Ab Initio Molecular Dynamics Study on the Interactions between Carboxylate Ions and Metal Ions in Water

Photodynamic gel-bombs enhance tumor penetration and downstream synergistic therapies

Nanoparticle-based drug delivery system remains a significant challenge in the current treatment of solid tumors, primarily due to their limited penetration capabilities. Herein, we successfully engineer photodynamic gel-bombs (DCM@OPR) capable of penetrating deeply into tumor tissues utilizing the photodynamic-triggered explosive energy and receptor-mediated transcytosis, significantly enhancing the therapeutic efficacy of breast cancer. The photodynamic gel-bombs were fabricated by loading powerful components of chlorin e6 and MnO2 nanoparticles, as well as Doxorubicin, into a crosslinked Ca2+-gel. Upon exposure to laser irradiation, the obtained photodynamic gel-bombs are capable of generating explosive energy, resulting in their fragmentation into numerous nanofragments. The photodynamic-triggered explosive energy subsequently drives these nanofragments to deeply penetrate into tumor tissues through gap leakage among tumor cells. In addition, the photodynamic-triggered explosive energy also promotes the escape of those therapeutic components (including chlorin e6, MnO2 nanoparticles, and doxorubicin) and nanofragments from lysosomes. In the subsequent stages, these nanofragments also exhibit excellent transcytosis capacity, facilitating deep penetration into tumor tissues. As expected, the enhanced penetration and accumulation of therapeutic components into tumor tissues can be achieved, significantly enhancing the anti-proliferation capacity against breast cancer.

Charge Arrangement Determines the Sensitivity of Aggregation Patterns between Peptide-Chains to the Surrounding Ionic Environment

The molecular basis for the liquid-liquid phase separation (LLPS) behavior of various biomolecular components in the cell is the formation of multivalent and low-affinity interactions. When the content of these components exceeds a certain critical concentration, the molecules will spontaneously coalesce to form a new liquid phase; i.e., LLPS occurs. Intrinsically disordered proteins (IDPs) are usually rich in amino acids with charged side-chains, and thus, LLPS-involving interactions between their side-chains are of great interest. However, the molecular details of the coalescence of such charged IDPs in a salt solution are still lacking. Here, we focus on two types of peptide-chains with oppositely charged amino acids in extreme arrangements and investigate their aggregation patterns in various ionic environments. The results show that the interaction patterns between peptide-chains with nonuniform charge arrangement sequences are more sensitive to the surrounding cationic environment, and Na+ ions are more likely to cause aggregation of ASP residues compared to Mg2+ ions. As the ionic concentration increases, the electrostatic interactions between oppositely charged residues are gradually converted into a negative-negative amino acid interaction network bridged by Na+ ions, while the positive charge-rich regions are more strongly inclined to be exposed to the solvent environment and gain greater freedom of movement. Simultaneously, this effect will reach saturation with a further increase of salt concentration. The present study enriches insights into the electrostatic dominant factors in phase separation phenomena at the atomic level, which will hopefully inspire the design and application of targeted LLPS in the future.

Initiation of Medial Calcification: Revisiting Calcium Ion Binding to Elastin

Pathological calcification of elastin, a key connective tissue protein in the medial layers of blood vessels, starts with the binding of calcium ions. This Mini-Review focuses on understanding how calcium ions interact with elastin to initiate calcification at a molecular level, and emphasizes water's critical role in mediating this interaction. In the past decade, great strides have been made in understanding and modeling ion-specific hydration and its effects on biomolecule interactions. However, these advances have been largely absent from our understanding of elastin calcification. Historically, charge-neutral backbone carbonyls and negatively charged carboxyl groups have been proposed as elastin's calcium binding sites. Recently, tropoelastin's only four carboxyl groups have been identified as binding sites from classical molecular dynamics (MD). While carboxyl groups have a much higher affinity for binding calcium ions than backbone carbonyls, conflicting evidence persists for both functional group's importance in elastin calcification. This can be attributed to the fact that divalent ions strongly polarize water, leading to a hydration shell that shields electrostatic forces. The hydration shell surrounding both a calcium ion and either of the proposed binding sites must be displaced to enable binding. Providing our own extended X-ray absorption fine structure (EXAFS) data and complementary simulations, we discuss the potential structures of calcium binding in elastin and review prior knowledge regarding the relative importance of the two proposed binding sites.

