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65cc66abe9ebbb4db952ba01
|
10.26434/chemrxiv-2024-83hjj
|
GREEN SYNTHESIS OF ZINC OXIDE NANOPARTICLES USING ALOE VERA: A STUDY ON OPTICAL PROPERTIES AND PHOTOCATALYTIC ACTIVITY
|
The emergence of green synthesis provides an environmentally conscious alternative to conventional methods in the pursuit of sustainable nanotechnology. Exploring this environmentally friendly territory, our research reveals the fascinating realm of zinc oxide nanoparticles (ZnO NPs), which are made using the botanical expertise of Aloe barbadensis miller, also referred to as aloe vera. This work sets out to investigate the optical properties and photocatalytic capabilities of these biosynthesized nanoparticles with an emphasis on their potential use in the methylene blue (MB) degradation process.
Green synthesis, a meticulous blend of botanical expertise and analytical precision, initiates with the careful synthesis of NPs using Aloe barbadensis miller leaves as reducing agent. The resultant Aloe Vera-assisted ZnO nanoparticles (AL-ZnO) exhibit significant optical properties, as unveiled by UV-vis spectroscopy, indicating a semiconductor behavior with an absorption peak at 310 nm. Tauc's equation reveals a bandgap energy of 4.37 eV, indicating direct electronic transitions within the AL-ZnO NPs. The particle size of 5.86nm was determined through a hyperbolic model. AL-ZnO showcases remarkable catalytic prowess in photocatalysis, achieving complete methylene blue degradation under soft sunlight within 105 minutes. This positions Aloe Vera-assisted ZnO NPs as potent catalysts for eco-friendly water treatment, marking a significant stride in green synthesis. The study also delves into the optical attributes of Al-doped ZnO nanoparticles, uncovering robust light-refracting capabilities and high optical conductivity. This positions them as ideal candidates for applications in solar cells and light-emitting devices, contributing to advancements in renewable energy technologies. In essence, the research establishes Aloe Vera-assisted ZnO NPs as multifaceted, powerful catalysts with significant implications for both environmentally conscious water treatment and the broader domain of green synthesis.
|
Sanju Singh; Bhawana Jain
|
Materials Science; Nanoscience; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-02-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cc66abe9ebbb4db952ba01/original/green-synthesis-of-zinc-oxide-nanoparticles-using-aloe-vera-a-study-on-optical-properties-and-photocatalytic-activity.pdf
|
67af06866dde43c908d1aec7
|
10.26434/chemrxiv-2025-vcwq2
|
Interaction of Metal Ion Stabilized Oligomeric Dipeptide with Lipid Membrane: Concurrent Observations of Supported Lipid Membrane, Wetting and Uptake
|
The interaction of biomolecules with cell membranes is crucial due to their important role in governing the cellular function and membrane dynamics. However, most of the studies predominantly focus on the interaction of monomeric forms of biomolecules with lipid membranes, leaving the effects of cytotoxic oligomeric self-aggregates largely unexplored. In this study, we present the first evidence that oligomeric intermediates of diphenylalanine exert diverse effects on lipid membranes, influenced by lipid phase and charge. Our findings reveal that the fibrillar morphology of diphenylalanine facilitates the formation of supported phospholipid membranes through liposome deformation. Importantly, metal ion stabilized oligomeric intermediates of diphenylalanine cause wetting, promote vesicle uptake, and induce coalescence, resulting in significant structural alterations of lipid membranes having different charges. These insights open new research directions with profound implications for biomedicine, nanotechnology, and help in fundamental biological understanding.
|
Priyanka Nath; Debanjan Bagchi; Avijit Maity; Huma Tabassum; Suman Choudhury; Naveen Kumar; Anjan Chakraborty
|
Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Biochemistry; Biophysical Chemistry; Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67af06866dde43c908d1aec7/original/interaction-of-metal-ion-stabilized-oligomeric-dipeptide-with-lipid-membrane-concurrent-observations-of-supported-lipid-membrane-wetting-and-uptake.pdf
|
60c74ce6bb8c1ac05f3db4d1
|
10.26434/chemrxiv.12567680.v1
|
The Effectiveness of a 3D Printed Hydrogel Membrane to Sustain Algal Growth
|
This experiment assessed whether the photosynthetic algae species <i>Chlorella Vulgaris </i>could growth within a carrageenan based hydrogel. This hydrogel variant was synthesized with a nanosilicate powder, used to strengthen the polymer bonds between the carrageenan which allows for more robust 3D printing. Using a chip hemocytometer, it was found that <i>Chlorella Vulgaris </i>showed signs of growth in the carrageenan hydrogel without the aid of additional nutrients.<div>This means that the algae could potentially be 3D printed into structures used for biofiltration of enviromental pollutants</div>
|
Ben Caroway; Satchel Malo; Frank Parsons
|
Biocompatible Materials; Biological Materials; Biodegradable Materials; Biochemistry; Bioengineering and Biotechnology; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ce6bb8c1ac05f3db4d1/original/the-effectiveness-of-a-3d-printed-hydrogel-membrane-to-sustain-algal-growth.pdf
|
675232d07be152b1d0163b00
|
10.26434/chemrxiv-2024-b8x26
|
A single outer-sphere amino-acid substitution turns on the NO reactivity of a hemerythrin-like protein
|
Mycobacterial hemerythrin-like proteins (HLPs) are important for the survival of pathogens in macrophages. Their molecular mechanisms of function remain poorly defined but recent studies point to their possible role in nitric oxide (NO) scavenging. Unlike any nonheme diiron protein studied so far, the diferric HLP from Mycobacterium kansasii (Mka-HLP) reacts with NO in a multistep fashion to consume four NO molecules per diiron center. HLPs are largely conserved across mycobacteria and we argued that comparative studies of distant orthologs may illuminate the role of the protein scaffold in this reactivity and yield intermediates with properties more favorable for detailed spectroscopic characterization. Herein, we show that HLP from Azotobacter vinelandii (Avi-HLP) requires a single T47F point mutation in the outer sphere of its diferric center to adopt a bridging mu-oxo diferric structure alike that of Mka-HLP that makes it reactive toward NO. Radical combination of NO with the mu-oxo bridge yields nitrite and a mixed valent Fe(III)Fe(II) cluster that further react with NO to produce a stable magnetically coupled Fe(III){FeNO}7 cluster. We report characterization of this stable cluster by electronic absorption, EPR, FTIR and resonance Raman spectroscopies and suggest ways Phe 46 (Mka numbering) might control the Fe(III) reduction potential and the NO reactivity of HLPs.
|
THERESE ALBERT; NATASHA PENCE; FANGFANG ZHONG; EKATERINA PLETNEVA; PIERRE MOENNE-LOCCOZ
|
Biological and Medicinal Chemistry; Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Reaction (Inorg.); Spectroscopy (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675232d07be152b1d0163b00/original/a-single-outer-sphere-amino-acid-substitution-turns-on-the-no-reactivity-of-a-hemerythrin-like-protein.pdf
|
645200e607c3f02937218322
|
10.26434/chemrxiv-2023-6bhsx
|
How reproducible is the synthesis of Zr--porphyrin metal--organic frameworks? An interlaboratory study
|
Metal--organic frameworks (MOFs) are a rapidly growing class of materials that offer great promise in various applications. However, the synthesis remains challenging: for example, a range of crystal structures can often be accessed from the same building blocks, which complicates the phase selectivity. Likewise, the high sensitivity to slight changes in synthesis conditions may cause reproducibility issues. This is crucial, as it hampers the research and commercialisation of affected MOFs. Here, we present the first-ever interlaboratory study of the synthetic reproducibility of two Zr--porphyrin MOFs, PCN-222 and PCN-224, to investigate the scope of this problem. For PCN-222, only one sample out of ten was phase pure and of the correct symmetry, while for PCN-224, three were phase pure, although none of these show the spatial linker order characteristic of PCN-224. Instead, these samples resemble dPCN-224 (disordered PCN-224), which was recently reported by us. The variability in thermal behaviour, defect content, and BET surface area of the synthesised samples are also studied. Our results have important ramifications for field of metal--organic frameworks and their crystallisation, by highlighting the synthetic challenges associated with a multi-variable synthesis space and flat energy landscapes characteristic of MOFs.
|
Hanna Boström; Sebastian Emmerling; Fabian Heck; Charlotte Koschnick; Andrew Jones; Matthew Cliffe; Rawan Al Natour; Mickaële Bonneau; Vincent Guillerm; Osama Shekhah; Mohamed Eddaoudi; Javier Lopez-Cabrelles; Shuhei Furukawa; Maria Romero-Angel; Carlos Marti-Gastaldo; Minliang Yan; Amanda Morris; Ignacio Romero-Muñiz; Ying Xiong; Ana Platero-Prats; Jocelyn Roth; Wendy Queen; Kalle Mertin; Danielle Schier; Neil Champness; Hamish Yeung; Bettina Lotsch
|
Inorganic Chemistry; Coordination Chemistry (Inorg.); Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic
|
CC BY 4.0
|
CHEMRXIV
|
2023-05-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645200e607c3f02937218322/original/how-reproducible-is-the-synthesis-of-zr-porphyrin-metal-organic-frameworks-an-interlaboratory-study.pdf
|
6360d1be55a0816558cd7f0a
|
10.26434/chemrxiv-2022-ppf2d-v2
|
Critical review on uranium and arsenic content and their chemical mobilization in the groundwater: A case study of the Malwa region Punjab, India
|
Groundwater played a pivotal role in the social and economic development of the Malwa Region. With the advent of the green revolution, water for irrigation and domestic use led to the development of groundwater resources. Slowly, the green revolution changed into a greed revolution, and the exploitation of groundwater resources converted into their overexploitation. Groundwater's overexploitation not only led to groundwater depletion but also led to a change in the chemistry of the Malwa region's aquifers. Researchers from academia and institutions worked and published their findings of the uranium and arsenic contaminations in the Malwa region of Punjab. In this article, we are the first to bring all the dispersed data to one commonplace. By studying the physicochemical parameters of groundwater of all districts of the Malwa region and their correlation, this paper is going to highlight the various chemical reactions occurring in the Malwa region's aquifer and how they impact groundwater chemistry. For understanding, we devised a hypothetical model to understand the complex interplay of this region's natural dynamics of groundwater aquifers. Finally, we tried to describe how the various chemical changes in the groundwater aquifer can be the reason for the mobilization of arsenic and uranium by making schematic chemical flow-charts of their mobilization. This article aims to highlight the importance of using a multidisciplinary and interdepartmental approach to comprehending the complex problem of groundwater management.
|
vajinder kumar; Sandip Saha; Avneesh Kumar; Arnab Maity; Tirtha Mukherjee; Atul Kumar
|
Earth, Space, and Environmental Chemistry; Environmental Science; Geochemistry; Hydrology and Water Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6360d1be55a0816558cd7f0a/original/critical-review-on-uranium-and-arsenic-content-and-their-chemical-mobilization-in-the-groundwater-a-case-study-of-the-malwa-region-punjab-india.pdf
|
62348f9b202c06afcdd830a6
|
10.26434/chemrxiv-2022-d6qn6
|
Cu-Catalyzed Cyclization/Coupling of Alkenyl Aldimines. Indolization of Aldehydes, Anilines and Arylzinc Reagents
|
We report a Cu(II)-catalyzed cyclization/coupling of alkenyl aldimines with arylzinc reagents to create complex indole-3-diarylmethane derivatives. The aldimines are readily available by simple dehydration, making the process a formal three-component reaction that strategically combines alkenyl aldehydes, anilines and arylzinc reagents to generate substituted indole-3-diarylmethane cores. Since the cyclization/coupling of alkenyl aldimines is unknown to date, the current method discloses an uncharted chemical space with regard to both the substrate and product diversity for this class of reaction.
|
Rishi R. Sapkota; Raj K. Tak; Vivek Aryal; Doleshwar Niroula; Nicholas C. Secosky; Roshan K. Dhungana; Ramesh Giri
|
Organic Chemistry; Catalysis; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62348f9b202c06afcdd830a6/original/cu-catalyzed-cyclization-coupling-of-alkenyl-aldimines-indolization-of-aldehydes-anilines-and-arylzinc-reagents.pdf
|
66c4bcf220ac769e5f2e1ad8
|
10.26434/chemrxiv-2024-8pjvp
|
Transforming Waste Fish Bones to Nanoparticles with Ultrasound and Aqueous Organic Acids
|
Nano-hydroxyapatite particles were prepared from Atlantic salmon bones using ultrasound in combination with heat, ball-milling and acid treatment. The smallest particles (d = 29 nm) were produced using aqueous propanoic acid and 15 min ultrasound exposure, whereas heat pre-treatment and ultrasound for 60 min led to more well-defined, spherical particles.
|
Sarah Boudreau; Sabahudin Hrapovic; Emma MacIsaac; Edmond Lam; Fabrice Berrué; Francesca Kerton
|
Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Minerals; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c4bcf220ac769e5f2e1ad8/original/transforming-waste-fish-bones-to-nanoparticles-with-ultrasound-and-aqueous-organic-acids.pdf
|
65be989e66c1381729e68ac3
|
10.26434/chemrxiv-2024-c8g75
|
UiO-66-NDC (1,4-Naphthalenedicarboxylic Acid): A Versatile Metal-Organic Framework-Based Catalyst for Photocatalytic Degradation of Dye Chemicals
|
Metal-organic frameworks (MOFs) have received significant attention for their use as photocatalysts and photocatalyst supports. These materials have a number of benefits, including stability, catalyst reusability, tunability, and the capacity for post-reaction separation. Here, the potential applications of UiO-66-NDC (1,4-Naphthalenedicarboxylic acid) as a photocatalyst for the degradation of reactive orange 16 (RO16), methyl orange (MO), and rhodamine B (RhB) were investigated. Due to its large surface area, adjustable characteristics, stability, effective light absorption, capacity for charge separation, and adaptability in design, UiO-66-NDC was chosen for photocatalytic dye degradation. A solvothermal process was used to synthesize the UiO-66-NDC, and methods including X-ray diffraction (XRD) and scanning electron microscopy (SEM) were used to characterize its structure. The zeta potential was used to determine the surface charge. In order to conduct the photocatalytic tests, dye solutions with defined concentrations were exposed to UVA light irradiation in the presence of UiO-66-NDC. UV-visible spectroscopy was used to monitor the degradation process, which made it possible to calculate the degradation rate constants and the percentage of dye removal. The removal efficiency of adsorption, which was also examined, was at a minimum (17% for RO16, 48% for MO, and 25% for RhB). The degradation of the dyes by UiO-66-NDC showed excellent photocatalytic activity, with degradation rates for RO16, MO, and RhB of 93%, 94%, and 91%, respectively, and good reusability. The research determined that 300 mg/L of catalyst was the ideal level. Three successive cycles of using UiO-66-NDC as a catalyst have demonstrated its reusability. It was possible to remove 97% of RO16, 99% of MO, and 95% of RhB at a high starting dye concentration (20 mg/L).
|
Elif Özcan; Hüseyin Cengiz Yatmaz; Yunus Zorlu
|
Materials Science; Inorganic Chemistry; Catalysis; Hybrid Organic-Inorganic Materials; Solid State Chemistry; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65be989e66c1381729e68ac3/original/ui-o-66-ndc-1-4-naphthalenedicarboxylic-acid-a-versatile-metal-organic-framework-based-catalyst-for-photocatalytic-degradation-of-dye-chemicals.pdf
|
67501ecff9980725cf014413
|
10.26434/chemrxiv-2024-52g9l
|
Chat-Microreactor: A Large-Language-Model-Based Assistant for Designing Continuous Flow Systems
|
Continuous flow in microchannels play pivotal roles in advancing automated chemical synthesis. However, frequent multiphase reactions pose key challenges for designing reactors that efficiently disperse phases. Although effort has been directed toward automating development processes, the unique nature of each existing study offers limited opportunities for generalization; consequently applying this knowledge to new microreactor designs is difficult. In this study, we introduce a self-optimizing workflow that uses large language models (LLMs) to extract key microreactor-system parameters, such as density, velocity, and Capillary number, from the literature. Minimal training led to a reduction in extraction time from 24 to 16 s, with the collected data processed by ensemble learning models delivering F1 scores greater than 70% when classifying flow patterns. Through interpretability analysis, we confirmed the machine learning model's alignment with human expertise. We then applied the model to an oil-water dispersion system for controlled alumina microsphere preparation and a piperacillin synthesis system, achieving accuracy rates of 83% and 94%, respectively. This study offers synthetic chemists an LLM-based tool for the development of microreactor systems, thereby pioneering the use of machine learning in literature-sparse fields.
|
Yongqi Pan; Qinfan Xiao; Fangyu Zhao; Zhenhao Li; Jianyang Liu; Shafqat Ullah; Kang Hui Lim; Tianyi Huang; Zhiyuan Yu; Claudia Li; Dingyan Zhang; Qiangqiang Xue; Qiang Chen; Sibudjing Kawi; Yujun Wang; Guangsheng Luo
|
Chemical Engineering and Industrial Chemistry; Process Control; Reaction Engineering; Transport Phenomena (Chem. Eng.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67501ecff9980725cf014413/original/chat-microreactor-a-large-language-model-based-assistant-for-designing-continuous-flow-systems.pdf
|
6581619066c13817298f90cf
|
10.26434/chemrxiv-2023-0xs54
|
Alared: environmentally sensitive fluorescent red amino acid for biomolecular interaction studies and live-cell imaging of bioactive peptides
|
To fill the need for environmentally sensitive fluorescent unnatural amino acids able to operate in the red region of the spectrum, we designed and synthesized Alared, a red solvatochromic and fluorogenic amino acid derived from the Nile Red chromophore. The new unnatural amino acid can be easily integrated into bioactive peptides by means of classical solid-phase peptide synthesis. The fluorescence quantum yield and the emission maximum of Alared-labeled peptides vary in a broad range depending on the peptide’s environment, making Alared a powerful reporter of biomolecular interactions. Due to its red-shifted absorption and emission spectra, Alared-labeled peptides could be monitored in living cells with minimal interference from cellular autofluorescence. Using ratiometric fluorescence microscopy, we were able to track the fate of the Alared-labeled peptide agonists of the apelin G protein-coupled receptor upon receptor activation and internalization. Due to its color-shifting environmentally sensitive emission, Alared allowed for distinguishing the fractions of peptides that are specifically bound to the receptor or unspecifically bound to different cellular membranes.
|
Antoine Mirloup; Yann Berthomé; Stéphanie Riché; Patrick Wagner; Fabien Hanser; Arthur Laurent; Xavier Iturrioz; Catherine Llorens-Cortes; Julie Karpenko; Dominique Bonnet
|
Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Organic Synthesis and Reactions; Imaging; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6581619066c13817298f90cf/original/alared-environmentally-sensitive-fluorescent-red-amino-acid-for-biomolecular-interaction-studies-and-live-cell-imaging-of-bioactive-peptides.pdf
|
60c7484a469df41874f43998
|
10.26434/chemrxiv.11312642.v2
|
Structure-Photochemical Function Relationships in Nitrogen-Containing Heterocyclic Aromatic Photobases Derived from Quinoline
|
<p>Photobases are compounds which become strong bases
after electronic excitaton into a charge-transfer excited state. Recent experimental studies have highlighted
the photobasicity of the 5-R quinoline compounds, demonstrating a strong
substituent dependence to the pK<sub>a</sub><sup>*</sup>. Here we describe our systematic
study of how the photobasicity of four families of nitrogen-containing
heterocyclic aromatics are tuned through substituents. We show that substituent position and
identity both significantly impact the pK<sub>a</sub><sup>*</sup>. We demonstrate that the substituent effects
are additive and identify many disubstituted compounds with substantially
greater photobasicity than the most photobasic 5-R quinoline compound identified
previously. We show that the addition of
a second fused benzene ring to quinoline, along with two electron-donating
substituents, lowers the vertical excitation energy into the visible while still maintaining a pK<sub>a</sub><sup>*</sup> > 14. Overall, the structure-function relationships
developed in this study provide new insights to guide the development of new
photocatalysts that employ photobasicity.
