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613b7443ac32197177779289
|
10.26434/chemrxiv-2021-l8c7b
|
Kinetically corrected Monte Carlo-molecular dynamics simulations of solid electrolyte interphase growth
|
We present a kinetic approach to the Monte Carlo-molecular dynamics (MC-MD) method for simulating reactive liquids using non-reactive forcefields. A graphical reaction representation allows definition of reactions of arbitrary complexity, including their local solvation environment. Reaction probabilities and molecular dynamics (MD) simulation times are derived from ab initio calculations. Detailed validation is followed by studying the development of the solid electrolyte interphase (SEI) in lithium-ion batteries. We reproduce the experimentally observed two-layered structure on graphite, with an inorganic layer close to the anode and an outer organic layer. This structure develops via a near-shore aggregation mechanism.
|
Joseph W Abbott; Felix Hanke
|
Theoretical and Computational Chemistry; Materials Science; Energy; Computational Chemistry and Modeling; Theory - Computational; Fuels - Energy Science
|
CC BY 4.0
|
CHEMRXIV
|
2021-09-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613b7443ac32197177779289/original/kinetically-corrected-monte-carlo-molecular-dynamics-simulations-of-solid-electrolyte-interphase-growth.pdf
|
6720ceef5a82cea2fa32358f
|
10.26434/chemrxiv-2024-hx5gr
|
Beyond Butler-Volmer equation for CO2 electro-reduction on Cu-based gas diffusion electrodes
|
We present a methodology for modelling gas diffusion electrodes with Cu-based catalysts. The applicability of the Butler Volmer equation (B-Ve) based on Tafel analysis is limited to single electron transfer reactions which are not typical of CO2 reduction reactions on Cu catalysts. We developed a method that involves linking the nanoscale effects encapsulated in a detailed calibrated microkinetic model (MKM) on Cu(100) electrodes to a mass transport model (MTM) on a low surface area, flooded agglomerate electrode. The MKM carries richer kinetic information of most reaction pathways described in contemporary literature for Cu(100). Polynomial equations are used to bridge kinetic and transport models without the need for excessive complexity. Our results show that using regression modelling, the microkinetic information at the microscopic level of the catalyst can be successfully linked with the macroscopic electrode models. We observe how mass transport parameters such as CO2 concentration, pH, and applied voltage, interacts with microkinetic information of the catalyst, influencing the reaction pathways and current densities of key products methane, ethylene, ethanol, and hydrogen. Although the model explores the medium to high voltage regimes, the methodology can address the oversimplification of CO2 reduction (CO2RR) kinetics and hydrogen evolution reaction (HER) for observed multiple kinetic regimes if comprehensive microkinetic models are integrated. It also serves as a foundational work for further experimental endeavours for the development of comprehensive microkinetic models. The holistic approach carried out in this work allows for the optimization of both reaction rates and mass transport, paving the way for rational optimisation of electrode designs and their scaling towards commercialization.
|
Peace Adesina; Joel Ager; Alexei Lapkin
|
Chemical Engineering and Industrial Chemistry; Reaction Engineering
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6720ceef5a82cea2fa32358f/original/beyond-butler-volmer-equation-for-co2-electro-reduction-on-cu-based-gas-diffusion-electrodes.pdf
|
62e05c03ed926ea4b1a73e2c
|
10.26434/chemrxiv-2022-44r17-v2
|
Sella, an open-source automation-friendly molecular saddle point optimizer
|
We present a new algorithm for the optimization of molecular structures to saddle points on the potential energy surface using a redundant internal coordinate system. This algorithm automates the procedure of defining the internal coordinate system, including the handling of linear bending angles, e.g. through the addition of dummy atoms. Additionally, the algorithm supports constrained optimization using the null-space sequential quadratic programming formalism. Our algorithm determines the direction of the reaction coordinate through iterative diagonalization of the Hessian matrix, and does not require evaluation of the full Hessian matrix. Geometry optimization steps are chosen using the restricted step partitioned rational function optimization method, and displacements are realized using a high-performance geodesic stepping algorithm. This results in a robust and efficient optimization algorithm suitable for use in automated frameworks.
We have implemented our algorithm in Sella, an open source software package designed to optimize atomic systems to saddle point structures. We also introduce a new benchmark test comprising 500 molecular structures that approximate saddle point geometries and show that our saddle point optimization algorithm outperforms the algorithms implemented in several leading electronic structure theory packages.
|
Eric Hermes; Khachik Sargsyan; Habib Najm; Judit Zádor
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Structure
|
CC BY 4.0
|
CHEMRXIV
|
2022-07-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e05c03ed926ea4b1a73e2c/original/sella-an-open-source-automation-friendly-molecular-saddle-point-optimizer.pdf
|
67987e296dde43c908ae048d
|
10.26434/chemrxiv-2025-8dzjk
|
Single-molecule junctions formed using different electrode metals under an inert atmosphere
|
The electrical and mechanical properties of single-molecule junctions, electronic devices approaching the limits of miniaturization, have typically been probed using inert gold electrodes. Such studies have clearly exposed the role of the molecular bridge and linker groups, as well as the impact of the surrounding environment (solvent, temperature, electric field), on interfacial charge transport and chemical reactivity. However, a complete understanding and the ultimate technological exploitation of molecular devices may only be realized if they can also be readily evaluated using non-gold electrode metals – a task broadly impeded by the rapid oxidation of such materials in air. Here we demonstrate that single-molecule junctions can be formed using seven metals (gold, silver, copper, platinum, zinc, nickel, cobalt) under an inert atmosphere inside of a glovebox. We identify the characteristic conductance features of atomic-sized junctions for each metal at room temperature and ambient pressure, a guiding signature of nanoscale electrode formation. We further show the conductance of single-molecule junctions comprising the same molecule and up to five different metals does not strongly correlate with electrode work function, corroborating previous reports and inviting future targeted studies to rationalize the trends observed. Snapback measurements on five metals reveal that the size of the nanogap opened upon breaking atomic point contacts exponentially correlates with the material’s melting point, a proxy for the rate of surface atom diffusion. Together, this work exposes exciting new opportunities to experimentally probe the influence of electrode metal on the formation, stability, and function of these nanoscale structures.
|
Thomas Czyszczon-Burton; Sawyer Lazar; Zelin Miao; Michael Inkpen
|
Physical Chemistry; Inorganic Chemistry; Nanoscience; Nanodevices; Self-Assembly; Transport phenomena (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67987e296dde43c908ae048d/original/single-molecule-junctions-formed-using-different-electrode-metals-under-an-inert-atmosphere.pdf
|
63e3c64c6d032916bb68a9fe
|
10.26434/chemrxiv-2022-f0fgw-v2
|
Modified Akuamma Alkaloids with Increased Potency at the Mu-opioid Receptor
|
Akuammine (1) and pseudo-akuammigine (2) are indole alkaloids found in the seeds of the akuamma tree (Picralima nitida). Both alkaloids are weak agonists of the mu opioid receptor (µOR); however, they produce minimal effects in animal models of antinociception. To probe the interactions of 1 and 2 at the opioid receptors, we have prepared a collection of 22 semi-synthetic derivatives. Evaluation of this collection at the µOR and kappa opioid receptor (κOR) revealed structural-activity relationship trends and derivatives with improved potency at the OR. Most notably, the introduction of a phenethyl moiety to the N1 of 2 produces a 70-fold increase in potency and a 7-fold increase in selectivity for the µOR. The in vitro potency of this compound resulted in increased efficacy in the tail-flick and hot-plate assays of antinociception. The improved potency of these derivatives highlights the promise of exploring natural product scaffolds to probe the opioid receptors.
|
Madeline Hennessy; Anna Gutridge; Alexander French; Elizabeth Rhoda; Yazan Meqbil; Meghna Gill; Yavnika Kashyap; Kevin Appourchaux; Barnali Pauli; Z. Jim Wang; Richard van Rijn; Andrew Riley
|
Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-02-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e3c64c6d032916bb68a9fe/original/modified-akuamma-alkaloids-with-increased-potency-at-the-mu-opioid-receptor.pdf
|
65ea6f389138d23161fc53cb
|
10.26434/chemrxiv-2024-g1cgf
|
Practical One Pot Synthesis of 2-Alkyl-substituted Benzothiazoles from Bis-(2-nitrophenyl)-disulfides.
|
2-Methyl benzothiazoles are widely used as key precursor for dyes, photosensitizers and fluorescent markers. Therefore, they are demanded in multigram and even kilogram amounts. Hereby, we propose a scalable single-step procedure for production of 2-alkylsubstituted benzothiazoles from corresponding bis-(2-nitrophenyl)-disulfides. Substrates containing various substituents including carboxylic and ester groups were introduced into reaction. Different sodium salts were tested as reducing agents, extensive optimization was performed. The products were obtained in the amounts of up to 350 g in a single run.
|
Volodymyr Puskov; Serhii Babii; Iryna Adamenko; Sviatoslava Melnychuk; Tetiana Druzhenko; Alexander Lyapunov; Sergey Popov; Dmytro Volochnyuk; Serhiy Ryabukhin
|
Organic Chemistry; Organic Synthesis and Reactions; Process Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ea6f389138d23161fc53cb/original/practical-one-pot-synthesis-of-2-alkyl-substituted-benzothiazoles-from-bis-2-nitrophenyl-disulfides.pdf
|
62d5db8a4e76bfc69c953dae
|
10.26434/chemrxiv-2022-tnc3f
|
SARS-CoV-2 and MERS-CoV spike protein binding studies support stable mimic of bound 9-O-acetylated sialic acids
|
Many disease-causing viruses target sialic acids (Sias), a class of nine-carbon sugars known to coat the surface of many cells including those in the lungs. Human beta coronaviradae, known for causing respiratory tract diseases, often bind Sias, some preferentially bind to those with 9-O-Ac-modification. Currently, co-binding of SARS-CoV-2, a beta coronavirus responsible for the COVID-19 pandemic, to human Sias has been reported and its preference towards α2-3-linked Neu5Ac shown. Nevertheless, O-acetylated Sias-protein binding studies are difficult, due to the ester lability. We studied the binding free energy differences between Neu5,9Ac2α2-3GalβpNP and its more stable 9-NAc mimics binding to SARS-CoV-2 spike protein using molecular dynamics and alchemical free energy simulations. We identified multiple Sias-binding pockets, including two novel sites, with similar binding affinities to those of MERS-CoV, a known co-binder of sialic acid. In our binding poses, 9-NAc and 9-OAc Sias bind similarly, suggesting an experimentally reasonable mimic to probe viral mechanisms.
|
Lisa Oh; Ajit Varki; Xi Chen; Lee-Ping Wang
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d5db8a4e76bfc69c953dae/original/sars-co-v-2-and-mers-co-v-spike-protein-binding-studies-support-stable-mimic-of-bound-9-o-acetylated-sialic-acids.pdf
|
60c74fc9bb8c1a1f973dba0d
|
10.26434/chemrxiv.12939776.v1
|
In Situ Electron Paramagnetic Resonance Correlated Spectroscopy and Imaging: A Tool for Lithium-Ion Batteries to Investigate Metallic Lithium Sub-Micrometric Structures Created by Plating and Stripping
|
<div>Monitoring the formation of dendrites or filaments of lithium is of paramount importance</div><div>for Li-based battery technologies, hence the intense activities in designing in situ techniques</div><div>to visualize their growth. Herein we report the benefit of correlating in situ electron para4 magnetic resonance (EPR) spectroscopy and EPR imaging to analyze the morphology and</div><div>location of metallic lithium in a symmetric Li/LiPF6/Li electrochemical cell during polariza6 tion. We exploit the variations in shape, resonance field and amplitude of the EPR spectra</div><div>to follow, operando, the nucleation of sub-micrometric Li particles (narrow and symmetrical</div><div>signal) that conjointly occurs with the fragmentation of bulk Li on the opposite electrode</div><div>(asymmetrical signal). Moreover, in situ EPR correlated spectroscopy and imaging (spectral10 spatial EPR imaging) allows the identification (spectral) and localization (spatial) of the sub11 micrometric Li particles created by plating (deposition) or stripping (altered bulk Li surface).</div><div>We finally demonstrate the possibility to visualize, via in situ EPR imaging, dendrites formed</div><div>through the separator in the whole cell. Such a technique could be of great help in mastering</div><div>the Li-electrolyte interface issues that plague the development of solid-state batteries.</div>
|
Charles-Emmanuel Dutoit; Mingxue Tang; Didier Gourier; Jean-Marie Tarascon; Hervé Vezin; Elodie Salager
|
Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-09-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fc9bb8c1a1f973dba0d/original/in-situ-electron-paramagnetic-resonance-correlated-spectroscopy-and-imaging-a-tool-for-lithium-ion-batteries-to-investigate-metallic-lithium-sub-micrometric-structures-created-by-plating-and-stripping.pdf
|
65aeec1466c138172909eb3f
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10.26434/chemrxiv-2024-5mdm9
|
Construction of Multi-Scale Dissipative Particle Dynamics (DPD) Models from other Coarse-Grained Models
|
We present a general scheme for converting coarse grained models into Dissipative Particle Dynamics (DPD) models. We build the corresponding DPD models by anal- ogy with the de novo DPD coarse graining scheme suggested by Groot and Warren (J. Chem. Phys., 1997). Electrostatic interactions between charged DPD particles are represented though the addition of a long-range Slater Coulomb potential as suggested by Gonz ́alez-Melchor et al (J. Chem. Phys 2006). The construction is illustrated by converting MARTINI models for various proteins into a DPD representation, but it not restricted to the usual potential form in the MARTINI model—viz Lennard-Jones potentials. We further extended the DPD scheme away from the typical use of homo- geneous particle sizes, and therefor faithfully representing the variations in the particle sizes seen in the underlying MARTINI model. The accuracy of the resulting construc- tion of our generalized DPD models with respect to several structural observables have been benchmarked favorably against all-atom and MARTINI models for a selected set of peptides and proteins, and variations in the scales of the coarse-graining of the water solvent.
|
Yinhan Wang; Rigoberto Hernandez
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65aeec1466c138172909eb3f/original/construction-of-multi-scale-dissipative-particle-dynamics-dpd-models-from-other-coarse-grained-models.pdf
|
62ea77de00ed9c921a2053e3
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10.26434/chemrxiv-2022-6lv34-v2
|
Modeling the expansion of virtual screening libraries
|
Recently, the growth of commercially-available molecules has been driven by “tangible” make-on-demand, virtual libraries. Such billion-molecule libraries can never be fully synthesized, tested, or even stored. The only way to explore this expanded chemical space is by computationally prioritizing particular molecules for synthesis and testing, often by docking. The success of this prioritization may depend on library properties: how diverse are the molecules, how similar are they to bio-like molecules, such as metabolites and drugs, how does receptor-fit improve with library size, and how does the presence of artifacts grow with library size? To begin to investigate these questions, we compare the characteristics and performance of a library of 3 million “in-stock” molecules with that of ever-larger tangible libraries, up to 3 billion molecules in size. The bias toward biologically precedented molecules of the 886-fold larger tangible library decreases 19,000-fold compared to the in-stock library. Looking at docking hits, and not the overall libraries, thousands of high-ranking synthesized and tested tangible compounds from five ultra-large library docking campaigns are also dissimilar to bio-like molecules. These observations imply that bio-likeness plays little role in the likelihood of binding, appearing to contradict multiple studies to the contrary. Another important aspect of library growth is whether screening ever-larger libraries leads to better ligands. Judged by docking score, better fitting molecules are found as the library grows, with score improving log-linearly with library size. Finally, it is possible to imagine that as library size increases, so too do the chances of rare events—molecules that cheat the scoring function and rank artifactually well. Both simulation and experimental results from ultra-large library screens suggest that this is true—as the libraries grow, more and more artifacts can crowd the very top-ranking molecules. Although the nature of these artifacts appears to change from target to target, the expectation of their occurrence does not, and simple strategies may be devised to minimize the impact of these rare-event artifacts on the success of large library screens.
|
Jiankun Lyu; John Irwin; Brian Shoichet
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ea77de00ed9c921a2053e3/original/modeling-the-expansion-of-virtual-screening-libraries.pdf
|
60c753274c89197a56ad427c
|
10.26434/chemrxiv.13414646.v1
|
Spatiotemporal Control of Supramolecular Polymerization and Gelation of Metal-Organic Polyhedra
|
In coordination-based supramolecular materials such as metallogels, simultaneous temporal and spatial control of their assembly remains challenging. Here, we demonstrate that the combination of light with acids as stimuli allows for the spatiotemporal control over the architectures, mechanical properties, and shape of porous soft materials based on metal-organic polyhedra (MOPs). First, we show that the formation of a colloidal gel network from a preformed kinetically trapped MOP solution can be triggered upon addition of trifluoroacetic acid (TFA), and that acid concentration determines the reaction kinetics. As determined by time-resolved dynamic light scattering, UV-vis absorption and <sup>1</sup>H NMR spectroscopies and rheology measurements, the consequences of the increase in acid concentration are (i) an increase in the cross-linking between MOPs; (ii) a growth in the size of the colloidal particles forming the gel network; (iii) an increase in the density of the colloidal network; and (iv) a decrease in the ductility and stiffness of the resulting gel. We then demonstrate that irradiation of a dispersed photoacid generator, pyranine, allows the spatiotemporal control of the gel formation by locally triggering the self-assembly process. Using this methodology, we show that the gel can be patterned into a desired shape. Such precise positioning of the assembled structures, combined with the stable and permanent porosity of MOPs, could allow their integration into devices for applications such as sensing, separation, catalysis, or drug release.
|
alexandre legrand; Li-Hao Liu; Philipp Royla; Takuma Aoyama; Gavin Craig; arnau carne-sanchez; Kenji Urayama; Jan J. Weigand; Chia-Her Lin; Shuhei Furukawa
|
Supramolecular Chemistry (Inorg.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2020-12-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753274c89197a56ad427c/original/spatiotemporal-control-of-supramolecular-polymerization-and-gelation-of-metal-organic-polyhedra.pdf
|
656b94cfcf8b3c3cd7a67aba
|
10.26434/chemrxiv-2023-9b9hj
|
Tuning Enantioselective Drug Adsorption in Isoreticular Homochiral Metal-Peptide Frameworks through Proximity Pore Interactions
|
Pharmaceutical research places great importance on the stereochemistry and enantioseparation of racemic drugs due to the potential variations in pharmacological and toxicological properties displayed by different enantiomers as they interact with the body’s metabolic pathway. Metal-organic frameworks (MOFs) are porous adsorbents that can be designed to possess homochirality within their structures, enabling tunable porosity and enantioselective adsorption. In our study, we present the synthesis of five novel and homochiral Co-L-GG(R) MOFs (where L-GG = glycyl-L(S)-glutamic acid and R = bipyridyl (bipy) pillar ligands). These isoreticular MOFs were synthesized using the ligand extension strategy. This approach allowed us to systematically control the pore sizes of the MOFs, enabling fine-tuning of the enantioselective adsorption of racemic drugs, primarily DL-Penicillamine (Pen). Our findings reveal that the pore size greatly influences enantioselective adsorption, where too large or too small pores hinder the proximity-driven dispersive interactions between the drug and the pore surface, resulting in poor enantioselective adsorption of Pen. We achieved an enantiomeric excess (ee) of 60.1% (L over D), increasing to a maximum 76.1% ee using Co-L-GGvinylbipy by tuning proximity interactions in saturated pores. These results were accomplished by controlling the drug saturation within the MOF pores, promoting favorable interactions.