Quantitative measurement of cation-mediated adhesion of DNA to anionic surfaces

Anionic polyelectrolytes, such as DNA, are attracted to anionic surfaces in the presence of multivalent cations. A major barrier toward molecular-level understanding of these attractive interactions is the paucity of measurements of the binding strength. Here, atomic force microscopy-based single molecule force spectroscopy was used to quantify the binding free energy of double-stranded DNA to an anionic surface, with complementary density functional theory calculations of the binding energies of metal ion-ligand complexes. The results support both electrostatic attraction and ion-specific binding. Our study suggests that the correlated interactions between counterions are responsible for attraction between DNA and an anionic surface, but the strength of this attraction is modulated by the identity of the metal ion. We propose a mechanism in which the strength of metal-ligand binding, as well as the preference for particular binding sites, influence both the concentration dependence and the strength of the DNA-surface interactions.

Double-hydrophilic block copolymer-metal ion associations: Structures, properties and applications

Hybrid polyionic complexes (HPICs), constructed from double-hydrophilic block copolymers and metal ions, have been largely developed with increasing interest in the past decade in the fields of catalysis, materials science and biological applications. The chemical natures of both blocks are very versatile, but one block should be able to interact with ions, and the second one should be neutral. Many metals have been used to form HPICs, which have, in their simplest architectural form, a core-shell structure of a few tens of nanometers in radius with an external shell made of the neutral block of the copolymer. In this review, we focus our discussion on the stability, shape, size and inner structure of these hybrid micelles. We then describe the most recent applications of HPICs, as reported in the literature, and point out the current challenges, missing structural information and future perspectives for this class of organized structures.

Phase Behavior of Ion-Containing Polymers in Polar Solvents: Predictions from a Liquid-State Theory with Local Short-Range Interactions

The thermodynamic phase behavior of charged polymers is a crucial property underlying their role in biology and various industrial applications. A complete understanding of the phase behaviors of such polymer solutions remains challenging due to the multi-component nature of the system and the delicate interplay among various factors, including the translational entropy of each component, excluded volume interactions, chain connectivity, electrostatic interactions, and other specific interactions. In this work, the phase behavior of partially charged ion-containing polymers in polar solvents is studied by further developing a liquid-state (LS) theory with local shortrange interactions. This work is based on the LS theory developed for fully-charged polyelectrolyte solutions. Specific interactions between charged groups of the polymer and counterions, between neutral segments of the polymer, and between charged segments of the polymer are incorporated into the LS theory by an extra Helmholtz free energy from the perturbed-chain statistical associating fluid theory (PC-SAFT). The influence of the sequence structure of the partially charged polymer is modeled by the number of connections between bonded segments. The effects of chain length, charge fraction, counterion valency, and specific short-range interactions are explored. A computational App for salt-free polymer solutions is developed and presented, which allows easy computation of the binodal curve and critical point by specifying values for the relevant model parameters.

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.

The Promoter Role of Amines in the Condensation of Silicic Acid: A First-Principles Investigation

