Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Time-Resolved Spectroscopic Study on the Photoredox Reaction of 2-(p-Hydroxymethyl)phenylAnthraquinone.

ABSTRACT: In this work, we report a combined time-resolved spectroscopic and density functional theory computational study on 2-(p-hydroxymethyl)phenylanthraquinone (PPAQ) in which the benzyl alcohol moiety is significantly farther away from the AQ ketone group compared to the compound 2-(1-hydroxyethyl) 9,10-anthraquinone (HEAQ) so as to investigate the photophysical and photochemical reactions of PPAQ in several solvents, especially for the photoredox reaction in a pH 2 aqueous solution. The results here indicate that PPAQ undergoes the photoredox reaction via a two-step pathway and that the low efficiency of the photoredox reaction of PPAQ compared to the related HEAQ molecule is caused by the longer distance between the benzyl alcohol moiety and the AQ ketone moieties.

SUBMITTER: Song Q

PROVIDER: S-EPMC5567363 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Time-Resolved Spectroscopic Study on the Photoredox Reaction of 2-(p-Hydroxymethyl)phenylAnthraquinone.

Song Qingqing Q Zhang Xiting X Ma Jiani J Guo Yan Y Phillips David Lee DL

Scientific reports 20170822 1

In this work, we report a combined time-resolved spectroscopic and density functional theory computational study on 2-(p-hydroxymethyl)phenylanthraquinone (PPAQ) in which the benzyl alcohol moiety is significantly farther away from the AQ ketone group compared to the compound 2-(1-hydroxyethyl) 9,10-anthraquinone (HEAQ) so as to investigate the photophysical and photochemical reactions of PPAQ in several solvents, especially for the photoredox reaction in a pH 2 aqueous solution. The results her ...[more]

PMID: 28831174

Similar Datasets

Time-Resolved Spectroscopic Study of N,N-Di(4-bromo)nitrenium Ions in Acidic Aqueous Solution.

Project description:Nitrenium ions are common reactive intermediates with high activities towards some biological nucleophiles. In this paper, we employed femtosecond transient absorption (fs-TA) and nanosecond transient absorption (ns-TA) as well as nanosecond time-resolved resonance Raman (ns-TR3) spectroscopy and density function theory (DFT) calculations to study the spectroscopic properties of the N(4,4'-dibromodiphenylamino)-2,4,6-trimethylpyridinium BF4- salt (1) in an acidic aqueous solution. Efficient cleavage of the N-N bond (4 ps) to form the N,N-di(4-bromophenyl)nitrenium ion (DN) was also observed in the acidic aqueous solution. As a result, the dication intermediate 4 appears more likely to be produced after abstracting a proton for the nitrenium ion DN in the acid solution first, followed by an electron abstraction to form the radical cation intermediate 3. These new and more extensive time-resolved spectroscopic data will be useful to help to develop an improved understanding of the identity, nature, and properties of nitrenium ions involved in reactions under acidic aqueous conditions.

| S-EPMC6862224 | biostudies-literature

Atomically resolved spectroscopic study of Sr2IrO4: experiment and theory.

Project description:Particularly in Sr2IrO4, the interplay between spin-orbit coupling, bandwidth and on-site Coulomb repulsion stabilizes a J(eff) = 1/2 spin-orbital entangled insulating state at low temperatures. Whether this insulating phase is Mott- or Slater-type, has been under intense debate. We address this issue via spatially resolved imaging and spectroscopic studies of the Sr2IrO4 surface using scanning tunneling microscopy/spectroscopy (STM/S). STS results clearly illustrate the opening of an insulating gap (150 ~ 250 meV) below the Néel temperature (TN), in qualitative agreement with our density-functional theory (DFT) calculations. More importantly, the temperature dependence of the gap is qualitatively consistent with our DFT + dynamical mean field theory (DMFT) results, both showing a continuous transition from a gapped insulating ground state to a non-gap phase as temperatures approach TN. These results indicate a significant Slater character of gap formation, thus suggesting that Sr2IrO4 is a uniquely correlated system, where Slater and Mott-Hubbard-type behaviors coexist.

| S-EPMC3810661 | biostudies-other

Analysis of the HindIII-catalyzed reaction by time-resolved crystallography.

Project description:In order to investigate the mechanism of the reaction catalyzed by HindIII, structures of HindIII-DNA complexes with varying durations of soaking time in cryoprotectant buffer containing manganese ions were determined by the freeze-trap method. In the crystal structures of the complexes obtained after soaking for a longer duration, two manganese ions, indicated by relatively higher electron density, are clearly observed at the two metal ion-binding sites in the active site of HindIII. The increase in the electron density of the two metal-ion peaks followed distinct pathways with increasing soaking times, suggesting variation in the binding rate constant for the two metal sites. DNA cleavage is observed when the second manganese ion appears, suggesting that HindIII uses the two-metal-ion mechanism, or alternatively that its reactivity is enhanced by the binding of the second metal ion. In addition, conformational change in a loop near the active site accompanies the catalytic reaction.

| S-EPMC4321485 | biostudies-literature

Time-Resolved Spectroscopic Study of <i>N</i>,<i>N</i>-Di(4-bromo)nitrenium Ions in Selected Solutions.