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James Ho; Ankit Yadav; Andrzej Gładysiak; Andrew Carpenter ; Anjali Verma; Matthew Cranswick; Adrian Henle; Mas Subramanian ; Joe Baio; Kyriakos Stylianou
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Inorganic Chemistry; Materials Chemistry
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CC BY NC 4.0
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CHEMRXIV
|
2023-12-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656b94cfcf8b3c3cd7a67aba/original/tuning-enantioselective-drug-adsorption-in-isoreticular-homochiral-metal-peptide-frameworks-through-proximity-pore-interactions.pdf
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60c75987ee301c5da2c7b916
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10.26434/chemrxiv.14707581.v1
|
Dissociative Electron Attachment in C2H via Electronic Resonances
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<div>
<div>
<div>
<div>
<p>Investigation of microwave-activated CH<sub>4</sub>/H<sub>2 </sub>plasma used in chemical vapor deposition of diamond revealed the presence of electronically excited C<sub>2</sub><sup>-</sup>(B<sup>2</sup>Σ<sub>u</sub><sup>+</sup>). Using high-level electronic structure methods, we investigate electronic structure of C<sub>2</sub>H<sup>-</sup> and suggest possible routes for formation of C<sub>2</sub><sup>-</sup> in the ground (X<sup>2</sup>Σ<sub>g</sub><sup>+</sup>) and excited (B<sup>2</sup>Σ<sub>u</sub><sup>+</sup>) states via electronic resonances. To describe electronically meta-stable states,
we employ the equation-of-motion coupled-cluster method augmented by the complex absorbing potential. The resonance wave-functions are analyzed using natural
transition orbitals. We identified several resonances in
C<sub>2</sub>H<sup>-</sup>, including the state that may lead to C<sub>2</sub><sup>-</sup>(B<sup>2</sup>Σ<sub>u</sub><sup>+</sup>). </p><p>
</p>
<p></p><p>
</p>
<p>
</p>
<p>
</p>
</div>
</div>
</div>
</div>
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Sahil Gulania; Anna Krylov
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Theory - Computational; Physical and Chemical Processes; Quantum Mechanics; Quasiparticles and Excitations; Spectroscopy (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-06-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75987ee301c5da2c7b916/original/dissociative-electron-attachment-in-c2h-via-electronic-resonances.pdf
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64f0b9a1dd1a73847fe5da37
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10.26434/chemrxiv-2023-0zzcd
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How poisoning is avoided in a step of relevance to the Haber-Bosch catalysis
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For a catalyst to be efficient and durable, it is crucial that the reaction products do not poison the catalyst. In the case of the Haber-Bosch iron based catalyst, the rate-limiting step is believed to be the decomposition of nitrogen molecules on the Fe(111) surface. This step leads to the production of atomic nitrogen on the surface N* that unless are hydrogenated and eventually released as NH3 molecules, remain on the surface. Thus, it is important to ascertain how a high N* coverage affects nitrogen dissociative chemisorption. To answer this question, we study the properties of the Fe(111) surface at different N* coverage both at room and operando temperature. Using state-of-the-art simulations, we have already found that, at high temperatures, the surface atoms are highly mobile and that the catalytic centers normally associated with the surface activity acquire a finite lifetime [1]. Here, we discover that the N* surface atoms are highly mobile and that coverage reduces but does not eliminate iron mobility. The N* atoms promote the formation of metastable iron triangular surface structures whose chemical composition can be described as F e_3^*N_i^* i = 1, 4. These structures are the result of the frustrated drive of the system towards a more stable Fe4N phase. As a consequence of the formation of these structures, nitrogen atoms tend to cluster, reducing their poisoning effect. At the same time, the reduction in the number of catalytic centers is counteracted by an increase in their lifetime. The combined effect is that the barrier for dissociation is not significantly altered at least up to the maximum coverage studied here of 50%.
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Shivam Tripathi; Luigi Bonati; Simone Perego; Michele Parrinello
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Catalysis; Heterogeneous Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
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2023-10-12
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f0b9a1dd1a73847fe5da37/original/how-poisoning-is-avoided-in-a-step-of-relevance-to-the-haber-bosch-catalysis.pdf
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60c74990842e65e989db2d7c
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10.26434/chemrxiv.12079587.v1
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On the Basis Set Selection for Calculations of Core-Level States: Different Strategies to Balance Cost and Accuracy
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<p>We present a study on basis set effect in correlated calculations of core-level states. While it is well recognized that the core-level states require using more extensive basis sets than their valence counterparts, the standard strategy has been to use large contracted basis sets, such as the cc-pVXZ or cc-pCXZ series. Building upon the ideas of Besley, Gilbert, and Gill [J. Chem. Phys. 130, 124308 (2009)], we show that much more effective strategy is to use uncontracted bases, such as core or fully uncontracted Pople's basis. The physical grounds behind this approach are explained and illustrated by numerical results. We also discuss other cost-saving strategies, such as virtual space truncation and using mixed precision execution.</p>
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Ronit Sarangi; Marta L. Vidal; Sonia Coriani; Anna Krylov
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Theory - Computational
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-04-10
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74990842e65e989db2d7c/original/on-the-basis-set-selection-for-calculations-of-core-level-states-different-strategies-to-balance-cost-and-accuracy.pdf
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61e1553ff81dfeff76b83237
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10.26434/chemrxiv-2022-3p3sd
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Detection of Few Hydrogen Peroxide Molecules using Self-Reporting Fluorescent Nanodiamond Quantum Sensors
|
Hydrogen peroxide (H2O2) plays an important role in various signal transduction pathways and regulates important cellular processes. However, monitoring and quantitatively assessing the distribution of H2O2 molecules inside living cells requires a nanoscale sensor with molecular-level sensitivity. Herein, we show the first demonstration of sub-10 nm-sized fluorescent nanodiamonds as a catalyst for the decomposition of H2O2 and the production of radical intermediates at the nanoscale. Furthermore, the NV quantum sensors inside the nanodiamonds are employed to quantify the aforementioned radicals. We believe that our method of combining the peroxidase-mimicking activities of the nanodiamonds with their intrinsic quantum sensor showcases their application as a self-reporting H2O2 sensor with molecular-level sensitivity and nanoscale spatial resolution. Given the robustness and the specificity of the sensor, our results promise a new platform for elucidating the role of H2O2 at the cellular level.
|
Yingke Wu; Priyadharshini Balasubramanian; Zhenyu Wang; Jaime A. S. Coelho; Mateja Prslja; Martin B. Plenio; Fedor Jelezko; Tanja Weil
|
Materials Science; Analytical Chemistry; Nanoscience; Carbon-based Materials; Optical Materials; Spectroscopy (Anal. Chem.)
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CC BY NC ND 4.0
|
CHEMRXIV
|
2022-01-17
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e1553ff81dfeff76b83237/original/detection-of-few-hydrogen-peroxide-molecules-using-self-reporting-fluorescent-nanodiamond-quantum-sensors.pdf
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60f8ddb9032114aee3b6f803
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10.26434/chemrxiv-2021-l3dhr
|
Essential Terminology Connects NMR and qNMR
Spectroscopy to Its Theoretical Foundation
|
Classical 1D 1H NMR spectra are prototypic for
NMR spectroscopy in that they represent a wealth
of chemical information encoded into convoluted
graphs or patterns that contain complex features
(aka multiplets), even for seemingly simple
molecules. Accordingly, the utility of NMR depends
on the theoretical and visual skills required to extract
all the physical parameters that represent usable
structural and quantitative information. Moreover, it
depends on the ability of the analyst to
communicate them effectively and reproducibly.
After decades of continuous development, NMR
spectroscopy has reached a stage where its
analytical capabilities have outgrown the typical
level of detail of interpretation, especially of 1D NMR
spectra. The quantum-mechanical (QM) foundation,
history, evolution, and (in-)consistency of widely
applied terminology calls for re-examination and
recalibration. In order to develop new perspectives
on solution-state NMR analysis, including the rapidly evolving quantitative NMR (qNMR), the
present study draws on the well-established NMR model systems and molecules (AB2C2,
strychnine, testosterone, α-santonin). Through well-documented key topics related to spectral
acquisition and analysis, the study builds the foundation for a modular, coherent, and
standardized nomenclature of NMR terminology. This is a necessary condition for a healthy
research data lifecycle including their management and reuse. This work presents experimental
evidence and connects with essential concepts of QM theory that clarify the distinct meaning of
the primary terms: resonance, signal, pattern, peak, line, transition; as well as other widely used
terms: splitting, multiplicity/multiplet, resolution, and dispersion. The proposed NMR terminology
was built through a consensus-finding process that evolved from extended pharmacopoeial and
research coordination efforts. It is supported by detailed figures and NMR data interpretation that
employs QM-based full spin analysis.
|
Guido Pauli; G. Joseph Ray; Anton Bzhelyansky; Birgit Jaki; Charlotte Corbett; Christina Szabo; Christoph Setinbeck; Dan Sørensen; Damien Jeannerat; Daneel Ferreira; David Lankin; James McAlpine; Jean-Nicholas Dumez; Jonathan Bisson; Krish Krishnamurty; Matthias Niemitz; Michael Nelson; Patrick Giraudeau; Samuli-Petrus Korhonen; Stefan Kuhn; Toru Miura; Lucy Botros
|
Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Natural Products; Analytical Chemistry - General; Spectroscopy (Anal. Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2021-07-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f8ddb9032114aee3b6f803/original/essential-terminology-connects-nmr-and-q-nmr-spectroscopy-to-its-theoretical-foundation.pdf
|
674b5bbdf9980725cf9ca081
|
10.26434/chemrxiv-2024-x7wgx
|
Photoinduced electron transfer across phospholipid bilayers in anaerobic and aerobic atmospheres
|
In natural photosynthesis, light-driven electron transfer across the thylakoid membrane enables efficient charge separation and the confinement of reaction spaces for generating NADPH and CO2 and oxidation of water. These reactions are complementary redox reactions and require different reaction conditions for optimal performance. However, current artificial photosynthesis studies only take place in the bulk and are sensitive towards oxygen and air, which limits their applicability under aerated and water-splitting conditions. Herein, we report light-driven electron transfer across a lipid bilayer membrane of liposome vesicles via a rigid oligoaromatic molecular wire that allows to electronically connect an oxidation and reduction reaction which are spatially separated by the membrane. The molecular wire has a simple, symmetric, easy-to-synthesize design based on benzothiadiazole and fluorene units and absorbs in the visible spectrum which makes it suitable for solar energy conversion. The model reactions in this study are light-driven NADH oxidation on one side of the membrane and light-driven reduction of an organic water-soluble dye in the bulk phase of liposomes. Additionally, the system is active in both aerobic and anaerobic atmospheres, rendering it ideal for aerobic conditions or reactions that produce oxygen such as solar-driven water splitting and artificial photosynthesis applications.
|
Novitasari Sinambela; Richard Jacobi; Dieter Sorsche; Leticia Gonzalez; Andrea Pannwitz
|
Physical Chemistry; Organic Chemistry; Catalysis
|
CC BY 4.0
|
CHEMRXIV
|
2024-12-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674b5bbdf9980725cf9ca081/original/photoinduced-electron-transfer-across-phospholipid-bilayers-in-anaerobic-and-aerobic-atmospheres.pdf
|
60c7453f0f50db5bc5396234
|
10.26434/chemrxiv.9999656.v1
|
Computational Screening of Transition Metal /p-block Hybrid Electrocatalysts for CO2 Reduction
|
Among all the pollutants in the atmosphere, CO2 has the highest impact on global warming and with the rising levels of this pollutant, studies on developing various technologies to convert CO2 into carbon neutral fuels and chemicals have become more valuable. In this work, we present a detailed computational study of electrochemical reduction of CO2 reduction (CO2RR) to methane and methanol over different transition metal-p block catalysts using Density Functional Theory calculations. In addition to the catalyst structure, we studied reaction mechanisms using free energy diagrams that explain the product selectivity with respect to the competing hydrogen evolution reaction. Furthermore, we developed scaling relations between all the active C bound intermediate species with ΔG (CO*) and O bound species with ΔG (OH*). The limiting potential lines with ΔG(OH*) as descriptor are much less negative compared to UL lines with ΔG(CO*) as descriptor indicating that catalyst materials following pathways via OH- bound intermediate species require more negative potentials than CO*HCO* and CO2 COOH* steps to convert into products. We developed thermodynamic volcano plots with two descriptors; CO* and OH* binding free energies and determined the best catalyst material among the initially investigated catalyst materials expecting this plot will provide guidance to the future work on improving the activity of transition metal-p block catalysts for this important reduction reaction.<br />
|
Sahithi Ananthaneni; Rees Rankin
|
Electrocatalysis; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-10-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453f0f50db5bc5396234/original/computational-screening-of-transition-metal-p-block-hybrid-electrocatalysts-for-co2-reduction.pdf
|
677f99e581d2151a026b31ce
|
10.26434/chemrxiv-2025-ttjb3
|
Nonbonded force field parameters derived from Atom-In-Molecules methods reproduce interactions in proteins from first--principles
|
Non-covalent interactions govern many chemical and biological phenomena and are crucial in protein-protein interactions, enzyme catalysis, and DNA folding. The size of these macromolecules and their various conformations demand computational inexpensive force fields that can accurately mimic the quantum chemical nature of the atomic non-covalent interactions. Accurate force fields, coupled with increasingly longer molecular dynamics (MD) simulations, may empower us to predict conformational changes associated with the biochemical function of proteins. Here, we aim to derive nonbonded protein force field parameters from the partitioned electron density of amino acids - the fundamental units of proteins - via the atoms-in-molecules (AIM) approach. The AIM parameters are validated using a database of charged, aromatic and hyrdrophilic side chain interactions in 610 conformations, primarily involving pi-pi interactions, as recently reported by one of us. Electrostatic and van der Waals interaction energies calculated with nonbonded force field parameters from different AIM methodologies were compared to first principle interaction energies from absolute localized molecular orbital - energy decomposition analysis (ALMO-EDA) at the wB97XV/def2TZVPD level. Our findings show that electrostatic interactions between side chains are accurately reproduced by atomic charges from the minimal basis iterative stockholder (MBIS) scheme with mean absolute errors of 4-7 kJ/mol. Meanwhile, C6 coefficients from the MBIS AIM method effectively predicts dispersion interactions with a mean error of -2 kJ/mol and a maximal error or -5 kJ/mol. As an outlook to use AIM methods in the development of protein force fields we present the constrained AIM method that allows to fix backbone parameters during the optimization of side chain interactions. Backbone dihedral parameters have been optimized to reproduce secondary structure elements in proteins and not altering them maintains compatibility with conventional protein force fields while improving the description of side chain interactions. Our validated AIM methods allow for the depiction of non-covalent, long-range interactions in proteins using cost-effective force fields that achieve chemical precision.
|
Carlos Castillo-Orellana; Farnaz Heidar-Zadeh; Esteban Vöhringer-Martinez
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677f99e581d2151a026b31ce/original/nonbonded-force-field-parameters-derived-from-atom-in-molecules-methods-reproduce-interactions-in-proteins-from-first-principles.pdf
|
60c74ecdbdbb89bdd2a39c49
|
10.26434/chemrxiv.12801125.v1
|
Wepy: A Flexible Software Framework for Simulating Rare Events with Weighted Ensemble Resampling
|
This paper describes the software tool "wepy", an implementation of the weighted ensemble algorithm in python. Wepy was designed to be a flexible simulation framework for rare or long-timescale molecular events, such as protein (un)folding, ligand (un)binding, and large-scale conformational changes or rearrangements. It is implemented as a pure python package, which works well with the OpenMM python library and can easily leverage other python tools for that are useful for molecular simulation and analysis such as mdtraj, scikit-learn, numpy and scipy. It has full support for high-dimensional adaptive resampling algorithms (WExplore and REVO) and provides a framework to easily facilitate the development of new resampling algorithms. Its modular design allows domain experts to write their own analysis functions and progress variables, while taking advantage of a vetted framework for parallel simulation and weighted ensemble resampling.
|
Samuel Lotz; Alex Dickson
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ecdbdbb89bdd2a39c49/original/wepy-a-flexible-software-framework-for-simulating-rare-events-with-weighted-ensemble-resampling.pdf
|
60c74c51469df4196af44080
|
10.26434/chemrxiv.12458579.v1
|
Persistent Organic Room-Temperature Phosphorescence in Cyclohexane-Trans-1,2-Bisphthalimide Derivatives: The Dramatic Impact of Heterochiral vs. Homochiral Interactions
|
Persistent metal-free Room-Temperature Phosphorescence (RTP) materials attract significant interest owing to the production of long-lived triplet excited states. Although several organic designs show RTP, the impact of intermolecular interactions on the triplet excitons stabilization and migrations remains hardly understood because obtaining different ordered intermolecular interactions while conserving identical molecular electronic properties is very challenging. We propose here a new strategy to circumvent this problem by taking advantage of the distinct molecular packing that can be found between enantiomer and racemic forms of a chiral molecule. Structural, photophysical and chiroptical investigations of chiral cyclohexane bisphthalimide derivatives showed that heterochiral and homochiral dimer interactions play a crucial role on the triplet excited state stabilization, resulting in higher RTP efficiency for enantiopure systems than for racemic one. This study paves the way to the use of molecular chirality to rationalize supramolecular properties arising from subtle intermolecular interactions.<br />
|
Ludovic Favereau; Cassandre Quinton; Cyril Poriel; Thierry Roisnel; Denis Jacquemin; Jeanne Crassous
|
Physical Organic Chemistry; Supramolecular Chemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c51469df4196af44080/original/persistent-organic-room-temperature-phosphorescence-in-cyclohexane-trans-1-2-bisphthalimide-derivatives-the-dramatic-impact-of-heterochiral-vs-homochiral-interactions.pdf
|
60c73d0fbdbb897955a37c04
|
10.26434/chemrxiv.5437255.v1
|
Photochemical Synthesis of 1-Aminonorbornanes via Strain-Driven, Formal [3+2] Cycloadditions
|
<p>This report describes a new route toward 1‑aminonorbornanes via
strain-driven, visible light-mediated formal [3+2] cycloadditions with
aminocyclopropanes. Lewis acidic salts (LiBF<sub>4</sub>, ZnCl<sub>2</sub>)
were found to facilitate the oxidation of a variety of amine-containing heterocycles,
and consequently, these additives led to improved conversion and isolated
yields. This operationally-simple method tolerates a variety of functional
handles (e.g. alcohols, protected amines), can generate optically-pure products
through diastereoselective variations, and affords entry to unique chemical
space through the diversity of accessible substitution patterns. Providing
flexible access to 1-aminonorbornanes is expected to benefit modern drug design
and development efforts seeking to incorporate more <i>sp<sup>3</sup></i>-rich motifs into lead scaffods. Further, gram-scale
operation proceeds smoothly in continuous flow, suggesting that this chemistry
can be readily translated beyond the academic- or discovery-scales.</p>
|
Daryl Staveness; Taylor Sodano; Corey Stephenson
|
Photochemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2017-09-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0fbdbb897955a37c04/original/photochemical-synthesis-of-1-aminonorbornanes-via-strain-driven-formal-3-2-cycloadditions.pdf
|
6771a80afa469535b92e9778
|
10.26434/chemrxiv-2025-6mk86
|
Optimised Process to Produce Calcium Acetate from Waste Blue Mussel Shells and its Use as a De-icer
|
The preparation of calcium acetate from mussel (Mytilus edulis) shells and acetic acid was optimised via design of experiments. The solid product was identified as the monohydrate via powder X-ray diffraction, IR spectroscopy and Thermogravimetric analysis. Comparisons were made to optical grade calcite in place of the bio-sourced calcium carbonate for the synthesis. An exploratory central composite design compared the yield of calcium acetate with respect to shell material used (shells dried in air at room temperature, dried at 220 °C or calcined), concentration of acetic acid, and time. The yield of Ca(CH₃COO)₂·H₂O was optimized further using heated, crushed shells using a custom optimal design. A maximum yield of 93% was reached after 32 h using 9% v/v CH₃COOH or an 85% yield using food-grade white vinegar after 24 h. De-icing experiments showed that Ca(CH₃COO)₂·H₂O produced from waste blue mussel shells melted 6 wt.% of ice at a concentration of 30% (m/v). For comparison, 11 wt.% defrosted using CaCl2 30% (m/v) and 13 wt.% defrosted using NaCl 30% (m/v).
|
Jennifer Murphy; Melissa Morgan; Sachel Christian-Robinson; Megan Fitzgerald; Francesca Kerton
|
Analytical Chemistry; Earth, Space, and Environmental Chemistry; Agriculture and Food Chemistry; Wastes; Chemoinformatics
|
CC BY NC 4.0
|
CHEMRXIV
|
2025-01-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6771a80afa469535b92e9778/original/optimised-process-to-produce-calcium-acetate-from-waste-blue-mussel-shells-and-its-use-as-a-de-icer.pdf
|
60c750de469df4a1aef44921
|
10.26434/chemrxiv.13079639.v1
|
Hydroxy-bridged Active Site States of [NiFe]-Hydrogenase Unraveled by Cryogenic Vibrational Spectroscopy and DFT Computations
|
The catalytic mechanism of H<sub>2</sub> conversion by [NiFe]-hydrogenase is subject of extensive research. Apart from at least four reaction intermediates of H<sub>2</sub>/H<sup>+</sup> cycling, there is also a number of resting states, which are formed under oxidizing conditions. While not directly involved in the catalytic cycle, knowledge of their molecular structure and reactivity is important, because these states usually accumulate in the course of hydrogenase purification, and they may also play a role <i>in vivo</i> during hydrogenase maturation. Here, we applied low-temperature infrared (cryo-IR) and nuclear resonance vibrational spectroscopy (NRVS) to the isolated catalytic subunit, HoxC, of the heterodimeric regulatory [NiFe]-hydrogenase (RH) from <i>Ralstonia eutropha</i>. Cryo-IR spectroscopy revealed that the HoxC protein can be enriched in almost pure redox states suitable for NRVS investigation. NRVS analysis of the hydrogenase catalytic center is usually hampered by strong spectral contributions of the FeS clusters of the small, electron-transferring subunit. Therefore, our approach to investigate the FeS cluster-free, <sup>57</sup>Fe labeled HoxC granted an unprecedented view onto the active site modes, including those obscured by FeS cluster-derived bands. Rationalized by density functional theory (DFT) calculations, our data allow the structural description of two hydroxy-containing resting states. Our work highlights the relevance of cryogenic vibrational spectroscopy and DFT to elucidate the structure of barely defined redox states of the [NiFe]-hydrogenase active site.
