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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.
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.
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.
In this case, one can use various free energy calculation methods to obtain the protonation free energy [15] such as biased Metropolis MC, [24] free-energy perturbation, [25] [26] thermodynamic integration, [27] [28] [29] the non-equilibrium work method [30] or the Bennett acceptance ratio method. [31] Note that the pK HH
Free energy relationships establish the extent at which bond formation and breakage happen in the transition state of a reaction, and in combination with kinetic isotope experiments a reaction mechanism can be determined. Free energy relationships are often used to calculate equilibrium constants since they are experimentally difficult to ...
In theoretical chemistry, the Empirical Valence Bond (EVB) approach is an approximation for calculating free-energies of a chemical reaction in condensed-phase.It was first developed by Israeli chemist Arieh Warshel, [1] and was inspired by the way Marcus theory uses potential surfaces to calculate the probability of electron transfer.
The Gibbs free energy for converting a mole of CO 2 to glucose is 114 kcal, whereas eight moles of photons of wavelength 600 nm contains 381 kcal, giving a nominal efficiency of 30%. [2] However, photosynthesis can occur with light up to wavelength 720 nm so long as there is also light at wavelengths below 680 nm to keep Photosystem II ...
While the Lineweaver–Burk plot has historically been used for evaluation of the parameters, together with the alternative linear forms of the Michaelis–Menten equation such as the Hanes–Woolf plot or Eadie–Hofstee plot, all linearized forms of the Michaelis–Menten equation should be avoided to calculate the kinetic parameters ...