Combinatorial Probes for High‐Throughput Electrochemical Analysis of Circulating Nucleic Acids in Clinical Samples

The analysis of circulating tumour nucleic acids (ctNAs) provides a minimally invasive way to assess the mutational spectrum of a tumour. However, effective and practical methods for analyzing this emerging class of markers are lacking. Analysis of ctNAs using a sensor‐based approach has notable challenges, as it is vital to differentiate nucleic acids from normal cells from mutation‐bearing sequences emerging from tumours. Moreover, many genes related to cancer have dozens of different mutations. Herein, we report an electrochemical approach that directly detects genes with mutations in patient serum by using combinatorial probes (CPs). The CPs enable detection of all of the mutant alleles derived from the same part of the gene. As a proof of concept, we analyze mutations of the EGFR gene, which has more than 40 clinically relevant alterations that include deletions, insertions, and point mutations. Our CP‐based approach accurately detects mutant sequences directly in patient serum.     

Chemoselective Suzuki-Miyaura reactions of 4-bromo-3-O-triflyl-estrone. Synthesis and atropisomerism of arylated estrones

4-Bromo-3-O-triflyl-estrone has been synthesized in 2 steps from estrone and was successfully employed in chemoselective palladium catalysed Suzuki-Miyaura reactions. Mono- and bis-arylations were carried out selectively by variation of ligands and solvents. Overall 19 derivatives of mono- and bis-arylated estrones were synthesized under optimized conditions in high yields. Various products showed atropisomerism which was studied in detail by NMR spectroscopy.     

The double Renner effect in the X(2)A" and A(2)A' electronic states of HO(2)

A theoretical investigation of the X(2)A" and A(2)A' electronic states of the HO(2) radical is reported. Both electronic states have nonlinear equilibrium geometries and they correlate with a (2)Pi state at linear geometries so that they exhibit the Renner effect. In highly excited bending states, there is tunneling between two equivalent minima (with geometries where the H nucleus is bound to one, or the other, of the two O nuclei), and the two linear geometries H-O-O and O-O-H become accessible to the molecule. Thus, HO(2) affords an example of the so-called double Renner effect. Three-dimensional potential energy surfaces for the X(2)A" and A(2)A' electronic states of HO(2) have been calculated ab initio and the global potential energy surfaces for the states have been constructed. These surfaces have been used, in conjunction with the computer program DR [Odaka et al., J. Mol. Structure 795, 14 (2006); Odaka et al., J. Chem. Phys. 126, 094301 (2007)], for calculating HO(2) rovibronic energies in the "double-Renner"-degenerate electronic states X(2)A" and A(2)A'. The results of the ab initio calculations, the rovibronic energies obtained, and analyses of the wavefunctions for selected states are presented.     

Synthesis and structural investigation of the compounds containing HF2 anions: Ca(HF2)2, Ba4F4(HF2)(PF6)3 and Pb2F2(HF2)(PF6)

Three new compounds Ca(HF₂)₂, Ba₄F₄(HF₂)(PF₆)₃ and Pb₂F₂(HF₂)(PF₆) were obtained in the system metal(II) fluoride and anhydrous HF (aHF) acidified with excessive PF₅. The obtained polymeric solids are slightly soluble in aHF and they crystallize out of their aHF solutions. Ca(HF₂)₂ was prepared by simply dissolving CaF₂ in a neutral aHF. It represents the second known compound with homoleptic HF environment of the central atom besides Ba(H₃F₄)₂. The compounds Ba₄F₄(HF₂)(PF₆)₃ and Pb₂F₂(HF₂)(PF₆) represent two additional examples of the formation of a polymeric zigzag ladder or ribbon composed of metal cation and fluoride anion (MF⁺)_n besides PbF(AsF₆), the first isolated compound with such zigzag ladder. The obtained new compounds were characterized by X-ray single crystal diffraction method and partly by Raman spectroscopy. Ba₄F₄(HF₂)(PF₆)₃ crystallizes in a triclinic space group P1¯ with a=4.5870(2) Å, b=8.8327(3) Å, c=11.2489(3) Å, α=67.758(9)°, β=84.722(12), γ=78.283(12)°, V=413.00(3) Å³ at 200 K, Z=1 and R=0.0588. Pb₂F₂(HF₂)(PF₆) at 200 K: space group P1¯, a=4.5722(19) Å, b=4.763(2) Å, c=8.818(4) Å, α=86.967(10)°, β=76.774(10)°, γ=83.230(12)°, V=185.55(14) ų, Z=1 and R=0.0937. Pb₂F₂(HF₂)(PF₆) at 293 K: space group P1¯, a=4.586(2) Å, b=4.781(3) Å, c=8.831(5) Å, α=87.106(13)°, β=76.830(13)°, γ=83.531(11)°, V=187.27(18) Å³, Z=1 and R=0.072. Ca(HF₂)₂ crystallizes in an orthorhombic Fddd space group with a=5.5709(6) Å, b=10.1111(9) Å, c=10.5945(10) Å, V=596.77(10) Å³ at 200 K, Z=8 and R=0.028.     

