Hydration of Y3+ ion: a Car-Parrinello molecular dynamics study

The solvation shell structure of Y3+ and the dynamics of the hydrated ion in an aqueous solution of 0.8 M YCl3 are studied in two conditions with and without an excess proton by using first principles molecular dynamics method. We find that the first solvation shell around Y3+ contains eight water molecules forming a square antiprism as expected from x-ray absorption near edge structure in both the conditions we examined. A detailed analysis relying upon localized orbitals reveals that the complexation of water molecules with yttrium cation leads to a substantial amount of charge redistribution particularly on the oxygen atoms, giving rise to the chemical shifts of approximately -20 ppm in 17O nuclear magnetic resonance relative to the computed nuclear shieldings of the bulk water.     

Synergistic effect of dicarbollide anions in liquid-liquid extraction: a molecular dynamics study at the octanol-water interface

We report a molecular dynamics study of chlorinated cobalt bis(dicarbollide) anions [(B(9)C(2)H(8)Cl(3))(2)Co](-)"CCD(-)" in octanol and at the octanol-water interface, with the main aim to understand why these hydrophobic species act as strong synergists in assisted liquid-liquid cation extraction. Neat octanol is quite heterogeneous and is found to display dual solvation properties, allowing to well solubilize CCD(-), Cs(+) salts in the form of diluted pairs or oligomers, without displaying aggregation. At the aqueous interface, octanol behaves as an amphiphile, forming either monolayers or bilayers, depending on the initial state and confinement conditions. In biphasic octanol-water systems, CCD(-) anions are found to mainly partition to the organic phase, thus attracting Cs(+) or even more hydrophilic counterions like Eu(3+) into that phase. The remaining CCD(-) anions adsorb at the interface, but are less surface active than at the chloroform interface. Finally, we compare the interfacial behavior of the Eu(BTP)(3)(3+) complex in the absence and in the presence of CCD(-) anions and extractant molecules. It is found that when the CCD(-)'s are concentrated enough, the complex is extracted to the octanol phase. Otherwise, it is trapped at the interface, attracted by water. These results are compared to those obtained with chloroform as organic phase and discussed in the context of synergistic effect of CCD(-) in liquid-liquid extraction, pointing to the importance of dual solvation properties of octanol and of the hydrophobic character of CCD(-) for synergistic extraction of cations.     

Surfactant behavior of "ellipsoidal" dicarbollide anions: a molecular dynamics study

We report a molecular dynamics study of cobalt bis(dicarbollide) anions [(B(9)C(2)H(8)X(3))(2)Co](-) (XCD(-)) commonly used in liquid-liquid extraction (X = H, Me, Cl, or Br), showing that these anions, although lacking the amphiphilic topology, behave as anionic surfactants. In pure water, they display "hydrophobic attractions", leading to the formation of aggregates of different sizes and shapes depending on the counterions. When simulated at a water/"oil" interface, the different anions (HCD(-), MeCD(-), CCD(-), and BrCD(-)) are found to be surface active. As a result, the simulated M(n+) counterions (M(n+) = Na(+), K(+), Cs(+), H(3)O(+), UO(2)(2+), Eu(3+)) concentrate on the aqueous side of the interface, forming a "double layer" whose characteristics are modulated by the hydrophobic character of the anion and by M(n+). The highly hydrophilic Eu(3+) or UO(2)(2+) cations that are generally "repelled" by aqueous interfaces are attracted by dicarbollides near the interface, which is crucial as far as the mechanism of assisted cation extraction to the oil phase is concerned. These cations interact with interfacial XCD(-) in their fully hydrated Eu(H(2)O)(9)(3+) and UO(2)(H(2)O)(5)(2+) forms, whereas the less hydrophilic monocharged cations display intimate contacts via their X substituents. The results obtained with the TIP3P and OPLS models for the solvents are confirmed with other water models (TIP5P or a polarizable 4P-Pol water) and with more polar "oil" models. The importance of interfacial phenomena is further demonstrated by simulations with a high oil-water ratio, leading to the formation of a micelle covered with CCD's. We suggest that the interfacial activity of dicarbollides and related hydrophobic anions is an important feature of synergism in liquid-liquid extraction of hard cations (e.g., for nuclear waste partitioning).     

