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60ff0d5a393cc904c94f1f18
|
10.26434/chemrxiv-2021-7rngq
|
An expanded LUXendin color palette for GLP1R
detection and visualization in vitro and in vivo
|
The glucagon-like peptide-1 receptor (GLP1R) is expressed in peripheral tissues and the brain, where it exerts pleiotropic actions on metabolic and inflammatory processes. Detection and visualization of GLP1R remains challenging, partly due to a lack of validated reagents. Previously, we generated LUXendins, antagonistic red and far-red fluorescent probes for specific labeling of GLP1R in live and fixed cells/tissue. We now extend this concept to the green and near-infrared color ranges by synthesizing and testing LUXendin492, LUXendin551, LUXendin615 and LUXendin762. All four probes brightly and specifically label GLP1R in cells and pancreatic islets. Further, LUXendin551 acts as chemical beta cell reporter in preclinical rodent models, while LUXendin762 allows non-invasive imaging, highlighting differentially-accessible GLP1R populations. We thus expand the color palette of LUXendins to seven different spectra, opening up a range of experiments using widefield microscopy available in most labs through super-resolution imaging and whole animal imaging. With this, we expect that LUXendins will continue to generate novel and specific insight into GLP1R biology.
|
Julia Ast; Alissa N. Novak; Tom Podewin; Nicholas H. F. Fine; Ben Jones; Alejandra Tomas; Ramona Birke; Kilian Roßmann; Bettina Mathes; Jenny Eichhorst; Martin Lehmann; Amelia K. Linnemann; David J. Hodson; Johannes Broichhagen
|
Biological and Medicinal Chemistry; Chemical Biology
|
CC BY 4.0
|
CHEMRXIV
|
2021-07-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ff0d5a393cc904c94f1f18/original/an-expanded-lu-xendin-color-palette-for-glp1r-detection-and-visualization-in-vitro-and-in-vivo.pdf
|
67db9efb81d2151a021de682
|
10.26434/chemrxiv-2025-12mdb
|
Toward Predictive Data-Driven Atomistic Modeling of Electrocatalyst Stability and Surface Reconstruction
|
Catalyst dissolution and surface restructuring are ubiquitous in electrocatalysis, often leading to formidable activity–stability trade-offs and obscure electrochemically-induced surface species that severely hinder the understanding and optimization of electrocatalysts under diverse harsh operating conditions. As even state-of-the-art characterization techniques lack the resolution and efficiency for the unambiguous elucidation of decomposition kinetics and reconstruction dynamics at electrocatalytic interfaces, many atomistic modeling approaches—following the recent advances in physics-driven machine learning—have been widely used to facilitate the atom-by-atom understanding and rational engineering of electrocatalyst stability and dynamics. This Perspective systematically assesses classical and data-driven approaches in theoretical surface science and computational catalysis, recognizing their achievements and highlighting their limitations in throughput, efficiency, accuracy, bias, transferability, and scalability toward enabling realistic and predictive modeling of electrocatalyst degradation and reconstruction. By examining different methods spanning first-principles simulations, surface sampling, neural network interatomic potentials, and generative deep learning models, it is underscored how such data-driven computational techniques help elucidate the precise nature of various key interfacial atomistic processes to address existing technical challenges in surface modeling and provide a new paradigm to optimize dissolution kinetics and restructuring dynamics for electrocatalyst design.
|
Jiayu Peng
|
Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Electrocatalysis; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67db9efb81d2151a021de682/original/toward-predictive-data-driven-atomistic-modeling-of-electrocatalyst-stability-and-surface-reconstruction.pdf
|
60c74f1dbb8c1a5f673db88c
|
10.26434/chemrxiv.12808415.v1
|
Can We See the Energy Densities? I. Insights from Real-Time Time-Dependent Density Functional Theory Simulations
|
In this work, we report a scheme to evaluate and analysis of energy density fluctuations during the real-time time-dependent density functional theory (RT-TDDFT) simulations. Using Ag<sub>4</sub>–N<sub>2</sub> complexes as examples, it is shown that the energy of each molecular fragment (such as Ag<sub>4</sub> and N<sub>2</sub>) can be readily computed by partitioning Kohn-Sham energy densities using Becke or fragment-based Hirshfeld (FBH) scheme. A strong orientation-dependence is observed for theenergy flow between the Ag<sub>4</sub> cluster and a nearby N<sub>2</sub> molecule in the RT-TDDFT simulations. Future applications of such an energy density analysis in electron dynamics simulations are<br />discussed.
|
junjie yang; Zheng Pei; Jingheng Deng; Qin Wu; Yuezhi Mao; Zhibo Yang; bin wang; Christine
M. Aikens; Wanzhen Liang; Yihan Shao
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f1dbb8c1a5f673db88c/original/can-we-see-the-energy-densities-i-insights-from-real-time-time-dependent-density-functional-theory-simulations.pdf
|
672bd2527be152b1d03b0c1f
|
10.26434/chemrxiv-2024-v3m2s
|
Prescreening of Liquid Density and Surface Tension for Synthetic Aviation Turbine Fuels by Nuclear Magnetic Resonance Atom Types
|
Prescreening of Synthetic (“Sustainable”) Aviation Turbine Fuel, referred to as SAF in this work, is becoming regarded as an essential technique to secure the early-stage development of SAF candidates. Prescreening refers to the study of small volumes of SAF at the early stages of product development for the purpose of assessing the compatibility of the SAF candidate with the American Society for Testing and Materials (ASTM) D4054 evaluation procedure for new aviation turbine fuels. The basis of the prescreening process relies on the availability of numerical models that can predict the fit-for-purpose properties of the ASTM evaluation procedure without the volumes of the SAF candidate needed to perform all the necessary measurements being available.
In this work, such models are developed that predict two important fit-for-purpose ASTM D4054 properties, the temperature dependent liquid density and temperature dependent surface tension of complex hydrocarbons mixtures. The basis of the method is the determination of atom type compositions by a 1H 13C Heteronuclear Single Quantum Coherence (HSQC) Nuclear Magnetic Resonance (NMR) spectroscopy methodology.
The dependence of each of, temperature dependent liquid density, and temperature dependent surface tension, on the range of atom types that comprise typical aviation fuel hydrocarbons is learned by the multiple linear regression modelling to a database of pure component and pure component mixture data gathered from the literature. A data base of 1,241 entries is gathered for density, and a data base of 1,260 entries gathered for surface. Each database is divided in an 80:20 ratio for model training and model testing. Extensive iterations of model training and testing objectively identify the same seven atom types as being most influential to each property. The collection of seven atom types, in addition to a temperature dependent term, is shown to be sufficient to determine each property quite precisely.
The models are then applied to the atom type compositions of two fossil-derived aviation fuels, four synthetic aviation fuels, and four reference gasoline fuels, as determined by 1H 13C HSQC NMR. The methodology shows high performance, predicting the unseen liquid density of these real fuels within an absolute error range of 0.00 – 5.59%, and surface tension within an absolute error range of 0.29 - 4.41%. It also successfully differentiates the relative magnitudes of each property across these fuels. This indicates that the method is valuable for prescreening applications.
|
Robert Parker; Mark Kelly; Tiarnán Watson-Murphy; Mohammad Reza Ghaani; Stephen Dooley
|
Physical Chemistry; Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672bd2527be152b1d03b0c1f/original/prescreening-of-liquid-density-and-surface-tension-for-synthetic-aviation-turbine-fuels-by-nuclear-magnetic-resonance-atom-types.pdf
|
60c74063bb8c1a09223d9da9
|
10.26434/chemrxiv.7640489.v2
|
Adsorption of Amino Acids on Graphene: Assessment of Current Force Fields
|
<div>
<div>
<div>
<p>We compare the free energies of adsorption (∆Aads) and the structural preferences of amino
acids obtained using the force fields — Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P,
OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid–graphene interactions are favorable irrespective of the force field. While the magnitudes of ∆Aads differ between the force
fields, the trends in the free energy of adsorption with amino acids are similar across the studied
force fields. ∆Aads positively correlates with amino acid–graphene and negatively correlates with
graphene–water interaction energies. Using a combination of principal component analysis and
density-based clustering technique, we grouped the structures observed in the graphene adsorbed
state. The resulting population of clusters, and the conformation in each cluster indicate that the
structures of the amino acid in the graphene adsorbed state vary across force fields. The differences
in the conformations of amino acids are more severe in the graphene adsorbed state compared to the
bulk state for all the force fields. Our findings suggest that while the thermodynamics of adsorption
of proteins and peptides would be described consistently across different force fields, the structural
preferences of peptides and proteins on graphene will be force field dependent.
</p>
</div>
</div>
</div>
|
Siva Dasetty; John K. Barrows; Sapna Sarupria
|
Biological Materials; Carbon-based Materials; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Thermodynamics (Chem. Eng.); Clusters; Self-Assembly; Statistical Mechanics; Structure; Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-01-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74063bb8c1a09223d9da9/original/adsorption-of-amino-acids-on-graphene-assessment-of-current-force-fields.pdf
|
667275e801103d79c58caf03
|
10.26434/chemrxiv-2024-9hhv5
|
Light-induced reversible switching of generation and extinction of an organic radical anion
|
Radicals play a crucial role across various domains, ranging from serving as catalysts in chemical reactions to materials for spintronic applications. Currently, a major challenge for the chemists is the development of the next generation of organic radicals controllable by photons. To tackle this challenge, here we introduce a dyad system that combines a dimethyldihydropyrene (DHP) photochromic unit with a naphthalene diimide (NDI) moiety. This system forms a stable organic NDI-based radical-anion upon exposure to light in a solvent containing a small amount of an amine that acts as an electron donor. The radical anion formtion has also been demonstrated with chemical reductant. The photoisomerization of this photochromic system converts it into a less-conjugated and less-electron-rich form, affecting the generation of the radical as well as its stability. Consequently, light-induced isomerization effectively quenches the radical. Thus, the formation and existence of the radical can be adjusted by manipulating the photoisomerization of the photochromic unit under diverse light sources. Additionally, the system exhibits significant differences in emission in the radical and the closed-shell state, thereby offering a dual readout of the state of the molecule.
|
Sheelbhadra Chatterjee; Palash Jana; Samyadeb Mahato; Subhajit Bandyopadhyay
|
Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-06-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667275e801103d79c58caf03/original/light-induced-reversible-switching-of-generation-and-extinction-of-an-organic-radical-anion.pdf
|
64f18dbbdd1a73847ff01671
|
10.26434/chemrxiv-2023-1b47d-v2
|
An Integrated Direct-to-Biology Platform for the Nanoscale Synthesis and Biological Evaluation of PROTACs
|
ABSTRACT: Proteolysis targeting chimeras (PROTACs) are heterobifunctional molecules that co opt the cell’s natural proteasomal degradation mechanisms to selectively tag and degrade undesired proteins. However, a challenge associated with PROTACs is the difficult optimisation required to identify new degraders, thus the development of high-throughput platforms for their synthesis and biological evaluation is required. In this study, we establish an ultra high-throughput experimentation (ultraHTE) platform for PROTAC synthesis, followed by direct addition of the crude reaction mixtures to cellular degradation assays without any purification. This ‘Direct-to-Biology’ (D2B) approach was validated, then exem-plified in a medicinal chemistry campaign to identify novel BRD4 PROTACs from a BRD4-binding scaffold previously unexplored for targeted protein degradation. Using the D2B platform, the synthesis of over 600 PROTACs was carried out in a 1536-well plate and subsequent biological evaluation of these candidates was performed by a single scientist in less than one month, to identify a set of picomolar BRD4 degraders. Due to its ability to hugely accelerate the optimisation of new degraders, we anticipate our platform to transform the synthesis and testing of PROTACs.
|
Rebecca Stevens; Enrique Bendito-Moll; David Battersby; Afjal Miah; Natalie Wellaway; Robert Law; Peter Stacey; Diana Klimaszewska; Justyna Macina; Glenn Burley; John Harling
|
Biological and Medicinal Chemistry; Organic Chemistry; Chemical Engineering and Industrial Chemistry; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems; Pharmaceutical Industry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f18dbbdd1a73847ff01671/original/an-integrated-direct-to-biology-platform-for-the-nanoscale-synthesis-and-biological-evaluation-of-prota-cs.pdf
|
60c74e0abb8c1a17643db6a7
|
10.26434/chemrxiv.11836251.v3
|
Single-Site Binding of Pyrene to Poly(ester-Imide)s Incorporating Long Spacer Units: Prediction of NMR Resonance-Patterns from a Fractal Model
|
Co-polycondensation
of the diimide-based diols<i> N</i>,<i>N</i>'-bis(2-hydroxyethyl)hexafluoro-isopropylidene-diphthalimide,
(HFDI), and <i>N</i>,<i>N</i>'-bis(2-hydroxy-ethyl)naphthalene-1,4,5,8-tetracarboxylic-diimide,
(NDI), with aliphatic diacyl chlorides ClOC(CH<sub>2</sub>)<i><sub>x</sub></i>COCl (<i>x</i> = 5
to 8) affords linear copoly(ester-imide)s. Such copolymers interact with pyrene
via supramolecular binding of the polycyclic aromatic molecule at NDI residues.
This results in upfield complexation shifts and sequence-related splittings of
the NDI <sup>1</sup>H NMR resonances, but gives a very different resonance-pattern
from the corresponding copolymer where <i>x</i>
= 2. Computational modelling of the polymer with <i>x</i> = 5 suggests that, in this system, each pyrene molecule binds to
just a single NDI residue rather than to an adjacent pair of NDI's in a tight
chain-fold ("dual-site" binding) as found for <i>x</i> = 2. The new single-site binding model enables the pattern of <sup>1</sup>H
NMR resonances for copolymers with longer spacers (<i>x</i> = 5 to 8) to be reproduced and assigned by simulation from sequence-specific
shielding factors based on the fractal known as the fourth-quarter Cantor set.
As this set also enables an understanding of dual-site binding systems, it
evidently provides a general numerical framework for supramolecular
sequence-analysis in binary copolymers.
|
Marcus Knappert; Tianqi Jin; Scott D. Midgley; Guanglu Wu; Oren Scherman; Ricardo Grau-crespo; Howard Colquhoun
|
Organic Polymers; Polymer chains
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e0abb8c1a17643db6a7/original/single-site-binding-of-pyrene-to-poly-ester-imide-s-incorporating-long-spacer-units-prediction-of-nmr-resonance-patterns-from-a-fractal-model.pdf
|
6571a35d5bc9fcb5c9449992
|
10.26434/chemrxiv-2023-zs9kp-v2
|
Quantifying Electrochemical Degradation in Single-crystalline LiNi0.8Mn0.1Co0.1O2–Graphite pouch cells through Operando X-ray and Post-mortem Investigations
|
Layered nickel-rich lithium transition metal oxides (LiNixMnyCo1−x−yO2; where x ≥ 0.8), with single-crystalline morphology, are promising future high-energy-density Li-ion battery cathodes due to their ability to mitigate particle-cracking-induced degradation. This is due to the absence of grain boundaries in these materials, which prevents the build-up of bulk crystallographic strain during electrochemical cycling. Compared to their polycrystalline counterparts, there is a need to study single-crystalline Ni-rich cathodes using operando X-ray methods in uncompromised machine-manufactured industry-like full cells to understand their bulk degradation mechanisms as a function of different electrochemical cycling protocols. This can help us identify factors to improve their long-term performance. Here, through in-house operando X-ray studies of pilot-line-built LiNi0.8Mn0.1Co0.1O2–Graphite A7 pouch cells, it is shown that their electrochemical capacity fade under harsh conditions (2.5–4.4 V and 40 °C for 100 cycles at C/3 rate) primarily stems from the high-voltage reconstruction of the cathode surface from a layered to a cubic (rock salt) phase that impedes Li+ kinetics and increases cell impedance. Post-mortem electron and X-ray microscopy show that these cathodes can withstand severe anisotropic structural changes and show no cracking when cycled under such conditions. Comparing these results to those from commercial Li-ion cells with surface-modified single-crystalline Ni-rich cathodes, it is identified that cathode surface passivation can mitigate this type of degradation and prolong cycle life. In addition to furthering our understanding of degradation in single-crystalline Ni-rich cathodes, this work also accentuates the need for practically relevant and reproducible fundamental investigations of Li-ion cells and presents a methodology for achieving this.
|
Ashok S. Menon; Nickil Shah; James A. Gott; Eleni Fiamegkou; Matthew J. W. Ogley; Galo J. Paez Fajardo; Naoum Vaenas; Ieuan Ellis; Nishitha Ravichandran; Peter Cloetens; Dmitry Karpov; Jay Warnett; Paul Malliband; David Walker; Geoff West; Melanie Loveridge; Louis Piper
|
Energy; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6571a35d5bc9fcb5c9449992/original/quantifying-electrochemical-degradation-in-single-crystalline-li-ni0-8mn0-1co0-1o2-graphite-pouch-cells-through-operando-x-ray-and-post-mortem-investigations.pdf
|
61e9f6f2b815cc80e39ccc6c
|
10.26434/chemrxiv-2021-jmk6d-v4
|
Arylboronic Acids Catalyzed Upgrade of Glucosamines for Deoxyfructosazine and Insights on Reaction Mechanism
|
Chitin is the most abundant N-containing polysaccharides in nature and D-glucosamine is one of most successful commercial monomer products in current market. Here we reported an arylboronic acids catalyzed upgrade of glucosamines in aqueous solution for deoxyfructosazine which is an important high-value compound in pharmaceutical and food industries, as well as a promising bio-based platform molecule for speciality chemicals and sustainable functional materials. Such direct integration of deoxyfructosazine into development of renewable chemicals/functional materials might be a practical way for utilization of chitin as a renewable nitrogen source. A mechanism focusing on catalytic cycle of arylboronic acid via a boron transfer was also proposed.
|
Meifeng Wang; Gan Zhu; Yiqun Li; Liuqun Gu
|
Organic Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Organocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-01-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e9f6f2b815cc80e39ccc6c/original/arylboronic-acids-catalyzed-upgrade-of-glucosamines-for-deoxyfructosazine-and-insights-on-reaction-mechanism.pdf
|
60c755d5bb8c1a154f3dc4c4
|
10.26434/chemrxiv.14171342.v1
|
Exploring the in Vitro Operating Window of Glycosyltransferase PtUGT1 from Polygonum Tinctorium for a Biocatalytic Route to Indigo Dye
|
The eobiotic compound indican lends itself to a compelling biocatalytic dyeing strategy for denim, in which the formation of corrosive by-products is avoided. However, the efficient and scalable production of indican remains a key bottleneck. This work focuses on the in vitro characterization of PtUGT1, a glycosyltransferase from Polygonum tinctorium that catalyzes the formation of indican via the glycosylation of indoxyl. Here, the buffer composition and enzyme concentration were identified as key parameters for enzyme activity and stability. The short lifetime of the enzyme under reaction conditions initiated an immobilization study. As a consequence, an amino-functionalized methacrylate resin was identified as a highly functional option for efficient immobilization of PtUGT1, allowing immobilization yields of > 98% for enzyme loadings up to 7.6 w-%. We further report a stabilization factor of 47 and significantly improved overall biocatalytic productivity. The straightforward handling and reuse of the described heterogeneous biocatalyst is demonstrated.