Though well-recognized, the molecular-level understanding of the multifunctional roles of amines in the condensation of polysilicic acids, which is one of the key processes in hydrothermal synthesis of zeolites, is still limited. Taking ethylamine as a prototype, we investigated the mechanism of polysilicic acid condensation in the existence of organic amines in aqueous solution with extensive first-principles-based calculations. Because of the high proton affinity, ethylamine exists as amine silicates and alters the subsequent condensation mechanisms from a 1-step lateral attack mechanism accompanied with simultaneous intermolecular proton transfer in neutral aqueous solution to a 2-step SN2-like mechanism. Specifically, the 5-coordinated Si species that were not observed on pathways of condensation in neutral solution are effectively stabilized by the ethylamine cations as intermediates, and the barriers for condensation of ortho-silicic acid are significantly reduced from 133 kJ/mol in neutral solution to 58 and 63 kJ/mol for formation of the 5-coordinated Si intermediate and proton transfer for water release, respectively. Similar variations of mechanisms and barriers for condensation were also observed in the formation of cyclic trimers as well as linear and cyclic tetramers of ortho-silicic acids. Based on these, it was proposed that apart from acting as structure-directing agents, pore fillers, and pH adjusters, organic amines can also function as promoters in the condensation of polysilicic acids.

Resolving the Equal Number Density Puzzle: Molecular Picture from Simulations of LiCl(aq) and NaCl(aq)

The change in number densities of aqueous solutions of alkali chlorides should be qualitatively predictable. Typically, as cations get larger, the number density of the solution decreases. However, aqueous solutions of lithium and sodium chloride exhibit at ambient conditions practically identical number densities at equal molalities despite different ionic sizes. Here, we provide an atomistic interpretation of this experimentally observed anomalous behavior using molecular dynamics simulations. The obtained results show that the rigidity of the Li⁺ first and second solvation shells and the associated compromised hydrogen bonding result in practically equal average water densities in the local hydration regions for Li⁺ and Na⁺ despite different sizes of the cations. In addition, in more distant regions from the cations, the water densities of these two solutions also coincide. These findings thus provide an atomistic interpretation for matching number densities of LiCl and NaCl solutions. In contrast, the number density differences between NaCl and KCl solutions as well as between LiCl and KCl solutions behave in a regular fashion with lower number densities of solutions observed for larger cations.

Exploring the effects of approach velocity on depletion force and coalescence in oil-in-water emulsions

An emulsion is a thermodynamically unstable system consisting of at least two immiscible liquid phases, one of which is dispersed in the other in the form of droplets of varying size. Most studies on emulsions have focused on the behaviour of emulsion droplets with diameter from ∼50 μm and upwards. However, the properties of smaller droplets may be highly relevant in order to understand the behaviour of emulsions, including their performance in numerous applications within the fields of food, industry, and medical science. The relatively long life-time and small size of these droplets compared to other emulsion droplets, make them suited for optical trapping and micromanipulation technologies. Optical tweezers have previously shown potential in the study of stabilized emulsions. Here we employ optical tweezers to examine unstable oil-in-water emulsions to determine the effects of system parameters on depletion force and coalescence times.

Hydration Mimicry by Membrane Ion Channels

Ions transiting biomembranes might pass readily from water through ion-specific membrane proteins if these protein channels provide environments similar to the aqueous solution hydration environment. Indeed, bulk aqueous solution is an important reference condition for the ion permeation process. Assessment of this hydration mimicry concept depends on understanding the hydration structure and free energies of metal ions in water in order to provide a comparison for the membrane channel environment. To refine these considerations, we review local hydration structures of ions in bulk water and the molecular quasi-chemical theory that provides hydration free energies. In doing so, we note some current views of ion binding to membrane channels and suggest new physical chemical calculations and experiments that might further clarify the hydration mimicry concept.

Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy

We combine Raman-MCR vibrational spectroscopy experiments with ab initio and classical MD simulations to gain molecular insights into carboxylate–cation binding.

