Ultrasensitivity of Water Exchange Kinetics to the Size of Metal Ion

Femtosecond Electron-Transfer Dynamics across the D2O/Cs+/Cu(111) Interface: The Impact of Hydrogen Bonding

Hydrogen bonding is essential in electron-transfer processes at water-electrode interfaces. We study the impact of the H-bonding of water as a solvent molecule on real-time electron-transfer dynamics across a Cs+-Cu(111) ion-metal interface using femtosecond time-resolved two-photon photoelectron spectroscopy. We distinguish in the formed water-alkali aggregates two regimes below and above two water molecules per ion. Upon crossing the boundary of these regimes, the lifetime of the excess electron localized transiently at the Cs+ ion increases from 40 to 60 fs, which indicates a reduced alkali-metal interaction. Furthermore, the energy transferred to a dynamic structural rearrangement due to hydration is reduced from 0.3 to 0.2 eV concomitantly. These effects are a consequence of H-bonding in the water-water interaction and the beginning formation of a nanoscale water network. This finding is supported by real-space imaging of the solvatomers and vibrational frequency shifts of the OH stretching and bending modes calculated for these specific interfaces.

Impact of hierarchical water dipole orderings on the dynamics of aqueous salt solutions

Ions exhibit highly ion-specific complex behaviours when solvated in water, which remains a mystery despite the fundamental importance of ion solvation in nature, science, and technology. Here we explain these ion-specific properties by the ion-induced hierarchical dipolar, translational, and bond-orientational orderings of ion hydration shell under the competition between ion-water electrostatic interactions and inter-water hydrogen bonding. We first characterise this competition by a new length λHB(q), explaining the ion-specific effects on solution dynamics. Then, by continuously tuning ion size and charge, we find that the bond-orientational order of the ion hydration shell highly develops for specific ion size and charge combinations. This ordering drastically stabilises the hydration shell; its degree changes the water residence time around ions by 11 orders of magnitude for main-group ions. These findings are fundamental to ionic processes in aqueous solutions, providing a physical principle for electrolyte design and application.

Tailoring water structure with high-tetrahedral-entropy for antifreezing electrolytes and energy storage at -80 °C

One of unsolved puzzles about water lies in how ion-water interplay affects its freezing point. Here, we report the direct link between tetrahedral entropy and the freezing behavior of water in Zn²⁺-based electrolytes by analyzing experimental spectra and molecular simulation results. A higher tetrahedral entropy leads to lower freezing point, and the freezing temperature is directly related to the entropy value. By tailoring the entropy of water using different anions, we develop an ultralow temperature aqueous polyaniline| |Zn battery that exhibits a high capacity (74.17 mAh g^-1) at 1 A g^-1 and -80 °C with ~85% capacity retention after 1200 cycles due to the high electrolyte ionic conductivity (1.12 mS cm^-1). Moreover, an improved cycling life is achieved with ~100% capacity retention after 5000 cycles at -70 °C. The fabricated battery delivers appreciably enhanced performance in terms of frost resistance and stability. This work serves to provide guidance for the design of ultralow temperature aqueous batteries by precisely tuning the water structure within electrolytes.

Nucleation Rate Theory for Coordination Number: Elucidating Water-Mediated Formation of a Zigzag Na2SO4 Morphology

Predicting and controlling nanostructure formation during nucleation can pave the way to synthesizing novel energy materials via crystallization. However, such control over nucleation and crystallization remains challenging due to an inadequate understanding of critical factors that govern evolving atomistic structures and dynamics. Herein, we utilize coordination number as a reaction coordinate and rate theory to investigate how sodium sulfate, commonly known as a phase-change energy material, nucleates in a supersaturated aqueous solution. In conjunction with ab initio and force field-based molecular dynamics simulation, the rate theoretical analysis reveals that sodium sulfate from an initially dissolved metastable state transits to a heterogeneous mixture of prenucleated clusters and finally to a large cylindrical zigzag morphology. Measurements of Raman spectra and their ab initio modeling confirm that this nucleated morphology contains a few waters for every sulfate. Rate processes such as solvent exchange and desolvation exhibit high sensitivity to the evolving prenucleation/nucleation structures, providing a means to distinguish between critical nucleation precursors. Desolvation and forming the first-shell interionic coordination structure via monomer-by-monomer addition around sulfates are found to explain the formation of large nuclei. Thus, a detailed understanding of the step-by-step structure formation across scales has been achieved. This can be leveraged to predict nucleation-related structures and dynamics and potentially control the synthesis of novel phase-change materials for energy applications.

