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Virtual Ligand-Assisted Optimization: A Rational Strategy for Ligand Engineering ChemRxiv Pub Date : 2024-04-25 Satoshi, Maeda, Wataru, Matsuoka, Taihei, Oki, Ren, Yamada, Tomohiko, Yokoyama, Shinichi, Suda, Yu, Harabuchi, Satoru, Iwata
Ligand engineering is one of the most important, but labor-intensive processes in the development of transition metal catalysis. Historically, this process has been streamlined by the invention of ligand descriptors such as Tolman’s electronic parameter and the cone angle. Analyzing reaction outcomes in terms of these parameters has enabled chemists to find important factors for designing optimal ligands
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De novo design of inhibitors of DNA methyltransferase 1: A critical comparison of ligand- and structure-based approaches ChemRxiv Pub Date : 2024-04-25 José L., Medina-Franco, Diana L., Prado-Romero, Fernanda I., Saldívar-González, Iván, López-Mata, Pedro A., Laurel-García, Norberto, Sánchez-Cruz
Designing and developing inhibitors against the epigenetic target DNA methyltransferase (DNMT) is an attractive strategy in epigenetic drug discovery. DNMT1 is one of the epigenetic enzymes with significant clinical relevance. Structure-based de novo design is a drug discovery strategy used in combination with similarity searching to identify a novel DNMT inhibitor with a novel chemical scaffold and
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Theoretical insight into complexation between cyclocarbons and C60 fullerene ChemRxiv Pub Date : 2024-04-25 Zeyu, Liu, Tian, Lu
This work conducts the comprehensive theoretical study on the non-covalent complexation between cyclocarbons of different sizes and C60 fullerene for the first time. The binding energy between cyclocarbons and C60 fullerene is observed to be significantly stronger than that between two C18 or two C60 fullerenes, indicating a particularly strong affinity between them. The cyclocarbons and C60 fullerene
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Intermolecular Formal [2π+2σ] Cycloaddition of Enol Silyl Ethers with Bicyclo[1.1.0]butanes Promoted by Lewis acids ChemRxiv Pub Date : 2024-04-25 Shi-Wu, Li, Shi-Jie, Zhu, Xue, Tian
A new approach to directly access bicyclo[2.1.1]hexanes (BCHs) from easily prepared enol silyl ethers and bicyclo[1.1.0]butanes (BCBs) through formal [2π+2σ] cycloaddition was developed involving two-electron mediated process promoted by commercially available Lewis acids. This new reaction tolerated a wide range of enol silyl ethers and BCBs. In addition, a scale-up experiment and the synthetic transformations
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CHARMM Molecular Simulation Observations of Carbonaceous Materials as Possible Templates for Prebiotic Nucleic Acid Oligomer Formation ChemRxiv Pub Date : 2024-04-25 Anna, Du, Barnas, Monteith
This research utilizes CHARMM molecular simulations for the purposes of an initial qualitative observational study of diamond-like carbon and related carbonaceous substrates as potential templates for the abiotic formation of RNA polymers,. While a number of research group have looked at nanodiamond, graphite and other carbon and non-carbon-based materials (especially clays) as possible solid templates
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Triptycene-like naphthopleiadene as a readily accessible scaffold for supramolecular and materials chemistry ChemRxiv Pub Date : 2024-04-25 Neil, McKeown, Md Khairul, Amin, Gary, Nichol, Shuhua, Pang, Chunchun, Ye, Yuancheng , Liu
Triptycene derivatives are used extensively in supramolecular and materials chemistry, however, most are prepared using multi-step synthesis involving the generation of a benzyne intermediate, which hinders production on a large scale. Inspired by the ease of the synthesis of resorcinarenes, we report the rapid and efficient preparation of triptycene-like 1,6,2’,7’-tetrahydroxynaphthopleiadene directly
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Radiotherapy Mediated Catalytic Prodrug Therapy with Higher Radiochemical Conversion than Hydrated Electrons ChemRxiv Pub Date : 2024-04-25 Wei, Cao, Jian, Wang, Yin, Liang, Sijie, Wu, Ruotong, Deng, Hanjie, Zhu
Using radiotherapy to activate chemotherapeutic conversion is a promising approach to reduce off-target toxicity in cancer therapy. Current radiation chemistry mostly relies on substrate to react with the primary species of water radiolysis, with the most abundant being hydrated electron (e−aq) and ·OH. However, only 280 nM e−aq is generated by 1 Gy radiation, fundamentally limiting the yield of conventional
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Peptide Macrocyclization via Intramolecular Interception of Visible-Light-Mediated Desulfurization ChemRxiv Pub Date : 2024-04-25 Nicholas, Mitchell, Frances, Smith, Rhys, Griffiths, Declan, Meehan, Harriet , Knowles, Peiyu, Zhang, Huw, Williams, Andrew, Wilson
