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Mathematical Modeling of a Supramolecular Assembly for Pyrophosphate Sensing

The power of sensing molecules is often characterized in part by determining their thermodynamic/dynamic properties, in particular the binding constant of a guest to a host. In many studies, traditional nonlinear regression analysis has been used to determine the binding constants, which cannot be a...

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Autores principales: Emami, Fereshteh, Abdollahi, Hamid, Minami, Tsyuoshi, Peco, Ben, Reliford, Sean
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8724255/
https://www.ncbi.nlm.nih.gov/pubmed/34993174
http://dx.doi.org/10.3389/fchem.2021.759714
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author Emami, Fereshteh
Abdollahi, Hamid
Minami, Tsyuoshi
Peco, Ben
Reliford, Sean
author_facet Emami, Fereshteh
Abdollahi, Hamid
Minami, Tsyuoshi
Peco, Ben
Reliford, Sean
author_sort Emami, Fereshteh
collection PubMed
description The power of sensing molecules is often characterized in part by determining their thermodynamic/dynamic properties, in particular the binding constant of a guest to a host. In many studies, traditional nonlinear regression analysis has been used to determine the binding constants, which cannot be applied to complex systems and limits the reliability of such calculations. Supramolecular sensor systems include many interactions that make such chemical systems complicated. The challenges in creating sensing molecules can be significantly decreased through the availability of detailed mathematical models of such systems. Here, we propose uncovering accurate thermodynamic parameters of chemical reactions using better-defined mathematical modeling-fitting analysis is the key to understanding molecular assemblies and developing new bio/sensing agents. The supramolecular example we chose for this investigation is a self-assembled sensor consists of a synthesized receptor, DPA (DPA = dipicolylamine)-appended phenylboronic acid (1) in combination with Zn(2+)(1.Zn) that forms various assemblies with a fluorophore like alizarin red S (ARS). The self-assemblies can detect multi-phosphates like pyrophosphate (PPi) in aqueous solutions. We developed a mathematical model for the simultaneous quantitative analysis of twenty-seven intertwined interactions and reactions between the sensor (1.Zn-ARS) and the target (PPi) for the first time, relying on the Newton-Raphson algorithm. Through analyzing simulated potentiometric titration data, we describe the concurrent determination of thermodynamic parameters of the different guest-host bindings. Various values of temperatures, initial concentrations, and starting pHs were considered to predict the required measurement conditions for thermodynamic studies. Accordingly, we determined the species concentrations of different host-guest bindings in a generalized way. This way, the binding capabilities of a set of species can be quantitatively examined to systematically measure the power of the sensing system. This study shows analyzing supramolecular self-assemblies with solid mathematical models has a high potential for a better understanding of molecular interactions within complex chemical networks and developing new sensors with better sensing effects for bio-purposes.
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spelling pubmed-87242552022-01-05 Mathematical Modeling of a Supramolecular Assembly for Pyrophosphate Sensing Emami, Fereshteh Abdollahi, Hamid Minami, Tsyuoshi Peco, Ben Reliford, Sean Front Chem Chemistry The power of sensing molecules is often characterized in part by determining their thermodynamic/dynamic properties, in particular the binding constant of a guest to a host. In many studies, traditional nonlinear regression analysis has been used to determine the binding constants, which cannot be applied to complex systems and limits the reliability of such calculations. Supramolecular sensor systems include many interactions that make such chemical systems complicated. The challenges in creating sensing molecules can be significantly decreased through the availability of detailed mathematical models of such systems. Here, we propose uncovering accurate thermodynamic parameters of chemical reactions using better-defined mathematical modeling-fitting analysis is the key to understanding molecular assemblies and developing new bio/sensing agents. The supramolecular example we chose for this investigation is a self-assembled sensor consists of a synthesized receptor, DPA (DPA = dipicolylamine)-appended phenylboronic acid (1) in combination with Zn(2+)(1.Zn) that forms various assemblies with a fluorophore like alizarin red S (ARS). The self-assemblies can detect multi-phosphates like pyrophosphate (PPi) in aqueous solutions. We developed a mathematical model for the simultaneous quantitative analysis of twenty-seven intertwined interactions and reactions between the sensor (1.Zn-ARS) and the target (PPi) for the first time, relying on the Newton-Raphson algorithm. Through analyzing simulated potentiometric titration data, we describe the concurrent determination of thermodynamic parameters of the different guest-host bindings. Various values of temperatures, initial concentrations, and starting pHs were considered to predict the required measurement conditions for thermodynamic studies. Accordingly, we determined the species concentrations of different host-guest bindings in a generalized way. This way, the binding capabilities of a set of species can be quantitatively examined to systematically measure the power of the sensing system. This study shows analyzing supramolecular self-assemblies with solid mathematical models has a high potential for a better understanding of molecular interactions within complex chemical networks and developing new sensors with better sensing effects for bio-purposes. Frontiers Media S.A. 2021-12-21 /pmc/articles/PMC8724255/ /pubmed/34993174 http://dx.doi.org/10.3389/fchem.2021.759714 Text en Copyright © 2021 Emami, Abdollahi, Minami, Peco and Reliford. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Chemistry
Emami, Fereshteh
Abdollahi, Hamid
Minami, Tsyuoshi
Peco, Ben
Reliford, Sean
Mathematical Modeling of a Supramolecular Assembly for Pyrophosphate Sensing
title Mathematical Modeling of a Supramolecular Assembly for Pyrophosphate Sensing
title_full Mathematical Modeling of a Supramolecular Assembly for Pyrophosphate Sensing
title_fullStr Mathematical Modeling of a Supramolecular Assembly for Pyrophosphate Sensing
title_full_unstemmed Mathematical Modeling of a Supramolecular Assembly for Pyrophosphate Sensing
title_short Mathematical Modeling of a Supramolecular Assembly for Pyrophosphate Sensing
title_sort mathematical modeling of a supramolecular assembly for pyrophosphate sensing
topic Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8724255/
https://www.ncbi.nlm.nih.gov/pubmed/34993174
http://dx.doi.org/10.3389/fchem.2021.759714
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