Browse
Submit Data
Databases
API
Help

Dataset Information

23 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effects of nonequilibrium fluctuations on ultrafast short-range electron transfer dynamics.

ABSTRACT: A variety of electron transfer (ET) reactions in biological systems occurs at short distances and is ultrafast. Many of them show behaviors that deviate from the predictions of the classic Marcus theory. Here, we show that these ultrafast ET dynamics highly depend on the coupling between environmental fluctuations and ET reactions. We introduce a dynamic factor, ? (0???????1), to describe such coupling, with 0 referring to the system without coupling to a "frozen" environment, and 1 referring to the system's complete coupling with the environment. Significantly, this system's coupling with the environment modifies the reaction free energy, ?G^?, and the reorganization energy, ?^?, both of which become smaller. This new model explains the recent ultrafast dynamics in flavodoxin and elucidates the fundamental mechanism of nonequilibrium ET dynamics, which is critical to uncovering the molecular nature of many biological functions.

SUBMITTER: Lu Y

PROVIDER: S-EPMC7272615 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Effects of nonequilibrium fluctuations on ultrafast short-range electron transfer dynamics.

Lu Yangyi Y Kundu Mainak M Zhong Dongping D

Nature communications 20200604 1

A variety of electron transfer (ET) reactions in biological systems occurs at short distances and is ultrafast. Many of them show behaviors that deviate from the predictions of the classic Marcus theory. Here, we show that these ultrafast ET dynamics highly depend on the coupling between environmental fluctuations and ET reactions. We introduce a dynamic factor, γ (0 ≤ γ ≤ 1), to describe such coupling, with 0 referring to the system without coupling to a "frozen" environment, and 1 referring to ...[more]

PMID: 32499536

Similar Datasets

Short-Range Electron Transfer in Reduced Flavodoxin: Ultrafast Nonequilibrium Dynamics Coupled with Protein Fluctuations.

Project description:Short-range electron transfer (ET) in proteins is an ultrafast process on the similar time scales as local protein-solvent fluctuation, and thus the two dynamics are coupled. Here we use semiquinone flavodoxin and systematically characterized the photoinduced redox cycle with 11 mutations of different aromatic electron donors (tryptophan and tyrosine) and local residues to change redox properties. We observed the forward and backward ET dynamics in a few picoseconds, strongly following a stretched behavior resulting from a coupling between local environment relaxations and these ET processes. We further observed the hot vibrational-state formation through charge recombination and the subsequent cooling dynamics also in a few picoseconds. Combined with the ET studies in oxidized flavodoxin, these results coherently reveal the evolution of the ET dynamics from single to stretched exponential behaviors and thus elucidate critical time scales for the coupling. The observed hot vibration-state formation is robust and should be considered in all photoinduced back ET processes in flavoproteins.

| S-EPMC7304529 | biostudies-literature

Understanding Short-Range Electron-Transfer Dynamics in Proteins.

Project description:Short-range electron-transfer (ET) reactions in biological systems are usually ultrafast, having transfer rates comparable to or even faster than corresponding environmental fluctuations, and often display nonexponential behaviors. To understand these nonequilibrium ET dynamics, we carried out detailed theoretical analyses based on the Sumi-Marcus model. It is shown that the ET dynamics is largely determined by the relative time scales of the ET reaction and its surrounding motions. Significantly, different environmental fluctuations can produce a variety of apparent ET dynamics even with the same driving force, ? Go, and reorganization energy, ?. We applied our analyses to an ultrafast ET process in DNA repair by (6-4) photolyase and directly obtained the inner and outer reorganization energies (?i and ?o) as well as the free energy ? Go of various mutants, providing mechanical insight into ultrafast short-range ET reactions in proteins.

| S-EPMC7258173 | biostudies-literature

Femtosecond dynamics of short-range protein electron transfer in flavodoxin.

Project description:Intraprotein electron transfer (ET) in flavoproteins is important for understanding the correlation of their redox, configuration, and reactivity at the active site. Here, we used oxidized flavodoxin as a model system and report our complete characterization of a photoinduced redox cycle from the initial charge separation in 135-340 fs to subsequent charge recombination in 0.95-1.6 ps and to the final cooling relaxation of the product(s) in 2.5-4.3 ps. With 11 mutations at the active site, we observed that these ultrafast ET dynamics, much faster than active-site relaxation, mainly depend on the reduction potentials of the electron donors with minor changes caused by mutations, reflecting a highly localized ET reaction between the stacked donor and acceptor at a van der Waals distance and leading to a gas-phase type of bimolecular ET reaction confined in the active-site nanospace. Significantly, these ultrafast ET reactions ensure our direct observation of vibrationally excited reaction product(s), suggesting that the back ET barrier is effectively reduced because of the decrease in the total free energy in the Marcus inverted region, leading to the accelerated charge recombination. Such vibrationally coupled charge recombination should be a general feature of flavoproteins with similar configurations and interactions between the cofactor flavin and neighboring aromatic residues.

| S-EPMC3909472 | biostudies-literature

Ultrafast Dynamics of Nonequilibrium Organic Exciton-Polariton Condensates.