Synthetic methods that enable the macrocyclisation of peptides facilitate the development of more effective therapeutic and diagnostic tools. Herein we report a peptide cyclisation strategy based on intramolecular interception of visible-light-mediated cysteine desulfurisation. This method allows cyclisation of unprotected peptides in an aqueous solution via the installation of a hydrocarbon linkage
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Borylation and rearrangement reactions of azasilaanthracenes to afford B,N-doped nanographenes ChemRxiv Pub Date : 2024-04-25 Yoann, Olivier, Elena, Zender, Danillo, Valverde, Robert, Neubaur, Sebastian, Karger, Alexander, Virovets, Michael, Bolte, Hans-Wolfram, Lerner, Matthias, Wagner
An air-stable B3,N3-containing dibenzobisanthene (8) was prepared in 29% yield by heating a 1,3,5-tri(azasilaanthryl)benzene (5) with BBr3 (180 °C). Under these conditions, the reaction does not stop after threefold SiMe2/BBr exchange but proceeds further via two rearrangement and two intramolecular C–H borylation steps. Some mechanistic details were unveiled by using smaller model systems and applying
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The paradoxical behavior of rough colloids at fluid interfaces ChemRxiv Pub Date : 2024-04-25 Peter, Beltramo, Md Anisur, Rahman
Colloidal particles adsorb and remain trapped at immiscible fluid interfaces due to strong interfacial adsorption energy, with a contact angle defined by the chemistry of the particle and fluid phases. An undulated contact line may appear due to either particle surface roughness or shape anisotropy, which results in a quadrupolar interfacial deformation and strong long range capillary interaction between
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Tracking Trash to Treasure: In situ monitoring of Single Microbial Cell Oil biosynthesis from Waste Cooking Oil using Raman Reverse Isotope Probing and Imaging ChemRxiv Pub Date : 2024-04-25 SURYA PRATAP, SINGH, Jiro, Karlo, Arto, Koistinen, Victor, Carrasco Navarro
Single microbial cell oil (SMCO) plays a fundamental role in maintaining the structure of cellular membranes and as energy reservoirs. Oleaginous microbes are known to have a high content of lipids, which often acts as a microbial factory for the bioremediation of waste cooking oil (WCO) which is a major pollutant contaminating land and water bodies. The biomass of microbes grown in WCO can be utilized
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Total Synthesis of Carbazomycins E and F ChemRxiv Pub Date : 2024-04-25 Kentaro, Okano, Atsunori, Mori, Yunosuke, Shima, Yuxuan, Feng
Total synthesis of carbazomycins E and F was achieved by double functionalization of an aryne intermediate generated from a 2-aminobiphenyl derivative. The tethered amino group underwent nucleophilic addition to the aryne intermediate to construct the carbazole skeleton. The resulting carbanion was formylated to give the multiply substituted carbazole. This formyl group caused several problems. For
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Validation of the identification reliability of known and assumed UDMH transformation products using gas chromatographic retention indices and machine learning ChemRxiv Pub Date : 2024-04-25 Anastasia, Karnaeva, Anastasia, Sholokhova
Thirty two commercially available standards were used to determine chromatographic retention indices (RIs) for three different stationary phases. The selected compounds were nitrogen-containing heterocycles and amides, which are unsymmetrical dimethylhydrazine (UDMH) transformation products or its assumed transformation products. UDMH is a highly toxic compound widely used in the space industry, that
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Thermally integrated photoelectrochemical devices with perovskite/silicon tandem solar cells: a modular approach for scalable direct water splitting ChemRxiv Pub Date : 2024-04-25 Muriel, Matheron, Angela, Maragno, Adina, Morozan, Jennifer, Fize, Vincent, Artero, Sophie, Charton
Direct solar water splitting appears as a promising route to produce hydrogen avoiding competition for electricity against other important economic uses. Halogenated hybrid perovskites recently enabled the demonstration of efficient and potentially low-cost photoelectrochemical cells and PV-coupled electrolysers, reaching high efficiencies but so far limited to small active area of a few mm2 so far
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Anisotropic porosity and interface synergy enhanced gas permselectivity in heterolayer metal-organic framework membrane ChemRxiv Pub Date : 2024-04-25 Ritesh, Haldar, Susmita, Kundu, Tanmoy, Maity, Suvendu, Panda
The pursuit of sustainable, carbon-free separation technology hinges on the efficient separation of gas mixtures with high separation factors and flow rates, i.e. high permselectivity. However, achieving this objective is arduous due to the meticulous engineering at the angstrom scale and intricate chemical manipulation required to design the pores within membranes. To address this challenge, a proof-of-concept