</p>
|
Sophya Alamudun; Kyle Tanovitz; April Fajardo; Kaitlind Johnson; Andy Pham; Tina Jamshidi Araghi; Andrew Petit
|
Photochemistry (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-02-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7484a469df41874f43998/original/structure-photochemical-function-relationships-in-nitrogen-containing-heterocyclic-aromatic-photobases-derived-from-quinoline.pdf
|
6393a276cfb5ff7d6264aea5
|
10.26434/chemrxiv-2022-3fh1t-v3
|
N-Metallocenyl Ynamides: Preparation, Reactivity and Synthesis of ansa[3]-Ferrocenylamides
|
The first synthesis of various N-metallocenyl ynamides has been developed and two strategies for the oxidative cyclization of N-ferrocenyl ynamide into ansa[3]-ferrocenylamide are also reported. The mechanism for the iodine(III)-triggered transfor-mation has been studied by means of DFT calculations, showing that it proceeds through a Concerted Iodination Deprotona-tion step.
|
Capucine Mahe; Olivier Blacque; Gilles Gasser; Vincent Gandon; Kevin Cariou
|
Biological and Medicinal Chemistry; Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions; Bioorganometallic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-12-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6393a276cfb5ff7d6264aea5/original/n-metallocenyl-ynamides-preparation-reactivity-and-synthesis-of-ansa-3-ferrocenylamides.pdf
|
6644c21591aefa6ce1126423
|
10.26434/chemrxiv-2024-nmcb0
|
Foaming enables material-efficient bioplastic products with minimal persistence
|
Mismanaged plastic products should be designed to inherently reduce their environmental impacts by optimizing material efficiency and minimizing environmental persistence. Foaming biodegradable bioplastics (i.e., introducing microstructural pores into the material) was hypothesized to achieve this objective. To test this hypothesis, the marine biodegradation of novel cellulose diacetate (CDA) foams of varying relative density (ρ_foam/ρ_solid =0.09-1.00) was evaluated in a flow-through seawater mesocosm. After 36 weeks, the CDA foams (ρ_foam/ρ_solid =0.09) lost 65-70% of their mass, while equivalent polystyrene foams persisted with no change in mass. The degradation rates of the CDA foams were ~15 times that of solid CDA and the fastest of any plastic reported in the ocean. Material indices, value functions, and qualitative descriptors for circularity indicated that CDA foams could be the favorable choice of material for food-packaging applications with potential benefits to society worth hundreds of millions of dollars annually. Foaming of biodegradable bioplastics thus represents a promising strategy toward minimizing the environmental impacts of frequently mismanaged consumer plastics.
|
Bryan James; Yanchen Sun; Kali Pate; Rahul Shankar; Mounir Izallalen; Sharmistha Mazumder; Steven Perri; Katelyn Houston; Brian Edwards; Jos de Wit; Christopher Reddy; Collin Ward
|
Polymer Science; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Cellulosic materials; Environmental Science; Industrial Manufacturing
|
CC BY 4.0
|
CHEMRXIV
|
2024-05-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6644c21591aefa6ce1126423/original/foaming-enables-material-efficient-bioplastic-products-with-minimal-persistence.pdf
|
6213982b0aec1a316a252606
|
10.26434/chemrxiv-2022-vnvzl
|
Two step activation of Ru‐PN3P pincer catalysts for CO2
hydrogenation
|
Activation of homogeneous catalysts is an important step in ensuring efficient operation of any catalytic system as a whole. For the majority of pincer catalysts, the activation step leans heavily on the metal ligand cooperative chemistry that allows these complexes to react with small molecule substrates and engage in catalytic transformations. While the majority of such
catalyst require a single activation event to become cooperative, herein we report an exception to this trend. Specifically we demonstrate that Ru‐PN3P aminopyridine pincer catalyst, that lacks conventional reactivity with hydrogen upon typical one‐fold activation, can engage in this reactivity when a sequential two‐step activation is performed. The resulting anionic complexes readily activate molecular hydrogen and react further with CO2 showing the previously unknown reactivity that is critical for CO2 hydrogenation catalyst. While active in CO2 hydrogenation, Ru‐PN3Ps are significantly more efficient in hydrogenation of bicarbonates – a likely consequence of the chemistry of these pincers requiring formation of anionic complexes for hydrogen activation.
|
Alex Tossaint; Christophe Rebreyend; Vivek Sinha; Manuela Weber; Stefano Canossa; Evgeny Pidko; Georgy Filonenko
|
Physical Chemistry; Inorganic Chemistry; Catalysis; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-02-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6213982b0aec1a316a252606/original/two-step-activation-of-ru-pn3p-pincer-catalysts-for-co2-hydrogenation.pdf
|
672a85945a82cea2fa25c228
|
10.26434/chemrxiv-2024-60b57
|
Simulating lithium deposition on planar anode: the role of particle reservoir and the influence of dendrite growth on current density profiles
|
In this work, we developed a computational model of lithium deposition on planar electrodes. With this model, we simulated several chronoamperometry experiments considering different deposition probabilities, i.e. cell overpotentials. Since the planar geometry induces an ion concentration gradient profile that continues to evolve toward the bulk electrolyte, we studied the influence of the lithium reservoir and rationalized its role in the real system. The solid electrolyte interface (SEI) is conceptualized as a thin layer whose thickness determines the ion diffusion profile. Additionally, the impact of dendrite formations on electrode roughness and current density profiles was analyzed by comparison with test simulations assuming inhibited dendrite growth. By presenting current density profiles in quantitatively meaningful units, our work narrows the gap for further comparison with experimental measurements. The util- ity of our simulations for determining the electrode area in lithium metal batteries is addressed.
|
Paula Valentina Saravia; Cecilia Andrea Calderón; Ezequiel Pedro Marcos Leiva; Sergio Alexis Paz
|
Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-11-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672a85945a82cea2fa25c228/original/simulating-lithium-deposition-on-planar-anode-the-role-of-particle-reservoir-and-the-influence-of-dendrite-growth-on-current-density-profiles.pdf
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62bf0edd08a0f9039c588364
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10.26434/chemrxiv-2022-ts9c6
|
Digging out the molecular connections between the active site of human lysosomal alpha-mannosidase and its pathophysiology
|
Human lysosomal alpha-mannosidase (hLAMAN) is a paradigmatic example of how few missense mutations can critically affect normal catabolism in the lysosome and cause the severe condition named alpha-mannosidosis. Here we have made use of computational chemistry methods to unveil the molecular basis of 4 missense mutations in hLAMAN with pathological consequences. We have simulated for the first time the all-atom catalytic reaction mechanism of hLAMAN by means of quantum mechanics/molecular mechanics metadynamics. Second, we show how the catalytically inactive variant D74E presents a significant increase of the free energy barrier. Third, we have identified that the D159N and E402K mutations are connected with the active site movement. Finally, we show that mutation R229W does not alter the balance between the hydrophilic and hydrophobic solvent accessible surface area in the protein, but does affect the active site dynamics. Our findings open up new opportunities for treatment of mannosidosis.
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Bruno Di Geronimo; Santiago Alonso-Gil; Bojan Zagrovic; Gilbert Reibnegger; Pedro Alejandro Sánchez-Murcia
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Biocatalysis
|
CC BY NC ND 4.0
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CHEMRXIV
|
2022-08-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bf0edd08a0f9039c588364/original/digging-out-the-molecular-connections-between-the-active-site-of-human-lysosomal-alpha-mannosidase-and-its-pathophysiology.pdf
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619e0d30dff1cc3065307f19
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10.26434/chemrxiv-2021-gfd9q
|
Understanding the Conformational Preference of Propeller-shaped Polycyclic Aromatic Hydrocarbons
|
The physico-chemical properties of chiral propeller-shaped PAHs (propellerenes) are strongly dependent on their conformational behavior. A sound, physical model to understand why propellerenes exhibit a conformation preference for either a C2 or D3 conformation that moves beyond a phenomenological explanation is needed. We have therefore performed a computational study to rationalize the conformational preference of propellerenes. Using an activation strain analysis approach, we find that the conformational preference of propellerenes is ultimately determined by the flexibility of the wings. When wings are relatively flexible, as is the case for ortho-substituted propellerenes, a favorable contraction of the radial bonds connecting the core and the propellerene wings is possible, and the more distorted C2 conformation will be preferred. The more rigid wings of benzenoid propellerenes, on the other hand, cannot deform sufficiently, and will therefore always adopt a D3 conformation. Our approach represents a unique method to pinpoint the conformational preferences of propellerenes, and, in principle, any sterically congested molecule.
|
Alex van der Ham; Thomas Hansen; Hermen S. Overkleeft; Dmitri V. Filippov; Grégory F. Schneider; Trevor A. Hamlin
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Theoretical and Computational Chemistry; Computational Chemistry and Modeling
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-11-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619e0d30dff1cc3065307f19/original/understanding-the-conformational-preference-of-propeller-shaped-polycyclic-aromatic-hydrocarbons.pdf
|
6532910ac3693ca993bcad0a
|
10.26434/chemrxiv-2023-89mz0
|
Metal-Peptidic Cages – Helical Oligoprolines Generate Highly Anisotropic Nanospaces with Emergent Isomer Control
|
The self-assembly of metal-organic cages enables the rapid creation of atomically defined, three-dimensional, nanoscale architectures reminiscent of proteins. However, existing metal-organic cages are almost exclusively built from rigid and flat aromatic panels, limiting binding selectivity and, often, water solubility. Herein, we disclose a new class of cages - metal-peptidic cages - which utilise water-soluble, chiral and helical oligoproline strands of varying length to generate highly anisotropic nanospaces. Further, we find formation of the cis isomer of the cage is strongly favoured, and is an emergent property of using complex and chiral building blocks in the formation of defined nanospaces. We demonstrate that the use of peptidic building blocks allows us to rapidly tune the size of the nanospace formed, from c. 1 - 4 nm, and that the use of biologically relevant components enables targeted binding of therapeutic molecules, highlighting the potential of these systems for selective drug delivery.
|
Ben Barber; Ellen Jamieson; Leah White; Charlie McTernan
|
Organic Chemistry; Inorganic Chemistry; Nanoscience; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-10-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6532910ac3693ca993bcad0a/original/metal-peptidic-cages-helical-oligoprolines-generate-highly-anisotropic-nanospaces-with-emergent-isomer-control.pdf
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663a438321291e5d1daa0090
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10.26434/chemrxiv-2024-v3mnv
|
Neuromodulating Alkaloids from Millipede Defensive Secretions
|
Natural products are commonly deployed as defensive agents and these molecules have formed the basis for today’s therapeutic agents. Millipedes have evolved specialized glands to store structurally diverse chemical defenses, including cyanide containing metabolites, alkaloids, and oxidized aromatics. A study into the excretions of an understudied millipede, Ischnocybe plicata, led to characterizing four new oxidized alkaloids (ischnocybines) with potent and selective binding affinity for sigma-1, an orphan neuroreceptor. Analysis by MS and 2D NMR revealed the relative configurations of these four ischnocybines. These molecules are structurally distinct from all other millipede metabolites and are the first metabolites to be shown to bind to a specific neuroreceptor with low nanomolar affinity (Ki 13.6 nM). In addition, this natural structural diversity establishes a structure activity relationship and supports a proposed biosynthetic pathway leading to the target compounds.
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Carla Menegatti; Paige Banks; Kenneth Knott; Anthony J. Briganti; Samuel V. G. McNally; Paul Marek; Anne M. Brown; Tappey Jones; Emily Mevers
|
Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Chemical Biology
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-05-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663a438321291e5d1daa0090/original/neuromodulating-alkaloids-from-millipede-defensive-secretions.pdf
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6447eb61df78ec50155e92f3
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10.26434/chemrxiv-2023-s6mp3
|
Hydrogen Generation by Hydrolysis of Magnesium Hydride in Organic Acids Solutions
|
Hydrolysis of MgH2 has a high theoretical hydrogen yield (15.2%) and is very attractive for onsite hydrogen production. However, the low solubility of Mg(OH)2 causes sluggish kinetics and incomplete utilization of MgH2. In this paper, we solve this problem by using organic acids (acetic, citric and oxalic) and nanoscale graphene-like carbon. The organic acid solution significantly increases the yield and rate of H2 generation due to its acidic nature. The hydrogen yield approaches 100% with a fast hydrolysis rate when the molar ratio Acid/MgH2 exceeds 0.9, 2.0 and 2.7 for the citric, oxalic and acetic acid, respectively. In doing so, pH of the reaction solutions after hydrolysis corresponds to 4.53, 2.11 and 4.28, accordingly, testifying about buffer nature of the solutions “citric acid / magnesium citrate” and “acetic acid / magnesium acetate”. The addition of graphene-like material (GLM) also significantly increases the yield and rate of H2 generation due to the decrease of particle size and increase of defects in the material, as well as due to stabilising the MgH2 nanoparticles and preventing their agglomeration. Additionally, GLM encapsulates the MgH2 particles thus suppressing the formation of MgO and, in turn, promoting achievement of the maximum hydrogen yield. In addition, this work presents layout and operation features of the developed apparatus for the controlled generation of pressurised hydrogen using hydrolysis of Mg or MgH2 in acidic solutions, as well as its testing results for the hydrolysis of Mg and MgH2 in the solution of citric acid.
|
Mykhaylo Lototskyy; Moegamat Wafeeq Davids; Tshepo Kgokane Sekgobela; Artem Arbuzov; Sergey Mozhzhukhin; Yongyang Zhu; Renheng Tang; Boris Tarasov
|
Physical Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Composites; Hydrogen Storage Materials; Chemical Kinetics
|
CC BY 4.0
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CHEMRXIV
|
2023-04-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6447eb61df78ec50155e92f3/original/hydrogen-generation-by-hydrolysis-of-magnesium-hydride-in-organic-acids-solutions.pdf
|
63e0c2e11f23f0032d42f1ce
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10.26434/chemrxiv-2022-4sgm6-v2
|
Stereospecific Synthesis of Enantiopure [6]Helicene Containing a Seven-Membered Ring and [7]Helicene via Acid-Promoted Stepwise Alkyne Annulations of Doubly Axial-Chiral Precursors
|
The enantiopure seven-membered ring embedded [6]helicene and carbo[7]helicene (>99% ee) with an opposite helicity were simultaneously and quantitatively (>99%) synthesized with a perfect stereospecificity through stepwise acid-promoted intramolecular alkyne annulations of doubly axial-chiral cyclization precursors. The helical handedness of the [6]- and [7]helicenes was fully stereo-controlled by the doubly axial chirality of the precursors as a result of complete axial-to-helical asymmetry transfer. The cyclizations proceeded in a stepwise manner; the first six-membered ring formation was followed by the kinetically-controlled seven- or six-membered ring formation with or without helix-inversion of a [4]helicene intermediate generated during the first cyclization step, thus quantitatively producing enantiopure circularly polarized luminescent [6]- and [7]helicenes with an opposite helicity, respectively.
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Tomoyuki Ikai; Kosuke Oki; Shoya Yamakawa; Eiji Yashima
|
Organic Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-02-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e0c2e11f23f0032d42f1ce/original/stereospecific-synthesis-of-enantiopure-6-helicene-containing-a-seven-membered-ring-and-7-helicene-via-acid-promoted-stepwise-alkyne-annulations-of-doubly-axial-chiral-precursors.pdf
|
60c7447abdbb89103ca38808
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10.26434/chemrxiv.9108461.v2
|
High-Throughput Discovery and Evaluation of a General Catalytic Method for N-Arylation of Weakly Nucleophilic Sulfonamides
|
Sulfonamides are poor nucleophiles in Pd C-N coupling catalysis, hindering synthesis of densely-functionalized N,N-diaryl sulfonamide motifs relevant to medicinal chemistry. Through targeted high-throughput experimentation (HTE), we have identified the Pd/AdBippyPhos catalyst system as an effective and general method to construct this difficult to access moiety. In particular, AdBippyPhos is critical for the installation of heteroaromatic groups. Computational steric parameterization of the investigated ligands reveals the potential importance of remote steric demand, where a large cone angle combined with an accessible Pd center is correlated to successful catalysts for C-N coupling reactions.<br />
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Joseph Becica; Damian Hruszkewycz; Janelle Steves; Jennifer Elward; David Leitch; Graham Dobereiner
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Combinatorial Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis; Catalysis; Ligand Design; Reaction (Organomet.)
|
CC BY NC ND 4.0
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CHEMRXIV
|
2019-09-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7447abdbb89103ca38808/original/high-throughput-discovery-and-evaluation-of-a-general-catalytic-method-for-n-arylation-of-weakly-nucleophilic-sulfonamides.pdf
|
6668341ae7ccf7753a80889d
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10.26434/chemrxiv-2024-tqjmw
|
Simulating Solid-State Battery Cathode Manufacturing via Wet-Processing with Resolved Active Material Geometries
|
Prior to the development of a solid-state battery cell, researchers have limited knowledge about the microstructure of the electrodes and how they are affected by manufacturing. Therefore, numerical simulations can be considered as a powerful tool to link the fabrication process to the final microstructure of the electrode. In this paper, a numerical simulation of a wet-processed solid-state battery cathode with a formulation of 75 % LiNi9Mn0.5Co0.5O2 (NMC), 17.5 %LPSCl, 5 % Timcal C65 and 2.5 % Polyisobutene (PIB) is presented. From nano-computed tomography images, realistic shapes of active material particles are extracted and used in the simulation, which is well-calibrated to experimental data. In particular, we study the effects of calendering on the microstructure of the simulated cathode and deduce structure-property relations.
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Dennis Weitze; Franco Zanotto; Diana Zapata-Dominguez; Alejandro A. Franco
|
Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Energy Storage
|
CC BY 4.0
|
CHEMRXIV
|
2024-06-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6668341ae7ccf7753a80889d/original/simulating-solid-state-battery-cathode-manufacturing-via-wet-processing-with-resolved-active-material-geometries.pdf
|
67895eaafa469535b95013c7
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10.26434/chemrxiv-2025-m49f0
|
Photoenzymatically-Induced Asymmetric Hydroarylation of Alkenes with (Hetero)aryl Halides
|
Herein we describe a set of privileged and stereocomplementary ene-reductase enzymes which, when induced by light and aided by an exogenous photocatalyst, catalyze the coupling of (hetero)aryl halides and alkenes in an asymmetric intermolecular hydroarylation process. Thus, carbon scaffolds containing C(sp2)-C(sp3) bonds are synthesized enzymatically from simple precursors in excellent enantiomeric excess. Furthermore, an intramolecular coupling is achieved through tethering of (hetero)aryl halides to their alkene reaction partners and in this manner problematic side reactions are suppressed and yields improved. This work extends the utility of photo-induced biocatalysis through the addition of the novel and pharmaceutically important (hetero)aromatic halide class of radical precursors.
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Corey L. Jones; Alandra Quinn; Xiaochun Wang; Jason K. Smith; Jeffrey M. Casavant; Simon Berritt; Thomas Knauber; Carolos A. Martinez; Jovan Livada; Scott France; Paul F. Richardson; Roger M. Howard; Hatice G. Yayla
|
Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2025-01-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67895eaafa469535b95013c7/original/photoenzymatically-induced-asymmetric-hydroarylation-of-alkenes-with-hetero-aryl-halides.pdf
|
629878d54f43d64ba02ce321
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10.26434/chemrxiv-2022-7zf68
|
Direct Solid-State Synthesis of the Superconductor NaMo6Se8: Single-Crystal Structure, Electrical and Magnetic Properties
|
Powder samples and single crystals of the ternary selenide NaMo6Se8 were obtained by direct solid-state reaction at high temperature for the first time. The structure was determined by single-crystal X-ray diffraction. NaMo6Se8 crystallizes in the trigonal space group R-3 (No. 148) with unit-cell parameters a = 9.5564 (2) Å, c = 11.7181 (3) Å and Z = 3. Full-matrix least-squares refinement on F2 using 911 independent reflections for 25 refinable parameters results in R1 = 0.0251 and wR2 = 0.0593. The structure contains Mo6Se8iSe6a cluster units (octahedral Mo6 cluster inscribed in a pseudo S8 cube) separated from each other by large voids which are filled up by eight-coordinate Na atoms. The evolution of the Mo-Mo distances of the octahedral Mo6 cluster with respect to the cationic charge in the selenide Chevrel phases is also discussed. NaMo6Se8 behaves as a p-type metal with relatively low electrical resistivity and becomes superconductor below 9.2 K.
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Patrick Gougeon; Philippe Gall
|
Inorganic Chemistry; Solid State Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-06-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629878d54f43d64ba02ce321/original/direct-solid-state-synthesis-of-the-superconductor-na-mo6se8-single-crystal-structure-electrical-and-magnetic-properties.pdf
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60c740210f50db84973958f8
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10.26434/chemrxiv.7645115.v1
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Modular, Stereocontrolled Cβ–H/Cα–C Activation of Alkyl Carboxylic Acids
|
<div>
<div>
<div>
<p>The union of two powerful transformations, directed C–H activation and decarboxylative cross-coupling, for the
enantioselective synthesis of vicinally functionalized alkyl, carbocyclic, and heterocyclic compounds is described. Starting from
simple carboxylic acid building blocks, this modular sequence exploits the residual directing group to access more than 50 scaffolds
that would be otherwise extremely difficult to prepare. The tactical use of these two transformations accomplishes a formal vicinal
difunctionalization of carbon centers in a way that is modular and thus amenable to rapid diversity incorporation. A simplification of
routes to known preclinical drug candidates is presented along with the rapid diversification of an antimalarial compound series.