Role of water-bridged interactions in metal ion coupled protein allostery

Allosteric communication between distant parts of proteins controls many cellular functions, in which metal ions are widely utilized as effectors to trigger the allosteric cascade. Due to the involvement of strong coordination interactions, the energy landscape dictating the metal ion binding is intrinsically rugged. How metal ions achieve fast binding by overcoming the landscape ruggedness and thereby efficiently mediate protein allostery is elusive. By performing molecular dynamics simulations for the Ca²⁺ binding mediated allostery of the calmodulin (CaM) domains, each containing two Ca²⁺ binding helix-loop-helix motifs (EF-hands), we revealed the key role of water-bridged interactions in Ca²⁺ binding and protein allostery. The bridging water molecules between Ca²⁺ and binding residue reduces the ruggedness of ligand exchange landscape by acting as a lubricant, facilitating the Ca²⁺ coupled protein allostery. Calcium-induced rotation of the helices in the EF-hands, with the hydrophobic core serving as the pivot, leads to exposure of hydrophobic sites for target binding. Intriguingly, despite being structurally similar, the response of the two symmetrically arranged EF-hands upon Ca²⁺ binding is asymmetric. Breakage of symmetry is needed for efficient allosteric communication between the EF-hands. The key roles that water molecules play in driving allosteric transitions are likely to be general in other metal ion mediated protein allostery.

Natural proteins often utilize allostery in executing a variety of functions. Metal ions are typical cofactors to trigger the allosteric cascade. In this work, using the Ca²⁺ sensor protein calmodulin as the model system, we revealed crucial roles of water-bridged interactions in the metal ion coupled protein allostery. The coordination of the Ca²⁺ to the binding site involves an intermediate in which the water molecule bridges the Ca²⁺ and the liganding residue. The bridging water reduces the free energy barrier height of ligand exchange, therefore facilitating the ligand exchange and allosteric coupling by acting as a lubricant. We also showed that the response of the two symmetrically arranged EF-hand motifs of CaM domains upon Ca²⁺ binding is asymmetric, which is directly attributed to the differing dehydration process of the Ca²⁺ ions and is needed for efficient allosteric communication.

Thermodynamic and Kinetic Studies on the Conversion of Solvent-Shared to Contact Ion Pairs in Sparingly Soluble MF2 (M = Mg2+ and Ca2+) Aqueous Solutions: Implications for Understanding Supersaturated Behavior and Association Constant Determination

The thermodynamic and kinetic behaviors of Mg²⁺-F^- ion pairing in aqueous solution are investigated theoretically and experimentally and are contrasted to those of Ca²⁺-F^-. Thermodynamically, similar to CaF_x(H₂O)₁₄^2-x (x = 1 and 2), MgF(H₂O)_y⁺ (y = 14-20) contact ion pairs (CIPs) are more stable than their solvent-shared ion pairs (SSIPs), whereas the CIPs and SSIPs of MF₂(H₂O)_y are almost isoenergetic. However, in kinetics, the conversion of SSIPs to CIPs for M²⁺-F^- (M = Mg²⁺ and Ca²⁺) ion pairing must overcome a high energy barrier due to the strong hydration of Mg²⁺ and F^-. The kinetics dominate after the thermodynamics and kinetics are balanced, which hinders the formation of M²⁺-F^- CIPs in practical MF₂ aqueous solutions (less than or equal to saturated concentrations). This result is also supported by the ¹⁹F nuclear magnetic resonance spectra of saturated MF₂ solutions. Although the interaction between Mg²⁺ and F^- is slightly stronger than that between Ca²⁺ and F^- due to the smaller radius of Mg²⁺, the formation of Mg²⁺-F^- CIPs needs to go through two rate-limiting steps, the dehydration and entrance of F^- (i.e., via exchange mode) with a higher energy barrier, due to the ability of strongly bound water molecules and rigorous octahedral coordinated configuration of Mg²⁺, while the formation of Ca²⁺-F^- CIPs only goes through a single rate-limiting step, the entrance of F^- (i.e., via swinging mode) with a lower energy barrier, due to the flexible coordination configuration of Ca²⁺. This is responsible for precipitation in MgF₂ aqueous solution requiring a larger supersaturation degree and a lower precipitation rate than in CaF₂. These kinetic factors lead to the association constants previously reported for MF⁺ determined by a fluoride ion-selective electrode (ISE) combined with the titration method, where the MF₂ solutions were always unsaturated at the titration end point, which actually corresponds to those of the ligand process going from completely free M²⁺ and F^- to their SSIPs. A possible strategy to accurately determine the association constants of MF⁺ and MF₂(aq) CIPs by fluoride ISEs is proposed. The present results suggest that judging the formation of M²⁺-F^- CIPs in practical solutions from a theoretical calculation perspective requires significant consideration of the kinetic factors, except for the thermodynamic factors.

