Electrostatics of phosphatidic acid monolayers: Insights from computer simulations

In this paper, we argue that many of the fascinating electrostatic effects that take place in amphiphilic systems are strongly related to the particular organization of the oxygen atoms within each individual molecule. In particular, we focus on two effects: charge inversion and dielectric overscreening. For that purpose, we present molecular dynamics simulations of phosphatidic acid (DMPA²⁻) in the presence of divalent counterions. Our results show that the many oxygens present in DMPA²⁻ cooperatively create strong binding sites for counterions, which in some cases lead to charge inversion. We also present an analysis of the role of interfacial water and relate our analysis to the phenomenon of dielectric overscreening. Several experimental implications are discussed in the conclusions.     

Improved separation of palladium species in biological matrices by using a combination of gel permeation chromatography and isotachophoresis

The binding of palladium to high-molecular-mass compounds in palladium-treated lettuce is investigated as an example for a biological matrix. The total palladium concentration in lettuce leaves is 10.3 ng/g wet weight. After homogenization, high-molecular-mass compounds (> 10 kDa) are isolated by ultrafiltration. For separation of these palladium species a combination of preparative gel permeation chromatography (GPC) and preparative isotachophoresis (ITP) is used. Palladium is determined in separated fractions by using a highly sensitive total reflection X-ray fluorescence (TXRF) method after preconcentration. After GPC separation, four main fractions of palladium species are collected, each containing palladium in ng quantities (3-10 ng). Two of these fractions are further separated by ITP, yielding at least three main peaks per GPC fraction, each containing palladium in the range of 0.3-3 ng. These palladium containing peaks are characterized by high-performance size exclusion chromatography (HPSEC) and capillary isotachophoresis (cITP) in parallel. HPSEC enables the estimation of the molecular mass of six main palladium peaks, covering a molecular mass range of 69-200 kDa. It is also shown that the estimation of molecular mass after separation is more reliable than the respective estimation directly in the first GPC run. However, cITP reveals that each of the separated peaks is still a mixture of at least five different compounds.     

Oxidation of nitrided si(100) by gaseous atomic and molecular oxygen

The nitridation of Si(100) by ammonia and the subsequent oxidation of the nitrided surface by both gaseous atomic and molecular oxygen was investigated under ultrahigh vacuum (UHV) conditions using X-ray photoelectron spectroscopy (XPS). Nitridation of Si(100) by the thermal decomposition of NH3 results in the formation of a subsurface nitride and a decrease in the concentration of surface dangling bond sites. On the basis of changes in the N1s spectra obtained after NH3 adsorption and decomposition, we estimate that the nitride resides about four to five layers below the vacuum-solid interface and that the concentration of surface dangling bonds after nitridation is only 59% of its value on Si(100)-(2 x 1). Oxidation of the nitrided surface is found to produce an oxide phase that remains in the outer layers of the solid and interacts only weakly with the underlying nitride for oxygen coverages up to 2.5 ML. Slight changes in the N1s spectra observed after oxidizing at 300 K are suggested to arise primarily from the introduction of strain within the nitride, and by the formation of a small amount of Si2=N-O species near the nitride-oxide interface. The nitrogen bonding environment changes negligibly after oxidizing at 800 K, which is indicative of greater phase separation at elevated surface temperature. Nitridation is also found to significantly reduce the reactivity of the Si(100) surface toward both atomic and molecular oxygen. A comparison of the oxygen uptake on the clean and nitrided surfaces shows quantitatively that the decrease in dangling bond concentration is responsible for the reduced activity of the nitrided surface toward oxidation, and therefore that dangling bonds are the initial adsorption site for both gaseous oxygen atoms and molecules. Increasing the surface temperature is found to promote the uptake of oxygen when O2 is used as the oxidant, but brings about only a small enhancement in the uptake of gaseous O-atoms. The different effects of surface temperature on the uptake of O versus O2 are interpreted in terms of the efficiency at which dangling bond pairs are regenerated on the surface at elevated temperature and the different site requirements for the adsorption of O and O2.     

Dual quartz crystal microbalance compensation using a submerged reference crystal. Effect of surface roughness and liquid properties

Absolute resonant frequency measurements were made on gold-coated AT-cut quartz crystals with one face in contact with a series of liquids. The effect of surface roughness and liquid properties (viscosity and density) was analyzed in terms of a “trapped liquid” model. In this model, liquid present in surface imperfections is viewed as rigidly coupled mass. In some of the literature this density-dependent, but not viscosity-dependent, term is viewed as being additive to the hydrodynamic shift seen for a smooth surface. Data obtained using 1 μm and 5 μm surface finish crystals are inconsistent with the predictions of the trapped liquid model. This suggests hydrodynamic coupling between liquid internal and external to the crevices. Despite the lack of a theoretical model for the liquid motion, it is possible to compensate for frequency variations resulting from changing liquid properties and for roughness effects by making direct measurements of the resonant frequency difference between two crystals exposed to the same solution. This novel procedure works to the extent that the two crystals have similar surface topographies. Compensation is excellent for 1 μm finish crystals and good for 5 μm finish crystals.     

