Structural and dynamic properties of concentrated alkali halide solutions: a molecular dynamics simulation study

The physicochemical properties of alkali halide solutions have long been attributed to the collective interactions between ions and water molecules in the solution, yet the structure of water in these systems and its effect on the equilibrium and dynamic properties of these systems are not clearly understood. Here, we present a systematic view of water structure in concentrated alkali halide solutions using molecular dynamics simulations. The results of the simulations show that the size of univalent ions in the solution has a significant effect on the dynamics of ions and other transport properties such as the viscosity that are correlated with the structural properties of water in aqueous ionic solution. Small cations (e.g., Li+) form electrostatically stabilized hydrophilic hydration shells that are different from the hydration shells of large ions (e.g., Cs+) which behave more like neutral hydrophobic particles, encapsulated by hydrogen-bonded hydration cages. The properties of solutions with different types of ion solvation change in different ways as the ion concentration increases. Examples of this are the diffusion coefficients of the ions and the viscosities of solutions. In this paper we use molecular dynamics (MD) simulations to study the changes in the equilibrium and transport properties of LiCl, RbCl, and CsI solutions at concentrations from 0.22 to 3.97 M.     

Understanding the pH-dependent behavior of graphene oxide aqueous solutions: a comparative experimental and molecular dynamics simulation study

Understanding the pH-dependent behavior of graphene oxide (GO) aqueous solutions is important to the production of assembled GO or reduced GO films for electronic, optical, and biological applications. We have carried out a comparative experimental and molecular dynamics (MD) simulation study to uncover the mechanisms behind the aggregation and the surface activity of GO at different pH values. At low pH, the carboxyl groups are protonated such that the GO sheets become less hydrophilic and form aggregates. MD simulations further suggest that the aggregates exhibit a GO-water-GO sandwichlike structure and as a result are stable in water instead of precipitating. However, at high pH, the deprotonated carboxyl groups are very hydrophilic such that individual GO sheets prefer to dissolve in bulk water like a regular salt. The GO aggregates formed at low pH are found to be surface-active and do not exhibit characteristic features of surfactant micelles. Our findings suggest that GO does not behave like conventional surfactants in pH 1 and 14 aqueous solutions. The molecular-level understanding of the solution behavior of GO presented here can facilitate and improve the experimental techniques used to synthesize and sort large, uniform GO dispersions in a solution phase.     

G-quadruplexes can maintain their structure in the gas phase

Several very extended (0.5-1 micros) molecular dynamics (MD) simulations of parallel and antiparallel G-quadruplex DNA strongly suggest that in the presence of suitable cations the quadruplex not only remains stable in the gas phase, but also displays a structure that closely resembles that found in extended (25-ns long) trajectories in aqueous solution. In the absence of the crucial cations, the trajectories become unstable and in general the quadruplex structure is lost. To our knowledge, this is the first physiologically relevant structure of DNA for which very large MD simulations suggest that the structure in water and in the gas phase are indistinguishable.     

Development and validation of an integrated computational approach for the study of ionic species in solution by means of effective two-body potentials. The case of Zn2+, Ni2+, and Co2+ in aqueous solutions

In this paper we have developed an effective computational procedure for the structural and dynamical investigation of ions in aqueous solutions. Quantum mechanical potential energy surfaces for the interaction of a transition metal ion with a water molecule have been calculated taking into account the effect of bulk solvent by the polarizable continuum model (PCM). The effective ion-water interactions have been fitted by suitable analytical potentials, and have been utilized in molecular dynamics (MD) simulations to obtain structural and dynamical properties of the ionic aqueous solutions. This procedure has been successfully applied to the Co2+-H2O open-shell system and, for the first time, Co-oxygen and Co-hydrogen pair potential functions have been determined and employed in MD simulations. The reliability of the whole procedure has been assessed by applying it also to the Zn2+ and Ni2+ aqueous solutions, and the structural and dynamical properties of the three systems have been calculated by means of MD simulations and have been found to be in very good agreement with experimental results. The structural parameters of the first solvation shells issuing from the MD simulations provide an effective complement to extended X-ray absorption fine structure (EXAFS) experiments.     

