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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...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
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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. |
format | Online Article Text |
id | pubmed-9352323 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
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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