Evaluation of cooperativity for phase transitions in two- and three-dimensional systems

Use of the so-called "cooperative unit" (readily obtainable from the midpoint slope of phase transition curves) is discussed for the determination of cluster sizes and cooperative interaction energies. This quantity has been commonly employed in a rather empirical way since its correct interpretation is known only for some special cases (linear systems, all-or-none transitions). It is shown in the framework of a lattice model (Ising model) that the cooperative unit may be interpreted in terms of correlation functions and that it defines an average cluster corresponding to the patch size as obtained from scattering experiments. Relations between the cooperative unit and a cooperativity parameter are given for various lattices. Different types of transition curves are discussed using a simple analytical formalism, the quasichemical approximation. Some important nonideality effects are investigated which may lead to a "smearing-out" of first-order transitions.     

Biorefining of platinum group metals from model waste solutions into catalytically active bimetallic nanoparticles

Bacteria can fabricate platinum group metal (PGM) catalysts cheaply, a key consideration of industrial processes and waste decontaminations. Biorecovery of PGMs from wastes is promising but PGM leachates made from metallic scraps are acidic. A two‐step biosynthesis ‘pre‐seeds’ metallic deposits onto bacterial cells benignly; chemical reduction of subsequent metal from acidic solution via the seeds makes bioscaffolded nanoparticles (NPs). Cells of Escherichia coli were seeded using Pd(II) or Pt(IV) and exposed to a mixed Pd(II)/Pt(IV) model solution under H₂ to make bimetallic catalyst. Its catalytic activity was assessed in the reduction of Cr(VI), with 2 wt% or 5 wt% preloading of Pd giving the best catalytic activity, while 1 wt% seeds gave a poorer catalyst. Use of Pt seeds gave less effective catalyst in the final bimetallic catalyst, attributed to fewer and larger initial seeds as shown by electron microscopy, which also showed a different pattern of Pd and Pt deposition. Bimetallic catalyst (using cells preloaded with 2 wt% Pd) was used in the hydrogenation of soybean oil which was enhanced by ~fourfold using the bimetallic catalyst made from a model waste solution as compared to 2 wt% Pd preloaded cells alone, with a similar selectivity to cis C18:1 product as found using a Pd‐Al₂O₃ commercial catalyst.     

Software techniques for two- and three-dimensional kinematic measurements of biological and biomimetic systems

Researchers studying aspects of locomotion or movement in biological and biomimetic systems commonly use video or stereo video recordings to quantify the behaviour of the system in question, often with an emphasis on measures of position, velocity and acceleration. However, despite the apparent simplicity of video analysis, it can require substantial investment of time and effort, even when performed with adequate software tools. This paper reviews the underlying principles of video and stereo video analysis as well as its automation and is accompanied by fully functional and freely available software implementation.     

Synthesis and application of methyleneoxy pseudodipeptide building blocks in biologically active peptides

Summary. Pseudodipeptides H-Phe[CH₂O]Phe-OH, H-Tyr[CH₂O] Asp-OH and H-Pro[CH₂O]-D-Thr-OH were synthesized using the intramolecular Williamson reaction via substituted morpholin-3-one ring with the nitrogen atom protected with bulky Boc group. This protection and the substituent at C₅ position induced the stereospecific alkylation at the C₂ position introducing the side chain of the C-terminal amino acid mimetic. In the first pseudodipeptide a quenching of the enolate with benzaldehyde was followed by dehydration and corresponding double bond was hydrogenated with high stereospecific purity. In the other pseudodipeptides, this alkylation was carried out directly by tert-butyl 2-bromoacetate or acetaldehyde. However, in the latter reaction an R configuration of C₃ substituent in conjugated lactame ring was determined using a NOE NMR. Consequently, after opening this ring by acidic hydrolysis, the C-terminal part of corresponding pseudodipeptide possessed the side-chain of D-Thr mimetic, contrary to former one. Synthesized pseudodipeptides were introduced into HIV protease inhibitors and into peptides with oostatic activity.     

DNA self-assembling systems: branched oligonucleotides as building blocks and monitoring by pyrene excimer band formation

The construction of a DNA self-assembling system created by four Y-shaped branched oligodeoxynucleotide building blocks has been studied. The assembly was verified by changes in the fluorescence emission spectra and revealed an additive effect in pyrene excimer band formation during DNA self-assembly.     

