Two-Dimensional Infrared Spectroscopy of Aqueous Solutions of Metal Nitrates: Slowdown of Spectral Diffusion in the Presence of Divalent Cations

The hydrogen-bonded network of water can be affected both structurally and dynamically by the presence of ions. In the present study, we have considered three aqueous solutions of metal nitrates to investigate the effects of divalent cations (Mg²⁺ and Ca²⁺), compared to that of monovalent Na⁺ ions, on hydrogen-bond fluctuations and vibrational spectral diffusion through calculations of linear and two-dimensional infrared spectra of these solutions at room temperature. We have employed the methods of molecular dynamics simulations using effective polarizable models of ions combined with quantum mechanical calculations of transition variables and statistical mechanical calculations of spectral response functions of vibrational spectroscopy. Divalent cations are found to have much stronger and longer-ranged effects on the structure and dynamics of the hydrogen-bonded network than that induced by the monovalent sodium ions. The blue shifts in the calculated linear spectra are found to follow the Hofmeister trend for the cations. The 2D-IR spectral lineshape and intensity corresponding to three-pulse echo peak shift (3PEPS) experiments are calculated. The timescales of these nonlinear spectral responses and also frequency-time correlations show significant slowing down of spectral diffusion for solutions containing divalent Mg²⁺ and Ca²⁺ ions compared to the corresponding dynamics of the solution containing Na⁺ ions. Unlike NaNO₃ solution, the relaxation of frequency and dipole orientational fluctuations of anion-bound water in Mg(NO₃)₂ and Ca(NO₃)₂ solutions are found to be somewhat slower than bulk water, which can be attributed to the presence of divalent cations whose effects go beyond their first solvation shells. This is also seen in the dynamics of bulk water in these solutions which is found to be notably slower for the solutions containing divalent cations than that in the NaNO₃ solution. Unlike Mg²⁺ and Ca²⁺ ions, no specific cationic effect is observed for the Na⁺ ions.

Microscopic Picture of Calcium-Assisted Lipid Demixing and Membrane Remodeling Using Multiscale Simulations

The specificity of anionic phospholipids-calcium ion interaction and lipid demixing has been established as a key regulatory mechanism in several cellular signaling processes. The mechanism and implications of this calcium-assisted demixing have not been elucidated from a microscopic point of view. Here, we present an overview of atomic interactions between calcium and phospholipids that can drive nonideal mixing of lipid molecules in a model lipid bilayer composed of zwitterionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)) and anionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (POPS)) lipids with computer simulations at multiple resolutions. Lipid nanodomain formation and growth were driven by calcium-enabled lipid bridging of the charged phosphatidylserine (PS) headgroups, which were favored against inter-POPS dipole interactions. Consistent with several experimental studies of calcium-associated membrane sculpting, our analyses also suggest modifications in local membrane curvature and cross-leaflet couplings as a response to such induced lateral heterogeneity. In addition, reverse mapping to a complementary atomistic description revealed structural insights in the presence of anionic nanodomains, at timescales not accessed by previous computational studies. This work bridges information across multiple scales to reveal a mechanistic picture of calcium ion's impact on membrane biophysics.

Pressure in Molecular Simulations with Scaled Charges. 1. Ionic Systems

Charge scaling, rationalized as MDEC (molecular dynamics in electronic continuum) or ECC (electronic continuum correction), has become a widely used simple approach to how to avoid self-consistent induced dipoles yet approximately take into account the effects of electronic polarizability. It has been assumed that the continuum permittivity does not depend on density; in turn, pressure is calculated by standard formulas. In this work, we elaborate a complementary approximation of density-independent molecular polarizability and derive formulas for pressure corrections within the MDEC framework; real behavior lies between these two extremes. The pressure corrections for test ionic systems are huge and negative, leading to sizable densities in constant-pressure MDEC simulations. A comparison of MDEC results with equivalent polarizable systems gives a good pressure match for a crystal but very low MDEC pressures for ionic liquids. These results witness about the importance of a correct density dependence not only of continuum permittivity in MDEC simulations but also of polarizability in polarizable simulations.

