Molecular modeling of the structure and dynamics of the interlayer species of ZnAlCl layered double hydroxide

Molecular dynamics simulations of the ZnAl layered double hydroxide containing interlayer chloride anions have been performed in the NpT and Np(zz)T statistical ensembles for metal Zn/Al ratios of 2 and 3. We have monitored the interlayer spacing as a function of the number of intercalated water molecules for each statistical ensemble. We have studied how these profiles are affected by the method of calculation of the charges of the hydroxide layer atoms. Diffusion coefficients of the interlayer water molecules have been calculated for different Zn/Al ratios. The calculation of the chemical potential of the interlayer water molecules has been carried out for three amounts of interlayer water molecules. The calculation showed a qualitative agreement with the bulk water chemical potential within a range of interlayer water molecule contents.     

Atomistic insights into the inhibition of cysteine proteases: first QM/MM calculations clarifying the stereoselectivity of epoxide-based inhibitors

Due to their important role in many diseases, cysteine proteases represent new promising drug targets. An important class of cysteine-protease inhibitors is derived from the naturally occurring compound E64, possessing an epoxysuccinyl moiety as warhead. Experimental studies show stereoselectivity concerning the inhibition potency, e.g., a trans-configured epoxide ring is essential for inhibition, and furthermore, in most cases, the ( S, S)-configured inhibitors have a higher inhibition potency than their ( R, R)-counterparts. However, the underlying effects are not fully understood. In this work, such effects are investigated by classical molecular dynamics simulations and combined quantum mechanics/molecular modeling (QM/MM) calculations for the E64c-cathepsin B complex. Our computations reveal that the hydrogen bonding network between the enzyme and the E64c (or its derivatives) determines the stereoselectivity of the subsequent ring opening reaction by governing the distance between the attacking thiolate and the attacked C2 atom of the epoxide ring. For the ( S, S)-configuration, a strong network can be realized which enables a close contact between the reacting centers, so that the irreversible step becomes very efficient. The ( R, S)-configuration ( cis-configuration) can only form networks in which the two reacting centers are so far away from each other that the irreversible step can hardly happen. The ( R, R)-configuration is in between, less optimal than the ( S, S)-configuration but much better than the ( R, S)-configuration. Exceptions where the ( R, R)-configurations shows higher potency than the ( S, S) ones are also explained.     

Molecular Lanthanide Switches for Magnetism and Photoluminescence

Solvation of [(CNT)Ln(η⁸-COT)] (Ln=La, Ce, Nd, Tb, Er; CNT=cyclononatetraenyl, i.e., C₉H₉⁻; COT=cyclooctatetraendiid, i.e., C₈H₈²⁻) complexes with tetrahydrofuran (THF) gives rise to neutral [(η⁴-CNT)Ln(thf)₂(η⁸-COT)] (Ln=La, Ce) and ionic [Ln(thf)_x(η⁸-COT)][CNT] (x=4 (Ce, Nd, Tb), 3 (Er)) species in a solid-to-solid transformation. Due to the severe distortion of the ligand sphere upon solvation, these species act as switchable luminophores and single-molecule magnets. The desolvation of the coordinated solvents can be triggered by applying a dynamic vacuum, as well as a temperature gradient stimulus. Raman spectroscopic investigations revealed fast and fully reversible solvation and desolvation processes. Moreover, we also show that a Nd:YAG laser can induce the necessary temperature gradient for a self-sufficient switching process of the Ce(III) analogue in a spatially resolved manner.     

Study of charge storage in the nanofibrous poly(ethylene terephthalate) electrets prepared by electrospinning or by corona discharge method

In this paper, the charge storage performance of electrospun poly(ethylene terephthalate) (PET) mats with high specific surface area was evaluated in comparison to that of PET film electrets. Corona discharge method was used to charge the electrospun PET mats and PET films. The surface potential decay measurements revealed that the corona charged РЕТ mats had higher initial values for the normalized surface potential compared to the РЕТ electret films. A tendency for stabilization of the electret charge to one and the same value for all charged samples (mats and films) after the 50th day was observed. The peaks at 90 °C in the thermally stimulated current (TSC) spectra of uncharged and charged in corona discharge electrospun PET mats were observed and attributed to a relaxation of the separated space charges, the dipole disorientation or injected charges within the bulk. It was found that the value of the storage charge in a corona charged electrospun PET mats was higher than that in PET mats prepared by electrospinning.     

Fast gas chromatography for pesticide residues analysis

The importance of method development in the area of pesticide residues analysis is apparent from legislative requirements continuously decreasing the maximum acceptable concentration levels in food and water. This covers also contribution in the science in the field of ultra-trace analysis of organic pollutants in complex mixtures. Analysis time is one of the most important aspects that should be considered in the choice of analytical methods for routine application. With this fact, fast gas chromatography (GC) has acquired a real importance in the pesticide residue analysis. This paper provides an overview of fast GC methods for analysis of pesticide residues in variety of matrices at ultra-trace concentration levels. Emphasis is put on the development in the last 6 years.     

