Hydration and Charge-Transfer Effects of Alkaline Earth Metal Ions Binding to a Carboxylate Anion, Phosphate Anion, and Guanine Nucleobase

To investigate the ability of alkaline earth metal ions to tune ion-mediated DNA adsorption, hydrated Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺ ions bound to a carboxylate anion, phosphate anion, and guanine nucleobase were modeled using density functional theory (DFT) and a combined explicit and continuum solvent model. The large first solvation shell of Ba²⁺ requires a larger solute cavity defined by a solvent-accessible surface, which is used to model all hydrated ions. Alkaline earth metal ions bind indirectly or directly to each binding site. DFT binding energies decrease with increasing ion size, which is likely due to ion size and hydration structure, rather than quantum effects such as charge transfer. However, charge transfer explains weaker ion binding to guanine compared to phosphate or carboxylate. Overall, carboxylate and phosphate anions are expected to compete equally for hydrated Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺ ions and larger alkaline earth metal ions may induce weaker ion-mediated adsorption. The ion size and hydration structure of alkaline earth metal ions may effectively tune ion-mediated adsorption processes, such as DNA adsorption to functionalized surfaces.

Comparison of the Microsolvation of CaX2 (X = F, Cl, Br, I) in Water: Size-Selected Anion Photoelectron Spectroscopy and Theoretical Calculations

To understand the microsolvation of alkaline-earth dihalides in water and provide information about the dependence of solvation processes on different halides, we investigated CaBr₂(H₂O)_n^-, CaI₂(H₂O)_n^-, and CaF₂(H₂O)_n^- (n = 0-6) clusters using size-selected anion photoelectron spectroscopy and conducted theoretical calculations on these clusters and their neutrals. The results are compared with those of CaCl₂(H₂O)_n^-/0 clusters reported previously. It is found that the vertical detachment energies (VDEs) of CaCl₂(H₂O)_n^-, CaBr₂(H₂O)_n^-, and CaI₂(H₂O)_n^- show a similar trend with increasing cluster size, while the VDEs of CaF₂(H₂O)_n^- show a different trend. The VDEs of CaF₂(H₂O)_n^- are much lower than those of CaCl₂(H₂O)_n^-, CaBr₂(H₂O)_n^-, and CaI₂(H₂O)_n^-. A detailed probing of the structures shows that a significant increase of the Ca-X distance (separation of Ca²⁺-X^- ion pair) in CaCl₂(H₂O)_n^-/0, CaBr₂(H₂O)_n^-/0, and CaI₂(H₂O)_n^-/0 clusters occurred at about n = 5. However, for CaF₂(H₂O)_n^-/0, no abrupt change of the Ca-F distance with the increasing cluster size has been observed. In CaCl₂(H₂O)₆^-/0, CaBr₂(H₂O)₆^-/0, and CaI₂(H₂O)₆^-/0, the Ca atom coordinates directly with 5 H₂O molecules. However, in CaF₂(H₂O)_n^-/0, the Ca atom coordinates directly with only 2 or 3 H₂O molecules. The similarity or differences in the structures and coordination numbers are consistent with the fact that CaCl₂, CaBr₂, and CaI₂ have similar solubility, while CaF₂ has much lower solubility.

Determination of van der Waals Parameters Using a Double Exponential Potential for Nonbonded Divalent Metal Cations in TIP3P Solvent

A double exponential (DE) functional form for Lennard-Jones (LJ) interactions, proposed in our previous study, has many advantages over LJ potentials including a natural softcore characteristic for the convenience of the pathway-based free-energy calculations, fast convergence, and flexibility in use. In this work, we put the first step on the application of the DE functional form by identifying a DE potential, coined DE-TIP3P, for molecular simulations using the TIP3P water model. The developed DE-TIP3 potential was better than LJ potential in reproducing the experimental water properties. Afterward, we developed the nonbonded models of 15 divalent metal ions, which frequently appear and play vital roles in biological systems, to be consistent with the DE-TIP3P potential and TIP3P water model. Our nonbonded models were as good as the complicated nonbonded dummy cationic models by Jiang et al. and the nonbonded 12-6-4 LJ models by Li and Merz in reproducing the experimental properties of those ions. Moreover, our nonbonded models achieved a better performance than the compromise (CM) LJ models and 12-6-4 LJ models, developed by Li and Merz, in reproducing the properties of MgCl₂ in aqueous solution.

