Ab Initio H2O in Realistic Hydrophilic Confinement

A protocol for the ab initio construction of a realistic cylindrical pore in amorphous silica, serving as a geometric nanoscale confinement for liquids and solutions, is presented. Upon filling the pore with liquid water at different densities, the structure and dynamics of the liquid inside the confinement can be characterized. At high density, the pore introduces long‐range oscillations into the water density profile, which makes the water structure unlike that of the bulk across the entire pore. The tetrahedral structure of water is also affected up to the second solvation shell of the pore wall. Furthermore, the effects of the confinement on hydrogen bonding and diffusion, resulting in a weakening and distortion of the water structure at the pore walls and a slowdown in diffusion, are characterized.     

Second Comes First: Switching Elementary Steps in Palladium-Catalyzed Cross-Coupling Reactions

The electron-poor palladium(0) complex L₃Pd (L=tris[3,5-bis(trifluoromethyl)phenyl]phosphine) reacts with Grignard reagents RMgX and organolithium compounds RLi via transmetalation to furnish the anionic organopalladates [L₂PdR]⁻, as shown by negative-ion mode electrospray-ionization mass spectrometry. These palladates undergo oxidative additions of organyl halides R′X (or related S_N2-type reactions) followed by further transmetalation. Gas-phase fragmentation of the resulting heteroleptic palladate(II) complexes results in the reductive elimination of the cross-coupling products RR′. This reaction sequence corresponds to a catalytic cycle, in which the order of the elementary steps of transmetalation and oxidative addition is switched relative to that of palladium-catalyzed cross-coupling reactions proceeding via neutral intermediates. An attractive feature of the palladate-based catalytic system is its ability to mediate challenging alkyl–alkyl coupling reactions. However, the poor stability of the phosphine ligand L against decomposition reactions has so far prevented its successful use in practical applications.     

Nitride Spinel: An Ultraincompressible High‐Pressure Form of BeP2N4

Owing to its outstanding elastic properties, the nitride spinel γ‐Si₃N₄ is of considered interest for materials scientists and chemists. DFT calculations suggest that Si₃N₄‐analog beryllium phosphorus nitride BeP₂N₄ adopts the spinel structure at elevated pressures as well and shows outstanding elastic properties. Herein, we investigate phenakite‐type BeP₂N₄ by single‐crystal synchrotron X‐ray diffraction and report the phase transition into the spinel‐type phase at 47 GPa and 1800 K in a laser‐heated diamond anvil cell. The structure of spinel‐type BeP₂N₄ was refined from pressure‐dependent in situ synchrotron powder X‐ray diffraction measurements down to ambient pressure, which proves spinel‐type BeP₂N₄ a quenchable and metastable phase at ambient conditions. Its isothermal bulk modulus was determined to 325(8) GPa from equation of state, which indicates that spinel‐type BeP₂N₄ is an ultraincompressible material.     

The Dynamics of the Neuropeptide Y Receptor Type 1 Investigated by Solid-State NMR and Molecular Dynamics Simulation

We report data on the structural dynamics of the neuropeptide Y (NPY) G-protein-coupled receptor (GPCR) type 1 (Y1R), a typical representative of class A peptide ligand GPCRs, using a combination of solid-state NMR and molecular dynamics (MD) simulation. First, the equilibrium dynamics of Y1R were studied using ¹⁵N-NMR and quantitative determination of ¹H-¹³C order parameters through the measurement of dipolar couplings in separated-local-field NMR experiments. Order parameters reporting the amplitudes of the molecular motions of the C-H bond vectors of Y1R in DMPC membranes are 0.57 for the Cα sites and lower in the side chains (0.37 for the CH₂ and 0.18 for the CH₃ groups). Different NMR excitation schemes identify relatively rigid and also dynamic segments of the molecule. In monounsaturated membranes composed of longer lipid chains, Y1R is more rigid, attributed to a higher hydrophobic thickness of the lipid membrane. The presence of an antagonist or NPY has little influence on the amplitude of motions, whereas the addition of agonist and arrestin led to a pronounced rigidization. To investigate Y1R dynamics with site resolution, we conducted extensive all-atom MD simulations of the apo and antagonist-bound state. In each state, three replicas with a length of 20 μs (with one exception, where the trajectory length was 10 μs) were conducted. In these simulations, order parameters of each residue were determined and showed high values in the transmembrane helices, whereas the loops and termini exhibit much lower order. The extracellular helix segments undergo larger amplitude motions than their intracellular counterparts, whereas the opposite is observed for the loops, Helix 8, and termini. Only minor differences in order were observed between the apo and antagonist-bound state, whereas the time scale of the motions is shorter for the apo state. Although these relatively fast motions occurring with correlation times of ns up to a few µs have no direct relevance for receptor activation, it is believed that they represent the prerequisite for larger conformational transitions in proteins.     

