Water-solubilisation and bio-conjugation of a red-emitting BODIPY marker

The synthesis and preliminary bio-conjugation studies of a novel water-soluble red-emitting di-styryl BODIPY dye are disclosed. Aggregation behaviour of this compound under physiological conditions was suppressed by specific introduction of a di-sulfonated peptide-based linker at the meso phenyl substituent, sultonated styryl arms and short polyethyleneglycol chains at the boron center. Thus, a good quantum yield of 22% in PBS for this red-emitting BODIPY was obtained. Introduction of an activated ester function enabled successful bio-conjugation to monoclonal antibodies and proteins.     

Sorption speciation of nickel(II) onto Ca-montmorillonite: batch, EXAFS techniques and modeling

The sorption speciation of Ni(II) on Ca-montmorillonite was evaluated using a combination of batch experiments, extended X-ray absorption fine structure (EXAFS) spectroscopy and modeling. The pH and temperature at the aqueous-montmorillonite interface affects both the extent of Ni(II) sorption as well as the local atomic structure of the adsorbed Ni(II) ions. At 0.001 mol L(-1) Ca(NO(3))(2) and low pH, the study reveals that the majority of Ni(II) is adsorbed in the interlayers of Ca-montmorillonite coordinated by six water molecules in an octahedron as an outer-sphere complex. At higher pH, inner-sphere surface complexes are formed. The Ni-Si/Al distances (R(Ni-Al) = 3.00 ?, R(Ni-Si1) = 3.10 ? and R(Ni-Si2) = 3.26 ?) determined by EXAFS confirm the formation of mononuclear complexes located at the edges of Ca-montmorillonite platelets at pH 7.5 and 8.5. At pH 10.0, the Ni-Ni/Si distances (R(Ni-Ni) = 3.07 ? and R(Ni-Si) = 3.26 ?) indicates the formation of Ni-phyllosilicate precipitates. A rise in temperature promotes inner-sphere complexation, which in turn leads to an increase in Ni(II) sorption on Ca-montmorillonite. Sorption edges are fitted excellently by surface complexation model (SCM) with the aid of surface species determined from EXAFS spectroscopy.     

Metal-containing peptide nucleic acid conjugates

Peptide Nucleic Acids (PNAs) are non-natural DNA/RNA analogues with favourable physico-chemical properties and promising applications. Discovered nearly 20 years ago, PNAs have recently re-gained quite a lot of attention. In this Perspective article, we discuss the latest advances on the preparation and utilisation of PNA monomers and oligomers containing metal complexes. These metal- conjugates have found applications in various research fields such as in the sequence-specific detection of nucleic acids, in the hydrolysis of nucleic acids and peptides, as radioactive probes or as modulators of PNA·DNA hybrid stability, and last but not least as probes for molecular and cell biology.     

Regioselective synthesis of 5-monostyryl and 2-tetracyanobutadiene BODIPY dyes

Several unsymmetrically 2,5-disubstituted BODIPY dyes were obtained from 2-substituted derivatives (iodo, ethynylaryl) using a regioselective Knoevenagel condensation reaction with dimethylaminobenzaldehyde. The unsaturated, unsymmetrical 2-ethynyl-5-styryl-BODIPY undergoes a regioselective [2 + 2] cycloaddition reaction with tetracyanoethylene leading to the 1,1,4,4-tetracyanobuta-1,3-diene (TCBD) derivative. This shows rich redox activity with two reversible oxidation and three reversible reduction waves at +0.72 V, +1.04 V; -0.32 V, -0.78 V, and -1.50 V, respectively.     

Prebiotic chemistry: A fuzzy field

If prebiotic chemistry is defined as the study of the chemical steps, which lead to the first organisms, a clear-cut definition of “living organism” is needed. Unfortunately, no unambiguous and universally accepted definition exists for the concept “living”. Under these conditions, fuzzy logic is probably the methodological tool that can best be used to handle questions pertaining to “the origin of life”. A conventional scale must, however, be defined which interestingly enough, depends necessarily on our present-day scientific knowledge.     

Oxyfold: A Simple and Efficient Solid‐Supported Reagent for Disulfide Bond Formation

The synthesis and use of novel polymer‐supported reagents for disulfide bond formation is described. This family of supported reagents consists of a series of oxidized methionines grafted onto a solid support. Their cost and the simplicity of their preparation through N‐carboxyanhydride polymerization on beads make them reactants of choice for the formation of disulfide bridges in peptides.     