Artificial Intelligence Resolves Kinetic Pathways of Magnesium Binding to RNA

Magnesium is an indispensable cofactor in countless vital processes. In order to understand its functional role, the characterization of the binding pathways to biomolecules such as RNA is crucial. Despite the importance, a molecular description is still lacking since the transition from the water-mediated outer-sphere to the direct inner-sphere coordination is on the millisecond time scale and therefore out of reach for conventional simulation techniques. To fill this gap, we use transition path sampling to resolve the binding pathways and to elucidate the role of the solvent in the binding process. The results reveal that the molecular void provoked by the leaving phosphate oxygen of the RNA is immediately filled by an entering water molecule. In addition, water molecules from the first and second hydration shell couple to the concerted exchange. To capture the intimate solute-solvent coupling, we perform a committor analysis as the basis for a machine learning algorithm that derives the optimal deep learning model from thousands of scanned architectures using hyperparameter tuning. The results reveal that the properly optimized deep network architecture recognizes the important solvent structures, extracts the relevant information, and predicts the commitment probability with high accuracy. Our results provide detailed insights into the solute-solvent coupling which is ubiquitous for kosmotropic ions and governs a large variety of biochemical reactions in aqueous solutions.

Role of entropy in determining the phase behavior of protein solutions induced by multivalent ions

Recent experiments have reported lower critical solution temperature (LCST) phase behavior of aqueous solutions of proteins induced by multivalent ions, where the solution phase separates upon heating. This phenomenon is linked to complex hydration effects that result in a net entropy gain upon phase separation. To decipher the underlying molecular mechanism, we use all-atom molecular dynamics simulations along with the two-phase thermodynamic method for entropy calculation. Based on simulations of a single BSA protein in various salt solutions (NaCl, CaCl₂, MgCl₂, and YCl₃) at temperatures (T) ranging 283-323 K, we find that the cation-protein binding affinity increases with T, reflecting its thermodynamic driving force to be entropic in origin. We show that in the cation binding process, many tightly bound water molecules from the solvation shells of a cation and the protein are released to the bulk, resulting in entropy gain. To rationalize the LCST behavior, we calculate the ζ-potential that shows charge inversion of the protein for solutions containing multivalent ions. The ζ-potential increases with T. Performing simulations of two BSA proteins, we demonstrate that the protein-protein binding is mediated by multiple cation bridges and involves similar dehydration effects that cause a large entropy gain which more than compensates for rotational and translational entropy losses of the proteins. Thus, the LCST behavior is entropy-driven, but the associated solvation effects are markedly different from hydrophobic hydration. Our findings have direct implications for tuning the phase behavior of biological and soft-matter systems, e.g., protein condensation and crystallization.

