Principles and calibration of collinear photofragmentation and atomic absorption spectroscopy

The kinetics of signal formation in collinear photofragmentation and atomic absorption spectroscopy (CPFAAS) are discussed, and theoretical equations describing the relation between the concentration of the target molecule and the detected atomic absorption in case of pure and impure samples are derived. The validity of the equation for pure samples is studied experimentally by comparing measured target molecule concentrations to concentrations determined using two other independent techniques. Our study shows that CPFAAS is capable of measuring target molecule concentrations from parts per billion (ppb) to hundreds of parts per million (ppm) in microsecond timescale. Moreover, the possibility to extend the dynamic range to cover eight orders of magnitude with a proper selection of fragmentation light source is discussed. The maximum deviation between the CPFAAS technique and a reference measurement technique is found to be less than 5 %. In this study, potassium chloride vapor and atomic potassium are used as a target molecule and a probed atom, respectively.     

On Certain Extensions of a Rotation Invariant Markov Process

Let (X _t ,P ^x ) be a rotation invariant (RI) Feller process on R ^d {0}, d2. We study certain type of strong Markov extensions of (X _t ,P ^x ) to R ^d . It turns out that that the unique (RI) extension always exists and is of that type. We give a kind of quasi-ergodicy condition (E) under which the (RI) extension is the only extension of that type. A class of processes fulfilling (E) is also characterized.     

The De Giorgi measure and an obstacle problem related to minimal surfaces in metric spaces

We study the existence of a set with minimal perimeter that separates two disjoint sets in a metric measure space equipped with a doubling measure and supporting a Poincaré inequality. A measure constructed by De Giorgi is used to state a relaxed problem, whose solution coincides with the solution to the original problem for measure theoretically thick sets. Moreover, we study properties of the De Giorgi measure on metric measure spaces and show that it is comparable to the Hausdorff measure of codimension one. We also explore the relationship between the De Giorgi measure and the variational capacity of order one. The theory of functions of bounded variation on metric spaces is used extensively in the arguments.     

Supramolecular chirogenesis in zinc porphyrins: interaction with bidentate ligands,formation of tweezer structures,and the origin of enhanced optical activity

The complexation behavior, binding properties, and spectral parameters of supramolecular chirality induction in the achiral host molecule, syn (face-to-face conformation) ethane-bridged bis(zinc porphyrin), upon interaction with chiral bidentate guests (diamines and amino alcohols) have been studied by means of UV-vis, CD, fluorescence, (1)H NMR, and ESI MS techniques. It was found that the guest structure plays a decisive role in the chirogenesis pathway. The majority of bidentate ligands (except those geometrically unsuitable) exhibit two major equilibria steps: the first guest ligation leading to formation of the 1:1 host-guest tweezer structure (K(1)) and the second guest molecule ligation (K(2)) forming the anti bis-ligated species (1:2). The second ligation is much weaker (K(1) > K(2)) due to the optimal geometry and stability of the 1:1 tweezer complex. The enhanced conformational stability of the tweezer complex ensures an efficient chirality transfer from the chiral guest to the achiral host, consequently inducing a remarkably high optical activity in the bis-porphyrin.     

MM-PBSA free energy analysis of endo-1,4-xylanase II (XynII)-substrate complexes: binding of the reactive sugar in a skew boat and chair conformation

The binding of xylotetraose in different conformations to the active site of endo-1,4-beta-xylanase II (XynII) from Trichoderma reesei was studied using molecular dynamics (MD) simulations and free energy analyses employing the MM-PBSA (Molecular Mechanics-Poisson-Boltzmann Surface Area) method. MD simulations of 1 ns were done for the substrate xylotetraose having the reactive sugar, which is bound in the -1 subsite of XynII in the 4C1 (chair) and 2So (skew boat) ground state conformations, and for the transition state of the XynII catalysed hydrolysis of the beta-glycosidic linkage. According to the simulations and free energy analysis, XynII binds the substrate with the -1 sugar in the 2So conformation 59.8 kJ mol(-1) tighter than the substrate with the sugar in the 4C1 conformation. The reactive 2So conformation resembles closely the reaction transition state and has the breaking glycosidic bond in a pseudo-axial orientation ready for facile bond cleavage. The transition state was calculated to be bound 77.1 kJ mol(-1) tighter than the 4C1 ground state conformation. The molecular mechanical interaction energy between the enzyme and the reactive pyranoside unit at the -1 subsite was 75.7 kJ mol(-1) more favorable for the binding of the 2So conformation than the 2C1 conformation, explaining the clearly tighter binding of the reactive structure The results of this study indicate that in the Michaelis complex XynII, a member of the family 11 xylanase, the substrate is bound in a skew boat conformation and in the catalytic reaction, the -1 sugar proceeds from the 4C1 conformation through 2So to the transition state with the -1 sugar in the 2,5B conformation.     