Calcium ion binding to calmodulin: binding free energy calculation using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method by incorporating implicit polarization

Binding of calcium ion to calcium-binding proteins (CBP) triggers a large number of biological processes in a cell. CBP are known to play important roles in various diseases, such as cancer, alzheimer, and neuronal problems. However, the calculation of the binding affinity of calcium ion to CBP still possesses a significant challenge to the computational investigators. One of the main reasons for this difficulty is the polarization of CBP due to the binding of calcium. In the current work, we have used the implicit polarization method of Leontyev et al. (PCCP, 13.7 (2011): 2613-2626) to calculate the binding free energy of calcium ion binding to calmodulin, an important CBP. We have used the widely used MM-PBSA method to find a good protocol of calculation with implicit polarization. We have also optimized the best value of the calcium radius to match the experimental results. Our results show incorporation of polarization improves the agreement between the calculated and experimental results, although still, some discrepancy remains. On the whole, this work shows implicit polarization when combined with the MM-PBSA method can give results better than calculation without any polarization, and further improvement is necessary to get a quantitative match with experiments.Communicated by Ramaswamy H. Sarma.

Molecular modeling of aqueous electrolytes at interfaces: Effects of long-range dispersion forces and of ionic charge rescaling

Molecular dynamics simulations of aqueous electrolytes generally rely on empirical force fields, combining dispersion interactions-described by a truncated Lennard-Jones (LJ) potential-and electrostatic interactions-described by a Coulomb potential computed with a long-range solver. Recently, force fields using rescaled ionic charges [electronic continuum correction (ECC)], possibly complemented with rescaling of LJ parameters [ECC rescaled (ECCR)], have shown promising results in bulk, but their performance at interfaces has been less explored. Here, we started by exploring the impact of the LJ potential truncation on the surface tension of a sodium chloride aqueous solution. We show a discrepancy between the numerical predictions for truncated LJ interactions with a large cutoff and for untruncated LJ interactions computed with a long-range solver, which can bias comparison of force field predictions with experiments. Using a long-range solver for LJ interactions, we then show that an ionic charge rescaling factor chosen to correct long-range electrostatic interactions in bulk accurately describes image charge repulsion at the liquid-vapor interface, and the rescaling of LJ parameters in ECCR models-aimed at capturing local ion-ion and ion-water interactions in bulk- describes well the formation of an ionic double layer at the liquid-vapor interface. Overall, these results suggest that the molecular modeling of aqueous electrolytes at interfaces would benefit from using long-range solvers for dispersion forces and from using ECCR models, where the charge rescaling factor should be chosen to correct long-range electrostatic interactions.

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.

Hierarchical phenomena in multicomponent liquids: simulation methods, analysis, chemistry

Complex, multicomponent, solutions have often been studied solely through the lens of specific applications of interest. Yet advances to both simulation methodologies (enhanced sampling, etc.) and analysis techniques (network analysis algorithms and others), are creating a trove of data that reveal transcending characteristics across vast compositional phase space. This perspective discusses technical considerations of the reliable and accurate simulations of complex solutions, followed by the advances to analysis algorithms that elucidate coupling of different length and timescale behavior (hierarchical phenomena). The different manifestations of hierarchical phenomena are presented across an array of solution environments, emphasizing fundamental and ongoing science questions. With a more advanced molecular understanding in hand, a quintessential application (solvent extraction) is discussed, where significant opportunities exist to re-imagine the technical scope of an established technology.

Dynamics of water trapped in transition metal oxide-graphene nano-confinement

Motivated by practical implementation of transition-metal oxide-graphene heterostructures, we use all atom molecular dynamics simulations to study dynamics of water in a nano slit bounded by a transition metal oxide surface, namely, TiO2termination of SrTiO3, and graphene. The resultant asymmetric, strong confinement produces square ice-like crystallites of water pinned at TiO2surface and drives enhanced hydrophobicity of graphene via the proximity effect to the hydrophilic TiO2surface. This importantly brings in dynamic heterogeneity, both in translational and rotational degrees of freedom, due to coupling between the slow relaxing, strongly adsorbed water layer at the hydrophilic oxide surface, and faster relaxation of subsequent water layers. The heterogeneity is signalled in the ruggedness of the effective free energy landscapes. We discuss possible implications of our findings in drug delivery.

Restructuring a Deep Eutectic Solvent by Water: The Nanostructure of Hydrated Choline Chloride/Urea

Deep eutectic mixtures are a promising sustainable and diverse class of tunable solvents that hold great promise for various green chemical and technological processes. Many deep eutectic solvents (DES) are hygroscopic and find use in applications with varying extents of hydration, hence urging a profound understanding of changes in the nanostructure of DES with water content. Here, we report on molecular dynamics simulations of the quintessential choline chloride-urea mixture, using a newly parametrized force field with scaled charges to account for physical properties of hydrated DES mixtures. These simulations indicate that water changes the nanostructure of solution even at very low hydration. We present a novel approach that uses convex constrained analysis to dissect radial distribution functions into base components representing different modes of local association. Specifically, DES mixtures can be deconvoluted locally into two dominant competing nanostructures, whose relative prevalence (but not their salient structural features) change with added water over a wide concentration range, from dry up to ∼30 wt % hydration. Water is found to be associated strongly with several DES components but remarkably also forms linear bead-on-string clusters with chloride. At high water content (beyond ∼50 wt % of water), the solution changes into an aqueous electrolyte-like mixture. Finally, the structural evolution of the solution at the nanoscale with extent of hydration is echoed in the DES macroscopic material properties. These changes to structure, in turn, should prove important in the way DES acts as a solvent and to its interactions with additive components.

