Dynamics of polydisperse hard-spheres under strong confinement

We use molecular simulation to probe the connection between local structure and the unusual re-entrant dynamics observed for polydisperse hard-sphere liquids confined in thin slit pores. The local structure is characterised by calculating 2-D bond-orientational order parameters associated with square and hexatic order for particles in the layer adjacent to the confining walls. When the wall separation is commensurate with the average particle size, the particles primarily exhibit local hexatic order, whereas local square order increases in prevalence for incommensurate geometries. The relaxation time extracted from the ensemble-averaged mean-square displacement increases exponentially with the static correlation length associated with hexatic local order in strongly confined commensurate geometries, in agreement with theoretical predictions for dynamical slowing. Square order, by contrast, is not associated with a growing length scale for either commensurate or incommensurate geometries, indicating that it is strongly geometrically frustrated. Our results suggest that the influence of bond-orientational order on dynamical slowing may be altered by changing the extent of confinement.     

Decoding the components of dynamics in three‐domain proteins

In this study, we examine the feasibility and limitations of describing the motional behavior of three‐domain proteins in which the domains are linearly connected. In addition to attempting the determination of the internal and overall reorientational correlation times, we investigate the existence of correlations in the motions between the three domains. Since in linearly arranged three‐domain proteins, there are typically no experimental data that can directly report on motional correlation between the first and the third domain, we address this question by dynamics simulations. Two limiting cases occur: (1) for weak repulsive potentials and (2) when strong repulsive potentials are applied between sequential domains. The motions of the terminal domains become correlated in the case of strong interdomain repulsive potentials when these potentials do not allow the angle between the sequential domains to be smaller than about 60°. Using the model‐free (MF) and extended MF formalisms of Lipari and Szabo, we find that the motional behavior can be separated into two components; the first component represents the concerted overall motion of the three domains, and the second describes the independent component of the motion of each individual domain. We find that this division of the motional behavior of the protein is maintained only when their timescales are distinct and can be made when the angles between sequential domains remain between 60° and 160°. In this work, we identify and quantify interdomain motional correlations. © 2013 Wiley Periodicals, Inc.     

Synthesis of μ2-Oxo-Bridged Iron(III) Tetraphenylporphyrin–Spacer–Nitroxide Dimers and their Structural and Dynamics Characterization by using EPR and MD Simulations

Iron(III) porphyrins have the propensity to form μ₂-oxo-dimers, the structures of which resemble two wheels on an axle. Whereas their crystal structure is known, their solution structure and internal dynamics is not. In the present work, the structure and dynamics of such dimers were studied by means of electron paramagnetic resonance (EPR) spectroscopy and quantum chemistry based molecular dynamics (MD) simulations by using the semiempirical tight-binding method (GFN-xTB). To enable EPR investigation of the dimers, a nitroxide was attached to each of the tetraphenylporphyrin cores through a linear and a bent linker. The inter-nitroxide distance distributions within the dimers were determined by continuous-wave (cw)-EPR and pulsed electron–electron double resonance (PELDOR or DEER) experiments and, with the help of MD, interpreted in terms of the rotation of the porphyrin planes with respect to each other around the Fe–O–Fe axis. It was found that such rotation is restricted to the four registers defined by the phenyl substituents. Within the registers, the rotation angle swings between 30° and 60° in the proximal and between 125° and 145° in the distal register. With EPR, all four angles were found to be equally populated, whereas the 30° and 145° angles are strongly favored to the expense of the 60° and 125° angles in the MD simulation. In either case, the internal dynamics of these dimers thus resemble the motion of a step motor.     

Ceramic fuel cells using novel proton-conducting BaCe0.5Zr0.3Y0.1Yb0.05Zn0.05O3-δ electrolyte

Journal of Solid State Electrochemistry - Protonic ceramic fuel cells have become extremely interesting due to their high power output at the intermediate temperature range...     

Reversed-phase liquid chromatography coupled on-line to estrogen receptor bioaffinity detection based on fluorescence polarization

We describe the development and validation of a high-resolution screening (HRS) platform which couples gradient reversed-phase high-performance liquid chromatography (RP-HPLC) on-line to estrogen receptor α (ERα) affinity detection using fluorescence polarization (FP). FP, which allows detection at high wavelengths, limits the occurrence of interference from the autofluorescence of test compounds in the bioassay. A fluorescein-labeled estradiol derivative (E2-F) was synthesized and a binding assay was optimized in platereader format. After subsequent optimization in flow-injection analysis (FIA) mode, the optimized parameters were translated to the on-line HRS bioassay. Proof of principle was demonstrated by separating a mixture of five compounds known to be estrogenic (17β-estradiol, 17α-ethinylestradiol and the phytoestrogens coumestrol, coumarol and zearalenone), followed by post-column bioaffinity screening of the individual affinities for ERα. Using the HRS-based FP setup, we were able to screen affinities of off-line-generated metabolites of zearalenone for ERα. It is concluded that the on-line FP-based bioassay can be used to screen for the affinity of compounds without the disturbing occurrence of autofluorescence.     

Can a synthetic thread act as an electrochemically switchable molecular device?

Here we report that at room temperature in acetonitrile after the reduction of the naphthalimide-site, a synthetic molecular thread undergoes a complete conformational change which makes possible an efficient conversion of chemical energy into mechanical work; such results point out the ability of the thread to act as a molecular device under electrochemical control.     

Electricity generation by an enriched phototrophic consortium in a microbial fuel cell

Microbial fuel cell (MFC) technology is a novel electricity generation process catalyzed by microorganisms. Much progress is made in the design and construction of MFCs, however the diversity of the electrochemically active microorganisms and the electricity generation mechanisms remain a black box. As sun is a predominantly unused energy resource, here we present a highly enriched phototrophic consortium that can produce electricity in an “H” typed MFC at a high power density (2650 mW m⁻², normalized to membrane area) in light, which was eightfold of that produced by non-enriched consortium in the same reactor. Light–dark shift experiments showed that light contributed to the electricity generation. A microbial excreted mediator assisted the electron transfer to the electrode. During the experiment, the accumulation of the mediator over time enhanced the electron transfer rate. The excitation–emission matrix fluorescence spectroscopy results indicated indole group containing compound representing the dominant mediator component.     

Conjugation of nucleosides and oligonucleotides by [3+2] cycloaddition

A procedure is presented for copper(I)-catalyzed [3+2] cycloaddition of nucleosides and nucleotides in near-quantitative yield. Azido-alkyne cycloaddition was applied for the preparation of a range of adenosine dimers and derivatives with versatile functionality, as well as for the smooth condensation of two oligonucleotide strands. The described technology may find valuable application in the synthesis of oligonucleotide dimers and conjugates.