<br />
|
Giorgio Caserta; Vladimir Pelmenschikov; Christian Lorent; Armel F.Tadjoung Waffo; Sagie Katz; Lars Lauterbach; Janna Schoknecht; Hongxin Wang; Yoshitaka Yoda; Kenji Tamasaku; Martin Kaupp; Peter Hildebrandt; Oliver Lenz; Stephen P. Cramer; Ingo Zebger
|
Theory - Computational; Biocatalysis; Biophysical Chemistry; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750de469df4a1aef44921/original/hydroxy-bridged-active-site-states-of-ni-fe-hydrogenase-unraveled-by-cryogenic-vibrational-spectroscopy-and-dft-computations.pdf
|
60c7453bbdbb895d48a389b2
|
10.26434/chemrxiv.9985118.v1
|
Reticular Growth of Graphene Nanoribbon 2D Covalent Organic Frameworks
|
Synthesis and characterization covalent organic frameworks (COFs) from a small molecule diamine and polydisperse cove type GNRs (c-GNRs) functionalized with aldehydes. The cGNR-COF films were found to contain crystalline regions (>100 nm<sup>2</sup>) of imine linked GNRs that could be chemically exfoliated into bilayer/trilayers utilizing a sonication protocol with <i>o</i>-dichlorobenzene (<i>o</i>-DCB).
|
Gregory Veber; Christian
S. Diercks; Cameron Rogers; Wade S. Perkins; Jim Ciston; Alex Liebman-Peláez; Chenhui Zhu; Felix R. Fischer
|
Carbon-based Materials; Nanostructured Materials - Materials; Thin Films; Conducting polymers; Organic Polymers; Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-10-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453bbdbb895d48a389b2/original/reticular-growth-of-graphene-nanoribbon-2d-covalent-organic-frameworks.pdf
|
653f76e3a8b423585a8fdd5c
|
10.26434/chemrxiv-2023-9f4xc-v2
|
Using BpyAla to generate Copper Artificial Metalloenzymes: a catalytic and structural study
|
Artificial metalloenzymes (ArMs) have emerged as a promising avenue in the field of biocatalysis, offering new reactivity. However, their design remains challenging due to the limited understanding of their protein dynamics and how the introduced cofactors alter the protein scaffold structure. Here we present the structures and catalytic activity of novel copper ArMs capable of (R)- or (S)-stereoselective control, utilizing a steroid carrier protein (SCP) scaffold. To incorporate 2,2’-Bipyridine (Bpy) into SCP, two distinct strategies were employed: either Bpy was introduced as an unnatural amino acid (2,2’-bipyridin-5-yl)alanine (BpyAla) using amber stop codon expression or via bioconjugation of bromomethyl-Bpy to cysteine residues. The resulting ArMs proved to be effective at catalysing an enantioselective Friedel-Crafts reaction with SCP_Q111BpyAla achieving the best selectivity with an enantioselectivity of 72% ee (S). Interestingly, despite using the same protein scaffold, different attachment strategies for Bpy at the same residue (Q111) led to a switch in the enantiopreference of the ArM.
|
Eva Klemencic; Richard Brewster; Hafiz Ali; Julia Richardson; Amanda Jarvis
|
Biological and Medicinal Chemistry; Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Bioengineering and Biotechnology; Biocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2023-10-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653f76e3a8b423585a8fdd5c/original/using-bpy-ala-to-generate-copper-artificial-metalloenzymes-a-catalytic-and-structural-study.pdf
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65a40d3fe9ebbb4db9241e9e
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10.26434/chemrxiv-2023-nl054-v2
|
Betaketothioesters in Organocatalysis: Harnessing Nucleophilic Reactivity, the Fluorophobic Effect, and Expanding the Substrate Repertoire
|
The use of thioesters as nucleophiles marks a considerable change in organic synthesis. This new method, propelled by gentle enolization with minimal catalyst loading, results in enantiomeric excesses surpassing 95% under ambient conditions, accomplishing total conversion in merely 6 hours. Remarkably, this method eliminates the need for additional functional groups in nitroalkenes for efficient chirality transfer from the organocatalyst. The exceptional reactivity of thioesters, combined with their water tolerance, enables reactions utilizing the hydrophobic effect, resulting in reaction times as short as 15 minutes and products with slightly enhanced stereoselectivity compared to analogous reactions in dichloromethane. Additionally, reactions performed in perfluorinated solvents outpace their homogenous counterparts in organic solvents, delivering products in shorter time with comparable stereoselectivity. This work highlights the rare utilization of the fluorous effect in organocatalysis. Simple squaramides also exhibit remarkable catalytic activity in the reactions of beta-keto thioesters with alpha-bromo nitroalkenes. As little as 0.1 mol% of the catalyst leads to product formation with an 86% yield (qNMR) and 93% enantiomeric excess. Upscaling the reaction does not significantly affect the enantiomeric excess but leads to a slight decrease in yield from 82% to 77%. It has been demonstrated that thioesters react more rapidly than their ketoester counterparts, and the two-step reaction leading to dihydrofuran ring closure is entirely accomplished by extending the reaction time, eliminating the need for additional base. The examples presented here expand the range of substrates derived from carboxylic acid esters in catalytic reactions, suggesting the potential for the synthesis of challenging reactions in analogues of alkoxyl esters.
|
Maciej Dajek; Paulina Kubiak; Julia Bąkowicz; Błażej Dziuk; Rafał Kowalczyk
|
Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a40d3fe9ebbb4db9241e9e/original/betaketothioesters-in-organocatalysis-harnessing-nucleophilic-reactivity-the-fluorophobic-effect-and-expanding-the-substrate-repertoire.pdf
|
673f8f897be152b1d03cb23b
|
10.26434/chemrxiv-2024-9v9nt
|
Chemical substitution and band gap tunability in chiral Ag3Au(Se,Te)2 solid solutions
|
Ag3AuSe2 and Ag3AuTe2 were previously predicted to be narrow direct gap semiconductors with the same chiral structure type. Recent computational studies using Perdew-Burke-Ernzerhof (PBE) functional highlighted their potential band gap tunability via strain application. For example, Ag3AuSe2 was predicted to exhibit full band closure above 4% tensile strain. In this study, we explored chemical substitution to examine the density functional theory (DFT) predictions, by replacing Se2− with larger Te2− anions. We synthesized and characterized the electronic and optical properties of Ag3Au[Se(1−x)Te(x)]2 solid solutions for x from 0 to 1. Our findings revealed that the lattice constants increase linearly with Te incorporation, reaching 3.6% expansion at 90% Se2− to Te2− substitution. The activation energy and optical band gap of Ag3Au(Se,Te)2 were determined using electrical resistivity and ultraviolet–visible (UV-Vis) diffuse reflectance measurements. The band gap decreased with increasing Te content, although hybrid functionals are necessary to correctly predict the gap. Further computational studies on the band structures of Ag3Au(Se,Te)2 alloys would shed light on the impact of lattice parameter modification via chemical substitution on band gap tunability.
|
Juyeon Won; Martin Gutierrez-Amigo; Akhila Mattapalli; Mohammad A. Ali; Daniel P. Shoemaker
|
Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673f8f897be152b1d03cb23b/original/chemical-substitution-and-band-gap-tunability-in-chiral-ag3au-se-te-2-solid-solutions.pdf
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60c743ba337d6ccebee26c87
|
10.26434/chemrxiv.9637001.v1
|
Thiopeptide Defense by an Ant’s Bacterial Symbiont
|
Fungus-growing
ants and their bacterial symbionts have emerged as a model animal-microbe
symbiosis and an ideal system for understanding antibiotic deployment in an
ecological context. We found that <i>Pseudonocardia</i>
symbionts of the ant <i>Trachymyrmex
septentrionalis</i> have strong antibiotic activity against their most likely
competitors: other strains of ant-associated bacteria. Activity-guided
fractionation revealed the defensive molecule produced by these bacteria to be
the thiopeptide antibiotic GE37468. Here we assign an ecological role –
host-associated niche defense – for this antibiotic, previously identified in a
biochemical screen and known only for its <i>in
vitro </i>activity against clinically-relevant pathogens. Genomic analysis
uncovered a split biosynthetic gene cluster for this molecule and suggests that
these symbionts acquired it from soil bacteria. Similar thiopeptide antibiotics
have recently been ascribed host-associated niche defense roles, and the
function of GE37468 in this insect niche intriguingly parallels thiopeptide
defense in the human microbiome. Molecular defenses from animal-associated
microbes may have particular promise as therapeutics, and indeed thiopeptide
antibiotics with high structural similarity to GE37468 are already under
clinical investigation.
|
Preston T. Chang; Krithika Rao; Lauren O. Longo; Elisabeth S. Lawton; Georgia Scherer; Ethan Van Arnam
|
Drug Discovery and Drug Delivery Systems; Environmental biology; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743ba337d6ccebee26c87/original/thiopeptide-defense-by-an-ant-s-bacterial-symbiont.pdf
|
63dbcb81a8f79476ca61b744
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10.26434/chemrxiv-2023-ddcr1
|
∆-Machine Learning for Quantum Chemistry Prediction of Solution-phase Molecular Properties at the Ground and Excited States
|
Due to the limitation of solvent models, quantum chemistry calculated solution-phase molecular properties often deviates from experimental measurements. Recently, ∆-machine learning (∆-ML) was shown to be a promising approach to correcting errors in the quantum chemistry calculation of solvated molecules. However, this approach's applicability to different molecular properties and its performance in various use cases are still unknown. In this work, we tested the performance of Δ-ML in correcting redox potential and absorption energy calculations using four types of input descriptors and various ML methods. We sought to understand the dependence of ∆-ML performance on the property to predict, the quantum chemistry method, the data set distribution/size, the type of input features, and the feature selection techniques. We found that ∆-ML can effectively correct the errors in redox potentials calculated by density functional theory (DFT) and absorption energies calculated by time-dependent DFT. For both properties, the ∆-ML corrected results showed less sensitivity to the DFT functional choice than the raw results. The optimal input descriptor depends on the property, regardless of the specific ML method used. The solvent-solute descriptor (SS) is the best for redox potential, whereas the combined molecular fingerprint (cFP) is the best for absorption energy. A detailed analysis of the feature space and the physical foundation of different descriptors well explained these observations. Feature selection did not further improve the Δ-ML performance. Finally, we analyzed the limitation of our Δ-ML solvent effects approach in data sets with molecules of varying degrees of electronic structure errors.
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Xu Chen; Pinyuan Li; Eugen Hruska; Fang Liu
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning
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CC BY NC ND 4.0
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CHEMRXIV
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2023-02-03
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dbcb81a8f79476ca61b744/original/machine-learning-for-quantum-chemistry-prediction-of-solution-phase-molecular-properties-at-the-ground-and-excited-states.pdf
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60c74f70567dfe43d9ec56ab
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10.26434/chemrxiv.12857927.v2
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Targeting Allosteric Pockets of SARS-CoV-2 Main Protease Mpro
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<h3>Repurposing of antivirals is an attractive therapeutic option for the treatment of COVID-19. M<sup>pro </sup>(also called 3CL<sup>pro</sup>) is a key protease of SARS-CoV-2 involved in viral replication, and is a promising drug target for testing the existing antivirals. A major challenge to test the efficacy of antivirals is the conformational plasticity of M<sup>pro</sup> and its future mutation prone flexibility. To address this, we hereby propose combination therapy by drugging two specific additional pockets of M<sup>pro</sup> probed in our studies. Long scale Molecular Dynamics (MD) simulations provide evidence of these additional sites being allosteric. Suitable choice of drugs in catalytic and allosteric pockets appear to be essential for combination therapy. Current study, based on docking and extensive set of MD simulations, finds the combination of Elbasvir, Glecaprevir, Ritonavir to be a viable candidate for further experimental drug testing/pharmacophore design for M<sup>pro</sup>. </h3>
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Zahoor Ahmad Bhat; Dheeraj Chitara; Jawed Iqbal1; Sanjeev. B.S.; Arumugam Madhumalar
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Computational Chemistry and Modeling
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CC BY NC ND 4.0
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CHEMRXIV
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2020-11-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f70567dfe43d9ec56ab/original/targeting-allosteric-pockets-of-sars-co-v-2-main-protease-mpro.pdf
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6138d15827d9060a7781898c
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10.26434/chemrxiv-2021-3gv6v
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Aromatic, or Antiaromatic, That Is the Question:
|
The term aromaticity in chemistry is reminiscent of symmetric, stable structures that have delocalized electrons and sustain diamagnetic ring currents in the presence of external magnetic fields. The two latter characteristics sometimes mistakenly are thought to be the same. In a groundbreaking discovery Liddle and co-workers synthesized a D3h complex with rare Th‒Th bonds. Studying the electronic structure of a neutral singlet model system, 3”, showed that the molecule has a delocalized HOMO between three Th atoms akin to a 2-electron 3-center bond. Employing nucleus independent chemical shift (NICS) computations and according to the pattern of the NICS scan plot on 3”, the authors suggested that the molecule is a σ-aromatic species as it is reflected also in the title of their paper. Unfortunately, NICS is an inappropriate tool for evaluation of the magnetic aromaticity among early and mid-transition metals (TM), the elements that share a characteristic with thorium; they all have low-energy unoccupied orbitals. In the following we explain why NICS fails to assess aromaticity of molecules containing TMs and prove that the Th3 ring is a weakly antiaromatic system. We introduce a simple protocol to examine the aromaticity of any molecule utilizing software packages, which have been used by the authors of the main article.
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Ben Joseph R Cuyacot; Cina Foroutan-Nejad
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Theoretical and Computational Chemistry; Inorganic Chemistry; Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling; Theory - Computational
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CC BY 4.0
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CHEMRXIV
|
2021-09-13
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6138d15827d9060a7781898c/original/aromatic-or-antiaromatic-that-is-the-question.pdf
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60c74abe337d6c4080e27980
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10.26434/chemrxiv.12250142.v1
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A SARS-CoV-2 Coronavirus Antigen-Detecting Half-Strip Lateral Flow Assay Towards the Development of Point of Care Tests Using Commercially Available Reagents
|
<p>The SARS-CoV-2 pandemic has
created an unprecedented need for rapid diagnostic testing to enable the
efficient treatment and mitigation of COVID-19. The primary diagnostic tool
currently employed is reverse transcription polymerase chain reaction (RT-PCR),
which can have good sensitivity and excellent specificity. Unfortunately, implementation
costs and logistical problems with reagents during the global SARS-CoV-2 pandemic
have hindered its universal on demand adoption. Lateral flow assays (LFAs) represent
a class of diagnostic that, if sufficiently clinically sensitive, may fill many
of the gaps in the current RT-PCR testing regime, especially in low- and
middle-income countries (LMICs). To date, many serology LFAs have been
developed, though none meet the performance requirements necessary for
diagnostic use cases, primarily due to the relatively long delay between
infection and seroconversion. However, based on previously reported results
from SARS-CoV-1, antigen-based SARS-CoV-2 assays may have significantly better
clinical sensitivity than serology assays. To date, only a very small number of
antigen-detecting LFAs have been developed. Development of a half-strip LFA is
a useful first step in the development of any LFA format. In this paper we
present a half-strip LFA using commercially available antibodies for the
detection of SARS-CoV-2. We have tested this LFA in buffer and measured an LOD
of 0.62 ng/mL using an optical reader with sensitivity equivalent to a visual
read. Further development, including evaluating the appropriate sample matrix,
will be required for this assay approach to be made useful in a point of care
setting, though this half-strip LFA may serve as a useful starting point for
others developing similar tests. </p>
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Benjamin D. Grant; Caitlin E. Anderson; John R Williford; Luis F. Alonzo; Veronika
A. Glukhova; David S. Boyle; Bernhard H. Weigl; Kevin P Nichols
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Biochemical Analysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-05-07
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74abe337d6c4080e27980/original/a-sars-co-v-2-coronavirus-antigen-detecting-half-strip-lateral-flow-assay-towards-the-development-of-point-of-care-tests-using-commercially-available-reagents.pdf
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60c74123469df43452f42d92
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10.26434/chemrxiv.7527680.v2
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Exploring the Thermodynamic Criteria for Responsive Adsorption Processes
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<div><div>We describe a general model to explore responsive adsorption processes in flexible porous materials.</div><div>This model combines mean field formalism of the osmotic potential, classical density functional theory of adsorption in slit pore models and generic potential functions which represent the Helmholtz free energy landscape of a porous system.</div><div>Using this model, we focus on recreating flexible adsorption phenomena observed in prototypical metal-organic frameworks, especially the recently discovered effect of negative gas adsorption (NGA).</div><div>We identify the key characteristics required for the model to generate unusual adsorption processes and subsequently employ an extensive parametric study to outline conditions under which gate-opening and NGA are observed.</div><div>This powerful approach will guide the design of responsive porous materials and the discovery of entirely new adsorption processes.</div></div>
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Jack D. Evans; Simon Krause; Stefan Kaskel; Martin B. Sweatman; Lev Sarkisov
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Computational Chemistry and Modeling; Physical and Chemical Processes; Structure; Surface; Thermodynamics (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
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2019-03-18
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74123469df43452f42d92/original/exploring-the-thermodynamic-criteria-for-responsive-adsorption-processes.pdf
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60c749d7567dfe07c2ec4c74
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10.26434/chemrxiv.12110862.v1
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Caffeine Alkaline Hydrolysis and in Silico Anticipation Reveal the Origin of Camellimidazoles
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<div>- Context. Camellimidazoles A–C were recently reported as new natural substances arising from what was described as new caffeine degradation pathway in Keemun black tea. <br />- Discoveries. Under alkaline hydrolysis conditions followed by spontaneous cascade reactions with formaldehyde or dichloromethane (as the key methylene group providers), we were able to achieve the synthesis of camellimidazoles B and C. A MetWork-based pipeline was also implemented highlighting a wealth of structurally diverse compounds formed in the course of the reaction and streamlining the isolation of the newly described camellimidazoles D-F, subsequently confirmed as anticipated in silico upon extensive spectroscopic analyses. Besides demonstrating the artefactual origin of camellimidazoles, the current investigation emphasizes the fitness of MetWork-tagging to illuminate the chemical diversity associated with seemingly simple reactive conditions.<br />- Methods. Organic synthesis, phytochemical analysis, in silico anticipation, molecular networking dereplication<br /><br /></div><div><br /></div>
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Pierre Le Pogam; Erwan POUPON; Grégory Genta-Jouve; Jean-François Gallard; Victor Turpin; Adam Skiredj; Karine Leblanc; Mehdi Beniddir
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Natural Products
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-04-13
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749d7567dfe07c2ec4c74/original/caffeine-alkaline-hydrolysis-and-in-silico-anticipation-reveal-the-origin-of-camellimidazoles.pdf
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60c758710f50db9328398442
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10.26434/chemrxiv.14423579.v2
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On the Amine-Catalyzed Suzuki-Miyaura Coupling Using a Catalysis-Based Fluorometric Method
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<p>The Suzuki-Miyaura coupling is one of the most frequently used reactions in organic synthesis. Recent work by others suggested that an arylamine, prepared by palladium catalysis and tricyclohexylphosphine, could catalyze Suzuki-Miyaura coupling reactions without transition metals. Herein, we used a fluorometric quantification method for palladium previously developed in our laboratory to unambiguously conclude that there is a correlation between the palladium content in the arylamine and the rate of a Suzuki-Miyaura coupling. Also, our mass spectroscopic analysis of the arylamine revealed the presence of a palladium-phosphine complex. When Pd(OAc)<sub>2</sub> was used as a catalyst for the same Suzuki-Miyaura coupling, tricyclohexylphosphine was detrimental to the coupling and that the arylamine played negligible role. This study demonstrates the utility of the fluorometric technology for catalysis research.<br /></p>
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Jincy K. Vinod; Annelise K. Wanner; Elizabeth James; Kazunori Koide
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Homogeneous Catalysis; Organocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-05-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758710f50db9328398442/original/on-the-amine-catalyzed-suzuki-miyaura-coupling-using-a-catalysis-based-fluorometric-method.pdf
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60c7509cbdbb890e3aa39f57
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10.26434/chemrxiv.13058024.v1
|
Method to Predict Reagents in Iridium-Based Photoredox Catalysis
|
Visible-light photoredox catalysts with oxidizing excited states have been broadly applied in organic synthesis. Following photon absorption by the photocatalyst, electron transfer from an organic reagent is the most common mechanistic outcome for this class of reaction. Reduction potentials for organic reagents are therefore useful to predict reactivity and DFT proved to be useful as a predictive tool in this regard. Due to the complex mechanisms that follow electron transfer, kinetics play a crucial role in the success of photoredox reactions. We extend the predictive tools of DFT to estimate the electron transfer <i>rates</i> between an excited photocatalyst and various organic substrates. To calibrate our model, 49 electron transfer rate constants were experimentally measured in acetonitrile for the catalyst Ir[dF(CF<sub>3</sub>)ppy]<sub>2</sub>(dtbpy)<sup>+</sup>. The rate constants, k<i><sub>q</sub></i>, gave a clear predictive trend when compared to calculated ionization energies in “frozen solvent”, which was a better predictor than standard reduction potentials in our case. The calculated k<i><sub>q</sub></i> gave an average error of 17% for log(k<sub>q</sub>) values between 4 and 11. This simple method can predict the reactivity of hundreds of reagents <i>in silico</i>. Notably, the calculations offered unexpected insight that we could translate into success for the C-H activation of acetylacetone as a proof-of-concept.
|
Antoine Juneau; Taylor O. Hope; Jason Malenfant; Mihai Mesko; Jacob A. Mcneill; Mathieu Frenette
|
Photocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
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2020-10-07
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7509cbdbb890e3aa39f57/original/method-to-predict-reagents-in-iridium-based-photoredox-catalysis.pdf
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644f35db6ee8e6b5ed6260e5
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10.26434/chemrxiv-2023-zltxf
|
Structural verification and new reactivity for Stang’s reagent, [PhI(CN)][OTf]
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The structure of Stang’s reagent [PhI(CN)][OTf] is confirmed by X-ray crystallography and is determined to be best described as an ion-pair in organic solution. It is found to be a strong Lewis acid, but reaction with pyridine ligands gives [Pyr-CN][OTf] salts via redox and represents the first path to a new derivative of the CDAP reagent widely used as an activation agent for polysaccharides.