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Analogies and differences in the photoactivation mechanism of bathy and canonical bacteriophytochromes revealed by multiscale modeling ChemRxiv Pub Date : 2024-04-25 Giacomo, Salvadori, Benedetta, Mennucci
Bacteriophytochromes are light-sensing biological machines that interconvert between two spectroscopically distinct states, Pr and Pfr. The relative stability of the two states is opposite in canonical and bathy bacteriophytochromes but in both cases the switch between them is triggered by a photoisomerization of an embedded bilin chromophore, the effects of which propagate throughout the protein with
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A Macrocyclic Parallel Dimer Showing Quantum Coherence of Quintet Multiexcitons at Room Temperature ChemRxiv Pub Date : 2024-04-25 Nobuhiro, Yanai, Wataru, Ishii, Masaaki, Fuki, Eman, M Bu Ali, Shunsuke, Sato, Bhavesh, Parmar, Akio, Yamauchi, Catherine, Helenna Mulyadi, Masanori, Uji, Samara, Medina Rivero, Go, Watanabe, Jenny, Clark, Yasuhiro, Kobori
Singlet fission (SF) is a promising approach in quantum information science because it can generate spin-entangled quintet triplet pairs by photoexcitation independent of temperature. However, it is still challenging to rationally achieve quantum coherence at room temperature, which requires precise control of the orientation and dynamics of triplet pairs. Here we show that the quantum coherence of
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Quantifying the Seasonal Variation of Environmental Pharmaceutical Residues ChemRxiv Pub Date : 2024-04-25 Tuomas, Nurmi, Toni, Kiljunen
Pharmaceutical substances, among other contaminants drained from wastewater treatment process and entered into aqueous environments, exhibit significant seasonal dependencies in their environmental concentrations. Although measurement data on removal of pharmaceutical residues in wastewater treatment plants and their degradation in the environment thereafter are readily available, the complexity and
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Lewis Acid-Catalyzed Unusual (4+3) Annulation of para-Quinone Methides with Bicyclobutanes: Access to Oxabicyclo [4.1.1]octanes ChemRxiv Pub Date : 2024-04-25 A T, Biju, Shiksha, Deswal, Avishek, Guin
Over the past few years, there has been a surge of interest in the chemistry of bicyclobutanes (BCBs). Although BCBs have been used to synthesize bicyclo[2.1.1]hexanes and bicyclo[3.1.1]heptanes, the synthesis of bicyclo[4.1.1]octanes has re-mained elusive. Herein, we report the first Lewis acid-catalyzed unexpected (4+3) annulation of para-quinonemethides (p-QMs) with BCBs allowing the synthesis of
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Design of metal-organic frameworks using deep dreaming approaches ChemRxiv Pub Date : 2024-04-25 Conor, Cleeton, Lev, Sarkisov
Exploring the expansive and largely untapped chemical space of metal-organic frameworks (MOFs) holds promise for revolutionising the field of materials science. MOFs, hailed for their modular architecture, offer unmatched flexibility in customising functionalities to meet specific application needs. However, navigating this chemical space to identify optimal MOF structures poses a significant challenge
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Solid-state cathode heterogeneity impact on utilization and fracture dynamics ChemRxiv Pub Date : 2024-04-25 Kelsey, Hatzell, Se Hwan, Park, Carlos Juarez, Yescas, Kaustubh, Naik, Yingjin , Wang, Yuting , Luo, Dhanya, Puthusseri, Patrick, Kwon, Bairav S. , Vishnugopi, Badri, Shyam, Heng, Yang, John, Cook, John, Okasinki, Andrew , Chaung, Xianghui , Xiao, Julia, Greer, Partha P. , Mukherjee, Beniamin , Zahiri, Paul, Braun
Structural heterogeneity in solid-state batteries can impact material utilization and fracture mechanisms. Dense crystallographically oriented lithium cobalt oxide cathodes serve as a model electrode system for exploring how density variability contributes to stress relief and build up during cycling. Real- and reciprocal-space operando and ex-situ synchrotron based experiments are utilized to understand
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Quality Control in the Mass Spectrometry Proteomics Core: a Practical Primer ChemRxiv Pub Date : 2024-04-25 Benjamin, Neely, Yasset, Perez-Riverol, Magnus, Palmblad
The past decade has seen widespread advances in quality control (QC) materials and software tools focused specifically on mass spectrometry-based proteomics, yet the rate of adoption is inconsistent. Despite the fundamental importance of QC, it typically falls behind learning new techniques, instruments, or software. Considering how important QC is in a core setting where data is generated for non-mass
