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66d0d66fa4e53c48760febaf | 10.26434/chemrxiv-2024-7gp9m-v3 | Effects of Functionalization on Photo-Actuatable Octa(dimethylsiloxy)silsesquioxane-Azobenzene Network Gels and their Substance Loading and Unloading Efficiencies | The synthesis, characterization, analysis, and effect on solvent uptake of styrene, alcohol, amino, and perfluoro functionalized silsesquioxane-azobenzene hybrid gels are discussed. 4,4’-diallyloxyazobenzene and octa(dimethylsiloxy)silsesquioxane (Q8M8H) gels are generated using hydrosilylation chemistry. These gels were modified through two routes: in-situ and post-synthesis modification, depending on the compatibility of the modifiers. The dynamic gel systems react to visible and UV light to expand and contract, giving them sponge-like properties. The general characteristics of each gel are illustrated through UV-Vis, ATR-FTIR, TGA, NMR, and SEM imaging. Effects on their solvent uptake load and preference for various solvents/pollutants are detailed below, and notable findings include preferences of the styrene material for aromatics, perfluoro for THF, and alcohol for acetone. This is accompanied by a low affinity for water, enabling them to remove organic solvents and particulate from water. We find that selectivity for certain substances can be obtained but at the cost of total absorptivity of the gel systems. | Cory Sims; Ethan Chandler; Herenia Espitia Armenta; Nai-hsuan Hu; Joseph Furgal | Materials Science; Polymer Science; Earth, Space, and Environmental Chemistry; Controlled-Release Systems; Hybrid Organic-Inorganic Materials; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d0d66fa4e53c48760febaf/original/effects-of-functionalization-on-photo-actuatable-octa-dimethylsiloxy-silsesquioxane-azobenzene-network-gels-and-their-substance-loading-and-unloading-efficiencies.pdf |
60eebd7db9b60196b2246c36 | 10.26434/chemrxiv-2021-b1qwb | Efficient direct nitrosylation of a-diimine rhenium tricarbonyl complexes to structurally nearly identical higher charge congeners activable towards photo-CO release | The reaction of rhenium a-diimine (N-N) tricarbonyl complexes with nitrosonium tetrafluoroborate yields the corresponding dicarbonyl-nitrosyl [Re(CO)2(NO)(N-N)X]+ species (where X = halide). The complexes, accessible in a single step in good yied, are structurally nearly identical higher charge congeners of the tricarbonyl molecules. Substitution chemistry aimed at the realization of equivalent dicationic species (intended for applications as potential antimicrobial agents), revealed that the reactivity of metal ion in [Re(CO)2(NO)(N-N)X]+ is closer to that of a harder Re(III) acid, probably due to the stronger p-acceptor properties of NO+ as compared to those of CO. The metal ion thus shows great affinity for p-basic ligands, which are consequently difficult to replace by e.g. s-donor or week p-acids like pyridine. Attempts of direct nitrosylation of a-diimine fac-[Re(CO)3]+ complexes bearing p-basic OR-type ligands gave the [Re(CO)2(NO)(N-N)(BF4)][BF4] salt, as the only product in good yield, featuring a stable Re-F-BF3 bond. The solid state crystal structure of nearly all molecules presented could be elucidated. A fundamental consequence of the chemistry of [Re(CO)2(NO)(N-N)X]+ complexes, it that the same can be photo-activated towards CO release and represent an entirely new class of photoCORMs. | Sara Nasiri Sovari; Isabelle Kolly; Kevin Schindler; Youri Cortat; Liu Shing-Chi ; Aurelien Crochet; Aleksandar Pavic; Fabio Zobi | Inorganic Chemistry; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60eebd7db9b60196b2246c36/original/efficient-direct-nitrosylation-of-a-diimine-rhenium-tricarbonyl-complexes-to-structurally-nearly-identical-higher-charge-congeners-activable-towards-photo-co-release.pdf |
64023ca19789de3dd9de35f5 | 10.26434/chemrxiv-2023-wgv41 | Spiroindoles as Intermediates/Products in Transition Metal Catalyzed Dearomatization of Indoles | Spirocyclic indole derivatives are fascinating tridimensional molecular scaffolds, from both a synthetic and biological point of view. Among the diversity of strategies developed to access this kind of structures, transition metal catalysis recently led to impressive advances, especially in order to tame the unique reactivity of the dearomatized spirocyclic intermediates. These species can indeed evolve towards both spirocyclic or non-spirocyclic products through rearomatization-driven processes which are at the same time highly challenging to control but also source of a large structural diversity. This review highlights the most prominent methods of the last decade allowing to trigger a spirocyclization on indole derivatives tethered with a transition metal-activable functional group, leading to both spirocyclic and rearomatized products. The discussion is particularly focused on the reactivity and the complex mechanistic features regarding the evolution of the spiroindoleninium intermediate, highly dependent on the catalytic system. | Floris Buttard; Xavier Guinchard | Organic Chemistry; Catalysis; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64023ca19789de3dd9de35f5/original/spiroindoles-as-intermediates-products-in-transition-metal-catalyzed-dearomatization-of-indoles.pdf |
643f08ac83fa35f8f6de889e | 10.26434/chemrxiv-2023-z282s | Water-based synthesis and nitrate release properties of a ZrIV-based metal-organic framework derived from L-aspartic acid | We report the synthesis and characterisation of a cationic metal-organic framework (MOF) based on ZrIV and L-aspartate and containing nitrate as extraframework counteranion, named MIP-202-NO3. The ion exchange properties of MIP-202-NO3 were preliminarily investigated to evaluate its potential as a platform for controlled release of nitrate, finding that it readily releases nitrate in aqueous solution. | Temitope Olabisi Abodunrin; Matous Kloda; Jan Demel; Marco Taddei | Inorganic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643f08ac83fa35f8f6de889e/original/water-based-synthesis-and-nitrate-release-properties-of-a-zr-iv-based-metal-organic-framework-derived-from-l-aspartic-acid.pdf |
646a7ae6a32ceeff2d02dd25 | 10.26434/chemrxiv-2023-18cn7 | Atypical swelling gelation of chitin physical hydrogel and the tunable mechanical properties | Atypical swelling gelation of chitin physical hydrogels were investigated. Only by tuning the amount of N-acetylation reagent, the degree of acetylation varied and the moldable chitin hydrogels with a wide variety of gel concentration (0.21–6.4 wt%) were obtained. In response to the gel concentration, the mechanical properties ranged from swollen soft gels to shrunk rigid gels (compressive E = 4.22–310 kPa). Thus-prepared chitin hydrogels, which are made only of chitin and water, exhibited high transparency and integrity. The swelling gelation of chitin physical hydrogels was achieved owing both to the cationic charge of the amino groups inducing the osmotic pressure and the toughness of chitin hydrogels that endured the large volume change. These previously-unnoticed advantageous aspects of chitin have pioneered a novel region of swellable physical gels that has been exclusive to chemical gels. | Yuto Kaku; Satoshi Okada; Shuji Fujisawa; Tsuguyuki Saito; Noriyuki Isobe | Physical Chemistry; Materials Science; Polymer Science; Biopolymers; Cellulosic materials; Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646a7ae6a32ceeff2d02dd25/original/atypical-swelling-gelation-of-chitin-physical-hydrogel-and-the-tunable-mechanical-properties.pdf |
65202828bda59ceb9a00bc8e | 10.26434/chemrxiv-2023-1mgbh | Ideal conductor/dielectric model (ICDM): A generalized technique to correct for finite-size effects in molecular simulations of hindered ion transport | Molecular simulations serve as indispensable tools for investigating the kinetics and elucidating the mechanism of hindered ion transport across nanoporous membranes. In particular, recent advancements in advanced sampling techniques have made it possible to access translocation timescales spanning several orders of magnitude. In our prior study (\href{https://doi.org/10.1021/acs.jctc.2c00375}{Shoemaker,~\emph{et al.},~\emph{J. Chem. Theory Comput.}, 18: 7142, {\bf 2022}}), we identified significant finite size artifacts in simulations of pressure-driven hindered ion transport through nanoporous graphitic membranes. We introduced the ideal conductor model, which effectively corrects for such artifacts by assuming the feed to be an ideal conductor. In the present work, we introduce the ideal conductor dielectric model (ICDM), a generalization of our earlier model, which accounts for the dielectric properties of both the membrane and the filtrate. Using the ICDM model substantially enhances the agreement among corrected free energy profiles obtained from systems of varying sizes, with notable improvements observed in regions proximate to the pore exit. Moreover, the model has the capability to consider secondary ion passage events, including the transport of a co-ion subsequent to the traversal of a counter-ion, a feature absent in our original model. We also investigate the sensitivity of the new model to various implementation details. The ICDM model offers a universally applicable framework for addressing finite size artifacts in molecular simulations of ion transport. It stands as a significant advancement in our quest to use molecular simulations to comprehensively understand and manipulate ion transport processes through nanoporous membranes. | Amir Haji-Akbari; Brian Shoemaker | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2023-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65202828bda59ceb9a00bc8e/original/ideal-conductor-dielectric-model-icdm-a-generalized-technique-to-correct-for-finite-size-effects-in-molecular-simulations-of-hindered-ion-transport.pdf |
60c745bcbdbb897032a38abc | 10.26434/chemrxiv.10246928.v1 | Size matters: Size Dependency of Gold Nanoparticles Interacting with Model Membranes | <p><b>The
rapid development of nanomaterials has led to an increase in the number and
variety of engineered nanomaterials (ENMs) in the environment. Gold
nanoparticles (AuNPs) are an example of a commonly studied ENM whose highly
tailorable properties have generated significant interest through a wide range
of research fields. In the present work, we report the first qualitative as
well as quantitative experimental characterisation of the AuNP-membrane
interaction. We investigate the interactions between citrate-stabilised AuNPs (diameters
5, 10, 25, 35, 50, 60 nm) and large unilamellar vesicles (LUVs) acting as a
model membrane system. LUVs were prepared in two different formulations using
1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) and
1,2-dileoyl-sn-glycero-3-phosphocholine (DOPC). Our results show that the
interaction between AuNPs and LUVs is size dependent; in particular, we reveal
the existence of two AuNP’s critical diameters which determine the fate of
AuNPs in contact with a lipid membrane. The results provide a new understanding
of the size dependent interaction between AuNPs and lipid bilayers of direct
relevance to nanotoxicology and to the design of NP vectors.</b></p> | Claudia Contini; James W. Hindley; Tom Macdonald; Joseph Barritt; Oscar Ces; Nick Quirke | Biophysical Chemistry; Interfaces; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745bcbdbb897032a38abc/original/size-matters-size-dependency-of-gold-nanoparticles-interacting-with-model-membranes.pdf |
60c7559ebdbb891140a3a860 | 10.26434/chemrxiv.14132258.v1 | Damming a Molecular Energy Reservoir: Ion-regulated Electronic Energy Shuttling in a [2]Rotaxane | Bidirectional
electronic energy shuttling is shown to occur between the molecular ring and
axle components of a rotaxane. The engineered energetic and kinetic parameters
give rise to long-lived, delayed luminescence.
Perturbation of the quasi-isoenergetic ring and stopper chromophore
excited-state energy levels upon cation binding influences the energy shuttling
process, and hence luminescence read-out, representing a new potential
mechanism in luminescent molecular chemosensor development | Shilin Yu; Arkady Kurpryakov; James Lewis; Vicente Martí-Centelles; Stephen Goldup; Jean-Luc Pozzo; Gediminas Jonusauskas; Nathan McClenaghan | Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7559ebdbb891140a3a860/original/damming-a-molecular-energy-reservoir-ion-regulated-electronic-energy-shuttling-in-a-2-rotaxane.pdf |
642eba320784a63aeea31200 | 10.26434/chemrxiv-2023-b0d6x | Expanding the Scope of Hypervalent Iodine Reagents in the Synthesis of Sulfinamides from Sulfenamides | This study presents a novel, efficient method for the synthesis of sulfinamidines via oxidative amination of sulfenamides using diacetoxyiodobenzene (PhI(OAc)2) and secondary amines under basic conditions. The technique achieves outstanding yields of up to 99%, streamlining the process under mild and metal-free conditions. In addition, two possible pathways are proposed to explain the observed molecular sequence of events in this reaction. The advanced approach expands the synthetic toolbox available to chemists, enabling the synthesis of valuable sulfinamidine compounds, and opening up potential applications in medicinal chemistry. Overall, this study highlights the potential of hypervalent iodine-mediated methods for efficient and streamlined organic synthesis. | Xunbo Lu; Guoling Huang; Jianlin Ye; Muhammad Adnan Bashir; Yuetong Chen; Wenjing Chen | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642eba320784a63aeea31200/original/expanding-the-scope-of-hypervalent-iodine-reagents-in-the-synthesis-of-sulfinamides-from-sulfenamides.pdf |
67d217d6fa469535b907e158 | 10.26434/chemrxiv-2025-95xv6-v2 | Metal ɑ-helix peptide frameworks | Metal-peptide frameworks (MPFs) are a growing class of metal–organic frameworks with promising applications in metalloprotein mimicry, chiral separations, and catalysis. There are limited examples of MPFs, especially those with both secondary structure and natural amino acid side chains that coordinate to metal nodes, which is important for accurately mimicking metalloprotein active sites. Here, we de-sign a robust and modular strategy based on short ɑ-helical peptides (9 amino acids long) to form frameworks with many types of bio-mimetic metal sites. Peptides were designed to have Glu and His metal-binding residues, hydrophobic residues, and noncanonical helix-enforcing residues. With Co(II), it was shown that mutagenesis of a single amino acid near the metal-binding residues generates a diverse library of frameworks with varying metal node coordination geometries and compositions. Structures for 16 out of 20 variants were characterized by single-crystal X-ray diffraction, revealing how noncovalent interactions impact the metal primary sphere. In one case, a point mutation turns on reversible ligand-triggered conformational changes, demonstrating that this platform allows for dynamic behavior like that observed in metalloproteins. Furthermore, we show that frameworks readily assemble with Mn(II), Fe(II), Cu(II), and Zn(II) ions, highlighting the generality of this approach. The ease-of-synthesis, modularity, and crystallinity of these materials make this a highly accessible platform for studying and engineering biomimetic metal centers in porous materials. | Ronnie Richardson-Matthews; Kateryna Velko; Bitan Bhunia; Sabari Ghosh; Julia Oktawiec; Joseph Brunzelle; Viet Thuc Dang; Andy Nguyen | Inorganic Chemistry; Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Solid State Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d217d6fa469535b907e158/original/metal-helix-peptide-frameworks.pdf |
635bd9beecdad5fc2bf0eec0 | 10.26434/chemrxiv-2022-mccfz | Ammonia - A Step Away from Traditional Fuels | With the economic and societal progress, a great escalation in energy demands has been witnessed over the years. A major proportion of total energy consumed globally is accounted by the transportation sector where fossil fuels or derivatives such as petrol, diesel and jet fuel are predominantly utilized. This has led to a very high contribution to greenhouse emissions by this sector. With focus on a sustainable future, there is a dire need for alternate green fuels. In this short review, we discuss the potential use of ammonia as a clean fuel; disadvantages and possible resolutions. | Dhairya Mittal; Aaftaab Sethi | Energy; Fuels - Energy Science | CC BY NC 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635bd9beecdad5fc2bf0eec0/original/ammonia-a-step-away-from-traditional-fuels.pdf |
60c74dcbf96a001f7c2879e6 | 10.26434/chemrxiv.12660722.v1 | Reducing CO2 to HCO2- at Mild Potentials: Lessons from Formate Dehydrogenase | The catalytic reduction of CO<sub>2</sub> to HCO<sub>2</sub><sup>-</sup>
requires a formal transfer of a hydride (two electrons, one proton). Synthetic
approaches for inorganic molecular catalysts have exclusively relied on classic
metal hydrides, where the proton and electrons originate from the metal (via heterolytic
cleavage of an M-H bond). An analysis of the scaling relationships that exist in
classic metal hydrides reveal that hydride donors sufficiently hydridic to
perform CO<sub>2</sub> reduction are only accessible at very reducing electrochemical
potentials, which is consistent with known synthetic electrocatalysts. By
comparison, the formate dehydrogenase enzymes operate at relatively mild
potentials. In contrast to reported synthetic catalysts, none of the major
mechanistic proposals for hydride transfer in formate dehydrogenase proceed
through a classic metal hydride. Instead, they invoke formal hydride transfer from
an orthogonal or bi-directional mechanism, where the proton and electron are
not co-located. We discuss the thermodynamic advantages of this approach for
favoring CO<sub>2</sub> reduction at mild potentials, along with guidelines for
replicating this strategy in synthetic systems. | Jenny Yang; Tyler Kerr; Xinran S. Wang; Jeffrey Barlow | Bioinorganic Chemistry; Organometallic Compounds; Small Molecule Activation (Inorg.); Homogeneous Catalysis; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dcbf96a001f7c2879e6/original/reducing-co2-to-hco2-at-mild-potentials-lessons-from-formate-dehydrogenase.pdf |
67d60f8d6dde43c908f3d541 | 10.26434/chemrxiv-2025-sgfdw | Elucidation of the Mechanism of Partial
Activation of EPAC1 Allosteric Modulators by
Markov State Modelling | The development of selective modulators of exchange protein activated by cAMP (EPAC1/RAPGEF3), which preferentially bind its cAMP-binding site, would pave
the way for novel therapeutic interventions in cardiac, metabolic, inflammatory, and oncologic disorders. Here we have applied a computational workflow using Markov
State Models (MSMs) and steered molecular dynamics (sMD) to probe the allosteric activation of EPAC1 by both cAMP and pharmaceutical hit compound I942. sMD
was used to examine the large-scale domain rearrangement EPAC1 undergoes during activation. Intermediate conformations accessed via sMD were then used as starting points for equilibrium MD simulations, which were pooled for the construction of MSMs. The resulting models capture the activation of wild-type (WT) EPAC1
by cAMP, and provide an explanation for the lack of response to cAMP shown by the L273W point mutant. sMD/MSM modelling also elucidated the structural basis
for partial activation of EPAC1 by ligand I942 and revealed the crucial contribution of ligand interactions with EPAC1’s catalytic region to achieve full activation. The mechanistic
insights from this study suggest a design strategy to guide the development of potent small-molecule EPAC1 activators. | Adele Hardie; Frederick Powell; Silvia Lovera; Stephen Yarwood; Graeme Barker; Julien Michel | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2025-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d60f8d6dde43c908f3d541/original/elucidation-of-the-mechanism-of-partial-activation-of-epac1-allosteric-modulators-by-markov-state-modelling.pdf |
642d2207a029a26b4cf05137 | 10.26434/chemrxiv-2023-7454p | Cu₂SiSe₃ as a promising solar absorber: harnessing cation dissimilarity to avoid killer antisites | Copper-chalcogenides are promising candidates for thin film photovoltaics due to their ideal electronic structure and potential for defect tolerance. To this end, we have theoretically investigated the optoelectronic properties of Cu₂SiSe₃, due to its simple ternary composition, and the favorable difference in charge and size between the cation species, limiting antisite defects and cation disorder. We find it to have an ideal, direct bandgap of 1.52 eV and a maximum efficiency of 30% for a 1.5 μm-thick film at the radiative limit. Using hybrid density functional theory, the formation energies of all intrinsic defects are calculated, revealing the p-type copper vacancy as the dominant defect species, which forms a perturbed host state. Overall, defect concentrations are predicted to be low and have limited impact on non-radiative recombination, as a consequence of the p - d coupling and antibonding character at the valence band maxima. Therefore, we propose that Cu₂SiSe₃ should be investigated further as a potential defect-tolerant photovoltaic absorber. | Adair Nicolson; Seán R. Kavanagh; Christopher N. Savory; Graeme W. Watson; David O. Scanlon | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Photovoltaics; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642d2207a029a26b4cf05137/original/cu2si-se3-as-a-promising-solar-absorber-harnessing-cation-dissimilarity-to-avoid-killer-antisites.pdf |