</p>
</div>
</div>
</div>
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Ming Shang; Karla S. Feu; Julien C. Vantourout; Lisa M. Barton; Heather
L. Osswald; Nobutaka Kato; Kerstin Gagaring; Case W. McNamara; Gang Chen; Liang Hu; Shengyang Ni; Paula Fernández-Canelas; Miao Chen; Rohan R. Merchant; Tian qin; Stuart Schreiber; Bruno Melillo; jin-quan yu; Phil Baran
|
Natural Products; Organic Synthesis and Reactions; Stereochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-01-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740210f50db84973958f8/original/modular-stereocontrolled-c-h-c-c-activation-of-alkyl-carboxylic-acids.pdf
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652de39c45aaa5fdbb280b9b
|
10.26434/chemrxiv-2023-4q2v2
|
Organic Optoelectronic Devices Based on Through-Space Interaction
|
Through-space interaction (TSI), including through-space conjugation (TSC) and through-space charge transfer (TSCT), has emerged as a promising strategy for designing functional materials and constructing superior optoelectronic devices. Because of the multichannel charge transport and structural flexibility, TSI-based devices often exhibit high-performance optoelectronic properties, such as excellent photoluminescence, high charge carrier mobility, and outstanding device efficiency. In this review, the principles and characteristics of TSI are briefly introduced. Then we mainly focused on the recent progress of optoelectronic device applications based on materials with TSC and TSCT. Various advanced optoelectronic devices, including organic fluorescence film sensors, organic light-emitting diodes, single-molecule junctions, and photoswitches are discussed in detail and possible breakthroughs are proposed for future molecular design and efficiency enhancement.
|
Jiaqi Peng; Liyuan Hou; Dan Liu; Zheng Zhao; Jianquan Zhang; Zijie Qiu; Ben Zhong Tang
|
Materials Science; Aggregates and Assemblies; Optical Materials
|
CC BY NC ND 4.0
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CHEMRXIV
|
2023-10-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652de39c45aaa5fdbb280b9b/original/organic-optoelectronic-devices-based-on-through-space-interaction.pdf
|
632d12fdcf382945a9aeca70
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10.26434/chemrxiv-2022-tz5ss
|
Tetraalkoxysilane Assisted Self-Emulsification Templating for Mesoporous Silica Nanoparticles with Controlled Mesostructures
|
Although mesoporous silica nanoparticles (MSNs) have been intensively investigated, their mesostructure and formation mechanism are still a topic of debate. Here, we demonstrate that the formation of MSNs is a result of dynamic two-level template collaborative self-assembly of microemulsion droplets and spherical micelles, whose surfaces are both partly covered by silicate species. The stability of microemulsion droplets spontaneously formed by water-surfactant-tetraalkoxysilanes (TAOS) ternary system determines the final morphology and particle size of MSNs, and we definitively confirms that the dendritic MSNs (DMSNs) with unique hierarchical pore structures is a metastable intermediate product, which could be kinetically transferred to regular MSNs undergoing a fast structural collapse of microemulsion droplets with the continuous consumption of TAOS. Our research further highlights the prominent role of self-emulsification of organic silane reagents in sol-gel chemistry to tune the morphology and structure of final products.
|
Bo Peng; Jia-Feng Zhou; Hui Chen; Meng Ding; Yi-Song Zhu; Belén Albela; Peng Wu; Laurent Bonneviot; kun zhang
|
Inorganic Chemistry; Nanoscience; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632d12fdcf382945a9aeca70/original/tetraalkoxysilane-assisted-self-emulsification-templating-for-mesoporous-silica-nanoparticles-with-controlled-mesostructures.pdf
|
6338304bba8a6d9dae63d46a
|
10.26434/chemrxiv-2022-0g9k0
|
Identifying chemistry students’ baseline systems thinking skills when constructing systems for a topic on climate change
|
Recently, increased attention towards systems thinking (ST) in chemistry education has aimed to bridge disciplines and equip citizens and scientists with skills needed to address global challenges such as sustainability and climate change. As a result, new resources have emerged for educators to implement systems thinking in chemistry education (STICE), including a proposed set of ST skills. While these efforts aim to make ST implementation easier, little is known about how to assess these skills in a chemistry context. Additionally, there are no studies that have investigated how chemistry students naturally engage with ST learning activities; such information would guide educators about where to place emphasis when teaching ST skills. In this study, we investigated ST skills employed by students who constructed visual representations (systems) of a topic related to climate change. Eighteen undergraduate chemistry students from first- to third-year participated in this study. We designed and implemented a ST intervention to capture how students engaged with three ST tasks, performed individually and collaboratively. In our analysis, we assessed eleven ST skills that aligned with the five characteristics of STICE proposed by York and Orgill. We found that most participants demonstrated these ST skills when assessing ST skills exactly as articulated in the literature. When further investigating the extent that participants demonstrated these skills, we identified aspects of these skills that participants did and did not demonstrate. We found that (1) participants’ systems lacked concepts and connections at the submicroscopic level, (2) participants’ systems included multiple types of connections in their systems but few circular loops and causal connections, (3) participants predicted how their systems changed over time but lacked multicomponent causal reasoning, and (4) participants’ systems demonstrated the breadth of connections but did not consider human connections to the underlying chemistry of climate change topics. These findings identify aspects of ST where chemistry educators need to place emphasis when teaching ST skills to chemistry students and when guiding learning activities and other assessments. Using our findings, we created a ST rubric for the chemistry community as a tool for assessing ST skills.
|
Alisha R. Szozda; Peter G. Mahaffy; Alison B. Flynn
|
Chemical Education
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6338304bba8a6d9dae63d46a/original/identifying-chemistry-students-baseline-systems-thinking-skills-when-constructing-systems-for-a-topic-on-climate-change.pdf
|
6324975bf764e62c60f8054b
|
10.26434/chemrxiv-2022-jfwjs-v3
|
BODIPY-labelled estrogens for fluorescence analysis of environmental microbial degradation
|
Biodegradation of estrogen hormone micropollutants is a well-established approach towards their remediation. Fluorescently labelled substrates are used extensively for rapid, near real-time analysis of biological processes and are a potential tool for studying biodegradation processes faster and more efficiently than conventional approaches. However, it is important to understand how the fluorescently tagged surrogates compare with the natural substrate in terms of chemical analysis and the intended application. We derivatized three natural estrogens with BODIPY fluorophores by azide-alkyne cycloaddition click reaction and developed an analytical workflow based on simple liquid-liquid extraction and HPLC-PDA analysis. The developed methods allow for concurrent analysis of both fluorescent and natural estrogens with comparable recovery, accuracy, and precision. We then evaluated the use of BODIPY-labelled estrogens as surrogate substrates for studying biodegradation using a model bacterium for estrogen metabolism. The developed analytical methods were successfully employed to compare the biological transformation of 17β-estradiol (E2), with and without BODIPY fluorescent tag. Through measuring the complete degradation of E2 and the transformation of BODIPY-estradiol to BODIPY-estrone in the presence of a co-substrate, we found that BODIPY-labelled estrogens are biologically viable surrogates for investigating biodegradation in environmental bacteria.
|
Celeste Felion; Ricardo Lopez-Gonzalez; Alan L. Sewell; Rodolfo Marquez; Caroline Gauchotte-Lindsay
|
Analytical Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-09-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6324975bf764e62c60f8054b/original/bodipy-labelled-estrogens-for-fluorescence-analysis-of-environmental-microbial-degradation.pdf
|
65658855cf8b3c3cd74be96b
|
10.26434/chemrxiv-2023-ml11l
|
Toward New Horizons in Verdazyl-Nitroxide High-Spin Systems: Thermally Robust Tetraradical with Quintet Ground State
|
High-spin organic tetraradicals with significant intramolecular exchange interactions have high potential for advanced technological applications and fundamental research, but reported to date examples exhibit limited stability and processability. In this work, we designed the first tetraradical based on an oxoverdazyl core and nitronyl nitroxide radicals and successfully synthesized it using a palladium-catalyzed cross-coupling reaction of oxoverdazyl radical bearing three iodo-phenylene moieties with a gold(I) nitronyl nitroxide-2-ide complex in the presence of a recently developed efficient catalytic system. The molecular and crystal structures of the tetraradical were confirmed by single crystal X-ray diffraction analysis. The tetraradical possesses good thermal stability with decomposition onset at ∼115 °C in an inert atmosphere. The resulting unique verdazyl-nitroxide conjugate was thoroughly studied using a complex of SQUID magnetometry of polycrystalline powders, EPR spectroscopy in various matrices, cyclic voltammetry (CV), and high-level quantum chemical calculations. All collected data confirm the high thermal stability of the resulting tetraradical and quintet multiplicity of its ground state, which makes the synthesis of this important paramagnet a new milestone in the field of creating high-spin systems.
|
Igor Zayakin; Pavel Petunin; Pavel Postnikov; Alexey Dmitriev; Nina Gritsan; Pavel Dorovatovskii; Alexander Korlyukov; Matvey Fedin; Artem Bogomyakov; Anna Akyeva; Mikhail Syroeshkin; Julia Burykina; Evgeny Tretyakov
|
Physical Chemistry; Materials Science; Magnetic Materials; Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65658855cf8b3c3cd74be96b/original/toward-new-horizons-in-verdazyl-nitroxide-high-spin-systems-thermally-robust-tetraradical-with-quintet-ground-state.pdf
|
668d8aab01103d79c5843a77
|
10.26434/chemrxiv-2024-36vjp
|
Soft magnetic hysteresis in a dysprosium amide-alkene complex up to 100 K
|
Lanthanides have recently shown magnetic memory at both the atomic and molecular level. The temperatures at which single-molecule magnets (SMMs) show magnetic hysteresis only increased from 4 K to 14 K in nearly 25 years since the discovery of the first SMM in 1993. However, since 2017 energy barriers to magnetic reversal (Ueff) from 1237(28)-1631(25) cm–1 and open magnetic hysteresis loops between 40-80 K have often been delivered by molecules featuring rigid aromatic ligands in axial dysprosium cyclopentadienyl complexes and their derivatives. Here we report a dysprosium bis(amide)-alkene complex, [Dy{N(SiiPr3)[Si(iPr)2C(CH3)=CHCH3]}{N(SiiPr3)(SiiPr2Et)}][Al{OC(CF3)3}4] (1-Dy), which shows Ueff = 1843(11) cm–1 and slow closing of magnetic hysteresis loops up to 100 K. Calculations show that the record Ueff value of 1-Dy arises from the charge-dense bis(silyl)amide ligands, with a pendant alkene taking a structural role to enforce a large N–Dy–N angle while imposing only a weak equatorial interaction. This leads to molecular spin dynamics up to one hundred times slower than the current best SMMs above 100 K.
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Jack Emerson-King; Gemma Gransbury; Benjamin Atkinson; William Blackmore; George Whitehead; Nicholas Chilton; David Mills
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Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Magnetism
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CC BY 4.0
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CHEMRXIV
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2024-07-15
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668d8aab01103d79c5843a77/original/soft-magnetic-hysteresis-in-a-dysprosium-amide-alkene-complex-up-to-100-k.pdf
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678a58086dde43c908f074ac
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10.26434/chemrxiv-2025-t42q4
|
Photochemical Chain Scissions Enhance Polyethylene Glycol Biodegradability:
From Probabilistic Modelling to Experimental Demonstration
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Polyethylene glycols (PEGs), a major class of water-soluble polymers (WSPs), are widely used in diverse applications which may lead to their release into the environment. This work investigates the reaction of PEGs with photochemically produced hydroxyl radicals (•OH), an important environmental oxidant, and assesses the effect of reaction-induced molecular weight (MW) decreases on PEG biodegradation dynamics in soil and sediment. Probabilistic kinetic modelling revealed a significant reduction in PEG MW after only a few •OH-induced chain scissions on initial PEG molecules. The simulation results were experimentally validated by reacting 13C-labeled PEGs (average MW = 6200 Da) with photochemically produced •OH, resulting in pronounced shifts in the size distribution of PEGs towards lower MWs with increasing reaction extents. Incubations of the initial non-reacted and three incrementally •OH-reacted PEG mixtures over a 150-day period in sediment and soil demonstrated increasing rates and extents of PEG biodegradation to 13CO2 with increasing •OH-reaction extent and thus decreasing PEG average MW. This study underscores the importance of considering the MW distributions of WSPs and their dynamic changes through biotic or abiotic chain scission reactions — showcased herein by reacting PEGs with photochemically produced •OH — in mechanistically understanding WSP biodegradability in natural and engineered receiving environments.
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Kevin Kleemann; Madalina Jaggi; Stefano M. Bernasconi; Robert Alexander Schmitz; Glauco Battagliarin; Andreas Künkel; Carsten Simon; Kristopher McNeill; Michael Sander
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Polymer Science; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry
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CC BY 4.0
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CHEMRXIV
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2025-01-28
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678a58086dde43c908f074ac/original/photochemical-chain-scissions-enhance-polyethylene-glycol-biodegradability-from-probabilistic-modelling-to-experimental-demonstration.pdf
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623b9bb82c501047e5864066
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10.26434/chemrxiv-2021-qr24p-v4
|
A crystalline tri-thorium cluster: σ-aromaticity vs charge-shift bonding
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Very recently, Boronski et al. reported the first thorium-thorium bond in a crystalline cluster prepared under normal experimental conditions. By using a range of experimental techniques and computational models, the authors found that the isolated actinide cluster contains at its heart two paired electrons delocalized over the tri-thorium ring. The recorded Raman spectrum allegedly confirmed the existence of a σ-aromatic three-center two-electron bond. In the following we demonstrate that the experimentally observed broad inelastic scattering bands between 60 and 135 cm-1, originally assigned by the authors to thorium-thorium vibrations, represent the combination of Th–Cl stretching and Th–Cl–Th bending modes, and they establish the existence of an unprecedented multicenter charge-shift bonding (ThCl2)3 rather than the σ-aromatic bonding Th3. In the light of the presented findings, the latter remains experimentally unproven and computationally questionable.
|
Dariusz Szczepanik
|
Theoretical and Computational Chemistry; Inorganic Chemistry; Bonding; Coordination Chemistry (Inorg.); Lanthanides and Actinides
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-03-25
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623b9bb82c501047e5864066/original/a-crystalline-tri-thorium-cluster-aromaticity-vs-charge-shift-bonding.pdf
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60c74bf90f50db8723396d53
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10.26434/chemrxiv.12330866.v2
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Magnetic Ordering via Itinerant Ferromagnetism in a Metal-Organic Framework
|
<b>Materials
that combine magnetic order with other desirable physical attributes offer to revolutionize
our energy landscape. Indeed, such materials could find transformative applications
in spintronics, quantum sensing, low-density magnets, and gas separations. As a result, efforts to design multifunctional magnetic materials have recently
moved beyond traditional solid-state materials to metal–organic solids. Among
these, metal–organic frameworks in particular bear structures that offer
intrinsic porosity, vast chemical and structural programmability, and tunability
of electronic properties. Nevertheless, magnetic order within metal–organic
frameworks has generally been limited to low temperatures, owing largely to challenges
in creating strong magnetic exchange in extended metal–organic solids. Here, we employ the phenomenon of itinerant ferromagnetism to realize magnetic
ordering at <i>T</i><sub>C</sub> = 225 K in
a mixed-valence chromium(II/III) triazolate compound, representing the highest ferromagnetic
ordering temperature yet observed in a metal–organic framework. The itinerant
ferromagnetism is shown to proceed via a double-exchange mechanism, the first such
observation in any metal–organic material. Critically, this mechanism results
in variable-temperature conductivity with barrierless charge transport below <i>T</i><sub>C</sub> and a large negative
magnetoresistance of 23% at 5 K. These observations suggest applications for double-exchange-based
coordination solids in the emergent fields of magnetoelectrics and spintronics. Taken together, the insights gleaned from these results are expected to provide
a blueprint for the design and synthesis of porous materials with synergistic
high-temperature magnetic and charge transport properties. </b>
|
Jesse Park; Brianna Collins; Lucy Darago; Tomce Runcevski; Michael Aubrey; Henry Z. H. Jiang; Ever Velasquez; Mark Green; Jason Goodpaster; Jeffrey R. Long
|
Hybrid Organic-Inorganic Materials; Magnetic Materials; Coordination Chemistry (Inorg.); Magnetism
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CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bf90f50db8723396d53/original/magnetic-ordering-via-itinerant-ferromagnetism-in-a-metal-organic-framework.pdf
|
62cd696f7aab58ced5ba5ebe
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10.26434/chemrxiv-2022-dtwbm
|
Unravelling the Ordered Phase of the Quintessential Hybrid Perovskite MAPbI3 – Thermophysics to the Rescue
|
Hybrid organic-inorganic perovskites continue to attract an enormous amount of attention, yet a robust microscopic picture of their different phases as well as the extent and nature of the disorder present remain elusive. Using specific-heat data along with high-resolution inelastic neutron scattering and ab initio modeling, we address
this ongoing challenge for the case of the ordered phase of the quintessential hybrid perovskite MAPbI3. At low-temperatures, the specific heat of MAPbI3 reveals strong
deviations from the Debye limit, a common feature of pure hybrid perovskites and their mixtures. We find that these deviations are exquisitely sensitive to the underlying low-energy phonon band structure, thus paving the way for a quantitative and robust assessment of available structural models beyond what has been possible to date. Our thermophysical analysis demonstrates that the (otherwise ordered) structure around the organic moiety is characterized by a substantial lowering of the local
symmetry relative to what can be inferred from crystallographic studies. The ab initio phonon calculations also provide a means of exploring in detail the physical origin of the observed thermophysical anomalies, which can now be unequivocally associated with excitations of sub-Terahertz optical phonons responsible for translational and librational distortions of the octahedral units. To the best of our knowledge, this is the first time that such a model-selection protocol using thermophysical properties as key input has been deployed with success in the study of this important class of materials.
|
Pelayo Marin-Villa; Ana Arauzo; Kacper Drużbicki; Felix Fernandez-Alonso
|
Theoretical and Computational Chemistry; Materials Science; Energy; Hybrid Organic-Inorganic Materials; Photovoltaics
|
CC BY NC ND 4.0
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CHEMRXIV
|
2022-07-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cd696f7aab58ced5ba5ebe/original/unravelling-the-ordered-phase-of-the-quintessential-hybrid-perovskite-ma-pb-i3-thermophysics-to-the-rescue.pdf
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61bd913a7284d039ddf02ea5
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10.26434/chemrxiv-2021-67nq5
|
Standard binding free energy and membrane desorption mechanism for a phospholipase C
|
Peripheral membrane proteins (PMPs) bind temporarily to cellular membranes and play important roles in signalling, lipid metabolism and membrane trafficking. Obtaining accurate membrane-PMP affinities using experimental techniques is more challenging than for protein-ligand affinities in aqueous solution. At the theoretical level, calculation of standard protein-membrane binding free energy using molecular dynamics simulations remains a daunting challenge owing to the size of the biological objects at play, the slow lipid diffusion and the large variation in configurational entropy that accompanies the binding process. To overcome these challenges, we used a computational framework relying on a series of potential-of-mean-force (PMF) calculations including a set of geometrical restraints on collective variables. This methodology allowed us to determine the standard binding free energy of a PMP to a phospholipid bilayer using an all-atom force field. Bacillus thuringiensis phosphatidylinositol-specific phospholipase C (BtPI-PLC) was chosen due to its importance as a virulence factor and owing to the host of experimental affinity data available. We computed a standard binding free energy of -8.2±1.4 kcal/mol in reasonable agreement with the reported experimental values (-6.6±0.2 kcal/mol). In light of the 2.3-μs separation PMF calculation, we investigated the mechanism whereby BtPI-PLC disengages from interactions with the lipid bilayer during separation. We describe how a short amphipathic helix engages in transitory interactions to ease the passage of its hydrophobes through the interfacial region upon desorption from the bilayer.
|
Emmanuel Moutoussamy; Hanif Muhammad Khan; Mary Fedarko Roberts; Anne Gershenson; Christophe Chipot; Nathalie Reuter
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-12-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61bd913a7284d039ddf02ea5/original/standard-binding-free-energy-and-membrane-desorption-mechanism-for-a-phospholipase-c.pdf
|
64788f59be16ad5c5748e891
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10.26434/chemrxiv-2023-hrpx0
|
Porous supramolecular gels produced by reversible self-gelation of ruthenium-based metal-organic polyhedra
|
Supramolecular gels based on metal-organic polyhedra (MOPs) represent a versatile platform to access processable soft materials with controlled porosity. Herein, we report a self-gelation approach that allows the reversible assembly of a novel Ru-based MOP in the form of colloidal gels. The presence of cationic mixed-valence [Ru2(COO)4]+ paddlewheel units allows for modification of the MOP charge via acid/base treatment, and therefore, its solubility. This feature enables control over supramolecular interactions, making it possible to reversibly force MOP aggregation to form nanoparticles, which further assemble to form a colloidal gel network. The gelation process was thoroughly investigated by time-resolved ζ-potential, pH, and dynamic light scattering measurements. This strategy leads to the evolution of hierarchically porous aerogel from individual MOP molecules without using any additional component. Furthermore, we demonstrate that the simplicity of this method can be exploited for the obtention of MOP-based gels through a one-pot synthetic approach starting from MOP precursors.