Beyond Thermodynamics: Assessing the Dynamical Softness of Hydrated Ions from First Principles

Ion (de)hydration is a key rate-determining step in interfacial processes from corrosion to electrochemical energy storage. However, predicting the kinetics of ion (de)hydration remains challenging, prompting the use of static proxies such as hydration energy and valence. While useful for assessing thermodynamic preferences, such descriptors cannot fully capture the dynamical softness of the hydration shell that dictates kinetics. Accordingly, we use first-principles molecular dynamics to analyze hydration shell softness for a diverse set of metal cations. Three dynamic metrics are introduced to intuitively describe the bond rigidity, shape deformability, and exchange fluidity of the solvation shell. Together, these metrics capture the relevant physics in the static descriptors, while offering a far more complete and efficient representation for the overall propensity for (de)hydration. Application to the hydrated ion set demonstrates a weak connection between dynamical softness and hydration energy, confirming that dynamical descriptors of hydration are key for correctly describing ion transfer processes.

Second Harmonic Scattering Reveals Ion-Specific Effects at the SiO2 and TiO2 Nanoparticle/Aqueous Interface

Ion-specific effects play a crucial role in controlling the stability of colloidal systems and regulating interfacial processes. Although mechanistic pictures have been developed to explain the electrostatic structure of solid/water colloidal interfaces, ion-specific effects remain poorly understood. Here we quantify the average interfacial water orientation and the electrostatic surface potential around 100 nm SiO2 and TiO2 colloidal particles in the presence of NaCl, RbCl, and CaCl2 using polarimetric angle-resolved second harmonic scattering. We show that these two parameters can be used to establish the ion adsorption mechanism in a low ionic strength regime (<1 mM added salt). The relative differences between salts as a function of the ionic strength demonstrate cation- and surface-specific preferences for inner- vs outer-sphere adsorption. Compared to monovalent Rb+ and Na+, Ca2+ is found to be preferentially adsorbed as outer-sphere on SiO2 surfaces, while a dominant inner-sphere adsorption is observed for Ca2+ on TiO2. Molecular dynamics simulations performed on crystalline SiO2 and TiO2 surfaces support the experimental conclusions. This work contributes to the understanding of the electrostatic environment around colloidal nanoparticles on a molecular level by providing insight into ion-specific effects with micromolar sensitivity.

Electrochemical Detection of Phosphate Ion in Body Fluids with a Magnesium Phosphate Modified Electrode

An electrochemical sensor for phosphate detection in body fluids was developed based on the hydration transition of magnesium hydrogen phosphate (newberyite, MgHPO₄·3H₂O). The sensor was fabricated through incubation of a multi-walled carbon nanotube/Nafion (MWCNT/Nafion) modified glassy carbon electrode (GCE) in magnesium phosphate solution, where MgHPO₄·3H₂O was self-assembled on the electrode surface (denoted as MgP/MWCNT/Nafion). An electrooxidation peak at 1.0 V vs. Ag/AgCl was observed when the as-prepared electrode was subjected to a differential pulse voltammetry (DPV) scan in the presence of phosphate in acetate solution. When the DPV scan was performed in 0.4 - 1.3 V vs. Ag/AgCl, a linear relationship was observed between the peak height and the phosphate concentration in the range from 0.01 to 25 μM in the presence of 0.1 mM Mg²⁺ in the acetate solution with a limit of detection of 32 nM. And the sensor was successfully applied for phosphate detection in human urine and saliva samples with recoveries of 94.7 - 104.4 and 96 - 103.3%, respectively.

Kinetic and thermodynamic analysis defines roles for two metal ions in DNA polymerase specificity and catalysis

Magnesium ions play a critical role in catalysis by many enzymes and contribute to the fidelity of DNA polymerases through a two-metal ion mechanism. However, specificity is a kinetic phenomenon and the roles of Mg²⁺ ions in each step in the catalysis have not been resolved. We first examined the roles of Mg²⁺ by kinetic analysis of single nucleotide incorporation catalyzed by HIV reverse transcriptase. We show that Mg.dNTP binding induces an enzyme conformational change at a rate that is independent of free Mg²⁺ concentration. Subsequently, the second Mg²⁺ binds to the closed state of the enzyme-DNA-Mg.dNTP complex (K_d = 3.7 mM) to facilitate catalysis. Weak binding of the catalytic Mg²⁺ contributes to fidelity by sampling the correctly aligned substrate without perturbing the equilibrium for nucleotide binding at physiological Mg²⁺ concentrations. An increase of the Mg²⁺ concentration from 0.25 to 10 mM increases nucleotide specificity (k_cat/K_m) 12-fold largely by increasing the rate of the chemistry relative to the rate of nucleotide release. Mg²⁺ binds very weakly (K_d ≤ 37 mM) to the open state of the enzyme. Analysis of published crystal structures showed that HIV reverse transcriptase binds only two metal ions prior to incorporation of a correct base pair. Molecular dynamics simulations support the two-metal ion mechanism and the kinetic data indicating weak binding of the catalytic Mg²⁺. Molecular dynamics simulations also revealed the importance of the divalent cation cloud surrounding exposed phosphates on the DNA. These results enlighten the roles of the two metal ions in the specificity of DNA polymerases.