Chitosan as an active support for assembly of metal nanoparticles and application of the resultant bioconjugates in catalysis

Metal nanoparticle-chitosan (NPs-chitosan) bioconjugates were formed by exposure of chitosan to an aqueous solution of metal salts under thermal treatment. The metal nanoparticles that are formed strongly bound to chitosan, which encouraged us to investigate their catalytic performance. It was demonstrated that the metal NPs-chitosan bioconjugates functioned as effective catalysts for the reduction of 4-nitrophenol in the presence of NaBH₄, which was monitored by means of spectrophotometry as a function of reaction time. The silver NPs-chitosan bioconjugates exhibited excellent catalytic activity and were reusable for up to seven cycles. In contrast, the gold NPs-chitosan catalyst displayed poor catalytic activity, even in the second cycle. A highlight of our approach is that chitosan simultaneously acts as an active support for the synthesis and assembly of nanoparticles, and the resultant bioconjugates bear the advantage of easy separation from the reaction medium.     

The elementary catalytic system model as a building unit of large enzymatic systems. General model

A model of an elementary catalytic system (ECS) is suggested, derived from the notions of the general theory of systems, which is capable of performing a single elementary catalytic act (ECA). For large chemical systems involving high numbers of ECAs occurring on various ECSs, the system's action becomes increasingly effective when component ECSs are coupled into complex structures. Models are suggested to describe these couples and several fundamental theorems are proved concerning the possible structures. Complex catalytic systems are shown to contain finite numbers of ECSs.     

Two three-dimensional metal-organic frameworks constructed by multiple building blocks of benzenetricarboxylate and bis(imidazole) ligands

Two novel metal-organic frameworks [Zn₃(BTC)₂(bbi)₃]_n (1) (H₃BTC = 1,3,5-benzenetricarboxylate, bbi = 1,1′-(1,4-butanediyl)bis(imidazole)) and{[Zn₃(BTC)₂(bix)₃ · 2.5H₂O]}_n (2) (bix = 1,4-bis(imidazole-1-ylmethyl)benzene) have been hydrothermally prepared and characterized. Analysis of the structure of 1 displays a 3D framework exhibiting a threefold interpenetration net of identical Zn_1.5(BTC)(bbi)_1.5 single frameworks. In the structure of 2, BTC³⁻ and bix build up infinite tubes extending to a 3D non-interpenetrated porous framework. Moderate fluorescent emissions in the solid state at room temperature were observed in both the compounds.     

Convenient solid-phase synthesis of oligopeptides using pentacoordinated phosphoranes with amino acid residue as building blocks

The reactive intermediates of pentacoordinated phosphoranes with amino acids (P(5)-AA) as building blocks, which were obtained by the reaction of O-phenylene phosphorochloridate with N,O-bis(trimethylsilyl)amino acids, were linked to a solid-phase support containing a hydroxymethyl polystyrene functional group. The first amino acid residue was coupled to the solid-phase support after washing the resin with organic solvent. Repeating the procedure led to oligopeptides linked on the resin. A series of free oligopeptides including tetra-Gly, di-Val, tri-Val, di-Leu, di-Phe, and Phe-Leu were obtained after cleavage from solid-phase support. The structure of these oligopeptides were determined by IR, (1)H NMR, FAB-MS, and HPLC.     

Label-free electrochemical aptasensor for thrombin detection with platinum nanoparticles and blocking reagent horseradish peroxidase as enhancers

A sensitive label-free electrochemical aptasensor was successfully fabricated for thrombin detection with platinum nanoparticles (Pt) and blocking reagent horseradish peroxidase (HRP) as enhancers. A Nafion?-graphene-coated electrode was first modified with an electrochemical probe of methylene blue (MB) through electrostatic interaction. Then Pt was electrodeposited onto an electrode for immobilization of the thrombin aptamer (TBA). Subsequently, HRP served as blocking reagent instead of bovine serum albumin (BSA). With the synergistic effect between Pt and HRP, the prepared aptasensor showed a superior catalytic efficiency toward H(2) O(2) in the presence of MB. After the combination of target thrombin on electrode surface, the TBA-thrombin complex made a barrier for electrocatalysis of Pt and HRP and inhibited the electrotransfer, resulting in a greater decrease in MB signals. As a result, the proposed approach showed a high sensitivity and a much wider linearity to thrombin in the range from 0.005 to 50 nM with a detection limit of 1 pM.     

