Resonant Raman Scattering of 4‐Nitrothiophenol

Thiophenol‐based molecules are commonly used reporter molecules for various experiments, especially within the scope of surface‐ and tip‐enhanced Raman spectroscopy. Due to their molecular structure, they bind covalently to noble metals and have a huge Raman scattering cross section. Herein, the widely uncharted optical properties of the frequently used probe molecule 4‐nitrothiophenol (p‐NTP or 4‐NTP) are analyzed by resonant Raman spectroscopy. Based on the three different types of samples, it is demonstrated that the molecule exhibits two intrinsic resonances at specific wavelengths. For a wide range of experiments, this is an important information since intrinsic resonances may give rise to an enhancement of the Raman intensity at these specific excitation wavelengths. The Raman cross section of p‐NTP in resonance at 1.9 eV (650 nm) to be 6 × 10−26 cm2 per molecule is also measured

Studien über variable Oberflächenloops der En-Reduktase NCR aus Zymomonas mobilis

The present work deals with the flavin-dependent ene reductases from the Old Yellow Enzyme family which catalyze a trans-hydrogenation of activated C=C double bonds with absolute stereospecificity due to the architecture of their active site. All family members possess as a structural backbone a barrel made of eight parallel beta-sheets, which are connected by loops with eight surrounding alpha-helices. Despite great structural and sequential similarities, the individual family members demonstrate significant differences in substrate specificity, thermostability and enantioselectivity. This fact leads to the question where the source of these different preferences of the individual ene reductases comes from. Comparing the amino acid composition as well as the spatial arrangement of the various family members, it is noticeable that the differences between these enzymes are located especially in so-called flexible beta/alpha loop regions on the surface of the catalytic interface. The central question of this work is the influence of these surface loop regions on enzyme´s properties and the evolutionary relationship and development of such loop regions within this enzyme family. In the first approach four beta/alpha loop regions between five selected ene reductases were shuffled by using the semi-rational Golden Gate Shuffling method. Based on a developed photometric activity assay, a total of five loop shuffling variants were selected for the characterization of the substrate spectrum. This characterization has shown that the random simultaneous shuffling of up to four surface loop regions resulted in enzyme variants demonstrating compared to wild type NCR an increased reduction activity towards standard substrates. In the second approach the family of the Old Yellow Enzymes was divided into five homologous subfamilies by using phylogenetic analysis based on the overall sequence identity. One of these subfamilies was investigated in more detail with regard on the occurrence, as well as the evolutionary relationship of surface loops. For this purpose two surface loops, Loop A and Loop B, in three different ene reductases were defined by a sequence-based secondary structure prediction. The generation of Hidden Markov loop profiles led to the conclusion that beta/alpha surface loops are composed of conserved, as well as variable amino acid positions and that individual family members can be assigned to certain loop profiles. Additionally to that Hidden Markov loop profiles pointed out that the presence of a common loop region at two different ene reductases is not depending on the overall sequence identity. Two widely related family members could exhibit the same loop profile. In the third approach the question, whether the loop length and/or the amino acid composition of a loop area possess a significant influence on the properties of an enzyme was addressed by the development of a rational loop design method. Therefore, a total of seven loop variants of the two structurally defined loop regions A and B of NCR from Z. mobilis were designed. The crystal structure determination of one of the loop grafting variants revealed that the exchange of loop regions led to changes that affect the complete enzyme structure. Furthermore, it was shown by the seven rational variants that both, the amino acid composition as well as the loop length of surface loops of TIM barrel proteins possess a significant effect on the properties of an enzyme. Thus, in contrast to Loop B changes in the Loop A region in length or amino acid composition led to a decreased stability of the enzyme. Additionally, it could be shown that it was possible to transfer properties of one enzyme to another by the grafting of surface loop regions, for example the cis/trans substrate specificity. In summary, the present work could demonstrate that TIM barrel based enzymes are able to tolerate large structural as well as sequential alterations within their surface loops without losing their catalytic activity. Based on the results obtained within this thesis it could be concluded that beta/alpha surface loop regions of Old Yellow Enzymes are representing "Enzyme Modifying Elements" that possess a significant influence on the