Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Elucidating dissociation activation energies in host-guest assemblies featuring fast exchange dynamics.

ABSTRACT: The ability to mediate the kinetic properties and dissociation activation energies (E _a) of bound guests by controlling the characteristics of "supramolecular lids" in host-guest molecular systems is essential for both their design and performance. While the synthesis of such systems is well advanced, the experimental quantification of their kinetic parameters, particularly in systems experiencing fast association and dissociation dynamics, has been very difficult or impossible with the established methods at hand. Here, we demonstrate the utility of the NMR-based guest exchange saturation transfer (GEST) approach for quantifying the dissociation exchange rates (k _out) and activation energy (E _a,out) in host-guest systems featuring fast dissociation dynamics. Our assessment of the effect of different monovalent cations on the extracted E _a,out in cucurbit[7]uril:guest systems with very fast k _out highlights their role as "supramolecular lids" in mediating a guest's dissociation E _a. We envision that GEST could be further extended to study kinetic parameters in other supramolecular systems characterized by fast kinetic properties and to design novel switchable host-guest assemblies.

SUBMITTER: Shusterman-Krush R

PROVIDER: S-EPMC8179218 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge.

Project description:In this study, we report binding free energy calculations of various drugs-of-abuse to Cucurbit-[8]-uril as part of the SAMPL8 blind challenge. Force-field parameters were obtained from force-matching with different quantum mechanical levels of theory. The Replica Exchange Umbrella Sampling (REUS) approach was used with a cylindrical restraint to enhance the sampling of host-guest binding. Binding free energy was calculated by pulling the guest molecule from one side of the symmetric and cylindrical host, then into and through the host, and out the other side (bidirectional) as compared to pulling only to the bound pose inside the cylindrical host (unidirectional). The initial results with force-matched MP2 parameter set led to RMSE of 4.68 [Formula: see text] from experimental values. However, the follow-up study with CHARMM generalized force field parameters and force-matched PM6-D3H4 parameters resulted in RMSEs from experiment of [Formula: see text] and [Formula: see text], respectively, which demonstrates the potential of REUS for accurate binding free energy calculation given a more suitable description of energetics. Moreover, we compared the free energies for the so called bidirectional and unidirectional free energy approach and found that the binding free energies were highly similar. However, one issue in the bidirectional approach is the asymmetry of profile on the two sides of the host. This is mainly due to the insufficient sampling for these larger systems and can be avoided by longer sampling simulations. Overall REUS shows great promise for binding free energy calculations.

| S-EPMC8131287 | biostudies-literature

Superstructured Biomaterials Formed by Exchange Dynamics and Host-Guest Interactions in Supramolecular Polymers.

Project description:Dynamic and reversible assembly of molecules is ubiquitous in the hierarchical superstructures of living systems and plays a key role in cellular functions. Recent work from the laboratory reported on the reversible formation of such superstructures in systems of peptide amphiphiles conjugated to oligonucleotides and electrostatically complimentary peptide sequences. Here, a supramolecular system is reported upon where exchange dynamics and host-guest interactions between β-cyclodextrin and adamantane on peptide amphiphiles lead to superstructure formation. Superstructure formation with bundled nanoribbons generates a mechanically robust hydrogel with a highly porous architecture that can be 3D printed. Functionalization of the porous superstructured material with a biological signal results in a matrix with significant in vitro bioactivity toward neurons that could be used as a supramolecular model to design novel biomaterials.

| S-EPMC8061421 | biostudies-literature

Temperature-sensitive transitions below LCST in amphiphilic dendritic assemblies: host-guest implications.

Project description:Oligo(ethylene glycol)-decorated supramolecular assemblies have been of great interest due to their charge-neutral character and thus their propensity to avoid nonspecific interactions. These systems are known to exhibit a macroscopic temperature-sensitive transition, where the assembly phase-separates from the aqueous phase at higher temperatures. While this so-called lower critical solution temperature (LCST) behavior has been well-studied, there have been no studies on the fate of these supramolecular assemblies below this transition temperature. The work here brings to light the presence of a second, sub-LCST transition, observed well below the LCST of oligo(ethylene glycol) (OEG)-based dendrons, where the host-guest properties of the assembly are significantly altered. This sub-LCST transition is accompanied by changes in the guest encapsulation stability and dynamics of host exchange.

| S-EPMC3706455 | biostudies-literature

Temporal and Triggered Evolution of Host-Guest Characteristics in Amphiphilic Polymer Assemblies.

Project description:An amphiphilic polymer with cleavable side chain and main chain functional groups has been designed and synthesized. Specific cleavage of either of its functional groups was found to have an effect on the morphology of the assembly. Degradation of the main chain is shown to cause morphology of the supramolecular assembly to evolve with time from a micelle-like assembly to a vesicular assembly. On the other hand, stimulus-induced cleavage of the side chains causes these nanoassemblies to disassemble. These temporal (main chain) and triggered (side chain) degradation processes have implications in the design of degradable polymers as supramolecular scaffolds for biological applications.

| S-EPMC4917414 | biostudies-literature

Catalysis of Synergistic Reactions by Host-Guest Assemblies: Reductive Carbonylation of Nitrobenzenes.

