Free energy components

Smith P E and W F van Gunsteren 1994b. When Are Free Energy Components Meemingful Journal Physical Chemistry 98 13735-13740. 

Once the electron density of the embedded molecule is evaluated by the SCRF calculations, the free-energy component which is due to the solvent polarization and can be expressed as ... 

Thermodynamic Pathways and Electrostatic Free Energy Components The PBFE Method... 

Other Free Energy Components MM/PBSA Methods... 

Archontis, G. Simonson, T. Karplus, M., Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase, J. Mol. Biol. 2001, 306, 307-327... 

Archontis, G. Simonson, T., Proton binding to proteins a free energy component analysis using a dielectric continuum model, Biophys. J. 2005, 88, 3888-3904... 

Molecular Dynamics Free Energy Yields Structures and Free Energy Components... 

The individual free energy components show the relative contributions from the electrostatic and the van der Waals interactions. The free energy change for the annihilation of the charges on the ligand in the complex and in solution is almost identical within the limits of the estimation. However, the van der Waals free energy component for the complex is more than that of the isolated ligand (Table 1). 

TABLE 5 Surface Free Energy Components of High Strength Carbon Fibers Studied by Two-Liquid Tensiometric Method (in mJ/m2)... 

Inspection of the free energy components points out the dominant role of AGeie in water, which amounts to around 145% of the experimental hydration free energy (Table 4-1). In turn, the non-electrostatic term, AGn-eie, gives rise to an unfavorable contribution to the hydration of these compounds, which reflects the larger magnitude of the cavitation term compared to the van der Waals one in water [15], Overall, except for hydrocarbons, the transfer of polar solutes from the gas phase to water is a favorable process, which mainly originates from the electrostatic interactions between solute and water molecules. 

We developed the Analytical Generalized Born plus Non-Polar (AGBNP) model, an implicit solvent model based on the Generalized Born model [37-40,44, 66] for the electrostatic component and on the decomposition of the nonpolar hydration-free energy into a cavity component based on the solute surface area and a solute-solvent van der Waals interaction free energy component modeled using an estimator based on the Born radius of each atom. 

Energies and Free Energy Components from Molecular Dynamics and Polsson-Boltzmann Calculations. Application to Amino Acid Recognition by Aspartyl-tRNA Synthetase. 

Table 4. Free energy components intermolecular harmonic vibration, g, and the potential energy, u, of structures at minimum potential energy. The differences defined as = 9w averaged over...

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