Calculating free energies of organic molecules on insulating substrates

• Julian Gaberle,
• David Z. Gao and
• Alexander L. Shluger

Beilstein J. Nanotechnol. 2017, 8, 667–674, doi:10.3762/bjnano.8.71

• molecular dynamics. Both molecules contain the same anchoring groups and benzene ring structures, yet differ in their flexibility. Therefore, the entropic contributions to their free energy differ, which affects surface processes. Using potential of mean force and thermodynamic integration techniques, free

• understanding dynamic processes of organic molecules on insulating substrates. Keywords: entropy; free energy; molecular dynamics; organic molecules; potential of mean force; thermodynamic integration surface step; Introduction In recent years molecular films and self-assembled monolayers have attracted a lot

• their energetics at nonzero temperatures will help to elucidate the mechanisms responsible for these processes. Thermodynamic integration and potential of mean force (PMF) calculations were employed in order to calculate entropies and free energies from classical MD. The dependence of the accuracy of

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

• Pavel V. Komarov,
• Pavel G. Khalatur and
• Alexei R. Khokhlov

Beilstein J. Nanotechnol. 2013, 4, 567–587, doi:10.3762/bjnano.4.65

• , which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25–50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the

• force for dissociation (association) of positively/negatively charged ions, H3O+ and SO3−, is dominantly of energetic or entropic nature, we examined the temperature dependence of pair correlation functions (PCFs) g+–(r) and the corresponding potential of mean force W+–(r) = –kBTlng+–(r). The value of W

• potential energy contribution. To demonstrate this, we performed a thermodynamic decomposition of the potential of mean force. If the standard state for free energy is defined as that for the infinitely separated cation and anion, r→∞, then one can write where W+–(∞) = 0 and ΔS = –∂W+–(r)/∂T. The entropic