Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies

We have estimated free energies for the binding of nine cyclic carboxylate guest molecules to the octa-acid host in the SAMPL4 blind-test challenge with four different approaches. First, we used standard free-energy perturbation calculations of relative binding affinities, performed at the molecular-mechanics (MM) level with TIP3P waters, the GAFF force field, and two different sets of charges for the host and the guest, obtained either with the restrained electrostatic potential or AM1-BCC methods. Both charge sets give good and nearly identical results, with a mean absolute deviation (MAD) of 4 kJ/mol and a correlation coefficient (R ²) of 0.8 compared to experimental results. Second, we tried to improve these predictions with 28,800 density-functional theory (DFT) calculations for selected snapshots and the non-Boltzmann Bennett acceptance-ratio method, but this led to much worse results, probably because of a too large difference between the MM and DFT potential-energy functions. Third, we tried to calculate absolute affinities using minimised DFT structures. This gave intermediate-quality results with MADs of 5–9 kJ/mol and R ² = 0.6–0.8, depending on how the structures were obtained. Finally, we tried to improve these results using local coupled-cluster calculations with single and double excitations, and non-iterative perturbative treatment of triple excitations (LCCSD(T0)), employing the polarisable multipole interactions with supermolecular pairs approach. Unfortunately, this only degraded the predictions, probably because of a mismatch between the solvation energies obtained at the DFT and LCCSD(T0) levels.     

The One-dimensional Fractional Supersymmetric Quantum Mechanical Operator of Momentum

In the case of the quantum generalization of stable Lévy processes, expressions for the Hermitian operator of momentum and its eigenfunctions are proposed. The normalization constant has been determined and its relation to the translation operator is shown. The interrelation between the momentum and the wave number has been generalized for the processes with a non-integer dimensionality α. The simplest nonlocal superalgebra is introduced.      

In vitro and in vivo biocompatibility study on laser 3D microstructurable polymers

Films and microstructured scaffolds have been fabricated using direct laser writing out of different polymers: hybrid organic-inorganic ORMOCORE b59, acrylate-based AKRE23, novel organic-inorganic Zr containing hybrid SZ2080, and biodegradable PEG-DA-258. Adult myogenic stem cells were grown on these surfaces in vitro. Their adhesion, growth, and viability test results suggest good potential applicability of the materials in biomedical practice. Pieces of these polymers were implanted in rat’s paravertebral back tissue. Histological examination of the implants and surrounding tissue ex vivo after 3 weeks of implantation was conducted and results show the materials to be at least as biocompatible as surgical clips or sutures. The applied direct laser writing technique seems to offer good future prospects in a polymeric 3D scaffold design for artificial tissue engineering with autologous stem cells.     

Preparation and characterization of Y1−xPrxBa2Cu3O7−δ single crystals

We present a reliable method for growing single crystals of Y_1−xPr_xBa₂Cu₃O_7−δ high-T_c superconductors in ZrO₂ crucibles. This method results in crystals with greatly improved superconducting properties compared to crystals grown with the previously reported methods which use Al₂O₃ crucibles. We describe techniques for crystal growth in both Al₂O₃ and ZrO₂ crucibles using an excess of BaCo₃ and CuO as the flux. The crystals were characterized by means of DC magnetic-susceptibility measurements, electrical-resistivity measurements, and electron microprobe analysis. The effects of Al contamination on the conditions for crystal growth and on the superconducting properties of the crystals are found to be quite significant.     

Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods

We have estimated affinities for the binding of 34 ligands to trypsin and nine guest molecules to three different hosts in the SAMPL3 blind challenge, using the MM/PBSA, MM/GBSA, LIE, continuum LIE, and Glide score methods. For the trypsin challenge, none of the methods were able to accurately predict the experimental results. For the MM/GB(PB)SA and LIE methods, the rankings were essentially random and the mean absolute deviations were much worse than a null hypothesis giving the same affinity to all ligand. Glide scoring gave a Kendall's τ index better than random, but the ranking is still only mediocre, τ = 0.2. However, the range of affinities is small and most of the pairs of ligands have an experimental affinity difference that is not statistically significant. Removing those pairs improves the ranking metric to 0.4-1.0 for all methods except CLIE. Half of the trypsin ligands were non-binders according to the binding assay. The LIE methods could not separate the inactive ligands from the active ones better than a random guess, whereas MM/GBSA and MM/PBSA were slightly better than random (area under the receiver-operating-characteristic curve, AUC = 0.65-0.68), and Glide scoring was even better (AUC = 0.79). For the first host, MM/GBSA and MM/PBSA reproduce the experimental ranking fairly good, with τ = 0.6 and 0.5, respectively, whereas the Glide scoring was considerably worse, with a τ = 0.4, highlighting that the success of the methods is system-dependent.     

Anisotropic enhancement of superconductivity in heavy-ion irradiated (K,Ba)BiO3

We have measured the specific heat, resistivity, and ac susceptibility of (K,Ba)BiO3 single crystals before and after introduction of either point or columnar defects by electron (EI) or heavy-ion irradiation (HII). While the magnetic field dependence of these properties remains mainly unaffected by EI, the irreversibility line and the location of the specific heat anomaly are both shifted up in temperature after HII. The shift is apparent only if the magnetic field is applied parallel to the ion tracks. For perpendicularly applied fields, both lines lie at the same field as in the pristine sample. These experiments call the nature of the vortex liquid state into question.     

The excited-state chemistry of protochlorophyllide a: a time-resolved fluorescence study.

The excited-state processes of protochlorophyllide a, the precursor of chlorophyll a in chlorophyll biosynthesis, are studied using picosecond time-resolved fluorescence spectroscopy. Following excitation into the Soret band, two distinct fluorescence components, with emission maxima at 640 and 647 nm, are observed. The 640 nm emitting component appears within the time resolution of the experiment and then decays with a time constant of 27 ps. In contrast, the 647 nm emitting component is built up with a 3.5 ps rise time and undergoes a subsequent decay with a time constant of 3.5 ns. The 3.5 ps rise kinetics are attributed to relaxations in the electronically excited state preceding the nanosecond fluorescence, which is ascribed to emission out of the thermally equilibrated S(1) state. The 27 ps fluorescence, which appears within the experimental response of the streak camera, is suggested to originate from a second minimum on the excited-state potential-energy surface. The population of the secondary excited state is suggested to reflect a very fast motion out of the Franck-Condon region along a reaction coordinate different from the one connecting the Franck-Condon region with the S(1) potential-energy minimum. The 27 ps-component is an emissive intermediate on the reactive excited-state pathway, as its decay yields the intermediate photoproduct, which has been identified previously (J. Phys. Chem. B 2006, 110, 4399-4406). No emission of the photoproduct is observed. The results of the time-resolved fluorescence study allow a detailed spectral characterization of the emission of the excited states in protochlorophyllide a, and the refinement of the kinetic model deduced from ultrafast absorption measurements.     

Immobilized Stationary Phases for Hydrophobic Interaction Chromatography of Proteins

Immobilized stationary phases for hydrophobic interaction chromatography (HIC) of proteins are prepared by coating macroporous silica Daisogel of different porosity with hydrophobized cellulose derivatives. The polymer adsorbed on the silica surface afterwards was cross-linked with bifunctional compounds. A uniform polymer nanocoating was indicated using the nitrogen gas adsorption method BET and scanning electron microscopy. The absence of non-specific protein sorption of the synthesized adsorbents shows that the developed polymeric coating isolates silica surface from contact with the sorbate. The retention data of bovine serum albumin (BSA) in the HIC mode on different synthesized adsorbents were evaluated. It was shown that sorption capacity of such phases may vary over a wide range and depends mainly on the substitution degree of the immobilized polymer. The dynamic sorption capacity of BSA was up to 63 mg mL⁻¹. The results proved that the new stationary phases have significant promise for the separation and purification of proteins in the HIC mode.