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A molecular thermodynamic theory is developed for polyampholytes from the coarse-grained charged hard-sphere chain model. The phase behavior of polyampholytes with variations in sequence and chain length is satisfactorily predicted by the theory, consistent with simulation results and experimental observations. At a fixed chain length, the phase envelope expands as the sequence of charge distribution becomes less random. With increasing chain length, the phase envelope expands for diblock and random polyampholytes, but shrinks for zwitterionic polyampholytes. The predicted critical temperature, density, and pressure exhibit scaling relations with chain length for all the three (diblock, random, and zwitterionic) polyampholytes. [ABSTRACT FROM AUTHOR]

Discusses an equation of state for thermodynamic properties of chain fluids. Crossover equation of state outside and inside the critical region; Comparisons with computer simulations for square-well chain fluids.

Studies the properties of polyelectrolyte solutions with stickiness between polyions and counterions at the molecular level. Derivation of the mathematical expressions for thermodynamic properties; Formation of polyion chains from the monomers; Measurement of charged hard-sphere chain contribution.

Proposes a molecular-thermodynamic modelling for polyelectrolyte solutions. Role of cavity-correlation function (CCF) in the identification of polyelectrolyte solution; Relationship between hypernetted-chain and mean-spherical closures; Details on the effective nearest-neighbor cavity correlation function.

Neurotransmission requires a continuously available pool of synaptic vesicles (SVs) that can fuse with the plasma membrane and release their neurotransmitter contents upon stimulation. After fusion, SV membranes and membrane proteins are retrieved from the presynaptic plasma membrane by clathrin-mediated endocytosis. After the internalization of a clathrin-coated vesicle, the vesicle must uncoat to replenish the pool of SVs. Clathrin-coated vesicle uncoating requires ATP and is mediated by the ubiquitous molecular chaperone Hsc70. In vitro, depolymerized clathrin forms a stable complex with Hsc70* ADP. This complex can be dissociated by nucleotide exchange factors (NEFs) that release ADP from Hsc70, allowing ATP to bind and induce disruption of the clathrin:Hsc70 association. Whether NEFs generally play similar roles in vesicle trafficking in vivo and whether they play such roles in SV endocytosis in particular is unknown. To address this question, we used information from recent structural and mechanistic studies of Hsp70:NEF and Hsp70:co-chaperone interactions to design a NEF inhibitor. Using acute perturbations at giant reticulospinal synapses of the sea lamprey (Petromyzon marinus), we found that this NEF inhibitor inhibited SV endocytosis. When this inhibitor was mutated so that it could no longer bind and inhibit Hspl 10 (a NEF that we find to be highly abundant in brain cytosol), its ability to inhibit SV endocytosis was eliminated. These observations indicate that the action of a NEF, most likely Hspl 10, is normally required during SV trafficking to release clathrin from Hsc70 and make it available for additional rounds of endocytosis. [ABSTRACT FROM AUTHOR]

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 Ca 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. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [ABSTRACT FROM AUTHOR]

The 70 kDa heat shock proteins (Hsp70s) play important roles in preventing the misfolding of proteins and repairing damage under stress by coupling ATP binding and hydrolysis to protein substrate release and binding, respectively. ATP binding is believed to induce closing of the Hsp70 nucleotide binding domain (NBD) around the nucleotide. We report here a combined computational-experimental study of this open-closed transition. All-atom molecular dynamics simulations were performed for isolated open state NBDs with and without bound ATP. The nucleotide-free NBD samples a wide range of open configurations exhibiting flexible rearrangements of its four subdomains (IA-IIB). In contrast, the ATP-bound Hsp70 NBD closes to a range of configurations that is substantially more closed than the conformation observed in crystals of ATP-complexed NBDs. The close approach of subdomains IB and IIB observed in the simulations results in a strong coordination of the fluorescence probe Trp90 of IB with Arg261 of IIB, a feature not seen in the crystal structures. To determine if this computationally observed conformation occurs in solution, we constructed an R261A mutant. The mutation was found to increase the Km and kcat for ATP and to significantly reduce the extent of the fluorescence quench observed upon ATP binding. Our results thus account for the previously unexplained ATP-driven change in Trp90 fluorescence seen in the isolated NBD. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

We report a molecular simulation study for the separation of industrially important gas mixtures (CO2/H2, CO2/CH4, and CO2/N2) in rho zeolite-like metal-organic framework (rho-ZMOF). Rho-ZMOF contains a wide-open anionic framework and charge-balancing extraframework Na+ ions. Two types of binding sites for Na+ ions are identified in the framework. Site I is in the single eight-membered ring, whereas site II is in the α-cage. Na+ ions at site I have a stronger affinity for the framework and thus a smaller mobility. The binding sites in rho-ZMOF resemble those in its inorganic counterpart rho-zeolite. CO2 is adsorbed predominantly over other gases because of its strong electrostatic interactions with the charged framework and the presence of Na+ ions acting as additional adsorption sites. At ambient temperature and pressure, the CO2 selectivities are 1800 for the CO2/H2 mixture, 80 for the CO2/CH4 mixture, and 500 for the CO2/N2 mixture. Compared with other MOFs and nanoporous materials reported to date, rho-ZMOF exhibits unprecedentedly high selective adsorption for these gas mixtures. This work represents the first simulation study to characterize extraframework ions and examine gas separation in a charged ZMOF. The simulation results reveal that rho-ZMOF is a promising candidate for the separation of syngas, natural gas, and flue gas. [ABSTRACT FROM AUTHOR]