Project description:Numerous chemical transformations require two or more catalytically active sites that act in a concerted manner; nevertheless, designing heterogeneous catalysts with such multiple functionalities remains an overwhelming challenge. Herein, it is shown that by the integration of acidic flexible polymers and Pd-metallated covalent organic framework (COF) hosts, the merits of both catalytically active sites can be utilized to realize heterogeneous synergistic catalysis that are active in the conversion of nitrobenzenes to carbamates via reductive carbonylation. The concentrated catalytically active species in the nanospace force two catalytic components into proximity, thereby enhancing the cooperativity between the acidic species and Pd species to facilitate synergistic catalysis. The resulting host-guest assemblies constitute more efficient systems than the corresponding physical mixtures and the homogeneous counterparts. Furthermore, this system enables easy access to a family of important derivatives such as herbicides and polyurethane monomers and can be integrated with other COFs, showing promising results. This study utilizes host-guest assembly as a versatile tool for the fabrication of multifunctional catalysts with enhanced cooperativity between different catalytic species.

| S-EPMC10466335 | biostudies-literature

Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field.

Project description:Molecular recognition is of paramount interest in many applications. Here we investigate a series of host-guest systems previously used in the SAMPL4 blind challenge by using molecular simulations and the AMOEBA polarizable force field. The free energy results computed by Bennett's acceptance ratio (BAR) method using the AMOEBA polarizable force field ranked favorably among the entries submitted to the SAMPL4 host-guest competition [Muddana, et al., J. Comput.-Aided Mol. Des., 2014, 28, 305-317]. In this work we conduct an in-depth analysis of the AMOEBA force field host-guest binding thermodynamics by using both BAR and the orthogonal space random walk (OSRW) methods. The binding entropy-enthalpy contributions are analyzed for each host-guest system. For systems of inordinate binding entropy-enthalpy values, we further examine the hydrogen bonding patterns and configurational entropy contribution. The binding mechanism of this series of host-guest systems varies from ligand to ligand, driven by enthalpy and/or entropy changes. Convergence of BAR and OSRW binding free energy methods is discussed. Ultimately, this work illustrates the value of molecular modelling and advanced force fields for the exploration and interpretation of binding thermodynamics.

| S-EPMC5102783 | biostudies-literature

Amplifying undetectable NMR signals to study host-guest interactions and exchange.

Project description:The characteristics of host-guest systems, such as molecular recognition, complexation, encapsulation, guest composition, and dynamic exchange, are manifested by changes in the chemical shifts (??) in the NMR spectrum. However, in cases where NMR signals cannot be detected, due to low concentrations, poor solubility, or relatively fast exchange, an alternative is needed. Here, we show that by using the magnetization transfer (MT) method, the undetectable NMR signals of host-guest assemblies can be amplified by two orders of magnitude. It is shown that the binding kinetics characteristics of a fluorinated guest and cucurbit[n]uril (CB[n]) hosts in aqueous solutions determine the NMR signal amplification of host-guest assemblies. In addition, by using the MT technique within the 19F-NMR framework, one can detect ?M concentrations of the complex and study the effect of different solutes on the resulting host-guest system. The results expand the "NMR toolbox" available to explore a wider range of dynamic host-guest systems in which NMR signals cannot be detected.

| S-EPMC5450594 | biostudies-literature

Ternary host-guest complexes with rapid exchange kinetics and photoswitchable fluorescence.

Project description:Confinement within molecular cages can dramatically modify the physicochemical properties of the encapsulated guest molecules, but such host-guest complexes have mainly been studied in a static context. Combining confinement effects with fast guest exchange kinetics could pave the way toward stimuli-responsive supramolecular systems-and ultimately materials-whose desired properties could be tailored "on demand" rapidly and reversibly. Here, we demonstrate rapid guest exchange between inclusion complexes of an open-window coordination cage that can simultaneously accommodate two guest molecules. Working with two types of guests, anthracene derivatives and BODIPY dyes, we show that the former can substantially modify the optical properties of the latter upon noncovalent heterodimer formation. We also studied the light-induced covalent dimerization of encapsulated anthracenes and found large effects of confinement on reaction rates. By coupling the photodimerization with the rapid guest exchange, we developed a new way to modulate fluorescence using external irradiation.

| S-EPMC9473544 | biostudies-literature

Host-guest interaction mediated polymeric assemblies: multifunctional nanoparticles for drug and gene delivery.

Project description:Novel core-shell structured nanoassemblies are assembled by a beta-cyclodextrin containing a positively charged host polymer and a hydrophobic guest polymer. The hydrophobic core of these types of assemblies serves as a nanocontainer to load and release the hydrophobic drugs, while the positively charged hydrophilic shell is able to condense the plasmid DNA and achieve its transfection/expression in osteoblast cells. These assemblies may be used as a new generation of multifunctional nanocarriers for simultaneous drug delivery and gene therapy.

| S-EPMC2835570 | biostudies-literature

Flow-induced-crystallization: tailoring host-guest supramolecular co-assemblies at the liquid-solid interface.

Project description:Here, we report that using the method of simply contacting a sample solution droplet with a piece of tissue paper can create a solvent flow (capillary force). During this process, the dynamics and solvent removal can promote the formation and stabilization of a meta-stable linear quasi-crystal composed of p-terphenyl-3,5,3',5'-tetracarboxylic acid (TPTC) molecules, which would otherwise pack into thermodynamically favored random tiling. The tailored quasi-crystal (linear) template allows atop it higher-efficiency accommodation of fullerene molecules (C60) from 40.1% to 97.5%, compared with that obtained in the random-tiling (porous) case. Overall, the result of this study presents an unusual yet remarkably simple strategy for tailoring complex host-guest supramolecular systems at the liquid-solid interface.

| S-EPMC9400487 | 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