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Neutron scattering is a very high-performance method for studying the structure and dynamics of condensed matter with similar approaches in wide ranges of space and time, matching dimensions in space from single atoms to macromolecules and in time from atomic vibrations over crystal phonons to low-lying transitions in the microwave range, and to motions of large molecular units. Concerning the number and depth of physical concepts, neutron scattering may be compared to modern nuclear magnetic resonance. Neutrons have contributed essential results to the understanding of atomic and molecular processes and are, in this respect, complementary to other materials science probes. Among others, three properties of thermal neutrons make them especially appropriate for such work: the neutron mass is similar to atomic masses, and both neutron energies and the wavelengths of the neutron material wave match typical values for condensed matter. A further important feature of neutron scattering, making it especially valuable in biochemistry and polymer sciences, is that hydrogen and deuterium atoms very significantly and specifically contribute to the signal in both diffraction and spectroscopy. Additionally, neutrons are scattered at the nuclei and directly reflect the nuclear structure and motions. Results from neutron scattering are of great general interest. This paper aims to provide an introduction for chemists on a level understandable also to students and researchers who are not going to become part of the neutron community and will not be involved in the experiments, but shall be able to understand the basic concepts of the method and its relevance to modern chemistry. The paper focuses on basic theory, typical experiments, and some examples demonstrating the applications. As for many modern experimental techniques, the interpretation of the results of neutron scattering is based on theoretical models and requires a significant mathematical overhead. Most results are only meaningful when compared with computer simulations. For understanding this, in this paper, the theory of scattering is developed, starting with intuitive models and presenting typical concepts such as the scattering triangle, energy and momentum transfer, and the relation of inelastic and elastic scattering to space- and time-dependent information. The interaction of neutrons with matter, scattering cross sections, beam attenuation, and coherent versus incoherent scattering are explained in detail. Two further typical concepts that are not generally familiar to scientists outside the community are the use of wave and particle equivalence, and of handling results as a scattering function that depends simultaneously on momentum and energy transfers. The possibility of obtaining neutron beams for scattering experiments at a few research centers around high-performance sources is explained, and experimentally relevant features of research reactors and spallation sources are mentioned. As neutron experiments always have to deal with small flux and extended beams and shielding, experimental conditions are very far away from laboratory methods where handling of samples and instruments is concerned. Experimental details are given for making experiments more understandable and familiarizing the reader with the method. Related to this are extended possibilities for handling samples in a large variety of different environments. In a further part of the manuscript, a variety of techniques and typical instruments are presented, together with some characteristic applications bringing alive the theory developed so far. This covers powder diffraction and structure of liquid water, triple-axis spectrometers and lattice phonons, backscattering spectrometry and rotational tunneling, time-of-flight spectrometry, and simultaneously probing the energy and shape of low lying vibrations and diffusion, filter spectrometer and vibrational spectroscopy without selection rules, small-angle neutron scattering and protein unfolding, as well as micelles, neutron spin echo spectroscopy, and polymer dynamics.
In general, concepts such as chemical equilibria and classical analytical chemistry, as well as instrumental methods such as potentiometry and flow injection analysis (FIA), are taught separately in the curricula of chemistry-related degree programs. However, FIA provides an opportunity to connect all of these important topics. This article shows how simple experiments can be used to link the fundamentals of FIA and potentiometry to the fundamentals of chemical equilibria and teach them in a sustainable way. The experiments were designed for undergraduate environmental science students with basic knowledge of chemical equilibria and classical analytical chemistry and minimal knowledge of electrochemistry. However, they can also be integrated into various courses on instrumental analysis in chemistry-related degree programs.
Marine algae produce complex polysaccharides, which can be degraded by marine heterotrophic bacteria utilizing carbohydrate-active enzymes. The red algal polysaccharide porphyran contains the methoxy sugar 6-O-methyl-D-galactose (G6Me). In the degradation of porphyran, oxidative demethylation of this monosaccharide towards D-galactose and formaldehyde occurs, which is catalyzed by a cytochrome P450 monooxygenase and its redox partners. In direct proximity to the genes encoding for the key enzymes of this oxidative demethylation, genes encoding for zinc-dependent alcohol dehydrogenases (ADHs) were identified, which seem to be conserved in porphyran utilizing marine Flavobacteriia. Considering the fact that dehydrogenases could play an auxiliary role in carbohydrate degradation, we aimed to elucidate the physiological role of these marine ADHs. Although our results reveal that the ADHs are not involved in formaldehyde detoxification, a knockout of the ADH gene causes a dramatic growth defect of Zobellia galactanivorans with G6Me as a substrate. This indicates that the ADH is required for G6Me utilization. Complete biochemical characterizations of the ADHs from Formosa agariphila KMM 3901T (FoADH) and Z. galactanivorans DsijT (ZoADH) were performed, and the substrate screening revealed that these enzymes preferentially convert aromatic aldehydes. Additionally, we elucidated the crystal structures of FoADH and ZoADH in complex with NAD+ and showed that the strict substrate specificity of these new auxiliary enzymes is based on a narrow active site.
