Viayna, Antonio Pinheiro, Silvana Curutchet, Carles Luque, F Javier Zamora, William J
Published in
Journal of computer-aided molecular design
Within the scope of SAMPL7 challenge for predicting physical properties, the Integral Equation Formalism of the Miertus-Scrocco-Tomasi (IEFPCM/MST) continuum solvation model has been used for the blind prediction of n-octanol/water partition coefficients and acidity constants of a set of 22 and 20 sulfonamide-containing compounds, respectively. The...
Holtomo, Olivier Hadidjatou, Hamadou Tandong, Ayiseh Frederick Nsangou, Mama Motapon, Ousmanou
Published in
Journal of Molecular Modeling
The present work investigates the infrared spectra and solvation free energies (SE) of PEHA ((E)-2-(Pyridin-2-yl) ethyl 3-(3,4-dihydroxyphenyl) acrylate) and their impact on the oxidation. The latter was examined through the ionization potential parameter (IP). These investigations were carried out by the DFT method at B3LYP/6-31G(d) for optimizati...
Krämer, Andreas Hudson, Phillip S Jones, Michael R Brooks, Bernard R
Published in
Journal of computer-aided molecular design
Accurately computing partition coefficients is a pivotal part of drug discovery. Specifically, octanol-water partition coefficients can provide information into hydrophobicity of drug-like molecules, as well as a de facto representation of membrane permeability. However, one challenge facing the computation of partition coefficients is the need to ...
Fan, Shujie Iorga, Bogdan I Beckstein, Oliver
Published in
Journal of computer-aided molecular design
All-atom molecular dynamics simulations with stratified alchemical free energy calculations were used to predict the octanol-water partition coefficient [Formula: see text] of eleven small molecules as part of the SAMPL6-[Formula: see text] blind prediction challenge using four different force field parametrizations: standard OPLS-AA with transfera...
Ouimet, Jonathan A Paluch, Andrew S
Published in
Journal of computer-aided molecular design
Blind predictions of octanol/water partition coefficients at 298 K for 11 kinase inhibitor fragment like compounds were made for the SAMPL6 challenge. We used the conventional, "untrained", free energy based approach wherein the octanol/water partition coefficient was computed directly as the difference in solvation free energy in water and 1-octan...
Procacci, Piero Guarnieri, Guido
Published in
Journal of computer-aided molecular design
In this paper, we compute, by means of a non equilibrium alchemical technique, the water-octanol partition coefficients (LogP) for a series of drug-like compounds in the context of the SAMPL6 challenge initiative. Our blind predictions are based on three of the most popular non-polarizable force fields, CGenFF, GAFF2, and OPLS-AA and are critically...
Zamora, William J Pinheiro, Silvana German, Kilian Ràfols, Clara Curutchet, Carles Luque, F Javier
Published in
Journal of computer-aided molecular design
The IEFPCM/MST continuum solvation model is used for the blind prediction of n-octanol/water partition of a set of 11 fragment-like small molecules within the SAMPL6 Part II Partition Coefficient Challenge. The partition coefficient of the neutral species (log P) was determined using an extended parametrization of the B3LYP/6-31G(d) version of the ...
Mecklenfeld, Andreas Raabe, Gabriele
Published in
Journal of computer-aided molecular design
Accurate solvation free energy ΔGsolv predictions require well parametrized force fields. In order to refit Lennard-Jones (LJ) parameters for improved ΔGsolv predictions for a variety of compound classes and chemical environments, a large number of ΔGsolv calculations is required. As the calculation of ΔGsolv is computational expensive, there is ne...
Roy, Dipankar Kovalenko, Andriy
Published in
Journal of computer-aided molecular design
The molecular solvation theory in the form of the Three-Dimensional Reference Interaction Site Model (3D-RISM) with Kovalenko-Hirata (KH) closure relation is benchmarked for use with dimethyl sulfoxide (DMSO) as solvent for (bio)-chemical simulation within the framework of integral equation formalism. Several force field parameters have been tested...
Hinge, Vijaya Kumar Roy, Dipankar Kovalenko, Andriy
Published in
Journal of computer-aided molecular design
The state-of-the-art molecular solvation theory is used to predict skin permeability of a large set of compounds with available experimental skin permeability coefficient (logKP). Encouraging results are obtained pointing to applicability of a novel quantitative structure activity model that uses statistical physics based 3D-RISM-KH theory for solv...
