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60c73db6f96a00d1ea285e04 | 10.26434/chemrxiv.6025658.v1 | Activation of CO2 at Chromia-Nanocluster-Modified Rutile and Anatase TiO2 | Converting CO<sub>2</sub>
to fuels is required to enable the production of sustainable fuels and to
contribute to alleviating CO<sub>2</sub> emissions. In considering conversion
of CO<sub>2</sub>, the initial step of adsorption and activation by the catalyst
is crucial. In addressing this difficult problem, we have examined how
nanoclusters of reducible metal oxides supported on TiO<sub>2</sub> can promote
CO<sub>2</sub> activation. In this paper we present density functional theory
(DFT) simulations of CO<sub>2</sub> activation on heterostructures composed of extended
rutile and anatase TiO<sub>2</sub> surfaces modified with chromia nanoclusters.
The heterostructures show non-bulk Cr and O sites in the nanoclusters and an
upshifted valence band edge that is dominated by Cr 3d- O 2p interactions. We
show that the supported chromia nanoclusters can adsorb and activate CO<sub>2 </sub>and
that activation of CO<sub>2</sub> is promoted whether the TiO<sub>2</sub>
support is oxidised or hydroxylated. Reduced heterostructures, formed by
removal of oxygen from the chromia nanocluster, also promote CO<sub>2</sub>
activation. In the strong CO<sub>2</sub> adsorption modes, the molecule bends
giving O-C-O angles of 127 - 132<sup>o</sup> and elongation of C-O distances up
to 1.30 Å; no carbonates are formed. The electronic properties show a strong CO<sub>2</sub>-Cr-O
interaction that drives the interaction of CO<sub>2</sub> with the nanocluster
and induces the structural distortions. These results highlight that a metal
oxide support modified with reducible metal oxide nanoclusters can activate CO<sub>2</sub>,
thus helping to overcome difficulties associated with the difficult first step
in CO<sub>2</sub> conversion. | Michael Nolan; Marco Fronzi | Catalysts; Nanocatalysis - Catalysts & Materials; Computational Chemistry and Modeling; Theory - Computational; Heterogeneous Catalysis; Photocatalysis; Catalysis; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2018-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73db6f96a00d1ea285e04/original/activation-of-co2-at-chromia-nanocluster-modified-rutile-and-anatase-ti-o2.pdf |
60c755ec469df45588f45227 | 10.26434/chemrxiv.14184929.v1 | Increased Antibacterial Properties of Indoline-Derived Phenolic Mannich Bases | <p>The search for antibacterial agents for the combat
of nosocomial infections is a timely problem, as antibiotic-resistant bacteria continue
to thrive. The effect of indoline substituents on the antibacterial properties
of aminoalkylphenols was studied, leading to the development of a library of
compounds with minimum inhibitory concentrations (MICs) as low as 1.18 µM. Two novel aminoalkylphenols were identified as particularly promising,
after MIC and minimum bactericidal concentrations (MBC) determination against a
panel of reference strain Gram-positive bacteria, and further confirmed against
40 clinical isolates (<i>Staphylococcus
aureus</i>, <i>S. epidermidis</i>, <i>Enterococcus</i> <i>faecalis</i>,<i> E. faecium</i>, and<i> Listeria monocytogenes</i>). The same two
aminoalkylphenols displayed low toxicity against two <i>in vivo</i> models (<i>Artemia salina</i> brine shrimp and <i>Saccharomyces cerevisiae</i>)<i>.
</i>The <i>in vitro</i> cytotoxicity evaluation
(on human keratinocytes and human embryonic lung fibroblast cell lines)
of the same compounds was also carried out. They demonstrated a particularly
toxic effect on the fibroblast cell lines, with IC<sub>50</sub> in the 1.7-5.1 mM range, thus narrowing their
clinical use. The desired increase in the antibacterial properties of the
alkylaminophenols, particularly indoline-derived phenolic Mannich bases, was
reached by introducing an additional nitro group in the indolinyl substituent
or by the replacement of a methyl by a bioisosteric trifluoromethyl substituent.
Notably, the introduction of an additional nitro moiety did not confer added
toxicity to the alkylaminophenols.</p> | Tatu Rimpilainen; Alexandra Nunes; Rita Calado; Ana Fernandes; Joana Andrade; Epole Ngolle; Gabriella Spengler; Nikoletta Szemeredi; João Rodrigues; João Paulo Gomes; Patricia Rijo; Nuno Candeias | Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755ec469df45588f45227/original/increased-antibacterial-properties-of-indoline-derived-phenolic-mannich-bases.pdf |
66cc4e18f3f4b052902499bf | 10.26434/chemrxiv-2024-qmvlw | Effect of Particle Size and Alloying with Gallium and Zinc in Copper Nanoparticles from Ab Initio Molecular Dynamics | Supported nanoparticles (NPs) are an intense field of research in both industry and academia due to their unique catalytic properties in particular. Yet, establishing relationships between structure and activity has remained a challenge due to multiple possible compositions, interfaces, and even alloy formation. This is especially pronounced for bimetallic NPs used in CO2 hydrogenation to methanol, where the structure responds dynamically to the chemical potential of the reactants and products, resulting in distinct surface structures depending on the exact reaction conditions. These phenomena have been highlighted by combining ab initio Molecular Dynamics (AIMD) and Metadynamics (MTD) in conjunction with in situ X-ray absorption spectroscopy, chemisorption, and CO-IR. Here, we aim to understand how particle size and simulation temperature influence the structure and dynamics of small Cu NPs using the diffusion coefficients and the radial distribution function/atomic pair density function as descriptors using unbiased AIMD simulations. We found that decreasing the particle size or increasing the simulation temperature results in increased atom mobility, highlighted by the increased metal diffusion and resulting in decreased particle crystallinity. We also find that alloying Cu with Ga significantly increases the diffusion of both elements in the particle compared to the monometallic ones, while such diffusion lies in between the individual elements composing the CuZn particles. | Andreas Müller; Aleix Comas-Vives; Christophe Copéret | Theoretical and Computational Chemistry; Catalysis; Theory - Computational; Heterogeneous Catalysis; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-08-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cc4e18f3f4b052902499bf/original/effect-of-particle-size-and-alloying-with-gallium-and-zinc-in-copper-nanoparticles-from-ab-initio-molecular-dynamics.pdf |
60c74930bdbb8928ffa39104 | 10.26434/chemrxiv.12040398.v1 | Enantioselective C(sp3)–C(sp3) Cross-Coupling of Non-activated Alkyl Electrophiles via Nickel Hydride Catalysis | Cross-coupling of two alkyl fragments is an
efficient method to produce organic molecules rich in sp<sup>3</sup>-hydridized
carbon centers, which are attractive candidate compounds in drug discovery.
Enantioselective C(sp<sup>3</sup>)-C(sp<sup>3</sup>) coupling, especially of
alkyl electrophiles without an activating group (aryl, vinyl, carbonyl) is
challenging. Here we report a strategy based on nickel hydride addition to
internal olefins followed by nickel-catalyzed alkyl-alkyl coupling. This
strategy enables enantioselective cross-coupling of non-activated alkyl iodides
with alkenyl boronates to produce chiral alkyl boronates. Employing readily
available and stable olefins as pro-chiral nucleophiles, the coupling proceeds
under mild conditions and exhibits broad scope and high functional group
tolerance. Applications in late-stage functionalization of natural products and
drug molecules, synthesis of chiral building blocks, and enantioselective
formal synthesis of (<i>S</i>)-(+)-Pregabalin are demonstrated.<br /> | Srikrishna Bera; Runze Mao; Xile Hu | Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74930bdbb8928ffa39104/original/enantioselective-c-sp3-c-sp3-cross-coupling-of-non-activated-alkyl-electrophiles-via-nickel-hydride-catalysis.pdf |
65db553a66c13817297f2cc2 | 10.26434/chemrxiv-2024-zpfbx | Highly Stable CsPbBr3@MoS2 Nanostructures: Synthesis and Optoelectronic Properties Towards Implementation into Solar Cells | Halide perovskites (HPs) have gained significant interest in the scientific and technological sectors due to their unique optical, catalytic, and electrical characteristics. However, the HPs are prone to decomposition when exposed to air, oxygen, or heat. The instability of HP materials limits their commercialization, prompting significant efforts to address and overcome these limitations. Meanwhile, the transition metal dichalcogenides, such as MoS2, are chemically stable and offer versatile properties suitable for electronic, optical, and catalytic applications. The layered structure of MoS2 allows for the development of protective coatings for other nanoparticles. In this study, we successfully synthesized a novel CsPbBr3@MoS2 core-shell nanostructure (CS-NS) by enveloping CsPbBr3 within a MoS2 shell for the first time. We also demonstrate a significant enhancement in the stability of CS-NSs when dispersed in polar solvents for extended periods. Remarkably, the hybrid CS-NSs exhibits an absorption spectrum closely aligned with MoS2 and photoluminescence (PL) quenching, indicating the potential for charge or energy transfer. We used finite difference time domain (FDTD) simulations to evaluate the efficiency of CS-NS-based solar cells and their potential for performance enhancement. This groundbreaking CS-NSs represents a significant advancement in harnessing halide perovskite materials for applications in photovoltaics and various optoelectronic devices. | Achiad Goldreich; Jonathan Prilusky; Neena Prasad; Lena Yadgarov | Materials Science; Nanoscience; Core-Shell Materials; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65db553a66c13817297f2cc2/original/highly-stable-cs-pb-br3-mo-s2-nanostructures-synthesis-and-optoelectronic-properties-towards-implementation-into-solar-cells.pdf |
631afd3cbada38d3bbbeb473 | 10.26434/chemrxiv-2022-w59zp | Massively Parallel Fragment-Based Quantum Chemistry for Large Molecular Systems: The Serestipy Software | We describe the Serestipy software, which is an add-on to the quantum-chemistry program Serenity. Serestipy is a representational-state transfer-oriented application programming interface written in the Python programming language enabling parallel subsystem density-functional theory calculations. We introduce approximate strategies in the context of frozen-density embedding time-dependent density-functional theory to make parallel large-scale excited-state calculations feasible. Their accuracy is carefully benchmarked with calculations for large assemblies of porphine molecules. We apply this framework to a theoretical model nanotube consisting of rings of porphine monomers, with 12,160 atoms (or 264,960 basis functions) in total. We obtain its electronic structure and absorption spectrum in less than a day of computation time.
| Patrick Eschenbach; Niklas Niemeyer; Johannes Neugebauer | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631afd3cbada38d3bbbeb473/original/massively-parallel-fragment-based-quantum-chemistry-for-large-molecular-systems-the-serestipy-software.pdf |
66eb3c4812ff75c3a1bcd800 | 10.26434/chemrxiv-2024-5mlml | Base-free palladium-catalyzed borylation of enol carboxylates and further reactivity toward deboronation and cross-coupling | A series of base-free Pd-catalyzed borylation procedures are reported for a number of alkenyl carboxylates. High-throughput experimentation was used to discover and optimize these reactions using in situ generated catalyst systems. With lactone or lactam substrates, the resulting alkenyl pinacol boronates are hydrolytically unstable, undergoing protodeboronation under even mildly basic aqueous conditions. Optimization of this protodeboronation resulted in a mild, two-step reduction of the C–O bond, achieving net-deoxygenation while leaving the alkene intact. In contrast, use of an alternative tetraalkoxydiboron source – B2EPin2 – was successful in catalysis, and offered improved stability of the resulting organoboron species. This enables further reactivity, such as cross-coupling, while suppressing protodeboronation. | Gregory Gaube; Douglas Miller; Rowan McCallum; Nahiane Pipaon Fernandez; David Leitch | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66eb3c4812ff75c3a1bcd800/original/base-free-palladium-catalyzed-borylation-of-enol-carboxylates-and-further-reactivity-toward-deboronation-and-cross-coupling.pdf |
6697955cc9c6a5c07a858675 | 10.26434/chemrxiv-2023-56kdv-v3 | A benchmark study of dioxygen complexes based on coupled cluster and density functional theory | A set of five compounds containing peroxo, superoxo or bis-mu-oxo moieties has been studied in the gas phase using CCSD(T)/aug-cc-pVQZ, also in combination with Goodson’s continued fraction approach. The corresponding analytical frequencies corroborate assignments of bands from experiments, and thus provide a consistent set of reference data that can be used for benchmarking a range of density functional approximations. A total of 100 density functionals have been checked for the general bond lengths, the specific peroxo/superoxo bond lengths, angles, and vibrational frequencies. There is not one density functional that performs equally well for all of these properties, not even within one class of density functionals. | Marcel Swart; Marc Reimann | Theoretical and Computational Chemistry; Inorganic Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6697955cc9c6a5c07a858675/original/a-benchmark-study-of-dioxygen-complexes-based-on-coupled-cluster-and-density-functional-theory.pdf |
6661ca8791aefa6ce1ebf01e | 10.26434/chemrxiv-2024-qmb1s-v2 | Unified, Biosynthesis-Inspired, Completely Stereocontrolled Total Synthesis of All Highest-Order [n+1] Oligocyclotryptamine Alkaloids | We describe the unified enantioselective total synthesis of the polycyclotryptamine natural products (+)-quadrigemine H, (+)-isopsychotridine C, (+)-oleoidine, and (+)-caledonine. Inspired by our hypothesis for the biogenesis of these alkaloids via an iterative concatenative addition of homochiral cyclotryptamines to a meso-chimonanthine headcap, we leverage the modular, diazene-directed assembly of stereodefined cyclotryptamines to introduce successive C3a−C7' quaternary stereocenters on a heterodimeric meso-chimonanthine surrogate with full stereochemical control at each quaternary linkage. We developed a new strategy for iterative aryl-alkyl diazene synthesis using increasingly complex oligomeric hydrazide nucleophiles and a bifunctional cyclotryptamine bearing a C3a leaving group and a pendant C7 pronucleophile. The utility of this strategy is demonstrated by the first total synthesis of heptamer (+)-caledonine and hexamer (+)-oleoidine. Enabled by our completely stereoselective total syntheses and expanded characterization data sets, we provide the first complete stereochemical assignment of pentamer (+)-isopsychotridine C, provide evidence that it is identical to the alkaloid known as (+)-isopsychotridine B, and report that tetramer (+)-quadrigemine H is identical to the alkaloid called (+)-quadrigemine I, resolving longstanding questions about the structures of the highest-order [n+1] oligocyclotryotamine alkaloids. | Tony Scott; Mohammad Movassaghi | Organic Chemistry; Natural Products; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6661ca8791aefa6ce1ebf01e/original/unified-biosynthesis-inspired-completely-stereocontrolled-total-synthesis-of-all-highest-order-n-1-oligocyclotryptamine-alkaloids.pdf |
6560c13c29a13c4d47e62d0b | 10.26434/chemrxiv-2023-0rcr2 | Computational screening of chemical properties of molecule based on DFT Homo & Lumo through python tool. | Computational chemistry software designed to compute the chemical properties of compounds falls under the category of dry research. The computational calculation of chemicals is a broad term. In this current study, chemical properties are estimated through computational methods, which is valuable for newly synthesis and altering chemicals compounds. After successful operation, computational chemistry software generates a log file. This newly developed software has interoperability with the density-functional theory software output file. Take only two inputs from the end user i.e. highest occupied molecule orbital (HOMO) and lowest un-occupied molecular orbital (LUMO) value and process on them; through this an automated, open source toolkit following outputs are prompt as a result: ionization energy, electron affinity, hardness, chemicalpotential, electronegativity and softness, electrophilicity index. Each parameter has its own unique value in chemistry. The acceptable result is 99.1 percent confidence interval. | Muhammad Aziz | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6560c13c29a13c4d47e62d0b/original/computational-screening-of-chemical-properties-of-molecule-based-on-dft-homo-lumo-through-python-tool.pdf |
60c7410b842e654ebfdb1de9 | 10.26434/chemrxiv.7295585.v2 | Comment on “Probing the Origins of Photodegradation in Organic- Inorganic Metal Halide Perovskites with Time-Resolved Mass Spectrometry”, Sustainable Energy & Fuels, 2018. | <div>This is a comment on an article in Sustainable Energy & Fuels reporting time-resolved mass spectrometry (MS) of
evolved gas species during photo-induced degradation of
methylammonium lead iodide perovskite (MAPbI3
).</div><div><br /></div><div>Note:<br /></div><div><br /></div><div>The authors of the commented article released a response to these observations on February 1, 2019. This document has been updated including new comments to their response on March 13, 2019, see page 4. For the original version of this comment, please see version 1.<br /><br /></div> | Emilio Jose Juarez-Perez | Hybrid Organic-Inorganic Materials; Mass Spectrometry; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7410b842e654ebfdb1de9/original/comment-on-probing-the-origins-of-photodegradation-in-organic-inorganic-metal-halide-perovskites-with-time-resolved-mass-spectrometry-sustainable-energy-fuels-2018.pdf |
62b2dc4b7da6ce2ddb1b3264 | 10.26434/chemrxiv-2022-qqxd1 | Data-driven multi-objective optimization tactics for catalytic asymmetric reactions | Optimization of catalyst structure to simultaneously improve multiple reaction objectives (e.g., yield, enantio-, and regioselectivity) remains a formidable challenge. Herein, we describe a machine learning workflow for the multi-objective optimization of catalytic reactions that employ chiral bisphosphine ligands. This was demonstrated through the optimization of two sequential reactions required in the asymmetric synthesis of an active pharmaceutical ingredient. To accomplish this, a density functional theory-derived database of >500 bisphosphine ligands was constructed and a designer chemical space mapping technique was established. The protocol used classification methods to identify active catalysts, followed by linear regression to model reaction selectivity. This led to the prediction and validation of significantly improved ligands for all reaction outputs suggesting a general strategy for the optimization of reactions where performance is controlled by bisphosphine ligands.
