Browse
Submit Data
Databases
API
Help

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

X-ray imaging of chemically active valence electrons during a pericyclic reaction.

ABSTRACT: Time-resolved imaging of chemically active valence electron densities is a long-sought goal, as these electrons dictate the course of chemical reactions. However, X-ray scattering is always dominated by the core and inert valence electrons, making time-resolved X-ray imaging of chemically active valence electron densities extremely challenging. Here we demonstrate an effective and robust method, which emphasizes the information encoded in weakly scattered photons, to image chemically active valence electron densities. The degenerate Cope rearrangement of semibullvalene, a pericyclic reaction, is used as an example to visually illustrate our approach. Our work also provides experimental access to the long-standing problem of synchronous versus asynchronous bond formation and breaking during pericyclic reactions.

SUBMITTER: Bredtmann T

PROVIDER: S-EPMC4263170 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

X-ray imaging of chemically active valence electrons during a pericyclic reaction.

Bredtmann Timm T Ivanov Misha M Dixit Gopal G

Nature communications 20141126

Time-resolved imaging of chemically active valence electron densities is a long-sought goal, as these electrons dictate the course of chemical reactions. However, X-ray scattering is always dominated by the core and inert valence electrons, making time-resolved X-ray imaging of chemically active valence electron densities extremely challenging. Here we demonstrate an effective and robust method, which emphasizes the information encoded in weakly scattered photons, to image chemically active vale ...[more]

PMID: 25424639

Similar Datasets

Intrinsic beam emittance of laser-accelerated electrons measured by x-ray spectroscopic imaging.

Project description:The recent combination of ultra-intense lasers and laser-accelerated electron beams is enabling the development of a new generation of compact x-ray light sources, the coherence of which depends directly on electron beam emittance. Although the emittance of accelerated electron beams can be low, it can grow due to the effects of space charge during free-space propagation. Direct experimental measurement of this important property is complicated by micron-scale beam sizes, and the presence of intense fields at the location where space charge acts. Reported here is a novel, non-destructive, single-shot method that overcame this problem. It employed an intense laser probe pulse, and spectroscopic imaging of the inverse-Compton scattered x-rays, allowing measurement of an ultra-low value for the normalized transverse emittance, 0.15 (±0.06) ? mm mrad, as well as study of its subsequent growth upon exiting the accelerator. The technique and results are critical for designing multi-stage laser-wakefield accelerators, and generating high-brightness, spatially coherent x-rays.

| S-EPMC4835856 | biostudies-other

In operando x-ray imaging of nanoscale devices: Composition, valence, and internal electrical fields.

Project description:We introduce a method for directly imaging depletion layers in operando with elemental specificity and chemical speciation at sub-100 nm spatial resolution applicable to today's three-dimensional electronic architectures. These typically contain complex, multicomponent designs consisting of epitaxial heterostructures, buried domains, or nanostructures with different shapes and sizes. Although the variety of devices is immense, they commonly rely on carrier separation in a built-in potential induced by composition or strain gradients. To image these, we scanned a focused synchrotron x-ray nanobeam over a single semiconductor nanowire heterostructure and simultaneously measured the current through the device and the emitted characteristic x-rays as a function of the incoming hard x-ray energy. With these results, it is possible to identify the compositional and molecular structure as well as localize the electrical fields present under typical working conditions. This information allows us to draw an energy band diagram consistent with the elemental distribution and a high-resolution chemical speciation map.

| S-EPMC5722647 | biostudies-literature

Perovskite With Tunable Active-Sites Oxidation State by High-Valence W for Enhanced Oxygen Evolution Reaction.

Project description:Perovskite oxides have been established as a promising kind of catalyst for alkaline oxygen evolution reactions (OER), because of their regulated non-precious metal components. However, the surface lattice is amorphous during the reaction, which gradually decreases the intrinsic activity and stability of catalysts. Herein, the precisely control tungsten atoms substituted perovskite oxides (Pr0.5Ba0.5Co1-xWxO3-δ) nanowires were developed by electrostatic spinning. The activity and Tafel slope were both dependent on the W content in a volcano-like fashion, and the optimized Pr0.5Ba0.5Co0.8W0.2O3-δ exhibits both excellent activity and superior stability compared with other reported perovskite oxides. Due to the outermost vacant orbitals of W6+, the electronic structure of cobalt sites could be efficiently optimized. Meanwhile, the stronger W-O bond could also significantly improve the stability of latticed oxide atoms to impede the generation of surface amorphous layers, which shows good application value in alkaline water splitting.

| S-EPMC8784603 | biostudies-literature

Mechanism of 3-Methylglutaconyl CoA Decarboxylase AibA/AibB: Pericyclic Reaction versus Direct Decarboxylation.

Project description:The enzyme 3-methylglutaconyl coenzyme A (CoA) decarboxylase (called AibA/AibB) catalyzes the decarboxylation of 3-methylglutaconyl CoA to generate 3,3-dimethylacrylyl-CoA, representing an important step in the biosynthesis of isovaleryl-coenzyme A in Myxococcus xanthus when the regular pathway is blocked. A novel mechanism involving a pericyclic transition state has previously been proposed for this enzyme, making AibA/AibB unique among decarboxylases. Herein, density functional calculations are used to examine the energetic feasibility of this mechanism. It is shown that the intramolecular pericyclic reaction is associated with a very high energy barrier that is similar to the barrier of the same reaction in the absence of the enzyme. Instead, the calculations show that a direct decarboxylation mechanism has feasible energy barriers that are in line with the experimental observations.

| S-EPMC7756340 | biostudies-literature

Distribution of valence electrons of the flavin cofactor in NADH-cytochrome b5 reductase.

