Literature DB >> 29380104

Assessment of tautomer distribution using the condensed reaction graph approach.

T R Gimadiev1,2, T I Madzhidov2, R I Nugmanov2, I I Baskin2,3, I S Antipin2, A Varnek4.   

Abstract

We report the first direct QSPR modeling of equilibrium constants of tautomeric transformations (logK T ) in different solvents and at different temperatures, which do not require intermediate assessment of acidity (basicity) constants for all tautomeric forms. The key step of the modeling consisted in the merging of two tautomers in one sole molecular graph ("condensed reaction graph") which enables to compute molecular descriptors characterizing entire equilibrium. The support vector regression method was used to build the models. The training set consisted of 785 transformations belonging to 11 types of tautomeric reactions with equilibrium constants measured in different solvents and at different temperatures. The models obtained perform well both in cross-validation (Q2 = 0.81 RMSE = 0.7 logK T units) and on two external test sets. Benchmarking studies demonstrate that our models outperform results obtained with DFT B3LYP/6-311 ++ G(d,p) and ChemAxon Tautomerizer applicable only in water at room temperature.

Entities:  

Keywords:  Condensed graphs of reaction; QSPR; Support vector regression; Tautomerism

Mesh:

Substances:

Year:  2018        PMID: 29380104     DOI: 10.1007/s10822-018-0101-6

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


  33 in total

1.  Generalized Gradient Approximation Made Simple.

Authors: 
Journal:  Phys Rev Lett       Date:  1996-10-28       Impact factor: 9.161

2.  Advanced exact structure searching in large databases of chemical compounds.

Authors:  Sergey V Trepalin; Andrey V Skorenko; Konstantin V Balakin; Anatoly F Nasonov; Stanley A Lang; Andrey A Ivashchenko; Nikolay P Savchuk
Journal:  J Chem Inf Comput Sci       Date:  2003 May-Jun

3.  Hydride transfer catalyzed by xylose isomerase: mechanism and quantum effects.

Authors:  Mireia Garcia-Viloca; Cristóbal Alhambra; Donald G Truhlar; Jiali Gao
Journal:  J Comput Chem       Date:  2003-01-30       Impact factor: 3.376

4.  SAMPL2 and continuum modeling.

Authors:  Anthony Nicholls; Stanislaw Wlodek; J Andrew Grant
Journal:  J Comput Aided Mol Des       Date:  2010-04-06       Impact factor: 3.686

5.  Prediction of SAMPL2 aqueous solvation free energies and tautomeric ratios using the SM8, SM8AD, and SMD solvation models.

Authors:  Raphael F Ribeiro; Aleksandr V Marenich; Christopher J Cramer; Donald G Truhlar
Journal:  J Comput Aided Mol Des       Date:  2010-04-01       Impact factor: 3.686

6.  Do not hesitate to use Tversky-and other hints for successful active analogue searches with feature count descriptors.

Authors:  Dragos Horvath; Gilles Marcou; Alexandre Varnek
Journal:  J Chem Inf Model       Date:  2013-06-13       Impact factor: 4.956

7.  Models for identification of erroneous atom-to-atom mapping of reactions performed by automated algorithms.

Authors:  Christophe Muller; Gilles Marcou; Dragos Horvath; João Aires-de-Sousa; Alexandre Varnek
Journal:  J Chem Inf Model       Date:  2012-12-05       Impact factor: 4.956

8.  So you think you understand tautomerism?

Authors:  Roger A Sayle
Journal:  J Comput Aided Mol Des       Date:  2010-03-23       Impact factor: 3.686

9.  Computational chemogenomics: is it more than inductive transfer?

Authors:  J B Brown; Yasushi Okuno; Gilles Marcou; Alexandre Varnek; Dragos Horvath
Journal:  J Comput Aided Mol Des       Date:  2014-04-27       Impact factor: 3.686

10.  Enumeration of ring-chain tautomers based on SMIRKS rules.

Authors:  Laura Guasch; Markus Sitzmann; Marc C Nicklaus
Journal:  J Chem Inf Model       Date:  2014-09-09       Impact factor: 4.956

View more
  5 in total

Review 1.  QSAR without borders.

Authors:  Eugene N Muratov; Jürgen Bajorath; Robert P Sheridan; Igor V Tetko; Dmitry Filimonov; Vladimir Poroikov; Tudor I Oprea; Igor I Baskin; Alexandre Varnek; Adrian Roitberg; Olexandr Isayev; Stefano Curtarolo; Denis Fourches; Yoram Cohen; Alan Aspuru-Guzik; David A Winkler; Dimitris Agrafiotis; Artem Cherkasov; Alexander Tropsha
Journal:  Chem Soc Rev       Date:  2020-05-01       Impact factor: 54.564

2.  Discovery of novel chemical reactions by deep generative recurrent neural network.

Authors:  William Bort; Igor I Baskin; Timur Gimadiev; Artem Mukanov; Ramil Nugmanov; Pavel Sidorov; Gilles Marcou; Dragos Horvath; Olga Klimchuk; Timur Madzhidov; Alexandre Varnek
Journal:  Sci Rep       Date:  2021-02-04       Impact factor: 4.379

Review 3.  Machine Learning of Reaction Properties via Learned Representations of the Condensed Graph of Reaction.

Authors:  Esther Heid; William H Green
Journal:  J Chem Inf Model       Date:  2021-11-04       Impact factor: 6.162

4.  Toward in Silico Modeling of Dynamic Combinatorial Libraries.

Authors:  Iuri Casciuc; Artem Osypenko; Bohdan Kozibroda; Dragos Horvath; Gilles Marcou; Fanny Bonachera; Alexandre Varnek; Jean-Marie Lehn
Journal:  ACS Cent Sci       Date:  2022-05-27       Impact factor: 18.728

5.  Comprehensive Analysis of Applicability Domains of QSPR Models for Chemical Reactions.

Authors:  Assima Rakhimbekova; Timur I Madzhidov; Ramil I Nugmanov; Timur R Gimadiev; Igor I Baskin; Alexandre Varnek
Journal:  Int J Mol Sci       Date:  2020-08-03       Impact factor: 5.923

  5 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.