We report a molecular simulation study for CO 2storage in metal−organic frameworks (MOFs). As compared to the aluminum-free and cation-exchanged ZSM-5 zeolites and carbon nanotube bundle, IRMOF1 exhibits remarkably higher capacity. Incorporation of Na +cations into zeolite increases the capacity only at low pressures. By variation of the metal oxide, organic linker, functional group, and framework topology, a series of isoreticular MOFs (IRMOF1, Mg-IRMOF1, Be-IRMOF1, IRMOF1-(NH 2) 4, IRMOF10, IRMOF13, and IRMOF14) are systematically examined, as well as UMCM-1, a fluorous MOF (F-MOF1), and a covalent−organic framework (COF102). The affinity with CO 2is enhanced by addition of a functional group, and the constricted pore is formed by interpenetration of the framework; both lead to a larger isosteric heat and Henry’s constant and subsequently a stronger adsorption at low pressures. The organic linker plays a critical role in tuning the free volume and accessible surface area and largely determines CO 2adsorption at high pressures. As a combination of high capacity and low framework density, IRMOF10, IRMOF14, and UMCM-1 are identified from this study to be the best for CO 2storage, even surpass the experimentally reported highest capacity in MOF-177. COF102 is a promising candidate with high capacity at considerably low pressures. Both gravimetric and volumetric capacities at 30 bar correlate well with the framework density, free volume, porosity, and accessible surface area. These structure−function correlations are useful for a priori prediction of CO 2capacity and for the rational screening of MOFs toward high-efficacy CO 2storage. [ABSTRACT FROM AUTHOR]

Recently we have investigated the storage and adsorption selectivity of CO 2and CH 4in three different classes of nanoporous materialssilicalite, IRMOF-1, and C 168schwarzite through Monte Carlo simulation (Babarao, R.; Hu, Z.; Jiang, J. Langmuir, 2007, 23, 659). In this work, the self-, corrected, and transport diffusivities of CO 2and CH 4in these materials are examined using molecular dynamics simulation. The activation energies at infinite dilution are evaluated from the Arrhenius fits to the diffusivities at various temperatures. As loading increases, the self-diffusivities in the three frameworks decrease as a result of the steric hindrance; the corrected diffusivities remain nearly constant or decrease approximately linearly depending on the adsorbate and framework; and the transport diffusivities generally increase except for CO 2in IRMOF-1. The correlation effects are identified to reduce from MFI, C 168to IRMOF-1, in accordance with the porosity increasing in the three frameworks. Predictions of self-, corrected, and transport diffusivities for pure CO 2and CH 4from the Maxwell−Stefan formulation match the simulation results well. In a CO 2/CH 4mixture, the self-diffusivities decreases with loading, and good agreement is found between simulated and predicted results. On the basis of the adsorption and self-diffusivity in the mixture, the permselectivity is found to be marginal in IRMOF-1, slightly enhanced in MFI, and greatest in C 168schwarzite. Although IRMOF-1 has the largest storage capacity for CH 4and CO 2, its selectivity is not satisfactory. [ABSTRACT FROM AUTHOR]

The spatial and temporal properties of water and ions in bionanoporous materialsprotein crystalshave been investigated using molecular dynamics simulations. Three protein crystals are considered systematically with different morphologies and chemical topologies:  tetragonal lysozyme, orthorhombic lysozyme, and tetragonal thermolysin. It is found that the thermal fluctuations of Catoms in the secondary structures of protein molecules are relatively weak due to hydrogen bonding. The solvent-accessible surface area per residue is nearly identical in the three protein crystals; the hydrophobic and hydrophilic residues in each crystal possess approximately the same solvent-accessible surface area. Water distributes heterogeneously and has different local structures within the biological nanopores of the three protein crystals. The mobility of water and ions in the crystals is enhanced as the porosity increases and also by the fluctuations of protein atoms particularly in the two lysozyme crystals. Anisotropic diffusion is found preferentially along the pore axis, as experimentally observed. The anisotropy of the three crystals increases in the order: tetragonal thermolysin < tetragonal lysozyme < orthorhombic lysozyme. [ABSTRACT FROM AUTHOR]

Hsp70s are essential chaperones with roles in a variety of cellular processes and representatives in all kingdoms of life. They are comprised of a nucleotide binding domain (NBD) and a protein substrate-binding domain (SBD). Structures of isolated NBDs and SBDs have been reported but, until recently, a functionally intact Hsp70 containing both the NBD and SBD has resisted structure determination. Here, it is reported that preparation of diffractionquality crystals of functionally intact bovine Hsc70 required (i) deletion of part of the protein to reduce oligomerization, (ii) point mutations in the interface between the SBD and NBD and (iii) use of high concentrations of the structure stabilizing agents glycerol and trimethylamine oxide (TMAO). The introduction of point mutations in interdomain interfaces and the use of the potent structure stabilizer TMAO may be generally useful in crystallization of multidomain proteins that exhibit interdomain motions. [ABSTRACT FROM AUTHOR]