| Jordan Dotson; Lucy van Dijk; Jacob Timmerman; Samantha Grosslight; Richard Walroth; Kurt Püntener; Francis Gosselin; Kyle Mack; Matthew Sigman | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Machine Learning; Catalysis | CC BY 4.0 | CHEMRXIV | 2022-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b2dc4b7da6ce2ddb1b3264/original/data-driven-multi-objective-optimization-tactics-for-catalytic-asymmetric-reactions.pdf |
6606688b66c13817292809df | 10.26434/chemrxiv-2024-jqkjv | ARKA: A framework of dimensionality reduction for machine-learning classification modeling, risk assessment, and data gap-filling of sparse environmental toxicity data | Toxicity assessment of environmental chemicals is an integral aspect of assessing the sustainability of flora and fauna constituting the aquatic and terrestrial ecosystems. A wide variety of living organisms are constantly being exposed to these chemicals, most of which generate toxic effects. Due to the lack of experimental toxicity data of environmental chemicals, there arises a need to fill data gaps by in silico approaches. One of the most commonly used in silico approaches for toxicity assessment of small datasets is the Quantitative Structure-Activity Relationship (QSAR), which generates predictive models for the efficient prediction of query compounds. However, the predictions from these models are often erroneous for some compounds, and the reliability of the predictions from QSARs derived from small datasets is often questionable from a statistical point of view. This is due to the presence of a larger number of descriptors as compared to the number of training compounds, which reduces the degree of freedom of the developed model. To reduce the overall prediction error for a particular QSAR model, we have proposed here the computation of the novel Arithmetic Residuals in K-groups Analysis (ARKA) descriptors. We have reduced the number of modeling descriptors, keeping the entire chemical space and preventing the loss of chemical information. We have used here five representative environmentally relevant endpoints (skin sensitization, earthworm toxicity, milk/plasma partitioning, algal toxicity, and rodent carcinogenicity of hazardous chemicals) with graded responses to which the ARKA framework was applied for classification modeling. On comparing the performance of the models generated using conventional QSAR descriptors and the ARKA descriptors, the prediction quality of the models derived from ARKA descriptors was found much better than the models derived from QSAR descriptors signifying the potential of ARKA descriptors in ecotoxicological classification modeling of small data sets. For the ease of users, a Java-based expert system has been developed that computes the ARKA descriptors from the input of QSAR descriptors. | Arkaprava Banerjee; Kunal Roy | Theoretical and Computational Chemistry; Theory - Computational; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6606688b66c13817292809df/original/arka-a-framework-of-dimensionality-reduction-for-machine-learning-classification-modeling-risk-assessment-and-data-gap-filling-of-sparse-environmental-toxicity-data.pdf |
60c748cc469df45554f43ac4 | 10.26434/chemrxiv.11916336.v1 | Automated Analysis of Contact Angle Goniometry Data Using DropPy | <p>Despite advances in contact angle data
collection and analysis, the opacity inherent to automated options forces most
non-expert researchers to rely on manual techniques and limit assessment of
available data. In tandem, with the emergence of inexpensive and
powerful hardware in increasingly small form-factors, the development of robust
and versatile software packages would enable interrogation of wetting phenomena
across a range of platforms. Here,
we introduce DropPy, an open-source Python implementation of the classic
axisymmetric drop shape analysis technique to fit droplet profiles from images
automatically while providing an easy interface through which casual users may
interpret their findings.</p> | Michael Orella; McLain Leonard; Yuriy Román-Leshkov; Fikile Brushett | Imaging; High-throughput Screening; Fluid Mechanics; Interfaces; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748cc469df45554f43ac4/original/automated-analysis-of-contact-angle-goniometry-data-using-drop-py.pdf |
60c757da469df41d74f4553d | 10.26434/chemrxiv.14265215.v2 | Reactive and Inelastic Scattering Dynamics of Hyperthermal O and O2 from a Carbon Fiber Network | The
reactive and inelastic scattering dynamics of
ground-state atomic and molecular oxygen from a carbon fiber network at 1023-1823 K was
investigated with a molecular beam-surface scattering technique. A molecular beam containing hyperthermal O and O<sub>2</sub>
with a mole ratio of 0.92:0.08 and nominal velocity of 8 km s<sup>-1</sup> was
directed at the network, and time-of-flight distributions of the scattered
products were collected at various angles with the use of a rotatable mass
spectrometer detector. O atoms exhibited both impulsive scattering (IS)
and thermal desorption (TD) dynamics, where the TD O-atom flux
increased with surface temperature and the IS O-atom flux remained relatively constant. While the
majority of the TD O atoms desorbed promptly after the beam pulse struck the
network, signatures of thermal processes occurring over long residence times
were also observed. Evidence of O<sub>2</sub> reactions was not observed, and
the behavior of the inelastically scattered O<sub>2</sub> was invariant to the
temperature of the network and showed both IS and TD dynamics. The dominant reactive product was CO, whereas CO<sub>2</sub>
was a minor product. Both these products showed only TD dynamics. The observed
flux of CO initially increased with temperature and then reached a plateau
above which the flux no longer increased with temperature, over the temperature
range studied. Thermally desorbed CO products exited the network promptly or
after relatively long residence times, and two populations of CO with long
residence times were distinguished. Hysteresis was observed in the
temperature-dependent flux of thermally desorbed O and CO, with opposing trends
for the two products. This work follows similar studies in our
laboratory where the target materials were vitreous carbon and highly oriented
pyrolytic graphite. The data suggest that the chemical reactivity of the three
forms of <i>sp</i><sup>2</sup> carbon surfaces
is similar and that the differences arise from the variations of the
morphology. <br /> | Savio Poovathingal; Min Qian; Vanessa Murray; Timothy Minton | Surface | CC BY 4.0 | CHEMRXIV | 2021-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757da469df41d74f4553d/original/reactive-and-inelastic-scattering-dynamics-of-hyperthermal-o-and-o2-from-a-carbon-fiber-network.pdf |
60c744ba567dfe9fc7ec4334 | 10.26434/chemrxiv.9895628.v1 | Monitoring and Modeling of Heavy Metals Contents in Vegetables Collected from Markets in Imo State, South-Eastern, Nigeria | <p>Vegetable
consumption is one major exposure route of heavy metal to humans, but few data
exist for Imo State. We assessed the contamination levels and associated health
risk of cadmium (Cd), cobalt (Co), copper (Cu), nickel (Ni), lead (Pb) and zinc
(Zn) in vegetables (<i>Telfairia
occidentalis</i>, <i>Pterocarpus mildbraedii</i>,
<i>Gongronenina latifolium</i> and <i>Vernonia amygdalina</i>) that are consumed frequently
from markets (n=16) in three zones of Imo State, Nigeria. After wet-digestion
of samples, the supernatant were analyzed by using atomic absorption
spectrophotometry. The mean concentrations in the<i> </i>four vegetables ranged from 0.006±0.003 mg/kg to 0.011±0.007 mg/kg
for Cd, 0.064±0.012 mg/kg to 1.225±0.226 mg/kg for Co, 10.711±1.968 mg/kg to
25.088±13.975 mg/kg for Cu, 0.062±0.013 mg/kg to 0.307±0.210 mg/kg for Ni,
0.006±0.005 mg/kg to 0.012±0.002 mg/kg for Pb and 63.55±4.055 mg/kg to
104.126±24.080 mg/kg for Zn. Except for Zn, all heavy metals in the various
vegetables were below the joint standard of Food and Agriculture Organization
(FAO) and World Health Organisation (WHO). Although, overall heavy metal load
was very low, Zn had the highest contamination factor in vegetables. Heavy
metals concentrations in vegetables generally showed low to high variations and
statistically different (p < 0.05). Average daily intake was below the
provisional tolerance limit except for Zn. The individual hazard index of
vegetables for both children and adults were below 1, indicating no potential
risk to the public. Overall, heavy metals hazard index were below 1, indicating
acceptable level of non-carcinogenic adverse health effect. However, potential
multi-element contamination from ingestion is possible as revealed by the
correlation profiling of heavy metals. </p> | Isiuku Beniah Obinna; Christian Enyoh | Analytical Chemistry - General; Environmental Analysis; Food | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744ba567dfe9fc7ec4334/original/monitoring-and-modeling-of-heavy-metals-contents-in-vegetables-collected-from-markets-in-imo-state-south-eastern-nigeria.pdf |
6494e390a2c387fa9ac9449b | 10.26434/chemrxiv-2023-l87m8 | An Electrochemical Proximity Assay (ECPA) for Antibody Detection Incorporating Flexible Spacers for Improved Performance | A clever approach for biosensing is to leverage the concept of the proximity effect, where analyte binding to probes can be coupled to a second, controlled binding event such as short DNA strands. This analyte-dependent effect has been exploited in various sensors with optical or electrochemical readouts. Electrochemical proximity assays (ECPA) are more amenable to miniaturization and adaptation to the point-of-care, yet ECPA has been generally targeted toward protein sensing with antibody-oligonucleotide probes. Antibodies themselves are also important as biomarkers, since they are produced in bodily fluids at the onset of a disease, often in low amounts. In this work, by using antigen-DNA conjugates, we targeted an ECPA method for antibody sensing and showed that the assay performance can be greatly enhanced using flexible spacers in the DNA conjugates. After adding flexible polyethylene glycol (PEG) spacers at two distinct positions, the spacers ultimately increased the antibody-dependent current by a factor of 4.0 without significant background increases, similar to our recent work using thermofluorimetric analysis (TFA). The optimized ECPA was applied to anti-digoxigenin antibody quantification at concentrations ranging over two orders of magnitude, from the limit-of-detection of 300 pM up to 50 nM. The assay was functional in 90% human serum, where increased ionic strength was used to counteract double-layer repulsion effects at the electrode. This flexible-probe ECPA methodology should be useful for sensing other antibodies in the future with high sensitivity, and the mechanism for signal improvement with probe flexibility may be applicable to other DNA-based electrochemical sensor platforms. | Amanda S.N. Kurian; Mainul Islam Mazumder; Asanka Gurukandure ; Christopher J. Easley | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Biochemical Analysis; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6494e390a2c387fa9ac9449b/original/an-electrochemical-proximity-assay-ecpa-for-antibody-detection-incorporating-flexible-spacers-for-improved-performance.pdf |
655ccc98dbd7c8b54bb6812b | 10.26434/chemrxiv-2023-tp7mj-v2 | Controlling the Nonadiabatic Dynamics of the Charge-Transfer Process with Chirped-Pulses: Insights from a Double-Pump Time-Resolved Fluorescence Spectroscopy Scheme. | The manipulation of the ultrafast quantum dynamics of a molecular system can be achieved through the application of tailored light fields. This has been achieved in many ways in the past. In our present investigations, we show that it is possible to exert specific control over the nonadiabatic dynamics of a generic model system describing ultrafast charge-transfer within a condensed dissipative environment by using frequency-chirped pulses. By adjusting the external photoexcitation conditions, such as the chirp parameter, we show that the final population of the excitonic and charge-transfer states can be significantly altered, thereby influencing the elementary steps controlling the transfer process. Besides, we introduce an excitation scheme based on double-pump time-resolved fluorescence spectroscopy using chirped-pulse excitations. Here, our findings reveal that chirped excitations enhance the vibrational system dynamics as evidenced by the simulated spectra, where a substantial signal intensity dependence on the chirp is observed. Our simulations show that chirped pulses are a promising tool for steering the dynamics of the charge-transfer process towards a desired target outcome. | Jia Hao Soh; Thomas L.C. Jansen; Elisa Palacino-González | Theoretical and Computational Chemistry; Physical Chemistry; Optics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655ccc98dbd7c8b54bb6812b/original/controlling-the-nonadiabatic-dynamics-of-the-charge-transfer-process-with-chirped-pulses-insights-from-a-double-pump-time-resolved-fluorescence-spectroscopy-scheme.pdf |
649fc7049ea64cc16741f3ec | 10.26434/chemrxiv-2023-m6279 | Transmittance modulation by gold nanoparticle mediated
wet chemical etching of silica | Wet etching in hydrofluoric acid (HF) is one of the most common routes for the surface texturing of silica, leading to improved optical properties, which find applications in several fields. In this work, wet etching of silica is mediated by the deposition of chemically synthesized gold nanoparticles on the substrate. Nanoparticles of different sizes are coated on silica and act as a mask when etching using HF. The effect of parameters such as etching time, nanoparticle size, and HF concentration on the surface morphologies and transmittance are studied and correlated with the chemical etching mechanism. This work reveals that a proper choice of masking and etching conditions can reduce the optical transmission of silica. Etching leads to the formation of arrays of micron-size elongated pits. The pit width and surface roughness are found to increase with
etching time and HF concentration, in turn leading to a decrease in transmittance. The results show that nanoparticle masking is an effective way to modulate silica etching and in turn, reduce the transmittance of the substrate | Neethu Thomas; Parasuraman Swaminathan | Materials Science; Nanoscience; Chemical Engineering and Industrial Chemistry; Coating Materials; Nanostructured Materials - Materials; Thin Films | CC BY 4.0 | CHEMRXIV | 2023-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649fc7049ea64cc16741f3ec/original/transmittance-modulation-by-gold-nanoparticle-mediated-wet-chemical-etching-of-silica.pdf |
670cc8df12ff75c3a15c2b0f | 10.26434/chemrxiv-2024-6nbfh-v2 | Synthesis of fully π-conjugated, pentagon-embedded non-alternant carbon nanobelts | Synthesis of carbon nanobelts (CNBs) with delocalized electronic structures and enhanced π-conjugation remains unclear but is fundamentally important. Herein, we present the first successful synthesis and characterization of fully π-conjugated, pentagon-embedded non-alternant CNBs, carefully designed with optimal strain and reactive site protection. These compounds were synthesized using an iterative Diels-Alder reaction followed by deoxygenative aromatization. Unlike all-benzenoid alternant CNBs, these CNBs exhibit smaller band gaps, stronger red emission, and more effective π-conjugation due to the incorporation of non-alternant moieties. One CNB can be oxidized into its dication, which exhibits an open-shell singlet ground state and intriguing global aromaticity, with theoretical calculations predicting two weakly coupled annulenes along the edges. This work opens new avenues for synthesizing complex carbon nanostructures with enhanced electronic properties. | Yi Han; Shaofei Wu; Koon Yong Shawn Khoo ; Chunyan Chi | Organic Chemistry; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670cc8df12ff75c3a15c2b0f/original/synthesis-of-fully-conjugated-pentagon-embedded-non-alternant-carbon-nanobelts.pdf |
6378623553ab8038472b2229 | 10.26434/chemrxiv-2022-rd3qj | Pd-Catalyzed site selective C(sp2)-H chalcogenation of amino acids and peptides using picolinamide auxiliary | Chalcogenated amino acids/peptides are recently being considered therapeutic drug candidates. This report describes a handy synthetic method for the Pd-catalyzed picolinamide directed site-selective C(sp2)-H chalcogenation of - amino acids and peptides with diaryl disulfides and diselenides reagents. A variety of -amino acids, benzylamines and phenethyl amines are chalcogenated in moderate to good yields bearing good selectivity. Importantly, this synthetic methodology provides the first late-stage peptide chalcogenation. Herein, ample substrate scopes with sensitive functionality, late-stage drug modification, various post-synthetic utilities including easy removal of directing group, and synthesis of indoline are systematically explored for the practical utility. | Nagendra Sharma; Raghunath Bag | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6378623553ab8038472b2229/original/pd-catalyzed-site-selective-c-sp2-h-chalcogenation-of-amino-acids-and-peptides-using-picolinamide-auxiliary.pdf |
60c7480f0f50db492c3966fd | 10.26434/chemrxiv.11854389.v1 | Basic Zinc Cubane-1,4-Dicarboxylate: A New MOF-5 Analogous with High Porosity and Robust Dynamics | A new metal-organic framework, basic zinc cubane-1,4-dicarboxylate, (1) was synthesized. 1 is a cubic framework of the same underlying topology, as basic zinc terephthalate, MOF-5, with similar lattice parameters, unique dynamics and competitive adsorption properties. It has a highsymmetry space group, Pm3,¯m with a lattice parameter of 12.776 Å, as determined by X-ray diffraction at 100 K. The structure consists of a random distribution of two perpendicular basic zinc carboxylate nodes and axially disordered cubylene spacers, so the observed high-symmetry structure is an average of several lower-symmetry unit cells. The binary orientational disorder of the nodes has significant influence on the uniaxial rotation of the edges, realizing a previous idea of robust dynamics1. The structural and dynamical ifferences of 1 and MOF-5 are based on the local symmetry and the electronic structure of the organic components: i) the lack of conjugation in cubane-1,4-dicarboxylate does not fix the orientation of the nodes; and ii) the incomplete match of the cubylene (rotor) and dicarboxylate (stator) units facilitates the rotation of the cubylene units even at 100 K. The calculated rotation barrier is unusually low, and it depends on the orientation of the adjacent carboxylate units. The crystals of 1 can be activated either at elevated temperature in vacuum or at ambient conditions by solvent exchange. The high surface area (3160 m2g-1) and the high capacity of hydrogen uptake promise future practical applications.<br /> | Dávid Földes; Éva Kováts; Gábor Bortel; Szilvia Klébert; Emma Jakab; Sándor Pekker | Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7480f0f50db492c3966fd/original/basic-zinc-cubane-1-4-dicarboxylate-a-new-mof-5-analogous-with-high-porosity-and-robust-dynamics.pdf |
65b771ba9138d23161f688a6 | 10.26434/chemrxiv-2024-wzmvs | The Direct β-C(sp3)–H Fluorination of Carboxylic Acids | Due to their widespread applications fluorine-containing compounds have become indispensable in various areas of our everyday lives. The ever-increasing demand for complex fluorinated molecules has raised a significant interest to develop new synthetic methodologies that selectively introduce fluorine into molecular scaffolds. While functional group interconversion approaches are well-established in this regard, their reliance on pre-installed reactive handles has encouraged organic chemists to investigate new strategies to enable a direct conversion of inert C–H bonds into C–F bonds. Transition-metal-catalyzed fluorination reactions have been recognized as a promising tool in this context, but fundamental challenges, such as the very high energetic barriers associated with the formation of C–F bonds by reductive elimination, amongst other reasons, remain to be addressed systematically. Arguably, research towards new concepts in fluorination chemistry should be conducted with substrates that are of immediate utility and imply a generalizability of the respective strategies. Carboxylic acids, owing to their versatile synthetic utility in organic synthesis and their comparably challenging use in C–H activation ideally fulfill these criteria. Herein, we here report a protocol that for the first time enables the β-C(sp3)–H fluorination of free carboxylic acids. The rational design of the oxidizing reagent proved to be crucial in establishing the protocol and introduces a new dimension to the rational design of synthetic methods in the field of C–H activation. The reported protocol gives access to a wide range of fluorinated carboxylic acids without the need to introduce an exogenous directing group. | Sourjya Mal; Friedrich Jurk; Kerstin Hiesinger; Manuel van Gemmeren | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Bond Activation; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b771ba9138d23161f688a6/original/the-direct-c-sp3-h-fluorination-of-carboxylic-acids.pdf |