|
Javier Troyano; Fuerkaiti Tayier; Phitchayapha Phattharaphuti; Takuma Aoyama; Kenji Urayama; Shuhei Furukawa
|
Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Coordination Chemistry (Inorg.); Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-06-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64788f59be16ad5c5748e891/original/porous-supramolecular-gels-produced-by-reversible-self-gelation-of-ruthenium-based-metal-organic-polyhedra.pdf
|
625f34afef2ade3f323644e8
|
10.26434/chemrxiv-2022-brd31
|
Magnetic field effects in biology from the perspective of the radical pair mechanism
|
A large and growing body of research shows that weak magnetic fields can significantly influence various biological systems, including plants, animals, and humans. However, the underlying mechanisms behind these phenomena remain elusive. It is remarkable that the magnetic energies implicated in these effects are much smaller than thermal energies. Here we review these observations, of which there are now hundreds, and we suggest that a viable explanation is provided by the radical pair mechanism, which involves the quantum dynamics of the electron and nuclear spins of naturally occurring transient radical molecules. While the radical pair mechanism has been studied in detail in the context of avian magnetoreception, the studies reviewed here show that magnetosensitivity is widespread throughout biology. We review magnetic field effects on various physiological functions, organizing them based on the type of the applied magnetic fields, namely static, hypomagnetic, and oscillating magnetic fields, as well as isotope effects. We then review the radical pair mechanism as a potential unifying model for the described magnetic field effects, and we discuss plausible candidate molecules that might constitute the radical pairs. We review recent studies proposing that the quantum nature of the radical pairs provides promising explanations for xenon anesthesia, lithium effects on hyperactivity, magnetic field and lithium effects on the circadian clock, and hypomagnetic field effects on neurogenesis and microtubule assembly. We conclude by discussing future lines of investigation in this exciting new area of quantum biology related to weak magnetic field effects.
|
Hadi ZADEH-HAGHIGHI; Christoph Simon
|
Biological and Medicinal Chemistry; Biochemistry; Biophysics; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-04-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625f34afef2ade3f323644e8/original/magnetic-field-effects-in-biology-from-the-perspective-of-the-radical-pair-mechanism.pdf
|
60c744fb337d6c300ae26ed5
|
10.26434/chemrxiv.9942380.v1
|
Defect Chemistry of Disordered Solid-State Electrolyte Li10GeP2S12
|
Several classes of materials, including thiophosphates, garnets, argyrodites, and anti-perovskites, have been considered as electrolytes for all-solid-state batteries. Native point defects and dopants play a critical role in impeding or facilitating fast ion conduction in these solid electrolytes. Despite its significance, comprehensive studies of the native defect chemistry of well-known solid electrolytes is currently lacking, in part due their compositional and structural complexity. Most of these solid-state electrolytes exhibit significant structural disorder, which requires careful consideration when modeling the point defect energetics. In this work, we model the native defect chemistry of a disordered solid electrolyte, Li<sub>10</sub>GeP<sub>2</sub>S<sub>12</sub> (LGPS), by uniquely combining ensemble statistics, accurate electronic structure, and modern first-principles defect calculations. We find that V<sub>Li</sub>, Li<sub>i</sub>, and P<sub>Ge</sub> are the dominant defects. From these calculations, we determine the statistics of defect energetics; formation energies of the dominant defects vary over ~140 meV. Combined with <i>ab initio</i> molecular dynamics simulations, we find that anti-sites P<sub>Ge</sub> promote Li ion conductivity, suggesting LGPS growth under P-rich/Ge-poor conditions will enhance ion conductivity. To this end, we offer practical experimental guides to enhance ion conductivity.
|
Prashun Gorai; Hai Long; Eric Jones; Shriram Santhanagopalan; Vladan Stevanovic
|
Electrochemistry; Main Group Chemistry (Inorg.); Solid State Chemistry; Theory - Inorganic; Computational Chemistry and Modeling; Theory - Computational; Energy Storage; Physical and Chemical Properties; Structure; Thermodynamics (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-10-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744fb337d6c300ae26ed5/original/defect-chemistry-of-disordered-solid-state-electrolyte-li10ge-p2s12.pdf
|
65b7fe07e9ebbb4db93b12a1
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10.26434/chemrxiv-2024-d4jbl
|
E_min: A First-Principles Thermochemical Descriptor for Predicting Molecular Synthesizability
|
Predicting the synthesizability of a new molecule remains an unsolved challenge that chemists have long tackled with heuristic approaches. Here, we report a new method for predicting synthesizability using a simple, yet accurate thermochemical descriptor. We introduce E_min, the energy difference between a molecule and its lowest energy constitutional isomer, as a synthesizability predictor that is accurate, physically meaningful, and first-principles based. We apply E_min to 134,000 molecules in the QM9 dataset and find that E_min is accurate when used alone and reduces incorrect predictions of "synthesizable" by up to 52% when used to augment commonly-used prediction methods. Our work illustrates how first-principles thermochemistry and heuristic approximations for molecular stability are complementary, opening a new direction for synthesizability prediction methods
|
Andrew Lee; Sarah N. Elliott; Hassan Harb; Logan Ward; Ian T. Foster; Larry A. Curtiss; Rajeev S. Assary
|
Theoretical and Computational Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2024-01-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b7fe07e9ebbb4db93b12a1/original/e-min-a-first-principles-thermochemical-descriptor-for-predicting-molecular-synthesizability.pdf
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65ae77639138d231617c37ef
|
10.26434/chemrxiv-2023-bdwh0-v3
|
Exploring the Chemical Subspace of RPLC: a Data Driven Approach
|
The chemical space is comprised of a vast number of possible structures, of which an unknown portion comprises the human and environmental exposome. Such samples are frequently analyzed using non-targeted analysis via liquid chromatography (LC) coupled to high-resolution mass spectrometry often employing a reversed phase (RP) column. However, prior to analysis, the contents of these samples are unknown and could be comprised of thousands of known and unknown chemical constituents. Moreover, it is unknown which part of the chemical space is sufficiently retained and eluted using RPLC. Therefore, we present a generic framework that uses a data driven approach to predict whether molecules fall "inside", "maybe" inside, or "outside" of the RPLC subspace. Firstly, three retention index random forest (RF) regression models were constructed that showed that molecular fingerprints are able to predict RPLC retention behavior. Secondly, these models were used to setup the dataset for building a RPLC RF classification model. The RPLC classification model was able to correctly predict whether a chemical belonged to the RPLC subspace with an accuracy of 92% for the testing set. Finally, applying this model to the 91737 small molecules (i.e., <=1000 Da) in NORMAN SusDat showed that 19.1% fall "outside" of the RPLC subspace. Knowing which chemicals are outside of the RPLC subspace can assist in reducing potential candidates for library searching and avoid screening for chemicals that will not be present in RPLC data.
|
Denice van Herwerden; Alexandros Nikolopoulos; Leon Barron; Jake O'Brien; Bob Pirok; Kevin Thomas; Saer Samanipour
|
Analytical Chemistry; Earth, Space, and Environmental Chemistry; Chemoinformatics; Mass Spectrometry
|
CC BY 4.0
|
CHEMRXIV
|
2024-01-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ae77639138d231617c37ef/original/exploring-the-chemical-subspace-of-rplc-a-data-driven-approach.pdf
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67b4e58f6dde43c90873d74c
|
10.26434/chemrxiv-2025-mlb1q
|
HFIP Solvent Effects on Enantioselectivity of Dirhodium Tetracar-boxylate-Catalyzed Cyclopropanation
|
In recent years, additives that modulate both reactivity and selectivity in rhodium catalyzed-reactions of aryldiazoacetaes have become increasingly prominent. 1,1,1,3,3,3-Hexafluoroisopropanol (HFIP) has been shown to have a profound effect on rhodium carbene reac-tivity and selectivity, especially on enabling carbene cyclopropanation in the presence of various nucleophilic poisons. HFIP also has a variable influence on the enantioselectivity of the reactions catalyzed by chiral dirhodium tetracarboxylates, and this study examines the fundamental properties of the rhodium carbene/HFIP system through experimentation, density functional theory (DFT), and molecu-lar dynamics (MD) simulations. These studies revealed that the C4-symmetric bowl-shaped catalysts, which have been previously consid-ered to be relatively rigid, experience far greater flexibility in this hydrogen bonding media, resulting in distortion of the bowl-shaped cata-lysts. These studies explain why even though a majority of the catalysts have a drop in enantioselectivity in HFIP, some catalysts such as Rh2(TCPTAD)4, lead to a switch in enantioselectivity, whereas others, such as Rh2(NTTL)4, lead to a considerably enhanced enantiose-lectivity.
|
Turki Alturaifi; Kristin Shimabukuro; Jack Sharland; Binh Khanh Mai; Evan Weingarten; Mithun Madhusudhanan; Djamaladdin Musaev; Peng Liu; Huw Davies
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b4e58f6dde43c90873d74c/original/hfip-solvent-effects-on-enantioselectivity-of-dirhodium-tetracar-boxylate-catalyzed-cyclopropanation.pdf
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67ceadecfa469535b9b3e2b2
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10.26434/chemrxiv-2025-2lb14-v2
|
Unleashing the power of machine learning in nanomedicine formulation development
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Artificial intelligence (AI) is being integrated into nearly every aspect of modern life, and the collaboration between machine learning (ML) – a subfield of AI – and microfluidic fabrication techniques has the potential to accelerate the development of nanomedicines. Here, we present a machine learning workflow designed to optimize the microfluidic-based formulation of nanomedicines. A database of almost 200 unique nanomedicine formulations with over 550 total measurements was curated by producing liposomes, lipid nanoparticles, and poly(lactic-co- glycolic acid) (PLGA) nanoparticles, either empty or loaded with the model therapeutic agent curcumin (CURC), using a benchtop microfluidic system. Materials and flow parameters (input features), including the reagent concentrations, total flow rates, and aqueous:organic flow rate ratios were systematically varied, and the resulting particles were characterized for their hydrodynamic diameter (dH), polydispersity index (PdI), and encapsulation efficiency (EE) (output parameters). These data were used to train, test, and validate 13 different ML models, using a freely available and open-source librries, with the task of returning the most accurate prediction of the nanomedicine attributes – dH, PdI, EE. The most accurate ML models, based on random forest regression, were implemented to yield particles with user-specified attributes. Finally, the proposed ML workflow, dubbed MicrofluidicML, was compared against generative large language models – Open AI ChatGPT, Google’s Gemini, DeepSeek. MicrofluidicML provides a workflow where the researcher has complete governance and control of the input data, the computational overhead is much lower compared to the amount of data required to train a generative AI model, and the post-hoc SHAP analysis provides key information towards the critical factors affecting nanoparticle formation. The application of ML in the field of nanomedicine is inevitable, and MicrofluidicML represents a step towards implementing a computationally lightweight ML framework for accelerating nanomedicine development.
|
Thomas Lee Moore; Cristiano Pesce; Antonietta Greco; Claudia Pisante; Greta Avancini; Valentina Di Francesco; Paolo Decuzzi
|
Materials Science; Nanoscience; Controlled-Release Systems
|
CC BY NC 4.0
|
CHEMRXIV
|
2025-03-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ceadecfa469535b9b3e2b2/original/unleashing-the-power-of-machine-learning-in-nanomedicine-formulation-development.pdf
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65a94f619138d2316138b51d
|
10.26434/chemrxiv-2024-sxkmc
|
Continuous Flow Scale-Up of Enantiospecific Solid-to-Solid Photodecarbonylation Chemistry Through Pulsed Flow Operation and Inline Crystallization
|
The enantioselective formation of C-C bonds is arguably one of the most important reactions in organic chemistry. While elegant solutions have been devised for the total synthesis of several natural products, active pharmaceutical ingredients (API), and related scaffolds, efficient methods that strive towards the principles of green chemistry remain highly desirable additions to the synthetic organic toolbox. Additionally, modern strategies become increasingly challenging when the desired structures are highly strained, sterically encumbered, or contain adjacent quaternary chiral centers. In this research, the hexasubstituted ketone d,l-2,4-dimethyl-3-oxo-2,4-diphenylpentanedinitrile was chosen as a highly strained and chiral proof-of-concept substrate to evaluate the scalability of solid state photoelimination chemistry. Performing the photodecarbonylation of easily accessible alpha-chiral ketones in the solid state physically restricts the mobility of the generated radical intermediates, resulting in high regio- and enantiospecificity. Additionally, aqueous suspensions can be used, resulting in a simple filtration as the only purification step. The continuous flow HANUTM 2X 15 photoreactor, preceded by a custom inline crystallization setup, were shown to be key enabling technologies to achieve the previously problematic continuous operation and scale-up of these reactions. A solid-to-solid photochemical process was successfully optimised, resulting in a STY of 3.9 kg h-1 m-3.
|
Bavo Vandekerckhove; Bart Ruttens; Bert Metten; Christian Stevens; Thomas Heugebaert
|
Organic Chemistry; Photochemistry (Org.); Process Chemistry; Stereochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a94f619138d2316138b51d/original/continuous-flow-scale-up-of-enantiospecific-solid-to-solid-photodecarbonylation-chemistry-through-pulsed-flow-operation-and-inline-crystallization.pdf
|
64992c861dcbb92a5e93a2ae
|
10.26434/chemrxiv-2023-8dclm
|
The LARGEST library of Bicyclo[1.1.1]pentanes for Drug Discovery enabled by Light
|
In 2012, bicyclo[1.1.1]pentanes were demonstrated to be bioisosteres of the phenyl ring. Today, after more than a decade, the difficulty in their large-scale preparation is still a problem, that often outweighs the corresponding derivatives to becoming clinical candidates. Here, we report a practical general reaction that gives bicyclo[1.1.1]pentanes on mg- to kg-quantities using just light. No additional additives or catalysts are needed. Using this strategy, we have prepared >300 functionalized bicyclo[1.1.1]pentanes on a (multi)gram scale. So far, this is the most general and practical approach to bicyclo[1.1.1]pentanes. Many of these molecules, which were previously commercialized, are already being used in drug discovery by pharmaceutical companies Gilead Sciences, Hoffman-La Roche, Idorsia, Merck, Janssen Pharm., etc.
This work should ease the transition of bicyclo[1.1.1]pentane-containing bioactive compounds to clinical candidates, and subsequently to drugs.
|
Vasyl Ripenko; Vadym Sham; Vitalina Levchenko; Serhii Holovchuk; Daniil Vysochyn; Ivan Klymov; Dmytro Kyslyi; Stanislav Veselovych; Serhii Zhersh; Yurii Dmytriv; Andrey Tolmachov; Iryna Sadkova; Irina Pishel; Pavel Mykhailiuk
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64992c861dcbb92a5e93a2ae/original/the-largest-library-of-bicyclo-1-1-1-pentanes-for-drug-discovery-enabled-by-light.pdf
|
632bc9c2975e9459478420b3
|
10.26434/chemrxiv-2022-l6jqr-v2
|
A Transferrable Range-Separated Force Field for Water:
Combining the Power of Both Physically-Motivated
Models and Machine Learning Techniques
|
An accurate, transferrable, and computationally efficient potential energy surface (PES) is of paramount importance for all molecular mechanics simulations. In this work, using water as example, we demonstrate how one can construct a reliable force field by combining the advantages of both physically-motivated and data-driven machine learning (ML) methods. Different to the existing water models based on many-body expansion, we adopt a separation scheme purely based on distances, and systematically investigate how the long-range asymptotic terms increase the transferability and the data efficiency of the ML potential. We also show how the ML model can be an ideal tool to fit the short-range interactions which used to post great challenges to the conventional physically-motivated force fields. The water force field we obtain is highly accurate and transferrable in different environments, and the distance-based separation scheme is easy to be extended to general molecular systems. Through this study, we show how the information we learn from small clusters can be extrapolated into larger systems, thus providing a general recipe for the intermolecular force field development at CCSD(T) level of theory in future.
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Lan Yang; Jichen Li; Feiyang Chen; Kuang Yu
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning
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CC BY 4.0
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CHEMRXIV
|
2022-09-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632bc9c2975e9459478420b3/original/a-transferrable-range-separated-force-field-for-water-combining-the-power-of-both-physically-motivated-models-and-machine-learning-techniques.pdf
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63516f64ecdad5ba68e5a93a
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10.26434/chemrxiv-2022-0g95w-v2
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Highly non-stoichiometric YAG ceramics with modified luminescence properties
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Yttrium aluminium garnet Y3Al5O12 (YAG) is a widely used phosphor host. Its optical properties are tuned by chemical substitution at its YO8 or AlO6/AlO4 sublattices, with emission wavelengths defined by a finite number of rare-earth (YO8 sublattice) and transition-metal (AlO6/AlO4 sublattice) dopants which have been explored extensively. Non-stoichiometric compositions Y3+xAl5-xO12 (x ≠ 0) may offer a route to new emission wavelengths by distributing dopants over multiple crystallographic sites, but deviation from Y3Al5O12 stoichiometry is difficult to achieve and limited generally to ≤ 1% excess Y3+. Here we report a series of highly non-stoichiometric YAG ceramics Y3+xAl5-xO12 (0 ≤ x ≤ 0.4), with up to 20% of the AlO6 sublattice substituted by Y3+, synthesised by advanced melt-quenching techniques. This impacts the up-conversion luminescence of Yb3+/Er3+-doped systems, whose yellow-green emission differs from the red-orange emission of their stoichiometric counterparts. This contrasts with YAG:Ce3+ where the dopant ions occupy the YO8 sublattice exclusively, with down-conversion luminescence that is hardly affected by host non-stoichiometry. Beyond YAG, analogous highly non-stoichiometric systems should be obtainable for a range of functional garnets, demonstrated here by the successful synthesis of Gd3.2Al4.8O12 and Gd3.2Ga4.8O12. This opens the way to property tuning by control of garnet host stoichiometry, and the prospect of improved performance or new applications for garnet-type materials.
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Weiwei Cao; Ana Isabel Becerro; Victor Castaing; Xue Fang; Pierre Florian; Franck Fayon; Didier Zanghi; Emmanuel Veron; Alessio Zandonà; Cécile Genevois; Michael Pitcher; Mathieu Allix
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Inorganic Chemistry; Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-10-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63516f64ecdad5ba68e5a93a/original/highly-non-stoichiometric-yag-ceramics-with-modified-luminescence-properties.pdf
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60c75863469df42692f45647
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10.26434/chemrxiv.14546946.v1
|
Operation Mechanism of Organic Electrochemical Transistors as Redox Chemical Transducers
|
<p>There is intense interest
in utilizing the redox activity of Organic Mixed Ionic Electronic Conductors
for faradaic chemical sensing. In particular, the investigation of organic
electrochemical transistors (OECTs) as biosensors due to their low operational
potentials, ease of fabrication (e.g. by inkjet printing), biocompatibility,
and large transconductance. </p>
<p>It has become common
practice in the OECT community to combine both chemical detection and
transistor function within the same compartment, assuming that the sensor
signal is amplified seamlessly by the sensing OECT. These devices however routinely
encounter several challenges whose origins often remained unclear. Some of
these challenges are 1) small changes in drain current, contradicting OECT’s oft-touted
current-amplifying abilities. 2) Irreversible chemical changes to the
semiconducting polymer electrodes. 3) Parasitic side reactions convoluting the
sensing signal, exacerbated by applied voltages.</p>
<p>In this manuscript, we
show that optimization of OECT-based sensors requires more rigorous
characterization of electrode potentials to elucidate electrochemical phenomena,
a practice that is often largely absent in current reports. Our analysis of fundamental
device physics of various OECT architectures shows that despite what a large
fraction of the organic bioelectronics community still believes, amperometric OECTs either 1) do not display
any transistor behavior, and in fact operate merely as electrodes or 2) Undergo
irreversible changes and are extremely complex to calibrate, or both 1) and 2).
</p>
<p>Indeed, to fully utilize
the OECT’s large transconductance, a separate 2-electrode Reaction Cell which
is utilized to gate a separate OECT is needed (RC-OECT). In this manuscript, in
addition to showing that the RC-OECT resolves the fundamentally and
irreconcilably contradicting design principles of amperometric OECTs, we demonstrate
that it provides great device and materials design flexibility. Finally, we elucidate
the basic principles on how to further optimize the RC-OECT.</p>
<p>We believe that our
findings will be of great interest to researchers in the fields of
bioelectronics as a call to action to re-evaluate present approaches of
utilizing OECTs for chemical detection and to help practitioners select
materials and designs to optimize redox sensors based on organic semiconductors.