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Jason Dutton; Jason Bennetts; Lachlan Barwise; Lachlan Sharp-Bucknall; Keith White; Conor Hogan
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Inorganic Chemistry; Main Group Chemistry (Inorg.)
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CC BY NC 4.0
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CHEMRXIV
|
2023-05-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644f35db6ee8e6b5ed6260e5/original/structural-verification-and-new-reactivity-for-stang-s-reagent-ph-i-cn-o-tf.pdf
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66ddd3ef51558a15ef6f3d0e
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10.26434/chemrxiv-2024-f9pf4
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Multilayer Molecular Moiré Superlattices of para Phenylene Diamine Exhibit Angle-dependent and pH Controlled High Interfacial Electrical Conductivity Through Tunneling
|
Here we report the formation of multilayered molecular moiré superlattices of para phenylene diamine that showed a ten-fold increase in the interfacial conductivity as compared to its mono-lattice counterpart. The increase in the interfacial current for moiré superlattices was due to the decrease in tunneling barrier and length at the interface of superlattice owing to the absence of intervening water molecules the presence of which increased the barrier in the 2D lattice. Fast Fourier transform was used to decipher the interfacial current from the conductive atomic force microscopy measurements on the multilayered superlattices. A monotonous decrease in the interfacial current was observed as the twist angles increased for the same superlattice. The twist angle was strongly correlated with the number of hydrogen bonds at the interface and thus a twist dependent variation in interfacial current was observed. Furthermore, a significant increase in the interfacial current upon protonation or deprotonation of the moiré superlattices was observed due to the increase in number of hydrogen bonds at the multi-lattice interfaces.
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Ujjala Dey; Arun Chattopadhyay
|
Physical Chemistry; Nanoscience; Interfaces; Quantum Mechanics; Self-Assembly; Materials Chemistry
|
CC BY NC ND 4.0
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CHEMRXIV
|
2024-09-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ddd3ef51558a15ef6f3d0e/original/multilayer-molecular-moire-superlattices-of-para-phenylene-diamine-exhibit-angle-dependent-and-p-h-controlled-high-interfacial-electrical-conductivity-through-tunneling.pdf
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66b0e11301103d79c5cdafca
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10.26434/chemrxiv-2024-rvkg6
|
Towards Precision CAR T-cell Immunotherapy: extended gate FET biosensor for personalized drug monitoring
|
Selection and optimization of therapies for cancer patients urgently needs personalization. Portable point-of-care electronic biosensors emerge as a groundbreaking solution to contribute to better decision-making in precision oncology. This study showcases the innovative use of extended gate field-effect transistor (EG-FET) biosensors to monitor the concentration and pharmacokinetics of immunotherapeutic drugs in vivo. Complementary positron emission tomography (PET) and radioactivity biodistribution studies in mice validate the EG-FET measurements. We introduce a novel indirect assay format for detecting target modules in an adapter CAR T-cell therapy model, effectively addressing the limitations of traditional potentiometric measurements. The EG-FET sensors exhibit exceptional sensitivity, and fulfill the requirements for immunotherapeutic drug monitoring without the need for complex radioactive labeling. In pharmacokinetic evaluations, the FET-based biosensor's performance aligns with standard radioactive measurements, revealing the distinct lifespans of small-sized TMs (15 minutes for scFv type) and larger TMs (14 hours for IgG4 type). These promising findings advocate for further exploration of next-generation biosensors in therapeutic monitoring roles. With their cost, size, and response time advantages, these biosensors hold immense potential for advancing personalized oncology, transcending the conventional diagnostic roles typically highlighted in the literature.
|
Trang-Anh Nguyen-Le; Christin Neuber; Isli Cela; Zeljko Janićijević; Liliana Rodrigues Loureiro; Lydia Hoffmann; Anja Feldmann; Michael Bachmann; Larysa Baraban
|
Biological and Medicinal Chemistry; Materials Science; Analytical Chemistry; Biochemical Analysis; Electrochemical Analysis; Bioengineering and Biotechnology
|
CC BY NC 4.0
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CHEMRXIV
|
2024-08-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b0e11301103d79c5cdafca/original/towards-precision-car-t-cell-immunotherapy-extended-gate-fet-biosensor-for-personalized-drug-monitoring.pdf
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62b508c37da6ce55a11de33e
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10.26434/chemrxiv-2022-1bvf1
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Critical analysis of radical scavenging properties of atorvastatin in methanol recently estimated via density functional theory
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In this communication we draw attention on serious flaws that plague recently reported antioxidant properties of
atorvastatin (ATV) in methanol. First and foremost, we emphasize that the O-H bond dissociation energies (BDE) of about 400\,kcal/mol previously reported are completely wrong. Further, we present results refuting the previous claim that the proton affinity (PA) of ATV is smaller than that of the ascorbic acid. That unfounded claim relies on incorrect data for PA's ascorbic acid (which we correct here) circulated in the literature. Further, we correct the values of the chemical reactivity indices (e.g., chemical hardness, electrophilicity index, electroaccepting and electrodonating
powers), which were inadequately estimated previously via Kohn-Sham HOMO and LUMO energies. Finally, our updated values for \ce{O-H} bond dissociation enthalpy (BDE = 91.4\,kcal/mol) and electron transfer enthalpy (ETE = 105.7\,kcal/mol) tentatively suggest that direct H-atom transfer (HAT) and sequential proton loss electron transfer (SPLET) may coexist.
|
Ioan Baldea
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysical Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-06-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b508c37da6ce55a11de33e/original/critical-analysis-of-radical-scavenging-properties-of-atorvastatin-in-methanol-recently-estimated-via-density-functional-theory.pdf
|
65456abda8b423585ae4cdaf
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10.26434/chemrxiv-2023-jfccx-v2
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A critical review of challenges and advances to produce 2G biodiesel with oleaginous microorganisms and lignocellulose.
|
Lignocellulose as carbon source and oleaginous microorganisms including yeast, bacterium, and fungi, have been studied extensively for oil and biodiesel production, however, several bottlenecks and challenges remain unresolved. Today commercial biodiesel production is stuck at the first generation using oleaginous seeds as palm, soybean, and others, but commercial oil production from oleaginous microorganisms is not cost-effective and sustainable. Before fermentation is necessary to get rich-sugars liquor from lignocellulose, but this is very difficult because lignin affects both enzyme activity and oleaginous microorganism growth, then hydrolysis is a process that easily could be stopped by several changes in adequate conditions that sometimes is almost impossible has the control as the strain ability to produce enzymes or cellulose polymerization degree by origin of lignocellulose. The oil production in the bioprocess is a challenge too because fermentations of oleaginous microorganisms are aerobic which means the need to supply oxygen constant during fermentation, this consumes energy, besides lipid production is low, and the lipid yield decreases in the extraction process. In this small review discuss those troubles related to sustainable lipid production with oleaginous microorganisms and lignocellulose as carbon source.
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Mijael Espinoza Gil; Octavio Loera-Corral; Rosa Olivia Cañizares-Villanueva; Ricardo Aguilar-López; Maria del Carmen Montes-Horcasitas
|
Energy; Chemical Engineering and Industrial Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-11-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65456abda8b423585ae4cdaf/original/a-critical-review-of-challenges-and-advances-to-produce-2g-biodiesel-with-oleaginous-microorganisms-and-lignocellulose.pdf
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64edf54ddd1a73847fc58fb7
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10.26434/chemrxiv-2023-vqqgv
|
An In Silico Database for Automated Feature Identification
of High-Resolution Tandem Mass Spectrometry 13C
Trimethylation Enhancement Using Diazomethane (13CTrEnDi)-
Modified Lipid Data
|
13C-Trimethylation enhancement using diazomethane (13C-TrEnDi) is a chemical derivatization technique that uses 13C-labeled diazomethane to increase mass spectrometry (MS) signal intensities for phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipid classes, both of which are of major interest in biochemistry. In silico mass spectrometry databases have become mainstays in lipidomics experiments; however, 13C-TrEnDi modified PC and PE species have altered m/z and fragmentation patterns from their native counterparts. To build a database of 13C-TrEnDi modified PC and PE species, a lipid extract from nutritional yeast was derivatized and fragmentation spectra of modified PC and PE species were mined using diagnostic fragmentation filtering by searching 13C-TrEnDi modified headgroups with m/z 199 (PC) and 202 (PE). Identities of 25 PC and 10 PE species were assigned after comparing to predicted masses from the Lipid Maps Structure Database with no false positive identifications observed; neutral lipids could still be annotated after derivatization. Collision energies from 16 to 52 eV were examined, resulting in three additional class-specific fragment ions emerging, as well as a combined sn1/sn2 fragment ion, allowing sum-composition level annotations to be assigned. Using the Lipid Blast templates, a NIST-compatible 13C-TrEnDi database was produced based on fragmentation spectra observed at 36 eV and tested on HEK 293T cell lipid extracts, identifying 47 PC and 24 PE species, representing a 1.8-fold and 2.2-fold increase in annotations, respectively. The 13C-TrEnDi database is freely available, MS vendor-independent and widely compatible with MS data processing pipelines, increasing the throughput and accessibility of TrEnDi for lipidomics applications.
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Joshua Roberts; Christian Rosales; Karl Wasslen; Angela Radnoff; Elena Godbout; Jean-Simon Diallo; Jeffrey Manthorpe; Jeffrey Smith
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Analytical Chemistry; Biochemical Analysis; Mass Spectrometry
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CC BY NC 4.0
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CHEMRXIV
|
2023-08-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64edf54ddd1a73847fc58fb7/original/an-in-silico-database-for-automated-feature-identification-of-high-resolution-tandem-mass-spectrometry-13c-trimethylation-enhancement-using-diazomethane-13c-tr-en-di-modified-lipid-data.pdf
|
60c75164567dfe2f19ec5a4e
|
10.26434/chemrxiv.13159994.v1
|
Photochemical Carbene Transfer Reactions of Aryl/Aryl Diazoalkanes – Experiment and Theory
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The photochemical carbene transfer reaction is a timely strategy in organic synthesis and generally proceeds via singlet carbene intermediates. In this combined experimental and computational studies, we show that the photolysis reaction of diaryl diazoalkanes gives access to both singlet and triplet diarylcarbene intermediates. The electronic properties of substituents of the aryl substituents show a strong influence on the electronic properties of the carbene intermediate and result in significantly reduced singlet triplet energy gaps. Depending on the spin state and electronic properties of the carbene intermediate, the reaction with alkynes provides access towards chemoselective cyclopropenation, cascade, or C-H functionalization reactions.
|
Sripati Jana; Chao Pei; Claire Empel; Rene Koenigs
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.); Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75164567dfe2f19ec5a4e/original/photochemical-carbene-transfer-reactions-of-aryl-aryl-diazoalkanes-experiment-and-theory.pdf
|
65bb3cdf9138d231612f2ab0
|
10.26434/chemrxiv-2024-wzql1
|
De novo design of nanopores for single-molecule detection that incorporates α-helix peptides
|
Nanopore sensing using transmembrane proteins enjoys great potential for rapid and low-cost single-molecule detection. Creating pore-forming proteins or peptides is an emerging frontier in the field of nanopore sensing. One of the approaches for constructing new nanopores is bottom-up De novo protein design. Due to the difficulties in designing and expressing transmembrane proteins, peptides are the first design target, but so far, de novo α-helical nanopores with sizes large enough to transport biomolecules have not been reported. Here, we constructed α-helical nanopores based on GX6G and GX3G motifs, named FFK and LEK. FFK formed multidisperse pores with diameters of 0.9 to 1.4 nm while LEK formed monodisperse pores with a diameter of 0.9 nm. Though the larger diameter of FFK nanopores provides opportunities for molecular translocation, the too-fast join and dissociate of peptide monomers make them unsuited for nanopore sensing. On the other hand, translocation of poly-L-lysine through LEK nanopore could be observed by electrical recording, revealing their possibility for amino-acid sequencing. Our findings provide new opportunities to create designer nanopores for nanopore sensing technologies.
|
Masataka Usami; Zugui Peng; Yusuke Sekiya; Batsaikhan Mijiddorj; Izuru Kawamura; Ryuji Kawano
|
Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bb3cdf9138d231612f2ab0/original/de-novo-design-of-nanopores-for-single-molecule-detection-that-incorporates-helix-peptides.pdf
|
674d8b377be152b1d0a89629
|
10.26434/chemrxiv-2024-bh4h4
|
Nanoconfinement-induced electrochemical ion-solvent cointercalation in pillared titanate host materials
|
Electrochemical ion-solvent cointercalation reactions are an avenue to reach improved kinetics compared to the corresponding intercalation of desolvated ions. Here, we demonstrate the impact of different structural pillar molecules on the electrochemical Li+ intercalation mechanism in expanded hydrogen titanate (HTO) electrode materials. We show that interlayer-expansion of HTO with organic pillars can enable cointercalation reactions. Their electrochemical reversibility is drastically improved when non-cross-linking pillars are employed that expand and separate the host material’s individual layers, underlining the impact of the electrochemo-mechanics of the nanoconfined interlayer space. This pillared HTO structure results in an increased Li+ storage capacity and reversibility compared to pristine HTO. We derive structural models of the pillared HTO host materials based on combined experiments and theoretical calculations, and employ electrochemical operando experiments to unambiguously demonstrate the nanoconfinement-induced cointercalation mechanism in pillared HTO electrode materials. The work demonstrates the potential of nanoconfined pillar molecules to modify host materials and enable highly reversible cointercalation reactions with improved capacity and kinetics.
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Mennatalla Elmanzalawy; Haohong Song; Maciej Tobis; Robert Leiter; Jaehoon Choi; Hyein Moon; Wan-Yu Tsai; De-en Jiang; Simon Fleischmann
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Physical Chemistry; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Materials Chemistry
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CC BY 4.0
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CHEMRXIV
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2024-12-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674d8b377be152b1d0a89629/original/nanoconfinement-induced-electrochemical-ion-solvent-cointercalation-in-pillared-titanate-host-materials.pdf
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66e31529cec5d6c142e2124f
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10.26434/chemrxiv-2024-q6dkh-v2
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Dynamic Nuclear Polarization with Conductive Polymers
|
The low sensitivity of liquid-state nuclear magnetic resonance (NMR) can be overcome by hyperpolarizing nuclear spins by dissolution dynamic nuclear polarization (dDNP). It consists of transferring the near-unity polarization of unpaired electron spins of stable radicals to the nuclear spins of interest at liquid helium temperatures, below 2 K, before melting the sample in view of hyperpolarized liquid-state magnetic resonance experiments. Reaching such a temperature is challenging and requires complex instrumentation, which impedes the deployment of dDNP. Here, we propose organic conductive polymers such as polyaniline (PANI) as a new class of polarizing matrices and report 1H polarizations of up to 5%. We also show that 13C spins of a host solution impregnated in porous conductive polymers can be hyperpolarized by relayed DNP. Such conductive polymers can be synthesized as chiral and display current induced spin selectivity leading to electron spin hyperpolarization close to unity without the need for low temperatures nor high magnetic fields. Our results show the feasibility of solid-state DNP in conductive polymers that are known to exhibit chirality-induced spin selectivity.
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Quentin Stern; Guillaume Verhaeghe; Théo El Daraï; Damien Montarnal; Nghia Huu Le; Laurent Veyre; Chloé Thieuleux; Charlotte Bocquelet; Olivier Cala; Sami Jannin
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Physical Chemistry; Analytical Chemistry; Spectroscopy (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
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2024-09-13
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e31529cec5d6c142e2124f/original/dynamic-nuclear-polarization-with-conductive-polymers.pdf
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6523ac3e45aaa5fdbb96d8e8
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10.26434/chemrxiv-2023-zt864
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Chemical imaging of sphingolipids and phospholipids at the single amyloid-β plaque level in post-mortem human Alzheimer’s disease brain
|
Lipids dysregulations have been critically implicated in Alzheimer’s disease (AD) pathology. Chemical analysis of amyloid-β (Aβ) plaque pathology in transgenic AD mouse models has demonstrated alterations in the microenvironment in direct proximity to Aβ plaque pathology. In mouse studies, differences in lipid patterns linked to structural polymorphism among Aβ pathology, such as diffuse, immature, and mature fibrillary aggregate have also been reported. To date, no comprehensive analysis of neuronal lipids microenvironment changes in human AD tissue has been performed.
Here, for the first time we leverage matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) though high speed and spatial resolution commercial time-of-light instrument, as well as high mass resolution in-house developed orbitrap system to characterize the lipid microenvironment in postmortem human brain tissue from AD patients carrying Presenilin 1 mutations (PSEN 1) that lead to familial forms of AD (fAD). Interrogation of the spatially resolved MSI data on a single Aβ plaque allowed us to verify nearly 40 sphingolipid and phospholipid species from diverse subclasses being enriched and depleted in relation to the Aβ deposits. This included monosialo-gangliosides (GM), ceramide monohexosides (HexCer), ceramide-1-phosphates (CerP), ceramide phosphoethanolamine conjugates (PE-Cer), sulfatides (ST), as well as phosphatidylinositols (PI), phosphatidylethanolamines (PE), and phosphatidic acid (PA) species (including Lyso-forms). Indeed, many of the sphingolipids species overlap with the species previously seen in transgenic AD mouse models. Interestingly, in comparison to the animal studies, we observed an increased localization of PE and PI species containing arachidonic acid (AA). These finding are highly relevant, demonstrating for the first time Aβ plaque pathology-related alteration in the lipid microenvironment in humans. They provide a basis for development of potential lipid biomarkers for AD characterization and insight into human-specific molecular pathway alterations.