Using a hierarchical multiscale approach combining quantum mechanics and molecular simulation, we have investigated the adsorption of pure CO2 and N2 and their mixture at room temperature in C168 schwarzite, as a model for nanoporous carbons. First, the adsorbate–adsorbent interaction potential is determined using ab initio quantum mechanics computations, and then the adsorption is predicted using full atomistic Monte Carlo simulations. The extents of adsorption, adsorption energies, and isosteric heats of pure CO2 and N2 simulated with the ab initio potential are found to be higher than those with the empirical Steele potential that had been developed from gas adsorption on planar graphite. The inclusion of the electric quadrupole moment of adsorbate in simulation has no discernible effect on N2 adsorption but results in a larger extent of CO2 adsorption at high coverages. The selectivity of CO2 over N2 in the C168 schwarzite from a model flue gas is predicted to be significantly larger with the ab initio potential than with the Steele potential. This illustrates the importance of an accurate adsorbate–adsorbent interaction potential in determining gas adsorption and suggests that nanoporous carbons might be useful for the separation of flue gases. As a comparison, the adsorption and selectivity of CO2 and N2 in ZSM-5 zeolites are also simulated with the experimentally validated potential parameters. The selectivity in the C168 schwarzite predicted with the ab initio or Steele potential is found to be larger than the selectivity in all-silica ZSM-5, but less than that in Na-exchanged ZSM-5 zeolites. [ABSTRACT FROM AUTHOR]

J-domains are widespread protein interaction modules involved in recruiting and stimulating the activity of Hsp70 family chaperones. We have determined the crystal structure of the J-domain of auxilin, a protein which is involved in uncoating clathrin-coated vesicles. Comparison to the known structures of J-domains from four other proteins reveals that the auxilin J-domain is the most divergent of all J-domain structures described to date. In addition to the canonical J-domain features described previously, the auxilin J-domain contains an extra N-terminal helix and a long loop inserted between helices I and II. The latter loop extends the positively charged surface which forms the Hsc70 binding site, and is shown by directed mutagenesis and surface plasmon resonance to contain side chains important for binding to Hsc70. [ABSTRACT FROM AUTHOR]

Among many factors that affect protein phase separation, solvent plays a pivotal role in the possible structuring of the solvent molecules around the protein. The effect of solvent structuring is influenced strongly by temperature because of the relative stability of hydrogen bonding at low temperatures. As a result, quantitative as well as qualitative changes in protein phase separation may be expected with change in temperature. Here, we use a temperature dependent pair potential to examine the effect of water in the phase separation of protein solutions. Using Gibbs ensemble Monte Carlo simulations, we observe both a lower critical solution temperature and an upper critical solution temperature, in good agreement with the experimental observations for a number of proteins and phenomenological, statistical thermodynamic arguments. It is found that the effect of solvent is significant at low temperatures as a result of the highly structured shell of water molecules around the protein molecules. Radial distribution functions also indicate that a thick shell of structured water exists around the protein molecules due to the formation of strong hydrogen bonds when temperature is low. The findings of this study suggest that a simple model with a reasonable physical basis can capture the general phase behavior of some proteins or biopolymers. [ABSTRACT FROM AUTHOR]

We study the effects of the size of polymer additives and ionic strength on the phase behavior of a nonglobular protein—immunoglobulin G (IgG)—by using a simple four-site model to mimic the shape of IgG. The interaction potential between the protein molecules consists of a Derjaguin–Landau–Verwey–Overbeek-type colloidal potential and an Asakura–Oosawa depletion potential arising from the addition of polymer. Liquid-liquid equilibria and fluid-solid equilibria are calculated by using the Gibbs ensemble Monte Carlo technique and the Gibbs–Duhem integration (GDI) method, respectively. Absolute Helmholtz energy is also calculated to get an initial coexisting point as required by GDI. The results reveal a nonmonotonic dependence of the critical polymer concentration ρPEG* (i.e., the minimum polymer concentration needed to induce liquid-liquid phase separation) on the polymer-to-protein size ratio q (equivalently, the range of the polymer-induced depletion interaction potential). We have developed a simple equation for estimating the minimum amount of polymer needed to induce the liquid-liquid phase separation and show that ρPEG*∼[q/(1+q)3]. The results also show that the liquid-liquid phase separation is metastable for low-molecular weight polymers (q=0.2) but stable at large molecular weights (q=1.0), thereby indicating that small sizes of polymer are required for protein crystallization. The simulation results provide practical guidelines for the selection of polymer size and ionic strength for protein phase separation and crystallization. [ABSTRACT FROM AUTHOR]

An ionic covalent-organic framework (ICOF-1 containing sp³ hybridized boron anionic centers formed by spiroborate linkage and dimethylammonium ions) is explored as an ion exchanger for the removal of lead (Pb2+) ions from aqueous solution. From molecular simulations, the Pb2+ ions are observed to exchange with the nonframework DMA+ ions in the ICOF-1. At a concentration of 600 ppm, the Pb2+ ions are completely exchanged and reside in the ICOF-1, while the DMA+ ions are in a dynamic equilibrium with the solution. It is revealed that the exchange between Pb2+ and DMA+ is governed by the stronger attraction of Pb2+ with the negatively charged ICOF-1 framework. The radial distribution functions and mean-squared displacements further show that the exchanged Pb2+ ions are in a closer proximity to the ICOF-1 framework with a smaller mobility than DMA+ ions. The simulation study provides microscopic insight into the ion-exchange process between Pb2+ and DMA+, and it suggests that the ICOF-1 might be an intriguing candidate for water purification. [ABSTRACT FROM AUTHOR]

