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The time-dependent approach to electronic spectroscopy, as popularized by Heller and coworkers in the 1980's, is applied here in conjunction with linear-response, time-dependent density functional theory to study vibronic absorption, emission and resonance Raman spectra of several diamondoids. Two-state models, the harmonic and the Condon approximations, are used for the calculations, making them easily applicable to larger molecules. The method is applied to nine pristine lower and higher diamondoids: adamantane, diamantane, triamantane, and three isomers each of tetramantane and pentamantane. We also consider a hybrid species “Dia = Dia” – a shorthand notation for a recently synthesized molecule comprising two diamantane units connected by a C[double bond, length as m-dash]C double bond. We resolve and interpret trends in optical and vibrational properties of these molecules as a function of their size, shape, and symmetry, as well as effects of “blending” with sp2-hybridized C-atoms. Time-dependent correlation functions facilitate the computations and shed light on the vibrational dynamics following electronic transitions.
Through the reactions of 1-aminomethyl-2-naphthol and substituted 1-aminobenzyl-2-naphthols with 3,4-dihydroisoquinoline or 6,7-dimethoxy-3,4-dihydroisoquinoline under microwave conditions, naphth[1,2-e][1,3]oxazino[2,3-a]-isoquinoline derivatives were prepared in good yields. The latter reaction was extended by using 2-aminoarylmethyl-1-naphthols, leading to isomeric naphth-[2,1-e][1,3]oxazino[2,3-a] isoquinolines. Beside the detailed NMR spectroscopic and theoretical study of both stereochemistry and dynamic behaviour of these new conformational flexible heterocyclic ring systems an unexpected dynamic process between two diastereomers was observed in solution, studied by variable temperature H-1 NMR spectroscopy and the mechanism proved by theoretical DFT computations.
Transcriptome analysis through next-generation sequencing technologies allows the generation of detailed gene catalogs for non-model species, at the cost of new challenges with regards to computational requirements and bioinformatics expertise. Here, we present TRAPID, an online tool for the fast and efficient processing of assembled RNA-Seq transcriptome data, developed to mitigate these challenges. TRAPID offers high-throughput open reading frame detection, frameshift correction and includes a functional, comparative and phylogenetic toolbox, making use of 175 reference proteomes. Benchmarking and comparison against state-of-the-art transcript analysis tools reveals the efficiency and unique features of the TRAPID system.
Silver nanoparticles (SNPs) are among the most commercialized nanoparticles because of their antibacterial effects. Besides being employed, e. g. as a coatingmaterial for sterile surfaces in household articles and appliances, the particles are also used in a broad range of medical applications. Their antibacterial properties make SNPs especially useful for wound disinfection or as a coating material for prostheses and surgical instruments. Because of their optical characteristics, the particles are of increasing interest in biodetection as well. Despite the widespread use of SNPs, there is little knowledge of their toxicity. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) and laser post-ionization secondary neutral mass spectrometry (Laser-SNMS) were used to investigate the effects of SNPs on human macrophages derived from THP-1 cells in vitro. For this purpose, macrophages were exposed to SNPs. The SNP concentration ranges were chosen with regard to functional impairments of the macrophages. To optimize the analysis of the macrophages, a special silicon wafer sandwich preparation technique was employed; ToF-SIMS was employed to characterize fragments originating from macrophage cell membranes. With the use of this optimized sample preparation method, the SNP-exposed macrophages were analyzed with ToF-SIMS and with Laser-SNMS. With Laser-SNMS, the three-dimensional distribution of SNPs in cells could be readily detected with very high efficiency, sensitivity, and submicron lateral resolution. We found an accumulation of SNPs directly beneath the cell membrane in a nanoparticular state as well as agglomerations of SNPs inside the cells.
Silver nanoparticles (SNP) are among the most commercialized nanoparticles. Here, we show that peptide-coated SNP cause functional impairment of human macrophages. A dose-dependent inhibition of phagocytosis is observed after nanoparticle treatment, and pretreatment of cells with N-acetyl cysteine (NAC) can counteract the phagocytosis disturbances caused by SNP.
