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6401c2c09789de3dd9d78562
|
10.26434/chemrxiv-2022-mbzrv-v2
|
Polymeric carbon nitride-based photocathodes for visible light-driven selective reduction of oxygen to hydrogen peroxide
|
Polymeric carbon nitrides (PCN) are sustainable, tunable, non-toxic and chemically stable materials that represent highly promising heterogeneous photocatalysts for light-driven hydrogen peroxide production via selective reduction of dioxygen. However, most of the studies on photocatalytic H2O2 production using PCN-based photocatalysts reported so far have used PCN powder suspensions and have been carried out in the presence of additional (sacrificial) electron donors, such as aliphatic or aromatic alcohols. Herein, we report the first multicomponent hybrid photocathode based on PCN that is capable of selective reduction of dioxygen to H2O2 under visible light irradiation (420 nm LED). A comparative analysis of various photocathode architectures is carried out using electronic absorption spectroscopy, surface photovoltage spectroscopy, open-circuit photopotential spectroscopy, and photocurrent measurements, including in-situ detection of formed H2O2 using microelectrodes. Notably, the ability of PCN-based photocathodes to catalyze the light-driven reduction of O2 to H2O2 in the absence of any additional electron donor is unambiguously demonstrated. Our study thus highlights the intrinsic nature of the photocatalytic activity of PCN in H2O2 production, and paves the way for the development of further PCN-based photocathodes in which PCN could be coupled with more effective light absorbers to increase the overall performance.
|
Hanna Braun; Dariusz Mitoraj; Joanna Kuncewicz; Andreas Hellmann; Mohamed M. Elnagar; Joachim Bansmann; Christine Kranz; Timo Jacob; Wojciech Macyk; Radim Beranek
|
Materials Science; Catalysis; Photocatalysis; Redox Catalysis; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-03-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6401c2c09789de3dd9d78562/original/polymeric-carbon-nitride-based-photocathodes-for-visible-light-driven-selective-reduction-of-oxygen-to-hydrogen-peroxide.pdf
|
6494345f853d501c005361af
|
10.26434/chemrxiv-2023-643mn
|
Time-resolved Mn2+–NO and NO–NO distance measurements reveal that catalytic asymmetry regulates alternating access in an ABC transporter
|
ATP-binding cassette (ABC) transporters shuttle diverse substrates across biological membranes. Transport is often achieved through a transition between an inward-facing (IF) and an outward-facing (OF) conformation of the transmembrane domains (TMDs). Asymmetric nucleotide-binding sites (NBSs) are present among several ABC subfamilies and their functional role remains elusive. Here we addressed this question using concomitant NO–NO, Mn2+–NO, and Mn2+–Mn2+ pulsed electron-electron double resonance spectroscopy of TmrAB in a time resolved manner. This type IV ABC transporter undergoes a reversible transition in the presence of ATP with a significantly faster forward transition. The impaired degenerate NBS stably binds Mn2+–ATP and Mn2+ is preferentially released at the active consensus NBS. ATP hydrolysis at the consensus NBS considerably accelerates reverse transition. Both NBSs fully open during each conformational cycle and the d-NBS may regulate the overall kinetics of this process.
|
Michael Rudolph; Robert Tampé; Benesh Joseph
|
Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Spectroscopy (Physical Chem.); Transport phenomena (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6494345f853d501c005361af/original/time-resolved-mn2-no-and-no-no-distance-measurements-reveal-that-catalytic-asymmetry-regulates-alternating-access-in-an-abc-transporter.pdf
|
639f4210518c1684723043e3
|
10.26434/chemrxiv-2022-nxhd6
|
Biodegradable Polyphosphoester Micelles Act as Both Background-free 31P Magnetic Resonance Imaging Agents and Drug Nanocarriers
|
Imaging and tracing materials inside the body is essential to develop functional materials for personalized therapies, including drug delivering nanocarriers and artificial tissues. Magnetic Resonance Imaging (MRI) is a key whole-body imaging technology, where heteronuclear MRI agents enable background-free, quantitative labeling. However, many MRI agents raised concerns due to environmental pollution and organ accumulation. As a solution, we developed a biodegradable, biocompatible polymer platform for heteronuclear 31P magnetic resonance imaging (MRI). We introduce polyphosphoester colloids for heteronuclear MRI using 31P-nucleus. 31P MRI has been severely hampered by unfavorable magnetic resonance properties of 31P, including intrinsic background and low sensitivity. We overcame these fundamental challenges in imaging of 31P by tailoring molecular and structural features of polymeric colloids. We have synthesized gradient-type polyphosphonate copolymers that self-assemble into well-defined micelles. The gradient leads to favorable MRI characteristics compared with homo- and block copolymers. Background-free imaging and biodegradation were proven in vivo in Manduca sexta. Furthermore, we demonstrate by encapsulation of the potent drug PROTAC ARV-825 that these amphiphilic copolymers can simultaneously deliver hydrophobic drugs and thus enable theranostics. We present a unique platform of biocompatible, degradable polyphosphoesters that inherently act as background-free MRI agents and delivery vehicles.
|
Olga Koshkina; Timo Rheinberger; Vera Flocke; Anton Windfelder; Pascal Bouvain; Naomi M. Hamelmann; Jos M.J. Paulusse; Hubert Hubert Gojzewski; Ulrich Flögel; Frederik Wurm
|
Biological and Medicinal Chemistry; Polymer Science; Nanoscience; Drug delivery systems; Organic Polymers; Polymer chains
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639f4210518c1684723043e3/original/biodegradable-polyphosphoester-micelles-act-as-both-background-free-31p-magnetic-resonance-imaging-agents-and-drug-nanocarriers.pdf
|
6787c29b81d2151a02427093
|
10.26434/chemrxiv-2024-3lvxl-v2
|
RhFe Alloying Promotes the Efficient and Selective Conversion of Syngas to Ethanol
|
The direct conversion of syngas to ethanol is a promising route for the sustainable production of value-added chemicals and fuels. While Fe-promoted Rh-based catalysts have long been studied because of their notable activity and selectivity towards ethanol, the nature of Rh-Fe interaction and the catalyst structure under reaction conditions remain poorly understood due to the intrinsic complexity of heterogeneous catalysts prepared by conventional approaches. In this work, we construct well-defined RhFe@SiO2 model catalysts via surface organometallic chemistry (SOMC), composed of small and narrowly distributed nanoparticles supported on silica. Such RhFe@SiO2 catalyst converts syngas into ethanol, reaching an overall selectivity of 38% ethanol among all products at 8.4% CO conversion, while the non-promoted Rh@SiO2 catalyst mostly yields methane (selectivity > 90%) and no ethanol. Detailed in situ XAS and DRIFTS studies reveal that the RhFe@SiO2 catalyst corresponds to an Rh-Fe alloy with ca. 3:1 Rh/Fe ratio alongside residual FeII single site. The alloy is stable under working conditions, promoting high activity and ethanol selectivity.
|
Zhou Wei; Scott Docherty; Erwin Lam; Christian Ehinger; Xiaoyu Zhou; Yuhui Hou; Paco Laveille; Christophe Copéret
|
Catalysis; Heterogeneous Catalysis
|
CC BY NC 4.0
|
CHEMRXIV
|
2025-01-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6787c29b81d2151a02427093/original/rh-fe-alloying-promotes-the-efficient-and-selective-conversion-of-syngas-to-ethanol.pdf
|
65561ad0dbd7c8b54b63319a
|
10.26434/chemrxiv-2023-3fk6j
|
Computational Discovery of Codoped Single-Atom Catalysts for Methane-to-Methanol Conversion
|
The absence of a synthetic catalyst that can selectively oxidize methane to methanol motivates extensive study of single-site catalysts that possess a high degree of tunability in their coordination environments and share similarities with natural enzymes that can catalyze this reaction. Single-atom catalysts (SACs), and in particular doped graphitic SACs, have emerged as a promising family of materials due to their high atom economy and scalability, but SACs have yet to be exhaustively screened for methane-to-methanol conversion. Modulating the coordination environment near single metal sites by means of codopants, we carry out a large-scale high-throughput virtual screen of 2,048 transition metal (i.e., Mn, Fe, Co, and Ru) SACs codoped with various elements (i.e, N, O, P and S) in numerous spin and oxidation (i.e., M(II)/M(III)) states for the challenging conversion of methane to methanol. We identify that ground state preference is metal- and oxidation-state dependent. We observe a weak negative correlation between the oxo formation energy (ΔE(oxo)) and the energy of hydrogen atom transfer (ΔE(HAT)) thanks to the high variation of the coordination environment. Therefore, codoped SACs demonstrate flexible tunability that disrupts linear free energy relationships in a similar manner to homogeneous catalysts without losing the high scalability of heterogeneous catalysts. We identify energetically favorable catalyst candidates along the Pareto frontier of ΔE(oxo) and ΔE(HAT). Further kinetic analysis reveals an intermediate-spin Fe(II) SAC and a low-spin Ru(II) SAC as promising candidates that merit further experimental exploration.
