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Overcoming of One More Pitfall in Boundary Element Calculations with Computer Simulations of Ion-Selective Electrode Response.

ABSTRACT: Computer simulations of ion-selective membrane electrodes using diffusion layer models based on finite-differences principle for calculating diffusion processes in both phases and taking into account the local ion exchange equilibrium at the interface are successfully used for clarifying and even predicting the influence of different diffusion factors on several time-dependent characteristics of electrodes. It is shown here that a well-established approach based on the assumption of the constant concentration of the interfering ion in the sample solution fails for solutions containing strongly interfering ions where the concentration of the interfering ion in the boundary layer of the solution can be far lower in comparison with its concentration in the bulk. The limitation is demonstrated by a drastic discrepancy between experimental and calculated curves for the dependence of potential on time. This limitation can be overcome by taking into account the change of the interfering ion concentration in the boundary layer in accordance with the electroneutrality condition. A good agreement between simulation results and experimental data is demonstrated.

SUBMITTER: Egorov VV

PROVIDER: S-EPMC6649265 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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Overcoming of One More Pitfall in Boundary Element Calculations with Computer Simulations of Ion-Selective Electrode Response.

Egorov Vladimir V VV Novakovskii Andrei D AD

ACS omega 20190118 1

Computer simulations of ion-selective membrane electrodes using diffusion layer models based on finite-differences principle for calculating diffusion processes in both phases and taking into account the local ion exchange equilibrium at the interface are successfully used for clarifying and even predicting the influence of different diffusion factors on several time-dependent characteristics of electrodes. It is shown here that a well-established approach based on the assumption of the constant ...[more]

PMID: 31459419

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Project description:Biological processes require DNA and RNA helices to pack together in specific interhelical orientations. While electrostatic repulsion between backbone charges is expected to be maximized when helices are in parallel alignment, such orientations are commonplace in nature. To better understand how the repulsion is overcome, we used experimental and computational approaches to investigate how the orientational preferences of DNA helices depend on the concentration and valence of mobile cations. We used Förster resonance energy transfer (FRET) to probe the relative orientations of two 24-bp helices held together via a freely rotating PEG linker. At low cation concentrations, the helices preferred more "cross"-like orientations over those closer to parallel, and this preference was reduced with increasing salt concentrations. The results were in good quantitative agreement with Poisson-Boltzmann (PB) calculations for monovalent salt (Na+). However, PB underestimated the ability of mixtures of monovalent and divalent ions (Mg2+) to reduce the conformational preference. As a complementary approach, we performed all-atom molecular dynamics (MD) simulations and found better agreement with the experimental results. While MD and PB predict similar electrostatic forces, MD predicts a greater accumulation of Mg2+ in the ion atmosphere surrounding the DNA. Mg2+ occupancy is predicted to be greater in conformations close to the parallel orientation than in conformations close to the crossed orientation, enabling a greater release of Na+ ions and providing an entropic gain (one bound ion for two released). MD predicts an entropy gain larger than that of PB because of the increased Mg2+ occupancy. The entropy changes have a negligible effect at low Mg2+ concentrations because the free energies are dominated by electrostatic repulsion. However, as the Mg2+ concentration increases, charge screening is more effective and the mixing entropy produces readily detectable changes in packing preferences. Our results underline the importance of mixing entropy of counterions in nucleic acid interactions and provide a new understanding on the impact of a mixed ion atmosphere on the packing of DNA helices.

Dataset Information

Overcoming of One More Pitfall in Boundary Element Calculations with Computer Simulations of Ion-Selective Electrode Response.

Publications

Overcoming of One More Pitfall in Boundary Element Calculations with Computer Simulations of Ion-Selective Electrode Response.

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