67372f167be152b1d0291577 | 10.26434/chemrxiv-2024-gsk41 | Large-scale characterization of chemical bonding and topology in the Materials Project database | Topology is key to the determination of many physical and chemical properties of materials, such as electrical and optical properties, magnetic properties, thermal and mechanical behaviour, etc. However, despite the growing number of databases of crystalline materials available, there has been very little systematic effort to date to analyze their topology. In this work, we have leveraged recent algorithmic advances in the analysis of chemical bonding and topology determination in order to perform high-throughput analysis of topology of materials on a large scale databases of existing and hypothetical materials, the Materials Project data set of more than 150,000 structures. Beyond the statistical analysis of the most frequent topologies and coordination environments, the publication of this topological data will allow researchers to search for materials by topology and chemical environment, paving the way to enhanced performance in materials screening for applications. We demonstrated two examples of the usefulness of topological considerations in such computational screening. | Lionel Zoubritzky; François-Xavier Coudert | Theoretical and Computational Chemistry; Materials Science | CC BY 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67372f167be152b1d0291577/original/large-scale-characterization-of-chemical-bonding-and-topology-in-the-materials-project-database.pdf |
645104001ca6101a45a93741 | 10.26434/chemrxiv-2023-nrgnw | Using Oriented External Electric Fields to Manipulate Rupture Forces of Mechanophores | Oriented External Electric Fields (OEEFs) can catalyze chemical reactions by selectively weakening bonds. This makes them a topic of interest in mechanochemistry, where mechanical force is used to rupture specific bonds in molecules. Using electronic structure calculations based on density functional theory (DFT), we investigate the effect of OEEFs on the mechanical force required to activate mechanophores. We demonstrate that OEEFs can greatly lower the rupture force of mechanophores, and that the degree of this effect highly depends on the angle relative to the mechanical force at which the field is being applied. The greatest lowering of the rupture force does not always occur at the point of perfect alignment between OEEF and the vector of mechanical force. By combining methods to simulate molecules in OEEFs with methods applying mechanical force, we present an effective tool for analyzing mechanophores in OEEFs and show that computationally determining optimal OEEFs for mechanophore activation can assist in the development of future experimental studies. | Tarek Scheele; Tim Neudecker | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645104001ca6101a45a93741/original/using-oriented-external-electric-fields-to-manipulate-rupture-forces-of-mechanophores.pdf |
60c74476f96a00618e2869ca | 10.26434/chemrxiv.9808241.v1 | Characterization of an L-Ascorbate Catabolic Pathway with Unprecedented Enzymatic Transformations | <p>L-Ascorbate (vitamin C) is ubiquitous in both our diet and the environment. <i>Ralstonia eutropha </i>H16 (<i>Cupriavidus necator </i>ATCC 17699) uses L-ascorbate as sole carbon source but lacks the genes encoding the known catabolic pathways. RNAseq identified eight candidate catabolic genes. Sequence similarity networks and genome neighborhood networks guided predictions for function of the encoded proteins; the predictions were confirmed by <i>in vitro</i> assays and <i>in vivo</i> growth phenotypes of gene deletion mutants. L-Ascorbate, a lactone, is oxidized and ring-opened by enzymes in the cytochrome b<sub>561</sub> and gluconolactonase families, respectively, to form 2,3-diketo-L-gulonate. A protein predicted to have a WD40-like fold catalyzes an unprecedented benzilic acid rearrangement involving migration of a carboxylate group to form 2-carboxy-L-lyxonolactone; the lactone is hydrolyzed by a member of the amidohydrolase superfamily to yield 2-carboxy-L-lyxonate. A member of the PdxA family of oxidative decarboxylases catalyzes a novel decarboxylation that uses NAD<sup>+</sup> catalytically. The product, L-lyxonate, is catabolized to alpha-ketoglutarate by a previously characterized pathway.</p> | Tyler Stack; Katelyn Morrison; Thomas Dettmer; Brendan Wille; Chan Kim; Ryan Joyce; Madison Jermain; Yadanar Than Naing; Khadija Bhatti; Brian San Francisco; Michael S. Carter; John A. Gerlt | Biochemistry; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74476f96a00618e2869ca/original/characterization-of-an-l-ascorbate-catabolic-pathway-with-unprecedented-enzymatic-transformations.pdf |
6566937ecf8b3c3cd75b79e2 | 10.26434/chemrxiv-2023-78vb3-v2 | Carbene-Catalyzed Atroposelective Construction of Chiral Diaryl Ethers | Atropoisomeric chemotypes of diaryl ethers related scaffolds are prevalent in naturally active compounds. Nevertheless, there remains considerable research to be carried out on the catalytic asymmetric synthesis of these axially chiral molecules. In this instance, we disclose the first N-heterocyclic carbene catalyzed synthesis of axially chiral diaryl ethers via atroposelective esterification of dialdehyde-containing diaryl ethers. The reaction proceeds mathematically through a desymmetrization method catalyzed by NHC, which results in the production of axially chiral diaryl ether atropisomers with good yields and high enantioselectivities in mild conditions. The chiral diaryl ether compounds can be utilized as precursors for further transformation into highly functionalized diaryl ethers with potential bioactivity and as chiral ligands with uses in asymmetric catalysis. | Yuheng Liu; Lutong Yuan; Linlong Dai; Qiaohong Zhu; Guofu Zhong; Xiaofei Zeng | Organic Chemistry; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6566937ecf8b3c3cd75b79e2/original/carbene-catalyzed-atroposelective-construction-of-chiral-diaryl-ethers.pdf |
6298709d23bf1f68dab21895 | 10.26434/chemrxiv-2022-8vs90 | Disassembly Mechanisms and Energetics of Polymetallic Rings and Rotaxanes with Ion Mobility Mass Spectrometry | Understanding the fundamental reactivity of polymetallic complexes is challenging due to the complexity of their structures with many possible bond breaking and forming processes. Here we apply ion mobility mass spectrometry (IM-MS) coupled with density functional theory (DFT) to investigate the disassembly mechanisms and energetics of a family of heterometallic rings and rotaxanes with the general formula [NH2RR’][Cr7MF8(O2CtBu)16] with M = MnII, FeII, CoII, NiII, CuII, ZnII, CdII. Our results show that their stability can be tuned both by altering the d-metal composition in the macrocycle and by the end groups of the secondary ammonium cation [NH2RR’]+. Ion mobility probes the conformational landscape of the disassembly process from intact complex to structurally distinct isobaric fragments, providing unique insights to how a given divalent metal tunes the structural dynamics.
| Niklas Geue; Tom S. Bennett; Alexandra A. Arama; Lennart A.I. Ramakers; George F.S. Whitehead; Grigore A. Timco; Peter B. Armentrout; Eric J.L. McInnes; Neil A. Burton; Richard E.P. Winpenny; Perdita E. Barran | Physical Chemistry; Inorganic Chemistry; Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6298709d23bf1f68dab21895/original/disassembly-mechanisms-and-energetics-of-polymetallic-rings-and-rotaxanes-with-ion-mobility-mass-spectrometry.pdf |
60c7426d0f50db9171395cef | 10.26434/chemrxiv.8273627.v1 | 2,2’-Dipyridylamine as Organic Molecular Electrocatalyst for Hydrogen Evolution Reaction in Acidic Electrolytes | Finding a low-cost and stable electrocatalyst for hydrogen evolution reaction (HER) as a replacement for scarce and expensive precious metal catalysts has attracted significant interest from chemical and materials research communities. Here, we demonstrate an organic catalyst based on 2,2’-dipyridylamine (dpa) molecules adsorbed on carbon surface, which shows remarkable hydrogen evolution activity and performance durability in strongly acidic polymer electrolytes without involving any metal. The HER onset potential at dpa adsorbed on carbon has been found to be less than 50 mV in sulfuric acid and in a Nafion-based membrane electrode assembly (MEA). At the same time, this catalyst has shown no performance loss in a 60-hour durability test. The HER reaction mechanisms and the low onset overpotential in this system are revealed based on electrochemical study. Density functional theory (DFT) calculations suggest that the pyridyl-N functions as the active site for H adsorption with a free energy of -0.13 eV, in agreement with the unusually low onset overpotential for an organic molecular catalyst.<br /> | Xi Yin; Ling Lin; Hoon T. Chung; Ulises Martinez; Andrew M. Baker; Sandipkumar Maurya; Piotr Zelenay | Catalysts; Computational Chemistry and Modeling; Electrocatalysis; Heterogeneous Catalysis; Organocatalysis; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426d0f50db9171395cef/original/2-2-dipyridylamine-as-organic-molecular-electrocatalyst-for-hydrogen-evolution-reaction-in-acidic-electrolytes.pdf |
6667dbe012188379d8d187ab | 10.26434/chemrxiv-2024-sdx0k | Metal-Free Site-Selective Functionalization with Cyclic Diaryl λ3-Chloranes: Suppression of Benzyne Formation for Ligand-Coupling Reactions | While hypervalent halogens are versatile reagents enabling diverse reactions in organic synthesis, the utility of hypervalent chlorine compounds, particularly cyclic λ3-chloranes, remains underdeveloped despite their unique electronic properties and innate enhanced reactivity. Herein, we illustrate the elusive ligand coupling reaction of cyclic λ3-chloranes that suppresses the more facile competing reaction modality involving benzyne intermediates. The methodology can be performed in three-component as well as two-component fashion, offering direct access to a wide range of unsymmetrically substituted biaryl molecules in very high yields and excellent ortho-regioselectivity. The reactions were scalable, and the versatility was demonstrated by constructing different types of C–S and C–N bonds under mild conditions. The reaction outcomes were also compared with corresponding λ3-iodanes and λ3-bromanes, demonstrating the superiority of cyclic λ3-chloranes in ligand-coupling reactions under metal-free conditions. | Koushik Patra; Manas Pratim Dey; Mahiuddin Baidya | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6667dbe012188379d8d187ab/original/metal-free-site-selective-functionalization-with-cyclic-diaryl-3-chloranes-suppression-of-benzyne-formation-for-ligand-coupling-reactions.pdf |
60c746c2bdbb894d60a38c77 | 10.26434/chemrxiv.11393928.v1 | Modulation of Prins Cyclization by Vibrational Strong Coupling | <div>Light-molecule strong coupling has emerged within the last decade as an entirely new method to control chemical reactions. A few years ago it was discovered that the chemical reactivity could be altered by vibrational strong coupling (VSC). While the potential of VSC in organic chemistry appears enormous, only a limited number of reactions have been investigated under VSC to date, including solvolysis and deprotection reactions. Here we investigate the effect of VSC on a series of aldehydes and ketones undergoing Prins cyclization, an important synthetic step in pharmaceutical chemistry. We observe a decrease of the second-order rate constant with VSC of the reactant carbonyl stretching groups. We measure an increased activation energy due to VSC, but proportional changes in activation enthalpy and entropy suggest no substantive change in reaction pathway. The addition of common cycloaddition reactions to the stable of VSC-modified chemical reactions is another step towards establishing VSC as a genuine tool for synthetic chemistry.</div> | Kenji Hirai; Rie Takeda; JAMES HUTCHISON; Hiroshi Uji-i | Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746c2bdbb894d60a38c77/original/modulation-of-prins-cyclization-by-vibrational-strong-coupling.pdf |
66e986e212ff75c3a19ade54 | 10.26434/chemrxiv-2024-ssj00 | Reversing the Chemoselectivity in Photocatalytic C–F Bond Cleavage Enabled by Zirconocene and Photoredox Catalysis | The development of chemoselective defluorination reactions is highly desirable due to the exceptional stability of the C–F bond compared to other functional groups. Recent advances in photocatalysis have enabled cataytic single-electron transfer (SET) processes, offering an alternative to stoichiometric methods that rely on strong reducing agents. However, these strategies have primarily focused on trifluoromethyl substrates, with limited success for compounds containing fewer fluorine atoms, which are inherently more resistant to SET. Herein, we report a novel defluorination strategy for α-fluorocarbonyl compounds, employing zirconocene and photoredox catalysis. Our method leverages the strong fluorine affinity of zirconocene and bypassed reliance on reduction potential, focusing instead on the bond dissociation energy of the fluorinated molecules. This methodology offers a complementary ap-proach for catalytic C–F bond cleavage under visible-light conditions. | Haruki Takimoto; Kazuhiro Aida; Yoshio Nishimoto; Daisuke Yokogawa; Eisuke Ota; Junichiro Yamaguchi | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2024-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e986e212ff75c3a19ade54/original/reversing-the-chemoselectivity-in-photocatalytic-c-f-bond-cleavage-enabled-by-zirconocene-and-photoredox-catalysis.pdf |
63d025c5246f16b96acb84a4 | 10.26434/chemrxiv-2023-182cb | Techno-economic assessment of a cost and quality-based algal biodiesel production process | The biggest obstacles to replacing petroleum-based diesel with less-polluting biodiesel are its cost and use of arable land for feedstock production, namely food crops. Microalgae are more suitable since they don’t require arable land; however, currently it is not cost-effective, and few previous studies have analyzed its quality. To overcome these two crucial challenges, we developed a novel Cost and Quality-based Algal Biodiesel Production Process (abbreviated as CQ-Biodiesel), which produces cost-effective biodiesel while exceeding the minimum quality defined by American Standards for Testing and Materials. CQ-Biodiesel is modeled in SuperPro Designer, implementing an innovative approach where we shift focus from product retention (as in previous research) to overall cost-effectiveness. This enables minor sacrifices in productivity for maximal overall energy efficiency, attaining 98.49%. A hybrid cultivation stage is introduced in this study to maximize lipid productivity at 0.13 g/L/day, a 10% increase compared to previous studies. A closed-loop hexane extraction method is developed to decrease solvent pollu- tion by 99.4% compared to previous studies. In the US, the computed selling price is $4.71/gallon, 15% less than diesel. The present study reveals that the CQ-Biodiesel model significantly improves upon existing algal biodiesel production processes in three key aspects—cost, quality, and reduced envi- ronmental impact. | Steven Liu; Jean-Francois Hamel | Energy; Chemical Engineering and Industrial Chemistry; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d025c5246f16b96acb84a4/original/techno-economic-assessment-of-a-cost-and-quality-based-algal-biodiesel-production-process.pdf |
64383a361d262d40ea66519b | 10.26434/chemrxiv-2023-d1b3l | Bridging physical intuition and hardware efficiency for correlated electronic states: the local unitary cluster Jastrow ansatz for electronic structure | A prominent goal in quantum chemistry is to solve the molecular electronic structure problem for the ground state energy with high accuracy. While classical quantum chemistry is a relatively mature field, the accurate and scalable prediction of strongly correlated states found, e.g., in bond breaking and polynuclear transition metal compounds remains an open problem. Within the context of a variational quantum eigensolver, we propose a new family of ansatzes which provides a more physically appropriate description of strongly correlated electrons than unitary coupled cluster with singles and doubles excitations, with vastly reduced quantum resource requirements. Specifically, we present a set of local approximations to the unitary cluster Jastrow wavefunction motivated by Hubbard physics. The resulting ansatz removes the need for SWAP gates and can be tailored to arbitrary qubit topologies (e.g., square, hex, heavy-hex). Our ansatz is well-suited to take advantage of continuous sets of quantum gates recently realized on superconducting devices with tunable couplers, while retaining a unique level of physical transparency and interpretability. As the capabilities of quantum computing devices continue to progress, we expect that the local cluster Jastrow ansatz to be a natural choice to encode both statically and dynamically correlated electronic wavefunctions. | Mario Motta; Kevin J. Sung; K. Birgitta Whaley; Martin Head-Gordon; James Shee | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64383a361d262d40ea66519b/original/bridging-physical-intuition-and-hardware-efficiency-for-correlated-electronic-states-the-local-unitary-cluster-jastrow-ansatz-for-electronic-structure.pdf |
6687d3f401103d79c51872d3 | 10.26434/chemrxiv-2024-r3l1b | Non-equilibrium Spatiotemporal Patterns of Charge-transfer Supramolecular Assembly | Spatiotemporal organization and patterns are a hallmark of life, exemplified by the spatiotemporal organization of microtubules during cell division. The emerging interest in lifelike materials has motivated a paradigm shift from equilibrium to non-equilibrium supramolecular assemblies. However, the next challenge is to program the self-assembly process to drive its spatiotemporal patterns, thereby controlling its structure and properties across both space and time. In this study, we integrate a redox-based dissipative self-assembly with a reaction-diffusion system to generate spatiotemporal patterns of supramolecular assemblies. Our findings reveal that the components of dissipative self-assemblies critically influence the emergent patterns, which can be precisely directed by external perturbations, such as the addition of oxidizing agent. This approach offers a versatile strategy for manipulating a broad range of monomers to generate diverse spatiotemporal patterns of supramolecular architectures of different shapes and material properties. This enables the investigation of their collective behaviour across various length scales. This strategy not only advances our understanding to build complex non-equilibrium supramolecular architectures but also paves the way for development of lifelike materials spatiotemporally tunable properties. | Surbhi Sharma; Mohit Kumar; Jessica Erlenbusch; Ankit Sakhuja; Subi J. George; Shikha Dhiman | Physical Chemistry; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6687d3f401103d79c51872d3/original/non-equilibrium-spatiotemporal-patterns-of-charge-transfer-supramolecular-assembly.pdf |
64ae01b9ba3e99daefee4851 | 10.26434/chemrxiv-2023-xvd0q-v2 | Tuning structural coloration through evanescent wave absorption at microscale concave interfaces | Here, structural color generated by total internal reflection (TIR) interference at microscale concave interfaces is tuned via evanescent wave absorption by dyes. Using quantitative angle-resolved spectral analysis combined with ray tracing simulation, it is demonstrated that the multibounce TIR trajectories enhance the efficiency of dye absorption and usefulness in modulating the reflected colors. Depending on the absorbance spectrum of the dye used, and the amount of dye coated at the TIR interface, the angle-dependent reflected colors can be predictably altered. The use of a near-infrared absorbing dye allows for the combination of overt color-shifting iridescent effects under illumination with visible wavelengths and covert optical-motion effects under near-infrared. This work, which explores an innovative approach for controlling the reflective properties of iridescent structurally colored materials, may be of interest both for fundamental research and for applications such as sensors, coatings, and security. | Krista Hirsch; Nathaniel Sturniolo; Caleb Meredith; Malak Rayes; Lauren Zarzar | Materials Science; Optical Materials; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ae01b9ba3e99daefee4851/original/tuning-structural-coloration-through-evanescent-wave-absorption-at-microscale-concave-interfaces.pdf |
