@article{SzatmariHeydenreichKochetal.2013, author = {Szatmari, Istvan and Heydenreich, Matthias and Koch, Andreas and Fulop, Ferenc and Kleinpeter, Erich}, title = {Unexpected isomerization of new naphth[1,3]oxazino[2,3-a] isoquinolines in solution, studied by dynamic NMR and supported by theoretical DFT computations}, series = {Tetrahedron}, volume = {69}, journal = {Tetrahedron}, number = {35}, publisher = {Elsevier}, address = {Oxford}, issn = {0040-4020}, doi = {10.1016/j.tet.2013.06.094}, pages = {7455 -- 7465}, year = {2013}, abstract = {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.}, language = {en} } @article{VanBelProostVanNesteetal.2013, author = {Van Bel, Michiel and Proost, Sebastian and Van Neste, Christophe and Deforce, Dieter and Van de Peer, Yves and Vandepoele, Klaas}, title = {TRAPID - an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes}, series = {Genome biology : biology for the post-genomic era}, volume = {14}, journal = {Genome biology : biology for the post-genomic era}, number = {12}, publisher = {BioMed Central}, address = {London}, issn = {1465-6906}, doi = {10.1186/gb-2013-14-12-r134}, pages = {10}, year = {2013}, abstract = {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.}, language = {en} } @article{DraudeGallaPelsteretal.2013, author = {Draude, F. and Galla, S. and Pelster, Axel and Tentschert, J. and Jungnickel, H. and Haase, Alfred and Mantion, Alexandre and Thuenemann, Andreas F. and Taubert, Andreas and Luch, A. and Arlinghaus, H. F.}, title = {ToF-SIMS and Laser-SNMS analysis of macrophages after exposure to silver nanoparticles}, series = {Surface and interface analysis : an international journal devoted to the development and application of techniques for the analysis surfaces, interfaces and thin films}, volume = {45}, journal = {Surface and interface analysis : an international journal devoted to the development and application of techniques for the analysis surfaces, interfaces and thin films}, number = {1}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0142-2421}, doi = {10.1002/sia.4902}, pages = {286 -- 289}, year = {2013}, abstract = {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.}, language = {en} } @article{TentschertDraudeJungnickeletal.2013, author = {Tentschert, J. and Draude, F. and Jungnickel, H. and Haase, A. and Mantion, Alexandre and Galla, S. and Thuenemann, Andreas F. and Taubert, Andreas and Luch, A. and Arlinghaus, H. F.}, title = {TOF-SIMS analysis of cell membrane changes in functional impaired human macrophages upon nanosilver treatment}, series = {Surface and interface analysis : an international journal devoted to the development and application of techniques for the analysis surfaces, interfaces and thin films}, volume = {45}, journal = {Surface and interface analysis : an international journal devoted to the development and application of techniques for the analysis surfaces, interfaces and thin films}, number = {1}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0142-2421}, doi = {10.1002/sia.5155}, pages = {483 -- 485}, year = {2013}, abstract = {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.}, language = {en} } @phdthesis{Rohrmann2013, author = {Rohrmann, Johannes}, title = {The transcription factors orchestra of ripening tomato fruits}, address = {Potsdam}, pages = {Ix, 136 S. + 1 CD-Rom}, year = {2013}, language = {en} } @article{ZhongAdelsbergerNiedermeieretal.2013, author = {Zhong, Qi and Adelsberger, Joseph and Niedermeier, M. A. and Golosova, Anastasi and Bivigou Koumba, Achille Mayelle and Laschewsky, Andr{\´e} and Funari, S. S. and Papadakis, Christine M. and M{\"u}ller-Buschbaum, Peter}, title = {The influence of selective solvents on the transition behavior of poly(styrene-b-monomethoxydiethylenglycol-acrylate-b-styrene) thick films}, series = {Colloid and polymer science : official journal of the Kolloid-Gesellschaft}, volume = {291}, journal = {Colloid and polymer science : official journal of the Kolloid-Gesellschaft}, number = {6}, publisher = {Springer}, address = {New York}, issn = {0303-402X}, doi = {10.1007/s00396-012-2879-4}, pages = {1439 -- 1451}, year = {2013}, abstract = {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.}, language = {en} } @article{CodorniuHernandezBoeseKusalik2013, author = {Codorniu-Hernandez, Edelsys and Boese, Adrian Daniel and Kusalik, Peter G.}, title = {The hemibond as an alternative condensed phase structure for the hydroxyl radical}, series = {Canadian journal of chemistry = Revue canadienne de chimie}, volume = {91}, journal = {Canadian journal of chemistry = Revue canadienne de chimie}, number = {7}, publisher = {NRC Research Press}, address = {Ottawa}, issn = {0008-4042}, doi = {10.1139/cjc-2012-0520}, pages = {544 -- 551}, year = {2013}, abstract = {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.