Methane-to-methanol oxidation by the hydrated iron(IV) oxo species in aqueous solution: a combined DFT and car-parrinello molecular dynamics study

Previously, we have shown that the ferryl ion ([FeIVO]2+) is easily produced from Fenton's reagent (i.e., a mixture of Fe2+ ions and H2O2 in aqueous solution), using DFT and Car-Parrinello MD calculations. To verify that the ferryl ion can indeed act as the active species in oxidation reactions with Fenton's reagent, we study in the present paper the reactivity of the ferryl ion toward an organic substrate, in particular the oxidation of methane to methanol. In the first part of this paper, we perform static DFT calculations on the reaction of CH4 with the [(H2O)5FeIVO]2+ complex in vacuo that show a strong prevalence of the oxygen-rebound mechanism over the methane coordination mechanism. This is in agreement with the static DFT results for methane oxidation by biocatalysts MMO and P450, but not with those for methane oxidation by bare metal-oxo ions, where the methane coordination mechanism prevails. The highest energy barrier in the oxygen-rebound mechanism is only 3 kcal/mol in vacuo, whereas in the methane coordination mechanism the highest barrier is 23 kcal/mol. Overall the oxidation reaction energy is downhill by 47 kcal/mol. We conclude that the ferryl ion can indeed act as the oxidative intermediate in the Fenton oxidation of organic species. In the second part of this paper, we perform a preliminary assessment of solvent effects on the oxidation by the ferryl ion in aqueous solution using the method of constrained (first principles) molecular dynamics. The free energy barrier of the H-abstraction reaction from methane by the ferryl ion (i.e., the first step in the rebound mechanism) in aqueous solution is, with 22 kcal/mol in solution, significantly higher than in vacuo. Given the fact that methane has a relatively strong C-H bond (ca. 10 kcal/mol stronger than the C-H bonds in the more typical Fenton's reagent substrates), we infer that for many organic substrates oxidation with the ferryl ion as an active intermediate may be a perfectly viable route.     

Characterizing hydrophobicity at the nanoscale: a molecular dynamics simulation study

We use molecular dynamics (MD) simulations of water near nanoscopic surfaces to characterize hydrophobic solute-water interfaces. By using nanoscopic paraffin like plates as model solutes, MD simulations in isothermal-isobaric ensemble have been employed to identify characteristic features of such an interface. Enhanced water correlation, density fluctuations, and position dependent compressibility apart from surface specific hydrogen bond distribution and molecular orientations have been identified as characteristic features of such interfaces. Tetrahedral order parameter that quantifies the degree of tetrahedrality in the water structure and an orientational order parameter, which quantifies the orientational preferences of the second solvation shell water around a central water molecule, have also been calculated as a function of distance from the plate surface. In the vicinity of the surface these two order parameters too show considerable sensitivity to the surface hydrophobicity. The potential of mean force (PMF) between water and the surface as a function of the distance from the surface has also been analyzed in terms of direct interaction and induced contribution, which shows unusual effect of plate hydrophobicity on the solvent induced PMF. In order to investigate hydrophobic nature of these plates, we have also investigated interplate dewetting when two such plates are immersed in water.     

Hydration of superoxide studied by molecular dynamics simulation

Molecular dynamics was used to study the hydration of superoxide (O). The Helmholtz free energy of hydration of O was estimated by the thermodynamic integration method. The diffusion of O and the water structure around O were also studied. Two water models were used in the calculations and the results were compared to experiments.     

Structural properties of polystyrene oligomers in different environments: a molecular dynamics study

We have performed detailed molecular dynamics simulations to investigate the effects of solvation and confinement on the structure of polystyrene (PS) oligomers in four different environments, melt, concentrated solution, dilute solution and confined concentrated solution at 450 K and 1 bar, respectively. Local packing of the monomers and the solvent (toluene, good solvent) molecules were monitored by means of radial distribution functions (RDFs). We have also investigated bond, angle, and dihedral angle distributions of the monomers. End-to-end distances, radii of gyration and persistence lengths were calculated to characterize the static properties. The chain in the dilute solution was found to exhibit more stretched conformations. Dilution effect of the solvent was observed in the RDFs between the monomer centers. Only slight conformational changes in the polymers were observed by solvation. The effect of confinement was mainly seen in the density profiles, which showed an oscillatory behavior in the confined system.     

