Testing the hypothesis that solvent exchange limits the rates of calcite growth and dissolution.

It is established that the rates of solvent exchange at interfaces correlate with the rates of a number of mineral reactions, including growth, dissolution and ion sorption. To test if solvent exchange is limiting these rates, quasi-elastic neutron scattering (QENS) is used here to benchmark classical molecular dynamics (CMD) simulations of water bound to nanoparticulate calcite. Four distributions of solvent exchanges are found with residence times of 8.9 ps for water bound to calcium sites, 14 ps for that bound to carbonate sites and 16.7 and 85.1 ps for two bound waters in a shared calcium-carbonate conformation. By comparing rates and activation energies, it is found that solvent exchange limits reaction rates neither for growth nor dissolution, likely due to the necessity to form intermediate states during ion sorption. However, solvent exchange forms the ceiling for reaction rates and yields insight into more complex reaction pathways.

Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints.

The routinely employed periodic boundary conditions complicate molecular simulations of physiologically relevant asymmetric lipid membranes together with their distinct solvent environments. Therefore, separating the extracellular fluid from its cytosolic counterpart has often been performed using a costly double-bilayer setup. Here, we demonstrate that the lipid membrane and solvent asymmetry can be efficiently modeled with a single lipid bilayer by applying an inverted flat-bottom potential to ions and other solute molecules, thereby restraining them to only interact with the relevant leaflet. We carefully optimized the parameters of the suggested method so that the results obtained using the flat-bottom and double-bilayer approaches become mutually indistinguishable. Then, we apply the flat-bottom approach to lipid bilayers with various compositions and solvent environments, covering ions and cationic peptides to validate the approach in a realistic use case. We also discuss the possible limitations of the method as well as its computational efficiency and provide a step-by-step guide on how to set up such simulations in a straightforward manner.

Evolution of the electrical double layer with electrolyte concentration probed by second harmonic scattering.

Investigating the electrical double layer (EDL) structure has been a long-standing challenge and has seen the emergence of several sophisticated techniques able to probe selectively the few molecular layers of a solid/water interface. While a qualitative estimation of the thickness of the EDL can be obtained using simple theoretical models, following experimentally its evolution is not straightforward and can be even more complicated in nano- or microscale systems, particularly when changing the ionic concentration by several orders of magnitude. Here, we bring insight into the structure of the EDL of SiO2 nanoparticle suspensions and its evolution with increasing ionic concentration using angle-resolved second harmonic scattering (AR-SHS). Below millimolar salt concentrations, we can successively characterize inner-sphere adsorption, diffuse layer formation, and outer-sphere adsorption. Moreover, we show for the first time that, by appropriately selecting the nanoparticle size, it is possible to retrieve information also in the millimolar range. There, we observe a decrease in the magnitude of the surface potential corresponding to a compression in the EDL thickness, which agrees with the results of several other electroanalytical and optical techniques. Molecular dynamics simulations suggest that the EDL compression mainly results from the diffuse layer compression rather than outer-sphere ions (Stern plane) moving closer to the surface.

Stealthy Player in Lipid Experiments? EDTA Binding to Phosphatidylcholine Membranes Probed by Simulations and Monolayer Experiments.

Ethylenediaminetetraacetic acid (EDTA) is frequently used in lipid experiments to remove redundant ions, such as Ca2+, from the sample solution. In this work, combining molecular dynamics (MD) simulations and Langmuir monolayer experiments, we show that on top of the expected Ca2+ depletion, EDTA anions themselves bind to phosphatidylcholine (PC) monolayers. This binding, originating from EDTA interaction with choline groups of PC lipids, leads to the adsorption of EDTA anions at the monolayer surface and concentration-dependent changes in surface pressure as measured by monolayer experiments and explained by MD simulations. This surprising observation emphasizes that lipid experiments carried out using EDTA-containing solutions, especially of high concentrations, must be interpreted very carefully due to potential interfering interactions of EDTA with lipids and other biomolecules involved in the experiment, e.g., cationic peptides, that may alter membrane-binding affinities of studied compounds.

Applicability of perturbed matrix method for charge transfer studies at bio/metallic interfaces: a case of azurin.