|
Haojun Jia; Chenru Duan; Ilia Kevlishvili; Aditya Nandy; Mingjie Liu; Heather Kulik
|
Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis
|
CC BY 4.0
|
CHEMRXIV
|
2023-11-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65561ad0dbd7c8b54b63319a/original/computational-discovery-of-codoped-single-atom-catalysts-for-methane-to-methanol-conversion.pdf
|
66ac7012c9c6a5c07acb96f1
|
10.26434/chemrxiv-2024-p71gj
|
The Proteomics Standards Initiative standardized formats for spectral libraries and fragment ion peak annotations: mzSpecLib and mzPAF
|
Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats used for encoding spectral libraries, but none have undergone a standardization process to ensure broad applicability to many applications. As part of the Human Proteome Organization Proteomics Standards Initiative (PSI), we have developed a standardized format for encoding spectral libraries, called mzSpecLib (https://psidev.info/mzSpecLib). It is primarily a data model that flexibly encodes metadata about the library entries using the extensible PSI-MS controlled vocabulary, and can be encoded in and converted between different serialization formats. We have also developed a standardized data model and serialization for fragment ion peak annotations, called mzPAF (https://psidev.info/mzPAF). It is defined as a separate standard since it may be used for other applications besides spectral libraries. The mzSpecLib and mzPAF standards are compatible with existing PSI standards such as ProForma 2.0 and the Universal Spectrum Identifier. The mzSpecLib and mzPAF standards have been primarily defined for peptides in proteomics applications, with basic small molecule support. They could be extended in the future to other fields that need to encode spectral libraries for non-peptidic analytes.
|
Joshua Klein; Henry Lam; Tytus Mak; Wout Bittremieux; Yasset Perez-Riverol; Ralf Gabriels; Jim Shofstahl; Helge Hecht; Pierre-Alain Binz; Shin Kawano; Tim Van Den Bossche; Jeremy Carver; Benjamin A. Neely; Luis Mendoza; Tomi Suomi; Tine Claeys; Thomas Payne; Douwe Schulte; Zhi Sun; Nils Hoffmann; Yunping Zhu; Steffen Neumann; Andrew R. Jones; Nuno Bandeira; Juan Antonio Vizcaíno; Eric W. Deutsch
|
Analytical Chemistry; Mass Spectrometry
|
CC BY 4.0
|
CHEMRXIV
|
2024-08-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ac7012c9c6a5c07acb96f1/original/the-proteomics-standards-initiative-standardized-formats-for-spectral-libraries-and-fragment-ion-peak-annotations-mz-spec-lib-and-mz-paf.pdf
|
64fa0964b338ec988a0fd7e8
|
10.26434/chemrxiv-2023-h82bh
|
Palladium-Catalyzed Regiodivergent Three Component Alkenylamination of Terminal Dienes with Alkyl and Aryl Amines
|
We report a palladium-catalyzed method for 4,3- or 4,1-selective alkenylamination of terminal dienes. Three component couplings proceed with alkenyl triflates and several amines, giving vicinal carboamination with a Xantphos-supported catalyst and distal difunctionalization with a phosphoramidite ligand. Experimental evidence indicates selectivity in the former reactions is largely influenced by the substrate whereas the latter is catalyst controlled, orchestrated by a key pi-stacking interaction among the ligand, solvent, and substrate.
|
Xiaoxiao Ma; Steven Malcolmson
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fa0964b338ec988a0fd7e8/original/palladium-catalyzed-regiodivergent-three-component-alkenylamination-of-terminal-dienes-with-alkyl-and-aryl-amines.pdf
|
60c73fde702a9b2f38189fa2
|
10.26434/chemrxiv.7505654.v1
|
Bioinspired Syntheses of Herqulines B and C from Cyclodipeptide Mycocyclosin
|
<div>A bioinspired approach for the syntheses of herqulines B and C is reported that takes advantage of an Ltyrosine-derived diketopiperazine, a mycocyclosin analog, as a synthetic precursor. The strategy relies on a series of consecutive reductions to adjust the mycocyclosin oxidation state to that observed in the herquline class of natural products. The strained and distorted L-tyrosine-based biaryl system characteristic for mycocyclosin is selectively converted to the 1,4-diketone structural motif common to the herqulines via initial hypervalent iodine-mediated dearomatization and a subsequent directed Birch reduction, enabled by an intramolecular H-source. The piperazine oxidation state is accessible in an iron-catalyzed reduction of the diketopiperazine precursor.</div>
|
Xu Zhu; Christopher C. McAtee; Corinna Schindler
|
Natural Products; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-12-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fde702a9b2f38189fa2/original/bioinspired-syntheses-of-herqulines-b-and-c-from-cyclodipeptide-mycocyclosin.pdf
|
66612b0d91aefa6ce1e2e942
|
10.26434/chemrxiv-2024-3z7tw-v2
|
On-Demand Reverse Design of Polymers with
PolyTAO
|
The forward screening and reverse design of drug molecules, inorganic molecules, and polymers with enhanced properties are vital for accelerating the transition from laboratory research to market application. Specifically, due to the scarcity of large-scale datasets, the discovery of polymers via materials informatics is particularly challenging. Nonetheless, scientists have developed various machine learning models for polymer structure-property relationships using only small polymer datasets, thereby advancing the forward screening process of polymers. However, the success of this approach ultimately depends on the diversity of the candidate pool, and exhaustively enumerating all possible polymer structures through human imagination is impractical. Consequently, achieving on-demand reverse design of polymers is essential.
In this work, we curate an immense polymer dataset containing nearly one million polymeric structure-property pairs based on expert knowledge. Leveraging this dataset, we propose a Transformer-Assisted Oriented pretrained model for on-demand polymer generation (PolyTAO). This model produces polymers with 99.27% chemical validity in top-1 generation mode (approximately 200k generated polymers), representing the highest reported success rate among polymer generative models. Additionally, the average R2 between the properties of the generated polymers and their expected values across 15 predefined properties is 0.96.
To further evaluate the pretrained model's performance in generating polymers with additional user-defined properties for downstream tasks, we conduct fine-tuning experiments on three publicly available small polymer datasets using both semi-template and template-free generation paradigms. Through these extensive experiments, we demonstrate that our pretrained model and its fine-tuned versions are capable of achieving on-demand reverse design of polymers with specified properties, whether in semi-template generation or the more challenging template-free generation scenarios, showcasing its potential as a unified pretrained foundation model for polymer generation.
|
Haoke Qiu; Zhao-Yan Sun
|
Theoretical and Computational Chemistry; Materials Science; Polymer Science; Organic Polymers; Theory - Computational; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66612b0d91aefa6ce1e2e942/original/on-demand-reverse-design-of-polymers-with-poly-tao.pdf
|
66600a6f91aefa6ce1d30621
|
10.26434/chemrxiv-2024-944lx
|
Role of Alkyl Chain Linker in the Conformational Preferences of N-phenylalkylsquaramates and bis-N,N'-diphenylalkylsquaramides
|
The conformational space of small molecules can be exploited to deploy the hierarchical nature of the intermolecular interactions such as hydrogen bonding and π-stacking in the crystal structures. Modulation of the conformational space was achieved by varying the alkyl chain length in N-phenylalkylsquaramates and bis-N,N'-diphenylalkylsquaramides, which were synthesized by condensation of dimethyl squarate with the corresponding phenyl alkylamines. In the crystal structures of these compounds, even though the catemeric N–H···O hydrogen bonding is the primary interaction and the hierarchy in the secondary interactions consisting of π-stacking and H···H bonding leads to a large variation in the molecular structures in the solid state.
|
Aman Pandey; G Naresh Patwari
|
Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66600a6f91aefa6ce1d30621/original/role-of-alkyl-chain-linker-in-the-conformational-preferences-of-n-phenylalkylsquaramates-and-bis-n-n-diphenylalkylsquaramides.pdf
|
61d6f211e7b75133288f3035
|
10.26434/chemrxiv-2022-xncgb
|
Quantum Mechanical Study of Protonation of Oxygen Ligands in the Laccase Active Site Based on X-Ray Structures of Subatomic Resolution
|
Laccases are enzymes catalyzing oxidation of a wide range of organic and inorganic substrates accompanied by molecular oxygen reduction to water. Previously studies of oxygen reduction by laccases have recently been reported. They were based on single-crystal serial X-ray crystallography with increasing absorption doses at subatomic resolution, As a result, coordinates of all non-hydrogen atoms of the active site have been determined with high precision for both oxidized and reduced states of the enzyme. Those data can be used to clarify the mechanism of molecular oxygen reduction by laccases. However, the X-ray data lack information about protonation states of the oxygen ligands involved. Applying quantum mechanical calculations, in the present work protonation of oxygen ligands in the active site of laccase was determined for both reduced and oxidized states of the enzyme (the stable states observed in experiments at reduction of molecular oxygen in laccase). The high precision of X-ray-determined atom coordinates allowed us to simplify preliminary calculations of molecular mechanics for models used in the quantum mechanical calculations.
