Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A combined crystallography and DFT study on ring-shaped Cucurbit[n]urils: structures, surface character, and host-guest recognition.

ABSTRACT: A combined crystallography and DFT study of cucurbit[n]urils (n = 5-8, 10) was carried out, and PBE0 was certified to be the most rational density functional method for optimization task. Steric hindrance and electronic effect of the hindered lone pair electrons in cucurbit[n]urils were qualitatively measured by bond order analysis, lone pair electron (LP) visualization and electrostatic potential (ESP) study. Together with energy decomposition analysis of some selected host-guest systems, we quantitatively verified the effect of size/cavity and noncovalent interaction in host-guest recognition. This solid study revealed that lone pairs electrons affect not only on host-guest identification mode but also on geometry stability, which pave the avenue for further sophisticated applications.

SUBMITTER: Zhu G

PROVIDER: S-EPMC8965660 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A combined crystallography and DFT study on ring-shaped Cucurbit[n]urils: structures, surface character, and host-guest recognition.

Zhu Guoxun G You Ao A Song Huacan H Li Zhengquan Z

RSC advances 20220330 16

A combined crystallography and DFT study of cucurbit[n]urils (n = 5-8, 10) was carried out, and PBE0 was certified to be the most rational density functional method for optimization task. Steric hindrance and electronic effect of the hindered lone pair electrons in cucurbit[n]urils were qualitatively measured by bond order analysis, lone pair electron (LP) visualization and electrostatic potential (ESP) study. Together with energy decomposition analysis of some selected host ...[more]

PMID: 35424911

Similar Datasets

Metal-Assisted Complexation of Fluorogenic Dyes by Cucurbit[7]uril and Cucurbit[8]uril: A DFT Evaluation of the Key Factors Governing the Host-Guest Recognition.

Project description:With the emergence of host-guest systems, a novel branch of complexation chemistry has found wide application in industries such as food, pharmacy, medicine, environmental protection and cosmetics. Along with the extensively studied cyclodextrins and calixarenes, the innovative cucurbiturils (CB) have enjoyed increased popularity among the scientific community as they possess even better qualities as cavitands as compared to the former molecules. Moreover, their complexation abilities could further be enhanced with the assistance of metal cations, which can interestingly exert a dual effect on the complexation process: either by competitively binding to the host entity or cooperatively associating with the CB@guest structures. In our previous work, two metal species (Mg2+ and Ga3+) have been found to bind to CB molecules in the strongest fashion upon the formation of host-guest complexes. The current study focuses on their role in the complex formation with three dye molecules: thiazole orange, neutral red, and thioflavin T. Various key factors influencing the process have been recognized, such as pH and the dielectric constant of the medium, the cavity size of the host, Mn+ charge, and the presence/absence of hydration shell around the metal cation. A well-calibrated DFT methodology, solidly based and validated and presented in the literature experimental data, is applied. The obtained results shed new light on several aspects of the cucurbituril complexation chemistry.

| S-EPMC9966945 | biostudies-literature

Broad-Spectrum Extracellular Antiviral Properties of Cucurbit[n]urils.

Project description:Viruses are microscopic pathogens capable of causing disease and are responsible for a range of human mortalities and morbidities worldwide. They can be rendered harmless or destroyed with a range of antiviral chemical compounds. Cucurbit[n]urils (CB[n]s) are a family of macrocycle chemical compounds existing as a range of homologues; due to their structure, they can bind to biological materials, acting as supramolecular "hosts" to "guests", such as amino acids. Due to the increasing need for a nontoxic antiviral compound, we investigated whether cucurbit[n]urils could act in an antiviral manner. We have found that certain cucurbit[n]uril homologues do indeed have an antiviral effect against a range of viruses, including herpes simplex virus 2 (HSV-2), respiratory syncytial virus (RSV) and SARS-CoV-2. In particular, we demonstrate that CB[7] is the active homologue of CB[n], having an antiviral effect against enveloped and nonenveloped species. High levels of efficacy were observed with 5 min contact times across different viruses. We also demonstrate that CB[7] acts with an extracellular virucidal mode of action via host-guest supramolecular interactions between viral surface proteins and the CB[n] cavity, rather than via cell internalization or a virustatic mechanism. This finding demonstrates that CB[7] acts as a supramolecular virucidal antiviral (a mechanism distinct from other current extracellular antivirals), demonstrating the potential of supramolecular interactions for future antiviral disinfectants.