60c75108337d6c7fdfe28485 | 10.26434/chemrxiv.13110212.v1 | First-Principles Investigations of Magnetic Anisotropy and Spin-Crossover Behavior of Fe(III)-TBP Complexes | <div>With the ongoing efforts to obtain mononuclear 3d-transition metal complexes that manifest slow relaxation of magnetization and hence, can behave as single molecule magnets (SMMs), we have modelled 14 novel Fe(III) complexes out of which nine behave as potential SMMs. These complexes possess large zero-field splitting (ZFS)</div><div>parameter D in the range of -40 to -60 cm<sup>-1</sup>. The first-principles investigation of the ground-spin state applying density functional theory (DFT) and wave-function based</div><div>multi-configurations methods e.g. SA-CASSCF/NEVPT2 are found to be quite consistent except for few delicate cases with near degenerate spin-states. In such cases, the</div><div>hybrid B3LYP functional is found to be biased towards high-spin (HS) state. Altering the percentage of exact exchange admixed in B3LYP functional leads to intermediate spin</div><div>(IS) ground state consistent with the multireference calculations. The origin of large zero field splitting (ZFS) in the Fe(III)-based trigonal bipyramidal (TBP) complexes</div><div>is investigated and the D-values are further tuned by varying the axial ligands with group XV elements (N, P and As) and equatorial halide ligands from F, Cl, Br and I. Furthermore, a number of complexes are identified with very small Gibbs free energy values indicating the possible spin-crossover phenomenon between the bi-stable spin-states.</div> | Rishu Khurana; Sameer Gupta; Md. Ehesan Ali | Theory - Inorganic; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75108337d6c7fdfe28485/original/first-principles-investigations-of-magnetic-anisotropy-and-spin-crossover-behavior-of-fe-iii-tbp-complexes.pdf |
60c748ca567dfe03c3ec4a74 | 10.26434/chemrxiv.11973141.v1 | Evidence for Photocatalyst Involvement in Oxidative Additions of Nickel-Catalyzed Carboxylate O-Arylations | In this study we use in situ infrared tracking to describe the kinetics of dual photo- and nickel-catalyzed carboxylate O-arylations. We examined both a state-of-the-art homogeneous (Ir(ppy)<sub>3</sub>) and heterogeneous (graphitic carbon nitride) photocatalyst, comparing their kinetics to each other, and to the existing mechanistic proposal. We argue against the current hypothesis, specifically that the photocatalyst is only involved to trigger a rate-limiting reductive elimination.<br /> | Jamal Malik; Amiera Madani; Bartholomäus Pieber; Peter H. Seeberger | Photocatalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748ca567dfe03c3ec4a74/original/evidence-for-photocatalyst-involvement-in-oxidative-additions-of-nickel-catalyzed-carboxylate-o-arylations.pdf |
60c753d3842e65ea4adb4019 | 10.26434/chemrxiv.13558151.v1 | Emergence of a Promiscuous Peroxidase Under Non-Equilibrium Conditions | <p><b>In the far from equilibrium state of
living matter, energy is consumed to fuel the metabolic networks of enzymatic
reactions. The emergence of
protometabolic pathways in primeval earth is intricately related to the
evolutionary journey of modern enzymes. Fundamental understanding of such
energy driven generation of early catalytic systems would help us recognize the
conditions required for the minimal metabolism that predated the chemical
emergence of life. Herein, we report substrate driven generation of a non-equilibrium
catalytic machinery from a single amino acid functionalized fatty acid in
presence of a cofactor hemin. The non-equilibrium assembled state showed
acceleration of catalytic potential resulting in degradation of the substrate
and subsequently led to disassembly. Controls that promoted equilibration could
not access the three-dimensional microphases and showed substantially lower
catalytic activity. Significantly, </b><b>the
assembled state showed latent catalytic function </b><b>by hydrolysing
a precursor to yield the same substrate</b>.<b> </b><b>Consequently, the assembly was
benefitted with augmented lifetime of the catalytic state exploiting a promiscuous
cascade and thus foreshadowing protometabolism. The results contribute towards
our understanding of energy driven generation of primitive catalytic
machineries that assisted the minimal metabolism of early life.</b><b></b></p> | Sumit Pal; Antara Reja; Subhajit Bal; Baishakhi Tikader; Sandip Kar; Dibyendu Das | Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753d3842e65ea4adb4019/original/emergence-of-a-promiscuous-peroxidase-under-non-equilibrium-conditions.pdf |
67ca159581d2151a0265b786 | 10.26434/chemrxiv-2025-nq14w | Discovery of a CNS active GSK3 degrader using orthogonally reactive linker screening | Bifunctional targeted protein degraders, also known as Proteolysis Targeting Chimeras (PROTACs), are an emerging drug modality that may offer a new approach to understand and treat neurodegenerative diseases. These molecules have a non-occupancy based, sub-stoichiometric mechanism of action which results in removal of target proteins from cells, presenting new opportunities to interrogate and intervene in pathogenic signalling. Identifying chemical starting points for PROTACs remains a largely empirical process and the design rules for identifying in vivo quality tools to interrogate new therapeutic hypotheses in the Central Nervous System (CNS) have yet to be established. We demonstrate a concept of using orthogonally reactive linker reagents, that allowed us to construct screening libraries varying the E3 ligase recruiting ligand, the target protein recruiting ligand and the linker simultaneously and test compounds directly in cells. This led us identify a molecule directly from our screen that upon further profiling demonstrated rapid and selective Glycogen Synthase Kinase 3 (GSK3) degradation in cells, as well as CNS in vivo activity in mouse. Our findings provide new opportunities to investigate the role of GSK3 paralogs in cellular and in vivo disease models and demonstrate a successful Direct-to-Biology approach, with broad potential for identifying in vivo quality bifunctional chemical probes for CNS disease concepts. | Andreas Holmqvist; Nur Mehpare Kocaturk; Christina Duncan; Jennifer Riley; Steve Baginski; Graham Marsh; Joel Cresser-Brown; Hannah Maple; Kristiina Juvonen; Nicola Morrice; Calum Sutherland; Kevin Read; William Farnaby | Biological and Medicinal Chemistry; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2025-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ca159581d2151a0265b786/original/discovery-of-a-cns-active-gsk3-degrader-using-orthogonally-reactive-linker-screening.pdf |
64ff131599918fe537c23eb0 | 10.26434/chemrxiv-2023-296cq | Phosphonium-substituted Diphosphaindenylide (PPI): Exploration of Biradical Character and Ligand Properties | Starting from C6H4(PCl2)2 and the TMS-substituted ylide (TMS)2C=PR3 (TMS = trimethylsilyl, R = p-tolyl), the phosphonium-substituted diphosphaindenylide PPI was prepared in two steps. CASSCF calculations as well as the reactivity toward diphenyl acetylene suggest a notable biradical character in PPI. Reaction with [Cr(CO)3(MeCN)3] affords the complex [Cr(CO)3(η5-PPI)] (5). This complex was employed to explore the ligand properties of PPI, which demonstrates considerable potential through the combination of strong metal-ligand interactions and the possibility of a pronounced indenyl effect. | Peter Coburger; Clara Schweinzer; Moritz Scharnhölz | Inorganic Chemistry; Organometallic Chemistry; Bonding; Coordination Chemistry (Organomet.); Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ff131599918fe537c23eb0/original/phosphonium-substituted-diphosphaindenylide-ppi-exploration-of-biradical-character-and-ligand-properties.pdf |
6329ff3f114b7e43b416c505 | 10.26434/chemrxiv-2022-wgz1j | Room for Improvement in the Initial Martini 3 Parameterization of Peptide Interactions | The Martini 3 coarse-grain force field has greatly improved upon its predecessor, having already been successfully employed in several applications. Here, we gauge the accuracy of Martini 2 and 3 protein interactions in two types of systems: coiled coil peptide dimers in water and transmembrane peptides. Coiled coil dimers form incorrectly under Martini 2 and not at all under Martini 3. With transmembrane peptides, Martini 3 represents better the membrane thickness–peptide tilt relationship, but shorter peptides do not remain transmembranar. We discuss related observations, and describe mitigation strategies involving either scaling interactions or restraining the system. | J. Karl Spinti; Fernando Neiva Nunes; Manuel Nuno Melo | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6329ff3f114b7e43b416c505/original/room-for-improvement-in-the-initial-martini-3-parameterization-of-peptide-interactions.pdf |
63364e3ae615026ceb2b9e69 | 10.26434/chemrxiv-2022-c9gn5 | Thiol and H2S Mediated NO Generation from Nitrate at Copper(II) | Nitrate fertilizer runoff poses chemical challenge for their remedial as relatively inert nitrate-oxoanions require stringent conditions for reduction. We present a novel strategy of using thiols RSH that represent biologically relevant reductants to convert nitrate to NO at a Cu(II) center under mild conditions with formation of disulfides RSSR. The bidentate b-diketiminato complex [Cl2NNF6]Cu(κ2-O2NO) engages in O-atom transfer (OAT) with various thiols (RSH) to form sulfenic acid (RSOH). Mechanistic studies indicate formation of the copper(II) nitrite complex [Cl2NNF6]Cu(κ2-O2N) upon OAT that further reacts with RSH to give S-nitrosothiols RSNO and [CuII]2(m-OH)2 en route to NO formation with [CuII]-SR intermediates. H2S, a physiologically potent agent and thiol congener, also reduces nitrate at copper(II) to NO generation, providing a lens into NO3-/H2S cross-talk in the biological milieu. | Pokhraj Ghosh; Molly Stauffer; Md Estak Ahmed; Jeffery Bertke; Richard Staples; Timothy Warren | Inorganic Chemistry; Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63364e3ae615026ceb2b9e69/original/thiol-and-h2s-mediated-no-generation-from-nitrate-at-copper-ii.pdf |
60c7523e9abda2624af8dd8e | 10.26434/chemrxiv.13270607.v1 | Double-Helix Supramolecular Nanofibers Assembled from Negatively Curved Nanographenes | The layered structures of graphite and related nanographene molecules play key roles in their physical and electronic functions. However, the stacking modes of negatively curved nanographenes remains unclear, owing to the lack of suitable nanographene molecules. Herein we report the synthesis and one-dimensional supramolecular self-assembly of negatively curved nanographenes without any assembly-assisting substituents. This curved nanographene self-assembles in various organic solvents and acts as an efficient gelator. The formation of nanofibers was confirmed by microscopic measurements, and an unprecedented double-helix assembly by continuous π-π stacking was uncovered by three-dimensional electron crystallography. This work not only reports the discovery of an all-sp<sup>2</sup>-carbon supramolecular π-organogelator with negative curvature, but also demonstrates the power of three-dimensional electron crystallography for the structural determination of submicrometer-sized molecular alignment. | Kenta Kato; Kiyofumi Takaba; Saori Maki-Yonekura; Nobuhiko Mitoma; Yusuke Nakanishi; Taishi Nishihara; Taito Hatakeyama; Takuma Kawada; Yuh Hijikata; Jenny Pirillo; Lawrence T. Scott; Koji Yonekura; Yasutomo Segawa; Kenichiro Itami | Supramolecular Chemistry (Org.); Self-Assembly; Crystallography – Organic | CC BY 4.0 | CHEMRXIV | 2020-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7523e9abda2624af8dd8e/original/double-helix-supramolecular-nanofibers-assembled-from-negatively-curved-nanographenes.pdf |
60c741e8702a9beac718a33e | 10.26434/chemrxiv.7865168.v4 | Convergent Total Synthesis of Principinol D, a Rearranged Kaurane Diterpenoid | <div>
<p>The total synthesis of principinol D, a rearranged kaurane diterpenoid, is reported. This grayanane natural product is constructed via a convergent fragment coupling approach, wherein the central 7-membered ring is synthesized at a late stage. The bicyclo[3.2.1]octane fragment is accessed by a Ni-catalyzed α-vinylation reaction. Strategic reductions include a diastereoselective SmI<sub>2</sub>-mediated ketone reduction with PhSH and a new protocol for selective ester reduction in the presence of ketones. The convergent strategy reported herein may be an entry point to the larger class of kaurane diterpenoids.</p>
</div> | Timothy Newhouse; Aneta Turlik; Yifeng Chen; Anthony Scruse | Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e8702a9beac718a33e/original/convergent-total-synthesis-of-principinol-d-a-rearranged-kaurane-diterpenoid.pdf |
63d884435391e5d2ea6cb71d | 10.26434/chemrxiv-2023-znxt1 | Insights of Oxygen Reduction Selectivity and Fe Leaching from Fe-N-C Nanozyme in Ascorbate Oxidation | Ascorbic acid (H2A) is a well-known antioxidant to protect cellular components from free radical damage, meanwhile it is also emerged as pro-oxidant in cancer therapy. However, such contradictory mechanisms underlying H2A oxidation are not well understood. Here, we report the discovery of Fe leaching during catalytic H2A oxidation using Fe-N-C nanozyme as a ferritin mimic and its influence in selectivity of oxygen reduction reaction (ORR). Owing to the heterogeneity, Fe-Nx sites in Fe-N-C primarily catalyzed the H2A oxidation and 4e ORR via an iron-oxo intermediate; meanwhile marginal N-C sites catalyzed the 2e ORR via an O2 intermediate with H2O2 production, although which was less favorable in kinetics and hardly observable in the early stage. Nonetheless, trace O2 accumulated and attacked Fe-Nx sites, leading to a linear leakage of unstable Fe ions up to 420 ppb when the concentration of H2A increased. As a result, a substantial fraction (~40%) of N-C sites on Fe-N-C were activated, and a new path for Fenton-type H2A oxidation was finally enabled. After Fe ions diffused into the bulk solution, the ORR at the N-C sites stopped at H2O2 production, which was the origin for the pro-oxidant effect by H2A. This work highlights the Fe-leakage occurring on Fe-N-C nanozymes and uncovers the multifaceted insights of ORR selectivity in H2A oxidation under realistic conditions.
| Xuwen Cao; Caixia Zhu; Qing Hong; Xinghua Chen; Kaiyuan Wang; Yanfei Shen; Songqin Liu; Yuanjian Zhang | Catalysis; Biocatalysis; Nanocatalysis - Reactions & Mechanisms; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d884435391e5d2ea6cb71d/original/insights-of-oxygen-reduction-selectivity-and-fe-leaching-from-fe-n-c-nanozyme-in-ascorbate-oxidation.pdf |
62f66e8ee78f709b7538f8a7 | 10.26434/chemrxiv-2022-nlb0m | Systematic exploration of privileged warheads for covalent kinase drug discovery | Kinase-targeted drug discovery for cancer therapy has advanced significantly in the last three decades. Currently, diverse kinase inhibitors or degraders have been reported, such as allosteric inhibitors, covalent inhibitors, macrocyclic inhibitors, and PROTAC degraders. Out of these, covalent kinase inhibitors (CKIs) have been attracting attention due to their enhanced selectivity and exceptionally strong affinity. Eight covalent kinase drugs have been FDA approved thus far. Here, we review current developments in CKIs. We explore the characteristics of the CKIs: the features of nucleophilic amino acids and the preferences of electrophilic warheads. We provide systematic insights into privileged warheads for repurposing to other kinase targets. Finally, we discuss trends in CKI development across the whole proteome. | Zheng Zhao; Philip E. Bourne | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f66e8ee78f709b7538f8a7/original/systematic-exploration-of-privileged-warheads-for-covalent-kinase-drug-discovery.pdf |
60c75152702a9ba2f418bf19 | 10.26434/chemrxiv.13148825.v1 | Equilibrium Between Tri- and Tetra-Coordinate Chalcogenuranes Is Critical for Cysteine Protease Inhibition | <div>There have been significant advances in the biological use of hypervalent selenium and tellurium compounds as cysteine protease inhibitors over the recent past. However, the full understanding of their reaction mechanisms in aqueous medium and the mechanism of cysteine proteases inhibition is still elusive. Kinetic studies suggest an irreversible inhibition mechanism, which was explained by forming a covalent bond between the enzyme sulfhydryl group and the chalcogen atom at its hypervalent state (+4). However, it is still unclear the active form of the inhibitor present in the aqueous biological media. To uncover this question, we performed a theoretical investigation using density functional theory (DFT). This study investigated chloride ligand exchange reactions by oxygen and sulfur nucleophiles on hypervalent selenium and tellurium compounds. All tetra- and tri-coordinate chalcogen compounds and distinct protonation states of the nucleophiles were considered, totaling 34 unique species, 7</div><div>nucleophiles and 155 free energies rections. We discovered that chloride is easily replaced by a nonprotonated nucleophile (SH<sup>–</sup> or OH<sup>– </sup>) in R<sub>2</sub>SeCl<sub>2</sub> . We also found that</div><div>tri-coordinate species are more stable than their tetra-coordinate counterparts, with selenoxide (R<sub>2</sub>SeO) protonation being strongly exergonic in acid pH. These results suggest that the protonated selenoxide (R<sub>2</sub>SeOH<sup>+</sup>) is the most probable active chemical species in biological media. The computed energetic profiles paint a possible picture for the selenurane activity, with successive exergonic steps leading to a covalent inhibition of thiol dependent enzymes, like cysteine proteases. A second less exergonic pathway has also been uncovered, with a direct reaction to chalcogenonium cation (R<sub>2</sub>SeCl<sup>+</sup>) as the inhibition step. The trends observed for the telluranes were similar, albeit with</div><div>more exergonic reactions and a stronger trend to form bonds with oxygen species then selenuranes.</div><div><br /></div> | Gabriela Dias SIlva; Rodrigo L O R Cunha; Mauricio Domingues Coutinho Neto | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75152702a9ba2f418bf19/original/equilibrium-between-tri-and-tetra-coordinate-chalcogenuranes-is-critical-for-cysteine-protease-inhibition.pdf |
60c758a0f96a0036ae288e80 | 10.26434/chemrxiv.14569461.v1 | Charge Density and Hydrophobicity-Dominated Regimes in the Phase Behavior of Complex Coacervates | <div>The role of hydrophobicity, and particularly nonionic hydrophobic comonomers, on the phase behavior of polyelectrolyte complex coacervates is not well-understood. Here, we address this problem by synthesizing a library of polymers with a wide range of charge densities and nonionic hydrophobic side chain lengths, and characterizing their phase behavior by optical turbidity. The polymers were prepared by post-polymerization modification of poly(N-acryloxy succinimide), targeting charge densities between 40 and 100% and nonionic aliphatic sidechains with lengths from 0 to 12 carbons long. Turbidity measurements on pairs of polycations and polyanions with matched charge densities and nonionic sidechain lengths revealed a complex salt response with distinct charge density-dominated and hydrophobicity-dominated regimes. The polymer solubilities were not directly correlated with the phase behavior of the coacervates, indicating the difficulty of understanding the coacervate phase behavior in terms of the polymer-water interaction parameter. This result suggests that there is significant room for further work to understand the mechanisms by which specific molecular-scale interactions moderate the phase behavior of complex coacervates.</div> | Jun Huang; Jennifer Laaser | Polyelectrolytes - Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758a0f96a0036ae288e80/original/charge-density-and-hydrophobicity-dominated-regimes-in-the-phase-behavior-of-complex-coacervates.pdf |
60c74ac9f96a002b242874be | 10.26434/chemrxiv.12241634.v1 | Receptor Determinant Analogues for All 9-O-Ac-Sialoglycan-Recognizing Corona Viruses | <p><b>In present study, analogues of receptor determinants were identified, which can mimic 9-O-Acsialoglycan-recognition by viruses and its usage in antiviral. It is well known that receptor determinants are part of host cell surface receptors which are recognized by virus surface glycoprotein as the first interaction of the target cell. This recognition governs the further processes of viral infection. Similar to other influenza viruses, Corona virus also processes through mechanisms of host interaction. This hostvirus interaction involves a conserved domain at interaction component of virus, which is known to be a key component during the process of virus infection. Therefore in the present study profile of possible Pharmacophore of conserved domain was used as a filter to identify analogues of receptor determinant from database ZINC database. The identified molecules were re-observed among the applicability domain defined by existing antiviral drugs as well as natural existing receptor determinant with sialic acid. The identified molecule needs to be further evaluated through in-vitro experiments. </b><br /></p> | Pratibha Preeti Maurya | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ac9f96a002b242874be/original/receptor-determinant-analogues-for-all-9-o-ac-sialoglycan-recognizing-corona-viruses.pdf |
