Kleinbundgaard9667

However, in the neighboring disordered domains, their C-termini penetrate deeper into the lipid bilayer. We conclude that local membrane order determines not only the affinity but also the mode of interaction of amyloid oligomers, which may have significant implications for disease mechanisms.Molecular dynamics (MD) simulations of biological membranes have achieved such levels of sophistication that are commonly used to predict unresolved structures and various properties of lipids and to substantiate experimental data. While achieving sufficient sampling of lipid dynamics remains a major challenge, a commonly used method to improve lipid sampling, e.g., in terms of specific interactions with membrane-associated proteins, is to randomize the initial arrangement of lipid constituents in multiple replicas of simulations, without changing the overall lipid composition of the membrane of interest. Here, we introduce a method that can rapidly generate multiple replicas of lipid bilayers with different spatial and conformational configurations for any given lipid composition. The underlying algorithm, which allows one to shuffle lipids at any desired level, relies on the application of an external potential, here referred to as the "carving potential", that removes clashes/entanglements before lipid positions are exchanged (shuffled), thereby minimizing the energy penalty due to abrupt lipid repositioning. The method is implemented as "Membrane Mixer Plugin (MMP) 1.0" in VMD, with a convenient graphical user interface that guides the user in setting various options and parameters. The plugin is fully automated and generates new membrane replicas more rapidly and conveniently than other analogous tools. The plugin and its capabilities introduced here can be extended to include additional features in future versions.The temperature-dependent X-ray emission spectra of liquid ethanol were calculated theoretically using a semi-classical approximation to the Kramers-Heisenberg formula, which includes the dynamical effects induced by a core-hole. Soft X-ray emission spectroscopic measurements were performed to discern the changes in the hydrogen bonding (h-bonding) structure of liquid ethanol using a temperature-controlled liquid cell at 241 and 313 K. The relative intensities of the peaks at approximately 526.5 and 527.1 eV varied with temperature, and the corresponding behavior was reproduced theoretically, although the variation with temperature in the calculated spectra were more enhanced than that in the experiment. The two peaks can be attributed to the 3a″ + 10a' mixed state and pure 3a″ state, respectively, depending on the behavior of the local h-bonding structure. The splitting of the 3a″ component occurred because of the h-bonding behavior of liquid ethanol. Furthermore, the size of the ethanol cluster decreased with an increase in temperature, mainly due to the breaking of the one-donor/one-acceptor type h-bonding. Our studies suggest that the electronic state of liquid ethanol reflects several types of h-bonding structures, and the ratios of these h-bonding types vary with temperature.The chemical bond between a transition metal and a methyl group (M-CH3) is typically defined as a single covalent bond, which is of fundamental significance and general interest in understanding the structural properties and reactivity of transition metal alkyl compounds. Herein, we demonstrate that the M-CH3 bonding involves varying σ and π components and thus should be best described in terms of the partial double M═CH3 bond. The often-neglected π bonding stems from an occupied π-symmetric orbital of the methyl group comprising all three C-H σ bonds (but one C-H' contributes more than the other two) and a vacant low-lying metal d(π) orbital, and is associated with the intramolecular C-H'···M agostic effect (i.e., an acute M-C-H' angle and a short H'···M distance), whose origin is still controversial. We quantify the geometric and energetic impacts of the π interaction involved in the M-CH3 bond by explicitly computing the intramolecular πCH' → dM interaction with the ab initio valence bond (VB) theory. Our computations of the ligand-free [TiCH3]3+ and a series of metallocene catalysts provide a direct proof for the presence of the π bonding in M-CH3 bonds, which is the cause for the agostic effect. The partial double M═CH3 bonding model is not only validated by a range of bonding analyses including VB self-consistent field (VBSCF)-based energy decomposition and quantum theory of atoms in molecules (QTAIM) but also authenticated by the specific activity of double M═CH3 bonds in the C-H activation and olefin insertion. More importantly, the σ bond gradually switches from a classical covalent bond to a novel charge-shift bond with the π bonding becoming increasingly significant. We anticipate that the recognition of the π interaction between electrophilic metal centers and C-H bonds can benefit the understanding of the nature of metal-carbon bonds in transition metal ethyl, alkyl, and carbene compounds.Vacancy and doping engineering are promising pathways to improve the electrocatalytic ability of nanomaterials for detecting heavy metal ions. However, the effects of the electronic structure and the local coordination on the catalytic performance are still ambiguous. Herein, cubic selenium vacancy-rich CoSe2 (c-CoSe2-x) and P-doped orthorhombic CoSe2-x (o-CoSe2-x|P) were designed via vacancy and doping engineering. An o-CoSe2-x|P-modified glass carbon electrode (o-CoSe2-x|P/GCE) acquired a high sensitivity of 1.11 μA ppb-1 toward As(III), which is about 40 times higher than that of c-CoSe2-x, outperforming most of the reported nanomaterial-modified glass carbon