Phenol adsorption on closed carbon nanotubes

We present the results of systematic studies of phenol adsorption on closed commercially available, unmodified carbon nanotubes. Phenol adsorption is determined by the value of tube-specific surface area, the presence of small amount of surface groups influence adsorption only in very small amount. Phenol can be applied as a probe molecule for comparative analysis of tube surface areas. Tube curvature influences adsorption from solution, i.e., we observe increasing adsorption energy (and slower desorption process) with the decrease in tube curvature. This is in full accordance with molecular simulation results.     

Theoretical studies on interactions between low energy electrons and protein-DNA fragments: valence anions of AT-amino acids side chain complexes

Electron attachment to trimeric complexes that mimic most frequent hydrogen bonding interactions between an amino acid side chain (AASC) and the Watson-Crick (WC) 9-methyladenine-1-methylthymine (MAMT) base pair has been studied at the B3LYP/6-31++G(d,p) level of theory. Although the neutral trimers will not occur in the gas phase due to unfavorable free energy of stabilization (G(stab)) they should form a protein-DNA complex where entropy changes related to formation of such a complex will more than balance its disadvantageous G(stab). The most stable neutrals possess an identical pattern of hydrogen bonds (HBs). In addition, the proton-acceptor (N7) and proton-donor (N10) atoms of adenine involved in those HBs are located in the main groove of DNA. All neutral structures support the adiabatically stable valence anions in which the excess electron is localized on a π* orbital of thymine. The vertical detachment energies (VDEs) of anions corresponding to the most stable neutrals are substantially smaller than that of the isolated WC MAMT base pair. Hence, electron transfer from the anionic thymine to the phosphate group and as a consequence formation of a single strand break (SSB) should proceed more efficiently in a protein-dsDNA complex than in the naked dsDNA as far as electron attachment to thymine is concerned.     

1,3,5-Triazine Nitrogen Mustards with Different Peptide Group as Innovative Candidates for AChE and BACE1 Inhibitors

A series of new analogs of nitrogen mustards (4a–4h) containing the 1,3,5-triazine ring substituted with dipeptide residue were synthesized and evaluated for the inhibition of both acetylcholinesterase (AChE) and β-secretase (BACE1) enzymes. The AChE inhibitory activity studies were carried out using Ellman’s colorimetric method, and the BACE1 inhibitory activity studies were carried out using fluorescence resonance energy transfer (FRET). All compounds displayed considerable AChE and BACE1 inhibition. The most active against both AChE and BACE1 enzymes were compounds A and 4a, with an inhibitory concentration of AChE IC₅₀ = 0.051 µM; 0.055 µM and BACE1 IC₅₀ = 9.00 µM; 11.09 µM, respectively.     

Examining the possibilities of applying high pressure to preserve yoghurt supplemented with probiotic bacteria

Natural yoghurt was subject to pressures of 200 and 250 MPa/4 and 18°C/15 min, after which milk-activated inocula of Lactobacillus acidophilus and Bifidobacterium sp. were added. The yoghurts were stored for 4 weeks at refrigeration temperature. After preparation and each week of storage, the count of bacteria, acidity, antibacterial property and an organoleptic assessment was determined. The highest survival rate was demonstrated by the bacteria of Lactobacillus delbrueckii ssp. bulgaricus, Streptococcus thermophilus and Bifidobacterium sp. in the yoghurt pressurised 200 MPa/15min at 4°C. Acidity increases in the control yoghurts were higher than in the pressurised ones. Pressurised yoghurts demonstrated weaker antibacterial effect in comparison to control yoghurts. Slight changes in the smell and taste were observed after pressurisation. Yoghurts pressurised at 18°C were characterised by more favourable organoleptic properties. Better conciseness of the curd and lower whey seep out were observed in pressurised yoghurt.     

Acid-catalyzed Hydrolysis of the cis-[Cr(1,10-phenanthroline)2(O2CO)]+ Ion Studied by the u.v.–vis Stopped Flow Method

The cis-[Cr(phen)₂(O₂CO)]⁺ ion was prepared through the displacement of two molecules of water from the cis-[Cr(phen)₂(OH₂)₂]³⁺ by the bidentate carbonate anion. It underwent two-phase hydrolysis reactions under acidic conditions (0.1 < [H⁺] < 2.7 m) at 5, 10, 15, 20 and 25 °C. Via slow carbonato chelate ring opening (first step k₁^slow) and a second fast decarboxylation(k₂^fast value). The first step was preceded by protonation of the coordinate bidentate carbonate ligand. The second step exhibited no pH dependence, while k₁^slow values increased with acid concentration that suggested the presence of both protonated and deprotonated reactant species. Based on these observations we have proposed a hydrolysis mechanism featuring H₂O-induced ring-opening of the coordinate CO₃²⁻ group in the first step k₁^slow followed by loss of CO₃²⁻ from two intermediates, [Cr(phen)₂(O₂COH)]²⁺ (k₁^slow) and [Cr(phen)₂(OH₂)(O₂COH)]²⁺ (k₂^fast).     