Water network dynamics at the critical moment of a peptide's beta-turn formation: a molecular dynamics study

All-atom molecular dynamics simulations for a single molecule of Leu-Enkephalin in aqueous solution have been used to study the role of the water network during the formation of beta-turns. We give a detailed account of the intramolecular hydrogen bonding, the water-peptide hydrogen bonding, and the orientation and residence times of water molecules focusing on the short critical periods of transition to the stable beta-turns. These studies suggest that, when intramolecular hydrogen bonding between the first and fourth residue of the beta-turn is not present, the disruption of the water network and the establishment of water bridges constitute decisive factors in the formation and stability of the beta-turn. Finally, we provide possible explanations and mechanisms for the formations of different kinds of beta-turns.     

Contact angle hysteresis at the nanoscale: a molecular dynamics simulation study

In this paper, the contact angle hysteresis (CAH) of nanodroplets on both rigid and flexible substrates with different wettabilities was studied using molecular dynamics (MD) simulations. The critical shear stress (CSS) that determines the motion of the contact line (CL) was investigated. A theoretical correlation between CAH and CSS was proposed. Both CAH and CSS reflect the energy dissipation at the CL of the droplet in response to the exerted force. MD results of CAH are qualitatively consistent with the theoretical model. Simulation results also show that, for the same liquid–solid interactions, CAH on the flexible substrate is larger than that on the rigid substrate. These findings aim to enhance our understanding of the mechanism of the CAH at the nanoscale.     

Spreading dynamics of chain-like monolayers: a molecular dynamics study

Using large-scale molecular dynamics simulations, we have shown previously that the spreading dynamics of sessile drops on solid surfaces can be described in detail using the molecular-kinetic theory of dynamic wetting. Here we present our first steps in extending this approach to investigate the spreading dynamics of Langmuir-Blodgett monolayers. We make use of a monolayer model originally developed by Karaborni and Toxvaerd, but somewhat simplified to facilitate large-scale simulations. Our preliminary results are in good agreement with recent experimental observations and also support a molecular-kinetic interpretation in which the driving force for spreading is the lateral pressure in the monolayer. Away from equilibrium, initial spreading rates are constant and logarithmically dependent on pressure. However, near equilibrium, spreading is pseudo-diffusive and follows the square root of time. In both regimes the controlling factor is the equilibrium frequency of molecular displacements within the monolayer.     

Hydrogen-bonded clusters and solvate structures in the supercritical CO2-water-o-hydroxybenzoic acid system: the car-parrinello molecular dynamics

Hydrogen-bonded clusters and solvate structures formed by o-hydroxybenzoic acid (o-HBA) and water in supercritical CO₂ were studied (T = 318 K, 348 K, ρ = 0.7 g/cm³). The atom-atom radial distribution functions, coordination numbers, average numbers of hydrogen bonds for individual atomic groups, and power spectrum were calculated by the Car-Parrinello molecular dynamics. Despite the high polarity of the cosolvent, the hydroxyl group of o-HBA predominantly forms intramolecular hydrogen bond, while hydrogen bonds with water involve only the atoms of carboxyl groups. The temperature effect on the stability of these bonds showed itself in different ways. The intermolecular interactions of o-HBA with carbon dioxide were found to be weaker than those with water. It was established that the Lewis acid-Lewis base interactions between CO₂ and the hydroxyl group of the solute increase with increasing temperature. Instantaneous configurations illustrating the temperature effects on the molecular structures were obtained.     

