Structural and dynamical characterization of poly-gamma-glutamic acid-based cross-linked nanoparticles

This work describes the formation of water-soluble hydrophilic nanoparticles from biosynthetic poly-γ-glutamic acid (PGA). Nanoparticles were formed by cross-linking using 2,2′-(ethylenedioxy) diethylamine in the presence of water-soluble carbodiimide. The structure was determined by nuclear magnetic resonance spectroscopy and the particle size by transmission electron microscopy (TEM), size exclusion chromatography (SEC), and dynamic light-scattering (DLS) measurements. The results from TEM, SEC, and DLS reveal that the particle size depends on the ratio of cross-linking. Particle size values measured by TEM were between 20 and 90 nm. Formation of cross-linked nanoparticles results in a dramatic viscosity drop compared to the viscosity of the corresponding solution of the parent PGA. The viscosity and DLS experiments disclose an intriguing interplay between intrachain and interchain cross-linking of the polymer chains, depending on the cross-linker density and polymer concentration. The SEC measurements show that the retention time of the major portion of particles increase because of the higher cross-linking ratio. At moderate cross-linker concentration, intramolecular cross-linking is the dominant process, whereas at higher cross-linker densities, the interpolymer cross-linking plays an important role. As a result, large clusters are also formed.     

GlycoMiner: a new software tool to elucidate glycopeptide composition

New computer software, GlycoMiner, has been developed to automatically identify tandem (MS/MS) spectra obtained in liquid chromatography/mass spectrometry (LC/MS) runs which correspond to N-glycopeptides. The program complements conventional proteomics analysis, and can be used in a high-throughput environment. The program interprets the spectra and determines the structure of the corresponding glycopeptides. GlycoMiner runs under Windows, can process spectra obtained on various instruments, and can be downloaded from our website (w3.chemres.hu/ms/glycominer). The algorithm works similarly to a human expert; evaluates the low mass oxonium ions; deduces oligosaccharide losses from the protonated molecule; and identifies the mass of the peptide residue. The program has been tested on tryptic digests of two glycopeptides: AGP (which has five different N-glycosylation sites) and transferrin (with two N-glycosylation sites). Results have been evaluated both manually and by GlycoMiner. Out of 3132 MS/MS spectra 338 were found to correspond to glycopeptides; identification by GlycoMiner showed a 0.1% false positive and 0.1% false negative rate. From these it was possible to identify 196 glycan structures manually; GlycoMiner correctly identified all of these, with no false positives. The rest were low quality spectra, not suitable for structure assignment.     

Additional Minor Phytoecdysteroids of Serratula wolffii

Three new and one known ecdysteroids were identified in the MeOH extract of the roots of Serratula wolffii. The new compounds isolated were (11α)‐11‐hydroxyshidasterone ( 1 ), (2β,3α,5β,14β,22R)‐2,3,20,22,25‐pentahydroxycholest‐7‐en‐6‐one ( 2 ), and (2β,3α,5β,22R)‐2,3,20,22,25‐pentahydroxycholest‐7‐en‐6‐one ( 3 ), together with the known ponasterone A ( 4 ). This latter compound was now better characterized than earlier. The structures of compounds 1 – 4 were established by extensive spectroscopic techniques, including one‐ and two‐dimensional NMR methods.     

How close can you get? Studies of ultrafast light-induced processes in ruthenium-[60] fullerene dyads with short pyrazolino and pyrrolidino links

Two pyrazoline- and one pyrrolidine-bridged Ru(II)bipyridine-[60]fullerene dyads have been prepared and studied by ultrafast time-resolved spectroscopy. A silver-assisted synthesis route, in which Ag(I) removes the chlorides from the precursor complex Ru(bpy) 2Cl 2 facilitates successful coordination of the [60]fullerene-substituted third ligand. Upon light excitation of the ruthenium moiety, the emission was strongly quenched by the fullerene. The main quenching mechanism is an exceptionally fast direct energy transfer ( k obs > 1 x 10 (12) s (-1) in the pyrazoline-bridged dyads), resulting in population of the lowest excited triplet state of fullerene. No evidence for electron transfer was found, despite the extraordinarily short donor-acceptor distance that could kinetically favor that process. The observations have implications on the ongoing development of devices built from Ru-polypyridyl complexes and nanostructured carbon, such as C 60 or nanotubes.     