Effect of Divalent Cations on the Interaction of Carboxylate Self-Assembled Monolayers

Interactions between organic molecules in aqueous environments, whether in the fluid phase or adsorbed on solids, are often affected by the cations present in the solution. We investigated, at nanometer scale, how surface carboxylate interactions are influenced by dissolved divalent cations: Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺. Self-assembled monolayer (SAM) surfaces with exposed terminations of alkyl, -CH₃, carboxylate, -COO^- , or dicarboxylate, -DiCOO^-, were deposited on gold-coated tips and substrates. We used atomic force microscopy (AFM), in chemical force mapping (CFM) mode, to measure adhesion forces between various combinations of SAMs on the tip and substrate, in solutions of 0.5 M NaCl, that contained 0.012 M of one of the divalent cations. The type of cation, the number of carboxyl groups that interact, and their structure on the SAM influenced adhesion between the surfaces. The effect of the reference solution, which only contains Na⁺ cations, on adhesion force was mainly attributed to van der Waals and hydrophobic forces, explaining the lower force in systems that are more hydrophilic, i.e., -COO^--COO^-, and higher force for more hydrophobic systems. For charged surfaces, i.e., -COO^- and -DiCOO^-, in divalent cation solutions results were consistent with ion bridging. The inclusion of a hydrophobic surface, i.e., the -CH₃-COO^- or -CH₃-DiCOO^- system, decreased the possibility for strong cation bridging with the charged surface, resulting in lower adhesion. For systems including -COO^-, the adhesion force series followed the inverse cation hydrated radius trend (Na⁺ ≈ Mg²⁺ < Sr²⁺ < Ca²⁺ < Ba²⁺) whereas -DiCOO^- was responsible for lower adhesion force and modified trends, depending on the corresponding surface in the system. Differences in force magnitude between the monolayers were correlated with lower charge availability on the -DiCOO^- surface as a result of fewer active sites, probably because of the tendency of exposed malonate surface groups to interact between them, as well as high rigidity, resulting from the molecule structure. The characteristic response of the -DiCOO^- surface in solutions of Sr²⁺ and Ca²⁺ was correlated with possible malonate complexation modes. Comparison with previous studies suggested that the strong response of a -DiCOO^- surface to Sr²⁺ resulted from bidentate chelation, whereas Ca²⁺ response was attributed to alpha-mode association to malonate.

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.

Specific Ion Effects on the Interaction of Hydrophobic and Hydrophilic Self-Assembled Monolayers

Interactions between mineral surfaces and organic molecules are fundamental to life processes. The presence of cations in natural environments can change the behavior of organic compounds and thus alter the mineral-organic interfaces. We investigated the influence of Na⁺, Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺ on the interaction between two models, self-assembled monolayers, that were tailored to have hydrophobic -CH₃ or hydrophilic -COO(H) terminations. Atomic force microscopy in chemical force mapping mode, where the tips were functionalized with the same terminations, was used to measure adhesion forces between the tip and substrate surfaces, to gather fundamental information about the role of these cations in the behavior of organic compounds and the surfaces where they adsorb. Adhesion force between hydrophobic surfaces in 0.5 M NaCl solutions that contained 0.012 M divalent cations did not change, regardless of the ionic potential, that is, the charge per unit radius, of the cation. For systems where one or the other surface was functionalized with carboxylate, -COO(H), mostly in its deprotonated form, -COO^-, a reproducible change in the adhesion force was observed for each of the ions. The trend of increasing adhesion force followed the pattern: Na⁺ ≈ Mg²⁺ < Sr²⁺ < Ca²⁺ < Ba²⁺, suggesting that ionic potential, thus hydrated radius, controls the interaction. The presence of a -CH₃ surface in the asymmetric system leads to lower adhesion forces than in the hydrophilic system, whereas the ionic trend remains the same. Although specific ion effects are felt in both systems, the lower adhesion force in the asymmetric system, compared with the hydrophilic system, implies that the -CH₃ surface plays an important role.

Multiscale partial charge estimation on graphene for neutral, doped and charged flakes

The minimal-basis iterative stockholder (MBIS) and restrained electrostatic potential (RESP) methods were applied to examine the effects of edges and of nitrogen and boron dopants on the atomic partial charges of neutral and charged graphene flakes. The results provided the parameters to fit a second-order atom-condensed Kohn-Sham DFT model (ACKS2), accurately determining the partial charges, the dipole and local electric fields in large graphene flakes with negligible cost. Our approach can lead to improvements of graphene force fields in charged conditions and guide the design of media for catalytic applications.