Opposite photo-induced deformations in azobenzene-containing polymers with different molecular architecture: molecular dynamics study

Photo-induced deformations in azobenzene-containing polymers (azo-polymers) are central to a number of applications, such as optical storage and fabrication of diffractive elements. The microscopic nature of the underlying opto-mechanical coupling is yet not clear. In this study, we address the experimental finding that the scenario of the effects depends on molecular architecture of the used azo-polymer. Typically, opposite deformations in respect to the direction of light polarization are observed for liquid crystalline and amorphous azo-polymers. In this study, we undertake molecular dynamics simulations of two different models that mimic these two types of azo-polymers. We employ hybrid force field modeling and consider only trans-isomers of azobenzene, represented as Gay-Berne sites. The effect of illumination on the orientation of the chromophores is considered on the level of orientational hole burning and emphasis is given to the resulting deformation of the polymer matrix. We reproduce deformations of opposite sign for the two models being considered here and discuss the relevant microscopic mechanisms in both cases.     

H-Bond in methanol: a molecular dynamics study

A set of molecular dynamics (MD) simulations of methanol-d₄ at three temperatures in the liquid range (200, 250 and 300K) have been carried out. The equations of motion of 256 molecules interacting through a potential model due to Haughney et al. [J. Phys. Chem., 91 (1987) 4934] were solved using the velocity version of the Verlet algorithm. This rather large number of molecules was required for studying the behaviour of the system at momentum transfers as low as 0.25 Å⁻¹. It was found that the system experiences long period fluctuations, and therefore very long MD runs (of the order of 100 ps) are necessary in order to obtain accurate statistical averages. Computed static properties are in good agreement with those reported by Haughney et al. and the neutron weighted g(r) and the static structure factor compare favourably with available neutron diffraction data. The study of time-dependent properties through centre-of-mass autocorrelation functions (VACF, F_s(Q,t) and F(Q,t)) and their memory functions reveals features unknown in simple liquids and very similar to those found in liquid water. A close agreement between centre-of-mass single-particle autocorrelation functions and the translational part of QENS data is also observed. The dynamic structure factor for the centres of mass show distinctive side peaks in the same region of the (Q,ω) plane where recently collective excitations have been studied using coherent neutron scattering thus establishing the presence of propagating short wavelength modes. fa]Presented at the International Symposium on Hydrogen Bond Physics held at Il Ciocco, Barga, Italy, 11–14 September 1990.     

Hydration of alkali ions from first principles molecular dynamics revisited

Structural and dynamical properties of the hydration of Li(+), Na(+), and K(+) in liquid water at ambient conditions were studied by first principles molecular dynamics. Our simulations successfully captured the different hydration behavior shown by the three alkali ions as observed in experiments. The present analyses of the dependence of the self-diffusion coefficient and rotational correlation time of water on the ion concentration suggest that Li(+) (K(+)) is certainly categorized as a structure maker (breaker), whereas Na(+) acts as a weak structure breaker. An analysis of the relevant electronic structures, based on maximally localized Wannier functions, revealed that the dipole moment of H(2)O molecules in the first solvation shell of Na(+) and K(+) decreases by about 0.1 D compared to that in the bulk, due to a contraction of the oxygen lone pair orbital pointing toward the metal ion.     

Computing the (1)H NMR spectrum of a bulk ionic liquid from snapshots of car-parrinello molecular dynamics simulations.

We have investigated the performance of several computational protocols in predicting the NMR spectrum of a molecular ion in a complex liquid phase such as an ionic liquid. To do this, we computed the proton NMR chemical shifts of the 1-ethyl-3-methylimidazolium cation [emim](+) in [emim][Cl]. Environmental effects on the imidazolium ring proton chemical shifts are quite significant and must be taken into account explicitly. Calculations performed on the isolated imidazolium cation as well as on the [emim][Cl] ion pair grossly fail to reproduce the correct spacing between proton signals. In contrast, calculations performed on clusters extracted from the trajectory of a Car-Parrinello molecular dynamics simulation yield very good results.     

Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions

The effect of molecular crowding on the structure and stability of biomolecules has become a subject of increasing interest because it can clarify how biomolecules behave under cell-mimicking conditions. Here, we quantitatively analyzed the effects of molecular crowding on the thermodynamics of antiparallel G-quadruplex formation via Hoogsteen base pairs and of antiparallel hairpin-looped duplex (HP duplex) formation via Watson-Crick base pairs. The free energy change at 25 degrees C for G-quadruplex formation decreased from -3.5 to -5.5 kcal mol(-1) when the concentration of poly(ethylene glycol) 200 was increased from 0 to 40 wt %, whereas that of duplex formation increased from -9.8 to -6.9 kcal mol(-1). These results showed that the antiparallel G-quadruplex is stabilized under molecular crowding conditions, but that the HP duplex is destabilized. Moreover, plots of stability (ln K(obs)) of the DNA structures versus water activity (ln a(w)) demonstrated that the ln K(obs) for G-quadruplex formation decreased linearly as the ln a(w) increased, whereas that for duplex formation increased linearly with the increase in ln a(w), suggesting that the slope approximately equals the number of water molecules released or taken up during the formation of these structures. Thus, molecular crowding affects the thermodynamics of DNA structure formation by altering the hydration of the DNA. The stabilization of the DNA structures with Hoogsteen base pairs and destabilization of DNA structures with Watson-Crick base pairs under molecular crowding conditions lead to structural polymorphism of DNA sequences regulated by the state of hydration.     

Microstructure of neat alcohols: a molecular dynamics study

Neat methanol and tert-butanol are studied by molecular dynamics with the focus on the microstructure of these two alcohols. The site-site radial distribution functions, the corresponding structure factors, and an effective local one-body density function are shown to be the appropriate statistical quantities that point in a complementary manner towards the same microstructure for any given liquid. Methanol is found to be a weakly associated liquid forming various chainlike patterns (open and closed) while tert-butanol is almost entirely associated and forms micellelike primary pattern. The presence of stable local microheterogeneity within homogeneous disordered phase appears as a striking feature of these liquids. The absence of any such apparent clustering in water--a stronger hydrogen bonding liquid--through the same two statistical quantities is analyzed.     

Adsorption of organosilanes at a Zn-terminated ZnO (0001) surface: molecular dynamics study

Four different organosilanes (octyltrihydroxysilane, butyltrihydroxysilane, aminopropyltrihydroxysilane, and thiolpropyltrihydroxysilane) adsorbed at a reconstructed Zn-terminated polar ZnO (0001) surface are studied via constant temperature (298 K) molecular dynamics simulations. Both single adsorbed silane molecules as well as adsorbed silane layers are modeled, and the energy, distance, orientation, and alignment of these adsorbates are analyzed. The adsorbed silane molecules exhibit behavior depending on the chemical nature of their tail (nonpolar or polar) as well as on the silane concentration at the solid surface (single adsorption or silane layer). In contrast to the O-terminated ZnO surface studied previously, now adsorption can only occur at the vacancies of this reconstructed crystal surface, thus leading to an arched structure of the liquid phase near the crystal surface. Nevertheless, both nonpolar and polar single adsorbed silanes show a similar orientation and alignment at the surface (orthogonal in the former, parallel in the latter case) as for the O-terminated ZnO surface, although the interaction energy with the surface is considerably increased for nonpolar silanes while it is nearly unaffected for the polar ones. For adsorbed silanes within silane layers, the difference to single adsorbed silanes depends on the polarity of the tail: nonpolar silanes again show an orthogonal alignment, while polar silanes exhibit two different orientations at the solid surface-a head and a tail down configuration. This leads to two completely different but nevertheless stable orientations of these silanes at the Zn-terminated ZnO surface.     

Adsorption and solvation of ethanol at the water liquid-vapor interface: a molecular dynamics study

The free energy profiles of methanol and ethanol at the water liquid-vapor interface at 310K were calculated using molecular dynamics computer simulations. Both alcohols exhibit a pronounced free energy minimum at the interface and, therefore, have positive adsorption at this interface. The surface excess was computed from the Gibbs adsorption isotherm and was found to be in good agreement with experimental results. Neither compound exhibits a free energy barrier between the bulk and the surface adsorbed state. Scattering calculations of ethanol molecules from a gas phase thermal distribution indicate that the mass accommodation coefficient is 0.98, and the molecules become thermalized within 10 ps of striking the interface. It was determined that the formation of the solvation structure around the ethanol molecule at the interface is not the rate-determining step in its uptake into water droplets. The motion of an ethanol molecule in a water lamella was followed for 30 ns. The time evolution of the probability distribution of finding an ethanol molecule that was initially located at the interface is very well described by the diffusion equation on the free energy surface.