properties of the entire enzyme. Furthermore, it was also shown for the first time that surface loops can be assigned to specific loop profiles consisting of conserved and variable regions. Based on the acquired understanding of the influence of loop regions on enzyme properties, it should in the near future be possible to create a tailor-made reductase with desired properties by rational loop design.Die vorliegende Arbeit beschäftigt sich mit Flavin-abhängigen En-Reduktasen der Old Yellow Enzyme Familie, die aufgrund der Architektur ihres aktiven Zentrums eine trans-Hydrierung von aktivierten C=C Doppelbindungen mit absoluter Stereospezifität katalysieren. Als strukturelles Grundgerüst besitzen alle Familienmitglieder ein Fass gebildet aus acht parallelen beta-Faltblätter, die mittels Loops mit acht umgebenden alpha-Helices verbunden sind. Trotz großer struktureller, sowie sequenzieller Gemeinsamkeiten, weisen die einzelnen Familienmitglieder deutliche Unterschiede bezüglich Substratspezifität, Thermostabilität und Enantioselektivität auf. Daraus ergibt sich die Frage, worin der Ursprung dieser unterschiedlichen Präferenzen der einzelnen En-Reduktasen begründet liegt. Vergleicht man nun dazu die Aminosäurezusammensetzung, sowie die räumliche Struktur der verschiedenen Familienmitglieder, fällt auf, dass sich diese Enzyme vor allem in sogenannten flexiblen beta/alpha Loopregionen an der Oberfläche des katalytischen Interface unterscheiden. Die zentrale Frage die sich nun stellt, und die in dieser Arbeit mittels drei verschiedenen Ansätze beantwortet werden soll ist, welchen Beitrag diese oberflächlichen Loopregionen für die Eigenschaften eines Enzymes leisten, sowie ob sich eine evolutive Entwicklung der Loopregionen erkennen lässt. Im ersten Ansatz ist es mittels der Methode des semi-rationalen Golden Gate Shufflings gelungen vier Loopregionen zwischen fünf ausgewählten En-Reduktasen simultan zu durchmischen. Basierend auf einem im Rahmen dieser Arbeit entwickelten, photometrischen Aktivitätsassay wurden fünf Loopaustausch Varianten ausgewählt, die hinsichtlich ihres Substratspektrums charakterisiert wurden. Es konnte gezeigt werden, dass durch das zufällige, simultane Austauschen von bis zu vier Loopregionen Enzymvarianten erhalten wurden, die im Vergleich zum NCR Wildtyp eine erhöhte Reduktaseaktivität gegenüber Standardsubstraten zeigten. Im zweiten Ansatz wurde die Familie der Old Yellow Enzyme mittels phylogenetischer Analysen basierend auf der Gesamtsequenzidentität in fünf homologe Unterfamilien unterteilt. Eine dieser Unterfamilien wurde hinsichtlich des Auftretens und der evolutiven Zusammenhänge von Oberflächenloops genauer untersucht. Dazu wurden in insgesamt drei En-Reduktasen je zwei Loopregionen durch Sekundärstrukturvorhersage bestimmt, Loop A und Loop B. Es konnte mittels der Erstellung von Hidden Markov Loop Profilen gezeigt werden, dass sich Loops aus konservierten, sowie variablen Aminosäuren zusammensetzen und dass sich einzelne Familienmitglieder bestimmten Loop-Profilen zuordnen lassen. Anhand der Loop-Profile wurde auch deutlich, dass das Vorkommen eines gemeinsamen Loopbereiches bei zwei verschiedenen En-Reduktasen nicht abhängig ist von der Gesamtsequenzidentität der beiden. Im dritten Ansatz wurde mittels der Entwicklung einer rationalen Loopdesign Methodik untersucht, ob die Looplänge sowie die Aminosäurezusammensetzung eines Loopbereiches einen entscheidenden Einfluss auf die Eigenschaften eines Enzyms ausübt. Dazu wurden insgesamt sieben rationale Loopvarianten der beiden strukturell definierten Loopbereiche A und B von NCR aus Z. mobilis erstellt. Die Kristallstrukturaufklärung einer Loopaustauschvariante brachte die Erkenntnis, dass der Austausch von Loopregionen zu Veränderungen führt, die die ganze Enzymstruktur betreffen. Des Weiteren konnte anhand der sieben rationalen Loopvarianten gezeigt werden, dass sowohl die Aminosäurezusammensetzung, als auch die Looplänge der beta/alpha Loops von TIM barrel Enzymen einen deutlichen Effekt auf die Eigenschaften eines Enzyms haben. So haben im Gegensatz zu Loop B Veränderungen im Loop A zu einer verminderten Stabilität des Enzymes geführt. Es konnte auch gezeigt werden, dass man anhand des Loopaustausches Eigenschaften von einem Enzym auf ein anderes übertragen kann wie zum Beispiel die cis/trans Substratspezifität. Zusammenfassend konnte anhand der hier vorliegenden Arbeit gezeigt werden, dass TIM barrel basierte Enzyme große strukturelle, wie auch sequentielle Änderungen in ihren Oberflächenloops tolerieren können ohne ihre katalytische Aktivität zu verlieren. Man kann dank der in dieser Arbeit gewonnenen Ergebnisse folgern, dass es sich bei beta/alpha Oberflächenloops von Old Yellow Enzymes um „Enzym modifizierende Elemente“ handelt, die einen deutlichen Einfluss auf die Eigenschaften des gesamten Enzyms haben. Außerdem wurde ebenfalls zum ersten Mal gezeigt, dass sich Oberflächenloops bestimmten Loop-Profilen zuordnen lassen und aus konservierten, sowie variablen Bereichen bestehen. Dank des hier erlangten Verständnisses des Einflusses von Loopregionen auf Enzymeigenschaften sollte es in naher Zukunft möglich sein anhand der designten Loopbereiche eine Reduktase mit gewünschten Eigenschaften rational zu erstellen