Backbonding contributions to small molecule chemisorption in a metal–organic framework with open copper(i) centers

Metal–organic frameworks are promising materials for applications such as gas capture, separation, and storage, due to their ability to selectively adsorb small molecules. The metal–organic framework Cu^I-MFU-4l, which contains coordinatively unsaturated copper(i) centers, can engage in backbonding interactions with various small molecule guests, motivating the design of frameworks that engage in backbonding and other electronic interactions for highly efficient and selective adsorption. Here, we examine several gases expected to bind to the open copper(i) sites in Cu^I-MFU-4l via different electronic interactions, including σ-donation, π-backbonding, and formal electron transfer. We show that in situ Cu L-edge near edge X-ray absorption fine structure (NEXAFS) spectroscopy can elucidate π-backbonding by directly probing excitations to unoccupied backbonding orbitals with Cu d-character, even for gases that participate in other dominant interactions, such as ligand-to-metal σ-donation. First-principles calculations based on density functional theory and time-dependent density functional theory additionally reveal the backbonding molecular orbitals associated with these spectroscopic transitions. The energies of the transitions correlate with the energy levels of the isolated small molecule adsorbates, and the transition intensities are proportional to the binding energies of the guest molecules within Cu^I-MFU-4l. By elucidating the molecular and electronic structure origins of backbonding interactions between electron rich metal centers in metal–organic frameworks and small molecule guests, it is possible to develop guidelines for further molecular-level design of solid-state adsorbents for energy-efficient separations of relevance to industry.

In situ near edge X-ray absorption fine structure spectroscopy directly probes unoccupied states associated with backbonding interactions between the open metal site in a metal–organic framework and various small molecule guests.     

Mapping of possible prion protein self-interaction domains using peptide arrays

Background  

The common event in transmissible spongiform encephalopathies (TSEs) or prion diseases is the conversion of host-encoded protease sensitive cellular prion protein (PrP^C) into strain dependent isoforms of scrapie associated protease resistant isoform (PrP^Sc) of prion protein (PrP). These processes are determined by similarities as well as strain dependent variations in the PrP structure. Selective self-interaction between PrP molecules is the most probable basis for initiation of these processes, potentially influenced by chaperone molecules, however the mechanisms behind these processes are far from understood. We previously determined that polymorphisms do not affect initial PrP^C to PrP^Sc binding but rather modulate a subsequent step in the conversion process. Determining possible sites of self-interaction could elucidate which amino acid(s) or amino acid sequences contribute to binding and further conversion into other isoforms. To this end, ovine – and bovine PrP peptide-arrays consisting of 15-mer overlapping peptides were probed with recombinant sheep PrP^C fused to maltose binding protein (MBP-PrP).     

Chemiluminescence from the oxidation of urea and ammonia with hypobromite and N-bromosuccinimide

The spectral distribution for the chemiluminescent oxidation of ammonia with hypobromite is significantly different to that for the oxidation of ammonia with N-bromosuccinimide. Therefore, in contrast to the assumptions of several authors, the action of N-bromosuccinimide is not solely derived from the in situ formation of hypobromite. Neither the oxidation of urea with hypobromite nor the oxidation of urea with N-bromosuccinimide involves an initial hydrolysis of urea to ammonia in the alkaline solution. However, these two reactions lead to a common emitter. The addition of xanthene dyes, such as dichlorofluorescein, enhance the chemiluminescence intensity by energy transfer to the efficient fluorophore, but reaction between the sensitiser and hypobromite can result in a significant increase in the background signal. A list of potential interferences has been compiled; particular attention was paid to guanidino compounds, as the chemiluminescence accompanying the oxidation of this functional group has not been previously discussed.     

OPTICAL AND THERMAL CHARACTERIZATION OF NATURAL (Sepia officinalis) MELANIN

Abstract The optical properties and the thermal diffusivity of natural cuttlefish ( Sepia officinalis ) melanin have been measured. The optical absorption and scattering properties of melanin particles were determined at 580 nm and 633 nm, using photometric and photothermal techniques. For the photometric studies, the absorption and the transport scattering coefficients were determined from the measurements of diffuse reflectance and transmittance. The scattering anisotropy was obtained from an additional measurement of the total attenuation coefficient and independently obtained by goniometry. For photothermal studies, pulsed photothermal radiometry was used to deduce the absorption and transport scattering coefficients via a model based on optical diffusion theory. Pulsed photothermal radiometry was also used to provide the thermal diffusivity of solid melanin pressed pellets.     

Elongated conformers of charge states +11 to +15 of bovine ubiquitin studied using ESI-FAIMS-MS

Recent advancements in high-field asymmetric waveform ion mobility spectrometry (FAIMS) have led to significant improvements in the application of this technology to the study of protein conformers. Compared with previous work, the maximum value of the separation voltage (i.e., the dispersion voltage) has increased, thereby enabling multiple, elongated conformers of individual charge states of bovine ubiquitin to be separated in the gas phase (e.g., four conformers of each of the +11 and +12 charge states were separated). The use of a carrier gas mixture of 40% nitrogen and 60% helium changed the separation selectivity compared with pure nitrogen and enhanced the signal intensity, especially for the +14 and +15 charge states (the latter was not detected in a nitrogen carrier gas). Conformer cross sections were determined using the FAIMS/energy-loss method and found to be similar within a given charge state. The cross sections for conformers of charge states +13, + 14, and +15 plateau at about 2000 A2 suggesting that the structure of bovine ubiquitin is essentially unfolded after the addition of the 13th proton.