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- ItemBenchmark of Simplified Time-Dependent Density Functional Theory for UV–Vis Spectral Properties of Porphyrinoids(Weinheim : Wiley-VCH Verlag, 2019) Batra, Kamal; Zahn, Stefan; Heine, ThomasTime-dependent density functional theory is thoroughly benchmarked for the predictive calculation of UV–vis spectra of porphyrin derivatives. With the aim to provide an approach that is computationally feasible for large-scale applications such as biological systems or molecular framework materials, albeit performing with high accuracy for the Q-bands, the results given by various computational protocols, including basis sets, density-functionals (including gradient corrected local functionals, hybrids, double hybrids and range-separated functionals), and various variants of time-dependent density functional theory, including the simplified Tamm–Dancoff approximation, are compared. An excellent choice for these calculations is the range-separated functional CAM-B3LYP in combination with the simplified Tamm–Dancoff approximation and a basis set of double-ζ quality def2-SVP (mean absolute error [MAE] of ≈0.05 eV). This is not surpassed by more expensive approaches, not even by double hybrid functionals, and solely systematic excitation energy scaling slightly improves the results (MAE ≈0.04 eV).
- ItemCurcuminoid–BF2 complexes: Synthesis, fluorescence and optimization of BF2 group cleavage(Frankfurt a.M. : Beilstein-Institut, 2017) Weiß, Henning; Reichel, Jeannine; Görls, Helmar; Schneider, Kilian R.A.; Micheel, Mathias; Pröhl, Michael; Gottschaldt, Michael; Dietzek, Benjamin; Weigand, WolfgangEight difluoroboron complexes of curcumin derivatives carrying alkyne groups containing substituents have been synthesized following an optimised reaction pathway. The complexes were received in yields up to 98% and high purities. Their properties as fluorescent dyes have been investigated. Furthermore, a strategy for the hydrolysis of the BF2 group has been established using aqueous methanol and sodium hydroxide or triethylamine.
- ItemCharacterization of Fluorescent Proteins with Intramolecular Photostabilization*(Weinheim : Wiley-VCH, 2021) Henrikus, Sarah S.; Tassis, Konstantinos; Zhang, Lei; van der Velde, Jasper H. M.; Gebhardt, Christian; Herrmann, Andreas; Jung, Gregor; Cordes, ThorbenGenetically encodable fluorescent proteins have revolutionized biological imaging in vivo and in vitro. Despite their importance, their photophysical properties, i. e., brightness, count-rate and photostability, are relatively poor compared to synthetic organic fluorophores or quantum dots. Intramolecular photostabilizers were recently rediscovered as an effective approach to improve photophysical properties of organic fluorophores. Here, direct conjugation of triplet-state quenchers or redox-active substances creates high local concentrations of photostabilizer around the fluorophore. In this paper, we screen for effects of covalently linked photostabilizers on fluorescent proteins. We produced a double cysteine mutant (A206C/L221C) of α-GFP for attachment of photostabilizer-maleimides on the β-barrel near the chromophore. Whereas labelling with photostabilizers such as trolox, a nitrophenyl group, and cyclooctatetraene, which are often used for organic fluorophores, had no effect on α-GFP-photostability, a substantial increase of photostability was found upon conjugation to azobenzene. Although the mechanism of the photostabilizing effects remains to be elucidated, we speculate that the higher triplet-energy of azobenzene might be crucial for triplet-quenching of fluorophores in the blue spectral range. Our study paves the way for the development of fluorescent proteins with photostabilizers in the protein barrel by methods such as unnatural amino acid incorporation. © 2021 The Authors. ChemBioChem published by Wiley-VCH GmbH
- Itemcorr2D: Implementation of Two-Dimensional Correlation Analysis in R(Los Angeles : UCLA, 2019) Geitner, Robert; Fritzsch, Robby; Bocklitz, Thomas W.; Popp, JürgenIn the package corr2D two-dimensional correlation analysis is implemented in R. This paper describes how two-dimensional correlation analysis is done in the package and how the mathematical equations are translated into R code. The paper features a simple tutorial with executable code for beginners, insight into the calculations done before the correlation analysis, a detailed look at the parallelization of the fast Fourier transformation based correlation analysis and a speed test of the calculation. The package corr2D offers the possibility to preprocess, correlate and postprocess spectroscopic data using exclusively the R language. Thus, corr2D is a welcome addition to the toolbox of spectroscopists and makes two-dimensional correlation analysis more accessible and transparent.
