Dataset Information

Condensed-Phase Molecular Representation to Link Structure and Thermodynamics in Molecular Dynamics.

ABSTRACT: Molecular design requires systematic and broadly applicable methods to extract structure-property relationships. The focus of this study is on learning thermodynamic properties from molecular-liquid simulations. The methodology relies on an atomic representation originally developed for electronic properties: the Spectrum of London and Axilrod-Teller-Muto representation (SLATM). SLATM's expansion in one-, two-, and three-body interactions makes it amenable to probing structural ordering in molecular liquids. We show that such representation encodes enough critical information to permit the learning of thermodynamic properties via linear methods. We demonstrate our approach on the preferential insertion of small solute molecules toward cardiolipin membranes and monitor selectivity against a similar lipid. Our analysis reveals simple, interpretable relationships between two- and three-body interactions and selectivity, identifies key interactions to build optimal prototypical solutes, and charts a two-dimensional projection that displays clearly separated basins. The methodology is generally applicable to a variety of thermodynamic properties.

SUBMITTER: Mohr B

PROVIDER: S-EPMC10373487 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature

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Publications

Condensed-Phase Molecular Representation to Link Structure and Thermodynamics in Molecular Dynamics.

Mohr Bernadette B van der Mast Diego D Bereau Tristan T

Journal of chemical theory and computation 20230703 14

Molecular design requires systematic and broadly applicable methods to extract structure-property relationships. The focus of this study is on learning thermodynamic properties from molecular-liquid simulations. The methodology relies on an atomic representation originally developed for electronic properties: the Spectrum of London and Axilrod-Teller-Muto representation (SLATM). SLATM's expansion in one-, two-, and three-body interactions makes it amenable to probing structural ordering in molec ...[more]

PMID: 37395557

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Project description:Lifshitz theory is widely used to calculate interfacial interaction energies and underpins established approaches to the interpretation of measurement data from experimental methods including the surface forces apparatus and the atomic force microscope. However, a significant limitation of Lifshitz theory is that it uses the bulk dielectric properties of the medium to predict the work of adhesion. Here, we demonstrate that a different approach, in which the interactions between molecules at surfaces and in the medium are described by a set of surface site interaction points (SSIPs), yields interaction free energies that are correlated better with experimentally determined values. The work of adhesion W(Lifshitz) between hydrocarbon surfaces was calculated in 260 liquids using Lifshitz theory and compared with interaction free energies ΔΔG calculated using the SSIP model. The predictions of these models diverge in significant ways. In particular, ΔΔG values for hydrocarbon surfaces are typically small and vary little, but in contrast, W(Lifshitz) values span 4 orders of magnitude. Moreover, the SSIP model yields significantly different ΔΔG values in some liquids for which Lifshitz theory predicts similar values of W(Lifshitz). These divergent predictions were tested using atomic force microscopy. Experimentally determined works of adhesion were closer to the values predicted using the SSIP model than Lifshitz theory. In mixtures of methanol and benzyl alcohol, even greater differences were found in the interaction energies calculated using the two models: the value of ΔΔG calculated using the SSIP model declines smoothly as the benzyl alcohol concentration increases, and values are well correlated with experimental data; however, W(Lifshitz) decreases to a minimum and then increases, reaching a larger value for benzyl alcohol than for methanol. We conclude that the SSIP model provides more reliable estimates of the work of adhesion than Lifshitz theory.

Dataset Information

Condensed-Phase Molecular Representation to Link Structure and Thermodynamics in Molecular Dynamics.

Publications

Condensed-Phase Molecular Representation to Link Structure and Thermodynamics in Molecular Dynamics.

Similar Datasets

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