Graphene membranes with nanoslits for seawater desalination via forward osmosis.

Stacked graphene (GE) membranes with cascading nanoslits can be synthesized economically compared to monolayer nanoporous GE membranes, and have potential for molecular separation. This study focuses on investigating the seawater desalination performance of these stacked GE layers as forward osmosis (FO) membranes by using molecular dynamics simulations. The FO performance is evaluated in terms of water flux and salt rejection and is explained by analysing the water density distribution and radial distribution function. The water flow displays an Arrhenius type relation with temperature and the activation energy for the stacked GE membrane is estimated to be 8.02 kJ mol-1, a value much lower than that of commercially available FO membranes. The study reveals that the membrane characteristics including the pore width, offset, interlayer separation distance and number of layers have significant effects on the desalination performance. Unlike monolayer nanoporous GE membranes, at an optimum layer separation distance, the stacked GE membranes with large pore widths and completely misaligned pore configuration can retain complete ion rejection and maintain a high water flux. Findings from the present study are helpful in developing GE-based membranes for seawater desalination via FO.

Ultrafast permeation of seawater pervaporation using single-layered C2N via strain engineering.

Emerging two-dimensional (2D) ultra-thin nanomaterials are ideal candidates for next-generation high-throughput membranes. 2D carbon nitride C2N possesses intrinsic regular and uniformly distributed sub-nanometer pores which probably allow a high permeation flux. This work reports on the investigation of seawater pervaporation through a single-layered C2N membrane via a combined approach of first-principles calculations and molecular dynamics simulations. The C2N layer remains stable when the strain is less than a threshold point of 12% at which the pore size is enlarged by 50%. The strained C2N membrane only allows water molecules from seawater to permeate, and the water flux in C2N is enhanced by one to four orders of magnitude compared to that in other membranes. The water flux exhibits an Arrhenius-type relation with temperature. The hydrogen-bonding interaction among water molecules in C2N is weaker and decays faster than that in bulk water, which is because it is energetically unfavorable for water molecules to enter C2N. This proof-of-concept study suggests that C2N might be an appealing membrane material for seawater pervaporation.

Corrugated graphene layers for sea water desalination using capacitive deionization.

The effect of the electric field and surface morphology of corrugated graphene (GE) layers on their capacitive deionization process is studied using molecular dynamics simulations. Deionization performances are evaluated in terms of water flow rate and ion adsorption and explained by analysing the water density distribution, radial distribution function and distribution of the ions inside the GE layers. The simulation results reveal that corrugation of GE layers reduces the water flow rate but largely enhances ion adsorption in comparison to the flat GE layers. Such enhancement is mainly due to the adsorption of ions on the GE layers due to the anchoring effect in the regions with wide interlayer distances. Moreover, it reveals that the entrance configuration of the GE layers also has a significant effect on the performance of deionization. Overall, the results from this study will be helpful in designing effective electrode configurations for capacitive deionization.

Molecular Environment Modulates Conformational Differences between Crystal and Solution States of Human ß-Defensin 2.

Human ß-defensin 2 is a cysteine-rich antimicrobial peptide. In the crystal state, the N-terminal segment (residues 1-11) exhibits a helical conformation. However, a truncated form, with four amino acids removed from the N-terminus, adopts nonhelical conformations in solution, as shown by NMR. To explore the molecular origins of these different conformations, we performed Hamiltonian replica exchange molecular dynamics simulations of the peptide in solution and in the crystal state. It is found that backbone hydration and specific protein-protein interactions are key parameters that determine the peptide conformation. The helical conformation in the crystal state mainly arises from reduced hydration as well as a salt bridge between the peptide and a symmetry-related neighboring monomer in the crystal. When the extent of hydration is reduced and the salt bridge is reintroduced artificially, the peptide is successfully folded back to the helical conformation in solution. The findings not only shed light on the development of accurate force field parameters for protein molecules but also provide practical guidance in the design of functional proteins and peptides.

Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

Aggregation is an irreversible form of protein complexation and often toxic to cells. The process entails partial or major unfolding that is largely driven by hydration. We model the role of hydration in aggregation using "Dehydrons." "Dehydrons" are unsatisfied backbone hydrogen bonds in proteins that seek shielding from water molecules by associating with ligands or proteins. We find that the residues at aggregation interfaces have hydrated backbones, and in contrast to other forms of protein-protein interactions, are under less evolutionary pressure to be conserved. Combining evolutionary conservation of residues and extent of backbone hydration allows us to distinguish regions on proteins associated with aggregation (non-conserved dehydron-residues) from other interaction interfaces (conserved dehydron-residues). This novel feature can complement the existing strategies used to investigate protein aggregation/complexation.

Covalent-organic framework as a template to assemble carbon nanotubes into a high-density membrane: computational demonstration.

Carbon nanotube (CNT) membranes have a wide range of important technological applications; however, the fabrication of high-density CNT membranes is challenging. Using molecular simulation, we demonstrate that a covalent-organic framework (COF-8) can act as a template promoting (9, 9) CNTs to assemble into a homogeneous high-density membrane. Surprisingly, the templated assembly is unique for (9, 9) CNTs and not observed for smaller or larger CNTs. The microscopic analysis based on the potential of mean force reveals that the highly selective assembly of (9, 9) CNTs into COF-8 is thermodynamically favorable, in contrast to other CNTs. This proof-of-concept computational study proposes a bottom-up strategy to produce high-density CNT membranes, and has a significant implication in CNT applications.

Self-assembly of amphiphilic peptide (AF)6H5K15: coarse-grained molecular dynamics simulation.

Amphiphilic peptides are receiving considerable interest for drug delivery because of their self-assembly nature. A molecular dynamics simulation study is reported here to investigate the self-assembly of FA32 peptide composed of 32 amino acid (AF)6H5K15. The peptide, as well as water and counterions, are represented by the MARTINI coarse-grained model. Within 5 µs simulation duration, the peptide is observed to form micelles. Ala and Phe stay in the hydrophobic core, Lys in the hydrophilic shell, and amphiphilic His at the interface. The assembly process and microscopic structures are analyzed in terms of the number of clusters, the radii of micelle, core and shell, and the density profiles of residues. A three-step process is proposed for the assembly: small clusters are initially aggregated and then merged into large clusters, eventually micelles are formed. The effects of simulation box size and peptide concentration are examined in detail. It is found that the micellar structures and microscopic properties are essentially independent of box size. With increasing concentration, quasi-spherical micelles change to elongated shape and micelle size generally increases. The simulation study provides microscopic insight into the assembly process of FA32 peptide and the microscopic structures.

Sorption-induced structural transition of zeolitic imidazolate framework-8: a hybrid molecular simulation study.

A new force field and a hybrid Monte Carlo/molecular dynamics simulation method are developed to investigate the structural transition of zeolitic imidazolate framework-8 (ZIF-8) induced by N2 sorption. At a high loading (approximately 50 N2 molecules per unit cell), ZIF-8 shifts from low-loading (LL) to high-loading (HL) structure. A stepped sorption isotherm is predicted with three distinct regions, which agrees well with experimental data. The orientation of imidazolate rings and the motion of framework atoms exhibit sharp changes upon structural transition. Furthermore, pronounced changes are observed in various contributions to potential energies (including stretching, bending, torsional, van der Waals, and coulombic). The analysis of radial distribution functions between N2 and framework atoms suggests N2 interacts strongly with the imidazolate rings in ZIF-8. The simulation reveals that the structural transition of ZIF-8 is largely related to the reorientation of imidazolate rings, as attributed to the enhanced van der Waals interaction between N2 and imidazolate rings as well as the reduced torsional interaction of framework in the HL structure. This is the first molecular simulation study to describe the continuous structural transition of ZIF-8 and, it provides microscopic insight into the underlying mechanism.

Liquid chromatographic separation in metal-organic framework MIL-101: a molecular simulation study.

