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A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules

[Image: see text] Closed-form, analytical approximations for electrostatic properties of molecules are of unique value as these can provide computational speed, versatility, and physical insight. Here, we have derived a simple, closed-form formula for the apparent surface charge (ASC) as well as for...

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Autores principales: Folescu, Dan E., Onufriev, Alexey V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2022
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9352323/
https://www.ncbi.nlm.nih.gov/pubmed/35936397
http://dx.doi.org/10.1021/acsomega.2c01484
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author Folescu, Dan E.
Onufriev, Alexey V.
author_facet Folescu, Dan E.
Onufriev, Alexey V.
author_sort Folescu, Dan E.
collection PubMed
description [Image: see text] Closed-form, analytical approximations for electrostatic properties of molecules are of unique value as these can provide computational speed, versatility, and physical insight. Here, we have derived a simple, closed-form formula for the apparent surface charge (ASC) as well as for the electric field generated by a molecular charge distribution in aqueous solution. The approximation, with no fitted parameters, was tested against numerical solutions of the Poisson equation, where it has produced a significant speed-up. For neutral small molecules, the hydration free energies estimated from the closed-form ASC formula are within 0.8 kcal/mol RMSD from the numerical Poisson reference; the electric field at the surface is in quantitative agreement with the reference. Performance of the approximation was also tested on larger structures, including a protein, a DNA fragment, and a viral receptor–target complex. For all structures tested, a near-quantitative agreement with the numerical Poisson reference was achieved, except in regions of high negative curvature, where the new approximation is still qualitatively correct. A unique efficiency feature of the proposed “source-based″ closed-form approximation is that the ASC and electric field can be estimated individually at any point or surface patch, without the need to obtain the full global solution. An open-source software implementation of the method is available: https://people.cs.vt.edu/~onufriev/CODES/aasc.zip.
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spelling pubmed-93523232022-08-05 A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules Folescu, Dan E. Onufriev, Alexey V. ACS Omega [Image: see text] Closed-form, analytical approximations for electrostatic properties of molecules are of unique value as these can provide computational speed, versatility, and physical insight. Here, we have derived a simple, closed-form formula for the apparent surface charge (ASC) as well as for the electric field generated by a molecular charge distribution in aqueous solution. The approximation, with no fitted parameters, was tested against numerical solutions of the Poisson equation, where it has produced a significant speed-up. For neutral small molecules, the hydration free energies estimated from the closed-form ASC formula are within 0.8 kcal/mol RMSD from the numerical Poisson reference; the electric field at the surface is in quantitative agreement with the reference. Performance of the approximation was also tested on larger structures, including a protein, a DNA fragment, and a viral receptor–target complex. For all structures tested, a near-quantitative agreement with the numerical Poisson reference was achieved, except in regions of high negative curvature, where the new approximation is still qualitatively correct. A unique efficiency feature of the proposed “source-based″ closed-form approximation is that the ASC and electric field can be estimated individually at any point or surface patch, without the need to obtain the full global solution. An open-source software implementation of the method is available: https://people.cs.vt.edu/~onufriev/CODES/aasc.zip. American Chemical Society 2022-07-19 /pmc/articles/PMC9352323/ /pubmed/35936397 http://dx.doi.org/10.1021/acsomega.2c01484 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Folescu, Dan E.
Onufriev, Alexey V.
A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules
title A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules
title_full A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules
title_fullStr A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules
title_full_unstemmed A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules
title_short A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules
title_sort closed-form, analytical approximation for apparent surface charge and electric field of molecules
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9352323/
https://www.ncbi.nlm.nih.gov/pubmed/35936397
http://dx.doi.org/10.1021/acsomega.2c01484
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