Project description:Nitrenium ions are important reactive intermediates in chemistry and biology. In this work, femtosecond and nanosecond transient absorption (fs-TA and ns-TA) along with nanosecond time-resolved resonance Raman (ns-TR³) experiments were employed to examine the photochemical pathways of N-(4,4'-dibromodiphenylamino)-2,4,6-trimethylpyridinium BF₄- (salt (DN) from just absorption of a photon of light to the production of the important N,N-di(4-bromophenyl)nitrenium ion 2. In acetonitrile (MeCN), the formation of halogenated diarylnitrenium ion 2 was observed within 4 ps, showing the vibrational spectra with strong intensity. The nucleophilic adduct reaction of ion 2 with H₂O was also examined in aqueous solutions. The direct detection of the unique ortho adduct intermediate 3 shows that there is an efficient and exclusive reaction pathway for 2 with H₂O. The results shown in this paper give new characterization of 2, which can be used to design time-resolved spectroscopy investigations of covalent addition reactions of nitrenium ions with other molecules in future studies.

| S-EPMC6321521 | biostudies-literature

PyLDM - An open source package for lifetime density analysis of time-resolved spectroscopic data.

Project description:Ultrafast spectroscopy offers temporal resolution for probing processes in the femto- and picosecond regimes. This has allowed for investigation of energy and charge transfer in numerous photoactive compounds and complexes. However, analysis of the resultant data can be complicated, particularly in more complex biological systems, such as photosystems. Historically, the dual approach of global analysis and target modelling has been used to elucidate kinetic descriptions of the system, and the identity of transient species respectively. With regards to the former, the technique of lifetime density analysis (LDA) offers an appealing alternative. While global analysis approximates the data to the sum of a small number of exponential decays, typically on the order of 2-4, LDA uses a semi-continuous distribution of 100 lifetimes. This allows for the elucidation of lifetime distributions, which may be expected from investigation of complex systems with many chromophores, as opposed to averages. Furthermore, the inherent assumption of linear combinations of decays in global analysis means the technique is unable to describe dynamic motion, a process which is resolvable with LDA. The technique was introduced to the field of photosynthesis over a decade ago by the Holzwarth group. The analysis has been demonstrated to be an important tool to evaluate complex dynamics such as photosynthetic energy transfer, and complements traditional global and target analysis techniques. Although theory has been well described, no open source code has so far been available to perform lifetime density analysis. Therefore, we introduce a python (2.7) based package, PyLDM, to address this need. We furthermore provide a direct comparison of the capabilities of LDA with those of the more familiar global analysis, as well as providing a number of statistical techniques for dealing with the regularization of noisy data.

| S-EPMC5460884 | biostudies-literature

Photochemical α-Cleavage Reaction of 3',5'-Dimethoxybenzoin: A Combined Time-Resolved Spectroscopy and Computational Chemistry Study.

Project description:Benzoin is one of the most commonly used photoinitiators to induce free radical polymerization. Here, improved benzoin properties could be accomplished by the introduction of two methoxy substituents, leading to the formation of 3',5'-dimethoxybenzoin (DMB) which has a higher photo-cleavage quantum yield (0.54) than benzoin (0.35). To elucidate the underlying reaction mechanisms of DMB and obtain direct information of the transient species involved, femtosecond transient absorption (fs-TA) and nanosecond transient absorption (ns-TA) spectroscopic experiments in conjunction with density functional theory/time-dependent density functional theory (DFT/TD-DFT) calculations were performed. It was found that the photo-induced α-cleavage (Norrish Type I reaction) of DMB occurred from the nπ* triplet state after a rapid intersystem crossing (ISC) process (7.6 ps), leading to the generation of phenyl radicals on the picosecond time scale. Compared with Benzoin, DMB possesses two methoxy groups which are able to stabilize the alcohol radical and thus result in a stronger driving force for cleavage and a higher quantum yield of photodissociation. Two stable conformations (cis-DMB and trans-DMB) at ground state were found via DFT calculations. The influence of the intramolecular hydrogen bond on the α-cleavage of DMB was elaborated.

| S-EPMC7435414 | biostudies-literature

Time-resolved spectroscopic studies of the AppA blue-light receptor BLUF domain from Rhodobacter sphaeroides.

