We derive a new model for the established concept of the molecular free energy surface density (MolFESD) yielding a more rigorous representation of local surface contributions to the overall hydrophobicity of a molecule. The model parametrization makes efficient use of both local and global information about solvation thermodynamics, as formulated earlier for the problem of predicting free energies of hydration. The free energy of transfer is separated into an interaction contribution and a term related to the cavity formation. Interaction and cavity components are obtained from the statistical three-dimensional (3D) free energy density and a linear combination of surface and volume terms, respectively. An appropriate molecular interaction field generated by the program Grid is used as an approximate representation of the interaction part of the 3D free energy density. We further compress the 3D density by means of a linear combination of localized surface functions allowing for the derivation of local hydrophobic contributions in the form of a free energy surface density. For a set of 400 compounds our model yields significant correlation (R(2) = 0.95, sigma = 0.57) between experimental and calculated log P values. The final model is applied to establish a correlation between partial free energies of transfer for a series of sucrose derivatives and their relative sweetness, as studied earlier in the group of the authors. We find considerable improvement regarding the rms error of the regression thus validating the presented approach.
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http://dx.doi.org/10.1021/ci025576h | DOI Listing |
Chem Sci
January 2025
Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University Suzhou Jiangsu 215123 China
Understanding the oxygen reduction reaction (ORR) mechanism and accurately characterizing the reaction interface are essential for improving fuel cell efficiency. We developed an active learning framework combining machine learning force fields and enhanced sampling to explore the dynamics and kinetics of the ORR on Fe-N/C using a fully explicit solvent model. Different possible reaction paths have been explored and the O adsorption process is confirmed as the rate-determining step of the ORR at the Fe-N/C-water interface, which needs to overcome a free energy barrier of 0.
View Article and Find Full Text PDFRSC Adv
January 2025
Department of Chemistry, Debre Tabor University Ethiopia.
DFT calculations were performed to investigate the possible reaction mechanisms underlying catalyst-free chloroboration reactions of carbonyl compounds with BCl. The interaction between BCl and the C[double bond, length as m-dash]O moiety of carbonyl compounds is a two-step reaction. In the first step, B of BCl forms a bond with the O of the C[double bond, length as m-dash]O moiety, followed by the 1,3-Cl migration process from BCl to the C of the carbonyl group.
View Article and Find Full Text PDFHeliyon
January 2025
Mechanical Power Engineering Department, Faculty of Engineering - Mataria, Helwan University, Cairo, 11718, Egypt.
Wind turbine control is critical in power generation from wind, thus assuring great efficiency and cost-effectiveness. This has been a subject of intense research, and its advancements are critical to developing even better and efficient wind turbines. This research looks at several passive flow control mechanisms for horizontal wind turbines.
View Article and Find Full Text PDFPhys Chem Chem Phys
January 2025
Department of Chemical Engineering, Indian Institute of Technology Jodhpur, Jodhpur-342037, India.
Correction for 'Structure, dynamic, and free energy analyses of 5-hydroxymethylfurfural in aprotic solvents and imidazolium ionic liquids using all-atom molecular dynamics simulations' by Sweta Jha , , 2024, , 28417-28430, https://doi.org/10.1039/D4CP02914C.
View Article and Find Full Text PDFPhys Chem Chem Phys
January 2025
Department of Chemistry, Hankuk University of Foreign Studies, Yongin 17035, Republic of Korea.
In our previous work, we studied the thermodynamics of two cases of intercompartmental transport through a carbon nanotube: one involving water molecules and the other involving nonpolar molecules. Free energy calculations indicate that transporting water molecules from one compartment to another a narrow channel is impossible, whereas for nonpolar molecules, only approximately half can be transported. Therefore, the interaction strength between transported molecules significantly affects molecular transport.
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