}, language = {en} } @article{TechenCzaplaMoellnitzetal.2013, author = {Techen, Anne and Czapla, Sylvia and M{\"o}llnitz, Kristian and Budach, Dennis B. and Wessig, Pablo and Kumke, Michael Uwe}, title = {Synthesis and spectroscopic characterization of fluorophore-labeled oligospiroketal rods}, series = {Helvetica chimica acta}, volume = {96}, journal = {Helvetica chimica acta}, number = {11}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0018-019X}, doi = {10.1002/hlca.201200616}, pages = {2046 -- 2067}, year = {2013}, abstract = {Fluorescence probes consisting of well-established fluorophores in combination with rigid molecular rods based on spirane-type structures were investigated with respect to their fluorescence properties under different solvent conditions. The attachment of the dyes was accomplished by 1,3-dipolar cycloaddition between alkynes and azides (click' reaction) and is a prime example for a novel class of sensor constructs. Especially, the attachment of two (different) fluorophores on opposite sides of the molecular rods paves the way to new sensor systems with less bulky (compared to the conventional DNA- or protein-based concepts), nevertheless rigid spacer constructs, e.g., for FRET-based sensing applications. A detailed photophysical characterization was performed in MeOH (and in basic H2O/MeOH mixtures) for i) rod constructs containing carboxyfluorescein, ii) rod constructs containing carboxyrhodamine, iii) rod constructs containing both carboxyfluorescein and carboxyrhodamine, and iv) rod constructs containing both pyrene and perylene parts. For each dye (pair), two rod lengths with different numbers of spirane units were synthesized and investigated. The rod constructs were characterized in ensemble as well as single-molecule fluorescence experiments with respect to i) specific roddye and ii) dyedye interactions. In addition to MeOH and MeOH/NaOH, the rod constructs were also investigated in micellar systems, which were chosen as a simplified model for membranes.}, language = {en} } @article{MondalDeyBaburinetal.2013, author = {Mondal, Suvendu Sekhar and Dey, Subarna and Baburin, Igor A. and Kelling, Alexandra and Schilde, Uwe and Seifert, Gotthard and Janiak, Christoph and Holdt, Hans-J{\"u}rgen}, title = {Syntheses of two imidazolate-4-amide-5-imidate linker-based hexagonal metal-organic frameworks with flexible ethoxy substituent}, series = {CrystEngComm}, volume = {15}, journal = {CrystEngComm}, number = {45}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1466-8033}, doi = {10.1039/c3ce41632a}, pages = {9394 -- 9399}, year = {2013}, abstract = {A rare example of in situ linker generation with the formation of soft porous Zn- and Co-MOFs (IFP-9 and -10, respectively) is reported. The flexible ethoxy groups of IFP-9 and -10 protrude into the 1D hexagonal channels. The gas-sorption behavior of both materials for H-2, CO2 and CH4 showed wide hysteretic isotherms, typical for MOFs having a flexible substituent which can give rise to a gate effect.}, language = {en} } @article{HerderUtechtManickeetal.2013, author = {Herder, Martin and Utecht, Manuel Martin and Manicke, Nicole and Grubert, Lutz and P{\"a}tzel, Michael and Saalfrank, Peter and Hecht, Stefan}, title = {Switching with orthogonal stimuli electrochemical ring-closure and photochemical ring-opening of bis(thiazolyl) maleimides}, series = {Chemical science}, volume = {4}, journal = {Chemical science}, number = {3}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {2041-6520}, doi = {10.1039/c2sc21681g}, pages = {1028 -- 1040}, year = {2013}, abstract = {The photochemistry as well as electrochemistry of novel donor-acceptor bis(morpholinothiazolyl)maleimides has been investigated. Proper substitution of these diarylethene-type molecular switches leads to the unique situation in which their ring-closure can only be accomplished electrochemically, while ring-opening can only be achieved photochemically. Hence, these switches operate with orthogonal stimuli, i.e. redox potential and light, respectively. The switch system could be optimized by introducing trifluoromethyl groups at the reactive carbon atoms in order to avoid by-product formation during oxidative ring closure. Both photochemical and electrochemical pathways were investigated for methylated, trifluoromethylated, and nonsymmetrical bis(morpholinothiazolyl) maleimides as well as the bis(morpholinothiazolyl) cyclopentene reference compound. With the aid of the nonsymmetrical "mixed" derivative, the mechanism of electrochemically driven ring closure could be elucidated and seems to proceed via a dicationic intermediate generated by two-fold oxidation. All experimental work has been complemented by density functional theory that provides detailed insights into the thermodynamics of the ring-open and closed forms, the nature of their excited states, and the reactivity of their neutral as well as ionized species in different electronic configurations. The particular diarylethene systems described herein could serve in multifunctional (logic) devices operated by different stimuli (inputs) and may pave the way to converting light into electrical energy via photoinduced "pumping" of redox-active meta-stable states.}, language = {en} }