Supramolecular chirogenesis in zinc porphyrins: equilibria, binding properties, and thermodynamics

Complexation mechanism, binding properties and thermodynamic parameters of supramolecular chirality induction in the achiral host molecule, syn (face-to-face conformation) ethane-bridged bis(zinc porphyrin), upon interaction with chiral monoamine and monoalcohol guests have been studied by means of the UV-vis, CD, (1)H NMR, and ESI MS techniques. It was found that the chirogenesis process includes three major equilibria steps: the first guest ligation to a zinc porphyrin subunit of the host (K(1)), syn to anti conformational switching (K(S)), and further ligation by a second guest molecule to the remaining ligand-free zinc porphyrin subunit (K(2)), thus forming the final bis-ligated species possessing supramolecular chirality. The validity of this equilibria model is confirmed by the excellent match between the calculated and experimentally observed spectral parameters of the bis-ligated species. The second ligation proceeds in a cooperative manner as K(2) > K(1) for all supramolecular systems studied, regardless of the structure of the chiral ligand used. The binding properties are highly dependent on the nature of the functional group (amines are stronger binders than alcohols) and on the structure of the chiral guests (primary and aliphatic amines have overall binding constant values greater than those of secondary and aromatic amines, respectively).     

Grafting of functionalized silica particles with poly(acrylic acid)

Two different methods to graft silica particles with poly(acrylic acid) (PAA) were studied. In the first method PAA was reacted with 1,1′‐carbonyldiimidazole to give functionalized PAA. The resulting activated carbonyl group reacted easily with 3‐aminopropyl‐functionalized silica at low temperatures. In the second method 3‐glycidoxypropyl‐functionalized silica particles were reacted directly with PAA by using magnesium chloride as a catalyst. Different molecular weights of PAAs were used in order to investigate the effect of molecular weight on grafting yields in both methods. The grafting yields were determined with thermogravimetric analysis (TGA). All products were also investigated with IR. The results showed that the yields of reactions performed at ambient temperature by using 1,1′‐carbonyldiimidazole‐functionalized PAA were the same as with a direct reaction of unfunctionalized PAA and 3‐aminopropyl‐functionalized silica performed at 153°C. Also in reactions between 3‐glycidoxypropyl‐functionalized silica and PAA the yields were satisfactory. Copyright © 2006 John Wiley & Sons, Ltd.     

Observation of topical catalysis by sphingomyelinase coupled to microspheres

Sphingomyelinase, SMase (EC 3.1.4.12), was coupled onto amino-derivatized acrylate microspheres and was shown to retain its catalytic activity. The immobilized enzyme allows one to carry out topical enzymatic reaction in a controlled manner. Accordingly, these spheres were held with a micropipet and using micromanipulator brought into contact with a giant liposome membrane composed of phosphatidylcholine and sphingomyelin (SOPC/C16:0-SM, 0.75:0.25, molar ratio), representing the substrate for the immobilized enzyme. The macroscopic consequences of the enzyme reaction were visualized using fluorescence microscopy as well as differential interference contrast microscopy. The surface contact of the giant vesicle and immobilized enzyme causes membrane microdomain formation and domain clustering (capping) in the membrane and subsequent shedding of small vesicles from the membrane into the interior of the giant liposome. The method described represents a novel approach to study enzymatic reactions and allows manipulating giant vesicles as well as cultured cells in a spatially controlled manner.     

Versatile bio-ink for covalent immobilization of chimeric avidin on sol-gel substrates

A bio-ink for covalent deposition of thermostable, high affinity biotin-binding chimeric avidin onto sol-gel substrates was developed. The bio-ink was prepared from heterobifunctional crosslinker 6-maleimidohexanoic acid N-hydroxysuccinimide which was first reacted either with 3-aminopropyltriethoxysilane or 3-aminopropyldimethylethoxysilane to form silane linkers 6-maleimide-N-(3-(triethoxysilyl)propyl)hexanamide or -(ethoxydimethylsilyl)propyl)-hexanamide. C-terminal cysteine genetically engineered to chimeric avidin was reacted with the maleimide group of silane linker in methanol/PBS solution to form a suspension, which was printed on sol-gel modified PMMA film. Different concentrations of chimeric avidin and ratios between silane linkers were tested to find the best properties for the bio-ink to enable gravure or inkjet printing. Bio-ink prepared from 3-aminopropyltriethoxysilane was found to provide the highest amount of active immobilized chimeric avidin. The developed bio-ink was shown to be valuable for automated fabrication of avidin-functionalized polymer films.