Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Large-Scale Flow Photochemical Synthesis of Functionalized trans-Cyclooctenes Using Sulfonated Silica Gel.

ABSTRACT: Functionalized trans-cyclooctenes are useful bioorthogonal reagents that are typically prepared using a flow photoisomerization method where the product is captured by AgNO₃ on silica gel. While this method is effective, the leaching of silver can be problematic when scaling up syntheses. It is shown here that Ag(I) immobilized on tosic silica gel can be used to capture trans-cyclooctene products at higher loadings without leaching. It is demonstrated that the sulfonated silica gel can be regenerated and reused with similar yields over multiple runs. Nine different trans-cyclooctenes were synthesized, including those commonly utilized in bioorthogonal chemistry as well as new amine and carboxylic acid derivatives.

SUBMITTER: Darko A

PROVIDER: S-EPMC8224989 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Three-Dimensional Large-Scale Fused Silica Microfluidic Chips Enabled by Hybrid Laser Microfabrication for Continuous-Flow UV Photochemical Synthesis.

Project description:We demonstrate a hybrid laser microfabrication approach, which combines the technical merits of ultrafast laser-assisted chemical etching and carbon dioxide laser-induced in situ melting for centimeter-scale and bonding-free fabrication of 3D complex hollow microstructures in fused silica glass. With the developed approach, large-scale fused silica microfluidic chips with integrated 3D cascaded micromixing units can be reliably manufactured. High-performance on-chip mixing and continuous-flow photochemical synthesis under UV irradiation at ~280 nm were demonstrated using the manufactured chip, indicating a powerful capability for versatile fabrication of highly transparent all-glass microfluidic reactors for on-chip photochemical synthesis.

| S-EPMC9026117 | biostudies-literature

Efficient low-cost preparation of <i>trans</i>-cyclooctenes using a simplified flow setup for photoisomerization.

Project description:AbstractBioorthogonal ligations have emerged as highly versatile chemical tools for biomedical research. The exceptionally fast reaction between 1,2,4,5-tetrazines and trans-cyclooctenes (TCOs), also known as tetrazine ligation, is frequently used in this regard. Growing numbers of applications for the tetrazine ligation led to an increased demand for TCO compounds, whose commercial availability is still very limited. Reported photochemical procedures for the preparation of TCOs using flow chemistry are straightforward and high yielding but require expensive equipment. Within this contribution, we present the construction and characterization of a low-cost flow photoreactor assembled from readily accessible components. Syntheses of all commonly used trans-cyclooctene derivatives were successfully carried out using the described system. We are convinced that the presented system for photoisomerization will promote access to bioorthogonally reactive TCO derivatives.Graphical abstract

| S-EPMC4785212 | biostudies-literature

A photochemical flow reactor for large scale syntheses of aglain and rocaglate natural product analogues.

Project description:Herein, we report the development of continuous flow photoreactors for large scale ESIPT-mediated [3+2]-photocycloaddition of 2-(p-methoxyphenyl)-3-hydroxyflavone and cinnamate-derived dipolarophiles. These reactors can be efficiently numbered up to increase throughput two orders of magnitude greater than the corresponding batch reactions.

| S-EPMC5696104 | biostudies-literature

The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material.

Project description:Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.

| S-EPMC7238428 | biostudies-literature

Enhancing reactivity for bioorthogonal pretargeting by unmasking antibody-conjugated trans-cyclooctenes.

Project description:The bioorthogonal cycloaddition reaction between tetrazine and trans-cyclooctene (TCO) is rapidly growing in use for molecular imaging and cell-based diagnostics. We have surprisingly uncovered that the majority of TCOs conjugated to monoclonal antibodies using standard amine-coupling procedures are nonreactive. We show that antibody-bound TCOs are not inactivated by trans-cis isomerization and that the bulky cycloaddition reaction is not sterically hindered. Instead, TCOs are likely masked by hydrophobic interactions with the antibody. We show that introducing TCO via hydrophilic poly(ethylene glycol) (PEG) linkers can fully preserve reactivity, resulting in >5-fold enhancement in functional density without affecting antibody binding. This is accomplished using a novel dual bioorthogonal approach in which heterobifunctional dibenzylcyclooctyne (DBCO)-PEG-TCO molecules are reacted with azido-antibodies. Improved imaging capabilities are demonstrated for different cancer biomarkers using tetrazine-modified fluorophore and quantum dot probes. We believe that the PEG linkers prevent TCOs from burying within the antibody during conjugation, which could be relevant to other bioorthogonal tags and biomolecules. We expect the improved TCO reactivity obtained using the reported methods will significantly advance bioorthogonal pretargeting applications.

| S-EPMC5022565 | biostudies-literature

Theoretical Studies of a Silica Functionalized Acrylamide for Calcium Scale Inhibition.

