Absolute free energy of binding

WL Jorgensen, JK Buckner, S Boudon, J Tirado-Rives. Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer m water. J Chem Phys 89 3742-3746, 1988. 

That said, for select systems it is possible to attempt to calculate an absolute free energy. This can be done by running two FEP or TI simulations and summing the results.44 For example, to calculate the absolute free energy of binding of a substrate to an enzyme, we perform the following simulations ... 

Tsui V, Case DA. Calculations of the absolute free energies of binding between RNA... 

W. Jorgensen, J. K. Buckner, S. Boudon, andj. Tirado-Rives,/. Ghem. Phys., 89,3742 (1988). Efficient Computation of Absolute Free Energy of Binding by Computer Simulations. Application to the Methane Dimer in Water. 

Most likely, the atom adsorbed on the surface will diffuse until it is trapped in a defect (seed formation). If the concentration of free transition metal atoms around the seed is large enough, a nanoparticle is formed from the atoms that are one by one trapped in the potential well formed by the seed. If one wants to obtain a material with uniform distribution of transition metal atoms bound to defect sites (or heteroatom inclusions), the system should be gradually heated in such a way that all defect sites will be occupied. The last is possible only if the absolute free energy of the cluster formation (per transition metal atom) is less than the absolute free energy of binding to a vacancy site. No data are available on the entropy of these elemental reactions nevertheless, since all degrees of freedom are constrained as... 

V. Tsui and D. A. Case, J. Phys. Chem. B, 105, 11314 (2001). Calculations of the Absolute Free Energies of Binding between RNA and Metal Ions Using Molecular Dynamics Simulations and Continuum Electrostatics. 

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