A molecular simulation study is reported to investigate liquid chromatographic separation in metal-organic framework MIL-101. Two mixtures are considered: three amino acids (Arg, Phe, and Trp) in aqueous solution and three xylene isomers (p-, m-, and o-xylene) dissolved in hexane. For the first mixture, the elution order is found to be Arg > Phe > Trp. The hydrophilic Arg has the strongest interaction with the polar mobile phase (water) and the weakest interaction with the stationary phase (MIL-101), and thus transports at the fastest velocity. Furthermore, Arg forms the largest number of hydrogen bonds with water and possesses the largest hydrophilic solvent-accessible surface area. For the second mixture, the elution order is p-xylene > m-xylene > o-xylene, consistent with available experimental observation. With the largest polarity as compared to p- and m-xylenes, o-xylene interacts the most strongly with the stationary phase and exhibits the slowest transport velocity. For both mixtures, the underlying separation mechanism is elucidated from detailed energetic and structural analysis. It is revealed that the separation can be attributed to the cooperative solute-solvent and solute-framework interactions. This simulation study, for the first time, provides molecular insight into liquid chromatographic separation in a MOF and suggests that MIL-101 might be an interesting material for the separation of industrially important liquid mixtures.

A highly permeable and selective zeolitic imidazolate framework ZIF-95 membrane for H2/CO2 separation.

Making use of the preferred adsorption affinity and capacity to CO(2) as well as the highly porous structure with huge cavities of 2.4 nm, a highly permeable and selective ZIF-95 molecular sieve membrane was developed for the separation of H(2) from CO(2).

Development of a force field for zeolitic imidazolate framework-8 with structural flexibility.

A force field is developed for zeolitic imidazolate framework-8 (ZIF-8) with structural flexibility by combining quantum chemical calculations and classical Amber force field. The predicted crystalline properties of ZIF-8 (lattice constants, bond lengths, angles, dihedrals, and x-ray diffraction patterns) agree well with experimental results. A structural transition from crystalline to amorphous as found in experiment is observed. The mechanical properties of ZIF-8 are also described fairly well by the force field, particularly the Young's modulus predicted matches perfectly with measured value. Furthermore, the heat capacity of ZIF-8 as a typical thermophysical property is predicted and close to experimental data available for other metal-organic frameworks. It is revealed the structural flexibility of ZIF-8 exerts a significant effect on gas diffusion. In rigid ZIF-8, no diffusive behavior is observed for CH(4) within the simulation time scale of current study. With the structural flexibility, however, the predicted diffusivities of CH(4) and CO(2) are close to reported data in the literature. The density distributions and free energy profiles of CH(4) and CO(2) in the pore of ZIF-8 are estimated to analyze the mechanism of gas diffusion.

A homochiral metal-organic framework membrane for enantioselective separation.

For the first time, a homochiral metal-organic framework membrane was prepared for the enantioselective separation of important chiral compounds, especially chiral drug intermediates, which will allow for the potential development of a new, sustainable and highly efficient chiral separation technique.

Metal-organic framework supported ionic liquid membranes for CO2 capture: anion effects.

IRMOF-1 supported ionic liquid (IL) membranes are investigated for CO(2) capture by atomistic simulation. The ILs consist of identical cation 1-n-butyl-3-methylimidazolium [BMIM](+), but four different anions, namely hexafluorophosphate [PF(6)](-), tetrafluoroborate [BF(4)](-), bis(trifluoromethylsulfonyl)imide [Tf(2)N](-), and thiocyanate [SCN](-). As compared with the cation, the anion has a stronger interaction with IRMOF-1 and a more ordered structure in IRMOF-1. The small anions [PF(6)](-), [BF(4)](-), and [SCN](-) prefer to locate near to the metal-cluster, particularly the quasi-spherical [PF(6)](-) and [BF(4)](-). In contrast, the bulky and chain-like [BMIM](+) and [Tf(2)N](-) reside near the phenyl ring. Among the four anions, [Tf(2)N](-) has the weakest interaction with IRMOF-1 and thus the strongest interaction with [BMIM](+). With increasing the weight ratio of IL to IRMOF-1 (W(IL/IRMOF-1)), the selectivity of CO(2)/N(2) at infinite dilution is enhanced. At a given W(IL/IRMOF-1), the selectivity increases as [Tf(2)N](-) < [PF(6)](-) < [BF(4)](-) < [SCN](-). This hierarchy is predicted by the COSMO-RS method, and largely follows the order of binding energy between CO(2) and anion estimated by ab initio calculation. In the [BMIM][SCN]/IRMOF-1 membrane with W(IL/IRMOF-1) = 1, [SCN](-) is identified to be the most favorable site for CO(2) adsorption. [BMIM][SCN]/IRMOF-1 outperforms polymer membranes and polymer-supported ILs in CO(2) permeability, and its performance surpasses Robeson's upper bound. This simulation study reveals that the anion has strong effects on the microscopic properties of ILs and suggests that MOF-supported ILs are potentially intriguing for CO(2) capture.