|
Philipp Petermeier; Cristina Fortuna; Kathrine M. Hübschmann; Gonzalo Nahuel Bidart Costoya; Thomas Tørring; David Tezé; Ditte Hededam Welner; Selin Kara
|
Bioorganic Chemistry; Natural Products; Organic Synthesis and Reactions; Biocatalysis; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755d5bb8c1a154f3dc4c4/original/exploring-the-in-vitro-operating-window-of-glycosyltransferase-pt-ugt1-from-polygonum-tinctorium-for-a-biocatalytic-route-to-indigo-dye.pdf
|
647ad85ebe16ad5c57636b44
|
10.26434/chemrxiv-2023-q8419-v2
|
VGAE-MCTS: a New Molecular Generative Model combining Variational Graph Auto-Encoder and Monte Carlo Tree Search
|
Molecular generation is crucial for advancing drug discovery, material design, and chemical exploration. It expedites the search for new drug candidates, facilitates tailored material creation, and enhances our understanding of molecular diversity. By employing artificial intelligence techniques, such as molecular generative models based on molecular graphs, researchers have tackled the challenge of efficiently molecules with desired properties. We proposed a new molecular generative model combining deep learning and reinforcement learning evaluated the validity, novelty, and optimized physicochemical properties of the generated molecules. Importantly, the model explored uncharted regions of chemical space, allowing for the efficient discovery and design of new molecules. This innovative approach has significant potential to revolutionize drug discovery, material science, and chemical research for accelerating scientific innovation. By leveraging advanced techniques and exploring previously unexplored chemical spaces, this study offers promising prospects for the efficient discovery and design of new molecules in the field of drug development.
|
Hiroaki Iwata; Taichi Nakai; Takuto Koyama; Shigeyuki Matsumoto; Ryosuke Kojima; Yasushi Okuno
|
Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems
|
CC BY 4.0
|
CHEMRXIV
|
2023-06-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647ad85ebe16ad5c57636b44/original/vgae-mcts-a-new-molecular-generative-model-combining-variational-graph-auto-encoder-and-monte-carlo-tree-search.pdf
|
6217523250b621c99cde6453
|
10.26434/chemrxiv-2022-33s1j
|
Synthesis, Structure and Thermal Properties of Volatile Group 11 Triazenides as Potential Precursors for Vapor Deposition
|
Group 11 thin films are desirable as interconnects in microelectronics. Although many M–N bonded Cu precursors have been explored for vapor deposition, there is currently a lack of suitable Ag and Au derivatives. Herein, we present monovalent Cu, Ag and Au 1,3-di-tert-butyltriazenides that have potential for use in vapor deposition. These compounds possess thermal stability and volatility that rival that of current state-of-the-art group 11 precursors with bidentate M–N bonded ligands. All compound sublime quantitatively between 120 and 130 °C at 0.5 mbar. Thermogravimetric analysis showed the Cu and Ag compounds both volatilized at ~200 °C with 0 and 2% residual mass, respectively. The Au triazenide showed two separated mass loss events at ~175 and 240 °C, and 35% residual mass. The crystal structure of the Cu compound showed a dimer, whilst the Ag and Au derivatives were tetrameric. Nuclear magnetic resonance spectroscopy showed dimers for the Cu and Au compounds and a dimer/tetramer equilibrium for the Ag compound. Electronic energies from density functional theory calculations confirmed dimeric preference for the Cu triazenide while Ag and Au preferred the tetrameric. However, all three compounds showed dimeric preference when accounting for entropy. Dimers are, therefore, expected to dominate in the gas phase for all three compounds during sublimation. Natural bond orbital analysis was used to identify orbital interactions important for the dimer/tetramer preference. Three factors were identified, in conjunction with strong metal-metal interactions, to increase the preference for rhombic tetramers.
|
Rouzbeh Samii; Anton Fransson; David Zanders; Atilla Varga; Sean Barry; Lars Ojamäe; Vadim Kessler; Nathan J. O'Brien
|
Inorganic Chemistry; Ligands (Inorg.); Transition Metal Complexes (Inorg.); Materials Chemistry; Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-02-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6217523250b621c99cde6453/original/synthesis-structure-and-thermal-properties-of-volatile-group-11-triazenides-as-potential-precursors-for-vapor-deposition.pdf
|
6453a2ab1ca6101a45c542a0
|
10.26434/chemrxiv-2023-7g4z2
|
Cobaltaelectro-Catalyzed C–H Annulation with Allenes for Atropochiral and P-stereogenic Compounds: Late-stage Diversification and Continuous Flow Scale up
|
The 3d metallaelectro-catalyzed C–H activation has been identified as an increasingly viable strategy to access valuable organic molecules in a sustainable fashion under exceedingly mild reaction conditions. However, the development of enantioselective 3d metallaelectro-catalyzed C–H activation is very challenging and in its infancy. Here, we disclose the merger of cobaltaelectro-catalyzed C–H activation with asymmetric catalysis for the highly enantioselective annulation of allenes. A broad range of C–N axially chiral and P-stereogenic compounds were thereby obtained in good yields of up to 98% with excellent enantioselectivities of up to >99% ee. The practicality of this approach was demonstrated by the diversification of complex bioactive compounds and drug molecules as well as decagram-scale enantioselective electrocatalysis in continuous flow.
|
Ye Lin; Tristan von Münchow; Lutz Ackermann
|
Catalysis; Electrocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2023-05-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6453a2ab1ca6101a45c542a0/original/cobaltaelectro-catalyzed-c-h-annulation-with-allenes-for-atropochiral-and-p-stereogenic-compounds-late-stage-diversification-and-continuous-flow-scale-up.pdf
|
62121ae2a6fb4da6df5c685a
|
10.26434/chemrxiv-2022-gn5fm
|
A Co-conformationally “Topologically” Chiral Catenane
|
As recognized in the early 1960s, catenanes composed of two achiral rings that are oriented (Cnh symmetry) as a result of the sequence of atoms they contain are topologically chiral. Here we present the first synthesis of a highly enantioenriched catenane containing a related but overlooked “co-conformationally ‘topologically’ chiral” stereogenic unit, which arises when a bilaterally symmetric Cnv ring is desymmetrised by the position of an oriented macrocycle.
|
Arnau Rodríguez-Rubio; Andrea Savoini; Florian Modicom; Patrick Butler; Stephen Goldup
|
Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry; Supramolecular Chemistry (Org.)
|
CC BY 4.0
|
CHEMRXIV
|
2022-02-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62121ae2a6fb4da6df5c685a/original/a-co-conformationally-topologically-chiral-catenane.pdf
|
645715b007c3f02937551966
|
10.26434/chemrxiv-2023-wgwn7
|
Template Synthesis to Solve the Unreachable Ortho C-H Func-tionalization Reaction of Iodobenzene
|
With the development of ortho C-H functionalization in Pd/NBE chemistry, the catalytic systems used are becoming increasingly complex. The increasingly complex catalytic systems may have created technical barri-ers for researchers in other fields to apply Pd/NBE chemical methods. This report describes the use of a simple Pd/NBE catalytic system to achieve ortho C-H oxylation and phosphonylation and other functionalization of iodobenzene through templated conversion reactions. The key point of this method is to explore the previous-ly unknown step of introducing dimethylamine in the ortho position of iodobenzene through C-H amination. Aryl dimethylamine is quickly converted to methyl quaternary ammonium salt precipitation, and methyl qua-ternary ammonium salt effectively avoids Hofmann elimination in the subsequent functionalization.
|
Bo-Sheng Zhang; Wan-Yuan Jia; Yi-Ming Wang; Svenja Warratz; Ze-Qiang Zhang; Xue-Ya Gou; Yong-Min Liang; Xi-Cun Wang; Zheng-Jun Quan; Lutz Ackermann
|
Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645715b007c3f02937551966/original/template-synthesis-to-solve-the-unreachable-ortho-c-h-func-tionalization-reaction-of-iodobenzene.pdf
|
6798e78b6dde43c908b7ced2
|
10.26434/chemrxiv-2025-2p0ln
|
High-yield prebiotic polymerization of 2’,3’-cyclic nucleotides under wet-dry cycling
|
The spontaneous formation of RNA polymers is one of the most crucial yet unsolved steps in the investigation of the origin of life. RNA oligomerization from nucleotide solutions has so far been reported only with low reactivity. Here we show that 2’,3’-cyclic nucleotides of all four nucleobases efficiently polymerize without external activators when dehydrated at room temperature in a mild alkaline pH range. Oligomerization yield, Y, and the polymer length further increase by wet-dry cycling, peaking at Y ≈ 70% in guanosine solutions and Y ≥ 20% for the other nucleobases when individually solubilized. Microscopy observation during drying indicates that the guanosine reactivity is enhanced over the other nucleobases by its self-assembly propensity. We show that at pH 11, a condition disfavoring guanosine structuring, polymerization in stoichiometrically balanced solution of the four nucleotides reaches Y = 36% and well distributed inclusion of nucleobases in the chains. The simplicity of the procedure, where only water is added at each cycle, makes this process a promising candidate for the prebiotic origin of RNA oligomers on early Earth.
|
Federico Caimi; Juliette Langlais; Francesco Fontana; Sreekar Wunnava; Tommaso Bellini; Dieter Braun; Tommaso Pietro FRACCIA
|
Physical Chemistry; Materials Science; Catalysis; Oligomers; Base Catalysis; Self-Assembly
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6798e78b6dde43c908b7ced2/original/high-yield-prebiotic-polymerization-of-2-3-cyclic-nucleotides-under-wet-dry-cycling.pdf
|
6683c79dc9c6a5c07a06adfb
|
10.26434/chemrxiv-2024-7dxzq
|
Asymmetric Syntheses of Aziridine-2-carboxylates via Reductive Kinetic Resolution of 2H-Azirines
|
Enantioenriched aziridine-2-carboxylates are valuable organic compounds thanks to their versatility as chiral building blocks. Several syntheses of bioactive molecules employ aziridine-2-carboxylates as a crucial synthetic intermediate, e.g. the total synthesis of dynobacin A. However, traditional strategies only access N-protected aziridines, which are poorly stable and can undergo unwanted side reactions as ring-opening. Herein, we present the first copper hydride kinetic resolution of racemic 2H-azirines for the asymmetric preparation of N-H aziridine-2-carboxylates and the corresponding enantioenriched 2H-azirines. This is relevant as N-H aziridine-2-carboxylates are a generally bench stable and easily diversifiable building block. After an extensive catalyst screening and reaction optimization, the N-H aziridines were obtained with excellent diastereoselectivity (>20:1) and high enantioselectivity (up to 94%). Additionally, we conducted a Hammett study and we observed a linear free energy relationship between the ΔΔG⧧ of the diastereomeric transition states and the σp- values.
|
Yinuo Zheng; Antonio Rizzo; Pauline Chiu
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Ligands (Organomet.); Transition Metal Complexes (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6683c79dc9c6a5c07a06adfb/original/asymmetric-syntheses-of-aziridine-2-carboxylates-via-reductive-kinetic-resolution-of-2h-azirines.pdf
|
633d17a40e3c6a1133343b20
|
10.26434/chemrxiv-2022-9d3z8
|
Translating Aqueous CO2 Hydrogenation Activity to Electrocatalytic Reduction with a Homogeneous Cobalt Catalyst
|
A molecular cobalt CO2 hydrogenation catalyst was explored for electrocatalytic CO2 reduction under aqueous conditions. The resulting pH-dependent selectivity between H2 and HCO2- is rationalized through thermodynamic analysis and stoichiometric experiments.
|
Xinran Wang; Jenny Yang
|
Inorganic Chemistry; Catalysis; Energy; Electrocatalysis; Homogeneous Catalysis; Fuels - Energy Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633d17a40e3c6a1133343b20/original/translating-aqueous-co2-hydrogenation-activity-to-electrocatalytic-reduction-with-a-homogeneous-cobalt-catalyst.pdf
|
644685e5df78ec5015511572
|
10.26434/chemrxiv-2023-71mjq-v2
|
Inverse design of metal-organic frameworks for direct air capture of CO2 via deep reinforcement learning
|
The combination of several interesting characteristics makes metal-organic frameworks (MOFs) a highly sought-after class of nanomaterials for a broad range of applications like gas storage and separation, catalysis, drug delivery, and so on. However, the ever-expanding and nearly infinite chemical space of MOFs makes it extremely challenging to identify the most optimal materials for a given application. In this work, we present a novel approach using deep reinforcement learning for the inverse design of MOFs, our motivation being designing promising materials for the important environmental application of direct air capture of CO2 (DAC). We demonstrate that the reinforcement learning framework can successfully design MOFs with critical characteristics important for DAC. Our top-performing structures populate two separate subspaces of the MOF chemical space: the subspace with high CO2 heat of adsorption and the subspace with preferential adsorption of CO2 from humid air, with few structures having both characteristics. Our model can thus serve as an essential tool for the rational design and discovery of materials for different target properties and applications.
|
Hyunsoo Park; Sauradeep Majumdar; Xiaoqi Zhang; Jihan Kim; Berend Smit
|
Theoretical and Computational Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Hybrid Organic-Inorganic Materials
|
CC BY 4.0
|
CHEMRXIV
|
2023-04-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644685e5df78ec5015511572/original/inverse-design-of-metal-organic-frameworks-for-direct-air-capture-of-co2-via-deep-reinforcement-learning.pdf
|
60c75781bdbb8994b8a3abf5
|
10.26434/chemrxiv.14411030.v1
|
On the Mechanism of Electrochemical Generation and Decomposition of Phthalimide N-oxyl (PINO)
|
Phthalimide <i>N</i>-oxyl (PINO)
is a potent hydrogen atom transfer (HAT) catalyst that can be generated
electrochemically from <i>N</i>-hydroxyphthalimide (NHPI). However, catalyst
decomposition has limited its application. This paper details mechanistic
studies of the generation and decomposition of PINO under electrochemical
conditions. Voltammetric data, observations from bulk electrolysis, and <a>computational</a> studies suggest two primary aspects.
First, base-promoted formation of PINO from NHPI occurs via multiple-site
concerted proton-electron transfer (MS-CPET). Second, PINO decomposition occurs
by at least two second-order paths, one of which is greatly enhanced by base. Optimal
catalytic efficiency in PINO-catalyzed oxidations occurs in the presence of
bases whose corresponding conjugate acids have <a>p<i>K</i><sub>a</sub></a>s in the range of 12-15,
which strike a balance between promoting PINO formation and minimizing its decay.
|
Cheng Yang; Luke Farmer; Derek Pratt; Stephen Maldonado; Corey Stephenson
|
Electrocatalysis; Organocatalysis; Redox Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75781bdbb8994b8a3abf5/original/on-the-mechanism-of-electrochemical-generation-and-decomposition-of-phthalimide-n-oxyl-pino.pdf
|
675131f6f9980725cf1cacd5
|
10.26434/chemrxiv-2024-kqrw0
|
Multigram Synthesis of 3-Azabicyclo[3.1.1]heptane Derivatives Including Bicyclic Thalidomide Analogs
|
An efficient approach to the multigram synthesis of 3-azabicyclo[3.1.1]heptanes is described. The method relied on the intramolecular imide formation in the properly 1,3-functionalized cyclobutane derivative. In turn, the latter compound was obtained via the diastereoselective Strecker reaction of readily accessible 3-oxocyclobutanecarboxylate. The resulting synthetic intermediate – 1-amino-3-azabicyclo[3.1.1]heptane-2,4-dione – was used to synthe¬size several monoprotected bicyclic diamines valuable as building blocks for medicinal chemistry, as well as a series of bridged analogs of Thalidomide, a known anticancer drug and a component of proteolysis-targeting chimeras (PROTACs).
|
Viacheslav Lysenko; Anton Portiankin; Oleh Shyshlyk; Timur Savchenko; Kostiantyn Nazarenko; Alexander Kostyuk; Oleksandr Golovchenko; Volodymyr Brovarets; Oleksandr Grygorenko
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY 4.0
|
CHEMRXIV
|
2024-12-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675131f6f9980725cf1cacd5/original/multigram-synthesis-of-3-azabicyclo-3-1-1-heptane-derivatives-including-bicyclic-thalidomide-analogs.pdf
|
64de36d201042bc1cc3548a9
|
10.26434/chemrxiv-2023-clnp1-v2
|
Cu-OFF/ERI zeolite: Intergrowth structure synergistically boosting NH3-SCR performance
|
Cu-SSZ-13 zeolite has been commercialized for selective catalytic reduction with ammonia (NH3-SCR) to remove NOx from diesel exhaust. As its synthesis usually requires toxic and costly organic templates, the discovery of alternative Cu-based zeolite catalysts with organotemplate-free synthesis and comparable or even superior NH3-SCR activity to Cu-SSZ-13 is of great academic and industrial significance. Herein, we, for the first time, demonstrated that the Cu-T catalyst with an intergrowth structure of offretite (OFF) and erionite (ERI) synthesized with organotemplate-free method showed better catalytic performance than Cu-ERI and Cu-OFF as well as Cu-SSZ-13. Structure characterizations and density functional theory (DFT) calculations indicated that the intergrowth structure promoted more isolated Cu2+ located at 6MR of intergrowth interface, resulting in a better hydrothermal stability of Cu-T than Cu-ERI and Cu-OFF. Strikingly, the low-temperature activity of Cu-T significantly increased after hydrothermal aging, while that of Cu-ERI and Cu-OFF substantially decreased. On the basis of in situ diffuse reflectance infrared Fourier transform spectra (DRIFTS) analysis and DFT calculations, the reason can be attributed to that the NH4NO3 formed on the CuxOy species within ERI polymorph of Cu-T underwent fast SCR reaction pathway with the assistance of Brønsted acid sites at the intergrowth interfaces under standard SCR reaction conditions. Significantly, Cu-T exhibited a wider temperature window at a catalytic activity over 90% than Cu-SSZ-13 (175 − 550 ℃ vs. 175 − 500 ℃ for fresh and 225 − 500 ℃ vs. 250 − 400 ℃ for hydrothermal treatment). This work provides a new direction for the design of high-performance NH3-SCR catalysts in terms of the interplay of intergrowth structure of zeolites.
|
Jinfeng Han; Junyan Li; Wenru Zhao; Lin Li; Mengyang Chen; Xin Ge; Sen Wang; Qingling Liu; Donghai Mei; Jihong Yu
|
Catalysis; Nanocatalysis - Reactions & Mechanisms; Redox Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64de36d201042bc1cc3548a9/original/cu-off-eri-zeolite-intergrowth-structure-synergistically-boosting-nh3-scr-performance.pdf
|
61dffa8f77a41672eccf8dcc
|
10.26434/chemrxiv-2022-vrsfr
|
Transition metal and radical free 1,2-dicarbofunctionalisation of 1,1-arylboryl alkenes through dual C(sp3)-C(sp3) bond formation
|
We reveal here the regioselective nucleophilic addition of C(sp3) to 1,1-arylboryl alkenes, followed by nucleophilic attack of the alpha-boryl carbanionic intermediates to C(sp3) electrophiles, at room temperature. We envisioned this goal through engaged C(sp3) chemical entities avoiding metal catalysts, additives, radical initiators or specific irradiation. This multicomponent reaction guarantees that the new tetrasubstituted carbon formed retains all the C atoms from the three starting materials involved in the assembly.
|
Elena Fernandez; Oriol Salvado; Sara Gonzalez
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61dffa8f77a41672eccf8dcc/original/transition-metal-and-radical-free-1-2-dicarbofunctionalisation-of-1-1-arylboryl-alkenes-through-dual-c-sp3-c-sp3-bond-formation.pdf
|
613ad21f42198ed2c57232b0
|
10.26434/chemrxiv-2021-pzp5m
|
Optoelectronic and elastic response of fluorinated hexagonal boron nitride monolayer
|
The inherited insulating behavior of hexagonal boron nitride (h-BN) monolayer restricts its application in several optoelectronic devices, so finding a technique to reduce the bandgap allows it to possess
the semiconducting functionality. Here, an experimentally feasible fluorinated hexagonal boron
nitride (FBNF), a structurally, dynamically, and mechanically stable monolayer is reported by using
density functional theory calculations. The significant geometrical transformation from planer h-BN
to buckled FBNF softens the structure by retaining the mechanical isotropy and structural symmetry.
