Vibrationally resolved valence and core photoionization and photoexcitation spectra of an electron-deficient trivalent boron compound: the case of catecholborane.

Compounds containing trivalent boron (TB) as the electron-deficient site(s) find numerous practical uses ranging from Lewis bases in organic synthesis to high-tech industry, with a number of novel applications anticipated. We present an experimental and theoretical study of the gas-phase valence photoionization (VUV-PES), core photoionization (XPS) and photoexcitation (NEXAFS) spectra of a representative TB compound catecholborane (CB). For modelling and assigning the spectra we used the ΔDFT and restricted single excitation space TD-DFT methods for the XPS and NEXAFS, and OVGF and EOM-CCSD for the VUV-PES. The vibrationally resolved structure was computed in the Franck-Condon (FC) and Herzberg-Teller (FCHT) approximations generally resulting in a good agreement with the observed spectral features. For the prediction of core-electron binding energies (CEBEs) several density functionals were tested. The best performance overall was furnished by ωB97X-D suggesting that including the dispersion correction is beneficial. The FCHT vibronic intensities are in clear discrepancy with the B 1s NEXAFS spectrum if the harmonic approximation is used for the B-H wagging mode both in the ground and in the first core-excited state. Instead, a much better agreement is obtained if the excited state potential is approximated to a symmetric double-well. The observed vibronic pattern could be a general fingerprint of the presence of TB centre(s), specifically, the transfer of the (core) density to the vacant boron p-orbital in the excited state.

A free-boundary model of a motile cell explains turning behavior.

To understand shapes and movements of cells undergoing lamellipodial motility, we systematically explore minimal free-boundary models of actin-myosin contractility consisting of the force-balance and myosin transport equations. The models account for isotropic contraction proportional to myosin density, viscous stresses in the actin network, and constant-strength viscous-like adhesion. The contraction generates a spatially graded centripetal actin flow, which in turn reinforces the contraction via myosin redistribution and causes retraction of the lamellipodial boundary. Actin protrusion at the boundary counters the retraction, and the balance of the protrusion and retraction shapes the lamellipodium. The model analysis shows that initiation of motility critically depends on three dimensionless parameter combinations, which represent myosin-dependent contractility, a characteristic viscosity-adhesion length, and a rate of actin protrusion. When the contractility is sufficiently strong, cells break symmetry and move steadily along either straight or circular trajectories, and the motile behavior is sensitive to conditions at the cell boundary. Scanning of a model parameter space shows that the contractile mechanism of motility supports robust cell turning in conditions where short viscosity-adhesion lengths and fast protrusion cause an accumulation of myosin in a small region at the cell rear, destabilizing the axial symmetry of a moving cell.

Characterisation of the electronic structure of galvinoxyl free radical by variable energy UPS, XPS and NEXAFS spectroscopy.

Insights into the electronic structure of galvinoxyl - a prototype persistent free radical species - are of interest to elucidate its attractive photophysical and magnetic properties and to pave way for a sensible design of novel applications. To this end, we study the photoionization and photoexcitation UPS, XPS and NEXAFS spectra of the gas-phase galvinoxyl in the valence and core (C 1s and O 1s) regions using synchrotron X-ray radiation. We observe significant variations of relative band intensities with photon energy for valence ionizations below 10 eV which are rationalized in terms of the properties of the corresponding valence molecular orbitals. We calculate the core electron binding energies and core-excited states by employing the spin-unrestricted ΔDFT (B3LYP, M06-2X, and ωB97xD) and time-dependent DFT (SRC2-BLYP) methods. A good correlation between the calculations and the measured C 1s and O 1s XPS and NEXAFS spectra is obtained if one assumes that the galvinoxyl sample has undergone a partial degradation (around 50%) to the saturated (closed-shell) phenolic-quinonic derivative known as galvinol. We carry out a comparative theoretical analysis of the XPS and NEXAFS spectra of galvinoxyl and galvinol by assigning the relevant absorptions and pointing out the most important relative differences. The calculations identify a band in the O 1s NEXAFS spectrum whose diminishing intensity is a most manifest indicator of the extent of the degradation. Such a feature may thus prove useful in monitoring the scavenging dynamics of galvinoxyl using the core-excitation spectroscopy.

Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology.

Hybrid deterministic-stochastic methods provide an efficient alternative to a fully stochastic treatment of models which include components with disparate levels of stochasticity. However, general-purpose hybrid solvers for spatially resolved simulations of reaction-diffusion systems are not widely available. Here we describe fundamentals of a general-purpose spatial hybrid method. The method generates realizations of a spatially inhomogeneous hybrid system by appropriately integrating capabilities of a deterministic partial differential equation solver with a popular particle-based stochastic simulator, Smoldyn. Rigorous validation of the algorithm is detailed, using a simple model of calcium 'sparks' as a testbed. The solver is then applied to a deterministic-stochastic model of spontaneous emergence of cell polarity. The approach is general enough to be implemented within biologist-friendly software frameworks such as Virtual Cell.

The study of the electronic structure of some N-heterocyclic carbenes (NHCs) by variable energy photoelectron spectroscopy.

The photoionization of three N-heterocyclic carbenes (NHCs) has been studied in the valence and core regions using synchrotron radiation. We observed different variations in the relative band intensities with photon energy for the NHCs in the valence ionization region. This is due to the intra-ring interactions between the C=C bond, nitrogen and carbene lone pairs in the heterocyclic ring of NHCs. In the core ionization region we observed chemical shifts which are consistent with the relative electron affinities of atoms and intramolecular electron density shifts. The core electron binding energies calculated via the unrestricted ΔDFT (B3LYP and M06-2X) approach are in very good agreement with the experiment. The shake-up portion of the core photoionization spectra is adequately described by the time-dependent DFT calculations relying on the CAM-B3LYP functional.

The Gibbs free energy of formation of halogenated benzenes, benzoates and phenols and their potential role as electron acceptors in anaerobic environments.

The sequence of redox reactions in the natural environment generally follows the electron affinity of the electron acceptors present and can be rationalized by the redox potentials of the appropriate half-reactions. Answering the question how halogenated aromatics fit into this sequence requires information on their Gibbs free energy of formation values. In 1992 Gibbs free energy data for various classes of halogenated aromatic compounds were systematically explored for the first time based on Benson's group contribution method. Since then more accurate quantum chemical calculation methods have become available. Here we use these methods to estimate enthalpy and Gibbs free energy of formation values of all chlorinated and brominated phenols. These data and similar state-of-the-art datasets for halogenated benzenes and benzoates were then used to calculate two-electron redox potentials of halogenated aromatics for standard conditions and for pH 7. The results underline the need to take speciation into consideration when evaluating redox potentials at pH 7 and highlight the fact that halogenated aromatics are excellent electron acceptors in aqueous environments.

Characterisation of the electronic structure of some stable nitroxyl radicals using variable energy photoelectron spectroscopy.

The photoionization of three stable nitroxyl radicals has been studied in the valence and core regions using synchrotron radiation. We observed different variations of the relative band intensities with the photon energy for two pyrrolidine nitroxyls (nitroxyl8 and nitroxyl9) in the valence ionization region. This is due to strong intramolecular interactions between the amide substituent and the ring π-orbital when present. In the core ionization region we observed chemical shifts which were consistent with the relative electron affinities of different atoms. We also observed the multiplet splitting of core level binding energies in the final ionic states. The core electron binding energies calculated via the restricted open shell Hartree-Fock based ΔSCF method exhibit good agreement with the experimental core ionization bands and with the assignment of the spectra by empirical analysis.

Electronic structure of two precursors for nanofabrication: [(CH3)3CN]2W[N(CH3)2]2 and Ti(NMe2)2(NEt2)2.

The electronic structures of bis(tert-butylimino)bis(dimethylamino) tungsten and bis(N-ethylethanaminato)bis(N-methylmethanaminato) titanium heteroleptic complexes, which are precursors for atomic layer deposition of metallic nitride on surfaces, have been investigated by HeI and HeII UV photoelectron spectroscopy and DFT/OVGF calculations. We discuss the electronic structures of these two and other related d(0)-type complexes in relation to the mechanism of adsorption and decomposition of metal alkylamide precursors on surfaces.