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Antimicrobial peptide coating of TiO2 nanoparticles for boosted antimicrobial effects ChemRxiv Pub Date : 2024-04-25 Lucrezia, Caselli, Tanja , Traini, Samantha , Micciulla, Federica , Sebastiani, Sebastian , Köhler, Emilie Marie , Nielsen, Ragna , Guldsmed Diedrichsen, Maximilian W. A. , Skoda, Martin, Malmsten
This study explores coating of photocatalytic nanoparticles with antimicrobial peptides (AMPs) for boosted antimicrobial effects, and how such effects depend on AMP properties. For this, TiO2 nanoparticles were coated with the AMP KYE21 or its hydrophobically enhanced variant WWWKYE21. Mirroring effects of the free peptides, coated nanoparticles displayed higher binding and UV-induced degradation for
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Computational Large-Scale Screening of Bioorthogonal 1,2,4,5-Tetrazine/trans-Cyclooctene Cycloadditions ChemRxiv Pub Date : 2024-04-25 Dennis, Svatunek
Bioorthogonal reactions between 1,2,4,5-tetrazines and trans-cyclooctenes have emerged as valuable chemical tools in the fields of chemical biology and material science, and they hold significant potential for medical applications. The most critical attribute of such reactions is their rate. Experimental investigations into the reactivity of 1,2,4,5-tetrazines are time-consuming and costly. In contrast
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Transition Behaviors of Isostructural sql-Topological Hydrogen-Bonded Frameworks Composed of Naphthalene, Quinoxaline, and Pyrazinopyrazine Derivatives ChemRxiv Pub Date : 2024-04-25 Ichiro, Hisaki, Haruka, Kubo, Shunsuke, Konishi, Ryusei, Oketani, Takashi, Hayashi
A series of isostructural reticular framework materials with systematic differences on chemical structures allows us to disclose correlations between specific structural factors and properties, providing insights for designing novel porous frameworks. However, even slight differences in the molecular structure often lead to non-isostructural polymorphic frameworks particularly in the case of hydrogen-bonded
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A guidebook for sustainability in laboratories ChemRxiv Pub Date : 2024-04-25 Thomas, Freese, Renate, Kat, Suzanne D., Lanooij, Tanja C., Böllersen, C. Maurits, De Roo, Nils, Elzinga, Meagan, Beatty, Brian, Setz, Roza R., Weber, Irene, Malta, Timea B., Gandek, Peter, Fodran, Robert, Pollice, Michael M., Lerch, Arjen, Krikken
This guidebook aims to improve lab users’ everyday practices to become more sustainable. Specifically, this guidebook provides practical suggestions on how to effectively use lab instruments and resources and on how to acquire data. We provide advice to labs covering disciplines such as biology, chemistry, computational science, engineering, life sciences, materials sciences, medicine, pharmacy, and
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Asymmetric Synthesis of Chiral-at-Iridium Complexes through Pd-Catalyzed Kinetic Resolution ChemRxiv Pub Date : 2024-04-25 Jiajia, Ma, Yun-Peng , Chu, Xue-Lin, Yue, De-Hai, Liu
Metal-centered chirality has been recognized for over one century, and chiral-at-metal complexes where chirality is exclusively attributed to the metal center due to the specific coordination pattern of achiral ligands around the metal ion, has been broadly utilized in diverse areas of natural sciences. However, synthesis of these molecules remains constrained. Notably, while asymmetric catalysis has
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Ditopic ligand effects on solution-phase equilibria and electrochemistry of atomically precise copper chalcogenide nanoclusters ChemRxiv Pub Date : 2024-04-25 Gwendolyn, Bailey, Michael, Trenerry
Atomically precise copper chalcogenide nanoclusters are an exceptionally diverse class of nanomaterials with potential applications in chemiluminescence, sensing, and catalysis. However, most previously reported nanoclusters have been characterized exclusively in the solid state, leaving open questions as to their stability and function in solution. In this work, we report the first detailed solution-phase
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Dynamic Behavior and Substrate Interactions of the Polymyxin Resistance Determinant MCR-1 Investigated by Extended Molecular Dynamics Simulations in the Membrane Environment ChemRxiv Pub Date : 2024-04-25 James, Spencer, Emily, Lythell, Reynier, Suardíaz, Philip, Hinchliffe, Sofia, Oliveira, Marc, van der Kamp, Adrian, Mulholland
The polymyxin colistin is an agent of last resort for treatment of severe infections by multiresistant Gram-negative opportunistic bacteria. Colistin resistance arises through covalent modification of lipid A disaccharide by phosphoethanolamine (PEtN) transferases, preventing colistin interaction. The Mobile Colistin Resistance (MCR) PEtN transferase is a plasmid-borne enzyme that is the major cause
