3D Printed Cellulose Nanofiber Aerogel Scaffold with Hierarchical Porous Structures for Fast Solar-Driven Atmospheric Water Harvesting.

Hygroscopic salt-based composite sorbents are considered ideal candidates for solar-driven atmospheric water harvesting. The primary challenge for the sorbents lies in exposing more hygroscopically active sites to the surrounding air while preventing salt leakage. Herein, a hierarchically structured scaffold is constructed by integrating cellulose nanofiber and lithium chloride (LiCl) as building blocks through 3D printing combined with freeze-drying. The milli/micrometer multiscale pores can effectively confine LiCl and simultaneously provide a more exposed active area for water sorption and release, accelerating both water sorption and evaporation kinetics of the 3D printed structure. Compared to a conventional freeze-dried aerogel, the 3D printed scaffold exhibits a water sorption rate that is increased 1.6-fold, along with a more than 2.4-fold greater water release rate. An array of bilayer scaffolds is demonstrated, which can produce 0.63 g g-1 day-1 of water outdoors under natural sunlight. This article provides a sustainable strategy for collecting freshwater from the atmosphere.

Geometric differences in the ribosome exit tunnel impact the escape of small nascent proteins.

The exit tunnel is the subcompartment of the ribosome that contains the nascent polypeptide chain and, as such, is involved in various vital functions, including regulation of translation and protein folding. As the geometry of the tunnel shows important differences across species, we focus on key geometrical features of eukaryote and prokaryote tunnels. We used a simple coarse-grained molecular dynamics model to study the role of the tunnel geometry in the post-translational escape of short proteins (short open reading frames [sORFs]) with lengths ranging from 6 to 56 amino acids. We found that the probability of escape for prokaryotes is one for all but the 12-mer chains. Moreover, proteins of this length have an extremely low escape probability in eukaryotes. A detailed examination of the associated single trajectories and energy profiles showed that these variations can be explained by the interplay between the protein configurational space and the confinement effects introduced by the constriction sites of the ribosome exit tunnel. For certain lengths, either one or both of the constriction sites can lead to the trapping of the protein in the "pocket" regions preceding these sites. As the distribution of existing sORFs indicates some bias in length that is consistent with our findings, we finally suggest that the constraints imposed by the tunnel geometry have impacted the evolution of sORFs.

Competing Effects of Hydration and Cation Complexation in Single-Chain Alginate.

Alginic acid, a naturally occurring anionic polyelectrolyte, forms strong physically cross-linked hydrogels in the presence of metal cations. The latter engage in electrostatic interactions that compete with intra- and intermolecular hydrogen bonds, determining the gel structure and properties of the system in aqueous media. In this study, we use all-atom molecular dynamics simulations to systematically analyze the interactions between alginic acid chains and Na+ and Ca2+ counterions. The formed alginates originate from the competition of intramolecular hydrogen bonding and water coordination around the polyelectrolyte. In contrast to the established interpretation, we show that calcium cations strongly bind to alginate by disrupting hydrogen bonds within (1 → 4)-linked ß-d-mannuronate (M) residues. On the other hand, Na+ cations enhance intramolecular hydrogen bonds that stabilize a left-hand, fourfold helical chain structure in poly-M alginate, resulting in stiffer chains. Hence, the traditionally accepted flexible flat-chain model for poly-M sequence is not valid in the presence of Na+. The two cations have a distinct effect on water coordination around alginate and therefore on its solubility. While Ca+ disrupts water coordination directly around the alginate chains, mobile Na+ cations significantly disrupt the second hydration layer.

United-Atom Molecular Dynamics Study of the Mechanical and Thermomechanical Properties of an Industrial Epoxy.

Epoxy resins are the most commonly used adhesives in industry due to their versatility, low cost, low toxicity, low shrinkage, high strength, resistance to moisture, and effective electrical resistance. These diverse properties can be tailored based on the chemical structure of the curing agent and the conditions of the curing process. Molecular simulations of epoxy resins have gained attention in recent years as a means to navigate the vast choice of chemical agents and conditions that will give the required properties of the resin. This work examines the statistical uncertainty in predicting thermodynamic and mechanical properties of an industrial epoxy resin using united atom molecular dynamics simulation. The results are compared with experimental measurements of the elastic modulus, Poisson's ratio, and the glass transition temperature obtained at different temperatures and degrees of curing. The decreasing trend of the elastic modulus with increasing temperature is accurately captured by the simulated model, though the uncertainty in the calculated average is large. The glass transition temperature is expectedly overpredicted due to the high rates accessible to molecular simulations. We find that Poisson's ratio is particularly sensitive to sample anisotropy as well as the method of evaluation, which explains the lack of consistent trends previously observed with molecular simulation at different degrees of crosslinking and temperatures.

