Literature DB >> 26606626

Searching for Computational Strategies to Accurately Predict pKas of Large Phenolic Derivatives.

Aida Mariana Rebollar-Zepeda1, Tania Campos-Hernández1, María Teresa Ramírez-Silva1, Alberto Rojas-Hernández1, Annia Galano1.   

Abstract

Twenty-two reaction schemes have been tested, within the cluster-continuum model including up to seven explicit water molecules. They have been used in conjunction with nine different methods, within the density functional theory and with second-order Møller-Plesset. The quality of the pKa predictions was found to be strongly dependent on the chosen scheme, while only moderately influenced by the method of calculation. We recommend the E1 reaction scheme [HA + OH(-) (3H2O) ↔ A(-) (H2O) + 3H2O], since it yields mean unsigned errors (MUE) lower than 1 unit of pKa for most of the tested functionals. The best pKa values obtained from this reaction scheme are those involving calculations with PBE0 (MUE = 0.77), TPSS (MUE = 0.82), BHandHLYP (MUE = 0.82), and B3LYP (MUE = 0.86) functionals. This scheme has the additional advantage, compared to the proton exchange method, which also gives very small values of MUE, of being experiment independent. It should be kept in mind, however, that these recommendations are valid within the cluster-continuum model, using the polarizable continuum model in conjunction with the united atom Hartree-Fock cavity and the strategy based on thermodynamic cycles. Changes in any of these aspects of the used methodology may lead to different outcomes.

Entities:  

Year:  2011        PMID: 26606626     DOI: 10.1021/ct2001864

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  7 in total

1.  7-O-Galloyltricetifavan: a promising natural radical scavenger.

Authors:  Le Trung Hieu; Tran Thi Van Thi; Nguyen Thi Hoa; Adam Mechler; Quan V Vo
Journal:  R Soc Open Sci       Date:  2022-06-22       Impact factor: 3.653

2.  Origin of the proton-transfer step in the cofactor-free (1H)-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase: effect of the basicity of an active site His residue.

Authors:  Aitor Hernandez-Ortega; Matthew G Quesne; Soi Bui; Dominic P H M Heuts; Roberto A Steiner; Derren J Heyes; Sam P de Visser; Nigel S Scrutton
Journal:  J Biol Chem       Date:  2014-01-30       Impact factor: 5.157

3.  Hydroxyl Radical Scavenging of Indole-3-Carbinol: A Mechanistic and Kinetic Study.

Authors:  Quan V Vo; Mai Van Bay; Pham Cam Nam; Adam Mechler
Journal:  ACS Omega       Date:  2019-11-08

4.  Structural Characterization of Mannoglucan Isolated from Ophiocordyceps sobolifera and Its Antioxidant Activities.

Authors:  Trung Hieu Le; Thi Van Thi Tran; Van Khoa Tran; Xuan Anh Vu Ho; Thanh Minh Tran; Dang Giang Chau Nguyen; Thi Hong Chuong Nguyen; Rajender S Varma; Tam Kiet Trinh; Thanh-Tam Ho; Thi Bach Hac Nguyen; Tansir Ahamad; Chinh Chien Nguyen; Quyet Van Le
Journal:  ACS Omega       Date:  2022-03-11

5.  A theoretical study of the radical scavenging activity of natural stilbenes.

Authors:  Quan V Vo; Pham Cam Nam; Mai Van Bay; Nguyen Minh Thong; Le Trung Hieu; Adam Mechler
Journal:  RSC Adv       Date:  2019-12-18       Impact factor: 3.361

6.  A thermodynamic and kinetic study of the antioxidant activity of natural hydroanthraquinones.

Authors:  Quan V Vo; Nguyen Minh Thong; Trinh Le Huyen; Pham Cam Nam; Nguyen Minh Tam; Nguyen Thi Hoa; Adam Mechler
Journal:  RSC Adv       Date:  2020-05-27       Impact factor: 4.036

7.  The antioxidant activity of natural diterpenes: theoretical insights.

Authors:  Quan V Vo; Nguyen Minh Tam; Le Trung Hieu; Mai Van Bay; Nguyen Minh Thong; Trinh Le Huyen; Nguyen Thi Hoa; Adam Mechler
Journal:  RSC Adv       Date:  2020-04-16       Impact factor: 4.036

  7 in total

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