Raman spectroscopic studies of terthiophenes for molecular electronics

The effect of thiol and selenol functionalization on the vibrational spectra and photochemical stability of terthiophene based molecular wires was investigated using surface-enhanced Raman scattering (SERS). The molecules were found to exhibit markedly different properties at the silver surface of the SERS substrate, despite having almost identical Raman spectra in solution and in the solid state. In contrast to terthiophene (3T), the bisthiolterthiophene (T3) and biselenol-terthiophene (Se3) molecules were stable against photoinduced structural changes when adsorbed to the metal surface at low concentrations. This indicates that the strong bonds to the silver surface, via S or Se terminal atoms, leads to a rapid decay of photoexcited states. Comparison with ab initio calculations shows that both T3 and Se3 bind with only one of the functional groups to the Ag surface.     

Direct probing of sorbent-solvent interactions for amylose tris(3,5-dimethylphenylcarbamate) using infrared spectroscopy, X-ray diffraction, solid-state NMR, and DFT modeling

The sorbent-solvent interactions for amylose tris(3, 5-dimethylphenylcarbamate) (ADMPC) with five commonly used solvents, hexane, methanol, ethanol, 2-propanol (IPA), and acetonitrile (ACN), are studied using attenuated total reflection infrared spectroscopy (ATR-IR) of thin sorbent films, X-ray diffraction (XRD) of thin films, (13)C cross polarization/magic angle spinning (CP/MAS) and MAS solid state NMR of polymer-coated silica beads (commercially termed "Chiralpak AD"), and DFT modeling. The ADMPC-polymer-coated silica beads are used commercially for analytical and preparative scale separations of chiral enantiomers. The polymer forms helical rods with intra- and inter-rod hydrogen bonds (H-bonds). There are various nm-sized cavities formed between the polymer side-chains and rods. The changes in the H-bonding states of the C=O and NH groups of the polymer upon absorption of each of the five solvents at 25 degrees C are determined with ATR-IR. The IR wavenumbers, the H-bonding interaction energies, and the H-bonding distances of the polymer side-chains with each of the solvent molecules are predicted using the DFT/B3LYP/6-311+g(d,p) level of theory. The changes in the polymer crystallinity upon absorption of each solvent are characterized with XRD. The changes in the polymer crystallinity and the H-bonding states of C=O groups are also probed with (13)C CP/MAS solid-state NMR. The changes in the polymer side-chain mobility are detected using (13)C MAS solid-state NMR. The H-bonding states of the polymer change upon absorption of each polar solvent and usually result in an increase in the polymer crystallinity and the side-chain mobility. The polymer rods are reorganized upon solvent absorption, and the distance between the rods increases with the increase in the solvent molecular size. These results have implications for understanding the role of the solvent in modifying the structure and behavior of the polymer sorbents.     

Eigenwaves in waveguides with dielectric inclusions: completeness

We formulate the definition of eigenwaves and associated waves in a nonhomogeneously filled waveguide using the system of eigenvectors and associated vectors of a pencil and prove its double completeness with a finite defect or without a defect. Then, we prove the completeness of the system of transversal components of eigenwaves and associated waves as well as the ‘mnimality’ of this system and show that this system is generally not a Schauder basis. This work is a continuation of the paper Eigenwaves in waveguides with dielectric inclusions: spectrum. Appl. Anal. 2013. doi:10.1080/00036811.2013.778980 by Y. Smirnov and Y. Shestopalov. Therefore, we omit the problem statements and all necessary basic definitions given in the previous paper.     

Updating the Chemiluminescence Oxygen‐Aftereffect Method for Determining the Rate Constant of the Peroxy‐Radical Self‐Reaction: Oxidation of Cyclohexene

Updating the facile chemiluminescence oxygen‐aftereffect method, most suitable for determining the rate constant (k_t) of the peroxy‐radical self‐reaction (main chemiluminescence channel), pertained to considering the sensitivity of such a method toward a disturbing influence of the peroxy radicals of the initiator of the chain oxidation process. Such a disturbance may derive from the side chemiluminescent reaction, which involves peroxy radicals of both hydrocarbon and initiator. To examine the applicability and limitations of the chemiluminescence method under present scrutiny, cyclohexene was used as the model oxidizable hydrocarbon substrate. Computer simulations of the reaction and chemiluminescence kinetics have demonstrated the validity of the considered methodology at the value of the rate constant of the propagation of the overall chain process by peroxy radicals of the initiator higher than 1 m ^?1 s^?1. Despite that the chemiluminescence time profile and the stationary level of the total chemiluminescence intensity depend on the kinetics of the side chemiluminescence channel and on the ratio of the excited‐state generation yields in the mentioned reaction channel and in the main chemiluminescence process, the value of k_t assessed by the oxygen‐aftereffect method has been found independent of variation of these characteristics.     