Collocation by singular splines

Splines determined by the kernel of the differential operator are known to be useful to solve the singular boundary value problems of the form . One of the most successful methods is the collocation method based on special Chebyshev splines. We investigate the construction of the associated B-splines based on knot-insertion algorithms for their evaluation, and their application in collocation at generalized Gaussian points. Specially, we show how to obtain these points as eigenvalues of a symmetric tridiagonal matrix of order k. This research was supported by Grant 037-1193086-2771, by the Ministry of science, education and sports of the Republic of Croatia.     

Rheological behavior of self-assembling PEG-beta-cyclodextrin/PEG-cholesterol hydrogels

The rheological properties of a recently developed self-assembling hydrogel system composed of beta-cyclodextrin (betaCD)- and cholesterol-derivatized 8-arm star-shaped poly(ethylene glycol) (PEG8) were investigated. To understand and predict the gel rheological properties, data fitting with the Maxwell model as well as comparing the system's concentration-dependent behavior with Cates' model for reversibly breaking chains were performed. To investigate the influence of the polymer architecture, networks were also prepared by replacing the cholesterol-derivatized 8-arm star-shaped PEG by linear bifunctional PEG-cholesterol or by using 4-arm instead of 8-arm polymers. Rheological analysis showed that the 8-arm polymer-based mixtures yielded tight viscoelastic networks, but their storage and loss moduli significantly deviated from those predicted by the Maxwell model. The scaling of the plateau moduli, relaxation times, and zero-shear viscosities with concentration for gels composed of 8-arm cholesterol- and betaCD-derivatized PEG followed a power law with exponents higher than predicted by Cates' model. On the other hand, hydrogels in which linear bifunctional PEG-cholesterol was used instead of 8-arm star-shaped PEG-cholesterol or which were based on 4-arm polymers showed a substantially better fit with the Maxwell model and reduced differences between empirical and Cates' theoretical scaling exponents. Rheological analysis also showed that the hydrogels were thermoreversible. At low temperatures, the gels showed viscoelastic behavior due to slow overall relaxation of the polymer chains. At higher temperatures, however, a reduced number of betaCD/cholesterol complexes and concomitant faster chain relaxation processes eventually led to liquid-like behavior. The relationship between temperature and the relaxation time was used to determine an activation energy of 46 kJ/mol for breaking and reptation of the polymers.     

Glycine enolates: the effect of formation of iminium ions to simple ketones on alpha-amino carbon acidity and a comparison with pyridoxal iminium ions