Diclofenac Ion Hydration: Experimental and Theoretical Search for Anion Pairs

Self-assembly of organic ions in aqueous solutions is a hot topic at the present time, and substances that are well-soluble in water are usually studied. In this work, aqueous solutions of sodium diclofenac are investigated, which, like most medicinal compounds, is poorly soluble in water. Classical MD modeling of an aqueous solution of diclofenac sodium showed equilibrium between the hydrated anion and the hydrated dimer of the diclofenac anion. The assignment and interpretation of the bands in the UV, NIR, and IR spectra are based on DFT calculations in the discrete-continuum approximation. It has been shown that the combined use of spectroscopic methods in various frequency ranges with classical MD simulations and DFT calculations provides valuable information on the association processes of medical compounds in aqueous solutions. Additionally, such a combined application of experimental and calculation methods allowed us to put forward a hypothesis about the mechanism of the effect of diclofenac sodium in high dilutions on a solution of diclofenac sodium.     

Redox entropy of plastocyanin: developing a microscopic view of mesoscopic polar solvation

We report applications of analytical formalisms and molecular dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of the theory required to describe polar solvation at the mesoscopic scale. The analytical techniques include a microscopic formalism based on structure factors of the solvent dipolar orientations and density and continuum dielectric theories. The microscopic theory employs the atomistic structure of the protein with force-field atomic charges and solvent structure factors obtained from separate MD simulations of the homogeneous solvent. The MD simulations provide linear response solvation free energies and reorganization energies of electron transfer in the temperature range of 280-310 K. We found that continuum models universally underestimate solvation entropies, and a more favorable agreement is reported between the microscopic calculations and MD simulations. The analysis of simulations also suggests that difficulties of extending standard formalisms to protein solvation are related to the inhomogeneous structure of the solvation shell at the protein-water interface combining islands of highly structured water around ionized residues along with partial dewetting of hydrophobic patches. Quantitative theories of electrostatic protein hydration need to incorporate realistic density profile of water at the protein-water interface.     

Coarse-grained molecular dynamics simulations of the sphere to rod transition in surfactant micelles

Surfactant molecules self-assemble in aqueous solutions to form various micellar structures such as spheres, rods, or lamellae. Although phase transitions in surfactant solutions have been studied experimentally, their molecular mechanisms are still not well understood. In this work, we show that molecular dynamics (MD) simulations using the coarse-grained (CG) MARTINI force field and explicit CG solvent, validated against atomistic MD studies, can accurately represent micellar assemblies of cetyltrimethylammonium chloride (CTAC). The effect of salt on micellar structures is studied for aromatic anionic salts, e.g., sodium salicylate, and simple inorganic salts, e.g., sodium chloride. Above a threshold concentration, sodium salicylate induces a sphere to rod transition in the micelle. CG MD simulations are shown to capture the dynamics of this shape transition and support a mechanism based on the reduction in the micelle-water interfacial tension induced by the adsorption of the amphiphilic salicylate ions. At the threshold salt concentration, the interface is nearly saturated with adsorbed salicylate ions. Predictions of the effect of salt on the micelle structure in different CG solvent models, namely, single-site standard water and three-site polarizable water, show qualitative agreement. This suggests that phase transitions in aqueous micelle solutions could be investigated by using standard CG water models which allow for 3 orders of magnitude reduction in the computational time as compared to that required for atomistic MD simulations.     

Molecular features of the air/carbonate solution interface

The nature of the air/carbonate solution interface is considered with respect to water structure by sum-frequency vibrational spectroscopy (SFVS) and molecular dynamics simulations (MDS). Results from this study provide further understating regarding previous observations that the surface tensions of structure making sodium carbonate solutions have been shown to be significantly greater than the surface tensions of structure breaking bicarbonate solutions at equivalent concentrations. This difference in surface tension and its variation with salt concentration is related to the organization of water and ions at the air/solution interface. Spectral results from SFVS show at equivalent concentrations that, for the carbonate solution, the strong water structure signal of 3200 cm(-1) at the air/carbonate solution interface is increased by a factor of 4 when compared to the same signal for the air/bicarbonate solution interface, which spectrum is weaker than the spectrum for the air/water interface in the absence of salt. These results from SFVS are explained by the results from MDS which show that in the case of carbonate solutions the structure making carbonate ions are excluded from the interfacial water region which region is extended in depth. On the other hand, in the case of bicarbonate solutions, the bicarbonate ions are accommodated in the interfacial water region and there is no evidence of an increase in the extent of water structure. These SFVS experimental and MD simulation results provide further information to understand interfacial phenomena of soluble salts at the molecular level.     

