A Nonlinear Group Contribution Method for Predicting the Free Energies of Inclusion Complexation of Organic Molecules with α- and β-Cyclodextrins

2001 ◽  
Vol 41 (5) ◽  
pp. 1266-1273 ◽  
Author(s):  
Takahiro Suzuki
Keyword(s):  
Organic Molecules ◽  
Inclusion Complexation ◽  
Group Contribution ◽  
Group Contribution Method ◽  
Free Energies

Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field.

2018 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Alejandro Lara ◽  
David L. Mobley ◽  
Toon Vestraelen ◽  
Adelio R Matamala ◽  
...  
Keyword(s):  
Force Field ◽  
Functional Groups ◽  
Electrostatic Interactions ◽  
Organic Molecules ◽  
Force Fields ◽  
Chemical Elements ◽  
Atomic Charges ◽  
Free Energies ◽  
Molecular Systems ◽  
Solvent Model

<div>Computer simulations of bio-molecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in bio-molecular systems and are therein described by atomic point charges.</div><div>In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the MBIS atomic charge method, including the solvent polarization, with a root mean square error of 2.0 kcal mol<sup>-1</sup> for the 613 organic molecules studied. The largest deviation was observed for phosphor-containing molecules and the molecules with amide, ester and amine functional groups.</div>

scholarly journals A Computational Protocol Combining DFT and Cheminformatics for Prediction of pH-Dependent Redox Potentials

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3978
Author(s):  
Rocco Peter Fornari ◽  
Piotr de Silva
Keyword(s):  
Organic Molecules ◽  
Ph Value ◽  
Computational Cost ◽  
Legendre Transform ◽  
Good Prediction ◽  
Redox Potentials ◽  
Free Energies ◽  
Hybrid Functional ◽  
Data Set ◽  
State Changes

Discovering new materials for energy storage requires reliable and efficient protocols for predicting key properties of unknown compounds. In the context of the search for new organic electrolytes for redox flow batteries, we present and validate a robust procedure to calculate the redox potentials of organic molecules at any pH value, using widely available quantum chemistry and cheminformatics methods. Using a consistent experimental data set for validation, we explore and compare a few different methods for calculating reaction free energies, the treatment of solvation, and the effect of pH on redox potentials. We find that the B3LYP hybrid functional with the COSMO solvation method, in conjunction with thermal contributions evaluated from BLYP gas-phase harmonic frequencies, yields a good prediction of pH = 0 redox potentials at a moderate computational cost. To predict how the potentials are affected by pH, we propose an improved version of the Alberty-Legendre transform that allows the construction of a more realistic Pourbaix diagram by taking into account how the protonation state changes with pH.

A group contribution method based on nonrandom lattice-hole theory with molecular bulkiness

1998 ◽  
Vol 15 (3) ◽  
pp. 246-251 ◽  
Author(s):  
Byung Heung Park ◽  
Min Sun Yeom ◽  
Ki-Pung Yoo ◽  
Chul Soo Lee
Keyword(s):  
Group Contribution ◽  
Group Contribution Method ◽  
Hole Theory
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