Cover Feature: OH Radical-Induced Oxidation in Nucleosides and Nucleotides Unraveled by Tandem Mass Spectrometry and Infrared Multiple Photon Dissociation Spectroscopy (ChemPhysChem 23/2023)

OH⋅-induced oxidation products of DNA nucleosides and nucleotides have been structurally characterized by collision-induced dissociation tandem mass spectrometry (CID-MS²) and Infrared Multiple Photon Dissociation (IRMPD) spectroscopy. CID-MS² results have shown that the addition of one oxygen atom occurs on the nucleobase moiety. The gas-phase geometries of +16 mass increment products of 2’-deoxyadenosine (dA(O)H⁺), 2’-deoxyadenosine 5’-monophosphate (dAMP(O)H⁺), 2’-deoxycytidine (dC(O)H⁺), and 2’-deoxycytidine 5’-monophosphate (dCMP(O)H⁺) are extensively investigated by IRMPD spectroscopy and quantum-chemical calculations. We show that a carbonyl group is formed at the C8 position after oxidation of 2’-deoxyadenosine and its monophosphate derivative. For 2’-deoxycytidine and its monophosphate derivative, the oxygen atom is added to the C5 position to form a C−OH group. IRMPD spectroscopy has been employed for the first time to provide direct structural information on oxidative lesions in DNA model systems.     

Photosensitization of bioinspired thymine-containing polymers

Here, we report a sensitization study on a family of water-soluble photopolymers based on thymine. The goal of this study was to determine whether the presence of sensitizer molecules would promote photocrosslinking/immobilization of the polymers using low-energy irradiation (520 nm) as compared to the UV irradiation (approximately 280 nm) necessary for the standard photoinduced process to take place. With the aid of Eosin Y Spirit Soluble (EY) as a sensitizer, water-soluble polystyrene copolymers of vinylbenzylthymine-vinylbenzyltriethylammonium chloride (VBT-VBA) were immobilized after exposure to visible irradiation. By exciting the sensitizer molecule in the presence of VBT copolymers at a wavelength where absorption by the latter does not occur, the triplet state of the sensitizer is generated in high yields, and consequently, polymer photocross-linking takes place. UV-vis spectroscopy has been used to study the effect of irradiation dose, copolymer composition, and sensitizer concentration on the photoreactivity of VBT polymers. These studies demonstrate the feasibility of using Eosin Y as a sensitizer to achieve the thymine photodimer formation, resulting in immobilization of VBT-VBA-EY films on PET substrate. This provides complementary information on photoinduced immobilization of VBT-VBA films that are crucial for developing new classes of environmentally benign materials and new energy-saving methods.     

Effect of hexyl substituent groups on photophysical and electrochemical properties of the poly[(9,9‐Dioctyluorene)−2,7‐diyl‐alt‐(4,7‐bis (3‐Hexylthien‐5‐Yl)−2,1,3‐Benzothiadiazole)−2′,2″‐diyl]

The effect of the presence of hexyl group in thiophene on the photophysical and electrochemical properties of poly[(9,9‐dioctyluorene)?2,7‐diyl‐alt‐(4,7‐bis(3‐hexylthien‐5‐yl)?2,1,3‐benzothiadiazole)?2′,2″‐diyl] (F8TBT) is investigated. The copolymers present electron donor–acceptor architecture and are synthesized by Suzuki coupling reaction. The UV/Vis spectra show absorption maximum in the wavelength range of blue and orange, which are associated with different segments of the polymer backbone. Addition of hexyl substituent groups has a positive effect on the molar absorptivity and increases the emission and absorption intensities due to fluorene and thiophene‐benzothiadiazole‐thiophene (TBT) units, although an increment in the bandgap is observed. Cyclic voltammetry study of the polymer films reveal irreversible reduction and oxidation processes of the TBT units in the polymer chain and the HOMO and LUMO energy levels suggest ambipolar character for the polymers, while the electrochemical bandgaps are consistent with the absorbance measurements. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 1975–1982     

Complexes of nucleolipid liposomes with single-stranded and double-stranded nucleic acids