Kinetic pathways of water exchange in the first hydration shell of magnesium

Water exchange between the coordination shells of metal cations in aqueous solutions is fundamental in understanding their role in biochemical processes. Despite the importance, the microscopic mechanism of water exchange in the first hydration shell of Mg²⁺ has not been resolved since the exchange dynamics is out of reach for conventional all-atom simulations. To overcome this challenge, transition path sampling is applied to resolve the kinetic pathways, to characterize the reaction mechanism and to provide an accurate estimate of the exchange rate. The results reveal that water exchange involves the concerted motion of two exchanging water molecules and the collective rearrangement of all water molecules in the first hydration shell. Using a recently developed atomistic model for Mg²⁺, water molecules remain in the first hydration shell for about 40 ms, a time considerably longer compared to the 0.1 ms predicted by transition state theory based on the coordinates of a single water molecule. The discrepancy between these timescales arises from the neglected degrees of freedom of the second exchanging water molecule that plays a decisive role in the reaction mechanism. The approach presented here contributes molecular insights into the dynamics of water around metal cations and provides the basis for developing accurate atomistic models or for understanding complex biological processes involving metal cations.

Charge Density of Cation Determines Inner versus Outer Shell Coordination to Phosphate in RNA

Divalent cations are often required to fold RNA, which is a highly charged polyanion. Condensation of ions, such as Mg²⁺ or Ca²⁺, in the vicinity of RNA renormalizes the effective charges on the phosphate groups, thus minimizing the intra RNA electrostatic repulsion. The prevailing view is that divalent ions bind diffusively in a nonspecific manner. In sharp contrast, we arrive at the exact opposite conclusion using a theory for the interaction of ions with the phosphate groups using RISM theory in conjunction with simulations based on an accurate three-interaction-site RNA model. The divalent ions bind in a nucleotide-specific manner using either the inner (partially dehydrated) or outer (fully hydrated) shell coordination. The high charge density Mg²⁺ ion has a preference to bind to the outer shell, whereas the opposite is the case for Ca²⁺. Surprisingly, we find that bridging interactions, involving ions that are coordinated to two or more phosphate groups, play a crucial role in maintaining the integrity of the folded state. Their importance could become increasingly prominent as the size of the RNA increases. Because the modes of interaction of divalent ions with DNA are likely to be similar, we propose that specific inner and outer shell coordination could play a role in DNA condensation, and perhaps genome organization as well.

Hydration structure and water exchange kinetics at xenotime-water interfaces: implications for rare earth minerals separation

Hydration of surface ions gives rise to structural heterogeneity and variable exchange kinetics of water at complex mineral-water interfaces. Here, we employ ab initio molecular dynamics (AIMD) simulations and water adsorption calorimetry to examine the aqueous interfaces of xenotime, a phosphate mineral that contains predominantly Y3+ and heavy rare earth elements. Consistent with natural crystal morphology, xenotime is predicted to have a tetragonal prismatic shape, dominated by the {100} surface. Hydration of this surface induces multilayer interfacial water structures with distinct OH orientations, which agrees with recent crystal truncation rod measurements. The exchange kinetics between two adjacent water layers exhibits a wide range of underlying timescales (5-180 picoseconds), dictated by ion-water electrostatics. Adsorption of a bidentate hydroxamate ligand reveals that {100} xenotime surface can only accommodate monodentate coordination with water exchange kinetics strongly depending on specific ligand orientation, prompting us to reconsider traditional strategies for selective separation of rare-earth minerals.

