相关论文: Hydration free energies of polypeptides from popul…
The interactions of hydrated ions with solution and interface partners are strong on a chemical energy scale. Here, we test the foremost \textit{ab initio theory} for evaluation of hydration free energies of ions, namely,…
A recently developed statistical mechanical Quasi-Chemical Theory (QCT) has led to significant insights into solvation phenomena for both hydrophilic and hydrophobic solutes. The QCT exactly partitions solvation free energies into three…
The quasi-chemical organization of the potential distribution theorem -- molecular quasi-chemical theory (QCT) -- enables practical calculations and also provides a conceptual framework for molecular hydration phenomena. QCT can be viewed…
A statistical thermodynamic development is given of a new implicit solvent model that avoids the traditional system size limitations of computer simulation of macromolecular solutions with periodic boundary conditions. This implicit solvent…
Molecular Density Functional Theory (MDFT) offers an efficient implicit- solvent method to estimate molecule solvation free-energies whereas conserving a fully molecular representation of the solvent. Even within a second order ap-…
K+(aq) ion is an integral component of many cellular processes, amongst which the most important, perhaps, is its role in transmitting electrical impulses along the nerve. Understanding its hydration structure and thermodynamics is crucial…
This paper organizes McMillan-Mayer theory, the potential distribution approach, and quasi-chemical theory to provide theory for the thermodynamic effects associated with longer spatial scales involving longer time scales, thus helping to…
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…
The hydration or binding free energy of a drug-like molecule is a key data for early stage drug discovery. Hundreds of thousands of evaluations are needed, which rules out the exhaustive use of atomistic simulations and free energy methods.…
Carbon dioxide hydrates are ice-like nonstoichiometric inclusion solid compounds with importance to global climate change, and gas transportation and storage. The thermodynamic and kinetic mechanisms that control carbon dioxide nucleation…
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.…
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 accurate prediction of solvation free energy is of significant importance as it governs the behavior of solutes in solution. In this work, we apply a variety of machine learning techniques to predict and analyze the alchemical free…
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…
We assess the performance of molecular densityfunctional theory (MDFT) to predict hydration freeenergies of the small drug-like molecules benchmark,FreeSolv. MDFT in the hyper-netted chain approx-imation (HNC) coupled with a pressure…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
The free energies to evacuate the first hydration shell around a solute and a cavity defined by the first hydration shell depend on the system size. This observation interpreted within the quasichemical theory shows that both the…
We consider the prediction of a basic thermodynamic property---hydration free energies---across a large subset of the chemical space of small organic molecules. Our in silico study is based on computer simulations at the atomistic level…
A system of patchy colloidal particles interacting with a solute that can associate multiple times in any direction is a useful model for patchy colloidal mixtures. Despite the simplicity of the interaction, because of the presence of…
We present mode-coupling equations for the description of the slow dynamics observed in supercooled molecular liquids close to the glass transition. The mode-coupling theory (MCT) originally formulated to study the slow relaxation in simple…