Revisiting Cation Complexation and Hydrogen Bonding of Single-Chain Polyguluronate Alginate.

Modifying the properties of bio-based materials has garnered increasing interest in recent years. In related applications, the ability of alginates to complex with metal ions has been shown to be effective in liquid-to-gel transitions, useful in the development of foodstuff and pharma products as well as biomaterials, among others. However, despite its ubiquitous use, alginate behavior as far as interactions with cations is not fully understood. Hence, this study presents a detailed comparison of alginate's complexation with Na+ and Ca2+ and the involved intramolecular hydrogen bonding and biomolecular chain geometry. Using all-atom molecular dynamics simulations, we find that in contrast to accepted models, calcium cations strongly bind to alginate chains by disruption of hydrogen bonds between neighboring residues, stabilizing a left-hand, 3-fold helical chain structure that enhances chain stiffness. Hence, while present, the traditionally accepted egg-box binding mode was a minor subset of possible conformations. For a single chain, most of the cation binding occurred as single-cation interaction with a carboxyl group, without the coordination of other alginate oxygens. The monovalent Na+ ions were found to be mostly nonlocalized around alginate and therefore do not compete with intramolecular hydrogen bonding. The different binding modes observed for Na+ and Ca2+ contribute toward explaining the different solubility of sodium and calcium alginate.

Expanding carbon capture capacity: uncovering additional CO2 adsorption sites in imine-linked porous organic cages.

With an increasing need to develop carbon capture technologies, research regarding the use of cage-based porous materials has garnered great interest. Typically, the study of gas adsorption in porous organic cages (POCs) has focused on the gas uptake inside the cage cavity. By using molecular dynamics simulation, this study reveals the presence of eight sites outside the cavity of a 15-crown-5 ether-substituted imine-linked POC which could enhance carbon dioxide adsorption capacity. Adsorption on these sites is likely stabilized by the functional groups on the cage vertices and the imine groups on the faces of the POC. These external adsorption sites have a higher CO2 adsorption capacity and greater sensitivity to temperature and pressure changes than the sites within the cage cavity. These characteristics are particularly favourable for applications based on pressure- and temperature-swing separation.

Negative Pressure within a Liquid-Fluid Interface Determines Its Thickness.

The density within the interface between two fluid phases at equilibrium gradually changes from that of one phase to that of the other. The main change in density, according to experimental measurements, practically occurs over a finite distance of O [1 nm]. If we assume that the average stress difference within the interface is on the order of magnitude of ambient pressure, then the Bakker equation implies that for a liquid with surface tensions, say ∼50 mN/m, we get an interface thickness of ∼500 nm. This is certainly too big because it contradicts experimental findings. Alternatively, if the thickness is assumed to be O [10 nm] or less, as is usually believed, the average stress difference must be ∼5 × 106 N/m2 or bigger, which is surprisingly high. This paper shows using a few approaches that such a high average stress difference is due to negative stresses in the interface.

Coarse-Grained Simulation of Protein-Imprinted Hydrogels.

The MARTINI force-field is adapted for acrylic functional monomers and used to simulate protein-imprinted polymers, including complexation in solution, cross-linking reaction, washing, and rebinding of the protein. A globally controlled grand canonical Monte Carlo simulation combined with molecular dynamics is used to achieve proper hydration and swelling of the gel. Two gel formulations are compared, one with only polar functional monomers and one with additional small number of charged monomers. Imprinted hydrogels are evaluated for two proteins, lysozyme, and cytochrome c and chosen due to their similarity in size and isoelectric point, though it is known that their imprinting behavior is very different. Analysis of diffusion of the proteins within the gel shows that their interaction with functional monomers and their diffusion mechanism differ substantially and hence affect their specific and nonspecific interactions with the gel.

The Relation between α-Helical Conformation and Amyloidogenicity.

