ChemRxiv
Not a member yet
27047 research outputs found
Sort by
Ligand-Induced Folding in a Dopamine-Binding DNA Aptamer
No full textAptamers are often employed as a molecular recognition element in the development of different
types of biosensors. Many of these biosensors take advantage of the aptamer having a ligand induced structure-formation binding mechanism. However, this binding mechanism is poorly
understood. Here we use isothermal titration calorimetry and NMR spectroscopy to study the
binding and ligand-induced structural change exhibited by the dopamine-binding DNA aptamer. We
analysed a series of aptamers where we shorten the terminal stem that contains the 5’ and 3’ termini
of the aptamer sequence. All aptamers bind dopamine in an enthalpically driven process
compensated by an unfavorable entropy. A general trend of the aptamer having a weaker binding
affinity is observed as the terminal stem is shortened. For all aptamers studied, numerous signals
appear in the imino region of the 1H NMR spectrum indicating that new structure forms with ligand
binding. However, it is only when this region of structure formation in the aptamer is brought close
to the sensor surface that we obtain a functional electrochemical aptamer-based biosensor
Multistep Enzymatic Low-density Polyethylene Degradation via Phenylalanine Monooxygenase and Isocitrate Lyase in Pseudomonas aeruginosa
No full textPlastics have become indispensable in modern industries; however, their resistance to natural degradation poses environmental challenges. Biological degradation technologies employing microorganisms offer promising solutions. Here, we analyzed the transcriptome and proteome of Pseudomonas aeruginosa, a plastic-degrading microorganism found in the gut of superworms, to identify the genes and enzymes upregulated during polyethylene degradation. Functional analyses of these upregulated genes and enzymes using the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology databases revealed an increase in lipid and hydrophobic amino acid metabolism, suggesting their involvement in polyethylene degradation. Based on these analyses, we identified phenylalanine monooxygenase, which is capable of oxidizing plastics, and isocitrate lyase, which is involved in C-C bond cleavage. To investigate the involvement of these enzymes in polyethylene degradation, phhA and aceA were transformed into Escherichia coli, and the enzymes were produced and purified. The purified enzymes were then reacted with polyethylene and analyzed. The results revealed the formation of hydroxyl (-OH) and C-O groups on the polyethylene surface after treatment with phenylalanine monooxygenase, confirming its ability to oxidize polyethylene. Isocitrate lyase alone did not affect polyethylene production; however, when combined with phenylalanine monooxygenase, it contributed to a reduction in molecular weight. This suggests a two-stage process of polyethylene degradation involving oxidation and depolymerization that requires sequential action of multiple enzymes. Thus, we identified the enzymes involved in each stage and demonstrated the degradation ability of polyethylene using purified enzymes
Femtosecond core-level spectroscopy reveals involvement of triplet states in the gas-phase photodissociation of Fe(CO)5
No full textExcitation of iron pentacarbonyl [Fe(CO)5], a prototypical photocatalyst, at 266 nm causes sequential loss of two CO ligands in the gas phase, creating catalytically active, unsaturated iron carbonyls. Despite numerous studies, major aspects of its ultrafast photochemistry remain unresolved because the early excited-state dynamics have so far eluded spectroscopic observation. This has led to the long-held assumption that ultrafast dissociation of gas-phase Fe(CO)5 proceeds exclusively on the singlet manifold. Herein, we present a combined experimental-theoretical study employing ultrafast extreme ultraviolet transient absorption spectroscopy near the Fe M2 ,3-edge, which features spectral evolution on 100-fs and 3-ps time scales, alongside high-level electronic structure theory, which enables characterization of the molecular geometries and electronic states involved in the ultrafast photodissociation of Fe(CO)5. We assign the 100-fs evolution to spectroscopic signatures associated with intertwined structural and electronic dynamics on the singlet metal-centered states during first CO loss, and the
3-ps evolution to the competing dissociation of Fe(CO)4 along the lowest singlet and triplet surfaces to form Fe(CO)3. Calculations of transient spectra in both singlet and triplet states as well as spin-orbit coupling constants along key structural pathways, provide evidence for intersystem crossing to the triplet ground state of Fe(CO)4. Thus, our work presents the first spectroscopic detection of transient excited states during ultrafast photodissociation of gas-phase Fe(CO)5 and challenges the long-standing assumption that triplet states do not play a role in the ultrafast dynamics
Prioritization of early-stage research and development of a hydrogel-encapsulated anaerobic technology for distributed treatment of high strength organic wastewater
No full textThis study aims to support the prioritization of research and development (R&D) pathways of hydrogel-encapsulated anaerobic technology to treat high-strength organic industrial wastewaters, enabling decentralized energy recovery and treatment to reduce organic loading on centralized treatment facilities. To characterize the sustainability implications of early-stage design decisions and to delineate R&D targets, an encapsulated anaerobic process model was developed and coupled with design algorithms for integrated process simulation, techno-economic analysis (TEA), and life cycle assessment (LCA) under uncertainty. Across the design space, a single-stage configuration with passive biogas collection was found to have the greatest potential for financial viability and the lowest life cycle carbon emission. Through robust uncertainty and sensitivity analyses, hydraulic retention time (HRT) and encapsulant volume were identified as the most impactful design decisions for the levelized cost and carbon intensity of chemical oxygen demand (COD) removal. Encapsulant longevity, a technological parameter, was the dominant driver of system sustainability and thus a clear R&D priority. Ultimately, we found encapsulated anaerobic systems with optimized fluidized bed design have significant potential to provide affordable, carbon-negative, distributed COD removal from high strength organic wastewaters if encapsulant longevity can be maintained at 5 years or above
On-Demand Reverse Design of Polymers with PolyTAO
No full textThe forward screening and reverse design of drug molecules, inorganic molecules, and polymers with enhanced properties are vital for accelerating the transition from laboratory research to market application. Specifically, due to the scarcity of large-scale datasets, the discovery of polymers via materials informatics is particularly challenging. Nonetheless, scientists have developed various machine learning models for polymer structure-property relationships using only small polymer datasets, thereby advancing the forward screening process of polymers. However, the success of this approach ultimately depends on the diversity of the candidate pool, and exhaustively enumerating all possible polymer structures through human imagination is impractical. Consequently, achieving on-demand reverse design of polymers is essential.
