Literature DB >> 27460058

Prediction of cyclohexane-water distribution coefficients with COSMO-RS on the SAMPL5 data set.

Andreas Klamt1,2, Frank Eckert3, Jens Reinisch3, Karin Wichmann3.   

Abstract

The Conductor-Like-Screening-Model for Real Solvents (COSMO-RS) method has been used for the blind prediction of cyclohexane-water distribution coefficients logD within the SAMPL challenge. The partition coefficient logP of the neutral species was calculated first and then corrected for dissociation or protonation, as appropriate for acidic or basic solutes, to obtain the cyclohexane-water logD. Using the latest version of the COSMOtherm implementation, this approach in combination with a rigorous conformational sampling yielded a predictive accuracy of 2.11 log units (RMSD) for the 53 compounds of the blind prediction dataset. By that it was the most accurate of all contest submissions and it also achieved the best rank order. The RMSD mainly arises from a group of outliers in the negative logD range, which at least partly may arise from dimerization or other experimental problems coming up for very polar molecules in very non-polar solvents.

Entities:  

Keywords:  COSMO-RS; Distribution coefficients; Molecular modeling; Molecular simulation; SAMPL5; Solvation

Mesh:

Substances:

Year:  2016        PMID: 27460058     DOI: 10.1007/s10822-016-9927-y

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  11 in total

1.  A Comprehensive Comparison of the IEFPCM and SS(V)PE Continuum Solvation Methods with the COSMO Approach.

Authors:  A Klamt; C Moya; J Palomar
Journal:  J Chem Theory Comput       Date:  2015-08-13       Impact factor: 6.006

2.  First Principles Calculations of Aqueous pKa Values for Organic and Inorganic Acids Using COSMO-RS Reveal an Inconsistency in the Slope of the pKa Scale.

Authors:  Andreas Klamt; Frank Eckert; Michael Diedenhofen; Michael E Beck
Journal:  J Phys Chem A       Date:  2003-11-06       Impact factor: 2.781

3.  On the performance of continuum solvation methods. A comment on "Universal approaches to solvation modeling".

Authors:  Andreas Klamt; Benedetta Mennucci; Jacopo Tomasi; Vincenzo Barone; Carles Curutchet; Modesto Orozco; F Javier Luque
Journal:  Acc Chem Res       Date:  2009-04-21       Impact factor: 22.384

4.  Prediction of the free energy of hydration of a challenging set of pesticide-like compounds.

Authors:  Andreas Klamt; Frank Eckert; Michael Diedenhofen
Journal:  J Phys Chem B       Date:  2009-04-09       Impact factor: 2.991

Review 5.  Design of drugs involving the concepts and theories of drug metabolism and pharmacokinetics.

Authors:  D A Smith; B C Jones; D K Walker
Journal:  Med Res Rev       Date:  1996-05       Impact factor: 12.944

6.  Calculation of solvation free energies with DCOSMO-RS.

Authors:  Andreas Klamt; Michael Diedenhofen
Journal:  J Phys Chem A       Date:  2015-02-10       Impact factor: 2.781

7.  COSMO-RSC: Second-Order Quasi-Chemical Theory Recovering Local Surface Correlation Effects.

Authors:  A Klamt
Journal:  J Phys Chem A       Date:  2016-03-18       Impact factor: 2.781

8.  Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge.

Authors:  Ariën S Rustenburg; Justin Dancer; Baiwei Lin; Jianwen A Feng; Daniel F Ortwine; David L Mobley; John D Chodera
Journal:  J Comput Aided Mol Des       Date:  2016-10-07       Impact factor: 3.686

9.  Probing carboxylate Gibbs transfer energies via liquid|liquid transfer at triple phase boundary electrodes: ion-transfer voltammetry versus COSMO-RS predictions.

Authors:  Stuart M MacDonald; Marcin Opallo; Andreas Klamt; Frank Eckert; Frank Marken
Journal:  Phys Chem Chem Phys       Date:  2008-05-22       Impact factor: 3.676

10.  Hydrophobicities of the nucleic acid bases: distribution coefficients from water to cyclohexane.

Authors:  P Shih; L G Pedersen; P R Gibbs; R Wolfenden
Journal:  J Mol Biol       Date:  1998-07-17       Impact factor: 5.469

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  21 in total

1.  The influence of hydrogen bonding on partition coefficients.

Authors:  Nádia Melo Borges; Peter W Kenny; Carlos A Montanari; Igor M Prokopczyk; Jean F R Ribeiro; Josmar R Rocha; Geraldo Rodrigues Sartori
Journal:  J Comput Aided Mol Des       Date:  2017-01-04       Impact factor: 3.686

2.  Prediction of partition and distribution coefficients in various solvent pairs with COSMO-RS.

Authors:  Sofja Tshepelevitsh; Kertu Hernits; Ivo Leito
Journal:  J Comput Aided Mol Des       Date:  2018-05-30       Impact factor: 3.686

3.  Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model.

Authors:  Sebastian Diaz-Rodriguez; Samantha M Bozada; Jeremy R Phifer; Andrew S Paluch
Journal:  J Comput Aided Mol Des       Date:  2016-08-26       Impact factor: 3.686

4.  Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections.

Authors:  Frank C Pickard; Gerhard König; Florentina Tofoleanu; Juyong Lee; Andrew C Simmonett; Yihan Shao; Jay W Ponder; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2016-09-19       Impact factor: 3.686

5.  Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge.

Authors:  Mehtap Işık; Teresa Danielle Bergazin; Thomas Fox; Andrea Rizzi; John D Chodera; David L Mobley
Journal:  J Comput Aided Mol Des       Date:  2020-02-27       Impact factor: 3.686

6.  COSMO-RS based predictions for the SAMPL6 logP challenge.

Authors:  Christoph Loschen; Jens Reinisch; Andreas Klamt
Journal:  J Comput Aided Mol Des       Date:  2019-11-26       Impact factor: 3.686

7.  Use of molecular dynamics fingerprints (MDFPs) in SAMPL6 octanol-water log P blind challenge.

Authors:  Shuzhe Wang; Sereina Riniker
Journal:  J Comput Aided Mol Des       Date:  2019-11-19       Impact factor: 3.686

8.  Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge.

Authors:  Caitlin C Bannan; Kalistyn H Burley; Michael Chiu; Michael R Shirts; Michael K Gilson; David L Mobley
Journal:  J Comput Aided Mol Des       Date:  2016-09-27       Impact factor: 3.686

9.  Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database.

Authors:  Guilherme Duarte Ramos Matos; Daisy Y Kyu; Hannes H Loeffler; John D Chodera; Michael R Shirts; David L Mobley
Journal:  J Chem Eng Data       Date:  2017-04-24       Impact factor: 2.694

Review 10.  High throughput methods to measure the propensity of compounds to form intramolecular hydrogen bonding.

Authors:  Giulia Caron; Maura Vallaro; Giuseppe Ermondi
Journal:  Medchemcomm       Date:  2017-04-27       Impact factor: 3.597

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