|
Sergei Gavryushov; Nikolay Kuzmich; Konstantin Polyakov
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Biophysics; Computational Chemistry and Modeling
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-01-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d6f211e7b75133288f3035/original/quantum-mechanical-study-of-protonation-of-oxygen-ligands-in-the-laccase-active-site-based-on-x-ray-structures-of-subatomic-resolution.pdf
|
65f051ce9138d231614f3c89
|
10.26434/chemrxiv-2024-3x9ns-v2
|
Acid-modified, Ti3C2-based MXene as catalysts for up-cycling polyethylene terephthalate
|
Plastics are indispensable materials for packaging and many products from our daily life and their recycling is essential to ensure a circular economy. In this study, −SO3H modified-MXene, Ti3C2, was used as a recoverable solid acid catalyst for up-cycling of polyethylene terephthalate (PET) to terephthalic acid (TPA) and ethylene glycol (EG) by hydrolysis. For the addition of −SO3H groups to the Ti3C2Tx surface (where Tx represents the surface moieties such as -OH or -O), sulfonation with an aryl diazonium salt obtained from sulfanilic acid was employed. X-ray photoelectron and Fourier transform infrared spectroscopies analyses provided a direct indication that sulfonation of the Ti3C2Tx was successfully performed, while X-ray diffraction and Transmission electron microscopy analyses evidence the presence of −SO3H groups in between the layers of Ti3C2Tx due to the increases of the interlayer spacing through the intercalation of functional groups. The higher the concentration of acid groups, the higher the interlayer spacing.
The depolymerisation of PET in water occurred with a very good isolated yield in TPA (99%) for the MXene with the highest amount of sulfonic acid groups. We can conclude that the acidity is mandatory to perform the hydrolysis reaction, in agreement with the acidity measurements, which shows that the MXene modified with the highest amount of derived sulfonic acids contains the highest amount of acidity. Nevertheless, the accessibility to the acidic sites is a key factor that promotes the 2D acid-modified MXene materials as important catalysts for PET up-cycling to TPA.
|
Iuliana Chirica; Anca Mirea; Tudor Suteu; Andrei Kuncser; Stefan Neatu; Mihaela Florea; Michel Barsoum; Florentina Neatu
|
Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f051ce9138d231614f3c89/original/acid-modified-ti3c2-based-m-xene-as-catalysts-for-up-cycling-polyethylene-terephthalate.pdf
|
62c2f312be884bfd9cfa8fc1
|
10.26434/chemrxiv-2022-qj35z-v2
|
Combining Deep Eutectic Solvents with TEMPO-based Polymer Electrodes: Influence of Molar Ratio on Electrode Performance
|
For sustainable storage of electrical energy, all-organic batteries based on redox-active polymers promise to become an alternative to conventional lithium ion batteries. Yet, polymers can only contribute to the goal of an all-organic cell as electrodes or as solid electrolytes. Here, we replace the electrolyte with a sustainable deep eutectic solvent (DES) composed of sodium bis(trifluoromethanesulfonyl)imide (NaTFSI) and N-methylacetamide (NMA), while using poly(2,2,6,6-tetramethylpiperidin-1-yl-oxyl methacrylate) (PTMA) as cathode. The successful combination of a DES with a polymer electrode is reported here for the first time. The electrochemical stability of PTMA electrodes in the DES at the eutectic molar ratio of 1:6 is comparable to conventional battery electrolytes. More viscous electrolytes with higher salt concentrations can hinder charging and discharging at high rates. Lower salt concentrations on the other hand lead to decreasing capacities and faster decomposition. The used eutectic mixture of 1:6 is best suited uniting high stability and moderate viscosity.
|
Matthias Uhl; Tanja Geng; Philipp A. Schuster; Benjamin W. Schick; Matthias Kruck; Alexander Fuoss; Alexander J. C. Kuehne; Timo Jacob
|
Physical Chemistry; Polymer Science; Energy; Organic Polymers; Energy Storage; Electrochemistry - Mechanisms, Theory & Study
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c2f312be884bfd9cfa8fc1/original/combining-deep-eutectic-solvents-with-tempo-based-polymer-electrodes-influence-of-molar-ratio-on-electrode-performance.pdf
|
60c741b1bdbb893fd1a383ba
|
10.26434/chemrxiv.8118995.v1
|
DNA Minor Groove Binding with Bisbenzamidine-Ru(II) Complexes
|
We report the first Ru(II) coordination compounds that interact with DNA through a canonical minor groove insertion mode and with selectivity for A/T rich sites. This was made possible by integrating a bis‑benzamidine minor groove DNA-binding agent with a ruthenium(II) complex. Importantly, one of the enantiomers (Δ‑[Ru(bpy)<sub>2</sub><b>b4bpy</b>]<sup>2+</sup>, <b>Δ‑4Ru</b>) shows a considerably higher DNA affinity than the parent organic ligand and than the other enantiomer, particularly for the AATT sequence, while the other enantiomer preferentially targets long AAATTT sites with overall lower affinity. Finally, we demonstrate that the photophysical properties of these new binders can be exploited for DNA cleavage using visible light.
|
Mateo I. Sánchez; Gustavo Rama; Renata Calo; Kübra Ucar; Per Lincoln; Miguel Vázquez López; Manuel Melle-Franco; José Luis Mascareñas; M. Eugenio Vázquez
|
Bioinorganic Chemistry; Supramolecular Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-05-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741b1bdbb893fd1a383ba/original/dna-minor-groove-binding-with-bisbenzamidine-ru-ii-complexes.pdf
|
619b2ca9a831ec181eda5948
|
10.26434/chemrxiv-2021-pt5gd
|
Quantum alchemy beyond singlets: Bonding in diatomic molecules with hydrogen
|
Bonding energies are key for the relative stability of molecules in chemical space. Therefore methods employed to search for relevant molecules in chemical space need to capture the bonding behavior for a wide range of molecules, including radicals. In this work, we investigate the ability of quantum alchemy to do so for exploring hypothetical chemical compounds, here diatomic molecules involving hydrogen with various electronic structures. We evaluate equilibrium bond lengths, ionization ener- gies, and electron affinities of these fundamental systems. We compare and contrast how well manual quantum alchemy calculations, i.e. quantum mechanical calculations in which the nuclear charge is altered, and quantum alchemy approximations using a Taylor series expansion can predict these molecular properties. We also investigate the extent of error cancellation of these approaches in terms of ionization energies and electron affinities when using thermodynamic cycles. Our results suggest that the accuracy of Taylor series expansions are greatly improved by error cancellation in thermodynamic cycles, and errors also appear to be generally system-dependent. Taken together, this work provides insights into how quantum alchemy predictions us- ing a Taylor series expansion may be applied to future studies of non-singlet systems as well as which challenges remain open for these cases.
|
Emily Eikey; Alex Maldonado; Charles Griego; Guido Falk von Rudorff; John Keith
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics
|
CC BY NC 4.0
|
CHEMRXIV
|
2021-11-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619b2ca9a831ec181eda5948/original/quantum-alchemy-beyond-singlets-bonding-in-diatomic-molecules-with-hydrogen.pdf
|
60c73e14702a9b101b189cbe
|
10.26434/chemrxiv.6304460.v1
|
Achilles' heel of Iron-Based Catalysts During Oxygen Reduction in Acidic Medium
|
Fuel cells efficiently convert chemical into electric energy, with promising application for clean transportation. In proton-exchange membrane fuel cells (PEMFCs), rare platinum metal catalyzes today the oxygen reduction reaction (ORR) while iron(cobalt)-nitrogen-carbon materials (Fe(Co)-N-C) are a promising alternative. Their active sites can be classified as atomically dispersed metal-ions coordinated to nitrogen atoms (MeNxCy moieties) or nitrogen functionalities (possibly influenced by sub-surface metallic particles). While their durability is a recognized challenge, its rational improvement is impeded by insufficient understanding of operando degradation mechanisms. Here, we show that FeNxCy moieties in a representative Fe-N-C catalyst are structurally stable but electrochemically unstable when exposed in acidic medium to H2O2, the main ORR byproduct. We reveal that exposure to H2O2 leaves iron-based catalytic sites untouched but decreases their turnover frequency (TOF) via oxidation of the carbon surface, leading to weakened O2 binding on iron-based sites. Their TOF is recovered upon electrochemical reduction of the carbon surface, demonstrating the proposed deactivation mechanism. Our results reveal a hitherto unsuspected deactivation mechanism during ORR in acidic medium. This study identifies the N-doped carbon surface as Achilles' heel during ORR catalysis in PEMFCs. Observed in acidic but not in alkaline electrolyte, these insights suggest that durable iron-nitrogen-carbon catalysts are within reach for PEMFCs if rational strategies minimizing the amount of H2O2 or reactive oxygen species (ROS) produced during ORR are developed.
