Statistical information on the edge surface area and edge crystallographic orientation of clay nanoparticle surfaces is essential for proper accounting of the protonation-deprotonation reactions as a part of mechanistic surface complexation models. A combination of atomic-force microscopy (AFM) measurements and molecular dynamics computer simulations made it possible to quantify the relative contributions of the most frequently occurring montmorillonite edge surfaces to the total edge surface area. Edge surfaces normal to the  and  crystallographic directions are found to be the most abundant (~60% and ~20%, respectively), in agreement with previous estimations.
The precise positioning of catalytic amino acids against the substrate in an enzyme active site is a crucial factor in biocatalysis. Biosynthesis of the chromophores of fluorescent proteins (FPs) is an autocatalytic process that must conform to these requirements. Here, we show that, in addition to the internal amino acid residues in the proximity of the chromophore, chromophore biosynthesis is influenced by the remote amino acids exposed on the outer surface of the β-barrel structure of the FP. It has been shown earlier that chromophore biosynthesis of the red FP from Zoanthus sp. (zoan2RFP) proceeds via an immature green state. At the same time, the green state is the final stage of chromophore biosynthesis of green FP (zoanGFP), which is highly homologous to zoan2RFP. It was also shown that a single N66D substitution in the chromophore-forming sequence of zoanGFP might trigger the synthesis of the red chromophore. However, in this case, the synthesis of the red chromophore is incomplete and occurs only at elevated temperatures. Here, we tried to uncover additional structural determinants that govern the biosynthesis of the red chromophore. A comparison of zoanGFP and zoan2RFP revealed intrabarrel amino acid differences at five positions. Exhaustive substitutions of these five positions in zoanGFP-N66D gave rise to zoanGFPmut with the same intrabarrel amino acid composition as zoan2RFP. zoanGFPmut showed only partial green-to-red chromophore transformation at elevated temperatures. To elucidate the extra factors that can affect red chromophore biosynthesis, we performed comparative molecular dynamics simulations of zoan2RFP and zoanGFPmut. The simulations revealed several external amino acids that might influence the arrangement and flexibility of the chromophore-surrounding amino acid residues in these proteins. Mutagenesis experiments confirmed the crucial role of these residues in red chromophore biosynthesis. The obtained zoanGFPmut2 exhibited complete green-to-red transformation, suggesting that the mutated amino acids exposed on the surface of the β-barrel contribute to red chromophore biosynthesis.
The siloxane surface of uncharged clays is known to be hydrophobic, which is supported by strong experimental and theoretical evidence. For the siloxane surface of charged clays, like smectites, the picture is not as clear. We are aiming to clarify this issue by molecular simulations in which smectite surface hydrophobicity is quantified through the separate contribution of the surface itself, and the contribution due to the presence of charge-balancing cations on the surface. In order to explore systematically the effects of the total smectite charge and its distribution in the structure, a series of molecular dynamics (MD) simulations was performed for several models of dioctahedral smectites and compared with the results for uncharged pyrophyllite.
The largest difference between the simulation results for smectite models with naturally present surface counterions and the models where these ions were artificially removed from the surface, while maintaining the same total charge balance of the model, is in the shape of the water coverage. In the former case, full surface wetting is observed and a relatively flat water film is forming on the surface. Its irregularity and thickness is connected with number of ions on the surface. However, in all cases of smectite surfaces artificially devoid of ions, a water droplet is always formed and the wetting is incomplete. The contact angles of the water droplets on charged montmorillonites are very similar to that on uncharged pyrophyllite surface and range roughly between 110o and 90o. These angles are also affected by the distribution of the octahedral and tetrahedral substitutions in the structure and by their ratio. In the case of purely tetrahedral substitutions the contact angle on the bare smectite surface can be as low as ~60o, but still far from complete wetting.