626bf9cd6c989c78e7c9f415 | 10.26434/chemrxiv-2022-hjg68 | Protein-Induced Delubrication: How plant-based and dairy proteins affect mouthfeel | Understanding how certain proteins cause astringency is necessary in order to improve the mouthfeel and popularity of plant-based foods. To this end, we studied protein interactions during oral processes using a PDMS-PDMS interface lubricated by ex-vivo human saliva. Friction measurements and in-contact imaging were implemented, while food consumption was simulated by introducing model plant and animal-based proteins. All but one of the protein samples caused an increase in measured friction and this correlated with astringency ratings from a human taste panel. This is attributed to delubrication as the salivary pellicle is removed, since food proteins interact with salivary proteins thus disrupting their adhesion. This interaction is shown to occur both on the surface and in the bulk of the fluid. However, the debonding of the pellicle requires frictional shear stress (i.e., rubbing). Food proteins in isolation are themselves shown to be surface-active and form boundary films, which can adhere following removal of the pellicle. The mechanical action of protein particles in the delubrication process was isolated by filtering and shown to account for a moderate (<33%) increase in friction magnitude accompanied by a significant (>90%) increase in frictional noise. The flow and deformation of these particles was also visualised thus demonstrating how the microscale breakdown of food can be studied. | Sorin-Cristian Vladescu; Maria Gonzalez Agurto; Connor Myant; Michael Boehm; Stefan Baier; Gleb Yakubov; Guy Carpenter; Tom Reddyhoff | Agriculture and Food Chemistry; Food | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626bf9cd6c989c78e7c9f415/original/protein-induced-delubrication-how-plant-based-and-dairy-proteins-affect-mouthfeel.pdf |
67bf3e7efa469535b90be62b | 10.26434/chemrxiv-2025-64bhb | Growing and Linking Optimizers: Synthesis-driven Molecule Design | In the present work, two reaction-based generative models for molecular design are presented: Growing Optimizer and Linking Optimizer. These models are designed to emulate real-life chemical synthesis by sequentially selecting building blocks and simulating the reactions between them to form new compounds. By focusing on the feasibility of the generated molecules, Growing Optimizer and Linking Optimizer offer several advantages, including the ability to restrict chemistry to specific building blocks, reaction types, and synthesis pathways, a crucial requirement in drug design. Unlike text-based models, which construct molecules by iteratively forming a textual representation of the molecular structure, and graph-based models, which assemble molecules atom by atom or fragment by fragment, our approach incorporates a more comprehensive understanding of chemical knowledge, making it relevant for drug discovery projects. Comparative analysis with REINVENT 4, a state-of-the-art molecular generative model, shows that Growing Optimizer and Linking Optimizer are more likely to produce synthetically accessible molecules while reaching molecules of interest with the desired properties. | Clarisse Descamps; Vincent Bouttier; Juan Sanz García; Quentin Perron; Hamza Tajmouati | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bf3e7efa469535b90be62b/original/growing-and-linking-optimizers-synthesis-driven-molecule-design.pdf |
67d6724dfa469535b9636520 | 10.26434/chemrxiv-2025-wn98j | Racemization-free peptide bond formation via 2-nitrobenzensulfonyl strategy for diastereoselective synthesis of (Z)-fluoroalkene-type peptidomimetcs | The Xaa-Pro-type (Z)-fluoroalkene dipeptide isostere (FADI) serves as a versatile surrogate for peptide bonds, effectively restricting cis–trans isomerization of the prolyl-amide bond and offering advantages in the development of conformationally constrained peptide analogues. However, the diastereoselective synthesis of tri-peptidomimetics incorporating Xaa-Pro-type FADIs is challenging due to the high susceptibility to racemization of the -stereogenic center during peptide bond formation. Here, we introduce a racemization- and epimerization-free coupling strategy for the stereoselective synthesis of fluoroalkene-type peptidomimetics by reacting Xaa-Pro-type FADIs with amino acid benzyl esters or peptides. This approach leverages the unique properties of the 2-nitrobenzenesulfonyl (Ns) group as an N-terminal protecting group, which promotes sulfonamide anion formation, effectively suppressing -deprotonation and thereby preventing racemization or epimerization. Our findings highlight the pivotal role of the N-Ns group in peptide synthesis and provide a robust platform for expanding the utility of FADIs in peptidomimetic designing. | Chihiro Iio; Kohei Sato; Nobuyuki Mase; Tetsuo NARUMI | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d6724dfa469535b9636520/original/racemization-free-peptide-bond-formation-via-2-nitrobenzensulfonyl-strategy-for-diastereoselective-synthesis-of-z-fluoroalkene-type-peptidomimetcs.pdf |
66a6030b5101a2ffa85ca797 | 10.26434/chemrxiv-2024-848r1 | The Role of sp3 Defects in Eliciting Divergent Fluorescence Response of Single-Walled Carbon Nanotubes to Dopamine and Serotonin | Modulating the optical response of fluorescent nanoparticles through rational modification of their surface chemistry can yield distinct optical signatures upon the interaction with compositionally analogous molecules. Herein, we present a novel method for tuning the fluorescence response of single-walled carbon nanotubes (SWCNTs) towards dopamine (DA) and serotonin, two compositionally similar monoamine-hydroxylated aromatic neurotransmitters, by introducing oxygen defects into (6,5) chirality-enriched SWCNTs suspended by sodium cholate (SC). This modification facilitated opposite optical responses towards these neurotransmitters, where DA significantly increased the fluorescence of the defect-induced SWCNTs (D-SWCNTs) six-fold, while serotonin notably decreased it. In contrast, pristine, defect-free SWCNTs exhibited similar optical responses to both neurotransmitters. The underlying mechanisms for the divergent fluorescence response were found to be polydopamine (PDA) surface adsorption in the case of DA’s fluorescence enhancement, while serotonin’s fluorescence decrease was attributed to enhanced solvent relaxation effects in the presence of defects. Importantly, the divergent optical response between DA and serotonin by D-SWCNTs via the introduction of defects was validated in complex biological environments, such as serum. Further, the generality of our approach was confirmed by the successful demonstrations of a divergent fluorescence response of D-SWCNT suspended by an additional dispersant, namely lipid–polyethylene glycol (PEG). This study offers promising avenues for the broad applicability of tailored surface functionalization of SWCNTs to achieve divergent responses towards compositionally similar molecules and advance innovative applications in sensing, imaging, and diagnostic technologies. | Srestha Basu; Adi Hendler-Neumark; Gili Bisker | Physical Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a6030b5101a2ffa85ca797/original/the-role-of-sp3-defects-in-eliciting-divergent-fluorescence-response-of-single-walled-carbon-nanotubes-to-dopamine-and-serotonin.pdf |
6731de65f9980725cfd25336 | 10.26434/chemrxiv-2024-xt0rj | Novel Imidazopyridine Derivatives Targeting Cytochrome bd Oxidase: A Promising Strategy to Combat Tuberculosis
| Tuberculosis (TB) treatment is time-consuming and is further worsened due to multi-drug resistance and toxicities. Hence, there is a need for the discovery of newer antituberculosis drugs. One of the important and emerging areas of discovering new drugs is by hindering the energy metabolism generator pathway like oxidative phosphorylation (OP) which helps the sustainability of both the replicating and dormant forms of the bacterium in the host. The drugs including Telacebec (Q203) and Bedaquiline target the OP pathway enzymes cytochrome bc1 complex and ATP synthase. However, the tuberculosis bacterium survives even after the inhibition of these enzymes due to the compensatory energy production by Mycobacterium tuberculosis-cytochrome bd oxidase enzyme leading to drug resistance. Additionally, this enzyme helps the survival of the organism in aerobic conditions and in the presence of stress factors including hypoxia conditions, reactive oxygen and nitrogen species. Hence, cytochrome bd oxidase is a promising target for the discovery of novel antitubercular lead candidates. Our work employed computational techniques to design and identify novel imidazopyridines that inhibit cytochrome bd oxidase for developing antitubercular drugs. SwissSimilarity screened structurally similar compounds from the ZINC database and resulted in 989 compounds containing different rings. However, we excluded all the non-bicyclic analogues and this resulted in a library of 824 drug-like candidates as most of the bicyclic compounds showed promising inhibitory action. Further, we considered the versatile nature of amine functionality in terms of synthetic feasibility and improving the antitubercular potency and selected 262 amine-modified derivatives of imidazopyridine (1 to 262). These 262 compounds along with three reported cytochrome bd oxidase inhibitors including amiloride derivative (1a), 2-(Quinolin-4-yloxy)acetamide (2a), and 2-Arylquinolone (3a) were docked against cytochrome bd oxidase (PDB ID: 7NKZ, 2.5 Å). This process identified 255 as the best lead candidate with a docking score of -8.38 than the other 268 compounds and the reported three compounds-1a (-7.47), 2a (-5.70) and 3a (-5.35). These results suggest that the imidazopyridine derivative 255 is a promising lead compound based on its docking score and favorable binding properties indicating strong potential for further development as an anti-TB agent. | Afzal Shaik; Sreecharan Ekambarapu ; Nitin Kalia; Srikanth Danaboina; Srinivas Nanduri | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6731de65f9980725cfd25336/original/novel-imidazopyridine-derivatives-targeting-cytochrome-bd-oxidase-a-promising-strategy-to-combat-tuberculosis.pdf |
647fbb2ae64f843f416e7f53 | 10.26434/chemrxiv-2023-2cvbs | Mutexa: A Computational Ecosystem for Intelligent
Protein Engineering | Protein engineering holds immense promise in shaping the future of biomedicine and biotechnology. This review focuses on our ongoing development of Mutexa, a computational ecosystem designed to enable "intelligent protein engineering". In this vision, researchers can seamlessly acquire sequences of protein variants with desired functions as biocatalysts, therapeutic peptides, and diagnostic proteins by interacting with a computational machine, similar to how we use Amazon Alexa in these days. The technical foundation of Mutexa has been established through the development of database that integrates enzyme structures with their respective functions (e.g., IntEnzyDB), workflow software packages that enable high-throughput protein modeling (e.g., EnzyHTP and LassoHTP), and scoring functions that map the sequence-structure-function relationship of proteins (e.g., EnzyKR and DeepLasso). We will showcase the applications of these tools in benchmarking the convergence conditions of enzyme functional descriptors across mutants, investigating protein electrostatics and cavity distributions in SAM-dependent methyltransferases, and understanding the role of non-electrostatic dynamic effects in enzyme catalysis. Finally, we will conclude by addressing the future steps and challenges in our endeavor to develop new Mutexa applications that facilitate the selection of beneficial mutants in enzyme engineering. | Zhongyue Yang; Qianzhen Shao; Yaoyukun Jiang; Christopher Jurich; Xinchun Ran; Reecan Juarez; Bailu Yan; Sebastian Stull; Anvita Gollu; Ning Ding | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Computational Chemistry and Modeling; Artificial Intelligence; Biocatalysis | CC BY NC 4.0 | CHEMRXIV | 2023-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647fbb2ae64f843f416e7f53/original/mutexa-a-computational-ecosystem-for-intelligent-protein-engineering.pdf |
6103ea4e8f6bf6461771f4ea | 10.26434/chemrxiv-2021-ls95s | Validation of a hemiacetal intermediate during absolute Soai autocatalytic amplification under heterogenous phase | Absolute asymmetric synthesis produces chiral molecules without any chiral polarization and is an interesting rational for the origin of homochirality. Remarkably, in the Soai reaction absolute asymmetric amplification of alkanol product is observed under heterogenous conditions. Reaction of iPr2Zn vapor on solid carbaldehyde produced corresponding alkanol with up to 96% ee. In a parallel amplification process, a chiral ester is produced with 98% ee. The latter is attributed to disproportionation of starting aldehyde into hemiacetal followed by a subsequent Claisen-Tishchenko mechanism. This observation provide evidence for the debated transient intermediate, and opens new perspectives in the elucidation of the mechanism of amplification of chirality in the Soai reaction. | Mohamed Amedjkouh; Giuseppe Rotunno | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Physical Organic Chemistry; Stereochemistry | CC BY NC 4.0 | CHEMRXIV | 2021-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6103ea4e8f6bf6461771f4ea/original/validation-of-a-hemiacetal-intermediate-during-absolute-soai-autocatalytic-amplification-under-heterogenous-phase.pdf |
65bce0fa66c1381729cef52e | 10.26434/chemrxiv-2024-kkn30 | Time-dependent deep learning manufacturing process model for battery electrode microstructure prediction | The manufacturing process of Lithium-ion battery electrodes directly affects the practical properties of the cells, such as their performance, durability, and safety. While computational physics-based modeling has been proved as a useful method to produce insights on the manufacturing properties interdependencies as well as the formation of electrode microstructures, their high computational costs avoid their direct utilization in electrode optimization loops. In this work, we report a novel time-dependent deep learning (DL) model of battery electrodes manufacturing process, demonstrated for calendering of NMC111 electrodes, and trained with time-series data arising from physics-based Discrete Element Method (DEM) simulations. The DL model predictions are validated by comparing evaluation metrics (e.g. MSE and R2 score) and electrode functional metrics (contact surface area, porosity, diffusivity and tortuosity factor), showing very good accuracy with respect to the DEM simulations. Our DL model can remarkably capture the elastic recovery of the electrode upon compression (spring-back phenomenon) and the main 3D electrode microstructure features without using the functional descriptors for its training. Furthermore, our DL model has a significantly less computational cost that the DEM simulations, paving the way towards quasi-real time optimization loops of the 3D electrode architecture predicting the calendering conditions to adopt in order to obtain the desired electrode performance. | Diego E. Galvez-Aranda; Tan Le Dinh; Utkarsh Vijay; Franco M. Zanotto; Alejandro A. Franco | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Theory - Computational; Artificial Intelligence; Energy Storage | CC BY 4.0 | CHEMRXIV | 2024-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bce0fa66c1381729cef52e/original/time-dependent-deep-learning-manufacturing-process-model-for-battery-electrode-microstructure-prediction.pdf |
67852c71fa469535b9d28d7b | 10.26434/chemrxiv-2024-zh4w2-v3 | Bridging Oxide Thermodynamics and Site-Blocking: A Computational Study of ORR Activity on Platinum Nanoparticles | The Oxygen Reduction Reaction (ORR) is a key reaction in fuel cells and metal-air batteries, where high overpotentials remain a critical challenge despite extensive research. While experimental studies have revealed the importance of surface oxidation, a unified computational framework capable of simultaneously capturing both the thermodynamic aspects of rate-determining steps and the kinetic effects of site-blocking on the overpotential has remained elusive. In this work, we present a novel computational approach that bridges this gap by combining grand-canonical Monte Carlo simulations with the MACE-MP-0 foundation model to study the ORR on experimentally reconstructed Pt nanoparticles. This framework enables the systematic investigation of oxidation effects across multiple scales, from atomic-level place-exchange mechanisms to macroscopic kinetic behavior. Our simulations reveal a strong dependence of system thermodynamics on oxygen coverage and successfully predict the place-exchange mechanism onset at 1.06 V vs. SHE, in agreement with experimental observations. Through established scaling relations and deletion energy analysis, we quantify both the rate-determining step and the distribution of reactive sites on the oxidized surface, providing insight into the complex interplay between surface oxidation and ORR activity. By linking our results with both theoretical and experimental benchmarks on multiple points, we ensure the viability of our assumptions and approach. Using a simplified kinetic model derived from our simulations, we demonstrate agreement with core experimental observations, validating the predictive power of foundation models in computational electrochemistry. This work not only provides a comprehensive understanding of oxide effects in ORR but also establishes a versatile computational methodology that can be readily extended to study similar electrochemical processes on other catalytic systems, offering a powerful new tool for rational catalyst design. | Tom Demeyere; Tom Ellaby; Misbah Sarwar; David Thompsett; Chris-Kriton Skylaris | Theoretical and Computational Chemistry; Catalysis; Machine Learning; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67852c71fa469535b9d28d7b/original/bridging-oxide-thermodynamics-and-site-blocking-a-computational-study-of-orr-activity-on-platinum-nanoparticles.pdf |
60d158a7261611c1128b9e68 | 10.26434/chemrxiv-2021-hvb1j-v2 | Observation of an Intermediate to H2 Binding in a Metal–organic Framework | Coordinatively-unsaturated metal sites within certain zeolites and metal–organic frameworks can strongly adsorb various molecules. While many classical examples involve electron-poor metal cations that interact with adsorbates largely through electrostatic interactions, unsaturated electron-rich metal centers housed within porous frameworks can often chemisorb guests amenable to redox activity or covalent bond formation. Despite the promise that materials bearing such sites hold in addressing myriad challenges in gas separations and storage, very few studies have directly interrogated mechanisms of chemisorption at open metal sites within porous frameworks. Here, we show that H<sub>2</sub>chemisorption at the trigonal pyramidal Cu<sup>+</sup>sites in the metal–organic framework Cu<sup>I</sup>‑MFU-4<i>l </i>occurs via the intermediacy of a metastable physisorbed precursor species. This finding demonstrates that adsorption at framework metal sites does not always follow a concerted pathway and underscores the importance of probing kinetics in the design of next-generation adsorbents<b>.</b> | Brandon R. Barnett; Hayden A. Evans; Gregory M. Su; Henry Z. H. Jiang; Romit Chakraborty; Didier Banyeretse; Tyler Hartman; Madison Martinez; Benjamin A. Trump; Jacob Tarver; Matthew Dods; Lena M. Funke; Jonas Börgel; Jeffrey A. Reimer; Walter S. Drisdell; Katherine Hurst; Thomas Gennett; Stephen A. FitzGerald; Craig M. Brown; Martin Head-Gordon; Jeffrey R. Long | Materials Science; Inorganic Chemistry; Hybrid Organic-Inorganic Materials; Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d158a7261611c1128b9e68/original/observation-of-an-intermediate-to-h2-binding-in-a-metal-organic-framework.pdf |
60c74f04469df4418df445ef | 10.26434/chemrxiv.12839261.v1 | Dendritic Fibrous Nanosilica (DFNS) for RNA Extraction from Cells | Efficient RNA extraction is critical for all
downstream molecular applications and techniques. Despite the availability of
several commercial kits, there is an enormous scope to develop novel materials
that have high binding and elution capacities. Here we show that RNA from the
cells can be extracted by dendritic fibrous nanosilica (DFNS) with higher efficiency