| S-EPMC9578052 | biostudies-literature

Host-guest interactions in nor-seco-cucurbit[10]uril: novel guest-dependent molecular recognition and stereoisomerism.

Project description:The unique monomer and excimer fluorescence emissions of pyrene were first exploited as distinctly photophysical signals to identify the possible diastereomers of guests within nor-seco-cucurbit[10]uril (NS-CB[10]) cavities. Further experiments revealed that balancing the hydrophilic and hydrophobic effects of the guest in aqueous solution can improve the molecular recognition and binding ability of NS-CB[10].

| S-EPMC6664405 | biostudies-literature

Modulating the Nucleated Self-Assembly of Tri-β(3) -Peptides Using Cucurbit[n]urils.

Project description:The modulation of the hierarchical nucleated self-assembly of tri-β(3) -peptides has been studied. β(3) -Tyrosine provided a handle to control the assembly process through host-guest interactions with CB[7] and CB[8]. By varying the cavity size from CB[7] to CB[8] distinct phases of assembling tri-β(3) -peptides were arrested. Given the limited size of the CB[7] cavity, only one aromatic β(3) -tyrosine can be simultaneously hosted and, hence, CB[7] was primarily acting as an inhibitor of self-assembly. In strong contrast, the larger CB[8] can form a ternary complex with two aromatic amino acids and hence CB[8] was acting primarily as cross-linker of multiple fibers and promoting the formation of larger aggregates. General insights on modulating supramolecular assembly can lead to new ways to introduce functionality in supramolecular polymers.

| S-EPMC6680354 | biostudies-literature

PSMA-Targeted Supramolecular Nanoparticles Prepared From Cucurbit[8]uril-Based Ternary Host-Guest Recognition for Prostate Cancer Therapy.

Project description:Nanomedicines play an important role in cancer therapy; however, some drawbacks including unsatisfactory efficacy and side effects arising from indiscriminate drug release retard their clinical applications. Although functionalization of nanomedicines through covalent interactions can improve the pharmacokinetics and efficacy of the loaded drugs, complicated and tedious synthesis greatly limits the exploration of multifunctional nanoparticles. Herein, we utilize a supramolecular strategy to design a nanomedicine for targeted drug delivery through cucurbit[8]uril-based host-guest ternary complexation and successfully prepare prostate-specific membrane antigen (PSMA)-targeted supramolecular nanoparticles encapsulating doxorubicin (DOX). In vitro studies exhibit targeted modification via noncovalent enhance anticancer efficiency of DOX due to the increased cell uptake on account of receptor-mediated endocytosis. This design provides a new strategy for the development of sophisticated drug delivery systems and holds perspective potentials in precise cancer treatments.

| S-EPMC8867089 | biostudies-literature

Evaluation of the complexation behaviour among functionalized diphenyl viologens and cucurbit[7] and [8]urils.