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Mixing order asymmetry in nanoparticle-polymer complexation and precipitation revealed by isothermal titration calorimetry ChemRxiv Pub Date : 2024-04-25 Jean-Francois, Berret, Leticia, Vitorazi
In recent years, there has been a renewed interest in complex coacervation, driven by concerted efforts to offer novel experimental and theoretical insights into electrostatic charge-induced association. While previous studies have primarily focused on polyelectrolytes, proteins or surfactants, our work explores the potential of using cerium (CeO2) and iron (γ-Fe2O3) oxide nanoparticles (NPs) to develop
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A versatile fabrication route for screening block copolymer membranes for bioprocessing ChemRxiv Pub Date : 2024-04-25 Stefan , Guldin, Ke, Meng, Alberto, Alvarez-Fernandez, Daniel G. , Bracewell
Traditional polyethersulfone (PES) filters, widely used for sterile, viral and ultrafil- tration often exhibit limited selectivity-permeability due to the heterogenous pore size distribution. Such limitations have sparked interest in developing novel isoporous mem- brane materials and fabrication techniques to overcome the selectivity-permeability upper bound. Among several promising candidates, block
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Scaling Laws for Optimal Herschel–Bulkley Yield Stress Fluid Flow in Self-Similar Tree-like Branching Networks ChemRxiv Pub Date : 2024-04-25 Ashish, Garg
This study analyzes optimal flow conditions and structures in tree-like branching networks for yield stress Herschel–Bulkley fluids. We focus on maximizing flow conductance under volume constraints, assuming fully developed laminar flow in circular tubes. We propose a conjecture that if the tube-wall stress, remains the same in the network for all branches, then an optimal solution exists. We find
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Electron Transfer Dynamics at Dye-Sensitized SnO2/TiO2 Core-Shell Electrodes in Aqueous/Nonaqueous Electrolyte Mixtures ChemRxiv Pub Date : 2024-04-25 Thomas, Mallouk, Langqiu, Xiao, Jacob, Spies, Colton, Sheehan, Zichen, Zeng, Yunhan, Gao, Tianyue, Gao, Annika, Ehrlacher, Michael, Zuerch, Gary, Brudvig
The dynamics and efficiency of photoinduced electron transfer were measured at dye-sensitized photoanodes in aqueous (acetate buffer), nonaqueous (acetonitrile), and mixed solvent electrolytes by nanosecond transient spectroscopy (TAS) and ultrafast optical-pump terahertz-probe spectroscopy (OPTP). Higher injection efficiencies were found in mixed solvent electrolytes for dye-sensitized SnO2/TiO2 core/shell
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Combined physics- and machine-learning-based method to identify druggable binding sites using SILCS-Hotspots ChemRxiv Pub Date : 2024-04-25 Alex, MacKerell, Erik, Nordquist, Mingtian, Zhao, Anmol, Kumar
Identifying druggable binding sites on proteins is an important and challenging problem, particularly for cryptic, allosteric binding sites that may not be obvious from X-ray, cryo-EM, or predicted structures. The Site-Identification by Ligand Competitive Saturation (SILCS) method accounts for the flexibility of the target protein using all-atom molecular simulations that include various small molecule
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Alzheimer's Disease: Exploring the Landscape of Cognitive Decline ChemRxiv Pub Date : 2024-04-25 Rumiana, Tenchov, Janet, Sasso, Qiongqiong Angela, Zhou
Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline, memory loss, and impaired daily functioning. The pathology of AD is marked by the accumulation of amyloid-beta plaques and tau protein tangles in brain, along with neuroinflammation and synaptic dysfunction. Genetic factors, such as mutations in APP, PSEN1, and PSEN2 genes, as well as APOE ε4 allele
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The Evolving Landscape of Parkinson's Disease Research: Current Challenges and Future Outlook ChemRxiv Pub Date : 2024-04-25 Rumiana, Tenchov, Janet, Sasso, Qiongqiong Angela, Zhou
Parkinson’s disease (PD) is a progressive neurodegenerative disorder that primarily affects movement. It occurs due to gradual loss of dopamine-producing brain cells, particularly in substantia nigra. The exact cause of Parkinson's disease is not fully understood, but it is believed to involve a combination of genetic and environmental factors. Currently available treatments provide symptomatic relief
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Inverse vaccines - Friend, Not Foe: How Inverse Vaccines Tackle Autoimmune Diseases ChemRxiv Pub Date : 2024-04-25 Rumiana, Tenchov, Qiongqiong Angela, Zhou
Inverse vaccines are a new and exciting approach to treating autoimmune diseases. Unlike traditional vaccines that train the immune system to fight off pathogens, inverse vaccines aim to reprogram the immune system to stop attacking healthy tissues.