Scaling Transform and Stretched States in Quantum Mechanics

We consider the Husimi Q(q, p)-functions which are quantum quasiprobability distributions on the phase space. It is known that, under a scaling transform (q; p) → (?q; ?p), the Husimi function of any physical state is converted into a function which is also the Husimi function of some physical state. More precisely, it has been proved that, if Q(q, p) is the Husimi function, the function ?² Q(?q; ?p) is also the Husimi function. We call a state with the Husimi function ?² Q(?q; ?p) the stretched state and investigate the properties of the stretched Fock states. These states can be obtained as a result of applying the scaling transform to the Fock states of the harmonic oscillator. The harmonic-oscillator Fock states are pure states, but the stretched Fock states are mixed states. We find the density matrices of stretched Fock states in an explicit form. Their structure can be described with the help of negative binomial distributions. We present the graphs of distributions of negative binomial coefficients for different stretched Fock states and show the von Neumann entropy of the simplest stretched Fock state.     

Absolute and relative quantification of sheep brain prion protein (PrP) allelic variants by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry

Transmissible spongiform encephalopathies (TSEs) are characterised by the accumulation in the tissues of affected individuals of an abnormal form (PrP(Sc)) of a protein naturally produced by the host, the cellular prion protein (PrP(C)). In sheep, susceptibility to TSEs is tightly controlled by polymorphism at positions 136 (A or V), 154 (R or H) and 171 (R or Q) of the Prnp gene encoding the prion protein (PrP). Quantification of PrP variants at positions 136, 154 and 171 can be achieved by matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometric analysis of the respective peptides 114-139, 152-159 and 160-171 obtained after tryptic digestion of the PrP protein. In this study we quantified the tryptic peptide 114-139 containing the first polymorphic site. Quantification was either relative, between variants of this peptide, or absolute with respect to the C-terminally (18)O-labelled peptide obtained by hydrolysing known amounts of recombinant protein with trypsin in H(2) (18)O. After purification of PrP(C) and PrP(Sc) from the brain of two heterozygous sheep carrying either the ARQ/VRQ or ARR/VRQ genotypes, the proportion of each variant was measured. In the ARQ/VRQ animal, while both variants were equally represented in the normal isoform, the VRQ variant was predominantly found in the abnormal PrP protein, suggesting dissimilar behaviour of the two variants in the pathological process. The situation was even more contrasted in the ARR/VRQ animal where PrP(Sc) was solely composed of the VRQ variant. These two examples clearly illustrate the value of MALDI-TOF analysis, combined with appropriate immunopurification techniques, in seeking a precise understanding of the influence of PrP polymorphisms on TSE pathogenesis.     

Interactions of Sea Anemone Toxins with Insect Sodium Channel—Insights from Electrophysiology and Molecular Docking Studies

Animal venoms are considered as a promising source of new drugs. Sea anemones release polypeptides that affect electrical activity of neurons of their prey. Voltage dependent sodium (Nav) channels are the common targets of Av1, Av2, and Av3 toxins from Anemonia viridis and CgNa from Condylactis gigantea. The toxins bind to the extracellular side of a channel and slow its fast inactivation, but molecular details of the binding modes are not known. Electrophysiological measurements on Periplaneta americana neuronal preparation revealed differences in potency of these toxins to increase nerve activity. Av1 and CgNa exhibit the strongest effects, while Av2 the weakest effect. Extensive molecular docking using a modern SMINA computer method revealed only partial overlap among the sets of toxins’ and channel’s amino acid residues responsible for the selectivity and binding modes. Docking positions support earlier supposition that the higher neuronal activity observed in electrophysiology should be attributed to hampering the fast inactivation gate by interactions of an anemone toxin with the voltage driven S4 helix from domain IV of cockroach Nav channel (NavPaS). Our modelling provides new data linking activity of toxins with their mode of binding in site 3 of NavPaS channel.     

Fast in-line bottom-up analysis of monoclonal antibodies: Toward an electrophoretic fingerprinting approach

For their characterization and quality control, monoclonal antibodies are frequently analyzed at the bottom-up level to generate specific fingerprints that can be used to tackle post-translational modifications or ensure production consistency between lots. To circumvent time-consuming and labor-intensive off-line sample preparation steps, the implementation of integrated methodologies from sample preparation to separation and detection is highly valuable. In this perspective, capillary zone electrophoresis appears as a choice technique since the capillary can subsequently be used as a vessel for sample preparation and electrophoretic discrimination/detection of the reaction products. Here, a fast in-line methodology for the routine quality control of mAbs at the bottom-up level is reported. Simultaneous denaturation and reduction (pretreatment step) were conducted with RapiGest® surfactant and dithiothreitol before in-line tryptic digestion. Reactant mixing was realized by transverse diffusion of laminar flow profile under controlled temperature. In-line digestion was carried out with a resistant trypsin to autolysis. The main parameters affecting the digestion efficiency (trypsin concentration and incubation conditions) were optimized to generate mAb electrophoretic profiles free from trypsin interferences. An acidic MS-compatible BGE was used to obtain high resolution separation of released peptides and in-line surfactant cleavage. The whole methodology was performed in less than two hours with good repeatability of migration times (RSD = 0.91%, n = 5) and corrected peak areas (RSD = 9.6%, n = 5). CE-fingerprints were successfully established for different mAbs and an antibody-drug conjugate.     

Reactive Phenanthrene Derivatives as Markers of Amino Groups in Fluorescence Microscopy of Surface Modified Micro-Zeolite L

Journal of Fluorescence - Two reactive phenanthrene derivatives, 4-(1H phenanthrol [9,10-d] imidazole-2-yl) benzaldehyde (PIB) and 6,9-dimethoxyphenanthro[9,10-c]furan-1,3-dione (PA) with high...