Kinetics and mechanism of the reactions of CH3CO and CH3C(O)CH2 radicals with O2. Low-pressure discharge flow experiments and quantum chemical computations

The reactions CH(3)CO + O(2)--> products (1), CH(3)CO + O(2)--> OH +other products (1b) and CH(3)C(O)CH(2) + O(2)--> products (2) have been studied in isothermal discharge flow reactors with laser induced fluorescence monitoring of OH and CH(3)C(O)CH(2) radicals. The experiments have been performed at overall pressures between 1.33 and 10.91 mbar of helium and 298 +/- 1 K reaction temperature. OH formation has been found to be the dominant reaction channel for CH(3)CO + O(2): the branching ratio, Gamma(1b) = k(1b)/k(1), is close to unity at around 1 mbar, but decreases rapidly with increasing pressure. The rate constant of the overall reaction, k(2), has been found to be pressure dependent: the fall-off behaviour has been analysed in comparison with reported data. Electronic structure calculations have confirmed that at room temperature the reaction of CH(3)C(O)CH(2) with O(2) is essentially a recombination-type process. At high temperatures, the further reactions of the acetonyl-peroxyl adduct may yield OH radicals, but the most probable channel seems to be the O(2)-catalysed keto-enol transformation of acetonyl. Implications of the results for atmospheric modelling studies have been discussed.     

Leading RNA tertiary interactions: structures, energies, and water insertion of A-minor and P-interactions. A quantum chemical view

Complex molecular shapes of ribosomal RNA molecules are stabilized by recurrent types of tertiary interactions involving highly specific and conserved non-Watson-Crick base pairs, triplets, and quartets. We analyzed the intrinsic structure and stability of the P-motif and the four basic types of A-minor interactions (types I, II, III, and 0), which represent the most prominent RNA tertiary interaction patterns refined in the course of evolution. In the studied interactions, the electron correlation component of the stabilization usually exceeds the Hartree-Fock (HF) term, leading to a strikingly different balance of forces as compared to standard base pairing stabilized primarily by the HF term. In other words, the A-minor and P-interactions are considerably more influenced by the dispersion energy as compared to canonical base pairs, which makes them particularly suitable to zip the folded RNA structures that are substantially hydrated even in their interior. Continuum solvent COSMO calculations confirm that the stability of the canonical GC base pair is affected (reduced) by the continuum solvent screening considerably more than the stability of the A-minor interaction. Among the studied systems, the strong A-minor II and weak A-minor III interactions require water molecules to stabilize the experimental geometry. Gas-phase optimization of the canonical A-minor II A/CG triplet without water results in a geometry that is clearly inconsistent with the RNA structure. The gas-phase structure of the P-interaction and the most stable A-minor I interaction nicely agrees with the geometries occurring in the ribosome. A-minor I can also adopt an alternative water-mediated substate rather often observed in X-ray and molecular dynamics studies. The A-minor I water bridge, however, does not appear to stabilize the tertiary contact, and its role is to provide structural flexibility to this binding pattern within the context of the RNA structure. Interestingly, the insertion of a polar water molecule in the A-minor I A/CG tertiary contact occurring in the A/C tertiary pair is stabilized primarily by the HF (electrostatic) interaction energy, while the dispersion-controlled A/G contact remains firmly bound. Thus, the intrinsic balance of forces as revealed by quantum mechanics (QM) calculations nicely correlates with many behavioral aspects of the studied interactions inside RNA. The comparison of interaction energies computed using quantum chemistry and an AMBER force field reveals that common molecular mechanics calculations perform rather well, except that the strength of the P-interaction is modestly overestimated. We also briefly discuss the non-negligible methodological differences when evaluating simple base-base nucleic acids base pairs and the complex RNA tertiary base pairing patterns using QM procedures.     