</p>
|
Siew Ting Melissa Tan; Scott Tom Keene; Alexander Giovannitti; Armantas Melianas; Maximilian Moser; Iain McCulloch; Alberto Salleo
|
Conducting polymers
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-05-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75863469df42692f45647/original/operation-mechanism-of-organic-electrochemical-transistors-as-redox-chemical-transducers.pdf
|
60c758e2842e65818fdb48f6
|
10.26434/chemrxiv.14597670.v1
|
Thermal Expansion of Metal–Organic Framework Crystal–Glass Composites
|
<a>Metal-organic
framework crystal-glass composites (MOF CGCs) are a class of materials
comprising a crystalline framework embedded within a MOF glass matrix. Here, we
investigate the thermal expansion behavior of three MOF CGCs, incorporating two
flexible (MIL-53(Al) and MIL-118) and one rigid (UL-MOF-1) MOF within a ZIF-62
glass matrix. Specifically, variable-temperature powder X-ray diffraction data and
thermo-mechanical analysis show the suppression of thermal expansivity in each
of these three crystalline MOFs when suspended within a ZIF-62 glass matrix. In
particular, for the two flexible frameworks, the average volumetric thermal
expansion (<i>β</i>) was
found to be near-zero in the crystal-glass composite.</a>
These results provide a route to engineering thermal expansivity in stimuli-responsive MOF glass composites.
|
Christopher Ashling; Giulio
I. Lampronti; Thomas J. F. Southern; Rachel Evans; Thomas Bennett
|
Composites; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Interfaces; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-05-20
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758e2842e65818fdb48f6/original/thermal-expansion-of-metal-organic-framework-crystal-glass-composites.pdf
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60c74a480f50db367c396a2b
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10.26434/chemrxiv.12152520.v1
|
Endowing TADF Luminophors with AIE Properties Though Adjusting Flexible Dendrons for Highly Efficient Solution-Processed Nondoped OLEDs.
|
<p><a>The amalgamation of thermally activated delayed
fluorescence (TADF) and aggregation-induced emission (AIE) properties, term
AIE-TADF, is a promising strategy to design novel robust luminescent materials.
Herein, we transform 2,3,4,5,6-penta(9H-carbazol-9-yl)benzonitrile (5CzBN) from
an ACQ molecule to AIEgens by simply decorating a 5CzBN core with alkyl chain-linked
spirobifluorene dendrons. By increasing the number of flexible dendrons, these
materials can not only show obvious AIE-TADF characteristics and uniform film
morphology, but also exhibit better resistance to isopropyl alcohol, which are
beneficial to the fully solution-processed OLEDs. Notably, 5CzBN-PSP show great
device efficiency with external quantum efficiency (EQE), current efficiency
and power efficiency of 20.1%, 58.7 cd A<sup>-1</sup> and 46.2 lm W<sup>-1</sup>,
respectively, which achieved record-breaking efficiency in solution-processed nondoped
OLEDs based on AIE emitters. It demonstrates a general approach to explore new
efficient emitters by the marriage of AIE and TADF what could potentially improve
their performance in various areas.</a></p>
|
Jingyi Wei; Dan Liu; Wenwen Tian; Wei Jiang; Yueming Sun; zheng zhao; Ben Zhong Tang
|
Organic Compounds and Functional Groups; Dyes and Chromophores
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-04-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a480f50db367c396a2b/original/endowing-tadf-luminophors-with-aie-properties-though-adjusting-flexible-dendrons-for-highly-efficient-solution-processed-nondoped-ole-ds.pdf
|
672382e25a82cea2faa05260
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10.26434/chemrxiv-2024-r2lsq
|
Towards a Universal Scaling Method for Predicting Equilibrium Constants of Polyoxometalates
|
The computational prediction of equilibrium constants is still an open problem for a wide variety of relevant chemical systems. Particularly, acid dissociation constants (pKa) are an essential asset in biological, synthetic or industrial chemistry whose prediction encounters several difficulties, requiring the development of novel strategies. The self-assembly of polyoxometalates (POMs) is another complex problem where acid-base reactions play a central role; a successful prediction of the formation constants of these structures is intimately linked with the limitations of pKa determination. Our methodology POMSimulator enables the prediction of these polyoxometalates formation constants from Density Functional Theory (DFT) calculations, using the experimental Kf values available in the literature to fit the resulting predictions. In this work, we carry out a systematic analysis of a very large number of POM formation constants already predicted through the application of POMSimulator. We then propose an universal scaling scheme for the adjustment of the DFT-based formation constants of POMs, relying on a linear scaling of the form y = mx + b. Here, the slope (m) is a constant parameter - hence, universal towards the nature of the polyoxometalate and the calculation method. The intercept (b), in contrast, is a system-dependent parameter that can be predicted with a multi-linear regression model trained with statistical aggregates of the non-scaled formation constants. Thus, we are able to successfully predict the speciation and phase diagrams of POM systems for which available experimental data is minimal, as well as providing a general scaling scheme that might be extended to other kinds of chemical systems.
|
Jordi Buils; Diego Garay-Ruiz; Enric Petrus; Mireia Segado-Centellas; Carles Bo
|
Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Clusters; Self-Assembly; Solution Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672382e25a82cea2faa05260/original/towards-a-universal-scaling-method-for-predicting-equilibrium-constants-of-polyoxometalates.pdf
|
60c74c279abda221adf8d217
|
10.26434/chemrxiv.8010311.v2
|
Transition between [R]- and [S]-Stereoisomers without Bond Breaking
|
We for the first time shown that transition between (R) and (S) stereoisomers via a planar transition state or an intermediate structure without having to break a bond is possible. Rigorous theoretical calculations have been used to study this novel phenomenon and to characterize the energetic, structure, dynamic and kinetic properties.
|
Shampa Raghunathan; Komal Yadav; V. C. Rojisha; Tanashree Jaganade; V. Prathyusha; Swetha Bikkina; Upakarasamy Lourderaj; U. Deva Priyakumar
|
Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c279abda221adf8d217/original/transition-between-r-and-s-stereoisomers-without-bond-breaking.pdf
|
66a13c3cc9c6a5c07ac9c7b7
|
10.26434/chemrxiv-2024-4xc02-v3
|
Comparing parameterized and self-consistent approaches to ab initio cavity quantum electrodynamics for electronic strong coupling
|
Molecules under strong or ultra-strong light-matter coupling present an intriguing route to modify chemical structure, properties, and reactivity. A rigorous theoretical treatment of such systems requires handling matter and photon degrees of freedom on an equal quantum mechanical footing. In the regime of molecular electronic strong or ultra-strong coupling to one or a few molecules, it is desirable to treat the molecular electronic degrees of freedom using the tools of ab initio quantum chemistry, yielding an approach referred to as ab initio cavity quantum electrodynamics (ai-QED), where the photon degrees of freedom are treated at the level of cavity quantum electrodynamics. We analyze two complementary approaches to ai-QED: (1) a parameterized ai-QED, a two-step approach where the matter degrees of freedom are computed using existing electronic structure theories, enabling the construction of rigorous ai-QED Hamiltonians in a basis of many-electron eigenstates, and (2) self-consistent ai-QED, a one-step approach where electronic structure methods are generalized to include coupling between electronic and photon degrees of freedom. Although these approaches are equivalent in their exact limits, we identify a disparity between the projection of the two-body dipole self-energy operator that appears in the parameterized approach and its exact counterpart in the self-consistent approach. We provide a theoretical argument that this disparity resolves only under the limit of a complete orbital basis and a complete many-electron basis for the projection. We present numerical results highlighting this disparity and its resolution in a particularly simple molecular system of helium hydride cation, where it is possible to approach these two complete basis limits simultaneously. In this same helium hydride system, we examine and compare the practical issue of computational cost required to converge each approach towards the complete orbital and many-electron bases limit. Finally, we assess the aspect of photonic convergence for polar and charged species, finding comparable behavior between parameterized and self-consistent approaches.
|
Ruby Manderna; Nam Vu; Jonathan Foley
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Optics
|
CC BY 4.0
|
CHEMRXIV
|
2024-07-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a13c3cc9c6a5c07ac9c7b7/original/comparing-parameterized-and-self-consistent-approaches-to-ab-initio-cavity-quantum-electrodynamics-for-electronic-strong-coupling.pdf
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6576858a29a13c4d472643e5
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10.26434/chemrxiv-2023-d43gk
|
Tetrahydrocannabinol and Dopamine D1 Receptor
|
Dopamine is a hormone that is released by the adrenal gland and influences motor control and motivation. Dopamine is known to have 5 receptors which are D1, D2, D3, D4 and D5, which are further categorized into 2 families: D1 family and D2 family. The D1 family is known to play a role in motivation and motor control whereas the D2 family is known to affect attention and sleep. THC, a type of cannabinoid, can lead to feelings of euphoria, anxiety, fear, distrust, or panic. THC is known to affect dopamine in regions such as the anterior cingulate cortex (ACC), and plays a role in fundamental cognitive processes. Although there is a vast amount of research between the relationship of THC on dopamine, there continues to be limited research in relation to THC on dopamine receptors. The D1 receptor plays a role in several essential functions, such as memory, attention, impulse control, regulation of renal function, and locomotion. Accordingly, this review is intended to summarize the relationship between THC and D1 receptors, highlighting key gaps in the literature and avenues for future research.
|
Jiwon Lee
|
Biological and Medicinal Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-12-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6576858a29a13c4d472643e5/original/tetrahydrocannabinol-and-dopamine-d1-receptor.pdf
|
60c75559469df44052f45146
|
10.26434/chemrxiv.14071247.v1
|
Curse or Blessing? Influence of Impurities on Cross-Coupling— Guideline for Elucidating Catalysts
|
Several efforts have been made for the replacement of noble metal palladium in cross-coupling reactions, maintaining high efficiency of the target transformation. In several cases it is possible to perform the chemistry of palladium with related metals, and their activity was supported with mechanistic studies. Moreover, the complete exclusion of palladium is also in focus. Very recently it was demonstrated that special amine organocatalysts could catalyse Suzuki-Miyaura coupling reaction. Here we show that in this recent transformation homeopathic palladium impurities and trace phosphorous species originated from the conditions used for the organocatalyst synthesis are responsible for the catalytic effect instead of the amine species. This finding confirms the power of palladium in cross-coupling and draw the attention of impurity effect in this field of chemical research. In this article, we represent general guidelines for elucidating the real catalyst of reactions.<br />
|
Zoltán Novák; Réka Adamik; János T. Csenki; Ferenc Béke; Regina Gavaldik; Bálint Varga; Bálint Nagy; Zoltán May; János Daru; Zsombor Gonda; Gergely L. Tolnai
|
Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-02-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75559469df44052f45146/original/curse-or-blessing-influence-of-impurities-on-cross-coupling-guideline-for-elucidating-catalysts.pdf
|
6772a75c81d2151a026264e7
|
10.26434/chemrxiv-2024-k8zj9
|
3-Oxabicyclo[3.1.1]heptanes as Isosteres of meta-Substituted Benzene Rings
|
Replacement of the aromatic rings in drug candidates with isosteric rigid sp3-rich scaffolds can improve physicochemical properties and increase the chance of progressing the molecule in the development and open new chemical space. Isosteres of meta-substituted benzenes remain challenging due to the difficulty of mimicking the exit vector angles and bond distances. Herein, we report the synthesis of 1,5-disubstituted 3-oxabicyclo[3.1.1]heptanes (oxa-BCHs), which can serve as saturated isosteres of meta-substituted phenyl rings, with similar geometric arrangement. This structural motif can be obtained under mild reaction conditions via acid-mediated isomerization of (2-oxaspiro[3.3]heptan-6-yl)methanols using catalytic quantities of pyridinium chloride (PyrHCl). We demonstrate the utility of this methodology by preparing various building blocks for use in medicinal chemistry and incorporating the 3-oxa-BCH into the anticancer drug Sonidegib, improving its physicochemical properties, such as permeability, metabolic stability and solubility.
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Jennifer Morvan; Evelien Renders; Peter JJA Buijnsters; Pavel Ryabchuk
|
Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6772a75c81d2151a026264e7/original/3-oxabicyclo-3-1-1-heptanes-as-isosteres-of-meta-substituted-benzene-rings.pdf
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67856a736dde43c9086460e1
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10.26434/chemrxiv-2025-77dmp
|
Linear-Scaling Quadruple Excitations in Local Pair Natural Orbital Coupled-Cluster Theory
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We present a fast, asymptotically linear-scaling implementation of the perturbative quadruples energy correction in coupled-cluster theory using local natural orbitals. Our work follows the domain-based local pair natural orbital (DLPNO) approach previously applied to lower levels of excitations in coupled-cluster theory. Our DLPNO-CCSDT(Q) algorithm uses converged doubles and triples amplitudes from a preceding DLPNO-CCSDT computation, to compute the quadruples amplitude and energy in the quadruples natural orbital (QNO) basis. We demonstrate the compactness of the QNO space, showing that more than 95% of the (Q) correction can be recovered using relatively loose natural orbital cutoffs, compared to the tighter cutoffs used in pair and triples natural orbitals at lower levels of coupled-cluster theory. We also highlight the accuracy of our algorithm in the computation of relative energies, which yields deviations of sub-kJ mol-1 in relative energy compared to the canonical CCSDT(Q). Timings are conducted on a series of growing linear alkanes (up to 10 carbons and 608 basis functions) and water clusters (up to 49 water molecules and 2842 basis functions), to establish the asymptotic linear-scaling of our DLPNO-(Q) algorithm.
|
Andy Jiang; Henry Schaefer III; Justin Turney
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics
|
CC BY 4.0
|
CHEMRXIV
|
2025-01-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67856a736dde43c9086460e1/original/linear-scaling-quadruple-excitations-in-local-pair-natural-orbital-coupled-cluster-theory.pdf
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654c06d86e0ec7777f8e492d
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10.26434/chemrxiv-2023-b4g1x-v2
|
ISMER: A Novel Frequency Attenuated Mechanical Metamaterial for High-Magnitude Earthquake Dampening at a Cost-Effective Approach
|
Materials with special geometrically designed microstructures, referred to as metamaterials, have gained significant attention in the world due to their unique properties of toughness and failure-resistance. The ability to simply alter the internal geometry of almost any material to exponentially increase strength is incredibly enticing due to the feasibility and possibilities of billions of designs that can change the entire scope of how a material behaves. However, mechanical metamaterials have yet to be majorly implemented at a large scale to solve our crucial problems. A major problem the world faces today is producing stronger construction materials to prevent events such as Earthquake collapses, while still maintaining scalability and cost-effectiveness for earthquake prone regions such as Syria and Turkey. This is where ISMER (Internal Structural Modification for Earthquake Resistance), a novel metamaterial design, finds its place in the world of lost-cost earthquake resistance. Convergent Finite Element Analysis methods were used to design and simulate the behavior of a special class of mechanical metamaterials under randomized-seismic loading and 3D printing techniques to fabricate the physical specimens. Afterwards, scaled models and nanoscale mechanics were explored with Scanning Electron Microscopy (SEM), ISMER was improved in terms of magnitude resistance. Within the methods of this study, 8 modular varieties, 2 to 16 units, are considered, as the structure transitions from an hourglass to honeycomb structure as distance increases, with 8 units being a perfectly vertical support and the control. These designs and measurements are proportional to the specimen itself, so ISMER can be implemented into any Newtonian solid. The study resulted in a rich understanding of how to manipulate any material’s strength by manipulating the microscale, in which a mathematical model was postulated, and prototype models were fabricated and tested. It was found that the 16 units case (honeycomb) was the most optimal for a variety of tests such as Frequency Attenuation and Richter Scale Simulations and has major potential to be feasibly implemented into manufacturing of housing materials as it showcased resistance to earthquakes of magnitude 6.
|
Suraj Reddy
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Metamaterials; Nanostructured Materials - Materials; Artificial Intelligence
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CC BY 4.0
|
CHEMRXIV
|
2023-11-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654c06d86e0ec7777f8e492d/original/ismer-a-novel-frequency-attenuated-mechanical-metamaterial-for-high-magnitude-earthquake-dampening-at-a-cost-effective-approach.pdf
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6462b69bf2112b41e99fb334
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10.26434/chemrxiv-2023-8hdmv
|
Graph transformer neural network for chemical reactivity prediction
|
Optimizing the properties of advanced drug candidates can be facilitated by directly introducing certain chemical groups without having to synthesize the molecules from scratch. However, their chemical complexity often renders reactivity predictions and synthesis planning challenging. Herein, we introduce a graph transformer neural network (GTNN) approach for computational reaction screening and identification of substrates suitable for late-stage functionalization, taking compound alkylation via Minisci-type chemistry as an example. GTNNs were trained on experimentally generated reactions obtained from miniaturized high-throughput experimentation and literature data. Trained models were prospectively applied to predicting the reactivity of 3180 advanced heterocyclic molecules, identifying potential substrates for Minisci-type alkylation. All predicted substrates were experimentally confirmed. Multiple chemical transformations were identified for each of these compounds. Selected hits were scaled up, isolated, and characterized, delivering 30 novel, suitably functionalized molecules for medicinal chemistry. These results positively advocate GTNN models for reactivity prediction in drug discovery.
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David F. Nippa; Kenneth Atz; Alex T. Müller; Jens Wolfard; Clemens Isert; Martin Binder; Oliver Scheidegger; David B. Konrad; Uwe Grether; Rainer E. Martin; Gisbert Schneider
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Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Drug Discovery and Drug Delivery Systems; Machine Learning; Artificial Intelligence
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-05-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6462b69bf2112b41e99fb334/original/graph-transformer-neural-network-for-chemical-reactivity-prediction.pdf
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641a49a32bfb3dc251262968
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10.26434/chemrxiv-2023-zmt04
|
Transcriptomic Analysis of Loratadine as an Antibiotic Adjuvant Against MRSA
|
Methicillin-resistant Staphylococcus aureus (MRSA) has evolved to become resistant to multiple classes of antibiotics. New antibiotics are costly to develop and deploy, and they have a limited effective lifespan. Antibiotic adjuvants are molecules that potentiate existing antibiotics through non-toxic mechanisms. We previously reported that loratadine, the active ingredient in Claritin potentiates multiple cell-wall active antibiotics in vitro and disrupts biofilm formation through a hypothesized inhibition of the master regulatory kinase Stk1. Loratadine and oxacillin combined repressed the expression of key antibiotic resistance genes in the bla and mec operons. We hypothesized that additional differentially expressed genes involved in antibiotic resistance, biofilm formation, and other cellular pathways would be modulated when looking transcriptome wide. To test this, we used RNA-seq to quantify transcript levels and found pleiotropic effects in gene expression, including genes implicated in antibiotic resistance, as well as genes critical for metabolism, transcription (RNA Polymerase subunits alpha and beta), and translation (a plethora of ribosomal protein genes and Elongation Factor Tu). Stk1 and its cognate phosphatase, stp, were also downregulated by loratadine. Together, this provides the most molecular details to date about loratadine’s function as an antibiotic adjuvant.