Antibacterial performance of alginic acid coating on polyethylene film.

Alginic acid coated polyethylene films were examined in terms of surface properties and bacteriostatic performance against two most representative bacterial strains, that is, Escherichia coli and Staphylococcus aureus. Microwave plasma treatment followed by brush formation in vapor state from three distinguished precursors (allylalcohol, allylamine, hydroxyethyl methacrylate) was carried out to deposit alginic acid on the substrate. Surface analyses via various techniques established that alginic acid was immobilized onto the surface where grafting (brush) chemistry influenced the amount of alginic acid coated. Moreover, alginic acid was found to be capable of bacterial growth inhibition which itself was significantly affected by the brush type. The polyanionic character of alginic acid as a carbohydrate polymer was assumed to play the pivotal role in antibacterial activity. The cell wall composition of two bacterial strains along with the substrates physicochemical properties accounted for different levels of bacteriostatic performance.

Extreme Serum Titanium Concentration Induced by Acetabular Cup Failure: Unveiling a Unique Scenario of Titanium Alloy Debris Accumulation.

The majority of contemporary total hip arthroplasty (THA) implants are constructed from Ti alloys, which are generally believed to generate fewer adverse local tissue reactions (ALTRs) compared to CoCr alloys. This study presents a case of unusual primary THA failure where a substantial release of Ti alloy debris was observed. A 52-year-old active male underwent THA after post-traumatic aseptic necrosis of the femoral head in 2006. Seventeen years after the procedure, the patient presented with groin pain and a restricted range of motion. X-rays revealed the protrusion of the alumina ceramic head through the Ti6Al4V acetabular cup. Trace element analysis indicated significantly elevated levels of serum Ti, Al, and V. CT and MRI confirmed Ti alloy cup failure and a severe ALTR. During revision surgery, it was found that the worn-out ceramic head was in direct contact with the acetabular cup, having protruded through a central hole it had created over time. No acetabular liner was found. Histological analysis of his tissue samples showed wear-induced synovitis with areas of multinucleated foreign body giant cells and the accumulation of numerous metal particles but no acute inflammatory response. Six months after the revision THA, the patient has experienced favourable outcomes. This case provides an instructive illustration for studying the consequences of the substantial release of Ti alloy debris from orthopedic implants.

Gibbs free energy of formation of chlordecone and potential degradation products: implications for remediation strategies and environmental fate.

Chlordecone (C(10)Cl(10)O; CAS number 143-50-0) has been used extensively as an organochlorine insecticide but is nowadays banned under The Stockholm Convention on Persistent Organic Pollutants (POPs). A search for chlordecone-respiring organisms and choosing between reductive versus oxidative remediation tools and strategies to clean up chlordecone-polluted environments would benefit from the availability of Gibbs free energy data of chlordecone and its potential dechlorination products. Presently such data are not available. Polycyclic "cage" molecules of which chlordecone is an example contain considerable strain energy. It is not a priori clear how this affects the thermodynamic properties of the chlorinated members of this unique class of compounds and to what extent redox potentials for the halogenated congeners are different from those of other aliphatic and aromatic organohalogens. We performed ab initio quantum chemical calculations to estimate Δ(f)H(m)° and Δ(f)G(m)° values of chlordecone and selected dechlorination products and used these data to calculate their Gibbs free energy and redox potential. With redox potentials in the range of 336-413 mV chlordecone has an E(o)' value similar to that of other organochlorines. The results indicate that there are no thermodynamic reasons why chlordecone-respiring or -fermenting organisms should not exist.

Anti-bacterial treatment of polyethylene by cold plasma for medical purposes.