Remarkably, the induced direct bandgap semiconducting behavior after fluorination enhances the
optical absorbance and reflectivity reduces energy loss, creates strong optical anisotropy, and makes
FBNF monolayer is a proper material in the optoelectronic and nanomechanical applications
|
Shambhu Bhandari Sharma
|
Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2021-09-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613ad21f42198ed2c57232b0/original/optoelectronic-and-elastic-response-of-fluorinated-hexagonal-boron-nitride-monolayer.pdf
|
60c757a6f96a0045f9288ce3
|
10.26434/chemrxiv.14444315.v1
|
SnO2 -SiO2 1D Core-Shell Nanowires Heterostructures for Selective Hydrogen Sensing
|
SnO2 is one of the most employed n-type semiconducting metal oxide (SMOX) in chemo-resistive gas-sensing although it presents serious limitations due to a low selectivity. Herein, we introduce one-dimensional (1D) SnO2-SiO2 core-shell nanowires (CSNWs). SnO2 nanowires (NWs) are synthesized by vapor–liquid–solid deposition and the amorphous SiO2-shell layer with varying thicknesses (1.8-10.5 nm) was grown by atomic layer deposition (ALD). SiO2-coated SnO2 CSNWs show lower baseline conductance as compared to the Pristine SnO2 NWs, due to an enhancement of the electron depletion layer. The SnO2-SiO2/N CSNWs (N representing the number of SiO 2 ALD cycles) sensors show a dramatic improvement of the selectivity towards hydrogen. Moreover, the sensing-response markedly depends on the thickness of the SiO2-shell layer and the working temperature. The SnO2-SiO2/60 CSNWs sensor (ca. 4.8 nm SiO2 shell thickness) was the best performing sensor in terms of selectivity and sensitivity exhibiting a response of 160 (ca. 7-folds higher than the pristine SnO2 NWs) towards 500 ppm of hydrogen at 500 °C with a lower detection limit at ppb-level (0.082 ppm). The selectivity and enhanced sensing-response are related to the masking effect of the SiO2 shell and an increased in the width of the electron depletion layer due to the strong electronic coupling between the SnO2 core and SiO2-shell layer, respectively. The remarkable sensing performances of the SnO2-SiO2/N CSNWs can be attributed to the homogeneous and conformal SiO2 shell layer by ALD,<br />electronic coupling between the core and the shell, the optimized shell thickness and high surface area provided by the 1D SnO2 NWs network.<br />
|
Muhammad Hamid Raza; Navpreet Kaur; Elisabetta Comini; Nicola Pinna
|
Nanostructured Materials - Materials; Sensors; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757a6f96a0045f9288ce3/original/sn-o2-si-o2-1d-core-shell-nanowires-heterostructures-for-selective-hydrogen-sensing.pdf
|
654b4f5e2c3c11ed71f510ac
|
10.26434/chemrxiv-2023-r9s9h-v2
|
Photochemical H2 Activation by an Zn–Fe Heterometallic:
A Mechanistic Investigation
|
Addition of H2 to a Zn–Fe heterometallic complex was observed to occur under photochemical conditions (390 or 428 nm LED) and leads to the formation of the corresponding metal dihydride. The reaction does not occur under thermal conditions and DFT calculations suggest this is an endergonic, light driven process. Through a combined experimental and computational approach, the plausible mechanisms for H2 activation were investigated. Inhibition experiments, double-label cross-over experiments, radical trapping experiments, EPR spectroscopy and DFT calculations were used to gain insight into this system. The combined data are consistent with two plausible mechanisms, the first involving ligand dissociation followed by oxidative addition of H2 at the Fe centre, the second involving homolytic fragmentation of the Zn–Fe heterometallic and formation of radical intermediates.
|
Marina Perez-Jimenez; Mark Crimmin
|
Inorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions; Main Group Chemistry (Inorg.); Transition Metal Complexes (Inorg.)
|
CC BY 4.0
|
CHEMRXIV
|
2023-11-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654b4f5e2c3c11ed71f510ac/original/photochemical-h2-activation-by-an-zn-fe-heterometallic-a-mechanistic-investigation.pdf
|
60c75068f96a008e82287e0f
|
10.26434/chemrxiv.13037993.v1
|
crystIT: Complexity and Configurational Entropy of Crystal Structures via Information Theory
|
<div>The information content of a crystal structure as conceived by information theory has recently proved as an intriguing approach to calculate the complexity of a crystal structure within a consistent concept. Given the relatively young nature of the field, theory development is still at the core of on-going research efforts. In this work we provide an update to the current theory, improving the formulas that evaluation of crystal structures with partial occupancies as frequently found in disordered system is feasible. To encourage wider application and further theory development we incorporate the updated formulas in crystIT (crystal structure & Information Theory), an open-source python-based program that allows for calculating various complexity measures of crystal structures based on a standardized *.cif file.</div>
|
Clemens Kaußler; Gregor Kieslich
|
Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75068f96a008e82287e0f/original/cryst-it-complexity-and-configurational-entropy-of-crystal-structures-via-information-theory.pdf
|
66218797418a5379b0227097
|
10.26434/chemrxiv-2024-5kkhf
|
Charge and spin transfer dynamics in a weakly coupled porphyrin dimer
|
The dynamics of electron and spin transfer in the radical cation and photogenerated triplet states of a tetramethylbiphenyl-linked zinc-porphyrin dimer were investigated, so as to test the relevant parameters for the design of a single-molecule spin valve, and the creation of a novel platforms for the photogeneration of high-multiplicity spin states. We used a combination of multiple techniques, including variable-temperature continuous wave EPR, pulsed proton electron–nuclear double resonance (ENDOR), transient EPR, and optical spectroscopy. The conclusions are further supported by density functional theory (DFT) calculations, and comparison to reference compounds. The low-temperature cw-EPR and room-temperature near-IR spectra of the dimer monocation demonstrate that the radical cation is spatially localized on one side of the dimer at any point in time, while the EPR spectra at 298 K reveal rapid hopping of the radical spin density between both sites of the dimer via reversible intramolecular electron transfer. The hyperfine interactions are modulated by electron transfers and can be quantified using ENDOR spectroscopy. This allowed simulation of the variable- temperature cw-EPR spectra with a two-site exchange model and provided information on the temperature-dependence of the electron transfer rate. The electron-transfer rates range from about 10.0 MHz at 200 K to about 53.9 MHz at 298 K. The activation enthalpies ∆‡H of the electron transfer were determined as ∆‡H = 9.55 kJ mol−1 and ∆‡H = 5.67 kJ mol−1 in a 1:1:1 solvent mixture of CD2Cl2:toluene-d8:THF-d8 and in 2-methyltetrahydrofuran, respectively, consistent with a Robin–Day class II mixed-valence compound. Investigation of the spin-density distribution of the photogenerated triplet state of the Zn-porphyrin dimer reveals localization of the triplet-spin density on a nanosecond time scale on one half of the dimer at 20 K in 2-methyltetrahydrofuran and at 250 K in a polyvinylcarbazole film. We highlight how these results impact the design of single-molecule spintronic devices, quantifying fundamental parameters for relevant building blocks, and offer the first step towards a novel platforms for photogenerated high-multiplicity spin states.
|
Sebastian Kopp; Ashley Redman; Igor Roncevic; Lisa Schröder; Lapo Bogani; Harry Anderson; Christiane Timmel
|
Physical Chemistry; Organic Chemistry; Nanoscience; Nanodevices; Chemical Kinetics; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66218797418a5379b0227097/original/charge-and-spin-transfer-dynamics-in-a-weakly-coupled-porphyrin-dimer.pdf
|
646def11be16ad5c57d53e19
|
10.26434/chemrxiv-2023-zt1r3-v3
|
Charged Chiral Derivatization for Enantioselective Imaging of D-, L-2-Hydroxyglutaric Acid Using Ion Mobility Spectrometry/Mass Spectrometry
|
A newly synthesized charged chiral tag enabled enantioselective imaging of D-, L-2-hydroxyglutaric acid, which are independently associated with the regulation of DNA methylation. The tag-conjugated diastereomers were ionized efficiently through MALDI, separated by ion mobility spectrometry, and further separated from other molecules in mass spectrometry. On-tissue chiral derivatization using the tag facilitated the visualization of different distributions of the two isomers in the mouse testis.
|
Eiji Sugiyama; Yuki Nishiya; Kenji Yamashita; Ryo Hirokawa; Yoshiteru Iinuma; Takashi Nirasawa; Hajime Mizuno; Yoshitaka Hamashima; Kenichiro Todoroki
|
Analytical Chemistry; Imaging; Mass Spectrometry; Separation Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646def11be16ad5c57d53e19/original/charged-chiral-derivatization-for-enantioselective-imaging-of-d-l-2-hydroxyglutaric-acid-using-ion-mobility-spectrometry-mass-spectrometry.pdf
|
6734c52b5a82cea2fa02902a
|
10.26434/chemrxiv-2024-xwcv5
|
Looking at High-Pressure Electrides Through the Lens of Quantum Crystallography: The Case of Simple Cubic Calcium
|
High-pressure electrides (HPEs) represent a unique class of materials characterized by the localization of electrons in non-bonding interstitial regions, distinct from typical atom-atom interactions. This study delves into the properties of calcium in its simple cubic (sc) phase (Ca-sc) under extreme pressure, a candidate for exhibiting HPE behavior. Through quantum crystallography (QCr), we meticulously analyze the electron density and bonding nature of Ca-sc at pressures up to 40 GPa. Our theoretical framework reveals a pressure-induced electronic transition from s- to d-character, resulting in the formation of multi-center bonds (MCBs) within Ca8 clusters. The topological analysis corroborates the existence of non-nuclear maxima (NNM) and electron localization features indicative of HPEs. These findings underscore the efficacy of QCr techniques in elucidating material behavior under extreme conditions, thereby establishing a pathway for experimental validation of HPEs like Ca-sc.
|
Stefano Racioppi; Eva Zurek
|
Theoretical and Computational Chemistry; Materials Science; Inorganic Chemistry; Bonding; Solid State Chemistry; Crystallography – Inorganic
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6734c52b5a82cea2fa02902a/original/looking-at-high-pressure-electrides-through-the-lens-of-quantum-crystallography-the-case-of-simple-cubic-calcium.pdf
|
60c758a0337d6c942ee29285
|
10.26434/chemrxiv.14458962.v2
|
On the Estimation of the Molecular Inaccessible Volume and the Molecular Accessible Surface of a Ligand in Protein Ligand Systems
|
<p>
In
this work, a novel approach is proposed based on the accurate
computation of a protein’s inaccessible volume as regards to a
ligand, plus the corresponding surface area, where the ligand can be
placed in order to “touch” the protein without any overlaps. The
proposed approach can be thought as an extension of the widely used
concept of the Solvent-Accessible Surface Area (SASA), evaluating the
surface generated by the ligand while being rolled over all the atoms
of the protein without penetrating them. Identification of the
inaccessible volume of each candidate protein-ligand pair is also
provided in the context of this study, along with the boundary
surface where the ligand can be placed so as to be in “contact”
with the protein, which is expected to significantly enhance the
ability to investigate specific protein drug interactions.</p>
|
Konstantinos Konstantinidis; Ioannis Karakasiliοtis; Kostas Anagnostopoulos; Georgios Boulougouris
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758a0337d6c942ee29285/original/on-the-estimation-of-the-molecular-inaccessible-volume-and-the-molecular-accessible-surface-of-a-ligand-in-protein-ligand-systems.pdf
|
6764037581d2151a02353be8
|
10.26434/chemrxiv-2024-07bbb-v2
|
Biogenic Aluminium-Potassium Hybrid Nanoparticles: Synthesis, Characterisation, and Antimicrobial Efficacy Against Multi-Drug Resistant Clinical Isolates of Staphylococcus Aureus, Salmonella Spp., And Streptococcus Spp.
|
The synthesis, characterization, and antimicrobial efficacy of biogenic aluminium-potassium hybrid nanoparticles (Pl-Al/KNPs) synthesized using Polyalthia longifolia leaf extract are presented. Aluminium chloride and potassium chloride were used as precursors, and the green synthesis approach leveraged the phytochemicals in P. longifolia for capping and stabilizing the nanoparticles. A significant colour change during the synthesis, attributed to Surface Plasmon Resonance (SPR), confirmed nanoparticle formation. Characterization using ATR-FTIR spectroscopy revealed the involvement of functional groups such as hydroxyl (-OH), carbonyl (-C=O), and phenolic (-C-OH) groups, which played crucial roles in reducing metal ions and stabilizing the nanoparticles. SEM micrographs indicated that the nanoparticles were predominantly spherical with sizes ranging from 70 to 103 nm. Slight agglomeration and non-uniform distribution were observed, likely due to the natural variability in phytochemical composition. EDX analysis confirmed the elemental composition of the nanoparticles, with aluminium (49.11%) and potassium (24.99%) as the primary constituents, along with trace elements like magnesium, silicon, and calcium, enhancing the stability and functionality of the nanoparticles. The antimicrobial efficacy of Pl-Al/KNPs was evaluated against multi-drug-resistant clinical isolates of Staphylococcus aureus, Salmonella spp., and Streptococcus spp. using the Kirby-Bauer disk diffusion method. Pl-Al/KNPs exhibited significant zones of inhibition: Staphylococcus aureus (18.5 mm), Salmonella spp. (16.8 mm), and Streptococcus spp. (17.3 mm), outperforming the zones observed with P. longifolia extract alone. These findings underscore the potential of Pl-Al/KNPs as eco-friendly antimicrobial agents, relevant for combating drug-resistant pathogens and advancing sustainable nanotechnology for healthcare applications.
|
Mathew Gideon; Nathan Aliyu Dikko
|
Biological and Medicinal Chemistry; Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Drug Discovery and Drug Delivery Systems
|
CC BY 4.0
|
CHEMRXIV
|
2024-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6764037581d2151a02353be8/original/biogenic-aluminium-potassium-hybrid-nanoparticles-synthesis-characterisation-and-antimicrobial-efficacy-against-multi-drug-resistant-clinical-isolates-of-staphylococcus-aureus-salmonella-spp-and-streptococcus-spp.pdf
|
676ccfbe6dde43c90857c4b5
|
10.26434/chemrxiv-2024-35f9j-v3
|
Chatbot-Assisted Quantum Chemistry for Explicitly Solvated Molecules
|
Advanced computational chemistry software packages have transformed chemical research by leveraging quantum chemistry and molecular simulations. Despite their capabilities, the complicated design and requirement for specialized computing hardware hinder their applications in the broad chemistry community. Here, we introduce AutoSolvateWeb, a chatbot-assisted computational platform that addresses both challenges simultaneously. This platform employs a user-friendly chatbot interface to guide non-experts through a multistep procedure involving various computational packages, enabling them to configure and execute complex quantum mechanical/molecular mechanical (QM/MM) simulations of explicitly solvated molecules. Moreover, this platform operates on cloud infrastructure, allowing researchers to run simulations without prerequisite computing hardware. As a proof of concept, AutoSolvateWeb demonstrates that combining virtual agents with cloud computing can democratize access to sophisticated computational research tools.
|
Rohit S. K. Gadde; Sreelaya Devaguptam; Fangning Ren; Rajat Mittal; Lechen Dong; Yao Wang; Fang Liu
|
Theoretical and Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676ccfbe6dde43c90857c4b5/original/chatbot-assisted-quantum-chemistry-for-explicitly-solvated-molecules.pdf
|
65b545499138d23161defe2a
|
10.26434/chemrxiv-2024-crzn6
|
Detection of chemometric-guided biomarkers associated with alcohol consumption in mice liver tissue using infrared spectroscopy
|
Among the leading contributors to fetal alcohol spectrum disorder (FASD), perinatal alcohol usage is characterized by neurodevelopmental dysfunction and growth retardation. This study aims to determine spectroscopic biomarkers referring to the results of early postnatal exposure to alcohol in the liver of newborn mice. The samples were divided into three groups: Negative control group, gavage control group (positive control), and group with gavage + alcohol which is treated between postnatal days (PD) 3 and 20 with 3.0 g/kg body weight of ethanol in a liter of artificially enhanced milk (.02 ml/g). After the decapitation of mice, liver tissues were removed and infrared data were obtained using Fourier Transform Infrared (FTIR) Spectroscopy. Spectral data was analyzed and evaluated using normalization, principal component analysis (PCA), and hierarchical cluster analysis (HCA). Possible chemometric biomarkers detected in this study are related to the lipids and found as follows: 2960 cm−1, 2873 cm−1, 1454 cm−1, and 1398 cm−1. According to the results of this study, it can be proposed that FTIR is an effective tool for the detection of chemometric-guided biomarkers related to the consequences of early postnatal alcohol consumption on female rats.
|
Arwa Dahham Qadawee; Ali Forat Algburi; Şebnem Garip Ustaoğlu; İlknur Dursun; Hakan Kaygusuz
|
Biological and Medicinal Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b545499138d23161defe2a/original/detection-of-chemometric-guided-biomarkers-associated-with-alcohol-consumption-in-mice-liver-tissue-using-infrared-spectroscopy.pdf
|
60c73e5b0f50db7f8239564b
|
10.26434/chemrxiv.6959627.v1
|
Dissolution and Performing Homogeneous Photocatalysis of Polymeric Carbon Nitride
|
<a></a><a>As a metal-free conjugated polymer, carbon
nitride (CN) has attracted tremendous attention as heterogeneous
(photo)catalysts. </a><a></a><a>By
following prototype of enzymes, making all catalytic sites of accessible via
homogeneous reactions is a promising approach toward maximizing CN activity,
but hindered
due to </a><a></a><a>the poor insolubility
of CN</a>.
