Molecular gradients: an efficient approach for optimizing the surface properties of biomaterials and biochips

A variety of molecular gradients of alkanethiols with the structure HS-(CH(2))(m)-X (m = 15; X = COOH, CH(2)NH(2), or CH(3)) and oligo(ethylene glycol)-terminated alkanethiols with the structures HS-(CH(2))(15)-CO-NH-Eg(n) (n = 2, 4, or 6), HS-(CH(2))(15)-CO-NH-Eg(2)-(CH(2))(2)-NH-CO-(CH(2))(4)-biotin, and HS-(CH(2))(15)-CO-NH-Eg(6)-CH(2)-COOH were prepared on polycrystalline gold films. These gradients were designed to serve as model surfaces for fundamental studies of protein adsorption and immobilization phenomena. Ellipsometry, infrared spectroscopy, and X-ray photoelectron spectroscopy, operating in scanning mode, were used to monitor the layer composition, gradient profiles, tail group conformation, and overall structural quality of the gradient assemblies. The gradient profiles were found to be 4-10 mm wide, and they increased in width with increasing difference in molecular complexity between the thiols used to form the gradient. The oligo(ethylene glycol) thiols are particularly interesting because they can be used to prepare so-called conformational gradients, that is, gradients that display a variation in oligo(ethylene glycol) chain conformation from all trans on the extreme Eg(2,4) sides, via an amorphous-like phase in the mixing regimes, to helical at the extreme Eg(6) sides. We demonstrate herein a series of experiments where the above gradients are used to evaluate nonspecific binding of the plasma protein fibrinogen, and in agreement with previous studies, the highest amounts of nonspecifically bound fibrinogen were observed on all-trans monolayers, that is, on the extreme Eg(2,4) sides. Moreover, gradients between Eg(2) and a biotinylated analogue have been prepared to optimize the conditions for the immobilization of streptavidin. Ellipsometry and infrared spectroscopy reveal high levels of immobilization over a fairly broad range of compositions in the gradient regime, with a maximum between 50 and 60% of the biotinylated analogue in the monolayer. A pI gradient composed of (NH(3)(+)/COO(-))-terminated thiols was also prepared and evaluated with respect to its ability to separate differently charged proteins, pepsin, and lysozyme, on a solid surface.     

Structure and dynamic stability of cyclodextrin inclusion complexes with 1,4-disubstituted bicyclo[2.2.2]octanes

The properties of inclusion complexes of 1,4-di-R-bicyclo[2.2.2]octaves (R = H (1), Me (2), Cl (3), Br (4), and OH (5)) with cyclodextrins have been studied by NMR, microcalorimetry, and force-field computations. The compounds2 and3 (but not the other compounds) give dynamically stable 1:2 guest-host complexes with -cyclodextrin. Microcalorimetry of5 in water indicates a moderately strong 1:1 complex with - but weak complexes with - or -cyclodextrin. The behaviour depends on the subtle interplay size, polarity, hydrophobicity and type of solvent.     

Crystal structure and pyroelectric coefficient of Co(IO3)2 and structural relationships among the anhydrous noncentrosymmetric 3d-transition metal lodates

Cobalt iodate, Co(IO₃)₂, is pyroelectric at room temperature and crystallizes in the trigonal space group P3 with four formulas in the unit cell. The pyroelectric coefficient p₃ = 5.1(5) × 10^?5 Cm^?2 K^?1, and the lattice constants at 298 K are a = 10.9597(1) and c = 5.0774(1)Å. The crystal structure was solved from the Patterson function and a consideration of the structural similarities among the anhydrous 3d-transition metal iodates. Refinement was by the method of least squares using 1825 observed reflections measured with a four-circle diffractometer. The final agreement factor R = 0.050. Two of the three independent octahedrally coordinated cobalt atoms are disordered. The absolute orientation of the polar axis was determined with respect to the crystal morphology. The iodine atoms in the trigonal pyramidal iodate ions point toward the morphologically undeveloped end of the crystals, as does the positive sense of the spontaneous polarization: It is this end that develops a positive polarization on heating. The spontaneous polarization is estimated at about 22 × 10^?2 Cm^?2. The iodate ion arrangement is very similar to that in α-LiIO₃. The anhydrous noncentrosymmetric 3d-iodates may be classified into three isomorphous sets, with space group P6₃ and corresponding maximal subgroups P3 and P2₁. All three sets are isostructural with α-LiIO₃ except for the cation distribution. The ability of the iodate ion framework to accept a range of cations of different valences is discussed in terms of the tricapped trigonal-prismatic environment about the iodine atoms.     

