Browse
Submit Data
Databases
API
Help

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Kinetic and Thermodynamic Modulation of Dynamic Imine Libraries Driven by the Hexameric Resorcinarene Capsule.

ABSTRACT: The composition of dynamic covalent imine libraries (DCL) adapts to the presence of the hexameric resorcinarene capsule. In the presence of the self-assembled capsule, a kinetic and thermodynamic modulation of the imine constituents of the DCLs was observed, which was induced by an unusual predatory action of the capsule on specific imine constituents. More complex 2 × 2 DCLs also adapt to the presence of the hexameric capsule, showing a thermodynamic and kinetic modulation of the constituents induced by the predatory action of the capsule. By cross-referencing experimental data, a good selectivity (up to 66%) for one constituent can be induced in a 2 × 2 DCL.

SUBMITTER: Gambaro S

PROVIDER: S-EPMC8010792 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Carbocation catalysis in confined space: activation of trityl chloride inside the hexameric resorcinarene capsule.

Project description:Carbocation catalysis can be performed inside the confined space of the hexameric resorcinarene capsule. The inner cavity of the capsule can host the trityl carbocation, which catalyses the Diels-Alder reaction between dienes and unsaturated aldehydes. Experimental results and in silico calculations show that the hexameric resorcinarene capsule C6 can promote the formation of the trityl carbocation from trityl chloride through the cleavage of the carbon-halogen bond promoted by OH⋯X- hydrogen bonding. Here it is shown that the combination of the nanoconfined space and the latent carbocation catalysis provides a convenient complementary strategy for the typical carbocation catalysis. The latent strategy bypasses the typical pitfalls associated with active carbocations and provides control of the reaction efficiency in terms of reaction rate, conversion, and selectivity.

| S-EPMC9337730 | biostudies-literature

The Hexameric Resorcinarene Capsule as a Bronsted Acid Catalyst for the Synthesis of Bis(heteroaryl)methanes in a Nanoconfined Space.

Project description:Herein, we show that the hexameric resorcinarene capsule C is able to catalyze the formation of bis(heteroaryl)methanes by reaction between pyrroles or indoles and carbonyl compounds (?-ketoesters or aldehydes) in excellent yields and selectivity. Our results suggest that the capsule can play a double catalytic role as a H-bond catalyst, for the initial activation of the carbonyl substrate, and as a Brønsted acid catalyst, for the dehydration of the intermediate alcohol.

| S-EPMC6817573 | biostudies-literature

Just Add Water: Modulating the Structure-Derived Acidity of Catalytic Hexameric Resorcinarene Capsules.

Project description:The hexameric undecyl-resorcin[4]arene capsule (C11R6) features eight discrete structural water molecules located at the vertices of its cubic suprastructure. Combining NMR spectroscopy with classical molecular dynamics (MD), we identified and characterized two distinct species of this capsule, C11R6-A and C11R6-B, respectively featuring 8 and 15 water molecules incorporated into their respective hydrogen-bonded networks. Furthermore, we found that the ratio of the C11R6-A and C11R6-B found in solution can be modulated by controlling the water content of the sample. The importance of this supramolecular modulation in C11R6 capsules is highlighted by its ability to perform acid-catalyzed transformations, which is an emergent property arising from the hydrogen bonding within the suprastructure. We show that the conversion of C11R6-A to C11R6-B enhances the catalytic rate of a model Diels-Alder cyclization by 10-fold, demonstrating the cofactor-derived control of a supramolecular catalytic process that emulates natural enzymatic systems.

| S-EPMC8517980 | biostudies-literature

New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities.

Project description:Most rotamer libraries are generated from subsets of the PDB and do not fully represent the conformational scope of protein side chains. Previous attempts to rectify this sparse coverage of conformational space have involved application of weighting and smoothing functions. We resolve these limitations by using physics-based molecular dynamics simulations to determine more accurate frequencies of rotameric states. This work forms part of our Dynameomics initiative and uses a set of 807 proteins selected to represent 97% of known autonomous protein folds, thereby eliminating the bias toward common topologies found within the PDB. Our Dynameomics derived rotamer libraries encompass 4.8 × 10(9) rotamers, sampled from at least 51,000 occurrences of each of 93,642 residues. Here, we provide a backbone-dependent rotamer library, based on secondary structure ?/? regions, and an update to our 2011 backbone-independent library that addresses the doubling of our dataset since its original publication.

| S-EPMC4715459 | biostudies-literature

An Atom-Economical Method for the Formation of Amidopyrroles Exploiting the Self-Assembled Resorcinarene Capsule.

Project description:Here is reported the first example of an organocatalyzed coupling between pyrrole and isocyanates in a nanoconfined space. The hexameric resorcinarene capsule C is able to catalyze the direct coupling between isocyanates and pyrroles to give amidopyrroles with excellent yields and selectivities. The reaction catalyzed by C prevents the use of expensive and poorly atom-economical reagents. As in natural enzymes, the cavity of C is able to discriminate between isomeric substrates.

| S-EPMC7997627 | biostudies-literature

To catalyze or not to catalyze: elucidation of the subtle differences between the hexameric capsules of pyrogallolarene and resorcinarene.