We report on the association of anionic liposomes from POP-Ade:POPC (1-palmitoyl-2-oleoyl-phosphatidyladenosine and 1-palmitoyl-2-oleoyl-phosphatidylcholine, respectively) with single- and double-strand nucleic acids, mediated by Ca(2+) bridging. The structural and dynamical features of such complexes are compared with those displayed when the nucleolipid is replaced by POPG (1-palmitoyl-2-oleoyl-sn-phosphatidyl-glycerol), characterized by the same apolar skeleton and negative charge as POP-Ade, but lacking the nucleic polar head. For single-stranded nucleic acids, we demonstrate that specific interactions drive the formation of complexes with nucleolipid liposomes, while no association is present for POPG-based samples. For double-stranded nucleic acids, Ca(2+) bridging promotes association with both liposomal formulations, but the corresponding complexes have different structural features, in terms of size, overall charge and internal liquid-crystalline structure.     

Aerobic,Copper‐Mediated Oxidation of Alkaline Formaldehyde to Fuel‐Cell Grade Hydrogen and Formate: Mechanism and Applications

Beyond nanopowders: Hydrogen and formate are produced through the oxidation of alkaline HCHO by CuO microparticles. The Cu microparticles formed in the purely electrochemical reduction of CuO preserve the morphology of CuO (left‐hand image: CuO; right‐hand image: Cu formed in the reduction of CuO by alkaline HCHO) and can be permeated by a gas. They react more efficiently than Cu nanoparticles with air to restore CuO.

     

Sequence determination of αs1‐casein isoforms from donkey by mass spectrometric methods

Four co‐eluting components, with experimentally measured M_r of 23 658, 23 786, 24 278 and 24 406 Da, were detected by reversed‐phase high‐performance liquid chromatography (RP‐HPLC) and matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) analysis in the dephosphorylated casein fraction of a milk sample collected at middle lactation stage from an individual donkey belonging to the Ragusano breed. By coupling RP‐HPLC, two‐dimensional polyacrylamide gel electrophoresis (2D‐PAGE), enzymatic digestions, MALDI‐TOF MS and capillary RP‐HPLC/nano‐electrospray ionization tandem mass spectrometry (nESI‐MS/MS) analyses, the four components were identified as donkey's α_s1‐CNs and their sequences completely characterized, using the known mare's α_s1‐CN (GenBank Acc. No. AAK83668; M_r 23750.7 Da) as reference. The proteins with M_r of 23 786 and 23 658 Da differ in the presence of a glutamine residue at position 83 in the full‐length component and present the amino acid substitutions Q⁸→H and H¹¹⁵→Y with respect to the mare's α_s1‐CN. The other two components with M_r 24 406 and 24 278 Da, which also differ in the presence of a glutamine residue at position 88 in the full‐length component, show the insertion of the pentapeptide HTPRE between Leu³³ and the Glu³⁴. The two α_s1‐CNs bearing the pentapeptide insertion were named variants A (202 amino acids; M_r 24 406) and A₁ (201 amino acids; M_r 24 278), whereas the two α_s1‐CNs without the pentapeptide were named variants B (197 amino acids; M_r 23 786) and B₁ (196 amino acids; M_r 23 658). Copyright © 2009 John Wiley & Sons, Ltd.     

A Serious Look at Changeable Silly Putty

Changeable Silly Putty is a thermochromic material. It changes color due to a change in temperature. This paper describes advanced experiments designed to find the mechanism of the color change, provides a discussion of proposed mechanisms, and describes three experiments using Changeable Silly Putty that are suitable for young children.     

A simulated annealing algorithm for transient optimization in gas networks

In this paper we present a simulated annealing approach for the gas network optimization problem. A gas network consists of a set of pipes to transport the gas from the sources to the sinks whereby gas pressure gets lost due to friction. Further on there are compressors, which increase gas pressure, and valves. The aim is to minimize fuel gas consumption of the compressors whereas demands of consumers have to be satisfied. The problem of transient (time-dependent) optimization of gas networks results in a highly complex mixed integer nonlinear program. We relax the equations describing the gas dynamic in pipes by adding these constraints combined with appropriate penalty factors to the objective function. A suitable neighborhood structure is developed for the relaxed problem where time steps as well as pressure and flow of the gas are decoupled. Our approach convinces with flexibility and very good computational results.