Equilibrium constants in D2O were determined by 1H NMR analyses for formation of imines/iminium ions from addition of glycine methyl ester to acetone and from addition of glycine to phenylglyoxylate. First-order rate constants, also determined by 1H NMR, are reported for deuterium exchange between solvent D2O and the alpha-amino carbon of glycine methyl ester and glycine in the presence of increasing concentrations of ketone and Br?nsted bases. These rate and equilibrium data were used to calculate second-order rate constants for deprotonation by DO- and by Br?nsted bases of the alpha-imino carbon of the ketone adducts. Formation of the iminium ion between acetone and glycine methyl ester and between phenylglyoxylate and glycine is estimated to cause 7 unit and 15 unit decreases, respectively, in the pKa's of 21 and 29 for deprotonation of the parent carbon acids. The effect of formation of iminium ions to phenylglyoxylate and to 5'-deoxypyridoxal (DPL) [Toth, K.; Richard, J. P. J. Am. Chem. Soc. 2007, 129, 3013-3021] on the carbon acidity of glycine is similar. However, DPL is a much better catalyst than phenylglyoxylate of deprotonation of glycine, because of the exceptionally large thermodynamic driving force for conversion of the amino acid and DPL to the reactive iminium ion.     

A Computational and Experimental Approach Linking Disorder,High‐Pressure Behavior,and Mechanical Properties in UiO Frameworks

Whilst many metal–organic frameworks possess the chemical stability needed to be used as functional materials, they often lack the physical strength required for industrial applications. Herein, we have investigated the mechanical properties of two UiO‐topology Zr‐MOFs, the planar UiO‐67 ([Zr₆O₄(OH)₄(bpdc)₆], bpdc: 4,4′‐biphenyl dicarboxylate) and UiO‐abdc ([Zr₆O₄(OH)₄(abdc)₆], abdc: 4,4′‐azobenzene dicarboxylate) by single‐crystal nanoindentation, high‐pressure X‐ray diffraction, density functional theory calculations, and first‐principles molecular dynamics. On increasing pressure, both UiO‐67 and UiO‐abdc were found to be incompressible when filled with methanol molecules within a diamond anvil cell. Stabilization in both cases is attributed to dynamical linker disorder. The diazo‐linker of UiO‐abdc possesses local site disorder, which, in conjunction with its longer nature, also decreases the capacity of the framework to compress and stabilizes it against direct compression, compared to UiO‐67, characterized by a large elastic modulus. The use of non‐linear linkers in the synthesis of UiO‐MOFs therefore creates MOFs that have more rigid mechanical properties over a larger pressure range.     

Electromembrane extraction of gonadotropin‐releasing hormone agonists from plasma and wastewater samples

In the present study, for the first time electromembrane extraction followed by high performance liquid chromatography coupled with ultraviolet detection was optimized and validated for quantification of four gonadotropin‐releasing hormone agonist anticancer peptides (alarelin, leuprolide, buserelin and triptorelin) in biological and aqueous samples. The parameters influencing electromigration were investigated and optimized. The membrane consists 95% of 1‐octanol and 5% di‐(2‐ethylhexyl)‐phosphate immobilized in the pores of a hollow fiber. A 20 V electrical field was applied to make the analytes migrate from sample solution with pH 7.0, through the supported liquid membrane into an acidic acceptor solution with pH 1.0 which was located inside the lumen of hollow fiber. Extraction recoveries in the range of 49 and 71% within 15 min extraction time were obtained in different biological matrices which resulted in preconcentration factors in the range of 82–118 and satisfactory repeatability (7.1 < RSD% < 19.8). The method offers good linearity (2.0–1000 ng/mL) with estimation of regression coefficient higher than 0.998. The procedure allows very low detection and quantitation limits of 0.2 and 0.6 ng/mL, respectively. Finally, it was applied to determination and quantification of peptides in human plasma and wastewater samples and satisfactory results were yielded.     

Homogeneous tritylation of cellulose in 1-butyl-3-methylimidazolium chloride

1-Alkyl-3-methylimidazolium-based ionic liquids, having chloride as a counter ion, were studied for cellulose solubility; and the influence of different alkyl chain lengths was also investigated. The alkyl chain length was incrementally varied from ethyl to decyl to determine structure-dissolution properties; a distinct odd-even effect was observed for short chain lengths. In addition, the tritylation of cellulose was performed in 1-butyl-3-methylimidazolium chloride using pyridine as base. The influences of reaction time and the ratio of trityl chloride per cellulose monomer unit on the degree of substitution were investigated in detail by elemental analysis and 1H NMR spectroscopy. A DS of around 1 was obtained after 3 h reaction time using a six fold excess of trityl chloride.