Related papers: Machine-Learned Electrostatic Potentials for Accur…
We present a method to accurately predict the Helmholtz harmonic free energies of molecular crystals in high-throughput settings. This is achieved by devising a computationally efficient framework that employs a Gaussian Process Regression…
Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…
Atomic partial charges are crucial parameters in molecular dynamics (MD) simulation, dictating the electrostatic contributions to intermolecular energies, and thereby the potential energy landscape. Traditionally, the assignment of partial…
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…
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…
Free energies govern the behavior of soft and liquid matter, and improving their predictions could have a large impact on the development of drugs, electrolytes or homogeneous catalysts. Unfortunately, it is challenging to devise an…
The solvation free energy of organic molecules is a critical parameter in determining emergent properties such as solubility, liquid-phase equilibrium constants, and pKa and redox potentials in an organic redox flow battery. In this work,…
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-…
We devise automated workflows for the calculation of Helmholtz and Gibbs free energies and their temperature and pressure dependence and provide the corresponding computational tools. We employ non-equilibrium thermodynamics for evaluating…
The effect of replacing individual contributions to an empirical energy function are assessed for halogenated benzenes (X-Bz, X = H, F, Cl, Br) and chlorinated phenols (Cl-PhOH). Introducing electrostatic models based on distributed charges…
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…
Multistate empirical valence bond (EVB) models provide an accurate description of the energetics of proton transfer and solvation in complex molecular systems and can be efficiently used in molecular dynamics computer simulations. Within…
We introduce a local machine-learning method for predicting the electron densities of periodic systems. The framework is based on a numerical, atom-centred auxiliary basis, which enables an accurate expansion of the all-electron density in…
In molecular simulations, machine-learning force fields can achieve ab initio accuracy at a lower cost but remain limited in the explicit modeling of electrons. In this work, we develop an electron-aware machine-learning force field, in…
Electrostatics is of paramount importance to chemistry, physics, biology, and medicine. The Poisson-Boltzmann (PB) theory is a primary model for electrostatic analysis. However, it is highly challenging to compute accurate PB electrostatic…
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…
The present paper proposes an adaptive biasing potential for the computation of free energy landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells…
Accurate phase diagram calculation from molecular dynamics requires systematic treatment and convergence of statistical averages. In this work we propose a Gaussian process regression based framework for reconstructing the free energy…
Free-energy-based adaptive biasing methods, such as Metadynamics, the Adaptive Biasing Force (ABF) and their variants, are enhanced sampling algorithms widely used in molecular simulations. Although their efficiency has been empirically…
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…