Solid-state molecular organization and solution behavior of methane-1,1-diphosphonic acid derivatives of heterocyclic amines: the role of the topochemical ring modification and the intramolecular hydrogen bonds in monosubstituted piperid-1-ylmethane-1,1-diphosphonic acids

The crystal structures of 3-methylpiperid-1-ylmethane-1,1-diphosphonic (2), 4-methylpiperid-1-ylmethane-1,1-diphosphonic (3), 2-ethylpiperid-1-ylmethane-1,1-diphosphonic (4), and 2-methylpiperid-1-ylmethane-1,1-diphosphonic (5) acids have been determined and are discussed with respect to their molecular organization and crystal-packing preferences. The chair conformation, predominant also in solution, favors equatorial positioning of the bulky substituents of the heterocyclic N and C atoms. The molecular geometry also provides access to intramolecular hydrogen-bond formation between the axial protons located on the nitrogen atoms, as well as the carbon atoms closest to it, and phosphonic/phosphonate oxygen atoms. The molecules preferably arrange in monolayers, observed in all crystals with an exception of 3. The layers are held in place in the third direction through van der Waals interactions. The analysis of two-dimensional hydrogen-bonded networks is concentrated on revealing how the substituent's topology of the molecule affects the solid-state organization in well-defined structures and is aimed at unraveling the consequences and the possible conformational changes by stepwise network disruption upon crystal dissolution in water. The solution NMR studies are focused on revealing the role that the topochemistry of the substituent plays for the stereodynamics in 2-5. It is demonstrated that in contrast to piperid-1-ylmethane-1,1-diphosphonic acid (1), in which the ring inversion/rotation around the C-N bond concerted with the N-H...O hydrogen-bond breaking/formation process leads to a mixture of two interconverting conformers, the concerted N-H...O breaking/rotation/N-H...O formation process in 2 and 3 allows for a predominance of one conformer in solution. However, placement of a substituent at 2-position in the ring hampers the rotation around the C-N bond; this makes 4 and 5 significantly less flexible relative to compounds 1-3. In addition, both compounds 4 and 5 are proved to exist as a mixture of two conformers, the equilibrium of which in acidic solution is shifted towards the conformer found in solid state. In alkaline solutions of 4 and 5, the equilibrium is shifted towards the conformer that is forced by the flipping of the heterocyclic ring. These results correlate well with recently documented differences in the biological potency of this group of compounds.     

Strong and electromagnetic J/ψ and ψ(2S) decays into pion and kaon pairs

We discuss interference effects important for the form factors extraction in the vicinity of J/ψ andψ(2S)resonances in combination with resonance parameters determination.The implementation to the Monte Carlo event generator PHOKHARA of the J/ψ and ψ(2S)contributions to the muon,pion and kaon pairs production associated with a photon at next-to-leading order is also described.     

Movement of proteins in an environment crowded by surfactant micelles: anomalous versus normal diffusion

Small proteins move in crowded cell compartments by anomalous diffusion. In many of them, e.g., the endoplasmic reticulum, the proteins move between lipid membranes in the aqueous lumen. Molecular crowding in vitro offers a systematic way to study anomalous and normal diffusion in a well controlled environment not accessible in vivo. We prepared a crowded environment in vitro consisting of hexaethylene glycol monododecyl ether (C(12)E(6)) nonionic surfactant and water and observed lysozyme diffusion between elongated micelles. We have fitted the data obtained in fluorescence correlation spectroscopy using an anomalous diffusion model and a two-component normal diffusion model. For a small concentration of surfactant (below 4 wt %) the data can be fitted by single-component normal diffusion. For larger concentrations the normal diffusion fit gave two components: one very slow and one fast. The amplitude of the slow component grows with C(12)E(6) concentration. The ratio of diffusion coefficients (slow to fast) is on the order of 0.1 for all concentrations of surfactant in the solution. The fast diffusion is due to free proteins while the slow one is due to the protein-micelle complexes. The protein-micelle interaction is weak since even in a highly concentrated solution (35% of C(12)E(6)) the amplitude of the slow mode is only 10%, despite the fact that the average distance between the micelles is the same as the size of the protein. The anomalous diffusion model gave the anomaly index (r(2)(t) approximately t(alpha)), alpha monotonically decreasing from alpha = 1 (at 4% surfactant) to alpha = 0.88 (at 37% surfactant). The fits for two-component normal diffusion and anomalous diffusion were of equally good quality, but the physical interpretation was only straightforward for the former.     

Methyl 3-methyl-2H-azirine-2-carboxylate photochemistry studied by matrix-isolation FTIR and DFT calculations

The aliphatic 2H-azirine, methyl 3-methyl-2H-azirine-2-carboxylate (MMAC), has been synthesized and its monomeric form investigated by IR spectroscopy in an argon matrix, at 10 K, as well as theoretically (DFT/B3LYP/6-311++G(d,p)). Two low-energy conformers of MMAC (Ct and Cc) were found in the matrix, both exhibiting the cis conformation around the C-O bond but differing in the arrangement around the C-C(alpha) bond. The two conformers were photoreactive upon in situ broadband UV excitation (lambda > 235 nm), yielding nitrile ylide (P1) and ketene imine (P2) type products, which resulted from cleavage of the C-C or C-N bond, respectively. The kinetics of the reactions leading to the formation of P1 and P2 are of first order, with the processes being favored when the reactant is in the Cc conformation. Very interestingly, the C-N bond photocleavage, which is unusual for aliphatic 2H-azirines, was found to be preferred over the generally favored in 2H-azirines C-C bond breakage. This behavior is attributed to the presence in the molecule of the electron-withdrawing methoxycarbonyl substituent, which accelerates the intersystem crossing toward the T(1) triplet state and, in this way, favors the C-N bond cleavage. In addition to the primary photoprocesses leading to formation of P1 and P2, secondary photoprocesses leading to the decarboxylation and decarbonylation of P2 have been also observed.