Project description:Exciton-polariton condensation in organic materials, arising from the coupling of Frenkel excitons to the electromagnetic field in cavities, is a phenomenon resulting in low-threshold coherent light emission among other fascinating properties. The exact mechanisms leading to the thermalization of organic exciton-polaritons toward condensation are not yet understood, partly due to the complexity of organic molecules and partly to the canonical microcavities used in condensation studies, which limit broadband studies. Here, we exploit an entirely different cavity design, i.e., an array of plasmonic nanoparticles strongly coupled to organic molecules, to successfully measure the broadband ultrafast dynamics of the strongly coupled system. Sharp features emerge in the transient spectrum originating from the formation of a condensate with a well-defined molecular vibrational composition. These measurements represent the first direct experimental evidence that molecular vibrations drive condensation in organic systems and provide a benchmark for modeling the dynamics of organic-based exciton-polariton condensates.

| S-EPMC6909230 | biostudies-literature

Equilibrium and ultrafast kinetic studies manipulating electron transfer: A short-lived flavin semiquinone is not sufficient for electron bifurcation.

Project description:Flavin-based electron transfer bifurcation is emerging as a fundamental and powerful mechanism for conservation and deployment of electrochemical energy in enzymatic systems. In this process, a pair of electrons is acquired at intermediate reduction potential (i.e. intermediate reducing power), and each electron is passed to a different acceptor, one with lower and the other with higher reducing power, leading to "bifurcation." It is believed that a strongly reducing semiquinone species is essential for this process, and it is expected that this species should be kinetically short-lived. We now demonstrate that the presence of a short-lived anionic flavin semiquinone (ASQ) is not sufficient to infer the existence of bifurcating activity, although such a species may be necessary for the process. We have used transient absorption spectroscopy to compare the rates and mechanisms of decay of ASQ generated photochemically in bifurcating NADH-dependent ferredoxin-NADP+ oxidoreductase and the non-bifurcating flavoproteins nitroreductase, NADH oxidase, and flavodoxin. We found that different mechanisms dominate ASQ decay in the different protein environments, producing lifetimes ranging over 2 orders of magnitude. Capacity for electron transfer among redox cofactors versus charge recombination with nearby donors can explain the range of ASQ lifetimes that we observe. Our results support a model wherein efficient electron propagation can explain the short lifetime of the ASQ of bifurcating NADH-dependent ferredoxin-NADP+ oxidoreductase I and can be an indication of capacity for electron bifurcation.

| S-EPMC5572931 | biostudies-literature

Nonequilibrium continuous phase transition in colloidal gelation with short-range attraction.

Project description:The dynamical arrest of attractive colloidal particles into out-of-equilibrium structures, known as gelation, is central to biophysics, materials science, nanotechnology, and food and cosmetic applications, but a complete understanding is lacking. In particular, for intermediate particle density and attraction, the structure formation process remains unclear. Here, we show that the gelation of short-range attractive particles is governed by a nonequilibrium percolation process. We combine experiments on critical Casimir colloidal suspensions, numerical simulations, and analytical modeling with a master kinetic equation to show that cluster sizes and correlation lengths diverge with exponents ~1.6 and 0.8, respectively, consistent with percolation theory, while detailed balance in the particle attachment and detachment processes is broken. Cluster masses exhibit power-law distributions with exponents -3/2 and -5/2 before and after percolation, as predicted by solutions to the master kinetic equation. These results revealing a nonequilibrium continuous phase transition unify the structural arrest and yielding into related frameworks.

| S-EPMC7367344 | biostudies-literature

Aqueous Photocurrent Measurements Correlated to Ultrafast Electron Transfer Dynamics at Ruthenium Tris Diimine-Sensitized NiO Photocathodes.

Project description:Understanding the structural and electronic factors governing the efficiency of dye-sensitized NiO photocathodes is essential to optimize solar fuel production in photoelectrochemical cells (PECs). For these purpose, three different ruthenium dyes, bearing either two or four methylphosphonate anchoring groups and either a bipyridine or a dipyridophenazine ancillary ligand, were synthesized and grafted onto NiO films. These photoelectrodes were fully characterized by XPS, ToF-SIMS, UV-vis absorption, time-resolved emission and femtosecond transient absorption spectroscopies. Increasing the number of anchoring groups from two to four proved beneficial for the grafting efficiency. No significant modification of the electronic properties compared to the parent photosensitizer was observed, in accordance with the non-conjugated nature of the grafted linker. The photoelectrochemical activity of the dye-sensitized NiO electrodes was assessed in fully aqueous medium in the presence of an irreversible electron acceptor and photocurrents reaching 190 ?A.cm-2 were recorded. The transient absorption study revealed the presence of two charge recombination pathways for each of the sensitizers and evidenced a stabilized charge separated state in the dppz derivative, supporting its superior photoelectrochemical activity.

| S-EPMC5493983 | biostudies-literature

Concurrent Ultrafast Electron- and Hole-Transfer Dynamics in CsPbBr<sub>3</sub> Perovskite and Quantum Dots.