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Wojciech Michno; Andrew Bowman; Durga Jha; Karolina Minta; Junyue Ge; Srinivas Koutarapu; Henrik Zetterberg; Kaj Blennow; Tammaryn Lashley; Ron Heeren; Jörg Hanrieder
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Biological and Medicinal Chemistry; Analytical Chemistry; Imaging; Mass Spectrometry; Biochemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-10-10
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6523ac3e45aaa5fdbb96d8e8/original/chemical-imaging-of-sphingolipids-and-phospholipids-at-the-single-amyloid-plaque-level-in-post-mortem-human-alzheimer-s-disease-brain.pdf
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60c745c6842e65d099db26c1
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10.26434/chemrxiv.8187629.v2
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Facile Electron Transfer to CO2 during Adsorption at the Metal | Solution Interface
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<i>We estimate the rate of electron transfer to CO2 at the Au (211)|water interface during adsorption in an electrochemical environment under reducing potentials. Based on density functional theory calculations at the generalized gradient approximation and hybrid levels of theory, we find electron transfer to adsorbed *CO2 to be very facile. This high rate of transfer is estimated by the energy distribution of the adsorbate-induced density of states as well as from the interaction between diabatic states representing neutral and negatively charged CO2. Up to 0.62 electrons are transferred to CO2, and this charge adiabatically increases with the bending angle to a lower limit of 137°. We conclude that this rate of electron transfer is extremely fast compared to the timescale of the nuclear degrees of freedom, that is, the adsorption process.</i><br />
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Joseph Gauthier; Meredith Fields; Michal Bajdich; Leanne D. Chen; Robert B. Sandberg; Karen Chan; Jens Kehlet Nørskov
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Computational Chemistry and Modeling; Electrocatalysis; Heterogeneous Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
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2019-10-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745c6842e65d099db26c1/original/facile-electron-transfer-to-co2-during-adsorption-at-the-metal-solution-interface.pdf
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61b80eb702d90d55416229c1
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10.26434/chemrxiv-2021-v0rdz
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Dendrite-free alkali-metal electrodeposition from contact-ion-pair state induced by mixing alkaline earth cation
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Alkali metals, such as lithium and sodium, have been expected to be used for rechargeable metal-anode batteries owing to their low electrode potentials and large capacities. However, the well-known fatal problem, “dendritic growth” causing a dangerous short circuit, is faced while charging the batteries. Here, through a comprehensive study with electrochemical experiments, Raman and soft X-ray emission spectroscopies, density-functional-theory calculation, and molecular dynamic simulations, we provide an advanced guideline for electrolyte design in which a mixture of alkaline earth (Mg, Ca, Ba) salts is used to inhibit dendrite growth of alkali metals (Li, Na) during electrodeposition. Especially, focusing on CaTFSA2, as a salient exemplary alkaline-earth-cation additive, we demonstrate that dendrite-free morphology upon alkali-metal electrodeposition can successfully be attained by modifying their solvation structures in the dual-cation electrolyte systems. Adding divalent Ca2+ promotes alkali cation (Li+ or Na+) to form the contact ion pairs (CIPs) with the counter anions, which replaces the solvent-separated ion pairs (SSIPs) commonly existing in single-cation electrolytes. Such CIPs related to alkali cations would separate Ca2+ ions distantly to shield the strong coulomb interaction among the divalent cations. The stronger binding of the CIPs would retard the desolvation kinetics of alkali cations and, consequently, realizes a severely constrained alkali-metal electrodeposition in a reaction-limited process that is required for the dendrite-free morphology. This work provides prospects to construct dual-cation electrolytes for dendrite-free alkali-metal-anode batteries utilizing the concerted interactions between monovalent and multivalent cations.
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Hongyi Li; Masaki Murayama; Tetsu Ichitsubo
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Physical Chemistry; Energy; Chemical Kinetics; Solution Chemistry; Materials Chemistry; Crystallography
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CC BY NC ND 4.0
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CHEMRXIV
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2021-12-14
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b80eb702d90d55416229c1/original/dendrite-free-alkali-metal-electrodeposition-from-contact-ion-pair-state-induced-by-mixing-alkaline-earth-cation.pdf
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65846b8366c1381729bc5f23
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10.26434/chemrxiv-2023-8l7pb
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Computational Prediction of an Antimony-based n-type Transparent Conducting Oxide: F-doped Sb2O5
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Transparent conducting oxides (TCOs) possess a unique combination of optical transparency and electrical conductivity, making them indispensable in optoelectronic applications. However, the heavy dependence on a small number of established materials limits the range of devices they can support. The discovery and development of additional wide bandgap oxides that can be doped to display metallic-like conductivity is therefore necessary. In this work, we use hybrid density functional theory to identify a binary Sb(V) system, Sb2O5, as a promising TCO with high conductivity and transparency when doped with fluorine. We have conducted a full point defect analysis, finding F-doped Sb2O5 to exhibit degenerate n-type transparent conducting behavior. The inherently large electron affinity found in antimony oxides also widens its application in organic solar cells. Following our previous work on zinc antimonate, this work provides additional support for designing Sb(V)-based oxides as cost-effective transparent conducting oxides for a broader range of applications.
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Ke Li; Joe Willis; Seán R. Kavanagh; David O. Scanlon
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Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry
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CC BY 4.0
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CHEMRXIV
|
2023-12-22
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65846b8366c1381729bc5f23/original/computational-prediction-of-an-antimony-based-n-type-transparent-conducting-oxide-f-doped-sb2o5.pdf
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6304da9fd858fbab9a5960e0
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10.26434/chemrxiv-2022-grzz3
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Two Theorems and Important Insight on How the Preferred Mechanism of Free Radical Scavenging Cannot Be Settled
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Totally ignoring that the five enthalpies of reaction --- bond dissociation enthalpy (BDE), adiabatic ionization potential (IP), proton dissociation enthalpy (PDE), proton affinity (PA), and electron transfer enthalpy (ETE) --- characterizing the three free radical scavenging mechanisms --- direct hydrogen atom transfer (HAT), sequential electron transfer proton transfer (SET-PT), and stepwise proton loss electron transfer (SPLET) --- are not independent of each other, a recent publication (Molecules, 2019, 24, 1646) on antioxidant activity of dietary vitamins compared and "found'' different quantities which should be strictly equal by virtue of energy conservation. Aiming at clarifying this point as well as at avoiding such mistakes in future studies or unraveling errors in previous literature, in the present paper
we formulate two theorems that any sound results on antioxidation should obey. The first theorem states that the sums of the enthalpies characterizing the individual steps of SET-PT and SPLET are equal: IP + PDE = PA + ETE (= H2). This is a mathematical identity emerging from the fact that both the reactants and the final products of SET-PT and SPLET are chemically identical. The second theorem, which is also a mathematical identity, states that H2 - BDE = IP_H > 0, where IP_H is the ionization potential of the H atom in the medium (e.g., gas or solvent) considered. Due to their general character, these theorems may/should serve as necessary sanity tests for any results on antioxidant activity whatever the method employed in their derivation. From a more general perspective, they should be a serious word of caution to attempts of assigning the preferred free radical scavenging pathway merely based on thermochemical descriptors.
|
Ioan Baldea
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Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Theory - Computational; Biophysical Chemistry
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CC BY NC 4.0
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CHEMRXIV
|
2022-08-24
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6304da9fd858fbab9a5960e0/original/two-theorems-and-important-insight-on-how-the-preferred-mechanism-of-free-radical-scavenging-cannot-be-settled.pdf
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649ee7a79ea64cc167397443
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10.26434/chemrxiv-2023-czgfb
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Erythronium Bonds: Noncovalent Interactions Involving Group 5 Elements as Electron Density Acceptors
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Analyses of the Cambridge Structural Database and theoretical calculations (PBE0-D3/def2-TZVP level, atoms-in-molecules, natural bond orbital studies) prove the formation of net attractive noncovalent interactions between group 5 elements and electron-rich atoms (neutral or anionic). These bondings are markedly different from coordination bonds formed by the same elements and possess the distinctive features of σ-hole interactions. The term erythronium bond is proposed to denote these bonds. X-ray structures of vanadate-dependent bromoperoxidases show these interactions are present also in biological systems.
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Miriam Calabrese; Rosa Gomila; Andrea Pizzi; Antonio Frontera; Giuseppe Resnati
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Theoretical and Computational Chemistry; Physical Chemistry; Organometallic Chemistry; Computational Chemistry and Modeling; Crystallography
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-07-03
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649ee7a79ea64cc167397443/original/erythronium-bonds-noncovalent-interactions-involving-group-5-elements-as-electron-density-acceptors.pdf
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6250ac2f742e9f76dd58073c
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10.26434/chemrxiv-2022-78vm2
|
High-throughput Nano-DESI Mass Spectrometry Imaging of
Biological Tissues Using an Integrated Microfluidic Probe
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Nanospray desorption electrospray mass spectrometry imaging (nano-DESI MSI) enables quantitative imaging of hundreds of molecules in biological samples with minimal sample pretreatment and a spatial resolution down to 10 µm. We have recently developed an integrated glass microfluidic probe (iMFP) for nano-DESI MSI, which simplifies the experimental setup and enables imaging with a spatial resolution of 25 µm. Herein, we describe an improved design of the iMFP for the high-throughput imaging of tissue sections. We increased the dimensions of the primary and spray channels and optimized the spray voltage and solvent flow rate to obtain a stable operation of the iMFP at both low (0.04 mm/s) and high (0.4 mm/s) scan rates. We demonstrate the performance of the high-throughput iMFP by imaging mouse uterine and brain tissue sections. We observe that the sensitivity, molecular coverage, and spatial resolution obtained using the iMFP do not change to a significant extent as the scan rate increases. Using a scan rate of 0.4 mm/s, we obtained high quality images of mouse uterine tissue sections (scan area: 3.2 mm×2.3 mm) in only 9.5 minutes and of mouse brain tissue (scan area: 7.0 mm×5.4 mm) in 21.7 minutes, which corresponds to a 10-15-fold improvement in the experimental throughput. We have also developed a quantitative metric for evaluating the quality of ion images obtained at different scan rates. Specifically, by defining regions of interest (ROI) in both a representative ion image and optical image of the tissue section, we calculated the spatial deviation between the two ROIs by counting the number of mismatched pixels. Using this metric, we demonstrate that the percent deviation increases slightly from 6.7% to 10.2 % with an increase in the scan rate from 0.02 to 0.4 mm/s. The maximum experimental throughput achieved in this study is limited by the acquisition rate of a mass spectrometer necessary to achieve the desired spatial resolution and may be further improved using a faster instrument. The ability to image biological tissues with high throughput using iMFP-based nano-DESI MSI will substantially speed up tissue mapping efforts.
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Xiangtang Li; Hang Hu; Ruichuan Yin; Yingju Li; Xiaofei Sun; Sudhansu K. Dey; Julia Laskin
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Analytical Chemistry; Biochemical Analysis; Imaging; Mass Spectrometry
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CC BY NC 4.0
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CHEMRXIV
|
2022-04-12
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6250ac2f742e9f76dd58073c/original/high-throughput-nano-desi-mass-spectrometry-imaging-of-biological-tissues-using-an-integrated-microfluidic-probe.pdf
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66f489d712ff75c3a178df84
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10.26434/chemrxiv-2024-nb231
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Unusual Directionality in Thioamide Hydrogen Bonds Can Stabilize β-Strands
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Though thioamides are considered weaker hydrogen-bond acceptors than oxoamides, recent calculations suggest they might enhance hydrogen bonds within the backbone of individual β-strands. We confirm this prediction through spectroscopic analysis of minimal amino-acid models. Further, incorporation of thioamides into the backbone of β-hairpin models high-lights opportunities to control β-strand stability.
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Haoliang Zheng; Robert W Newberry
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Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Physical Organic Chemistry; Chemical Biology
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CC BY NC 4.0
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CHEMRXIV
|
2024-10-01
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f489d712ff75c3a178df84/original/unusual-directionality-in-thioamide-hydrogen-bonds-can-stabilize-strands.pdf
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67cdc80281d2151a02c065c7
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10.26434/chemrxiv-2025-1k503
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Difluoro(methoxy)methyl is a Neglected Group for Medicinal Chemistry – Revival via CF2OMe Containing Amines
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Here we present four key advancements toward the efficient synthesis and application of gem-difluoromethoxyamines from thionoesters. A robust and scalable method was developed for thionoester preparation, employing an imidate-based strategy. Fluorodesulfuration using DAST was systematically evaluated, identifying structural factors influencing reactivity and enabling access to novel CF2OMe-functionalized amines. Stability assessments of hydrolytic resistance compared N-protected derivatives with their hydrochloride counterparts. Additionally, transesterification of thionoesters with primary alcohols expanded the synthetic utility of these intermediates, offering a versatile route to fluorinated building blocks for medicinal chemistry applications.
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Мykhailo Pashko; Dmitriy Granat; Dmytro Leha; Yurii Yagupolskii; Dmytro Volochnyuk; Serhiy Ryabukhin
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Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
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CC BY NC ND 4.0
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CHEMRXIV
|
2025-03-12
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cdc80281d2151a02c065c7/original/difluoro-methoxy-methyl-is-a-neglected-group-for-medicinal-chemistry-revival-via-cf2o-me-containing-amines.pdf
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640a97576642bf8c8f43e3f8
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10.26434/chemrxiv-2023-wgntf
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In Vivo Chemiluminescence Induced Combinational
Chemo-Photodynamic Therapy for Tumor Inhibition
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The combination of stimuli-activable prodrug based chemotherapy and photodynamic therapy (PDT) has attracted increasing attention. Recent studies have verified the effectiveness of this strategy in the treatment of multiple aggressive cancers. However, in such combination, the stimuli-responsive chemotherapy and PDT have their own problems that need to be overcome. The uneven distribution of endogenous stimuli within tumor tissues makes it difficult for prodrug to be completely activated. And the inadequate tissue penetration depth of external light results in low efficiency of PDT. Aiming at these two bottlenecks, we designed a biocompatible dextran based - multi-component nanomedicine (PCL-NPs) that integrate a chemiluminescence agent luminol, a photosensitizer chlorine e6 (Ce6), and a reactive oxygen species (ROS)-activable thioketal-based paclitaxel (PTX) prodrug. The presence of overexpressed hydrogen peroxide (H2O2) inside tumor oxidizes the luminol moiety to generate in-situ light for PDT through chemiluminescence resonance energy transfer (CRET). The singlet oxygen (1O2) produced in this process not only directly kills tumor cells but also amplifies oxidative stress to accelerate the activation of PTX prodrug. We propose that the PCL-NPs have great therapeutic potential by simultaneously enhancing chemotherapy and PDT in a combination therapy.
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Chendi Ding; Zhaoqing Shi; Meitong Ou; Yingbang Li; Li Huang; Wenyan Wang; Qili Huang; Meihang Li; Chunbo Chen; Xiaowei Zeng; Hongzhong Chen; Lin Mei
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Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-03-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640a97576642bf8c8f43e3f8/original/in-vivo-chemiluminescence-induced-combinational-chemo-photodynamic-therapy-for-tumor-inhibition.pdf
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60c74a0d0f50dbfff43969de
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10.26434/chemrxiv.12148446.v1
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Surface and Catalyst Driven Singlet Oxygen Formation in Li-O2 Cells
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Large overpotentials upon discharge and charge of Li-O2 cells have motivated extensive research into heterogeneous solid electrocatalysts or non-carbon electrodes with the aim to improve rate capability, round-trip efficiency and cycle life. These features are equally governed by parasitic reactions, which are now recognized to be caused by the highly reactive singlet oxygen (1O2). However, the link between the presence of electrocatalysts and 1O2 formation in metal-O2 cells is unknown. Here, we show that, compared to pristine carbon black electrodes, a representative selection of electrocatalysts or non-carbon electrodes (noble metal, transition metal compounds) may both slightly reduce or severely increase the 1O2 formation. The individual reaction steps, where the surfaces impact the 1O2 yield are deciphered, showing that 1O2 yield from superoxide disproportionation as well as the decomposition of trace H2O2 are sensitive to catalysts. Transition metal compounds in general are prone to increase 1O2. <br />
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Aleksej Samojlov; David Schuster; Jürgen Kahr; Stefan Freunberger
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Catalysts; Energy Storage; Electrochemistry - Mechanisms, Theory & Study
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-04-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a0d0f50dbfff43969de/original/surface-and-catalyst-driven-singlet-oxygen-formation-in-li-o2-cells.pdf
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60d226a4403d9947b2bbf442
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10.26434/chemrxiv-2021-g285c-v2
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Systematic Study of the Thermal Properties of Zeolitic Frameworks
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We report a systematic study of the thermal and mechanical properties of 134 pure SiO2 zeolites through DFT-based calculations by making use of the quasi-harmonic approximation (out of a total of 242 known fully ordered zeolitic frameworks). The comparison of our results with reported experimental data for several zeolites revealed a very good accuracy and validated our simulation methodology. We observe a wide range of thermal expansion coefficients (from −5 to −35 MK−1), highlighting the great influence of the framework topology over this physical property, while demonstrating that all pure-silica zeolites exhibit negative thermal expansion (NTE). Our simulations also provide a path for the computation of the bulk modulus for each structure, as well as its pressure and temperature dependence. Results revealed a large gamut of bulk modulus values (from 8 to 134 GPa), showing that most frameworks display pressure-induced softening — but not all!
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Maxime Ducamp; François-Xavier Coudert
|
Theoretical and Computational Chemistry; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-06-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d226a4403d9947b2bbf442/original/systematic-study-of-the-thermal-properties-of-zeolitic-frameworks.pdf
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60c746bd337d6c1fb2e271f5
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10.26434/chemrxiv.11383659.v1
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Bioorthogonal Tetrazine Carbamate Cleavage by Highly Reactive Trans-Cyclooctene
|
<p>The high reaction rate of the 'click-to-release' reaction between allylic substituted <i>trans</i>-cyclooctene and tetrazine has enabled exceptional control over chemical and biological processes. Here we report the development of a new bioorthogonal cleavage reaction based on <i>trans</i>-cyclooctene and tetrazine with up to 3 orders of magnitude higher reactivity compared to the parent reaction, and 4 to 6 orders higher than other cleavage reactions. In this new pyridazine elimination mechanism, wherein the roles a reversed, a <i>trans</i>-cyclooctene activator reacts with a tetrazine that is substituted with a methylene-linked carbamate, leading to an 1,4-elimination of the carbamate and liberation of an amine. Through a series of mechanistic studies, we identified the 2,5-dihydropyridazine tautomer as the releasing species and found factors that govern its formation and subsequent fragmentation. The bioorthogonal utility was demonstrated by the selective cleavage of a tetrazine-linked antibody-drug conjugate by <i>trans</i>-cyclooctenes, affording efficient drug liberation in plasma and cell culture. Finally, the parent and the new reaction were compared at low concentration, showing that the use of a highly reactive <i>trans</i>-cyclooctene as activator leads to a complete reaction with antibody-drug conjugate in seconds <i>vs</i>. hours for the parent system. We believe that this new reaction may allow markedly reduced click-to-release reagent doses <i>in vitro</i> and <i>in vivo</i> and could expand the application scope to conditions wherein the <i>trans</i>-cyclooctene has limited stability. </p>
|
Arthur van Onzen; Ron M. Versteegen; Freek
J. M. Hoeben; Ivo A.W. Filot; Raffaella Rossin; tong zhu; Jeremy Wu; Peter J. Hudson; Henk M. Janssen; Wolter ten Hoeve; Marc Robillard
|
Bioorganic Chemistry; Organic Synthesis and Reactions; Chemical Biology; Drug Discovery and Drug Delivery Systems
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CC BY NC ND 4.0
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CHEMRXIV
|
2019-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746bd337d6c1fb2e271f5/original/bioorthogonal-tetrazine-carbamate-cleavage-by-highly-reactive-trans-cyclooctene.pdf
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62a3a829a784d13a517a31a8
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10.26434/chemrxiv-2022-sn16v
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Photoinduced transfer hydrogenation of nitrogen to ammonia using a Mo-catalyst and a Hantzsch ester donor is demonstrated with and without an Ir-photoredox co-catalyst
|
Whereas photoredox catalysis using molecular systems enjoys considerable utility in small molecule transformations and reactions relevant to organic synthesis, to date there are no related examples of photodriven catalytic nitrogen fixation. We wondered whether a photoinduced transfer hydrogenation strategy might provide a viable pathway toward such a reaction. Hantzsch esters (and related organic structures) offer an opportunity for catalysis design in this context as they can behave as photoreductants, though to our knowledge they had yet to be shown to be compatible with such a redox intensive process (6 e–/6 H+). In the present study we demonstrate that fully reduced Hantzsch esters (abbreviated as HEH2) successively deliver stored H2-equivalents to N2, producing NH3 catalytically, in the presence of a molecular precatalyst (Mo) under blue-light irradiation but otherwise ambient conditions. While not required for the observed photocatalysis, the addition of a photoredox catalyst (Ir) to the reaction mixture enhances both the rate and turnover number of the net transformation. Encouraging with respect to future studies toward recycling the donor, electrochemically or via hydrogenation, other N-heterocycle H2-donors are also compatible with catalysis in the presence of the photoredox catalyst. The reduction of N2 to NH3 by HEH2 or H2 are thermodynamically very similar (ΔΔGf(NH3) = 1.8 kcal mol–1 in acetonitrile). However, whereas the combination of H2 with N2 to produce NH3 is accomplished via high temperature and pressure over a metal catalyst, the needed overpotential to drive the reduction of N2 by HEH2 can instead be derived from light. This study hence illustrates a promising photoredox catalysis approach toward deep reduction of robust small molecule substrates via photoinduced transfer hydrogenation, with the complete reduction of the triple bond of N2 providing a vivid example.
