Unbinding Molecular Recognition Force Maps of Localized Single Receptor Molecules by Atomic Force Microscopy

Atomic force microscopy is a technique capable to study biological recognition processes at the single‐molecule level. In this work we operate the AFM in a force‐scan based mode, the jumping mode, where simultaneous topographic and tip–sample adhesion maps are acquired. This approach obtains the unbinding force between a well‐defined receptor molecule and a ligand attached to the AFM tip. The method is applied to the avidin–biotin system. In contrast with previous data, we obtain laterally resolved adhesion maps of avidin–biotin unbinding forces highly correlated with single avidin molecules in the corresponding topographic map. The scanning rate 250 pixel s^?1 (2 min for a 128×128 image) is limited by the hydrodynamic drag force. We are able to build a rupture‐force distribution histogram that corresponds to a single defined molecule. Furthermore, we find that due to the motility of the polymer used as spacer to anchor the ligand to the tip, its direction at rupture does not generally coincide with the normal to the tip–sample, this introduces an appreciable error in the measured force.     

Time‐Dependent Density Functional Theory Molecular Dynamics Simulations of Liquid Water Radiolysis

The early stages of the Coulomb explosion of a doubly ionized water molecule immersed in liquid water are investigated with time‐dependent density functional theory molecular dynamics (TD–DFT MD) simulations. Our aim is to verify that the double ionization of one target water molecule leads to the formation of atomic oxygen as a direct consequence of the Coulomb explosion of the molecule. To that end, we used TD–DFT MD simulations in which effective molecular orbitals are propagated in time. These molecular orbitals are constructed as a unitary transformation of maximally localized Wannier orbitals, and the ionization process was obtained by removing two electrons from the molecular orbitals with symmetry 1B₁, 3A₁, 1B₂ and 2A₁ in turn. We show that the doubly charged H₂O²⁺ molecule explodes into its three atomic fragments in less than 4 fs, which leads to the formation of one isolated oxygen atom whatever the ionized molecular orbital. This process is followed by the ultrafast transfer of an electron to the ionized molecule in the first femtosecond. A faster dissociation pattern can be observed when the electrons are removed from the molecular orbitals of the innermost shell. A Bader analysis of the charges carried by the molecules during the dissociation trajectories is also reported.     

Probing the beta-1,3:1,4 glucanase, CtLic26A, with a thio-oligosaccharide and enzyme variants

The substrate binding regions of a beta-1,3:1,4 glucanase are revealed through structural analysis with a thio-oligosaccharide and kinetics of enzyme variants.     

Full-field photonic biosensors based on tunable bio-doped sol-gel glasses

A full-field generic photonic biosensor approach, which relies on a bio-doped polymeric strip waveguide configuration, is described. We show the potential of tailor-made hybrid polymeric materials prepared by sol-gel technology for the fabrication of ultra-compact biosensor devices, where both the transducer and the recognition elements are merged into one single microstructure. Such devices were fabricated by micromolding in capillaries (MIMIC) soft lithographic technique. In contrast to evanescent field sensors, the sensor response does not only rely on the interaction of the evanescent wave with the recognition element, but on the interaction of the whole field, thus enabling a reduction of the sensor dimensions and/or a decrease of its limit of detection (LOD). The potential of this generic approach was demonstrated by developing a biosensor for the detection of H(2)O(2) using horseradish peroxidase (HRP) as the doping agent. Solutions containing 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic) acid (ABTS) and different concentrations of H(2)O(2) were dispensed over the waveguide and the green-coloured cation radical ABTS*(+) product was mainly obtained inside the photonic structure, resulting in a maximum absorption increase of 2.5 a.u. at a set working wavelength of 670 nm over the H(2)O(2) concentration range studied. The sensor exhibited a sensitivity of (3.1+/-0.2) x 10(3) a.u./mol L(-1) and a limit of detection (LOD) of 4.4 x 10(-5) mol L(-1) H(2)O(2). These results anticipate that full-field waveguide microstructures based on bio-doped sol-gel polymers will enable the fabrication of cost-effective photonic biosensors. Moreover, the ease of fabrication by a soft lithography technique and the use of such polymeric materials are fully compatible with their integration in compact automatic analysis systems.     

The structure of the lanthanide aquo ions in solution as studied by 17O NMR spectroscopy and DFT calculations

The (17)O NMR shifts of aqueous samples of lanthanide triflates were measured and analysed. In these systems the triflate anion does not enter the first coordination sphere. The contact contribution to the shifts showed a break at Eu(III), which reflects a change in the number of water molecules in the first coordination sphere of the Ln(III) ion from 9 for La-Sm to 8 for the heavier lanthanides. This change in hydration number is accompanied by a change in the parameters governing the pseudo-contact shifts. Fitting of the data with tricapped trigonal prism and square antiprismatic geometries obtained by DFT (density function theory) calculations showed that the crystal field parameters for these geometries differ by an order of magnitude. The hyperfine coupling constant for both geometries was determined to be A/(Planck's constant)= -4.2 x 10(6) rad s(-1).     