The potential of several ion-sensitive electrodes responds to the incorporated cations and anions. This has led some authors to misinterpret the potential of metal salt membrane electrodes and of electrodes of the second kind. Neglecting the kinetics of potential establishment and interpreting the potentials solely based on thermodynamics produce completely irrelevant data and suggest that ion concentrations down to 10−45 mol L−1 are accessible by simple potentiometric measurements. The switching from cation to anion response mechanism cannot be derived from thermodynamic equations. It bears complete similarity to the switching of response in the case of foreign interfering ions.
In teaching electrochemistry, it is of primary importance to make students always aware of the relations between electrochemistry and all the non-electrochemical topics, which are taught. The vast majority of students will not specialise in electrochemistry, but they all can very much benefit from the basics and concepts of electrochemistry. This paper is aimed to give suggestions how the teaching of electrochemistry can easily be interrelated to topics of inorganic, organic, analytical, environmental chemistry, biochemistry and biotechnology.
Electrochemical Raman spectroscopy can provide valuable insights into electrochemical reaction mechanisms. However, it also shows various pitfalls and challenges. This paper gives an overview of the necessary theoretical background, crucial practical considerations for successful measurement, and guidance for in situ/in operando electrochemical Raman spectroscopy. Several parameters must be optimized for suitable reaction and measurement conditions. From the experimental side, considerations for the setup, suitable signal enhancement methods, choice of material, laser, and objective lens are discussed. Different interface phenomena are reviewed in the context of data interpretation and evaluation.
Heteroleptic molybdenum complexes bearing 1,5-diaza-3,7-diphosphacyclooctane (P2N2) and non-innocent dithiolene ligands were synthesized and electrochemically characterized. The reduction potentials of the complexes were found to be fine-tuned by a synergistic effect identified by DFT calculations as ligand-ligand cooperativity via non-covalent interactions. This finding is supported by electrochemical studies combined with UV/Vis spectroscopy and temperature-dependent NMR spectroscopy. The observed behavior is reminiscent of enzymatic redox modulation using second ligand sphere effects.
Marine Bacteroidetes that degrade polysaccharides contribute to carbon cycling in the ocean. Organic matter, including glycans from terrestrial plants, might enter the oceans through rivers. Whether marine bacteria degrade structurally related glycans from diverse sources including terrestrial plants and marine algae was previously unknown. We show that the marine bacterium Flavimarina sp. Hel_I_48 encodes two polysaccharide utilization loci (PULs) which degrade xylans from terrestrial plants and marine algae. Biochemical experiments revealed activity and specificity of the encoded xylanases and associated enzymes of these PULs. Proteomics indicated that these genomic regions respond to glucuronoxylans and arabinoxylans. Substrate specificities of key enzymes suggest dedicated metabolic pathways for xylan utilization. Some of the xylanases were active on different xylans with the conserved β-1,4-linked xylose main chain. Enzyme activity was consistent with growth curves showing Flavimarina sp. Hel_I_48 uses structurally different xylans. The observed abundance of related xylan-degrading enzyme repertoires in genomes of other marine Bacteroidetes indicates similar activities are common in the ocean. The here presented data show that certain marine bacteria are genetically and biochemically variable enough to access parts of structurally diverse xylans from terrestrial plants as well as from marine algal sources.
The vast majority of RNA splicing in today‘s organisms is achieved by the highly regulated and precise removal of introns from pre-mRNAs via the spliceosome. Here we present a model of how RNA splicing may have occurred in earlier life forms. We have designed a hairpin ribozyme derived spliceozyme that mediates two RNA cleavages and one ligation event at specific positions and thus cuts a segment (intron) out of a parent RNA and ligates the remaining fragments (exons). The cut-out intron then performs a downstream function, acting as a positive regulator of the activity of a bipartite DNAzyme. This simple scenario shows how small RNAs can perform complex RNA processing dynamics, involving the generation of new phenotypes by restructuring segments of given RNA species, as well as delivering small RNAs that may play a functional role in downstream processes.
Enzymes, the driving biocatalysts in living organisms, are typically not suited for large-scale industrial use. In the last decade, enzyme engineering has evolved into the key technology to design tailor-made enzymes for chemical and pharmaceutical applications. We highlight current trends in enzyme engineering and biocatalysis based on outstanding examples from the pharmaceutical industry.