Ionic Environment Affects Bacterial Lipopolysaccharide Packing and Function

The interaction of lipopolysaccharides (LPS) with metal cations strongly affects the stability and function of the Gram-negative bacterial outer membrane. The sensitivity of deep rough (Re) LPS packing and function to the ionic environment, as affected by cation valency and ionic radius, has been determined using molecular dynamics simulations and Langmuir balance experiments. The degree of LPS aggregation within the LPS models in the presence of different cations is assessed by measuring the effective mean molecular area (Â_m) of each LPS molecule projected onto the interfacial plane at the end of the equilibration. These results are compared to the LPS mean molecular area from experimental measurements in which the LPS monolayers are assembled at the air-water interface using a Langmuir film balance. We found that packing of the LPS arrays is sensitive to the ionic radius and ion valency of the cations present in solution during LPS array packing. Using enhanced sampling of the free energy for the intercalation of oligo(allylamine HCl) (OAH) into deep rough Salmonella enterica LPS bilayers, we obtained the affinity of the core section of LPS to OAH as a function of the nature of the metal cations present in solution. We found that packing of the solvated LPS bilayer models is sensitive to ionic radius and ion valency of the neutralizing cations. This further suggests that ion bridging and steric barriers rather than charge shielding are important factors in mitigating ligand intercalation under conditions with low ionic concentrations.

Short solvent model for ion correlations and hydrophobic association

Coulomb interactions play a major role in determining the thermodynamics, structure, and dynamics of condensed-phase systems, but often present significant challenges. Computer simulations usually use periodic boundary conditions to minimize corrections from finite cell boundaries but the long range of the Coulomb interactions generates significant contributions from distant periodic images of the simulation cell, usually calculated by Ewald sum techniques. This can add significant overhead to computer simulations and hampers the development of intuitive local pictures and simple analytic theory. In this paper, we present a general framework based on local molecular field theory to accurately determine the contributions from long-ranged Coulomb interactions to the potential of mean force between ionic or apolar hydrophobic solutes in dilute aqueous solutions described by standard classical point charge water models. The simplest approximation leads to a short solvent (SS) model, with truncated solvent-solvent and solute-solvent Coulomb interactions and long-ranged but screened Coulomb interactions only between charged solutes. The SS model accurately describes the interplay between strong short-ranged solute core interactions, local hydrogen-bond configurations, and long-ranged dielectric screening of distant charges, competing effects that are difficult to capture in standard implicit solvent models.

How cations affect the electric double layer and the rates and selectivity of electrocatalytic processes

Electrocatalysis is central to the production of renewable fuels and high-value commodity chemicals. The electrolyte and the electrode together determine the catalytic properties of the liquid/solid interface. In particular, the cations of the electrolyte can greatly change the rates and reaction selectivity of many electrocatalytic processes. For this reason, the careful choice of the cation is an essential step in the design of catalytic interfaces with high selectivity for desired high-value products. To make such a judicious choice, it is critical to understand where in the electric double layer the cations reside and the various distinct mechanistic impacts they can have on the electrocatalytic process of interest. In this perspective, we review recent advances in the understanding of the electric double layer with a particular focus on the interfacial distribution of cations and the cations' hydration states in the vicinity of the electrode under various experimental conditions. Furthermore, we summarize the different ways in which cations can alter the rates and selectivity of chemical processes at electrified interfaces and identify possible future areas of research in this field.

Theory and simulations for RNA folding in mixtures of monovalent and divalent cations

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.

Dynamics of metal ions around an RNA molecule

Noncoding RNA molecules take part in many biological processes, while metal ions play crucial roles in helping RNAs to perform their functions. However, the statics and dynamics of these metal ions around RNA molecules are still not well understood. In this work, we report a detailed molecular dynamics study of the type-I preQ_{1}-bound riboswitch aptamer domain (PRAD) at different ionic conditions (K^{+}, Na^{+}, and Mg^{2+}). The results show that the structural properties and flexibility of the PRAD molecule greatly influence the distributions and dynamics of metal ions around it. Simultaneously, Na^{+} ions show a stronger competitiveness with Mg^{2+} ions than K^{+} ions, and the three types of metal ions have different modes of interaction with the RNA molecule. Furthermore, we have also investigated specific binding sites of metal ions on the PRAD molecule and found that the dynamics and hydration structures of metal ions located at the ion-binding sites were obviously affected by the RNA structure near these ion-binding sites. These results may be useful to understand the role of the metal ions in noncoding RNA functions.