|
Christian Johansen; Emily Boyd; Jonas Peters
|
Organic Chemistry; Inorganic Chemistry; Catalysis; Small Molecule Activation (Inorg.); Photocatalysis; Redox Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-06-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a3a829a784d13a517a31a8/original/photoinduced-transfer-hydrogenation-of-nitrogen-to-ammonia-using-a-mo-catalyst-and-a-hantzsch-ester-donor-is-demonstrated-with-and-without-an-ir-photoredox-co-catalyst.pdf
|
63eab983fcfb27a31fbb9f86
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10.26434/chemrxiv-2023-bg1f9
|
Building a nucleic acid nanostructure with DNA-epitope conjugates for a versatile electrochemical protein detection platform
|
The recent surge of effort in nucleic acid-based electrochemical (EC) sensors has been fruitful, and some have even shown real-time quantification of drugs in the blood of living animals. Yet there remains a need for more generalizable EC platforms for the detection of multiple classes of clinically relevant targets. Our group has recently reported a nucleic acid nanostructure that permits simple, economical, and generalizable EC readout of a wide range of analytes (small molecules, peptides, large proteins, or antibodies). The DNA nanostructure is built through on-electrode enzymatic ligation of three oligonucleotides for attachment, binding, and signaling. However, the signaling mechanism predominantly relies on tethered diffusion of methylene blue at the electrode surface, limiting the detection of larger proteins that have no readily available small molecule binding partners. In this study, we adapted the nanostructure sensor to quantify larger proteins in a more generic manner, through conjugating the proteins minimized antibody-binding epitope to the central DNA strand of the nanostructure (DNA-peptide conjugate). This concept was verified using creatine kinase (CK-MM), an important biomarker of muscle damage, myocardial infarction, overexertion/rhabdomyolysis, or neuromuscular disorders where clinical outcomes could be improved with rapid sensing. DNA-epitope conjugates permitted a competitive immunoassay protocol at the electrode surface for quantifying CK protein. Square-wave voltammetry (SWV) signal suppression was proportional to the amount of surface-bound antibody with a limit of detection (LOD) of 5 nM and a response time as low as 3 minutes, and displacement of antibody by native CK-MM protein analyte could also be assayed. CK was quantified from the LOD of 14 nM up to 100 nM, overlapping well with the normal (non-elevated) human clinical range of 3 37 nM, and the sensor response was validated in 98% human serum. While a need for improved DNA-epitope conjugate purification was identified, overall this approach not only allows the detection of a generic protein- or peptide-binding antibody, but it also should facilitate future quantitative EC readout of various clinically relevant protein analytes that were previously inaccessible to EC techniques.
|
Asanka Gurukandure; Subramaniam Somasundaram; Amanda S. N. Kurian; Niamat Khuda; Christopher J. Easley
|
Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Biochemical Analysis; Electrochemical Analysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-02-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63eab983fcfb27a31fbb9f86/original/building-a-nucleic-acid-nanostructure-with-dna-epitope-conjugates-for-a-versatile-electrochemical-protein-detection-platform.pdf
|
67acaae0fa469535b909c2d7
|
10.26434/chemrxiv-2025-n2wh8
|
Revealing a novel intercalation nature of high-capacity conversion cathode materials for Fluoride-Ion Batteries by Operando Studies
|
To rationalize and improve the performance of high energy density electrode materials for all-solid-state fluoride ion batteries and abstract the increasing demands of energy storage, it is important to gain a fundamental understanding of structure/phase evolution during cell operation, which is closely correlated to capacity fading upon cycling. Here, we design an operando cell for laboratory X-ray diffraction, by which we monitor the real-time structure evolution of BiF3 cathode materials and the degradation of superior ionic conductor BaSnF4 over the negative cell potential range against Sn/SnF2 anode at an elevated temperature (100 °C). The results, together with ex-situ XRD measurements, reveal that BiF3 undergoes multiple-step phase transformations upon defluorination (from original o-BiF3 to c-BiF3 and then o’-BiF3) before the formation of Bi metal, showing an intercalation-type mechanism. In addition, the formation of Bismuth oxidefluoride (BiOF) at later discharged state (beyond a capacity of 200 mAh g-1) is observed, which is attributed to oxygen impurities from the solid electrolyte introduced by the applied solid state synthesis method. Operando XAS measurements confirm the continuous reduction of the Bi oxidation state from +3 to 0 and the formation of multi-intermediate phases during the defluorination process. Through Rietveld analysis on operando XRD patterns we obtain the quantification of phase fractions and crystal structure information of intermediate phases during the defluorination process, from which we are able to derive a model for the first defluorination process of BiF3 at elevated temperatures. Furthermore, the comparison between the results from operando XAS and operando XRD indicates that BaSnF4 plays a crucial role on the transport process of not only F- but also oxygen impurities within the BiF3 cathode composite, contributing to the formation of the oxidefluoride phase. In addition, BaSnF4 shows a rather wide potential window, with degradation taking place at a potential below -200 mV (against Sn/SnF2 anode).
|
Hong Chen; Roland Schoch; Jean-Noel Chotard; Yannick Thiebes; Kerstin Wissel; Rainer Niewa; Matthias Bauer; Oliver Clemens
|
Materials Science; Fuels - Materials; Nanostructured Materials - Materials
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67acaae0fa469535b909c2d7/original/revealing-a-novel-intercalation-nature-of-high-capacity-conversion-cathode-materials-for-fluoride-ion-batteries-by-operando-studies.pdf
|
654e13f2dbd7c8b54b020dcd
|
10.26434/chemrxiv-2023-xk0cp
|
Room temperature sensing of volatile organic compounds using hybrid SnO nanoflower and Laser-Induced Graphitic carbon devices
|
Volatile organic compounds (VOCs) are a common risk to human health in industrial and domestic settings. VOCs are often present at concentrations that cannot be detected through human odor perception. VOC sensors are, therefore, urgently needed for home and workplace environmental monitoring, including wearable sensors for workers. However, current chemiresistive VOC sensors typically require high-energy fabrication processes with large environmental footprints, significant mass-loadings of critical raw materials and/or elevated operating temperatures, which hamper widespread, sustainable deployment. We demonstrate a simple, low-energy hybrid fabrication route for chemiresistive VOC sensors, comprising additively-produced laser-induced graphene (LIG) electrodes on plastic substrates, decorated with SnO nanoflowers. The SnO nanoflowers were synthesized below 100C at ambient pressure and offer a low-energy alternative to conventional SnO2 or other metal-oxide nanoparticle devices. These chemiresistive sensors can detect methanol vapor at room temperature (∼18C) and typical humidity levels (∼55% RH), with a limit of detection (170±40 ppm) below 8-hour worker safety exposure levels (200 ppm). The sensors also demonstrated stable DC resistance responses DeltaR/R = 9±2% to 710 ppm of methanol for over 21 days in ambient laboratory conditions. First principles density functional theory simulations are used to elucidate the origin of the performance of the LIG-SnO sensors. LIG-SnO hybrid sensors thus present a resource-efficient route to develop chemiresistive sensors for low-power applications, such as wearable worker safety or Internet of Things edge-sensing.
|
Richard Murray; Arbresha Muriqi; Cathal Larrigy; Alida Russo; Mintesinot Tamiru; Daniela Iacopino; Michael Nolan; Aidan Quinn
|
Theoretical and Computational Chemistry; Analytical Chemistry; Electrochemical Analysis; Environmental Analysis; Computational Chemistry and Modeling; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-11-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654e13f2dbd7c8b54b020dcd/original/room-temperature-sensing-of-volatile-organic-compounds-using-hybrid-sn-o-nanoflower-and-laser-induced-graphitic-carbon-devices.pdf
|
66fd2aa651558a15efcde9d9
|
10.26434/chemrxiv-2024-62g35
|
Development of an orally bioavailable covalent STING inhibitor
|
Pharmacological inhibition of cGAS-STING-controlled innate immune pathway is an emerging therapeutic strategy for a myriad of inflammatory diseases, including autoimmune disease, ulcerative colitis, non-alcoholic fatty liver disease and aging-related neurodegeneration. Here we report GHN105 as an orally bioavailable covalent STING inhibitor. Late-stage diversification of the briarane-type diterpenoid excavatolide B allowed the installation of solubility-enhancing functional groups while enhancing its activity as a covalent STING inhibitor against multiple human STING variants, including the S154 variant responsible for a genetic autoimmune disease. Selectively engaging the membrane-proximal Cys91 residue of STING, GHN105 dose-dependently inhibited cGAS-STING signaling and type I interferon responses in cells and in vivo. Orally administered GHN105 exerted marked therapeutic efficacy and reversed key pathological features in a delayed-treatment acute colitis mouse model. Notably, we also showed that GHN105 covalently engaged STING in the colon tissues. Our study provided proof of concept that synthetic briarane analog GHN105 serves as a safe and orally active covalent STING inhibitor. With a growing number of chronic inflammatory diseases linked to aberrant STING activation, orally bioavailable STING inhibitors would benefit patients by lowering the infection risk from frequent injections while allowing long-term systemic administration.
|
GUANG-HAO NIU; Wan-Chi Hsiao; Po-Hsun Lee; Li-Guo Zheng; Yu-Shao Yang; Wei-Cheng Huang; Chih-Chien Hsieh; Tai-Yu Chiu; Jing-Ya Wang; Ching-Ping Chen; Chen-Lung Huang; May-Su You; Yi-Ping Kuo; Chien-Ming Wang; Zhi-Hong Wen; Guann-Yi Yu; Chiung-Tong Chen; Ya-Hui Chi; Chun-Wei Tung; Shu-Ching Hsu; Teng-Kuang Yeh; Ping-Jyun Sung; Mingzi M. Zhang; Lun Kelvin Tsou
|
Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fd2aa651558a15efcde9d9/original/development-of-an-orally-bioavailable-covalent-sting-inhibitor.pdf
|
60c746ca702a9b79bd18ac90
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10.26434/chemrxiv.11409417.v1
|
The Problem of Aspartimide Formation During Protein Chemical Synthesis Using SEA-Mediated Ligation
|
Aspartimide formation often complicates the solid phase synthesis of peptides. Much less discussed is the potential occurrence of this side-reaction during the coupling of peptide segments using chemoselective peptide bond forming reactions such as the native chemical ligation and extended methods. Here we describe how to manage this problem using bis(2-sulfenylethyl)amido (SEA)-mediated ligation and SUMO-2/SUMO-3 as protein targets.<br />
|
Jennifer Bouchenna; Magalie Sénéchal; Hervé Drobecq; Jérôme Vicogne; Oleg Melnyk
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Biochemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-12-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746ca702a9b79bd18ac90/original/the-problem-of-aspartimide-formation-during-protein-chemical-synthesis-using-sea-mediated-ligation.pdf
|
60c748d9ee301c6265c79989
|
10.26434/chemrxiv.11988516.v1
|
Palladium-Catalyzed Denitrative Mizoroki–Heck Reaction
|
<div><p>We have developed a Mizoroki–Heck reaction of nitroarenes with alkenes under palladium catalysis. The use of a Pd/BrettPhos catalyst promoted the alkenylation, whereas other catalysts led to a decrease in the product yield. In addition to nitroarenes, nitroheteroarenes were also applicable to the present reaction. Combination of a nucleophilic aromatic substitution (S<sub>N</sub>Ar) with the denitrative alkenylation produced a multi-functionalized arene in a one-pot operation.</p></div>
|
Toshimasa Okita; Kitty K. Asahara; Kei Muto; Junichiro Yamaguchi
|
Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748d9ee301c6265c79989/original/palladium-catalyzed-denitrative-mizoroki-heck-reaction.pdf
|
666b596f01103d79c527317b
|
10.26434/chemrxiv-2024-3149c-v2
|
The Electrochemical Peroxydisulfate-Oxalate Autocatalytic Reaction
|
Aqueous solutions containing both the strong oxidant, peroxydisulfate (S2O82‒), and the strong reductant, oxalate (C2O42‒), are thermodynamically unstable due to the highly exothermic homogeneous redox reaction: S2O82‒ + C2O42‒ ® 2 SO42‒ + 2 CO2 (DG0 = −490 kJ/mol). However, at room temperature, this reaction does not occur to a significant extent over the timescale of a day due to its inherently slow kinetics. We demonstrate that the S2O82‒/C2O42‒ redox reaction occurs rapidly, once initiated by the Ru(NH3)62+-mediated 1e– reduction of S2O82‒ to form S2O83•‒ at a glassy carbon electrode. Theoretically, the mediated electrochemical generation of a single molecule of S2O83•‒ is capable of initiating an autocatalytic cycle that consumes both S2O82‒ and C2O42‒ in bulk solution. Several experimental demonstrations of S2O82‒/C2O42‒ autocatalysis are presented. Differential electrochemical mass spectrometry measurements demonstrate that CO2 is generated in solution for at least 10 minutes following a 30-s initiation step during which S2O83•‒ is generated. Quantitative bulk electrolysis of S2O82‒ in solutions containing excess C2O42‒ is initiated by electrogeneration of immeasurably small quantities of S2O83•‒. Capture of CO2 as BaCO3 during electrolysis additionally confirms the autocatalytic generation of CO2. First- principles density functional theory calculations, ab initio molecular dynamics simulations, and finite difference simulations of cyclic voltammetric responses are presented that support and provide additional insights into the initiation and mechanism of the S2O82‒/C2O42‒ autocatalytic reaction. Preliminary evidence indicates that autocatalysis also results in a chemical traveling reaction front that propagates into the solution normal to the planar electrode surface.
|
Jordyn Janusz; Joshua Beeler; Seyyedamirhossein Hosseini; Mayank Tanwar; Rui Zeng; Hongsen Wang; Héctor Abruña; Matthew Neurock; Henry White
|
Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Mass Spectrometry; Computational Chemistry and Modeling; Electrochemistry - Mechanisms, Theory & Study
|
CC BY 4.0
|
CHEMRXIV
|
2024-06-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666b596f01103d79c527317b/original/the-electrochemical-peroxydisulfate-oxalate-autocatalytic-reaction.pdf
|
6182d2b992abe0b26733ca4b
|
10.26434/chemrxiv-2021-cznr1
|
Functional reconstitution of the insect odorant receptor co-receptor in a tethered lipid bilayer membrane
|
As membrane proteins are among the most important drug targets, it is critical to study membrane proteins to improve drug design. However, due to the myriad roles fulfilled by the cellular membrane, it is a highly complex environment and challenging to study. Tethered membranes reproduce the basic physicochemical properties of the cellular membrane without their inherent complexity, and their high electrical resistance and stability makes them ideal to study membrane proteins, particularly ion channels. However, due to the close proximity of the membrane to the support and the reduced fluidity and high packing density, they are unsuitable to study larger membrane proteins. We present here a tethered membrane system into which the functional the odorant receptor coreceptor from Drosophila melanogaster, a tetrameric ionotropic receptor was incorporated and its sensitivity to various ligands was examined via electrochemical impedance spectroscopy and atomic force microscopy.
|
David Kleinheinz; Chiara D'Onofrio; Ulrich Ramach; Colm Carraher; Bernhard Schuster; Wolfgang Knoll; Jakob Andersson
|
Physical Chemistry; Nanoscience; Interfaces; Self-Assembly; Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-02-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6182d2b992abe0b26733ca4b/original/functional-reconstitution-of-the-insect-odorant-receptor-co-receptor-in-a-tethered-lipid-bilayer-membrane.pdf
|
60c74bb0ee301c3427c79efd
|
10.26434/chemrxiv.12374249.v1
|
Ultralow Surface Tension Solvents Enable Facile COF Activation with Reduced Pore Collapse
|
<p>Covalent Organic Frameworks (COFs) are organic,
crystalline, highly porous materials attractive for applications such as gas
storage, gas separations, catalysis, contaminant adsorption and membrane
filtration. Activation of COFs removes adsorbed solvents and impurities, but
common methods for COF activation can result in collapse of porous structure
and loss of accessible surface areas. Here, we present a study of the impact of
solvent surface tension on the activation process and demonstrate that
activation using the ultralow surface tension solvent perfluorohexane (PFH) is
simple and effective for a range of COF materials. We synthesized six different
imine-based COFs through imine condensation reactions between tris(4-aminophenyl)
benzene (TAPB) or 2,4,6-tris(4-aminophenyl)-1,3,5-triazine (TAPT) and
multi-functional di- and tri-benzaldehydes with different aromatic
substituents. For each COF, we performed a solvent wash followed by vacuum
drying using six solvents varying in surface tension from 11.9 – 72.8 mN m<sup>-1</sup>.
Through powder X-ray diffraction (PXRD) measurements combined with nitrogen
adsorption and desorption analysis, we found that some COF chemistries readily
lost their porosity during activation with higher surface tension solvents
while others were more robust. However, all COFs could be effectively activated
using PFH to produce materials with excellent crystallinity and high surface
areas, comparable to those for samples activated using supercritical CO<sub>2</sub>.
This work demonstrates that the solvent surface tension used during activation
has a strong impact on potential pore collapse, and activation using PFH
provides a simple and effective activation method to produce COFs with
excellent crystallinities and pore structures.</p>
|
Dongyang Zhu; Rafael Verduzco
|
Nanostructured Materials - Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bb0ee301c3427c79efd/original/ultralow-surface-tension-solvents-enable-facile-cof-activation-with-reduced-pore-collapse.pdf
|
62c43f08f51939ba317f2998
|
10.26434/chemrxiv-2022-l8vk8-v2
|
FAIR assessment of nanosafety data reusability with community standards
|
New nanomaterials improve our society. Understanding their effects on biological systems is of importance to improve our understanding of their properties and safety. However, reusability of previously produced data to help developing computational risk assessment tools is still limited, due to the inconsistency in experimental reporting, the lack of generally accepted machine-readable metadata standards, and the ability to combine between such standards. Fortunately, the research community has developed multiple minimum reporting standards (MRS) to address a number of these issues. This makes the development of a machine-friendly approach possible to annotate and assess datasets' reusability according to those standards. In this work, we identified twelve published minimum reporting standards relevant to nanosafety research and converted them into a machine-readable representation in the form of FAIR maturity indicators. Moreover, as part of this NanoSafety Data Reusability Assessment framework, we developed a metadata generator web application to be integrated into experimental data management. Finally, a new web application can summarize the nanosafety-related reusability of digital resources against one or more subsets of maturity indicators selected, aimed at specific computational risk assessment use cases. With this approach, we show that we can transparently record and communicate the reusability of experimental data and metadata. This improved FAIR approach will help the community make nanosafety research more reusable for exploration, toxicity prediction, and regulation.
|
Ammar Ammar; Chris Evelo; Egon Willighagen
|
Nanoscience
|
CC BY 4.0
|
CHEMRXIV
|
2022-07-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c43f08f51939ba317f2998/original/fair-assessment-of-nanosafety-data-reusability-with-community-standards.pdf
|
60c7422bf96a005595286576
|
10.26434/chemrxiv.8230172.v1
|
Energizing Listless Pyrimidines by Pre-Distortion for the General Synthesis of 7-Aza-Indazoles from 2-Hydrazonylpyrimidines via Intramolecular Diels-Alder Reactions
|
<p>Pyrimidines are almost unreactive partners in Diels-Alder cycloadditions with alkenes and alkynes, and usually only reactions under drastic conditions were historically reported. We describe how 2-hydrazonylpyrimidines, easily obtained in two steps from commercially available 2-halopyrimidines can be exceptionally activated by trifluoro acetylation. This allows a Diels-Alder cycloaddition under very mild conditions, leading to a large diversity of <i>aza</i>-indazoles, a ubiquitous scaffold in medicinal chemistry. This reaction is general, scalable and has an excellent functional group tolerance. Quantum mechanical calculations show how the simple <i>N</i>-trifluoromethylation of 2-hydrazonylpyrimidines distorts the substrate into a transition state-like geometry that readily undergoes the intramolecular Diels-Alder cycloaddition. </p>
|
Vincent Le Fouler; yu Chen; Vincent Gandon; Vincent Bizet; Christophe Salomé; Thomas Fessard; Fang Liu; K. N. Houk; Nicolas Blanchard
|
Organic Synthesis and Reactions; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-06-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7422bf96a005595286576/original/energizing-listless-pyrimidines-by-pre-distortion-for-the-general-synthesis-of-7-aza-indazoles-from-2-hydrazonylpyrimidines-via-intramolecular-diels-alder-reactions.pdf
|
6426a012647e3dca99cd7b57
|
10.26434/chemrxiv-2023-qr03r
|
Partial replacement of Pb2+ in MAPbI2.6Cl0.4 perovskite films and their photovoltaic performance
|
Replacing lead atoms in halide perovskite materials is of significant importance for the development of environmentally friendly perovskite solar cells. In this paper, we investigated the effect of doping the MAPbI2.6Cl0.4 hybrid perovskite (MA-methyl ammonium) with non-toxic elements, such as alkaline earth metal ions (Mg2+) and transition metal ions (Zn2+). The structural, morphological, and optical properties of the prepared samples were analyzed using X-ray diffraction (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM), and UV-Vis. spectroscopy. Finally, the doped films were used as photoactive layers in solar devices in order to evaluate their photovoltaic performance. Zn proved to be more appropriate to replace partially Pb and films with higher quality were obtained. As a result, the MAPb1-xZnxI2.6Cl0.4 based solar cells have demonstrated a slight improvement of the photovoltaic performances, resulting in a uniform and narrower PCEs (power conversion efficiency) range, compared to pristine MAPbI2.6Cl0.4 based devices.