Coupling of Conformational Switches in Calcium Sensor Unraveled with Local Markov Models and Transfer Entropy

Proteins often have multiple switching domains that are coupled to each other and to the binding of ligands in order to realize signaling functions. Here we investigate the C2A domain of Synaptotagmin-1 (Syt-1), a calcium sensor in the neurotransmitter release machinery and a model system for the large family of C2 membrane binding domains. We combine extensive molecular dynamics (MD) simulations with Markov modeling in order to model conformational switching domains, their states, and their dependence on bound calcium ions. Then, we use transfer entropy to characterize how the switching domains are coupled via directed or allosteric mechanisms and give rise to the calcium sensing function of the protein. Our proposed switching mechanism contributes to the understanding of the neurotransmitter release machinery. Furthermore, the methodological approach we develop serves as a template to analyze conformational switching domains and the broad study of their coupling in macromolecular machines.

Development of a Force Field for the Simulation of Single-Chain Proteins and Protein-Protein Complexes

The accuracy of atomistic physics-based force fields for the simulation of biological macromolecules has typically been benchmarked experimentally using biophysical data from simple, often single-chain systems. In the case of proteins, the careful refinement of force field parameters associated with torsion-angle potentials and the use of improved water models have enabled a great deal of progress toward the highly accurate simulation of such monomeric systems in both folded and, more recently, disordered states. In living organisms, however, proteins constantly interact with other macromolecules, such as proteins and nucleic acids, and these interactions are often essential for proper biological function. Here, we show that state-of-the-art force fields tuned to provide an accurate description of both ordered and disordered proteins can be limited in their ability to accurately describe protein-protein complexes. This observation prompted us to perform an extensive reparameterization of one variant of the Amber protein force field. Our objective involved refitting not only the parameters associated with torsion-angle potentials but also the parameters used to model nonbonded interactions, the specification of which is expected to be central to the accurate description of multicomponent systems. The resulting force field, which we call DES-Amber, allows for more accurate simulations of protein-protein complexes, while still providing a state-of-the-art description of both ordered and disordered single-chain proteins. Despite the improvements, calculated protein-protein association free energies still appear to deviate substantially from experiment, a result suggesting that more fundamental changes to the force field, such as the explicit treatment of polarization effects, may simultaneously further improve the modeling of single-chain proteins and protein-protein complexes.

An electric double layer structure and differential capacitance at the electrode interface of tributylmethylammonium bis(trifluoromethanesulfonyl)amide studied using a molecular dynamics simulation

A molecular dynamics simulation at the electrode interface of a quaternary ammonium ionic liquid, tributylmethylammonium bis(trifluoromethanesulfonyl)amide ([N₁₄₄₄⁺][TFSA^-]), has been performed. Unlike the commonly used cations, such as 1-alkyl-3-methylimidazolium and 1,1-alkylmethylpyrrolidinium cations, N₁₄₄₄⁺ has multiple long-alkyl groups (three butyl groups). The behavior of ions at the electrode interface, especially these butyl groups, has been investigated. N₁₄₄₄⁺ at the first layer mainly has two types of orientations, lying and standing. The lying orientation is dominant at moderately negative potentials. However, the standing one becomes dominant at the more negative potentials. Due to this orientational change, the number of N₁₄₄₄⁺ increases at the first layer as the potential becomes negative even at the potentials where the anions are completely depleted there. The change in orientation results in the upward deviation of the differential capacitance from the theoretical prediction at the negative potentials. The results suggest that the orientational preference caused by the steric constraint between alkyl groups plays an important role in the behavior of the electric double layer of the ionic liquids.

