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| Format: | Preprint |
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2025
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| Online-Zugang: | https://arxiv.org/abs/2509.22430 |
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| _version_ | 1866910109773332480 |
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| author | Carvalho, Felipe Silva McMahon, Alexander Case, David A. Luchko, Tyler |
| author_facet | Carvalho, Felipe Silva McMahon, Alexander Case, David A. Luchko, Tyler |
| contents | Accurate modeling of aqueous monovalent ions is essential for understanding the function of biomolecules, such as nucleic acid stability and binding of charged drugs to protein targets. The 1D and 3D reference interaction site models (1D- and 3D-RISM) of molecular solvation, as implemented in the AmberTools molecular modeling suite, are well suited for modeling mixtures of ionic species around biomolecules across a wide range of concentrations. However, the available ion model parameters were optimized for molecular dynamics simulations, not for the RISM framework, which includes a closure approximation. To address this, we optimized the Lennard-Jones 12-6 model for monovalent ions for 1D-RISM with the partial series expansion of order 3 closure by fitting to experimental values of ion-oxygen distance (IOD), hydration free energy (HFE), partial molar volume (PMV) and mean activity coefficient. The new parameter set demonstrated significant improvement in HFE, IOD, and mean activity coefficients, whereas no overall change was observed for the PMV. A second optimization step was necessary to account for the cation-anion interactions that affect the mean activity coefficients. The new parameters were validated at finite salt concentrations against experimental data for 16 ion pairs and showed improved accuracy for 14 of them, while the results for CsI and CsF were the second best. 1D-RISM results obtained with the new NaCl parameters were used to calculate the preferential interaction parameter of the ions around the 24L B-DNA using 3D-RISM. The new parameters demonstrated better agreement with experiment at physiological and higher concentrations. At lower concentrations, the results primarily depended on the closure with little effect from the ion parameters. Overall, the ion parameters specifically developed for RISM show improved accuracy at infinite dilution and finite concentrations. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2509_22430 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Development of an Optimized Parameter Set for Monovalent Ions in the Reference Interaction Site Model of Solvation Carvalho, Felipe Silva McMahon, Alexander Case, David A. Luchko, Tyler Chemical Physics Accurate modeling of aqueous monovalent ions is essential for understanding the function of biomolecules, such as nucleic acid stability and binding of charged drugs to protein targets. The 1D and 3D reference interaction site models (1D- and 3D-RISM) of molecular solvation, as implemented in the AmberTools molecular modeling suite, are well suited for modeling mixtures of ionic species around biomolecules across a wide range of concentrations. However, the available ion model parameters were optimized for molecular dynamics simulations, not for the RISM framework, which includes a closure approximation. To address this, we optimized the Lennard-Jones 12-6 model for monovalent ions for 1D-RISM with the partial series expansion of order 3 closure by fitting to experimental values of ion-oxygen distance (IOD), hydration free energy (HFE), partial molar volume (PMV) and mean activity coefficient. The new parameter set demonstrated significant improvement in HFE, IOD, and mean activity coefficients, whereas no overall change was observed for the PMV. A second optimization step was necessary to account for the cation-anion interactions that affect the mean activity coefficients. The new parameters were validated at finite salt concentrations against experimental data for 16 ion pairs and showed improved accuracy for 14 of them, while the results for CsI and CsF were the second best. 1D-RISM results obtained with the new NaCl parameters were used to calculate the preferential interaction parameter of the ions around the 24L B-DNA using 3D-RISM. The new parameters demonstrated better agreement with experiment at physiological and higher concentrations. At lower concentrations, the results primarily depended on the closure with little effect from the ion parameters. Overall, the ion parameters specifically developed for RISM show improved accuracy at infinite dilution and finite concentrations. |
| title | Development of an Optimized Parameter Set for Monovalent Ions in the Reference Interaction Site Model of Solvation |
| topic | Chemical Physics |
| url | https://arxiv.org/abs/2509.22430 |