than commercially available silica. This could be because of the unique fibrous
morphology, high accessible surface area, and nano-size particles of DFNS. We
studied various fundamental aspects, including the role of particle size,
morphology, surface area, and charge on silica surface on RNA extraction
efficiency. Infrared spectroscopy (FTIR) studies revealed the interaction of
functional groups of the RNA with the silica surface, causing selective
binding. Due to the sustainable synthesis protocol of DFNS, the simplicity of
various buffers and washing solutions used, this RNA extraction kits can be assembled
in any lab. In addition to the fundamental aspects of DFNS-RNA interactions,
this study has the potential to initiate the development of indigenous DFNS
based kits for RNA extraction. | Ayan Maity; U. S. Sandra; Ullas Kolthur-Seetharam; Vivek Polshettiwar | Biochemical Analysis; Nanostructured Materials - Nanoscience; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f04469df4418df445ef/original/dendritic-fibrous-nanosilica-dfns-for-rna-extraction-from-cells.pdf |
67819b93fa469535b982b707 | 10.26434/chemrxiv-2025-nvv8h | Identifying driving and spectator phonon modes in pentacene exciton transport | In organic semiconductors, crystal packing motif is known to modify electronic properties, like exciton transport dynamics. Phonon vibrations can drive or hinder exciton transport and understanding the role of these intermolecular vibrations can aid in the rational design of materials for improved solar cell efficiency. In this paper, we use a double pulse spatially offset femtosecond stimulated Raman spectroscopy (SOFSRS) to identify the functional role of phonon modes in pentacene exciton transport. In SOFSRS, we photoexcite our sample at a spatially offset position relative to the Raman pump and probe, which allows us to track changes in the excited state structure over micron length scales and femtosecond timescales during exciton transport. We first measure the phonon modes in a single crystal and then use optical pulse shaping to selectively amplify each mode and measure the resulting exciton transport dynamics along the fast and slow transport axes using SOFSRS. We compare the resulting dynamics with a single pulse excitation SOFSRS to unambiguously assign driving and spectator phonon modes. We find that a 91 cm-1 phonon mode drives exciton transport preferentially along the slow transport axis. We also find two modes at 161 and 176 cm-1 that drive an increase in the overall excited state population and use computations to assign a plausible mechanism. This study presents a new experimental method that is capable of determining the functional role of phonon vibrations in mediating exciton transport. | Pauline Lynch; Renee Frontiera | Physical Chemistry; Energy; Photovoltaics; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2025-01-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67819b93fa469535b982b707/original/identifying-driving-and-spectator-phonon-modes-in-pentacene-exciton-transport.pdf |
663d730421291e5d1de320b5 | 10.26434/chemrxiv-2024-jqp0c | A three-component hydrogen bonded framework | A porous three-component hydrogen bonded framework, 1∙biphen∙TP, was prepared from a tetra-amidinium component (14+) and two different dianions, benzene-1,4-dicarboxylate (terephthalate, TP2–) and biphenyl-4,4′-dicarboxylate (biphen2–). Interestingly, when the framework was prepared in ethanol/water, 1∙biphen∙TP forms even when an excess of either dicarboxylate is present. However, when only water is used as solvent, only two-component frameworks are formed. | Phonlakrit Muang-Non; Meabh Perry-Britton; Lauren Macreadie; Nicholas White | Organic Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.); Materials Chemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663d730421291e5d1de320b5/original/a-three-component-hydrogen-bonded-framework.pdf |
63885c270058eb8a3d6c2349 | 10.26434/chemrxiv-2022-9vlxl-v2 | Fluorescent Organometallic Dyads and Triads: Establishing spatial Relationships | FRET pairs involving up to three different Bodipy dyes are utilized to provide information on the assembly/disassembly of organometallic complexes. Azolium salts tagged with chemically robust and photostable blue or green or red fluorescent Bodipy, respectively, were synthesized and the azolium salts used to prepare metal complexes [(NHC_blue)ML], [(NHC_green)ML] and [(NHC_red)ML] (ML = Pd(allyl)Cl, IrCl(cod), RhCl(cod), AuCl, Au(NTf2), CuBr). The blue and the green Bodipy and the green and the red Bodipy, respectively, were designed to allow the formation of efficient FRET pairs with minimal cross-talk. Organometallic dyads formed from two subunits enable the transfer of excitation energy from the donor dye to the acceptor dye. The blue, green and red emission provide three information channels on the formation of complexes, which is demonstrated for alkyne or sulfur bridged digold species and for ion pairing of a red fluorescent cation and a green fluorescent anion. This approach is extended to probe an assembly of three different subunits. In such a triad, each component is tagged with either a blue, a green or a red Bodipy and the energy transfer blue green red proves the formation of the triad. The tagging of molecular components with robust fluorophores can be a general strategy in (organometallic) chemistry to establish connectivities for intermediates in homogeneous catalysis | Herbert Plenio; Yoshinao Shinozaki; Stepan Popov | Organometallic Chemistry; Spectroscopy (Organomet.); Transition Metal Complexes (Organomet.) | CC BY 4.0 | CHEMRXIV | 2022-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63885c270058eb8a3d6c2349/original/fluorescent-organometallic-dyads-and-triads-establishing-spatial-relationships.pdf |
60c74e47bb8c1ae2a73db70f | 10.26434/chemrxiv.12732137.v1 | Polarised Covalent Thorium(IV)- and Uranium(IV)-Silicon Bonds | We report the synthesis and characterisation of isostructural thorium(IV)- and uranium(IV)-
silanide complexes, providing the first structurally authenticated Th-Si bond and a rare example of a
molecular U-Si bond. These complexes therefore present the first opportunity to directly compare the
chemical bonding of Th-Si and U-Si bonds. Quantum chemical calculations show significant and
surprisingly similar 7s, 6d, and 5f orbital contributions from both actinide (An) elements in polarised
covalent An-Si bonds | Benjamin Reant; Victoria
E. J. Berryman; John A. Seed; Annabel Basford; Alasdair Formanuik; Ashley J. Wooles; Nikolas Kaltsoyannis; Stephen T. Liddle; David Mills | Lanthanides and Actinides; Organometallic Compounds; Theory - Inorganic; Coordination Chemistry (Organomet.); Ligands (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e47bb8c1ae2a73db70f/original/polarised-covalent-thorium-iv-and-uranium-iv-silicon-bonds.pdf |
623b53f321e2d0f661ae4911 | 10.26434/chemrxiv-2022-5jwkz | Surface Modified Nano-Electrospray Needles Improve Sensitivity for Native Mass Spectrometry | Native mass spectrometry (MS) and charge detection-mass spectrometry (CD-MS) have become versatile tools for characterizing a wide range of proteins and macromolecular complexes. Both commonly use nano-electrospray ionization (nESI) from pulled borosilicate needles, but some analytes are known to nonspecifically adsorb to the glass, which may lower sensitivity and limit the quality of the data. To improve the sensitivity of native MS and CD-MS, we modified the surface of nESI needles with inert surface modifiers, including polyethylene-glycol. We found that the surface modification improved the signal intensity for native MS of proteins and for CD-MS of adeno-associated viral capsids. These surface modified needles provide a simple and inexpensive method for improving the sensitivity of challenging analytes. | Marius Kostelic; Chih-Chieh Hsieh; Ciara Zak; Jack Ryan; Erin Baker; Craig Aspinwall; Michael Marty | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623b53f321e2d0f661ae4911/original/surface-modified-nano-electrospray-needles-improve-sensitivity-for-native-mass-spectrometry.pdf |
64e0fbde00bbebf0e675223b | 10.26434/chemrxiv-2023-kxck8 | Dependence of the structure and properties of Ba6Co6O15+δCl on the starting materials | Structural refinements of Ba6Co6O15+δCl prepared using two different sources of barium oxide reveals that two different values of δ, 0.574(3) and 0.914(8), are obtained on synthesis at the same temperature in air. The refinements are based on powder X-ray diffraction data obtained with high intensity synchrotron radiation, performed to increase the sensitivity of the refinements to the oxygen contents. The magnetic and electronic properties of the materials, measured and reported here, support the differences in formula and structure but are not changed dramatically by the change in oxygen content. | Seth Walensky; Danrui Ni; Robert Cava | Materials Science; Inorganic Chemistry; Magnetic Materials; Nanostructured Materials - Materials; Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e0fbde00bbebf0e675223b/original/dependence-of-the-structure-and-properties-of-ba6co6o15-cl-on-the-starting-materials.pdf |
612224c2f71bc838fc2a7000 | 10.26434/chemrxiv-2021-lsxnx | Bioorthogonal photocatalytic decaging-enabled spatiotemporal proteomics | Spatiotemporally resolved dissection of subcellular proteome is crucial to our understanding of cellular functions in health and disease. Although enzyme-based proximity labeling strategies have emerged as powerful methods to portray the compartmentalized proteome of diverse organelles, current approaches still suffer from limitations such as the genetic operation that is not compatible with hard-to-transfect cells as well as overexpression of the fusion protein that may cause altered intracellular localization. We herein report a non-genetic strategy termed bioorthogonal and photocatalytic decaging-mediated proximity labeling (CAT-Prox) for spatiotemporally resolved proteome profiling in living cells. Our systematic survey of the organometallic photocatalysts has led to the identification of Ir(ppy)2bpy as a bioorthogonal and mitochondria-targeting complex that allowed photo-controlled, rapid rescue of azidobenzyl-caged quinone methide as a highly reactive Michael acceptor for proximity-based protein labelings. By coupling with quantitative mass spectrometry, CAT-Prox revealed the dynamic mitochondria proteome of cancer cells and macrophage cells under normal and stressed conditions. Furthermore, by targeting the photocatalyst to cell membrane receptors, CAT-Prox allowed microdomain proteome profiling on live cell surface. Together, CAT-Prox integrated the advantages of both enzymatic and chemical-based proximity labeling approaches as a general spatiotemporal proteomics platform for diverse subcellular spaces and cell types. | Zongyu Huang; Ziqi Liu; Xiao Xie; Ruxin Zeng; Zujie Chen; Linghao Kong; Xinyuan Fan; Peng Chen | Organic Chemistry; Catalysis; Organometallic Chemistry; Photocatalysis; Catalysis; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612224c2f71bc838fc2a7000/original/bioorthogonal-photocatalytic-decaging-enabled-spatiotemporal-proteomics.pdf |
61457db478257b341f20e31f | 10.26434/chemrxiv-2021-47f84 | High-Temperature Decomposition of Diisopropyl Methylphosphonate (DIMP) on Alumina: Mechanistic Predictions from Ab Initio Molecular Dynamics | The enhanced degradation of organophosphorous-based chemical warfare agents (CWAs) on metal-oxide surfaces holds immense promise for neutralization efforts; however, the underlying mechanisms in this process remain poorly understood. We utilize large-scale quantum calculations for the first time to probe the high-temperature degradation of diisopropyl methylphosphonate (DIMP), a nerve agent simulant. Our Born-Oppenheimer molecular dynamics (BOMD) calculations show that the gamma-Al2O3 surface shows immense promise for quickly adsorbing and destroying CWAs. We find that the alumina surface quickly adsorbs DIMP at all temperatures, and subsequent decomposition of DIMP proceeds via a propene elimination. Our BOMD calculations are complemented with metadynamics simulations to produce free energy paths, which show that the activation barrier decreases with temperature and DIMP readily decomposes on gamma-Al2O3. Our first-principle BOMD and metadynamics simulations provide crucial diagnostics for sarin decomposition models and mechanistic information for examining CWA decomposition reactions on other candidate metal oxide surfaces. | Sohag Biswas; Bryan Wong | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Theory - Computational; Physical and Chemical Properties; Surface | CC BY 4.0 | CHEMRXIV | 2021-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61457db478257b341f20e31f/original/high-temperature-decomposition-of-diisopropyl-methylphosphonate-dimp-on-alumina-mechanistic-predictions-from-ab-initio-molecular-dynamics.pdf |
678f5685fa469535b9f331d1 | 10.26434/chemrxiv-2025-pspxs-v2 | Ni-catalyzed Heteroaryl C‒O Bond Arylation and Homocoupling via Controlled Metal−Ligand Redox Cooperativity | Aryl ethers derived from natural sources offer a sustainable alternative to traditional aryl halides in transition-metal-catalyzed cross-coupling reactions, and challenges in their selective activation have been addressed over the past 40 years. Building on these successful researches, the focus has now shifted to bioactive molecules, such as heteroaryl ethers. Here we reported a selective C–O arylation for methoxy-heteroarene and further homocoupling by Nickel catalyst. Detailed mechanistic studies showed a 2-electron pathway was involved in C–O arylation by in-situ monitoring X-ray absorption spectroscopy (XAS) and secondary kinetic isotope experiments. Metal-ligand redox cooperation between nickel center and pyridine derivatives caused a single-electron homocoupling to form bipyridine skeleton, which is proved via XAS, in-situ monitoring ESR experiments, and characterization of isolated Ni(I) intermediates. Moreover, broad substrate scope of arylpyridines and bipyridines were applied with this synthetic strategy. It also provides a mechanistic perspective for nickel-catalyzed cross coupling via metal-ligand redox cooperation. | Chen-Hsun Hung; Jiun-Shian Shen; Tiow-gan Ong; Manman Zhu; Jia-Huei Luoh; Jie-Ting Fu; Chih-Wen Pao; Glenn P. A. Yap; Ping-Yu Chen; Lili Zhao Zhao; Ting-Hsuan Wang | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Bond Activation; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678f5685fa469535b9f331d1/original/ni-catalyzed-heteroaryl-c-o-bond-arylation-and-homocoupling-via-controlled-metal-ligand-redox-cooperativity.pdf |
60c75544ee301c6574c7b14a | 10.26434/chemrxiv.13875842.v2 | Enzymatic RNA Production from NTPs Synthesized from Nucleosides and Trimetaphosphate | <p>A mechanism of nucleoside triphosphorylation would have been critical in an evolving “RNA world” to provide high-energy substrates for reactions such as RNA polymerization. However, synthetic approaches to produce ribonucleoside triphosphoates (rNTPs) have suffered from conditions such as high temperatures or high pH that lead to increased RNA degradation, as well as substrate production that cannot sustain replication. We demonstrate that cyclic trimetaphosphate (cTmp) can react with nucleosides to form rNTPs under mild, prebiotically-relevant conditions, with second-order rate constants ranging from 1.7 x 10<sup>–6</sup> to 6.5 x 10<sup>–6</sup> M<sup>–1</sup> s<sup>–1</sup>. The ATP reaction shows a linear dependence on pH and Mg<sup>2+</sup>, and an enthalpy of activation of 88 ± 4 kJ/mol. At millimolar nucleoside and cTmp concentrations, the rNTP production rate is sufficient to facilitate RNA synthesis by both T7 RNA polymerase and a polymerase ribozyme. We suggest that the optimized reaction of cTmp with nucleosides may provide a viable connection between prebiotic nucleotide synthesis and RNA replication.</p> | Fabio Chizzolini; Alexandra Kent; Luiz F. M. Passalacqua; Andrej Lupták | Bioorganic Chemistry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75544ee301c6574c7b14a/original/enzymatic-rna-production-from-nt-ps-synthesized-from-nucleosides-and-trimetaphosphate.pdf |
6706a93612ff75c3a1f8c995 | 10.26434/chemrxiv-2024-91h02 | Intrinsic point defect tolerance in selenium for indoor and tandem photovoltaics | Selenium has reemerged as a promising absorber material for tandem and indoor photovoltaic (PV) devices due to its elemental simplicity, unique structural features, and wide band gap. However, despite rapid recent improvements, record Se solar cells only reach a third of their achievable efficiencies at the radiative limit, primarily due to a low open-circuit voltage relative to the band gap. The origins of this voltage deficit, along with the high doping densities often reported for trigonal selenium (t-Se), remain unclear. Here, we explore the point defect chemistry of t-Se combining first-principles calculations with experimental studies of thin-films from state- of-the-art PV devices. Our findings reveal a remarkable ability of the helical t-Se chains to reconstruct and form low-energy amphoteric defects, particularly in the case of self-vacancies and hydrogen, pnictogen, and halogen impurities. While chalcogen impurities and self-interstitials also form low-energy defects, these are electrically neutral. We also find that both intrinsic and extrinsic point defects do not contribute significantly to doping, either due to electrical inactivity (chalcogens) or self-compensation (hydrogen, halogens, pnictogens). Finally, we show that intrinsic point defects do not form detrimental non-radiative recombination centres and propose that PV performance is instead limited by other factors. These findings highlight the potential of Se as a defect-tolerant absorber, while optimising interfaces and extended structural imperfections is key to unlocking its full performance potential. | Seán R. Kavanagh; Rasmus S. Nielsen; John L. Hansen; Rasmus S. Davidsen; Ole Hansen; Alp E. Samli; Peter C. Vesborg; David O. Scanlon; Aron Walsh | Theoretical and Computational Chemistry; Materials Science; Thin Films; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6706a93612ff75c3a1f8c995/original/intrinsic-point-defect-tolerance-in-selenium-for-indoor-and-tandem-photovoltaics.pdf |
64017e3e37e01856dc0e2636 | 10.26434/chemrxiv-2023-dlx9v | Dielectric relaxation and dielectric decrement in ionic acetamide deep eutectic solvents: Spectral decomposition and comparison with experiments | Frequency dependent dielectric relaxation in the three deep eutectic solvents (DESs), (acetamide+LiClO4/NO3/Br), was investigated in the temperature range, 329T/K358, via molecular dynamics (MD) simulations. Subsequently, decomposition of the real and the imaginary components of the simulated dielectric spectra was carried out to separate the rotational (dipole-dipole), translational (ion-ion) and ro-translational (dipole-ion) contributions. The dipolar contribution, as expected, was found to dominate all the frequency dependent dielectric spectra over the entire frequency regime, while the other two components together made tiny contributions only. The translational (ion-ion) and the cross ro-translational contributions appeared in the THz regime in contrast to the viscosity dependent dipolar relaxations that dominated the MHz-GHz frequency window. Our simulations predicted, in agreement with experiments, anion dependent decrement of the static dielectric constant (_s ~ 20 - 30) for acetamide (_s ~66) in these ionic DESs. Simulated dipole-correlations (Kirkwood g factor) indicated significant orientational frustrations. The frustrated orientational structure was found to be associated with the anion dependent damage of the acetamide H-bond network. Single dipole reorientation time distributions suggested slowed down acetamide rotations but did not indicate presence of any rotationally frozen molecules. The dielectric decrement is, therefore, largely static in origin. This provides a new insight into the ion dependence of the dielectric behaviour of these ionic DESs. A good agreement between the simulated and the experimental timescales was also noticed. | Dhrubajyoti Maji; RANJIT Biswas | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64017e3e37e01856dc0e2636/original/dielectric-relaxation-and-dielectric-decrement-in-ionic-acetamide-deep-eutectic-solvents-spectral-decomposition-and-comparison-with-experiments.pdf |
60c73f5abb8c1a631e3d9aa3 | 10.26434/chemrxiv.6974024.v2 | Exploring peptide capture by anti-protein antibodies for LC-MS-based biomarker determination | <p>Immunocapture LC-MS/MS is a
promising technique to ensure high sensitivity and selectivity of low-abundant
protein biomarkers. For this purpose, the use of monoclonal antibodies (mAb) is
especially attractive as they are renewable reagents that can be standardized.