Amyloid fibrils are stable aggregates of misfolded proteins and polypeptides that are insoluble and resistant to protease activity. Abnormal formation of amyloid fibrils in vivo may lead to neurodegenerative disorders and other systemic amyloidosis, such as Alzheimer's, Parkinson's, and atherosclerosis. Because of their clinical importance, amyloids are under intense scientific research. It is believed that short polypeptide segments within proteins are responsible for the transformation of correctly folded proteins into parts of larger amyloid fibrils and that this transition is modulated by environmental factors, such as pH, salt concentration, interaction with the cell membrane, and interaction with metal ions. Most studies on amyloids focus on the amyloidogenic sequences. The focus of this study is on the structure of the amyloidogenic α-helical segments because the α-helical secondary structure has been recognized to be a key player in different stages of the amyloidogenesis process. We have previously shown that the α-helical conformation may be expressed by two parameters (θ and ρ) that form orthogonal coordinates based on the Ramachandran dihedrals (φ and ψ) and provide an illuminating interpretation of the α-helical conformation. By performing statistical analysis on α-helical conformations found in the Protein Data Bank, an apparent relation between α-helical conformation, as expressed by θ and ρ, and amyloidogenicity is revealed. Remarkably, random amino acid sequences, whose helical structures were obtained from the most probable dihedral angles, revealed the same dependency of amyloidogenicity, suggesting the importance of α-helical structure as opposed to sequence.

The selectivity of protein-imprinted gels and its relation to protein properties: A computer simulation study.

Polymer-based protein recognition systems have enormous potential within clinical and diagnostic fields due to their reusability, biocompatibility, ease of manufacturing, and potential specificity. Imprinted polymer matrices have been extensively studied and applied as a simple technique for creating artificial polymer-based recognition gels for a target molecule. Although this technique has been proven effective when targeting small molecules (such as drugs), imprinting of proteins have so far resulted in materials with limited selectivity due to the large molecular size of the protein and aqueous environment. Using coarse-grained molecular simulation, we investigate the relation between protein makeup, polymer properties, and the selectivity of imprinted gels. Nonspecific binding that results in poor selectivity is shown to be strongly dependent on surface chemistry of the template and competitor proteins as well as on polymer chemistry. Residence time distributions of proteins diffusing within the gels provide a transparent picture of the relation between polymer constitution, protein properties, and the nonspecific interactions with the imprinted gel. The pronounced effect of protein surface chemistry on imprinted gel specificity is demonstrated.

Sequence-dependent association of alginate with sodium and calcium counterions.

Molecular dynamics simulation is used to study in detail the binding of sodium and calcium ions to alginate chains, and its dependence on the content of guluronic (G) acid residues. Our previous studies showed that chains with different G content associate through different structural mechanisms due to differing degrees of rigidity of the ion-alginate chain complexes. Polymannuronate and polyguluronate chains form highly ordered structures due to their more rigid nature. Heteropolymer chains are more flexible and hence associate at higher ion and alginate concentrations, however, with association behavior that has a clear dependence on G content. The nature of interactions of sodium and calcium ions are shown to differ for poly-M, poly-G, and the heteropolymer compositions. Scattering curves of Ca2+-alginate solutions where found to have good agreement with the broken-rod SAXS model with nontrivial but clear dependence on G content, which is explained by chain flexibility and its relation to ion condensation.

A closer look into the α-helix basin.

α-Helices are the most abundant structures found within proteins and play an important role in the determination of the global structure of proteins and their function. Representation of α-helical structures with the common (φ, ψ) dihedrals, as in Ramachandran maps, does not provide informative details regarding the helical structure apart for the abstract geometric meaning of the dihedrals. We present an alternative coordinate system that describes helical conformations in terms of residues per turn (ρ) and angle (ϑ) between backbone carbonyls relative to the helix direction through an approximate linear transformation between the two coordinates system (φ, ψ and ρ, ϑ). In this way, valuable information on the helical structure becomes directly available. Analysis of α-helical conformations acquired from the Protein Data Bank (PDB) demonstrates that a conformational energy function of the α-helix backbone can be harmonically approximated on the (ρ, ϑ) space, which is not applicable to the (φ, ψ) space due to the diagonal distribution of the conformations. The observed trends of helical conformations obtained from the PDB are captured by four conceptual simulations that theoretically examine the effects of residue bulkiness, external electric field, and externally applied mechanical forces. Flory's isolated pair hypothesis is shown to be partially correct for α-helical conformations.

Structural Characterization of Sodium Alginate and Calcium Alginate.