Microsecond simulations have been performed to investigate CH4 hydrate formation from gas/water two-phase systems between silica and graphite surfaces, respectively. The hydrophilic silica and hydrophobic graphite surfaces exhibit substantially different effects on CH4 hydrate formation. The graphite surface adsorbs CH4 molecules to form a nanobubble with a flat or negative curvature, resulting in a low aqueous CH4 concentration, and hydrate nucleation does not occur during 2.5 μs simulation. Moreover, an ordered interfacial water bilayer forms between the nanobubble and graphite surface thus preventing their direct contact. In contrast, the hydroxylated-silica surface prefers to be hydrated by water, with a cylindrical nanobubble formed in the solution, leading to a high aqueous CH4 concentration and hydrate nucleation in the bulk region; during hydrate growth, the nanobubble is gradually covered by hydrate solid and separated from the water phase, hence slowing growth. The silanol groups on the silica surface can form strong hydrogen bonds with water, and hydrate cages need to match the arrangements of silanols to form more hydrogen bonds. At the end of the simulation, the hydrate solid is separated from the silica surface by liquid water, with only several cages forming hydrogen bonds with the silica surface, mainly due to the low CH4 aqueous concentrations near the surface. To further explore hydrate formation between graphite surfaces, CH4/water homogeneous solution systems are also simulated. CH4 molecules in the solution are adsorbed onto graphite and hydrate nucleation occurs in the bulk region. During hydrate growth, the adsorbed CH4 molecules are gradually converted into hydrate solid. It is found that the hydrate-like ordering of interfacial water induced by graphite promotes the contact between hydrate solid and graphite. We reveal that the ability of silanol groups on silica to form strong hydrogen bonds to stabilize incipient hydrate solid, as well as the ability of graphite to adsorb CH4 molecules and induce hydrate-like ordering of the interfacial water, are the key factors to affect CH4 hydrate formation between silica and graphite surfaces. [ABSTRACT FROM AUTHOR]

Water channels are essential to life sciences and many biological processes. We report a molecular simulation study on dipeptides embedded in a lipid (dipalmitoylphosphatidylcholine) membrane as synthetic water channels. Five dipeptides are examined including FF, FL, LF, and LL (with hydrophilic channels) and AV (with hydrophobic channel). It is found that AV is unstable in the lipid membrane due to incompatible interaction between the hydrophilic external surface of AV and the hydrophobic lipid tails; whereas FF, FL, LF, and LL with hydrophobic external surface exhibit good stability. In the four hydrophilic channels FF, FL, LF, and LL, water chains are formed; the number of chains ranges from multiple, two to one depending on channel diameter; moreover, water undergoes single-file diffusion and the mobility is enhanced with increasing channel diameter. The permeation rate of water in the FF channel is 9.20/ns, about three times that in aquaporin; however, the rate in FL, LF, and LL is much slower. Intriguingly, the rate can be tuned by a lateral stress/strain on the lipid membrane. The simulation study provides fundamental understanding on the stability of dipeptide channels embedded in a lipid membrane, quantitatively characterizing water structure, dynamics, and permeation in the channels. These microscopic insights are useful for the development of new water channels. [ABSTRACT FROM AUTHOR]

Zirconium (Zr) metal-organic frameworks (MOFs) have received considerable interest due to their superior hydrolytic, thermal, and chemical stability. On the basis of 40 topological nets, 120 Zr-MOFs with 8-, 10-, and 12-coordination are designed in this study with nitrogen-rich CO2-philic tetrazolate toward CO2 capture. The Zr-tetrazolate MOFs are revealed to exhibit substantially stronger CO2 adsorption than their carboxylate counterparts of identical topologies. By synergizing multiscale modeling from molecular simulation to breakthrough prediction, MOF-eft-P is identified among the 120 Zr-MOFs to possess the largest isosteric heat at infinite dilution and uptake at 1 bar for CO2, as well as the highest CO2/N2 selectivity; it outperforms many typical MOFs and other adsorbents reported in the literature. The breakthrough time of CO2 in MOF-eft-P is predicted to be 25 min and significantly longer than that of N2, indicating excellent CO2/N2 separation. This study demonstrates the bottom-up strategy to design Zr-MOFs and suggests MOF-eft-P to be an interesting candidate for CO2 capture. [ABSTRACT FROM AUTHOR]

Malek et al (2005 Nanotechnology 16 S522) studied the diffusion of water and sodium counter-ions in a b-lactoglobulin (bLG) crystal from a 5 ns molecular dynamics simulation. They presented water density in the main pore, and water mobility in the core and surface zones. Unfortunately, their results were incorrect and misleading. In this comment, we provide the results from our analysis for the same system. [ABSTRACT FROM AUTHOR]