Properties of Lipid Models of Lung Surfactant Containing Cholesterol and Oxidized Lipids: A Mixed Experimental and Computational Study

We introduce and study a multicomponent lipid film mimicking lipid composition of the human lung surfactant. It consists of phospholipids with various lipid headgroups and tail saturation. Furthermore, it includes cholesterol and oxidized lipids. Langmuir trough and fluorescence microscopy experiments are combined with fully atomistic molecular dynamics simulations. The considered lipid mixtures form complex interfacial films with properties modulated by lateral compression. Cholesterol laterally condenses, and oxidized lipids laterally expand the films; both types of molecules increase film miscibility. Oxidized lipids also alter the lipid-water interface enhancing film hydration; this effect can be partially reversed by cholesterol. Regarding presentation of different chemical moieties toward the aqueous subphase, the zwitterionic phosphatidylcholine groups dominate at the lipid-water interface, while both the negatively charged phosphatidylglycerol and hydroxyl group of cholesterol are less exposed. The investigated synthetic lipid-only mimic of the lung surfactant may serve as a basis for further studies involving nonlipid pulmonary surfactant components.

Calculation of salt-dependent free energy of binding of β-lactoglobulin homodimer formation and mechanism of dimer formation using molecular dynamics simulation and three-dimensional reference interaction site model (3D-RISM): diffuse salt ions and non-polar interactions between the monomers favor the dimer formation

There are several important phenomena in chemistry, biology, and physics where molecules (or parts of a molecule) having charges of the same sign come closer together and become stable. DNA condensation, RNA folding, colloid-colloid interactions are some of the examples of this kind. In the current work, we have investigated how β-lactoglobulin, a protein found in milk, in spite of carrying +13 charge, favors the homodimer formation in the presence of salt. We have focussed on calculating the protein-protein binding free energy in the presence of salt and identifying the thermodynamic and microscopic mechanism of the process. Estimation of binding free energy of this salt-dependent process is done by combining molecular dynamics simulation with statistical mechanical theory of three-dimensional reference interaction site model (3D-RISM). Binding free energy is evaluated from the chemical potential of the solutes as opposed to potential of mean force calculation, which gives only a constrained free energy. Our calculated values semi-quantitatively match with the experimental results. By examining the different components of binding free energy, we have found that the role of salt ions (especially of Cl^-) is to shift the equilibrium towards the dimer. Non-polar (Lennard-Jones) interactions between the monomers is also favorable to the binding free energy. However, water slightly disfavors the dimer formation. For the microscopic mechanism, heterogeneous of both Na⁺ and Cl^- near the charged residues at the binding interface and change of this charge distribution on dimer formation contribute to the stability. A fine-tuning of enthalpic and entropic effects of salt ions is found to operate at different salt concentrations. Both thermodynamic and microscopic mechanism of dimer formation gives detailed insight into the complex electrostatics of charged protein-protein binding.

On the transferability of ion parameters to the TIP4P/2005 water model using molecular dynamics simulations

Countless molecular dynamics studies have relied on available ion and water force field parameters to model aqueous electrolyte solutions. The TIP4P/2005 model has proven itself to be among the best rigid water force fields, whereas many of the most successful ion parameters were optimized in combination with SPC/E, TIP3P, or TIP4P/Ew water. Many researchers have combined these ions with TIP4P/2005, hoping to leverage the strengths of both parameter sets. To assess if this widely used approach is justified and to provide a guide in selecting ion parameters, we investigated the transferability of various commonly used monovalent and multivalent ion parameters to the TIP4P/2005 water model. The transferability is evaluated in terms of ion hydration free energy, hydration radius, coordination number, and self-diffusion coefficient at infinite dilution. For selected ion parameters, we also investigated density, ion pairing, chemical potential, and mean ionic activity coefficients at finite concentrations. We found that not all ions are equally transferable to TIP4P/2005 without compromising their performance. In particular, ions optimized for TIP3P water were found to be poorly transferable to TIP4P/2005, whereas ions optimized for TIP4P/Ew water provided nearly perfect transferability. The latter ions also showed good overall agreement with experimental values. The one exception is that no combination of ion parameters and water model considered here was found to accurately reproduce experimental self-diffusion coefficients. Additionally, we found that cations optimized for SPC/E and TIP3P water displayed consistent underpredictions in the hydration free energy, whereas anions consistently overpredicted the hydration free energy.

Polarizable MD simulations of ionic liquids: How does additional charge transfer change the dynamics?

A new model for treating charge transfer in ionic liquids is developed and applied to 1-ethyl-3-methylimidazolium tetrafluoroborate. The model allows for us to examine the roles of charge transfer, polarizability, and charge scaling effects on the dynamics of ionic liquids.