Fast and accurate circularization of a Rydberg atom

Preparation of a so-called circular state in a Rydberg atom where the projection of the electron angular momentum takes its maximum value is challenging due to the required amount of angular momentum transfer. Currently available protocols for circular state preparation are either accurate but slow or fast but error-prone. Here, we show how to use quantum optimal control theory to derive pulse shapes that realize fast and accurate circularization of a Rydberg atom. In particular, we present a theoretical proposal for optimized radio-frequency pulses that achieve high fidelity in the shortest possible time, given current experimental limitations on peak amplitudes and spectral bandwidth. We also discuss the fundamental quantum speed limit for circularization of a Rydberg atom, when lifting these constraints.Comment: 10 pages, 6 figure

Collective States in Molecular Monolayers on 2D Materials

Collective excited states form in organic two-dimensional layers through the Coulomb coupling of the molecular transition dipole moments. They manifest as characteristic strong and narrow peaks in the excitation and emission spectra that are shifted to lower energies compared to the monomer transition. We study experimentally and theoretically how robust the collective states are against homogeneous and inhomogeneous broadening as well as spatial disorder that occur in real molecular monolayers. Using a microscopic model for a two-dimensional dipole lattice in real space we calculate the properties of collective states and their extinction spectra. We find that the collective states persist even for 1-10% random variation in the molecular position and in the transition frequency, with similar peak position and integrated intensity as for the perfectly ordered system. We measure the optical response of a monolayer of the perylene-derivative MePTCDI on two-dimensional materials. On the wide band-gap insulator hexagonal boron nitride it shows strong emission from the collective state with a line width that is dominated by the inhomogeneous broadening of the molecular state. When using the semimetal graphene as a substrate, however, the luminescence is completely quenched. By combining optical absorption, luminescence, and multi-wavelength Raman scattering we verify that the MePTCDI molecules form very similar collective monolayer states on hexagonal boron nitride and graphene substrates, but on graphene the line width is dominated by non-radiative excitation transfer from the molecules to the substrate. Our study highlights the transition from the localized molecular state of the monomer to a delocalized collective state in the two-dimensional molecular lattice that is entirely based on Coulomb coupling between optically active excitations of the electrons or molecular vibrations

Plasmonic bimetallic two-dimensional supercrystals for H2 generation

Sunlight-driven H-2 generation is a central technology to tackle our impending carbon-based energy collapse. Colloidal photocatalysts consisting of plasmonic and catalytic nanoparticles are promising for H-2 production at solar irradiances, but their performance is hindered by absorption and multiscattering events. Here we present a two-dimensional bimetallic catalyst by incorporating platinum nanoparticles into a well-defined supercrystal of gold nanoparticles. The bimetallic supercrystal exhibited an H-2 generation rate of 139mmolg(cat)(-1)h(-1) via formic acid dehydrogenation under visible light illumination and solar irradiance. This configuration makes it possible to study the interaction between the two metallic materials and the influence of this in catalysis. We observe a correlation between the intensity of the electric field in the hotspots and the boosted catalytic activity of platinum nanoparticles, while identifying a minor role of heat and gold-to-platinum charge transfer in the enhancement. Our results demonstrate the benefits of two-dimensional configurations with optimized architecture for liquid-phase photocatalysis

The patterning toolbox FIB-o-mat: Exploiting the full potential of focused helium ions for nanofabrication