Hydrogen bonding mediated ion pairs of some aprotic ionic liquids and their structural transition in aqueous solution

Ion pair speciation of ionic liquids(ILs) has an important effect on the physical and chemical properties of ILs and recognition of the structure of ion pairs in solution is essential. It has been reported that ion pairs of some ILs can be formed by hydrogen bonding interactions between cations and anions of them. Considering the fact that far-IR(FIR) spectroscopy is a powerful tool in indicating the intermolecular and intramolecular hydrogen bonding, in this work, this spectroscopic technique has been combined with molecular dynamic(MD) simulation and nuclear magnetic resonance hydrogen spectroscopy(~1H NMR) to investigate ion pairs of aprotic ILs [Bmim][NO_3], [BuPy][NO_3], [Pyr_(14)][NO_3], [PP_(14)][NO_3] and [Bu-choline][NO_3] in aqueous IL mixtures. The FIR spectra have been assigned with the aid of density functional theory(DFT) calculations, and the results are used to understand the effect of cationic nature on the structure of ion pairs. It is found that contact ion pairs formed in the neat aprotic ILs by hydrogen bonding interactions between cation and anion, were still maintained in aqueous solutions up to high water mole fraction(say 0.80 for [BuPy][NO3]). When water content was increased to a critical mole fraction of water(say 0.83 for [BuPy][NO3]), the contact ion pairs could be transformed into solvent-separated ion pairs due to the formation of the hydrogen bonding between ions and water. With the further dilution of the aqueous ILs solution, the solvent-separated ion pairs was finally turned into free cations and free anions(fully hydrated cations or anions). The concentrations of the ILs at which the contact ion pairs were transformed into solvent-separated ion pairs and solvent-separated ion pairs were transformed into free ions(fully hydrated ion) were dependent on the cationic structures. These information provides direct spectral evidence for ion pair structures of the aprotic ILs in aqueous solution. MD simulation and ~1H NMR results support the conclusion drawn from FIR spectra investigations.     

An extensible interface for QM/MM molecular dynamics simulations with AMBER

We present an extensible interface between the AMBER molecular dynamics (MD) software package and electronic structure software packages for quantum mechanical (QM) and mixed QM and classical molecular mechanical (MM) MD simulations within both mechanical and electronic embedding schemes. With this interface, ab initio wave function theory and density functional theory methods, as available in the supported electronic structure software packages, become available for QM/MM MD simulations with AMBER. The interface has been written in a modular fashion that allows straight forward extensions to support additional QM software packages and can easily be ported to other MD software. Data exchange between the MD and QM software is implemented by means of files and system calls or the message passing interface standard. Based on extensive tests, default settings for the supported QM packages are provided such that energy is conserved for typical QM/MM MD simulations in the microcanonical ensemble. Results for the free energy of binding of calcium ions to aspartate in aqueous solution comparing semiempirical and density functional Hamiltonians are shown to demonstrate features of this interface. © 2013 Wiley Periodicals, Inc.     

Unified molecular picture of the surfaces of aqueous acid, base, and salt solutions

The molecular structure of the interfacial regions of aqueous electrolytes is poorly understood, despite its crucial importance in many biological, technological, and atmospheric processes. A long-term controversy pertains between the standard picture of an ion-free surface layer and the strongly ion specific behavior indicating in many cases significant propensities of simple inorganic ions for the interface. Here, we present a unified and consistent view of the structure of the air/solution interface of aqueous electrolytes containing monovalent inorganic ions. Molecular dynamics calculations show that in salt solutions and bases the positively charged ions, such as alkali cations, are repelled from the interface, whereas the anions, such as halides or hydroxide, exhibit a varying surface propensity, correlated primarily with the ion polarizability and size. The behavior of acids is different due to a significant propensity of hydronium cations for the air/solution interface. Therefore, both cations and anions exhibit enhanced concentrations at the surface and, consequently, these acids (unlike bases and salts) reduce the surface tension of water. The results of the simulations are supported by surface selective nonlinear vibrational spectroscopy, which reveals among other things that the hydronium cations are present at the air/solution interface. The ion specific propensities for the air/solution interface have important implications for a whole range of heterogeneous physical and chemical processes, including atmospheric chemistry of aerosols, corrosion processes, and bubble coalescence.     

羟基磷灰石界面水行为的分子模拟

本文采用分子动力学模拟(MD)方法研究了羟基磷灰石(HAP)(001)和(100)晶面上的水分子行为，发现HAP晶面间的水是处在高电场和高内压的环境下，并可在晶面处形成2～3层高度结构化的水层，这些水具有有序结构和类冰固化特征。其中在HAP晶体的[001]方向具有较强的极性，相对于[100]方向能诱导产生更多的有序结构化水层。研究发现HAP-水界面处钙和磷酸根位点分布和水分子的吸附位点相关，并且水在HAP界面上的吸附形式具有多样性。该工作揭示了HAP界面结构化水层的形成及其结构细节特征。HAP晶面附近的结构化水层可阻止溶液离子自由出入晶面，对HAP颗粒在水溶液中的动力学稳定性具有重要的影响。     