Solvate ionic liquids based on lithium bis(trifluoromethanesulfonyl)imide–glyme systems: coordination in MD simulations with scaled charges

Charge scaling in molecular dynamics simulations of lithium bis(trifluoromethanesulfonyl)imide–glyme solvate ionic liquids yields better agreement with experiments.

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.

Improved Cation Binding to Lipid Bilayers with Negatively Charged POPS by Effective Inclusion of Electronic Polarization

Phosphatidylserine (PS) lipids are important signaling molecules and the most common negatively charged lipids in eukaryotic membranes. The signaling can be often regulated by calcium, but its interactions with PS headgroups are not fully understood. Classical molecular dynamics (MD) simulations can potentially give detailed description of lipid-ion interactions, but the results strongly depend on the used force field. Here, we apply the electronic continuum correction (ECC) to the Amber Lipid17 parameters of 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (POPS) lipid to improve its interactions with K⁺, Na⁺, and Ca²⁺ ions. The partial charges of the headgroup, glycerol backbone, and carbonyls of POPS, bearing a unit negative charge, were scaled with a factor of 0.75, derived for monovalent ions, and the Lennard-Jones σ parameters of the same segments were scaled with a factor of 0.89. The resulting ECC-POPS model gives more realistic interactions with Na⁺ and Ca²⁺ cations than the original Amber Lipid17 parameters when validated using headgroup order parameters and the "electrometer concept". In ECC-lipids simulations, populations of complexes of Ca²⁺ cations with more than two PS lipids are negligible, and interactions of Ca²⁺ cations with only carboxylate groups are twice more likely than with only phosphate groups, while interactions with carbonyls almost entirely involve other groups as well. Our results pave the way for more realistic MD simulations of biomolecular systems with anionic membranes, allowing signaling processes involving PS and Ca²⁺ to be elucidated.

Charge Scaling Manifesto: A Way of Reconciling the Inherently Macroscopic and Microscopic Natures of Molecular Simulations

Electronic polarization effects play an important role in the interactions of charged species in biologically relevant aqueous solutions, such as those involving salt ions, proteins, nucleic acids, or phospholipid membranes. Explicit inclusion of electronic polarization in molecular modeling is tedious both from the point of view of force field parametrization and actual performance of the simulations. Therefore, the vast majority of biomolecular simulations is performed using nonpolarizable force fields, which can lead to artifacts such as dramatically overestimated ion pairing, particularly when polyvalent ions are involved. Here, we show that many of these issues can be remedied without extra computational costs by including electronic polarization in a mean field way via charge rescaling. We also lay the solid physical foundations of this approach and reconcile from this perspective the microscopic versus macroscopic natures of nonpolarizable force fields.

Accurate Biomolecular Simulations Account for Electronic Polarization

In this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of classical molecular dynamics simulations of biomolecules. While the effects of electronic polarization are highly pronounced for molecules with an opposite total charge, they are also non-negligible for interactions with overall neutral molecules. For instance, neglecting these effects in important biomolecules like amino acids and phospholipids affects the structure of proteins and membranes having a large impact on interpreting experimental data as well as building coarse grained models. With the combined advances in theory, algorithms and computational power it is currently realistic to perform simulations with explicit polarizable dipoles on systems with relevant sizes and complexity. Alternatively, the effects of electronic polarization can also be included at zero additional computational cost compared to standard fixed-charge force fields using the electronic continuum correction, as was recently demonstrated for several classes of biomolecules.

Sequential activation of STIM1 links Ca2+ with luminal domain unfolding

The stromal interaction molecule 1 (STIM1) has two important functions, Ca2+ sensing within the endoplasmic reticulum and activation of the store-operated Ca2+ channel Orai1, enabling plasma-membrane Ca2+ influx. We combined molecular dynamics (MD) simulations with live-cell recordings and determined the sequential Ca2+-dependent conformations of the luminal STIM1 domain upon activation. Furthermore, we identified the residues within the canonical and noncanonical EF-hand domains that can bind to multiple Ca2+ ions. In MD simulations, a single Ca2+ ion was sufficient to stabilize the luminal STIM1 complex. Ca2+ store depletion destabilized the two EF hands, triggering disassembly of the hydrophobic cleft that they form together with the stable SAM domain. Point mutations associated with tubular aggregate myopathy or cancer that targeted the canonical EF hand, and the hydrophobic cleft yielded constitutively clustered STIM1, which was associated with activation of Ca2+ entry through Orai1 channels. On the basis of our results, we present a model of STIM1 Ca2+ binding and refine the currently known initial steps of STIM1 activation on a molecular level.

