Aqueous Contact Ion Pairs of Phosphate Groups with Na+, Ca2+ and Mg2+ – Structural Discrimination by Femtosecond Infrared Spectroscopy and Molecular Dynamics Simulations
7
Citation
46
Reference
10
Related Paper
Citation Trend
Abstract:
Abstract The extent of contact and solvent shared ion pairs of phosphate groups with Na + , Ca 2+ and Mg 2+ ions in aqueous environment and their relevance for the stability of polyanionic DNA and RNA structures is highly debated. Employing the asymmetric phosphate stretching vibration of dimethyl phosphate (DMP), a model system of the sugar-phosphate backbone of DNA and RNA, we present linear infrared, femtosecond infrared pump-probe and absorptive 2D-IR spectra that report on contact ion pair formation via the presence of blue shifted spectral signatures. Compared to the linear infrared spectra, the nonlinear spectra reveal contact ion pairs with increased sensitivity because the spectra accentuate differences in peak frequency, transition dipole moment strength, and excited state lifetime. The experimental results are corroborated by long time scale MD simulations, benchmarked by density functional simulations on phosphate-ion-water clusters. The microscopic interpretation reveals subtle structural differences of ion pairs formed by the phosphate group and the ions Na + , Ca 2+ and Mg 2+ . Intricate properties of the solvation shell around the phosphate group and the ion are essential to explain the experimental observations. The present work addresses a challenging to probe topic with the help of a model system and establishes new experimental data of contact ion pair formation, thereby underlining the potential of nonlinear 2D-IR spectroscopy as an analytical probe of phosphate-ion interactions in complex biological systems.Keywords:
Solvation shell
First-principles molecular dynamics simulations have been performed on the solvation of Na+ in water. Consistent with the available experimental data, we find that the first solvation shell of Na+ contains on average 5.2 water molecules. A significant number of water exchanges between the first and second solvation shells are observed. However, the simulations are not long enough to reliably measure the rate of water exchange. Contrary to several previous studies, we do not find any effect of Na+ on the orientation of water molecules outside of the first solvation shell. Furthermore, the complete set of structural properties determined by first-principles molecular dynamics is not predicted by any of the known classical simulations.
Solvation shell
Implicit solvation
Cite
Citations (244)
Solvation shell
Cite
Citations (33)
(DFT) calculations were also performed to correlate the results with the experimental data and then further extended to other similar systems. It was found that the number of coordinating solvent molecules decreases with increasing Ca2+ concentration and increasing solvent molecule sizes. From the EXAFS data, it was observed that the first solvation shell of Ca2+ splits into two Ca-O distances in a methanol solution and the counter ion Cl- might also be within the first shell at high concentrations. For the first time, the effects of solvents with different polarities and sizes on the ion solvation environment were systematically evaluated.
Solvation shell
Cite
Citations (0)
Based on the theoretically calculated m.o. values for the binding energy of water molecules in the first and second solvation sphere of cations, the relation between bonding energies and experimentally observed hydration energies is discussed. Furthermore, the experimental values for the activation energy of water exchange in the first solvation layer are related to the binding energies of these water molecules, leading to strong support for an exchange mechanism involving the second hydration shell and a higher coordinated transition state.
Solvation shell
Quantum chemical
Cite
Citations (26)
(DFT) calculations were also performed to correlate the results with the experimental data and then further extended to other similar systems. It was found that the number of coordinating solvent molecules decreases with increasing Ca2+ concentration and increasing solvent molecule sizes. From the EXAFS data, it was observed that the first solvation shell of Ca2+ splits into two Ca-O distances in a methanol solution and the counter ion Cl- might also be within the first shell at high concentrations. For the first time, the effects of solvents with different polarities and sizes on the ion solvation environment were systematically evaluated.
Solvation shell
Cite
Citations (1)
The number of solvent molecules in the solvation shell of the title complex ion has been found to be 10, the stepwise equilibrium constants for the replacement of the 10 water molecules by 10 dimethyl sulphoxide molecules have been obtained, and the free energy increment per replacement step has been found to be ∼+1.42 kJ mol–1.
Solvation shell
Cite
Citations (1)
Abstract The first part of the article deals with the structure of the solvation shell of simple ions, particularly those with the inert gas structure, in aqueous and non‐aqueous solution. It is nowadays possible in favorable cases, to determine the solvation number or the coordination number in the first sphere. The solvation shells appear to be “more liquid” than was formerly believed. The hydration of neutral inert particles in aqueous solution is discussed in the second part. Caution is advised in the postulation of particular structural arrangements in the solution.
Solvation shell
Inert
Inert gas
Implicit solvation
Cite
Citations (45)
The flexibility of the hydrogen-bonded network of water is the basis for its excellent solvation properties. Accordingly, it is valuable to understand the properties of water in the solvation shell surrounding small molecules and biomolecules. Recent high-quality Raman spectra analyzed with Self-Modeling Curve Resolution (SMCR) have provided Raman spectra of small-molecule solvation shells. Here we apply SMCR to the complementary technique of Fourier transform infrared (FTIR) spectroscopy in the attenuated total reflection (ATR) configuration to extract the IR spectra of solvation shells. We first illustrate the method by obtaining the IR-MCR solvation shell spectra of tert-butanol (TBA), before applying it to antifreeze protein type III. Our results show that IR-SMCR spectroscopy is a powerful method for studying the solvation shell structure of small molecules and biomolecules. Given the wide availability of FTIR-ATR instruments, the method could prove to be an impactful tool for studying solvation and solvent-mediated interactions.
Solvation shell
Biomolecule
Attenuated total reflection
Implicit solvation
Cite
Citations (32)
Abstract The solvation of some neutral and charged organic molecules (phenol, nitroanilines, tetraalkylammonium) in binary solvent mixtures was investigated by means of intermolecular 1 H‐NOESY NMR spectroscopy. The solvation shell of the solute is, in most cases, selectively enriched in one of the cosolvents (preferential solvation). The origin of preferential solvation is discussed in terms of solute–solvent interactions and microheterogeneity in the solvent mixture. Copyright © 2002 John Wiley & Sons, Ltd.
Solvation shell
Cite
Citations (40)
Solvation shell
Hydroxylamine
Cite
Citations (6)