A new grand-canonical potential for the thermodynamic description of the reactions in solutions with constant pH

[Display omitted] •Legendre transformation makes reaction free energy dependent on pH of the solution.•For the different pH, different sites on the target molecule can be attacked.•Migration of the Pt-complex along the substrate in pH dependence can be explained.•Strategy for calculation of a relati...

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Vydané v:Journal of molecular liquids Ročník 335; s. 115979
Hlavní autori: Zimmermann, Tomáš, Šebesta, Filip, Burda, Jaroslav V.
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: Elsevier B.V 01.08.2021
Predmet:
Bioinorganic interactions
DFT calculations
Gibbs-Alberty free energy
Legendre transformation
Reaction at constant pH
Gibbs-Alberty free energy
Reaction at constant pH
Bioinorganic interactions
DFT calculations
Legendre transformation
ISSN:0167-7322, 1873-3166
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Shrnutí:[Display omitted] •Legendre transformation makes reaction free energy dependent on pH of the solution.•For the different pH, different sites on the target molecule can be attacked.•Migration of the Pt-complex along the substrate in pH dependence can be explained.•Strategy for calculation of a relatively very accurate pKa is suggested. This review emphasizes the necessity to perform additional Legendre transformation of the free energy for a correct thermodynamic description of reactions in the environment with constant pH. The power of this new thermodynamic potential (Gibbs-Alberty free energy ΔGA0) is demonstrated on three examples. First example, a DFT-based study of interaction of cisplatin with glycine, demonstrates the grand canonical character of the potential, which is manifested by the fact that ΔGA0 energy is not dependent on a concrete form of molecules (protonated or deprotonated) used for energy evaluation. This independence on concrete molecular form strongly contradicts to the standard quantum–mechanical approach where only a single protonation state is used to represent each molecule. Second example, the reaction of hydroxo form of cisplatin with methionine which exhibits quite interesting pH dependency, demonstrates that it is possible to predict metal coordination sites of the amino acid based on proton (hydronium) concentration in solution: in neutral environment the metal binds to thio-group, in basic solutions to amino-group of the amino acid, and in acidic solutions to carboxyl group. This prediction is in the remarkable agreement with the pH-dependent migration of the coordination site observed experimentally in Reedijk laboratory. The final example is the combination of the approach with QM/MM MD simulations of the interaction of (hydrated) mercury cation with thymine. In this reaction, ΔGA0 changes from endergonic to exergonic when the pH passes from acidic to basic values.
ISSN:0167-7322
1873-3166
DOI:10.1016/j.molliq.2021.115979