An effective partial charge model for bulk and surface properties of cubic ZrO2, Y2O3 and yttrium-stabilised zirconia

In this work a newly parametrised Coulomb plus Buckingham potential formulation for cubic ZrO₂, Y₂O₃ and yttrium-stabilised zirconia (YSZ) is presented. The density and pair distributions obtained for neat ZrO₂ and Y₂O₃ under ambient conditions are in excellent agreement with experimental data, while the vibrational power spectra are highly similar compared to those obtained via ab initio molecular dynamics simulations at the PBEsol level. In addition, it is shown that the use of effective partial charges has several advantages compared to interaction potentials employing the oxidation states in the evaluation of the coulombic interactions: (i) the diffusion coefficient and the associated activation energy of oxygen ions evaluated for YSZn (n = 4 to 12) display the best agreement with experimental data; (ii) no unphysical reorganisation of the interface and the bulk are observed in simulations of the (110) and (111) surfaces of cubic ZrO₂ and Y₂O₃, while due to the strong coulombic contributions in the case of the tested full-charge models a pronounced restructuring of the interface and the bulk is observed in the ZrO₂ case, and (iii) the use of effective partial charges ensures compatibility with existing solvent models and force-fields for the treatment of molecular compounds.

Dielectric Decrement for Aqueous NaCl Solutions: Effect of Ionic Charge Scaling in Nonpolarizable Water Force Fields

We investigate the dielectric constant and the dielectric decrement of aqueous NaCl solutions by means of molecular dynamic simulations. We thereby compare the performance of four different force fields and focus on disentangling the origin of the dielectric decrement and the influence of scaled ionic charges, as often used in nonpolarizable force fields to account for the missing dynamic polarizability in the shielding of electrostatic ion interactions. Three of the force fields showed excessive contact ion pair formation, which correlates with a reduced dielectric decrement. In spite of the fact that the scaling of charges only weakly influenced the average polarization of water molecules around an ion, the rescaling of ionic charges did influence the dielectric decrement, and a close-to-linear relation of the slope of the dielectric constant as a function of concentration with the ionic charge was found.

A force field of Li+, Na+, K+, Mg2+, Ca2+, Cl-, and SO4 2- in aqueous solution based on the TIP4P/2005 water model and scaled charges for the ions

In this work, a force field for several ions in water is proposed. In particular, we consider the cations Li⁺, Na⁺, K⁺, Mg²⁺, and Ca²⁺ and the anions Cl^- and SO₄ ^2-. These ions were selected as they appear in the composition of seawater, and they are also found in biological systems. The force field proposed (denoted as Madrid-2019) is nonpolarizable, and both water molecules and sulfate anions are rigid. For water, we use the TIP4P/2005 model. The main idea behind this work is to further explore the possibility of using scaled charges for describing ionic solutions. Monovalent and divalent ions are modeled using charges of 0.85 and 1.7, respectively (in electron units). The model allows a very accurate description of the densities of the solutions up to high concentrations. It also gives good predictions of viscosities up to 3 m concentrations. Calculated structural properties are also in reasonable agreement with the experiment. We have checked that no crystallization occurred in the simulations at concentrations similar to the solubility limit. A test for ternary mixtures shows that the force field provides excellent performance at an affordable computer cost. In summary, the use of scaled charges, which could be regarded as an effective and simple way of accounting for polarization (at least to a certain extend), improves the overall description of ionic systems in water. However, for purely ionic systems, scaled charges will not adequately describe neither the solid nor the melt.

Giant Thermoelectric Response of Nanofluidic Systems Driven by Water Excess Enthalpy

Nanofluidic systems could in principle be used to produce electricity from waste heat, but current theoretical descriptions predict a rather poor performance as compared to thermoelectric solid materials. Here we investigate the thermoelectric response of NaCl and NaI solutions confined between charged walls, using molecular dynamics simulations. We compute a giant thermoelectric response, 2 orders of magnitude larger than the predictions of standard models. We show that water excess enthalpy-neglected in the standard picture-plays a dominant role in combination with the electro-osmotic mobility of the liquid-solid interface. Accordingly, the thermoelectric response can be boosted using surfaces with large hydrodynamic slip. Overall, the heat harvesting performance of the model systems considered here is comparable to that of the best thermoelectric materials, and the fundamental insight provided by molecular dynamics suggests guidelines to further optimize the performance, opening the way to recycle waste heat using nanofluidic devices.