|
Chang Hyuck Choi; Hyung-Kyu Lim; Gajeon Chon; Min Wook Chung; Abdulrahman Altin; Nastaran Ranjbar Sahraie; Moulay-Tahar Sougrati; Lorenzo Stievano; Hyun Seok Oh; Eun Soo Park; Fang Luo; Peter Strasser; Goran Drazic; Karl J. J. Mayrhofer; Hyungjun Kim; Frederic Jaouen
|
Electrocatalysis; Fuel Cells
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-05-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e14702a9b101b189cbe/original/achilles-heel-of-iron-based-catalysts-during-oxygen-reduction-in-acidic-medium.pdf
|
60c74706842e65ac36db28f9
|
10.26434/chemrxiv.11475405.v1
|
Principal Interacting Spin Orbital: Understanding the Fragment Interactions in Open-Shell Systems
|
Due to the recent rise in the interests and research effort on first-row transition metal catalysis and other radical-related reactions, open-shell system is playing a much more important role in modern chemistry. However, the development of bonding analysis tools for open-shell system is still lagging behinid. In this work, we will present the principal interacting spin orbital (PISO) analysis, which is an analysis framework developed based on our previous principal interacting orbital (PIO) analysis. We will demonstrate the power of our framework to analyze different kinds of open-shell systems, ranging from simple organic radicals to much more complicated coordination complexes, from which we can see how different kinds of odd electron bonds could be identified. We will also illustrate its ability to be used in the analysis of chemical reaction, through which we can observe subtle patterns that could be helpful for tuning or rational design of related reactions.<br />
|
Fu Kit Sheong; Jing-Xuan Zhang; Zhenyang Lin
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74706842e65ac36db28f9/original/principal-interacting-spin-orbital-understanding-the-fragment-interactions-in-open-shell-systems.pdf
|
64f7abc879853bbd782c75d1
|
10.26434/chemrxiv-2023-xjl84
|
Open-ComBind: Harnessing unlabeled data for improved binding pose prediction
|
Determination of the bound pose of a ligand is a critical first step in many in silico drug discovery tasks. Molecular docking is the main tool for the prediction of non-covalent binding of a protein and ligand system. Molecular docking pipelines often only utilize the information of one ligand binding to the protein despite the commonly held hypothesis that different ligands share binding interactions when bound to the same receptor. Here we describe Open-ComBind, an easy-to-use, open-source version of the ComBind molecular docking pipeline that leverages information from multiple ligands without known bound structures to enhance pose selection. We first create distributions of feature similarities between ligand pose pairs, comparing near-native poses with all sampled docked poses. These distributions capture the likelihood of observing similar features, such as hydrogen bonds or hydrophobic contacts, in different pose configurations. These similarity distributions are then combined with a per-ligand docking score to enhance overall pose selection by 8.5% and 4.5% for high-affinity and congeneric series helper ligands, respectively. Open-ComBind reduces the average RMSD of ligands in our benchmark dataset by 8.2%. We provide Open-ComBind as an easy-to-use command line and Python API to increase pose prediction performance at www.github.com/drewnutt/open-combind.
|
Andrew McNutt; David Koes
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2023-09-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f7abc879853bbd782c75d1/original/open-com-bind-harnessing-unlabeled-data-for-improved-binding-pose-prediction.pdf
|
67d04cb9fa469535b9de7580
|
10.26434/chemrxiv-2025-r9r1x
|
Copper(I)-Catalyzed Asymmetric Intermolecular [3+2] Cycloaddition of Azomethine Ylides with Isatin-derived Trifluoromethyl Acrylates
|
An efficient, reliable and atom-economic strategy employing azomethine ylides and isatin-derived trifluoromethyl acrylates via intermolecular [3+2] cycloaddition for construction of valuable highly substituted pyrroledines bearing adjacent all-carbon quaternary stereocenters (one of which is a spirocyclic all-carbon quaternary stereocenter and the other is a trifluoromethylated all-carbon quaternary stereocenter) at C3 and C4 positions has been developed for the first time. The corresponding products with a broad substrate scope, good functional group tolerance and high stereoselectivity (29 examples, 60-96% yields, 80->99% ee, dr >20:1). In addition, subsequent amplification experiment and derivations further demonstrated the applicability of the synthetic methodology.
|
Shi-Wu Li; Xiaoying Cao; Zhifei Zhao; Jixing Zhao
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d04cb9fa469535b9de7580/original/copper-i-catalyzed-asymmetric-intermolecular-3-2-cycloaddition-of-azomethine-ylides-with-isatin-derived-trifluoromethyl-acrylates.pdf
|
66626cd821291e5d1d3fa433
|
10.26434/chemrxiv-2024-tndtk
|
Cu(II)/THPTA-Mediated Thiazolidine Deprotection for Living Phages and Cell Surfaces Labeling
|
Incorporating unnatural bioorthogonal groups into peptides and proteins offers an excellent opportunity to endow them with new properties in a precise and controlled manner. Among these, the α-oxo aldehyde group is particularly suitable for the post-functionalization of peptides and proteins due to its versatility and stability in aqueous buffers. However, the facile and site-specific incorporation of α-oxo aldehyde into proteins, especially in living systems, remains a long-lasting challenge. Here, we describe a novel Cu(II)/THPTA-Mediated Thiazolidine Deprotection (CUT-METHOD) strategy for post-installation of a highly-active α-oxo aldehyde moiety, which is released from a thiazolidine ring borne by a genetically encoded unnatural amino acid ThzK. This reaction is performed under physiological conditions, thereby enabling the chemoselective and site-specific modification of proteins via oxime ligation without compromising their integrity and function. To validate its versatility, we successfully performed site-specific incorporation of α-oxo aldehyde into recombinant proteins and those displayed on M13 filamentous bacteriophage particles and bacterial cell surfaces. In addition, by leveraging Spycatcher/Spytag chemistry and oxime ligation, the bacterial cells bearing aldehyde generated via the CUT-METHOD could be simultaneously decorated with two distinct functional molecules, providing a novel one-pot dual labeling platform for the construction of living bacterial cell-based cancer targeting systems. Put together, we have demonstrated that the CUT-METHOD strategy is a significant addition to the current bioorthogonal chemistry toolbox with broad applications anticipated in the near future.
|
Chengyun Ma; Guoqing Liu; Jianan Sun; Disheng Luo; Juan Yin; Dechun Yang; Shuo Pang; Wei Hou; Xinya Hemu; Bang-Ce Ye; Xiaobao Bi
|
Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Analytical Chemistry - General; Bioengineering and Biotechnology; Chemical Biology
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-06-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66626cd821291e5d1d3fa433/original/cu-ii-thpta-mediated-thiazolidine-deprotection-for-living-phages-and-cell-surfaces-labeling.pdf
|
60d3776c67d49116df9599f0
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10.26434/chemrxiv-2021-pl384
|
C-H Oxidation in Fluorenyl Benzoates Does Not Proceed Through a Stepwise Pathway: Revisiting Asynchronous Proton-Coupled Electron Transfer
|
2-fluorenyl benzoates were recently shown to undergo C–H bond oxidation through intramolecular proton transfer coupled with electron transfer to an external oxidant. Kinetic analysis revealed unusual rate-driving force relationships and indicated a mechanism of multi-site concerted proton-electron transfer (MS-CPET) for all reactions. More recently, an alternative interpretation of the data was proposed to explain the rate-driving force relationships, invoking a crossover from CPET to a stepwise mechanism with an initial intramolecular proton transfer (PT) (Costentin, Savéant, Chem. Sci., 2020, 11, 1006). Here, we show that this proposed alternative pathway is untenable based on new experimental assessments of the intramolecular PT equilibrium constant and rates. Measurement of the fluorenyl 9-C–H pKa, H/D exchange experiments, and kinetic modelling eliminate the possibility of a stepwise mechanism for C–H oxidation in the fluorenyl benzoate series. Implications for asynchronous MS-CPET mechanisms are discussed with respect to classical Marcus theory and the quantum-mechanical treatment of CPET.
