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Título: THE RECONCILIATION BETWEEN THE EXPERIMENTAL AND CALCULATED OCTANOL-WATER PARTITION COEFFICIENT OF 1,2-DIPALMITOYL-SNGLYCERO-3-PHOSPHATIDYLCHOLINE USING ATOMISTIC MOLECULAR DYNAMICS: AN OPEN QUESTION
Autor: RAYLA KELLY MAGALHAES COSTA
Colaborador(es): ANDRE SILVA PIMENTEL - Orientador
Catalogação: 18/MAI/2023 Língua(s): PORTUGUESE - BRAZIL
Tipo: TEXT Subtipo: THESIS
Notas: [pt] Todos os dados constantes dos documentos são de inteira responsabilidade de seus autores. Os dados utilizados nas descrições dos documentos estão em conformidade com os sistemas da administração da PUC-Rio.
[en] All data contained in the documents are the sole responsibility of the authors. The data used in the descriptions of the documents are in conformity with the systems of the administration of PUC-Rio.
Referência(s): [pt] https://www.maxwell.vrac.puc-rio.br/projetosEspeciais/ETDs/consultas/conteudo.php?strSecao=resultado&nrSeq=62569&idi=1
[en] https://www.maxwell.vrac.puc-rio.br/projetosEspeciais/ETDs/consultas/conteudo.php?strSecao=resultado&nrSeq=62569&idi=2
DOI: https://doi.org/10.17771/PUCRio.acad.62569
Resumo:
The octanol-water partition coefficient of the compost 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) molecule wasinvestigated using the methods of thermodynamic integration and umbrellasampling through atomistic molecular dynamics simulations. TheAMBER/GAFF and CHARMM/CGenFF force fields were used with sixwater models (SPC, TIP3P, TIP4P, TIP5P, OPC3, and OPC4) widely usedin molecular dynamics simulations. Among the models used, the OPC4water model with the two force fields provided the best agreement with theexperimental octanol-water partition coefficient of the DPPC. However,there is still much room for improvement in water models that correctlyestimate the surface tension. Using the OPC4 water model, the Gibbs freeenergy of transferring DPPC from octanol to the aqueous phase wascalculated to be 19.8(plus minus)0.3 and 20.2(plus minus)0.3 kcal mol-1, estimating an octanolwater partition coefficient of 14.5(plus minus)0.4 and 14.8(plus minus)0.3 for the AMBER/GAFFand CHARMM/CGenFF force fields, respectively. Umbrella samplingpresented issues of molecules being dragged between the two phases,generating artifacts, and consequently underestimating the values of freeenergy and octanol-water partition coefficient. This study shows theimportance of developing new models of water that accurately reproduceall its experimental characteristics. The reconciliation betweenexperimental measurements and theoretical calculations of partitioncoefficients of amphiphilic molecules. This study may have greatimportance in many areas of scientific and industrial applications, such asbiophysics, surfactant, colloids, membranes, medicine, nanotechnology,and food and pharmaceutical industries.
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