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Brianna Viering; Halie Balogh; Luke Akers; Meghan Blackledge; Heather Miller
|
Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Chemical Biology; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641a49a32bfb3dc251262968/original/transcriptomic-analysis-of-loratadine-as-an-antibiotic-adjuvant-against-mrsa.pdf
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6231cd368ab37305e0669b50
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10.26434/chemrxiv-2022-xkxc6
|
State-specific solvation for restricted active space spin-flip (RAS-SF) wave functions based on the polarizable continuum formalism
|
The restricted active space spin-flip (RAS-SF) formalism is a particular form of single-reference configuration interaction that can describe some forms of strong correlation at relatively low cost, and which has recently been formulated for the description of charge-transfer excited states. Here, we introduce both equilibrium and nonequilibrium versions of a state-specific solvation correction for vertical transition energies computed using RAS-SF wave functions, based on the framework of a polarizable continuum model (PCM). Ground-state polarization is described using the solvent's static dielectric constant and in the nonequilibrium solvation approach that polarization is modified upon vertical excitation using the solvent's optical dielectric constant. Benchmark calculations are reported for well-studied models of photo-induced charge transfer including
naphthalene dimer, C2H4...C2F4, pentacene dimer, and perylene diimide (PDI) dimer, several of which are important in organic photovoltaic applications. For the PDI dimer, we demonstrate that the charge-transfer character of the excited states is enhanced in the presence of a low-dielectric medium (static dielectric constant epsilon = 3) as compared to a gas-phase calculation (epsilon = 1). This stabilizes mechanistic traps for singlet fission and helps to explain experimental singlet fission rates. We also examine the effects of nonequilibrium solvation on charge-separated states in an intramolecular singlet fission chromophore, where we demonstrate that the energetic ordering of the states changes as a function of solvent polarity. The RAS-SF + PCM methodology that is reported here provides a framework to study charge-separated states in solution and in photovoltaic materials.
|
Bushra Alam; Hanjie Jiang; Paul Zimmerman; John Herbert
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Theory - Computational; Spectroscopy (Physical Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2022-03-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6231cd368ab37305e0669b50/original/state-specific-solvation-for-restricted-active-space-spin-flip-ras-sf-wave-functions-based-on-the-polarizable-continuum-formalism.pdf
|
616d080f7d3da5481efba8ea
|
10.26434/chemrxiv-2021-4qh4f-v2
|
High-Resolution Ion-Flux Imaging of Proton Transport Through Graphene|Nafion Membranes
|
In 2014, it was reported that protons can traverse between aqueous phases separated by nominally pristine monolayer graphene and hexagonal boron nitride (h-BN) films (membranes) under ambient conditions. This “intrinsic proton conductivity” of the one-atom-thick crystals, with proposed through-plane conduction, challenged the notion that graphene is impermeable to atoms, ions and molecules. More recent evidence points to a defect-facilitated transport mechanism, analogous to transport through conventional ion-selective membranes based on graphene and h-BN. To clarify the nature of proton transmission through graphene, local ion-flux imaging is performed herein on graphene|Nafion membranes using an “electrochemical ion (proton) pump cell” mode of scanning electrochemical cell microscopy (SECCM). Targeting regions that are free from visible macroscopic defects (e.g., cracks, holes etc.), and assessing hundreds to thousands of different sites across the graphene surfaces in a typical experiment, most of the graphene|Nafion membrane is impermeable to proton transport, with transmission typically occurring at only ≈20 – 60 localized sites across a ≈0.003 mm2 area of membrane (>5000 measurements, total). When localized proton transport occurs, it can be a highly dynamic process, with new transmission sites “opening” and a small number of sites “closing” under an applied electric field, on the seconds timescale. Applying a simple equivalent circuit model of ion-transport through a cylindrical nanopore, the local transmission sites are estimated to possess dimensions (radii) on the (sub)nanometer-scale, implying that rare atomic defects are responsible for proton conductance through monolayer graphene. Overall, this work reinforces SECCM as a premier tool for the structure−property mapping of microscopically complex (electro)materials, with the local ion-flux mapping configuration introduced herein being widely applicable for functional membrane characterization and beyond, e.g., for diagnosing failure mechanisms in protective surface coatings.
|
Cameron Bentley; Minkyung Kang; Saheed Bukola; Stephen Creager; Patrick Unwin
|
Physical Chemistry; Materials Science; Carbon-based Materials; Electrochemistry - Mechanisms, Theory & Study; Interfaces
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616d080f7d3da5481efba8ea/original/high-resolution-ion-flux-imaging-of-proton-transport-through-graphene-nafion-membranes.pdf
|
618f423f9960f3bfe7aa35e2
|
10.26434/chemrxiv-2021-skp0w
|
Mixing, Domains, and Fast Li-ion Dynamics in Ternary Li-Sb-Bi Battery Anode Alloys
|
Antimony and bismuth can both alloy with up to three molar equivalents of lithium and are therefore attractive candidates for replacing graphite in Li-ion battery anodes. Li3Sb and Li3Bi have the same cubic structure (Fm3 ̅m), but the ternary Li-Sb-Bi system has not been studied. We synthesized Li3(SbxBi1-x) with different Sb mole fractions at room temperature by ball-milling. These ternary alloys all have cubic crystal structures, as determined by XRD, but show a tendency towards phase segregation for x = 0.25 and 0.50. For x = 0.25, the lattice parameter presents a clear positive deviation from Vegard’s law in XRD, while for x = 0.50, XRD reveals two phases after milling, with the Bi-rich minority phase diminishing after thermal annealing. Solid-state nuclear magnetic resonance spectroscopy provides evidence for a Sb-enriched environment around the Li atoms for Li3Sb0.25Bi0.75, and nuclear spin-lattice relaxation measurements of the binary and ternary alloy phases point to low activation energies and rapid Li ion diffusion in Li3Bi.
|
Peter Kalisvaart; Madhusudan Chaudhary, ; Amit Bhattacharya; Vladimir Michaelis ; Jillian Buriak
|
Materials Science; Energy; Alloys; Nanostructured Materials - Materials; Energy Storage; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2021-11-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618f423f9960f3bfe7aa35e2/original/mixing-domains-and-fast-li-ion-dynamics-in-ternary-li-sb-bi-battery-anode-alloys.pdf
|
63939cef0fd99254a43fa800
|
10.26434/chemrxiv-2022-20kq3
|
AI-assisted reaction impurity prediction and inverse structure elucidation
|
Identification and control of impurities play a critical role in chemical process development for drug substance synthesis. Most chemical reactions result in a number of by-products and side-products, along with the intended major product. While chemists can predict many of the main process impurities, it remains challenging to enumerate the possible minor impurities and even more of a challenge to track and propagate impurities derived from raw materials or from step to step. Further, in the absence of a systematic means for listing out possible-low-level impurities and performing impurity propagation, inverse structure elucidation -- that is, identifying unknown impurities post hoc from analytical data, such as mass spectrometry data -- presents a significant challenge. In this work, impurity prediction was established by developing an AI-based reaction predictor that takes as input the main reactants, and reagents, solvents, and impurities in these materials. Further, the predictor was run iteratively to track impurity propagation in multi-step reactions. For inverse structure elucidation, a chemistry-informed language model was developed to translate mass spectrometry data to potential molecular structures, which can then be checked for matches against the predicted chemical reaction products. The impurity prediction tool was applied to synthesis of common small molecule drugs –- paracetamol and ibuprofen. The inverse structure elucidation tool was used for the identification of chemical structures from publicly available electrospray ionization mass spectrometry data.
|
Somesh Mohapatra; Daniel Griffin
|
Theoretical and Computational Chemistry; Analytical Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-12-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63939cef0fd99254a43fa800/original/ai-assisted-reaction-impurity-prediction-and-inverse-structure-elucidation.pdf
|
63ad504eff46516bd33aec2f
|
10.26434/chemrxiv-2022-60tmd
|
Pyridine-Boryl Radical-Catalyzed [2 + 2] Cycloaddition of Bicyclo[1.1.0]butanes with Alkenes
|
Bicyclo[2.1.1]hexanes (BCHs) represent an intriguing class of structurally rigid hydrocarbons that can serve as the bioisosteres of benzenoids in medicinal chemistry. Methods for the synthesis of BCHs are, however, limiting. Reported herein is a facile synthesis of BCHs via a strain-release-driven [2 + 2] cycloaddition of bicyclo[1.1.0]butanes (BCBs) with alkenes facilitated by a pyridine-boryl radical catalyst. The mild reaction conditions, broad substrate scope, and decent functional group tolerance of this protocol render it appealing in relevant fields of drug design and synthesis. Theoretical mechanistic studies reveal a radical relay mechanism involved. Synthetic applications of the products are conducted.
|
Honggen Wang; Yuan Liu; Shuang Lin; Yin Li; Jiang-Hao Xue; Qingjiang Li
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Organocatalysis; Redox Catalysis
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-12-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ad504eff46516bd33aec2f/original/pyridine-boryl-radical-catalyzed-2-2-cycloaddition-of-bicyclo-1-1-0-butanes-with-alkenes.pdf
|
645ffa9ef2112b41e97fba81
|
10.26434/chemrxiv-2023-wdd12
|
Identification of compounds from natural
Peruvian sources as potential inhibitors of
SARS-CoV-2 Mpro mutations by virtual
screening and computational simulations
|
The COVID-19 pandemic continues to be a public health problem worldwide. Several therapeutic targets of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been identified, whereas the main protease (Mpro) is necessary for virus replication. Since SARS-CoV-2 Mpro mutation rates are inherently high, searching for new inhibitors remains challenging. Herein, this work aimed to evaluate eighty-four natural compounds from Peruvian sources against different mutations on the Mpro target. Using computational technics, we applied virtual screening, all-atom molecular dynamics simulations, and binding free energy estimation by MM/GBSA methods. The virtual screening results helped us identify rutin as the top compound against different Mpro mutations. Likewise, the computational simulations demonstrated the high structural stability of the Mpro-rutin system. Our results demonstrated the antiviral capacity of compounds from Peruvian sources against SARS-CoV-2 Mpro and its mutations, which could significantly prevent and treat SARS-CoV-2 infection.
|
Haruna Luz Barazorda Ccahuana; Luis Daniel Goyzueta Mamani; Eymi Gladys Cárcamo Rodriguez; Angela Emperatriz Centeno Lopez; Margot Inés Paco Chipana; Miguel Angel Chávez Fumagalli
|
Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645ffa9ef2112b41e97fba81/original/identification-of-compounds-from-natural-peruvian-sources-as-potential-inhibitors-of-sars-co-v-2-mpro-mutations-by-virtual-screening-and-computational-simulations.pdf
|
669fdc9101103d79c55fb620
|
10.26434/chemrxiv-2024-pj99z
|
Strain-Induced Photochemical Opening of Ferrocene[6]cycloparaphenylene: Uncaging of Fe2+ with Visible Light
|
We present the synthesis, structure and remarkable reactivity of the first carbon nanohoop that incorporates ferrocene in the macrocyclic backbone. The high strain imposed on the ferrocene by the curved nanohoop structure enables unprecedent photochemical reactivity of this otherwise photochemically inert metallocene complex. Visible light activation triggers a ring-opening of the nanohoop structure dissociating the Fe–cyclopentadienyl bond in the presence of 1,10-phenanthroline. This process uncages Fe2+ ions captured in the form of [Fe(phen)3]2+ complex in high chemical yield and can operate efficiently in a water-rich solvent. The measured quantum yields of [Fe(phen)3]2+ formation show that embedding ferrocene into a strained nanohoop boosts its photoreactivity by three orders of magnitude compared to an unstrained ferrocene macrocycle or ferrocene itself. Our data suggest that the dissociation occurs by intercepting the photoexcited triplet state of the nanohoop by the nucleophilic ligand. The strategy portrayed in this work proposes that new, tunable reactivity of analogous metallamacrocycles can be achieved with spatial and temporal control, which will aid development of responsive materials for metal ions delivery and organometallic, supramolecular, or polymer chemistry.
|
Remigiusz Kręcijasz; Juraj Malinčík; Simon Mathew; Peter Štacko; Tomáš Šolomek
|
Organic Chemistry; Organometallic Chemistry; Photochemistry (Org.); Physical Organic Chemistry; Transition Metal Complexes (Organomet.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-07-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669fdc9101103d79c55fb620/original/strain-induced-photochemical-opening-of-ferrocene-6-cycloparaphenylene-uncaging-of-fe2-with-visible-light.pdf
|
62134103bd05a03b720e6886
|
10.26434/chemrxiv-2022-x72mz
|
Non-Covalent Interactions Atlas Benchmark Data Sets 4: σ-Hole Interactions
|
The SH250×10 dataset presented here extends the Non-Covalent Interactions Atlas database (www.nciatlas.org) to complexes bound by σ-hole interactions – halogen, chalcogen and pnictogen bonds. It comprises 250 complexes where Cl, Br, I, S, Se, P and As interact with diverse electron donors. An accurate CCSD(T)/CBS benchmark is provided for ten points along a dissociation curve of each complex. The SH250×10 set is used in testing a wide variety of DFT functionals and semiempirical quantum-mechanical methods. In DFT calculations, the new data set exposes large errors of some functionals related to exaggerated charge transfer. The size and diversity of the data set have also been exploited in the reparametrization of a halogen-bond correction for the PM6 semiempirical method.
|
Kristian Kříž; Jan Řezáč
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-02-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62134103bd05a03b720e6886/original/non-covalent-interactions-atlas-benchmark-data-sets-4-hole-interactions.pdf
|
64eb25ef3fdae147faf17961
|
10.26434/chemrxiv-2023-xbf2b
|
Molecular Driving Forces in the Self-Association of Silaffin Peptide R5 from MD Simulations
|
The 19-residue silaffin-R5 peptide has been widely studied for its ability to precipitate uniform SiO2 particles through mild temperature and pH pathways, in the absence of any organic solvents. There is consensus that post-translational modification (PTM) of side chains has a large impact on the biomineralization process. Thus, it is imperative to understand the precise mechanisms that dictate the formation of SiO2 from R5 peptide, including the effects of PTM on peptide aggregation and peptide-surface adsorption. In this work, we use molecular dynamics (MD) simulations to study the aggregation of R5 dimer with multiple PTMs, with the presence of different ions in solution. Since this system has strong interactions with deep metastable states, we use parallel bias metadynamics with partitioned families to efficiently sample the different states of the system. We find that peptide aggregation is a prerequisite for biomineralization. We observe that the electrostatic interactions are essential in the R5 dimer aggregation; for wild type R5 that only has positively charged residues, phosphate ions HPO42- in the solution form a bridge between two peptides and are essential for peptide aggregation. Alternatively, the post translational modification phosphorylation, which renders neutral serine residues negative, enables R5 to aggregate without phosphate ion. The extent of phosphorylation and location of phosphorylated residues on R5 peptide results in different behavior and extent of aggregation - the aggregation trend of R5 peptide that we observe is in line with SiO2 precipitation observed in previous experimental studies, proving that peptide aggregation is a prerequisite for biomineralization.
|
Coco Mao; Janani Sampath; Jim Pfaendtner
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64eb25ef3fdae147faf17961/original/molecular-driving-forces-in-the-self-association-of-silaffin-peptide-r5-from-md-simulations.pdf
|
657aaa0f9138d231619c1c83
|
10.26434/chemrxiv-2023-z4pjw
|
Catalyst-Free Late-Stage Functionalization to Assemble α-acyloxyenamide Electrophiles for Selectively Profiling Conserved Lysine Residues
|
Covalent probes coupled with chemical proteomics represent a powerful method for investigating small molecule and protein interactions. However, the creation of a reactive warhead within various ligands to form covalent probes has been a major obstacle. Herein, we report a convenient and robust process to assemble a unique electrophile, an α-acyloxyenamide, through a one-step late-stage coupling reaction. This procedure demonstrates remarkable tolerance towards other functional groups and facilitates ligand-directed labeling in proteins of interest. The reactive group has been successfully incorporated into a clinical drug targeting the EGFR L858R mutant, erlotinib, and a pan-kinase inhibitor. The resulting probes have been shown to be able to covalently engage a lysine residue proximal to the ATP-binding pocket of the EGFR L858R mutant. A series of active sites, and Mg2+, ATP-binding sites of kinases, such as K33 of CDK1, CDK2, CDK5; K278 of PAK2 and K270 of KPYM were detected. This is the first report of engaging these conserved catalytic lysine residues in kinases with covalent inhibition. Further application of this methodology to natural products has demonstrated its success in profiling ligandable conserved lysine residues in whole proteome. These findings offer insights for the development of new targeted covalent inhibitors (TCIs) and pave the way for future advancements in drug discovery and chemical proteomics.
|
Yuanyuan Zhao; Kang Duan; Youlong Fan; Shengrong Li; Liyan Huang; Zhengchao Tu; Jing Yang; Pinghua Sun; Yi Tan; Ke Ding; Zhengqiu Li
|
Biological and Medicinal Chemistry; Chemical Biology
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-12-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657aaa0f9138d231619c1c83/original/catalyst-free-late-stage-functionalization-to-assemble-acyloxyenamide-electrophiles-for-selectively-profiling-conserved-lysine-residues.pdf
|
65c9f0bf9138d23161ecc7b7
|
10.26434/chemrxiv-2024-fmlx0
|
CageCavityCalc (C3): A computational tool for calculating and visualizing cavities in Molecular Cages
|
Organic(porous) and metal-organic cages are promising biomimetic platforms with diverse applications spanning recognition, sensing and catalysis. The key to the emergence of these functions is the presence of well-defined inner cavities capable of binding a wide range of guest molecules and modulating their properties. However, despite the myriad cage architectures currently available, the rational design of structurally diverse and functional cages with specific host–guest properties remain challenging. Efficiently predicting such properties is critical for accelerating the discovery of novel functional cages.
Herein, we introduce CageCavityCalc (C3), a Python-based tool for calculating the cavity size of molecular cages. The code is available on GitHub at https://github.com/VicenteMartiCentelles/CageCavityCalc. C3 utilizes a novel algorithm that enables the rapid calculation of cavity sizes for a wide range of molecular structures and porous systems. Moreover, C3 facilitates easy visualization of the computed cavity size alongside hydrophobic and electrostatic potentials, providing insights into host-guest interactions within the cage. Furthermore, the calculated cavity can be visualized using widely available visualization software, such as PyMol, VMD, or Chimera. To enhance user accessibility, a PyMol plugin has been created, allowing non-specialists to use this tool without requiring computer programming expertise. We anticipate that the deployment of this computational tool will significantly streamline cage cavity calculations, thereby accelerating the discovery of functional cages.
|
Vicente Martí-Centelles; Tomasz Krzysztof Piskorz; Fernanda Duarte
|
Theoretical and Computational Chemistry; Organic Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.); Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2024-02-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c9f0bf9138d23161ecc7b7/original/cage-cavity-calc-c3-a-computational-tool-for-calculating-and-visualizing-cavities-in-molecular-cages.pdf
|
60c73ed9ee301c9540c787d1
|
10.26434/chemrxiv.7125656.v1
|
Conformational Effects on Physical-Organic Descriptors – the Case of Sterimol Steric Parameters
|
<div>
<div>
<div>
<p>Mathematical relationships which relate chemical structure with selectivity have provided quantitative insights underlying
catalyst design and informing mechanistic studies. Flexible compounds, however, can adopt several distinct geometries and
so can be challenging to describe using a single structure-based descriptor. How best to quantify the structural characteristics
of an ensemble of structure poses both practical and technical difficulties. In this work we introduce an automated
computational workflow which can be used to obtain multidimensional Sterimol parameters for a conformational ensemble
of a given substituent from a single command. The Boltzmann-weighted Sterimol parameters obtained from this approach
are shown to be useful in multivariate models of enantioselectivity, while the range of values from conformers within 3
kcal/mol of the most stable structure provides a visual way to capture a possible source of uncertainty arising in the resulting
models. Implementing our approach requires no programming expertise and can be executed from within a graphical user
interface using open-source programs.
