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The separation of trivalent actinides and lanthanides is a key step in the sustainable development of nuclear energy, and it is currently mainly realized via liquid–liquid extraction techniques. The underlying mechanism is complicated and remains ambiguous, which hinders the further development of extraction. Herein, to better understand the mechanism of the extraction, the contributing factors for the extraction are discussed (specifically, the sulfur-donating ligand, Cyanex301) by combing molecular dynamics simulations and experiments. This work is expected to contribute to improve our systematic understanding on a molecular scale of the extraction of lanthanides and actinides, and to assist in the extensive studies on the design and optimization of novel ligands with improved performance. [ABSTRACT FROM AUTHOR]

The octadentate hydroxypyridonate ligand 3,4,3-LI(1,2-HOPO) (t-HOPO) shows strong binding affinity with actinide cations and is considered as a promising decorporation agent used to eliminate in vivo actinides, while its dynamics in its unbound and bound states in the condensed phase remain unclear. In this work, by means of MD simulations, the folding dynamics of intact t-HOPO in its neutral (t-HOPO0) and in its deprotonated state (t-HOPO4−) were studied. The results indicated that the deprotonation of t-HOPO in the aqueous phase significantly narrowed the accessible conformational space under the simulated conditions, and it was prepared in a conformation that could conveniently clamp the cations. The simulation of UIV-t-HOPO showed that the tetravalent uranium ion was deca-coordinated with eight ligating O atoms from the t-HOPO4− ligand, and two from aqua ligands. The strong electrostatic interaction between the U4+ ion and t-HOPO4− further diminished the flexibility of t-HOPO4− and confined it in a limited conformational space. The strong interaction between the U4+ ion and t-HOPO4− was also implicated in the shortened residence time of water molecules. [ABSTRACT FROM AUTHOR]

Cyanex301 is considered as an important extractant in liquid–liquid extraction, while its dynamics in condensed phase remains unclear. By means of molecular dynamics simulations, the biphasic behavior of Cyanex301 in water–toluene binary solvents is addressed and compared to that of its two analogs, Cyanex272 and Cyanex302. The simulations shows that deprotonated ligands retard the de‐mixing of the binary solvents compared to their neutral counterparts, but display higher surface activity, and assemble in a more orderly manner at the interface. Increasing their concentrations results in the formation of microtubule‐like structures to maximize their contact with aqueous phase, which is not observed for their native states. The presence of counterion Na+ "salts out" ligands and enhances their distribution at the interface. This work complements experimental studies of the ligands with details of their conformations and distributions at the molecular level, and is expected to contribute to the extensive development of their applications in hydrometallurgy. [ABSTRACT FROM AUTHOR]

The adsorption of [UO2(H2O)5]2+ on a hydroxylated α-SiO2(001) surface was studied by periodic density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulation. The effects of pH, CO2, aqua solution and anionic ligands (OH−, NO3− and Cl−) on the adsorption geometry and stability were investigated. The results show that the adsorption of uranyl on a hydroxylated α-SiO2(001) surface leads to the formation of inner-sphere complexes, in which the bidentate complex at the double deprotonated site is most favored. The binding strengths of bidentate and monodentate complexes at the same site are similar, and they become weaker as the number of protons increases at the adsorption site, indicating an enhancement of the adsorption strength at higher pH values within a certain range. Strong chemical interaction plays an important role in all inner-sphere complexes. The hydrogen bonds are formed between uranyl and the hydroxylated surface in all inner- and outer-sphere complexes. The presence of CO2 weakens the adsorption of uranyl on the surface by forming uranyl carbonate (CO32−, HCO3−) complexes. The effect of the anion ligands depends on their charged state and their concentration in solutions. The explicit treatment of water environment in the models has a slight effect on the adsorption configuration. These results are consistent with the experimental observations. [ABSTRACT FROM AUTHOR]

A diverse superfamily of phospholipases consisting of the type VI lipase effectors Tle1-Tle5 secreted by the bacterial type VI secretion system (T6SS) have recently been identified as antibacterial effectors that hydrolyze membrane phospholipids. These effectors show no significant homology to known lipases, and their mechanism of membrane targeting and hydrolysis of phospholipids remains unknown. Here, the crystal structure of Tle1 (∼96.5 kDa) from Pseudomonas aeruginosa refined to 2.0 Å resolution is reported, representing the first structure of this superfamily. Its overall structure can be divided into two distinct parts, the phospholipase catalytic module and the putative membrane-anchoring module; this arrangement has not previously been observed in known lipase structures. The phospholipase catalytic module has a canonical α/β-hydrolase fold and mutation of any residue in the Ser-Asp-His catalytic triad abolishes its toxicity. The putative membrane-anchoring module adopts an open conformation composed of three amphipathic domains, and its partial folds are similar to those of several periplasmic or membrane proteins. A cell-toxicity assay revealed that the putative membrane-anchoring module is critical to Tle1 antibacterial activity. A molecular-dynamics (MD) simulation system in which the putative membrane-anchoring module embedded into a bilayer was stable over 50 ns. These structure-function studies provide insight into the hydrolysis and membrane-targeting process of the unique phospholipase Tle1. [ABSTRACT FROM AUTHOR]