- ItemRaman and infrared spectroscopy reveal that proliferating and quiescent human fibroblast cells age by biochemically similar but not identical processes(San Francisco : Public Library of Science, 2018) Eberhardt, Katharina; Matthäus, Christian; Marthandan, Shiva; Diekmann, Stephan; Popp, JürgenDermal fibroblast cells can adopt different cell states such as proliferation, quiescence, apoptosis or senescence, in order to ensure tissue homeostasis. Proliferating (dividing) cells pass through the phases of the cell cycle, while quiescent and senescent cells exist in a non-proliferating cell cycle-arrested state. However, the reversible quiescence state is in contrast to the irreversible senescence state. Long-term quiescent cells transit into senescence indicating that cells age also when not passing through the cell cycle. Here, by label-free in vitro vibrational spectroscopy, we studied the biomolecular composition of quiescent dermal fibroblast cells and compared them with those of proliferating and senescent cells. Spectra were examined by multivariate statistical analysis using a PLS-LDA classification model, revealing differences in the biomolecular composition between the cell states mainly associated with protein alterations (variations in the side chain residues of amino acids and protein secondary structure), but also within nucleic acids and lipids. We observed spectral changes in quiescent compared to proliferating cells, which increased with quiescence cultivation time. Raman and infrared spectroscopy, which yield complementary biochemical information, clearly distinguished contact-inhibited from serum-starved quiescent cells. Furthermore, the spectra displayed spectral differences between quiescent cells and proliferating cells, which had recovered from quiescence. This became more distinct with increasing quiescence cultivation time. When comparing proliferating, (in particular long-term) quiescent and senescent cells, we found that Raman as well as infrared spectroscopy can separate these three cellular states from each other due to differences in their biomolecular composition. Our spectroscopic analysis shows that proliferating and quiescent fibroblast cells age by similar but biochemically not identical processes. Despite their aging induced changes, over long time periods quiescent cells can return into the cell cycle. Finally however, the cell cycle arrest becomes irreversible indicating senescence.Dermal fibroblast cells can adopt different cell states such as proliferation, quiescence, apoptosis or senescence, in order to ensure tissue homeostasis. Proliferating (dividing) cells pass through the phases of the cell cycle, while quiescent and senescent cells exist in a non-proliferating cell cycle-arrested state. However, the reversible quiescence state is in contrast to the irreversible senescence state. Long-term quiescent cells transit into senescence indicating that cells age also when not passing through the cell cycle. Here, by label-free in vitro vibrational spectroscopy, we studied the biomolecular composition of quiescent dermal fibroblast cells and compared them with those of proliferating and senescent cells. Spectra were examined by multivariate statistical analysis using a PLS-LDA classification model, revealing differences in the biomolecular composition between the cell states mainly associated with protein alterations (variations in the side chain residues of amino acids and protein secondary structure), but also within nucleic acids and lipids. We observed spectral changes in quiescent compared to proliferating cells, which increased with quiescence cultivation time. Raman and infrared spectroscopy, which yield complementary biochemical information, clearly distinguished contact-inhibited from serum-starved quiescent cells. Furthermore, the spectra displayed spectral differences between quiescent cells and proliferating cells, which had recovered from quiescence. This became more distinct with increasing quiescence cultivation time. When comparing proliferating, (in particular long-term) quiescent and senescent cells, we found that Raman as well as infrared spectroscopy can separate these three cellular states from each other due to differences in their biomolecular composition. Our spectroscopic analysis shows that proliferating and quiescent fibroblast cells age by similar but biochemically not identical processes. Despite their aging induced changes, over long time periods quiescent cells can return into the cell cycle. Finally however, the cell cycle arrest becomes irreversible indicating senescence.
- ItemRole of electronic correlations in photoionization of NO2 in the vicinity of the 2A1/2B2 conical intersection(Cambridge : The Royal Soc. of Chemistry, 2017) Brambila, Danilo S.; Harvey, Alex G.; Houfek, Karel; Mašín, Zdeněk; Smirnova, OlgaWe present the first ab initio multi-channel photoionization calculations for NO2 in the vicinity of the 2A1/2B2 conical intersection, for a range of nuclear geometries, using our newly developed set of tools based on the ab initio multichannel R-matrix method. Electronic correlation is included in both the neutral and the scattering states of the molecule via configuration interaction. Configuration mixing is especially important around conical intersections and avoided crossings, both pertinent for NO2, and manifests itself via significant variations in photoelectron angular distributions. The method allows for a balanced and accurate description of the photoionization/photorecombination for a number of different ionic channels in a wide range of photoelectron energies up to 100 eV. Proper account of electron correlations is crucial for interpreting time-resolved signals in photoelectron spectroscopy and high harmonic generation (HHG) from polyatomic molecules.
