540 Chemie und zugeordnete Wissenschaften
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Although iron-based catalysts are regarded as a promising alternative to precious metal catalysts, their precise electronic structures during catalysis still pose challenges for computational descriptions. A particularly urgent question is the influence of the environment on the electronic structure, and how to describe this properly with computational methods. Here, we study an iron porphyrin chloride complex adsorbed on a graphene sheet using density functional theory calculations to detail how much the electronic structure is influenced by the presence of a graphene layer. Our results indicate that weak interactions due to van der Waals forces dominate between the porphyrin complex and graphene, and only a small amount of charge is transferred between the two entities. Furthermore, the interplay of the ligand field environment, strong p − d hybridization, and correlation effects within the complex are strongly involved in determining the spin state of the iron ion. By bridging molecular chemistry and solid state physics, this study provides first steps towards a joint analysis of the properties of iron-based catalysts from first principles.
Vibrational energy transfer (VET) is emerging as key mechanism for protein functions, possibly playing an important role for energy dissipation, allosteric regulation, and enzyme catalysis. A deep understanding of VET is required to elucidate its role in such processes. Ultrafast VIS-pump/IR-probe spectroscopy can detect pathways of VET in proteins. However, the requirement of having a VET donor and a VET sensor installed simultaneously limits the possible target proteins and sites; to increase their number we compare six IR labels regarding their utility as VET sensors. We compare these labels in terms of their FTIR, and VET signature in VET donor-sensor dipeptides in different solvents. Furthermore, we incorporated four of these labels in PDZ3 to assess their capabilities in more complex systems. Our results show that different IR labels can be used interchangeably, allowing for free choice of the right label depending on the system under investigation and the methods available.
Vanadium and Manganese Carbonyls as Precursors in Electron-Induced and Thermal Deposition Processes
(2022)
The material composition and electrical properties of nanostructures obtained from focused electron beam-induced deposition (FEBID) using manganese and vanadium carbonyl precursors have been investigated. The composition of the FEBID deposits has been compared with thin films derived by the thermal decomposition of the same precursors in chemical vapor deposition (CVD). FEBID of V(CO)6 gives access to a material with a V/C ratio of 0.63–0.86, while in CVD a lower carbon content with V/C ratios of 1.1–1.3 is obtained. Microstructural characterization reveals for V-based materials derived from both deposition techniques crystallites of a cubic phase that can be associated with VC1−xOx. In addition, the electrical transport measurements of direct-write VC1−xOx show moderate resistivity values of 0.8–1.2 × 103 µΩ·cm, a negligible influence of contact resistances and signatures of a granular metal in the temperature-dependent conductivity. Mn-based deposits obtained from Mn2(CO)10 contain ~40 at% Mn for FEBID and a slightly higher metal percentage for CVD. Exclusively insulating material has been observed in FEBID deposits as deduced from electrical conductivity measurements. In addition, strong tendencies for postgrowth oxidation have to be considered.
Liquid-jet photoelectron spectroscopy was applied to determine the first acid dissociation constant (pKa) of aqueous-phase glucose while simultaneously identifying the spectroscopic signature of the respective deprotonation site. Valence spectra from solutions at pH values below and above the first pKa reveal a change in glucose’s lowest ionization energy upon the deprotonation of neutral glucose and the subsequent emergence of its anionic counterpart. Site-specific insights into the solution-pH-dependent molecular structure changes are also shown to be accessible via C 1s photoelectron spectroscopy. The spectra reveal a considerably lower C 1s binding energy of the carbon site associated with the deprotonated hydroxyl group. The occurrence of photoelectron spectral fingerprints of cyclic and linear glucose prior to and upon deprotonation are also discussed. The experimental data are interpreted with the aid of electronic structure calculations. Our findings highlight the potential of liquid-jet photoelectron spectroscopy to act as a site-selective probe of the molecular structures that underpin the acid–base chemistry of polyprotic systems with relevance to environmental chemistry and biochemistry.
The absolute-scale electronic energetics of liquid water and aqueous solutions, both in the bulk and at associated interfaces, are the central determiners of water-based chemistry. However, such information is generally experimentally inaccessible. Here we demonstrate that a refined implementation of the liquid microjet photoelectron spectroscopy (PES) technique can be adopted to address this. Implementing concepts from condensed matter physics, we establish novel all-liquid-phase vacuum and equilibrated solution–metal-electrode Fermi level referencing procedures. This enables the precise and accurate determination of previously elusive water solvent and solute vertical ionization energies, VIEs. Notably, this includes quantification of solute-induced perturbations of water's electronic energetics and VIE definition on an absolute and universal chemical potential scale. Defining and applying these procedures over a broad range of ionization energies, we accurately and respectively determine the VIE and oxidative stability of liquid water as 11.33 ± 0.03 eV and 6.60 ± 0.08 eV with respect to its liquid-vacuum-interface potential and Fermi level. Combining our referencing schemes, we accurately determine the work function of liquid water as 4.73 ± 0.09 eV. Further, applying our novel approach to a pair of exemplary aqueous solutions, we extract absolute VIEs of aqueous iodide anions, reaffirm the robustness of liquid water's electronic structure to high bulk salt concentrations (2 M sodium iodide), and quantify reference-level dependent reductions of water's VIE and a 0.48 ± 0.13 eV contraction of the solution's work function upon partial hydration of a known surfactant (25 mM tetrabutylammonium iodide). Our combined experimental accomplishments mark a major advance in our ability to quantify electronic–structure interactions and chemical reactivity in liquid water, which now explicitly extends to the measurement of absolute-scale bulk and interfacial solution energetics, including those of relevance to aqueous electrochemical processes.