|
Scott Coste; Anna Brezny; Brian Koronkiewicz; James Mayer
|
Physical Chemistry; Organic Chemistry; Chemical Kinetics; Thermodynamics (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-06-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d3776c67d49116df9599f0/original/c-h-oxidation-in-fluorenyl-benzoates-does-not-proceed-through-a-stepwise-pathway-revisiting-asynchronous-proton-coupled-electron-transfer.pdf
|
60c743330f50dbe18a395e82
|
10.26434/chemrxiv.8976347.v1
|
Simultaneous Evaluation of Multiple Microarray Surface Chemistries Through Real-Time Interferometric Imaging
|
<p>Surface chemistry is one of the most crucial aspects for microarray modality biosensor development. As a matter of fact, the immobilization capability of the functionalized surface is one of the limiting factors for the final yield of the binding reaction. In this work, we locally deposited many reactive polymers on a single solid support, allowing for a direct comparison of functionality of probes immobilized on different polymers and demonstrating a new way of multiplexing. Our goal was to investigate the immobilization efficiency of reactive polymers, as well as the resulting affinity of the molecular probes, in a single experiment. This idea was demonstrated by spotting a large number of different reactive polymers on an untreated Si/SiO<sub>2</sub> chip, and depositing the same molecular probe on all the spots immediately after. This method proved to be efficient and could be used as an initial qualitative assay to decide which functionalization better suits a certain application. We also showed that the localized functionalization method is applicable to proteins as well as oligonucleotides. Moreover, by means of real-time binding measurements performed with the Interferometric Reflectance Imaging Sensor (IRIS), we demonstrated that this functionalization technique is comparable to the uniformity of classical flat-coating solution. The comparison between the binding curves that were obtained from different polymer spots with the same probe allowed us to decide which polymers would work better to immobilize a model protein, α-Lactalbumin, as well as a peptide extracted from the latter, namely LAC-1. The final outcome is promising, and it highlights the multiplexing power of this method: first, it allows to characterize dozens of polymers at once, within a single 60-minutes experiment. Secondly, it removes the limitation, related to coated surfaces, that only molecules with the same functional groups can be tethered to the same solid support. By applying this innovative protocol, there is no more restriction on the type of molecules that can be studied simultaneously and immobilization for each molecular probe can be individually optimized.</p>
|
Elisa Chiodi; Laura Sola; Dario Brambilla; Marina Cretich; Allison Marn; M. Selim Ünlü; Marcella Chiari
|
Inorganic Polymers; Polymer morphology; Imaging
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-07-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743330f50dbe18a395e82/original/simultaneous-evaluation-of-multiple-microarray-surface-chemistries-through-real-time-interferometric-imaging.pdf
|
60c7495e469df41686f43bcd
|
10.26434/chemrxiv.12056142.v1
|
A CONTINUOUS FLOW SULFURYL CHLORIDE BASED REACTION – SYNTHESIS OF A KEY INTERMEDIATE IN A NEW ROUTE TOWARD EMTRICITABINE AND LAMIVUDINE
|
<p>We
demonstrate a continuous two-step sequence where a sulfenyl chloride is formed,
trapped by vinyl acetate and chlorinated further via a Pummerer rearrangement.
This sequence produces a key intermediate in our new approach to the
oxathiolane core used to prepare the anti-retroviral medicines Emtricitabine
and Lamivudine. During batch scale-up to tens of grams, we found that the sequence
featured a strong exotherm, temperature and pressure sensitivity, and evolution
of hydrogen chloride and sulfur dioxide. These reactions are ideal candidates
for implementation in a continuous, mesoscale system for the sake of superior
control. In addition, we found that fast reagent additions at controlled
temperatures decreased byproduct formation. Herein, we discuss the flow implementation
and the final reactor design that led to a 141g/h throughput system. </p>
|
Juliana de Souza; Mateo Berton; David Snead; D. Tyler McQuade
|
Organic Synthesis and Reactions; Process Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7495e469df41686f43bcd/original/a-continuous-flow-sulfuryl-chloride-based-reaction-synthesis-of-a-key-intermediate-in-a-new-route-toward-emtricitabine-and-lamivudine.pdf
|
60c756ca0f50db51a0398151
|
10.26434/chemrxiv.14330384.v1
|
Electrochemistry in an Optical Fiber Microcavity - Optical Monitoring of Electrochemical Processes in Picoliter Volumes
|
In this work, we
demonstrate a novel method for multi-domain analysis of properties of analytes in
volumes as small as picoliter, combining electrochemistry and optical
measurements. A microcavity in-line Mach-Zehnder interferometer (µIMZI)
obtained in a standard single-mode optical fiber using femtosecond laser
micromachining was able to accommodate a microelectrode and optically monitor electrochemical
processes inside the fiber. The interferometer shows exceptional sensitivity to
changes in optical properties of analytes in the microcavity. We show that the
optical readout follows the electrochemical reactions. Here, the redox probe (ferrocenedimethanol)
undergoing reactions of oxidation and reduction changes the optical properties
of the analyte (refractive index and absorbance) that are monitored by the µIMZI.
Measurements have been supported by numerical analysis of both optical and
electrochemical phenomena. On top of a capability of the approach to perform
analysis in microscale, the difference between oxidized and reduced forms in
the near-infrared can be clearly measured using the µIMZI, which is hardly possible using other optical
techniques. The proposed multi-domain concept is a promising approach for
highly reliable and ultrasensitive chemo- and biosensing.
|
Tomasz Gabler; Andrzej Krześniak; Monika Janik; Anna Myśliwiec; Marcin Koba; Joanna Buczyńska; Martin Jönsson-Niedziolka; Mateusz Śmietana
|
Electrochemistry - Mechanisms, Theory & Study; Optics; Spectroscopy (Physical Chem.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2021-03-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756ca0f50db51a0398151/original/electrochemistry-in-an-optical-fiber-microcavity-optical-monitoring-of-electrochemical-processes-in-picoliter-volumes.pdf
|
674de05e5a82cea2fabd6eca
|
10.26434/chemrxiv-2024-w7cc1-v2
|
Selective chemical reduction of Nitrobenzene to Aniline by Fe doped 1T MoS2 nanozyme
|
The selective reduction of nitro group in reactive substituents of Nitrobenzene is a substantial challenge for industrial applications and academia. Inspired by unique Lewis acid character and the malleable oxidation state of Iron element. Fe doped MoS2 exhibits excellent catalytic reduction activity and selectivity towards nitrobenzene. DFT calculations have shown that charge transfer between Fe and Mo atoms is crucial for promoting S2- adsorption and rapid conversion of nitrobenzene. The kinetic study revealed that the reaction is first order with respect to Nitrobenzene and second order with respect to sulphide ion. The turn over number (TON), turn over frequency (TOF) for Fe reaction center and activation energy of the reaction were calculated as 1,291,800 molAn/molFe, 86,120 hr-1 and 22.091 kJ.mol-1 respectively. 5 % Fe-MoS2 showed high stability in N2 flow and retained 100 % selectivity and 80 % of activity for 5 cycles.
|
Ibrahim Ul Islam; Boxu Dong; 建陶(Jiantao) 宰(Zai); Xuefeng Qian
|
Catalysis; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674de05e5a82cea2fabd6eca/original/selective-chemical-reduction-of-nitrobenzene-to-aniline-by-fe-doped-1t-mo-s2-nanozyme.pdf
|
60c74dd3bdbb894809a39a8c
|
10.26434/chemrxiv.12662315.v1
|
Polymerization Photoinitiators with Near-Resonance Enhanced Two-Photon Absorption Cross-Section: Towards High-Resolution Photoresists with Improved Sensitivity
|
Synthesis of novel photoinitiators, spectroscopic (UV vis, fluorescence, steady state and time resolved), electrochemical and EPR studies of their photoinduced radical generation mechanisms, Z-scan measurements of their two-photon absorption cross section, two-photon polymerization at 532 nm, with a pulsed ns laser, material evaluation by scanning electron microscopy<br />
|
Caroline Arnoux; tatsuki konishi; Emma Van Elslande; Eric Aymé Poutougnigni; jean-christophe Mulatier; Lhoussain Khrouz; Christophe Bucher; Elise Dumont; Kenji Kamada; Chantal Andraud; Patrice L. Baldeck; Ákos Bányász; Cyrille Monnereau
|
Nanostructured Materials - Materials; Optical Materials; Interfaces; Photochemistry (Physical Chem.); Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dd3bdbb894809a39a8c/original/polymerization-photoinitiators-with-near-resonance-enhanced-two-photon-absorption-cross-section-towards-high-resolution-photoresists-with-improved-sensitivity.pdf
|
647aee0f4f8b1884b7c21bf9
|
10.26434/chemrxiv-2023-f7h9q
|
Control of H-related defects in γ-MnO2 in a hydrothermal synthesis
|
Manganese dioxide is a good candidate for effective energy storage and conversion as it possesses a rich electrochemistry. The compound also shows a wide polymorphism. The γ-variety, an intergrowth of β- and R-MnO2, has been extensively studied in several types of batteries (e.g. Zn/MnO2, Li-ion) and is a common electrode material for commercial batteries. It is well known that the insertion of protons thermodynamically stabilises γ-MnO2 with respect to β-MnO2. Protons can enter the structure either by forming groups of 4 hydroxyls around a Mn4+ vacancy, called a Ruetschi defect, or by forming a hydroxyl group near a Mn3+ ion, called a Coleman defect. These defects differently affect the electrochemistry of manganese oxide, and tailoring their amount in the structure can be used to tune the material properties. Previous studies have addressed the proton insertion process, but the role of the synthesis pathway on the amount of defects created is not well understood. We here investigate how the parameters in a hydrothermal synthesis of γ-MnO2 nanoparticles influence the amount and type of H-related defects. Structural investigations are carried out using Pair Distribution Function analysis, X-ray absorption spectroscopy, thermogravimetric analysis, and inelastic neutron scattering. We demonstrate the possibility to control the amount and type of defects introduced during the synthesis. While the amount of Ruetschi defects increases with synthesis temperature, it decreases with extended synthesis time, along with the amount of Coleman defects. Moreover, we discuss the arrangement of the defects in the γ-MnO2 nanoparticles.