Crystal structures of two- and three-dimensional polymeric complexes assembled by metal pseudohalides and 4-aminobenzoic acid via hydrogen bonds and covalent bonds

Four polymeric complexes [M(SCN)₂(4-abaH)₂]_n [M=Co(II) (1) or Cd(II) (2), 4-abaH=4-aminobenzoic acid], [Zn(N₃)(4-aba)]_n (3) and [Cd(N₃)(4-aba)(H₂O)]_n (4) were prepared from the reactions of 4-abaH with M(SCN)₂ [M=Co(II) or Cd(II)] and M(N₃)₂ [M=Zn(II) or Cd(II)] at different pH values. Their crystal structures have been determined by single-crystal X-ray diffraction. Both 1 and 2 consist of one-dimensional chains [M(μ-1,3-SCN)₂(4-abaH)₂]_n, in which each pair of the lateral carboxylic groups form double hydrogen bonds to furnish infinite two-dimensional sheets. In 3, the Zn(II) atoms are bridged by μ-1,1-azide groups and μ₂-carboxylate-O,O′ groups into an infinite zigzag chain featuring six-membered (ZnNZnOCO)_n rings, which are further connected by the 4-aba-N,O,O′ groups to generate a two-dimensional network. In 4, however, adjacent Cd(II) atoms are bridged by μ-1,1,3-azide groups to form an infinite chain with both four-membered Cd₂(μ-1,1-N₃)₂ and eight-membered Cd₂(μ-1,3-N₃)₂ rings. These chains are further connected by the 4-aba-N,O groups to generate a three-dimensional brickwall-like network. The results show significant effect of pH on the formation of the network structures.     

Base-pairing systems related to TNA containing phosphoramidate linkages: synthesis of building blocks and pairing properties

As part of a project that aims at screening TNA-related oligonucleotide systems in which threose backbone units may have some or all of their oxygen functions replaced by nitrogen, two TNA analogs containing (2'NH)- and (3'NH)-phosphoramidate groups, respectively, in place of phosphodiester groups were synthesized. They show base-pairing properties that are very similar to those of TNA itself. We also synthesized 2',3'-diamino analogs of alpha-L-threofuranosyl mononucleosides, yet attempts to convert them to TNA analogs containing phosphodiamidate linker groups were not successful. Such 2',3'-diamino derivatives of threofuranosyl nucleosides may be of interest, however, as building blocks of TNA analogs that contain non-phosphorous linker groups.     

Liposomes with polyribonucleotides as model of precellular systems

A study of the encapsulation of poly(U) and poly(C) within liposomes made from dipalmitoylphosphatidyl choline (DPPC), from egg yold phosphatidyl choline (PC), and from PC with cholesterol (CHOL) was made. The liposomes were prepared under anoxic conditions following the reverse-phase evaporation method. Determinations showed that 36 to 70% of the available lipids form liposomes and 2 to 5% of the polyribonucleotides can be entrapped by liposomes. The encapsulation of polyribonucleotides has also been measured in the presence of urea, cyanamide and Zn⁺⁺, condensing agents in prebiotic polymerization reactions. DPPC and PC:CHOL liposomes were formed in the presence of 1.0 M urea, although no PC liposomes were formed. The three types of liposomes were readily formed at 0.01 M urea, but in no case an enhancement of encapsulation efficiency of poly(U) was observed due to the presence of urea. Similar results were obtained with cyanamide. An enhanced encapsulation of poly(U) by the three types of liposomes was observed when Zn⁺⁺ was in the range of 0.001 to 0.01 M. Poly(U) encapsulation was 15 to 25 times higher when liposomes were prepared from DPPC at 0.01 M Zn⁺⁺. Similar results were obtained with poly(C). The advantages of DPPC-polyribonucleotide liposomes as precellular systems are discussed.     

