Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Caveat when using ADC(2) for studying the photochemistry of carbonyl-containing molecules.

ABSTRACT: Several electronic-structure methods are available to study the photochemistry and photophysics of organic molecules. Among them, ADC(2) stands as a sweet spot between computational efficiency and accuracy. As a result, ADC(2) has recently seen its number of applications booming, in particular to unravel the deactivation pathways and photodynamics of organic molecules. Despite this growing success, we demonstrate here that care has to be taken when studying the nonradiative pathways of carbonyl-containing molecules, as ADC(2) appears to suffer from a systematic flaw.

SUBMITTER: Marsili E

PROVIDER: S-EPMC8207513 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Caveat when using ADC(2) for studying the photochemistry of carbonyl-containing molecules.

Marsili Emanuele E Prlj Antonio A Curchod Basile F E BFE

Physical chemistry chemical physics : PCCP 20210601 23

Several electronic-structure methods are available to study the photochemistry and photophysics of organic molecules. Among them, ADC(2) stands as a sweet spot between computational efficiency and accuracy. As a result, ADC(2) has recently seen its number of applications booming, in particular to unravel the deactivation pathways and photodynamics of organic molecules. Despite this growing success, we demonstrate here that care has to be taken when studying the nonradiative pathways of carbonyl- ...[more]

PMID: 34085679

Similar Datasets

Studying manganese carbonyl photochemistry in a permanently porous metal-organic framework.

Project description:Mn(diimine)(CO)3X (X = halide) complexes are critical components of chromophores, photo- and electrocatalysts, and photoactive CO-releasing molecules (photoCORMs). While these entities have been incorporated into metal-organic frameworks (MOFs), a detailed understanding of the photochemical and chemical processes that occur in a permanently porous support is lacking. Here we site-isolate and study the photochemistry of a Mn(diimine)(CO)3Br moiety anchored within a permanently porous MOF support, allowing for not only the photo-liberation of CO from the metal but also its escape from the MOF crystals. In addition, the high crystallinity and structural flexibility of the MOF allows crystallographic snapshots of the photolysis products to be obtained. We report these photo-crystallographic studies in the presence of coordinating solvents, THF and acetonitrile, showing the changing coordination environment of the Mn species as CO loss proceeds. Using time resolved experiments, we report complementary spectroscopic studies of the photolysis chemistry and characterize the final photolysis product as a possible Mn(ii) entity. These studies inform the chemistry that occurs in MOF-based photoCORMs and where these moieties are employed as catalysts.

| S-EPMC10498678 | biostudies-literature

Chiral photochemistry of achiral molecules.

Project description:Chirality is a molecular property governed by the topography of the potential energy surface (PES). Thermally achiral molecules interconvert rapidly when the interconversion barrier between the two enantiomers is comparable to or lower than the thermal energy, in contrast to thermally stable chiral configurations. In principle, a change in the PES topography on the excited electronic state may diminish interconversion, leading to electronically prochiral molecules that can be converted from achiral to chiral by electronic excitation. Here we report that this is the case for two prototypical examples - cis-stilbene and cis-stiff stilbene. Both systems exhibit unidirectional photoisomerization for each enantiomer as a result of their electronic prochirality. We simulate an experiment to demonstrate this effect in cis-stilbene based on its interaction with circularly polarized light. Our results highlight the drastic change in chiral behavior upon electronic excitation, opening up the possibility for asymmetric photochemistry from an effectively nonchiral starting point.

| S-EPMC9019051 | biostudies-literature

Reciprocal carbonyl-carbonyl interactions in small molecules and proteins.

