Themis: A Software to Assess Association Free Energies via Direct Estimative of Partition Functions

Abstract

<div>We present the program <i>Themis</i> - a computer implementation of a standard statistical mechanics framework to compute free energies, average energies and entropic contributions for association processes of two atom-based structures. The partition functions are computed analytically using a discrete grid in the phase space, whose size and degree of coarseness can be controlled to allow efficient calculations and to achieve the desired level of accuracy. With this strategy, applications ranging from molecular recognition, chiral discrimination, surface adsorption and even the interactions involving molecules in electronic excited states can be handled.</div>

How Domain Segregation in Ionic Liquids Stabilizes Nanoparticles and Establishes Long-Range Ordering─A Computational Study

“…Potential of Mean Force Calculations. For the initial structure used in the pmf calculations, the Themis software 56 was used to locate the structure with minimum energy for a pair of NPs in contact (Figure 6) by performing rigid-body rotations and translations of the two NPs and computing the interaction energy using the same parameters employed in the simulations. The dimer with the lowest energy was solvated with ILs using Packmol.…”