Propensity of heavier halides for the water/vapor interface revisited using the Amoeba force field

Valorisation of agricultural waste derived biochars in aquaculture to remove organic micropollutants from water - experimental study and molecular dynamics simulations

In this work, we evaluated the valorisation of agricultural waste materials by transforming coconut husks and shells, corncobs and rice straw into biochar for water treatment in aquaculture. We compared the biochars' suitability for removal of organic micropollutants (acetaminophen, oxytetracycline, tetracycline, enrofloxacin, atrazine, diuron and diclofenac) from surface water needed for aquaculture. The biochars were prepared by three methods ranging from inexpensive drum kilns (200 °C) to pyrolysis with biogasfication (350-750 °C). Overall, antibiotics tetracycline and enrofloxacin were the most strongly sorbed micropollutants, and coconut husk biochar prepared at 750 °C was the best sorbent material. Molecular Dynamics simulations indicated that the major sorption mechanism is via π-π stacking interactions and there is a possibility of multilayer sorption for some of the micropollutants. We observed, a strong impact of ionic strength (salinity), which is an important consideration in coastal aquaculture applications. High salinity decreased the sorption for antibiotics oxytetracycline, tetracycline and enrofloxacin but increased diclofenac, atrazine and diuron sorption. We considered coconut husk biochar produced in drum kilns the most practical option for biochar applications in small-scale coastal aquacultures in South Asia. Pilot trials of canal water filtration at an aquaculture farm revealed that micropollutant sorption by coconut husk biochar under real-world conditions might be 10-500 times less than observed in the laboratory studies. Even so, biochar amendment of sand enhanced the micropollutant retention, which may facilitate subsequent biodegradation and improve the quality of brackish surface water used for food production in coastal aquaculture.

Image-charge effects on ion adsorption near aqueous interfaces

Electrostatic interactions near surfaces and interfaces are ubiquitous in many fields of science. Continuum electrostatics predicts that ions will be attracted to conducting electrodes but repelled by surfaces with lower dielectric constant than the solvent. However, several recent studies found that certain "chaotropic" ions have similar adsorption behavior at air/water and graphene/water interfaces. Here we systematically study the effect of polarization of the surface, the solvent, and solutes on the adsorption of ions onto the electrode surfaces using molecular dynamics simulation. An efficient method is developed to treat an electrolyte system between two parallel conducting surfaces by exploiting the mirror-expanded symmetry of the exact image-charge solution. With neutral surfaces, the image interactions induced by the solvent dipoles and ions largely cancel each other, resulting in no significant net differences in the ion adsorption profile regardless of the surface polarity. Under an external electric field, the adsorption of ions is strongly affected by the surface polarization, such that the charge separation across the electrolyte and the capacitance of the cell is greatly enhanced with a conducting surface over a low-dielectric-constant surface. While the extent of ion adsorption is highly dependent on the electrolyte model (the polarizability of solvent and solutes, as well as the van der Waals radii), we find the effect of surface polarization on ion adsorption is consistent throughout different electrolyte models.

Molecular Simulations of Hydrophobic Gating of Pentameric Ligand Gated Ion Channels: Insights into Water and Ions

Ion channels are proteins which form gated nanopores in biological membranes. Many channels exhibit hydrophobic gating, whereby functional closure of a pore occurs by local dewetting. The pentameric ligand gated ion channels (pLGICs) provide a biologically important example of hydrophobic gating. Molecular simulation studies comparing additive vs polarizable models indicate predictions of hydrophobic gating are robust to the model employed. However, polarizable models suggest favorable interactions of hydrophobic pore-lining regions with chloride ions, of relevance to both synthetic carriers and channel proteins. Electrowetting of a closed pLGIC hydrophobic gate requires too high a voltage to occur physiologically but may inform designs for switchable nanopores. Global analysis of ∼200 channels yields a simple heuristic for structure-based prediction of (closed) hydrophobic gates. Simulation-based analysis is shown to provide an aid to interpretation of functional states of new channel structures. These studies indicate the importance of understanding the behavior of water and ions within the nanoconfined environment presented by ion channels.

Induced Polarization in Molecular Dynamics Simulations of the 5-HT3 Receptor Channel

Ion channel proteins form water-filled nanoscale pores within lipid bilayers, and their properties are dependent on the complex behavior of water in a nanoconfined environment. Using a simplified model of the pore of the 5-HT3 receptor (5HT3R) which restrains the backbone structure to that of the parent channel protein from which it is derived, we compare additive with polarizable models in describing the behavior of water in nanopores. Molecular dynamics simulations were performed with four conformations of the channel: two closed state structures, an intermediate state, and an open state, each embedded in a phosphatidylcholine bilayer. Water density profiles revealed that for all water models, the closed and intermediate states exhibited strong dewetting within the central hydrophobic gate region of the pore. However, the open state conformation exhibited varying degrees of hydration, ranging from partial wetting for the TIP4P/2005 water model to complete wetting for the polarizable AMOEBA14 model. Water dipole moments calculated using polarizable force fields also revealed that water molecules remaining within dewetted sections of the pore resemble gas phase water. Free energy profiles for Na+ and for Cl- ions within the open state pore revealed more rugged energy landscapes using polarizable force fields, and the hydration number profiles of these ions were also sensitive to induced polarization resulting in a substantive reduction of the number of waters within the first hydration shell of Cl- while it permeates the pore. These results demonstrate that induced polarization can influence the complex behavior of water and ions within nanoscale pores and provides important new insights into their chemical properties.

