Improved physics in SIMNRA 7 Mayer, M.
Nuclear instruments & methods in physics research. Section B, Beam interactions with materials and atoms,
08/2014, Letnik:
332
Journal Article
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SIMNRA is an analytical code for the simulation of ion beam analysis energy spectra obtained by Rutherford backscattering, non-Rutherford scattering, elastic recoil detection analysis, and nuclear ...reaction analysis. Improvements of the simulation physics in SIMNRA version 7 include among others the skewness of all energy spread distributions, improved handling of scattering or reaction cross-sections with structure, generalized layer roughness, and sample porosity.
Hsp70 proteins are central components of the cellular network of molecular chaperones and folding catalysts. They assist a large variety of protein folding processes in the cell by transient ...association of their substrate binding domain with short hydrophobic peptide segments within their substrate proteins. The substrate binding and release cycle is driven by the switching of Hsp70 between the low-affinity ATP bound state and the high-affinity ADP bound state. Thus, ATP binding and hydrolysis are essential in vitro and in vivo for the chaperone activity of Hsp70 proteins. This ATPase cycle is controlled by co-chaperones of the family of J-domain proteins, which target Hsp70s to their substrates, and by nucleotide exchange factors, which determine the lifetime of the Hsp70-substrate complex. Additional co-chaperones fine-tune this chaperone cycle. For specific tasks the Hsp70 cycle is coupled to the action of other chaperones, such as Hsp90 and Hsp100.
Proton-coupled electron transfer (PCET) reactions are increasingly being studied in nonaqueous conditions, where the thermochemistry of PCET substrates is largely unknown. Herein, we report a method ...to obtain electrochemical standard potentials and calculate the corresponding bond dissociation free energies (BDFEs) of stable PCET reagents in nonaqueous solvents, using open-circuit potential (OCP) measurements. With this method, we measure PCET thermochemistry in acetonitrile and tetrahydrofuran for substrates with O-H and N-H bonds that undergo 1
/1H
and 2
/2H
redox processes. We also report corrected thermochemical values for the
/
H
(g)/H
and H
/H
(
) couples in several organic solvents. For 2
/2H
couples, OCP measurements provide the multielectron/multiproton standard potential and the average of the two X-H BDFEs. In contrast to traditional approaches for calculating BDFEs from electrochemical measurements, the OCP method directly measures the overall PCET reaction thermodynamics and avoids the need for a p
scale in the solvent of interest. Consequently, the OCP approach yields more accurate thermochemical values and should be general to any solvent mixture compatible with electrochemical measurements. The longer time scale of OCP measurements enables accurate thermochemical measurements for redox couples with irreversible or distorted electrochemical responses by cyclic voltammetry, provided the PCET reaction is chemically reversible. Recommendations for successful OCP measurements and limitations of the approach are discussed, including the current inability to measure processes involving C-H bonds. As a straightforward and robust technique to determine nonaqueous PCET thermochemistry, these OCP measurements will be broadly valuable, with applications ranging from fundamental reactivity studies to device development.
Upon the introduction of autonomous vehicles into daily traffic, it becomes increasingly likely that autonomous vehicles become involved in accident scenarios in which decisions have to be made about ...how to distribute harm among involved parties. In four experiments, participants made moral decisions from the perspective of a passenger, a pedestrian, or an observer. The results show that the preferred action of an autonomous vehicle strongly depends on perspective. Participants' judgments reflect self-protective tendencies even when utilitarian motives clearly favor one of the available options. However, with an increasing number of lives at stake, utilitarian preferences increased. In a fifth experiment, we tested whether these results were tainted by social desirability but this was not the case. Overall, the results confirm that strong differences exist among passengers, pedestrians, and observers about the preferred course of action in critical incidents. It is therefore important that the actions of autonomous vehicles are not only oriented towards the needs of their passengers, but also take the interests of other road users into account. Even though utilitarian motives cannot fully reconcile the conflicting interests of passengers and pedestrians, there seem to be some moral preferences that a majority of the participants agree upon regardless of their perspective, including the utilitarian preference to save several other lives over one's own.