A molecular simulation study is reported for water desalination through five zeolitic imidazolate framework (ZIF) membranes, namely ZIF-25, -71, -93, -96, and -97. The five ZIFs possess identical rho-topology but differ in functional groups. The rejection of salt (NaCl) is found to be around 97% in ZIF-25, and 100% in the other four ZIFs. The permeance ranges from 27 to 710 kg/(m²•h•bar), about one~two orders of magnitude higher compared with commercial reverse osmosis membranes. Due to a larger aperture size da, ZIF-25, -71, and -96 exhibit a much higher water flux than ZIF-93 and -97; however, the flux in ZIF-25, -71, and -96 is governed by the polarity of functional group rather than da. With the hydrophobic CH3 group, ZIF-25 has the highest flux despite the smallest da among ZIF-25, -71, and -96. The lifetime of hydrogen bonding in ZIF-25 is shorter than that in ZIF-71 and -96. Furthermore, water molecules undergo a fast flushing motion in ZIF-25, but frequent jumping in ZIF-96 and particularly in ZIF-97. An Arrhenius-type relationship is found between water flux in ZIF-25 and temperature, and the activation energy is predicted to be 6.5 kJ/mol. This simulation study provides a microscopic insight into water desalination in a series of ZIFs, reveals the key factors (aperture size and polarity of functional group) governing water flux, and suggests that ZIF-25 might be an interesting reverse osmosis membrane for high-performance water desalination. [ABSTRACT FROM AUTHOR]

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 ML 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. [ABSTRACT FROM AUTHOR]

We report a molecular simulation study for gas permeation in two membranes constructed from polymers of intrinsic microporosity (PIM-1 and PIM-7). With rigid ladder polymer chains, the membranes posses approximately 47.7 and 46.6% fractional free volumes (FFVs) in PIM-1 and PIM-7, respectively. The voids in the membranes have a diameter up to 9 Å and are largely interconnected. The sorption and diffusion of four gases (H2, O2, CH4 and CO2) were calculated by Monte Carlo and molecular dynamics simulations. The solubility coefficients increase in the order of H2 < O2 < CH4 < CO2, while the diffusion coefficients increase in the following order: CH4 < CO2 < O2 < H2. The simulation results agree well with experimental data, particularly for the solubility coefficients. The solubility and diffusion coefficients correlate well separately with the critical temperatures and effective diameters of gases. These molecular-based correlations can be used in the prediction for other gases. As attributed to the microporous structure, PIM-1 and PIM-7 outperform most glassy polymeric membranes in sorption and diffusion. PIM-1 has larger solubility and diffusion coefficients than PIM-7 because the cyano groups in PIM-1 lead to a stronger affinity and a larger FFV. The simulated solubility, diffusivity and permeation selectivities of CO2/H2, CO2/O2 and CO2/CH4 are consistent with experimental data. The quantitative microscopic understanding of gas permeation in the PIM membranes is useful for the new development of high-performance membranes. [ABSTRACT FROM AUTHOR]

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 α-glycine molecules using molecular dynamics. The validation of the force field is carried out in both solution and crystal/solution environments. The molecule α-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. [ABSTRACT FROM AUTHOR]

Storage of pure CO2and CH4and separation of their binary mixture in three different classes of nanostructured adsorbentssilicalite, C168schwarzite, and IRMOF-1have been compared at room temperature using atomistic simulation. CH4is represented as a spherical Lennard-Jones molecule, and CO2is represented as a rigid linear molecule with a quadrupole moment. For pure component adsorption, CO2is preferentially adsorbed than CH4in all the three adsorbents over the pressure range under this study, except in C168schwarzite at high pressures. The simulated adsorption isotherms and isosteric heats match closely with available experimental data. A dual-site Langmuir−Freundlich equation is used to fit the isotherms satisfactorily. Compared to silicalite and C168schwarzite, the gravimetric adsorption capacity of pure CH4and CO2separately in IRMOF-1 is substantially larger. This implies that IRMOF-1 might be a potential storage medium for CH4and CO2. For adsorption from an equimolar binary mixture, CO2is preferentially adsorbed in all three adsorbents. Predictions of mixture adsorption with the ideal-adsorbed solution theory on the basis of only pure component adsorption agree well with simulation results. Though IRMOF-1 has a significantly higher adsorption capacity than silicalite and C168schwarzite, the adsorption selectivity of CO2over CH4is found to be similar in all three adsorbents. [ABSTRACT FROM AUTHOR]

The article presents the highly porous nanofiber-supported monolayer graphene membranes for ultrafast organic solvent nanofiltration. Topics discussed include demonstrate a facile and versatile electrospinning approach to realize nanoporous graphene membranes on different polymeric supports; and the conductive graphene works as an excellent receptor for deposition of highly porous nanofibers during electrospinning, thereby enabling direct attachment of graphene to the support.

We report a new lattice density functional theory for polymer solutions at the solid-liquid interface. The theory accounts for the nearest-neighbor interactions and the long-range correlations due to chain connectivity. A Helmholtz free-energy functional is developed with an exact free-energy functional expression for the ideal chains and a thermodynamic model of lattice polymer solutions for the excess contributions. The local and weighted density approximations are used to calculate the contributions due to the athermal entropy of mixing and the internal energy of mixing, respectively. Mayer function and propagator formalism are adopted to obtain the segment-density distributions for various conformations including adsorbed trains, tails, loops, and free polymers. The predicted density distributions of polymer adsorption are in good agreement with simulation results. The results imply that as a counterbalance between energy and conformational entropy, the weighted density approximation used in the functional can rationally capture the segment-segment correlations. [ABSTRACT FROM AUTHOR]