Correlation between surface tension and void fraction in ionic liquids

An effort to systematize published and new data on the surface tension gamma of ionic liquids (ILs) is based on the hypothesis that the dimensionless surface tension parameter gamma V v (2/3)/ kT is a function of the void fraction x v = V v/ V m. The void volume V v is defined as the difference between the liquid volume V m occupied by an ion pair (known from cationic and anionic masses and liquid density measurements) and the sum V (+) + V (-) of the cationic and anionic volumes (known from crystal structures), while kT is the thermal energy. Our hypothesis that gamma V m (2/3)/ kT = G( x v) is initially based on cavity theory. It is then refined based on periodic lattice modeling, which reveals that the number N of voids per unit cell (hence the dimensionless surface tension) must depend on x v. Testing our hypothesis against data for the five ILs for which surface tension and density data are available over a wide range of temperatures collapses all of these data almost on a single curve G( x v), provided that slight (4%) self-consistent modifications are introduced on published crystallographic data for V (+) and V (-). An attempt to correlate the surface tension vs temperature data available for inorganic molten salts is similarly successful, but at the expense of larger shifts on the published ionic radii (8.8% for K; 3.3% for I). The collapsed G( x v) curves for ILs and inorganic salts do not overlap anywhere on x v space, and appear to be different from each other. The existence of a relation between gamma and x v is rationalized with a simple capillary model minimizing the energy. Our success in correlating surface tension to void fraction may apply also to other liquid properties.     

Conformational and electronic effects on the regioselectivity of the glycosylation of different anomers of N-dimethylmaleoyl-protected glucosamine acceptors

In a previous paper (Bohn et al., Carbohydr. Res., 2007, 342, 2522) the relative O3/O4 reactivities of both alpha- and beta-methyl glycosides of N-dimethylmaleoyl (DMM) glucosamine acceptors protected at O6 with three different groups were assessed by us, using two glycosyl donors. The alpha-anomers showed preferential or exclusive substitution at O3, whereas the beta-anomers gave preferential or exclusive substitution at O4. A DFT study of analogs of the reported acceptors indicates that whereas the beta-anomers carry the DMM ring parallel to the C2-H2 bond for steric reasons, the alpha-anomers tilt this ring producing a strong hydrogen bond between the H(O)3 and one of the DMM carbonyl groups. In this way, the O3 group becomes more nucleophilic and thus more reactive: both charge and Fukui functions on O3 and O4 in the model compounds support the experimental results. Surprisingly, the previously mentioned hydrogen bond is not the only driving force for the slant of the DMM group: the axial methoxyl group of the alpha-anomers also plays a role. The ease of rotation around the C2-N2 bond for DMM-protected analogs was assessed with different models. MP2 calculations using higher basis sets yield similar relative energy and charge values to those calculated using DFT.     

The energy landscape of a selective tumor-homing pentapeptide

Recently, a potentially powerful strategy based on phage-display libraries has been presented to target tumors via homing peptides attached to nanoparticles. The Cys-Arg-Glu-Lys-Ala (CREKA) peptide sequence has been identified as a tumor-homing peptide that binds to clotted plasmas proteins present in tumor vessels and interstitium. The aim of this work consists of mapping the conformational profile of CREKA to identify the bioactive conformation. For this purpose, a conformational search procedure based on modified simulated annealing combined with molecular dynamics was applied to three systems that mimic the experimentally used conditions: (i) the free peptide; (ii) the peptide attached to a nanoparticle; and (iii) the peptide inserted in a phage display protein. In addition, the free peptide was simulated in an ionized aqueous solution environment, which mimics the ionic strength of the physiological medium. Accessible minima of all simulated systems reveal a multiple interaction pattern involving the ionized side chains of Arg, Glu, and Lys, which induces a beta-turn motif in the backbone observed in all simulated CREKA systems.     

Graphite-silicone rubber composite electrode: Preparation and possibilities of analytical application

Composite electrodes were prepared using graphite powder and silicone rubber in different compositions. The use of such hydrophopic materials interned to diminish the swallowing observed in other cases when the electrodes are used in aqueous solutions for a long time. The composite was characterized for the response reproducibility, ohmic resistance, thermal behavior and active area. The voltammetric response in relation to analytes with known voltammetric behavior was also evaluated, always in comparison with the glassy carbon. The 70% (graphite, w/w) composite electrode was used in the quantitative determination of hydroquinone (HQ) in a DPV procedure in which a detection limit of 5.1x10(-8)molL(-1) was observed. HQ was determined in a photographic developer sample with errors lower then 1% in relation to the label value.     

Application of the aza-Wittig reaction to the synthesis of pyrazinothienotriazolopyrimidinones: a new tetracyclic ring system

A simple one-pot and efficient method is described for the synthesis of pyrazinothienopyrimidines 6 by domino processes involving aza-Wittig/intermolecular nucleophilic addition/intramolecular cyclization. A tandem aza-Wittig reaction of phosphazenes 7, derived from 6, with heterocumulenes (isocyanates, carbon disulfide or carbon dioxide) generates the pyrazinothienotriazolopyrimidinones 9, 11 and 12, respectively. Pyrazino[2′,3′:4,5]thieno[3,2-d]-1,2,4-triazolo[1,5-a]pyrimidin-4(3H)-ones 15 and bis(pyrazinothienotriazolopyrimidinones) 17 were synthesized by the intermolecular aza-Wittig reaction of phosphazenes 7 with acyl chlorides or α,ω-dichlorides followed by heterocyclization via imidoyl chloride intermediate 16. Further S-alkylation of 11 and reaction of 6 with phosgeniminium chloride produce 2-alkylthio- and 2-N,N-dimethylaminopyrazinothienotriazolopyrimidinones 13 and 19, respectively.