Amalgamation,interpolation and epimorphisms in algebraic logic

In his landmark paper on amalgamation published in Algebra Universalis in 1971, Don Pigozzi posed some open questions in connection with amalgamation of subclasses of cylindric algebras. Some of these questions were originally raised by Comer, Daigneault, Johnson, McKenzie and others. In this paper we give answers to all these as well as a number of other related questions. Most of the solutions were found by the authors of this paper. However, a few were contributed by others who will of course be given due credit at the appropriate points. This paper is dedicated to Don Pigozzi on his retirement. Presented by R. W. Quackenbush. The first author’s research was supported by the Hungarian National Foundation for Scientific Research grants no T30314 and T23234. The second author’s research was supported by the Hungarian National Foundation for Scientific Reserach OKTA grant no T30314. All the new results in this article were announced by Judit Madarász in the Workshop on Abstract Algebraic Logic, held in Centre de Recerca Matematica Bellaterra, Spain July 1–5, 1997. Received December 15, 2002; accepted in final form January 3, 2006.     

Theoretical study on the structure, stability, and electronic properties of the guanine-Zn-cytosine base pair in M-DNA

M-DNA is a type of metalated DNA that forms at high pH and in the presence of Zn, Ni, and Co, with the metals placed in between each base pair, as in G-Zn-C. Experiments have found that M-DNA could be a promising candidate for a variety of nanotechnological applications, as it is speculated that the metal d-states enhance the conductivity, but controversy still clouds these findings. In this paper, we carry out a comprehensive ab initio study of eight G-Zn-C models in the gas phase to help discern the structure and electronic properties of Zn-DNA. Specifically, we study whether a model prefers to be planar and has electronic properties that correlate with Zn-DNA having a metallic-like conductivity. Out of all the studied models, there is only one which preserves its planarity upon full geometry optimization. Nevertheless, starting from this model, one can deduce a parallel Zn-DNA architecture only. This duplex would contain the imino proton, in contrast to what has been proposed experimentally. Among the nonplanar models, there is one that requires less than 8 kcal/mol to flatten (both in gas and solvent conditions), and we propose that it is a plausible model for building an antiparallel duplex. In this duplex, the imino proton would be replaced by Zn, in accordance with experimental models. Neither planar nor nonplanar models have electronic properties that correlate with Zn-DNA having a metallic-like conductivity due to Zn d-states. To understand whether density functional theory (DFT) can describe appropriately the electronic properties of M-DNAs, we have investigated the electronic properties of G-Co-C base pairs. We have found that when self-interaction corrections (SIC) are not included the HOMO state contains Co d-levels, whereas these levels are moved below the HOMO state when SIC are considered. This result indicates that caution should be exercised when studying the electronic properties of M-DNAs with functionals that do not account for strong electronic correlations.     

Cyclometallated platinum(II) compounds with imine ligands derived from amino acids: Synthesis and oxidative addition reactions

The reactions of [PtMe₂(μ-SMe₂)]₂ with imines 4-ClC₆H₄CHNCHRCO₂Me (R = H (1a), Me (1b), ⁱPr (1c), CH₂C₆H₄(4’-OH) (1d), C₆H₅ (1e), CH₂C₆H₅(1f)) derived from natural amino acids produced under mild conditions cyclometallated platinum(II) compounds [PtMe{κ²-(C,N)-4-ClC₆H₃CHNCHRCO₂Me}(SMe₂)] (2a-2f). These compounds gave the corresponding phosphine derivatives [PtMe{κ²-(C,N)-4-ClC₆H₃CHNCHRCO₂Me}(PPh₃)] (3a-3f). The corresponding cyclometallated platinum(IV) compounds [PtMe₂I{κ²-(C,N)-4-ClC₆H₃CHNCHRCO₂Me}(PPh₃)] (4) arising from intermolecular oxidative addition of methyl iodide were obtained with a high degree of stereo selectivity. Analogous results were obtained for imine 2,6-Cl₂C₆H₃CHNCH(CH₂C₆H₅)CO₂Me (1g) in a process involving intramolecular oxidative addition of a C-Cl bond. The obtained compounds were fully characterized including structure determinations for compounds 3f, 4d and 4f.     

Isolation and structure determination of new 4,12-dideoxyphorbol esters from Euphorbia pannonica Host.

Phytochemical study of the aerial parts of Euphorbia pannonica led to the isolation of two new tigliane diterpenes, 4,12-dideoxy(4β)phorbol-20-benzoate-13-isobutyrate (1) and 4,12-dideoxy(4β)phorbol-20-benzoate-13-isovalerianate (2). The structures and relative stereochemistry were elucidated on the basis of extensive spectroscopic analyses, including 1D and 2D NMR experiments (¹H NMR, JMOD, COSY, NOESY, HSQC and HMBC).