Project description:Flavin compounds such as flavin adenine dinucleotide (FAD), flavin mononucleotide and riboflavin make up the active centers in flavoproteins that facilitate various oxidoreductive processes. The fine structural features of the hydrogens and valence electrons of the flavin molecules in the protein environment are critical to the functions of the flavoproteins. However, information on these features cannot be obtained from conventional protein X-ray analyses at ordinary resolution. Here we report the charge density analysis of a flavoenzyme, NADH-cytochrome b5 reductase (b5R), at an ultra-high resolution of 0.78?Å. Valence electrons on the FAD cofactor as well as the peptide portion, which are clearly visualized even after the conventional refinement, are analyzed by the multipolar atomic model refinement. The topological analysis for the determined electron density reveals the valence electronic structure of the isoalloxazine ring of FAD and hydrogen-bonding interactions with the protein environment. The tetrahedral electronic distribution around the N5 atom of FAD in b5R is stabilized by hydrogen bonding with C?H of Tyr65 and amide-H of Thr66. The hydrogen bonding network leads to His49 composing the cytochrome b5-binding site via non-classical hydrogen bonds between N5 of FAD and C?H of Tyr65 and O of Tyr65 and C?H of His49.

| S-EPMC5320556 | biostudies-literature

Quantum Suppression of Intramolecular Deuterium Kinetic Isotope Effects in a Pericyclic Hydrogen Transfer Reaction.

Project description:It is generally accepted that hydrogen tunneling enhances both primary and secondary H/D kinetic isotope effects (KIEs) over what would be expected under the assumptions of classical barrier transition. Previous studies have exclusively shown that the effects of tunneling upon primary H/D KIEs have been much larger than those observed for secondary H/D KIEs. Here we present a series of experimental H/D KIE results associated with the Chugaev elimination of methyl xanthate derived from ?-phenylethanol over the temperature range of 180 to 290 °C. Intramolecular H/D KIEs computed according to classical transition state theory (TST) are markedly overestimated relative to experimentally measured values. Experimental intermolecular H/D KIEs and direct dynamic calculations based on canonical variational transition state theory (CVT) with small-curvature tunneling correction (SCT) reveal that this result is largely the consequence of extraordinary tunneling enhancement of the secondary H/D KIE. This unexpected behavior is examined in the context of other similar hydrogen transfer reactions.

| S-EPMC6661151 | biostudies-literature

Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering.

Project description:Strong-field photoelectron holography and laser-induced electron diffraction (LIED) are two powerful emerging methods for probing the ultrafast dynamics of molecules. However, both of them have remained restricted to static systems and to nuclear dynamics induced by strong-field ionization. Here we extend these promising methods to image purely electronic valence-shell dynamics in molecules using photoelectron holography. In the same experiment, we use LIED and photoelectron holography simultaneously, to observe coupled electronic-rotational dynamics taking place on similar timescales. These results offer perspectives for imaging ultrafast dynamics of molecules on femtosecond to attosecond timescales.

| S-EPMC5481729 | biostudies-literature

Generation and Identification of the Linear OCBNO and OBNCO Molecules with 24 Valence Electrons.

Project description:Two structural isomers containing five second-row element atoms with 24 valence electrons were generated and identified by matrix-isolation IR spectroscopy and quantum chemical calculations. The OCBNO complex, which is produced by the reaction of boron atoms with mixtures of carbon monoxide and nitric oxide in solid neon, rearranges to the more stable OBNCO isomer on UV excitation. Bonding analysis indicates that the OCBNO complex is best described by the bonding interactions between a triplet-state boron cation with an electron configuration of (2s)0 (2pσ )0 (2pπ )2 and the CO/NO- ligands in the triplet state forming two degenerate electron-sharing π bonds and two ligand-to-boron dative σ bonds.

| S-EPMC7839540 | biostudies-literature

Hot electrons in a nanowire hard X-ray detector.

Project description:Nanowire chip-based electrical and optical devices such as biochemical sensors, physical detectors, or light emitters combine outstanding functionality with a small footprint, reducing expensive material and energy consumption. The core functionality of many nanowire-based devices is embedded in their p-n junctions. To fully unleash their potential, such nanowire-based devices require - besides a high performance - stability and reliability. Here, we report on an axial p-n junction GaAs nanowire X-ray detector that enables ultra-high spatial resolution (~200 nm) compared to micron scale conventional ones. In-operando X-ray analytical techniques based on a focused synchrotron X-ray nanobeam allow probing the internal electrical field and observing hot electron effects at the nanoscale. Finally, we study device stability and find a selective hot electron induced oxidization in the n-doped segment of the p-n junction. Our findings demonstrate capabilities and limitations of p-n junction nanowires, providing insight for further improvement and eventual integration into on-chip devices.

| S-EPMC7501287 | biostudies-literature

Probing Transient Valence Orbital Changes with Picosecond Valence-to-Core X-ray Emission Spectroscopy.

Project description:We probe the dynamics of valence electrons in photoexcited [Fe(terpy)2]2+ in solution to gain deeper insight into the Fe-ligand bond changes. We use hard X-ray emission spectroscopy (XES), which combines element specificity and high penetration with sensitivity to orbital structure, making it a powerful technique for molecular studies in a wide variety of environments. A picosecond-time-resolved measurement of the complete 1s X-ray emission spectrum captures the transient photoinduced changes and includes the weak valence-to-core (vtc) emission lines that correspond to transitions from occupied valence orbitals to the nascent core-hole. Vtc-XES offers particular insight into the molecular orbitals directly involved in the light-driven dynamics; a change in the metal-ligand orbital overlap results in an intensity reduction and a blue energy shift in agreement with our theoretical calculations and more subtle features at the highest energies reflect changes in the frontier orbital populations.

| S-EPMC5453616 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data