In this article we investigated the possibility of using mAbs developed against
intact proteins (anti-protein antibodies) to capture proteotypic epitope
peptides. Three mAbs were tested, and all selectively extracted proteotypic
epitope peptides from a complex sample. Compared to intact protein extraction,
this concept which we call peptide capture by anti-protein antibodies provided
cleaner extracts, which further improved the sensitivity. Analysis of three
patient samples demonstrated that p can be used for the determination of
different endogenous protein levels. </p><p></p> | Maren Levernæs; Bassem Farhat; Inger Oulie; Sazan S. Abdullah; Elisabeth Paus; Léon Reubsaet; Trine Grønhaug Halvorsen | Analytical Chemistry - General; Mass Spectrometry; Separation Science; Biochemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5abb8c1a631e3d9aa3/original/exploring-peptide-capture-by-anti-protein-antibodies-for-lc-ms-based-biomarker-determination.pdf |
655483b5dbd7c8b54b4d1d6d | 10.26434/chemrxiv-2023-tsppg | Nanometric determination of the thickness of aqueous samples for accurate molar absorption coefficients of water-soluble molecules in the mid-infrared region | Absorption spectra of aqueous samples measured by transmission need to be acquired using very thin cells (5-50 μm) when targeting the mid-infrared (mid-IR) region, due to the strong background absorbance of liquid water. The thickness of the cell used controls the pathlength of the light through the sample, a value needed for instance to transform absorption spectra into molar absorption coefficient spectra, or to determine solute concentrations from absorption spectra. The most accurate way to determine the thickness of a thin empty cell (i.e., filled with air) is from the period of an interference pattern, known as interference fringes, that arises when the cell is placed perpendicular to the path of light in the spectrometer. However, this same approach is not directly applicable to determine the thickness of a cells filled with an aqueous solution, due partially to the smaller amplitude of the interference fringes but fundamentally caused by its complex waveform, with a wavenumber-dependent oscillation period. Here, using Fresnel equations, we derived analytical expressions to model interference fringes in absorption spectra obtained by transmission, valid also for aqueous samples. We also present a novel Fourier-based analysis of the interference fringes that, in combination with the derived analytical expressions, allowed us to determine the pathlength of aqueous samples with an error below 50 nm. We implemented this novel approach to analyze interference fringes as a Live Script running in the software Matlab. As an application, we measured absorption spectra of a 97 mM solution of MES buffer (at low and high pH) using cells of various nominal thicknesses (6, 25 and 50 μm). The molar absorption coefficient spectrum for the acidic and basic forms of MES, worked out using pathlengths values determined using the present approach, were virtually identical regardless of the nominal thickness of the cells used, indicating that the thickness determined for the cells were consistent and likely very accurate. These results illustrate the performance of the presented method to determine the pathlength of aqueous samples, as well as for its utility to obtain accurate molar absorption coefficient spectra of water-soluble molecules in the mid-IR region. | Mónica Gutierrez-Salazar; Victor A. Lorenz Fonfria | Analytical Chemistry; Spectroscopy (Anal. Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655483b5dbd7c8b54b4d1d6d/original/nanometric-determination-of-the-thickness-of-aqueous-samples-for-accurate-molar-absorption-coefficients-of-water-soluble-molecules-in-the-mid-infrared-region.pdf |
624236b974104f4d17b632d4 | 10.26434/chemrxiv-2022-zxwhj | Solid Phase Extraction on Reverse Phase Chromatographic Media Subjected to Stresses Expected for Extraterrestrial Implementation | Sample preparation techniques, such as solid phase extraction, will likely be required for in situ analysis of liquid samples collected from bodies in our solar system that contain liquid, to concentration and desalt analytes of interest from the expected brines on these Ocean Worlds. Media to be used for these extraction procedures will have to survive the stresses of the long spaceflight required to reach these bodies, and remain functional once at that location. This work utilized tryptophan as an initial representative analyte to evaluate capture and desalting efficiencies in silica and polymeric reverse phase media, to determine how these solid phases might withstand stresses they could experience during deployment, including vacuum exposure, freezing, and heating/sonication treatments. Further experimentation on irradiation and long term freezing of media with an expanded array of analytes evaluated the utility of reverse phase media for this application. Kromasil® C-18 silica particles performed well, showing no loss in capture or desalting efficiency for the initial stress treatments or irradiation, but long term freezing after irradiation caused issues with this media. Oasis® HLB polymeric particles performed better, with 100% capture efficiency and 90% recovery of the tryptophan analyte for all treated and the untreated media. Onyx C-18 guard cartridges, a reverse phase C-18 modified silica monolithic media, exhibiting 100% capture efficiency and > 90% recovery of tryptophan for both untreated and treated monoliths but also had issues after irradiation and long term frozen storage. Chromolith® RP-18e silica monolithic guard cartridges showed issues with consistency and reproducibility. In expanding the list of analytes, the Oasis® HLB media showed the best performance, capturing more of the analytes tested and remaining fully functional through both irradiation and long term storage treatments. Other media with additional reverse phase capture characteristics were also evaluated but none performed as well on the selected analytes as the Oasis® HLB media. | Jerome Ferrance | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Space Chemistry; Analytical Chemistry - General; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624236b974104f4d17b632d4/original/solid-phase-extraction-on-reverse-phase-chromatographic-media-subjected-to-stresses-expected-for-extraterrestrial-implementation.pdf |
657c758066c138172941164c | 10.26434/chemrxiv-2023-ft12w | Electrophoretic Mobility of Nanoparticles in Water | Classical equations for colloidal mobility anticipate linear proportionality between the nanoparticle mobility and zeta potential caused by combined electrostatics of free charges at the nanoparticle and screening bound charges of the polar solvent. Polarization of the interfacial liquid, either spontaneous due to molecular asymmetry of the solvent (water) or induced by non-electrostatic (e.g., charge-transfer) interactions, is responsible for a static interface charge adding to the overall electrokinetic charge of the nanoparticle. The particle mobility gains a constant offset term formally unrelated to the zeta potential. The static charge is multiplied with the static dielectric constant of the solvent in the expression for the electrokinetic charge and is sufficiently large in magnitude to cause electrophoretic mobility of even neutral particles. At a larger scale, nonlinear electrophoresis linked to the interface quadrupole moment can potentially contribute a sufficiently negative charge to a micrometer-size nanoparticle. | Dmitry Matyushov | Physical Chemistry; Biophysical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657c758066c138172941164c/original/electrophoretic-mobility-of-nanoparticles-in-water.pdf |
65773cf6bec7913d27607180 | 10.26434/chemrxiv-2023-kkmsm | Electrochemical nitrate reduction to ammonia in a BPM-MEA system | Electrochemical nitrate reduction reaction (NO3RR) has garnered increasing attention as a pathway for converting a harmful pollutant (nitrate) into a value-added product (ammonia). Technologies that take advantage of this reaction also allow for a reduction in nitrogen waste accumulation enabling more balance in the global nitrogen cycle. However, high selectivity toward ammonia (NH3) is imperative for process viability. Recent studies suggest that proton plays a role in achieving high NH3 production; yet, systematic examination of the impact of proton on NO3RR selectivity is not widely conducted due to the lack of effective control over proton availability during electrolysis. Here, we employed a bipolar membrane (BPM)-based membrane electrode assembly (MEA) system to investigate the influence of protons on the selectivity of NO3RR. The BPM generates a robust proton flux during electrocatalytic reactions, making it a suitable candidate for investigating the proton effects on NO3RR. We employed the interposer layer (mixed cellulose ester membrane filter) and proton scavenger (CO32-) as an approach to control the proton flux. Furthermore, we redesigned the configuration of BPM-based MEA cells, allowing us to regulate the mass transfer of the reactants (e.g. proton and nitrate), creating local environments that favor ammonia formation. We find that a moderate proton supply allowed for an increase in ammonia yield by 576% when compared to the standard membrane electrode assembly, and a high selectivity of 26 (NH3 over NO2-) was achieved at an applied current density of 200 mA cm-2 with electrolyte mirrors that found in wastewater. Our work introduces a novel approach to address the selectivity of NO3RR from the perspective of cell design and the findings lay the groundwork for a deeper understanding of the influence of proton on selective NH3 synthesis from nitrate.
| Po-Wei Huang; Hakhyeon Song; Jaeyoung Yoo; Danae Chipoco Haro; Hyuck Mo Lee; Andrew Medford; Marta Hatzell | Catalysis; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Transport Phenomena (Chem. Eng.); Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65773cf6bec7913d27607180/original/electrochemical-nitrate-reduction-to-ammonia-in-a-bpm-mea-system.pdf |
6585323a66c1381729c645d4 | 10.26434/chemrxiv-2023-94r25-v2 | Nanocellulose in Textiles: A Potential Resource for Sustainable Textile Manufacturing | In recent times, there has been a discernible focus on the development of environmentally friendly and sustainable biomaterials obtained from renewable sources. Scientists are now investigating the prospective applications of nanocellulose, a biocompatible substance derived from natural cellulose. The aforementioned substance exhibits notable characteristics, such as a substantial surface area to volume ratio, with its compatibility with biological systems and capacity to undergo degradation. Nanocellulose has the capability to undergo transformation into nanofibers and nanocrystals, so enabling the generation of diverse structures, including elongated nanofibers, suspensions, and films. In the textile industry, there is a growing need to adopt sustainable techniques in order to address and minimize the negative environmental impacts. The current focus is on the advancement of environmentally sustainable alternatives in the realm of textile production, namely cellulose-based materials. These textiles are being created using processes that aim to minimize water pollution. In addition, recent advancements in dyeing methods have used nanocellulose to effectively reduce water consumption and eliminate the need for toxic materials. Nanocellulose nanocomposites, such as nanofibrillated celluloses (NFCs) and cellulose nanocrystals (CNCs), are increasingly used as fillers in textile nanocomposites to enhance their mechanical characteristics due to their cost-effectiveness and recyclability. The advancements achieved in the field of nanocellulose-based materials and technology exhibit considerable promise in the development of ecologically friendly solutions across several industries. | Sayam | Materials Science; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6585323a66c1381729c645d4/original/nanocellulose-in-textiles-a-potential-resource-for-sustainable-textile-manufacturing.pdf |
630039c7d147b26733b169e5 | 10.26434/chemrxiv-2022-x7ggk-v2 | Stereospecific Acylative Suzuki-Miyaura Cross-Coupling: A General Access to Optically Active α-Aryl Carbonyl Compounds | A novel strategy for the stereospecific Pd-catalyzed
acylative cross-coupling of enantiomerically enriched alkylboron compounds has been developed. The protocol features an extremely high level of enantiospecificity to allow facile access to synthetically challenging and valuable chiral ketones and carboxylic acid derivatives. The use of a sterically encumbered and electron-rich phosphine ligand proved to be crucial for the success of the reaction. Furthermore, based on experimental and computational studies, a unique mechanism for the transmetalation of the C(sp3)-based organoboron reagent has been identified.
| Byeongdo Roh; Abdikani Omar Farah; Beomsu Kim; Taisiia Feoktistova; Finn Moeller; Paul Ha-Yeon Cheong; Hong Geun Lee | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630039c7d147b26733b169e5/original/stereospecific-acylative-suzuki-miyaura-cross-coupling-a-general-access-to-optically-active-aryl-carbonyl-compounds.pdf |
62bead48d66f68680ab920e2 | 10.26434/chemrxiv-2022-p2h8r | Efficient and Site-Specific C–H Hydroxylation of Enones via a New Mechanism Useful for the Late-Stage Functionalization of Drugs and Natural Products | A mild and efficient method for the direct C(sp3)–H hydroxylation of enones in a site-specific way was developed via visible-light-induced hydrogen-atom transfer (HAT), which facilitates -hydroxylation of primary, secondary, and tertiary C–H bonds of different enones without involving metal and peroxide. The mechanistic study showed a new catalytic view, where Na2-eosin Y served as both the photocatalyst and the source of catalytic bromine radical species in the HAT-based catalytic cycle, and finally sacrificed itself completely by oxidative degradation to produce bromine radical and a major product phthalic anhydride in an environmentally friendly way. This scalable method was demonstrated by plenty of substrates to be extremely useful for the late-stage functionalization of drugs and natural products, and, in particular, has potential application in industry for large-scale production. | Cheng-Yu Zheng; Jian-Min Yue | Organic Chemistry; Natural Products; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bead48d66f68680ab920e2/original/efficient-and-site-specific-c-h-hydroxylation-of-enones-via-a-new-mechanism-useful-for-the-late-stage-functionalization-of-drugs-and-natural-products.pdf |
6580a658e9ebbb4db938e76a | 10.26434/chemrxiv-2023-ctlbz | Lead-based paint detection using perovskite fluorescence and X-ray fluorescence | Ingestion of flakes of Pb-based paint by infants remains a health hazard with life-long consequences throughout the world. Pb-based paint was banned for residential use in the US and Western Europe decades ago but is still sold in many countries. This study evaluates the performance of a new kit for detecting exposed Pb-based paint. The kit relies on the formation of Pb-halide perovskite that fluoresces bright green under a UV flashlight after spraying a non-toxic reagent. Tests with the Lumetallix kit were conducted in parallel with X-fluorescence and inductively-coupled plasma atomic emission analysis upon acid digestion using paint currently sold in Ivory Coast and samples of older US paint. Comparison of the three different methods indicates a detection limit for the Lumetallix kit of approximately 500 ppm Pb in paint, with a sensitivity of 95% and a selectivity of 94% relative to that threshold (n=76). This detection limit is an order of magnitude below the US definition of Pb-based paint of 0.5% Pb by weight. Because the kit is easy to use, exposed paint posing a risk could therefore reliably be screened at scale by the general public. Any follow-up for confirmation and mitigation based on XRF measurements will need to consider that Pb-based paint covered with paint without Pb will not respond to the kit but will be detected through the upper layer by XRF. | Alexander van Geen; Lukas Helmbrecht; Eric Ritter; Ernest Kouassi Ahoussi; Petanki Soro; Jacques Gardon; Willem Noorduin | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Geochemistry; Analytical Chemistry - General; Environmental Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6580a658e9ebbb4db938e76a/original/lead-based-paint-detection-using-perovskite-fluorescence-and-x-ray-fluorescence.pdf |
60c74ae7337d6c2d4be279ac | 10.26434/chemrxiv.12253463.v1 | Designing of Cytotoxic and Helper T Cell Epitope Map Provides Insights into the Highly Contagious Nature of the Pandemic Novel Coronavirus SARS-CoV2 | This study provides key insights into the contagious nature of SARS-CoV2 through analyses of T cell epitopes designed from SARS-CoV2 proteome. All top-scoring cytotoxic T cell epitopes from ORF1ab and helper T cell epitopes identified from all proteins were utilized to provide crucial insights into its pathogenesis. These T cell epitopes can be used as prophylactic or therapeutic multi-subunit vaccine or as diagnostic tools.<br /> | Dr. Seema Mishra | Biochemistry; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ae7337d6c2d4be279ac/original/designing-of-cytotoxic-and-helper-t-cell-epitope-map-provides-insights-into-the-highly-contagious-nature-of-the-pandemic-novel-coronavirus-sars-co-v2.pdf |
60ed4638609d0d4885da3b96 | 10.26434/chemrxiv-2021-fpp4n | Interaction of nanoparticles with lipid films: the role of symmetry | When nanomaterials are put in contact with living organisms, their interaction with biomacromolacules and biological barriers will determine their bioactivity, biological fate and cytotoxicity. In this context, the role of symmetry/shape anisotropy of both the nanomaterials and the biological interfaces on their interaction mechanism, is a relatively unaddressed issue. Here, we study the interaction of gold nanoparticles (NPs) of different shape (nanospheres and nanorods) with biomimetic membranes of different symmetry, i.e. flat membranes (of 2D symmetry, representative of the most common plasma membrane geometry), and cubic membranes (of 3D symmetry, representative of non-lamellar membranes, encountered in Nature in peculiar biological conditions). Through an ensemble of structural techniques (Neutron Reflectometry, Grazing Incidence Small-Angle Neutron Scattering), we found that, on a nanometric lengthscale, the structural stability of the membrane towards NPs is dependent on the topological characteristic of the lipid assembly and of the NPs, with higher symmetry related to higher stability. In addition, Confocal Laser Scanning Microscopy analyses highlight, on a micrometric legthscale, that cubic and lamellar phases interact with NPs according to two distinct mechanisms, related to the different structures of the lipid assemblies. This study represents a first attempt to systematically study the role of membrane symmetry on the interaction with NPs; the results will contribute to improve the fundamental knowledge on nano-bio interfaces and, more in general, will provide new insights on the biological function of non-lamellar cubic arrangements of interfacial membranes as a response strategy. | Lucrezia Caselli; Andrea Ridolfi; Gaetano Mangiapia; Pierfrancesco Maltoni; Jean-Francois Moulin; Debora Berti; Nina-Juliane Steinke; Emil Gustafsson; Tommy Nylander; Costanza Montis | Physical Chemistry; Nanoscience; Interfaces; Physical and Chemical Properties; Self-Assembly; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ed4638609d0d4885da3b96/original/interaction-of-nanoparticles-with-lipid-films-the-role-of-symmetry.pdf |
60c74ab9bb8c1a6c423db07a | 10.26434/chemrxiv.6723929.v2 | Effect of Surface Structure on Peptide Adsorption on Soft Surfaces | Using molecular dynamics simulations the adsorption of peptides onto nanostructured surfaces, consisting of alternating hydrophilic-hydrophobic stripes, was investigated. The adsorption strength, calculated using metadynamics, was found to decrease as the stripe width gets smaller. | David Cheung | Biocompatible Materials; Nanostructured Materials - Materials; Computational Chemistry and Modeling; Theory - Computational; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ab9bb8c1a6c423db07a/original/effect-of-surface-structure-on-peptide-adsorption-on-soft-surfaces.pdf |
65f1684ce9ebbb4db99c2984 | 10.26434/chemrxiv-2024-01sv9 | Harnessing ultrasound-derived hydroxyl radicals for the selective oxidation of aldehyde functions | Ultrasonic irradiation holds potential for the selective oxidation of non-volatile organic substrates in the aqueous phase by harnessing hydroxyl radicals as chemical initiators. Here, a mechanistic description of hydroxyl radical-initiated glyoxal oxidation is constructed by gleaning insights from photolysis and radiation chemistry to explain the yields and kinetic trends for oxidation products. The mechanistic description and kinetic measurements reported herein reveal that increasing the formation rate of hydroxyl radicals by changing the ultrasound frequency increases both the rates of glyoxal consumption and the selectivity towards C2 acid products over those from C-C cleavage. Glyoxal consumption also occurs more rapidly and with greater selectivity towards C2 acids under acidic conditions, which favor the protonation of carboxylate intermediates into their less reactive acidic forms. Leveraging such pH and frequency effects is crucial to mitigating product degradation by secondary reactions with hydroxyl radicals and oxidation products (specifically H2O2 and •O2–). These findings demonstrate the potential of ultrasound as a driver for the selective oxidation of aldehyde functions to carboxylic acids, offering a sustainable route for converting biomass-derived platform molecules into valuable products. | Ari F. Fischer; Teseer Bahry; Zhangyue Xie; Kaicheng Qian; Renhong Li; James Kwan; François Jérôme; Sabine Valange; Wen Liu; Prince N. Amaniampong; Tej S. Choksi | Physical Chemistry; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Chemical Kinetics; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f1684ce9ebbb4db99c2984/original/harnessing-ultrasound-derived-hydroxyl-radicals-for-the-selective-oxidation-of-aldehyde-functions.pdf |