Herein, we report the dissolution of CN in environment-friendly methane sulfonic
acid and the homogeneous photocatalysis driven by CN for the first time with
the activity boosted up to 10-times, comparing to the heterogeneous
counterparts. Moreover, facile recycling and reusability, the <a>hallmark</a> of heterogeneous catalysts, were kept
for the homogeneous CN photocatalyst via reversible precipitation using poor
solvents. It opens new vista of CN in homogeneous catalysis and offers a
successful example of polymeric
catalysts in bridging gaps of homo/heterogeneous catalysis.
|
Chaofeng Huang; Jing Wen; Yanfei Shen; Fei He; Li Mi; Ziyu Gan; Jin Ma; Songqin Liu; Haibo Ma; Yuanjian Zhang
|
Polymers; Heterogeneous Catalysis; Homogeneous Catalysis; Photocatalysis; Solution Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-08-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e5b0f50db7f8239564b/original/dissolution-and-performing-homogeneous-photocatalysis-of-polymeric-carbon-nitride.pdf
|
6690e02801103d79c5cb42f9
|
10.26434/chemrxiv-2024-1lbpg-v2
|
Automated Analysis of Interfaces, Interactions and Self-Assembly in Soft Matter Simulations
|
Molecular dynamics simulations have become an essential tool in the study of soft matter and biological macromolecules. The large amount of high-dimensional data produced by such simulations does not immediately elucidate the atomistic mechanisms that underlie complex materials and molecular processes. Analysis of these simulations is complicated: the dynamics intrinsic to soft matter simulations necessitates careful application of specific, and often complex, algorithms to extract meaningful molecular scale understanding. There is an ongoing need for high-quality, automated computational workflows to facilitate this analysis in a reproducible manner with minimal user input. In this work, we introduce a series of molecular simulation analysis tools for investigating interfaces, molecular interactions (including ring-ring stacking), and self-assembly. In addition, we include a number of auxiliary tools, including a useful function to unwrap molecular structures that are greater than half the length of their corresponding simulation box. These tools are contained in the PySoftK software package, making application of these algorithms straightforward for the user. These new simulation analysis tools within PySoftK will support high-quality, reproduce analysis of soft matter and biomolecular simulations to bring about new predictive understanding in nano- and biotechnology.
|
Raquel Lopez-Rios de Castro; Alejandro Santana-Bonilla; Robert M. Ziolek; Christian D. Lorenz
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Materials Science; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2024-07-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6690e02801103d79c5cb42f9/original/automated-analysis-of-interfaces-interactions-and-self-assembly-in-soft-matter-simulations.pdf
|
61d6f14ea16050881495f3c2
|
10.26434/chemrxiv-2022-cj4cz
|
Revisiting the Assignment of Innocent and Non-Innocent Counter ions in Lanthanide(III) Solution Chemistry
|
Lanthanides are found in critical applications from display technology to renewable energy. Often these rare earth elements are used as alloys or functional materials, yet the access to them are trough solution processes. In aqueous solution the rare earths are found predominantly as trivalent ions and charge balance dictates that counter ions are present. The fast ligand exchange and lack of directional bonding in lanthanides complexes has led to questions regarding the speciation of Ln3+ solvates in the presence of various counter ions, and to the distinction between innocent = non-coordinating, and non-innocent = coordinating counter ions. There is limited agreement as to which counter ions that belong to each group, which lead to this report. By using Eu3+ luminescence, it was possible to clearly distinguish between coordinating and non-coordinating ions. To interpret the results it was required to bridge the descriptions of ion pairing and coordination. The da-ta—in form of Eu3+ luminescence spectra and luminescence lifetimes from solutions with varying concentrations of acetate, chloride, nitrate, fluoride, sulfate, perchlorate and triflate—were contrasted to those obtained with ethylenediaminetet-raaceticacid (EDTA), which allowed for the distinction between three Ln3+-anion interaction types. It was possible to con-clude which counter ions are truly innocent (e.g. ClO4- and OTf-), and which clearly coordinate (e.g. NO3- and AcO-). Finally, the considerate amount of data from systems studied under similar conditions allowed the minimum perturbation arising from inner sphere or outer sphere coordination in Eu3+ complexes to be identified.
|
Nicolaj Kofod; Maria Storm Thomsen; Patrick Nawrocki; Thomas Just Sørensen
|
Physical Chemistry; Inorganic Chemistry; Lanthanides and Actinides; Spectroscopy (Inorg.); Solution Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-01-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d6f14ea16050881495f3c2/original/revisiting-the-assignment-of-innocent-and-non-innocent-counter-ions-in-lanthanide-iii-solution-chemistry.pdf
|
64cc1525dfabaf06ffa78c13
|
10.26434/chemrxiv-2023-jm56l
|
Synthesis of Secondary Amines via Self-Limiting Alkylation of N-Aminopyridinium Salts
|
Partial amine alkylation to prepare secondary amines is challenging due to the enhanced N-nucleophilicity that accompanies alkylation. Here we introduce N-aminopyridinium salts as ammonia surrogates for the synthesis of secondary amines via self-limiting alkylation chemistry. A one-pot protocol based on N-aminopyridinium arylation followed by N-alkylation and in situ depyridylation provides access to aryl alkyl amines. The method is compatible with complex molecular settings and overcomes classical challenges in selective amine alkylation by accomplishing alkylation via transient pyridinium ylide intermediates. These findings both establish N-aminopyridinium salts as ammonia synthons and provide a new disconnection for the construction of structurally complex secondary amines.
|
Pritam Roychowdhury; Saim Waheed; Uddalak Sengupta; Roberto Herrera; David Powers
|
Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64cc1525dfabaf06ffa78c13/original/synthesis-of-secondary-amines-via-self-limiting-alkylation-of-n-aminopyridinium-salts.pdf
|
657b0e8766c13817292aa275
|
10.26434/chemrxiv-2023-t5jp6
|
Chemical Micromotors Move Faster at Oil-Water Interfaces
|
Many real-world scenarios involve interfaces, particularly liquid-liquid interfaces, that can fundamentally al-ter the dynamics of colloids. This is poorly understood for chemically active colloids that release chemicals into their environment. We report here the surprising discovery that micromotors—colloids that convert chemical fuels into self-propulsion—move significantly faster at an oil-water interface than on a glass substrate. Typical speed increases ranged from 3-6 times up to an order of magnitude, and were observed for different types of chemical motors or oils. Such speed increases are likely caused by faster chemical reactions at an oil-water interface than a glass-water interface, but the exact mechanism remains unknown. Our results provide valuable insights into the complex interactions between chemical micromotors and their environments, which are important for applications in the human body or in the removal of organic pollutants from water. In addi-tion, this study also suggests that chemical reactions occur faster at an oil-water interface, and that micromo-tors can serve as a probe for such an effect.
|
Jiayu Liu; Zhou Yang; Zuyao Yan; Shifang Duan; Xiaowen Chen; Donghao Cui; Dezhou Cao; Ting Kuang; Xing Ma; Wei Wang
|
Physical Chemistry; Nanoscience; Interfaces; Transport phenomena (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657b0e8766c13817292aa275/original/chemical-micromotors-move-faster-at-oil-water-interfaces.pdf
|
60c7582b9abda28872f8e87d
|
10.26434/chemrxiv.14515845.v1
|
An Investigation of Five Component [3+2] Self-Assembled Cage Formation Using amidinium...carboxylate Hydrogen Bonds
|
The assembly of hydrogen bonded cages using amidinium∙∙∙carboxylate hydrogen bonding interactions was
investigated. A new tris-amidinium hydrogen bond donor tecton based on a tetraphenylmethane scaffold was
prepared and its self–assembly with the terephthalate anion studied, and a new tricarboxylate hydrogen bond
acceptor tecton was synthesized and its assembly with the 1,3-benzenebis(amidinium) hydrogen bond donor
explored. In both cases, molecular modelling indicated that the formation of the cages was geometrically feasible
and 1H NMR spectroscopic evidence was consistent with interactions between the components in competitive d6-
DMSO solvent mixtures. DOSY NMR spectroscopy of both systems indicated that both components diffuse at the
same rate as each other, and diffusion coefficients were consistent with cage formation, and with the formation of
assemblies significantly larger than the individual components. An X-ray crystal structure showed that one of the
assemblies did not have the desired cage structure in the solid state
|
Chriso Thomas; Emer Foyle; Samuel Walker; Nicholas White
|
Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7582b9abda28872f8e87d/original/an-investigation-of-five-component-3-2-self-assembled-cage-formation-using-amidinium-carboxylate-hydrogen-bonds.pdf
|
65caebfa66c138172982def4
|
10.26434/chemrxiv-2024-v9lhr
|
N-Heterocyclic carbene-catalyzed silicon-free sulfur fluoride exchange reactions of sulfonimidoyl fluorides
|
As the monoaza analogous of sulfonates and sulfonamides, sulfonimidate ester and sulfonimidamide have attracted growing attention in recent years. In this paper. We report an organocatalytic silicon-free sulfur fluoride exchange (SuFEx) reaction of sulfonimidoyl fluorides for the synthesis of these valuable organosulfurs. Under the catalysis of 10 mol% N-heterocyclic carbene (NHC), and MS 4Å, sulfonimidoyl fluorides reacted with phenols to produce sulfonimidate esters in 55-99% yields. In addition, under the relay catalysis of 10 mol% NHC and HOBt, various amines coupled with sulfonimidoyl fluorides to give sulfonimidamides in 55-99% yields.
|
Muze Lin; Yu Xie; Shuangjun Li; Zhihua Cai; Lin He; Guangfen Du
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Organocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2024-02-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65caebfa66c138172982def4/original/n-heterocyclic-carbene-catalyzed-silicon-free-sulfur-fluoride-exchange-reactions-of-sulfonimidoyl-fluorides.pdf
|
664825c221291e5d1d94581b
|
10.26434/chemrxiv-2024-3x7wm
|
Antibacterial and antileishmanial activity of 1,4-dihydropyridine derivatives
|
We have synthesized twenty-three 1,4-dihydropyridine derivatives (1,4-DHPs) by using a microwave-assisted one-pot multicomponent Hantzsch reaction and evaluated their antibacterial activity against a representative panel of cariogenic bacteria and their in vitro antileishmanial activity against Leishmania (L.) amazonensis promastigotes. Thirteen compounds were moderately active against Streptococcus sanguinis, Streptococcus mitis, and Lactobacillus paracasei. Compound 22 (diethyl 4-(3-methoxy-4-hydroxyphenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate) displayed moderate antibacterial activity against S. mitis and S. sanguinis, with a Minimum Inhibitory Concentration (MIC) of 500 µg/mL); compounds 8 (diethyl 4-(3-chlorophenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate ) and 10 (diethyl 4-(3-nitrophenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate) were moderately active against S. sanguinis (MIC = 500 µg/mL) and very active against L. amazonensis promastigotes (IC50 = 43.08 and 34.28 µM, respectively). Among the eight 1,4-DHPs that were active (IC50 < 50 µM) against L. amazonensis promastigotes, compound 13 (diethyl 4-(3,4,5-trimethoxyphenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate) gave the lowest IC50 (24.62 µM). On the basis of our results, asymmetric 1,4-DHPs derived from dimedone exhibit antileishmanial potential.
|
Thaís Oliveira; Jackson Silva; Nagela Silva; Paulo Félix; Andreia Oliveira; Carlos Martins; Lizandra Magalhães; Antônio Crotti
|
Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems; Microbiology
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-05-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664825c221291e5d1d94581b/original/antibacterial-and-antileishmanial-activity-of-1-4-dihydropyridine-derivatives.pdf
|
60c75781702a9bc34f18caea
|
10.26434/chemrxiv.14371916.v2
|
Quercetin Induces Lipid Domain-Dependent Permeability
|
In this work, we present our results on quercetin interaction with distinct model membranes exploring the importance of lipid phases, ld, ld/lo and ld+lo+so, to the action of this flavonoid in bilayers and possibly contributing to clarifying some controversial aspects related to quercetin multiple activities. We found out that quercetin is able to increase membrane permeability in a manner dependent on the presence and characteristics of lipid domains. In the presence of sphingomyelin, we found the greatest increase in mean membrane permeability (at least 10 times higher than the other lipid compositions). We also observed the presence of micrometric domains whose shape and size were disturbed by the action of quercetin. The presence of cholesterol increased membrane rigidity. This effect was enhanced with the presence of quercetin, but for chol-sphingomyelin combination, the bilayers became more flaccid at low quercetin/lipid proportions (< 1/5) and moderately rigid at proportions of the 1/1 order. The affinity parameters were higher for the most homogeneous systems and with larger areas and extensions of disordered liquid phase than for those systems of higher heterogeneity.
|
Natalia Slade; Danubia Batista Martins; Marcia P. dos Santos Cabrera
|
Biophysics; Cell and Molecular Biology; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75781702a9bc34f18caea/original/quercetin-induces-lipid-domain-dependent-permeability.pdf
|
677583c76dde43c908ffe86b
|
10.26434/chemrxiv-2024-bf4n8-v2
|
Martini 3 building blocks for Lipid Nanoparticle design
|
Lipid nanoparticles (LNPs) represent a promising platform for advanced drug and gene delivery, yet optimizing these particles for specific cargos and cell targets poses a complex, multifaceted challenge. Furthermore, there is a pressing need for a more comprehensive understanding of the underlying technology. Experimental studies are costly and often provide low-resolution information. Molecular dynamics (MD) simulations allow us to study these particles at a higher resolution, enhancing our understanding. However, studying these systems at atomic resolutions is both challenging and computationally expensive, as well as time-consuming. Coarse-grained (CG) models, such as Martini 3, are positioned as promising tools for studying LNPs. To enable CG-MD studies of LNPs, accurate and validated models of their components are needed. Here, we present a substantial extension of the Martini 3 library of lipids, covering the most important LNP components, including over a hundred of ionizable lipid (IL) models, along with natural occurring sterol models and PEGylated lipid models. We furthermore present initial protocols for screening fusion efficacy across different lipid formulations and for constructing whole LNPs at CG resolution, enabling future studies of these nanoparticles.
|
Lisbeth Ravnkilde Kjølbye; Mariana Valério; Markéta Paloncýová; Luis Borges-Araújo; Roberto Pestana-Nobles; Fabian Grünewald; Bart M. H. Bruininks; Rocío Araya-Osorio; Martin Šrejber; Raul Mera-Adasme; Luca Monticelli; Siewert J. Marrink; Michal Otyepka; Sangwook Wu; Paulo C.T. Souza
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2025-01-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677583c76dde43c908ffe86b/original/martini-3-building-blocks-for-lipid-nanoparticle-design.pdf
|
64deeecc00bbebf0e65e7a38
|
10.26434/chemrxiv-2023-ttt8q
|
Bispecific Antibodies Produced via Chemical Site-Specific Conjugation Technology: AJICAP Second Generation
|
Bispecific antibodies are biotherapeutics that amalgamate the specificities of two distinct antibodies into one molecule. Bispecific antibodies can be utilized in a broad range of diagnostic and therapeutic applications; however, their engineering requires genetic modification and remains time-consuming. Therefore, in this study, we used AJICAP second-generation technology, which drives the production of site-specific antibody-drug conjugates in a practical and robust manner, without genetic modification requirements, to generate bispecific antibodies. Using haloketone chemistry as an alternative to maleimide chemistry, which carries reaction risks, we successfully produced site-specific antibody conjugates. Pharmacokinetic studies revealed that the haloketone-based antibody conjugate was stable in the rat plasma. The resultant bispecific antibodies were rigorously evaluated, and surface plasmon resonance measurements and flow cytometry analyses confirmed that antigen binding remained intact. Additionally, the affinity for the neonatal Fc receptor (FcRn) was retained after conjugation. Further cytotoxicity evaluation emphasized the pronounced activity of the generated bi-specific antibodies. These preliminary findings highlight the potential of AJICAP second-generation technology in BisAb production. This novel approach introduces a fully chemical, site-specific strategy capable of producing bispecific antibodies, heralding a new era in the field of biotherapeutics.
|
Tomohiro Fujii; Kenichiro Ito; Kazutoshi Takahashi; Tsubasa Aoki; Takuya Seki; Yusuke Iwai; Rika Takasugi; Tomohiro Watanabe; Ryusuke Hirama; Ryo Tsumura; Hirobumi Fuchigami; Masahiro Yasunaga; Yutaka Matsuda
|
Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64deeecc00bbebf0e65e7a38/original/bispecific-antibodies-produced-via-chemical-site-specific-conjugation-technology-ajicap-second-generation.pdf
|
666b2cd201103d79c525474f
|
10.26434/chemrxiv-2024-4p9dq
|
Electrically-polarized nanoscale surfaces generate reactive oxygenated and chlorinated species for deactivation of microorganisms
|
Due to dwindling supply of new antibiotics, recent outbreaks of infectious diseases, and the emergence of antibiotic-resistant microorganisms, it is imperative to develop new effective strategies for deactivating a broad-spectrum of microorganisms and viruses. We have implemented electrically polarized nanoscale metallic coatings (ENM) that deactivate a wide range of microorganisms including Gram-negative and Gram-positive bacteria with greater than six-log reduction, in less than ten minutes of treatment. The electrically-polarized devices were also effective in deactivating lentivirus and C. albicans. The key to high deactivation effectiveness of ENM devices is electrochemical production of micromolar cuprous ions, which mediated reduction of oxygen to hydrogen peroxide. Formation of highly damaging species, hydroxyl radicals and hypochlorous acid, from hydrogen peroxide contributed to antimicrobial properties of the ENM devices. The electric polarization of nanoscale coatings represents an unconventional tool for deactivating a broad-spectrum of microorganisms through in-situ production of reactive oxygenated and chlorinated species.
|
Punit Kohli; Annie Y. Vargas-Lizarazo; M. Aswad Ali; Nehal A. Mazumder; Gitanjali M. Kohli; Miroslava Zaborska; Tyler Sons; Michelle Garnett; Ishani Senanayake; Boyd Goodson; José Vargas-Muñiz; Amber Pond; Philip J. Jensik; Michael E. Olson; Scott D. Hamilton-Brehm
|
Materials Science; Nanoscience; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666b2cd201103d79c525474f/original/electrically-polarized-nanoscale-surfaces-generate-reactive-oxygenated-and-chlorinated-species-for-deactivation-of-microorganisms.pdf
|
62c69154332f02c19bde9798
|
10.26434/chemrxiv-2022-tbtb8-v2
|
Materials discovery and design limits in MDABCO perovskites
|
We report the structures of three new materials in the MDABCO-based perovskite family. Analysis of the Goldschmidt tolerance factor and octahedral factor enable us to propose compositional limits for pseudo-cubic perovskite phase formation and suggest directions for further materials discovery in this family of new ferroelectrics.
|
Samuel D. Gale; Harry J. Lloyd; Louise Male; Mark R. Warren; Lucy K. Saunders; Paul A. Anderson; Hamish Yeung
|
Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-07-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c69154332f02c19bde9798/original/materials-discovery-and-design-limits-in-mdabco-perovskites.pdf
|
65c2bf68e9ebbb4db9cfe522
|
10.26434/chemrxiv-2024-t2bk9
|
Profiling the natural product-likeness of Latin American compound libraries
|
Compound databases of natural products play a crucial role in drug discovery and development projects and have implications in other areas, such as food chemical research, ecology and metabolomics. Recently, we put together the first version of the Latin American Natural Product database (LANaPDB) as a collective effort of researchers from six countries to ensemble a public and representative library of natural products in a geographical region with a large biodiversity. The present work aims to conduct a comparative and extensive profiling of the natural product-likeness of a recently updated version of LANaPDB and the individual ten compound databases that form part of LANaPDB. The natural product-likeness profile of the Latin American compound databases is contrasted with the profile of other major natural product databases in the public domain and a set of small-molecule drugs approved for clinical use. As part of the extensive characterization, we employed several chemoinformatics metrics of natural product likeness. The results of this study will capture the attention of the global community engaged in natural product databases, not only in Latin America but across the world.
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Alejandro Gómez-García; Ann-Kathrin Prinz; Daniel A. Acuña Jiménez; William J. Zamora; Haruna L. Barazorda-Ccahuana; Miguel Á. Chávez-Fumagalli; Marilia Valli; Adriano D. Andricopulo; Vanderlan da S. Bolzani; Dionisio A. Olmedo; Pablo N. Solís; Marvin J. Núñez; Johny R. Rodríguez Pérez; Hoover A. Valencia Sánchez; Héctor F. Cortés Hernández; Oscar M. Mosquera Martinez; Oliver Koch; José L. Medina-Franco
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Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Agriculture and Food Chemistry; Chemoinformatics - Computational Chemistry
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CC BY 4.0
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CHEMRXIV
|
2024-02-08
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c2bf68e9ebbb4db9cfe522/original/profiling-the-natural-product-likeness-of-latin-american-compound-libraries.pdf
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60c7573c0f50db123a39822d
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10.26434/chemrxiv.13568366.v3
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In situ Lithiated ALD Niobium Oxide for Improved Long Term Cycling of Layered Oxide Cathodes: A Thin-Film Model Study
|
<p>Protective
coatings applied to cathodes help to overcome interface stability issues and
extend the cycle life of Li-ion batteries. However, within 3D cathode
composites it is difficult to isolate the effect of the coating because of the
additives and non-ideal interfaces. In this study we investigate niobium oxide
(NbO<sub>x</sub>) as cathode coating in a thin-film model system, which provides
simple access to the cathode-coating-electrolyte interface. The conformal NbO<sub>x</sub>
coating was applied by atomic layer deposition (ALD) onto thin-film LiCoO<sub>2</sub>
cathodes. The cathode/coating stacks were annealed to lithiate the NbO<sub>x</sub>
and ensure sufficient ionic conductivity. A range of different coating
thicknesses were investigated to improve the electrochemical cycling with
respect to the uncoated cathode. At a NbO<sub>x</sub> thickness of 30 nm, the
cells retained 80% of the initial capacity after 493 cycles at 10 C, more than
doubling the cycle life of the uncoated cathode film. At the same thickness, the
coating also showed a positive impact on the rate performance of the cathode: 47%
of the initial capacity was accessible even at ultrahigh charge-discharge rates
of 100 C. Using impedance spectroscopy measurements, we found that the enhanced
performance is due to suppressed interfacial resistance growth during cycling.