The angular distributions of the H2O dipole vectors as a function of distance from the smectite surface show two preferred surface-oriented types of water molecules when counterions are present, and the total surface is highly hydrophilic. However, for surfaces devoid of ions, a population with dipole angles close to ~90o is dominating, and the smectite surfaces can be considered hydrophobic. It can be thus concluded that, independent of the structural charge, bare smectite surfaces by themselves are either hydrophobic or only moderately hydrophilic. Their experimentally observed highly hydrophilic character is almost entirely due to the charge balancing cations present on the surface.
Magnetic nanocomposites involving tetraborate ion (TB)-intercalated Mg–Al-layered double hydroxide (LDH) shell supported on magnesium ferrite core particles are synthesized, characterized, and compared with their non-magnetic analogues. The compositions of the obtained nanocomposites were determined and structural investigations were made by powder X-ray diffraction and Fourier transform infrared spectroscopy. Particle characteristics were examined by size distribution, specific surface area measurements, scanning electron microscopy and transmission electron microscopy. Room-temperature magnetic measurements were performed with a vibrating sample magnetometer. The dynamics and structure of the interlayer water molecules and borate ions were studied by molecular dynamics simulations. Analytical and modeling studies verified that the TB ions were arranged between the LDH layers in oblique positions. The products were found to carry ca. 6% boron (10**17 B atom/μg nanocomposite). The magnetic nanocomposite showed superparamagnetic properties and can potentially find applications in biomedical fields for the site-specific delivery of bio-potent boron agents.
Due to their high durability and immobilization properties, cementitious materials have found a considerable application in the design and construction of radioactive waste repositories in the last decades. During cement paste production, organic additives are introduced to modify various properties of cement. The presence of such organic complexants may negatively affect the immobilizing properties of cement with respect to radionuclides. For better understanding and prediction of the effects of interactions between organic molecules and cementitious materials with radionuclides, we have developed several representative models consisting of three principal components: (i) calcium silicate hydrate (C-S-H) phase - the main binding phase of cement; (ii) gluconate, a simple well-described molecule, as a representative of organic additives; (iii) U(VI), as one of the most studied radionuclides of the actinide series. The C-S-H phase with low Ca/Si ratio (~0.83) typical for â€œlow-pHâ€ and degraded cement pastes has been selected for this modelling study. Structural, and energetic aspects of the sorption processes of uranyl, gluconate, and their mutual correlations on the surface of cement were quantitatively modeled by classical molecular dynamics (MD) and potential of mean force (PMF) calculations. The ternary surface complex formation between uranyl hydroxides and Ca2+ cations at the C-S-H aqueous interfaces is shown to have an important role in the overall sorption process. In the presence of gluconate, U(VI) sorption on C-S-H is facilitated by weakening the Ca2+ binding with the surface. Additionally, Na+ is proven to be an important competitor for certain surface sorption sites and can potentially affect the equilibrium properties of the interface.
We performed constant reservoir composition molecular dynamics (CRC-MD) simulations at 323 K and 124 bar to quantitatively study the partitioning of fluid species between the nano- and mesopores of clay and a bulk reservoir containing an equimolar mixture of CO2 and CH4. The results show that the basal (001) and protonated edge (010) surfaces of illite both demonstrate a strong preference for CO2 over CH4 adsorption; that the (001) surfaces show a stronger preference for CO2 than the (010) surfaces, especially with K+ as the exchangeable cation; and that the structuring of the near-surface CO2 by K+ is stronger than that by Na+. The protonated (010) surfaces have a somewhat greater preference for CH4, with the concentration near them close to that in the bulk fluid. The effects of the surfaces on the fluid composition extend to approximately 2.0 nm from them, with the fluid composition at the center of the pore becoming essentially the same as the bulk composition at a pore thickness of ~5.7 nm. The preference of nano- and mesopores bounded by clay minerals for CO2 over CH4 suggests that injection of CO2 into tight reservoirs is likely to displace CH4 into larger pores, thus enhancing its production.