electrodes. Besides, o-CoSe2-x|P/GCE displayed good selectivity toward As(III) compared with other divalent heavy metal cations, which also exhibited excellent stability, repeatability, and practicality. X-ray absorption fine structure spectroscopy and density functional theory calculation demonstrate that electrons transferred from Co and Se to P sites through Co-P and Se-P bonds in o-CoSe2-x|P. P sites obtained plentiful electrons to form active centers, which also had a strong orbital coupling with As(III). In the detection process, As(III) was bonded with P and reduced by the electron-rich sites in o-CoSe2-x|P, thus acquiring a reinforced electrochemical sensitivity. This work provides an in-depth understanding of the influence of the intrinsic physicochemical properties of sensitive materials on the behavior of electroanalysis, thus offering a direct guideline for creating active sites on sensing interfaces.MA'AT analysis has been applied to methyl β-d-ribofuranoside (3) and methyl 2-deoxy-β-d-erythro-pentofuranoside (4) to demonstrate the ability of this new experimental method to determine multi-state conformational equilibria in solution. Density functional theory (DFT) was used to obtain parameterized equations for >20 NMR spin-coupling constants sensitive to furanose ring conformation in 3 and 4, and these equations were used in conjunction with experimental spin-couplings to produce unbiased MA'AT models of ring pseudorotation. These models describe two-state north-south conformational exchange consistent with results obtained from traditional treatments of more limited sets of NMR spin-couplings (e.g., PSEUROT). While PSEUROT, MA'AT, and aqueous molecular dynamics models yielded similar two-state models, MA'AT analysis gives more reliable results since significantly more experimental observables are employed compared to PSEUROT, and no assumptions are needed to render the fitting tractable. MA'AT models indicate a roughly equal distribution of north and south ring conformers of 4 in aqueous (2H2O) solution compared to ∼80% north forms for 3. Librational motion about the mean pseudorotation phase angles P of the preferred north and south conformers of 3 in solution is more constrained than that for 4. The greater rigidity of the β-ribo ring may be caused by synergistic stereoelectronic effects and/or noncovalent (e.g., hydrogen-bonding) interactions in solution that preferentially stabilize north forms of 3. MA'AT analysis of oligonucleotides and other furanose ring-containing biomolecules promises to improve current experimental models of sugar ring behavior in solution and help reveal context effects on ring conformation in more complex biologically important systems.Controllable regulation of enzyme activity is an important prerequisite for the in-depth application of enzymes, especially in today's intelligent era. However, irreversible regulation and cumbersome operation make this goal difficult to achieve. see more Here, by adopting magnetism and a harmless, noncontact, and time- and space-controllable physical element, we developed a system that could conveniently and reversibly regulate the activity of DNAzyme. In this system, the strands of the DNAzyme could be stretched or folded by applying or removing a magnetic field. Thereby, the conformation-dependent endonuclease activity of the DNAzyme could be facilely switched between an "OFF" and "ON" state. This system provides a reusable platform for the control of enzyme catalytic activity through magnetism, which provides guidance for further application in some related scientific research, especially the regulation of the activity of conformation-dependent polymers (DNAzymes, aptamers, and peptides).Iron phosphide nanoparticles (NPs) are promising noble metal-free electrocatalysts for the hydrogen evolution reaction (HER), but they usually show inferior activity due to the limited surface area and oxidative passivation. We reported a facile synthetic method to prepare FeP hollow NPs (HNPs) with various precursors. It was proven that the structural parameters (i.e., size, phosphating temperature, phase, and surfactant) of oxide precursors were correlated to the electrochemically active surface area (ECSA), phase purity, surface oxidation, and hollow morphology of FeP HER catalysts, thus affecting the HER activity. Among the three FeP HNPs, the 9 nm FeP HNPs prepared using the Fe3O4 precursor exhibited the highest overall activity with the lowest overpotential of 76 mV to drive a cathodic current density of 10 mA·cm-2 due to the highest ECSA, while 25 nm FeP prepared using the Fe2O3 precursor showed the highest turnover frequency because of the high phase purity and low surface oxidation degree.Renewable power-derived green hydrogen distributed via natural gas networks is considered one of the viable routes to drive the decarbonization of transportation and distributed power generation, while a trace amount of sulfur impurities is one of the key factors that affect the durability and life cycle expense of proton-exchange membrane fuel cells (PEMFCs) for end users. Herein, we explore the underlying effect of sulfur resistance for Pt-based hydrogen oxidation reaction (HOR) electrocatalysts devoted to high-performance and durable PEMFCs. Two typical electrocatalysts, Pt/C with pure Pt nanoparticles (NPs) and PtCo/C with Pt3Co-alloy-core-Pt-skin NPs, were investigated to demonstrate the structure-property relation for Pt-based electrocatalysts. It was revealed that the PtCo/C demonstrated alleviated sulfur poisoning with the adsorption rate constant reduced by 21.7% compared with Pt/C, and the desorption of the adsorbed sulfur was also more favorable with Pt-S bond decomposition temperature lowered by approximately 25 °C.