Time-dependent DFT studies of metal core-electron excitations in Mn complexes

Time-dependent density functional theory (TDDFT) has been applied to study core excitations from 1s and 2p Mn orbitals in a series of manganese complexes with oxygen and nitrogen donor ligands. The effect of basis set and functional on the excitation energy was evaluated in detail for one complex, Mn(acac)2 x (H2O)2. The results obtained for a range of compounds, namely, [Mn(Im)6]Cl2, Mn(CH3COO)2 x 4 H2O, Mn(acac)3, Mn(SALADHP)2 and [Mn(SALPN)O]2, show good consistency with the data from X-ray absorption spectroscopy (XAS), confirming the relation between the Mn K-edge energy and the oxidation state of the Mn atom. The energies predicted for 2p core excitations show a dependence on the metal oxidation state very similar to that determined experimentally by 1s2p resonant inelastic X-ray scattering (RIXS) studies for Mn(acac)2 x (H2O)2, Mn(acac)3, and Mn(sal)2(bipy). The reliability of the K-edge energies obtained in the present study indicates that TDDFT can be used in determining the oxidation states of Mn atoms in different computational models of the manganese cluster of photosystem II (PSII).     

Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds

We conduct computational analyses of ion permeation characteristics in a model glycine receptor (GlyR) modified by photo-sensitive compounds. In particular, we consider hypothetical attachment to the channel of charge-neutral chemical groups which can be photo-activated by shining light of an appropriate wavelength on the system. After illumination, the attached molecules become charged via a photodissociation process or excited into a charge-separated state (thus generating a significant electric dipole). We carry out Brownian Dynamics simulations of ion flow through the channel in the presence of the additional charges generated in this fashion. Based on these calculations, we predict that photo-activation of appropriately positioned photo-sensitive compounds near the channel mouth can significantly modify the rate of ion permeation and the current rectification ratio. Possible implications for GlyR-based device designs are briefly discussed.     

Strong inhibition of cholera toxin binding by galactose dendrimers

Galactose-containing dendrimers with long spacer arms inhibit cholera toxin binding as strongly as the natural ganglioside GM1 oligosaccharide does.     

Measuring flux distributions for diffusion in the small-numbers limit

For the classical diffusion of independent particles, Fick's law gives a well-known relationship between the average flux and the average concentration gradient. What has not yet been explored experimentally, however, is the dynamical distribution of diffusion rates in the limit of small particle numbers. Here, we measure the distribution of diffusional fluxes using a microfluidics device filled with a colloidal suspension of a small number of microspheres. Our experiments show that (1) the flux distribution is accurately described by a Gaussian function; (2) Fick's law, that the average flux is proportional to the particle gradient, holds even for particle gradients down to a single particle difference; (3) the variance in the flux is proportional to the sum of the particle numbers; and (4) there are backward flows, where particles flow up a concentration gradient, rather than down it. In addition, in recent years, two key theorems about nonequilibrium systems have been introduced: Evans' fluctuation theorem for the distribution of entropies and Jarzynski's work theorem. Here, we introduce a new fluctuation theorem, for the fluxes, and we find that it is confirmed quantitatively by our experiments.     

Investigating direct current potentials that affect native protein conformation during trapped ion mobility spectrometry–mass spectrometry

Trapped ion mobility spectrometry–time-of-flight mass spectrometry (TIMS-TOFMS) has emerged as a tool to study protein conformational states. In TIMS, gas-phase ions are guided across the IM stages by applying direct current (DC) potentials (D1–6), which, however, might induce changes in protein structures through collisional activation. To define conditions for native protein analysis, we evaluated the influence of these DC potentials using the metalloenzyme bovine carbonic anhydrase (BCA) as primary test compound. The variation of DC potentials did not change BCA-ion charge and heme content but affected (relative) charge-state intensities and adduct retention. Constructed extracted-ion mobilograms and corresponding collisional cross-section (CCS) profiles gave useful insights in (alterations of) protein conformational state. For BCA, the D3 and D6 potential (which are applied between the deflection transfer and funnel 1 [F1] and the accumulation exit and the start of the ramp, respectively) had most profound effects, showing multimodal CCS distributions at higher potentials indicating gradual unfolding. The other DC potentials only marginally altered the CCS profiles of BCA. To allow for more general conclusions, five additional proteins of diverse molecular weight and conformational stability were analyzed, and for the main protein charge states, CCS profiles were constructed. Principal component analysis (PCA) of the obtained data showed that D1 and D3 exhibit the highest degree of correlation with the ratio of folded and unfolded protein (F/U) as extracted from the mobilograms obtained per set D potential. The correlation of D6 with F/U and protein charge were similar, and D2, D4, and D5 showed an inverse correlation with F/U but were correlated with protein charge. Although DC boundary values for induced conformational changes appeared protein dependent, a set of DC values could be determined, which assured native analysis of most proteins.     

Intrinsic relaxation rates of polarized Cs vapor in miniaturized cells

The intrinsic relaxation rates of the vector magnetization of cesium vapor enclosed in microfabricated atomic magnetometer cells are investigated. Two methods—the optically detected magnetic resonance and the ground-state Hanle effect—are used to carry out automated measurements in dependence on cell temperature and nitrogen buffer gas pressure. The experimental results are compared with expected contributions of the different relaxation processes and in this way allow the discrimination between them to help further optimization of cell design. The methods are compared in terms of basic features, data quality, and practical applicability.     

Reaction to Paul’s Column “Where do we find the graphs from PT programmes showing measurement performance?”

The tentative arguments mentioned by Paul De Bievre are discussed and alternatives are given that may lead to different insights.     

Sokodosides, steroid glycosides with an isopropyl side chain, from the marine sponge Erylus placenta

Two novel steroid glycosides, sokodosides A and B (1 and 2, respectively), were isolated from the marine sponge Erylus placenta as growth-inhibitory principles against several strains of yeast and a cancer cell line. Sokodosides possess the novel carbon skeleton as characterized by the presence of a combination of isopropyl side chain and the 4,4-dimethyl steroid nucleus. Sokodoside B has another unique characteristic in the presence of delta(8,14,16) unsaturation. The structures of sokodosides were determined by analysis of spectral data and chemical degradation. The absolute stereochemistry of sokodoside A (1) was determined by the application of the modified Mosher analysis to the aglycon obtained by acid hydrolysis, whereas the absolute stereochemistry of the monosaccharide units in 1 and 2 was determined by chiral GC analyses of the acid hydrolysates.