependence on the ionic charge, as predicted by the Born model. We analyze this behavior using second-order perturbation theory. This provides effective methods to…
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…
In transitions between different environmental settings, a molecular system inevitably undergoes a range of detectable changes, and the ability to accurately simulate such responses, e.g., in the form of shifts to molecular energies,…
Reported here are results of theoretical calculations on the hexaaquoferric complex and deprotonated products to investigate the molecular mechanisms of hydrolysis of ferric ion in water. The combination of density functional electronic…
We propose a new simple computational model to estimate adsorption energies of atoms and molecules to low-temperature amorphous water ice, and we present the adsorption energies of carbon (3P), nitrogen (4S), and oxygen (3P) atoms based on…
Solvation in 1-ethyl-3-methylmidazolium chloride and in 1-ethyl-3-methylimidazolium hexafluorophosphate near equilibrium is investigated via molecular dynamics computer simulations with diatomic and benzenelike molecules employed as probe…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…
Accurate predictions of the hydration free energy for anions typically have been more challenging than for cations. Hydrogen bond donation to the anion in hydrated clusters such as $\mathrm{F(H_2O)}_n{}^-$ can lead to delicate structures.…
The free energy of mixing and the entropy of mixing for Cu$_{x}$Al$_{1-x}$ liquid binary alloys have been systematically investigated by using the electronic theory of metals along with the perturbation approach at a thermodynamic state…
One of the main applications of atomistic computer simulations is the calculation of ligand binding energies. The accuracy of these calculations depends on the force field quality and on the thoroughness of configuration sampling. Sampling…
We briefly review the effects of selective solvation of ions in aqueous mixtures, where the ion densities and the composition fluctuations are strongly coupled. We then examine the surface tension \gamma of a liquid-liquid interface in the…
The microscopic approach to calculating the free energy of a three-dimensional Ising-like system in a homogeneous external field is developed in the higher non-Gaussian approximation (the $\rho^6$ model) at temperatures above the critical…
Recent laboratory measurements have confirmed that chemical desorption (desorption of products due to exothermic surface reactions) can be an efficient process. The impact of including this process into gas-grain chemical models entirely…
A methodology for calculating the contribution of charged defects to the configurational free energy of an ionic crystal is introduced. The temperature-independent Wang-Landau Monte Carlo technique is applied to a simple model of a solid…
Understanding design principles of biomolecular recognition is a key question of molecular biology. Yet the enormous complexity and diversity of biological molecules hamper the efforts to gain a predictive ability for the free energy of…
We analyse the finite-size corrections to the free energy of crystals with a fixed center of mass. When we explicitly correct for the leading ($\ln N/N$) corrections, the remaining free energy is found to depend linearly on 1/N.…
We present a parameterized analytical model of alchemical molecular binding. The model describes accurately the free energy profiles of linear single-decoupling alchemical binding free energy calculations. The parameters of the model, which…
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li+, Cl-, and Ag+ ions. Using the Perdew-Burke-Ernzerhof…
The total energies of a large number of diatomic (or two-center) one-electron $A^{+} B^{+} e^{-}$ ions with unit electrical charges are determined numerically to high accuracy. Based on these results we derive some accurate…