On the internally contracted multireference CI method with full contraction

The configuration interaction (CI ) method where the efficiency of the generators of the unitary group is most fully exploited is the internally contracted multireference CI method. In the most recent version of this method the semi-internal configurations were kept uncontracted, which means that the number of configurations can still be quite large. In the present study the necessary formulas are derived for the case where the semi-internal states are also contracted. The highest density matrix that appears in these formulas is of order 5, and the computational treatment of this large matrix is discussed in detail.     

What Is a Quantum-Mechanical “Weak Value” the Value of?

A so called “weak value” of an observable in quantum mechanics (QM) may be obtained in a weak measurement + post-selection procedure on the QM system under study. Applied to number operators, it has been invoked in revisiting some QM paradoxes (e.g., the so called Three-Box Paradox and Hardy’s Paradox). This requires the weak value to be interpreted as a bona fide property of the system considered, a par with entities like operator mean values and eigenvalues. I question such an interpretation; it has no support in the basic axioms of quantum mechanics and it leads to unreasonable results in concrete situations.     

Development and application of an analytical protocol for evaluation of treatment processes for landfill leachates. II. Evaluation of leachate treatment efficiency of different steps in a constructed pilot plant

Different methods for treatment of leachate from a municipal solid waste (MSW) landfill were tested in a pilot plant. Raw leachate was pre-treated with aeration and sedimentation, followed by several parallel individual steps such as bioremediation, chemical oxidation, ozonation, and geo-bed filters. The efficiency of different treatment steps was evaluated according to one previously developed protocol, which includes measurements of several parameters such as conductivity, pH, nutrients, chloride, metals, organic compounds, and acute toxicity before and after a treatment step. The treatment steps which showed the highest efficiency towards organic pollutants in leachate were ozone treatment and chemical oxidation. The use of an adsorption filter, a geo-bed with a mixture of peat and bottom ash with ca 10% remaining carbon, also had good effects. A combination of pre-treatment and a geo-bed filter with peat and carbon ash gave the best overall treatment results when water-quality parameters such as total organic carbon and ammonia-nitrogen were also considered.     

Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor

Prediction of 3D structures of membrane proteins, and of G-protein coupled receptors (GPCRs) in particular, is motivated by their importance in biological systems and the difficulties associated with experimental structure determination. In the present study, a novel method for the prediction of 3D structures of the membrane-embedded region of helical membrane proteins is presented. A large pool of candidate models are produced by repacking of the helices of a homology model using Monte Carlo sampling in torsion space, followed by ranking based on their geometric and ligand-binding properties. The trajectory is directed by weak initial restraints to orient helices towards the original model to improve computation efficiency, and by a ligand to guide the receptor towards a chosen conformational state. The method was validated by construction of the β₁ adrenergic receptor model in complex with (S)-cyanopindolol using bovine rhodopsin as template. In addition, models of the dopamine D₂ receptor were produced with the selective and rigid agonist (R)-N-propylapomorphine ((R)-NPA) present. A second quality assessment was implemented by evaluating the results from docking of a library of 29 ligands with known activity, which further discriminated between receptor models. Agonist binding and recognition by the dopamine D₂ receptor is interpreted using the 3D structure model resulting from the approach. This method has a potential for modeling of all types of helical transmembrane proteins for which a structural template with sequence homology sufficient for homology modeling is not available or is in an incorrect conformational state, but for which sufficient empirical information is accessible.