scholarly journals Benchmarking computational methods to calculate the octanol/water partition coefficients of a diverse set of organic molecules

Author(s):  
Alondra López-Colón ◽  
Mariela E. Santiago-Mercado ◽  
Jonathan I. Aguirre-Santiago ◽  
Ariana de Jesús-Hernández ◽  
Jenlyan Negrón-Hernández ◽  
...  

In the discovery process of new drugs and the development of novel therapies in medicine, computational modeling is a complementary tool for the design of new molecules by predicting for example their solubility in different solvents. Here, we benchmarked several computational methods to calculate the partition coefficients of a diverse set of 161 organic molecules with experimental logP values obtained from the literature. In general, density functional theory methods yielded the best correlations and lower average deviations. Although results are obtained faster with semiempirical and molecular mechanics methodologies, these methods yielded higher average deviations and lower correlation coefficients than hybrid density functional theory methods. We recommend the use of an empirical formula to correct the calculated values with each methodology tested.

2013 ◽  
Vol 15 (12) ◽  
pp. 123028 ◽  
Author(s):  
Oliver T Hofmann ◽  
Viktor Atalla ◽  
Nikolaj Moll ◽  
Patrick Rinke ◽  
Matthias Scheffler

2021 ◽  
pp. 1-12
Author(s):  
Halimeh Rajabzadeh ◽  
Ayla Sharafat ◽  
Maryam Abbasi ◽  
Maryam Eslami Gharaati ◽  
Iraj Alipourfard

Favipiravir (Fav) has become a well-known drug for medication of patients by appearance of COVID-19. Heterocyclic structure and connected peptide group could make changes for Fav yielding different features from those required features. Therefore, it is indeed a challenging task to prepare a Fav compound with specific features of desired function. In this work, existence of eight Fav structures by tautomeric formations and peptide group rotations were obtained using density functional theory (DFT) optimization calculations. Gas phase, octanol solution, and water solution were employed to show impact of solution on features of Fav besides obtaining partition coefficients (LogP) for Fav compounds. Significant impacts of solutions were seen on features of Fav with the obtained LogP order: Fav-7 >  Fav-8 >  Fav-4 >  Fav-3 >  Fav-2 >  Fav-5 >  Fav-1 >  Fav-6. As a consequence, internal changes yielded significant impacts on features of Fav affirming its carful medication of COVID-19 patients.


2016 ◽  
Vol 121 (1) ◽  
pp. 392-401 ◽  
Author(s):  
Mathew E. McKenzie ◽  
Sushmit Goyal ◽  
Sung Hoon Lee ◽  
Hyun-Hang Park ◽  
Elizabeth Savoy ◽  
...  

2017 ◽  
Vol 53 (27) ◽  
pp. 3830-3833 ◽  
Author(s):  
Andreia de Almeida ◽  
Andreia F. Mósca ◽  
Darren Wragg ◽  
Margot Wenzel ◽  
Paul Kavanagh ◽  
...  

The mechanism of inhibition of water and glycerol permeation via human aquaglyceroporin-3 (AQP3) by gold(iii) complexes has been described, for the first time, using molecular dynamics (MD), combined with density functional theory (DFT) and electrochemical studies.


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