Project description:The calcium carbonate (CaCO3) scale is one of the most common oilfield scales and oil and gas production bane. CaCO3 scale can lead to a sudden halt in production or, worst-case scenario, accidents; therefore, CaCO3 scale formation prevention is essential for the oil and gas industry. Scale inhibitors are chemicals that can mitigate this problem. We used two popular theoretical techniques in this study: Density Functional Theory (DFT) and Ab Initio Molecular Dynamics (AIMD). The objective was to investigate the inhibitory abilities of mixed oligomers, specifically acrylamide functionalized silica (AM-Silica). DFT studies indicate that Ca2+ does not bind readily to acryl acid and acrylamide; however, it has a good binding affinity with PAM and Silica functionalized PAM. The highest binding affinity occurs in the silica region and not the -CONH functional groups. AIMD calculations corroborate the DFT studies, as observed from the MD trajectory that Ca2+ binds to PAM-Silica by forming bonds with silicon; however, Ca2+ initially forms a bond with silicon in the presence of water molecules. This bonding does not last long, and it subsequently bonds with the oxygen atoms present in the water molecule. PAM-Silica is a suitable calcium scale inhibitor because of its high binding affinity with Ca2+. Theoretical studies (DFT and AIMD) have provided atomic insights on how AM-Silica could be used as an efficient scale inhibitor.

| S-EPMC9230130 | biostudies-literature

Fluorogenic Bifunctional trans-Cyclooctenes as Efficient Tools for Investigating Click-to-Release Kinetics.

Project description:The inverse electron demand Diels-Alder pyridazine elimination reaction between tetrazines and allylic substituted trans-cyclooctenes (TCOs) is a key player in bioorthogonal bond cleavage reactions. Determining the rate of elimination of alkylamine substrates has so far proven difficult. Here, we report a fluorogenic tool consisting of a TCO-linked EDANS fluorophore and a DABCYL quencher for accurate determination of both the click and release rate constants for any tetrazine at physiologically relevant concentrations.

| S-EPMC7496853 | biostudies-literature

Amine-Functionalized Nanoporous Silica Monoliths for Heterogeneous Catalysis of the Knoevenagel Condensation in Flow.

Project description:Porous carrier materials functionalized with organocatalysts offer substantial advantages compared to homogeneous catalysts, e.g., easy separation of the catalyst, scalability, and an improved implementation in continuous operations. Here, we report the immobilization of (3-aminopropyl)trimethoxysilane (APTMS) onto self-prepared silica monoliths and its application as a heterogeneous catalyst in the Knoevenagel condensation between cyano ethylacetate and various aromatic aldehydes under continuous-flow conditions. The meso-macroporous silica monoliths (6-7 cm in length) were optimized to be used in flow taking advantage of their hierarchical meso- and macroporosity. The monoliths were cladded with a poly(ether ether ketone) (PEEK) tube by a refined procedure to guarantee tight connection between the carrier material and PEEK. Functionalization of the bare silica monoliths consisting of APTMS can be efficiently performed in flow in ethanol and toluene. While a large grafting gradient is obtained for toluene, the grafting in ethanol proceeds homogenously throughout the monolith, as evidenced by elemental analysis and time-of-flight secondary ion mass spectrometry (ToF-SIMS). The silica monoliths exhibit high conversion up to 95% with concurrent low back pressures, which is of importance in flow catalysis. By connecting two monoliths, high conversions can be maintained for several flow rates. Two types of monoliths were synthesized, possessing different mesopore sizes. The monolith bearing the larger mesopore size showed an enhanced turnover frequency (TOF), while the monolith with the smaller mesopores allowed for larger quantities of the product to be synthesized, due to the higher surface area. A long-term stability test showed that the functionalized monoliths were still active after 66 h of continuous usage, while the overall yield decreased over time.

| S-EPMC7807742 | biostudies-literature

96 mRRBS libraries: Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA

Project description:Sequencing based approaches have led to new insights about DNA methylation. While many different techniques for genome-scale mapping of DNA methylation have been employed, throughput has been a key limitation for most. To further facilitate the mapping of DNA methylation, we describe a protocol for gel-free multiplexed reduced representation bisulfite sequencing (mRRBS) that reduces the workload dramatically and enables processing of 96 or more samples per week. mRRBS achieves similar CpG coverage as the original RRBS protocol, while the higher throughput and lower cost make it better suited for large-scale DNA methylation mapping studies including cohorts of cancer samples.

2012-08-29 | GSE40429 | GEO