Literature DB >> 18510372

Calculation of quantum-mechanical descriptors for QSPR at the DFT level: is it necessary?

Tomasz Puzyn1, Noriyuki Suzuki, Maciej Haranczyk, Janusz Rak.   

Abstract

Most of the recently published quantitative structure-property relationship (QSPR) models, which can be used to predict environmentally relevant physicochemical data for persistent organic pollutants (e.g., polychlorinated dibenzo- p-dioxins, dibenzofurans, and biphenyls), employ molecular descriptors obtained by means of relatively costly calculations at the density functional theory (DFT) level. However, new semiempirical methods, PM6 and RM1, have recently been developed by J. J. P. Stewart's group. In this study, we compared various QSPR models based on DFT (B3LYP functional) descriptors with the same models based on semiempirical (PM6 and RM1) descriptors. We recalibrated 10 previously published models (for different properties and groups of congeneric compounds) employing PM6 and RM1 descriptors instead of B3LYP ones. We demonstrated that by applying RM1 and PM6 descriptors, we could obtain QSPR models with quality similar to that of models based on B3LYP descriptors. This level of accuracy was out of reach for the models employing AM1- and PM3-based descriptors.

Entities:  

Year:  2008        PMID: 18510372     DOI: 10.1021/ci800021p

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   4.956


  18 in total

1.  CORAL: QSPR models for solubility of [C60] and [C70] fullerene derivatives.

Authors:  Alla P Toropova; Andrey A Toropov; Emilio Benfenati; Giuseppina Gini; Danuta Leszczynska; Jerzy Leszczynski
Journal:  Mol Divers       Date:  2010-03-27       Impact factor: 2.943

2.  Geometry optimization method versus predictive ability in QSPR modeling for ionic liquids.

Authors:  Anna Rybinska; Anita Sosnowska; Maciej Barycki; Tomasz Puzyn
Journal:  J Comput Aided Mol Des       Date:  2016-02-01       Impact factor: 3.686

3.  QSAR-modeling of toxicity of organometallic compounds by means of the balance of correlations for InChI-based optimal descriptors.

Authors:  A A Toropov; A P Toropova; E Benfenati
Journal:  Mol Divers       Date:  2009-05-19       Impact factor: 2.943

4.  A combined LS-SVM & MLR QSAR workflow for predicting the inhibition of CXCR3 receptor by quinazolinone analogs.

Authors:  Antreas Afantitis; Georgia Melagraki; Haralambos Sarimveis; Panayiotis A Koutentis; Olga Igglessi-Markopoulou; George Kollias
Journal:  Mol Divers       Date:  2009-05-30       Impact factor: 2.943

5.  How the energy evaluation method used in the geometry optimization step affect the quality of the subsequent QSAR/QSPR models.

Authors:  Asmund Rinnan; Niels Johan Christensen; Søren Balling Engelsen
Journal:  J Comput Aided Mol Des       Date:  2009-11-27       Impact factor: 3.686

6.  Interaction between alkaline earth cations and oxo-ligands. DFT study of the affinity of the Ca2+ cation for carbonyl ligands.

Authors:  Leonardo Moreira da Costa; José Walkimar de Mesquita Carneiro; Gilberto Alves Romeiro; Lilian Weitzel Coelho Paes
Journal:  J Mol Model       Date:  2010-04-30       Impact factor: 1.810

7.  Estimating persistence of brominated and chlorinated organic pollutants in air, water, soil, and sediments with the QSPR-based classification scheme.

Authors:  T Puzyn; M Haranczyk; N Suzuki; T Sakurai
Journal:  Mol Divers       Date:  2010-04-13       Impact factor: 2.943

8.  Using nano-QSAR to predict the cytotoxicity of metal oxide nanoparticles.

Authors:  Tomasz Puzyn; Bakhtiyor Rasulev; Agnieszka Gajewicz; Xiaoke Hu; Thabitha P Dasari; Andrea Michalkova; Huey-Min Hwang; Andrey Toropov; Danuta Leszczynska; Jerzy Leszczynski
Journal:  Nat Nanotechnol       Date:  2011-02-13       Impact factor: 39.213

9.  DFT studies of imino and thiocarbonyl ligands with the pentaaqua Mg²⁺ cation: affinity and associated parameters.

Authors:  Leonardo Moreira da Costa; Glaucio Braga Ferreira; José Walkimar de M Carneiro
Journal:  J Mol Model       Date:  2013-03-28       Impact factor: 1.810

10.  Modeling the overall persistence and environmental mobility of sulfur-containing polychlorinated organic compounds.

Authors:  Aleksandra Mostrag; Tomasz Puzyn; Maciej Haranczyk
Journal:  Environ Sci Pollut Res Int       Date:  2010-02       Impact factor: 4.223

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