618d31bfda1506a1c99e63b9 | 10.26434/chemrxiv-2021-g856r | Pd(II)-catalyzed enantioselective C(sp3)–H arylation of cy-clopropanes and cyclobutanes guided by tertiary alkyla-mines. | ABSTRACT: Strained aminomethyl-cycloalkanes are a recurrent scaffold in medicinal chemistry due to their unique structural features that give rise to a range of biological properties. Here, we report a palladium-catalyzed enantioselective C(sp3)–H arylation of aminome-thyl-cyclopropanes and -cyclobutanes with aryl boronic acids. A range of native tertiary alkylamine groups are able to direct C–H cleavage and forge carbon-aryl bonds on the strained cycloalkanes framework as single diastereomers and with excellent enantiomeric ratios. Cen-tral to the success of this strategy is the use of a simple N-acetyl amino acid ligand, which not only controls the enantioselectivity but also promotes -C–H activation of over other pathways. Computational analysis of the cyclopalladation step provides an understanding of how enantioselective C–H cleavage occurs and revealed distinct transition structures to our previous work on enantioselective desymme-trization of N-iso-butyl tertiary alkylamines. This straightforward and operationally simple method simplifies the construction of func-tionalized aminomethyl-strained cycloalkanes, which we believe will find widespread use in academic and industrial settings relating to the synthesis of biologically active small molecules. | Matthew Gaunt; Jesus Rodrigalvarez; Luke Reeve; Javier Miro | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2021-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618d31bfda1506a1c99e63b9/original/pd-ii-catalyzed-enantioselective-c-sp3-h-arylation-of-cy-clopropanes-and-cyclobutanes-guided-by-tertiary-alkyla-mines.pdf |
60ccc312261611dd098b1048 | 10.26434/chemrxiv-2021-db11k | Machine learning for functional group identification in vibrational spectroscopy: A pedagogical lab for undergraduate chemistry students | Here we report a computational activity that introduces undergraduate physical chemistry students to machine learning (ML) in the context of vibrational spectroscopy. In the first part of the activity, students use ML binary classification algorithms to distinguish between carbonyl-containing and non-carbonyl-containing molecules on the basis of their infrared absorption spectra and test modifications to this basic analysis. In a further extension of the activity, students implement a multiclass classification to predict whether carbonyl-containing molecules contain a ketone, a carboxylic acid, or another carbonyl group. This activity is designed to introduce students both to the basic workflow of a ML classification analysis and to some of the ways in which machine learning analyses can fail. We provide a comprehensive handout for the activity, including theoretical background and a detailed protocol, as well as datasets and code to implement the exercise in Python or Mathematica. | Elizabeth Thrall; Seung Eun Lee; Joshua Schrier; Yijun Zhao | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Education; Machine Learning; Artificial Intelligence; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ccc312261611dd098b1048/original/machine-learning-for-functional-group-identification-in-vibrational-spectroscopy-a-pedagogical-lab-for-undergraduate-chemistry-students.pdf |
60c751efbdbb893053a3a184 | 10.26434/chemrxiv.13234877.v1 | Great Location: About Effects of Surface Bound Neighboring Groups for Passive and Active Fine-Tuning of CO2 Adsorption Properties in Carbon Capture Materials | Better carbon capture materials are crucial for managing today’s and the future CO<sub>2</sub> level in the atmosphere. The past focus was on increasing adsorption capacities. One knows by now that controlling the heat of adsorption (DH<sub>ads</sub>) is equally important. Is it too low, CO<sub>2</sub> uptake takes place at unfavorable conditions far from ambient and with insufficient selectivity. Is it too high, chemisorption occurs, and the materials can hardly be regenerated. The conventional approach for influencing DH<sub>ads</sub> is the modification of the adsorbing center. This paper proposes an alternative strategy. The hypothesis is that fine-tuning of the molecular environment in direct vicinity to the adsorbing center (primary amines) is a powerful tool for the adjustment of CO<sub>2</sub>-binding properties. Via click chemistry, any desired neighboring group (NG) can be incorporated on the surfaces of the resulting bifunctional, nanoporous organosilica materials. Passive NGs induce a change of the polarity of the surface, whereas active NGs are capable of a direct interaction with the active-center/ CO<sub>2</sub>pair. The effects on DH<sub>ads</sub> and also on the selectivity are studied in detail. A situation can be realized on the surface which resembles frustrated Lewis acid-base pairs, and the investigation of the binding-species by <sup>13</sup>C solid-state NMR indicate that the push-pull effects could play an essential role not only for CO<sub>2 </sub>adsorption but also for its activation. | Nele Klinkenberg; Sophia Kraft; Sebastian Polarz | Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751efbdbb893053a3a184/original/great-location-about-effects-of-surface-bound-neighboring-groups-for-passive-and-active-fine-tuning-of-co2-adsorption-properties-in-carbon-capture-materials.pdf |
62a3417470f8a73972fd9d35 | 10.26434/chemrxiv-2022-k6x89 | Non-physical species in chemical kinetic models: A case study of diazenyl hydroxy and diazenyl peroxide | Predictive chemical kinetic models often consider hundreds to thousands of intermediate chemical species. An even greater number of species, that might not participate in the model directly, are required to generate pressure-dependent reaction networks for gas-phase systems. As this immense chemical search space is being explored using automated software tools by applying reaction templates, it is probable
that non-physical species will infiltrate the model without being recognized by the compute or a human as such. These nonphysical species might obey chemical intuition as well as requirements coded in the software, e.g., obeying electron valence constraints of chemical elements, and may consequently remain unnoticed. Nonphysical
species become an acute problem when their presence affects the model observables. The present work discusses and analyzes two specific cases of such species, diazenyl hydroxy (·NNOH) and diazenyl peroxide (·NNOOH), both previously suggested as intermediates in nitrogen combustion systems. A comprehensive conformational search did not identify any non-fragmented energy well for either of the two species, and energy scans performed for diazenyl peroxide (·NNOOH), both at DFT and CCSD(T), show that they barrierlessly decompose. This work highlights a broad implication for future automated chemical kinetic model generation, and provides a significant motivation to standardize non-physical species identification in chemical kinetic models. | Nelly Mitnik; Sharon Haba; Alon Grinberg Dana | Physical Chemistry; Chemical Kinetics; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a3417470f8a73972fd9d35/original/non-physical-species-in-chemical-kinetic-models-a-case-study-of-diazenyl-hydroxy-and-diazenyl-peroxide.pdf |
60c744790f50db5e3a3960e5 | 10.26434/chemrxiv.9817208.v1 | Colloidal Dispersions of Oxide Nanoparticles in Ionic Liquids: Elucidating the Key Parameters | <p><b>This work presents a novel and comprehensive approach to predict and understand the stabilisation mechanisms of dispersions of nanoparticles in ionic liquids which </b><b>is at present unpredictable. This opens up applications with new materials combining the properties of both nanoparticles and ionic liquids.</b></p> | Jesse Cornelius Riedl; Mohammad Ali Akhavan Kazemi; Fabrice Cousin; Emmanuelle DUBOIS; Sébastien Fantini; Sandrine Lois; Régine Perzynski; Véronique Peyre | Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Interfaces; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744790f50db5e3a3960e5/original/colloidal-dispersions-of-oxide-nanoparticles-in-ionic-liquids-elucidating-the-key-parameters.pdf |
62f1f0275f687037c2b183c9 | 10.26434/chemrxiv-2022-h7s7m | Mechanoelectronics: Flexible Organic Semiconducting Single Crystals for Durable All-Flexible Field-Effect Transistors | Although many examples of mechanically flexible crystals
are currently known, their utility in all-flexible devices is not yet demonstrated, despite their immense potential for fabricating high-performance flexible devices. We report two alkylated diketopyrrolopyrrole (DPP) semiconducting single crystals, one of which displays impressive elastic mechanical flexibility whilst the other is brittle. Using the single crystal structures and density functional theory (DFT) calculations, we show that the methylated diketopyrrolopyrrole (DPP-diMe) crystals, with dominant π-stacking interactions and large contributions from dispersive interactions, are superior in terms of their stress tolerance and field-effect mobility (µFET) when compared to the brittle crystals of ethylated diketopyrrolopyrrole derivative (DPP-diEt). The field effect transistors (FETs) made of flexible substrates using elastic microcrystals of DPPdiMe retained µFET (from 0.019 cm2/Vs to 0.014 cm2/Vs ) more efficiently even after 40 bending cycles when compared to the brittle microcrystals of DPP-diEt which showed a significant drop in µFET just after 10 bending cycles. Our results not only provide valuable insights
into bending mechanism but also demonstrate the untapped potential of mechanically flexible semiconducting crystals for designing all flexible durable devices. | Ranita Samanta; Susobhan Das; Saikat Mondal; Tamador Alkhidir; Sharmarke Mohamed; Satyaprasad P Senanayak; Chilla Malla Reddy | Materials Science; Elastic Materials; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f1f0275f687037c2b183c9/original/mechanoelectronics-flexible-organic-semiconducting-single-crystals-for-durable-all-flexible-field-effect-transistors.pdf |
6780b88281d2151a028c1eef | 10.26434/chemrxiv-2025-mw3nk | α-N-Phthalimido-Oxy Isobutyrate-Mediated Deoxygenative Arylation: Total Synthesis of Alanenses A and B
| Inspired by our biosynthetic hypothesis for alanense A, we developed two distinct methods for the deoxygenative arylation of α-N-phthalimido-oxy isobutyrate (NPIB), derived from hydroxyl groups adjacent to or conjugated with a carbonyl moiety. One approach utilizes photoredox catalysis to achieve a radical-mediated arylation reaction. Alternatively, we designed an acid-mediated arylation method that proceeds through a cationic intermediate. The acid-mediated approach was successfully applied to the total syntheses of alanenses A and B, as well as O7′-methyllacinilene E. | Young Eum Hyun; Jeonguk Kweon; Thi Hieu Linh Phan; Dongwook Kim; Sunkyu Han | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6780b88281d2151a028c1eef/original/n-phthalimido-oxy-isobutyrate-mediated-deoxygenative-arylation-total-synthesis-of-alanenses-a-and-b.pdf |
60c741229abda216fcf8bde6 | 10.26434/chemrxiv.7931966.v1 | Aiming for a Standardized Protocol for Preparing a Process Green Synthesis Report and for Ranking Multiple Synthesis Plans to a Common Target Product | This paper proposes a standardized format for the preparation of process green synthesis reports that can be applied to chemical syntheses of active pharmaceutical ingredients (APIs) of importance to the pharmaceutical industry. Such a report is comprised of the following eight sections: a synthesis scheme, a synthesis tree, radial pentagons and step E-factor breakdowns for each reaction step, a tabular summary of key material efficiency step and overall metrics for a synthesis plan, a mass process block diagram, an energy consumption audit based on heating and cooling reaction and auxiliary solvents, a summary of environmental and safety-hazard impacts based on organic solvent consumption using the Rowan solvent greenness index, and a cycle time process schedule. Illustrative examples of process green synthesis reports are given for the following pharmaceuticals: 5-HT2B and 5-HT7 receptors antagonist (Astellas Pharma), brivanib (Bristol-Myers Squibb), and orexin receptor agonist (Merck). Methods of ranking synthesis plans to a common target product are also discussed using 6 industrial synthesis plans of apixaban (Bristol-Myers Squibb) as a working example. The Borda count method is suggested as a facile and reliable computational method for ranking multiple synthesis plans to a common target product using the following 4 attributes obtained from a process green synthesis report: process mass intensity, mass of sacrificial reagents used per kg of product, input enthalpic energy for solvents, and Rowan solvent greenness index for organic solvents.<br /> | john andraos | Bioorganic Chemistry; Process Chemistry; Pharmaceutical Industry | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741229abda216fcf8bde6/original/aiming-for-a-standardized-protocol-for-preparing-a-process-green-synthesis-report-and-for-ranking-multiple-synthesis-plans-to-a-common-target-product.pdf |
65af5b5fe9ebbb4db9c604da | 10.26434/chemrxiv-2024-8rx3v | Revisiting the benzene excimer using [2,2] paracyclophane model
system: Experiment and theory | We report high-level calculations of the excited states of [2,2]-paracyclophane
(PCP), which was recently investigated experimentally by ultrafast pump-probe experiments
on oriented single crystals [Haggag et al., ChemPhotoChem 6 e202200181
(2022)]. PCP, in which the orientation of the two benzene rings and their range of
motion are constrained, serves as a model for studying benzene exciplex formation.
The character of the excimer state and the state responsible for the brightest transition
are similar to those in benzene dimer. The constrained structure of PCP allows
one to focus on the most important degree of freedom, the inter-ring distance. The
calculations explain the main features of the transient absorption spectral evolution.
This brightest transition of the excimer is polarized along the inter-fragment axis.
The absorption of light polarized in the plane of the rings reveals the presence of
other absorbing states of Rydberg character, with much weaker intensities. We also
report new transient absorption data obtained by a broadband 8 fs pump, which
time-resolve strong modulations of the excimer absorption. The combination of theory
and experiment provides a detailed picture of the evolution of the electronic
structure of the PCP excimer in the course of a single molecular vibration. | Omer S. Haggag; Roi Baer; Sanford Ruhman; Anna I. Krylov | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65af5b5fe9ebbb4db9c604da/original/revisiting-the-benzene-excimer-using-2-2-paracyclophane-model-system-experiment-and-theory.pdf |
6671eca35101a2ffa8e64431 | 10.26434/chemrxiv-2024-cj0nl | Role of intermolecular interactions in Deep Eutectic solvents for CO2 capture: Vibrational spectroscopy and quantum chemical studies | Recent research and reviews on CO2 capture methods, along with advancements in the industry, have highlighted high costs and the energy-intensive nature as the primary limitations of conventional direct air capture and storage (DACS) methods. In response to these challenges, deep eutectic solvents (DESs) have emerged as a promising absorbents due to their scalability, selectivity, and lower environmental impact compared to other absorbents. However, the molecular origins of their enhanced thermal stability and selectivity for DAC applications have not been explored before. Therefore, the current study focuses on a comprehensive investigation into the molecular interactions within an alkaline DES composed of potassium hydroxide (KOH) and ethylene glycol (EG). Combining FT-IR and quantum chemical calculations, the study reports structural changes and intermolecular interactions induced in EG upon adding KOH and its implications on CO2 capture. Experimental and computational spectroscopic studies confirm the presence of noncovalent interactions (hydrogen bonds) within both EG and the KOH-EG system and point to the aggregation of ions at higher KOH concentrations. Additionally, molecular electrostatic potential (MESP) surface analysis, natural bond orbital (NBO) analysis, quantum theory of atoms-in-molecules (QTAIM) analysis, and reduced density gradient-noncovalent interaction (RDG-NCI) plot analysis elucidate changes in polarizability, charge distribution, hydrogen bond types, noncovalent interactions, and characterize interaction strengths, respectively. Evaluation of explicit and hybrid models assesses their effectiveness in representing intermolecular interactions. This research enhances our understanding of molecular interactions in the KOH-EG system, which are essential for both absorption and desorption of CO2. The study also aids in predicting and selecting DES components, optimizing their ratios with salts, and fine-tuning the properties of similar solvents and salts for enhanced CO2 capture efficiency. | Rashmi Mishra; Rajan Bhawnani; Rohit Chauhan; Rohan Sartape; Amey Thorat; Meenesh Singh; Jindal Shah | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Computational Chemistry and Modeling; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6671eca35101a2ffa8e64431/original/role-of-intermolecular-interactions-in-deep-eutectic-solvents-for-co2-capture-vibrational-spectroscopy-and-quantum-chemical-studies.pdf |
659168229138d23161e416f3 | 10.26434/chemrxiv-2024-xplqh | Total Synthesis of the Zwitterionic Trisaccharide Repeating Unit of Fusobacterium nucleatum ATCC 51191 O-antigen | Herein, we report an efficient total synthesis of Fusobacterium nucleatum ATCC 51191 zwitterionic trisaccharide repeating unit. Striking features of the target molecule are the presence of rare sugars, six nitrogen atoms dispersed over three sugars and functionalities like carboxylic acids and an amide. Challenges such as installation of 1,2-cis glycosidic linkage in AAT sugar, glycosylation using GlcNAcA donors with less reactive 4-OH of GlcNAcA, orthogonal late-stage amino acid coupling in the sterically hindered site, and synthesis of orthogonally protected rare amino sugars have been addressed. The total synthesis of target molecule accomplished via longest linear sequence of 22 steps in 2.3 % overall yield. | Aishwarya Shelke; Amar Kumar Mishra; Bhaswati Ghosh; Roberta Marchetti; Alba Silipo; Suvarn Kulkarni | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659168229138d23161e416f3/original/total-synthesis-of-the-zwitterionic-trisaccharide-repeating-unit-of-fusobacterium-nucleatum-atcc-51191-o-antigen.pdf |
63247379e61502ffd71b0555 | 10.26434/chemrxiv-2022-j57mb | Encapsulating Metal Nanoparticles into a Layered Zeolite Precursor with Surface Silanol Nests Enhances Sintering Resistance | Supported metal nanoparticles are widely used as heterogeneous catalysts but often deactivated due to sintering under harsh conditions, especially at high temperatures. Sintering can be prevented by confining metal species into a porous matrix, although supports rarely provide additional stabilization effects. Herein, we used silanol-rich layered zeolite, IPC-1P, to stabilize ultra-small Rh nanoparticles. By adjusting the interlayer space of the precursor through swelling, we prepared various architectures, including microporous Rh@IPC-4_C12 and disordered mesoporous Rh@IPC_C22. By in-situ scanning transmission electron microscopy, we confirmed that immobilized Rh nanoparticles are resistant to sintering at high temperatures (650 oC for 2hrs). Our density functional theory (DFT) calculations indicated that small Rh clusters strongly bind to the surface silanol quadruplets at IPC-1P layers through hydrogen transfer to the metallic particles, while high silanol density hinders migration on the surface. Ultimately, combining swelling with long-chain surfactant and utilizing metal-silanol interactions resulted in a novel, catalytically active zeolitic material termed Rh@IPC_C22. | Ang Li; Yuyan Zhang; Christopher Heard; Kinga Gołabek; Xiaohui Ju; Jiří Čejka; Michal Mazur | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Acid Catalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63247379e61502ffd71b0555/original/encapsulating-metal-nanoparticles-into-a-layered-zeolite-precursor-with-surface-silanol-nests-enhances-sintering-resistance.pdf |
60c74d5df96a007f6b287911 | 10.26434/chemrxiv.12543089.v2 | Water-Soluble Pyrene Tags Enable the Detection of Carbohydrates by Label-Assisted Laser Desorption/ionisation Mass Spectrometry | <div>Matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS) is widely used for the analysis of biomolecules. Label-assisted laser desorption/ionisation mass spectrometry (LALDI-MS) is a matrix-free variant of MALDI-MS, in which only analytes covalently attached to a laser desorption/ionisation (LDI) enhancer are detected. LALDI-MS has shown promise in overcoming limitations of MALDI-MS in terms of sample preparation and MS analysis. In this work, we have developed water-soluble pyrene-based LDI reagents (LALDI tags) that can be used for (in situ) labelling and LALDI-MS analysis of reducing carbohydrates from complex (biological) samples without the need for additional chemical derivatisation or purification. We have systematically explored the suitability of four pyrene-based LDI enhancers and three aldehyde-reactive handles, optimised sample preparation, and exemplified the use of a LALDI tag by the detection of lactose in cow’s milk. These results demonstrate that LALDI-MS is a promising technique for the analysis of reducing carbohydrates in biological samples, and pave the way for the development of LALDI-MS for glycomics and diagnostics.</div> | Jacob R Hauser; Edmund T Bergström; Alexander N. Kulak; Stuart L Warriner; Jane E Thomas-Oates; Robin Bon | Bioorganic Chemistry; Mass Spectrometry; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2020-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d5df96a007f6b287911/original/water-soluble-pyrene-tags-enable-the-detection-of-carbohydrates-by-label-assisted-laser-desorption-ionisation-mass-spectrometry.pdf |