Maximum likelihood estimates of diffusion coefficients from single-particle tracking experiments
(2021)
Single-molecule localization microscopy allows practitioners to locate and track labeled molecules in biological systems. When extracting diffusion coefficients from the resulting trajectories, it is common practice to perform a linear fit on mean-squared-displacement curves. However, this strategy is suboptimal and prone to errors. Recently, it was shown that the increments between the observed positions provide a good estimate for the diffusion coefficient, and their statistics are well-suited for likelihood-based analysis methods. Here, we revisit the problem of extracting diffusion coefficients from single-particle tracking experiments subject to static noise and dynamic motion blur using the principle of maximum likelihood. Taking advantage of an efficient real-space formulation, we extend the model to mixtures of subpopulations differing in their diffusion coefficients, which we estimate with the help of the expectation–maximization algorithm. This formulation naturally leads to a probabilistic assignment of trajectories to subpopulations. We employ the theory to analyze experimental tracking data that cannot be explained with a single diffusion coefficient. We test how well a dataset conforms to the assumptions of a diffusion model and determine the optimal number of subpopulations with the help of a quality factor of known analytical distribution. To facilitate use by practitioners, we provide a fast open-source implementation of the theory for the efficient analysis of multiple trajectories in arbitrary dimensions simultaneously.
The β-barrel assembly machinery (BAM) consisting of the central β-barrel BamA and four other lipoproteins mediates the folding of the majority of the outer membrane proteins. BamA is placed in an asymmetric bilayer and its lateral gate is suggested to be the functional hotspot. Here we used in situ pulsed electron-electron double resonance spectroscopy to characterize BamA in the native outer membrane. In the detergent micelles, the data is consistent with mainly an inward-open conformation of BamA. The native membrane considerably enhanced the conformational heterogeneity. The lateral gate and the extracellular loop 3 exist in an equilibrium between different conformations. The outer membrane provides a favorable environment for occupying multiple conformational states independent of the lipoproteins. Our results reveal a highly dynamic behavior of the lateral gate and other key structural elements and provide direct evidence for the conformational modulation of a membrane protein in situ.
Vibrational energy transfer (VET) is essential for protein function. It is responsible for efficient energy dissipation in reaction sites, and has been linked to pathways of allosteric communication. While it is understood that VET occurs via backbone as well as via non-covalent contacts, little is known about the competition of these two transport channels, which determines the VET pathways. To tackle this problem, we equipped the β-hairpin fold of a tryptophan zipper with pairs of non-canonical amino acids, one serving as a VET injector and one as a VET sensor in a femtosecond pump probe experiment. Accompanying extensive non-equilibrium molecular dynamics simulations combined with a master equation analysis unravel the VET pathways. Our joint experimental/computational endeavor reveals the efficiency of backbone vs. contact transport, showing that even if cutting short backbone stretches of only 3 to 4 amino acids in a protein, hydrogen bonds are the dominant VET pathway.
Understanding the physics of strongly correlated electronic systems has been a central issue in condensed matter physics for decades. In transition metal oxides, strong correlations characteristic of narrow d bands are at the origin of remarkable properties such as the opening of Mott gap, enhanced effective mass, and anomalous vibronic coupling, to mention a few. SrVO3 with V4+ in a 3d1 electronic configuration is the simplest example of a 3D correlated metallic electronic system. Here, the authors' focus on the observation of a (roughly) quadratic temperature dependence of the inverse electron mobility of this seemingly simple system, which is an intriguing property shared by other metallic oxides. The systematic analysis of electronic transport in SrVO3 thin films discloses the limitations of the simplest picture of e–e correlations in a Fermi liquid (FL); instead, it is shown show that the quasi-2D topology of the Fermi surface (FS) and a strong electron–phonon coupling, contributing to dress carriers with a phonon cloud, play a pivotal role on the reported electron spectroscopic, optical, thermodynamic, and transport data. The picture that emerges is not restricted to SrVO3 but can be shared with other 3d and 4d metallic oxides.
Anti-inflammatory effects of low-dose irradiation often follow a non-linear dose–effect relationship. These characteristics were also described for the modulation of leukocyte adhesion to endothelial cells. Previous results further revealed a contribution of reactive oxygen species (ROS) and anti-oxidative factors to a reduced leukocyte adhesion. Here, we evaluated the expression of anti-oxidative enzymes and the transcription factor Nrf2 (Nuclear factor-erythroid-2-related factor 2), intracellular ROS content, and leukocyte adhesion in primary human microvascular endothelial cells (HMVEC) upon low-dose irradiation under physiological laminar shear stress or static conditions after irradiation with X-ray or Carbon (C)-ions (0–2 Gy). Laminar conditions contributed to increased mRNA expression of anti-oxidative factors and reduced ROS in HMVEC following a 0.1 Gy X-ray and 0.5 Gy C-ion exposure, corresponding to reduced leukocyte adhesion and expression of adhesion molecules. By contrast, mRNA expression of anti-oxidative markers and adhesion molecules, ROS, and leukocyte adhesion were not altered by irradiation under static conditions. In conclusion, irradiation of endothelial cells with low doses under physiological laminar conditions modulates the mRNA expression of key factors of the anti-oxidative system, the intracellular ROS contents of which contribute at least in part to leucocyte adhesion, dependent on the radiation source.