Alchemical free energy calculations are a useful tool for predicting free energy differences
associated with the transfer of molecules from one environment to another. The hallmark of …

Publisher Summary In an alchemical transformation, a chemical species is transformed into
another via a pathway of nonphysical (alchemical) states. Many physical processes, such as …

We attempt to optimize the efficiency of thermodynamic integration, as defined by the
minimal number of unphysical intermediate states required for the computation of accurate …

We investigate the relative efficiency of thermodynamic integration, three variants of the
exponential formula, also referred to as thermodynamic perturbation, and Bennett's …

Alchemical free energy calculations are an increasingly important modern simulation
technique to calculate free energy changes on binding or solvation. Contemporary …

There is a significant need for improved tools to validate thermophysical quantities
computed via molecular simulation. In this paper we present the initial version of a …

Understanding the differences in behavior of different chemical systems is a central goal of
chemistry. Investigators would like, for example, to predict and explain the relative affinity of …

We present a comparison of four free energy calculation methods: thermodynamic
integration (TI); traditional free energy perturbation (FEP); Bennett's acceptance ratio method …

Background The calculation of free energy changes is fundamental for the thermodynamic
characterization of reaction pathways and chemical equilibria. The conventional …

Introduction 1988 marked the 25th anniversary of the publication of two classic papers in the
evolution of theoretical organic chemistry, Roald Hoffmann's report of ex-tended Hiickel …