As the field of nanoelectronics based on biomolecules such as peptides and proteins rapidly grows, there is a need for robust computational methods able to reliably predict charge transfer properties at bio/metallic interfaces. Traditionally, hybrid quantum-mechanical/molecular-mechanical techniques are employed for systems where the electron hopping transfer mechanism is applicable to determine physical parameters controlling the thermodynamics and kinetics of charge transfer processes. However, these approaches are limited by a relatively high computational cost when extensive sampling of a configurational space is required, like in the case of soft biomatter. For these applications, semi-empirical approaches such as the perturbed matrix method (PMM) have been developed and successfully used to study charge-transfer processes in biomolecules. Here, we explore the performance of PMM on prototypical redox-active protein azurin in various environments, from solution to vacuum interfaces with gold surfaces and protein junction. We systematically benchmarked the robustness and convergence of the method with respect to the quantum-centre size, size of the Hamiltonian, number of samples, and level of theory. We show that PMM can adequately capture all the trends associated with the structural and electronic changes related to azurin oxidation at bio/metallic interfaces.

Ionic Strength and Solution Composition Dictate the Adsorption of Cell-Penetrating Peptides onto Phosphatidylcholine Membranes.

Adsorption of arginine-rich positively charged peptides onto neutral zwitterionic phosphocholine (PC) bilayers is a key step in the translocation of those potent cell-penetrating peptides into the cell interior. In the past, we have shown both theoretically and experimentally that polyarginines adsorb to the neutral PC-supported lipid bilayers in contrast to polylysines. However, comparing our results with previous studies showed that the results often do not match even at the qualitative level. The adsorption of arginine-rich peptides onto 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) may qualitatively depend on the actual experimental conditions where binding experiments have been performed. In this work, we systematically studied the adsorption of R9 and K9 peptides onto the POPC bilayer, aided by molecular dynamics (MD) simulations and fluorescence cross-correlation spectroscopy (FCCS) experiments. Using MD simulations, we tested a series of increasing peptide concentrations, in parallel with increasing Na+ and Ca2+ salt concentrations, showing that the apparent strength of adsorption of R9 decreases upon the increase of peptide or salt concentration in the system. The key result from the simulations is that the salt concentrations used experimentally can alter the picture of peptide adsorption qualitatively. Using FCCS experiments with fluorescently labeled R9 and K9, we first demonstrated that the binding of R9 to POPC is tighter by almost 2 orders of magnitude compared to that of K9. Finally, upon the addition of an excess of either Na+ or Ca2+ ions with R9, the total fluorescence correlation signal is lost, which implies the unbinding of R9 from the PC bilayer, in agreement with our predictions from MD simulations.

Reorganization free energy of copper proteins in solution, in vacuum, and on metal surfaces.

Metalloproteins, known to efficiently transfer electronic charge in biological systems, recently found their utilization in nanobiotechnological devices where the protein is placed into direct contact with metal surfaces. The feasibility of oxidation/reduction of the protein redox sites is affected by the reorganization free energies, one of the key parameters determining the transfer rates. While their values have been measured and computed for proteins in their native environments, i.e., in aqueous solution, the reorganization free energies of dry proteins or proteins adsorbed to metal surfaces remain unknown. Here, we investigate the redox properties of blue copper protein azurin, a prototypical redox-active metalloprotein previously probed by various experimental techniques both in solution and on metal/vacuum interfaces. We used a hybrid quantum mechanical/molecular mechanical computational technique based on density functional theory to explore protein dynamics, flexibility, and corresponding reorganization free energies in aqueous solution, vacuum, and on vacuum gold interfaces. Surprisingly, the reorganization free energy only slightly decreases when azurin is dried because the loss of the hydration shell leads to larger flexibility of the protein near its redox site. At the vacuum gold surfaces, the energetics of the structure relaxation depends on the adsorption geometry; however, significant reduction of the reorganization free energy was not observed. These findings have important consequences for the charge transport mechanism in vacuum devices, showing that the free energy barriers for protein oxidation remain significant even under ultra-high vacuum conditions.

The "good," the "bad," and the "hidden" in neutron scattering and molecular dynamics of ionic aqueous solutions.

