Solvent Quality and Nonbiological Oligomer Folding: Revisiting Conventional Paradigms
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2024
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| author | Foumthuim, Cedrix J. Dongmo Arcangeli, Tobia Škrbić, Tatjana Giacometti, Achille |
| author_facet | Foumthuim, Cedrix J. Dongmo Arcangeli, Tobia Škrbić, Tatjana Giacometti, Achille |
| contents | We report on extensive molecular dynamics atomistic simulations of a \textit{meta}-substituted \textit{poly}-phenylacetylene (pPA) foldamer dispersed in three solvents, water \ce{H2O}, cyclohexane \ce{cC6H12}, and \textit{n}-hexane \ce{nC6H14}, and for three oligomer lengths \textit{12mer}, \textit{16mer} and \textit{20mer}. At room temperature, we find a tendency of the pPA foldamer to collapse into a helical structure in all three solvents but with rather different stability character, stable in water, marginally stable in n-hexane, unstable in cyclohexane. In the case of water, the initial and final number of hydrogen bonds of the foldamer with water molecules is found to be unchanged, with no formation of intrachain hydrogen bonding, thus indicating that hydrogen bonding plays no role in the folding process. In all three solvents, the folding is found to be mainly driven by electrostatics, nearly identical in the three cases, and largely dominant compared to van der Waals interactions that are different in the three cases.
This scenario is also supported by the analysis of distribution of the bond and dihedral angles and by a direct calculation of the solvation and transfer free energies via thermodynamic integration. The different stability in the case of cyclohexane and n-hexane notwithstanding their rather similar chemical composition can be traced back to the different entropy-enthalpy compensation that is found similar for water and n-hexane, and very different for cyclohexane.
A comparison with the same properties for \textit{poly}-phenylalanine oligomers underscores the crucial differences between pPA and peptides.
To highlight how these findings can hardly be interpreted in terms of a simple "good" and "poor" solvent picture, a molecular dynamics study of a bead-spring polymer chain in a Lennard-Jones fluid is also included. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2407_20686 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Solvent Quality and Nonbiological Oligomer Folding: Revisiting Conventional Paradigms Foumthuim, Cedrix J. Dongmo Arcangeli, Tobia Škrbić, Tatjana Giacometti, Achille Soft Condensed Matter We report on extensive molecular dynamics atomistic simulations of a \textit{meta}-substituted \textit{poly}-phenylacetylene (pPA) foldamer dispersed in three solvents, water \ce{H2O}, cyclohexane \ce{cC6H12}, and \textit{n}-hexane \ce{nC6H14}, and for three oligomer lengths \textit{12mer}, \textit{16mer} and \textit{20mer}. At room temperature, we find a tendency of the pPA foldamer to collapse into a helical structure in all three solvents but with rather different stability character, stable in water, marginally stable in n-hexane, unstable in cyclohexane. In the case of water, the initial and final number of hydrogen bonds of the foldamer with water molecules is found to be unchanged, with no formation of intrachain hydrogen bonding, thus indicating that hydrogen bonding plays no role in the folding process. In all three solvents, the folding is found to be mainly driven by electrostatics, nearly identical in the three cases, and largely dominant compared to van der Waals interactions that are different in the three cases. This scenario is also supported by the analysis of distribution of the bond and dihedral angles and by a direct calculation of the solvation and transfer free energies via thermodynamic integration. The different stability in the case of cyclohexane and n-hexane notwithstanding their rather similar chemical composition can be traced back to the different entropy-enthalpy compensation that is found similar for water and n-hexane, and very different for cyclohexane. A comparison with the same properties for \textit{poly}-phenylalanine oligomers underscores the crucial differences between pPA and peptides. To highlight how these findings can hardly be interpreted in terms of a simple "good" and "poor" solvent picture, a molecular dynamics study of a bead-spring polymer chain in a Lennard-Jones fluid is also included. |
| title | Solvent Quality and Nonbiological Oligomer Folding: Revisiting Conventional Paradigms |
| topic | Soft Condensed Matter |
| url | https://arxiv.org/abs/2407.20686 |