|
Nicolas Magnard; Andrea Kirsch; Mads R. V. Jørgensen; Innokenty Kantor; Daniel R. Sørensen; Simo Huotari; Svemir Rudic; Heloisa N. Bordallo; Kirsten Jensen
|
Inorganic Chemistry; Solid State Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647aee0f4f8b1884b7c21bf9/original/control-of-h-related-defects-in-mn-o2-in-a-hydrothermal-synthesis.pdf
|
612358928a6faa14d39e4bbf
|
10.26434/chemrxiv-2021-9b9p2
|
Triplet-to-Singlet Exciton Transfer in Hyperfluorescent OLED materials
|
Hyperfluorescent organic light-emitting diodes combine two kinds of dopants to maximize device efficiency: one molecule exhibiting thermally activated delayed fluorescence (TADF) and another molecule with a high fluorescence rate and narrow emission spectrum. The postulated role of a TADF sensitizer is to enable up-conversion of triplet to singlet excitons through the reverse intersystem crossing mechanism, which is followed by a Förster energy transfer to the fluorescent emitter. However, a second mechanism based on the direct triplet-to-singlet exciton transfer between TADF molecules is a priori possible, but its role in hyperfluorescence has not been investigated. Here we employ first-principles electronic structure and kinetic Monte Carlo simulations to study the hyperfluorescence mechanism in four pairs of TADF/fluorescent emitters. We demonstrate how the triplet-to-singlet energy transfer mechanism is, in some cases, the main driver for the quantum efficiency boost observed in hyperfluorescent devices.
|
Leonardo Evaristo de Sousa; Larissa dos Santos Born; Pedro Henrique de Oliveira Neto; Piotr de Silva
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Optical Materials; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-08-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612358928a6faa14d39e4bbf/original/triplet-to-singlet-exciton-transfer-in-hyperfluorescent-oled-materials.pdf
|
627574dfa42e9c794036b8af
|
10.26434/chemrxiv-2022-3nvt6
|
Highly stretchable ionically crosslinked acrylate elastomers based on polyelectrolyte complexes
|
Dynamic bonds are a powerful approach to tailor the mechanical properties of elastomers and introduce shape-memory, self-healing, and recyclability. Among the library of dynamic crosslinks, electrostatic interactions among oppositely charged ions have been shown to enable tough and resilient elastomers and hydrogels. In this work, we investigate the mechanical properties of ionically crosslinked ethyl acrylate-based elastomers assembled from oppositely charged copolymers. Using both infrared and Raman spectroscopy, we confirm that ionic interactions are established among polymer chains. We find that the glass transition temperature of the complex is in between the two individual copolymers, while the complex demonstrates higher stiffness and more recovery, indicating that ionic bonds can strengthen and enhance recovery of these elastomers. We compare cycles to increasing strain levels at different strain rates, and hypothesize that at fast strain rates ionic bonds dynamically break and reform while entanglements do not have time to slip, and at slow strain rates ionic interactions are disrupted and these entanglements slip significantly. Further, we show that a higher ionic to neutral monomer ratio can increase the stiffness, but its effect on recovery is minimal. Finally, taking advantage of the versatility of acrylates, ethyl acrylate is replaced with the more hydrophilic 2-hydroxyethyl acrylate, and the latter is shown to exhibit better recovery and self-healing at a cost of stiffness and strength. The design principles uncovered for these easy-to-manufacture polyelectrolyte complex-based bulk materials can be broadly applied to tailor elastomer stiffness, strength, inelastic recovery, and self-healing for various applications.
|
Hongyi Cai; Zhongtong Wang; Yuval Vidavsky; Meredith N. Silberstein
|
Materials Science; Polymer Science; Elastic Materials; Organic Polymers; Polyelectrolytes - Polymers
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-05-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627574dfa42e9c794036b8af/original/highly-stretchable-ionically-crosslinked-acrylate-elastomers-based-on-polyelectrolyte-complexes.pdf
|
669272445101a2ffa847a353
|
10.26434/chemrxiv-2024-vzssl
|
A Nano size COVID-19: Human death and Asymptomatic mechanism
|
COVID-19 has a spike protein and positive –sense RNA. Virus size is about 65 to 125 nm (diameter). The spike protein length is around 20 nm which is responsible for the infection. Based on the chemical concept, the metal ions are ready to form a complex with proteins. In this view, the spike protein can form a complex with various metal ions and the infection property of spike protein is prevented. Moreover, hemoglobin has Fe3+/Fe2+, the spike protein can also interact with the Fe3+/Fe2+ and form a complex. The spike protein length is 20nm which may sufficient to insert inside the hemoglobin molecule and form a complex with Fe. Ultimately, the hemoglobin loses its oxygen transfer property with the result to human death. The other type of corona virus spike protein length may not sufficient to insert inside the hemoglobin. Hence the COVID-19 virus is a major cause for human death. In this view, to prevent the virus infection non-toxic metal ions can be used to form a complex with spike protein. These interactions make the virus death / asymptomatic and prevents further replication.
|
Kannan Chellapandian; G. Vidhyalakshmi; K. Karthika devi; S. Senthur selvi; M. Krishnaveni
|
Biological and Medicinal Chemistry; Inorganic Chemistry; Nanoscience; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669272445101a2ffa847a353/original/a-nano-size-covid-19-human-death-and-asymptomatic-mechanism.pdf
|
60c743b59abda275e7f8c232
|
10.26434/chemrxiv.9598442.v1
|
Spontaneous Formation of Autocatalytic Sets with Self-Replicating Inorganic Metal Oxide Clusters
|
Biological self-replication is driven by complex machinery requiring large amounts of sequence information too complex to have formed spontaneously. This presents a fundamental problem for understanding the origins self-replication and by extension, life. One route for the emergence of self-replicators is via autocatalytic sets, but experimentally these have been based on RNA and require sequence information. Showing an example outside of biology, would give insights into how the universal ‘life-like’ chemistry can be. Here we show how a simple inorganic salt can spontaneously form information-rich, autocatalytic sets of replicating inorganic molecules that work via molecular recognition based on the {PMo12} Keggin ion, and {Mo36} cluster. These small clusters are involved in an autocatalytic network, where the assembly of gigantic molybdenum blue wheel (Mo154-blue), {Mo132} ball containing 154 and 132 molybdenum atoms, and a new {PMo12}Ì{Mo124 Ce4} nanostructure are templated by the smaller clusters which are themselves able to catalyse their own formation. Kinetic investigations revealed key traits of autocatalytic systems including molecular recognition and kinetic saturation. A stochastic model confirms the presence of an autocatalytic network driven by molecular recognition, where the larger clusters are the only products stabilised by information contained in the cycle, isolated due to a critical transition in the network. This study demonstrates how information-rich autocatalytic sets, based on simple inorganic salts, can spontaneously emerge which are capable of collective self-reproduction outside of biology.<br />
|
Haralampos N. Miras; Cole Mathis; Weimin Xuan; De-Liang Long; Robert Pow; Leroy Cronin
|
Coordination Chemistry (Inorg.); Kinetics and Mechanism - Inorganic Reactions; Supramolecular Chemistry (Inorg.); Computational Chemistry and Modeling; Nanocatalysis - Reactions & Mechanisms; Chemical Kinetics; Self-Assembly; Statistical Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b59abda275e7f8c232/original/spontaneous-formation-of-autocatalytic-sets-with-self-replicating-inorganic-metal-oxide-clusters.pdf
|
619dc25da12923d5f64c1383
|
10.26434/chemrxiv-2021-f9sf1
|
EnzyHTP: A High-Throughput Computational Platform for Enzyme Modeling
|
Molecular simulations, including quantum mechanics (QM), molecular mechanics (MM), and multiscale QM/MM modeling, have been extensively applied to understand the mechanism of enzyme catalysis and to design new enzymes. However, molecular simulations typically require specialized, manual operation ranging from model construction to post-analysis to complete the entire life-cycle of enzyme modeling. The dependence on manual operation makes it challenging to simulate enzymes and enzyme variants in a high-throughput fashion. In this work, we developed a Python software, EnzyHTP, to automate molecular model construction, QM, MM, and QM/MM computation, and analyses of modeling data for enzyme simulations. To test the EnzyHTP, we used fluoroacetate dehalogenase (FAcD) as a model system and simulated the enzyme interior electrostatics for 100 FAcD mutants with a random single amino acid substitution. For each enzyme mutant, the workflow involves structural model construction, 1 ns molecular dynamics simulations, and quantum mechnical calculations in 100 MD-sampled snapshots. The entire simulation workflow for 100 mutants was completed in 7 hours with 10 GPUs and 160 CPUs. EnzyHTP is expected to improve the efficiency and reproducibility of computational enzyme, facilitate the fundamental understanding of catalytic origins across enzyme families, and accelerate the optimization of biocatalysts for non-native substrate transformation.
|
Qianzhen Shao; Yaoyukun Jiang; Zhongyue Yang
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-11-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619dc25da12923d5f64c1383/original/enzy-htp-a-high-throughput-computational-platform-for-enzyme-modeling.pdf
|
60c74e910f50db810e397279
|
10.26434/chemrxiv.12751718.v1
|
Need for Assessing the Inhalation of Micro(nano)plastic Debris Shed from Masks, Respirators, and Home-Made Face Coverings During the COVID-19 Pandemic
|
<p>This urgent need, as we point out in the manuscript title,
stems from the fact that a regulatory gap widely exists in current quality standards
and regulations on masks and respirators. By surveying the relevant ASTM,
NOISH, EU, China, and ISO standards, as listed in the manuscript, we found no regulation
or recommendation pertinent to this type of respirable hazard. Non-medical
substitutes, such as face coverings, are also subject to such risks if made
with improper household materials.</p><p><br /></p>
<p>There are numerous studies on assessing the filtration
efficiency of masks, respirators, and recently, cloth face coverings (<i>ACS
Nano</i>, <b>2020</b>, 14, 6339; <i>Nano Lett</i>, <b>2020</b>,<b> </b>10.1021/acs.nanolett.0c02211).