We characterize a concentrated 7.3 m CaCl2 solution, combining neutron diffraction with chloride isotopic substitution (Cl-NDIS) in null water and molecular dynamics (MD) simulations. We elucidate the solution structure, thermodynamic properties, and extent of ion pairing previously suggested as concentration-dependent and often not observed at lower concentrations. Our Cl-NDIS measurements designate the solvent-shared ion pairing as dominant and the contact ion pairing (CIP) as insignificant even under conditions close to the solubility limit. The MD models parameterized against neutron diffraction with calcium isotopic substitution (Ca-NDIS) overestimate CIP despite successfully reproducing most of the Cl-NDIS signal. This drawback originates from the fact that Ca2+-Cl- interactions were primarily "hidden" in the Ca-NDIS signal due to overlapping with Ca2+-Ow and Ca2+-Hw contributions to the total scattering. Contrary, MD models with moderate CIP and possessing generally good performance at high concentrations fail to reproduce the NDIS measurements accurately. Therefore, the electronic polarization, introduced in most of the recent MD models via scaling ionic charges, resolves some but not all parameterization drawbacks. We conclude that despite improving the quality of MD models "on average," the question "which model is the best" has not been answered but replaced by the question "which model is better for a given research." An overall "good" model can still be inappropriate or, in some instances, "bad" and, unfortunately, produce erroneous results. The accurate interpretation of several NDIS datasets, complemented by MD simulations, can prevent such mistakes and help identify the strengths, weaknesses, and convenient applications for corresponding computational models.

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.

Surface Potential and Interfacial Water Order at the Amorphous TiO2 Nanoparticle/Aqueous Interface.

Colloidal nanoparticles exhibit unique size-dependent properties differing from their bulk counterpart, which can be particularly relevant for catalytic applications. To optimize surface-mediated chemical reactions, the understanding of the microscopic structure of the nanoparticle-liquid interface is of paramount importance. Here we use polarimetric angle-resolved second harmonic scattering (AR-SHS) to determine surface potential values as well as interfacial water orientation of ∼100 nm diameter amorphous TiO2 nanoparticles dispersed in aqueous solutions, without any initial assumption on the distribution of interfacial charges. We find three regions of different behavior with increasing NaCl concentration. At very low ionic strengths (0-10 µM), the Na+ ions are preferentially adsorbed at the TiO2 surface as inner-sphere complexes. At low ionic strengths (10-100 µM), a distribution of counterions equivalent to a diffuse layer is observed, while at higher ionic strengths (>100 µM), an additional layer of hydrated condensed ions is formed. We find a similar behavior for TiO2 nanoparticles in solutions of different basic pH. Compared to identically sized SiO2 nanoparticles, the TiO2 interface has a higher affinity for Na+ ions, which we further confirm with molecular dynamics simulations. With its ability to monitor ion adsorption at the surface with micromolar sensitivity and changes in the surface potential, AR-SHS is a powerful tool to investigate interfacial properties in a variety of catalytic and photocatalytic applications.

Oxalic Acid Adsorption on Rutile: Molecular Dynamics and ab Initio Calculations.

Detailed analysis of the adsorption of oxalic acid ions, that is, oxalate and hydrogenoxalate, on the rutile (110) surface was carried out using molecular dynamics augmented by free energy calculations and supported by ab initio calculations. The predicted adsorption on perfect nonhydroxylated and hydroxylated surfaces with surface charge density from neutral to +0.208 C/m2 corresponding to pH values of about 6 and 3.7, respectively, agrees with experimental adsorption data and charge-distribution multisite ion complexation model predictions obtained using the most favorable surface complexes identified in our simulations. We found that outer-sphere complexes are the most favorable, owing to strong hydrogen binding of oxalic acid ions with surface hydroxyls and physisorbed water. The monodentate complex, the most stable among inner-sphere complexes, was about 15 kJ/mol higher in energy, but separated by a large energy barrier. Other inner-sphere complexes, including some previously suggested in the literature as likely adsorption structures such as bidentate and chelate complexes, were found to be unstable both by classical and by ab initio modeling. Both the surfaces and (hydrogen)oxalate ions were modeled using charges scaled to 75% of the nominal values in accord with the electronic continuum theory and our earlier parameterization of (hydrogen)oxalate ions, which showed that nominal charges exaggerate ion-water interactions.