Surface activity and redox behavior of a non-ionic surfactant containing a phenothiazine group

A novel non-ionic surfactant, -(phenothiazinylhexyl)-ω-hydroxy-oligo(ethylene oxide) (PCPEG) containing phenothiazine as an electro-active group has been synthesized. Fundamental interfacial behavior of the surfactant at the air/water interface has been investigated by means of surface tensiometry to provide an insight into the relationship between the structure of the hydrophobic moiety and the surfactant properties. A comparison of diffusivity of PCPEG in the aqueous phase with that in the acetonitrile solution at high PCPEG concentrations shows that micellization has a pronounced effect on the redox behavior of PCPEG. The electrochemical responses for PCPEG aqueous solutions at the interface of a glassy carbon electrode are fairly dependent on the concentration of PCPEG. Above CMC, PCPEG molecules self-associate to form micellar aggregates and the formation and disruption of micelles can be reversibly controlled by change in the redox state of the phenothiazine group. The cyclic voltammetric responses for PCPEG aqueous solutions have been correlated with the dissolved states to explain the distinctive feature of the surfactant.     

Molecular dynamics simulation of the A-DNA to B-DNA transition in aqueous RbCl solution

Unrestrained molecular dynamics (MD) simulations have been carried out to characterize the stability of DNA conformations and the dynamics of A-DNA→B-DNA conformational transitions in aqueous RbCl solutions. The PARM99 force field in the AMBER8 package was used to investigate the effect of RbCl concentration on the dynamics of the A→B conformational transition in the DNA duplex d(CGCGAATTCGCG)2 . Canonical Aand B-form DNA were assumed for the initial conformation and the final conformation had a length per complete turn that matched the canonical B-DNA. The DNA structure was monitored for 3.0 ns and the distances between the C5′ atoms were obtained from the simulations. It was found that all of the double stranded DNA strands of A-DNA converged to the structure of B-form DNA within 1.0 ns during the unrestrained MD simulations. In addition, increasing the RbCl concentration in aqueous solution hindered the A→B conformational transition and the transition in aqueous RbCl solution was faster than that in aqueous NaCl solution for the same electrolyte strength. The effects of the types and concentrations of counterions on the dynamics of the A→B conformational transition can be understood in terms of the variation in water activity and the number of accumulated counterions in the major grooves of A-DNA. The rubidium ion distributions around both fixed A-DNA and B-DNA were obtained using the restrained MD simulations to help explain the effect of RbCl concentration on the dynamics of the A→B conformational transition.     

Hydrophobic and electrostatic interactions in adsorption of surface-active substances. Tetraalkylammonium salts

A relationship between the standard free energies of adsorption from aqueous solution at the oil/water interface and the radii of organic cations as exemplified by symmetric tetraakylammonium salts has been studied. Hydrophobic effects are shown to be major contributors to the interaction of surfactants with the interface. An adsorption coefficient to quantitate the hydrophobic effects and to specify the changes of standard adsorption energy depending upon the cavity surface area of the detergent hydrocarbon radical in aqueous solution has been proposed. A new formulation of the Traube rule, taking into account the hydrophobic effects concomitant with a transfer of surfactants from the water bulk onto the interface, has also been given.Standard free energies for the adsorption of organic and inorganic ions from aqueous solution at the interface of immiscible liquids have been found. The proposed method is based on an extrapolation of the relationship between the standard adsorption energy of tetraalkylammonium salts and the square of cationic radius to zero ionic radius. The standard free energy of adsorption for an inorganic counter-ion is derived from an intercept on the y-axis cut off by a straight line. The experimental adsorption data on inorganic salts have been used to calculate the standard free energies of adsorption for a variety of ions.A method of estimating the difference in potential at the oil/water interface between the adsorption plane and the aqueous solution has been proposed. The sign of potential provides a clue to the orientation of water molecules at the interface between immiscible liquids.     