Using the surface-sensitive mode of time-of-flight secondary ion mass spectrometry, in combination with multivariate statistical methods, we studied the composition of cell membranes in human macrophages upon exposure to SNP with and without NAC preconditioning. This method revealed characteristic changes in the lipid pattern of the cellular membrane outer leaflet in those cells challenged by SNP. Statistical analyses resulted in 19 characteristic ions, which can be used to distinguish between NAC pretreated and untreated macrophages. The present study discusses the assignments of surface cell membrane phospholipids for the identified ions and the resulting changes in the phospholipid pattern of treated cells. We conclude that the adverse effects in human macrophages caused by SNP can be partially reversed through NAC administration. Some alterations, however, remained.
Thick poly(styrene-b-monomethoxydiethylenglycol-acrylate-b-styrene) [P(S-b-MDEGA-b-S)] films (thickness 5 mu m) are prepared from different solvents on flexible substrates by solution casting and investigated with small-angle X-ray scattering. As the solvents are either PS- or PMDEGA-selective, micelles with different core-shell micellar structures are formed. In PMDEGA-selective solvents, the PS block is the core and PMDEGA is the shell, whereas in PS-selective solvents, the order is reversed. After exposing the films to liquid D2O, the micellar structure inside the films prepared from PMDEGA-selective solvents remains unchanged and only the PMDEGA (shell part) swells. On the contrary, in the films prepared from PS-selective solvents, the micelles revert the core and the shell. This reversal causes more entanglements of the PMDEGA chains between the micelles. Moreover, the thermal collapse transition of the PMDEGA block in liquid D2O is significantly broadened. Irrespective of the solvent used for film preparation, the swollen PMDEGA shell does not show a prominent shrinkage when passing the phase transition, and the transition process occurs via compaction. The collapsed micelles have a tendency to densely pack above the transition temperature.
Despite the critical importance of the hydroxyl radical in major scientific fields, there are still open questions on the behavior of this species in the aqueous phase. In particular, there has been much debate on the existence of a hemibonded interaction between the hydroxyl radical and water molecules. While some reports indicate that the hemibonded radical might explain some experimental data, others have claimed that this interaction is simply a density functional theory (DFT) artifact. Here, we provide results from high level (basis set limit of coupled-cluster levels up to single, double, triple excitations (CCSD(T)) and beyond) ab initio calculations of different OH center dot(H2O)(n) clusters in the gas phase to accurately explore the existence of the hemibonded interaction and its energy difference with respect to other well-defined hydrogen bond interactions. Additional comparisons with second order perturbation theory (MP2) and DFT are also presented. Constrained molecular dynamics was applied to determine the free energy for the formation/disruption and ice systems. Overall, our findings confirm that the hemibond can be an alternative structure for the hydroxyl radical in the condensed phase when the formation of hydrogen bonds is impeded. These results will aid the understanding of theoretical and experimental data and help future experimental designs for the detection of this important species.
We present and discuss the results of crystallographic and electron paramagnetic resonance (EPR) spectroscopic analyses of five tetrachloridocuprate(II) complexes to supply a useful tool for the structural characterisation of the [CuCl4]2− moiety in the liquid state, for example in ionic liquids, or in solution. Bis(benzyltriethylammonium)-, bis(trimethylphenylammonium)-, bis(ethyltriphenylphosphonium)-, bis(benzyltriphenylphosphonium)-, and bis(tetraphenylarsonium)tetrachloridocuprate(II) were synthesised and characterised by elemental, IR, EPR and X-ray analyses. The results of the crystallographic analyses show distorted tetrahedral coordination geometry of all [CuCl4]2− anions in the five complexes and prove that all investigated complexes are stabilised by hydrogen bonds of different intensities. Despite the use of sterically demanding ammonium, phosphonium and arsonium cations to obtain the separation of the paramagnetic Cu(II) centres for EPR spectroscopy no hyperfine structure was observed in the EPR spectra but the principal values of the electron Zeeman tensor, g∥ and g⊥, could be determined. With these EPR data and the crystallographic parameters we were able to carry out a correlation study to anticipate the structural situation of tetrachloridocuprates in different physical states. This correlation is in good agreement with DFT calculations.