Warren et al analyze the thermochemistry of proton-coupled electron transfer reagents. They highlight the mechanisms of certain transfer reactions and their link with hydrogen atom transfers, as well ...as compare concerted proton-electron transfer and stepwise pathways.
Conspectus Proton-coupled electron transfer (PCET) covers a wide range of reactions involving the transfer(s) of electrons and protons. The best-known PCET reaction, hydrogen atom transfer (HAT), has ...been studied in detail for more than a century. HAT is generally described as the concerted transfer of a hydrogen atom (H• ≡ H+ + e –) from one group to another, Y + H–X → Y–H + X, but a strict definition of HAT has been difficult to establish. Distinctions are more challenging when the transfer of “H•” involves e – and H+ that transfer to/from spatially distinct sites or even completely separate reagents (multiple-site concerted proton–electron transfer, MS-CPET). MS-CPET reactivity is increasingly proposed in biological and synthetic contexts, and some reactions typically described as HAT more resemble MS-CPET. Despite that HAT and MS-CPET reactions “look different,” we argue here that these reactions lie on a reactivity continuum, and that they are governed by many of the same key parameters. This Account walks the reader across this PCET reactivity continuum, using a series of studies to show the strong similarities of reactions that move protons and electrons in seemingly different ways. To prepare for our stroll, we describe the thermochemical and kinetic frameworks for HAT and MS-CPET. The driving force for a solution HAT reaction is most easily discussed as the difference in the bond dissociation free energies (BDFEs) of the reactants and products. BDFEs can be analyzed as sums of electron and proton transfer steps and can therefore be obtained from pK a and E° values. Even though MS-CPET reactions do not make and break H–X bonds in the same way as HAT, the same thermochemical description can be used with the introduction of an effective BDFE (BDFEeff). The BDFEeff of a reductant/acid pair is the free energy of that pair to form H•, which can be obtained from pK a and E° values in an analogous fashion to a standard BDFE. When the PCET thermochemistry is known, HAT and PCET rate constants can be understood and often predicted using linear free energy relationships (the Brønsted catalysis law) and Marcus theory type approaches. After this background, we walk the reader through a continuum of PCET reactivity. Our journey begins with a study of metal-mediated HAT from hydrocarbon substrates to a metal-oxo complex and travels to the MS-CPET end of the reactivity spectrum, involving the transfer of H+ and e – from the hydroxylamine TEMPOH to two completely separate molecules. These examples, and those in between, are all analyzed within the same thermodynamic and kinetic framework. A description of the first examples of MS-CPET with C–H bonds uses the same framework and highlights the importance of hydrogen bonding and preorganization. The examples and analyses show that the reactions along the PCET continuum are more similar than they are different, and that attempts to divide these reactions into subcategories can obscure much of the essential chemistry. We hope that developing the many common features of these reactions will help experts and newcomers alike to explore exciting new territories in PCET reactivity.
The program STRUCTNRA for the simulation of ion beam analysis charged particle spectra from arbitrary two-dimensional distributions of materials is described. The code is validated by comparison to ...experimental backscattering data from a silicon grating on tantalum at different orientations and incident angles. Simulated spectra for several types of rough thin layers and a chessboard-like arrangement of materials as example for a multi-phase agglomerate material are presented. Ambiguities between back-scattering spectra from two-dimensional and one-dimensional sample structures are discussed.
Proton-coupled electron transfer (PCET) reactions involve the concerted transfer of an electron and a proton. Such reactions play an important role in many areas of chemistry and biology. Concerted ...PCET is thermochemically more favorable than the first step in competing consecutive processes involving stepwise electron transfer (ET) and proton transfer (PT), often by >=1 eV. PCET reactions of the form X-H + Y X + H-Y can be termed hydrogen atom transfer (HAT). Another PCET class involves outersphere electron transfer concerted with deprotonation by another reagent, Y+ + XH-B Y + X-HB+. Many PCET/HAT rate constants are predicted well by the Marcus cross relation. The cross-relation calculation uses rate constants for self-exchange reactions to provide information on intrinsic barriers. Intrinsic barriers for PCET can be comparable to or larger than those for ET. These properties are discussed in light of recent theoretical treatments of PCET.
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