In this work, we curate an immense polymer dataset containing nearly one million polymeric structure-property pairs based on expert knowledge. Leveraging this dataset, we propose a Transformer-Assisted Oriented pretrained model for on-demand polymer generation (PolyTAO). This model produces polymers with 99.27% chemical validity in top-1 generation mode (approximately 200k generated polymers), representing the highest reported success rate among polymer generative models. Additionally, the average R2 between the properties of the generated polymers and their expected values across 15 predefined properties is 0.96.
To further evaluate the pretrained model\u27s performance in generating polymers with additional user-defined properties for downstream tasks, we conduct fine-tuning experiments on three publicly available small polymer datasets using both semi-template and template-free generation paradigms. Through these extensive experiments, we demonstrate that our pretrained model and its fine-tuned versions are capable of achieving on-demand reverse design of polymers with specified properties, whether in semi-template generation or the more challenging template-free generation scenarios, showcasing its potential as a unified pretrained foundation model for polymer generation
Synchronized Photoluminescence and Electrical Mobility Enhancement in 2D WS2 through Sequence-Specific Chemical Passivation
No full textTwo-dimensional (2D) semiconducting dichalcogenides hold exceptional promise as optoelectronic materials for next-generation electronic and photonic devices, as well as their hybrid circuits. Despite this potential, the pervasive presence of defects in 2D dichalcogenides results in carrier mobility and photoluminescence (PL) that fall significantly short of theoretical predictions. Although defect passivation offers a potential solution, its effects have been inconsistent. This inconsistency arises from the current materials and methods, which fail to achieve the desired binding chemistry and band structure engineering necessary to enhance optical and electrical properties simultaneously. In this work, we uncover new binding chemistry using a sequence-specific chemical passivation (SSCP) protocol based on 2-furanmethanothiol (FSH) and bis(trifluoromethane) sulfonimide lithium salt (Li-TFSI), which allows us to demonstrate a synchronized 100-fold enhancement in both carrier mobility and photoluminescence (PL) in WS2 monolayers. We propose a novel synergistic defect passivation mechanism, supported by ultrafast transient absorption spectroscopy (TA), Hard X-ray photoelectron spectroscopy (HAXPES), and density functional theory (DFT) calculations. Our findings establish a new performance benchmark for the optical and electronic properties of WS2 monolayers, paving the way for the development of more efficient and sustainable 2D semiconductor technologies
Metal-Organic Framework (MOF)-based Smart E-textile Supercapacitors
No full textWearable electronic textiles, also known as e-textiles, have surfaced as a promising means of seamless and unobstructed incorporation of electronic health monitoring gadgets into our daily routines. Yet, creating high-performance and flexible energy storage solutions still presents a notable hurdle in advancing these technologies. Nevertheless, creating efficient, adaptable, and expandable energy storage solutions continues to pose a noteworthy obstacle in powering these devices. This study demonstrates a facile strategy to design and fabricate MOF-based smart wearable e-textiles for all-solid-state textile supercapacitors. We report the fabrication of highly flexible and washable e-textiles by exploiting screen printing, pad-dry coating and inkjet print technology utilising a standalone MOF. The fabricated e-textiles were used as electrodes for an all-solid-state textile supercapacitor. The high areal capacitance of ~221.51 mF cm-2, ~359.4 mF cm-2 and ~353.5 mF cm-2 were achieved at a scan rate of 1 mVs-1 for screen print, pad-dry coating and inkjet printing technology respectively. With high energy densities of ~123.06 µWh cm−2 (screen print), ~199.66 µWh cm−2 (coating) and ~196.39 µWh cm−2 (inkjet print) and very high-power densities ~55 377.5 µW cm−2 (screen print) ~55 291.54 µW cm−2 (coating) ~54 385.38 µW cm−2 (inkjet print), the supercapacitors also showed outstanding capacitance retention (⁓97.4-97.9%) after 1 000 cycles. Our findings successfully demonstrate the potential of MOF-based smart textiles for wearable electronics applications, especially opening a new pathway for high-performance textile-based energy storage solutions
A Voltage-Controlled Strategy for Modular Shono-Type Amination