Waste-recycling Monte Carlo with optimal estimates: application to free energy calculations in alloys

The estimator proposed recently by Delmas and Jourdain for waste-recycling Monte Carlo achieves variance reduction optimally with respect to a control variate that is evaluated directly using the simulation data. Here, the performance of this estimator is assessed numerically for free energy calculations in generic binary alloys and is compared to those of other estimators taken from the literature. A systematic investigation with varying simulation parameters of a simplified system, the anti-ferromagnetic Ising model, is first carried out in the transmutation ensemble using path-sampling. We observe numerically that (i) the variance of the Delmas-Jourdain estimator is indeed reduced compared to that of other estimators; and that (ii) the resulting reduction is close to the maximal possible one, despite the inaccuracy in the estimated control variate. More extensive path-sampling simulations involving an FeCr alloy system described by a many-body potential additionally show that (iii) gradual transmutations accommodate the atomic frustrations; thus, alleviating the numerical ergodicity issue present in numerous alloy systems and eventually enabling the determination of phase coexistence conditions.     

Reachability,persistence, and constructive chemical reaction networks (part II): a formalism for species composition in chemical reaction network theory and application to persistence

Chemical Reaction Network Theory uses mathematics to study systems of reactions and infer their properties from their structure. At the onset is an abstract definition of a chemical reaction network which is very general and is pertinent beyond chemistry, e.g. in modeling interactions of microscopic and macroscopic living species. This allows the theory to provide widely applicable theorems. It also results in that the idea of chemical composition is mostly used implicitly in examples to illustrate theorems, not explicitly to establish new properties. In this paper we propose a formalism for species composition in a way that generalizes the idea of atomic composition—for instance, elementary species will extend the idea of atoms. We envision that this formalism could lead to more theorems on classes of networks that are of interest in biochemistry. Toward that prospect, we prove that if there is no isomerism among elementary species, and if a newly formalized and widely applicable reversibility condition holds, then a reaction network is vacuously persistent: no species will tend to extinction if all species are implicitly present at initial time. This paper is the second in a series of three articles. The first paper studies vacuous persistence and the third one probes a class of enzymatic networks.     

Chemistry at boron: synthesis and properties of red to near-IR fluorescent dyes based on boron-substituted diisoindolomethene frameworks

A general method for the synthesis of difluorobora-diisoindolomethene dyes with phenyl, p-anisole, or ethyl-thiophene substituents has been developed. The nature of the substituents allows modulation of the fluorescence from 650 to 780 nm. Replacement of the fluoro ligands by ethynyl-aryl or ethyl residues is facile using Grignard reagents. Several X-ray molecular structures have been determined, allowing establishment of structure-fluorescence relationships. When the steric crowding around the boron center is severe, the aromatic substituents α to the diisoindolomethene nitrogens are twisted out of coplanarity, and hypsochromic shifts are observed in the absorption and emission spectra. This shift reached 91 nm with ethyl substituents compared to fluoro groups. When ethynyl linkers are used, the core remains flat, and a bathochromic shift is observed. All the fluorophores exhibit relatively high quantum yields for emitters in the 650-800 nm region. When perylene or pyrene residues are connected to the dyes, almost quantitative energy transfer from them to the dye core occurs, providing large virtual Stokes shifts spanning from 8000 to 13,000 cm(-1) depending on the nature of the dye. All the dyes are redox active, providing the Bodipy radical cation and anion in a reversible manner. Stepwise reduction or oxidation to the dication and dianion is feasible at higher potentials. We contend that the present work paves the way for the development of a new generation of stable, functionalized luminophores for bioanalytical applications.     

Spectral estimation on the sphere with needlets: high frequency asymptotics

The angular power spectrum of a stationary random field on the sphere is estimated from the needlet coefficients of a single realization, observed with increasingly fine resolution. The estimator we consider is the one recently used in practice by (Faÿ et al. 2008) to estimate the power spectrum of the Cosmic Microwave Background. The consistency of the estimator, in the asymptotics of high frequencies, is proved for a model with a stationary Gaussian field corrupted by heteroscedastic noise and missing data.