Zeolitic imidazolate framework-8 as a reverse osmosis membrane for water desalination: insight from molecular simulation.

A molecular simulation study is reported for water desalination in zeolitic imidazolate framework-8 (ZIF-8) membrane. The simulation demonstrates that water desalination occurs under external pressure, and Na(+) and Cl(-) ions cannot transport across the membrane due to the sieving effect of small apertures in ZIF-8. The flux of water permeating the membrane scales linearly with the external pressure, and exhibits an Arrhenius-type relation with temperature (activation energy of 24.4 kJ∕mol). Compared with bulk phase, water molecules in ZIF-8 membrane are less hydrogen-bonded and the lifetime of hydrogen-bonding is considerably longer, as attributed to the surface interactions and geometrical confinement. This simulation study suggests that ZIF-8 might be potentially used as a reverse osmosis membrane for water purification.

Molecular simulations for energy, environmental and pharmaceutical applications of nanoporous materials: from zeolites, metal-organic frameworks to protein crystals.

Nanoporous materials have widespread applications in chemical industry, but the pathway from laboratory synthesis and testing to practical utilization of nanoporous materials is substantially challenging and requires fundamental understanding from the bottom up. With ever-growing computational resources, molecular simulations have become an indispensable tool for material characterization, screening and design. This tutorial review summarizes the recent simulation studies in zeolites, metal-organic frameworks and protein crystals, and provides a molecular overview for energy, environmental and pharmaceutical applications of nanoporous materials with increasing degree of complexity in building blocks. It is demonstrated that molecular-level studies can bridge the gap between physical and engineering sciences, unravel microscopic insights that are otherwise experimentally inaccessible, and assist in the rational design of new materials. The review is concluded with major challenges in future simulation exploration of novel nanoporous materials for emerging applications.

Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal.

Different biomolecular force fields (OPLS-AA, AMBER03, and GROMOS96) in conjunction with SPC, SPC/E and TIP3P water models are assessed for molecular dynamics simulations in a tetragonal lysozyme crystal. The root mean square deviations for the C(a) atoms of lysozymes are about 0.1 to 0.2 nm from OPLS-AA and AMBER03, smaller than 0.4 nm from GROMOS96. All force fields exhibit similar pattern in B-factors, whereas OPLS-AA and AMBER03 accurately reproduce experimental measurements. Despite slight variations, the primary secondary structures are well conserved using different force fields. Water diffusion in the crystal is approximately ten-fold slower than in bulk phase. The directional and average water diffusivities from OPLS-AA and AMBER03 along with SPC/E model match fairly well with experimental data. Compared to GROMOS96, OPLS-AA and AMBER03 predict larger hydrophilic solvent-accessible surface area of lysozyme, more hydrogen bonds between lysozyme and water, and higher percentage of water in hydration shell. SPC, SPC/E and TIP3P water models have similar performance in most energetic and structural properties, but SPC/E outperforms in water diffusion. While all force fields overestimate the mobility and electrical conductivity of NaCl, a combination of OPLS-AA for lysozyme and the Kirkwood-Buff model for ions is superior to others. As attributed to the steric restraints and surface interactions, the mobility and conductivity in the crystal are reduced by one to two orders of magnitude from aqueous solution.

Chiral separation of racemic phenylglycines in thermolysin crystal: a molecular simulation study.