Project description:AppA is a blue-light and redox-responding regulator of photosynthesis gene expression in Rhodobacter sphaeroides. Detailed time-resolved fluorescence spectroscopy and subpicosecond transient absorption spectroscopy study of the BLUF domain is presented for wild-type AppA (AppAwt) and a photoinactive Y21F mutant of AppA. The main findings discussed here are that (1) time-resolved laser excitation studies on dark-adapted protein show that AppAwt and Y21F mutant protein exhibits a fluorescence decay with a lifetime of 0.6 ns. Dark-adapted AppAwt but not Y21F also exhibits slower fluorescence decay with a lifetime of 1.7 ns. Analysis of AppAwt that was light-excited to a stable light-adapted form prior to data collection shows monoexponential fluorescence decay with a lifetime of 1.0 ns. This component disappeared after 1 min of data collection after which the original "dark-adapted" values were recovered, demonstrating the presence of a approximately 1 min lifetime intermediate during the return of AppA from light- to dark-adapted form. (2) Transient absorption spectral analysis reveals a very fast rising of transient absorption (<1 ps) for AppAwt. This fast component is missing in the Y21F mutant, which lacks Tyr21, giving rise to a slower transient absorption at 4-6 ps. In the AppAwt transient spectra, most ground states recover within approximately 30 ps, compared to approximately 90-130 ps in the mutant Y21F. We propose that a temporary electron transfer occurs from Tyr21 to the N5 of flavin in AppAwt and is a triggering event for subsequent hydrogen-bond rearrangements. Dynamics of the AppA photocycle is discussed in view of the currently solved crystallographic structure of AppA.

| S-EPMC2744204 | biostudies-literature

Time-resolved spectroscopic and electrophysiological data reveal insights in the gating mechanism of anion channelrhodopsin.

Project description:Channelrhodopsins are widely used in optogenetic applications. High photocurrents and low current inactivation levels are desirable. Two parallel photocycles evoked by different retinal conformations cause cation-conducting channelrhodopsin-2 (CrChR2) inactivation: one with efficient conductivity; one with low conductivity. Given the longer half-life of the low conducting photocycle intermediates, which accumulate under continuous illumination, resulting in a largely reduced photocurrent. Here, we demonstrate that for channelrhodopsin-1 of the cryptophyte Guillardia theta (GtACR1), the highly conducting C = N-anti-photocycle was the sole operating cycle using time-resolved step-scan FTIR spectroscopy. The correlation between our spectroscopic measurements and previously reported electrophysiological data provides insights into molecular gating mechanisms and their role in the characteristic high photocurrents. The mechanistic importance of the central constriction site amino acid Glu-68 is also shown. We propose that canceling out the poorly conducting photocycle avoids the inactivation observed in CrChR2, and anticipate that this discovery will advance the development of optimized optogenetic tools.

| S-EPMC8121809 | biostudies-literature

Time-resolved x-ray crystallography capture of a slow reaction tetrahydrofolate intermediate.

Project description:Time-resolved crystallography is a powerful technique to elucidate molecular mechanisms at both spatial (angstroms) and temporal (picoseconds to seconds) resolutions. We recently discovered an unusually slow reaction at room temperature that occurs on the order of days: the in crystalline reverse oxidative decay of the chemically labile (6S)-5,6,7,8-tetrahydrofolate in complex with its producing enzyme Escherichia coli dihydrofolate reductase. Here, we report the critical analysis of a representative dataset at an intermediate reaction time point. A quinonoid-like intermediate state lying between tetrahydrofolate and dihydrofolate features a near coplanar geometry of the bicyclic pterin moiety, and a tetrahedral sp 3 C6 geometry is proposed based on the apparent mFo-DFc omit electron densities of the ligand. The presence of this intermediate is strongly supported by Bayesian difference refinement. Isomorphous Fo-Fo difference map and multi-state refinement analyses suggest the presence of end-state ligand populations as well, although the putative intermediate state is likely the most populated. A similar quinonoid intermediate previously proposed to transiently exist during the oxidation of tetrahydrofolate was confirmed by polarography and UV-vis spectroscopy to be relatively stable in the oxidation of its close analog tetrahydropterin. We postulate that the constraints on the ligand imposed by the interactions with the protein environment might be the origin of the slow reaction observed by time-resolved crystallography.

| S-EPMC6397045 | biostudies-literature

Spectroscopic Study of a Cinchona Alkaloid-Catalyzed Henry Reaction.

Project description:A spectroscopic study of an organocatalytic Henry reaction between nitroalkanes and aldehydes catalyzed by a quinidine-derived Cinchona alkaloid is described. The binding modes of the reaction substrates are investigated using electronic absorption and fluorescence spectroscopy and further corroborated by nuclear magnetic resonance measurements. Aldehydes are shown to associate with both the 6'-OH group and the basic quinuclidine nitrogen of the catalyst, whereas nitroalkanes do not exhibit a clear binding mode. Reaction progress kinetic analysis reveals that the reaction is first-order in both of the substrates and the catalyst. Second, the reaction proceeds approximately five times faster in the excess of the nitroalkanes than in the excess of the aldehydes, suggesting that binding of the aldehydes results in the inhibition of the catalyst. Aldehydes deactivate the basic quinuclidine site, thus suppressing the deprotonation of the nitroalkanes which is the proposed initial step in the reaction cycle.

| S-EPMC5830691 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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