61d1d7e57284d0304200a252 | 10.26434/chemrxiv-2021-csr9s-v3 | A simple setup miniaturization with multiple benefits for Green Chemistry in nanoparticle synthesis | The development of nanomaterials often relies on wet-chemical syntheses performed in reflux-setups using round-bottom-flasks. An alternative approach to synthesize nanomaterials is here presented that uses glass tubes designed for NMR analysis as reactors. This approach uses less solvent, uses less energy, generates less waste, provides safer conditions, is less prone to contamination and is compatible with high throughput screening. The benefits of this approach are illustrated by an in breadth study with the synthesis of gold, iridium, osmium and copper sulfide nanoparticles. | Jette Mathiesen; Susan Cooper; Andy Anker; Tiffany Kinnibrugh; Kirsten Jensen; Jonathan Quinson | Materials Science; Nanoscience; Materials Processing; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d1d7e57284d0304200a252/original/a-simple-setup-miniaturization-with-multiple-benefits-for-green-chemistry-in-nanoparticle-synthesis.pdf |
62f161a5e78f707e8c341180 | 10.26434/chemrxiv-2022-fxm6q | The Performance of Different Water Models on the Structure and Function of Cytochrome P450 Enzymes | Modelling approaches and modern simulations to investigate the biomolecular structure and function rely on various methods, one among which is the choice of the water model. Water molecules play a crucial role in all sorts of chemistry. Cytochrome P450 (CYP450), in particular, water molecules are crucial for the formation of active oxidants which perform the oxidation and metabolism of several substrates. Computational chemistry tools such as MD simulations and QM/MM calculations, nowadays, have become complementary tools to study the structure and functions of CYP450 enzymes, and therefore, accurate modeling of water molecules is crucial. In the present study, we have highlighted the behavior of the three most widely used water models—TIP3P, SPC/E, and OPC for three different CYP450 enzymes—CYP450BM3, CYP450OleT, and CYP450BSβ during MD simulations and QM/MM calculations. We studied the various properties such as RMSD, RMSF, H-bond, water occupancy in the first solvation shell, and Hydrogen Atom Transfer (HAT) using QM/MM calculations and compared them for all the three water models. Our study shows that the stability of the enzyme structure is well maintained in all three water models. However, OPC water model performs well for the polar active sites, i.e., in CYP450OleT, CYP450BSβ while the TIP3P water model is superior for the hydrophobic site such as CYP450BM3. | Shalini Yadav; Vandana Kardam; Ankita Tripathi; Shruti T G; Kshatresh Dubey | Theoretical and Computational Chemistry; Inorganic Chemistry; Catalysis; Kinetics and Mechanism - Inorganic Reactions; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f161a5e78f707e8c341180/original/the-performance-of-different-water-models-on-the-structure-and-function-of-cytochrome-p450-enzymes.pdf |
628b6a68d555501372a43029 | 10.26434/chemrxiv-2022-hcgq2 | Crystal chemistry and first principles devising of C4 as the simplest dense carbon allotrope | From crystal chemistry rationale and geometry optimization onto ground state structures with DFT-based computations, a novel ultra-hard body centered tetragonal C4 (tet-C4) is proposed as the simplest dense carbon allotrope. tet-C4 is identified as cohesive as diamond, and likewise built of corner sharing C4 tetrahedra in all directions. Qualified as mechanically stable from the elastic constants combinations, tet-C4 has Vickers hardness identical to that of both cubic and hexagonal (lonsdaleite) diamond. Dynamical stability of tet-C4 derived from all positive phonon bands also allows obtaining heat capacity close to the experimental data of diamond. The electronic band structure shows insulating tet-C4 with a large indirect band gap of 5 eV. | Samir F. Matar; Vladimir L. Solozhenko | Theoretical and Computational Chemistry; Materials Science; Carbon-based Materials; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628b6a68d555501372a43029/original/crystal-chemistry-and-first-principles-devising-of-c4-as-the-simplest-dense-carbon-allotrope.pdf |
67c69b71fa469535b9dbab5f | 10.26434/chemrxiv-2025-dwlbl | Photophysics of Resveratrol Derivatives for Singlet Oxygen Formation | Trans-resveratrol, a naturally occurring antioxidant, undergoes significant photochemical transformations upon UV irradiation, producing photoisomers and derivatives such as cis-resveratrol, 2,4,6-trihydroxy-phenanthrene (THP), and resveratrone. Using quantum chemical methods, we investigated the photophysical properties of these species, including their absorption spectra, fluorescence, and intersystem crossing (ISC) rates, to assess their potential for singlet oxygen generation. Our results indicate that while trans- and cis-resveratrol exhibit limited ISC, resveratrone and THP exhibit competitive ISC and fluorescence rates, making them suitable photosensitizers for singlet oxygen production at the same excitation energy as trans-resveratrol. However, THP is experimentally more abundant than resveratrone upon trans-resveratrol excitation and also demonstrates favorable ISC properties, suggesting that it plays a predominant role in singlet oxygen generation. These findings highlight the potential of resveratrone and THP in photodynamic applications, expanding the functional versatility of resveratrol-derived compounds. | Mariana Yoshinaga; Josene M. Toldo; Willian R. Rocha; Mario Barbatti | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c69b71fa469535b9dbab5f/original/photophysics-of-resveratrol-derivatives-for-singlet-oxygen-formation.pdf |
65beb92966c1381729e7d7c9 | 10.26434/chemrxiv-2024-qjdpn | Valorisation of Brewer’s Spent Grain: Lignocellulosic Fractionation and its Potential for Polymer and Composite Material Applications | An estimated amount of 40 million t/a of Brewer’s Spent Grain (BSG) is produced and is currently used for low-value valorisation or disposed of in landfills. In an era where non-renewable resources stocks are depleting and products such as plastics accumulate in the environment, the need for more sustainable resources, products and production strategies is substantial. Lignocellulosic biomasses, when their production is not in competition with the food sector, could be an answer to this challenge through the use of biorefineries. This review aims at gathering the advantages of BSG’s valorisation through the prism of building block production for polymer synthesis and its use as natural filler for composite material. BSG will also be compared to other biomasses by exploring the conditions available for its fractionation. The examples listed herein depict promising valorisation strategies with a myriad of building blocks available for the synthesis of organic compounds and polymers. The use of BSG as filler in composite materials, however, faces limitations in terms of performances that will need to be tackled in future works. A lot of research has yet to be performed on BSG’s valorisation to help shift the polymer and material industry towards a more sustainable horizon. | Sacha Pérocheau Arnaud | Polymer Science; Agriculture and Food Chemistry; Biopolymers; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65beb92966c1381729e7d7c9/original/valorisation-of-brewer-s-spent-grain-lignocellulosic-fractionation-and-its-potential-for-polymer-and-composite-material-applications.pdf |
657febe2e9ebbb4db92a8d79 | 10.26434/chemrxiv-2023-28rqm | Polyethylene Materials Bearing In-chain Mechanophores | Polyethylenes are recognized as fundamental plastic materials that are manufactured in the largest quantities among all synthetic polymers. The chemical inert nature of the saturated hydrocarbon chains is important for the storage and usage of polyolefin plastics, whereas has given rise to significant environmental challenges regarding plastic pollution. Here we report the synthesis of polyethylene materials bearing in-chain mechanophores via catalytic copolymerization of ethylene with cyclobutene-fused polar comonomers. Cyclobutane-fused mechanophores serve as mechanical gates to regulate the degradability of the polyethylene materials. Upon ultrasonication treatment, saturated hydrocarbon chains will transform to degradable backbones bearing acyclic imide units. Subsequent hydrolysis enables polymer chemical recycling to bifunctional small molecules. Such polyethylene materials possess an ideal combination of stability and accessible degradability. | Xiaohui Zhang; Yajun Zhao; Meng Chen; Shan Tang | Polymer Science; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657febe2e9ebbb4db92a8d79/original/polyethylene-materials-bearing-in-chain-mechanophores.pdf |
64207683647e3dca998a7d20 | 10.26434/chemrxiv-2023-0ndm7 | Radical Simplification of Complex Molecule Retrosynthesis Enabled by
Electrocatalytic Cross-Coupling of α-Substituted Carboxylic Acids | The polar retrosynthetic analysis has been widely employed in the field of organic synthesis and
forms the basis of undergraduate curriculum. Although most reactions in organic synthesis rely on
this rubric to guide their strategic application, their implementation often requires a long list of
ancillary considerations to mitigate chemoselectivity and oxidation state issues involving
protecting groups and precise reaction choreography. Here we demonstrate a complete departure
from this norm by the use of a radical based Ni/Ag-electrocatalytic cross coupling of α-substituted
carboxylic acids, thereby enabling an intuitive and modular approach to accessing complex
molecular architectures. This new method relies on a key silver additive that forms an active Ag-nanoparticle
coated electrode surface in situ along with carefully chosen ligands that modulate the
reactivity of Ni. Through judicious choice of conditions and ligands, the cross-couplings can be
rendered highly diastereoselective. To demonstrate the simplifying power of these reactions,
exceedingly concise syntheses of 14 natural products and two medicinally relevant molecules were
completed. | Benxiang Zhang; Jiayan He; Yang Gao; Laura Levy; Martins Oderinde; Maximilian Palkowitz; T. G. Murali Dhar; Michael Mandler; Michael Collins; Daniel Schmitt; Philippe Bolduc; TeYu Chen; Sebastian Clementson; Nadia Petersen; Gabriele Laudadio; Yu Kawamata; Phil Baran | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64207683647e3dca998a7d20/original/radical-simplification-of-complex-molecule-retrosynthesis-enabled-by-electrocatalytic-cross-coupling-of-substituted-carboxylic-acids.pdf |
66622680418a5379b03e896d | 10.26434/chemrxiv-2024-t8f81 | Arenesulfenyl Fluorides: Synthesis, Structure, and Reactivity | Sulfenyl fluorides are organic compounds of sulfur in formal oxidation state +2 with the formula R–S–F. Although the chloride, bromide, and iodide analogues have been extensively described in the literature, organic sulfenyl fluorides remain essentially unstudied. These structures have been implicated as putative intermediates in established processes to access polyfluorinated sulfur species; however, definitive and direct evidence of their existence has not been achieved, nor has a systematic understanding of their reactivity. Here, we report the synthesis, isolation, and spectroscopic characterization of several arenesulfenyl fluorides, including structural analysis of 2,4-dinitrobenzenesulfenyl fluoride by single-crystal X-ray diffraction. The functional group undergoes direct, efficient, and highly regioselective anti-addition to alkenes and alkynes, as well as insertion by carbenes. The resulting α- or β-fluoro thioether adducts can be readily transformed into useful fluorinated motifs, for example by modification of the sulfur groups (to sulfonamides or sulfonyl fluorides), by sulfur elimination (to generate formal C–H fluorination products), or by Julia–Kocienski olefination (to form vinyl fluorides). Thus, we establish that sulfenyl fluorides are unexpectedly accessible and stable compounds. Further, they serve as versatile reagents for the production of fluorinated organic compounds. | Nathan H. Faialaga; Dana P. Gephart; Breno D. Silva; Richard Liu | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66622680418a5379b03e896d/original/arenesulfenyl-fluorides-synthesis-structure-and-reactivity.pdf |
6516b6f8a69febde9eeacf2e | 10.26434/chemrxiv-2023-lbp9n | Elucidating the impact of Li3InCl6-coated LiNi0.8Co0.15Al0.05O₂ on the electro-chemo mechanics of Li6PS5Cl-based solid-state batteries | Li6PS5Cl has attracted much attention due to its high Li-ion conductivity and ease in processibility, which allows large-scale applications of solid-state batteries. However, when combined with high-voltage cathodes, Li6PS5Cl suffers from detrimental side reactions. Due to the stability towards high voltages combined with a relatively high Li-ion conductivity Li3InCl6 has been considered as catholyte with the potential to compensate Li6PS5Cl shortcomings. Despite previous claims about its (electro)chemical instability, we hypothesize that Li3InCl6 remains a promising choice when (i) triple junctions between Li3InCl6, Li6PS5Cl, and Ni-rich cathodes are avoided and (ii) the cut-off voltage is below 3.6 V (vs Li/In). Therefore, a core-shell-structured cathode, i.e., LiNi0.8Co0.15Al0.05O₂ particles with a 100 nm thick pin-hole-free Li3InCl6 layer, has been developed using mechanofusion. When employed in a solid-state battery with a cut-off voltage of 3.58V (vs Li/In) a specific capacity enhancement of about 80 mAh/g at any C-rate (0.1 to 1C) was achieved. The stability of Li3InCl6 as well as its functionality to prevent Li6PS5Cl from decomposition and cathode particles from mechanical degradation has been demonstrated, by synchrotron operando XRD and, e.g., post-mortem analysis using Plasma FIB SEM and XPS. This study shows that Li3InCl6 can be used as catholyte when applied appropriately. | Feng Jin; Hung Quoc Nguyen; Laras Fadillah; Torgeir Matre Sandvik; Yu Liu; Adrian Gacia-Martin; Elena Salagre; Enrique García Michel; Dragos Stoian; Kenneth Marshall; Wouter Van Beek; Daniel Rettenwander; Mir Mehraj Ud Din; Günther Redhammer | Physical Chemistry; Materials Science; Energy; Coating Materials; Energy Storage | CC BY 4.0 | CHEMRXIV | 2023-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6516b6f8a69febde9eeacf2e/original/elucidating-the-impact-of-li3in-cl6-coated-li-ni0-8co0-15al0-05o2-on-the-electro-chemo-mechanics-of-li6ps5cl-based-solid-state-batteries.pdf |
60c73dabbdbb8941caa37cbe | 10.26434/chemrxiv.6022919.v1 | Anti-proliferative Activity of N-Heterocyclic Carbenes Derived from Guanosine | Palladium(II) and platinum(II) complexes bearing N-heterocyclic carbene derived from Guanosine are synthesized via oxidative addition. Cytotoxicity of the compounds is evaluated with human embryonic kidney (HEK293) cells, glioblastoma (U251) cervical cancer (HeLa) cells and prostate cancer (PC3) cells. Compounds 2a, 2b and 3a are highly selective for glioblastoma.<br /> | Maria Inês Leitão; Federico Herrera; Ana Petronilho | Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems; Bioorganometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2018-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dabbdbb8941caa37cbe/original/anti-proliferative-activity-of-n-heterocyclic-carbenes-derived-from-guanosine.pdf |
60c751bc4c89194839ad4004 | 10.26434/chemrxiv.13200959.v1 | Investigation of Island/ Single Core and Archipelago/ Multicore Enriched Asphaltenes and Their Solubility Fractions by Thermal Analysis Coupled to High Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry | <p>Despite extensive research, the molecular-level chemical characterization of asphaltenes, a highly aromatic solubility fraction of petroleum, remains an analytical challenge. This fraction is related to diverse problems in crude oil exploration, transportation, and refining. Two asphaltene architecture motifs are commonly discussed in literature, “island” (single core) and “archipelago” (multicore) type structures. The thermal desorption and pyrolysis behavior of island- and archipelago-enriched as-phaltenes and their extrography fractions was investigated. For this purpose, the evolved chemical pattern was investigated by thermal analysis coupled to ultrahigh resolution mass spectrometry (FT-ICR MS). Soft atmospheric pressure chemical ionization preserved the molecular information of the thermal emission profile. Time/temperature-resolved analysis allowed the chemical characterization of occluded material as well as of asphaltene building blocks during pyrolysis.</p><p>Regarding the thermogravimetric information, the island-type enriched sample (Wyoming asphal-tenes) revealed a significantly higher coke residue after the pyrolysis process compared to the archi-pelago-type enriched sample (Athabasca asphaltenes). In contrast to whole asphaltenes, extrograph-ic fractions revealed occluded material evolved during the desorption phase. For the acetone frac-tion, this effect was most abundant and suggests cooperative aggregation.</p><p>Pyrolysis revealed a bimodal behavior for most of the compound classes suggesting the presence of both architecture motifs in each asphaltene. DBE versus #C diagrams of the pyrolysis molecular pro-file revealed specific compositional trends: compounds with high DBE values and short alkylation likely to be originated from island-type asphaltenes, whereas species with low DBE values and high carbon numbers likely derive from archipelago-type asphaltenes.</p><p>In the asphaltene structural debate, thermal analysis ultrahigh resolution mass spectrometry serves as additional technique and supplements results obtainable by other techniques, such as direct infu-sion approaches. Consistent results on the structural motifs are indicated by the molecular finger-print visualized by DBE versus #C diagrams and serve as measure for the dominance of a structural motif.</p> | Anika Neumann; Martha L. Chacón-Patiño; Ryan P. Rodgers; Christopher Rüger; Ralf Zimmermann | Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751bc4c89194839ad4004/original/investigation-of-island-single-core-and-archipelago-multicore-enriched-asphaltenes-and-their-solubility-fractions-by-thermal-analysis-coupled-to-high-resolution-fourier-transform-ion-cyclotron-resonance-mass-spectrometry.pdf |
62a97a52eb1f0c561089748f | 10.26434/chemrxiv-2022-lc84d | Deep Learning-Based Increment Theory for Formation Enthalpy Predictions | Quantitative predictions of molecular thermochemistry, such as formation enthalpy, have been limited for complicated species due to a lack of available training data. Such predictions would be important in predicting reaction thermodynamics and constructing kinetic models. We introduce a graph-based deep learning approach that can separately learn the enthalpy contribution of each atom in its local environment and consider the effect of overall molecular structure. Because this approach follows the additivity scheme of increment theory, it can be generalized to larger and more complicated species not present in the training data. We demonstrate that our model can outperform the conventional increment theory in the predictions of formation enthalpy. We expect this approach will also enable rapid prediction of other extensive properties of large molecules that are difficult to derive from experiments or ab initio calculation. | Lung-Yi Chen; Ting-Wei Hsu; Tsai-Chen Hsiung; Yi-Pei Li | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a97a52eb1f0c561089748f/original/deep-learning-based-increment-theory-for-formation-enthalpy-predictions.pdf |
61a51cd75f114d0e3f6b5355 | 10.26434/chemrxiv-2021-knxg8 | Understanding Solution State Conformation and Aggregate Structure of Conjugated Polymers via Small Angle X-ray Scattering | Donor-acceptor (D-A) conjugated polymers are high-performance organic electronic materials that exhibit complex aggregation behavior. Understanding the solution state conformation and aggregation of conjugated polymers is crucial for controlling morphology during thin-film deposition and the subsequent electronic performance. However, a precise multiscale structure of solution state aggregates is lacking. Here, we present an in-depth small angle X-ray scattering (SAXS) analysis of the solution state structure of an isoindigo-bithiophene based D-A polymer (PII-2T) as our primary system. Modeling the system as a combination of hierarchical fibrillar aggregates mixed with dispersed polymers, we extract information about conformation and multiscale aggregation and also clarify the physical origin of features often observed but unaddressed or misinterpreted in small-angle scattering patterns of conjugated polymers. The persistence length of the D-A polymer extracted from SAXS agrees well with a theoretical model based on the dihedral potentials. Additionally, we show that the broad high q structure factor peak seen in scattering profiles can be attributed to lamellar stacking occurring within the fibril aggregates and that the low q aggregate scattering is strongly influenced by the polymer molecular weight. Overall, the SAXS profiles of D-A polymers in general exhibit a sensitive dependence on the co-existence of fibrillar aggregate and dispersed polymer chain populations. We corroborate our findings from SAXS with electron microscopy of freeze-dried samples for direct imaging of fibrillar aggregates. Finally, we demonstrate the generality of our approach by fitting the scattering profiles of a variety of D-A polymers. The results presented here establish a picture of the D-A polymer solution state structure and provide a general method of interpreting and analyzing their scattering profiles. | Justin J. Kwok; Kyung Sun Park; Bijal B. Patel; Rishat Dilmurat; David Beljonne; Xiaobing Zuo; Byeongdu Lee; Ying Diao | Materials Science; Polymer Science; Nanoscience; Aggregates and Assemblies; Fibers; Conducting polymers | CC BY 4.0 | CHEMRXIV | 2021-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a51cd75f114d0e3f6b5355/original/understanding-solution-state-conformation-and-aggregate-structure-of-conjugated-polymers-via-small-angle-x-ray-scattering.pdf |