Amino acids are the building blocks for protein biosynthesis and find use in myriad industrial applications including in food for humans, in animal feed, and as precursors for bio-based plastics, among others. However, the development of efficient chemical methods to convert abundant and renewable feedstocks into amino acids has been largely unsuccessful to date. To that end, here we report a heterogeneous catalyst that directly transforms lignocellulosic biomass-derived α-hydroxyl acids into α-amino acids, including alanine, leucine, valine, aspartic acid, and phenylalanine in high yields. The reaction follows a dehydrogenation-reductive amination pathway, with dehydrogenation as the rate-determining step. Ruthenium nanoparticles supported on carbon nanotubes (Ru/CNT) exhibit exceptional efficiency compared with catalysts based on other metals, due to the unique, reversible enhancement effect of NH3 on Ru in dehydrogenation. Based on the catalytic system, a two-step chemical process was designed to convert glucose into alanine in 43% yield, comparable with the well-established microbial cultivation process, and therefore, the present strategy enables a route for the production of amino acids from renewable feedstocks. Moreover, a conceptual process design employing membrane distillation to facilitate product purification is proposed and validated. Overall, this study offers a rapid and potentially more efficient chemical method to produce amino acids from woody biomass components. [ABSTRACT FROM AUTHOR]

By synergizing molecular dynamics and dissipative particle dynamics simulations, we investigate the assembly of amphiphilic grafted copolymers into vesicles and the loading/release of doxorubicin hydrochloride (DOX·HCl). The copolymers, PAE-g-PEGLA, comprise pH-sensitive poly(β-amino ester) grafted with hydrophilic poly(ethylene glycol) and hydrophobic poly(d,l-lactide). The vesicle formation is revealed to follow an aggregation-rearrangement mechanism, in which small clusters first form, then rearrange, and finally merge into bilayer-structured vesicles. The vesicle interior size and membrane thickness are substantially affected by the exchange quantity and frequency between tetrahydrofuran and water. At pH = 7, DOX·HCl is loaded into the vesicle interior, and the loading efficiency increases with increasing polymer concentration. At pH > 7, PAE blocks are protonated and hydrophilic, which causes the structure transition of membrane thus tuning membrane permeability for DOX·HCl release. When PLA blocks become longer, vesicle stability is enhanced and DOX·HCl release is suppressed. To mimic controlled release, a mixture of two copolymers is proposed, which form hybrid vesicles and lead to a moderate release rate of DOX·HCl. After multiple sequential pH variations between acidic and neutral circulatory environment, DOX·HCl is gradually released from the hybrid vesicles. This multiscale simulation study identifies the key factors governing vesicle formation and drug loading/release, and provides bottom-up insights toward the design and optimization of new amphiphilic polymers for high-efficacy drug delivery. [ABSTRACT FROM AUTHOR]

Recently, there has been growing interest in hafnium (Hf) metal-organic frameworks (MOFs). These MOFs may perform better as gas adsorbents than zirconium (Zr) MOFs due to the presence of Brønsted acid sites with high affinity toward adsorbates, together with the outstanding chemical and hydrothermal stabilities similar to their Zr analogues. However, Hf-MOFs have been rarely reported due to the lack of effective synthetic methods. We herein report a modulated hydrothermal synthesis of UiO-66(Hf)-type MOFs. Among these MOFs, UiO-66(Hf)-(OH)2 possesses a very high CO2 gravimetric uptake of 1.81 mmol g-1 at 0.15 bar and 298 K, which is 400% higher than that of UiO-66(Hf) (0.36 mmol g-1). It also exhibits a record-high volumetric CO2 uptake of 167 v/v at 1 bar and 298 K. Ideal adsorbed solution theory calculations showed a CO2/N2 (molar ratio 15:85) selectivity of 93 and CO2/H2 (molar ratio 30:70) selectivity above 1700. Breakthrough simulations also confirmed its optimal CO2 separation attribute. Our results have demonstrated for the first time the strong potential of Hf-MOFs for advanced adsorbents for high-performance CO2-related separations. [ABSTRACT FROM AUTHOR]

The latest high-throughput sequencing technologies show that there are more than 1000 types of microbiota in the human gut. These microbes are not only important to maintain human health, but also closely related to the occurrence and development of various diseases. With the development of transplantation technologies, allogeneic transplantation has become an effective therapy for a variety of end-stage diseases. However, complications after transplantation still restrict its further development. Post-transplantation complications are closely associated with a host's immune system. There is also an interaction between a person's gut microbiota and immune system. Recently, animal and human studies have shown that gut microbial populations and diversity are altered after allogeneic transplantations, such as liver transplantation (LT), small bowel transplantation (SBT), kidney transplantation (KT) and hematopoietic stem cell transplantation (HTCT). Moreover, when complications, such as infection, rejection and graft versus host disease (GVHD) occur, gut microbial populations and diversity present a significant dysbiosis. Several animal and clinical studies have demonstrated that taking probiotics and prebiotics can effectively regulate gut microbiota and reduce the incidence of complications after transplantation. However, the role of intestinal decontamination in allogeneic transplantation is controversial. This paper reviews gut microbial status after transplantation and its relationship with complications. The role of intervention methods, including antibiotics, probiotics and prebiotics, in complications after transplantation are also discussed. Further research in this new field needs to determine the definite relationship between gut microbial dysbiosis and complications after transplantation. Additionally, further research examining gut microbial intervention methods to ameliorate complications after transplantation is warranted. A better understanding of the relationship between gut microbiota and complications after allogeneic transplantation may make gut microbiota as a therapeutic target in the future. [ABSTRACT FROM AUTHOR]