Structural and thermodynamic aspects of ionic solvation in concentrated aqueous poly(ethylene glycol)

Solvation of ions in concentrated aqueous poly(ethylene glycol) (PEG) has been studied from thermodynamic and structural viewpoints using ion-transfer voltammetry at the interface between aqueous and nitrobenzene phases and X-ray absorption fine structure (XAFS). Systematic changes in the ion-transfer potential from water to aqueous PEG have been confirmed for several ions relative to the corresponding potential of tetraethylammonium ion (Et4N+), which is almost independent of PEG concentration. The results obtained for alkali cations strongly suggest the involvement of their complexation with PEG even in relatively diluted PEG solutions. It has been implied that the solvation circumstances of Br- and ClO4- are drastically altered when the PEG concentration becomes higher than particular critical values (e.g., 30-50% PEG200), where free water molecules are diminished because of the hydration of PEG. XAFS measurements have also been performed for K+ and Br- to get direct evidence for these findings. Although the spectra at the K K-edge clearly indicate the presence of a PEG complex of K+ in relatively diluted PEG solutions ( approximately 33% PEG200), an obvious increase in its ion-transfer potential has been detected at lower PEG concentrations, indicating that complexes formed at the interface rather than in bulk solution are transferred into an organic phase. Br- is fully hydrated in 0-50% PEG solutions, whereas some water molecules are replaced by PEG when the PEG concentration increases. Increasing the PEG concentration causes decreases in the coordination number from 6 in water to 2-3 in neat PEG. Thus, the present approach not only has elucidated the structural and thermodynamic aspects of ionic solvation in aqueous PEG but also has provided the information of the hydration of PEG.     

Role of counterion condensation in the self-assembly of SDS surfactants at the water-graphite interface

The aggregate structure of sodium dodecyl sulfate (SDS) adsorbed at the graphite-water interface has been studied with the aid of molecular dynamics (MD) simulations. As expected, our results show that adsorbed SDS yields hemi-cylindrical micelles. The hemi-cylindrical aggregates in our simulations closely resemble all structural and morphological details provided by previous solution atomic force microscopy (AFM) experiments. More interestingly, our data indicate that SDS head groups do not provide a complete shield to the hydrophobic tails. Instead, we found regions in which the hydrophobic tails are exposed to the aqueous solution. By conducting a parametric study for SDS-like nonionic surfactants we show that electrostatic interactions between SDS head groups and counterions are responsible for the unexpected result. Our interpretation is corroborated by density profiles, analysis of the coordination states, and mean square displacement data for both the adsorbed SDS surfactants and the counterions in solution. Counterion condensation appears to be a physical phenomenon that could be exploited to direct the assembly of advanced nanostructured materials.     

All-atom Molecular Dynamics Simulationsand NMR Spectroscopy Study on Interactions and Structures in N-Glycylglycine Aqueous Solution

All-atom molecular dynamics (MD) simulation and the NMR spectra are used to investi-gate the interactions in N-glycylglycine aqueous solution. Different types of atoms exhibit different capability in forming hydrogen bonds by the radial distribution function analysis. Some typical dominant aggregates are found in different types of hydrogen bonds by the statistical hydrogen-bonding network. Moreover, temperature-dependent NMR are used to compare with the results of the MD simulations. The chemical shifts of the three hydrogen atoms all decrease with the temperature increasing which reveals that the hydrogen bonds are dominant in the glycylglycine aqueous solution. And the NMR results show agreement with the MD simulations. All-atom MD simulations and NMR spectra are successful in revealing the structures and interactions in the N-glycylglycine-water mixtures.     

Aggregation and adsorption behavior of low concentration aqueous solutions of hexadecyltrimethylammonium ortho, meta, and parafluorobenzoate

The aggregation properties of 2-, 3-, and 4-fluorobenzoic acids (2FBA, 3FBA, and 4FBA, respectively) and their salts with hexadecyltrimethylammonium cations (HTA2FB, HTA3FB, and HTA4FB) in water were studied with a battery of techniques. Their activity at the air/solution interface has been also studied. The position of the fluorine atom in the acid affected the solubility, adsorption, and aggregation in the pure acids solutions. The 4FBA is less water soluble, more hydrophobic, and has the lower critical aggregation concentration of the three isomers. The behavior of the HTA2FB compound in aqueous solution is different from that of HTA3FB and HTA4FB. The critical micelle concentration, critical concentration for sphere-to-rod-like micelle transition, and Krafft point of HTA3FB and HTA4FB are lower than those of the other surfactant but their surface activities are higher. The differences between the HTA2FB and the other two surfactants have been explained on the basis of the regular solution theory of mixed micelles and in light of the analysis of the hydration shell of the acids through molecular dynamic simulations. The results of the present work suggest that the different behaviors are due to a combination of different dehydration tendencies and the steric possibility of inclusion of the counterions in the micelle palisade layer. The formation of rod-like micelles by HTA2FB, while the tetradecyltrimethylammonium 2-fluorobenzoate only forms spherical aggregates, is explained on the basis of the packing parameter. The mentioned factors are complementary to others presented in literature. These conditions may be used in the rational design of micelles by means of molecular dynamics simulations, reducing the trial-and-error approach used to date.