Hydration processes of barium chloride: Size-selected anion photoelectron spectroscopy and theoretical calculations of BaCl2-water clusters

In order to understand the hydration processes of BaCl₂, we investigated BaCl₂(H₂O)_n ^- (n = 0-5) clusters using size-selected anion photoelectron spectroscopy and theoretical calculations. The structures of neutral BaCl₂(H₂O)_n clusters up to n = 8 were also investigated by theoretical calculations. It is found that in BaCl₂(H₂O)_n ^-/0, the Ba-Cl distances increase very slowly with the cluster size. The hydration process is not able to induce the breaking of a Ba-Cl bond in the cluster size range (n = 0-8) studied in this work. In small BaCl₂(H₂O)_n clusters with n ≤ 5, the Ba atom has a coordination number of n + 2; however, in BaCl₂(H₂O)_6-8 clusters, the Ba atom coordinates with two Cl atoms and (n - 1) water molecules, and it has a coordination number of n + 1. Unlike the previously studied MgCl₂(H₂O)_n ^- and CaCl₂(H₂O)_n ^-, negative charge-transfer-to-solvent behavior has not been observed for BaCl₂(H₂O)_n ^-, and the excess electron of BaCl₂(H₂O)_n ^- is mainly localized on the Ba atom rather on the water molecules. No observation of Ba²⁺-Cl^- separation in current work is consistent with the lower solubility of BaCl₂ compared to MgCl₂ and CaCl₂. Considering the BaCl₂/H₂O mole ratio in the saturated solution, one would expect that about 20-30 H₂O molecules are needed to break the first Ba-Cl bond in BaCl₂.

Molecular dynamics simulations of alkaline earth metal ions binding to DNA reveal ion size and hydration effects

Classical molecular dynamics simulations reveal size-dependent trends of alkaline earth metal ions binding to DNA are due to ion size and hydration behavior.

Ab initio molecular dynamics studies of hydroxide coordination of alkaline earth metals and uranyl

Ab initio molecular dynamics (AIMD) simulations of the Mg2+, Ca2+, Sr2+ and UO22+ ions in either a pure aqueous environment or an environment containing two hydroxide ions have been carried out at the density functional level of theory, employing the generalised gradient approximation via the PBE exchange-correlation functional. Calculated mean M-O bond lengths in the first solvation shell of the aquo systems compared very well to existing experimental and computational literature, with bond lengths well within values measured previously and coordination numbers in line with previously calculated values. When applied to systems containing additional hydroxide ions, the methodology revealed increased bond lengths in all systems. Proton transfer events (PTEs) were recorded and were found to be most prevalent in the strontium hydroxide systems, likely due to the low charge density of the ion and the consequent lack of hydroxide coordination. For all alkaline earths, intrashell PTEs which occurred outside of the first solvation shell were most prevalent. Only three PTEs were identified in the entire simulation data of the uranium dihydroxide system, indicating the clear impact of the increased charge density of the hexavalent uranium ion on the strength of metal-oxygen bonds in aqueous solution. Broadly, systems containing more charge dense ions were found to exhibit fewer PTEs than those containing ions of lower charge density.