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.

The origin of facet selectivity and alignment in anatase TiO2 nanoparticles in electrolyte solutions: implications for oriented attachment in metal oxides

Oriented attachment (OA) is an important nonclassical pathway for crystal growth from solution, occurring by the self-assembly of nanoparticles and often leading to highly organized three-dimensional crystal morphologies. The forces that drive nanocrystal reorientation for face-selective attachment and exclude improperly aligned particles have remained unknown. Here we report evidence at the microscopic level that ion correlation forces arising from dynamically interacting electrical double layers are responsible for face-selective attraction and particle rotation into lattice co-alignment as particles interact at long range. Atomic-to-mesoscale simulations developed and performed for the archetype OA system of anatase TiO₂ nanoparticles in aqueous HCl solutions show that face-selective attraction from ion correlation forces outcompetes electrostatic repulsion at several nanometers apart, drawing particle face pairs into a metastable solvent-separated captured state. The analysis of the facet and pH dependence of interparticle interactions is in quantitative agreement with the observed decreasing frequency of attachment between the (112), (001), and (101) face pairs, revealing an adhesion barrier that is largely due to steric hydration forces from structured intervening solvents. This finding helps open new avenues for controlling crystal growth pathways leading to highly ordered three-dimensional nanomaterials.

Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential

As the second most abundant cation in human body, zinc is vital for the structures and functions of many proteins. Zinc-containing matrix metalloproteinases (MMPs) have been widely investigated as potential drug targets in a range of diseases ranging from cardiovascular disorders to cancers. However, it remains a challenge in theoretical studies to treat zinc in proteins with classical mechanics. In this study, we examined Zn(2+) coordination with organic compounds and protein side chains using a polarizable atomic multipole based electrostatic model. We find that polarization effect plays a determining role in Zn(2+) coordination geometry in both matrix metalloproteinase (MMP) complexes and in zinc-finger proteins. In addition, the relative binding free energies of selected inhibitors binding with MMP13 have been estimated and compared with experimental results. While not directly interacting with the small molecule inhibitors, the permanent and polarizing field of Zn(2+) exerts a strong influence on the relative affinities of the ligands. The simulation results also reveal the polarization effect on binding is ligand dependent and thus difficult to be incorporated into fixed-charge models implicitly.

Effects of nonadditive interactions on ion solvation at the water/vapor interface: a molecular dynamics study

The solvation of halide ions at the water/vapor interface is investigated by using molecular dynamics simulations with nonpolarizable molecular mechanical (MM), polarizable MM, and quantum mechanical (QM)/MM methods. The free energy profile of the ion solvation is decomposed into the energy and the entropic contributions along the ion displacement from inside to the surface of water. It is found that the surface affinity of the ion, relative to the bulk value, is determined by a subtle balance between the energetic destabilization and the entropic stabilization with the ion displacement. The amount of energetic destabilization is found to be reduced when nonadditive interactions are included, as in the polarizable MM and QM/MM models. The structure of water around the ion at the interface is also largely modified when the higher order effects are considered. For example, the induced dipole effect enhances the solvation structure around the ion at the interface significantly and thus reduces the amount of entropic stabilization at the interface, relative to in the bulk. It is found that this induced dipole effect causes the slowing in the ion-water hydrogen bond dynamics at the interface. On the other hand, the higher order induced multipole effects in the QM/MM method suppress both the excessive enhancement of the solvation structure and the slowing of the ion-water hydrogen bond dynamics at the interface. The present study demonstrates that not only the induced dipole moment but also the higher order induced multipole moments, which are neglected in standard empirical models, are essential for the correct description of the ion solvation at the water/vapor interface.

Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications

A current emphasis in empirical force fields is on the development of potential functions that explicitly treat electronic polarizability. In the present article, the commonly used methodologies for modelling electronic polarization are presented along with an overview of selected application studies. Models presented include induced point-dipoles, classical Drude oscillators, and fluctuating charge methods. The theoretical background of each method is followed by an introduction to extended Langrangian integrators required for computationally tractable molecular dynamics simulations using polarizable force fields. The remainder of the review focuses on application studies using these methods. Emphasis is placed on water models, for which numerous examples exist, with a more thorough discussion presented on the recently published models associated with the Drude-based CHARMM and the AMOEBA force fields. The utility of polarizable models for the study of ion solvation is then presented followed by an overview of studies of small molecules (e.g. CCl(4), alkanes, etc) and macromolecule (proteins, nucleic acids and lipid bilayers) application studies. The review is written with the goal of providing a general overview of the current status of the field and to facilitate future application and developments.