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Biocompatible Cobalt Oxide Nanoparticles for X-ray Fluorescence Microscopy ChemRxiv Pub Date : 2024-04-25 Sophia, Miller, Christian , Scott, Craig Eliot, Barnes, Martina, Ralle, Pierre, Moenne-Loccoz
The synthesis of water-soluble nanoparticles is a well-developed field for ferrite-based nanoparticles with the majority consisting of iron oxide or mixed metal iron oxide nanoparticles. However, the synthesis of non-agglomerated non-ferrite metal/metal oxide NPs is not as well established. The synthesis and characterization of uniform 20 nm, biologically compatible cobalt oxide (CoO) nanoparticles
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Charting electron beam-induced lattice reorientation in molecular nanocrystals ChemRxiv Pub Date : 2024-04-25 Niko, Vlahakis, Arden, Clauss, Jose, Rodriguez
High-energy electrons induce sample damage and motion at the nanoscale to fundamentally limit determination of molecular structures by electron diffraction. Using fast event-based electron counting (EBEC) detectors, we characterize electron beam-induced crystal lattice reorientations (BIR) that appear to broadly affect molecular microcrystals. These lattice reorientations are sufficiently large to
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Paired Electrolysis Enables Reductive Heck Coupling of Unacti-vated (Hetero)Aryl Halides and Alkenes ChemRxiv Pub Date : 2024-04-25 Phillip, Milner, Yihuan, Lai
The formation of carbon-carbon (C–C) bonds is a cornerstone of organic synthesis. Among various methods to construct Csp2–Csp3 bonds, the reductive Heck reaction between (hetero)aryl halides and alkenes stands out due to its potential efficiency and broad substrate availability. However, traditional reductive Heck reactions are limited by the use of pre-cious metal catalysts and/or limited aryl halide
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Adjusting the energy profile for CH–O interactions leads to improved stability of RNA stem-loop structures in MD simulations ChemRxiv Pub Date : 2024-04-25 Maria, Nagan, Lauren, Raguette, Sarah, Gunasekera, Rebeca, Ventura Diaz, Ethan, Aminov, Jason, Linzer, Diksha, Parwana, Qin, Wu, Carlos, Simmerling
The role of RNA in biology continues to grow but insight into important aspects of RNA behavior is lacking, such as dynamic structural ensembles in different environments, how flexibility is coupled to function, and how function might be modulated by small molecule binding. In the case of proteins, much progress in these areas has been made by complementing experiments with atomistic simulations, but
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Fluorescence imaging using deep-red Indocyanine Blue (ICB) a complementary partner for near infrared Indocyanine Green (ICG) ChemRxiv Pub Date : 2024-04-25 Bradley, Smith, Rananjaya , Gamage
Indocyanine Blue (ICB) is the deep-red, pentamethine analogue of the widely used clinical near-infrared heptamethine cyanine dye, Indocyanine Green (ICG). The two fluorophores have the same number of functional groups and molecular charge and vary only by a single vinylene unit in the polymethine chain which produces a predictable difference in spectral and physicochemical properties. We find that
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Site-Specific Template Generative Approach for Retrosynthetic Planning ChemRxiv Pub Date : 2024-04-25 Yu, Shee, Haote, Li, Pengpeng, Zhang, Andrea, Nikolic, Sanil, Sreekumar, Frédéric, Buono, Jinhua, Song, Timothy, Newhouse, Victor, Batista
Retrosynthesis, the strategy of devising laboratory pathways for small molecules by working backwards from the target compound, remains a rate limiting step in multi-step synthesis of complex molecules, particularly in drug discovery. Enhancing retrosynthetic efficacy requires overcoming the vast complexity of chemical space, the limited known interconversions between molecules, and the challenges
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Unlocking Metal-Ligand Cooperative Catalytic Photochemical Benzene Carbonylation: A Mechanistic Approach ChemRxiv Pub Date : 2024-04-25 Niklas, von Wolff, Francesco, Crisanti, Michael, Montag, David, Milstein, Julien, Bonin
A key challenge in green synthesis is the catalytic transformation of renewable substrates at high atom and energy efficiency, with minimal exergonicity (ΔG≈0). Non-thermal pathways, i.e., electrochemical and photochemical, can be used to leverage renewable energy resources to drive chemical processes at well-defined energy input and efficiency. Within this context, photochemical benzene carbonylation
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WS24: A diverse data set for predicting metal-organic framework stability in water and harsh environments with data-driven models ChemRxiv Pub Date : 2024-04-24 Heather, Kulik, Gianmarco, Terrones, Shih-Peng, Huang, Matt, Rivera, Shuwen, Yue, Alondra, Hernandez
Metal-organic frameworks (MOFs) are porous materials with applications in gas separations and catalysis, but a lack of water stability often limits their practical use given the ubiquity of water in air and the environment. Consequently, it is useful to predict whether a MOF is water-stable before investing time and resources into synthesis. Existing heuristics for designing water-stable MOFs lack