- ItemInvestigation of an Ablation-dominated Arc in a Model Chamber by Optical Emission Spectroscopy(Praha : Czech Technical University in Prague, Faculty of Electrical Engineering, Department of Physics, 2017) Methling, R.; Khakpour, A.; Wetzeler, S.; Uhrlandt, D.A switching arc in a model chamber is investigated by means of optical emission spectroscopy. Ignition wire is applied to initiate an arc of several kiloampere between tungsten−copper electrodes. Radiation emitted by the arc plasma is absorbed by a surrounding PTFE nozzle, leading to an ablation–dominated discharge. Video spectroscopy is carried out using an imaging spectrometer combined with a high–speed video camera. Carbon ion and fluorine atom line emission from the heating channel as well as copper, oxygen and nitrogen from ignition wire and ambient air are analyzed with focus on the low–current phases at the beginning of discharge and near current zero. Additionally, electrical parameters and total pressure are recorded while the general behavior of the discharge is observed by another video camera. Considering rotational symmetry of the arc the corresponding radial emission coefficients are determined. Finally, radial temperature profiles are calculated.
- ItemAntioxidant and hydrophilic poly(lactic acid) fibers obtained through their modification with amines and ferulic acid(New York, NY [u.a.] : Wiley, 2017) Wojciechowska, Dorota; Herczyńska, Lucyna; Simon, Frank; Puchalski, Michał; Stawski, DawidThe ferulic acid (FA) is a natural antioxidant, abundantly present in plants, which acts as the plant's immune system. In order to take advantage of its properties, a method has been developed, which combines antioxidant FA with bio-based biodegradable poly(lactic acid) fibers and biocompatible hydrophilic polyallylamine, enabling the production of versatile base material that could be used for active anti-inflammatory wound dressings. The fibers are first subjected to aminolysis in order to obtain amino moieties on the surface, able to react with the molecules of FA. Next, the FA was attached to the aminolyzed fibers surface with use of 1-ethyl-3–(3-dimethylaminopropyl) carbodiimide and N-hydroxysuccinimide. The anti-inflammatory properties of the modified fibers were assessed using 2,2-diphenyl-1-picrylhydrazyl radical scavenging assay. Presence of FA on the fibers’ surface was investigated through X-ray photoelectron spectroscopy analysis and Folin–Ciocalteu (total phenolic content) test.
- ItemTime-reversal symmetry breaking type-II Weyl state in YbMnBi2(London : Nature Publishing Group, 2019) Borisenko, S.; Evtushinsky, D.; Gibson, Q.; Yaresko, A.; Koepernik, K.; Kim, T.; Ali, M.; van den Brink, J.; Hoesch, M.; Fedorov, A.; Haubold, E.; Kushnirenko, Y.; Soldatov, I.; Schäfer, R.; Cava, R.J.Spectroscopic detection of Dirac and Weyl fermions in real materials is vital for both, promising applications and fundamental bridge between high-energy and condensed-matter physics. While the presence of Dirac and noncentrosymmetric Weyl fermions is well established in many materials, the magnetic Weyl semimetals still escape direct experimental detection. In order to find a time-reversal symmetry breaking Weyl state we design two materials and present here experimental and theoretical evidence of realization of such a state in one of them, YbMnBi2. We model the time-reversal symmetry breaking observed by magnetization and magneto-optical microscopy measurements by canted antiferromagnetism and find a number of Weyl points. Using angle-resolved photoemission, we directly observe two pairs of Weyl points connected by the Fermi arcs. Our results not only provide a fundamental link between the two areas of physics, but also demonstrate the practical way to design novel materials with exotic properties.
- ItemTailor-made nanostructures bridging chaos and order for highly efficient white organic light-emitting diodes(London : Nature Publishing Group, 2019) Li, Y.; Kovačič, M.; Westphalen, J.; Oswald, S.; Ma, Z.; Hänisch, C.; Will, P.-A.; Jiang, L.; Junghaehnel, M.; Scholz, R.; Lenk, S.; Reineke, S.Organic light-emitting diodes (OLEDs) suffer from notorious light trapping, resulting in only moderate external quantum efficiencies. Here, we report a facile, scalable, lithography-free method to generate controllable nanostructures with directional randomness and dimensional order, significantly boosting the efficiency of white OLEDs. Mechanical deformations form on the surface of poly(dimethylsiloxane) in response to compressive stress release, initialized by reactive ions etching with periodicity and depth distribution ranging from dozens of nanometers to micrometers. We demonstrate the possibility of independently tuning the average depth and the dominant periodicity. Integrating these nanostructures into a two-unit tandem white organic light-emitting diode, a maximum external quantum efficiency of 76.3% and a luminous efficacy of 95.7 lm W−1 are achieved with extracted substrate modes. The enhancement factor of 1.53 ± 0.12 at 10,000 cd m−2 is obtained. An optical model is built by considering the dipole orientation, emitting wavelength, and the dipole position on the sinusoidal nanotexture.
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