相关论文: Hydration Free Energies of Linear Alkanes: Systema…
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…
We examine five different popular rigid water models (SPC, SPCE, TIP3P, TIP4P and TIP5P) using MD simulations in order to investigate the hydrophobic hydration and interaction of apolar Lennard-Jones solutes as a function of temperature in…
Experiments show that at 298~K and 1 atm pressure the transfer free energy, $\mu^{\rm ex}$, of water from its vapor to liquid normal alkanes $C_nH_{2n+2}$ ($n=5\ldots12$) is negative. Earlier it was found that with the united-atom TraPPe…
Parametrizing energy functions for ionic systems can be challenging. Here, the total energy function for an eutectic system consisting of water, SCN$^-$, K$^+$ and acetamide is improved vis-a-vis experimentally measured properties. Given…
We present a family of alchemical perturbation potentials that enable the calculation of hydration free energies of small to medium-sized molecules in a concerted single alchemical coupling step instead of the commonly used sequence of two…
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…
Direct, all-atom calculations of the free energy of hydration of aqueous deca-alanine structures --- holistically including backbone and side-chain interactions together --- show that attractive interactions and the thermal expansion of the…
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…
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…
We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a non-equilibrium umbrella sampling method, in this case the recently developed…
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…
The accurate treatment of long-range energy terms such as van der Waals interactions is crucial for reliable free energy calculations in molecular simulations. Methods like force switching, potential switching, potential shifting, and Ewald…
Isothermal-isobaric molecular dynamics simulations are used to examine the microscopic structure and some properties of water-methanol liquid mixture. The TIP4P/2005 and SPC/E water models are combined with the united atom TraPPE and the…
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…
Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic for others. In paper I…
Recent studies of the hydration of micro- and nanoscale solutes have demonstrated a strong {\it coupling} between hydrophobic, dispersion and electrostatic contributions, a fact not accounted for in current implicit solvent models. We…
In this work, the tetrahydrofuran (THF) hydrate-water interfacial free energy is determined at $500\,\text{bar}$, at one point of the univariant two-phase coexistence line of the THF hydrate, by molecular dynamics simulation. The Mold…
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…
Hydrophobic hydration at metal/water interfaces actively contributes to the energetics of electrochemical reactions, e.g. CO$_2$ and N$_2$ reduction, where small hydrophobic molecules are involved. In this work, constant applied potential…
We compute ionic free energy adsorption profiles at aqueous graphene interface by developing a self-consistent approach. To do so, we design a microscopic model for water and put the liquid on an equal footing with the graphene described by…