Related papers: Activation entropy of electron transfer reactions
It is well known that collisionless systems are dissipation free from the perspective of particle collision and thus conserve entropy. On the other hand, processes such as magnetic reconnection and turbulence appear to convert large-scale…
We propose a new method to compute the free energy or enthalpy of fluids or disordered solids by computer simulation . The main idea is to construct a reference system by freezing one representative configuration, and then carry out a…
The process of deriving an interatomic potentials represents an attempt to integrate out the electronic degrees of freedom from the full quantum description of a condensed matter system. In practice it is the derivatives of the interatomic…
Treating water as a linearly responding dielectric continuum on molecular length scales allows very simple estimates of solvation structure and thermodynamics for charged and polar solutes. While this approach can successfully account for…
Most methods for estimating configurational entropy from molecular simulation data yield upper limits except for harmonic systems where they are exact. Problems arise at diffusive systems and the presence of conformational transitions.…
The extension of thermodynamic principles to active matter remains a challenge due to the non-equilibrium nature inherent to active systems. In this study, we introduce a framework to assess entropy in our minimal macroscopic experiment…
We translate the problem of calculating the entropy of a set of binary configurations/signals into a sequence of supervised classification tasks. Subsequently, one can use virtually any machine learning classification algorithm for…
We resolve a seeming paradox arising from a common misinterpretation of Ben-Naim's theorem, which rests on a pairwise decomposition of the Hamiltonian of a molecular solute/solvent system into pairwise solute-solvent and solvent-solvent…
In this contribution I critically revise the alchemical reversible approach in the context of the statistical mechanics theory of non covalent bonding in drug receptor systems. I show that most of the pitfalls and entanglements for the…
In the framework of irreversible thermodynamics, we study autonomous systems of reaction-diffusion equations to show how the entropy and free energy of an open and irreversible reactor depend on concentrations. To do this, we find a…
We present a method for computing free-energy differences using thermodynamic integration with a neural network potential that interpolates between two target Hamiltonians. The interpolation is defined at the sample distribution level, and…
In the aim of completing our previous efforts devoted to local and Rydberg transitions in organic compounds, we provide a series of highly-accurate vertical transition energies for intramolecular charge-transfer transitions occurring in…
Using molecular simulation, we study the nucleation of liquid droplets from binary mixtures and determine the free energy of nucleation along entropic pathways. To this aim, we develop the $\mu_1 \mu_2 VT-S$ method, based on the…
We consider a molecular junction immersed in a solvent where the electron transfer is dominated by Marcus-type steps. However, the successive nature of the charge transfer through the junction does not imply that the solvent reach thermal…
Solvation free energy is an important quantity in Computational Chemistry with a variety of applications, especially in drug discovery and design. The accurate prediction of solvation free energies of small molecules in water is still a…
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…
Using a one-dimensional macromolecule in aqueous solution as an illustration, we demonstrate that the relative entropy from information theory, $\sum_k p_k\ln(p_k/p_k^*)$, has a natural role in the energetics of equilibrium and…
Methods for estimating the correlation energy of molecules and other electronic systems are discussed based on the assumption that the correlation energy can be partitioned between atomic regions. In one method, the electron density is…
A general approach to calculate the diabatic surfaces for electron-transfer reactions is presented, based on first-principles molecular dynamics of the active centers and their surrounding medium. The excitation energy corresponding to the…
An elementary collision model of a molecular reservoir is considered upon which an external field is applied and the work is dissipated into heat. To realize macroscopic irreversibility at the microscopic level, we introduce a ``graceful''…