Project description:Carbonyl-carbonyl n→π* interactions where a lone pair (n) of the oxygen atom of a carbonyl group is delocalized over the π* orbital of a nearby carbonyl group have attracted a lot of attention in recent years due to their ability to affect the 3D structure of small molecules, polyesters, peptides, and proteins. In this paper, we report the discovery of a "reciprocal" carbonyl-carbonyl interaction with substantial back and forth n→π* and π→π* electron delocalization between neighboring carbonyl groups. We have carried out experimental studies, analyses of crystallographic databases and theoretical calculations to show the presence of this interaction in both small molecules and proteins. In proteins, these interactions are primarily found in polyproline II (PPII) helices. As PPII are the most abundant secondary structures in unfolded proteins, we propose that these local interactions may have implications in protein folding.Carbonyl-carbonyl π* non covalent interactions affect the structure and stability of small molecules and proteins. Here, the authors carry out experimental studies, analyses of crystallographic databases and theoretical calculations to describe an additional type of carbonyl-carbonyl interaction.

| S-EPMC5517579 | biostudies-literature

Understanding dynamics using sensitivity analysis: caveat and solution.

Project description:BackgroundParametric sensitivity analysis (PSA) has become one of the most commonly used tools in computational systems biology, in which the sensitivity coefficients are used to study the parametric dependence of biological models. As many of these models describe dynamical behaviour of biological systems, the PSA has subsequently been used to elucidate important cellular processes that regulate this dynamics. However, in this paper, we show that the PSA coefficients are not suitable in inferring the mechanisms by which dynamical behaviour arises and in fact it can even lead to incorrect conclusions.ResultsA careful interpretation of parametric perturbations used in the PSA is presented here to explain the issue of using this analysis in inferring dynamics. In short, the PSA coefficients quantify the integrated change in the system behaviour due to persistent parametric perturbations, and thus the dynamical information of when a parameter perturbation matters is lost. To get around this issue, we present a new sensitivity analysis based on impulse perturbations on system parameters, which is named impulse parametric sensitivity analysis (iPSA). The inability of PSA and the efficacy of iPSA in revealing mechanistic information of a dynamical system are illustrated using two examples involving switch activation.ConclusionsThe interpretation of the PSA coefficients of dynamical systems should take into account the persistent nature of parametric perturbations involved in the derivation of this analysis. The application of PSA to identify the controlling mechanism of dynamical behaviour can be misleading. By using impulse perturbations, introduced at different times, the iPSA provides the necessary information to understand how dynamics is achieved, i.e. which parameters are essential and when they become important.

| S-EPMC3070647 | biostudies-literature

Caveat Mutator

Project description:The use of whole genome microarrays for monitoring mutagenised or otherwise engineered genetic derivatives is a potentially powerful tool for checking genomic integrity. Using comparative genomic hybridization of a number of unrelated, directed deletion mutants in Escherichia coli K-12 MG1655 we identified unintended secondary genomic deletions in the flhDC region in deltafnr, deltacrp, and deltacreB mutants. These deletions were confirmed by PCR and phenotypic tests. Our findings show that non-motile progeny are found in some populations of MG1655 directed deletion mutants, and studies on the effects of gene knock-outs should be viewed with caution when the mutants have not been screened for the presence of secondary deletions, or confirmed by other methods. Keywords: comparative genomic hybridisation

2007-09-30 | GSE7695 | GEO

High-Performance Orange-Red Organic Light-Emitting Diodes with External Quantum Efficiencies Reaching 33.5% based on Carbonyl-Containing Delayed Fluorescence Molecules.

Project description:Developing orange to red purely organic luminescent materials having external quantum efficiencies (ηext s) exceeding 30% is challenging because it generally requires strong intramolecular charge transfer, efficient reverse intersystem crossing (RISC), high photoluminescence quantum yield (ΦPL ), and large optical outcoupling efficiency (Φout ) simultaneously. Herein, by introducing benzoyl to dibenzo[a,c]phenazine acceptor, a stronger electron acceptor, dibenzo[a,c]phenazin-11-yl(phenyl)methanone, is created and employed for constructing orange-red delayed fluorescence molecules with various acridine-based electron donors. The incorporation of benzoyl leads to red-shifted photoluminescence with accelerated RISC, reduced delayed lifetimes, and increased ΦPL s, and the adoption of spiro-structured acridine donors promotes horizontal dipole orientation and thus renders high Φout s. Consequently, the state-of-the-art orange-red organic light-emitting diodes are achieved, providing record-high electroluminescence (EL) efficiencies of 33.5%, 95.3 cd A-1 , and 93.5 lm W-1 . By referring the control molecule without benzoyl, it is demonstrated that the presence of benzoyl can exert significant positive effect over improving delayed fluorescence and enhancing EL efficiencies, which can be a feasible design for robust organic luminescent materials.