67111a9fcec5d6c1426c6d3c | 10.26434/chemrxiv-2024-kbcdf-v2 | Atomic View of Photosynthetic Metabolite Permeability Pathways and Confinement in Cyanobacterial Carboxysomes | Carboxysomes are protein microcompartments found in cyanobacteria, whose shell encapsulates rubisco at the heart of carbon fixation in the Calvin-cycle. Carboxysomes are thought to locally concentrate CO2 in the shell interior to improve rubisco efficiency through selective metabolite permeability, creating a concentrated catalytic center. However, permeability coefficients have not previously been determined for these gases, or for Calvin-cycle intermediates such as bicarbonate (HCO3-), 3-phosphoglycerate (3-PGA), or ribulose-1,5-bisphosphate (RuBP). Starting from a high resolution cryo-EM structure of a synthetic beta-carboxysome shell, we perform unbiased all-atom molecular dynamics (MD) to track metabolite permeability across the shell. The synthetic carboxysome shell structure, lacking the BMC trimer proteins and encapsulation peptides, is found to have similar permeability coefficients for multiple metabolites, and is not selectively permeable to HCO3- relative to CO2. To resolve how these comparable permeabilities can be reconciled with the clear role of the carboxysome in the CO2-concentrating mechanism in cyanobacteria, complementary atomic-resolution Brownian Dynamics (ARBD) simulations estimate the mean first passage time for CO2 assimilation in a crowded model carboxysome. Despite a relatively high CO2 permeability of approximately 10^-2 cm/s across the carboxysome shell, the shell proteins reflect enough CO2 back towards rubisco that 2650 CO2 molecules can be fixed by rubisco for every 1 CO2 molecule that escapes under typical conditions. The permeabilities determined from all-atom molecular simulation are key inputs into flux modeling, and the insight gained into carbon fixation can facilitate the engineering of carboxysomes and other bacterial microcompartments for multiple applications. | Daipayan Sarkar; Christopher Maffeo; Markus Sutter; Aleksei Aksimentiev; Cheryl Kerfeld; Josh Vermaas | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2024-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67111a9fcec5d6c1426c6d3c/original/atomic-view-of-photosynthetic-metabolite-permeability-pathways-and-confinement-in-cyanobacterial-carboxysomes.pdf |
60c750ea469df4432ef44934 | 10.26434/chemrxiv.13096601.v1 | Exploration and Optimization in Crystal Structure Prediction: Combining Basin Hopping with Quasi-Random Sampling | We describe the implementation of a Monte Carlo basin hopping global optimization procedure for the prediction of molecular crystal structure. The basin hopping method is combined with quasi-random structure generation in a hybrid method for crystal structure prediction, QR-BH, which combines the low-discrepancy sampling provided by quasi-random sequences with basin hopping's efficiency at locating low energy structures. Through tests on a set of single-component molecular crystals and co-crystals, we demonstrate that QR-BH provides faster location of low energy structures than pure quasi-random sampling, while maintaining the efficient location of higher energy structures that are important for identifying important polymorphs. | Shiyue Yang; Graeme Day | Supramolecular Chemistry (Org.); Computational Chemistry and Modeling; Self-Assembly; Structure; Materials Chemistry; Crystallography; Crystallography – Organic | CC BY 4.0 | CHEMRXIV | 2020-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750ea469df4432ef44934/original/exploration-and-optimization-in-crystal-structure-prediction-combining-basin-hopping-with-quasi-random-sampling.pdf |
65e2949266c1381729fed226 | 10.26434/chemrxiv-2024-1bg6h | Colorimetric detection of fentanyl using a supramolecular displacement assay | Fentanyl is a potent synthetic opioid with an alarmingly low lethal dosage of 2 mg. The equipment necessary to detect fentanyl in field settings (e.g., handheld spectrometers) is restricted to highly trained, well-funded, and specialized personnel. Established point-of-need technologies, such as lateral flow immunochromatographic strips, are available; however, they often involve multiple contact-based steps (e.g., collection, mixing) that pose a higher risk to users handling unknown substances. Herein, we developed a colorimetric displacement assay capable of contactless detection of fentanyl as liquid or solid samples. The basis of our assay relies on the presence of fentanyl to displace a redox mediator, ferrocene carboxylic acid, inclusively bound in the cavity of a supramolecular host, CB[7]. The displacement is only possible in the presence of high affinity binding guests, like fentanyl (KA ~ 106 M-1). The liberated redox guest can then react with indicator reagents that are free in solution, producing either: (i) a distinct blue color to indicate the presence of fentanyl or (ii) remain a pale blue tint in the absence of fentanyl. We demonstrate rapid and specific detection of fentanyl free base and fentanyl derivatives (e.g., acetyl fentanyl, furanyl fentanyl) against a panel of 9 other common drugs of abuse (e.g., morphine, cocaine, heroin). Furthermore, we highlight the intended use of this assay by testing grains of fentanyl derivatives on a surface with a drop (i.e., 25 µL) of assay reagent. We anticipate this approach can be applied broadly to identify the presence of fentanyl at the point of need. | Andrea C. Mora; Madeline Vara; Patrick Reust; Amanda Code; Piercen Oliver; Charles R. Mace | Physical Chemistry; Analytical Chemistry; Analytical Chemistry - General; Environmental Analysis; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e2949266c1381729fed226/original/colorimetric-detection-of-fentanyl-using-a-supramolecular-displacement-assay.pdf |
64fb69c5b338ec988a215f3f | 10.26434/chemrxiv-2023-7dspf-v2 | Catalytic Photoredox Carbobromination of Unactivated Alkenes with a-Bromocarbonyls via Mechanistically Distinct Radical-Addition Radical-Pairing Pathway | We disclose a catalytic photoredox carbobromination of unactivated alkenes with -bromocarbonyl compounds under a blue LED light. The reaction proceeds with -bromoesters, -bromonitriles and -bromo--lactones along with terminal and 1,2-disubstituted internal alkenes. Reactions with indenes and 1,1-disubstituted alkenes generate alkylated alkenes. Mecha-nistic studies by product selectivity and three-way competitive crossover experiments suggest that the reaction operates by a unique radical-addition radical-pairing (RARP) mechanism. The catalytic turnover is achieved by a single electron reduction of PC•+ by Br‒, rather than by alkyl radical (R•), and the product is generated by the pairing of Br• and R•, instead of the combination of Br‒ and a carbocation (R+). | Harshvardhan Singh; Raj Kumar Tak; Dhruba Poudel; Ramesh Giri | Organic Chemistry; Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fb69c5b338ec988a215f3f/original/catalytic-photoredox-carbobromination-of-unactivated-alkenes-with-a-bromocarbonyls-via-mechanistically-distinct-radical-addition-radical-pairing-pathway.pdf |
60c7488cbb8c1a42e73dacbf | 10.26434/chemrxiv.11925618.v1 | Recognition-Control and Host-Guest Interactions in High-Symmetry Cocrystals of Fullerenes with Cubane and Mesitylene | The limited success in the prediction of structure is one of the most serious problems in the engineering of molecular crystals. Here we show that the packing of high-symmetry molecules such as ball-shaped rotating fullerenes, cube-shaped cubane and octahedral-shaped mesitylene dimers give rise to the formation of cubic cocrystals with easily predictable lattice parameters. We present the synthesis and structure determination of Sc3N@C80-Ih cocrystals with cubane (C8H8) and mesitylene (C9H12) and compare the new materials with related C60 and C70 based structures. In this family of materials, most atom-to-atom interactions are averaged out by the symmetry and the crystal structures can be described in terms of classical molecule-to-molecule interactions. Size-dependent homo- and heteromolecular contacts control the stability of the ball-cube and ball-octahedron systems creating several host-guest and recognition-controlled regions. The analysis of the global phase diagrams explains not only the stability of the observed materials, but also the instability of a missing derivative. | Gábor Bortel; Éva Kováts; Dávid Földes; Emma Jakab; Gábor Durkó; Sándor Pekker | Carbon-based Materials; Supramolecular Chemistry (Inorg.); Theory - Computational; Structure; Crystallography; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7488cbb8c1a42e73dacbf/original/recognition-control-and-host-guest-interactions-in-high-symmetry-cocrystals-of-fullerenes-with-cubane-and-mesitylene.pdf |
60c74761469df4955bf437e2 | 10.26434/chemrxiv.11514189.v2 | RASS-Enabled S/P–C and S–N Bond Formation for DEL Synthesis | DNA Encoded Libraries have shown promise as a valuable technology for democratizing the hit discovery process. Although DEL provides relatively inexpensive access to libraries of unprecedented size, their production has been hampered by the idiosyncratic needs of the encoding DNA tag relegating DEL compatible chemistry to dilute aqueous environments. Recently Reversible Adsorption to Solid Support (RASS) has been demonstrated as a promising method to expand DEL reactivity using standard organic synthesis protocols. Here we demonstrate a suite of on-DNA chemistries to incorporate medicinally relevant and C–S, C–P and N–S linkages into DELs, which are underrepresented in the canonical methods. | Dillon T. Flood; Xuejing Zhang; Xiang Fu; Zhenxiang Zhao; Shota Asai; Brittany Sanchez; Emily J. Sturgell; Julien C. Vantourout; Paul Richardson; Mark E. Flanagan; David W. Piotrowski; Dominik K Kölmel; Jinqiao Wan; Yong Chang; Zhao Wang; Jason Chen; Phil Baran; Philip Dawson | Bioorganic Chemistry; Combinatorial Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74761469df4955bf437e2/original/rass-enabled-s-p-c-and-s-n-bond-formation-for-del-synthesis.pdf |
62be7421f5193953b47acbbc | 10.26434/chemrxiv-2022-p3nsg | Metal-support interactions in molecular single-site cluster catalysts | This study provides atomistic insights into the interface between a single-site catalyst and a transition metal chalcogenide support and illustrates how their cooperativity can be harnessed to modulate catalytic activity. A molecular platform MCo6Se8(PEt3)4(L)2 (1-M, M = Cr, Mn, Fe, Co, Cu, Zn) was designed in which the active site (M)/support (Co6Se8) interactions are interrogated by sys-tematically probing the electronic and structural changes that occur as the identity of the metal varies. All 3d transition metal 1-M clusters display remarkable catalytic activity for coupling tosyl azide and tert-butyl isocyanide, with Mn and Co derivatives show-ing the fastest turnover in the series. Detailed structural, electronic, and magnetic characterization of the clusters was performed using single crystal X-ray diffraction, 1H and 31P nuclear magnetic resonance spectroscopy, electronic absorption spectroscopy, cyclic voltammetry, and computational methods. Distinct metal/support redox regimes can be accessed in 1-M based on the energy of the edge metal’s frontier orbitals with respect to those of the cluster support. As the degree of electronic interaction between the edge and the support increases, a cooperative regime is reached wherein the support can deliver electrons to the catalytic site, in-creasing the reactivity of key metal-nitrenoid intermediates. | Benjamin S. Mitchell; Andrei Chirila; Jonathan A. Kephart; Andrew C. Boggiano; Sebastian M. Krajewski; Dylan Rogers; Werner Kaminsky; Alexandra Velian | Inorganic Chemistry; Nanoscience; Nanocatalysis - Catalysts & Materials; Coordination Chemistry (Inorg.); Reaction (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62be7421f5193953b47acbbc/original/metal-support-interactions-in-molecular-single-site-cluster-catalysts.pdf |
60c750e49abda2198bf8dafb | 10.26434/chemrxiv.13086023.v1 | Instrument-Free Protein Microarray Fabrication for Accurate Affinity Measurements | Protein microarrays have gained popularity as an attractive tool for
various fields, including drug and biomarker development, and diagnostics.
Thus, multiplexed binding affinity measurements in microarray format has become
crucial. The preparation of microarray-based protein assays relies on precise dispensing
of probe solutions to achieve efficient immobilization onto an active
surface. The prohibitively high cost of
equipment and the need for trained personnel to operate high complexity robotic
spotters for microarray fabrication are significant detriments for researchers,
especially for small laboratories with limited resources. Here, we present a
low-cost, instrument-free dispensing technique by which users who are
familiar with micropipetting can manually create multiplexed protein assays
that show improved capture efficiency and noise level in comparison to that of
the robotically spotted assays. In this study, we compare the efficiency of
manually and robotically dispensed α-Lactalbumin probe spots by analyzing
the binding kinetics obtained from the interaction with anti-α-Lactalbumin
antibodies, using the interferometric reflectance imaging sensor platform. We
show that the protein arrays prepared by micropipette manual spotting meet and
exceed the performance of those prepared by state-of-the-art robotic spotters.
These instrument-free protein assays have higher binding signal (~4-fold
improvement) and a ~3-fold better signal-to-noise ratio (SNR) in binding curves,
when compared to the data acquired by averaging of 75 robotic spots
corresponding to the same effective sensor surface area. We demonstrate the
potential of determining antigen-antibody binding coefficients in 24-multiplexed
chip format with less than 5% measurement error. | Iris Celebi; Matthew T. Geib; Elisa Chiodi; Nese Lortlar Ünlü; Fulya Ekiz Kanik; M. Selim Ünlü | Bioengineering and Biotechnology; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750e49abda2198bf8dafb/original/instrument-free-protein-microarray-fabrication-for-accurate-affinity-measurements.pdf |
60c7551b567dfe189bec61d1 | 10.26434/chemrxiv.14043740.v1 | Materials Genes of Heterogeneous Catalysis from Clean Experiments and Artificial Intelligence | Heterogeneous catalysis is an example of a complex materials function, governed by an intricate interplay of several processes, e.g., the different surface chemical reactions, and the dynamic re-structuring of the catalyst material at reaction conditions. Modelling the full catalytic progression via first-principles statistical mechanics is impractical, if not impossible. Instead, we show here how a tailored artificial-intelligence approach can be applied, even to a small number of materials, to model catalysis and determine the key descriptive parameters ("materials genes") reflecting the processes that trigger, facilitate, or hinder catalyst performance. We start from a consistent experimental set of "clean data", containing nine vanadium-based oxidation catalysts. These materials were synthesized, fully characterized, and tested according to standardized protocols. By applying the symbolic-regression SISSO approach, we identify correlations between the few most relevant materials properties and their reactivity. This approach highlights the underlying physicochemical processes, and accelerates catalyst design.<br /> | Lucas Foppa; Luca Ghiringhelli; Frank Girgsdies; Maike Hashagen; Pierre Kube; Michael Hävecker; Spencer J. Carey; Andrey Tarasov; Peter Kraus; Frank Rosowski; Robert Schlögl; Annette Trunschke; Matthias Scheffler | Catalysts; Kinetics and Mechanism - Inorganic Reactions; Reaction (Inorg.); Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2021-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7551b567dfe189bec61d1/original/materials-genes-of-heterogeneous-catalysis-from-clean-experiments-and-artificial-intelligence.pdf |
632dd805e665bda75a1002f8 | 10.26434/chemrxiv-2022-77x33 | Testing the Efficacy of the ‘Corsi-Rosenthal’ Box Fan Filter in an Active Classroom Environment | Poor ventilation in classrooms can increase the risk of infectious disease transmission, such as COVID-19, because it allows respiratory aerosol particles that may contain viruses to accumulate. Air purifiers can effectively reduce transmission rates in community spaces, including classrooms, because they increase the air change rate in the room and reduce particle concentrations. In this study, we investigate the effectiveness of Corsi-Rosenthal Boxes (C-R Box) in reducing particle concentrations in active, occupied classroom settings. A C-R Box is a do-it-yourself, cost-effective alternative to commercial air purifiers built from a box fan, four readily available filters, cardboard, and duct tape. We collected measurements of coarse (particles with diameters > 2.5μm) and fine (particles with diameters 0.5μm - 2.5 μm) particle number concentrations and PM2.5 (particles with diameter < 2.5μm) mass concentrations. Specifically, we compared measurements in occupied classrooms before and after we turned the C-R Boxes on. In our testing, C-R Boxes reduced fine particle number concentrations by 56-91% and PM2.5 mass concentrations by over 70% after we turn on the C-R Boxes. We also simulated velocity profiles in the classrooms with running C-R Boxes showing mixing throughout the classroom ensuring that all air can encounter the filter. | William Gasparrini; Sharmin Akter; Britney Russell; Fayekah Assanah; Doug Brugge; Michelle Cole; Marina Creed; Sarah Laskowski; Angela Starkweather; Kristina Wagstrom | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632dd805e665bda75a1002f8/original/testing-the-efficacy-of-the-corsi-rosenthal-box-fan-filter-in-an-active-classroom-environment.pdf |
62cdabd327b1e4837836ea9a | 10.26434/chemrxiv-2022-w2th1 | A Monoboranyl Analogue of 1,2-bis(di-tert-butylphosphino)ethane | Examples of unsymmetric diphosphines, especially those with customized secondary coordination spheres, are rare. Herein, we provide an approach towards a Lewis acid-containing analogue of the bulky diphosphine, 1,2-bis(di-tert-butylphosphino)ethane that contains a single boron moiety. The coordination chemistry of this ligand and its allyl precursor have been explored using nickel(0). | Marissa Clapson; Harvey Sharma; Joseph Zurakowski; Marcus Drover | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Coordination Chemistry (Organomet.); Ligands (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cdabd327b1e4837836ea9a/original/a-monoboranyl-analogue-of-1-2-bis-di-tert-butylphosphino-ethane.pdf |
643561d20784a63aeeef257c | 10.26434/chemrxiv-2023-gbtx9 | Merging Boron and Carbonyl based MR-TADF Emitter Designs to Achieve High Performance Deep Blue OLEDs | Multiresonant thermally activated delayed fluorescence (MR-TADF) compounds are attractive as emitters for organic light-emitting diodes (OLEDs) as they simultaneously can harvest both singlet and triplet excitons to produce light and show very narrowband emission, which translates to excellent colour purity. Here, we report the first example of a MR-TADF emitter (DOBDiKTa) that fuses together fragments from the two major classes of MR-TADF compounds, those containing boron and those containing carbonyl groups as acceptor fragments in the polycyclic aromatic hydrocarbon skeleton. Using this molecular design, this compound shows desirable narrowband deep blue emission and efficient TADF character. The OLED with DOBDiKTa as the emitter and mCP:PPT (1:1) as the co-host exhibits an EQEmax of 17.4%, an efficiency roll-off of 32% at 100 cd m-2, and CIE coordinates of (0.14, 0.12). Compared to DOBNA and DiTKa, DOBDiKTa shows higher device efficiency with reduced efficiency roll-off while maintaining a narrow pure blue electroluminescence, which demonstrates the promise of the proposed molecular design. | Sen Wu; Le Zhang; Jingxiang Wang; Abhishek Kumar Gupta; Ifor Samuel; Eli Zysman-Colman | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643561d20784a63aeeef257c/original/merging-boron-and-carbonyl-based-mr-tadf-emitter-designs-to-achieve-high-performance-deep-blue-ole-ds.pdf |
6611a6f591aefa6ce1f97f05 | 10.26434/chemrxiv-2024-vptmp-v2 | Modern Electrospray Ionization Mass Spectrometry Techniques for the Characterisation of Supramolecules and Coordination Compounds | Mass spectrometry is routinely used for myriad applications in clinical, industrial, and research laboratories worldwide. Developments in the areas of ionisation sources, high-resolution mass analysers, tandem mass spectrometry, and ion mobility have significantly extended the repertoire of mass spectrometrists, however for coordination compounds and supramolecules, mass spectrometry remains underexplored and arguably underappreciated. Here, the reader is guided through different tools of modern electrospray ionization mass spectrometry that are suitable for larger inorganic complexes. All steps, from sample preparation and technical details to data analysis and interpretation are discussed. The main target audience of this tutorial are synthetic chemists as well as technicians/mass spectrometrists with little experience in characterising labile inorganic compounds. | Niklas Geue | Inorganic Chemistry; Analytical Chemistry; Mass Spectrometry; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6611a6f591aefa6ce1f97f05/original/modern-electrospray-ionization-mass-spectrometry-techniques-for-the-characterisation-of-supramolecules-and-coordination-compounds.pdf |