Elemental analysis using TOF-SIMS and XPS further revealed a bulk and surface
contribution of the NbO<sub>x</sub> coating. These results show that in situ
lithiated ALD NbO<sub>x</sub> can significantly improve the performance of
layered oxide cathodes by enhancing interfacial charge transfer and inhibiting surface
degradation of the cathode, resulting in better rate performance and cycle
life.</p>
|
Abdessalem Aribia; Jordi Sastre; Xubin Chen; Evgeniia Gilshtein; Ayodhya N. Tiwari; Yaroslav E. Romanyuk
|
Energy Storage
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-03-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7573c0f50db123a39822d/original/in-situ-lithiated-ald-niobium-oxide-for-improved-long-term-cycling-of-layered-oxide-cathodes-a-thin-film-model-study.pdf
|
648a525ce64f843f41cb9c0f
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10.26434/chemrxiv-2023-sqdkg
|
Green and Sustainable Solvents for Solid-Phase Peptoid Synthesis
|
Peptoids are a class of sequence-controlled polymers that provide a versatile platform for the design of bioinspired materials. Solid-phase synthetic methods offer absolute control over the polypeptoid sequence and have been optimized to improve reaction efficiency and versatility. However, these solid-phase strategies rely on the use of reprotoxic and restricted solvents, N,N-dimethylformamide (DMF) and N-methyl-2-pyrrolidone (NMP), resulting in significant hazardous solvent consumption and waste generation. Here we report the solid-phase synthesis of peptoids with complete elimination of DMF and NMP and their replacement with greener solvents and binary mixtures to minimize the environmental impact and improve the sustainability of peptoid synthesis. We investigate the resin swelling performance of the green solvents and show that the purity profile and yield of the final peptoids are not adversely affected when compared to those synthesized in traditional solid-phase solvents. Furthermore, we adapt these greener methods for use on automated synthesizers for the synthesis of peptoids with different sequences and longer chain lengths. The replacement of hazardous solvents in solid-phase peptoid synthesis represents an advance in the sustainability of peptoid research, which could improve the translation of peptoids from academic labs to industry.
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Abigail Clapperton; Katya Naomi Marín Vera; Jon Babi; Helen Tran
|
Organic Chemistry; Polymer Science; Biopolymers
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-06-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648a525ce64f843f41cb9c0f/original/green-and-sustainable-solvents-for-solid-phase-peptoid-synthesis.pdf
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63f64e9032cd591f12534067
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10.26434/chemrxiv-2022-7wr7n-v2
|
Perovskite oxides as an opportunity to systematically study the Electrooxidation of alcohols and Polyols on materials based on abundant elements: Learning from the experience using pure metals and metallic oxides in (Electro-)catalysis
|
The cost-effective production of green hydrogen is one of the most important challenges for a sustainable energy transition. To decrease the cost in the production of hydrogen through electrolysis, there are several obstacles that must be overcome. For instance, more active and stable anodes made of abundant and cheap materials will contribute to lowering the capital and operational expenditure of the process. It is well-known that the oxidation of water requires high overpotentials, which is the main limitation for the performance of the device. In this context, substituting the oxidation of water (OER) at the anode of electrolyzers by the oxidation of biomass-derived substances contribute to the overall process by decreasing the power input of the devices and, in some cases, by producing value-added chemicals.
Herein, we re-visited some of the most important fundamental aspects of the (electro-)oxidation of alcohols and polyols on metal-based catalysts, focusing on reaction descriptors. Then, we moved to the (electro-)oxidation of these molecules on metal oxides, re-visiting some of the literature about their application in heterogeneous catalysis and for OER, to get insights about the relation of the structure of the materials and their activity.
Due to the lack of fundamental knowledge about the electro-oxidation of alcohols and polyols on metallic oxides and to the vast literature about the use of perovskite oxides for OER, we propose to start systematic studies using perovskite oxides for the electrooxidation of alcohols and polyols. Consequently, we presented results for LaCoO3, LaFeO3, LaMnO3, and LaNiO3, and propose a mechanism for the electro-oxidation of glycerol based on the formation and reactivity of MOH(O) species. We believe that fundamental and systematic studies in this topic would permit the establishment of reaction descriptors, speeding up the searching for suitable materials for this reaction and paving the way for a most cost-effective production of green hydrogen.
|
Patricia Santiago; Swathi Patchaiammal Raju; Karthik Akkiraju; Rafael Vicente; Mariane Da Silva; Shuai Yuan; Daniela Zanchet; Yang Shao-Horn; Pablo Sebastián Fernández
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Catalysis; Electrocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-02-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f64e9032cd591f12534067/original/perovskite-oxides-as-an-opportunity-to-systematically-study-the-electrooxidation-of-alcohols-and-polyols-on-materials-based-on-abundant-elements-learning-from-the-experience-using-pure-metals-and-metallic-oxides-in-electro-catalysis.pdf
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60c754b6ee301c6db3c7afe4
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10.26434/chemrxiv.13717819.v1
|
Planar Tetracoordinate Carbons in Allene-Type Structures
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<p>The exhaustive exploration of the potential energy surfaces of CE<sub>2</sub>M<sub>2</sub> (E = Si-Pb, M = Li, and Na) revealed seven global minima containing a planar tetracoordinate carbon (ptC). The design was based on a π-localization strategy, resulting in a ptC embedded in a linear or a bent allene-type E=C=E motif. The magnetic response showed a σ-aromaticity in the bent E=C=E fragments. The bonding analysis indicated that the ptCs form C-E covalent bonds and C-M electrostatic interactions.<b></b></p>
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Meng-hui Wang; Mesías Orozco-Ic; luis leyva-parra; William Tiznado; jorge barroso; Yi-hong Ding; Zhong-hua Cui; Gabriel Merino
|
Theory - Computational
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-02-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754b6ee301c6db3c7afe4/original/planar-tetracoordinate-carbons-in-allene-type-structures.pdf
|
60c750efbdbb8927ada39fa7
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10.26434/chemrxiv.13102172.v1
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In Silico Design of Peptides with Binding to the Receptor Binding Domain (RBD) of the SARS-CoV-2 and Their Utility in Bio-Sensor Development for SARS-CoV-2 Detection
|
<p>The severe
acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions of
people across the globe and created not only a health emergency but also a
financial crisis. This virus attacks on the angiotensin-converting enzyme 2 (ACE2)
receptor situated on the surface of the host cell membrane. The spike protein
of the virus binds to this receptor which is a critical step of infection. </p>
<p>A molecule
which can specifically stop this binding could be a potential therapeutic. In
this study, we have tested 12 potential peptides which can bind to the receptor
binding domain (RBD) of the spike protein of the virus and thus can potentially
inhibit the binding of the latter on ACE2 receptor. These peptides are screened
based on their binding with RBD of the spike protein and aqueous stability,
obtained using several atomistic molecular dynamic simulations. The potential
of mean force calculation of two most promising peptides confirmed their
binding to the RBD of the spike protein. </p>
<p>Furthermore, these
two potential peptides were tested for their use in a biosensing application for
SARS-CoV-2 detection. Two types of biosensing platforms, a graphene sheet and a
carbon nano tube (CNT), were tested. The peptides were modified in order to
functionalize the graphene and CNT. Based on the interaction between the substrate,
peptide and spike protein, the utility of screened peptide for a given bio
sensing platform is discussed and recommended.
</p>
|
Yogesh Badhe; Rakesh Gupta; Beena Rai
|
Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750efbdbb8927ada39fa7/original/in-silico-design-of-peptides-with-binding-to-the-receptor-binding-domain-rbd-of-the-sars-co-v-2-and-their-utility-in-bio-sensor-development-for-sars-co-v-2-detection.pdf
|
60c743f14c89197925ad2723
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10.26434/chemrxiv.9700427.v1
|
Two-Dimensional Infrared Spectroscopy From the Gas to Liquid Phase: Density Dependent J-Scrambling, Vibrational Relaxation, and the Onset of Liquid Character
|
Ultrafast 2DIR spectra and pump-probe responses of the N2O n 3 asymmetric stretch in SF6 as a function of density from the gas to supercritical phase and liquid are reported. 2DIR spectra unequivocally reveal free rotor character at all densities studied in the gas and supercritical region. Analysis of the 2DIR spectra determines that J-scrambling or rotational relaxation in N2O is highly efficient, occurring in ~1.5 to ~2 collisions with SF6 at all non-liquid densities. In contrast, N2O n 3 vibrational energy relaxation requires ~15 collisions, and complete vibrational equilibrium occurs on the ~ns scale at all densities. An independent binary collision model is sufficient to describe these supercritical state point dynamics. The N2O n 3 in liquid SF6 2DIR spectrum shows no evidence of free rotor character or spectral diffusion. Using these 2DIR results, hindered rotor or liquid-like character is found in gas and all supercritical solutions for SF6 densities ³ r * = 0.3, and increases with SF6 density. 2DIR spectral analysis offers direct time domain evidence of critical slowing for SF6 solutions closest to the critical point density. Applications of 2DIR to other high density and supercritical solution dynamics and descriptions are discussed. <br />
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Greg Ng Pack; Matthew Rotondaro; Parth Shah; Aritra Mandal; Shyamsunder Erramilli; Lawrence Ziegler
|
Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f14c89197925ad2723/original/two-dimensional-infrared-spectroscopy-from-the-gas-to-liquid-phase-density-dependent-j-scrambling-vibrational-relaxation-and-the-onset-of-liquid-character.pdf
|
61dfb9f5db4d9f591597319c
|
10.26434/chemrxiv-2022-m8xj2
|
Oxidative Addition of Aryl Halides to a Ni(I)-Bipyridine Complex
|
The oxidative addition of aryl halides to bipyridine- or phenanthroline-ligated nickel(I) is a commonly proposed step in nickel catalysis. However, there is a scarcity of complexes of this type that both are well-defined and undergo oxidative addition with aryl halides, hampering organometallic studies of this process. We report the synthesis of a well-defined Ni(I) complex, [(CO2Etbpy)NiCl]4 (1). Its solution-phase speciation is characterized by a significant population of monomer and a redox equilibrium that can be perturbed by π-acceptors and σ-donors. 1 reacts readily with aryl bromides, and mechanistic studies are consistent with a mechanism proceeding through an initial Ni(I) → Ni(III) oxidative addition. Such a process was demonstrated stoichiometrically for the first time, affording a structurally characterized Ni(III) aryl complex.
|
Stephen Ting; Wendy Williams; Abigail Doyle
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions; Transition Metal Complexes (Organomet.)
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CC BY NC 4.0
|
CHEMRXIV
|
2022-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61dfb9f5db4d9f591597319c/original/oxidative-addition-of-aryl-halides-to-a-ni-i-bipyridine-complex.pdf
|
63a87d59518c16eb08383072
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10.26434/chemrxiv-2022-zdb5j
|
β-Peptides incorporating polyhydroxylated cyclohexane β-amino acids: synthesis and conformational study
|
We describe the synthesis of trihydroxylated cyclohexane β-amino acids from (–)-shikimic acid, in their cis and trans configuration, and the incorporation of the trans isomer into a trans-2-aminocyclohexanecarboxylic acid peptide chain. Subsequently, the hydroxyl groups were partially or totally deprotected. The structural study of the new peptides by FTIR, CD, solution NMR and DFT calculations revealed that they all fold into a 14-helix secondary structure, similarly to the homooligomer of trans-2-aminocyclohexanecarboxylic acid. This means that the high degree of substitution of the cyclohexane ring of the new residue is compatible with the adoption of a stable helical secondary structure and opens opportunities for the design of more elaborate peptidic foldamers with oriented polar substituents at selected positions of the cycloalkane residues.
|
David Reza; Rosalino Balo; Jose M. Otero; Ai M. Fletcher; Rebeca García-Fandino; Victor M. Sanchez-Pedregal; Stephen G. Davies; Ramon J. Estevez; Juan C. Estevez
|
Organic Chemistry; Organic Synthesis and Reactions; Supramolecular Chemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-12-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a87d59518c16eb08383072/original/peptides-incorporating-polyhydroxylated-cyclohexane-amino-acids-synthesis-and-conformational-study.pdf
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676aa8ecfa469535b9a48401
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10.26434/chemrxiv-2024-wdtz9-v2
|
Machine learning for transition state geometry prediction
|
The calculation of transition state (TS) geometries is essential for understanding reaction mechanisms and rational synthetic methodology design. However, traditional methods like density functional theory (DFT) are often too computationally expensive for large-scale TS identification and are significantly slower than high-throughput experimental screening methods. Recent advancements in machine learning (ML) offer promising alternatives, enabling the direct prediction of TS geometries, reducing the reliance on expensive quantum mechanical (QM) calculations and affording predictions ahead of experiment. The works explored here include the broader application of ML in reaction property prediction, emphasising how accurate TS geometries can serve as vital input data to improve model accuracy. A comprehensive review of ML methods developed to explicitly predict TS geometries are then presented, with attention to their application in downstream tasks, such as energy barrier calculations, and their use as initial structures for further optimisation via QM methods. Finally, a critical evaluation of the accuracy and limitations of existing TS prediction methods are discussed, highlighting challenges that impede wider adoption and areas where further research is needed.
|
Isaac W. Beaglehole; Miles J. Pemberton; Elliot H. E. Farrar; Matthew N. Grayson
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2024-12-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676aa8ecfa469535b9a48401/original/machine-learning-for-transition-state-geometry-prediction.pdf
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60c75201337d6c3d74e28646
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10.26434/chemrxiv.13239488.v1
|
Electrostatically Tuning the Photodissociation of the Irgacure 2959 Photoinitiator in the Gas Phase by Cation Binding
|
<div><div><div><p>Our paper reports a combined experimental and computational investigation of the electrostatic tuning of Irgacure 2959, a Norrish-type I photoinitiator, in the presence of bound cations (H<sup>+</sup> , Li<sup>+</sup> , Na<sup>+</sup> , K<sup>+</sup> , Zn<sup>2+</sup> , Ca<sup>2+</sup> and Mg2+). Laser photodissociation action spectroscopy is deployed to acquire photodissociation spectra of mass- selected cation complexes. Quantum chemical calculations (TD-DFT and SCS-CC2) reveal that the cations are acting as point charges such that shifts of the key ππ* and nπ* states can be modelled as perturbations by an oriented electric field (OEF). The model agrees with the experimental photodissociation action spectra.</p></div></div></div>
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Samuel Marlton; Benjamin I. McKinnon; Nicholas Hill; Michelle Coote; Adam Trevitt
|
Photochemistry (Physical Chem.); Physical and Chemical Properties; Quantum Mechanics; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75201337d6c3d74e28646/original/electrostatically-tuning-the-photodissociation-of-the-irgacure-2959-photoinitiator-in-the-gas-phase-by-cation-binding.pdf
|
659bdb849138d231617227cd
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10.26434/chemrxiv-2024-3rldf
|
Gold-catalysed Heck Reactions: Fact or Fiction?
|
Two recent high-profile publications reported the formation of Heck-type arylated alkenes catalysed by MeDalPhosAuCl / AgOTf (J. Am. Chem. Soc. 2023, 145, 8810) and their cyclisation to tetralines (Angew. Chem. Int. Ed. 2023, e202312786). It was claimed that these were the first demonstrations in gold catalysis of alkene insertion into Au-aryl bonds, β-H elimination and chain-walking by Au-H cations. We show here that in fact this chemistry is a two-stage process. Only the first step, the production of an alkyl triflate ester as the primary organic product by the well-known alkene heteroarylation sequence, involves gold. The subsequent formation of Heck-type olefins and their cyclisation to tetralines represent classical H+-triggered carbocationic chemistry. These steps proceed in the absence of gold with identical results. Literature claims of new gold reactivity such as chain walking by the putative [LAuH]2+ dication have no basis in fact.
|
Peter H. M. Budzelaar; Manfred Bochmann; Martina Landrini; Luca Rocchigiani
|
Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions; Transition Metal Complexes (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659bdb849138d231617227cd/original/gold-catalysed-heck-reactions-fact-or-fiction.pdf
|
63b53a6304902a34bd1adc9b
|
10.26434/chemrxiv-2023-76wll-v2
|
Total Synthesis of Tetrodotoxin and 9-epiTetrodotoxin
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Tetrodotoxin and congeners are specific voltage-gated sodium channel blockers that exhibit remarkable anesthetic and an-algesic effects. Here, we present a scalable asymmetric synthesis of TTX and 9-epiTTX from the abundant chemical feed-stock furfuryl alcohol. The optically pure cyclohexane skeleton was assembled via a stereoselective Diels-Alder reaction. The dense heteroatom substituents were established sequentially by a series of functional group interconversions on highly oxygenated cyclohexane frameworks, including a chemoselective cyclic anhydride opening, and a decarboxylative hydrox-ylation. An innovative SmI2-mediated concurrent fragmentation, an oxo-bridge ring opening and ester reduction followed by an Upjohn dihydroxylation delivered the highly oxidized skeleton. Ruthenium-catalyzed oxidative alkyne cleavage and formation of the hemiaminal and orthoester under acidic conditions enabled the rapid assembly of TTX, anhydro-TTX, 9-epiTTX, and 9-epi lactone-TTX.
|
Peihao chen; Jing Wang; Yan Wang; Yuze Sun; Songlin Bai; Qingcui Wu; Shuangfeng Zhang; Xinyu Cheng; Peng Cao; Xiangbing Qi
|
Organic Chemistry; Natural Products; Organic Synthesis and Reactions; Stereochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-01-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b53a6304902a34bd1adc9b/original/total-synthesis-of-tetrodotoxin-and-9-epi-tetrodotoxin.pdf
|
60c746c6bdbb8920eaa38c9f
|
10.26434/chemrxiv.11362373.v1
|
Access to Substituted Indenol Ethers via a Regioselective Intermolecular Carbopalladation Cascade
|
Alkyne
carbopalladation reactions represent a powerful approach to generating multiple
new C–C bonds and substituted alkenes, however regioselectivity is often
challenging for intermolecular variants. By utilizing ynol ethers as polarized
alkynes we observe complete regiocontrol of migratory insertion with Pd–Ar
species. A Heck reaction was used to turn-over the catalytic cycle by
intercepting the vinyl-Pd adduct of carbopalladation with a pendant alkene.
