Liquids, Volume 4, Issue 3 (September 2024) – 3 articles

Years of massive applications of high-throughput atomistic modeling tools such as molecular docking and end-point free energy calculations in the drug industry and academic exploration have made them indispensable parts of hierarchical screening. While the similarities between host–guest and protein–ligand complexes lead to the direct extension of techniques for protein–ligand screening to host–guest systems, the practical performance of these hit identification tools remains unclear in host-–-guest binding. Recent reports on specific host–guest complexes suggest that the experience on the accuracy ladder accumulated from protein–ligand cases could be invalid in host–guest complexes, which makes it an urgent need to perform a systematic benchmark to secure solid numerical supports and guidance of practical setups. Concerning molecular docking, there still lacks a comprehensive benchmark considering popular docking programs. As for end-point reranking, quantitative and rigorous free energy estimation via end-point formulism requires establishing statistically meaningful measurements of uncertainties due to finite sampling, which is neglected or underestimated by a significant portion in almost all main-stream applications. Further, a face-to-face comparison between different screening tools is required for the design of a hierarchical workflow. To fill the above-mentioned critical gaps, in this work, using a dataset containing tens of host–guest complexes involving basket-like macromolecular hosts from the octa acid family, we extensively benchmark seven academic docking protocols and perform post-docking end-point rescoring with twenty protocols. The resulting comprehensive benchmark provides conclusive pictures of the practical value of docking and end-point screening in OA host–guest binding. Full article

Mole fraction of solubilities are reported for the: o-acetoacetanisidide, anthracene, benzoin, 4-tert-butylbenzoic acid, 3-chlorobenzoic acid, 3-chlorobenzoic acid, 2-chloro-5-nitrobenzoic acid, 4-chloro-3-nitrobenzoic acid, 3,4-dichlorobenzoic acid, 2,3-dimethoxybenzoic acid, 3,4-dimethoxybenzoic acid, 3,5-dimethoxybenzoic acid, 3,5-dinitrobenzoic acid, diphenyl sulfone, 2-ethylanthraquinone, 2-methoxybenzoic acid, 4-methoxybenzoic acid, 2-methylbenzoic acid, 3-methylbenzoic acid, 2-methyl-3-nitrobenzoic acid, 3-methyl-4-nitrobenzoic acid, 4-methyl-3-nitrobenzoic acid, 2-naphthoxyacetic acid, 3-nitrobenzoic acid, 4-nitrobenzoic acid, salicylamide, thioxanthene-9-one, 3,4,5-trimethoxybenzoic acid, and xanthene dissolved in isobutyl acetate at 298.15 K. The results of our experimental measurements, combined with the published literature data, were used to obtain Abraham model equations for isobutyl acetate. The mathematical correlations presented in the current study describe the observed molar solubility ratios of the solutes dissolved in isobutyl acetate to within an overall standard deviation of 0.12 log units or less. Full article

Vaporization enthalpies and vapor pressures of 5α-androstane and 5α-cholestane are reported using correlation gas chromatography (CGC). The results for 5α-cholestane are compared to both estimated and experimental values reported previously for 5α-cholestane. The results are generally in agreement with the literature within the reported uncertainties. A simple method for reducing the amount of curvature in logarithm plots of vapor pressures as a function of K/T when using n-alkanes as standards in CGC experiments is also reported. This may prove useful in evaluating vapor pressures of rigid hydrocarbons at high temperatures. Full article