|
Sarah Derbali; Lucia Leonat; Viorica Stancu; Andrei Tomulescu; Aurelian Galca; Khalid Nouneh ; Ioana Pintilie; M. Ebn Touhami ; Mihaela Florea
|
Energy; Photovoltaics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6426a012647e3dca99cd7b57/original/partial-replacement-of-pb2-in-ma-pb-i2-6cl0-4-perovskite-films-and-their-photovoltaic-performance.pdf
|
60c7546abdbb89a05ea3a645
|
10.26434/chemrxiv.13655435.v1
|
Local Decomposition of Hybridization Functions: Chemical Insight into Correlated Molecular Adsorbates
|
Hybridization functions are an established tool for investigating the
coupling between a correlated subsystem (often a single transition metal
atom) and its uncorrelated environment (the substrate and any ligands
present). The hybridization function can provide valuable insight into
why and how strong correlation features such as the Kondo effect can be
chemically controlled in certain molecular adsorbates. To deepen this
insight, we introduce a local decomposition of the hybridization
function, based on a truncated cluster approach, enabling us to study
individual effects on this function coming from specific parts of the
systems (e.g., the surface, ligands, or parts of larger ligands). It is
shown that a truncated-cluster approach can reproduce the Co 3<em>d</em> and Mn 3<em>d</em> hybridization functions from periodic boundary conditions in Co(CO)<sub>4</sub>/Cu(001)
and MnPc/Ag(001) qualitatively well. By locally decomposing the
hybridization functions, it is demonstrated at which energies the
transition metal atoms are mainly hybridized with the substrate or with
the ligand. For the Kondo-active the 3d<sub>x2−y2</sub> orbital in Co(CO)<sub>4</sub>/Cu(001),
the hybridization function at the Fermi energy is substrate-dominated,
so we can assign its enhancement compared with ligand-free Co to an
indirect effect of ligand–substrate interactions. In MnPc/Ag(001), the
same is true for the Kondo-active orbital, but for two other orbitals,
there are both direct and indirect effects of the ligand, together
resulting in such strong screening that their potential Kondo activity
is suppressed. A local decomposition of hybridization functions could
also be useful in other areas, such as analyzing the electrode
self-energies in molecular junctions.
|
Marc Philipp Bahlke; Michaela Schneeberger; Carmen Herrmann
|
Theory - Computational; Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7546abdbb89a05ea3a645/original/local-decomposition-of-hybridization-functions-chemical-insight-into-correlated-molecular-adsorbates.pdf
|
60c7522f4c89193010ad40bc
|
10.26434/chemrxiv.13265312.v1
|
Titanium-interlayer Mediated Hydroxyapatite Coating on Polyetheretherketone: A Prospective Study in Patients with Single-level Cervical Degenerative Disc Disease
|
Currently, there are limited reports regarding investigation of the biological
properties of polyetheretherketone (PEEK) coated with titanium (Ti) and
hydroxyapatite (HA) in human. The objective of this study is to evaluate the in vivo
response of the PEEK cages coated with Ti and HA versus uncoated PEEK cages after
anterior cervical discectomy and fusion (ACDF) in patients with single-level cervical
degenerative disc disease (CDDD). Twenty-four patients with PEEK cages coated with
Ti and HA (PEEK/Ti/HA group) were matched one-to-one with patients with uncoated
PEEK cages (PEEK group) based on age, gender, and operative segment. All patients
had been followed up for more than 2 years. Radiological assessments included
intervertebral height (IH), C2-7 angle(C2-7a), segmental alignment (SA), and fusion
rate. Clinical parameters included Visual Analogue Scale (VAS) and Japanese
Orthopedic Association (JOA) scores. There was no statistical difference in SA, IH,
and C2-7a between the two groups before and after surgery and all these parameters
were restored postoperatively. The fusion rate of PEEK/Ti/HA group was significantly
higher than PEEK group at 3-month post-operation (87.5% vs. 62.5%). At the last
follow-up, the fusion rate of the both groups achieved 100%. The VAS and JOA scores
were comparable between two groups and improved postoperatively. In conclusion, in
patients with single-level ACDF, PEEK cage coated with Ti and HA provided a higher
fusion rate than uncoated PEEK cage at 3-month post-operation, while both of the two
cages could achieve solid osseous fusion at the last follow up. Compared with the
uncoated PEEK cage, PEEK/Ti/HA cage yielded similar favorable segmental and
overall cervical lordosis, IH, and clinical outcomes after the surgery.
|
Ce zhu; Miaomiao He; Lili Mao; Tao LI; Li Zhang; Limin Liu; Ganjun Feng; Yueming Song
|
Biological Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7522f4c89193010ad40bc/original/titanium-interlayer-mediated-hydroxyapatite-coating-on-polyetheretherketone-a-prospective-study-in-patients-with-single-level-cervical-degenerative-disc-disease.pdf
|
6327ab01e665bd53510993f0
|
10.26434/chemrxiv-2022-9vlcf
|
Unlocking record capacity and rate capability of HxCrS2 by proton-exchange pretreatment
|
Unsustainable mining and limited availability of lithium-ion battery materials have created a driving need to develop alternatives such as sodium hosts.[1–4] The development of suitable anode materials remains a major challenge facing sodium-ion battery development. Efforts into studying the charge storage of sodium in transition metal sulfides have gained traction due to improved kinetics compared with oxides.[5] Van der Waals CrS2 has been predicted to be a good intercalation host for Na but has not been isolated as a bulk phase. Rather, [CrS2 ]− layers exist in delafossite-related materials such as NaCrS2 , which has only a moderate reversible capacity of about 100 mAh/g.[6] Here we present a new material, “HxCrS2” (denotes approximate composition) formed by proton-exchange of NaCrS2 which has a measured capacity of 728 mAh/g with significant improvements to capacity retention, sustaining over 700 mAh/g during cycling experiments. This is the highest reported capacity for a sulfide electrode and is higher than the capacity of antimony (576 mAh/g) which has been the most promising anode to date, pairing high capacity with high rates.[7] Pretreatment by proton-exchange offers a route to materials such as HxCrS2 which provide fast diffusion and high capacities for sodium-ion batteries.
|
Joseph Stiles; Anna Soltys; Xiaoyu Song; Saul Lapidus; Craig Arnold; Leslie Schoop
|
Materials Science; Energy; Materials Processing; Nanostructured Materials - Materials; Energy Storage; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6327ab01e665bd53510993f0/original/unlocking-record-capacity-and-rate-capability-of-hx-cr-s2-by-proton-exchange-pretreatment.pdf
|
62fd2557350acf2b9d470215
|
10.26434/chemrxiv-2022-35fwp
|
Ritonavir Form III: A New Polymorph After 24 Years
|
Polymorphism occurs widely in pharmaceutical solids, and must be thoroughly studied during product development. Twenty-four years after ritonavir (RTV) Form II materialized, we report a new polymorph, Form III, discovered via melt crystallization. Form III has a unique PXRD pattern, Raman spectrum, lower melting point and heat of fusion, compared to the known polymorphs, Form I and Form II. It is the least stable form, monotropically, among the three polymorphs. Form III differs from Form I and Form II in conformation and hydrogen bonding motifs. Nucleation from RTV supercooled liquid is slow, and selected Form III exclusively. The discovery of RTV Form III demonstrates the importance of crystal nucleation studies. Crystallization from supercooled liquids should be incorporated as part of polymorph screening workflow.
|
GEOFF ZHANG; Xin Yao; Rodger Henry
|
Physical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fd2557350acf2b9d470215/original/ritonavir-form-iii-a-new-polymorph-after-24-years.pdf
|
6233b0c08ab3732b56687bad
|
10.26434/chemrxiv-2022-89l57
|
Directed, Nickel-Catalyzed 1,2-Alkylsulfenylation of Alkenyl Carbonyl Compounds
|
We report a regioselective, nickel-catalyzed syn-1,2-carbosulfenylation of non-conjugated alkenyl carbonyl compounds with alkyl/arylzinc nucleophiles and tailored N–S electrophiles. This method allows the simultaneous installation of a variety of C(sp3) and S(Ar) (or Se(Ar)) groups on to unactivated alkenes, which complements previously developed 1,2-carbosulfenylation methodology in which only C(sp2) nucleophiles are compatible. A bidentate directing auxiliary controls regioselectivity, promotes high syn-stereoselectivity with a variety of E- and Z- internal alkenes, and enables the use of a variety of electrophilic sulfenyl (and seleno) electrophiles. Among compatible electrophiles, those with N-alkyl-benzamide leaving groups were found to be especially effective, as determined through comprehensive structure–reactivity mapping.
|
Zi-Qi Li; Wen-Ji He; Hui-Qi Ni; Keary Engle
|
Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6233b0c08ab3732b56687bad/original/directed-nickel-catalyzed-1-2-alkylsulfenylation-of-alkenyl-carbonyl-compounds.pdf
|
625e21c1ed4d888741106713
|
10.26434/chemrxiv-2022-c3vg6
|
Carbonylative Olefin Hydroacylation with Alkyl Halides by Multiphoton Tandem Photoredox Catalysis in Flow
|
The abundance, structural diversity and versatility of ketones give prominence to this carbonyl functional group in synthetic chemistry. The assembly of ketones via the carbonylative hydroacylation alkenes represents a powerful modular strategy for the synthesis of unsymmetric ketone products. Here, we report the first photocatalytic carbonylative hydroacylation of alkenes with unactivated alkyl halides. This protocol unifies the visible-light multiphoton catalytic cycle of [Ir(ppy)2(dtb-bpy)]+ with flow chemistry to engage energy demanding alkyl bromides and iodides at moderate pressures of carbon monoxide. The mild and practical methodology was employed to prepare a diverse array of 43 unsymmetric dialkyl ketones from primary, secondary and tertiary unactivated alkyl halides. We demonstrate the application of flow chemistry technology to achieve spatially resolved chemoselectivity, scalability and the generation of biologically relevant ketone products.
|
Jose Forni; Vir Gandhi; Anastasios Polyzos
|
Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-04-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625e21c1ed4d888741106713/original/carbonylative-olefin-hydroacylation-with-alkyl-halides-by-multiphoton-tandem-photoredox-catalysis-in-flow.pdf
|
65cd01c69138d231611fcba8
|
10.26434/chemrxiv-2024-s6n9r-v2
|
Interplay of Luminophores and Photoinitiators During Synthesis of Bulk and Patterned Luminescent Photopolymer Blends
|
Four-dimensional printing with embedded photoluminescence is emerging as an exciting area in additive manufacturing. Slim polymer films patterned with three-dimensional lattices of multimode, cylindrical waveguides (waveguide-encoded lattices, WELs) with enhanced fields of view can be fabricated by localizing light as self-trapped beams within a photopolymerizable formulation. Luminescent WELs have potential applications as solar cell coatings and smart, planar optical components. However, as luminophore-photoinitiator interactions are expected to change photopolymerization kinetics, the design of robust luminescent photopolymer sols is non-trivial. Here, we use model photopolymer systems based on methacrylate-siloxane and epoxide homopolymers, and their blends to investigate the influence of the luminophore Lumogen® Violet (LV) on the photolysis kinetics of the Omnirad™ 784 photoinitiator through UV/Vis absorbance spectroscopy. Initial rate analysis with different bulk polymers reveals differences in the first-order rate constants in the absence and presence of LV, with a notable increase (40%) in the photolysis rate for the 1:1 blend. Fluorescence quenching studies, coupled with density functional theory calculations, establish that these differences arise due to electron transfer from photoexcited LV to the ground state photoinitiator molecules. We also demonstrate an in-situ UV/Vis absorbance technique that enables real-time monitoring of both waveguide formation and photoinitiator consumption during the fabrication of WELs. The in-situ photolysis kinetics confirm that LV-photoinitiator interactions also influence the photopolymerization process during WEL formation. Our findings show that luminophores play a non-innocent role in photopolymerization and highlight the necessity for both careful consideration of the photopolymer formulation and a real-time monitoring approach to enable the fabrication of high-quality micropatterned luminescent polymeric films.
|
Helen Tunstall García; Takashi Lawson; Kathryn Benincasa; Andrew Prentice; Kalaichelvi Saravanamuttu; Rachel Evans
|
Polymer Science; Polymer blends; Polymerization (Polymers); Polymerization kinetics; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cd01c69138d231611fcba8/original/interplay-of-luminophores-and-photoinitiators-during-synthesis-of-bulk-and-patterned-luminescent-photopolymer-blends.pdf
|
64453a16e4bbbe4bbf21410f
|
10.26434/chemrxiv-2023-p8mb4
|
Discovery of Non-Classical Self-Assembly in Janus Particle-Based Surfactants and the Field-Triggered Breakdown of Surface Activity and Amphiphilic Properties
|
The use of colloidal particles as models to understand processes on a smaller size-scale is a highly valuable approach. Compared to molecules, particles are less defined but their architecture can be more complex, so is their long-range interaction. Sometimes one can observe phenomena which are unknown or much more difficult to realize on the molecular level. The current paper focuses on particle-based surfactants and reports about numerous unexpected properties. The main goal is the creation of an amphiphilic system with responsiveness in surface activity and associated self-organization phenomena depending on the application of an external trigger, preferably a physical field. A key step is the creation of a Janus-type particle characterized by two types of dipoles (electric and magnetic) which geometrically stand orthogonal to each other. In a field, one can control which contribution and which direction dominates the inter-particle interactions and as a result one can change the properties of the system drastically. The features of ferrite-core organosilica-shell particles with grain-like morphology modified by click chemistry is studied in response to spatially isotropic and anisotropic triggers. A highly unusual aggregation-dissolution-reaggregation sequence was discovered. Using a magnetic field, one can even switch off the amphiphilic properties and use this for the field-triggered breaking of multiphase systems such as emulsions.
|
Cornelia Lanz; Yasar Krysiak; Xu Liu; Manuel Hohgardt; Peter Jomo Walla; Sebastian Polarz
|
Physical Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Surfactants; Self-Assembly; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64453a16e4bbbe4bbf21410f/original/discovery-of-non-classical-self-assembly-in-janus-particle-based-surfactants-and-the-field-triggered-breakdown-of-surface-activity-and-amphiphilic-properties.pdf
|
60c73f1a0f50dbda44395732
|
10.26434/chemrxiv.7231058.v1
|
Random Forest Refinement of the KECSA2 Knowledge-based Scoring Function for Protein Decoy Detection
|
In this work, via the use
of the ‘comparison’ concept, Random Forest (RF) models were successfully
generated using unbalanced data sets that assign different importance factors
to atom pair potentials to enhance their ability to identify native proteins
from decoy proteins. Individual and combined data sets consisting of twelve
decoy sets were used to test the performance of the RF models. We find that RF
models increase the recognition of native structures without affecting their
ability to identify the best decoy structures. We also created models using
scrambled atom types, which create physically unrealistic probability
functions, in order to test the ability of the RF algorithm to create useful
models based on inputted scrambled probability functions. From this test we
find that we are unable to create models that are of similar quality relative
to the unscrambled probability functions. Next we created uniform probability
functions where the peak positions as the same as the original, but each
interaction has the same peak height. Using these uniform potentials we were
able to recover models as good as the ones using the full potentials suggesting
all that is important in these models are the experimental peak positions.
|
Jun Pei; Zheng Zheng; Kenneth M. Merz Jr.
|
Computational Chemistry and Modeling; Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-10-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1a0f50dbda44395732/original/random-forest-refinement-of-the-kecsa2-knowledge-based-scoring-function-for-protein-decoy-detection.pdf
|
6482d9dbbe16ad5c57af1937
|
10.26434/chemrxiv-2023-jsjwx
|
A Protein-Ligand Interaction-focused 3D Molecular Generative Framework for Generalizable Structure-based Drug Design
|
Deep generative models have been the subject of immense interest in various fields of science. While seeking a molecule that favorably binds to a target is a long-established goal of drug design, various generative models have emerged to reach the goal. Here, we employ the concept of intermolecular interactions between a protein and a ligand in a 3D molecular generative model, empowering the generalizable structure-based drug design. Inspired by how the practitioners manage to improve the potency of a ligand toward a target protein, we devised a strategy where prior knowledge of appropriate interactions navigates the ligand generation. We thus propose an interaction-focused generative framework, which establishes a local interaction condition to capture the surrounding pocket environment. We demonstrate that the condition enables precise control of ligand generation, justifying its effectiveness in guiding a ligand design inside a binding pocket. Through this strategy, the generated ligands could stably bind to the target pocket by forming favorable interactions, regardless of pocket type. Furthermore, we highlight the broad applicability of our framework by leveraging the site-specific interaction condition suitable for designing ligands for various purposes.
|
Wonho Zhung; Hyeongwoo Kim; Woo Youn Kim
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6482d9dbbe16ad5c57af1937/original/a-protein-ligand-interaction-focused-3d-molecular-generative-framework-for-generalizable-structure-based-drug-design.pdf
|
65b77e829138d23161f74850
|
10.26434/chemrxiv-2024-2qq61
|
Blocking Effects on the Hydrogen Oxidation Reaction on Polycrystalline Pt Electrodes
|
We report differential electrochemical mass spectrometry (DEMS) measurements on blocking effects induced by adsorbed CO or surface oxide on the hydrogen oxidation reaction (HOR) on a polycrystalline Pt electrode, comparing also with earlier results obtained on a thin-film Pt/Vulcan supported catalyst electrode.
|
Zenonas Jusys; R. Juergen Behm
|
Physical Chemistry; Physical and Chemical Processes
|
CC BY 4.0
|
CHEMRXIV
|
2024-01-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b77e829138d23161f74850/original/blocking-effects-on-the-hydrogen-oxidation-reaction-on-polycrystalline-pt-electrodes.pdf
|
6512de440065940912ea1aa6
|
10.26434/chemrxiv-2023-69qzs-v2
|
A prodrug activated by H2O2 and mitochondrial hydroxide: an improvement of cancer cells versus neutrophils selectivity
|
Many known chemotherapeutic anticancer agents exhibit neutropenia as a dose-limiting side effect. In this paper we suggest a prodrug concept solving this problem for camptothecin (HO-cpt). The prodrug is programmed according to Boolean “AND” logic. It requires for its activation the simultaneous presence of triggers T1 (H2O2) and T2 (pH 8 in mitochondria: Mit). The level of H2O2 in cancer cells is higher than that in normal cells. Thus, T1 discriminates cancer cells from the majority of normal cells excluding neutrophils, known to produce elevated levels of H2O2. T2 discriminates cancer cells from neutrophils, since the former cells have a higher number of Mit. We demonstrated that our prodrug exhibits antitumor activity both in vitro and in vivo, but is not toxic to normal cell and neutrophils in contrast to known single trigger prodrugs and the parent drug HO-cpt.