Quantifying Mg2+ Binding to ssDNA Oligomers: A Self-Consistent Field Theory Study at Varying Ionic Strengths and Grafting Densities

The performance of aptamer-based biosensors is crucially impacted by their interactions with physiological metal ions, which can alter their structures and chemical properties. Therefore, elucidating the nature of these interactions carries the utmost importance in the robust design of highly efficient biosensors. We investigated Mg2+ binding to varying sequences of polymers to capture the effects of ionic strength and grafting density on ion binding and molecular reorganization of the polymer layer. The polymers are modeled as ssDNA aptamers using a self-consistent field theory, which accounts for non-covalent ion binding by integrating experimentally-derived binding constants. Our model captures the typical polyelectrolyte behavior of chain collapse with increased ionic strength for the ssDNA chains at low grafting density and exhibits the well-known re-entrant phenomena of stretched chains with increased ionic strength at high grafting density. The binding results suggest that electrostatic attraction between the monomers and Mg2+ plays the dominant role in defining the ion cloud around the ssDNA chains and generates a nearly-uniform ion distribution along the chains containing varying monomer sequences. These findings are in qualitative agreement with recent experimental results for Mg2+ binding to surface-bound ssDNA.

Predicting RNA-Metal Ion Binding with Ion Dehydration Effects

Metal ions play essential roles in nucleic acids folding and stability. The interaction between metal ions and nucleic acids can be highly complicated because of the interplay between various effects such as ion correlation, fluctuation, and dehydration. These effects may be particularly important for multivalent ions such as Mg²⁺ ions. Previous efforts to model ion correlation and fluctuation effects led to the development of the Monte Carlo tightly bound ion model. Here, by incorporating ion hydration/dehydration effects into the Monte Carlo tightly bound ion model, we develop a, to our knowledge, new approach to predict ion binding. The new model enables predictions for not only the number of bound ions but also the three-dimensional spatial distribution of the bound ions. Furthermore, the new model reveals several intriguing features for the bound ions such as the mutual enhancement/inhibition in ion binding between the fully hydrated (diffuse) ions, the outer-shell dehydrated ions, and the inner-shell dehydrated ions and novel features for the monovalent-divalent ion interplay due to the hydration effect.

Manifestations of Weak O-H···F Hydrogen Bonding in M(H2O) n(B12F12) Salt Hydrates: Unusually Sharp Fourier Transform Infrared ν(OH) Bands and Latent Porosity (M = Mg-Ba, Co, Ni, Zn)

Eight M(H₂O) _n(Z) salt hydrates were characterized by single-crystal X-ray diffraction (Z^2- = B₁₂F₁₂^2-): M = Ca, Sr, n = 7; M = Mg, Co, Ni, Zn, n = 6; M = Ba, n = 4, 5. Weak O-H···F hydrogen bonding between the M(H₂O) _n²⁺ cations and Z^2- resulted in room-temperature Fourier transform infrared (FTIR) spectra having sharp ν(OH) bands, with full widths at half max of 10-30 cm^-1, which are much more narrow than ν(OH) bands in room temperature FTIR spectra of most salt hydrates. Clearly resolved ν_asym(OH/OD) and ν_sym(OH/OD) bands with Δν(OH) as small as 17 cm^-1 and Δν(OD) as small as 11 cm^-1 were observed (Δν(OX) = ν_asym(OX) - ν_sym(OX)). The isomorphic hexahydrates ( R3̅) have two fac-(H₂O)₃ sets of H₂O ligands and nearly octahedral coordination spheres. They exhibited four resolvable ν(OH) bands, one ν_asym(OH)/ν_sym(OH) pair for H₂O ligands with longer O(H)···F distances and one ν_asym(OH)/ν_sym(OH) pair for H₂O ligands with shorter O(H)···F distances. The ν(OH) bands for the three H₂O molecules with shorter, slightly stronger O(H)···F hydrogen bonds were broader, more intense, and red-shifted by ca. 25 cm^-1 relative to the bands for the three other H₂O molecules, the first time that such small differences in relatively weak O(H)···F hydrogen bonds in the same crystalline hexahydrate have resulted in observable IR spectroscopic differences at room temperature. For the first time room temperature ν(OH) values for salt hexahydrates showed the monotonic progression Mg²⁺ > Co²⁺ > Ni²⁺ > Zn²⁺, essentially the same progression as the p K_a values for these metal ions in aqueous solution. A further manifestation of the weak O-H···F hydrogen bonding in these hydrates is the latent porosity exhibited by Ba(H₂O)_5,8(Z), Sr(H₂O) _n,m(Z), and Ca(H₂O)_4,6(Z). Finally, the H₂O/D₂O exchange reaction Co(D₂O)₆(Z) → Co(H₂O)₆(Z) was ca. 50% complete in 1 h at 50 °C in N₂/17 Torr H₂O( g).