No full textShono-type oxidation to generate functionalized heterocycles is a powerful method for late-stage diversification of relevant pharmacophores; how-ever, development beyond oxygen-based nucleophiles remains underdeveloped. The limited scope can often be ascribed to constant current electrolysis resulting in potential drifts that oxidize a desired nucleophilic partner. Herein, we report a voltage-controlled strategy to selectively oxidize a broad scope of substrates, enabling modular C–N bond formation from protected amine nucleophiles. We implement an electroanalytically-guided workflow using cyclic voltammetry (CV) and differential pulse voltammetry (DPV) to identify oxidation potentials across a range of heterocyclic substrates. Controlled potential electrolysis (CPE) selectively generates -functionalized C–N products in moderate to good yields using carbamate-, sulfonamide-, and benzamide-derived nucleophiles. The importance of voltage control is further exemplified in two cases: (1) change in selectivity at different potentials with a morpholine substrate and (2) analysis of reaction outcomes between Celecoxib and an N-Boc or N-Ns-pyrrolidine substrate; the latter requires a potential more anodic than Celecoxib and does not yield desired product. Lastly, sequential voltage-controlled C–N and C–O functionalization of a model substrate generates difunctionalized pyrrolidines further broadening the utility of this reaction
Cu(II)/THPTA-Mediated Thiazolidine Deprotection for Living Phages and Cell Surfaces Labeling
No full textIncorporating unnatural bioorthogonal groups into peptides and proteins offers an excellent opportunity to endow them with new properties in a precise and controlled manner. Among these, the α-oxo aldehyde group is particularly suitable for the post-functionalization of peptides and proteins due to its versatility and stability in aqueous buffers. However, the facile and site-specific incorporation of α-oxo aldehyde into proteins, especially in living systems, remains a long-lasting challenge. Here, we describe a novel Cu(II)/THPTA-Mediated Thiazolidine Deprotection (CUT-METHOD) strategy for post-installation of a highly-active α-oxo aldehyde moiety, which is released from a thiazolidine ring borne by a genetically encoded unnatural amino acid ThzK. This reaction is performed under physiological conditions, thereby enabling the chemoselective and site-specific modification of proteins via oxime ligation without compromising their integrity and function. To validate its versatility, we successfully performed site-specific incorporation of α-oxo aldehyde into recombinant proteins and those displayed on M13 filamentous bacteriophage particles and bacterial cell surfaces. In addition, by leveraging Spycatcher/Spytag chemistry and oxime ligation, the bacterial cells bearing aldehyde generated via the CUT-METHOD could be simultaneously decorated with two distinct functional molecules, providing a novel one-pot dual labeling platform for the construction of living bacterial cell-based cancer targeting systems. Put together, we have demonstrated that the CUT-METHOD strategy is a significant addition to the current bioorthogonal chemistry toolbox with broad applications anticipated in the near future
Photosensitizer-Free Singlet Oxygen Generation via Charge Transfer Transition involving Molecular O2 toward Highly Efficient Oxidative Coupling of Arylamines to Azoaromatics
No full textPhotosensitizer (PS)‐mediated generation of singlet oxygen, O2 (a1Δg) is a well‐explored phenomenon in chemistry and biology. However, the requirement of appropriate PS with optimum excited state properties is a prerequisite of this approach which limits its widespread application. Herein, we report the generation of O2 (a1Δg) via direct charge-transfer (CT) excitation of solvent‐O2 (X3Σ_g^-) collision complex without any PS and utilize it for the catalyst-free oxidative coupling of arylamines to azoaromatics under ambient conditions in aqueous medium. The electron paramagnetic resonance (EPR) spectroscopy revealed the formation of O2 (a1Δg) upon direct excitation with 370 nm light. The present approach shows broad substrate scope, fast reaction kinetics (90 min), high selectivity (100%), excellent yields (up to 100%), and works well for both homo‐ and hetero‐coupling of arylamines. The oxidative coupling of arylamines was found to proceed through the generation of amine radicals via electron transfer (ET) from amines to O2 (a1Δg). Notably, electron‐rich amines show higher yields of azo products compared to electron‐deficient amines. Detailed mechanistic investigations using various spectroscopic tools revealed the formation of hydrazobenzene as an intermediate along with superoxide radicals which subsequently transform to hydrogen peroxide. The present study is unique in a way that molecular O2 simultaneously acts as a light absorbing chromophore (solvent‐O2 complex) as well as an efficient oxidant (O2 (a1Δg)) in the same reaction. This is the first report for the efficient, selective, and sustainable synthesis of azo compounds in aqueous medium under an ambient atmosphere without any PCs/PSs and paves the way for further in-depth understanding of the chemical reactivity of O2 (a1Δg) generated directly via CT excitation of solvent‐O2 complex toward various photochemical and photobiological transformations