|
Insa Klemt; Viktor Reshetnikov; Subrata Dutta; Galyna Bila; Rostyslav Bilyy; Itziar Cossío Cuartero; Andrés Hidalgo; Adrian Wünsche; Maximilian Böhm; Marit Wondrak; Leoni Kunz-Schughart; Rainer Tietze; Frank Beierlein; Petra Imhof; Sabrina Gensberger-Reigl; Monika Pischetsrieder; Marlies Körber; Tina Jost; Andriy Mokhir
|
Biological and Medicinal Chemistry; Organic Chemistry; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6512de440065940912ea1aa6/original/a-prodrug-activated-by-h2o2-and-mitochondrial-hydroxide-an-improvement-of-cancer-cells-versus-neutrophils-selectivity.pdf
|
61dd577681f3fee94fa326f6
|
10.26434/chemrxiv-2022-kwv4b
|
Next-generation biomonitoring of the early-life chemical exposome in neonatal and infant development
|
Exposure to man-made and natural chemicals is a major, yet not sufficiently considered, environmental risk factor in the etiology of chronic diseases. Current human biomonitoring approaches typically measure a limited number of exposures rather than investigating complex mixtures. The latter would be fundamental and necessary for a holistic assessment of chemical exposure in exposome-wide association studies. In this work, an highly-sensitive liquid chromatography-tandem mass spectrometry approach was developed and thoroughly-validated. The assay enables the simultaneous and targeted assessment of more than 80 highly-diverse xenobiotics in the investigated body fluids of urine, serum/plasma, and breast milk; the detection limit for most toxicants are in the pg-ng/mL range. In the plasma of extremely-premature infants (gestational age <28 weeks, birth weight <1 kg) a total of 27 different xenobiotics are identified; including severe contamination with synthetic plasticizers, perfluorinated alkylated substances and parabens. In an independent sample set of breast milk that was longitudinally collected over the first 211 days post-partum, a total of 29 analytes is detected, including the first-ever identification of pyrrolizidine- and tropane alkaloids in this matrix. Based on the generated data, a preliminary estimation of daily toxicant intake via breast milk is conducted. In conclusion, our proof-of-principle experiments show significant early-life co-exposure to multiple toxicants, and demonstrate the method’s applicability in future large-scale exposomics-type cohort studies in vulnerable populations.
|
Thomas Jamnik; Mira Flasch; Dominik Braun; Yasmin Fareed; Daniel Wasinger; David Seki; David Berry; Angelika Berger; Lukas Wisgrill; Benedikt Warth
|
Analytical Chemistry; Earth, Space, and Environmental Chemistry; Agriculture and Food Chemistry; Analytical Chemistry - General; Environmental Analysis; Mass Spectrometry
|
CC BY 4.0
|
CHEMRXIV
|
2022-01-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61dd577681f3fee94fa326f6/original/next-generation-biomonitoring-of-the-early-life-chemical-exposome-in-neonatal-and-infant-development.pdf
|
60c75413469df40874f44e98
|
10.26434/chemrxiv.12480794.v2
|
Pillared Mo2TiC2 MXene for High-Power and Long-life Lithium and Sodium-ion Batteries
|
<p></p><p>In this work, we
apply an amine-assisted silica pillaring method to create the first example of a
porous Mo<sub>2</sub>TiC<sub>2 </sub>MXene with nanoengineered interlayer
distances. The pillared Mo<sub>2</sub>TiC<sub>2</sub> has a surface area of 202
m<sup>2</sup> g<sup>-1</sup>, which is among the highest reported for any MXene,
and has a variable gallery height between 0.7 and 3 nm. The expanded interlayer
distance leads to significantly enhanced cycling performance for Li-ion storage,
with superior capacities, rate capabilities and cycling stabilities in
comparison to the non-pillared version. The pillared Mo<sub>2</sub>TiC<sub>2</sub>
achieved capacities over 1.7 times greater than multilayered MXene at 20 mA g<sup>-1</sup>
(≈ 320
mAh g<sup>-1</sup>) and 2.5 times higher at 1 A g<sup>-1</sup> (≈ 150
mAh g<sup>-1</sup>). The fast-charging properties of pillared Mo<sub>2</sub>TiC<sub>2</sub>
are further demonstrated by outstanding stability even at 1 A g<sup>-1</sup>
(under 8 min charge time), retaining 80% of the initial capacity after 500
cycles. Furthermore, we use a combination of spectroscopic techniques (i.e.
XPS, NMR and Raman) to show unambiguously that the charge storage mechanism of
this MXene occurs by a conversion reaction through the formation of Li<sub>2</sub>O.
This reaction increases by 2-fold the capacity beyond intercalation, and
therefore, its understanding is crucial for further development of this family
of materials. In addition, we also investigate for the first time the sodium
storage properties of the pillared and non-pillared Mo<sub>2</sub>TiC<sub>2</sub>.</p><br /><p></p>
|
Philip
A. Maughan; Luc Bouscarrat; Valerie R. Seymour; Shouqi Shao; Sarah J Haigh; Richard Dawson; Nuria Tapia-Ruiz; Nuno Bimbo
|
Nanostructured Materials - Nanoscience; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75413469df40874f44e98/original/pillared-mo2ti-c2-m-xene-for-high-power-and-long-life-lithium-and-sodium-ion-batteries.pdf
|
628b165e59f0d64ce39a2491
|
10.26434/chemrxiv-2022-g7mfn
|
Molecular-Property Prediction with Sparsity
|
Machine learning models for molecular-property prediction typically work with molecular
representations in the form of fingerprints, descriptors, or graphs. In case of fingerprints
and descriptors, molecular representations usually comprise thousands of features, which
causes the curse of dimensionality for many tabular models. In this work, we introduce
penalized linear models enforcing sparsity on grouped molecular representations. Loosely
speaking, sparsity penalties aim to select a relatively small number of features to improve
the interpretability and computational convenience of machine learning models.
|
Sanjar Adilov
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence
|
CC BY 4.0
|
CHEMRXIV
|
2022-05-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628b165e59f0d64ce39a2491/original/molecular-property-prediction-with-sparsity.pdf
|
6338de46975e943145903382
|
10.26434/chemrxiv-2022-6c4p3-v2
|
Electrochemical and Degradation Studies on One-Dimensional Tunneled Sodium Zirconogallate + Yttria-Stabilized Zirconia Composite, Mixed Sodium and Oxygen Ion Conductor
|
In recent years, multi-phase materials capable of multi-ion transport have emerged as attractive candidates for a variety of electrochemical devices. Here, we provide experimental results for fabricating a composite electrolyte made up of a one-dimensional fast sodium-ion conductor, sodium zirconogallate, and an oxygen-ion conductor, yttria-stabilized zirconia. The composite is synthesized through a vapor phase conversion mechanism, and the kinetics of this process are discussed in detail. The samples are characterized using diffraction, electron microscopy, and electrochemical impedance spectroscopy techniques. Samples with a finer grain structure exhibit higher kinetic rates due to larger three-phase boundaries (TPBs) per unit area. The total conductivity is fitted to an Arrhenius type equation with activation energies ranging from 0.23 eV at temperatures below 550 °C to 1.07 eV above 550 °C. The electrochemical performance of multi-phase multi-species, mixed sodium- and oxygen-ion conductors, is tested under both oxygen chemical potential gradient as well as sodium chemical potential gradient, before and after reaching equilibrium, are discussed using the Goldman-Hodgkin-Kats (GHK) and the Nernst equation. The total conductivity of the degraded cathode and anode terminals is investigated using electrochemical impedance spectroscopy. The degradation investigation of samples indicates a decrease in conductivity adjacent to the anode terminal, the loss of sodium content, and the formation of β-gallia adjacent to the fuel electrode after ~396h at 1463 K.
|
POOYA ELAHI; Jude A. Horsley; Taylor D. Sparks
|
Physical Chemistry; Materials Science; Inorganic Chemistry; Ceramics; Composites; Electrochemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-10-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6338de46975e943145903382/original/electrochemical-and-degradation-studies-on-one-dimensional-tunneled-sodium-zirconogallate-yttria-stabilized-zirconia-composite-mixed-sodium-and-oxygen-ion-conductor.pdf
|
634f81713e8d996c7e1f82bd
|
10.26434/chemrxiv-2022-2kd0k
|
Chemical fuel-driven dissipative living materials
|
Dissipative behaviors in biology are fuel-driven processes controlled by living cells and shape the structural and functional complexities in biological materials. It has inspired the development of various forms of synthetic dissipative materials controlled by time-dependent consumption of chemical or physical fuels, such as reactive chemical species, light, and electricity. To this date, synthetic living material featuring dissipative behaviors directly controlled by the fuel consumption of their constituent cells is unprecedented. In this paper, we report a chemical fuel-driven dissipative behavior of living materials comprising S. epidermidis and telechelic block copolymers. The macroscopic phase transition is controlled by D-glucose which serves a dual role of a competitive disassembling agent and a biological fuel source for living cells. Our work is a significant step towards constructing a synthetic dissipative living system and provides a new tool and knowledge to design emergent living materials.
|
Hyuna Jo; Serxho Selmani; Zhibin Guan; Seunghyun Sim
|
Polymer Science; Hydrogels; Organic Polymers; Polymer scaffolds; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634f81713e8d996c7e1f82bd/original/chemical-fuel-driven-dissipative-living-materials.pdf
|
61e116a977a4166a71d0acd8
|
10.26434/chemrxiv-2022-1fvp4
|
A Theoretical Study of Tridentenes
|
As substances corresponding to annulenes in Y-aromatic compounds, tridentenes were proposed by the authors. In this description, by revision of existing papers, a discussion on the magic number of tridentenes, which corresponds to Hückel’s 4N+2 rule, and arguments regarding typhoon tridentene and cyclone tridentene, which are expected to have stereoselective inclusion forming ability, are presented.
|
OHMAE TAKAYUKI OHMAE
|
Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-01-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e116a977a4166a71d0acd8/original/a-theoretical-study-of-tridentenes.pdf
|
60c74cb54c891916faad36c2
|
10.26434/chemrxiv.7498622.v2
|
Conductivity and Photoconductivity of a p-type Organic Semiconductor under Ultra-Strong Coupling
|
It
has been shown that light-matter strong coupling of materials can lead to
modified and often improved properties which has stimulated considerable
interest. While charge transport can be enhanced in n-type organic
semiconductors by coupling the electronic transition and thereby splitting the
conduction band into polaritonic states, it is not clear whether the same
process can also influence carrier transport in the valence band of p-type
semiconductors. Here we demonstrate for the first time that it is indeed
possible to enhance both the conductivity and photoconductivity of a p-type
semiconductor rr-P3HT that is ultra-strongly coupled to plasmonic modes. It is
due to the hybrid light-matter character of the virtual polaritonic excitations
affecting the linear-response of the material. Furthermore, in addition to
being enhanced, the photoconductivity of rr-P3HT shows modified spectral
response due to the formation of the hybrid polaritonic states. This
illustrates the potential of engineering the vacuum electromagnetic environment
to improve the opto-electronic properties of organic materials.
|
Kalaivanan Nagarajan; Jino George; Anoop Thomas; Eloïse Devaux; Thibault Chervy; Stefano Azzini; Jouaiti Aziz; Mir Wais Hosseini; Anil Kumar; Cyriaque Genet; Nicola Bartolo; Cristiano Ciuti; Thomas Ebbesen
|
Conducting polymers
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cb54c891916faad36c2/original/conductivity-and-photoconductivity-of-a-p-type-organic-semiconductor-under-ultra-strong-coupling.pdf
|
665de4dc418a5379b0ff1734
|
10.26434/chemrxiv-2024-hf8jh
|
Theoretical Investigation of Interactions between HIV-1 Tat and p53 proteins
|
HIV-1 Tat (transactivator of transcription) protein is the main arsenal of HIV, playing numerous roles during viral infection. This protein is inherently disordered, lacking any secondary structures. This plasticity allows HIV-1 Tat to engage in interaction with multiple proteins and biological molecules, resulting in either collapse of the immune system or severe damage to tissues. Proteomic studies previously revealed p53, commonly cited as the guardian angel of the genome to interact with the Tat protein through its tetramerization domain. As p53 is crucial in terms of whether the cell dies or lives, its interaction with the Tat protein is of broad interest in the pathogenesis of HIV infection. For this reason, we investigated the complexation between the Tat protein and the tetramerization domain of p53 using molecular docking and molecular dynamics simulations. We believe that the results reported in this manuscript are of great significance for developing novel therapeutic agents targeting the p53/Tat interaction.
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Sinem Koseoglu; Cansu Yenici; Sena Celikbas; Serra Aygun; Y. Dicle Altun; Sefer Baday; Onur Alpturk
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Theoretical and Computational Chemistry; Biological and Medicinal Chemistry
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CC BY 4.0
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CHEMRXIV
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2024-06-04
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665de4dc418a5379b0ff1734/original/theoretical-investigation-of-interactions-between-hiv-1-tat-and-p53-proteins.pdf
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659f21fc66c138172929b894
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10.26434/chemrxiv-2024-1ls4s
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Bismaleimide - Aluminium sulphate blends as 3D printing ink
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Aluminium Sulphate (AS) used a precursor for Al based compounds has the capabilities of flocculation and coagulation imparting strength to the material it gets added to. Bismaleimide (BMI) on the other hand is a high temperature resin used for aerospace applications. An AS-BMI resin has therefore been studied in this communication having potential application as a 3D printing ink
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Arnab Bhattacharyya; Tridha Ghosh; Priyanshu Kumar
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Materials Science; Polymer Science; Composites; Inorganic Polymers; Materials Chemistry
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CC BY 4.0
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CHEMRXIV
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2024-01-12
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659f21fc66c138172929b894/original/bismaleimide-aluminium-sulphate-blends-as-3d-printing-ink.pdf
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60c74755702a9b311e18ad92
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10.26434/chemrxiv.11634786.v1
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On the Terrestrial Gravitational Bending of Quantum Fields during Optics, Enzymatics and Catalyses of Biomolecular and Nanoscale Chemical Reactions
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<div>The death of cancer cells under zero gravity or simulated zero gravity has an unknown cause. A prior theory of gravity by fractional, reversible fissing of matter and fusing of space to target is presented for explaining this mystery of gravitational killing of cancer cells. With this new theory a new math of divergent differentiations and divergent integrations are outlined to explain mysteries. By the mechanism given the variation in source gravity as computed by the new math can thereby explain effects on biology as the biology and chemistry have divergent differentiations and divergent integrations, which couple source of gravities and couple changing gravities to surrounding spaces and targets in surrounding spaces. Greater effects of</div><div>gravities in nano-scales than molecular scales are reasoned as nano-sizes have mass effects and greater collectivity relative to molecular scales. The mechanism also postulates superluminosity of rare with slowing to luminous with denseness (space reversal) for explaining inertia, denseness and back and forth time reversal. The loss of inertia due to space reversal is reasoned! Mass to energy and vice versa dynamics are involved relativistically. By such new mechanics there are differences in denseness as the superlumes fiss to rare so surrounding rare can couple and the superluminous rare concentrates to slow so as to couple to dense. There are limits of such superluminosity as by the vast distances and the vast, composite, dense spaces of matter and the slowness (inertia). These new mechanics of composite matter/space manifest group dispersion (by new divergent calculus) as provided by hidden mechanics as by self-interacting self-deforming conformations to explain observable phase dispersed (older calculus). The observables are manifested by phase dispersions of matter and space as by new divergent calculus via constructive self interactions. The new math is contrasted with the Newtonian integrals and derivatives, which are more finite in actions and consequences whereas the divergent integrals and divergent differentiations are more ∞ in actions and consequences. If dynamic ∞ and count ∞, then the counting and mechanics can be as demonstrated here by many ∞(s) or counter ∞(s).</div>
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Reginald Little
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Biophysical Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2020-01-20
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74755702a9b311e18ad92/original/on-the-terrestrial-gravitational-bending-of-quantum-fields-during-optics-enzymatics-and-catalyses-of-biomolecular-and-nanoscale-chemical-reactions.pdf
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670c036212ff75c3a14f1f09
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10.26434/chemrxiv-2024-nkmq7-v2
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A Comparison of Modern Solvation Models for Oxygen Reduction at the Pt(111) Interface
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Solvation effects play an important role in the thermodynamics of catalytic reactions, however, current implicit solvation models often fail to accurately capture specific local effects, such as hydrogen bonding, limiting their ability to systematically incorporate solvation effects into quantum mechanical simulations. In this study, we investigate the Reference Interaction Site Model (RISM) and apply it to the Platinum (111) interface, using the Oxygen Reduction Reaction as a case study. We compare RISM to the Charge-Asymmetric Nonlocally Determined Local-Electric (CANDLE) solvation model, which belongs to the class of Poisson-Boltzmann models. Our results demonstrate that RISM, with the appropriately parametrized water model, can accurately describe properties of the solvated Pt(111) surface such as solvation free energies, workfunctions, capacitances and capture subtle effects due to electrolyte concentration and explicit adsorbates. We find that including lone pairs in the water model proves to be crucial for obtaining accurate results, highlighting the importance of water non-bonding orbitals in solvation effects at the Pt(111) interface. Furthermore, RISM enables the computation of previously inaccessible properties, such as the solvent/electrolyte density near charged electrodes, providing valuable insights into the electrochemical double layer structure. Our findings suggest that RISM could serve as a computationally efficient alternative for studying electrode-electrolyte interfaces, paving the way for systematically incorporating solvation effects into computational studies.
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Tom Demeyere; Chris-Kriton Skylaris
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Theoretical and Computational Chemistry; Catalysis; Electrocatalysis; Heterogeneous Catalysis
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CC BY 4.0
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CHEMRXIV
|
2024-10-16
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670c036212ff75c3a14f1f09/original/a-comparison-of-modern-solvation-models-for-oxygen-reduction-at-the-pt-111-interface.pdf
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66fde74e51558a15efe4159a
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10.26434/chemrxiv-2024-g2pzn
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Selection of two types of self-assembled configurational isomers from a dynamic library via a multivariant optimization process
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Mimicking biological functions using simple artificial molecules is a rational approach to understanding complicated phenomena in living systems. Selection of a suitable species from a library in response to external stimuli is a key event in evolution, adaptation, and switching. In this study, we developed an artificial molecular system in which two types of self-assemblies were selected from a dynamic library consisting of configurational isomers of hexameric cube-shaped entities assembled from CS-symmetric gear-shaped amphiphiles (GSAs) upon binding mainly two or three template guest molecules. Selection in the energy landscape of dynamic equilibrium occurs via multivariant optimization of the spatial arrangements of GSAs and guest molecules in the cavities of assemblies. Certain guest molecules induced both types of assemblies, and their distributions were controlled by the temperature and the guest concentration.
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Hongye Chen; Shuichi Hiraoka
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Organic Chemistry; Supramolecular Chemistry (Org.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-10-04
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fde74e51558a15efe4159a/original/selection-of-two-types-of-self-assembled-configurational-isomers-from-a-dynamic-library-via-a-multivariant-optimization-process.pdf
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66d8e9d9cec5d6c14228025f
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10.26434/chemrxiv-2024-0ldq8
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Macroscopic Assembly of Materials with Engineered Bacterial Spores via Coiled-Coil Interaction
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Herein, we report macroscopic materials formed by an assembly of engineered bacterial spores. Spores were engineered using a T7-driven expression system to display a high density of pH-responsive self-associating proteins on their surface. The engineered surface protein on the spore surface enabled pH-dependent binding at the protein level and enabled the assembly of granular materials. Mechanical properties remained largely constant with changing pH, but erosion stability was pH-dependent in a manner consistent with the pH-dependent interaction between the A-coils. Our finding utilizes synthetic biology for designs of macroscopic materials and illuminates the impact of coiled-coil interaction across various length scales.
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Lucas Korbanka; Ju-An Kim; Seunghyun Sim
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Materials Science; Biological Materials; Granular Materials; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-09-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d8e9d9cec5d6c14228025f/original/macroscopic-assembly-of-materials-with-engineered-bacterial-spores-via-coiled-coil-interaction.pdf
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6148c3e8b1d4a6e3068e132e
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10.26434/chemrxiv-2021-c13nz
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Discovery and characterization of benzyloxy piperidine based dopamine 4 receptor antagonists
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Abstract: The dopamine receptor 4 (D4R) is highly expressed in both motor, associative and limbic subdivisions of the coritico-basal ganglia network. Due to the distribution in the brain, there is mounting evidence pointing to a role for the D4R in the modulation of this network and its subsequent involvement in L-DOPA induced dyskinesias in Parkinson’s disease. As part of our continued effort in the discovery of novel D4R antagonists, we report the discovery and characterization of a new 3- or 4-benzyloxypiperidine scaffold as D4R antagonists. We report several D4R selective compounds (>30-fold vs. other dopamine receptor subtypes) with improved in vitro and in vivo stability over previously reported D4R antagonists.
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Kirsten Tolentino; Viktoriya Mashinson; Anish Vadukoot; Corey Hopkins
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Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems
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CC BY NC 4.0
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CHEMRXIV
|
2021-09-22
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6148c3e8b1d4a6e3068e132e/original/discovery-and-characterization-of-benzyloxy-piperidine-based-dopamine-4-receptor-antagonists.pdf
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