A molecular-dynamics (MD) simulation study of two heptapeptides containing α- and β-amino acid residues is presented. According to NMR experiments, the two peptides differ in dominant fold when solvated in MeOH: peptide 3 adopts predominantly β-hairpin-like conformations, while peptide 8 adopts a 14/ 15-helical fold. The MD simulations largely reproduce the experimental data. Application of NOE atomatom distance restraining improves the agreement with experimental data, but reduces the conformational sampling. Peptide 3 shows a variety of conformations, while still agreeing with the NOE and 3 J-coupling data, whereas the conformational ensemble of peptide 8 is dominated by one helical conformation. The results confirm the suitability of the GROMOS 54A7 force field for simulation or structure refinement of mixed α/ β-peptides in MeOH. [ABSTRACT FROM AUTHOR]

Abstract: The substrate bound heme-O2 complexes (ferrous dioxygen, S4 and ferric peroxo, S5) of P450cam (CYP101) have been studied by combined quantum mechanical/molecular mechanical (QM/MM) calculations. The oxyheme (without side chains) is treated with density functional theory and the protein/solvent environment by the CHARMM22 force field. The B3LYP/CHARMM calculations are found to give reasonable descriptions of the oxyheme complexes. An open-shell singlet is predicted to be the ground state for S4 with small energy separations to the excited states. This result is consistent with previous experimental and QM studies. Comparisons with analogous calculations on the isolated QM system in the gas phase show that the protein/solvent environment reduces the open-shell singlet-quintet energy gap which should facilitate the spin inversion upon the binding of the atmospheric oxygen. An intact ferric peroxo complex S5 is found only in the doublet state whereas the quartet and sextet states dissociate upon QM/MM optimization (uncoupling). [Copyright &y& Elsevier]

Abstract In this paper, the influence of humic acid (HA) and fulvic acid (FA) on biomineralization behaviour was evaluated. The results showed HA and FA did not obviously inhabit or promote the precipitation of U-phosphate minerals. The data from molecular dynamic simulation indicated that the free energy for the dissociation of uranyl the PO 4 3− -uranyl was 202.49 kJ/mol, which was much larger than that form HA-uranyl (88.3 kJ/mol). These simulated results revealed the less competitiveness of HA and FA with PO 4 3− for uranyl and explained why HA and FA had less impacted on the formation of U-phosphate minerals. However, the influence of HA/FA on the morphology was obvious, the microstructure of the bio-minerals changed from small particles to lamellar stacking structure with the addition of HA or FA. The findings of this study are helpful for us to gain a better understanding natural U-phosphate biomineralization behaviour. High lights • The influence of humic/fulvic acid on U-biomineralization was firstly discussed. • The humic/fulvic acid hadn't a decided impact on the U-phosphate precipitation. • The main effects of humic/fulvic acid on U-biomineralization reflected on morphology. • The introduction of humic and fulvic acid could promote the grain refinement. • The complexion of uranyl with phosphate was calculated by molecular dynamics method. [ABSTRACT FROM AUTHOR]

The cyclic octa-peptide octreotide and its derivatives are used as diagnostics and therapeutics in relation to particular types of cancers. This led to investigations of their conformational properties using spectroscopic, NMR and CD, methods. A CF 3 -substituted derivative, that was designed to stabilize the dominant octreotide conformer responsible for receptor binding, turned out to have a lower affinity. The obtained spectroscopic data were interpreted as to show an increased flexibility of the CF 3 derivative compared to the unsubstituted octreotide, which could then explain the lower affinity. In this article, we use MD simulation without and with time-averaged NOE distance and time-averaged local-elevation 3 J -coupling restraining representing experimental NMR data to determine the conformational properties of the different peptides in the different solvents for which experimental data are available, that are compatible with the NOE atom–atom distance bounds and the 3 J HNHα -couplings as derived from the NMR measurements. The conformational ensembles show that the CF 3 substitution in combination with the change of solvent from water to methanol leads to a decrease in flexibility and a shift in the populations of the dominant conformers that are compatible with the experimental data. [ABSTRACT FROM AUTHOR]