SERS intensity optimization by controlling the size and shape of faceted gold nanoparticles

In this work, we experimentally investigated the surface‐enhanced Raman spectroscopy (SERS) activity of faceted gold nanoparticles, which have been theoretically predicted to yield giant enhancements. Glycine was used to determine the SERS activity as a function of pH and ionic strength and to estimate the corresponding enhancement factor (EF). By optimizing the synthesis conditions of the flat prismatic nanoparticles, it was possible to control their size and shape. We demonstrate that the maximum SERS intensity increases with the edge length of the triangle, reaching a maximum EF of ∼10¹³ for 1.9 µm triangles (the largest tested). The corresponding glycine detection limit was as low as 10⁻¹² M , close to the single‐molecule threshold. Copyright © 2007 John Wiley & Sons, Ltd.     

High-resolution mass spectrometric analysis of secondary organic aerosol produced by ozonation of limonene

Chemical composition of secondary organic aerosol (SOA) formed from the ozone-initiated oxidation of limonene is characterized by high-resolution electrospray ionization mass spectrometry in both positive and negative ion modes. The mass spectra reveal a large number of both monomeric (m/z < 300) and oligomeric (m/z > 300) condensed products of oxidation. A combination of high resolving power (m/Deltam approximately 60,000) and Kendrick mass defect analysis makes it possible to unambiguously determine the molecular composition of hundreds of individual compounds in SOA samples. Van Krevelen analysis shows that the SOA compounds are heavily oxidized, with average O : C ratios of 0.43 and 0.50 determined from the positive and negative ion mode spectra, respectively. A possible reaction mechanism for the formation of the first generation SOA molecular components is considered. The discussed mechanism includes known isomerization and addition reactions of the carbonyl oxide intermediates generated during the ozonation of limonene. In addition, it includes isomerization and decomposition pathways for alkoxy radicals resulting from unimolecular decomposition of carbonyl oxides that have been disregarded by previous studies. The isomerization reactions yield numerous products with a progressively increasing number of alcohol and carbonyl groups, whereas C-C bond scission reactions in alkoxy radicals shorten the carbon chain. Together these reactions yield a large number of isomeric products with broadly distributed masses. A qualitative agreement is found between the number and degree of oxidation of the predicted and measured reaction products in the monomer product range.     

Characterization of platinum anticancer drug protein-binding sites using a top-down mass spectrometric approach

A proof-of-principle study on the application of a top-down electrospray ionization Fourier transform ion cyclotron resonance mass spectrometric approach for characterization of the primary binding sites of the platinum anticancer agents cisplatin, transplatin, and oxaliplatin on ubiquitin is presented. Through employment of different fragmentation techniques, the binding sites of cisplatin and oxaliplatin were found at N-terminal methionine-containing ubiquitin fragments, while transplatin was observed to be attached to 19Pro-Ser-Asp-Thr-Ile-Glu24. The binding to proteins is of particular relevance for the mode of action of metallodrugs with regard to (de)activation, transport, excretion, etc. To the best of our knowledge, this is the first top-down mass spectrometric study on the protein binding site characterization of transition-metal anticancer agents and demonstrates the potential of the applied technique for investigating metal drug-protein interactions.     

Influence of Environmental Parameters on the Stability of the DNA Molecule

Fluctuations in viscosity within the cell nucleus have wide limits. When a DNA molecule passes from the region of high viscosity values to the region of low values, open states, denaturation bubbles, and unweaving of DNA strands can occur. Stabilization of the molecule is provided by energy dissipation—dissipation due to interaction with the environment. Separate sections of a DNA molecule in a twisted state can experience supercoiling stress, which, among other things, is due to complex entropic effects caused by interaction with a solvent. In this work, based on the numerical solution of a mechanical mathematical model for the interferon alpha 17 gene and a fragment of the Drosophila gene, an analysis of the external environment viscosity influence on the dynamics of the DNA molecule and its stability was carried out. It has been shown that an increase in viscosity leads to a rapid stabilization of the angular vibrations of nitrogenous bases, while a decrease in viscosity changes the dynamics of DNA: the rate of change in the angular deviations of nitrogenous bases increases and the angular deformations of the DNA strands increase at each moment of time. These processes lead to DNA instability, which increases with time. Thus, the paper considers the influence of the external environment viscosity on the dissipation of the DNA nitrogenous bases’ vibrational motion energy. Additionally, the study on the basis of the described model of the molecular dynamics of physiological processes at different indicators of the rheological behavior of nucleoplasm will allow a deeper understanding of the processes of nonequilibrium physics of an active substance in a living cell to be obtained.