Alginate readily aggregates and forms a physical gel in the presence of cations. The association of the chains, and ultimately gel structure and mechanics, depends not only on ion type, but also on the sequence and composition of the alginate chain that ultimately determines its stiffness. Chain flexibility is generally believed to decrease with guluronic residue content, but it is also known that both polymannuronate and polyguluronate blocks are stiffer than heteropolymeric blocks. In this work, we use atomistic molecular dynamics simulation to primarily explore the association and aggregate structure of different alginate chains under various Ca(2+) concentrations and for different alginate chain composition. We show that Ca(2+) ions in general facilitate chain aggregation and gelation. However, aggregation is predominantly affected by alginate monomer composition, which is found to correlate with chain stiffness under certain solution conditions. In general, greater fractions of mannuronic monomers are found to increase chain flexibility of heteropolymer chains. Furthermore, differences in chain guluronic acid content are shown to lead to different interchain association mechanisms, such as lateral association, zipper mechanism, and entanglement, where the mannuronic residues are shown to operate as an elasticity moderator and therefore promote chain association.

Comparison of descriptors for predicting selectivity of protein-imprinted polymers.

Molecular imprinting is a technique that is used to create artificial receptors by the formation of a polymer network around a template molecule, creating a molecularly imprinted polymer. These artificial receptors may be used in applications that require molecular recognition, such as enantioseparations, biosensors, artificial catalysis, drug delivery and others. Small molecules, such as drugs, have been imprinted with high efficiency and, combined with the low cost of preparation, molecularly imprinted polymers have acquired commercial usage. While attempts at imprinting proteins have been significantly less successful, the great potential of protein-imprinted polymers (PIPs) in medicine and industry attracted much research. Multifunctionality, conformational flexibility, large size of the proteins, and aqueous polymerization environment are some of the obstacles faced by protein imprinting. We explore the relation between PIP selectivity and the properties of the template and competitor proteins. A comprehensive statistical analysis of published studies reveals a statistically significant correlation between four protein descriptors and the corresponding selectivity of PIPs. Namely, a PIP will generally be more selective against large competitor proteins with a smooth surface, whose isoelectric point and aspect ratio are significantly different than those of the template protein. The size of the protein, as measured by its molecular weight, appears to be independent of the template protein characteristics. Copyright © 2016 John Wiley & Sons, Ltd.

Cytosine derivatized bis(2,2'-bithienyl)methane molecularly imprinted polymer for selective recognition of 6-thioguanine, an antitumor drug.

A molecularly imprinted polymer (MIP) was designed and synthesized to serve as a functional material for selective recognition of 6-thioguanine (6TG), an antitumor drug. For that, the newly synthesized functional monomer, cytosine-bis(2,2'-bithienyl)-(4-carboxyphenyl)methane ester (Cyt-S4), revealed Watson-Crick type nucleobase pairing of 6TG. Formation of the Cyt-S4 and 6TG complex of the 2:1 stoichiometry was postulated based on the DFT calculations at the B3LYP/3-21G((⁎)) level and experimentally confirmed by fluorescence titration. The molecularly imprinted polymer (MIP) film was deposited by potentiodynamic electropolymerization on a Pt disk electrode as well as on an Au-coated glass slide and on an Au-quartz crystal resonator. The statistical model of formation of this film was successfully simulated by molecular dynamics. Completeness of the subsequent 6TG template extraction from MIP was confirmed by the UV-visible spectroscopy. An imprinting factor of 2.9 for the MIP film was determined by piezoelectric microgravimetry using ECQM. The double-layer capacity and alternating current measurements under flow-injection analysis (FIA) conditions were selected to transduce the 6TG recognition signal into the change of the double-layer capacity dependence on the 6TG concentration in solution for different supporting electrolyte concentrations. Detectability of the resulting chemosensor was 10 µM 6TG for the 0.5 M KF carrier solution in FIA. Selectivity of the chemosensor with respect to common interferences was high, e.g., it exceeded 130 to 2-amino-6-methylmercaptopurine, a 6TG metabolite.

Conformational changes of globular proteins upon adsorption on a hydrophobic surface.

This paper presents a study of protein adsorption and denaturation using coarse-grained Monte Carlo simulations with simulated annealing. Intermolecular interactions are modeled using the Miyazawa-Jernigan (MJ) knowledge-based potential for an implicit solvent. Three different hydrophobicity scales are tested for adsorption of fibronectin on a hydrophobic surface. The hydrophobic scale BULDG was chosen for further analysis due to its greater stability during heating and its partial regenerative ability upon slow cooling. Differences between helical and sheet structures are observed upon denaturation -α-helices undergo spreading of their native helical order to an elliptical perturbed shape, while ß-sheets transform into random coils and other more structured conformations. Electronic calculations carried out on rebuilt all-atom coordinates of adsorbed lysozymes revealed consistent destabilization of helices, while beta sheets show a greater variety of trends.

