Accessible Surface Area-based Method
The free energy of solvation of a solute molecule in the simplest ASA-based method is given by:
where is accessible surface area of atom i, and is solvation parameter of atom i, i.e. a contribution to the free energy of solvation of the particular atom i per surface unit area. The required solvation parameters for different types of atoms (C, N, O, S, etc.) are usually determined by least squares fit of the calculated and experimental transfer free energies for a series of organic compounds. The experimental energies are determined from partition coefficients of these compounds between different solutions or media using standard mole concentrations of the solutes.
It is noteworthy that solvation energy is free energy required to transfer a solute molecule from a solvent to “vacuum” (gas phase). This solvation energy can supplement the intramolecular energy in vacuum calculated in molecular mechanics. Therefore, the required atomic solvation parameters were initially derived from water-gas partition data. However, the dielectric properties of proteins and lipid bilayers are much more similar to those of nonpolar solvents than to vacuum. Newer parameters have therefore been derived from water-octanol partition coefficients or other similar data. Such parameters actually describe transfer energy between two condensed media or the difference of two solvation energies.
Read more about this topic: Implicit Solvation
Famous quotes containing the words accessible, surface and/or method:
“When he has seen, that it is not his, nor any man’s, but it is the soul which made the world, and that it is all accessible to him, he will know that he, as its minister, may rightfully hold all things subordinate and answerable to it.”
—Ralph Waldo Emerson (1803–1882)
“Night City was like a deranged experiment in Social Darwinism, designed by a bored researcher who kept one thumb permanently on the fast-forward button. Stop hustling and you sank without a trace, but move a little too swiftly and you’d break the fragile surface tension of the black market; either way, you were gone ... though heart or lungs or kidneys might survive in the service of some stranger with New Yen for the clinic tanks.”
—William Gibson (b. 1948)
“Argument is conclusive ... but ... it does not remove doubt, so that the mind may rest in the sure knowledge of the truth, unless it finds it by the method of experiment.... For if any man who never saw fire proved by satisfactory arguments that fire burns ... his hearer’s mind would never be satisfied, nor would he avoid the fire until he put his hand in it ... that he might learn by experiment what argument taught.”
—Roger Bacon (c. 1214–1294)