This particular issue, however, has been widely neglected by the scientific
community. Studies on masks and respirators as a source of respirable debris were
found to be anecdotal (<i>Ann. Occup. Hyg.</i> <b>1986</b>, 20, 131−133). Recent
discussions on disposable masks and respirators focused on their widespread use
during the current pandemic and disposal into the environment (<i>Sci Total
Environ</i> <b>2020</b>, 737:140279; <i>Waste Manage</i> <b>2020</b>, 108, 202-205).</p><p><br /></p>
<p>By putting several top-selling medical face masks and
N95 respirators under microscopes, we found plenty of micro(nano)plastic debris
on their inner facings, with some appearing to be loosely attached while others
still connected to their structural fibers. The two types of debris often appear
in the same cluster with similar morphology and texture. <b>Figure 1</b> in the
manuscript shows examples of these, and we have
submitted a file containing additional images with methods and QA/QC as further
evidence.</p><p><br /></p>
With
the novel coronavirus still looming in our communities, there is a strong ongoing
demand for personal respiratory protection devices. Supported by the latest guidance from WHO, many regulatory
bodies have made these a compulsory requirement for the public when using
public transport, or in certain settings where it is difficult to maintain adequate
physical distancing. Respirable hazards such as micro(nano)plastics in
these, if pervasively exist, may pose a public health concern. Children, the elderly,
and individuals having chronic respiratory diseases may be particularly
sensitive to this type of inhalable contaminants. With a growing body of
evidence on their adverse effects, micro(nano)plastics is an active research
domain with a quickly expanding scope. Researchers studying their inhalation, via
atmospheric or other anthropogenic sources, are now facing the reality that
there is a piece of plastic garment on top of the mouth and nose of millions of
people every day. With these becoming a necessity for many in their daily life
and work, questions must be raised over this apparent regulatory gap concerning
their long-term use safety. The current pandemic, if anything, should bring this
particular issue under scrutiny.
|
Jie Han; Shanshan He
|
Atmospheric Chemistry; Environmental Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e910f50db810e397279/original/need-for-assessing-the-inhalation-of-micro-nano-plastic-debris-shed-from-masks-respirators-and-home-made-face-coverings-during-the-covid-19-pandemic.pdf
|
65830fbae9ebbb4db95c3bfd
|
10.26434/chemrxiv-2022-znxrn-v2
|
Achieving Decentralized, Electrified, and Decarbonized Ammonia Production
|
The rapid reduction in the cost of renewable energy has motivated the transition from carbon-intensive chemical manufacturing to renewable, electrified, and decarbonized technologies. Although electrified chemical manufacturing technologies differ greatly, the feasibility of each electrified approach is largely related to the energy efficiency and capital cost of the system. Here, we examine the feasibility of ammonia production systems driven by wind and photovoltaic energy. We identify the optimal regions where wind and photovoltaic electricity production may be able to meet local demand for ammonia-based fertilizers. To account for growing concerns regarding access to water, geospatial optimization takes into account water stress caused by new ammonia facilities, and recommendations ensure that the identified regions do not experience an increase in water stress. Reducing water stress by 99% only increases costs by 1.4%. Furthermore, a movement toward a more decentralized ammonia supply chain driven by wind and photovoltaic electricity can reduce the transportation distance for ammonia by up to 76% while resulting in an increase in production costs by 18% if an energy efficiency of 40% is achieved.
|
Carlos Fernandez; Oliver Chapman; Marilyn Brown; Christian Alvarez Pugliese; Marta Hatzell
|
Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Thermodynamics (Chem. Eng.); Fuels - Energy Science; Photovoltaics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65830fbae9ebbb4db95c3bfd/original/achieving-decentralized-electrified-and-decarbonized-ammonia-production.pdf
|
65eebe13e9ebbb4db96f3ad1
|
10.26434/chemrxiv-2024-kld98
|
Scalable Synthesis of TiO2@IrOx Core-Shell Catalyst for Proton Exchange Membrane Water Electrolysis with Low Iridium Loading
|
The widespread application of green hydrogen production technologies requires cost reduction of crucial elements. To achieve this, a viable pathway to reduce the iridium loading in proton exchange membrane water electrolysis (PEMWE) is explored. Herein, we present a scalable synthesis method based on a photodeposition process for a TiO2@IrOx core-shell catalyst with a reduced iridium content as low as 40 wt%. Using this synthesis route, we obtain titania support particles homogeneously coated with a thin iridium oxide shell of only 2.1 ± 0.4 nm. The catalyst exhibits not only high ex situ activity, but also decent stability compared to commercially available catalysts. Furthermore, the unique core-shell structure provides a threefold increased electrical powder conductivity compared to structures without the shell. In addition, the low iridium content facilitates the fabrication of sufficiently thick catalyst layers at decreased iridium loadings mitigating the impact of crack formation in the catalyst layer during PEMWE operation. We demonstrate that the novel TiO2@IrOx core-shell catalyst clearly outperforms the commercial reference in single-cell tests with an iridium loading below 0.3 mgIr cm 2 exhibiting a superior iridium-specific power density of 17.9 kW gIr-1 compared to 10.4 kW gIr-1 for the commercial reference.
|
Darius Hoffmeister; Selina Finger; Lena Fiedler; Tien-Ching Ma; Andreas Körner; Matej Zlatar; Birk Fritsch; Kerstin Witte-Bodnar; Simon Carl; Alexander Götz; Benjamin Apeleo Zubiri; Johannes Will; Erdmann Spiecker; Serhiy Cherevko; Anna T. S. Freiberg; Karl J. J. Mayrhofer; Simon Thiele; Andreas Hutzler; Chuyen Van Pham
|
Materials Science; Nanoscience; Energy; Catalysts; Core-Shell Materials; Nanostructured Materials - Materials
|
CC BY 4.0
|
CHEMRXIV
|
2024-03-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65eebe13e9ebbb4db96f3ad1/original/scalable-synthesis-of-ti-o2-ir-ox-core-shell-catalyst-for-proton-exchange-membrane-water-electrolysis-with-low-iridium-loading.pdf
|
6515f79fade1178b244ef0fc
|
10.26434/chemrxiv-2022-dct7l-v3
|
MASSA Algorithm: automated rational sampling of training and test subsets for QSAR modelling
|
QSAR models capable of predicting biological, toxicity, and pharmacokinetic properties were widely used to search lead bioactive molecules in chemical databases. The dataset’s preparation to build these models has a strong influence on the quality of the generated models, and sampling requires that the original dataset be divided into training (for model training) and test (for statistical evaluation) sets. This sampling can be done randomly or rationally, but the rational division is superior. In this paper, we present MASSA, a Python tool that can be used to automatically sample datasets by exploring the biological, physicochemical, and structural spaces of molecules using PCA, HCA, and K-modes. The proposed algorithm is very useful when the variables used for QSAR are not available or to construct multiple QSAR models with the same training and test sets, producing models with lower variability and better values for validation metrics. These results were obtained even when the descriptors used in the QSAR/QSPR were different from those used in the separation of training and test sets, indicating that this tool can be used to build models for more than one QSAR/QSPR technique. Finally, this tool also generates useful graphical representations that can provide insights into the data.