Diffusion of Gold Nanoparticles in Inverse Opals Probed by Heterodyne Dynamic Light Scattering

The diffusive behavior of nanoparticles inside porous materials is attracting a lot of interest in the context of understanding, modeling, and optimization of many technical processes. A very powerful technique for characterizing the diffusive behavior of particles in free media is dynamic light scattering (DLS). The applicability of the method in porous media is considered, however, to be rather difficult due to the presence of multiple sources of scattering. In contrast to most of the previous approaches, the DLS method was applied without ensuring matching refractive indices of solvent and porous matrix in the present study. To test the capabilities of the method, the diffusion of spherical gold nanoparticles within the interconnected, periodic nanopores of inverse opals was analyzed. Despite the complexity of this system, which involves many interfaces and different refractive indices, a clear signal related to the motion of particles inside the porous media was obtained. As expected, the diffusive process inside the porous sample slowed down compared to the particle diffusion in free media. The obtained effective diffusion coefficients were found to be wave vector-dependent. They increased linearly with increasing spatial extension of the probed particle concentration fluctuations. On average, the slowing-down factor measured in this work agrees within combined uncertainties with literature data.

     

HILITE—A tool to investigate interactions of matter and light

Detailed investigations of laser–ion interactions require well-defined ion targets and detection techniques for high-sensitivity measurements of reaction educts and products. To this end, we have designed and built the High-Intensity Laser-Ion Trap Experiment Penning trap setup, which features various ion-target preparation techniques including selection, cooling, compression, and positioning as well as destructive and non-destructive measurement techniques to determine the number of stored ions for all charge states individually and simultaneously. We have recently performed first commissioning experiments of ion deceleration and dynamic ion capture with highly charged ion bunches from an electron beam ion source. We have characterized our single-pass non-destructive ion counter in detail and were able to determine the ion velocity as well as the number of ions from the signals acquired.     

Isotope Effect on Diffusion in Nafion Studied by NMR Diffusometry

Applied Magnetic Resonance - The isotope effect H → D on diffusion in proton-exchange membrane Nafion 212 is investigated using 1H and 2H nuclear magnetic resonance (NMR)...     

Effects of diclofenac on EPC liposome membrane properties

In this work the interaction of a non-steroidal anti-inflammatory drug (NSAID), diclofenac, with egg yolk phosphatidylcoline (EPC) liposomes, used as cell-membrane models, was quantified by determination of the partition coefficient. The liposome/aqueous phase partition coefficient was determined by derivative spectrophotometry, fluorescence quenching, and measurement of zeta-potential. Theoretical models based on simple partition of the diclofenac between two different media, were used to fit the experimental data, enabling the determination of K_p. The three techniques used yielded similar results. The effects of the interaction on the membranes characteristics were further evaluated, either by studying membrane potential changes or by effects on membrane fluidity. The liposome membrane potential and the size and size-homogeneity of liposomes were measured by light scattering. The effects of diclofenac on the internal viscosity or fluidity of the membrane were determined by use of spectroscopic probes—a series of n-(9-anthroyloxy) fatty acids in which the carboxyl terminal group is located at the interfacial region of the membrane and the fluorescent anthracene group is attached at different positions along the fatty acid chain. The location of the diclofenac on the membrane was also evaluated, by fluorescence quenching using the same series of fluorescent probes. Because the fluorescent anthracene group is attached at different positions along the fatty acid chain, it is possible to label at a graded series of depths in the bilayer. The interactions between the drug and the probe are a means of predicting the location of the drug on the membrane.     

Crystallographic and Computational Studies of Non-Covalent Interactions of Molecular Clips with a Series of Small Solvent Molecules

Molecular clips hold the potential of self-association and the ability to form host–guest complexes. Here we describe the synthesis of a 1,2-dimethoxyphenyl terminated glycoluril molecular clip (2) that binds with smaller solvent molecules by π?H–C and C=O?H–O non-covalent interactions. We obtained single crystals of 2 and 2 + CH₂Cl₂, CH₃OH, CH₃CN, and DMF solvents complexed within the clip. These solvents always form two π?H–C interactions between the aromatic rings in the clip, and CH₃OH formed an additional C=O?H–O hydrogen bond with the glycoluril carbonyl group. Based on single crystal data we found that π?H–C interactions of 2 + CH₂Cl₂ are stronger than 2 + CH₃CN and 2?+?DMF, due to the presence of stronger electron withdrawing groups in CH₂Cl₂, which lead to a decrease in dihedral angle of two glycoluril aromatic planes. We also investigated the non-covalent interaction energies of these solvent molecules with 2 using computational methods.

Graphical Abstract

Several solvent adducts of a glycoluril derivative have been isolated and characterized by single crystal X-ray diffraction, revealing two common pi?H–C non-covalent bonds within the molecular clip.

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