Thiosemicarbazone-derivatised palladium nanoparticles as efficient catalyst for the Suzuki-Miyaura cross-coupling of aryl bromides with phenylboronic acid

Thiosemicarbazone-derivatised palladium nanoparticles with average crystallite size 16.2 nm have been prepared and characterized by XRD and SEM. The nanoparticles were found to efficiently catalyze the Suzuki-Miyaura cross-coupling of aryl bromides (from electron-rich to electron poor) with phenylboronic acid even at room temperature, and they can be recovered and reused.     

Immobilized metal ion affinity partitioning of cells in aqueous two-phase systems: erythrocytes as a model

Immobilized metal ion affinity partitioning of erythrocytes from different species is described. We have explored the affinity between transition metal chelates and metal-binding sites situated on the cell surface by partitioning in aqueous two-phase system composed of poly(ethylene glycol) and dextran. Soluble metal-chelate-poly(ethylene glycol) was prepared by fixing metal ions to poly(ethylene glycol) via the covalently bonded chelator, iminodiacetic acid. The partitioning behaviour of erythrocytes in systems at different concentrations of the ligand was tested. The copper-chelate-poly(ethylene glycol) was quite effective in the affinity extraction of human and rabbit erythrocytes, while the zinc-chelate-poly(ethylene glycol) displayed significant affinity only to the rabbit cells. Furthermore, the influence of various effectors such as imidazole, sialic acid on immobilized metal ion affinity partitioning of erythrocytes was examined.     

Design and construction of self-assembling supramolecular protein complexes using artificial and fusion proteins as nanoscale building blocks

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Aptamer based photoelectrochemical cytosensor with layer-by-layer assembly of CdSe semiconductor nanoparticles as photoelectrochemically active species

A label-free photoelectrochemical cytosensor for highly sensitive and specific detection of Ramos cell was developed based on photoactive films. The films were fabricated by a layer-by-layer (LBL) assembly of positively charged poly(dimethyldiallylammonium chloride) (PDDA) and negatively charged CdSe semiconductor nanoparticles (NPs) capped with mercaptoacetic acid. The resulting modified electrodes were tested as sensors for Ramos cell through the recognition of DNA aptamer which was covalently bound to the electrode using the classic coupling reactions between -COOH groups on the surfaces of CdSe NPs and -NH(2) groups of the aptamer. The newly developed cytosensor exhibited excellent sensitivity and selectivity. The linear range was from 160 to 1600 cells/mL and the detection limit was 84 cells/mL.     

alpha,alpha'-disubstituted amino acids with silylated side chains as lipophilic building blocks for the synthesis of peptaibol analogues

New alpha,alpha'-disubstituted amino acids with silylated side chains have been synthesized in racemic form. Starting from a Schiff base of glycine tert-butyl ester, a large variety of alpha,alpha'-dialkylated amino acids has been obtained, depending on the alkylating reagents. The application of a hydrosilylation methodology enabled the synthesis of the same unnatural amino acids in an enantiomerically pure form. The ability of these bulky amino acids to be incorporated into peptides by solution-phase methodology has also been demonstrated, since constrained silylated dipeptides have been synthesized. These new lipophilic building blocks could be useful and innovative in the design of peptaibol analogues.     

Redox and fungicidal properties of phthalocyanine metal complexes as related to active oxygen

Some chemical and fungicidal effects of 20 phthalocyanines of Co, Fe, Cu, and Al were studied. Under dark conditions, these complexes reduced nitroblue tetrazolium in the presence of KCN, accelerated the autoxidation of ascorbate or hydroquinone and decomposed hydrogen peroxide. In the later reaction, hydroxyl radical was generated as evidenced with the deoxyribose assay. The inhibition by superoxide dismutase and catalase of catalyzed autoxidation of ascorbate suggests the participation of superoxide anion-radical and hydrogen peroxide in the reaction. Most complexes were toxic to the fungus Magnaporthe grisea which causes blast disease of rice. The toxicity was enhanced by light being diminished by antioxidant reagents sequestering active oxygen species. Some complexes (including nontoxic ones), after 1-day contact with a leaf surface of the disease-susceptible rice cultivar, induced the fungitoxicity of leaf diffusate. This toxicity was also light-activated and sensitive to antioxidant reagents. Several complexes, when added to inocula, decreased 2-3 times the frequency of the compatible symptoms of the blast. It is suggested that in planta, the dark redox activity of phthalocyanines along with their photosensitization promote the generation of active oxygen, which damages the parasite and, therefore, favors disease resistance.