Size and Structure of Empty and Filled Nanocontainer Based on Peptide Dendrimer with Histidine Spacers at Different pH

Novel peptide dendrimer with Lys-2His repeating units was recently synthesized, studied by NMR (Molecules, 2019, 24, 2481) and tested as a nanocontainer for siRNA delivery (Int. J. Mol. Sci., 2020, 21, 3138). Histidine amino acid residues were inserted in the spacers of this dendrimer. Increase of their charge with a pH decrease turns a surface-charged dendrimer into a volume-charged one and should change all properties. In this paper, the molecular dynamics simulation method was applied to compare the properties of the dendrimer in water with explicit counterions at two different pHs (at normal pH with neutral histidines and at low pH with fully protonated histidines) in a wide interval of temperatures. We obtained that the dendrimer at low pH has essentially larger size and size fluctuations. The electrostatic properties of the dendrimers are different but they are in good agreement with the theoretical soft sphere model and practically do not depend on temperature. We have shown that the effect of pairing of side imidazole groups is much stronger in the dendrimer with neutral histidines than in the dendrimer with protonated histidines. We also demonstrated that the capacity of a nanocontainer based on this dendrimer with protonated histidines is significantly larger than that of a nanocontainer with neutral histidines.     

Rapid monitoring of the nature and interconversion of supported catalyst phases and of their influence upon performance: CO oxidation to CO2 by gamma-Al2O3 supported Rh catalysts

Spatially and temporally resolved energy-dispersive EXAFS (EDE) has been utilised in situ to study supported Rh nanoparticles during CO oxidation by O2 under plug-flow conditions. Three distinct phases of Rh supported upon Al2O3 were identified by using EDE at the Rh K-edge during CO oxidation. Their presence and interconversion are related to the efficiency of the catalysts in oxidising CO to CO2. A metallic phase is only found at higher temperatures (>450 K) and CO fractions (CO/O2 > 1); an oxidic phase resembling Rh2O3 dominates the active catalyst under oxygen-rich conditions. Below about 573 K, and in CO-rich environments, high proportions of isolated Rh(I)(CO)2 species are found to co-exist with metallic Rh nanoparticles. Alongside these discrete situations a large proportion of the active phase space comprises small Rh cores surrounded by layers of active oxide. Confinement of Rh to nanoscale domains induces structural lability that influences catalytic behaviour. For CO oxidation over Rh/Al2O3 there are two redox phase equilibria alongside the chemistry of CO and O adsorbed upon extended Rh surfaces.     

Computation of hydration free energies of organic solutes with an implicit water model

A new approach for computing hydration free energies DeltaG(solv) of organic solutes is formulated and parameterized. The method combines a conventional PCM (polarizable continuum model) computation for the electrostatic component DeltaG(el) of DeltaG(solv) and a specially detailed algorithm for treating the complementary nonelectrostatic contributions (DeltaG(nel)). The novel features include the following: (a) two different cavities are used for treating DeltaG(el) and DeltaG(nel). For the latter case the cavity is larger and based on thermal atomic radii (i.e., slightly reduced van der Waals radii). (b) The cavitation component of DeltaG(nel) is taken to be proportional to the volume of the large cavity. (c) In the treatment of van der Waals interactions, all solute atoms are counted explicitly. The corresponding interaction energies are computed as integrals over the surface of the larger cavity; they are based on Lennard Jones (LJ) type potentials for individual solute atoms. The weighting coefficients of these LJ terms are considered as fitting parameters. Testing this method on a collection of 278 uncharged organic solutes gave satisfactory results. The average error (RMSD) between calculated and experimental free energy values varies between 0.15 and 0.5 kcal/mol for different classes of solutes. The larger deviations found for the case of oxygen compounds are probably due to a poor approximation of H-bonding in terms of LJ potentials. For the seven compounds with poorest fit to experiment, the error exceeds 1.5 kcal/mol; these outlier points were not included in the parameterization procedure. Several possible origins of these errors are discussed.     