Project description:The closely related, self-assembled resorcinarene and pyrogallolarene capsules display contrasting and puzzling encapsulation behaviors. Herein, we elucidate the reasons for these differences by combining experimental studies and DFT calculations. Furthermore, we report that, in contrast to the resorcinarene capsule, the pyrogallolarene derivative is not capable of catalyzing reactions with cationic transition states. The molecular mechanisms responsible for these observations are probed in detail.

| S-EPMC5364520 | biostudies-literature

Optimized iminium-catalysed 1,4-reductions inside the resorcinarene capsule: achieving >90% ee with proline as catalyst.

Project description:In previous work, we demonstrated that iminium-catalysed 1,4-reductions inside the supramolecular resorcinarene capsule display increased enantioselectivities as compared to their regular solution counterparts. Utilizing proline as the chiral catalyst, enantioselectivities remained below 80% ee. In this study, the reaction conditions were optimized by determining the optimal capsule loading and HCl content. Additionally, it was found that alcohol additives increase the enantioselectivity of the capsule-catalysed reaction. As a result, we report enantioselectivities of up to 92% ee for iminium-catalysed 1,4-reductions relying on proline as the sole chiral source. This is of high interest, as proline is unable to deliver high enantioselectivities for 1,4-reductions in a regular solution setting. Investigations into the role of the alcohol additive revealed a dual role: it not only slowed down the background reaction but also increased the capsule-catalysed reaction rate.

| S-EPMC8278068 | biostudies-literature

Thermodynamic and kinetic modeling of transcriptional pausing.

Project description:We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived from structural models of the transcription elongation complex (EC). Our algorithm is based on the thermodynamic stability of the EC along the DNA template calculated from the sequence-dependent free energy of DNA-DNA, DNA-RNA, and RNA-RNA base pairing associated with (i) the translocational and size fluctuations of the transcription bubble; (ii) changes in the associated DNA-RNA hybrid; and (iii) changes in the cotranscriptional RNA secondary structure upstream of the RNA exit channel. The calculations involve no adjustable parameters except for a cutoff used to discriminate paused from nonpaused complexes. When applied to 100 experimental pauses in transcription elongation by Escherichia coli RNA polymerase on 10 DNA templates, the approach produces statistically significant results. We also present a kinetic model for the rate of recovery of backtracked paused complexes. A crucial ingredient of our model is the incorporation of kinetic barriers to backtracking resulting from steric clashes of EC with the cotranscriptionally generated RNA secondary structure, an aspect not included explicitly in previous attempts at modeling the transcription elongation process.

| S-EPMC1450190 | biostudies-literature

Sesquiterpene Cyclisations Catalysed inside the Resorcinarene Capsule and Application in the Short Synthesis of Isolongifolene and Isolongifolenone.

Project description:Terpenes constitute the largest class of natural products and serve as an important source for medicinal treatments. Despite constant progress in chemical synthesis, the construction of complex polycyclic sesqui- and diterpene scaffolds remains challenging. Natural cyclase enzymes, however, are able to form the whole variety of terpene structures from just a handful of linear precursors. Man-made catalysts able to mimic such natural enzymes are lacking. Here, we describe the examples of sesquiterpene cyclisations inside an enzyme-mimicking supramolecular catalyst. This strategy allowed the formation of the tricyclic sesquiterpene isolongifolene in only four steps. The mechanism of the catalysed cyclisation reaction was elucidated using 13C-labelling studies and DFT calculations.

| S-EPMC6130823 | biostudies-literature

Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway.

Project description:The past decade has seen a wealth of 3D structural information about complex structured RNAs and identification of functional intermediates. Nevertheless, developing a complete and predictive understanding of the folding and function of these RNAs in biology will require connection of individual rate and equilibrium constants to structural changes that occur in individual folding steps and further relating these steps to the properties and behavior of isolated, simplified systems. To accomplish these goals we used the considerable structural knowledge of the folded, unfolded, and intermediate states of P4-P6 RNA. We enumerated structural states and possible folding transitions and determined rate and equilibrium constants for the transitions between these states using single-molecule FRET with a series of mutant P4-P6 variants. Comparisons with simplified constructs containing an isolated tertiary contact suggest that a given tertiary interaction has a stereotyped rate for breaking that may help identify structural transitions within complex RNAs and simplify the prediction of folding kinetics and thermodynamics for structured RNAs from their parts. The preferred folding pathway involves initial formation of the proximal tertiary contact. However, this preference was only ∼10 fold and could be reversed by a single point mutation, indicating that a model akin to a protein-folding contact order model will not suffice to describe RNA folding. Instead, our results suggest a strong analogy with a modified RNA diffusion-collision model in which tertiary elements within preformed secondary structures collide, with the success of these collisions dependent on whether the tertiary elements are in their rare binding-competent conformations.

| S-EPMC5003260 | 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