When using <i>o</i>-iodo styrenes substrates
the resulting products are oligosubstituted 1-indenol ethers with defined
stereochemistry based on the initial alkene geometry. By blocking β-hydride
elimination we demonstrated C–H and C–C reductive elimination steps for catalyst
turnover. Herein we report the optimization of reaction conditions, scope, and
alternative termination steps.
|
Brandon L. Coles-Taylor; Maximilian S. McCallum; Andrés G. Muñoz; Brian Michel
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Catalysis; Reaction (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-12-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746c6bdbb8920eaa38c9f/original/access-to-substituted-indenol-ethers-via-a-regioselective-intermolecular-carbopalladation-cascade.pdf
|
6708fc1b12ff75c3a1205788
|
10.26434/chemrxiv-2024-q804g
|
Molecular Structural Control of the Amorphous-Crystalline Balance in Solids: Structure-Phase Correlation in DADQs with Enhanced/Switchable Fluorescence
|
The amorphous/crystalline (A/C) assembly in molecular solids has a direct bearing on their attributes and applications, including mechanical, pharmaceutical, electronic and photophysical. However, a precise understanding of the molecular features and interactions that govern such assemblies has rarely been realized. The enhanced fluorescence of select classes of molecular materials with various applications in displays, sensing and imaging, is strongly influenced by their crystallinity; the subtle balance between the A and C forms is key to their use as functional phase change materials. We have synthesized and structurally characterized two series of alkoxyalkyl diaminodicyanoquinodimethanes (ROR′-DADQs) exhibiting enhanced and tunable fluorescence from the solution, to the A state, to the C state. An exhaustive study of their photophysical responses, thermal characteristics and A-C phase changes reveal significant correlations with the molecular structural features (R and R′ moieties), key interactions like H-bonds, and molecular orientations in the lattice. These observations provide novel insights into the molecular structural control of the A/C states in molecular solids, and A-C phase change systems; fluorescence switching is exploited as a signature of the phase transformations. The factors promoting the A or C forms of molecular solids can guide the design of novel materials and devices exploiting such supramolecular structures and their interconversions.
|
Ritesh Singh Maurya; T. P. Radhakrishnan
|
Materials Science; Aggregates and Assemblies; Optical Materials; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6708fc1b12ff75c3a1205788/original/molecular-structural-control-of-the-amorphous-crystalline-balance-in-solids-structure-phase-correlation-in-dad-qs-with-enhanced-switchable-fluorescence.pdf
|
60c74d06337d6cee84e27d1e
|
10.26434/chemrxiv.12582101.v1
|
Experimental Evidence of Two-fold Electromagnetic Enhancement Mechanism of Surface-Enhanced Raman Scattering
|
The surface-enhanced Raman scattering (SERS) electromagnetic
(EM) enhancement mechanism is a two-fold enhancement process in which both the
incident and scattered Raman fields are enhanced. In this letter, we present
new direct evidence of the two-fold EM mechanism by using an Ag nanorod
array/SiO<sub>2</sub> dielectric layer/Ag mirror multilayer thin film
"local plasmon resonator". The
two-fold EM enhancement mechanism of SERS was confirmed by analyzing the
optical absorption and Raman scattering spectra of the local plasmon resonator for
excitation and scattered light. The effect of light interference was
altered by varying the film thickness of the SiO<sub>2</sub> phase control
layer (PCL), and the absorbance in the Raman scattering wavelength range was
reduced from 90% to 0%. We also demonstrated that the intensity of the
background emission is closely related to the enhancement of the scattered
field and provides substantial evidence for a two-fold SERS enhancement
mechanism.
|
Samir Kumar; Kouta Tokunaga; Kyoko Namura; Takao Fukuoka; Motofumi Suzuki
|
Multilayers; Nanostructured Materials - Materials; Optical Materials; Thin Films; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d06337d6cee84e27d1e/original/experimental-evidence-of-two-fold-electromagnetic-enhancement-mechanism-of-surface-enhanced-raman-scattering.pdf
|
60c73e3b337d6cce31e262e1
|
10.26434/chemrxiv.6729113.v1
|
Organic Nanosynthesis of Ancient Windmill-like Window Gridarenes at Molecular Scale
|
We
focus on another kind of square-type unit nanogrids with starlike divergent extensibility.
As a result, square windmill-like nanogrid <b>WG4</b>
have been successfully synthesized by two different kinds of fluorene-based nanosynthons,
namely I-shape nanosynthon and L-shape nanosynthon synthesis method. Besides <b>WG4</b>, triangle and hexagon windmill-like
nanogrids (<b>WG3</b> and <b>WG5</b>) are also obtained via one-pot nanosynthesis of I-shape nanosynthon with <b>WG3</b>
as the main product. For the L-shape nanosynthon synthetic method, the
cyclization process possesses higher selectivity, resulting to an excellent yield
for <b>WG</b>4. In addition, two
stereoisomers of the triangle nanogrids, <i>cis-trans</i>-<b>WG3</b> and <i>cis-cis-</i><b>WG3</b>, were
separated and characterized from the single-crystal X-ray diffraction and <sup>1</sup>H
NMR analyses for getting insight into the configuration of the triangle nanogrids
with the skeleton planarization for the <i>trans</i>-configuration
and deplanarization for the <i>cis</i>-configuration.
|
Ying Wei; Quanyou Feng; Hui Liu; Xiuling Wang; Dongqing Lin; Fengning Guo; Changjin Ou; Songlin Xie; Mingdong Yi; Linghai Xie; Wei Huang
|
Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-07-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e3b337d6cce31e262e1/original/organic-nanosynthesis-of-ancient-windmill-like-window-gridarenes-at-molecular-scale.pdf
|
6780c78681d2151a028cfccf
|
10.26434/chemrxiv-2025-vfmm7
|
Mechanism of Cationic Peptide-Induced Assembly of Gold Nanoparticles: Modulation of Electrostatic Repulsion
|
The aggregation of plasmonic nanoparticles can lead to new and controllable properties useful for numerous applications. We recently showed the reversible aggregation of gold nanoparticles (AuNPs) via a small, cationic di-arginine peptide; however, the mechanism underlying this aggregation is not yet comprehensively understood. Here, we seek insights into the intermolecular interactions of cationic peptide-induced assembly of citrate-capped AuNPs by empirically measuring how peptide identity impacts AuNP aggregation. We examined the nanoscale interactions between the peptides and the AuNPs via UV-vis spectroscopy to determine the structure-function relationship of peptide length and charge on AuNP aggregation. Careful tuning of the sequence of the di-arginine peptide demonstrated that the mechanism of assembly is driven by a reduction in electrostatic repulsion. We show that an acetylated N-terminal and a carboxylic acid C-terminal decrease the peptide effectiveness in inducing AuNP aggregation. The increase in peptide size through addition of glycine or proline units hinders aggregation and leads to less redshift. Arginine-based peptides were also found to be more effective in assembling the AuNPs than cysteine-based peptides of equivalent length. We also illustrate that aggregation is independent of peptide stereochemistry. Finally, we demonstrate the modulation of peptide-AuNP behavior through changes to the pH, salt concentration, and temperature. Notably, histidine-based and tyrosine-based peptides could reversibly aggregate the AuNPs in response to the pH.
|
Benjamin Lam; Robert Ramji; Margaret Mullooly; Kristina D. Closser; Tod A. Pascal; Jesse V. Jokerst
|
Materials Science; Nanoscience; Chemical Engineering and Industrial Chemistry; Aggregates and Assemblies; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6780c78681d2151a028cfccf/original/mechanism-of-cationic-peptide-induced-assembly-of-gold-nanoparticles-modulation-of-electrostatic-repulsion.pdf
|
638665209b5b80521adaa44c
|
10.26434/chemrxiv-2022-hxvcc
|
Augmenting Polymer Datasets by Iterative Rearrangement
|
One of the biggest obstacles to successful polymer property prediction is an effective representation that accurately captures the sequence of repeat units in a polymer. Motivated by the successes of data augmentation in computer vision and natural language processing, we explore augmenting polymer data by rearranging the molecular representation while preserving the correct connectivity, revealing additional substructural information that is not present in a single representation. We evaluate the effects of this technique on the performance of machine learning models trained on three experimental polymer datasets and compare them to common molecular representations. Data augmentation improves deep learning property prediction performance compared to equivalent (non-augmented) representations. In datasets where the target property is primarily influenced by the polymer sequence rather than experimental parameters, this data augmentation technique provides the molecular embedding with more information to improve property prediction accuracy.
|
Stanley Lo; Martin Seifrid; Théophile Gaudin; Alán Aspuru-Guzik
|
Theoretical and Computational Chemistry; Polymer Science; Organic Polymers; Machine Learning
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-11-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638665209b5b80521adaa44c/original/augmenting-polymer-datasets-by-iterative-rearrangement.pdf
|
60c74b68ee301cd67fc79e67
|
10.26434/chemrxiv.12327554.v1
|
Using the SARS Infection Transcriptional Signature to Identify Potential Treatments for Covid-19
|
Gene expression data associated with viral infection of human cell lines is harnessed to define a conserved viral response signature. Drugs that tend to drive gene expression in the direction of the cellular viral response are significantly enriched for those with established antiviral activity. Transcription therefore facilitates a simple and effective filtering of candidate drugs to be put forward for bioassay validation.
|
Richard Killick; Clive Ballard; Patrick Doherty; Gareth Williams
|
Bioinformatics and Computational Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b68ee301cd67fc79e67/original/using-the-sars-infection-transcriptional-signature-to-identify-potential-treatments-for-covid-19.pdf
|
630f08a7f07ee1b3c4f869fd
|
10.26434/chemrxiv-2022-j0p8n
|
Competing single-chain folding and multi-chain aggregation pathways control solution-phase aggregate morphology of organic semiconducting polymers
|
Understanding the solution-phase behaviour of organic semiconducting polymers is important for systematically improving the performance of devices based on solution-processed thin films of these molecules. Conventional polymer theory predicts that polymer conformations become more compact as solvent quality decreases, but recent experiments have shown the high-performance organic-semiconducting polymer P(NDI2OD-T2) to form extended rod-like aggregates much larger than a single chain in poor solvents, with the formation of these extended aggregates correlated with enhanced electron mobility in films deposited from these solutions. We explain the unexpected formation of extended aggregates using a novel coarse-grained simulation model of P(NDI2OD-T2) that we have developed to study the effect of solvent quality on its solution-phase behaviour. In poor solvents, we find that aggregation through only a few monomers gives effectively inseparable chains, leading to the formation of extended structures of partially overlapping chains via non-equilibrium assembly. This behaviour requires that multi-chain aggregation occurs faster than chain folding, which we show is the case for the chain lengths and concentrations shown experimentally to form rod-like aggregates. This kinetically controlled process introduces a dependence of aggregate structure on concentration, chain length, and chain flexibility, which we show is able to reconcile experimental findings and is generalisable to the solution-phase assembly of other semiflexible polymers.
|
Belinda Boehm; Christopher McNeill; David Huang
|
Theoretical and Computational Chemistry; Materials Science; Polymer Science; Conducting polymers; Polymer morphology; Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2022-09-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630f08a7f07ee1b3c4f869fd/original/competing-single-chain-folding-and-multi-chain-aggregation-pathways-control-solution-phase-aggregate-morphology-of-organic-semiconducting-polymers.pdf
|
6452f82327fccdb3ea73640e
|
10.26434/chemrxiv-2023-w44vg
|
Unexpected C–O Bond Cleavage by a Copper–Phosphido Compound
|
Copper methoxide compound IPrCuOMe was unexpectedly formed in a reaction of IPrCuPPh2 with methyl acrylate. The alkoxide product was identified from the reaction mixture spectroscopically and structurally characterized. This C–O bond cleavage re-action likely depends on nucleophilicity of the Cu–P bond of IPrCuPPh2.
|
Steven G. Dannenberg; Rory Waterman
|
Inorganic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6452f82327fccdb3ea73640e/original/unexpected-c-o-bond-cleavage-by-a-copper-phosphido-compound.pdf
|
67ae18d0fa469535b930bbff
|
10.26434/chemrxiv-2025-ngxc3
|
Automation Accelerated screening of H-Bond-Rich Iridium Photosensitisers for Hydrogen Generation
|
In the pursuit of a stable hydrogen evolution photosensitiser, we demonstrate the incorporation of a series of our H-bond rich guanidine-styled iridium (III) complexes into a catalytic system. Using automation accelerated catalysis screening techniques we optimised our system quickly and effectively to observe how these strongly H-bonding complexes may perform. Proven to be photo-electronically suitable, and with effective electron transfer abilities evidenced by Stern-Volmer mechanistic studies, the complexes showed modest levels of H2 evolution in comparison to previously investigated photosensitisers with general formula [Ir(C^N)2(N^N)].
|
T. Harri Jones; Christopher Bradshaw; John Ward; Barry Blight
|
Inorganic Chemistry; Catalysis; Photocatalysis; Redox Catalysis
|
CC BY NC 4.0
|
CHEMRXIV
|
2025-02-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ae18d0fa469535b930bbff/original/automation-accelerated-screening-of-h-bond-rich-iridium-photosensitisers-for-hydrogen-generation.pdf
|
60c749c7567dfea121ec4c4c
|
10.26434/chemrxiv.12098478.v1
|
Formation Mechanism of Sub-Micron Pharmaceutical Composite Particles derived from Far- and Near Field Raman microscopy
|
Surface-enhanced Raman spectroscopy (SERS) and confocal Raman
microscopy are applied to investigate the structure and the molecular
arrangement of a sub-micron pharmaceutical organic composite. As a model system,
sub-micron Furosemide and polyvinylpyrrolidone (Furosemide/PVP) particles produced
by spray flash evaporation (SFE) from a single solution are investigated. The morphology,
size and crystallinity of Furosemide/PVP composites are first analyzed by
scanning electron microscopy (SEM) and X-ray powder diffraction (XRPD).
Afterwards, reference far-field Raman spectra and confocal far-field Raman maps
of Furosemide/PVP particles are interpreted based on the far-field Raman
spectra of pure Furosemide and pure PVP precursors. Confocal far-field Raman
microscopy shows that Furosemide/PVP particles feature an intermixture of Furosemide
and PVP molecules at the sub-micron scale. In order to have a better insight on
the molecular arrangement of PVP and Furosemide in composite particles, SERS
and surface-enhanced confocal Raman microscopy (SECoRM) are performed on Furosemide,
PVP and Furosemide/PVP composites particles sputtered with silver (40 nm).
Surface-sensitive SERS and SECoRM maps reveal that Furosemide/PVP particle
surfaces mainly consist of PVP molecules coating Furosemide domains. Overall, the
combination surface and bulk sensitive analyses allows drawing a clear picture
of the particle morphology and the molecular arrangement in Furosemide/PVP
sub-micron particles. Namely, SFE-produced Furosemide/PVP sub-micron particles
are formed by the agglomeration of primary particles consisting of Furosemide
nano-crystals embedded in a thin PVP matrix. Interestingly, both far-field (bulk-sensitive)
and surface-enhanced (surface-sensitive) confocal Raman microscopies provide molecular
information on a statistically-relevant amount of sub-micron particles in a single
microscopic map; this combination is thus an effective and time-saving and tool
for investigating organic and inorganic sub-micron composites.
|
Jakob Hübner; Jean-Baptiste Coty; Yan Busby; Denis Spitzer
|
Microscopy; Spectroscopy (Anal. Chem.); Structure
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749c7567dfea121ec4c4c/original/formation-mechanism-of-sub-micron-pharmaceutical-composite-particles-derived-from-far-and-near-field-raman-microscopy.pdf
|
65ba3816e9ebbb4db9594577
|
10.26434/chemrxiv-2024-rghs4
|
Electronic coherences built by an attopulse control the forces on the nuclei
|
Attopulses have an energy bandwidth broad enough to coherently excite several electronic states of molecules. Towards the control of chemical reactivity by attopulses we derive the quantum mechanical expression for the force exerted on the nuclei in such a vibronic wave packet both during and after the exciting pulse. Tuning the pulse parameters allows accessing specific electronic coherences that determine the force strength and direction during and after the pulse. Following the pulse, the force due to the non adiabatic interactions accelerates or slows down the motion of the vibronic wave packet on the excited electronic states and its sign controls the direction of population transfer. Computational results for the LiH and LiT molecules and the probing by the emission dipole are discussed.
|
Manuel Cardosa-Gutierrez; Raphael D. Levine; Francoise Remacle
|
Physical Chemistry; Photochemistry (Physical Chem.); Quantum Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ba3816e9ebbb4db9594577/original/electronic-coherences-built-by-an-attopulse-control-the-forces-on-the-nuclei.pdf
|
6266c3c611b146462a2f9bf1
|
10.26434/chemrxiv-2022-4bf85
|
Symmetry-Driven Total Synthesis of Myrioneurinol
|
We report a total synthesis of the Myrioneuron alkaloid myrioneurinol enabled by the recognition of hidden symmetry within its polycyclic structure. Our approach traces myrioneurinol’s complex framework back to a symmetrical diketone precursor, a double reductive amination of which forges its central piperidine unit. By employing an inexpensive chiral amine in this key desymmetrizing event, four stereocenters of the natural product including the core quaternary stereocenter are set in an absolute sense, providing the first asymmetric entry to this target. Other noteworthy strategic maneuvers include utilizing a bicyclic alkene as a latent cis-1,3-bis(hydroxymethyl) synthon and a topologically controlled alkene hydrogenation. Overall, our synthesis proceeds in 18 steps and ~1% yield from commercial materials.
|
Jake M. Aquilina; Myles W. Smith
|
Organic Chemistry; Natural Products; Organic Synthesis and Reactions
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-04-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6266c3c611b146462a2f9bf1/original/symmetry-driven-total-synthesis-of-myrioneurinol.pdf
|
667c99d5c9c6a5c07a796eee
|
10.26434/chemrxiv-2024-tl9wv
|
Rapid Synthesis of Phase-Engineered Tungsten Carbide Electrocatalysts via Flash Joule Heating for High-Current-Density Hydrogen Evolution
|
Fabricating durable and high-performance electrocatalysts operating at high current densities for industrial acidic hydrogen evolution remains a daunting challenge. Tailoring the phase composition of electrocatalysts is a promising strategy to harness synergistic effects and improve charge transfer, thereby optimizing their performance. This work presents a fast, green method based on flash joule heating (FJH) to synthesize phase-engineered tungsten carbide electrocatalysts for the acidic hydrogen evolution reaction (HER) at high current densities. Tungsten carbide electrodes with varying FJH treatment durations (3, 10, 30, and 60 seconds) are fabricated to fine-tune the mixture of tungsten monocarbide (WC) and tungsten semicarbide (W2C) phases. Results show that samples with a 30-second treatment (TC-3) exhibit an optimal balance between these phases, leading to a low overpotential of 387 mV at a high current density of 4 A/cm2. Notably, the TC-3 electrocatalysts remain stable for over 6 days at 4 A/cm2 due to their controlled phases and excellent corrosion-resistant properties. This work highlights a new method to fabricate cost-effective, high-performance tungsten carbide electrocatalysts with well-controlled phase compositions.
|
Amirarsalan Mashhadian; Shiwen Wu; Yun Hao; Mahdi Mosadegh; Kyeongjae Cho; Majid Minary-Jolandan; Guoping Xiong
|
Catalysis; Energy; Electrocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2024-07-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667c99d5c9c6a5c07a796eee/original/rapid-synthesis-of-phase-engineered-tungsten-carbide-electrocatalysts-via-flash-joule-heating-for-high-current-density-hydrogen-evolution.pdf
|
60c7500b9abda285a8f8d973
|
10.26434/chemrxiv.12985892.v1
|
Predicting Chemical Reaction Outcomes: A Grammar Ontology-based Transformer Framework
|
<p>Discovering and designing novel materials is a challenging problem as it often requires searching a combinatorially large space of potential candidates. Evaluation of all candidates experimentally is typically infeasible as it requires great amounts of effort, time, expertise, and money. The ability to predict reaction outcomes without performing extensive experiments is, therefore, important. Towards that goal, we report an approach that uses context-free grammar (CFG) based representations of molecules in a neural machine translation framework. We formulate the reaction-prediction task as a machine translation problem that involves discovering the transformations from the source sequence (comprising the reactants and agents) to the target sequence (comprising the major product) in the reaction. The grammar ontology-based representation of molecules hierarchically incorporates rich molecular structure information that, in principle, should be valuable for modeling chemical reactions. We achieve an accuracy of 80.1% on a standard reaction dataset using a model characterized by only a fraction of the number of training parameters in other sequence-to-sequence models based works in this area. Moreover, 99% of the predictions made on the same reaction dataset were found to be syntactically valid. We conclude that CFGs-based ontological representations could be an efficient way of incorporating structural information, ensuring chemically valid predictions, and overcoming overfitting in complex machine learning architectures employed in reaction prediction tasks.<br /></p>
|
Vipul Mann; Venkat Venkatasubramanian
|
Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-09-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7500b9abda285a8f8d973/original/predicting-chemical-reaction-outcomes-a-grammar-ontology-based-transformer-framework.pdf
|
60c750a7702a9b6dfa18be19
|
10.26434/chemrxiv.13066724.v1
|
Evaluation of PC12 Cell Neural Differentiation on Graphene Coated ITO Microchips
|
In this study, the impact of graphene on neuronal
differentiation of PC12 cells into neuron-like cells was evaluated in
conjunction with electrical stimuli. First, an ITO (Indium Tin Oxide) microchip
with a certain number of electrodes was fabricated using photolithography and
then a chemically synthesized graphene was coated on the microchip. The
electrical stimulation was applied through the ITO-microchip. Following
optimization of neuronal differentiation conditions, the effect of AC and DC electrical
stimulation on both bare and graphene-coated ITO-microchips for neuronal
differentiation was investigated. According to the results, it was observed
that electrical stimulation with direct current for 30 minutes caused a large
degree of neuronal cell differentiation on the graphene coated ITO-microchips.