Polyethylene (PE) is one of the most widely used polymers in many industrial applications. Biomedical uses seem to be attractive, with increasing interest. However, PE it prone to infections and its additional surface treatment is indispensable. An increase in resistance to infections can be achieved by treating PE surfaces with substances containing antibacterial groups such as triclosan (5-Chloro-2-(2,4-dichlorophenoxy)phenol) and chlorhexidine (1,1'-Hexamethylenebis[5-(4-chlorophenyl)biguanide]). This work has examined the impact of selected antibacterial substances immobilized on low-density polyethylene (LDPE) via polyacrylic acid (PAA) grafted on LDPE by low-temperature barrier discharge plasma. This LDPE surface treatment led to inhibition of Escherichia coli and Staphylococcus aureus adhesion; the first causes intestinal disease, peritonitis, mastitis, pneumonia, septicemia, the latter is the reason for wound and urinary tract infections.

Electronic structure analysis of riboflavin: OVGF and EOM-CCSD study.

The computational simulation of the photoelectron spectrum of active form of vitamin B2 is reported in the gas phase. In this work, we determine relative stability of eight riboflavin conformers by conformational search first with molecular mechanics AMMP potential in VEGA software at 553 K. Relative abundance of conformers was deduced from Boltzmann population weighting method (BPW). The three most stable conformers were then selected for computing valence, vertical ionization energies. We used high-level Equation-of-Motion Coupled-Cluster (EOM-IP-CCSD) method to obtain valence ionization energies (IP). In order to characterize the nature of ionization processes pertaining to different spectral bands, natural bonding orbital (NBO) method and molecular electrostatic potentials (MEP) were used to obtain orbital electron densities. The influence of the electronic structure of riboflavin on its biological activity is manifested via reduction of ionization energies of outermost orbitals which makes electron densities of these orbitals more readily available to participate in ligand-receptor bonding.

Modification of Hot-Melt Adhesives Based on Metallocene Poly(ethylene-propylene) Copolymer for High Adhesion to Polar Surfaces.

A procedure is described of grafting the acrylic acid onto an oxygen/ozone-activated metallocene poly(ethylene-co-propylene). Consequently, the grafted copolymer is applied as a component in a metallocene polyolefin-based hot-melt adhesive composition with increased adhesion. The surface properties and adhesion strength of the prepared hot-melt adhesive (HMA) were determined and used to account for the effect of grafting. The application of grafted polyolefin as one of the components of the HMA mixture provides significant increase in adhesive strength, and it also results in increased compatibility and negligible effects on the technological parameters of the final composition. The obtained results may have significant impact for the practical application of prepared HMA for book bonding.

Total Knee Replacement with an Uncemented Porous Tantalum Tibia Component: A Failure Analysis.

Porous tantalum has been extensively used in orthopaedic surgery, including uncemented total knee arthroplasty (TKA). Favourable results were reported with earlier monobloc tibial components and the design evolved to modular implants. We aimed to analyse possible causes for extensive medial tibia bone loss, resulting in modular porous tantalum tibia baseplate fracture after primary TKA. Retrieved tissue samples were scanned with 3 MeV focused proton beam for Proton-Induced X-ray Emission (micro-PIXE) elemental analysis. Fractographic and microstructural analysis were performed by stereomicroscopy. A full 3D finite-element model was made for numerical analysis of stress-strain conditions of the tibial baseplate. Histological examination of tissue underneath the broken part of the tibial baseplate revealed dark-stained metal debris, which was confirmed by micro-PIXE to consist of tantalum and titanium. Fractographic analysis and tensile testing showed that the failure of the tibial baseplate fulfilled the criteria of a typical fatigue fracture. Microstructural analysis of the contact surface revealed signs of bone ingrowth in 22.5% of the surface only and was even less pronounced in the medial half of the tibial baseplate. Further studies are needed to confirm the responsibility of metal debris for an increased bone absorption leading to catastrophic tibial tray failure.

Diffusion amid random overlapping obstacles: similarities, invariants, approximations.

Efficient and accurate numerical techniques are used to examine similarities of effective diffusion in a void between random overlapping obstacles: essential invariance of effective diffusion coefficients (D(eff)) with respect to obstacle shapes and applicability of a two-parameter power law over nearly entire range of excluded volume fractions (φ), except for a small vicinity of a percolation threshold. It is shown that while neither of the properties is exact, deviations from them are remarkably small. This allows for quick estimation of void percolation thresholds and approximate reconstruction of D(eff) (φ) for obstacles of any given shape. In 3D, the similarities of effective diffusion yield a simple multiplication "rule" that provides a fast means of estimating D(eff) for a mixture of overlapping obstacles of different shapes with comparable sizes.