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CO2-to-methanol electroconversion on a molecular cobalt catalyst facilitated by acidic cations ChemRxiv Pub Date : 2024-04-24 Sunmoon, Yu, Hiroki, Yamauchi, Junghwa, Kim, Botao, Huang, Hongbin, Xu, Daniel, Zheng, Xiao, Wang, Haldrian, Iriawan, Davide, Menga, Yang, Shao-Horn, Shuo, Wang, Abhishek, Aggarwal
The crucial role of electrolyte cations in CO2 electroreduction has received intensive attention. One prevailing theory is that through electrostatic interactions or direct coordination, larger cations such as Cs+ can better stabilize the key intermediate species for CO and multicarbon (C2+) product generation, for example, on silver and copper, respectively. Herein, we show that smaller, more acidic
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Europium-rich ternary phases with noble metals Eu2M2X (M = Pd, Pt; X = Al, Ga, Ge, Cd), and their structural relationship to the Laves phase Ca2Pt3Al1–xAgx ChemRxiv Pub Date : 2024-04-24 Simeon, Ponou, Anja-Verena, Mudring
The combination of divalent Eu with high magnetic moment and strong spin-orbit coupling (SOC) on Pd or Pt atoms in a single substance, makes Eu-Pd/Pt-X ternary phases attractive for materials with exotic physical properties. For that reason, compositions according to Eu2M2X (M = Pd, Pt; X = Al, Ga, Ge, Cd) were explored. X-ray diffraction analyses revealed that the three Pd analogues Eu2Pd2Al, Eu2Pd2Ga
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δ-Bonding and Electron Localisation in Crystalline Divalent Rare Earth Arene Complexes ChemRxiv Pub Date : 2024-04-24 Conrad, Goodwin, Ross, MacKenzie, Tomáš, Hajdu, John, Seed, George, Whitehead, Ralph, Adams, Nicholas, Chilton, David, Collison, Eric, McInnes
Landmark advances in rare earth (RE) chemistry have shown that formally divalent complexes can be isolated with non-Aufbau 4fn5d(dz2)1 or 4fn{5d/6s}1 electron configurations, which facilitate novel bonding motifs and phenomenal magnetic properties. We report an unprecedented series of divalent bis-tethered arene complexes, [RE(NHAriPr6)2] (2RE; RE = Sc, Y, La, Sm, Eu, Tm, Yb; NHAriPr6 = {N(H)C6H3-2
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[45Ti]Ti-DOTA: En route towards aza-macrocyclic 45Ti-based radiopharmaceuticals ChemRxiv Pub Date : 2024-04-24 Tamal, Roy, Eduard, Pogorilyy, Chubina Pathma, Kumarananthan, Unni Augestad, Kvitastein, Marco, Foscato, Tom Christian Holm, Adamsen, Erwan, Le Roux, Karl Wilhelm, Törnroos
We report the first use of DOTA as a chelator for titanium. The resulting complex is fully characterized and extended to the radiolabelling of DOTA with titanium-45.
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Cost-Effective and Wireless Portable Device for Rapid and Sensitive Quantification of Micro/Nanoplastics ChemRxiv Pub Date : 2024-04-24 Tianxi, Yang, Haoxin, Ye, Xinzhe , Zheng, Haoming , Yang, Matthew , Kowal, Teresa , Seifried, Gurvendra , Pal Singh, Krishna , Aayush, Guang , Gao, Edward , Grant, David , Kitts, Rickey , Yada
The accumulation of micro/nanoplastics (MNPs) in ecosystems poses tremendous environmental risks for terrestrial and aquat-ic organisms. Designing rapid, field-deployable, and sensitive devices for assessing the potential risks of MNPs pollution is critical. However, current techniques for MNPs detection have limited effectiveness. Here, we design a wireless portable de-vice that allows rapid, sensitive
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Albumin Nanoparticles in Cancer Therapeutics: Clinical Status, Challenges, and Future Directions ChemRxiv Pub Date : 2024-04-24 HACHEMI, KADRI, Mouhamad, Khoder, Mesk, Alshatfa, Feras Z, Alsalloum, Abdelbary, Elhissi, Anis, Daou
Cancer, a global health burden, is characterized by uncontrolled cell growth and metastasis, often resulting in debilitating treatments and mortality. While conventional therapeutic strategies have improved survival rates, they are limited by challenges such as off-target toxicity and drug resistance. With their design to enable targeted drug delivery, nanoparticles have presented a promising avenue
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Evaluation performance to assess accurate exchange-correlation functional in van der Waals TMD Materials AB2 (A = Mo, W and B = S, Se and Te) ChemRxiv Pub Date : 2024-04-24 Sushant Kumar, Behera, Praveen C, Ramamurthy
Two-dimensional (2D) transition metal dichalcogenides (TMDs) show multi-functionality due to their highly adjustable chemical, physical, and electronic properties. Here, structural, electronic, and phonon response are systematically studied for 06 TMDs systems via density functional theory (DFT) simulations. A reversible phase transition is revealed between the semiconducting (2H) phase and the metallic
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Assessing the accurate exchange-correlation functional in van der Waals TMD Materials AB2 (A = Nb, Ta and B = S, Se, Te) ChemRxiv Pub Date : 2024-04-24 Sushant Kumar, Behera, Praveen C, Ramamurthy