Thermal stability limits of proteins in solution and adsorbed on a hydrophobic surface.

A coarse-grained Monte Carlo simulation is used to study thermal denaturation of small proteins in an infinitely dilute solution and adsorbed on a flat hydrophobic surface. Intermolecular interactions are modeled using the Miyazawa-Jernigan (MJ) knowledge-based potential for implicit solvent with the BULDG hydrophobicity scale. We analyze the thermal behavior of lysozyme for its prevalence of α-helices, fibronectin for its prevalence of ß-sheets, and a short single helical peptide. Protein dimensions and contact maps are studied in detail before and during isothermal adsorption and heating. The MJ potential is shown to correctly predict the native conformation in solution under standard conditions, and the anticipated thermal stabilization of adsorbed proteins is observed when compared with heating in solution. The helix of the peptide is found to be much less stable thermally than the helices of lysozyme, reinforcing the importance of long-range forces in defining the protein structure. Contact map analysis of the adsorbed proteins shows correlation between the hydrophobicity of the secondary structure and their thermal stability on the surface.

A brief review of coarse-grained and other computational studies of molecularly imprinted polymers.

Molecular imprinting is an established method for the creation of artificial recognition sites in synthetic materials through polymerization and cross-linking in the presence of template molecules. Removal of the templates leaves cavities that are complementary to the template molecules in size, shape, and functionality. In recent years, various theoretical and computational models have been developed as tools to aid in the design of molecularly imprinted polymers (MIPs) or to provide insight into the features that determine MIP performance. These studies can be grouped into two general approaches-screening for possible functional monomers for particular templates and macromolecular models focusing on the structural characterization of the imprinted material. In this review, we pay special attention to coarse-grained models that characterize the functional heterogeneity in imprinted pores, but also cover recent advances in atomistic and first principle studies. We offer a critical assessment of the potential impact of the various models towards improving the state-of-the-art of molecular imprinting.

Simulation of protein-imprinted polymers. 3. Imprinting selectivity.

Molecular imprinting has been extensively studied and applied as a simple technique for creating artificial polymer-based recognition gels for a target molecule. Although this technique is effective when targeting small molecules, attempts to extend it to larger templates, such as proteins, have, for the most part, failed to show similar success. Our group has developed a simple simulation model to study protein imprinting. In our previous studies, we investigated the structure of the protein-imprinted pore and imprinting factors of various model proteins. Here, we concentrate on imprinting conditions that affect the separation factor, or the ratio between the interaction energies of the template and a competitor protein. We study the effect of size, charge density, and surface charge distribution of the template protein and calculate the separation factor for various polymerization conditions. Our model captures the known effect of increasing imprinting factor (ratio of binding of the protein in an imprinted polymer to that of a nonimprinted polymer) with increasing surface functionality of the polymer but at the cost of reduced selectivity. Most interestingly, we observe that the surface charge distribution of the protein plays an important role in selectivity of the protein-imprinted polymer, suggesting that some proteins may be better candidates for molecularly imprinted polymers than others.

Simulation of protein-imprinted polymers. 2. Imprinting efficiency.

Molecular imprinting allows the creation of artificial recognition sites in synthetic materials through polymerization and cross-linking in the presence of template molecules. Removal of the templates leaves cavities that are complementary to the template molecules in size, shape, and functionality. Although this technique is effective when targeting small molecules, attempts to extend it to larger templates, such as proteins, have failed to show similar success. Here we present the second report on our model simulation study of protein imprinting, in which we apply on-lattice Monte Carlo simulations for an imprinting process using radical polymerization of hydrogels as a simple model for protein-imprinted polymers (PIPs). In this part we focus on two gel types: PIPs and templated polymers (TPs), which are polymerized in the presence of charged and neutral proteins, respectively. We calculate the imprinting factor (IF) for gels formed at various conditions and compare it for both gel types. Our results show a significantly higher IF for PIPs, and though the strongest influence on IF is found to be the monomer concentration (Φ), charge concentrations on the protein and in solution also affect IF. The percolation limit of protein-sized pores is found to be a significant turning point for the effect of concentration of functional sites within the gels on IF.