Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States)
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States)
- National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States)
- Department of Mathematics, Michigan State University, East Lansing, Michigan 48824 (United States)
- Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States)
Implicit solvent models are important tools for calculating solvation free energies for chemical and biophysical studies since they require fewer computational resources but can achieve accuracy comparable to that of explicit-solvent models. In past papers, geometric flow-based solvation models have been established for solvation analysis of small and large compounds. In the present work, the use of realistic experiment-based parameter choices for the geometric flow models is studied. We find that the experimental parameters of solvent internal pressure p = 172 MPa and surface tension γ = 72 mN/m produce solvation free energies within 1 RT of the global minimum root-mean-squared deviation from experimental data over the expanded set. Our results demonstrate that experimental values can be used for geometric flow solvent model parameters, thus eliminating the need for additional parameterization. We also examine the correlations between optimal values of p and γ which are strongly anti-correlated. Geometric analysis of the small molecule test set shows that these results are inter-connected with an approximately linear relationship between area and volume in the range of molecular sizes spanned by the data set. In spite of this considerable degeneracy between the surface tension and pressure terms in the model, both terms are important for the broader applicability of the model.
- OSTI ID:
- 22251323
- Journal Information:
- Journal of Chemical Physics, Vol. 139, Issue 20; Other Information: (c) 2013 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA); ISSN 0021-9606
- Country of Publication:
- United States
- Language:
- English
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