Methodology to Assess the Effects of Rice Cultivation Under Flooded Conditions on van Genuchten’s Model Parameters and Pore Size Distribution

The effects of rice (Oryza sativa L.) cultivation under flooded conditions on soil’s physical-hydraulic properties were studied in this article, using a new methodology based on a combined analysis on soil water retention curve (WRC) and pore size distribution (PSD). WRC analysis was carried out through the changes of van Genuchten’s model parameters, the characteristics of WRC at the inflection point, and the specific water capacity curve. Analysis of PSD was performed on the volume changes of porosity fractions through a detailed pore size classification, while different pore size classifications based on their hydraulic and structural characteristics were also used. The methodology was applied using a small dataset obtained from fine-textured Entisol soils which were subjected to rice cultivation under flooded conditions in Axios River plain (Northern Greece). Measurements of WRC were obtained at four depths of the soil profile from two fields, before and after the growing season of rice. The analysis indicated that the van Genuchten’s model parameters (θ _s, a, and n) and the WRC characteristics at the inflection point (pressure head h _i , pore equivalent diameter D _i , and slope S _i ) significantly changed after the growing season following similar patterns, along the soil profile in both fields. The parameters θ _s, a, D _i , and S _i were decreased, while n and h _i were increased. The h _i and a were the most sensitive parameters, while the values of (h _i and 1/a) in each layer before and after the growing season for each field were linearly correlated and shifted to higher values because of compaction, indicating that it could be applied as a tool to evaluate the degree of soil compaction to similarly textured soils. The peaks of the specific water capacity curves were compressed (lower values of slope S _i ) and shifted to lower water potentials (h _i ) that corresponded to pores of equivalent diameter D _i between 2 and 6 μm. The soils had few structural pores (>9 μm) and low air-filled porosity (>30 μm) before the growing season, which presented accessory reduction after the growing season in both fields. Total porosity was reduced at the expense of structural porosity along the soil profile, while the pore size class of 5–3 μm was identified as the threshold where the smaller pores’ volume started to increase in all layers of both fields. The results indicated that the changes in the WRC and the PSD follow specific trends, which can be used in future studies to model temporal variability of soil’s physical-hydraulic properties.     

Ferroelectric switching behavior of pulsed laser deposited Ba0.8Sr0.2TiO3 thin films

The effect of pulse amplitude on the ferroelectric and switching properties of pulsed laser deposited Ba_0.8Sr_0.2TiO₃ thin films has been studied. The structural and morphological analysis revealed that the films had a well crystallized perovskite phase and grain size of about 30–40 nm. A well saturated P–E hysteresis loop was observed with a remnant polarization (P_r) ≈ 4.8 μC/cm² and a coercive field ≈ 100 kV/cm at a frequency of 1 kHz. The P_r has been found to be decreased only 4.3% after passing 8.0 × 10⁸ cycles. The analysis of switching response with nucleation limited switching model reveals that characteristic switching time (t₀) variance is due to the random distribution of the local electric fields. The peak value of polarization current and t₀ exhibits exponential dependence on reciprocal of pulse amplitude.     

Ab initio many-body calculations of the (3)H(d,n)(4)He and (3)He(d,p)(4)He fusion reactions

We apply the ab initio no-core shell model combined with the resonating-group method approach to calculate the cross sections of the (3)H(d,n)(4)He and (3)He(d,p)(4)He fusion reactions. These are important reactions for the big bang nucleosynthesis and the future of energy generation on Earth. Starting from a selected similarity-transformed chiral nucleon-nucleon interaction that accurately describes two-nucleon data, we performed many-body calculations that predict the S factor of both reactions. Virtual three-body breakup effects are obtained by including excited pseudostates of the deuteron in the calculation. Our results are in satisfactory agreement with experimental data and pave the way for microscopic investigations of polarization and electron-screening effects, of the (3)H(d,γn)(4)He bremsstrahlung and other reactions relevant to fusion research.