Calculation of protein-ligand binding free energy by using a polarizable potential

The binding of charged ligands benzamidine and diazamidine to trypsin was investigated by using a polarizable potential energy function and explicit-water molecular dynamics simulations. The binding free energies were computed from the difference between the free energies of decoupling the ligand from water and protein environments. Both the absolute and the relative free energies from the perturbation simulations agree with experimental measurements to within 0.5 kcal.mol(-1). Comparison of free-energy components sampled from different thermodynamic paths indicates that electrostatics is the main driving force behind benzamidine recognition of trypsin. The contribution of electronic polarization to binding appears to be crucial. By computing the free-energy contribution caused by the polarization between the ligand and its surroundings, we found that polarization has the opposite effect in dissimilar environments. Although polarization favors ligand solvation in water, it weakens the protein-ligand attraction by screening the electrostatic interaction between trypsin and benzamidine. We also examined the relative binding free energies of a benzamidine analog diazamidine to trypsin. The changes in free energy on benzamidine-diazamidine substitution were tens of kilocalories in both water and trypsin environments; however, the change in the total binding free energy is <2 kcal.mol(-1) because of cancellation, consistent with the experimental results. Overall, our results suggest that the use of a polarizable force field, given adequate sampling, is capable of achieving chemical accuracy in molecular simulations of protein-ligand recognition.

Solvation behavior of short-chain polystyrene sulfonate in aqueous electrolyte solutions: a molecular dynamics study

We analyze the solvation behavior of short-chain polystyrene sulfonate (PSS) in aqueous electrolyte solutions by isothermal-isochoric molecular dynamics simulation to determine the solvation effects on the structure and conformation of the polyelectrolyte as a function of the aqueous environment. To that end, we study these aqueous systems including the explicit atomistic description of water, the PSS chain, and their interactions with all species in solution. In addition, we investigate the effect of the degree of sulfonation and its distribution along the PSS chain on the resulting conformation as well as solvation structure. Moreover, we assess the impact of added salts on the net charge of the PSS backbone, placing emphasis on the valence of the counterion and the extent of the ion-pair formation between the sulfonate group and the counterions. Finally, we present evidence for the so-called like-charge attraction between sulfonate groups through the formation of counterion-mediated interchain sulfonate-sulfonate and water-mediated intrachain sulfonate-sulfonate bridges, as well as between unlike counterion-counterion interactions.

A theoretical investigation of the interactions between water molecules and ionic liquids

Quantum chemical calculations have been used to investigate the interaction between water molecules and ionic liquids based on the imidazolium cation with the anions [Cl(-)], [Br(-)], [BF(4)(-)], and [PF(6)(-)]. The predicted geometries and interaction energies implied that the water molecules interact with the Cl(-), Br(-), and BF(4)(-0 anions to form X(-)...W (X = Cl or Br, W = H(2)O), 2X-...2W, BF(4)(-)...W, and W...BF(4)(-)...W complexes. The hydrophobic PF(6)(-) anion could not form a stable complex with the water molecules at the density functional theory (DFT) level. Further studies indicate that the cation could also form a strong interaction with the water molecules. The 1-ethyl-3-methylimidazolium cation (Emim(+)) has been used as a model cation to investigate the interaction between a water molecule and a cation. In addition, the interaction between the ion pairs and the water was studied by using 1-ethyl-3-methylimidazolium chloride (Emim x Cl) as a model ionic liquid. The strengths of the interactions in these categories follow the trend anion-W > cation-W > ion pair-W.

Theoretical study of the hydrated Gd3+ ion: Structure, dynamics, and charge transfer

The dynamical processes taking place in the first coordination shells of the gadolinium (III) ion are important for improving the contrast agent efficiency in magnetic-resonance imaging. An extensive study of the gadolinium (III) ion solvated by a water cluster is reported, based on molecular dynamics simulations. The AMOEBA force field [P. Y. Ren and J. W. Ponder, J. Phys. Chem. B 107, 5933 (2003)] that includes many-body polarization effects is used to describe the interactions among water molecules, and is extended here to treat the interactions between them and the gadolinium ion. In this purpose accurate ab initio calculations have been performed on Gd(3+)-H(2)O for extracting the relevant parameters. Structural data of the first two coordination shells and some dynamical properties such as the water exchange rate between the first and second coordination shells are compared to available experimental results. We also investigate the charge transfer processes between the ion and its solvent, using a fluctuating charges model fitted to reproduce electronic structure calculations on [Gd(H(2)O)(n)](3+) complexes, with n ranging from 1 to 8. Charge transfer is seen to be significant (about one electron) and correlated with the instantaneous coordination of the ion.