Project description:Ultrafast charge-transfer (i.e., electron and hole) dynamics has been investigated between the cesium lead bromide (CsPbBr3, CPB) perovskite nanocrystals (NCs) and cadmium selenide (CdSe) quantum dots (QDs) as a new composite material for photocatalytic and photovoltaic applications. The CPB NCs have been synthesized and characterized by high-resolution transmission electron microscopy (HR-TEM) and X-ray diffraction (XRD) pattern. The redox levels (i.e., conduction band (CB) and valence band (VB)) of the CPB NCs and CdSe QDs suggest the feasibility of photoexcited electron transfer from CPB NCs to CdSe QDs and photoexcited hole transfer from CdSe QDs to CPB NCs, and it has been confirmed by both steady-state and time-resolved spectroscopy. To investigate the electron- and hole-transfer dynamics in ultrafast time scale, we have performed femtosecond up-conversion and femtosecond transient absorption studies. The measured electron-transfer time from CPB NCs to CdSe QDs and hole-transfer time from CdSe QDs to CPB NCs were found to be 550 and 750 fs, respectively. Interestingly, the charge-transfer process found to be restricted in CPB/CdSe@CdS core-shell system where electron transfer from CPB NCs to core shell takes place, but the hole transfer from core shell to CPB NCs found to be restricted due to CdS shell making the process thermodynamically nonviable. Our observation has suggested that after the photoexcitation of CPB NCs/CdSe QDs composite system, a charge-separated state is formed where the electrons are localized in CB of CdSe QDs and holes are localized in VB of CPB NCs. This makes the composite system a better material for efficient light harvesting and photocatalytic material as compared to the individual ones.

| S-EPMC6641258 | biostudies-literature

Ultrafast direct electron transfer at organic semiconductor and metal interfaces.

Project description:The ability to control direct electron transfer can facilitate the development of new molecular electronics, light-harvesting materials, and photocatalysis. However, control of direct electron transfer has been rarely reported, and the molecular conformation-electron dynamics relationships remain unclear. We describe direct electron transfer at buried interfaces between an organic polymer semiconductor film and a gold substrate by observing the first dynamical electric field-induced vibrational sum frequency generation (VSFG). In transient electric field-induced VSFG measurements on this system, we observe dynamical responses (<150 fs) that depend on photon energy and polarization, demonstrating that electrons are directly transferred from the Fermi level of gold to the lowest unoccupied molecular orbital of organic semiconductor. Transient spectra further reveal that, although the interfaces are prepared without deliberate alignment control, a subensemble of surface molecules can adopt conformations for direct electron transfer. Density functional theory calculations support the experimental results and ascribe the observed electron transfer to a flat-lying polymer configuration in which electronic orbitals are found to be delocalized across the interface. The present observation of direct electron transfer at complex interfaces and the insights gained into the relationship between molecular conformations and electron dynamics will have implications for implementing novel direct electron transfer in energy materials.

| S-EPMC5694661 | biostudies-literature

Gaussian fluctuations and linear response in an electron transfer protein.

Project description:In response to charge separation or transfer, polar liquids respond in a simple linear fashion. A similar linear response for proteins might be expected from the central limit theorem and is postulated in widely used theories of protein electrostatics, including the Marcus electron transfer theory and dielectric continuum theories. Although these theories are supported by a variety of experimental data, the exact validity of a linear protein dielectric response has been difficult to determine. Molecular dynamics simulations are presented that establish a linear dielectric response of both protein and surrounding solvent over the course of a biologically relevant electron transfer reaction: oxido-reduction of yeast cytochrome c in solution. Using an umbrella-sampling free energy approach with long simulations, an accurate treatment of long-range electrostatics and both classical and quantum models of the heme, good agreement is obtained with experiment for the redox potential relative to a heme-octapeptide complex. We obtain a reorganization free energy that is only half that for heme-octapeptide and is reproduced with a dielectric continuum model where the heme vicinity has a dielectric constant of only 1.1. This value implies that the contribution of protein reorganization to the electron transfer free energy barrier is reduced almost to the theoretical limit (a dielectric of one), and that the fluctuations of the electrostatic potential on the heme have a simple harmonic form, in accord with Marcus theory, even though the fluctuations of many individual protein groups (especially at the protein surface) are anharmonic.

| S-EPMC124439 | 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