Focused beams of helium ions are a powerful tool for high-fidelity machining with spatial precision below 5 nm. Achieving such a high patterning precision over large areas and for different materials in a reproducible manner, however, is not trivial. Here, we introduce the Python toolbox FIB-o-mat for automated pattern creation and optimization, providing full flexibility to accomplish demanding patterning tasks. FIB-o-mat offers high-level pattern creation, enabling high-fidelity large-area patterning and systematic variations in geometry and raster settings. It also offers low-level beam path creation, providing full control over the beam movement and including sophisticated optimization tools. Three applications showcasing the potential of He ion beam nanofabrication for two-dimensional material systems and devices using FIB-o-mat are presented

A cost–benefit analysis of acclimation to low irradiance in tropical rainforest tree seedlings: leaf life span and payback time for leaf deployment

The maintenance in the long run of a positive carbon balance under very low irradiance is a prerequisite for survival of tree seedlings below the canopy or in small gaps in a tropical rainforest. To provide a quantitative basis for this assumption, experiments were carried out to determine whether construction cost (CC) and payback time for leaves and support structures, as well as leaf life span (i) differ among species and (ii) display an irradiance-elicited plasticity. Experiments were also conducted to determine whether leaf life span correlates to CC and payback time and is close to the optimal longevity derived from an optimization model. Saplings from 13 tropical tree species were grown under three levels of irradiance. Specific-CC was computed, as well as CC scaled to leaf area at the metamer level. Photosynthesis was recorded over the leaf life span. Payback time was derived from CC and a simple photosynthesis model. Specific-CC displayed only little interspecific variability and irradiance-elicited plasticity, in contrast to CC scaled to leaf area. Leaf life span ranged from 4 months to >26 months among species, and was longest in seedlings grown under lowest irradiance. It was always much longer than payback time, even under the lowest irradiance. Leaves were shed when their photosynthesis had reached very low values, in contrast to what was predicted by an optimality model. The species ranking for the different traits was stable across irradiance treatments. The two pioneer species always displayed the smallest CC, leaf life span, and payback time. All species displayed a similar large irradiance-elicited plasticity

The patterning toolbox FIB-o-mat: Exploiting the full potential of focused helium ions for nanofabrication

Focused beams of helium ions are a powerful tool for high-fidelity machining with spatial precision below 5 nm. Achieving such a high patterning precision over large areas and for different materials in a reproducible manner, however, is not trivial. Here, we introduce the Python toolbox FIB-o-mat for automated pattern creation and optimization, providing full flexibility to accomplish demanding patterning tasks. FIB-o-mat offers high-level pattern creation, enabling high-fidelity large-area patterning and systematic variations in geometry and raster settings. It also offers low-level beam path creation, providing full control over the beam movement and including sophisticated optimization tools. Three applications showcasing the potential of He ion beam nanofabrication for two-dimensional material systems and devices using FIB-o-mat are presented

Association of early life stress and cognitive performance in patients with schizophrenia and healthy controls

As core symptoms of schizophrenia, cognitive deficits contribute substantially to poor outcomes. Early life stress (ELS) can negatively affect cognition in patients with schizophrenia and healthy controls, but the exact nature of the mediating factors is unclear. Therefore, we investigated how ELS, education, and symptom burden are related to cognitive performance. The sample comprised 215 patients with schizophrenia (age, 42.9 ± 12.0 years; 66.0 % male) and 197 healthy controls (age, 38.5 ± 16.4 years; 39.3 % male) from the PsyCourse Study. ELS was assessed with the Childhood Trauma Screener (CTS). We used analyses of covariance and correlation analyses to investigate the association of total ELS load and ELS subtypes with cognitive performance. ELS was reported by 52.1 % of patients and 24.9 % of controls. Independent of ELS, cognitive performance on neuropsychological tests was lower in patients than controls (p < 0.001). ELS load was more closely associated with neurocognitive deficits (cognitive composite score) in controls (r = −0.305, p < 0.001) than in patients (r = −0.163, p = 0.033). Moreover, the higher the ELS load, the more cognitive deficits were found in controls (r = −0.200, p = 0.006), while in patients, this correlation was not significant after adjusting for PANSS. ELS load was more strongly associated with cognitive deficits in healthy controls than in patients. In patients, disease-related positive and negative symptoms may mask the effects of ELS-related cognitive deficits. ELS subtypes were associated with impairments in various cognitive domains. Cognitive deficits appear to be mediated through higher symptom burden and lower educational level