60c74eb7337d6c1a33e2800b | 10.26434/chemrxiv.12790256.v1 | Label-free Lipidome Study of Paraventricular Thalamic Nucleus (PVT) of Rat Brain with Post-Traumatic Stress Injury by Raman Imaging | <a>Post-traumatic stress disorder (PTSD) is a
widespread psychiatric injury that develops serious life-threatening symptoms
like substance abuse, severe depression, cognitive impairments
and persistent
anxiety. However, the mechanisms of post-traumatic stress injury in brain is
poorly understood due to the lack of practical methods to reveal biochemical alterations
in various brain regions affected by this type of injury. Here, we introduce a
novel method that provides quantitative results from Raman maps in paraventricular
nucleus of the thalamus (PVT) region. By means of this approach, we have shown
a lipidome comparison in PVT regions of control and PTSD rat brains. Matrix-assisted
laser desorption/ionization (MALDI) mass spectrometry was also employed for validation
of the Raman results. Lipid alterations can reveal invaluable information
regarding the PTSD mechanisms in affected regions of brain. We have showed that
the concentration of cholesterol, cholesteryl palmitate, phosphatidylinositol,
phosphatidylserine, phosphatidylethanolamine, sphingomyelin, ganglioside,
glyceryl tripalmitate and sulfatide changes in the PVT region of PTSD compared to
control rats. Higher concentration of cholesterol suggests the higher level of
corticosterone in brain.</a><sup>1</sup> Moreover, concentration changes of
phospholipids and sphingolipids suggest the alteration of phospholipase A2
(PLA2) which is associated with inflammatory processes in the brain. Our
results have broadened the understanding of biomolecular mechanisms for PTSD in
PVT region of brain. This is the first report regarding the application of
Raman spectroscopy for PTSD studies. This method has a wide spectrum of
applications and can be applied to various other brain related disorders or
other regions of brain. | Ardalan Chaichi; Syed Mohammad Abid Hasan; Nishir Mehta; Fabrizio Donnarumma; Philip Ebenezer; Kermit Murray; Joseph Francis; Manas Ranjan Gartia | Biochemical Analysis; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eb7337d6c1a33e2800b/original/label-free-lipidome-study-of-paraventricular-thalamic-nucleus-pvt-of-rat-brain-with-post-traumatic-stress-injury-by-raman-imaging.pdf |
60c74a78842e65040adb2f53 | 10.26434/chemrxiv.12206384.v1 | Straightforward Preparation of Supramolecular Janus Nanorods by Hydrogen Bonding of End-Functionalized Polymers | Janus cylinders are one-dimensional colloids that have two faces with different compositions and functionalities and are useful as building blocks for advanced functional materials. Such anisotropic objects are difficult to prepare with nanometric dimensions. Here we describe a robust and versatile strategy to form micrometer long Janus nanorods with diameters in the 10-nanometer range, by self-assembly in water of end-functionalized polymers. For the first time, the Janus topology is not a result of the phase segregation of incompatible polymer arms, but is driven by the interactions between unsymmetrical and complementary hydrogen bonded stickers. It is therefore independent of the actual polymers used and works even for compatible polymers. To illustrate their applicative potential, we show that these Janus nanorods can efficiently stabilize oil-in-water emulsions. | Shuaiyuan Han; Sandrine Pensec; Cédric Lorthioir; Jacques Jestin; Jean-Michel Guigner; Jutta Rieger; François Stoffelbach; Erwan Nicol; Olivier Colombani; Laurent Bouteiller | Aggregates and Assemblies | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a78842e65040adb2f53/original/straightforward-preparation-of-supramolecular-janus-nanorods-by-hydrogen-bonding-of-end-functionalized-polymers.pdf |
60c74cbdee301c4468c7a14c | 10.26434/chemrxiv.12047376.v2 | Electron Trajectories in Molecular Orbitals | The time-dependent Schrödinger equation can be rewritten so that its interpretation is no longer probabilistic. Two well-known and related reformulations are Bohmian mechanics and quantum hydrodynamics. In these formulations, quantum particles follow real, deterministic trajectories influenced by a quantum force. Generally, trajectory methods are not applied to electronic structure calculations, since they predict that the electrons in a ground state, real, molecular wavefunction are motionless. However, a spin-dependent momentum can be recovered from the non-relativistic limit of the Dirac equation. Therefore, we developed new, spin-dependent equations of motion for the quantum hydrodynamics of electrons in molecular orbitals. The equations are based on a Lagrange multiplier, which constrains each electron to an isosurface of its molecular orbital, as required by the spin-dependent momentum. Both the momentum and the Lagrange multiplier provide a unique perspective on the properties of electrons in molecules. | Isaiah Sumner; Hannah Anthony | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cbdee301c4468c7a14c/original/electron-trajectories-in-molecular-orbitals.pdf |
611e14a9f71bc827382856ab | 10.26434/chemrxiv-2021-phwsx | In-Silico Structural prediction and functional annotation of uncharacterized protein Q7TLC7 (Y14_SARS) presence in SARS-COV2 | Protein structure prediction strategies point to predict the structures of proteins from their amino acid sequences, utilizing different computational calculations. Basically, the prediction of 3D structure of a protein from its amino acid sequence is one of the foremost critical indecisive issues in computational biology. This paper endeavors to grant a comprehensive presentation of the foremost later exertion and advance on protein structure prediction. Taking after the common flowchart of structure prediction, related concepts and strategies are displayed and experimentally established. In addition, brief presentations are made to a few widely-used prediction methods and the community-wide basic appraisal of protein structure prediction experiments. Here we can see Unknown proteins exist but have not been characterized or connected to known qualities. Domains of unknown function are experimentally distinguished proteins with no known functional or structural domain. In this paper, the examination and characterization of the likely useful perspectives of a hypothetical protein: coronavirus Q7TLC7 (Y14_SARS) was performed utilizing different computational strategies and tools. As the protein tertiary structure not accessible within the Protein Data Bank, the basic demonstrate expectation with its structural and functional annotation is well explained in this paper which consequently, gives an understanding into this hypothetical protein ( Q7TLC7) .In this manner, unleashes an opportunity for medicate and immunization focusing on against the disease by COVID19 investigation will be of significance in understanding the mechanism of the infections and will demonstrate to be advantageous within the revelation of new drugs | MD. Ashiqur Rahman; Rumana Akter Rumi | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611e14a9f71bc827382856ab/original/in-silico-structural-prediction-and-functional-annotation-of-uncharacterized-protein-q7tlc7-y14-sars-presence-in-sars-cov2.pdf |
61cc54e97f367e059663d465 | 10.26434/chemrxiv-2021-rdjkn-v2 | Modulating the Frontier Orbitals of an Aluminylene for Facile Dearomatization of Inert Arenes | Lewis bases are well known to stabilize electron-deficient species. We demonstrate herein that the redox property of a monocoordinated aluminylene 1 featuring only four valence electrons for the shell of Al can be boosted by a Lewis base. The coordination of 1 with an N-heterocyclic carbene (NHC) effectively shrinks the HOMO−LUMO gap, thereby enhancing the reactivity of the ensuing acyclic mono-NHC-stabilized aluminylene 2, which is isoelectronic with singlet carbenes. Moreover, such base coordination completely reverses the predominant chemical reactivity (i.e. electrophilicity/nucleophilicity) of aluminylenes. In marked contrast to 1, 2 readily undergoes a [4+1] cycloaddition reaction with naphthalene and biphenylene at room temperature. Remarkably, the enhanced ambiphilic nature of Al in 2 also enables facile cleavage of aromatic C−C bonds of inert arenes in both intra- and intermolecular fashion affording 3 and 5. The formation of 5 represents the first example of the cleavage of aromatic C(3)−C(4) bond in biphenylene by a single atom center. | Xin Zhang; Liu Leo Liu | Inorganic Chemistry; Organometallic Chemistry; Bond Activation; Coordination Chemistry (Organomet.); Main Group Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61cc54e97f367e059663d465/original/modulating-the-frontier-orbitals-of-an-aluminylene-for-facile-dearomatization-of-inert-arenes.pdf |
65f43fc166c13817290cd3df | 10.26434/chemrxiv-2024-plwn8 | Coupled-Cluster Treatment of Complex Open-Shell Systems: The Case of Single-Molecule Magnets | We investigate the reliability of two cost-effective coupled-cluster methods for computing spin-state energetics and spin-related properties of a set of open-shell transition-metal complexes. Specifically, we employ the second-order approximate coupled-cluster singles and doubles (CC2) method and projection-based embedding that combines equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) with density functional theory (DFT). The performance of CC2 and EOM-CCSD-in-DFT is assessed against EOM-CCSD. The chosen test set includes two hexaaqua transition-metal complexes containing Fe(II) and Fe(III), and a large Co(II)-based single-molecule magnet with a non-aufbau ground state. We find that CC2 describes
the excited states more accurately, reproducing EOM-CCSD excitation energies within 0.05 eV. However, EOM-CCSD-in-DFT excels in describing transition orbital angular momenta and spin-orbit couplings. Moreover, for the Co(II) molecular
magnet, using EOM-CCSD-in-DFT eigenstates and spin-orbit couplings, we compute spin-reversal energy barriers, as well as temperature-dependent and field-dependent magnetizations and magnetic susceptibilities that closely match experimental values within spectroscopic accuracy. These results underscore the efficiency of CC2 in computing state energies of multi-configurational, open-shell systems and highlight the utility of the more cost-efficient EOM-CCSD-in-DFT for computing spin-orbit couplings and magnetic properties of complex and large molecular magnets. | Maristella Alessio; Garrette Pauley Paran; Cansu Utku; Andreas Grueneis; Thomas-C. Jagau | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f43fc166c13817290cd3df/original/coupled-cluster-treatment-of-complex-open-shell-systems-the-case-of-single-molecule-magnets.pdf |
61b798e79e56b87c9bbb5d4f | 10.26434/chemrxiv-2021-412k8 | The Role of an Inert Electrode Support in Plasmonic
Electrocatalysis | Plasmonic nanostructures loaded onto catalytically inert conductive support materials are
believed to be advantageous for maximizing photocatalytic effects in photoelectrochemical
systems due to the increased efficiency of Schottky barrier-free architectures in collecting hot
charge carriers. However, the systematic mechanistic investigation and description of the inert
electrode support contribution to plasmonic electrocatalysis is missing. Herein, we
systematically investigated the effect of the supporting electrode material on the observed
photocatalytic enhancement by comparing photoelectrocatalytic properties of AuNPs supported
on highly oriented pyrolytic graphite (HOPG) and on indium tin oxide (ITO) electrodes using
electrocatalytic benzyl alcohol (BnOH) oxidation as a model system. Upon illumination, only
~(3 ± 1)% enhancement in catalytic current was recorded on the AuNP/ITO electrodes in
contrast to ~(42 ± 6)% enhancement on AuNP/HOPG electrodes. Our results showed that the
local heating due to light absorption by the electrode material itself independent of localized
surface plasmon effects is the primary source of the observed significant photo-induced
enhancement on the HOPG electrodes in comparison to the ITO electrodes. Moreover, we demonstrated that an increased interfacial charge transfer at elevated temperatures, and not
faster substrate diffusion is the main source of the enhancement. This work highlights the
importance of systematic evaluation of contributions of all parts, even if they are catalytically
inert, to the light-induced facilitation of catalytic reactions in plasmonic systems. | Sagar Ganguli; Alina Sekretareva | Physical Chemistry; Catalysis; Energy; Electrocatalysis; Photocatalysis; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b798e79e56b87c9bbb5d4f/original/the-role-of-an-inert-electrode-support-in-plasmonic-electrocatalysis.pdf |
60c7418f0f50db9e2a395b24 | 10.26434/chemrxiv.8066264.v1 | Leveraging Atropisomerism to Obtain a Selective Inhibitor of RET Kinase with Secondary Activities Towards EGFR Mutants | <p>Unstable atropisomerism is innate
in many common scaffolds in drug discovery, commonly existing as freely
rotating aryl-aryl bonds. Such compounds can access the majority of dihedral
conformations around the bond axis, however most small-molecules bind their target
within a narrow range of these available conformations. The remaining accessible
conformations can interact with other proteins leading to compound promiscuity.
Herein, we leverage atropisomerism to restrict the accessible low energy
dihedral conformations available to a promiscuous kinase inhibitor and achieve
highly selective and potent inhibitors of the oncogenic target RET kinase. We then
evaluate our lead inhibitor against kinases that were predicted to bind compounds
in a similar conformational window to RET, discovering a potent inhibitor of drug
resistant EGFR mutants including L858R/T790M/C797S EGFR. Leveraging atropisomerism
to restrict accessible conformational space should be a generally applicable
strategy due to the prevalence of unstable atropisomerism in drug discovery.</p> | Sean T. Toenjes; Valeria Garcia; Sean M. Maddox; Greg A. Dawson; Maria A. Ortiz; F. Javier Piedrafita; Jeffrey Gustafson | Bioorganic Chemistry; Physical Organic Chemistry; Stereochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7418f0f50db9e2a395b24/original/leveraging-atropisomerism-to-obtain-a-selective-inhibitor-of-ret-kinase-with-secondary-activities-towards-egfr-mutants.pdf |
6385f9c70949e169ec5a3c32 | 10.26434/chemrxiv-2022-c0zqg | The Mechanochemical Fries Rearrangement: Manipulating Isomer Ratios in the Synthesis of p-Hydroxyacetophenone at Different Scales | Here, we present the first mechanochemical Fries rearrangement for the industrially important synthesis of para hydroxyacetophenone, inside a ball mill and a twin-screw extruder. Our approach leads to quantitive conversion in as little as 90 minutes. Furthermore, the utilisation of liquid-assisted grinding can shift the isomer ratio resulting in an excess of the desired para product. The multigram scale-up via a continuous extrusion process leads to similar results in only three minutes of residence time while completely avoiding solvents. The extrusion temperature of 75-100 °C can even further be reduced by combining extrusion at 50°C with a subsequent ageing step. | Daniel Baier; Tilo Rensch; Konrad Bergheim; Viktoria Pietryga; Sven Graetz; Lars Borchardt | Organic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Process Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6385f9c70949e169ec5a3c32/original/the-mechanochemical-fries-rearrangement-manipulating-isomer-ratios-in-the-synthesis-of-p-hydroxyacetophenone-at-different-scales.pdf |
6114a3d918911d63d0dec8c4 | 10.26434/chemrxiv-2021-d3dr8 | ZIF-C as non-viral delivery system for CRISPR/Cas9 mediated hTERT knockdown in cancer cells | Telomerase, a ribonucleoprotein coded by the hTERT gene, plays an important role in cellular immortalization and carcinogenesis. hTERT is a suitable target for cancer therapeutics as its activity is highly upregulated in 85-90% of cancer cells but absent in normal somatic cells. Here, we target the hTERT gene at the DNA level by applying the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9 technology encapsulated in a recently discovered Metal-Organic Framework (MOF). We show that the MOF subtype ‘ZIF-C’ can efficiently load the hTERT targeting CRISPR system (CrhTERT@ZIF-C) and protect it from enzymatic degradation. The CrhTERT@ZIF-C is endocytosed by cancer cells and successfully disrupts the hTERT gene. The resultant inhibition of hTERT decreases cellular proliferation and causes apoptotic cancer cell death. Furthermore, hTERT knockdown shows a significant reduction in tumor metastasis and alters protein expression. Thus, our results conclusively establish ZIF-C based targeting of hTERT as a highly promising and novel approach for gene therapy in cancer. | Suneela Pyreddy ; Arpita Poddar ; Francesco Carraro; Shakil Ahmed Polash ; Chaitali Dekiwadia ; Zeyad Nasa ; Srinivasa Reddy Telukutla ; Paolo Falcaro; Ravi Shukla | Materials Science; Biocompatible Materials; Biological Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6114a3d918911d63d0dec8c4/original/zif-c-as-non-viral-delivery-system-for-crispr-cas9-mediated-h-tert-knockdown-in-cancer-cells.pdf |
60d5ec01c6229572e61b08e6 | 10.26434/chemrxiv-2021-0spz9 | Light sensitive phenacyl crosslinked dextran hydrogels for controlled delivery | Stimuli-responsive soft materials enable controlled release of loaded drug molecules and biomolecules. Controlled release of potent chemotherapeutic or immunotherapeutic agent is crucial to reduce unwanted side effects. In an effort to develop controlled release strategies that can be triggered using Cerenkov luminescence, we have developed polymer hydrogels that can release doxorubicin, bovine serum albumin and immunoglobulin G using light (254 nm – 375 nm) as a trigger. We describe the synthesis and photochemical characterisation of two light sensitive phenacyl bis-azide crosslinkers that are used to prepare transparent self-supporting hydrogel patches. One crosslinker was designed to optimize the overlap with the Cerenkov luminescence emission window, bearing an -extended phenacyl core, resulting in a high quantum yield (14%) of photocleavage when irradiated with 375 nm light. We used the extended phenacyl crosslinker for the preparation of protein-loaded dextran hydrogel patches, which showed efficient and selective dosed release of bovine serum albumin or immunoglobulin G after irradiation with 375 nm light. Based on the high quantum yield, efficient release and large overlap with the Cerenkov window, we envision application of these photosensitive soft materials in radiation targeted drug release. | Rienk Eelkema; Antonia Denkova; Tobias Breve; Sven Weerdenburg; Stefan van der Griend; Tim Groeneveld; Mike Filius | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d5ec01c6229572e61b08e6/original/light-sensitive-phenacyl-crosslinked-dextran-hydrogels-for-controlled-delivery.pdf |
679728c5fa469535b9033ef2 | 10.26434/chemrxiv-2025-9t733-v2 | Comprehensive Analysis for Low-cost and Highly Efficient Perovskite Solar Cells Using SCAPS-1D with Inexpensive Hole Transport Material, Electron Transport Material and Back Contact Considering the Toxicity | Perovskite solar cells are gaining popularity day by day due to the continuous effort of solar
scientists. However, there are several barriers to the commercialization of this solar cell. Various
materials can be used to achieve higher efficiency of perovskite solar cell design. Some of these
materials may also contain lead (Pb), which harms human life and the environment. Another
crucial hindrance for perovskite solar cells is the cost regarding hole transport material (HTM),
electron transport material (ETM), and back contact; most of the common HTM, ETM, and back
contact materials are expensive. In this study, we have chosen inexpensive HTM, ETM, and back
contact to determine highly efficient and less expensive cell structures. Eleven non-toxic and three
Pb-based absorber materials have been simulated using SCAPS-1D simulator where ETM (ZnO)
and HTM (PEDOT: PSS+WO3) are constant to determine the best absorber material. Later the
effect of thickness, temperature, back and front contact, electron affinity, defect density, and series
resistance are also considered. After simulation and optimization, it is found that Ni is the least
expensive back contact material for providing optimal efficiency, MAPbI3 is the best Pb-based
absorber material with open circuit voltage (Voc) =1.10V, short circuit current (Jsc) =28.47
mA/cm2, fill factor (FF) =86.42%, power conversion efficiency (eta(%)) =27.10%. In contrast, the
best non-toxic material is MASnI3 with Voc =0.97V, Jsc =34.89mA/cm2, FF =82.51% and eta (%)