Two-dimensional (2D) transition metal dichalcogenides (TMDs) exhibit diverse functionalities owing to their highly tunable chemical, physical, and electronic attributes. In this study, we systematically investigate the structural, electronic, and phonon responses of six TMD systems using density functional theory (DFT) simulations. Our analysis unveils a reversible phase transition between the semiconducting
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Semisynthetic Ferritin-based Nanoparticles with High Magnetic Anisotropy for Spatial Magnetic Manipulation and Inductive Heating ChemRxiv Pub Date : 2024-04-24 Andreas, Neusch, Ulf, Wiedwald, Iuliia P., Novoselova, Daniel A., Kuckla, Sarah, Sadik, Philipp, Hagemann, Nikolaos, Tetos, Michael, Farle, Cornelia, Monzel
The human iron storage protein ferritin represents an appealing template to realise a semisynthetic magnetic nanoparticle (MNP) for spatial manipulation or inductive heating applications on a nanoscale. Ferritin consists of a protein cage of well-defined size (12 nm), which is genetically modifiable, biocompatible, and into which a magnetic core is synthesised. Here, we probe the magnetic response
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Design of Experiments-Based Optimization of an Electrochemical Decarboxylative Alkylation using a Spinning Cylinder Electrode Reactor ChemRxiv Pub Date : 2024-04-24 David, Cantillo, Nikola, Petrović, Graham R., Cumming, Christopher A., Hone, María José, Nieves- Remacha, Pablo, García-Losada, Óscar, de Frutos, C. Oliver, Kappe
A design of experiments model has been developed to optimize an electrochemical protocol for the decarboxylative N-alkylation of pyrazole in a spinning cylinder electrode reactor. The electrochemical reaction requires the incorporation of molecular sieves as an additive to ensure the absence of moisture and prevent potential electrode corrosion issues. The spinning cylinder electrode reactor proved
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Retrieval Augmented Docking using Hierarchical Navigable Small Worlds ChemRxiv Pub Date : 2024-04-24 Michael, Keiser, Brendan, Hall
Make-on-demand chemical libraries have drastically increased the reach of molecular docking, with the enumerated ready-to-dock ZINC library approaching 5 billion molecules. While ever-growing libraries result in better-scoring molecules, the computational resources required to dock all of ZINC make this endeavor infeasible for most. Here, we organize and traverse chemical space with hierarchical navigable
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Migratory Aryl Cross-Coupling ChemRxiv Pub Date : 2024-04-24 Richard, Liu, Yoshiya, Sekiguchi, Polpum, Onnuch, Yuli, Li
A fundamental property of cross-coupling reactions is regiospecificity, meaning that the site of bond formation is determined by the leaving group’s location on the electrophile. Typically, to achieve a different substitution pattern requires synthesis of a new, corresponding starting-material isomer. As an alternative, we proposed the development of cross-coupling variants that afford access to multiple
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Electrolytomics: A unified big data approach for electrolyte design and discovery ChemRxiv Pub Date : 2024-04-24 Chibueze, Amanchukwu, Ritesh, Kumar, Minh, Canh Vu, Peiyuan, Ma
Electrolyte discovery is the bottleneck for developing next generation batteries. For example, lithium metal batteries (LMBs) promise to double the energy density of current Li-ion batteries (LIBs) while next generation LIBs are desired for operations at extreme temperature conditions and with high voltage cathodes. However, there are no suitable electrolytes to support these battery chemistries. Electrolyte
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Bipolar electrochemical growth of conductive microwires for cancer spheroid integration: A step forward in conductive biological circuitry ChemRxiv Pub Date : 2024-04-24 Frankie, Rawson, Andie, Robinsons, Craig , McBeth, Ruman, Rahman, Richard, Hague
The field of bioelectronics is developing exponentially. There is now a drive to interface electronics with biology for the development of new technologies to improve our understanding of electrical forces in biology. This builds on our recently published work in which we show wireless electrochemistry could be used to grow bioelectronic functional circuitry in 2 dimensional (2D) cell layers. To date
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High Yielding, Multigram-Scale Synthesis of TBAJ-876 Fragment, 876A-B ChemRxiv Pub Date : 2024-04-24 Michel C., Nuckols, Douglas A., Klumpp, Pankaj V., Khairnar, Chiranjeevi, Barreddi, Nakul, Telang, Saeed, Ahmad, B. Frank, Gupton
TBAJ-876 is an anti-tuberculosis drug shown to have high activity against multi-drug resistant tuberculosis (TB). We report a very efficient synthesis of the TBAJ-876 fragment 876A-B using an aldol condensation strategy starting from 6-bromo-3,4-dihydroquinolin-2(H)-one. The synthesis has been accomplished at multigram scale without the need of chromatography purification steps.