Triangular Ag nanoprisms are a type of most-studied noble-metal nanostructures over the past decade owing to their special structural architecture and outstanding optical and catalytic properties for a wide range of applications. Nevertheless, in contrast to active research for the synthesis of phase-pure Ag nanoprisms, no asymmetric heterodimers containing Ag prisms have been developed so far, probably due to lack of suitable synthetic methods. Herein, we devise a simple ion-exchange method to synthesize Ag2/Ag heterodimers at room temperature, through which Ag nanoprisms with controllable size and thickness can be fabricated. Formation chemistry and optical properties of the heterodimers have been investigated. These semiconductor/metal heterodimers have exhibited remarkable bactericidal activity to E. coli cells under visible light illumination. [ABSTRACT FROM AUTHOR]

Hydrous manganese dioxide nanostructures were synthesized via a catalytic oxidation reaction mechanism at mild temperatures. It was found that the morphology of the manganese dioxide nanostructures was significantly influenced by the pH of the reaction system. With increasing pH the morphology of manganese dioxide nanostructures changed from urchin-like structures to nanobelts. The capacitive performance was investigated by using cycle voltammetry and galvanostatic charge/discharge techniques. Hydrous manganese dioxide nanostructures obtained from a basic solution exhibited a capacitance of 262 F g [?] 1 at a current density of 250 mA g [?] 1 and a capacitive retention of 75% after 1200 cycles, suggesting that this is a promising electrode material for supercapacitors. The high specific capacitance is attributed to the hydrous nature coupled with a high surface area (181 m2 g [?] 1) of the manganese dioxide nanostructure. [ABSTRACT FROM AUTHOR]

Synthesis, structure, and gas adsorption properties of three Metal Organic Frameworks (MOFs) synthesized from predesigned ligands 4-(1H-tetrazole-5-yl)benzoic acid (4-TBA) and 2-fluoro-4-(1H-tetrazole-5-yl)benzoic acid (2F-4-TBA) along with Cu(II) as an metal precursor has been reported. Among these MOFs, Cu9(4-TBA)10(C2H5OH)2(Cu-TBA-1) and Cu2(4-TBA)2(DMF)(C2H5OH) (Cu-TBA-2) are structural isomers. Whereas, Cu2(4-TBA)2(DMF)(C2H5OH) (Cu-TBA-2) and Cu2(2-F-4-TBA)2(DMF)2(Cu-TBA-2F) have similar crystal structure. N2adsorption isotherms of the activated sample of Cu-TBA-1 and -2 exhibit types-I sorption behavior with a Langmuir and Brunauer–Emmett–Teller (BET) surface area of 686, 402 m2/g and 616, 356 m2/g, respectively. It is noteworthy that Cu-TBA-1 and -2 adsorbs 1.16 and, 1.54 wt % H2, while Cu-TBA-2F adsorbs 0.67 wt % at 77 K and 1 atm. On the other hand, Cu-TBA-1 and -2 adsorb 3.08 and 2.54 mmol/g, while Cu-TBA-2F adsorbs 1.27 mmol/g of CO2at 298 K and 1 bar pressure. H2adsorption sites in Cu-TBA-2 and -2F have been analyzed by molecular simulation. [ABSTRACT FROM AUTHOR]

A reaction density functional theory (R-DFT) is developed for chemical reactions in confined space by integrating reaction thermodynamics and DFT for chain fluids. The theory is applied to investigate DNA melting in slit pores, with nucleotides represented by coarse-grained charged Lennard-Jones particles. Three types of slit pores are considered for DNA melting: repulsive pore, attractive pore, and under electric field. In repulsive pores, the melting temperature increases slightly with reducing pore width, and the increase magnitude is nearly the same for DNA of different chain lengths. The double-strand DNA (dsDNA) and single-strand DNA (ssDNA) are located in the slit center, particularly for long DNA due to the effect of configuration entropy. In attractive pores, the melting temperature increases with increasing wall−fluid interaction. The DNA chains are preferentially adsorbed near the slit walls with a strong wall−fluid interaction. Under electric field, the melting temperature increases slightly and is more distinct for shorter DNA. [ABSTRACT FROM AUTHOR]

A weighted density functional theory is developed for Yukawa chain fluids confined in a nanoslit. The excess free-energy functional is separated into repulsive and attractive contributions. A simple Heaviside function is used as the weighting function to calculate the weighted density in both contributions. The excess free-energy functional of repulsive interaction is calculated by the equation of state developed by Liu et al., while the contribution to excess free-energy functional by attractive interaction is calculated using the statistical associating fluids theory for chain molecules with attractive potentials of variable range. For pure fluids, the predicted density profiles near the nanoslit wall are in good agreement with simulations. The effect of cut-off introduced in the weighting function for the attractive part is examined; in addition, the surface excess and partition coefficient are calculated. The density profiles are also predicted for mixtures of two Yukawa chain fluids with different chain lengths, hard-core diameters, fluid-fluid and wall-fluid interactions. This work reveals that it is important to decompose the excess free-energy functional into repulsive and attractive contributions, and a simple weighting function can be used for both contributions. [ABSTRACT FROM AUTHOR]