=27.98%. | Rukon Uddin; Sayem Ul Alam; Subrata Bhowmik | Energy; Photovoltaics | CC BY 4.0 | CHEMRXIV | 2025-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679728c5fa469535b9033ef2/original/comprehensive-analysis-for-low-cost-and-highly-efficient-perovskite-solar-cells-using-scaps-1d-with-inexpensive-hole-transport-material-electron-transport-material-and-back-contact-considering-the-toxicity.pdf |
60c73f18469df44234f429c7 | 10.26434/chemrxiv.7215332.v1 | The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination | <p>In the many scientific endeavors that are driven by organic chemistry, unambiguous identification of small molecules is of paramount importance. Over the past 50 years, NMR and other powerful spectroscopic techniques have been developed to address this challenge. While almost all of these techniques rely on inference of connectivity, the unambiguous determination of a small molecule’s structure requires X-ray and/or neutron diffraction studies. In practice, however, x-ray crystallography is rarely applied in routine organic chemistry due to intrinsic limitations of both the analytes and the technique. Here we report the use of the CryoEM method MicroED to provide routine and unambiguous structural determination of small organic molecules. From simple powders, with minimal sample preparation, we could collect high quality MicroED data from nanocrystals (~100x100x100 nm, ~10<sup>–15</sup>g) resulting in atomic resolution (<1 Å) crystal structures in minutes.</p> | Christopher G. Jones; Michael
W. Martynowycz; Johan Hattne; Tyler J. Fulton; Brian M. Stoltz; Jose A. Rodriguez; Hosea Nelson; Tamir Gonen | Natural Products; Organic Synthesis and Reactions; Microscopy; Nanodevices | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f18469df44234f429c7/original/the-cryo-em-method-micro-ed-as-a-powerful-tool-for-small-molecule-structure-determination.pdf |
6627c16c91aefa6ce1341752 | 10.26434/chemrxiv-2024-0p6l8 | Borylation via Iridium catalysed C-H activation: a new concise route to duocarmycin derivatives | The synthesis of the ethyl ester analogue of the ultapotent antitumour antibiotic seco-duocarmycin SA has been achieved in eleven linear steps from commercially available starting materials. The DSA alkylation subunit can be made in ten linear steps from the same precursor. The route involves CH activation at the equivalent of the C7 position on indole leading to a borylated intermediate 9 that is stable enough for coupling reactions but can be easily converted to the free hydroxyl analogue. | Marco Cominetti; Zoe Goddard; Bethany Hood; Andrew Beekman; Maria O'Connell; Mark Searcey | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2024-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6627c16c91aefa6ce1341752/original/borylation-via-iridium-catalysed-c-h-activation-a-new-concise-route-to-duocarmycin-derivatives.pdf |
67545ab7f9980725cf57b3e0 | 10.26434/chemrxiv-2024-38npb | A Carnitine-based BODIPY Photosensitizer | Organelle-selective photodynamic therapy (PDT) has emerged as a promising approach to enhance the precision and efficacy of cancer treatment by targeting key cellular structures. In this study, we report the design of a novel carnitine-based BODIPY photosensitizer, probe 1, which retains mitochondrial selectivity while acting as both a fluorescent probe and a potent photosensitizer. Building on our previously developed mitochondria-targeting probe (R)-BCT-2, which is transported into the mitochondrial matrix by the inner membrane protein carnitine-acylcarnitine translocase (CAC), probe 1 incorporates two bromine atoms that enhance intersystem crossing, leading to a singlet oxygen quantum yield of 80%, while retaining sufficient fluorescence for effective cell staining in fluorescence microscopy. Theoretical calculations indicate that the carnitine moiety distorts chromophore planarity, reducing oscillator strength but enhancing spin-orbit coupling, which, together with the extended triplet lifetime, contributes to increased phototoxicity. Probe 1 co-localizes in both mitochondria and, to a lesser extent, in lysosomes, and this dual targeting may synergistically enhance phototoxic activity by amplifying cellular stress responses. Importantly, probe 1 demonstrated high phototoxicity upon green light irradiation, with IC50 values of 52 nM under normoxia and 117 nM under hypoxia, while remaining non-cytotoxic in the dark. These results suggest that probe 1 is a promising candidate for organelle-targeted PDT, particularly in hypoxic tumor environments where its dual organelle targeting could enhance therapeutic efficacy. | Larissa Maierhofer; Ruth Prieto-Montero; Tamara Cubiella; Aitor Diaz-Andres; David Casanova; Virginia Martinez-Martinez; Maria D. Chiara; Enrique A. Mann; Jose Luis Chiara | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Computational Chemistry and Modeling; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67545ab7f9980725cf57b3e0/original/a-carnitine-based-bodipy-photosensitizer.pdf |
67736357fa469535b94f4832 | 10.26434/chemrxiv-2024-tl36p-v2 | Day-Level Long Persistent Luminescence in Purely Organic Polymers via Cascade Hole Trap Mechanism | In recent years, organic long persistent luminescence (OLPL) materials have made significant progress in achieving hour-level OLPL through the charge-separation mechanism in host-guest composites. However, it remains a considerable challenge for OLPL materials to achieve such performance using commonly available, cost-effective optoelectronic-inert polymers as the host component. In this work, electron-deficient naphthalenediimide derivatives are utilized as guest molecules, which are dispersed into various polymers, achieving hour-level OLPL for the first time in widely used, low-cost optoelectronic-inert hosts, such as poly(methyl methacrylate) (PMMA), poly(L-lactic acid) (PLLA), poly(vinyl acetate) (PVAc), and polystyrene (PS). By combining commercially available PMMA with polycarbonate (PC), an unprecedented day-level OLPL phenomenon is observed. A cascade polymer hole trap mechanism is proposed to elucidate this exceptional OLPL performance. Additionally, these materials can be applied not only for large-area fabrication and nighttime illumination but also for stable emission in diverse extreme environments, as well as for multi-layer information encryption. This innovation opens new possibilities for OLPL materials to potentially replace conventional inorganic materials in future applications. | Wei-Guang Chen; Zhi-Jian Chen; Yan Wang; Yan-Fang Zhuang; Lu-Yu Wang; Yi-Fan Lv; Jing Chang; yong wang; Yin Xiao; Yu Chen | Materials Science; Optical Materials; Photosensitizers; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67736357fa469535b94f4832/original/day-level-long-persistent-luminescence-in-purely-organic-polymers-via-cascade-hole-trap-mechanism.pdf |
62853937f053df9a6d208577 | 10.26434/chemrxiv-2022-3b427 | Diversity in a Bottle: Iminium Ions as a Platform for N-(Hetero)Aryl Piperidine Synthesis | Piperidines are prevalent throughout FDA-approved drugs and current drug candidates, thus robust methods for preparing these heterocycles are desirable for efficiently probing structure activity relationships (SAR) during drug discovery campaigns. N-heteroaryl piperidines are particularly important in pharmaceutical applications, but they remain problematic synthetic targets because traditional approaches based on transition metal catalyzed cross-coupling and or SNAr reactions routinely fail. We report here a general platform for the rapid synthesis of densely functionalized N-(hetero)aryl piperidine derivatives using a common precursor. First, we disclose an expeditious synthesis of bench-stable cyclic iminium salts starting from widely abundant heteroaryl amine and ketoacrylate feedstocks. We then show that these intermediates are readily elaborated into a wide variety of complex piperidines via derivatization reactions employing common reagents. This chemistry facilitates incorporation of trifluoromethyl, methyl, and cyano nucleophiles at C2, in addition to substitution at C3 using a variety of carbon electrophiles. Additionally, sequential C3 and C2 functionalization of the iminium salts allows for modular construction of piperidine derivatives having very complex substitution patterns. Finally, we show that the key iminium species can be generated and transformed in situ, providing access to desired compounds in a single-pot through-process. | Jacob Greenwood; Matthew Larsen; Samantha Burgess; Justin Newman; Yuan Jiang; Aaron C. Sather | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62853937f053df9a6d208577/original/diversity-in-a-bottle-iminium-ions-as-a-platform-for-n-hetero-aryl-piperidine-synthesis.pdf |
615d244aaa918d1e2a216c7c | 10.26434/chemrxiv-2021-m0np8 | FRET Pumping of Rhodamine-Based Probe in Light-Harvesting Nanoparticles for Highly Sensitive Detection of Cu2+ | In this work we presented novel strategy for increasing the performance of popular fluorescent probes on the basis of rhodamine-lactam platform. This strategy is based on the incorporation of probe molecules into the light-harvesting nanoparticles to pump modulated optical signal by Förster resonant energy transfer. Using the commercially available Cu2+ probe as a reference chemical, we have developed an efficient approach to significantly improve its sensing performance. Within obtained nanoparticles coumarin-30 nanoantenna absorbs excitation light and pumps incorporated sensing molecules providing bright fluorescence to a small number of emitters, while changing the probe-analyte equilibrium from liquid-liquid to solid-liquid significantly increased the apparent association constant, which together provided a ~100-fold decrease in the detection limit. The developed nanoprobe allows highly sensitive detection of Cu2+ ions in aqueous media without organic co-solvents usually required for dissolution of the probe, and demonstrate compatibility with inexpensive fluorometers and the ability to detect low concentrations with the naked eye. | Aleksandr Mironenko; Mikhail Tutov; Aleksandr Chepak; Svetlana Bratskaya | Analytical Chemistry; Nanoscience; Nanodevices; Nanofabrication; Plasmonic and Photonic Structures and Devices; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615d244aaa918d1e2a216c7c/original/fret-pumping-of-rhodamine-based-probe-in-light-harvesting-nanoparticles-for-highly-sensitive-detection-of-cu2.pdf |
60c74c86469df4699bf440da | 10.26434/chemrxiv.11522133.v2 | A Simple Method for Including Polarization Effects in Solvation Free Energy Calculations When Using Fixed-Charge Force Fields: Alchemically Polarized Charges. | <div><div>The incorporation of polarizability in classical force-field molecular simulations is an ongoing area of research. We focus here on its application to hydration free energy simulations of organic molecules. In contrast to computationally complex approaches involving the development of explicitly polarizable force fields, we present herein a simple methodology for incorporating polarization into such simulations using standard fixed-charge force-fields, which we call the Alchemically Polarized Charges (APolQ) method. APolQ employs a standard classical alchemical free energy change simulation to calculate the free energy difference between a fully polarized solute particle in a condensed phase and its unpolarized state in a vacuum. One electronic structure (ES) calculation to of the electron densities is required for each state: for the former, we use a Polarizable Continuum Model (PCM), and for the latter we use vacuum-phase electronic structure calculations.</div><div><br /></div><div>We applied APolQ to hydration free energy data for a test set of 45 neutral solute molecules in the FreeSolv database, and compared results obtained using three different water models (SPC/E, TIP3P, OPC3) and using MBIS and RESP partial charge methodologies. ES calculations were carried out at the MP2 level of theory and with cc-pVTZ and aug-cc-pVTZ basis sets. In comparison with AM1-BCC, we found that APolQ outperforms it for the test set. Despite our method using default GAFF parameters, the MBIS partial charges yield Absolute Average Deviations (AAD) 1.5 to 1.9 kJ·mol<sup>−1</sup> lower than AM1-BCC.</div><div><br /></div><div>We conjecture that this method can be further improved by fitting the Lennard-Jones and torsional parameters to partial charges derived using MBIS or RESP methodologies. </div></div> | Braden Kelly; William Smith | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c86469df4699bf440da/original/a-simple-method-for-including-polarization-effects-in-solvation-free-energy-calculations-when-using-fixed-charge-force-fields-alchemically-polarized-charges.pdf |
60c74372842e65ba97db2281 | 10.26434/chemrxiv.9166787.v1 | Controlling the Reactivity of Enzymes in Mechanochemistry: Inert Surfaces Protect β-Glucosidase Activity During Ball Milling | Although cellulose has been
identified as the foremost candidate for the replacement of fossil fuels, its
recalcitrant nature prevents the full deployment of technologies based on its
saccharification. We recently reported a possible strategy to resolve this
conundrum: using cellulases under “RAging” - a solvent-free process that
utilizes enzymes under mechanochemical conditions - to achieve fast, efficient
hydrolytic depolymerization of cellulosic materials into glucose.
β-Glucosidases catalyze the last and often limiting step of this process, <i>i.e.</i> the formation of glucose from
cellobiose. Here, we reveal the high sensitivity of β-glucosidases to ball
milling, as well as an unexpected stabilization effect of inert surfaces,
enabling the protection of β-glucosidases under mechanochemical treatment. This
approach provides an unexpected strategy to control the reactivity of enzymes
under mechanochemical conditions. Finally, our results also provide the very
first demonstration of enzymatic equilibrium under mechanochemical conditions. | Fabien Hammerer; Shaghayeh Ostadjoo; Tomislav Friscic; Karine Auclair | Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74372842e65ba97db2281/original/controlling-the-reactivity-of-enzymes-in-mechanochemistry-inert-surfaces-protect-glucosidase-activity-during-ball-milling.pdf |
60c7512aee301cfc64c7a9bd | 10.26434/chemrxiv.13129640.v1 | Protect to Detect: A Golgi Apparatus Targeted Probe to Image Mobile Zinc Through the Use of a Lipophilic Cell-Labile Protecting Group Strategy | The Golgi apparatus requires zinc for its normal function, but the role it plays in these
processes at the sub-cellular level is not well-understood due to the lack of appropriate tools
to image it. Herein, a small molecule Golgi apparatus targeted probe was developed to image
mobile Zn2+. A trityl group was used to protect a Golgi apparatus targeting cysteine residue to
increase membrane permeability, which was then removed in cellulo within 24 hours,
revealing the free cysteine targeting motif to anchor the probe to the Golgi apparatus. The
probe shows good photophysical properties, good selectivity and Zn2+ response over a wide
range of pH as well as low cellular toxicity. The probe was shown to be capable of targeting
the Golgi apparatus and responding to Zn2+ in a number of different cell lines and was also
applied to monitor the change of concentration of mobile Zn2+ in the Golgi apparatus in
response to oxidative stress. | Le Fang; Rachel Crespo Otero; Christopher Jones; Mike Watkinson | Supramolecular Chemistry (Org.); Sensors; Supramolecular Chemistry (Inorg.); Theory - Inorganic; Cell and Molecular Biology; Chemical Biology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7512aee301cfc64c7a9bd/original/protect-to-detect-a-golgi-apparatus-targeted-probe-to-image-mobile-zinc-through-the-use-of-a-lipophilic-cell-labile-protecting-group-strategy.pdf |
62cd260b244ce0626a4632c6 | 10.26434/chemrxiv-2022-1xw3b | Enhanced ciprofloxacin removal from aqueous solution using a chemically modified biochar derived from bamboo sawdust: Adsorption process optimization with response surface methodology | Contamination of water by ciprofloxacin has become a significant concern due to its adverse health effects and growing evidence of antimicrobial-resistant genes evolution. To this end, a chemically modified bamboo biochar was prepared from bamboo sawdust to effectively remove ciprofloxacin (CIP) from an aqueous solution. Under similar adsorption conditions, the modified bamboo biochar (MBC) has an excellent CIP removal efficiency (96%) compared to unmodified bamboo biochar (UBC) efficiency (45%). Thus, MBC was used in batch adsorption experiments and the process was optimized with the central composite design (CCD) framework of response surface methodology (RSM). Sorption process parameters such as initial CIP concentration, pH, adsorbent dose, and contact time were studied and found to have a significant effect on CIP removal. The optimal CIP removal (96%) was obtained at MBC dose (0.5 g L-1), CIP initial concentration (20 mg L-1), pH (7.5), and contact time (46 min). The adsorption kinetic data were well described by the pseudo-second-order model (R2 = 0.999), and both Langmuir (R2 = 0.994) and Freundlich (R2 = 0.972) models gave the best fit in CIP adsorption isotherm analysis. The maximum monolayer adsorption capacity of the MBC was 78.43 mg g-1 based on the Langmuir isotherm model. These results suggest that CIP adsorption was mainly controlled by chemisorption. Moreover, the CIP adsorption process was endothermic and spontaneous. Overall, MBC is a low-cost, efficient, and recyclable adsorbent for eliminating emerging contaminants such as ciprofloxacin from an aqueous solution. | wondimu kebede Wakejo; Beteley Tekola Meshasha; Joon Wun Kang; Yonas Chebude Chebude | Chemical Engineering and Industrial Chemistry; Water Purification | CC BY NC 4.0 | CHEMRXIV | 2022-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cd260b244ce0626a4632c6/original/enhanced-ciprofloxacin-removal-from-aqueous-solution-using-a-chemically-modified-biochar-derived-from-bamboo-sawdust-adsorption-process-optimization-with-response-surface-methodology.pdf |
60c756bc469df46817f4536a | 10.26434/chemrxiv.14315615.v1 | KAT Ligation for Rapid and Facile Covalent Attachment of Biomolecules to Surfaces | <p>The efficient and bioorthogonal chemical ligation reaction between potassium acyltrifluoroborates (KATs) and hydroxylamines (HAs) was used for the surface functionalization</p><p>of a self-assembled monolayer (SAM) with biomolecules. An alkane thioether molecule with one terminal KAT group (S-KAT) was synthesized and adsorbed onto a gold surface, placing a KAT</p><p>group on the top of the monolayer (KAT-SAM). As an initial test case, an aqueous solution of a hydroxylamine (HA) derivative of PEG (HA-PEG) was added to this KAT-SAM at room temperature to perform the surface KAT ligation. Quartz crystal microbalance with dissipation (QCM-D) monitoring confirmed the rapid attachment of the PEG moiety onto the SAM.</p><p>The covalent conjugation of PEG by amide-bond formation was established by complementary surface characterization methods including contact angle, ellipsometry, and X-ray photoelectron</p>
<p>spectroscopy (XPS). To test the applicability of this surface KAT ligation for the attachment of biomolecules to the surfaces, this KAT-SAM was subjected to the reaction with HA derivative of</p>
<p>protein. A HA-derivatized green fluorescent protein (HA-GFP) was added in dilute concentrations to the KAT-SAM under aqueous conditions and rapid protein attachment was observed in real-time by QCM. Despite the fact that such biomolecules have a variety of unprotected functional groups within their structures, the surface KAT reaction proceeded efficiently in a selective manner. Our results clearly demonstrate the versatile applicability of the KAT ligation for the covalent attachment of a variety of biomolecules onto surfaces under dilute and biocompatible</p>
<p>conditions to form stable, natural amide bonds.</p> | Alessandro Fracassi; Ankita Ray; Nako Nakatsuka; Cristiana Passiu; Matthias Tanriver; Dominik Schauenburg; Simon Scherrer; S.N Ramakrishna; Jeffrey Bode; Nicholas D. Spencer; Antonella Rossi; Yoko Yamakoshi | Aggregates and Assemblies; Biological Materials; Nanostructured Materials - Materials; Thin Films; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756bc469df46817f4536a/original/kat-ligation-for-rapid-and-facile-covalent-attachment-of-biomolecules-to-surfaces.pdf |
62729e0d6cae1c3bb5fd1d67 | 10.26434/chemrxiv-2022-q4h2z | Synthesis and styrene copolymerization of novel alkoxy ring-substituted octyl phenylcyanoacrylates | Novel alkoxy ring-substituted octyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2(CH2)6CH3 (where R is 2-methoxy, 3-methoxy, 4-methoxy, 2-ethoxy, 3-ethoxy, 4-ethoxy, 4-propoxy, 4-butoxy, 4-hexyloxy) were prepared and copolymerized with styrene. The acrylates were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-substituted benzaldehydes and octyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. All the acrylates were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis. | David R. Graykowski; Marlena D. Hadas; Marianna C. Haddad; Jacqueline Jimenez; Marcelina A. Skowronski; Jade D. Smith; Brendan S. Van Voorhis; Zoe M. Varsbergs; Sara M. Rocus; William S. Schjerven; Gregory B Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62729e0d6cae1c3bb5fd1d67/original/synthesis-and-styrene-copolymerization-of-novel-alkoxy-ring-substituted-octyl-phenylcyanoacrylates.pdf |