A Kirkwood-Buff derived force field for alkaline earth halide salts

The activity and function of many macromolecules in cellular environments are coupled with the binding of divalent ions such as calcium or magnesium. In principle, computer simulations can be used to understand the molecular level aspects of how many important macromolecules interact with ions. However, most of the force fields currently available often fail to accurately reproduce the properties of divalent ions in aqueous environments. Here we develop classical non-polarizable force fields for the aqueous alkaline earth metal halides (MX₂), where M = Mg²⁺, Ca²⁺, Sr²⁺, Ba²⁺ and X = Cl^-, Br^-, I^-, which can be used in bimolecular simulations and which are compatible with the Simple Point Charge/Extended (SPC/E) water model. The force field parameters are specifically developed to reproduce the experimental Kirkwood-Buff integrals for aqueous solutions and thereby the experimental activity derivatives, partial molar volumes, and excess coordination numbers. This ensures that a reasonable balance between ion-ion, ion-water, and water-water distributions is obtained. However, this requires a scaling of the cation to water oxygen interaction strength in order to accurately reproduce the integrals. The scaling factors developed for chloride salts are successfully transferable to the bromide and iodide salts. Use of these new models leads to reasonable diffusion constants and dielectric decrements. However, the performance of the models decreases with increasing salt concentration (>4m), and simulations of the pure crystals exhibited unstable behavior.

Computer simulations of alkali-acetate solutions: Accuracy of the forcefields in difference concentrations

When proteins are solvated in electrolyte solutions that contain alkali ions, the ions interact mostly with carboxylates on the protein surface. Correctly accounting for alkali-carboxylate interactions is thus important for realistic simulations of proteins. Acetates are the simplest carboxylates that are amphipathic, and experimental data for alkali acetate solutions are available and can be compared with observables obtained from simulations. We carried out molecular dynamics simulations of alkali acetate solutions using polarizable and non-polarizable forcefields and examined the ion-acetate interactions. In particular, activity coefficients and association constants were studied in a range of concentrations (0.03, 0.1, and 1M). In addition, quantum-mechanics (QM) based energy decomposition analysis was performed in order to estimate the contribution of polarization, electrostatics, dispersion, and QM (non-classical) effects on the cation-acetate and cation-water interactions. Simulations of Li-acetate solutions in general overestimated the binding of Li⁺ and acetates. In lower concentrations, the activity coefficients of alkali-acetate solutions were too high, which is suggested to be due to the simulation protocol and not the forcefields. Energy decomposition analysis suggested that improvement of the forcefield parameters to enable accurate simulations of Li-acetate solutions can be achieved but may require the use of a polarizable forcefield. Importantly, simulations with some ion parameters could not reproduce the correct ion-oxygen distances, which calls for caution in the choice of ion parameters when protein simulations are performed in electrolyte solutions.

Ion-Specific Effects in Carboxylate Binding Sites

Specific ion binding by carboxylates (-COO^-) is a broadly important topic because -COO^- is one of the most common functional groups coordinated to metal ions in metalloproteins and synthetic polymers. We apply quantum chemical methods and the quasi-chemical free-energy theory to investigate how variations in the number of -COO^- ligands in a binding site determine ion-binding preferences. We study a series of monovalent (Li⁺, Na⁺, K⁺, Cs⁺) and divalent (Zn²⁺, Ca²⁺) ions relevant to experimental work on ion channels and ionomers. Of two competing hypotheses, our results support the ligand field strength hypothesis and follow the reverse Hofmeister series for ion solvation and ion transfer from aqueous solution to binding sites with the preferred number of ligands. New insight arises from the finding that ion-binding sequences can be manipulated and even reversed just by constraining the number of carboxylate ligands in the binding sites. Our results help clarify the discrepancy in ion association between molecular ligands in aqueous solutions and ionomers, and their chemical analogues in ion-channel binding sites.