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Calculation of Crystal-Solution Dissociation Constants

The calculation of dissociation constants is an important problem in molecular biophysics. For such a calculation, it is important to correctly calculate both terms of the binding free energy; that is, the enthalpy and entropy of binding. Both these terms can be computed using molecular dynamics sim...

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Autores principales: Garbuzynskiy, Sergiy O., Finkelstein, Alexei V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8961641/
https://www.ncbi.nlm.nih.gov/pubmed/35204648
http://dx.doi.org/10.3390/biom12020147
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author Garbuzynskiy, Sergiy O.
Finkelstein, Alexei V.
author_facet Garbuzynskiy, Sergiy O.
Finkelstein, Alexei V.
author_sort Garbuzynskiy, Sergiy O.
collection PubMed
description The calculation of dissociation constants is an important problem in molecular biophysics. For such a calculation, it is important to correctly calculate both terms of the binding free energy; that is, the enthalpy and entropy of binding. Both these terms can be computed using molecular dynamics simulations, but this approach is very computationally expensive, and entropy calculations are especially slow. We develop an alternative very fast method of calculating the binding entropy and dissociation constants. The main part of our approach is based on the evaluation of movement ranges of molecules in the bound state. Then, the range of molecular movements in the bound state (here, in molecular crystals) is used for the calculation of the binding entropies and, then (using, in addition, the experimentally measured sublimation enthalpies), the crystal-to-vapor dissociation constants. Previously, we considered the process of the reversible sublimation of small organic molecules from crystals to vapor. In this work, we extend our approach by considering the dissolution of molecules, in addition to their sublimation. Similar to the sublimation case, our method shows a good correlation with experimentally measured dissociation constants at the dissolution of crystals.
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spelling pubmed-89616412022-03-30 Calculation of Crystal-Solution Dissociation Constants Garbuzynskiy, Sergiy O. Finkelstein, Alexei V. Biomolecules Article The calculation of dissociation constants is an important problem in molecular biophysics. For such a calculation, it is important to correctly calculate both terms of the binding free energy; that is, the enthalpy and entropy of binding. Both these terms can be computed using molecular dynamics simulations, but this approach is very computationally expensive, and entropy calculations are especially slow. We develop an alternative very fast method of calculating the binding entropy and dissociation constants. The main part of our approach is based on the evaluation of movement ranges of molecules in the bound state. Then, the range of molecular movements in the bound state (here, in molecular crystals) is used for the calculation of the binding entropies and, then (using, in addition, the experimentally measured sublimation enthalpies), the crystal-to-vapor dissociation constants. Previously, we considered the process of the reversible sublimation of small organic molecules from crystals to vapor. In this work, we extend our approach by considering the dissolution of molecules, in addition to their sublimation. Similar to the sublimation case, our method shows a good correlation with experimentally measured dissociation constants at the dissolution of crystals. MDPI 2022-01-18 /pmc/articles/PMC8961641/ /pubmed/35204648 http://dx.doi.org/10.3390/biom12020147 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Garbuzynskiy, Sergiy O.
Finkelstein, Alexei V.
Calculation of Crystal-Solution Dissociation Constants
title Calculation of Crystal-Solution Dissociation Constants
title_full Calculation of Crystal-Solution Dissociation Constants
title_fullStr Calculation of Crystal-Solution Dissociation Constants
title_full_unstemmed Calculation of Crystal-Solution Dissociation Constants
title_short Calculation of Crystal-Solution Dissociation Constants
title_sort calculation of crystal-solution dissociation constants
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8961641/
https://www.ncbi.nlm.nih.gov/pubmed/35204648
http://dx.doi.org/10.3390/biom12020147
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