Project description:The complexation behaviour of Diphenyl viologens (DPVs) with Cucurbit[n]urils (CB[n]) was evaluated in detail and the results were reported. In this work, we present the synthesis of various DPVs functionalised with electron withdrawing and electron donating groups (EWGs & EDGs) and investigate their complexation behaviour with CB[7] and CB [8]. Carboxylic acid functionalized DPV's (DPV-COOH) complexation with CB[8] gives additional insights, i.e., indicates hydrogen bonding plays an effective role in the complexation. The formation of a 2:2 quaternary complex of DPV-COOH/CB[8] under neutral pH conditions was supported by various analytical techniques. The complexation of DPVs with CB[7] specifies that irrespective of the functional group attached, they all form a 1:2 ternary complex, but the findings elaborate that the pattern followed in the complexation depends on the EW or EDG attached to the DPVs. The competition experiments conducted between functionalized DPVs and CB[7], CB[8] shows that they have more affinity towards CB[8] than CB[7] because of the better macrocyclic confinement effect of CB[8], as confirmed using UV-Vis spectroscopy. The binding affinity among EWG and EDG functionalised DPVs with CB[8] concludes EDG functionalised DPVs show better affinity towards CB[8], because they can form a charge transfer complex inside the CB[8] cavity. Exploring these host-guest interactions in more complex biological or environmental settings and studying their impact on the functionality of DPVs could be an exciting avenue for future research.

| S-EPMC10924918 | biostudies-literature

Controllable Synthesis and Catalytic Performance of Gold Nanoparticles with Cucurbit[n]urils (n = 5⁻8).

Project description:A series of gold nanoparticles (AuNPs) was prepared in situ with different cucurbit[n]urils (CB[n]s) in an alkaline aqueous solution. The nanoparticle sizes can be well controlled by CB[n]s (n = 5, 6, 7, 8) with different ring sizes. The packing densities of CB[5⁻8] and free surface area on AuNPs were determined. A direct relationship was found between the ring size and packing density of CB[n]s with respect to the AuNP-catalyzed reduction of 4-nitrophenol in the presence of NaBH₄. The larger particle size and higher surface coverage of bigger CB[n]-capped AuNPs significantly decreased the catalytic activity. Furthermore, this work could lead to new applications that utilize AuNPs under an overlayer of CB[n]s for catalysis, sensing, and drug delivery.

| S-EPMC6316165 | biostudies-literature

A DFT-Assisted Topological Analysis of Four Polymorphic, S-Shaped Aβ42 Fibril Structures.

Project description:Amyloid β 42 (Aβ42) is an inherently disordered peptide, whose toxic actions are believed to play important roles in the etiology of Alzheimer's disease. Four fibril structures of the peptide that display broadly similar characteristics were recently published, but a systematic comparison of these structures is lacking. In this paper, a topological framework was created to enable such understanding and produced new insights into subtle structural elements that underlie the overall structural diversity. A DFT-based analysis illuminated some of the energetic differences that arise as a consequence.

| S-EPMC6713286 | biostudies-literature

Generation of hexagonal close-packed ring-shaped structures using an optical vortex.

Project description:An optical vortex possesses a ring-shaped spatial profile and orbital angular momentum (OAM) owing to its helical wavefront. This form of structured light has garnered significant attention in recent years, and it has enabled new investigations in fundamental physics and applications. One such exciting application is laser-based material transfer for nano-/micro-fabrication. In this work, we demonstrate the application of a single-pulse optical vortex laser beam for direct printing of ring-shaped structures composed of hexagonal close-packed, mono-/multi-layered nanoparticles which exhibit 'structural color'. We compare and contrast the interaction of the vortex beam with both dielectric and metallic nanoparticles and offer physical insight into how the OAM of vortex beams interacts with matter. The demonstrated technique holds promise for not only photonic-based nano-/micro-fabrication, but also as a means of sorting particles on the nanoscale, a technology which we term 'optical vortex nanoparticle sorting'.

| S-EPMC11501167 | biostudies-literature

Host-guest complexation of cucurbit[8]uril with two enantiomers.

Project description:Host-guest complexation of cucurbit[8]uril (Q[8]) with two enantiomers, D-3-(2-naphthyl)-alanine (D-NA) and L-3-(2-naphthyl)-alanine (L-NA), has been fully investigated. Experimental data indicate that double guests reside within the cavity of Q[8] in both aqueous solution and solid state, generating highly stable homoternary complexes D-NA2@Q[8] and L-NA2@Q[8].

| S-EPMC5353740 | biostudies-literature