Achieving epitaxy between incommensurate materials by quasicrystalline interlayers

Epitaxial interfaces of commensurate periodic materials can be characterized by a locking into registry of their atomic structure. This characteristic is identified as a natural framework to capture the essence of epitaxy also for systems including quasicrystalline materials. The resulting general definition for epitaxy requires a matching of reciprocal lattice points. The consequences for the real space structure of an epitaxial interface between quasiperiodic and periodic materials are explored and an experimental realization of such an interface is presented. It is demonstrated that due to their higher number of reciprocal lattice basis vectors (exceeding three), quasicrystals can provide interlayers epitaxially linking incommensurate materials.     

Modeling the 2-His-1-carboxylate facial triad: iron-catecholato complexes as structural and functional models of the extradiol cleaving dioxygenases

Mononuclear iron(II)- and iron(III)-catecholato complexes with three members of a new 3,3-bis(1-alkylimidazol-2-yl)propionate ligand family have been synthesized as models of the active sites of the extradiol cleaving catechol dioxygenases. These enzymes are part of the superfamily of dioxygen-activating mononuclear non-heme iron enzymes that feature the so-called 2-His-1-carboxylate facial triad. The tridentate, tripodal, and monoanionic ligands used in this study include the biologically relevant carboxylate and imidazole donor groups. The structure of the mononuclear iron(III)-tetrachlorocatecholato complex [Fe(L3)(tcc)(H2O)] was determined by single-crystal X-ray diffraction, which shows a facial N,N,O capping mode of the ligand. For the first time, a mononuclear iron complex has been synthesized, which is facially capped by a ligand offering a tridentate Nim,Nim,Ocarb donor set, identical to the endogenous ligands of the 2-His-1-carboxylate facial triad. The iron complexes are five-coordinate in noncoordinating media, and the vacant coordination site is accessible for Lewis bases, e.g., pyridine, or small molecules such as dioxygen. The iron(II)-catecholato complexes react with dioxygen in two steps. In the first reaction the iron(II)-catecholato complexes rapidly convert to the corresponding iron(III) complexes, which then, in a second slow reaction, exhibit both oxidative cleavage and auto-oxidation of the substrate. Extradiol and intradiol cleavage are observed in noncoordinating solvents. The addition of a proton donor results in an increase in extradiol cleavage. The complexes add a new example to the small group of synthetic iron complexes capable of eliciting extradiol-type cleavage and provide more insight into the factors determining the regioselectivity of the enzymes.     

Enantioselective chemisorption of propylene oxide on a 2-butanol modified Pd(111) surface: the role of hydrogen-bonding interactions

The enantioselective chemisorption of R- and S-propylene oxide has been measured either on clean Pd(111) that has been exposed to S-2-butanol at various temperatures to vary the proportion of 2-butanol and 2-butoxide species or by adsorbing S-2-butanol on oxygen-covered Pd(111) to form exclusively 2-butoxide. The results reveal that enantioselective chemisorption is only found when 2-butanol is present on the surface. This is ascribed to enantiospecific hydrogen-bonding interactions between 2-butanol and propylene oxide. Measurements of the variation in enantiospecificity with 2-butanol exposure suggest that propylene oxide can interact either with a single adsorbed 2-butanol molecule or, at higher coverages, with two adsorbed 2-butanol species to form enantioselective sites.     

Enveloping distribution sampling: a method to calculate free energy differences from a single simulation

The authors present a method to calculate free energy differences between two states A and B "on the fly" from a single molecular dynamics simulation of a reference state R. No computer time has to be spent on the simulation of intermediate states. Only one state is sampled, i.e., the reference state R which is designed such that the subset of phase space important to it is the union of the parts of phase space important to A and B. Therefore, an accurate estimate of the relative free energy can be obtained by construction. The authors applied the method to four test systems (dipole inversion, van der Waals interaction perturbation, charge inversion, and water to methanol conversion) and compared the results to thermodynamic integration estimates. In two cases, the enveloping distribution sampling calculation was straightforward. However, in the charge inversion and the water to methanol conversion, Hamiltonian replica-exchange molecular dynamics of the reference state was necessary to observe transitions in the reference state simulation between the parts of phase space important to A and B, respectively. This can be explained by the total absence of phase space overlap of A and B in these two cases.     

Haloduracin α binds the peptidoglycan precursor lipid II with 2:1 stoichiometry

The two-peptide lantibiotic haloduracin is composed of two post-translationally modified polycyclic peptides that synergistically act on gram-positive bacteria. We show here that Halα inhibits the transglycosylation reaction catalyzed by PBP1b by binding in a 2:1 stoichiometry to its substrate lipid II. Halβ and the mutant Halα-E22Q were not able to inhibit this step in peptidoglycan biosynthesis, but Halα with its leader peptide still attached was a potent inhibitor. Combined with previous findings, the data support a model in which a 1:2:2 lipid II:Halα:Halβ complex inhibits cell wall biosynthesis and mediates pore formation, resulting in loss of membrane potential and potassium efflux.     

Free energy calculations offer insights into the influence of receptor flexibility on ligand–receptor binding affinities

Docking algorithms for computer-aided drug discovery and design often ignore or restrain the flexibility of the receptor, which may lead to a loss of accuracy of the relative free enthalpies of binding. In order to evaluate the contribution of receptor flexibility to relative binding free enthalpies, two host–guest systems have been examined: inclusion complexes of α-cyclodextrin (αCD) with 1-chlorobenzene (ClBn), 1-bromobenzene (BrBn) and toluene (MeBn), and complexes of DNA with the minor-groove binding ligands netropsin (Net) and distamycin (Dist). Molecular dynamics simulations and free energy calculations reveal that restraining of the flexibility of the receptor can have a significant influence on the estimated relative ligand–receptor binding affinities as well as on the predicted structures of the biomolecular complexes. The influence is particularly pronounced in the case of flexible receptors such as DNA, where a 50% contribution of DNA flexibility towards the relative ligand–DNA binding affinities is observed. The differences in the free enthalpy of binding do not arise only from the changes in ligand–DNA interactions but also from changes in ligand–solvent interactions as well as from the loss of DNA configurational entropy upon restraining.     

A quantum-dot based protein module for in vivo monitoring of protease activity through fluorescence resonance energy transfer

Here, we present a new generation of nanoscale probes for in vivo monitoring of protease activity by fluorescence resonance energy transfer (FRET). The approach is based on a genetically programmable protein module carrying a fluorescently labeled, protease-specific sequence that can self-assemble onto quantum dots. The protein module was used for real-time detection of human immunodeficiency virus type-1 protease (HIV-1 Pr) activity as well as quantitative assessment of inhibitor efficiency.     

Towards the Development of a Selective Ruthenium‐Catalyzed Hydroformylation of Olefins

The ruthenium‐catalyzed hydroformylation of 1‐ and 2‐octene to give preferentially the corresponding linear aldehyde is reported. The catalyst system comprising of Ru₃(CO)₁₂ and an imidazole‐substituted monophosphine ligand allows for high chemo‐ and regioselectivity. The hydroformylation proceeds with unprecedented rates for a ruthenium‐based catalyst.