A hybrid density functional theory (DFT) is developed for adsorption of copolymers in a selective nanoslit. The DFT incorporates a single-chain simulation for the ideal-gas free energy functional with two weighted density approximations for the residual free energy functional. The theory is found to be insensitive to the width parameter used in the weighted density. Theoretical predictions are in excellent agreement with simulation results in the segment density profiles and the adsorption configurations including tail, loop, and train for copolymers with various sequences over a wide range of surface affinity. The bridge conformation is also observed in multiblock copolymers. Ordered assembly is facilitated in copolymers with longer chain/block and at stronger attraction between segment B and the slit wall. While diblock copolymer shows the longest tail, alternating copolymer has the shortest. As the attraction between segment B and the slit wall increases, the average size and fraction decrease for tail, but increase for loop and train. [ABSTRACT FROM AUTHOR]

A new statistical mechanics model is developed to calculate the surface tensions of liquid mixtures, based on an equation of state for chain fluids and the scaled particle theory. Transferrable molecular parameters fitted to experimental phase equilibrium properties are used in this model. The feasibility of the model has been systematically tested in the correlations of 62 binary mixtures and in the predictions of 7 binary and 5 ternary mixtures, including nonassociating, self-associating, and cross-associating systems with overall average absolute relative deviations of 0.31%, 0.86%, and 0.92%, respectively. The accuracy of the new model makes it particularly well-suited in the calculation of surface tensions for a wide range of complex liquid mixtures. [ABSTRACT FROM AUTHOR]

We report a molecular simulation study on the assembly of an (A7B5)5/A7B5copolymer blend on nanopatterned surfaces. The density distributions, anisotropic radii of gyration, and conformations of both copolymers are quantitatively characterized. As the width of stripes on the surface decreases, the shape and thickness of the assembled film are found to be in qualitative agreement with those from experiments. The simulation results indicate that the shape and conformation of ordered film can be modulated by tuning the adsorption energy between the surface and the polymer or by adjusting the width of the stripes on the surface. We can regulate the width of the stripes to obtain a desired polymer conformation without altering the assembled film. In remarkable contrast to the pure copolymer, the radii of gyration of the blend in three directions are consistently smaller. The simulation reveals that the addition of a short chain during assembly is of central importance in restructuring the conformations of the long chain. [ABSTRACT FROM AUTHOR]

The vapor−liquid equilibria of binary systems containing imidazolium-based ionic liquids (ILs) have been investigated using an equation of state (EOS) for the heteronuclear square-well chain fluids (hetero-SWCFs). ILs are represented by “diblock compounds”, with the alkyl group as one block and the imidazolium ring−anion pair as the other block. Model parameters of the imidazolium ring−anion block are obtained by fitting the experimental pressure−volume−temperature (pVT) data of ILs, and they are combined with those of the alkyl block from our previous work to correlate and predict the molar volumes of homologous imidazolium ILs, with the average deviations of 0.62% and 3.24%, respectively. Vapor−liquid equilibria (VLE) of 22 binary systems that contain imidazolium ILs and solvents are correlated, with an average deviation of 5.38%. The results reveal that the imidazolium ILs can be regarded as diblock compounds fairly well and the hetero-SWCF−EOS is well-suited for calculation of their thermophysical properties. [ABSTRACT FROM AUTHOR]

By integrating polymer density function theory (DFT) and single-chain molecular simulation, a hybrid DFT is developed for homopolymer mixtures confined in a selective nanoslit. Two weighting functions are adopted separately in the polymer DFT for repulsive and attractive contributions to the excess free energy functional. The theoretical results agree well with simulation data for the density profiles, configurations (tail, loop and train), adsorption amounts, layer thicknesses, and partition coefficients. The polymer−slit interaction is found to have a large effect on the density profiles and partition coefficients but is found to have a small effect on the average sizes and percentages of the configurations. Nearly half of the polymer segments form tails, and the other half form trains. In addition, bridges are observed to form for sufficiently long polymer chains. As the length difference between two polymers increases, the effect of chain connectivity becomes increasingly important. [ABSTRACT FROM AUTHOR]

The recognition of multiblock copolymers on nanopatterned surfaces has been investigated by molecular simulations. All the copolymers (AnB12-n)5are composed of 60 square-well segments, but with various architectures by changing n. Segment density profiles, radii of gyration, pattern transfer parameters, and three adsorption conformations (tail, loop, and train) are examined quantitatively. It is found that the copolymer can recognize the adsorbing stripes on surface and the surface vicinity. The recognition affinity becomes stronger with increasing the stripe width, the adsorption strength, and the number of adsorbing segments in copolymer chain. From surface to bulk phase, the shape of copolymer changes from elongated to elliptical, and finally to globular. Among the three adsorption conformations, tail has the greatest average size while train has the smallest. With the increased number of nonadsorbing segments, the average size shows an increase in tail but a decrease in train. [ABSTRACT FROM AUTHOR]

Metal-organic frameworks (MOFs), NTU-111, 112, 113, were assembled from diversely "click"-extended tetracarboxylates. Since the MOFs were incorporated with exposed metal sites and accessible nitrogen-rich triazole units, they exhibited high CO2-selective capture capabilities supported by experimental investigations and molecular simulation studies. [ABSTRACT FROM AUTHOR]