| S-EPMC8787409 | biostudies-literature

Caveat Mutator

Project description:The use of whole genome microarrays for monitoring mutagenised or otherwise engineered genetic derivatives is a potentially powerful tool for checking genomic integrity. Using comparative genomic hybridization of a number of unrelated, directed deletion mutants in Escherichia coli K-12 MG1655 we identified unintended secondary genomic deletions in the flhDC region in fnr, crp, and creB mutants. These deletions were confirmed by PCR and phenotypic tests. Our findings show that non-motile progeny are found in some populations of MG1655 directed deletion mutants, and studies on the effects of gene knock-outs should be viewed with caution when the mutants have not been screened for the presence of secondary deletions, or confirmed by other methods. We used the CGH method to genetically characterize a series of regulatory gene deletion mutants we had made in MG1655 using the lamda-Red method of Datsenko and Wanner. A number of strains were tested using CGH, and each strain was tested only once. Genomic DNA isolated from wt MG1655 was used as a reference in all hybridisations.

2007-09-30 | E-GEOD-7695 | biostudies-arrayexpress

T memory stem cell formation: Caveat mTOR.

Project description: Not available

| S-EPMC4776221 | biostudies-literature

Forging isopeptide bonds using thiol-ene chemistry: site-specific coupling of ubiquitin molecules for studying the activity of isopeptidases.

Project description:Chemical methods for modifying proteins can enable studies aimed at uncovering biochemical function. Herein, we describe the use of thiol-ene coupling (TEC) chemistry to report on the function of branched (also referred to as forked) ubiquitin trimers. We show how site-specific isopeptide (N?-Gly-L-homothiaLys) bonds are forged between two molecules of Ub, demonstrating the power of TEC in protein conjugation. Moreover, we demonstrate that the N?-Gly-L-homothiaLys isopeptide bond is processed to a similar extent by deubiquitinases (DUBs) as that of a native N?-Gly-L-Lys isopeptide bond, thereby establishing the utility of TEC in the generation of Ub-Ub linkages. TEC is then applied to the synthesis of branched Ub trimers. Interrogation of these branched derivatives with DUBs reveals that the relative orientation of the two Ub units has a dramatic impact on how they are hydrolyzed. In particular, cleavage of K48C-linkages is suppressed when the central Ub unit is also conjugated through K6C, whereas cleavage proceeds normally when the central unit is conjugated through either K11C or K63C. The results of this work presage a role for branched polymeric Ub chains in regulating linkage-selective interactions.

| S-EPMC4373626 | biostudies-literature

Identification and quantification of carbonyl-containing α-pinene ozonolysis products using <i>O</i>-<i>tert</i>-butylhydroxylamine hydrochloride.

Project description:The yields of carbonyl-containing reaction products from the ozonolysis of α-pinene have been investigated using concentrations of ozone found in the indoor environment ([O3] ≤ 100 ppb). An impinger was used to collect gas-phase oxidation products in water, where the derivatization agent O-tert-butylhydroxylamine hydrochloride (TBOX) and gas chromatography-mass spectrometry were used to identify carbonyl-containing species. Seven carbonyl-containing products were observed. The yield of the primary product, pinonaldehyde was measured to be 76 %. Using cyclohexane as a hydroxyl radical (OH) scavenger, the yield of pinonaldehyde decreased to 46 %, indicating the influence secondary OH radicals have on α-pinene ozonolysis products. Furthermore, the use of TBOX, a small molecular weight derivatization agent, allowed for the acquisition of the first mass spectral data of oxopinonaldehyde, a tricarbonyl reaction product of α-pinene ozonolysis. The techniques described herein allow for an effective method for the collection and identification of terpene oxidation products in the indoor environment.

| S-EPMC5502832 | 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