The results were also verified by real-time qPCR.
|
Tansu Golcez; Fikri seven; Ozan Karaman; Mustafa Sen
|
Carbon-based Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750a7702a9b6dfa18be19/original/evaluation-of-pc12-cell-neural-differentiation-on-graphene-coated-ito-microchips.pdf
|
64e117a3694bf1540ca2e3b5
|
10.26434/chemrxiv-2023-4rw80
|
CO2 Capture and Conversion to Ethylene using a Bipolar Membrane Electrolysis System
|
Electrochemical CO2 reduction (CO2RR) has attracted significant interest as a pathway for achieving a carbon-neutral society. However, conventional gas-phase CO2 electrolysis configurations suffer from low CO2 utilization and expensive integration with carbon capture. Here, we demonstrate experimentally how a bipolar membrane (BPM) membrane electrode assembly (MEA) electrolysis cell can convert CO2 released from carbon capture solutions (K2CO3) directly into ethylene (C2H4). Using an optimized Cu-Ag electrocatalyst we demonstrate the conversion of CO2 to C2H4 with a 10% Faradaic efficiency (with a partial current density of 10 mA cm-2). During all tests, the BPM-MEA electrolysis cell also achieved ~100% CO2 utilization efficiency over 24 hours. Additionally, we discuss the impact of the cost of electricity and water loss play on the economic feasibility of BPM-MEA systems.
|
Hakhyeon Song; Carlos Fernandez; Anush Venkataraman; Victor Brandao; Sandeep Dhingra; Sukaran S. Arora; Carlos Villa; Daniela Ferrari; Carsten Sievers; Sankar Nair; Marta Hatzell
|
Catalysis; Electrocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e117a3694bf1540ca2e3b5/original/co2-capture-and-conversion-to-ethylene-using-a-bipolar-membrane-electrolysis-system.pdf
|
60c74a3fee301ca619c79c19
|
10.26434/chemrxiv.12174744.v1
|
Impacts of Ion-Pairing Effects on Linear and Nonlinear Photophysical Properties of Polymethines Dyes
|
Ion-pairing between cationic heptamethine and small bromine anion in a non-dissociating solvent results in a symmetry breaking towards a dipolar type chromophore, a transition that is never observed in presence of a bulky B(C<sub>6</sub>F<sub>5</sub>)<sub>4</sub> anion. For the first time, the effects of ion-pairing on the linear and nonlinear photophysical properties is investigated and reveals significant discrepancies between cyanine and dipolar states.<br />
|
Simon Pascal; San-Hui Chi; Joseph W. Perry; Chantal Andraud; Olivier MAURY
|
Spectroscopy (Physical Chem.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2020-04-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a3fee301ca619c79c19/original/impacts-of-ion-pairing-effects-on-linear-and-nonlinear-photophysical-properties-of-polymethines-dyes.pdf
|
66dd067f12ff75c3a1bcb6ff
|
10.26434/chemrxiv-2024-nslhn-v2
|
Characterization by LC-MS/MS of two conjugate vaccines using KLH as carrier protein
|
Keyhole limpet haemocyanins (KLH1 and KLH2) from Megathura crenulata, are large ( 3900 amino acids) multi-subunit oxygen-carrying metalloproteins, that are widely used as carrier proteins in conjugate vaccines and in immunotherapy. KLHs and their derived conjugate vaccines are poorly characterized by mass spectrometry due to the very stable supramolecular structures with megadalton molecular mass, and the resistance to be efficiently digested with standard protocols using specific proteases. KLH1 and KLH2 proteins were conjugated to the conserved twenty-one amino acids pP0 peptide, derived from the P0 acidic ribosomal protein of Rhipicephalus sp. ticks by using the maleimide-thiol chemistry. The resultant KLH1- and KLH2-Cys1pP0 conjugate vaccines were efficiently digested using the MED-FASP procedure, and analyzed by LC-MS/MS allowing approximately 85% sequence coverage of both conjugates. New PTMs not described for the KLH such as oxidized species were identified. The conjugation sites and Cys-His thioether bonds were determined by identifying cross-linked peptides using software developed for cross-linking mass spectrometry experiments. Conjugation sites were validated by combining sequence coverage, the presence of diagnostic and linker fragment ions in the MS/MS spectra, and the multi-peak pattern in the extracted ion chromatograms. In summary, 124 out of 170 Lys (75%) and 99 out 150 Lys (66%) were found conjugated to Cys1pP0 in KLH1 and KLH2, respectively. In total, four and seven Cys-His thioether bonds were experimentally determined in KLH1 and KLH2, respectively. This is the first report of the conjugation sites identification of two KLH-based vaccines determined by mass spectrometry
|
Satomy Pousa; Pablo E. Ramos-Bermúdez; Vladimir Besada; Ania Cabrales-Rico; Hilda Elisa Garay; Alina Rodríguez-Mallón; Katharina Zettl; Jacek R Wiśniewski; Luis Javier González
|
Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66dd067f12ff75c3a1bcb6ff/original/characterization-by-lc-ms-ms-of-two-conjugate-vaccines-using-klh-as-carrier-protein.pdf
|
6337112fcf3829502db81551
|
10.26434/chemrxiv-2022-qpcfh
|
Highly Efficient Light Harvesting of Eu(III) Complex in a Host-Guest Film by Triplet Sensitization
|
Lanthanide complexes are attractive light emitters owing to their ideal high color purity. Sensitization using ligands with high absorption efficiency is a powerful approach to enhancing photoluminescence intensity. However, the development of antenna ligands that can be used for sensitization is limited due to difficulties in controlling the coordination structures of lanthanides. Here, we demonstrate a system comprising triazine-based host molecules and Eu(hfa)3(TPPO)2 (hfa: hexafluoroacetylacetonato, TPPO: triphenylphosphine oxide), which shows drastically improved total photoluminescence intensity compared to conventional luminescent Eu(III) complexes. Time-resolved spectroscopic studies revealed that the energy transfer from the host molecules to Eu(III) occurs via the triplet states over several molecules with nearly unity efficiency. Our discovery paves the way for efficient light harvesting of Eu(III) complexes with simple fabrication using a solution process.
|
Shiori Miyazaki; Kenichi Goushi; Yuichi Kitagawa; Yasuchika Hasegawa; Chihaya Adachi; Kiyoshi Miyata; Ken Onda
|
Physical Chemistry; Photochemistry (Physical Chem.); Physical and Chemical Properties; Spectroscopy (Physical Chem.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6337112fcf3829502db81551/original/highly-efficient-light-harvesting-of-eu-iii-complex-in-a-host-guest-film-by-triplet-sensitization.pdf
|
60c74bc2469df45768f43f80
|
10.26434/chemrxiv.12362243.v1
|
‘Sacrificial’ Supramolecular Assembly and Pressure-Induced Polymerization: Toward Sequence-Defined Functionalized Nanothreads
|
<div><div><div><p>Limited supramolecular strategies have been utilized to synthesize sequence-defined polymers, despite the high utility of noncovalent interactions in materials design. Herein, we illustrate the utility of ‘sacrificial’ aryl-perfluoroaryl supramolecular synthons to synthesize sp3-hybridized nanothreads from sp2-enriched reactants. Our strategy features A-B reactant pairs in the form a phenol:pentafluorophenol co-crystal that is preorganized for an electronically-biased sequence-defined polymerization. The polymerization, initiated at 12 GPa, affords an alternating copolymer featuring exogenous –OH functionalities. The nanothread polymer exhibits crystallinity, as evidenced by a hexagonal X-ray diffraction pattern. The presence of the external substitution is confirmed through IR and Raman spectroscopy. Our approach realizes the first example of a functionalized sequence-defined nanothread through sacrificial supramolecular preorganization and presents a further approach for de novo design of complex nanothreads.</p></div></div></div>
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Margaret Gerthoffer; Sikai Wu; Bo Chen; Tao Wang; Steven Huss; Shalisa M Oburn; Vincent Crespi; John Badding; Elizabeth Elacqua
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Supramolecular Chemistry (Org.); Polymerization (Polymers)
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-05-28
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bc2469df45768f43f80/original/sacrificial-supramolecular-assembly-and-pressure-induced-polymerization-toward-sequence-defined-functionalized-nanothreads.pdf
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63fdee2f897b18336f40609f
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10.26434/chemrxiv-2023-rdtfc
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Active Site Descriptors from 95Mo NMR Signatures of Silica-supported Mo-based Olefin Metathesis Catalysts
|
The catalytic activity of silica-supported molybdenum oxides for olefin metathesis depends strongly on the metal loading and preparation conditions indicating that the nature and/or amounts of the active sites vary across catalysts. This is illustrated by comparing Mo-based (pre)catalysts prepared by impregnation with different metal loadings (2.5-15.6 wt% Mo) and a well-defined model material (2.3 wt% Mo) prepared via a surface organometallic chemistry (SOMC) synthetic approach. Analyses of FTIR, UV-vis, and Mo K-edge X-ray absorption spectra provide strong evidence that all the (pre)catalysts are composed predominantly of similar isolated Mo dioxo sites; however, they exhibit very different proportions of reducible surface sites and catalytic reaction properties. Specifically, the SOMC-derived catalyst is more active for liquid and gas-phase olefin metathesis conditions than a classical catalyst of similar Mo loading by a factor of 1.5-1.9, depending on precise reaction conditions. Most notably, solid-state 95Mo NMR spectra of these catalysts show distinct features, particularly evident under state-of-the-art high-field (28.2 T) measurement conditions where at least four distinct types of surface Mo dioxo sites are resolved, the distribution of which depends on the preparation methods. In particular, the presence of Mo sites with a specific deshielded 95Mo NMR signal correlates with the catalysts reducibility and metathesis activity; such sites are most prominent in the SOMC-derived catalyst. First-principles calculations show that the 95Mo NMR parameters, specifically the isotropic chemical shift and quadrupolar coupling constant, are good descriptors for local strain and coordination environment: acute (SiO-Mo(O)2-OSi) angles and low coordination numbers at the Mo sites leads to highly deshielded iso chemical shifts and small CQ values, respectively. Orbital and natural chemical shift analyses indicate that the deshielded 95Mo iso values of strained species are directly related to low LUMO energies, consistent with their higher reducibility and corresponding reactivity. Overall, this study shows that solid-state NMR is particularly powerful for the identification of distinct supported Mo dioxo species and that their 95Mo chemical shifts are related to their specific local electronic structures, providing a powerful descriptor for the propensity of Mo sites towards reduction and the formation of active sites.
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Zachariah Berkson; Ran Zhu; Christian Ehinger; Lukas Lätsch; Stefan Schmid; Darryl Nater; Stephan Pollitt; Olga Safonova; Snædís Björgvinsdóttir ; Alexander Barnes; Yuriy Román-Leshkov; Gregory Price; Glenn Sunley; Christophe Copéret
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Physical Chemistry; Inorganic Chemistry; Catalysis; Spectroscopy (Inorg.); Heterogeneous Catalysis; Spectroscopy (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-03-01
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fdee2f897b18336f40609f/original/active-site-descriptors-from-95mo-nmr-signatures-of-silica-supported-mo-based-olefin-metathesis-catalysts.pdf
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639b4458a2da4bcbc604f9ac
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10.26434/chemrxiv-2022-gn7r2-v2
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Process-informed adsorbent design guidelines for direct air capture
|
Direct air capture using solid adsorbents is a proven technology critical to reducing our net greenhouse gas emissions to zero and beyond. Currently, academic research into the technology mainly focuses on the development of new adsorbents. However, there is a discord between the adsorbent design and process performance. Many materials scientists focus on maximising metrics such as the CO2 capacity of their adsorbent. Here, we combine detailed process modelling, machine learning, and extensive global sensitivity analysis, which entails varying all of the model parameters together, on a direct air capture process to show that the dry CO2 adsorption capacity does not influence process performance for an amine-functionalised adsorbent operating in a temperature vacuum swing adsorption (TVSA) process, while it is important in a steam-assisted TVSA (S-TVSA) process. In fact, adsorption kinetics, density, and thermal conductivity are all critical attributes to obtaining a low energy penalty and reduced costs. The analysis also highlights the importance of heat transfer, directing process engineers to (alternative) adsorber designs that maximise this. By an in-depth evaluation of how process performance indicators are affected by materials properties and process operating parameters, this work provides guidance to both material scientists and process engineers towards the design of a "unicorn adsorbent" and intensified DAC processes. This will improve the performance of solid adsorbent direct air capture and help drive down the costs of this vital technology to avert the worst impacts of climate change.
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John Young; Fergus Mcilwaine; Berend Smit; Susana Garcia; Mijndert van der Spek
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Energy; Chemical Engineering and Industrial Chemistry
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CC BY 4.0
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CHEMRXIV
|
2022-12-16
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639b4458a2da4bcbc604f9ac/original/process-informed-adsorbent-design-guidelines-for-direct-air-capture.pdf
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64607555f2112b41e98559f3
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10.26434/chemrxiv-2023-m6t16
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Simulating Excited-State Complex Ensembles: Fluorescence and Solvatochromism in Amine-Arene Exciplexes
|
Exciplexes are excited-state complexes formed as a result of partial charge-transfer from the donor to the acceptor species. They are formed when one moiety of the donor-acceptor pair is electronically excited. The arene-amine exciplex formed between oligo-(p-phenylene) (OPP) and triethylamine (TEA) is of interest in photoredox catalysis for CO2 reduction as it can compete with complete quenching and electron transfer to OPP. Formation of the exciplex can therefore hinder the generation of a radical anion OPP·− necessary for subsequent CO2 reduction. We report an implementation of a workflow automating quantum-chemistry calculations that generate and characterize an ensemble of structures to represent this exciplex state. We use FireWorks, Pymatgen, and Custodian python packages for high-throughput ensemble generation via TDDFT optimization, verification of excited-state minima, and exciplex characterization with natural transition orbitals, exciton analysis, excited-state Mulliken charges, and energy decomposition analysis. Fluorescence spectra computed for these ensembles using Boltzmann-weighted contributions from each structure agree better with experiment than our previous work that employed a single representative exciplex structure (Kron, K. J. et al. J. Phys. Chem. A, 2022, 126, 2319–2329). The ensemble description of the exciplex state also reproduces an experimentally observed red shift of the emission spectrum of [OPP-4−TEA]∗ relative to [OPP-3−TEA]∗. The workflow developed here streamlines otherwise labor-intensive calculations that would require significant user intervention.
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Abhilash Patra; Anna Krylov; Shaama Mallikarjun Sharada
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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
|
2023-05-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64607555f2112b41e98559f3/original/simulating-excited-state-complex-ensembles-fluorescence-and-solvatochromism-in-amine-arene-exciplexes.pdf
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60c75900842e6566f3db4944
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10.26434/chemrxiv.13618988.v2
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The Key Role of the Latent N-H Group in Milstein's Catalyst for Ester Hydrogenation
|
<p>We previously demonstrated that Milstein’s seminal
diethylamino-substituted PNN-pincer-ruthenium catalyst for ester hydrogenation is
activated by dehydroalkylation of the pincer ligand, releasing ethane and
eventually forming an NHEt-substituted derivative that we proposed is the
active catalyst. In this paper, we present a computational and experimental mechanistic
study supporting this hypothesis. Our DFT analysis shows that the minimum-energy
pathways for hydrogen activation, ester hydrogenolysis, and aldehyde
hydrogenation rely on the key involvement of the nascent N-H group. We have
isolated and crystallographically characterized two catalytic intermediates, a
ruthenium dihydride and a ruthenium hydridoalkoxide, the latter of which is the
catalyst resting state. A detailed kinetic study shows that catalytic ester
hydrogenation is first-order in ruthenium and hydrogen, shows saturation
behavior in ester, and is inhibited by the product alcohol. A global fit of the
kinetic data to a simplified model incorporating the hydridoalkoxide and
dihydride intermediates and three kinetically relevant transition states showed
excellent agreement with the results from DFT. <b></b></p><br />
|
John Pham; Cole Jarczyk; Eamon Reynolds; Sophie Kelly; Thao Kim; Tianyi He; Jason Keith; Anthony Chianese
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Catalysis; Kinetics and Mechanism - Organometallic Reactions; Theory - Organometallic
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CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75900842e6566f3db4944/original/the-key-role-of-the-latent-n-h-group-in-milstein-s-catalyst-for-ester-hydrogenation.pdf
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60c748da337d6c5097e2760c
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10.26434/chemrxiv.11985231.v1
|
Possible Drug Candidates for COVID-19
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COVID-19, has been officially labeled as a pandemic by the World Health Organisation. This paper presents cloperastine and vigabatrin as two possible drug candidates for combatting the disease along with the process by which they were discovered. The paper presents the discoveries made by using a connectivity map and the docking configurations used to simulate the docking.