60c74476842e652c8adb246b | 10.26434/chemrxiv.9795338.v1 | A Transient Directing Group Strategy Enables Enantioselective Reductive Heck Hydroarylation of Alkenes | <p>Metal-coordinating directing groups have seen extensive use in the field of transition-metal-mediated functionalization of alkenes; however, their waste-generating installation and removal steps limit the efficiency and practicality of reactions that rely on their use. Inspired by developments in the field of C–H activation, herein we report a transient directing group approach to reductive Heck hydroarylation of alkenyl benzaldehyde substrates that proceeds under mild conditions. Highly stereoselective migratory insertion is facilitated by in situ formation of an imine from catalytic amounts of commercially available amino acid additive. Computational studies reveal an unusual mode of enantioinduction by the remote chiral center in the transient directing group.</p> | Lucas Oxtoby; Zi-Qi Li; Van Tran; Tuğçe Erbay; Ruohan Deng; Peng Liu; Keary Engle | Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74476842e652c8adb246b/original/a-transient-directing-group-strategy-enables-enantioselective-reductive-heck-hydroarylation-of-alkenes.pdf |
61042cd2032114ad33b8dc9a | 10.26434/chemrxiv-2021-7pdz9 | CRISPR-Click Enables Multi-Gene Editing with Modular Synthetic sgRNAs | Gene editing systems such as CRISPR/Cas9 readily enable individual gene phenotypes to be studied through loss-of-function. However, in certain instances, gene compensation can obfuscate the results of these studies, necessitating the editing of multiple genes to properly identify biological pathways and protein function. Performing multiple genetic modifications in cells remains difficult due to the requirement for multiple rounds of gene editing. While fluorescently labeled guide RNAs (gRNAs) are routinely used in laboratories for targeting CRISPR/Cas9 to disrupt individual loci, technical limitations in single guide RNA (sgRNA) synthesis hinder the expansion of this approach to multi-color cell sorting. Here, we describe a modular strategy for synthesizing sgRNAs where each target sequence is conjugated to a unique fluorescent label, which enables fluorescence-assisted cell sorting (FACS) to isolate cells that incorporate the desired combination of gene-editing constructs. We demonstrate that three short strands of RNA functionalized with strategically placed 3’-azide and 5’-alkyne terminal deoxyribonucleotides can be assembled in a one-step, template-assisted, copper-catalyzed alkyne-azide cycloaddition (CuAAC) to generate fully functional, fluorophore-modified sgRNAs. Using these synthetic sgRNA in combination with FACS, we achieved selective cleavage of two targeted genes, either separately as a single color experiment or in combination as a dual-color experiment. These data indicate that our strategy for generating doubly-clicked sgRNA allows for Cas9 activity in cells. By minimizing the size of each RNA fragment to 41 nucleotides or less, this strategy is well suited for custom, scalable synthesis of sgRNAs. | Hansol Park; Eiman Osman; Christopher Cromwell; Christopher St. Laurent; Yuning Liu; Elena Kitova; John Klassen; Basil Hubbard; Matthew Macauley; Julianne Gibbs | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61042cd2032114ad33b8dc9a/original/crispr-click-enables-multi-gene-editing-with-modular-synthetic-sg-rn-as.pdf |
65a74e07e9ebbb4db954d764 | 10.26434/chemrxiv-2024-t95cn | Synthesis and Characterization of Naphthalimide Diazene-Based Fluorescence Turn-on Molecules Responsive to Sulfinates | The synthesis and characterization of sulfinate addition-responsive turn-on fluorescent molecules are described. Sulfinate addition to diazene-substituted naphthalimide under sulfonyl radical conditions afforded the sulfonyl hydrazides with high quantum yields (up to 0.91 in THF and 0.54 in methanol), which exhibited a large Stokes shift (105 nm) in protic methanol solvent. | Hiroki Tanimoto; Shogo Kyogaku; Aoi Otsuki; Takenori Tomohiro | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a74e07e9ebbb4db954d764/original/synthesis-and-characterization-of-naphthalimide-diazene-based-fluorescence-turn-on-molecules-responsive-to-sulfinates.pdf |
677d0a466dde43c90899f1d7 | 10.26434/chemrxiv-2025-pf0tn | Investigating substrate binding mechanism in prolyl oligopeptidase through molecular dynamics | Prolyl oligopeptidase (PREP) has gained attention for its role in neurodegenerative diseases, particularly through protein-protein interactions with amyloid proteins such as alpha-synuclein and Tau. Although significant research has focused on PPIs, the substrate-binding dynamics within the catalytic pocket of PREP is less understood. This study combines molecular docking and molecular dynamics simulations to investigate the behavior of known PREP substrates, including thyrotropin-releasing hormone. Our simulations reveal that TRH transitions between three preferred regions within the binding pocket, one of which is favorable for catalytic activity. The absence of a single fixed binding site near the catalytic triad region may suggest a dynamic substrate-processing mechanism. Additionally, the potential of the TRH precursor as a substrate is evaluated. Our findings highlight the utility of computational methods in the analysis of protein dynamics and enzymatic mechanisms, offering insights into the functional versatility of PREP. | Sylwia Czach; Katarzyna Walczewska-Szewc | Theoretical and Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677d0a466dde43c90899f1d7/original/investigating-substrate-binding-mechanism-in-prolyl-oligopeptidase-through-molecular-dynamics.pdf |
65707f43cf8b3c3cd7e9721a | 10.26434/chemrxiv-2023-qdbkr-v4 | Catalytic transfer hydrogenolysis of switchgrass lignin with ethanol using spinel-type mixed-metal oxide catalysts affords control of the oxidation state of isolated aromatic products | Chemical reductions of lignin are useful to remove oxygen and create product slates that can function as renewable platform molecules for new fuels and chemicals. Catalytic transfer hydrogenolysis (CTH) is an underexplored method to conduct reductions of lignin that obviates the use of dangerous and non-renewable hydrogen gas. While noble metals are used extensively as catalysts for transfer hydrogenation, one major challenge for their deployment is related to their sustainability. In this work, we synthesized mixed-metal oxides of earth-abundant Co and Ni. We characterized these catalysts using powder x-ray diffraction (XRD) and tested their reactivity for CTH of acetophenone. Among the catalysts we tested, we noted that the spinel NiCo2O4 demonstrated the highest conversion of acetophenone (75%) and highest selectivity for ethylbenzene (90%), so we applied it to valorization of switchgrass lignin extracted under mild operating conditions by cosolvent enhanced lignocellulosic fractionation (CELF). The catalytically depolymerized lignin showed an increase in selectively deoxygenated monomeric compounds. Using 2D-NMR spectroscopy, we demonstrated the lignin displayed highly reduced aliphatic carbons resulting from the reduction reaction at the Cα sites mediated by our catalyst material. These results are critical to the further development of the lignin-first biorefinery as they demonstrate the use of sustainable catalyst materials and mild transformation conditions to generate and refine a suite of new bioproducts. | James Godwin; Jonah Babusci; Nichole Wonderling; Jeffrey Shallenberger; Kendhl Seabright; David Harper; Stephen Chmely | Catalysis; Agriculture and Food Chemistry; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65707f43cf8b3c3cd7e9721a/original/catalytic-transfer-hydrogenolysis-of-switchgrass-lignin-with-ethanol-using-spinel-type-mixed-metal-oxide-catalysts-affords-control-of-the-oxidation-state-of-isolated-aromatic-products.pdf |
62c62a42244ce0d43b3cf0e6 | 10.26434/chemrxiv-2022-4ngk1 | Anti-Kasha Fluorescence in Molecular Entities: The Central Role of the Electron-Vibrational Coupling
| According to Kasha’s rule, emission of a photon in a molecular system always comes from the lowest excited state. A corollary of this rule, i.e., the Kasha-Vavilov rule, states that the emission spectra are independent of the excitation wavelength. Although these rules apply for most of the molecular systems, violations of these rules are often reported for molecular systems. The prototypical case of a Kasha’s rule violation is the fluorescence observed from S2 in azulene. Thanks to the advances in both theoretical and experimental research, other types of anomalous fluorescence arising from higher-lying excited states (e.g., excitation energy transfer (EET)-based dual emissions, thermally-activated fluorescence etc.), and which mechanistically differ from the azulene-like anomalous fluorescence, are more recurrently reported in the literature. However, the underlying mechanisms leading to these anomalous emissions can be numerous and they are not yet well understood.
In order to shed some light into the above phenomena, this account provides a comprehensive review on this topic. We herein report quantum chemical investigations in target molecular systems breaking Kasha’s rule. The latter molecules were chosen as they were unambiguously reported to display anti-Kasha fluorescence. Our studies highlight three different types of anti-Kasha scenarios. Specifically, i) the strong electronic-, weak vibrational-nonadiabatic coupling (NAC) regime (here named as Type I case, i.e., azulene-like); ii) the strong electronic-, strong vibrational-NAC regime (Type II case, i.e., thermally-activated S2 fluorescence); and the iii) very weak electronic NAC regime (Type III case, i.e., EET dyads). In addition, by combining state-of-the-art quantum chemical calculations with excited-state decay rate theories and appropriate excited-state kinetic models, we provide semi-quantitative estimations of photoluminescence quantum yields for the most rigid molecular entities. Finally, we propose the use of simple theoretical descriptors relying on calculations of the excited-state density difference and the electron-vibrational coupling to classify anomalous emissions according to their coupling scenario.
Besides the fundamental interest of the above investigations, the herein developed computational protocols and descriptors will be useful for the tailored design of dyes with tunable and unconventional fluorescence properties and their exploitation in a wide range of areas, i.e., from organic-light emitting diodes (OLEDs) to bioimaging, small molecule fluorescent probes and photocatalysis. Finally, our theoretical framework enables attaining a holistic understanding of the interconversion processes between excited states, where the electron-vibrational coupling is shown to play a central role in determining the efficacy.
| Koen Veys; Daniel Escudero | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c62a42244ce0d43b3cf0e6/original/anti-kasha-fluorescence-in-molecular-entities-the-central-role-of-the-electron-vibrational-coupling.pdf |
64c260649ed5166e938e8632 | 10.26434/chemrxiv-2023-hgfxs | Experimental and Computational Investigation of Fluid Dynamics and Solid Transport in Split-and-Recombine Oscillatory Flow Reactors Using Water as Medium | In processing of chemical reactions involving solid phases, the physical properties of reagent suspensions is of critical importance. Therefore, we present herein a comprehensive analysis of fluid dynamics and solid transport in split-and-recombine oscillatory flow reactors. The research aims to improve the understanding of the mechanisms behind the resuspension capacity of solids in flow driven by the proven efficacy of such reactors in processing of reactions involving multiple phases. On the basis of its importance as a sustainable reaction medium, water was utilized as liquid phase during our comprehensive analysis. Experiments in a commercially available flow reactor (HANU 2X 5) verified a six-fold reduction of particle deposition in case of oscillatory flow compared to constant flow conditions using SiO2 slurries. Further investigations with a full factorial Design of Experiment approach revealed that the tuning of oscillation parameters enables the system to reach an optimal homogeneous suspension instead of incipient clogging. The net slurry flow rate was also found to significantly influence solids suspension capabilities. Under optimized conditions, quantitative transport of up to 10 wt% SiO2 slurries was achieved. A computational fluid dynamics model was developed to give insight into the multiphase fluid flow within the reactor geometry. It was found that oscillatory flow creates large recirculation regions and remarkable positive vertical velocities near the static mixers within the reactor plate that generate upward forces facilitating particle resuspension. By employing oscillations, suspension capabilities improved up to 5 times compared to stationary flow conditions. It was also observed that strategic asymmetries within the reactor could enhance resuspension, while the cross flow section aspect ratio exhibited only minimal influence. By utilizing a novel calculation method for Lagrangian particle tracing simulations, computational times for acquiring particle positions under oscillatory flow conditions were reduced by 82%. The simulation validated the benefits of oscillations in sustaining particle suspension. Oscillatory flow demonstrated a significant reduction in particle deposition at the reactor bottom compared to constant flow. The combination of experimental and computational approaches provides valuable insights for optimizing oscillatory flow reactor design, further advancing their utilization in chemical reaction technology and also potentially in manufacturing. | Filippo Nanto; Sandor B. Otvos; C. Oliver Kappe; Paolo Canu | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Reaction Engineering; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c260649ed5166e938e8632/original/experimental-and-computational-investigation-of-fluid-dynamics-and-solid-transport-in-split-and-recombine-oscillatory-flow-reactors-using-water-as-medium.pdf |
60c754330f50db92de397cdc | 10.26434/chemrxiv.13625783.v1 | Copper-Free One-Pot Sonogashira-Type Coupling for the Efficient Preparation of Symmetric Diarylalkyne Ligands for Metal-Organic Cages | <div>
<p>Bipyridine- and benzimidazole-based ligands for the
self-assembly of Co<sub>4</sub>L<sub>6</sub> cages were synthesised in short
reaction times and high isolated yields directly from aryl halide precursors
using a copper-free one-pot Sonogashira-type coupling. This one-pot method
circumvents the often time-consuming and challenging ligand synthesis for the
preparation and application of cages.</p>
</div>
<br /> | Marc Lehr; Tobias Paschelke; Victoria Bendt; André Petersen; Lorenz Pietsch; Patrick Harders; Anna McConnell | Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754330f50db92de397cdc/original/copper-free-one-pot-sonogashira-type-coupling-for-the-efficient-preparation-of-symmetric-diarylalkyne-ligands-for-metal-organic-cages.pdf |
64b563f2ae3d1a7b0dde20cc | 10.26434/chemrxiv-2023-z8thj | Application of Chiral Transfer Reagents to Improve
Stereoselectivity and Yields in the Synthesis of the Anti-Tuberculosis Drug Bedaquiline | Bedaquiline (BDQ) is an important drug for treating multidrug-resistant tuberculosis (MDR-TB), a
worldwide disease that causes more than 1.6 million deaths yearly. The current synthetic strategy adopted
by the manufacturers to assemble this molecule relies on a nucleophilic addition reaction of two complex
starting materials, but suffers from low conversion and no stereoselectivity, which subsequently increases
the cost of manufacturing BDQ. M4ALL has developed a new approach to this process that not only allows
high conversion of starting materials, but also results in good diastereo- and enantioselectivity towards the
desired BDQ stereoisomer. A variety of chiral lithium amides derived from amino acids were studied, and
it was found that lithium (R)-2-(methoxymethyl)pyrrolidide, obtained from D-proline, results in high assay
yield of the syn-diastereomer pair (82 %) and with considerable stereocontrol (d.r. = 13.6:1, e.r. = 3.6:1, 56
% ee) providing bedaquiline in up to 64 % assay yield before purification steps towards the final API. This
represents a considerable improvement in the BDQ yield compared to previously reported conditions and
could be critical to further lowering the cost of this life-saving drug. | Juliana Robey; Sanjay Maity; Sarah Aleshire; Angshuman Ghosh; Ajay Yadaw; Subho Roy; Sarah Mear; Timothy Jamison; Gopal Sirasani; Chris Senanayake; Rodger Stringham; B. Frank Gupton; Kai Donsbach; Ryan Nelson; Charles Shanahan | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b563f2ae3d1a7b0dde20cc/original/application-of-chiral-transfer-reagents-to-improve-stereoselectivity-and-yields-in-the-synthesis-of-the-anti-tuberculosis-drug-bedaquiline.pdf |
663424d191aefa6ce1027144 | 10.26434/chemrxiv-2024-05z1q-v2 | Distribution of Single-Particle Resonances Determines Plasmonic Response of Disordered Nanoparticle Ensembles | Understanding how colloidal soft materials interact with light is crucial to rational design of optical metamaterials. Electromagnetic simulations are computationally expensive and have primarily been limited to model systems described by a small number of particles -- dimers, small clusters, and small periodic unit cells of superlattices. In this work, we study the optical properties of bulk, disordered materials comprising a large number of plasmonic colloidal nanoparticles using Brownian dynamics simulations and the mutual polarization method. We investigate the far-field and near-field optical properties of both colloidal fluids and gels, which require thousands of nanoparticles to describe statistically. We show that these disordered materials exhibit a distribution of particle-level plasmonic resonance frequencies that determines their ensemble optical response. Nanoparticles with similar resonant frequencies form anisotropic and oriented clusters embedded within the otherwise isotropic and disordered microstructures. These collectively resonating morphologies can be tuned with the frequency and polarization of incident light. Knowledge of particle resonant distributions may help to interpret and compare the optical responses of different colloidal structures, correlate and predict optical properties, and rationally design soft materials for applications harnessing light. | Zachary M. Sherman; Delia J. Milliron; Thomas M. Truskett | Theoretical and Computational Chemistry; Materials Science; Optical Materials; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663424d191aefa6ce1027144/original/distribution-of-single-particle-resonances-determines-plasmonic-response-of-disordered-nanoparticle-ensembles.pdf |
67dc901a6dde43c908a37b28 | 10.26434/chemrxiv-2025-q3mwr-v2 | AlphaFold2-RAVE: Protein Ensemble Generation with Physics-Based Sampling | We introduce AlphaFold2-RAVE (af2rave), an open-source Python package that integrates machine learning-based structure prediction with physics-driven sampling to generate alternative protein conformations efficiently. Protein structures are not static but exist as ensembles of conformations, many of which are functionally relevant yet challenging to resolve experimentally. While deep learning models like AlphaFold2 can predict structural ensembles, they lack explicit physical validation. af2rave addresses this limitation by combining reduced multiple sequence alignment (MSA) AlphaFold2 predictions with molecular dynamics (MD) simulations to efficiently explore local conformational space. A feature selection module identifies key structural degrees of freedom, and the State Predictive Information Bottleneck (SPIB) method uncovers the underlying conformational topology, classifying functionally relevant states. Under the Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE) protocol, either unbiased or biased sampling can be performed to further explore the conformation ensembles. We validate af2rave on multiple systems, including E. coli adenosine kinase (ADK) and human DDR1 kinase, successfully identifying distinct functional states with minimal prior biological knowledge. Furthermore, we demonstrate that af2rave achieves conformational sampling efficiency comparable to long unbiased MD simulations on the SARS-CoV-2 spike protein receptor-binding domain while significantly reducing computational cost. The af2rave package provides a streamlined workflow for researchers to generate and analyze alternative protein conformations, offering an accessible tool for drug discovery and structural biology. | Da Teng; Vanessa J. Meraz; Akashnathan Aranganathan; Xinyu Gu; Pratyush Tiwary | Biological and Medicinal Chemistry; Biochemistry; Bioinformatics and Computational Biology; Biophysics | CC BY 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dc901a6dde43c908a37b28/original/alpha-fold2-rave-protein-ensemble-generation-with-physics-based-sampling.pdf |