A microscopic understanding of chiral separation mechanisms in liquid chromatography is significant in the pharmaceutical industry to facilitate the rational design of novel stationary phases and the optimization of separation processes. A molecular simulation study is reported to investigate the chiral separation of racemic D/L-phenylglycines. Thermolysin crystal and water act as the chiral stationary phase and the mobile phase, respectively. D-phenylglycine is observed to transport more slowly than L-phenylglycine, in accord with experimentally observed elution order. A slower flowing rate of the mobile phase enhances separation efficacy. From the energetic and structural analysis, it is found that D-phenylglycine interacts more strongly with thermolysin than L-phenylglycine; consequently, it stays more proximally to thermolysin for a longer time. The chiral discrimination of D/L-phenylglycines is attributed to the collective contribution from the chiral centers of thermolysin residues. This study suggests that, as a bionanoporous material, thermolysin has enantioselectivity capability and demonstrates the feasibility of molecular simulations in mimicking enantioseparation processes and probing underlying mechanisms.

Separation of amino acids in glucose isomerase crystal: insight from molecular dynamics simulations.

The separation of amino acids (Arg, Phe and Trp) in a liquid chromatography is investigated using molecular dynamics simulations. A bioorganic nanoporous material--glucose isomerase crystal--is used as the stationary phase and water as the mobile phase. The transport velocities of amino acids decrease in the order Arg>Phe>Trp, consistent with experimental measurement. The elution order is not affected by the solute concentration or by the flowing rate of mobile phase. Arg is highly hydrophilic and charged, interacts with water the most strongly, and thus moves with flowing water the fastest. Trp has the largest van der Waals volume and encounters the largest steric hindrance, leading to the slowest velocity. From the number distributions of amino acids around protein surface, Trp and Phe are found to stay closer to protein than Arg. The solvent-accessible surface areas of amino acids and the numbers of hydrogen bonds between amino acids and water further elucidate the observed velocity difference. The simulation results provide useful microscopic insight into the retention mechanisms in chromatographic separation process and suggest that glucose isomerase crystal has the capability to separate amino acids.

Force field for molecular dynamics studies of glycine/water mixtures in crystal/solution environments.

Defining a force field for the theoretical predictions of the structure and growth of pharmaceutical crystals is very difficult because of the complex intermolecular bonding found in these crystals. Here, we investigate the accuracy of the AMBER ff03 force field for alpha-glycine molecules using molecular dynamics. The validation of the force field is carried out in both solution and crystal/solution environments. The molecule alpha-glycine is chosen because it has a simple molecular structure while displaying complex intermolecular interactions typical of pharmaceutical crystals. We estimate the atomic charge for glycine from density-functional theory and represent water by the extended simple point charge (SPC/E) model. In a pure solution environment, our simulation results agree well with the experimental data available for solution density, radial distribution functions, hydration number, and diffusion coefficient of glycine. In the crystal/solution environment, the lattice energy calculations are in agreement with the available literature results and also the force field is able to identify the hydrophilic nature of the (010) surface of glycine crystal. The good agreement between simulation results and experimental data indicates that the chosen force field can be used to investigate the growth of glycine crystals from aqueous solutions.

Water in hydrated orthorhombic lysozyme crystal: Insight from atomistic simulations.

Biologically important water in orthorhombic lysozyme crystal is investigated using atomistic simulations. A distinct hydration shell surrounding lysozyme molecules is found from the number distribution of water molecules. While the number of water molecules in the hydration shell increases, the percentage decreases as the hydration level rises. Adsorption of water in the lysozyme crystal shows type-IV behavior. At low hydration levels, water molecules primarily intercalate the minor pores and cavity in the crystal due to the strong affinity between protein and water. At high hydration levels, the major pores are filled with liquidlike water as capillary condensation occurs. A type-H4 hysteresis loop is observed in the adsorption and desorption isotherms. The locations of the water molecules identified from simulation match fairly well with the experimentally determined crystallographic hydration sites. As observed in experiment, water exhibits anomalous subdiffusion because of the geometric restrictions and interactions of protein. With increasing hydration level, this anomaly is reduced and the diffusion of water tends to progressively approach normal Brownian diffusion. The flexibility of protein framework slightly enhances water mobility, but this enhancement decreases with increasing hydration level.