Prediction of the n‑octanol/water partition coefficients in the SAMPL6 blind challenge from MST continuum solvation calculations

The IEFPCM/MST continuum solvation model is used for the blind prediction of n-octanol/water partition of a set of 11 fragment-like small molecules within the SAMPL6 Part II Partition Coefficient Challenge. The partition coefficient of the neutral species (log P) was determined using an extended par...

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Detalles Bibliográficos
Autores: Zamora Ramírez, William J., Pinheiro, Silvana de Souza, German, Kilian, Ràfols Llach, Clara, Curutchet Barat, Carles E., Luque Garriga, F. Xavier
Tipo de recurso: artículo
Estado:Versión aceptada para publicación
Fecha de publicación:2019
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:2445/170228
Acceso en línea:https://hdl.handle.net/2445/170228
Access Level:acceso abierto
Palabra clave:Solvatació
Bioquímica
Farmacologia
Solvation
Biochemistry
Pharmacology
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spelling Prediction of the n‑octanol/water partition coefficients in the SAMPL6 blind challenge from MST continuum solvation calculationsZamora Ramírez, William J.Pinheiro, Silvana de SouzaGerman, KilianRàfols Llach, ClaraCurutchet Barat, Carles E.Luque Garriga, F. XavierSolvatacióBioquímicaFarmacologiaSolvationBiochemistryPharmacologyThe IEFPCM/MST continuum solvation model is used for the blind prediction of n-octanol/water partition of a set of 11 fragment-like small molecules within the SAMPL6 Part II Partition Coefficient Challenge. The partition coefficient of the neutral species (log P) was determined using an extended parametrization of the B3LYP/6-31G(d) version of the Miertus-Scrocco-Tomasi continuum solvation model in n-octanol. Comparison with the experimental data provided for partition coefficients yielded a root-mean square error (rmse) of 0.78 (log P units), which agrees with the accuracy reported for our method (rmse = 0.80) for nitrogen-containing heterocyclic compounds. Out of the 91 sets of log P values submitted by the participants, our submission is within those with an rmse < 1 and among the four best ranked physical methods. The largest errors involve three compounds: two with the largest positive deviations (SM13 and SM08), and one with the largest negative deviations (SM15). Here we report the potentiometric determination of the log P for SM13, leading to a value of 3.62 ± 0.02, which is in better agreement with most empirical predictions than the experimental value reported in SAMPL6. In addition, further inclusion of several conformations for SM08 significantly improved our results. Inclusion of these refinements led to an overall error of 0.51 (log P units), which supports the reliability of the IEFPCM/MST model for predicting the partitioning of neutral compounds.Springer Verlag2020202020192020info:eu-repo/semantics/articleinfo:eu-repo/semantics/acceptedVersion9 p.application/pdfapplication/pdfhttps://hdl.handle.net/2445/170228Articles publicats en revistes (Nutrició, Ciències de l'Alimentació i Gastronomia)reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésVersió postprint del document publicat a: https://doi.org/10.1007/s10822-019-00262-4Journal of Computer-Aided Molecular Design, 2019, vol. 34, p. 443-451https://doi.org/10.1007/s10822-019-00262-4(c) Springer Verlag, 2019info:eu-repo/semantics/openAccessoai:recercat.cat:2445/1702282026-05-29T05:05:01Z
dc.title.none.fl_str_mv Prediction of the n‑octanol/water partition coefficients in the SAMPL6 blind challenge from MST continuum solvation calculations
title Prediction of the n‑octanol/water partition coefficients in the SAMPL6 blind challenge from MST continuum solvation calculations
spellingShingle Prediction of the n‑octanol/water partition coefficients in the SAMPL6 blind challenge from MST continuum solvation calculations
Zamora Ramírez, William J.
Solvatació
Bioquímica
Farmacologia
Solvation
Biochemistry
Pharmacology
title_short Prediction of the n‑octanol/water partition coefficients in the SAMPL6 blind challenge from MST continuum solvation calculations
title_full Prediction of the n‑octanol/water partition coefficients in the SAMPL6 blind challenge from MST continuum solvation calculations
title_fullStr Prediction of the n‑octanol/water partition coefficients in the SAMPL6 blind challenge from MST continuum solvation calculations
title_full_unstemmed Prediction of the n‑octanol/water partition coefficients in the SAMPL6 blind challenge from MST continuum solvation calculations
title_sort Prediction of the n‑octanol/water partition coefficients in the SAMPL6 blind challenge from MST continuum solvation calculations
dc.creator.none.fl_str_mv Zamora Ramírez, William J.
Pinheiro, Silvana de Souza
German, Kilian
Ràfols Llach, Clara
Curutchet Barat, Carles E.
Luque Garriga, F. Xavier
author Zamora Ramírez, William J.
author_facet Zamora Ramírez, William J.
Pinheiro, Silvana de Souza
German, Kilian
Ràfols Llach, Clara
Curutchet Barat, Carles E.
Luque Garriga, F. Xavier
author_role author
author2 Pinheiro, Silvana de Souza
German, Kilian
Ràfols Llach, Clara
Curutchet Barat, Carles E.
Luque Garriga, F. Xavier
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Solvatació
Bioquímica
Farmacologia
Solvation
Biochemistry
Pharmacology
topic Solvatació
Bioquímica
Farmacologia
Solvation
Biochemistry
Pharmacology
description The IEFPCM/MST continuum solvation model is used for the blind prediction of n-octanol/water partition of a set of 11 fragment-like small molecules within the SAMPL6 Part II Partition Coefficient Challenge. The partition coefficient of the neutral species (log P) was determined using an extended parametrization of the B3LYP/6-31G(d) version of the Miertus-Scrocco-Tomasi continuum solvation model in n-octanol. Comparison with the experimental data provided for partition coefficients yielded a root-mean square error (rmse) of 0.78 (log P units), which agrees with the accuracy reported for our method (rmse = 0.80) for nitrogen-containing heterocyclic compounds. Out of the 91 sets of log P values submitted by the participants, our submission is within those with an rmse < 1 and among the four best ranked physical methods. The largest errors involve three compounds: two with the largest positive deviations (SM13 and SM08), and one with the largest negative deviations (SM15). Here we report the potentiometric determination of the log P for SM13, leading to a value of 3.62 ± 0.02, which is in better agreement with most empirical predictions than the experimental value reported in SAMPL6. In addition, further inclusion of several conformations for SM08 significantly improved our results. Inclusion of these refinements led to an overall error of 0.51 (log P units), which supports the reliability of the IEFPCM/MST model for predicting the partitioning of neutral compounds.
publishDate 2019
dc.date.none.fl_str_mv 2019
2020
2020
2020
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/170228
url https://hdl.handle.net/2445/170228
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Versió postprint del document publicat a: https://doi.org/10.1007/s10822-019-00262-4
Journal of Computer-Aided Molecular Design, 2019, vol. 34, p. 443-451
https://doi.org/10.1007/s10822-019-00262-4
dc.rights.none.fl_str_mv (c) Springer Verlag, 2019
info:eu-repo/semantics/openAccess
rights_invalid_str_mv (c) Springer Verlag, 2019
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 9 p.
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Springer Verlag
publisher.none.fl_str_mv Springer Verlag
dc.source.none.fl_str_mv Articles publicats en revistes (Nutrició, Ciències de l'Alimentació i Gastronomia)
reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,811543

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