Taking into Account the Ion-induced Dipole Interaction in the Nonbonded Model of Ions

Metal ions exist in almost half of the proteins in the protein databank and they serve as structural, electron-transfer and catalytic elements in the metabolic processes of organisms. Molecular Dynamics (MD) simulation is a powerful tool that provides information about biomolecular systems at the atomic level. Coupled with the growth in computing power, algorithms like the Particle Mesh Ewald (PME) method have become the accepted standard when dealing with long-range interactions in MD simulations. The nonbonded model of metal ions consists of an electrostatic plus 12-6 Lennard Jones (LJ) potential and is used largely because of its speed relative to more accurate models. In previous work we found that ideal parameters do not exist that reproduce several experimental properties for M(II) ions simultaneously using the nonbonded model coupled with the PME method due to the underestimation of metal ion-ligand interactions. Via a consideration of the nature of the nonbonded model, we proposed that the observed error largely arises from overlooking charge-induced dipole interactions. The electrostatic plus 12-6 LJ potential model works reasonably well for neutral systems but does struggle with more highly charged systems. In the present work we designed and parameterized a new nonbonded model for metal ions by adding a 1/r4 term to the 12-6 model. We call it the 12-6-4 LJ-type nonbonded model due to its mathematical construction. Parameters were determined for 16 +2 metal ions for the TIP3P, SPC/E and TIP4PEW water models. The final parameters reproduce the experimental hydration free energies (HFE), ion-oxygen distances (IOD) in the first solvation shell and coordination numbers (CN) accurately for the metal ions investigated. Preliminary tests on MgCl2 at different concentrations in aqueous solution and Mg2+--nucleic acid systems show reasonable results suggesting that the present parameters can work in mixed systems. The 12-6-4 LJ-type nonbonded model is readily adopted into standard force fields like AMBER, CHARMM and OPLS-AA with only a modest computational overhead. The new nonbonded model doesn't consider charge-transfer effects explicitly and, hence, may not suitable for the simulation of systems where charge-transfer effects play a decisive role.

Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent

Metal ions play significant roles in biological systems. Accurate molecular dynamics (MD) simulations on these systems require a validated set of parameters. Although there are more detailed ways to model metal ions, the nonbonded model, which employs a 12-6 Lennard-Jones (LJ) term plus an electrostatic potential is still widely used in MD simulations today due to its simple form. However, LJ parameters have limited transferability due to different combining rules, various water models and diverse simulation methods. Recently, simulations employing a Particle Mesh Ewald (PME) treatment for long-range electrostatics have become more and more popular owing to their speed and accuracy. In the present work we have systematically designed LJ parameters for 24 +2 metal (M(II)) cations to reproduce different experimental properties appropriate for the Lorentz-Berthelot combining rules and PME simulations. We began by testing the transferability of currently available M(II) ion LJ parameters. The results showed that there are differences between simulations employing Ewald summation with other simulation methods and that it was necessary to design new parameters specific for PME based simulations. Employing the thermodynamic integration (TI) method and performing periodic boundary MD simulations employing PME, allowed for the systematic investigation of the LJ parameter space. Hydration free energies (HFEs), the ion-oxygen distance in the first solvation shell (IOD) and coordination numbers (CNs) were obtained for various combinations of the parameters of the LJ potential for four widely used water models (TIP3P, SPC/E, TIP4P and TIP4PEW). Results showed that the three simulated properties were highly correlated. Meanwhile, M(II) ions with the same parameters in different water models produce remarkably different HFEs but similar structural properties. It is difficult to reproduce various experimental values simultaneously because the nonbonded model underestimates the interaction between the metal ions and water molecules at short range. Moreover, the extent of underestimation increases successively for the TIP3P, SPC/E, TIP4PEW and TIP4P water models. Nonetheless, we fitted a curve to describe the relationship between ε (the well depth) and radius (Rmin/2) from experimental data on noble gases to facilitate the generation of the best possible compromise models. Hence, by targeting different experimental values, we developed three sets of parameters for M(II) cations for three different water models (TIP3P, SPC/E and TIP4PEW). These parameters we feel represent the best possible compromise that can be achieved using the nonbonded model for the ions in combination with simple water models. From a computational uncertainty analysis we estimate that the uncertainty in our computed HFEs is on the order of ±1kcal/mol. Further improvements will require more advanced non-bonded models likely with inclusion of polarization.