</p>
</div>
</div>
</div>
|
Alexandre Brethomé; Stephen P. Fletcher; Robert Paton
|
Physical Organic Chemistry; Stereochemistry; Chemoinformatics; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed9ee301c9540c787d1/original/conformational-effects-on-physical-organic-descriptors-the-case-of-sterimol-steric-parameters.pdf
|
66a7afb0c9c6a5c07a68e1fd
|
10.26434/chemrxiv-2024-bkzp3
|
Ribosomal Synthesis of Ketone-containing Peptide Backbone via O to C Acyl Shift
|
Despite tremendous efforts to engineer translational machinery, replacing the encoded peptide backbone with new-to-Nature structures remains a significant and largely unmet challenge. C, H, O, and N are the elements of life, and yet ribosomes are only capable of forming C–N bonds as amides, C–O bonds as esters, and C–S bonds as thioesters; there is no current strategy to form C–C bonds as ketones embedded in the backbone of ribosomal products. We discovered that peptides containing a dehydrolactic acid motif rapidly isomerize to generate a backbone-embedded α,γ-diketoamide via a spontaneous formal O to C acyl shift. The dehydrolactic acid motif can be introduced into peptides ribosomally or via solid-phase synthesis using α-hydroxy phenylselenocysteine followed by oxidation. Subsequent incubation at physiological pH produces an α,γ-diketoamide that can be diversified using a variety of nucleophiles, including hydrazines and hydroxylamines to form pyrazoles and oximes, respectively. All of these groups remain embedded directly within the polypeptide backbone. This general strategy, predicated on an intricate cascade of acyl rearrangements, provides the first example of a C–C bond forming reaction to take place within the peptide backbone, as well as the first ribosomal strategy for generating protein-like materials with diverse, backbone-embedded heterocycles. The genetically encoded, new-to-nature biopolymers produced should accelerate the discovery of genetically encoded molecules whose properties better resemble those of bioactive natural products.
|
Carly Schissel; Helena Roberts-Mataric; Isaac Garcia; Hana Kang; Matthew Francis; Alanna Schepartz
|
Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a7afb0c9c6a5c07a68e1fd/original/ribosomal-synthesis-of-ketone-containing-peptide-backbone-via-o-to-c-acyl-shift.pdf
|
66fd8cda51558a15efdc3044
|
10.26434/chemrxiv-2023-m33nt-v3
|
Encapsulation of degraded DNA in alginate hydrogels: rheological characterization and applicability to forensic science
|
Forensic biomaterials are on the rise, with efforts in developing ex vivo tissue and blood mimetics. Incorporation of small and degraded DNA into these materials has implications for research and training across many areas of forensic science. Large fragments of highly concentrated genomic and phage DNA in solution have been characterized using rheology; however, this amount and size of DNA are atypical in DNA extracted from forensic evidence. In this work, we investigated how adding synthetic DNA oligos and genomic DNA extracted from bloodstains deposited for up to 19 months influenced the rheological properties of polymer systems intended for forensic biomaterial synthesis. We found that encapsulating DNA within an alginate-based, ionically crosslinked hydrogel produced the greatest differentiation in rheological profiles among DNA with varying physical properties. The different conformations and sizes of encapsulated DNA oligos exhibited significantly different responses during strain amplitude sweeps (p<0.05). We also observed moderate correlations between the rheological responses and the time since deposition of bloodstains used for DNA extraction (r = -0.57 to r = 0.62). This indicates that dilute, polydisperse and degraded genomic DNA extracts can effectively modulate the rheological properties of the encapsulating hydrogel. Our results demonstrate the viability of using rheology as a technique to analyze encapsulated dilute DNA oligos and degraded DNA while highlighting the need to consider the type of oligos included in forensic biomaterials.
|
Colin Elliott; Theresa Stotesbury
|
Materials Science; Analytical Chemistry; Polymer Science; Biological Materials; Biopolymers; Analytical Chemistry - General
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fd8cda51558a15efdc3044/original/encapsulation-of-degraded-dna-in-alginate-hydrogels-rheological-characterization-and-applicability-to-forensic-science.pdf
|
62bfa2049c9c6b76472939cb
|
10.26434/chemrxiv-2022-ztpbc-v3
|
On the prospects of optical cycling in diatomic cations: Effects of transition metals, spin-orbit couplings, and multiple bonds
|
Molecules with optical cycling centers (OCCs) are highly desirable in the context of fundamental studies as well as applications (e.g., quantum computing) because they can be effectively cooled to very low temperatures by repeated absorption and emission (hence, cycling). Charged species offer additional advantages for experimental control and manipulation. We present a systematic computational study of a series of diatomic radical-cations made of a d-block metal and a p-block ligand, that are isoelectronic (in their valence shell) to the successfully laser-cooled neutral molecules. Using high-level electronic structure methods, we characterize state and transition properties of low-lying electronic states and compute Franck-Condon factors. The computed branching ratios and radiative lifetimes reveal that the electronic transitions analogous to those successfully used in the laser cooling of neutral molecules are less than optimal in the cations. We propose alternative transitions suitable for optical cycling and highlight trends that could assist future designs of OCCs in charged or neutral molecules.
|
Paweł Wójcik; Eric R. Hudson; Anna I. Krylov
|
Theoretical and Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-07-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bfa2049c9c6b76472939cb/original/on-the-prospects-of-optical-cycling-in-diatomic-cations-effects-of-transition-metals-spin-orbit-couplings-and-multiple-bonds.pdf
|
63b9a7072840d8353ba7c7b3
|
10.26434/chemrxiv-2023-bg4bg-v2
|
Impact of nitrite-embedded packaging film on quality and sensory attributes of alternatively-cured and nitrite-free bologna
|
Nitrite-embedded film (NEF) was studied for its impact on quality attributes of alternatively-cured (with a natural source of nitrite from celery juice powder (AC)) bologna and nitrite-free bologna. The objectives of the study were to determine the effects of nitrite-embedded film (NEF) packaging following thermal processing of AC and nitrite-free bologna on quality attributes including lipid oxidation, instrumental color, pigment concentrations, and sensory properties such as cured meat flavor, aroma, and color. Three bologna formulations, each packaged with two packaging films were produced. A conventionally-cured control formulation (with nitrite from sodium nitrite; CON), a nitrite-free formulation (UCC), and an alternatively cured formulation (nitrite from cultured celery juice powder; AC) were packaged in conventional (CF) or nitrite-embedded (NEF) film. Instrumental a* values (measured during both light and dark storage at intervals of 7 or 14 days over 126 days of storage) and cured pigment concentration (measured at 14-day intervals over 84 days of storage) were significantly greater (P < 0.05) for the UCC-NEF treatment compared to its conventional film counterpart, UCC-CF. No significant differences (P > 0.05) for lipid oxidation (TBARS values) were observed with NEF. Trained sensory panelists, who evaluated samples at 14-day intervals over 70 days of storage, found significantly greater (P < 0.05) cured aroma, cured flavor, pink color and less off-flavor for uncured bologna packaged in NEF compared to conventional film. For the uncured bologna formulation, NEF packaging provided cured meat attributes comparable to the control formulation that included nitrite. This is the first time that cured aroma and cured flavor have been observed when nitrite from packaging film is added to heat-denatured (cooked) myoglobin in an anaerobic environment.
|
Michael Cropp; Rodrigo Tarté; Kenneth Prusa; James Dickson; Angela Shaw; Terry Houser; Rachel Crowley; Leah Reever; Joseph Sebranek
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Agriculture and Food Chemistry; Food
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-01-09
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b9a7072840d8353ba7c7b3/original/impact-of-nitrite-embedded-packaging-film-on-quality-and-sensory-attributes-of-alternatively-cured-and-nitrite-free-bologna.pdf
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61a7f48e6d4e8f1aa2a6bb85
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10.26434/chemrxiv-2021-6csxm
|
Excited-state distortions control the reactivities and regioselectivities of photochemical 4π-electrocyclizations of fluorobenzenes
|
The photochemistry of benzene is complex and non-selective because numerous mechanistic pathways are accessible in the ground- and excited-states. Fluorination is a known strategy to increase the chemoselectivities for Dewar-benzenes via 4π-disrotatory electrocyclization. However, the origin of the chemo- and regioselectivities of fluorobenzenes remains unexplained because of experimental limitations in resolving the excited-state structures on ultrafast timescales. The computational cost of multiconfigurational nonadiabatic molecular dynamics simulations is also generally prohibitive. We now provide high-fidelity structural information and reaction outcome predictions with machine-learning-accelerated photodynamics simulations of a series of fluorobenzenes, C6F6-nHn, n=0–3 to study their S1→S0 decay in 4 ns. We trained neural networks with XMS-CASPT2(6,7)/aug-cc-pVDZ calculations, which reproduced the S1 absorption features with mean absolute errors of 0.04 eV (< 2 nm). The predicted S1 excited-state lifetimes for C6F4H2, C6F6, C6F5H, and C6F3H3 are 64, 40, 18, and 8 ps, respectively. The trend is in excellent agreement with the experimental lifetimes. Our calculations show that the pseudo Jahn-Teller distortions create the S1 minimum region that prolongs the excited-state lifetime of fluorobenzenes. The pseudo Jahn-Teller distortions reduce when fluorination decreases. Characterization of the surface hopping structures suggests that the S1 relaxation first involves a cis-trans isomerization of a 𝜋C-C-bond in the benzene ring, promoted by the pseudo-Jahn-Teller distortions. A branching plane analysis revealed that the conical intersections favoring 4π-electrocyclization are less energetically accessible through the S1 relaxation; lower-energy conical intersections resemble the reactant and favor reversion.
|
Jingbai Li; Steven Lopez
|
Theoretical and Computational Chemistry; Organic Chemistry; Photochemistry (Org.); Computational Chemistry and Modeling; Machine Learning
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CC BY NC ND 4.0
|
CHEMRXIV
|
2021-12-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a7f48e6d4e8f1aa2a6bb85/original/excited-state-distortions-control-the-reactivities-and-regioselectivities-of-photochemical-4-electrocyclizations-of-fluorobenzenes.pdf
|
67510a945a82cea2fa077b1c
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10.26434/chemrxiv-2025-b1fh6
|
Enantioselective Synthesis of Complex Carbocycles by Donor/Donor Carbenes C-H insertion
|
A range of benzene-fused carbocyclic molecules are accessed by the enantioselective C–H insertion of rhodium donor/donor carbenes. The reaction is chemoselective for insertion into carbon centers appended with an electron-donating heteroatom, including a range of ethers, a free hydroxyl group, and a range of nitrogen substituents, including basic amines. DFT calculations support a step-wise mechanism of this process and provide insight into the origin of both stereoselectivity and the preference for C–H versus O–H insertion.
|
Jose Ruiz; Dylan Turner; Mingchun Gao; Wentao Guo; Tania Shahvali; Emily Jimenez Andrade; Kevin Kong; Beck Miller; James Fettinger; Matthew Sigman; Dean Tantillo; Jared Shaw
|
Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions
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CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67510a945a82cea2fa077b1c/original/enantioselective-synthesis-of-complex-carbocycles-by-donor-donor-carbenes-c-h-insertion.pdf
|
635fcbba1db0bde76340cc2c
|
10.26434/chemrxiv-2022-sb307
|
Phosphine reactivity and its implications for pyrolysis experiments and astrochemistry
|
Despite the importance of phosphorus-bearing molecules for life and their abundance outside Earth, the chemistry of those compounds still is poorly described. The present study investigated phosphine (PH3) decomposition and formation pathways. The reactions studied include phosphine thermal dissociation, conversion into PO, PN, and reactions in the presence of H2O+. The thermodynamic and rate coefficients of all reactions were calculated in the range of 50 – 2000 K considering the CCSD(T)/6-311G(3df,3pd)//B97xD/6-311G(3df,3pd) electronic structure data. The rate coefficients were calculated by RRKM and SCTST theories. According to the results, PH3 is stable due to thermal decomposition at T < 100 K but can be formed promptly by a reaction mechanism involving PH, PO, and PN. In the presence of radiation or ions, PH3 is readily decomposed. For this reason, it should be mainly associated with dust grains or icy mantles to be observed. The intersystem crossing associated with the dissociation of the isomers PON, NPO, and PNO was accessed by multireference methods, and its importance for the gas-phase PH3 formation/destruction was discussed. Also, the impact of the present outcomes on the phosphorus space chemistry was highlighted.
|
Leonardo Baptista; Amaury de Almeida
|
Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Space Chemistry; Chemical Kinetics; Physical and Chemical Properties
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CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635fcbba1db0bde76340cc2c/original/phosphine-reactivity-and-its-implications-for-pyrolysis-experiments-and-astrochemistry.pdf
|
66b3d4325101a2ffa8724773
|
10.26434/chemrxiv-2024-04kgm-v2
|
Extensive Biotransformation Profiling of AZD8205, an Anti-B7-H4 Antibody-Drug Conjugate, Elucidates Pathways Underlying its Stability In Vivo
|
What happens to macromolecules in vivo? What drives structure-activity relationship and in vivo stability for antibody-drug conjugates (ADCs)? These interrelated questions are increasingly relevant due to the re-emerging importance of ADCs as an impactful therapeutic modality and the gaps that exist in our understanding of ADC structural determinants that underlie ADC in vivo stability. Complex macromolecules, such as ADCs may undergo changes in vivo due to their intricate structure as biotransformations may occur on the linker, the payload and/or at the modified conjugation site. Furthermore, dissection of ADC metabolism presents a substantial analytical challenge due to the difficulty in identification or quantification of minor changes on a large macromolecule. We employed immunocapture-LCMS methods to evaluate in vivo changes in drug-antibody ratio (DAR) profile in four different lead ADCs. This comprehensive characterization revealed that a critical structural determinant contributing to ADC design was the selection of the linker as the competition between the retro-Michael deconjugation and thio-succinimide hydrolysis reactions resulted in superb conjugation stability in vivo. These data, in conjunction with additional factors, informed the selection of AZD8205, a B7-H4-directed cysteine-conjugated ADC bearing a novel topoisomerase I inhibitor payload, with durable DAR, currently being studied in the clinic for the potential treatment of solid malignancies (NCT05123482). These results highlight the relevance of studying macromolecule biotransformation and elucidating the ADC structure-in vivo stability relationship. The comprehensive nature of this work increases confidence in our understanding of these processes. We hope this analytical approach can inform future development of bioconjugate drug candidates.
|
Yue Huang; Hui Yin Tan; Jiaqi Yuan; Ruipeng Mu; Junyan Yang; Kathryn Ball; Balakumar Vijayakrishnan; Luke Masterson; Krista Kinneer; Nadia Luheshi; Meina Liang; Anton Rosenbaum
|
Analytical Chemistry; Mass Spectrometry
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CC BY 4.0
|
CHEMRXIV
|
2024-08-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b3d4325101a2ffa8724773/original/extensive-biotransformation-profiling-of-azd8205-an-anti-b7-h4-antibody-drug-conjugate-elucidates-pathways-underlying-its-stability-in-vivo.pdf
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66faf38012ff75c3a1f7fae3
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10.26434/chemrxiv-2024-pc891
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On the Compatibility of Halide Bilayer Separators for All-Solid-State Batteries
|
Considering the lack of solid electrolytes that are electrochemically stable in contact with a high-voltage cathode and a low-voltage metallic anode, bilayer separators in all-solid-state batteries are gaining increasing attention. However, previous studies have shown that the chemical reactivity between the materials comprising the electrolyte bilayer is one of the contributing factors to the deterioration of battery performance during cycling. Here, we computationally screen the chemical compatibility of an extensive range of materials forming a bilayer separator using first-principles calculations. Notably, several bilayer separators are found to be thermodynamically stable, amongst them, the stability of the Li3PO4/Li3InCl6 pairing is further verified experimentally using a combination of X-ray diffraction, solid-state nuclear magnetic resonance, and X-ray photoelectron spectroscopy. This study underscores the importance of understanding the chemical compatibility of bilayer separators when engineering high-energy density all-solid-state batteries.
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Abhishek A. Panchal; Tyler Pennebaker; Elias Sebti; Yan Li; Yuheng Li; Raphaële Clement; Pieremanuele Canepa
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Ceramics; Interfaces
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CC BY 4.0
|
CHEMRXIV
|
2024-10-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66faf38012ff75c3a1f7fae3/original/on-the-compatibility-of-halide-bilayer-separators-for-all-solid-state-batteries.pdf
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66b5e89f5101a2ffa8b18014
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10.26434/chemrxiv-2024-7w3v0-v2
|
Development of Peptoid-Based Heteroaryl-Decorated Histone Deacetylase (HDAC) Inhibitors with Dual-Stage Antiplasmodial Activity
|
Dynamics of epigenetic modifications such as acetylation and deacetylation of histone proteins have been shown to be crucial for the life cycle development and survival of Plasmodium falciparum, the deadliest malaria parasite. In this study, we present a novel series of peptoid-based histone deacetylase (HDAC) inhibitors incorporating nitrogen-containing bicyclic heteroaryl residues as a new generation of antiplasmodial peptoid-based HDAC inhibitors. We synthesized the HDAC inhibitors by an efficient multicomponent protocol based on the Ugi four-component reaction. The subsequent screening of 16 compounds from our mini-library identified 6i as the most promising candidate, demonstrating potent activity against asexual blood-stage parasites (IC50 Pf3D7 = 30 nM; IC50 PfDd2 = 98 nM), low submicromolar activity against liver-stage parasites (IC50 PbEEF = 0.25 µM), excellent microsomal stability (t1/2 > 60 min), and low cytotoxicity to HEK293 cells (IC50 = 136 µM).
|
Daniel Stopper; Lais Pessanha de Carvalho; Mariana Laureano de Souza; Cindy-Esther Kponomaizoun; Elizabeth Winzeler; Jana Held; Finn Kristian Hansen
|
Biological and Medicinal Chemistry
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CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b5e89f5101a2ffa8b18014/original/development-of-peptoid-based-heteroaryl-decorated-histone-deacetylase-hdac-inhibitors-with-dual-stage-antiplasmodial-activity.pdf
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6229935a97f21045f0043fe8
|
10.26434/chemrxiv-2022-73d0t
|
Density Functional Theory of Water with the Machine-Learned DM21 Functional
|
The delicate interplay between functional-driven and density-driven errors in density functional theory (DFT) has hindered traditional density functional approximations (DFAs) from providing an accurate description of water for over 30 years. Recently, the deep-learned DeepMind 21 (DM21) functional has been shown to overcome the limitations of traditional DFAs as it is free of delocalization error. To determine if DM21 can enable a molecular-level description of the physical properties of aqueous systems within Kohn-Sham DFT, we assess the accuracy of the DM21 functional for neutral, protonated, and deprotonated water clusters. We find that the ability of DM21 to accurately predict the energetics of aqueous clusters varies significantly with cluster size. Additionally, we introduce the many-body MB-DM21 potential derived from DM21 data within the many-body expansion of the energy and use it in simulations of liquid water as a function of temperature at ambient pressure. We find that size-dependent functional-driven errors identified in the analysis of the energetics of small clusters calculated with the DM21 functional result in the MB-DM21 potential systematically overestimating the hydrogen-bond strength and, consequently, predicting a more ice-like local structure of water at room temperature.
|
Etienne Palos; Eleftherios Lambros; Saswata Dasgupta; Francesco Paesani
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Physical and Chemical Properties; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-03-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6229935a97f21045f0043fe8/original/density-functional-theory-of-water-with-the-machine-learned-dm21-functional.pdf
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667a784e5101a2ffa873f3ee
|
10.26434/chemrxiv-2024-vdkfj-v5
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Photoswitchable catalysis by a self-assembled molecular cage
|
A heteroleptic [Pd2L2L'2]4+ coordination cage containing a photoswitchable azobenzene-derived ligand catalyzes the Michael addition reaction between methyl vinyl ketone and benzoyl nitromethane within its cavity. The correspond-ing homoleptic cages are catalytically inactive. The heteroleptic cage can be reversibly disassembled and reassembled using 530 nm light and 405 nm light, respectively, allowing catalysis within the cage to be switched ON and OFF at will.
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Ray G. DiNardi; Samina Rasheed; Simona S. Capomolla; M. Him Chak; Isis A. Middleton; Lauren K. Macreadie; Jake P. Violi; William A. Donald; Paul J. Lusby; Jonathon E. Beves
|
Organic Chemistry; Inorganic Chemistry; Nanoscience; Photochemistry (Org.); Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.)
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CC BY NC 4.0
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CHEMRXIV
|
2024-06-25
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667a784e5101a2ffa873f3ee/original/photoswitchable-catalysis-by-a-self-assembled-molecular-cage.pdf
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6466a1b0f2112b41e9c6e055
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10.26434/chemrxiv-2023-g3pkc
|
Autonomous Execution of Highly Reactive Chemical Transformations in the Schlenkputer
|
We demonstrate how it is possible to design a modular programmable inert-atmosphere Schlenkputer (Schlenk-line-computer) for the synthesis and manipulation of the most highly reactive compounds including those which are air- and moisture sensitive or pyrophoric. To do this we have designed and built a programmable Schlenk Line using the Chemputer architecture for the inertization of glassware which can achieve a vacuum line pressure of 1.5 10^-3 mbar and integrated a range of automated Schlenk glassware for the handling, storage, and isolation of reactive compounds at sub ppm levels of O2 and H2O. Utilising this hardware in conjunction with our platform has allowed the automation of a range of common organometallic reaction types for the synthesis of four highly reactive compounds from across the periodic table: [Cp2TiIII(MeCN)2]+ , CeIII{N(SiMe3)2}3, B(C6F5)3 and {DippNacNacMgI}2 which are variously sensitive to temperature, pressure, water and oxygen. Automated purification by crystallisation, filtration and sublimation are each demonstrated along with analysis using inline NMR or reaction sampling for UV/Vis. Finally, we demonstrate automated ultra-low temperature reactivity, down to −90 °C as well as safe handling and quenching of alkali metal reagents, using dynamic feedback from an in-situ temperature probe.
|
Lee Cronin; Nicola Bell; Florian Boser; Andrius Bubliauskas; Dominic Willcox; Victor Luna
|
Inorganic Chemistry; Chemical Engineering and Industrial Chemistry; Reaction Engineering
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CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6466a1b0f2112b41e9c6e055/original/autonomous-execution-of-highly-reactive-chemical-transformations-in-the-schlenkputer.pdf
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67a352b16dde43c908ad4645
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10.26434/chemrxiv-2025-gr8r6
|
Multiscale and multimodal image fusion. Coping with differences in scanned area and spatial resolution for Raman/fluorescence images of labelled cells.
|
Multiscale and multimodal image fusion is a challenge derived from the diversity of chemical and spatial information provided by the current hyperspectral image platforms. Efficient image fusion approaches are essential to exploit the complementary chemical information across different zoom scales. Most current image fusion algorithms tend to work by equalizing the spatial characteristics of the platforms to be combined, i.e., downsampling pixel size and cropping non-common scanned sample areas if required. In this work, a new image unmixing algorithm based on a flexible mathematical framework is proposed to enable working with all available image information while preserving the original spatial properties of every imaging measurement.