Concurrent Compression of Phospholipid Membranes by Calcium and Cholesterol

Regulation of cell metabolism, membrane fusion, association of proteins with cellular membranes, and cellular signaling altogether would not be possible without Ca²⁺ ions. The distribution of calcium within the cell is uneven with the negatively charged inner leaflet of the plasma membrane being one of the primary targets of its accumulation. Therefore, we decided to map the influence of Ca²⁺ on the properties of lipid bilayers closely resembling natural lipid membranes. We combined fluorescence spectroscopy (analysis of time-resolved emission spectra of Laurdan probe and derived parameters: integrated relaxation time related to local lipid mobility, and total emission shift reflecting membrane polarity and hydration) with molecular dynamics simulations to determine the effect of the increasing CaCl₂ concentration on model lipid membranes containing POPC, POPS, and cholesterol. On top of that, the impact of calcium on the plasma membranes isolated from HEK293 cells was investigated using the steady-state fluorescence of Laurdan. We found that calcium increases rigidity of all the model lipid membranes used, elevates their thickness, increases lipid packing and ordering, and impedes the local lipid mobility. All these effects were to a great extent similar to those elicited by cholesterol. However, the changes of the membrane properties induced by calcium and cholesterol seem largely independent from each other. At sufficiently high concentrations of calcium or cholesterol, the steric effects hindered a further alteration of membrane organization, i.e., the compressibility limit of membrane structures was reached. We found no indication for mutual interaction between Ca²⁺ and cholesterol, nor competition of Ca²⁺ ions and hydroxyl groups of cholesterol for binding to phospholipids. Fluorescence measurements indicated that Ca²⁺ adsorption decreases mobility within the carbonyl region of model bilayers more efficiently than monovalent ions do (Ca²⁺ ≫ Li⁺ > Na⁺ > K⁺ > Cs⁺). The effects of calcium ions were to a great extent mitigated in the plasma membranes isolated from HEK293 cells when compared to the model lipid membranes. Noticeably, the plasma membranes showed remarkably higher resistance toward rigidification induced by calcium ions even when compared with the model membranes containing cholesterol.

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.

Ion Transport and the True Transference Number in Nonaqueous Polyelectrolyte Solutions for Lithium Ion Batteries

Nonaqueous polyelectrolyte solutions have been recently proposed as high Li+ transference number electrolytes for lithium ion batteries. However, the atomistic phenomena governing ion diffusion and migration in polyelectrolytes are poorly understood, particularly in nonaqueous solvents. Here, the structural and transport properties of a model polyelectrolyte solution, poly(allyl glycidyl ether-lithium sulfonate) in dimethyl sulfoxide, are studied using all-atom molecular dynamics simulations. We find that the static structural analysis of Li+ ion pairing is insufficient to fully explain the overall conductivity trend, necessitating a dynamic analysis of the diffusion mechanism, in which we observe a shift from largely vehicular transport to more structural diffusion as the Li+ concentration increases. Furthermore, we demonstrate that despite the significantly higher diffusion coefficient of the lithium ion, the negatively charged polyion is responsible for the majority of the solution conductivity at all concentrations, corresponding to Li+ transference numbers much lower than previously estimated experimentally. We quantify the ion-ion correlations unique to polyelectrolyte systems that are responsible for this surprising behavior. These results highlight the need to reconsider the approximations typically made for transport in polyelectrolyte solutions.

Tubulin response to intense nanosecond-scale electric field in molecular dynamics simulation

Intense pulsed electric fields are known to act at the cell membrane level and are already being exploited in biomedical and biotechnological applications. However, it is not clear if electric pulses within biomedically-attainable parameters could directly influence intra-cellular components such as cytoskeletal proteins. If so, a molecular mechanism of action could be uncovered for therapeutic applications of such electric fields. To help clarify this question, we first identified that a tubulin heterodimer is a natural biological target for intense electric fields due to its exceptional electric properties and crucial roles played in cell division. Using molecular dynamics simulations, we then demonstrated that an intense - yet experimentally attainable - electric field of nanosecond duration can affect the bβ-tubulin’s C-terminus conformations and also influence local electrostatic properties at the GTPase as well as the binding sites of major tubulin drugs site. Our results suggest that intense nanosecond electric pulses could be used for physical modulation of microtubule dynamics. Since a nanosecond pulsed electric field can penetrate the tissues and cellular membranes due to its broadband spectrum, our results are also potentially significant for the development of new therapeutic protocols.