63dc8645068fd759791b4407 | 10.26434/chemrxiv-2023-pmrfw-v2 | Outlier-Based Domain of Applicability Identification for Materials Property Prediction Models | Machine learning models have been widely applied for material property prediction. However, practical application of these models can be hindered by a lack of information about how well they will perform on previously unseen types of materials. Because machine learning model predictions depend on the quality of the available training data, different domains of the material feature space are predicted with different accuracy levels by such models. The ability to identify such domains enables the ability to find the confidence level of each prediction, to determine when and how the model should be employed depending on the prediction accuracy requirements of different tasks, and to improve the model for domains with high errors. In this work, we propose a method to find domains of applicability using a large feature space and also introduce analysis techniques to gain more insight into the detected domains and subdomains. | Gihan Panapitiya; Emily Saldanha | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dc8645068fd759791b4407/original/outlier-based-domain-of-applicability-identification-for-materials-property-prediction-models.pdf |
60c73cbfee301c683cc78480 | 10.26434/chemrxiv.14743167.v1 | Self-Colorimetric Determination of Bio-Ethanol Using Permanganate in Fermentation Samples | <p>Without the aid of chromatographic techniques, quantification of bio-ethanol in fermentation-broth distillate becomes inconvenient. Potassium permanganate is preferable over potassium dichromate because of the latter well-known toxic properties, it is common used in ethyl alcohol determination either by visible determination of Cr(III) green optical density, a consumed Cr(VI) determination in strong acid medium by measuring band absorbance decrease at 267 nm or the unreacted Cr(VI) determination iodometrically after alcohol oxidation. Nevertheless, these titre methods arise difficulties experience analysts from multiple solutions preparation, standardization that should be carried out every day and to successful end point detection in the presence of Cr(III) green color which leads to a significant ethanol quantification error. Noteworthy permanganate-iodometrydrawbacks as same as titre dichromate difficult practical procedures and multiple reagents employed.</p><p>In this laboratory a self colorimetric method was developed in neutral medium as alcohol-specific oxidizing agent precludes both of its undesirable high oxidizing properties and difficult titrimetric methodologies for bio-ethanol quantification. It is based on unreacted permanganate optical density difference between a non ethanol-containing sample as a blank and ethanol-containing sample is directly proportional to the consumed permanganate amount in ethanol red-ox reaction and consequently directly proportional to ethanol content. This optical density difference versus ethanol concentration 1-6% v/v obeys Beer-Lampert law provides limit of detection, limit of quantification and correlation coefficient equal 0.17%, 0.56% and 0.999 respectively. <br /></p><p><br /></p> | Mohamed Abdelazim Abulela | Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cbfee301c683cc78480/original/self-colorimetric-determination-of-bio-ethanol-using-permanganate-in-fermentation-samples.pdf |
637eb2d40949e1273853d5f5 | 10.26434/chemrxiv-2022-f19xz | Metal-support interactions regulate substrate binding in Fe/Co/Se cluster catalysts | Here, we investigate the stereo-electronic requirements of a family of Fe/Co6Se8 molecular clusters to achieve a Goldilocks regime of substrate affinity for the catalytic coupling of tosyl azide and tert-butyl isocyanide. The reactivity of a catalytically competent iron-nitrenoid intermediate, observed in situ, is explored towards nitrene transfer and hydrogen atom abstraction. The dual role of isocyanide, which on one hand prevents catalyst degradation, but, in large amounts, slows down reactivity is exposed. The impact of distal changes (number of neighboring active sites and identity of supporting ligands) on substrate affinity, electronic properties, and catalytic activity is investigated. Overall, the study reveals that the dynamic, push-pull interactions between the substrate (tBuNC), active site (Fe), and support (Co6Se8) create a regime where increased substrate activation occurs concomitantly with expedited dissociation. | Benjamin Mitchell; Andrei Chirila; Daniel Zhou; Jonathan Kephart; Alexandra Velian | Inorganic Chemistry; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637eb2d40949e1273853d5f5/original/metal-support-interactions-regulate-substrate-binding-in-fe-co-se-cluster-catalysts.pdf |
60c74473567dfe4969ec4293 | 10.26434/chemrxiv.9791540.v1 | Boosting the Rate and Cycling Performance of β-LixV2O5 Nanorods for Li Ion Battery by Electrode Surface Decoration | The <i>β-</i>phase lithium vanadium oxide bronze (<i>β-</i>Li<i><sub>x</sub></i>V<sub>2</sub>O<sub>5</sub>)
with high theoretic specific capacity up to 440 mAh g<sup>-1</sup> is
considered as promising cathode materials, however, their practical application
is hindered by its poor ionic and electronic conductivity, resulting in unsatisfied
cyclic stability and rate capability. Herein, we report the surface decoration
of <i>β-</i>Li<i><sub>x</sub></i>V<sub>2</sub>O<sub>5</sub> cathode using both reduced
oxide graphene and ionic conductor LaPO<sub>4</sub>, which significantly promotes the electronic transfer and Li<sup>+</sup>
diffusion rate, respectively. As a result, the rGO/LaPO<sub>4</sub>/Li<i><sub>x</sub></i>V<sub>2</sub>O<sub>5</sub>
composite exhibits excellent electrochemical performance in terms of high reversible
specific capacity of 275.7 mAh g<sup>-1</sup> with high capacity retention of
84.1% after 100 cycles at a current density of 60 mA g<sup>-1</sup>, and
acceptable specific capacity of 170.3 mAh g<sup>-1</sup> at high current
density of 400 mA g<sup>-1</sup>. The cycled electrode is also analyzed by
electrochemical impedance spectroscopy, <i>ex-situ
</i>X-ray diffraction and scanning electron microscope, providing further
insights into the improvement of electrochemical performance. Our results
provide an effective approach to boost the electrochemical properties of
lithium vanadates for practical application in lithium ion batteries. | Panpan Wang; Yue Du; Baoyou Zhang; Yanxin Yao; Yuchen Xiao; Lijie Ci; Chengyan Xu; Liang Zhen | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74473567dfe4969ec4293/original/boosting-the-rate-and-cycling-performance-of-lix-v2o5-nanorods-for-li-ion-battery-by-electrode-surface-decoration.pdf |
6364d535ecdad5745bf9e2b2 | 10.26434/chemrxiv-2022-l9vp2 | Carboxysome-inspired electrocatalysis using enzymes for the reduction of CO2 at low concentrations | The electrolysis of dilute CO2 streams suffers from low concentrations of dissolved substrate and its rapid depletion at the electrolyte-electrocatalyst interface. These limitations require first energy-intensive CO2 capture and concentration, before electrolyzers can achieve acceptable performances. For direct electrocatalytic CO2 reduction from low-concentration sources, we in-troduce a strategy that mimics the carboxysome in cyanobacteria by utilizing microcompart-ments with nanoconfined and concentrated enzymes in a porous electrode. A carbonic anhy-drase accelerates CO2 hydration kinetics and minimizes substrate depletion by making all dis-solved carbon available for utilization, while a highly efficient formate dehydrogenase reduces CO2 cleanly to formate; down to even atmospheric concentrations of CO2. This bio-inspired concept demonstrates that the carboxysome provides a viable blueprint and strategy to achieve the reduction of low-concentration CO2 streams to chemicals. | Samuel Cobb; Azim Dharani; Ana Rita Oliveira; Ines Pereira; Erwin Reisner | Catalysis; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2022-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6364d535ecdad5745bf9e2b2/original/carboxysome-inspired-electrocatalysis-using-enzymes-for-the-reduction-of-co2-at-low-concentrations.pdf |
6415c939dab08ad68f52318a | 10.26434/chemrxiv-2023-qx77k | Selective Chemical Substitution in Intermetallic Compounds: DFT Study of Two Representative Cases: Cu5Zn3Sb2 and InPd2Cu | The unique site substitution of Zn in the structure of tetragonal Cu3Zn2Sb2 and the substitution of Cu in the binary InPd3, followed by the formation of Cu5Zn3Sb2 and InPd2Cu has been addressed from fundamental perspectives. First principles total energy calculations, and semi-empirical electronic structure calculations using both the density of states, crystal orbital Hamilton population, and Mulliken population analysis were performed to understand the observed compositional range for both the titled cases and to address the “coloring problem” for the experimentally observed site preferences. | NILANJAN ROY; Sandip Kumar Kuila | Theoretical and Computational Chemistry; Inorganic Chemistry; Bonding; Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2023-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6415c939dab08ad68f52318a/original/selective-chemical-substitution-in-intermetallic-compounds-dft-study-of-two-representative-cases-cu5zn3sb2-and-in-pd2cu.pdf |
60e6ef0c88258247fda6217a | 10.26434/chemrxiv-2021-vnn23 | Divergent Total Syntheses of Aspidospermidine, N-Methylaspidospermidine, N-Acetylaspidospermidine and Aspido-spermine via a Tandem Cyclization of Tryptamine-Ynamide | The divergent total syntheses of aspidospermidine, N-methylaspidospermidine, N-acetylaspidospermidine and aspidosperm-ine were achieved from a common pentacyclic indoline intermediate. The common pentacyclic indoline intermediate was synthesized on a gram scale through a Stork-type alkylation of 1H-pyrrolo[2,3-d]carbazole derivatives, which was prepared based on a Brønsted acid-catalyzed tandem cyclization of tryptamine-ynamide. Scalable synthesis of 1H-pyrrolo[2,3-d]carbazole afforded a facile access and practical approach to the Aspidosperma indole alkaloid family. | Lu Yang; Siwen Huang; Rongkang Huang; Anbin Hou; Sen Zhang; Hongwei Su; Xiaohong Ding; Bin Lin; Maosheng Cheng; Yongxiang Liu | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e6ef0c88258247fda6217a/original/divergent-total-syntheses-of-aspidospermidine-n-methylaspidospermidine-n-acetylaspidospermidine-and-aspido-spermine-via-a-tandem-cyclization-of-tryptamine-ynamide.pdf |
60c9e3b1c763713b6668cd9a | 10.26434/chemrxiv.14781855.v1 | [Co(TPP)]–Catalyzed Carbene Transfer from Acceptor–Acceptor Iodonium Ylides via N-enolate Carbene Radicals | <b>Abstract: </b>Square-planar cobalt(II)-systems have emerged as powerful carbene transfer catalysts for the synthesis of a variety of (hetero)cyclic compounds via redox non-innocent Co(III)-carbene radical intermediates. Spectroscopic detection and characterization of these reactive carbene radical intermediates has thus far been limited to a few scattered experiments, in part due to the fact that most studies have focused on mono-substituted carbene precursors. In this work, we demonstrate the unique formation of disubstituted cobalt(III)-carbene radicals in reactions between a cobalt(II)-porphyrin com-plex with acceptor-acceptor iodaneylidenes (iodonium ylides) as the carbene precursors. We report detailed spectroscopic characterization of the resulting reactive carbene radical species, and their application in styrene cyclopropanation. In particular, we demonstrate that iodonium ylides generate novel bis-carbenoid species leading to reversible substrate-promoted ligand modification of the commercially available [Co(TPP)]-catalyst. Two interconnected catalytic cycles are involved in the overall catalytic reaction with a mono-terminal carbene radical and an unprecedented N-enolate-carbene radical intermediate as the respective key species for the mono- and bis-carbene cycles. Notably, N-enolate formation is not a catalyst deactivation pathway, and both the N-enolate and the carbene radical moieties can be transferred as carbene units to styrene. The studies provide a detailed picture of the new [Co(TPP)]-catalyzed carbene transfer reactions from iodonium ylides. The findings are supported by detailed and unequivocal characterization of the reactive N-enolate & carbene radical intermediates and their deactivation products (EPR, UV-Vis, HR-MS, NMR, in-situ ATR-FT-IR, SC-XRD), Hammett analysis, mechanistic control experiments, DFT reaction pathway profiling and NEVPT2-CASSCF electronic structure calculations.<br /> | Roel F.J. Epping; Mees M. Hoeksma; Eduard O. Bobylev; Simon Mathew; Bas de Bruin | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9e3b1c763713b6668cd9a/original/co-tpp-catalyzed-carbene-transfer-from-acceptor-acceptor-iodonium-ylides-via-n-enolate-carbene-radicals.pdf |
60c74fe09abda25c21f8d91e | 10.26434/chemrxiv.12948638.v1 | A Versatile Protocol for Functionalization of Covalent Organic Frameworks via Suzuki-Miyaura Cross-Coupling | Post-synthetic
modification (PSM) is a prevalent and powerful strategy to introduce desired
functionalities into covalent organic frameworks (COFs) for functional products,
expediting their applications vastly. Herein, we demonstrate a PSM strategy for
functionalizing brominated COFs <i>via</i>
the well-developed Suzuki-Miyaura cross-coupling. By this protocol, a variety
of functionalities were installed into COFs efficiently, while the
crystallinity and porosity of COFs retained well. As a proof-of-concept,
BrCOF-2 was modified with trifluoromethyl groups to produce a SF<sub>6</sub>
adsorbent with remarkably enhanced properties. This facile and versatile
approach opens a new door for the synthesis of functional COFs, and greatly
expands the scope of their structural design aiming for various properties and
applications. | Qiaobo Liao; Can Ke; Xin Huang; Dongni Wang; Qingwen Han; Yifan Zhang; Yiying Zhang; Kai Xi | Materials Processing; Nanostructured Materials - Materials; Organic Polymers; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fe09abda25c21f8d91e/original/a-versatile-protocol-for-functionalization-of-covalent-organic-frameworks-via-suzuki-miyaura-cross-coupling.pdf |
60c7512cbdbb897ff6a3a038 | 10.26434/chemrxiv.13132814.v1 | Calculating the Full Free Energy Profile for Covalent Modification of a Druggable Cysteine in Bruton’s Tyrosine Kinase | <p>Targeted Covalent Inhibitors bind to their targets both covalent and non-covalent modes, providing exceptionally high affinity and selectivity. These inhibitors have been effectively employed as inhibitors of protein kinases, with Taunton and coworkers (<i>Nat. Chem. Biol.</i> <b>2015</b>, 11 (7), 525–531) reporting a notable example of a TCI with a cyanoacrylamide warhead that forms a covalent thioether linkage to an active-site cysteine (Cys481) of Bruton's tyrosine kinase. The specific mechanism of the binding and the relative importance of the covalent and non-covalent interactions is difficult to determine experimentally, but established simulation methods for calculating the absolute binding affinity of an inhibitor cannot describe the covalent bond forming steps. Here, an integrated approach using alchemical free energy perturbation</p><p>and QM/MM molecular dynamics methods was employed to model the complete Gibbs energy profile for the covalent inhibition of BTK by a cyanoacrylamide TCI. These calculations provide a rigorous and complete absolute Gibbs energy profile of the covalent modification binding process. The mechanism is ionic, where the target cysteine is deprotonated to form a nucleophilic thiolate, which then undergoes a facile conjugate addition to the electrophilic functional group to form a bond with the non covalently bound ligand. This model predicts that the formation of the covalent linkage makes binding 19.3 kcal/mol more exergonic than the non-covalent binding alone. Nevertheless, non-covalent interactions between the ligand and individual amino acid residues in the binding pocket of the enzyme are also essential for ligand binding,</p><p>particularly, van der Waals dispersion forces that have a larger contribution to the binding energy than the covalent component in absolute terms. This model also shows that the mechanism of covalent modification of a protein occurs through a complex series of steps and that entropy, conformational flexibility, non-covalent interactions, and the formation of covalent linkage are all significant factors in the ultimate</p><p>binding affinity of a covalent drug to its target.</p> | Ernest Awoonor-Williams; Christopher Rowley | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7512cbdbb897ff6a3a038/original/calculating-the-full-free-energy-profile-for-covalent-modification-of-a-druggable-cysteine-in-bruton-s-tyrosine-kinase.pdf |
6694c5dbc9c6a5c07a52602b | 10.26434/chemrxiv-2024-50ctc | Studying Superheated Stevia with Polynomial Chaos in Quantum ESPRESSO: opEn-Source Package for Research in Electronic Structure, Simulation, and Optimization | Coffee is one of the most consumed beverages by people on a daily basis. Many coffee drinkers use stevia to sweeten their drinks. Here we show the superheating of microwaved coffee upon adding stevia, where according to critical bubble theory, stevia granules act as nucleation sites for bubbles to form and the first-order phase transition to occur. Based on quantum mechanical simulations of the active component of stevia's structural relaxation by minimum ground state electron density energy forces, a hypothesis is devised for the origin of this stevia-induced superheating due to interactions with higher frequency, mobile carboxyl and hydroxyl group side-chains present above the base molecular plane of steviol [1], which enable stevia granules to act as bubble nucleation sites. Superheating of water upon adding pebbles after sealed microwaving has been previously observed [2]; however, the observation of superheating of coffee upon added stevia is currently not understood, even though the rise above the boiling point could be captured within the uncertainty of Newtonian cooling dynamics by polynomial chaos expansion. This study has implications for understanding the superheating of particulate accumulation in high-temperature, ambient-pressure environments, such as fuel in engines. | Saleem Al Dajani | Theoretical and Computational Chemistry; Physical Chemistry; Agriculture and Food Chemistry; Computational Chemistry and Modeling; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6694c5dbc9c6a5c07a52602b/original/studying-superheated-stevia-with-polynomial-chaos-in-quantum-espresso-op-en-source-package-for-research-in-electronic-structure-simulation-and-optimization.pdf |
66bb4da5f3f4b05290bccb6e | 10.26434/chemrxiv-2024-pxb4f | From High Dimensions to Human Comprehension: Exploring Dimensionality Reduction for Chemical Space Visualization | Dimensionality reduction is an important exploratory data analysis method that allows high-dimensional data to be represented in a human-interpretable lower-dimensional space. It is extensively applied in the analysis of chemical libraries, where chemical structure data — represented as high-dimensional feature vectors—are transformed into 2D or 3D chemical space maps. In this paper, commonly used dimensionality reduction techniques — Principal Component Analysis (PCA), t-Distributed Stochastic Neighbor Embedding (t-SNE), Uniform Manifold Approximation and Projection (UMAP), and Generative Topographic Mapping (GTM) — are evaluated for exploration of subsets of small molecule organic compounds from ChEMBL database. The performance of these methods is examined in terms of neighborhood preservation and visualization capabilities, and the strengths and limitations are discussed. | Alexey Orlov ; Tagir Akhmetshin; Dragos Horvath; Gilles Marcou; Alexandre Varnek | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bb4da5f3f4b05290bccb6e/original/from-high-dimensions-to-human-comprehension-exploring-dimensionality-reduction-for-chemical-space-visualization.pdf |
65b26f24e9ebbb4db9f6efeb | 10.26434/chemrxiv-2024-r1vxg | Pyridinium-activated alkyne-based spontaneous amino-yne click polymerization toward n-pi conjugated polyelectrolytes | Thanks to its high efficiency, excellent selectivity, simple operation and mild reaction conditions, the click polymerization has become a powerful tool for the synthesis of polymers. Among the reported click polymerizations, the activated alkyne-based one has drawn much attention. However, the preparation of conjugated polymers with charged main chains by this click polymerization has rarely been reported. Herein, by connection of ethynyl group with pyridinium moiety at its para-position, we present a new spontaneous click polymerization of pyridinium-activated diynes and aromatic diamines toward regioregular n-pi conjugated polyelectrolytes. The resultant polymers possess excellent thermal stability and good film forming properties. Thus, this pyridinium-activated alkyne-based spontaneous amino-yne click polymerization provides a powerful and straightforward tool for the preparation of main-chain charged n-pi conjugated polymers, which greatly expands the scope of click polymerization and opens up new avenues for the development of functional polymers. | Chunyang Li; Wuhua Liu; Bingnan Wang; Anjun Qin; Ben Zhong Tang | Polymer Science; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b26f24e9ebbb4db9f6efeb/original/pyridinium-activated-alkyne-based-spontaneous-amino-yne-click-polymerization-toward-n-pi-conjugated-polyelectrolytes.pdf |
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