The algorithm is tested on a challenging image fusion scenario of fluorescence and Raman images collected on labelled HeLa cells. The system is relevant from an analytical point of view, since smart fluorescence labelling allows profiting from the excellent morphological information without causing interferences in the rich chemical information furnished by Raman. From a data handling perspective, it offers a challenging multiscale problem, where the fast fluorescence imaging acquisition allows recording full cell images, and the slower Raman image acquisition is focused on scanning only relevant small regions of the cells analyzed. By applying the image fusion algorithm proposed, an improved morphological and chemical characterization of cell constituents in the full cell area is obtained despite the different spatial scales used in the original imaging measurements.
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Albert Sicre Conesa; Maria Marsal; Adrián Gómez-Sánchez; Pablo Loza-Álvarez; Anna de Juan
|
Analytical Chemistry; Imaging; Microscopy; Spectroscopy (Anal. Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2025-02-06
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a352b16dde43c908ad4645/original/multiscale-and-multimodal-image-fusion-coping-with-differences-in-scanned-area-and-spatial-resolution-for-raman-fluorescence-images-of-labelled-cells.pdf
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67253b087be152b1d0b37724
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10.26434/chemrxiv-2024-bkmwz
|
Modeling Solid-Liquid Interfaces in MARTINI 3
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The MARTINI force field has become increasingly popular in material science by virtue of its versatility and its building block approach. However, force field parametrization is primarily based on reproducing structural and thermodynamic properties of the building blocks in solution, which may not be the most suitable strategy for regular, extended surfaces at solid-liquid interfaces, e.g., the planar facets of nanoparticles. In this study, we propose a novel strategy for parametrizing MARTINI planar surfaces in contact with liquids. While the choice of bead types in MARTINI models for molecules and ions in solution is often dictated by their chemistry, we suggest that surface-liquid interactions can be refined through a top-down approach. Specifically, we propose tuning the density of particles in the model surface to reproduce available experimental data on contact angles. In addition, we suggest several possible solutions to mitigate an artifact of the force field, that is, the excessive ordering of the liquid in contact with regular surfaces. Our findings demonstrate that water ordering can be reduced by tuning surface roughness and the level of coarse-graining of water. Eventually, we validate our approach on silica surfaces functionalized by alkyl chains.
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Sonia Cambiaso; Andrea Tagliabue; Davide Bochicchio; Antonio Tinti; Fabio Rasera Figueiredo; Alberto Giacomello; Luca Monticelli; Giulia Rossi
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Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Interfaces; Surface
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CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67253b087be152b1d0b37724/original/modeling-solid-liquid-interfaces-in-martini-3.pdf
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67510ae37be152b1d0fdf8c9
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10.26434/chemrxiv-2024-383sc
|
A Nonaromatic Room-Temperature Phosphorescent Hydrogel with Shape Memory Effect and Ultra-High Elastic Modulus based on Partially Hydrolyzed Polyacrylonitrile
|
Organic room-temperature phosphorescent (RTP) hydrogels hold great potential for various applications. However, the development of hydrogels with long phosphorescence lifetimes remains challenging because of quenching by water. Moreover, achieving multifunctionality alongside long lifetimes presents additional challenges. Herein, a series of partially hydrolyzed polyacrylonitrile (PHPAN) hydrogels are prepared. The initial PHPAN-Na-ori (PHPAN-Na+-original) hydrogel exhibits RTP, and the hydrogel treated with Zn2+ and a heating-cooling process, namely the PHPAN-Zn-hc hydrogel, exhibits a long phosphorescence lifetime of 178.48 ms, an ultra-high elastic modulus of 161 MPa, and a shape memory effect. Experiment results show that the phosphorescence of the PHPAN-Na-ori hydrogel originates form the hydrophobic aggregation of the cyano groups, and the photoluminescent and mechanical characteristics of the PHPAN-Zn-hc hydrogel is because Zn2+ forms coordinate bond with carboxylate and the coordinate bond is weakened and re-forms with optimal conformations during the heating-cooling process, which stiffens the hydrogel network and suppress noradiative decay. This work proposes a reliable strategy for designing nonaromatic RTP hydrogels, and provides a hydrogel for multifunctional applications.
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Wendi Xie; Junwen Deng; Yalu Cai; Yanle Wang; Shuning He; Yunhao Bai; Jinsheng Xiao; Xuanshu Zhong; Junyao Jiang; Huiliang Wang
|
Polymer Science; Hydrogels
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CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67510ae37be152b1d0fdf8c9/original/a-nonaromatic-room-temperature-phosphorescent-hydrogel-with-shape-memory-effect-and-ultra-high-elastic-modulus-based-on-partially-hydrolyzed-polyacrylonitrile.pdf
|
60c74853ee301ca42bc79855
|
10.26434/chemrxiv.11831103.v2
|
Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like Protease (3CLpro) Structure: Virtual Screening Reveals Velpatasvir, Ledipasvir, and Other Drug Repurposing Candidates
|
<p>We prepared the three-dimensional model of the 2019-nCoV 3C-like protease (3CL<sup>pro</sup>) using the crystal structure of the highly-similar (96% identity) ortholog from the SARS-CoV. All residues involved in the catalysis, substrate binding and dimerisation are 100% conserved. Comparison of the polyprotein PP1AB sequences showed 86% identity. The 3C-like cleavage sites on the coronaviral polyproteins are highly conserved. Based on the near-identical substrate specificities and high sequence identities, we are in the opinion that some of the previous progress of specific inhibitors development for the SARS-CoV enzyme can be conferred on its 2019-nCoV counterpart. With the 3CL<sup>pro</sup> molecular model, we performed virtual screening for purchasable drugs and proposed 16 candidates for consideration. Among these, the antivirals ledipasvir or velpatasvir are particularly attractive as therapeutics to combat the 2019-nCoV with minimal side effects, commonly fatigue and headache. The drugs Epclusa (velpatasvir / sofosbuvir) and Harvoni (ledipasvir / sofosbuvir) could be very effective owing to their dual inhibitory actions on two viral enzymes.</p>
|
Yu Wai Chen; Chin-Pang Yiu; Kwok-Yin Wong
|
Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-02-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74853ee301ca42bc79855/original/prediction-of-the-sars-co-v-2-2019-n-co-v-3c-like-protease-3c-lpro-structure-virtual-screening-reveals-velpatasvir-ledipasvir-and-other-drug-repurposing-candidates.pdf
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65082cd9b338ec988ab0b303
|
10.26434/chemrxiv-2023-xxn7s-v2
|
Real-time Optical Tracking of Protein Corona Formation on Single Nanoparticles in Serum
|
Significant advances in synthesis and functionalization have provided state-of-the-art technology in controlling the physico-chemical properties of nanomaterials. These are finding numerous applications including in the biomedical field whereby nanoparticles are injected in vivo for medical imaging, theranostics and biosensing. However, interactions with proteins contained in biological fluids lead to the formation of a shell on the surface of the nanoparticles called "protein corona" (PC). PC plays a detrimental role for the intended applications as it may modify the interface of the nanoparticle and thereby block functional groups needed for recognition. It is therefore essential to understand the mechanisms of formation of these PCs in order to control the surface chemistry of the nanoparticles in complex biological fluids. Current characterization techniques can identify and quantify the composition of PCs using mass spectroscopy and electrophoresis. However, most of them do not enable real-time measurement in complex media because they require washing steps to remove excess protein. Finally, most techniques provide ensemble averages and are unable to access inter-particle heterogeneity. Here, we demonstrate the use of single-particle scattering microscopy combined with a microfluidic system to study PC formation in real-time at the single-nanoparticle level. The method is label-free and operates in undiluted blood serum. We probe PC formation on both, metallic and dielectric nanoparticles with different surface chemistries. Analysis of protein adsorption revealed unexpectedly strong heterogeneity whereby the amount of accumulated protein varies by up to a factor of 10 between the particles. Furthermore, it is found that the surface roughness of the nanoparticles affects the kinetics of the PC formation. The results of this in-situ characterization are a powerful tool to optimize the surface chemistry in order to minimize the formation of PCs and thus increase the efficiency of nanoparticles for applications such as targeted drug delivery.
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Mathias Dolci; Yuyang Wang; Sjoerd W. Nooteboom; Paul E.D. Soto Rodriguez; Samuel Sanchez; Lorenzo Albertazzi; Peter Zijlstra
|
Physical Chemistry; Materials Science; Nanoscience; Plasmonic and Photonic Structures and Devices; Biophysical Chemistry; Optics
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CC BY NC 4.0
|
CHEMRXIV
|
2023-09-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65082cd9b338ec988ab0b303/original/real-time-optical-tracking-of-protein-corona-formation-on-single-nanoparticles-in-serum.pdf
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60c740a6f96a0002df28631b
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10.26434/chemrxiv.7812680.v1
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Interplay of Catalyst Structure and Temperature for NMR Signal Amplification by Reversible Exchange
|
SABRE has brought up the many possibilities for chemical and medical researches. However, the current SABRE catalyst has multi-limitations, including the time-consuming activation, activation stability and temperature compatibility. In this report, synthesis of several variants of an iridium-based organometallic catalyst showed accelerated activation performance and enhanced stability, during NMR Signal Amplification By Reversible Exchange (SABRE) in solution under upon administration of parahydrogen (pH2)-enriched gas in methanol mixture containing the “variant” catalyst and the substrate (pyridine or nicotinamide). Furthermore, such series of newly discovered SABRE catalysts are opening a door to a much high activation efficiency and higher low temperature performances for the potential future applications in larger and more challenging application fields, as well the relevant theoretical study of SABRE mechanism.<br />
|
Fan Shi
|
Biophysical Chemistry; Chemical Kinetics; Quantum Mechanics; Spectroscopy (Physical Chem.); Statistical Mechanics; Structure
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a6f96a0002df28631b/original/interplay-of-catalyst-structure-and-temperature-for-nmr-signal-amplification-by-reversible-exchange.pdf
|
60c74627bb8c1a8fcd3da817
|
10.26434/chemrxiv.7927061.v2
|
Lysosome Targeting Chimeras (LYTACs) for the Degradation of Secreted and Membrane Proteins
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<p>Targeted protein degradation is a powerful strategy to address the canonically undruggable proteome. However, current technologies are limited to targets with cytosolically-accessible and ligandable domains. Here, we designed and synthesized conjugates capable of binding both a cell surface lysosome targeting receptor and the extracellular domain of a target protein. These lysosome targeting chimeras (LYTACs) consist of an antibody fused to agonist glycopeptide ligands for the cation-independent mannose-6-phosphate receptor (CI-M6PR). LYTACs enabled a CRISPRi knockdown screen revealing the biochemical pathway for CI-M6PR-mediated cargo internalization. We demonstrated that LYTACs mediate efficient degradation of Apolipoprotein-E4, epidermal growth factor receptor (EGFR), CD71, and programmed death-ligand 1 (PD-L1). LYTACs represent a modular strategy for directing secreted and membrane proteins for degradation in the context of both basic research and therapy. <b></b></p>
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Steven Banik; Kayvon Pedram; Simon Wisnovsky; Nicholas Riley; Carolyn Bertozzi
|
Bioorganic Chemistry; Cell and Molecular Biology; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-11-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74627bb8c1a8fcd3da817/original/lysosome-targeting-chimeras-lyta-cs-for-the-degradation-of-secreted-and-membrane-proteins.pdf
|
60c7443d4c8919987bad279c
|
10.26434/chemrxiv.9762332.v1
|
Synthesis, Characterization and Reactivity of Chromium(VI) Alkylidenes
|
Chromium(VI)
dialkyls are remarkably acidic, yielding a new set of anionic chromium
alkylidenes upon deprotonation with KN(TMS)<sub>2</sub>. We describe the characterization of three
anionic chromium alkylidenes of the type [(ArN)<sub>2</sub>Cr(=CHR)(CH<sub>2</sub>R]<sup>-</sup>
(R = <i><sup>t</sup></i>Bu, SiMe<sub>3</sub>,
Ph; Ar = 2,6-diisopropylphenyl). NEt<sub>4</sub>[(ArN)<sub>2</sub>Cr(=CHSiMe<sub>3</sub>)(CH<sub>2</sub>SiMe<sub>3</sub>)]
has been structurally characterized by X-ray diffraction. We have also studied the C-H activation of
cyclohexane effected by the transient neopentylidene (ArN)<sub>2</sub>Cr(=CHCMe<sub>3</sub>).
This reaction generated a tri-nuclear chromium(IV) complex, namely ‘[Cr(NAr)<sub>2</sub>]<sub>3</sub>’,
as well as the two organic products cyclohexene and neopentane. A probable
intermediate in this reaction could be trapped by PPh<sub>3</sub> to form (ArN)<sub>2</sub>Cr(PPh<sub>3</sub>)<sub>2</sub>. The latter undergoes ligand substitution
reactions with ethylene and CO to produce p-acid complexes of
tetravalent chromium.
|
Pengcheng Wu; Glenn P. A. Yap; Klaus Theopold
|
Kinetics and Mechanism - Organometallic Reactions; Ligands (Organomet.); Reaction (Organomet.); Transition Metal Complexes (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7443d4c8919987bad279c/original/synthesis-characterization-and-reactivity-of-chromium-vi-alkylidenes.pdf
|
60c745f6bb8c1a855a3da7b3
|
10.26434/chemrxiv.10887914.v1
|
Strong and Confined Acid Catalysts Impart Stereocontrol onto the Non-Classical 2-Norbornyl Cation
|
In 1949, S. Winstein and D. Trifan proposed that
the 2-norbornyl cation adopts a bridged, non-classical structure with a
3-center, 2-electron unit much like the bonding in diborane. While some embraced this
proposal, others firmly refuted it, giving rise to the vituperative 2-norbornyl
cation controversy. After 60 years of debate,
the long-sought crystallographic proof was eventually collected in 2013. Several decades after the
first non-classical formulation, we became interested in imparting
stereocontrol over the 2-norbornyl cation, a positively charged, simple
hydrocarbon that, due to its structural features, offers a major challenge to
asymmetric catalysis. Our investigation began by reversing the original
experiment by Winstein. Specifically, we found that IDPi catalysts are competent chiral acids
for carrying out a diastereo- and enantioselective C-C bond forming reaction
between racemic <i>exo</i>- and <i>endo</i>-norbornyl trichloroacetimidates and
1,3,5-trimethoxybenzene to exclusively deliver the <i>exo</i>-product with excellent enantioselectivities. We also found that
several structurally-different substrates can be converted to the same product
with good to excellent enantioselectivities, pointing to the existence of a
common cationic intermediate. Mechanistic and kinetic studies
were conducted to elucidate relevant aspects of the reaction.
|
Roberta Properzi; Philip S. J. Kaib; Markus Leutzsch; Gabriele Pupo; Raja Mitra; Chandra Kanta De; Peter R. Schreiner; Benjamin List
|
Acid Catalysis; Homogeneous Catalysis; Organocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-11-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745f6bb8c1a855a3da7b3/original/strong-and-confined-acid-catalysts-impart-stereocontrol-onto-the-non-classical-2-norbornyl-cation.pdf
|
61172e5745805d0dd3870af8
|
10.26434/chemrxiv-2021-kc81w-v2
|
Insight into subsurface adsorption derived from a lattice-gas model of atomic oxygen on Ag(111)
|
Theoretical gas-surface models that describe adsorption over a wide range of coverages can provide qualitative insight into chemical phenomena that occur at intermediate to high coverages, such as subsurface adsorption, surface reconstruction, and industrial heterogeneous catalysis. However, most atomistic, quantum-mechanical models of gas-surface adsorption are limited to low adsorbate coverage due to the large computational cost of models built using many surface atoms and adsorbates. To investigate adsorption in the subsurface of a crystalline solid with increasing coverage, we present a lattice-gas adsorption model that includes surface and subsurface sites of the solid, and is fully parametrized using density functional theory. We apply the model to study the competition between surface and subsurface adsorption of atomic oxygen on the Ag(111) surface. Oxygen population distributions calculated using the model show the onset of subsurface adsorption at a total coverage of approximately 1/4 monolayer and a greater accumulation of oxygen in the second rather than the first subsurface at total coverages greater than 1/2 monolayer. Computation of core-electron binding energies and projected density of states of an oxygen distribution predicted by the model reveal qualitative differences in oxygen-silver bonding at the surface and subsurface, suggesting that oxygen adsorbed in the two regions could play distinct roles in surface chemistry.
|
Carson Mize; Sara Isbill; Sharani Roy
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Quantum Mechanics; Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-08-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61172e5745805d0dd3870af8/original/insight-into-subsurface-adsorption-derived-from-a-lattice-gas-model-of-atomic-oxygen-on-ag-111.pdf
|
66fdf34712ff75c3a13e75cf
|
10.26434/chemrxiv-2024-13rlh
|
Pi-Extended Hypervalent Iodine Macrocycles and their Supramolecular Assembly with Buckminster Fullerene
|
A series of valine functionalized supramolecular hypervalent iodine macrocycles (HIMs) with enlarged aromatic cores, including naphthalene and anthraquinone, have been synthesized. Single crystal analysis shows the macrocycles consist of a slightly distorted cyclic planner interior with three carbonyl oxygens from the amino acid residues facing towards the center of the cage and all three alkyl groups above one plane. Owing to the enlarged aromatic core, the naphthalene-based HIMs were successfully co-crystallized with Buckminster Fullerene (C60) into a long-range columnar supramolecular structure. The assembled architecture displays a long-range pattern between HIM and C60 in a 2:3 ratio, respectively. Disassembly of the HIMs can be accomplished by adding anions of tetrabutylammonium (TBA) salts that selectively bind with the electron deficient iodine center in HIM systems. A comparative study of the associations constants and the binding energies for different aromatic-based HIMs with TBA(Cl) and TBA(Br) is presented.
|
Krishna Pandey; Samsul Arafin; Grayson Venus; Eli Jones; Yachu Du; Mina Dumre Pandey; Tahir Awais; Lichang Wang; Kyle Plunkett
|
Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fdf34712ff75c3a13e75cf/original/pi-extended-hypervalent-iodine-macrocycles-and-their-supramolecular-assembly-with-buckminster-fullerene.pdf
|
630fc221f9e99c3c35913cc3
|
10.26434/chemrxiv-2022-lfkl3
|
Electrochemical fabrication of nanostructured Ni with single diamond morphology
|
Mesoporous nickel with extremely high surface area was successfully fabricated for the first time using a monoolein-based bicontinuous cubic phase as a template. The 3-D nanoarchitecture of the deposited nickel films was confirmed by SAXS, TEM and elctrochemical analysis. The SAXS analysis revealed that the templated nickel has a single diamond structure (Fd3m symmetery).
|
Nassar ABDELRAHIM; Adam Squires; Joanne Elliott
|
Physical Chemistry; Materials Science; Nanoscience; Nanofabrication; Structure; Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630fc221f9e99c3c35913cc3/original/electrochemical-fabrication-of-nanostructured-ni-with-single-diamond-morphology.pdf
|
668ff349c9c6a5c07afae8e4
|
10.26434/chemrxiv-2023-t3k48-v3
|
Phytosterols in human serum as measured using a liquid chromatography tandem mass spectrometry
|
Phytosterols are lipophilic compounds found in plants with structural similarity to mammalian cholesterol. They cannot be endogenously produced by mammals and therefore always originate from diet. There has been increased interest in dietary phytosterols over the last few decades due to their association with a variety of beneficial health effects including low-density lipoprotein cholesterol lowering, anti-inflammatory and anti-cancerous effects. They are proposed as potential moderators for diseases associated with the central nervous system where cholesterol homeostasis is found to be imperative (multiple sclerosis, dementia, etc.) due to their ability to reach the brain. Here we utilised an enzyme-assisted derivatisation for sterol analysis (EADSA) in combination with a liquid chromatography tandem mass spectrometry (LC-MSn) to characterise phytosterol content in human serum. As little as 100 fg of plant sterol was injected on a reversed phase LC column. The method allows semi-quantitative measurements of phytosterols and their derivatives simultaneously with measurement of cholesterol metabolites. The identification of phytosterols in human serum was based on comparison of their LC retention times and MS2, MS3 spectra with a library of authentic standards. Free campesterol serum concentration was in the range from 0.30 - 4.10 µg/mL, β-sitosterol 0.16 - 3.37 µg/mL and fucosterol was at lowest concentration range from 0.05 - 0.38 µg/mL in ten individuals. This analytical methodology could be applied to the analysis of other biological fluids and tissues.
|
Kersti Karu; Marie Claire Gielen; Yu Chun Teng; Nina M De Gruijter; Coziana Ciurtin; Elizabeth C Rosser
|
Analytical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668ff349c9c6a5c07afae8e4/original/phytosterols-in-human-serum-as-measured-using-a-liquid-chromatography-tandem-mass-spectrometry.pdf
|
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