66382d3c91aefa6ce1408a72 | 10.26434/chemrxiv-2024-f7dh4 | Insights into the catalytic promotion of propylene self-metathesis over silica-supported molybdenum oxide using substituted olefins | Olefin metathesis is a versatile strategy for functional group interconversion around C=C bonds. Here, we investigate in detail a recently discovered promotional effect, where co-feeding 2,3-dimethyl-2-butene isomers (4MEs) increases propylene self-metathesis rates on silica-supported Mo and W oxides by orders of magnitude. Through detailed kinetic measurements on MoOx/SiO2, we validate a dynamic site renewal and decay cycle, analogous to WOx/SiO2, which operates in tandem with the Chauvin cycle and can be effectively modulated by co-feeding 4MEs. Active site titrations indicate that the promotional effect results from an increased density of active sites rather than enhanced per-site catalytic activity. Spectroscopic analyses reveal that the renewal and decay of Mo alkylidene active sites involve proton-transfer mediated by proximal acidic Si-OH groups. Additionally, the co-fed promoters not only reduce Mo (VI) to Mo (IV), thereby increasing the number of pre-active sites, but also act as proton relays, enhancing proton-transfer steps. This dual functionality elucidates the mechanism underlying the enhanced metathesis activity observed with promoter addition. | Ran Zhu; Husain Adamji; Zachariah Berkson; Jie Zhu; Ashley Head; Heather Kulik; Christophe Copéret; Yuriy Román-Leshkov | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66382d3c91aefa6ce1408a72/original/insights-into-the-catalytic-promotion-of-propylene-self-metathesis-over-silica-supported-molybdenum-oxide-using-substituted-olefins.pdf |
638422b24b1a5f168c8f902f | 10.26434/chemrxiv-2022-xx3vr-v2 | Promoting Cu Catalyzed CO2 electroreduction to multi-carbon products by tuning the activity of H2O | The electrochemical reduction of CO2 to multi-carbon products is a sustainable route for the synthesis of energy dense chemical feedstocks. Cu is the only material known to produce multi-carbon (C2+) products with appreciable selectivity. However, the generation of C2+ products compete with the formation of C1 products and the reduction of H2O to hydrogen. Here, we tuned the activity of H2O from 0.97 to 0.47 by using a NaClO4-based H2O-in-salt-electrolyte. Commercial Cu-nanoparticle electrodes evaluated in pH 9 NaClO4 with a H2O activity of 0.66 achieved a Faradaic Efficiency of ~ 73% for C2+ products (ethylene, ethanol, and propanol) with a C2+ partial current density of −110 mA cm–2 at –0.88 vs. Reversible Hydrogen Electrode. Furthermore, we were able to modulate the C2+/C1 ratios between 1 to 20 by altering only the H2O activity, demonstrating unrivaled tunability between C1 and C2+ products. Analysis of the Tafel slopes and reaction orders on model Cu electrodes revealed that the mechanism for forming C2 products was unchanged across a wide range of H2O activities, while C1 products and H2 had mechanisms which changed as the activity of H2O was lowered. Therefore, we can conclude that protons are part of the rate-determining step for the formation of C1 products, but not C2 products. We have demonstrated that tuning the activity of H2O in an aqueous solvent is a powerful new guiding principle for improving the reduction of CO2 to C2 and C3 products. | Hao Zhang; Jiaxin Gao; Anthony Shoji Hall | Physical Chemistry; Catalysis; Energy; Electrocatalysis; Chemical Kinetics; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638422b24b1a5f168c8f902f/original/promoting-cu-catalyzed-co2-electroreduction-to-multi-carbon-products-by-tuning-the-activity-of-h2o.pdf |
61db9b22db4d9f0ae2929eff | 10.26434/chemrxiv-2022-px3r8 | AutoSolvate: A Toolkit for Automating Quantum Chemistry Design and Discovery of Solvated Molecules | The availability of large, high-quality data sets is crucial for artificial intelligence design and discovery in chemistry. Despite the essential roles of solvents in chemistry, the rapid computational data set generation of solution-phase molecular properties at the quantum mechanical level of theory was previously hampered by the complicated simulation procedure. Software toolkits that can automate the procedure to set up high-throughput explicit-solvent quantum chemistry (QC) calculations for arbitrary solutes and solvents in an open-source framework are still lacking. We developed AutoSolvate, an open-source toolkit to streamline the workflow for QC calculation of explicitly solvated molecules. It automates the solvated-structure generation, force field fitting, configuration sampling, and the final extraction of microsolvated cluster structures that QC packages can readily use to predict molecular properties of interest. AutoSolvate is available through both a command line interface and a graphical user interface, making it accessible to the broader scientific community. To improve the quality of the initial structures generated by AutoSolvate, we investigated the dependence of solute-solvent closeness on solute/solvent identities and trained a machine learning model to predict the closeness and guide initial structure generation. Finally, we tested the capability of AutoSolvate for rapid data set curation by calculating the outer-sphere reorganization energy of a large data set of 166 redox couples, which demonstrated the promise of the AutoSolvate package for chemical discovery efforts. | Eugen Hruska; Ariel Gale; Xiao Huang; Fang Liu | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61db9b22db4d9f0ae2929eff/original/auto-solvate-a-toolkit-for-automating-quantum-chemistry-design-and-discovery-of-solvated-molecules.pdf |
60c74833337d6c8691e274e1 | 10.26434/chemrxiv.10318043.v2 | Strategies for Design of Potential Singlet Fission Chromophores Utilizing a Combination of Ground State and Excited State Aromaticity Rules | Singlet exciton fission photovoltaics requires chromophores with their lowest excited states arranged so that 2<i>E</i>(T<sub>1</sub>) < <i>E</i>(S<sub>1</sub>) and <i>E</i>(S<sub>1</sub>) < <i>E</i>(T<sub>2</sub>). Herein, qualitative theory and quantum chemical calculations are used to develop explicit strategies on how to use Baird’s 4<i>n</i> rule on excited state aromaticity, combined with Hückel’s 4<i>n</i>+2 rule for ground state aromaticity, to tailor new potential chromophores for singlet fission. We first analyze the <i>E</i>(T<sub>1</sub>), <i>E</i>(S<sub>1</sub>) and <i>E</i>(T<sub>2</sub>) of benzene and cyclobutadiene (<b>CBD</b>) as, respectively, excited state antiaromatic and aromatic archetypes, and reveal that <b>CBD </b>fulfils the criteria on the state ordering for a singlet fission chromophore. We then look at fulvenes, a class of compounds that can be tuned by choice of substituents from Baird-antiaromatic to Baird-aromatic in T<sub>1</sub> and S<sub>1</sub>, and from Hückel-aromatic to Hückel-antiaromatic in S<sub>0</sub>. The T<sub>1</sub> and S<sub>1</sub> states of most substituted fulvenes (159 of 225) are described by singly excited HOMO→LUMO configurations, providing a rational for the simultaneous tuning of <i>E</i>(T<sub>1</sub>) and <i>E</i>(S<sub>1</sub>) along an approximate (anti)aromaticity coordinate. Key to the tunability is the exchange integral (K<sub>H,L</sub>), which ideally is constant throughout the compound class, providing a constant D<i>E</i>(S<sub>1</sub>-T<sub>1</sub>). This leads us to a geometric model for identification of singlet fission chromophores, and we explore what factors limit the model. Candidates with calculated <i>E</i>(T<sub>1</sub>) of ~1 eV or higher are identified among benzannelated 4<i>n</i>pi-electron compound classes and siloles. In brief, it is clarified how the joint utilization of Baird’s 4<i>n</i> and Hückel’s 4<i>n</i>+2 rules, together with substituent effects (electronic and steric) and benzannelation, can be used to tailor new chromophores with potential use in singlet fission photovoltaics.<br /> | Ouissam El Bakouri; Joshua R. Smith; Henrik Ottosson | Physical Organic Chemistry; Computational Chemistry and Modeling; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74833337d6c8691e274e1/original/strategies-for-design-of-potential-singlet-fission-chromophores-utilizing-a-combination-of-ground-state-and-excited-state-aromaticity-rules.pdf |
676e5842fa469535b9f3e47e | 10.26434/chemrxiv-2024-2pc7l | Excited-state aromatization drives non-equilibrium planarization dynamics | Excited-state aromaticity is one of the most widely applied concepts in the field of chemistry, often used as a rational guideline for predicting conformational changes of cyclic π-conjugated systems induced by photoexcitation. Yet, the details of the relationship between the corresponding photoinduced electronic and structural dynamics have remained unclear. In this work, we applied femtosecond transient absorption and time-resolved time-domain Raman spectroscopies to track a nonequilibrium planarization dynamics of cyclooctatetraene (COT) derivative upon the onset of the excited-state aromaticity. In the femtosecond time-resolved Raman data, the bent-to-planar structural change was clearly captured as a continuous peak shift of the marker band, which was unambiguously identified with 13C-labeling. Our findings show that the planarization occurs after a significant change in the electronic structure, suggesting that the system first becomes aromatic, followed by a conformational change. This work provides a unique framework for understanding the excited-state aromaticity from a dynamical aspect. | Yusuke Yoneda; Tomoaki Konishi; Kensuke Suga; Shohei Saito; Hikaru Kuramochi | Physical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676e5842fa469535b9f3e47e/original/excited-state-aromatization-drives-non-equilibrium-planarization-dynamics.pdf |
6436cf6a73c6563f14b97730 | 10.26434/chemrxiv-2023-x82w3-v2 | Self-Dissociation of Polar Molecules in a Confined Infrared Vacuum | <p>Coherent light-matter interaction of molecular media in infrared (IR) cavities is a promising tool for manipulating and controlling chemical reactivity and light emission. We study the wavepacket dynamics of a single hydrogen fluoride (HF) molecule in electromagnetic environment, using the multiconfiguration time-dependent Hartree (MCTDH) method. We show that in the absence of additional thermal or coherent external sources, a single-mode cavity vacuum can efficiently dissociate a HF bond that is suddenly prepared in the vibrational ground level. We predict dissociation probabilities of up to 20% in less than 200 fs for a bare vacuum field that is resonant with the fundamental vibration frequency at the onset of the ultrastrong coupling regime. Additional enhancements of the dissociation probability can be expected for cavity with thermal excitations and multimode cavities. The results are understood analytically as the result of a Bloch-Siegert shift by using the extended-multi-level quantum Rabi model in a polaron frame that highlights the influence of the permanent dipole moments in the light-matter dynamics. Our work highlights the fundamental differences that can be expected for reactive dynamical processes inside infrared cavities and plasmonic nanostructures relative to free space.</p> | Johan F. Triana; Felipe Herrera | Physical Chemistry; Photochemistry (Physical Chem.); Physical and Chemical Processes; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6436cf6a73c6563f14b97730/original/self-dissociation-of-polar-molecules-in-a-confined-infrared-vacuum.pdf |
652704288bab5d2055239f17 | 10.26434/chemrxiv-2023-n2wct | A Supported Ziegler-Type Organohafnium Site Metabolizes Polypropyl-ene | Cp2Hf(CH3)2 reacts with silica containing strong aluminum Lewis acid sites to form Cp2Hf–13CH3+ paired to aluminate ani-ons. Solid-state NMR characterization shows that this reaction also forms neutral organohafnium and hafnium sites lacking methyl groups. Cp2Hf–13CH3+ reacts with isotatic polypropylene (iPP, Mn = 13.3 kDa; Đ = 2.4; mmmm = 94 %; ~110 C3H6/Hf) in the presence of H2 to form oils with moderate molecular weights (Mn = 290 - 1200 Da) in good yields. The ali-phatic oils show characteristic 13C{1H} NMR properties consistent with complete loss of diastereoselectivity and formation of regioirregular errors under 1 atm H2. These results show that a typical Ziegler-Natta type active site is compatible in a common reaction used to digest waste plastic into smaller aliphatic fragments. | Kavyasripriya Samudrala; Matthew Conley | Inorganic Chemistry; Catalysis; Organometallic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652704288bab5d2055239f17/original/a-supported-ziegler-type-organohafnium-site-metabolizes-polypropyl-ene.pdf |
640383d99789de3dd9eb80c4 | 10.26434/chemrxiv-2022-1rnqh-v2 | Mapping the chemical space of active-site targeted covalent ligands for protein tyrosine phosphatases | Protein tyrosine phosphatases (PTPs) are an important class of enzymes that modulate essential cellular processes through protein dephosphorylation and are dysregulated in various disease states. There is demand for new compounds that target the active sites of these enzymes, for use as chemical tools to dissect their biological roles or as leads for the development of new therapeutics. In this study, we explore an array of electrophiles and fragment scaffolds to investigate the required chemical parameters for covalent inhibition of tyrosine phosphatases. Our analysis juxtaposes the intrinsic electrophilicity of these compounds with their potency against several classical PTPs, revealing chemotypes that inhibit tyrosine phosphatases while minimizing excessive, potentially non-specific reactivity. We also assess sequence divergence at key residues in PTPs to explain their differential susceptibility to covalent inhibition. We anticipate that our study will inspire new strategies to develop covalent probes and inhibitors for tyrosine phosphatases. | Suk ho Hong; Sarah Y Xi; Andrew C Johns; Lauren C Tang; Allyson Li; Madeleine N Hum; Cassandra A Chartier; Marko Jovanovic; Neel H Shah | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2023-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640383d99789de3dd9eb80c4/original/mapping-the-chemical-space-of-active-site-targeted-covalent-ligands-for-protein-tyrosine-phosphatases.pdf |
674d934d5a82cea2fab381b4 | 10.26434/chemrxiv-2024-0q272 | Modular perovskite-BiVO4 artificial leaves towards syngas synthesis on a m2 scale | Metal halide perovskite-based artificial leaves have emerged in recent years as a promising design towards direct solar fuel synthesis. However, the complexity of these layered devices and reliance on solution-based techniques hinders the scalability and performance of existing prototypes. Here, we utilise vacuum processing of the perovskite light absorbers, as an industrially compatible method to produce large-scale devices. Accordingly, we fabricate fully evaporated 10 cm2 PV devices sustaining a 1 V photovoltage, which allow perovskite-BiVO4 tandem photoelectrochemical devices with a selective Cu92In8 alloy catalyst to sustain unassisted water and CO2 splitting over 36 hours. To demonstrate the modularity of this design, we designed a 0.70.5 m2 “artificial tree” reactor containing a 1010 array of artificial leaves, which was benchmarked during the 3-days final outdoor demonstration of the EIC Horizon Prize “Fuel From the Sun”, at the Joint Research Center of the European Commission in Ispra, Italy. Such real-world tests reveal key insights into practical operation that are not encountered during standardised laboratory experiments, but are crucial for upscaling of emerging solar fuel technologies. | Virgil Andrei; Yu-Hsien Chiang; Motiar Rahaman; Miguel Anaya; Taeheon Kang; Edoardo Ruggeri; Samuel D. Stranks; Erwin Reisner | Catalysis; Energy; Heterogeneous Catalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2024-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674d934d5a82cea2fab381b4/original/modular-perovskite-bi-vo4-artificial-leaves-towards-syngas-synthesis-on-a-m2-scale.pdf |
6743505f5a82cea2faa75dcb | 10.26434/chemrxiv-2024-8c02l | DFT-based Polarizable Ion Models for Molten Rare-earth Chlorides: from Lanthanum to Europium | We developed a systematic polarizable force field for molten trivalent rare-earth chlorides, from lanthanum to europium, based on first-principle calculations. The proposed model was employed to investigate the local structure and physico-chemical properties of pure molten salts and their mixtures with sodium chloride. We computed densities, heat capacities, surface tensions, viscosities and diffusion coefficients and disclosed their evolution along the lanthanide series, filling the gaps for poorly studied elements, such as promethium and europium. The analysis of the local arrangement of chloride anions around lanthanide cations revealed broad coordination number distributions with a typical [from six to nine]-fold environment, the maximum of which shifts towards lower values with the increase of atomic number as well as upon dilution of the salt in sodium chloride. The neighbouring lanthanide-chloride complexes were found to be connected by sharing a corner or an edge of the corresponding polyhedra. | Kateryna Goloviznina; Maria-Chiara Notarangelo; Julien Tranchida; Emeric Bourasseau; Mathieu Salanne | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Computational Chemistry and Modeling; Thermodynamics (Physical Chem.); Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6743505f5a82cea2faa75dcb/original/dft-based-polarizable-ion-models-for-molten-rare-earth-chlorides-from-lanthanum-to-europium.pdf |
667479fb01103d79c5b801c7 | 10.26434/chemrxiv-2024-85hg8 | Hetero-confinement in single CdTe nanoplatelets | Dimension-engineered synthesis of atomically thin II-VI nanoplatelets (NPLs) remains an open
challenge. While CdSe NPLs have been made with confinement ranging from 2-11 monolayers
(ML), CdTe NPLs have been significantly more challenging to synthesize and separate. Here we
provide detailed mechanistic insight into the layer-by-layer growth kinetics of CdTe NPLs.
Combining ensemble and single particle spectroscopic and microscopic tools, our work suggests
that beyond 2 ML CdTe NPLs, higher ML structures initially appear as hetero-confined materials
with co-localized multilayer structures. In particular, we observe strongly colocalized 3 and 4 ML
emissions accompanied by a broad trap emission. Accompanying transient absorption, single
particle optical and atomic force microscopy suggests islands of different MLs on the same NPL.
To explain the non-standard nucleation and growth of these hetero-confined structures, we
simulated the growth conditions of NPLs and quantified how monomer binding energy modifies
the kinetics and permits single NPLs with multi-ML structures. Our findings suggest that the
lower bond energy associated with CdTe relative to CdSe limits higher ML syntheses and explains
the observed differences between CdTe and CdSe growth. | Tasnim Ahmed; Xuanheng Tan; Barry Li; Jillian Williams; Elijah Cook; Sophia Tiano; Stephanie Tenney; Dugan Hayes; Justin Caram | Physical Chemistry; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667479fb01103d79c5b801c7/original/hetero-confinement-in-single-cd-te-nanoplatelets.pdf |
60c73e16f96a0027c7285e8a | 10.26434/chemrxiv.6530570.v1 | Non-Radiative Transitions in Metal-Free Octaethylporphyrin and 2-Nitrofluorene Donor-Acceptor System | <div><b>The aim of our work is to investigate the photoinduced electron transfer
in non-covalent metal-free octaethyl porphyrin and 2 nitrofluorene
system by electronic spectra and quantum chemical calculations.</b></div> | Mihir Ghosh; Shivraj; B. Siddlingeshwar; Anup Thomas; Subrata Sinha | Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2018-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e16f96a0027c7285e8a/original/non-radiative-transitions-in-metal-free-octaethylporphyrin-and-2-nitrofluorene-donor-acceptor-system.pdf |
614dbf4f6fc3a828edab9e90 | 10.26434/chemrxiv-2021-k0w7q | Semi-automated high-throughput substrate screening assay for nucleoside kinases | Nucleoside kinases (NKs) are key enzymes involved in the in vivo phosphorylation of nucleoside analogues used as drugs to treat cancer or viral infections. Having different specificities, the characterization of NKs is essential for drug design and the production of nucleotide analogues in an in vitro enzymatic process. Therefore, a fast and reliable substrate screening assay for NKs is of great importance. Here, we report the validation of a well-known luciferase-based assay for the detection of NK activity in 96-well plate format. The assay was semi-automated using a liquid handling robot. A good linearity was demonstrated (r² >0.98) in the range of 0 to 500 µM ATP, and it was shown that also alternative phosphate donors like dATP or CTP were accepted by the luciferase. The developed high-throughput assay revealed comparable results to HPLC analysis. The assay was exemplary used for the comparison of the substrate spectra of four nucleoside kinases using 20 (8 natural and 12 modified) substrates. The screening results correlated well with literature data and, additionally, previously unknown substrates were identified for three of the NKs studied. Our results demonstrate that the developed semi-automated high-throughput assay is suitable to identify best performing NKs for a wide range of substrates. | Katja Hellendahl; Maryke Fehlau; Sebastian Hans; Peter Neubauer; Anke Kurreck | Biological and Medicinal Chemistry | CC BY 4.0 | CHEMRXIV | 2021-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614dbf4f6fc3a828edab9e90/original/semi-automated-high-throughput-substrate-screening-assay-for-nucleoside-kinases.pdf |
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