Interfacial structural crossover and hydration thermodynamics of charged C60 in water

Classical molecular dynamics simulations of the hydration thermodynamics, structure, and dynamics of water in hydration shells of charged buckminsterfullerenes are presented in this study. Charging of fullerenes leads to a structural transition in the hydration shell, accompanied by creation of a significant population of dangling O-H bonds pointing toward the solute. In contrast to the well accepted structure-function paradigm, this interfacial structural transition causes nearly no effect on either the dynamics of hydration water or on the solvation thermodynamics. Linear response to the solute charge is maintained despite significant structural changes in the hydration shell, and solvation thermodynamic potentials are nearly insensitive to the altering structure. Only solvation heat capacities, which are higher thermodynamic derivatives of the solvation free energy, indicate some sensitivity to the local hydration structure. We have separated the solvation thermodynamic potentials into direct solute-solvent interactions and restructuring of the hydration shell and analyzed the relative contributions of electrostatic and nonpolar interactions to the solvation thermodynamics.

Metal Ion Interactions with Crude Oil Components: Specificity of Ca2+ Binding to Naphthenic Acid at an Oil/Water Interface

On the basis of dynamic interfacial tension measurements, Ca2+ has been shown specifically to interact with naphthenic acid (NA) at the n-heptane/water interface, consistent with NA adsorption followed by interfacial complexation and formation of a more ordered interfacial film. Optimum concentrations of Ca2+ and NA have been found to yield lower, time-dependent interfacial tensions, not evident for Mg2+ and Sr2+ or for several alkali metal ions studied. The results reflect the specific hydration and coordination chemistry of Ca2+ seen in biology. Owing to the ubiquitous presence of Ca2+ in oilfield waters, this finding has potential relevance to the surface chemistry underlying crude oil recovery. For example, “locking” acidic components at water/oil interfaces may be important for crude oil emulsion stability, or in bonding bulk oil to mineral surfaces through an aqueous phase, potentially relevant for carbonate reservoirs. The relevance of the present results to low salinity waterflooding as an enhanced crude oil recovery technique is also discussed.

Density functional theory studies on the solvent effects in Al(H2O)63+ water-exchange reactions: the number and arrangement of outer-sphere water molecules

Density functional theory (DFT) calculations combined with cluster models are performed at the B3LYP/6-311+G(d,p) level for investigating the solvent effects in Al(H₂O)₆³⁺ water-exchange reactions. A "One-by-one" method is proposed to obtain the most representative number and arrangement of explicit H₂Os in the second hydration sphere. First, all the possible ways to locate one explicit H₂O in second sphere (N_m' = 1) based on the gas phase structure (N_m' = 0) are examined, and the optimal pathway (with the lowest energy barrier) for N_m' = 1 is determined. Next, more explicit H₂Os are added one by one until the inner-sphere is fully hydrogen bonded. Finally, the optimal pathways with N_m' = 0-7 are obtained. The structural and energetic parameters as well as the lifetimes of the transition states are compared with the results obtained with the "Independent-minimum" method and the "Independent-average" method, and all three methods show that the pathway with N_m' = 6 may be representative. Our results give a new idea for finding the representative pathway for water-exchange reactions in other hydrated metal ion systems.