RNA molecules cannot fold in the absence of counterions. Experiments are typically performed in the presence of monovalent and divalent cations. How to treat the impact of a solution containing a mixture of both ion types on RNA folding has remained a challenging problem for decades. By exploiting the large concentration difference between divalent and monovalent ions used in experiments, we develop a theory based on the reference interaction site model (RISM), which allows us to treat divalent cations explicitly while keeping the implicit screening effect due to monovalent ions. Our theory captures both the inner shell and outer shell coordination of divalent cations to phosphate groups, which we demonstrate is crucial for an accurate calculation of RNA folding thermodynamics. The RISM theory for ion–phosphate interactions when combined with simulations based on a transferable coarse-grained model allows us to predict accurately the folding of several RNA molecules in a mixture containing monovalent and divalent ions. The calculated folding free energies and ion-preferential coefficients for RNA molecules (pseudoknots, a fragment of the rRNA, and the aptamer domain of the adenine riboswitch) are in excellent agreement with experiments over a wide range of monovalent and divalent ion concentrations. Because the theory is general, it can be readily used to investigate ion and sequence effects on DNA properties.
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Computational predictions of metal–macrocycle stability constants require accurate treatments of local solvent and pH effects
Rational design of molecular chelating agents requires a detailed understanding of physicochemical ligand–metal interactions in solvent phase. Computational quantum chemistry methods should be able to provide this, but computational reports have shown poor accuracy when determining absolute binding constants for many chelating molecules. To understand why, we compare and benchmark static- and dynamics-based computational procedures for a range of monovalent and divalent cations binding to a conventional cryptand molecule: 2.2.2-cryptand ([2.2.2]). The benchmarking comparison shows that dynamics simulations using standard OPLS-AA classical potentials can reasonably predict binding constants for monovalent cations, but these procedures fail for divalent cations. We also consider computationally efficient static procedure using Kohn–Sham density functional theory (DFT) and cluster-continuum modeling that accounts for local microsolvation and pH effects. This approach accurately predicts binding energies for monovalent and divalent cations with an average error of 3.2 kcal mol −1 compared to experiment. This static procedure thus should be useful for future molecular screening efforts, and high absolute errors in the literature may be due to inadequate modeling of local solvent and pH effects.
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- Award ID(s):
- 1705592
- PAR ID:
- 10310191
- Date Published:
- Journal Name:
- Physical Chemistry Chemical Physics
- Volume:
- 23
- Issue:
- 15
- ISSN:
- 1463-9076
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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