|
Navan Chauhan
|
Analytical Chemistry - General; Drug Discovery and Drug Delivery Systems
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CC BY 4.0
|
CHEMRXIV
|
2020-03-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748da337d6c5097e2760c/original/possible-drug-candidates-for-covid-19.pdf
|
60c74ae0842e6578f7db2ffb
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10.26434/chemrxiv.12254393.v1
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Molecular Structure of Pyrazinamide: a Critical Assessment of Modern Gas Electron Diffraction Data from Three Laboratories
|
<div><div>Accuracy and precision of molecular parameters determined by modern gas electron diffraction method</div><div>have been investigated. Diffraction patterns of gaseous pyrazinamide have been measured independently in three laboratories, in Bielefeld (Germany), Ivanovo (Russia) and Moscow (Russia). All data sets have been analysed in equal manner using highly controlled background elimination procedure and flexible restraints in molecular structure refinement. In detailed examination and comparison of the obtained results we have determined the average experimental precision of 0.004 Å for bond lengths and 0.2 degrees for angles. The corresponding average deviations of the refined parameters from the ae-CCSD(T)/ccpwCVTZ theoretical values were 0.003 Å and 0.2 degrees. The average precision for refined amplitudes of interatomic vibrations was determined to be 0.005 Å. It is recommended to take into account these values in calculations of total errors for refined parameters of other molecules with comparable complexity.</div></div><div><br /></div>
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Arseniy A. Otlyotov; Georgiy V. Girichev; Anatolii N. Rykov; Timo Glodde; Yury Vishnevskiy
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Spectroscopy (Physical Chem.); Structure
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-05-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ae0842e6578f7db2ffb/original/molecular-structure-of-pyrazinamide-a-critical-assessment-of-modern-gas-electron-diffraction-data-from-three-laboratories.pdf
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65252ef68bab5d2055071cb0
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10.26434/chemrxiv-2023-5f3q9
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MetalDock: an open access docking tool for easy and reproducible docking of metal complexes
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Despite the proven potential of metal complexes as therapeutics, the lack of computational tools available for high-throughput screening their interaction with proteins is a limiting factor towards clinical developments. To address this challenge, we introduce MetalDock, an easy-to-use, open access docking program for docking metal complexes to proteins. Our tool integrates the AutoDock docking engine with three quantum software packages to automate the docking of metal-organic complexes to proteins. We used a Monte Carlo sampling scheme to obtain the missing Lennard Jones parameters for 12 metal atom types and demonstrated that these parameters generalise exceptionally well. Our results show that the poses obtained by MetalDock are highly accurate as they predict the binding geometries experimentally determined by crystal structures with high spatial reproducibility. Three different case studies are presented which demonstrate the versatility of MetalDock for the docking of diverse metal-organic compounds to different biomacromolecules.
|
Matthijs Hakkennes; Francesco Buda; Sylvestre Bonnet
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
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CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65252ef68bab5d2055071cb0/original/metal-dock-an-open-access-docking-tool-for-easy-and-reproducible-docking-of-metal-complexes.pdf
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66023f24e9ebbb4db98821fe
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10.26434/chemrxiv-2024-6nhr1
|
Accurate and robust static hydrophobic contact angle measurements using machine learning
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Recent years has seen a surge in new approaches to material discovery. However, in order to validate and characterise these novel materials that are being discovered at unprecedented speeds, methods of experimental characterisation must match the pace of discovery. This is only possible through the use of high throughput autonomous approaches. % Automation addresses sources of human error To address this need, and to overcome the shortcomings in present methods, we present a machine learning (ML) approach to static contact angle measurement that is more accurate and faster than current best practice methods. The ML model was trained on a large data-set (> 7.2 million) generated via solutions of the Young-Laplace equation where the contact angle is known a priori, removing all sources of error from human input. The data-set included the effects of surface roughness, gravity, the size of drop relative to the image, reflections of the drop on the surface, and contact angles from 110° to 180°. The presented ML model (valid for contact angles >110°), in combination with a new automated image and contour processing approach, is shown to be more accurate than other methods when benchmarked against an experimental data-set, with an estimated error of 1 degree. The ML model is also two orders of magnitude faster at predicting contact angles than Young-Laplace fitting (the current best practice approach). The accuracy and speed of the presented approach provides a viable pathway towards robust and reproducible high-throughput contact angle analysis. The open-source software Conan-ML is provided for use and development of new approaches to goniometry.
|
Daniel Shaw; Ran Liang; Tian Zheng; Jianzhong Qi; Joseph Berry
|
Physical Chemistry; Analytical Chemistry; High-throughput Screening; Physical and Chemical Properties; Surface; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-03-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66023f24e9ebbb4db98821fe/original/accurate-and-robust-static-hydrophobic-contact-angle-measurements-using-machine-learning.pdf
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60c7531b4c89191656ad4267
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10.26434/chemrxiv.13387934.v1
|
Probing the Catalytically Active Species in POM-Catalyzed DNAmodel Hydrolysis
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<div>Phosphoester hydrolysis is an important chemical step in DNA repair. One archetypal molecular model of phosphoesters is para-nitrophenylphosphate (pNPP). It has been shown previously that the presence of molecular metal oxide [Mo7O24]6– may catalyse the hydrolysis of pNPP through the partial decomposition of polyoxomolybdate framework resulting in a [(PO4)2Mo5O15]6– product. Real-time monitoring of the catalytic system using electrospray ionisation mass spectrometry (ESI-MS) provided a glance into the species present in the reaction mixture. Following up on the obtained spectrometric data, Density Functional Theory (DFT) calculations were carried out to characterise the hypothetical intermediate [Mo5O15(pNPP)2(H2O)6]6–</div><div>that would be required to form under the</div><div>hypothesised transformation. Surprisingly, our results point to the dimeric [Mo2O8]4- anion resulting from the decomposition of [Mo7O24]6– as the active catalytic species involved in the hydrolysis of pNPP rather than the originally assumed {Mo5O15} skeleton. A similar study was carried out involving the same species but substituting Mo by W. The mechanism involving W species showed a higher barrier and less stable products in agreement with the non-catalytic effect found in experimental results.</div>
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Frederico Martins; Ángel Sanchez-Gonzalez; Jose Lanuza; Haralampos Miras; Xabier Lopez; Nuno Bandeira; Adrià Gil
|
Computational Chemistry and Modeling
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CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7531b4c89191656ad4267/original/probing-the-catalytically-active-species-in-pom-catalyzed-dn-amodel-hydrolysis.pdf
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60c73cc9567dfe6688ec356c
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10.26434/chemrxiv.14769693.v1
|
Synthesis, Photophysical Properties and Catalytic Activity of Ƙ3-SCS Pincer Palladium (II) Complex of N,N'-Di-Tert-Butylbenzene-1,3-Dicarbothioamide Supported by DFT Analysis
|
The title complex [PdCl(L)] (1), is obtained from the reaction of SCS pincer ligand HL (where, HL = N,N'-di-tert-butylbenzene-1,3-dicarbothioamide) with lithium tetrachloropalladate (II) in methanol. The compound 1 is characterized by elemental analysis, FTIR, 1H, and 13C-NMR spectroscopy, UV-Vis spectroscopy, powder X-ray diffraction and X-ray crystallographic techniques. At room temperature, 1 emits luminescence light of wavelength 460 nm in the solid state upon excitation by UV light of wavelength 280 nm. The average emission lifetime indicates that, both the ligand and complex emission is fluorescence in nature and involves mainly ligand centers π-π* deexcitation. It also shows good catalytic activity towards Mizoroki-Heck and Suzuki-Miyaura cross-coupling reactions of aryl bromides with tert-butyl acrylate and p-tolylboronic acid respectively. For both type of reactions, more than 99% conversion of the substrates is found to occur for electronically activated p-nitro bromobenzene using 1 mol % of 1. Further, modern DFT calculations are performed to decipher the mechanistic insight on the preferable pathways of the Mizoroki-Heck cross-coupling reaction. Stepwise free energy of reactions for various probable reaction pathways suggest that the catalytic route has profound preference for Pd(0)-Pd(II) over Pd(II)-Pd(IV) pathway.<br />
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Debasish Das; S. Kannan; Mukesh Kumar; Biswajit Sadhu; Liladhar B. Kumbhare
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Coordination Chemistry (Inorg.); Organometallic Compounds; Homogeneous Catalysis; Catalysis; Coordination Chemistry (Organomet.); Transition Metal Complexes (Organomet.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-06-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc9567dfe6688ec356c/original/synthesis-photophysical-properties-and-catalytic-activity-of-3-scs-pincer-palladium-ii-complex-of-n-n-di-tert-butylbenzene-1-3-dicarbothioamide-supported-by-dft-analysis.pdf
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60c7593b702a9bc9d318ce7a
|
10.26434/chemrxiv.14672136.v1
|
Catalytic Benzolactamization Through Isonitrile Insertion Enabled 1,4-Palladium Shift
|
<b>Isoindolinone is a class
of versatile <i>N</i>-heterocycles embedded in
many bioactive molecules and natural products. The invention of new methods to synthesize
these heterocyclic compounds with easily accessible chemicals is always attractive.
Herein, a conceptually novel approach to access this bicyclic system via isonitrile
insertion enabled 1,4-pallaidum shift is described. Compared with conventional
isonitrile participated C-H bond activation, both carbon and nitrogen atoms in
isonitrile moiety are engaged in new bond formation. Notably, two different
isoindolinones can be obtained selectively by switching the bases employed. Mechanistic
studies including DFT calculations have shed lights on the reaction mechanism
and explained the selectivity led to different products. Moreover, the power of
current benzolactamization is further demonstrated by providing concise routes
to key intermediates of indoprofen, indobufen, aristolactams, lennoxamine and
falipamil.</b>
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Fulin Zhang; Ruihua Zhao; Lei Zhu; Yinghua Yu; Saihu Liao; Zhi-Xiang Wang; Xueliang Huang
|
Organic Synthesis and Reactions
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CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7593b702a9bc9d318ce7a/original/catalytic-benzolactamization-through-isonitrile-insertion-enabled-1-4-palladium-shift.pdf
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64ba520ab053dad33aa35cc3
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10.26434/chemrxiv-2023-kpx9w
|
ASHA:A Chemical Sapce Navigator app for Dual–Target-Directed-Inhibitor design
|
Motivation: Screening large libraries virtually can be impractical and computationally expensive, especially when designing dual inhibitors. This is because each target must be screened separately, which further increases the time and resources required. One solution to this problem is to explore the biologically relevant chemical space for both targets, as visualizing chemical spaces simplifies the analysis of molecular datasets and reduces information to the level of human perception. This approach has potential applications in chemical library design, high-throughput screening, diversity analysis, and outlier detection. To aid in dual-inhibitor design, we have developed a freely available online tool that allows for the visualization and navigation of the chemical space of two targets of interest. By comparing these spaces, overlapping chemical space can be identified, facilitating the development of dual inhibitors. Results: This programme gives the user the ability to explore the overlap chemical space, fragment and ring distribution, shape analysis and oral drug availability via lipinsiki rule of five of user-defined molecules of interest for dual inhibitor-design and dataset similarity check. This web-app requires only a 3D SDF file of inhibitors against a target of interest to be uploaded, after which the user need only click a button to see the results. Web-app can be access through: https://chemproj1-b0cgo4zrqd.streamlit.app/
|
akhil kumar
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
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CHEMRXIV
|
2023-07-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ba520ab053dad33aa35cc3/original/asha-a-chemical-sapce-navigator-app-for-dual-target-directed-inhibitor-design.pdf
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60c7599cbdbb897b65a3b0a1
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10.26434/chemrxiv.14672685.v2
|
Sulfonium Ion-Promoted Traceless Schmidt Reaction of Alkyl Azides
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Schmidt reaction by sulfonium ions is described. General primary,
secondary, and tertiary alkyl azides were converted to the corresponding
carbonyl or imine compounds without any trace of the activators. This
bond scission reaction showcased ring-opening, -expansion, and one-pot
further conversion of the substrates as well as the application with C-H
azidation.
|
Bayu Ardiansah; Hiroki Tanimoto; Takenori Tomohiro; Tsumoru Morimoto; Kiyomi Kakiuchi
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Organic Synthesis and Reactions
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-05-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7599cbdbb897b65a3b0a1/original/sulfonium-ion-promoted-traceless-schmidt-reaction-of-alkyl-azides.pdf
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66e00b4e51558a15ef9430ea
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10.26434/chemrxiv-2024-ltgwp
|
Transfection of Macrophages with PAMAM-Pyrrolidone Dendrimers Complexed with Cu(II)- or Zn(II)- ions as Carriers of Genetic Material.
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Zn(II) and Cu(II) complexes of a generation 4 DAB-core PAMAM dendrimer with 5-methoxycarbonyl-2-pyrrolidinone (Pyrr) surface groups were prepared and investigated as carriers for siRNA in different cell lines. The Cu(II) complex (CuSO4)18@DAB-dendr-(Pyrr)64 is significantly better than lipofectamine for transfection of macrophages, while the Zn(II) complex only show low transfection activity. Both complexes are more cytotoxic than the free metal ions.
|
Anna Janaszewska; Monika Marcinkowska; Piotr Tarach; Julia Debicka; Barbara Klajnert-Maculewicz; Jørn Bolstad Christensen
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Biological and Medicinal Chemistry; Nanoscience; Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY 4.0
|
CHEMRXIV
|
2024-09-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e00b4e51558a15ef9430ea/original/transfection-of-macrophages-with-pamam-pyrrolidone-dendrimers-complexed-with-cu-ii-or-zn-ii-ions-as-carriers-of-genetic-material.pdf
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660172ebe9ebbb4db97c85d6
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10.26434/chemrxiv-2024-mwjvw
|
Long Excited-State Lifetimes in Three-Coordinate Copper(I) Com-plexes via Triplet–Triplet Energy Transfer to Pyrene-Decorated Isocy-anides
|
There has been much effort to improve excited-state lifetimes in photosensitizers based on earth-abundant first-row transition metals. Copper(I) complexes have gained significant attention in this field, and in most cases, sterically-driven approaches are used to optimize their lifetimes. This study presents a series of three-coordinate copper(I) complexes (Cu1–Cu3) where the excited-state lifetime is extended by triplet-triplet energy transfer. The heteroleptic compounds feature a cyclohexyl-substituted β-diketiminate (CyNacNacMe) paired with aryl isocyanide ligands, giv-ing the general formula Cu(CyNacNacMe)(CN-Ar) (CN-dmp = 2,6-dimethylphenyl isocyanide for Cu1; CN-pyr = 1-pyrenyl isocyanide for Cu2; CN-dmp-pyr = 2,6-dimethyl-4-(1-pyrenyl)phenyl isocyanide for Cu3). The nature, energies, and dynamics of the low-energy triplet excited states are assessed with a combination of photoluminescence measurements at room temperature and 77 K, ultrafast transient absorp-tion (UFTA) spectroscopy, and DFT calculations. The complexes featuring pyrene-decorated isocyanides (Cu2 and Cu3) exhibit extended excited-state lifetimes resulting from triplet–triplet energy transfer (TTET) between the short-lived charge-transfer excited state (3CT) and the long-lived pyrene-centered triplet state (3pyr). This TTET process is irreversible in Cu3, producing exclusively the 3pyr state, and in Cu2 the 3CT and 3pyr states are nearly isoenergetic, enabling reversible TTET and long-lived 3CT luminescence. The improved photophysical proper-ties in Cu2 and Cu3 result in photocatalytic activity for stilbene E/Z isomerization via triplet energy transfer and photoredox reactivity in trans-formations involving hydrodebromination and C–O bond activation. These results illustrate that the extended excited-state lifetimes achieved through TTET resulted in newly conceived photosynthetically-relevant earth-abundant transition metal complexes.
|
Dooyoung Kim; Michael C. Rosko; Felix N. Castellano; Thomas G. Gray; Thomas S. Teets
|
Physical Chemistry; Inorganic Chemistry; Catalysis; Transition Metal Complexes (Inorg.); Photocatalysis; Photochemistry (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660172ebe9ebbb4db97c85d6/original/long-excited-state-lifetimes-in-three-coordinate-copper-i-com-plexes-via-triplet-triplet-energy-transfer-to-pyrene-decorated-isocy-anides.pdf
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642b2d48a029a26b4cdca6cd
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10.26434/chemrxiv-2023-qqjkn
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Comonomer Isomers Result in Varied Optical Properties for Long Wavelength Infrared-Transmitting ORMOCHALC Polymers
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Inverse vulcanization is a method by which sulfur is combined with comonomer molecules to develop stable materials termed organically modified chalcogenide (ORMOCHALC) polymers. Although various comonomers have been used in the fabrication of ORMOCHALC polymers in prior studies, this study was performed to determine the effect of using molecular isomers, as comonomers in separate reactions, on the optical properties of ORMOCHALC polymers. For the study, meta-divinylbenzene (m-DVB) and para-divinylbenzene (p-DVB) were separately combined with sulfur in equivalent atomic percentage amounts to form poly(S-r-m-DVB) and poly(S-r-p-DVB), respectively. The use of these isomers resulted in polymers with notable differences in their optical properties, including the polymer color, optical transmission and refractive index. The impact of comonomer selection on the optical character of ORMOCHALC polymers is investigated and the results detailed.
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Darryl Boyd; Vinh Nguyen; Frederic Kung; Nia Pollard; Jason Myers; Daniel Gibson; Collin McClain; Colin Baker; Andre Clayborne; Woohong Kim; Jasbinder Sanghera
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Materials Science; Polymer Science; Hybrid Organic-Inorganic Materials; Optical Materials; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2023-04-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642b2d48a029a26b4cdca6cd/original/comonomer-isomers-result-in-varied-optical-properties-for-long-wavelength-infrared-transmitting-ormochalc-polymers.pdf
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60e0c13278e478a482b6c9bc
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10.26434/chemrxiv-2021-47tqn
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Amide-to-ester substitution as a strategy for optimizing PROTAC permeability and cellular activity
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Bifunctional PROTAC degraders belong to "beyond Rule of 5" chemical space, and criteria for predicting their drug-like properties are underdeveloped. PROTAC components are often combined via late-stage amide couplings, due to the reliability and robustness of amide bond formation. Amides, however, can give rise to low cellular permeability and poor ADME properties. We hypothesized that a bioisosteric replacement of an amide with a less polar ester could lead to improvements in both physicochemical properties and bioactivity. Using a library of model compounds, bearing either amides or esters at various linker-warhead junctions, we identify parameters for optimal compound lipophilicity and permeability. We next applied these learnings to design a set of novel amide-to-ester substituted, VHL-based BET degraders with increased permeability. Our ester-PROTACs remarkably retained intracellular stability, were overall more potent degraders than their amide counterparts and showed an earlier onset of the hook effect. These enhanced cellular features were found to be driven by greater cell permeability rather than improvements in ternary complex formation. This largely unexplored amide-to-ester substitution therefore provides a simple and practical strategy to enhance PROTAC permeability and degradation performance. Such approach could prove equally beneficial to other classes of beyond Ro5 molecules.
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Victoria Klein; Adam Bond; Conner Craigon; R. Scott Lokey; Alessio Ciulli
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Biological and Medicinal Chemistry; Biophysics; Chemical Biology; Drug Discovery and Drug Delivery Systems
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CC BY 4.0
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CHEMRXIV
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2021-07-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e0c13278e478a482b6c9bc/original/amide-to-ester-substitution-as-a-strategy-for-optimizing-protac-permeability-and-cellular-activity.pdf
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67cf47076dde43c9084f4e5f
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10.26434/chemrxiv-2025-r7p8m
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Transformation of pseudocapacitance at rate-determining step reveals the onset potential for oxygen evolution reaction at the Pt surface
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Onset potential is a measure of electrocatalytic activity and depends on the physicochemical processes occurring at the electrocatalyst/electrolyte interface. Conventionally, techniques like tangent intersection as the current transitions from non-Faradaic to Faradaic region are utilized for establishing onset potential. The electrochemical impedance spectroscopy (EIS) analysis can reveal physicochemical processes at the onset potential with the help of equivalent electrical circuits obtained from reaction mechanism analysis (RMA). The circuits estimated from the RMA are arranged into Ladder, Voigt, and Maxwell models. We demonstrate that in all these model circuits, the capacitance generated by the OH adsorption shows the maxima at the onset potential. The nature of adsorbing species is supported by Tafel slope analysis, wherein the low Tafel region, the Tafel slope of 122.5mV/dec indicates S-OH adsorption step as the rate determining step (RDS).
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Maurya Gyanprakash; S Ramanathan; Raj Ganesh Pala
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Physical Chemistry; Catalysis; Energy; Electrocatalysis; Electrochemistry - Mechanisms, Theory & Study
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CC BY NC ND 4.0
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CHEMRXIV
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2025-03-13
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cf47076dde43c9084f4e5f/original/transformation-of-pseudocapacitance-at-rate-determining-step-reveals-the-onset-potential-for-oxygen-evolution-reaction-at-the-pt-surface.pdf
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