Related papers: Alchemical Transformations for Concerted Hydration…
Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased Molecular…
Chemical thermodynamic models of solvent and solute activities predict the equilibrium behaviour of aqueous solutions. How-ever, these models are semi-empirical. They represent micro-scale ion and solvent behaviours that control the…
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…
Solvation free energy is an important design parameter in reaction kinetics and separation processes, making it a critical property to predict during process development. In previous research, directed message passing neural networks…
Experimental studies on ion-water clusters have provided insights into the microscopic aspects of hydration phenomena. One common view is that extending those experimental studies to larger cluster sizes would give the single ion absolute…
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…
Accurate calculation of free energies and their derivatives is central to assessing the thermodynamic stability of molecular and particulate systems across length scales. Yet such quantities can be difficult to compute reliably in strongly…
Aqueous lithium chloride solutions up to very high concentrations were investigated in classical molecular dynamics simulations. Various force fields based on the 12-6 Lennard-Jones model, parametrized for non-polarizable water solvent…
Recent molecular simulation and integral equation results alkali-halide ion pair potentials-of-mean-force in water are discussed. Dielectric model calculations are implemented to check that these models produce that characteristic structure…
"Alchemical" interpolation paths, i.e.~coupling systems along fictitious paths that without realistic correspondence, are frequently used within materials and molecular modeling and simulation protocols for the estimation of relative…
Performing alchemical transformations, in which one molecular system is nonphysically changed to another system, is a popular approach adopted in performing free energy calculations associated with various biophysical processes, such as…
We study the chemical potential of water as a function of charge based on perturbation theory. By calculating the electrostatic-energy fluctuations of two states (fully charged and uncharged) we are able to determine accurate values for the…
Doping compounds can be considered a perturbation to the nuclear charges in a molecular Hamiltonian. Expansions of this perturbation in a Taylor series, i.e. quantum alchemy, has been used in literature to assess millions of derivative…
For the family of model soft Coulomb potentials represented by V(r) = -\frac{Z}{(r^q+\beta^q)^{\frac{1}{q}}}, with the parameters Z>0, \beta>0, q \ge 1, it is shown analytically that the potentials and eigenvalues, E_{\nu\ell}, are…
Recent advances in machine learning and their applications have lead to the development of diverse structure-property relationship models for crucial chemical properties, and the solvation free energy is one of them. Here, we introduce a…
In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is broken. This causes a problem in the evaluation of…
The design of accurate helium-solute interaction potentials for the simulation of chemically complex molecules solvated in superfluid helium has long been a cumbersome task due to the rather weak but strongly anisotropic nature of the…
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…
Interplay of Coulomb interaction energy, free ion entropy, and conformational elasticity is a fascinating aspect in polyelectrolytes (PEs). We develop a theory for complexation of two oppositely charged PEs, a process known to be the…
The high-energy tail of the distribution of solute-solvent interaction energies is poorly characterized for condensed systems, but this tail region is of principal interest in determining the excess free energy of the solute. We introduce…