An idea to explore: Visualization of ionization of amino acids using Mathematica.

Ionization of amino acids (AA) is very important concept in biochemistry. We integrate the mathematical concept of probability with biochemically relevant process of AA ionization. We visualize the ionization process with Mathematica software discussing intramolecular interactions between weakly acidic/basic functional groups and charge-pH variation of amino acids in water solution. The visualizations rely on the notion of probability of ionization of functional groups and demonstrate how the extent of ionization and charge varies with pH of the solution. The examples described include amino acids and weak diprotic acids and bases. The aim is to help students better appreciate the importance and consequences of AA ionization and correct some misconceptions.

Discharge Plasma Treatment as an Efficient Tool for Improved Poly(lactide) Adhesive-Wood Interactions.

Poly(lactide) (PLA) films obtained by thermoforming or solution-casting were modified by diffuse coplanar surface barrier discharge plasma (300 W and 60 s). PLA films were used as hot-melt adhesive in joints in oak wood. It was demonstrated that lap shear strength increased from 3.4 to 8.2 MPa, respectively, for the untreated and plasma-treated series. Pull-off tests performed on particleboard for the untreated and treated PLA films showed 100% cohesive failure. Pull-off strength tests on solid oak demonstrated adhesion enhancement from 3.3 MPa with the adhesion failure mode to 6.6 MPa with the cohesion failure mode for untreated and treated PLA. XPS revealed that carbonyl oxygen content increased by two-to-three-fold, which was confirmed in the Fourier-transform infrared spectroscopy experiments of the treated PLA. The water contact angle decreased from 66.4° for the pristine PLA to 49.8° after treatment. Subsequently, the surface free energy increased from 47.9 to 61.05 mJ/m2. Thus, it was clearly proven that discharge air plasma can be an efficient tool to change surface properties and to strengthen adhesive interactions between PLA and woody substrates.

Polysaccharides coatings on medical-grade PVC: a probe into surface characteristics and the extent of bacterial adhesion.

Medical-grade polyvinyl chloride was coated by polysaccharides through a novel physicochemical approach. An initial surface activation was performed foremost via diffuse coplanar surface barrier discharge plasma in air at ambient temperature and pressure. Then, radical graft copolymerization of acrylic acid through grafting-from pathway was directed to render a well-defined brush of high density, and finally a chitosan monolayer and chitosan/pectin alternating multilayer were bound onto the functionalized surfaces. Surface characteristics were systematically investigated using several probe techniques. In vitro bacterial adhesion and biofilm formation assays indicated that a single chitosan layer was incapable of hindering the adhesion of a Staphylococcus aureus bacterial strain, while up to 30% reduction was achieved by the chitosan/pectin layered assembly. On the other hand, chitosan and chitosan/pectin multilayer could retard Escherichia coli adhesion by 50% and 20%, respectively. Furthermore, plasma treated and graft copolymerized samples were also found effective to diminish the degree of adherence of Escherichia coli.

Diffusion in cytoplasm: effects of excluded volume due to internal membranes and cytoskeletal structures.

The intricate geometry of cytoskeletal networks and internal membranes causes the space available for diffusion in cytoplasm to be convoluted, thereby affecting macromolecule diffusivity. We present a first systematic computational study of this effect by approximating intracellular structures as mixtures of random overlapping obstacles of various shapes. Effective diffusion coefficients are computed using a fast homogenization technique. It is found that a simple two-parameter power law provides a remarkably accurate description of effective diffusion over the entire range of volume fractions and for any given composition of structures. This universality allows for fast computation of diffusion coefficients, once the obstacle shapes and volume fractions are specified. We demonstrate that the excluded volume effect alone can account for a four-to-sixfold reduction in diffusive transport in cells, relative to diffusion in vitro. The study lays the foundation for an accurate coarse-grain formulation that would account for cytoplasm heterogeneity on a micron scale and binding of tracers to intracellular structures.