Development of Nonbonded Models for Metal Cations Using the Electronic Continuum Correction

The parametrization of classical nonbonded models of metal ions has been widely addressed in the recent years. Despite the continuous development of novel and more physically inspired functional forms, the 12-6 Lennard-Jones plus Coulomb potential is still the most adopted force field in molecular dynamics (MD) codes, owing to its simple form and easy implementation. However, due to the integer formal charge, unpolarizable force fields of ions may suffer from overestimated interatomic electrostatic interactions, leading to nonphysical clustering or repulsion between such full charges. The electronic continuum correction (ECC) can fix this problem through a simple inclusion of solvent polarization effects via ionic charge rescaling. In this work, the development of novel nonbonded models for mono, divalent, and highly charged metal ions is presented. For each metal species, the ionic charge has been scaled, according to the ECC. Lennard-Jones parameters have been optimized using experimental structural and thermodynamic properties as target quantities. Performances of the proposed models are discussed and compared with the literature data, while transferability attitudes among different and well-known water models are evaluated. © 2019 Wiley Periodicals, Inc.

Quantifying the Strength of a Salt Bridge by Neutron Scattering and Molecular Dynamics

The molecular structure and strength of a model salt bridge between a guanidinium cation (side chain group of arginine) and the acetate carboxylic group in an aqueous solution is characterized by a combination of neutron diffraction with isotopic substitution and molecular dynamics simulations. The present neutron scattering experiments provide direct information about ion pairing in the solution. At the same time, these measurements are used to assess the quality of the force field employed in the simulation. We show that a standard nonpolarizable force field overestimates the strength of salt bridges. In contrast, accounting for electronic polarization effects via charge scaling allows to quantitatively reproduce the experiment. Such simulations are used to quantify the weak character of a fully hydrated salt bridge. Finally, on top of the canonical hydrogen-bonding binding mode, we uncover another interaction motif involving an out-of-plane hydrophobic contact of the acetate methyl group with the guanidinium cation.

New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 1. Theory and accuracy

Polarizabilities and London dispersion forces are important to many chemical processes. Force fields for classical atomistic simulations can be constructed using atom-in-material polarizabilities and C n (n = 6, 8, 9, 10…) dispersion coefficients. This article addresses the key question of how to efficiently assign these parameters to constituent atoms in a material so that properties of the whole material are better reproduced. We develop a new set of scaling laws and computational algorithms (called MCLF) to do this in an accurate and computationally efficient manner across diverse material types. We introduce a conduction limit upper bound and m-scaling to describe the different behaviors of surface and buried atoms. We validate MCLF by comparing results to high-level benchmarks for isolated neutral and charged atoms, diverse diatomic molecules, various polyatomic molecules (e.g., polyacenes, fullerenes, and small organic and inorganic molecules), and dense solids (including metallic, covalent, and ionic). We also present results for the HIV reverse transcriptase enzyme complexed with an inhibitor molecule. MCLF provides the non-directionally screened polarizabilities required to construct force fields, the directionally-screened static polarizability tensor components and eigenvalues, and environmentally screened C6 coefficients. Overall, MCLF has improved accuracy compared to the TS-SCS method. For TS-SCS, we compared charge partitioning methods and show DDEC6 partitioning yields more accurate results than Hirshfeld partitioning. MCLF also gives approximations for C8, C9, and C10 dispersion coefficients and quantum Drude oscillator parameters. This method should find widespread applications to parameterize classical force fields and density functional theory (DFT) + dispersion methods.

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.

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.

Induction of rare conformation of oligosaccharide by binding to calcium-dependent bacterial lectin: X-ray crystallography and modelling study

Pathogenic micro-organisms utilize protein receptors (lectins) in adhesion to host tissues, a process that in some cases relies on the interaction between lectins and human glycoconjugates. Oligosaccharide epitopes are recognized through their three-dimensional structure and their flexibility is a key issue in specificity. In this paper, we analysed by X-ray crystallography the structures of the LecB lectin from two strains of Pseudomonas aeruginosa in complex with Lewis x oligosaccharide present on cell surfaces of human tissues. An unusual conformation of the glycan was observed in all binding sites with a non-canonical syn orientation of the N-acetyl group of N-acetyl-glucosamine. A PDB-wide search revealed that such an orientation occurs only in 4% of protein/carbohydrate complexes. Theoretical chemistry calculations showed that the observed conformation is unstable in solution but stabilised by the lectin. A reliable description of LecB/Lewis x complex by force field-based methods had proven especially challenging due to the special feature of the binding site, two closely apposed Ca²⁺ ions which induce strong charge delocalisation. By comparing various force-field parametrisations, we propose a general strategy which will be useful in near future for designing carbohydrate-based ligands (glycodrugs) against other calcium-dependent protein receptors.