Related papers: Predicting binding free energies in solution

Core-electron x-ray photoelectron spectroscopy is a powerful technique for studying the electronic structure and chemical composition of molecules, solids and surfaces. However, the interpretation of measured spectra and the assignment of…

Here, we quantitatively determine the impact of III-V/Si interface atomic configuration on the wetting properties of the system. Based on a description at the atomic scale using density functional theory, we first show that it is possible…

We present an extensive first-principles database of solute-vacancy, homoatomic, heteroatomic solute-solute, and solute-solute-vacancy binding energies of relevant alloying elements in aluminum. We particularly focus on the systems with…

Solvation free energies are efficiently predicted by molecular density functionnal theory (MDFT) if one corrects the overpressure introduced by the usual homogeneous reference fluid approximation. Sergiievskyi et al. [Sergiievskyi et al.,…

Recent progress in simulation methodologies and in computer power allow first principle simulations of condensed systems with Born-Oppenheimer electronic energies obtained by Quantum Monte Carlo methods. Computing free energies and…

We review the free energy approach to the kinetics of surfactant adsorption at fluid/fluid interfaces. The formalism is applied to several systems. For non-ionic surfactant solutions the results coincide with previous models while…

We calculate binding energies of four molecular solids using the Hartree-Fock (HF) and second-order M{\o}ller-Plesset perturbation theory (MP2). We obtain the energies within many-body expansion (MBE) as well as using periodic boundary…

Exact density functionals for the exchange and correlation energies are approximated in practical calculations for the ground-state electronic structure of a many-electron system. An important exact constraint for the construction of…

In this work we introduce a metal-oxide bond-energy model for alloy oxides based on pure-phase bond energies and bond synergy factors that describe the effect of alloying on the bond energy between cations and oxygen, an important quantity…

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…

Nuclear quantum effects, such as zero-point energy and tunneling, cause significant changes to the structure and dynamics of hydrogen bonded systems such as liquid water. However, due to the current inability to simulate liquid water using…

An analytic method for deriving the free energy of a three-dimensional Ising-like system near the critical point in a homogeneous external field is developed in the $\rho^6$ model approximation. The mathematical description proposed for…

We present an inequality that gives a lower bound on the expectation value of certain two-body interaction potentials in a general state on Fock space in terms of the corresponding expectation value for thermal equilibrium states of…

A gaussian distribution of binding energies, but conditioned to exploit generally available information on packing in liquids, provides a statistical-thermodynamic theory of liquid water that is structurally non-committal, molecularly…

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…

We investigate the role of order/disorder transitions in alchemical simulations of protein-ligand absolute binding free energies. We show, in the context of a potential of mean force description, that for a benchmarking system (the complex…

In a dense plasma environment, the energy levels of an ion shift relative to the isolated ion values. This shift is reflected in the optical spectrum of the plasma and can be measured in, for example, emission experiments. In this work, we…

Charge hydration asymmetry (CHA)--a characteristic dependence of hydration free energy on the sign of the solute charge--quantifies the asymmetric response of water to electric field at microscopic level. Accurate estimates of CHA are…

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…

Proton ordering in water ice is a paradigmatic order-disorder transition in a locally constrained system. The ice rules require exactly two hydrogens close to each oxygen, restricting the disorder to an exponentially large yet strongly…