Oxalic Acid Adsorption on Rutile: Experiments and Surface Complexation Modeling to 150 °C.

Here, we characterize oxalate adsorption by rutile in NaCl media (0.03 and 0.30 m) and between pH 3 and 10 over a wide temperature range which includes the near hydrothermal regime (10-150 °C). Oxalate adsorption increases with decreasing pH (as is typical for anion binding by metal oxides), but systematic trends with respect to ionic strength or temperature are absent. Surface complexation modeling (SCM) following the CD-MUSIC formalism, and as constrained by molecular modeling simulations and IR spectroscopic results from the literature, is used to interpret the adsorption data. The molecular modeling simulations, which include molecular dynamics simulations supported by free-energy and ab initio calculations, reveal that oxalate binding is outer-sphere, albeit via strong hydrogen bonds. Conversely, previous IR spectroscopic results conclude that various types of inner-sphere complexes often predominate. SCMs constrained by both the molecular modeling results and the IR spectroscopic data were developed, and both fit the adsorption data equally well. We conjecture that the discrepancy between the molecular simulation and IR spectroscopic results is due to the nature of the rutile surfaces investigated, that is, the perfect (110) crystal faces for the molecular simulations and various rutile powders for the IR spectroscopy studies. Although the (110) surface plane is most often dominant for rutile powders, a variety of steps, kinks, and other types of surface defects are also invariably present. Hence, we speculate that surface defect sites may be primarily responsible for inner-sphere oxalate adsorption, although further study is necessary to prove or disprove this hypothesis.

Surface Characterization of Colloidal Silica Nanoparticles by Second Harmonic Scattering: Quantifying the Surface Potential and Interfacial Water Order.

The microscopic description of the interface of colloidal particles in solution is essential to understand and predict the stability of these systems, as well as their chemical and electrochemical reactivity. However, this description often relies on the use of simplified electrostatic mean field models for the structure of the interface, which give only theoretical estimates of surface potential values and do not provide properties related to the local microscopic structure, such as the orientation of interfacial water molecules. Here we apply polarimetric angle-resolved second harmonic scattering (AR-SHS) to 300 nm diameter SiO2 colloidal suspensions to experimentally determine both surface potential and interfacial water orientation as a function of pH and NaCl concentration. The surface potential values and interfacial water orientation change significantly over the studied pH and salt concentration range, whereas zeta-potential (ζ) values remain constant. By comparing the surface and ζ-potentials, we find a layer of hydrated condensed ions present in the high pH case, and for NaCl concentrations ≥1 mM. For milder pH ranges (pH < 11), as well as for salt concentrations <1 mM, no charge condensation layer is observed. These findings are used to compute the surface charge densities using the Gouy-Chapman and Gouy-Chapman-Stern models. Furthermore, by using the AR-SHS data, we are able to determine the preferred water orientation in the layer directly in contact with the silica interface. Molecular dynamics simulations confirm the experimental trends and allow deciphering of the contributions of water layers to the total response.

Modeling of solid-liquid interfaces using scaled charges: rutile (110) surfaces.

Electronic continuum correction (ECC) has been proven to bring significant improvement in the modeling of interactions of ions (especially multivalent) in aqueous solutions. We present a generalization and the first application of this approach to modeling solid-liquid interfaces, which are omnipresent in physical chemistry, geochemistry, and biophysics. Scaling charges of the top layer of surface atoms makes the existing solid models compatible with the ECC models of ions and molecules, allowing the use of modified force fields for a more accurate investigation of interactions of various metal and metal-oxide surfaces with aqueous solutions, including complex biomolecules and multivalent ions. We have reparametrized rutile (110) models with different surface charge densities (from 0 to -0.416 C m-2) and adopted/developed scaled charge force fields for ions, namely Na+, Rb+, Sr2+, and Cl-. A good agreement of the obtained molecular dynamics (MD) data with X-ray experiments and previously reported MD results was observed, but changes in the occupancy of various adsorption sites were observed and discussed in detail.