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The atomic binding energy of the atom is the energy required to disassemble an atom into free electrons and a nucleus. [4] It is the sum of the ionization energies of all the electrons belonging to a specific atom. The atomic binding energy derives from the electromagnetic interaction of the electrons with the nucleus, mediated by photons.
In thermodynamics, the Gibbs free energy (or Gibbs energy as the recommended name; symbol ) is a thermodynamic potential that can be used to calculate the maximum amount of work, other than pressure–volume work, that may be performed by a thermodynamically closed system at constant temperature and pressure.
This free-energy map is also known as a potential of mean force (PMF). Free-energy perturbation calculations only converge properly when the difference between the two states is small enough; therefore it is usually necessary to divide a perturbation into a series of smaller "windows", which are computed independently.
The binding constant, or affinity constant/association constant, is a special case of the equilibrium constant K, [1] and is the inverse of the dissociation constant. [2] It is associated with the binding and unbinding reaction of receptor (R) and ligand (L) molecules, which is formalized as: R + L ⇌ RL
In 1884, Jacobus van 't Hoff proposed the Van 't Hoff equation describing the temperature dependence of the equilibrium constant for a reversible reaction: = where ΔU is the change in internal energy, K is the equilibrium constant of the reaction, R is the universal gas constant, and T is thermodynamic temperature.
Ligand efficiency is a measurement of the binding energy per atom of a ligand to its binding partner, such as a receptor or enzyme. [1]Ligand efficiency is used in drug discovery research programs to assist in narrowing focus to lead compounds with optimal combinations of physicochemical properties and pharmacological properties.
The Poisson–Boltzmann equation can be applied to biomolecular systems. One example is the binding of electrolytes to biomolecules in a solution. This process is dependent upon the electrostatic field generated by the molecule, the electrostatic potential on the surface of the molecule, as well as the electrostatic free energy. [13]
Except for the C/G initiation term, the first term represents the free energy of the first base pair, CG, in the absence of a nearest neighbor. The second term includes both the free energy of formation of the second base pair, GC, and stacking interaction between this base pair and the previous base pair. The remaining terms are similarly defined.