|
Gabriel Corrêa Veríssimo; Simone Queiroz Pantaleão; Philipe de Oliveira Fernandes; Jadson Castro Gertrudes; Thales Kronenberger; Kathia Maria Honório; Vinicius Gonçalves Maltarollo
|
Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6515f79fade1178b244ef0fc/original/massa-algorithm-automated-rational-sampling-of-training-and-test-subsets-for-qsar-modelling.pdf
|
60c740044c89195253ad2051
|
10.26434/chemrxiv.7581764.v1
|
Ipomoeassin F Binds Sec61α to Inhibit Protein Translocation
|
The ipomoeassin
family of natural resin glycosides is underexplored chemical space with potent antitumor
activity revealed in the NCI-60 cell lines screen; however, its mode of action
has so far remained unexplored. In this
manuscript, we report our chemical proteomics and subsequent biology studies that
transform our collective knowledge of the ipomoeassin glycolipids from Organic Synthesis and Medicinal
Chemistry to biological
mechanism and provide a step change in our understanding of its action at a
cellular level. Hence, we created an
ipomoeassin F-based biotin affinity probe and used it in live cells to isolate
the ER membrane protein Sec61α as its presumptive molecular target. A direct interaction between Sec61α and ipomoeassin
F was confirmed by cell imaging, pulldown from purified ER membranes and
competition studies using a photo-crosslinking analogue of the cyclodepsipeptide cotransin,
a known Sec61α inhibitor. Crucially, we then
showed that ipomoeassin F binding has a profound effect on Sec61 function,
using both in vitro and in vivo assays for protein translocation and protein secretion
respectively. Although structurally quite distinct, the potency of ipomoeassin
F is comparable to that of mycolactone, a recently identified and intensely
studied inhibitor of Sec61. The ~1,000 fold increase
in the ipomoeassin F resistance of two cell lines expressing mutant forms of Sec61α
strongly supports our conclusion that the effect of the compound on Sec61α is
the primary basis for its potent cytotoxicity. However, we also provide evidence that ipomoeassin
F is mechanistically distinct from known Sec61α inhibitors, suggesting that it is
a novel structural class that may offer new opportunities to explore the Sec61
protein translocation complex as a therapeutic target for drug discovery.
|
Wei Shi; Guanghui Zong; Zhijian Hu; Sarah O’Keefe; Dale Tranter; Ludivine Baron; Michael Iannotti; Belinda Hall; Katherine Corfield; Anja Paatero; Mark Henderson; Peristera Roboti; Jianhong Zhou; Xianwei Sun; Mugunthan Govindarajan; Jason M. Rohde; Nicolas Blanchard; Rachel Simmonds; James Inglese; Yuchun Du; Caroline Demangel; Stephen High; Ville Paavilainen
|
Natural Products; Biochemistry; Cell and Molecular Biology; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740044c89195253ad2051/original/ipomoeassin-f-binds-sec61-to-inhibit-protein-translocation.pdf
|
64b79915b053dad33a852ea9
|
10.26434/chemrxiv-2023-05387
|
An Extrusion Strategy for On-demand SF5Cl Gas Generation from a Commercial Disulfide
|
Herein, we report a novel methodology for the ex-situ generation of SF5Cl by employing 4,4′-dipyridyl disulfide as a safe commercial reagent obviating the need for lecture bottles. The method is applicable to certain SF5Cl-involving transformations using a two-chamber reactor. Moreover, easily applying SF5Cl in both polar and non-polar media is rendered feasible while avoiding the use of glovebox techniques. This report also suggests 1H-19F HOESY as a simple and fast stereochemistry indication for chloropentafluorosulfanylated olefins.
|
Reza Kordnezhadian; Tim De Bels; Kexin Su; Luc Van Meervelt; Ermal Ismalaj; Joachim Demaerel; Wim De Borggraeve
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b79915b053dad33a852ea9/original/an-extrusion-strategy-for-on-demand-sf5cl-gas-generation-from-a-commercial-disulfide.pdf
|
61ac8f067ce056c56d89c055
|
10.26434/chemrxiv-2021-tdg7f
|
Systemic Evolutionary Chemical Space Exploration For Drug Discovery
|
Chemical space exploration is a major task of the hit-finding process during the pursuit of novel chemical
entities. Compared with other screening technologies, computational de novo design has become a popular
approach to overcome the limitation of current chemical libraries. Here, we reported a de novo design platform
named systemic evolutionary chemical space explorer (SECSE). The platform was conceptually inspired by
fragment-based drug design, that miniaturized a “lego-building” process within the pocket of a certain target.
The key of virtual hits generation was then turned into a computational search problem. To enhance search and
optimization, human intelligence and deep learning were integrated. Application of SECSE against PHGDH,
proved its potential in finding novel and diverse small molecules that are attractive starting points for further
validation. This platform is open-sourced and the code is available at http://github.com/KeenThera/SECSE.
|
Chong Lu; Shien Liu; Weihua Shi; Jun Yu; Zhou Zhou; Xiaoxiao Zhang; Xiaoli Lu; Faji Cai; Ning Xia; Yikai Wang
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Artificial Intelligence
|
CC BY NC 4.0
|
CHEMRXIV
|
2021-12-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ac8f067ce056c56d89c055/original/systemic-evolutionary-chemical-space-exploration-for-drug-discovery.pdf
|
60c74020842e657fc0db1c23
|
10.26434/chemrxiv.6983264.v2
|
Electronic Structure Benchmark Calculations of Inorganic and Biochemical Carboxylation Reactions
|
<div><div><div><p>Carboxylation reactions represent a very special class of chemical reactions that is characterized by the presence of a carbon dioxide (CO2) molecule as reactive species within its global chemical equation. These reactions work as fundamental gear to accomplish the CO2 fixation and thus to build up more complex molecules through different technological and biochemical processes. In this context, a correct description of the CO2 electronic structure turns out to be crucial to study the chemical and electronic properties associated with this kind of reactions. Here, a sys- tematic study of CO2 electronic structure and its contribution to different carboxylation reaction electronic energies has been carried out by means of several high-level ab-initio post-Hartree Fock (post-HF) and Density Functional Theory (DFT) calculations for a set of biochemistry and inorganic systems. We have found that for a correct description of the CO2 electronic correlation energy it is necessary to include post-CCSD(T) contributions (beyond the gold standard). These high-order excitations are required to properly describe the interactions of the four π-electrons as- sociated with the two degenerated π-molecular orbitals of the CO2 molecule. Likewise, our results show that in some reactions it is possible to obtain accurate reaction electronic energy values with computationally less demanding methods when the error in the electronic correlation energy com- pensates between reactants and products. Furthermore, the provided post-HF reference values allowed to validate different DFT exchange-correlation functionals combined with different basis sets for chemical reactions that are relevant in biochemical CO2 fixing enzymes.</p></div></div></div>
|
Oscar A. Douglas-Gallardo; David A. Sáez; Stefan Vogt-Geisse; Esteban Vöhringer-Martinez
|
Reaction (Inorg.); Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-12-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74020842e657fc0db1c23/original/electronic-structure-benchmark-calculations-of-inorganic-and-biochemical-carboxylation-reactions.pdf
|
60c74ea5567dfe53cbec554e
|
10.26434/chemrxiv.12777578.v1
|
Remdesivir Strongly Binds to both RNA-dependent RNA Polymerase and Main Protease of SARS-CoV-2: Evidence from Molecular Simulations
|
The outbreak of a new coronavirus SARS-CoV-2 (severe acute respiratory syndrome–<br />coronavirus 2) has caused a global CoVid-19 (coronavirus disease 2019) pandemic, resulting in millions of infections and thousands of deaths around the world. There is currently no drug or vaccine for CoVid-19, but it has been revealed that some commercially available drugs are promising, at least for treating symptoms. Among them, Remdesivir, which can block the activity of RNA-dependent RNA polymerase (RdRp) in old SARS-CoV and MERS-CoV viruses, has been prescribed to CoVid-19 patients in many countries. A recent experiment showed that Remdesivir binds to SARS-CoV-2 with an inhibition constant of μM, but the exact target has not been reported. In this work, combining molecular docking, steered molecular dynamics and umbrella sampling we examined its binding affinity to two targets including the main protease (Mpro), also known as 3C-like protease, and RdRp. We showed that Remdesivir binds to Mpro slightly weaker than to RdRp and the corresponding inhibition constants, consistent with the experiment, fall to the μM range. The binding mechanisms of<br />Remdesivir to two targets differ in that electrostatic interaction is the main force in stabilizing the RdRp-Remdesivir complex, while the van der Waals interaction dominates in the MproRemdesivir case. Our result indicates that Remdesivir can target not only RdRp but also Mpro, which can be invoked to explain why this drug is effective in treating Covid-19. We have identified residues of the target protein that make the most important contribution to binding affinity, and this information is useful for drug development for this disease.
<br />
|
Hoang Linh Nguyen; Thai Nguyen; Duc Toan Truong; Mai Suan Li
|
Biophysics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ea5567dfe53cbec554e/original/remdesivir-strongly-binds-to-both-rna-dependent-rna-polymerase-and-main-protease-of-sars-co-v-2-evidence-from-molecular-simulations.pdf
|
673bede85a82cea2fa9a8730
|
10.26434/chemrxiv-2024-gtf8v
|
Ordered B2 phase in a disordered FCC matrix: Current state of research on the development of low-density B2-strengthened Fe-Mn-Al-Ni-C steels
|
Over the last five years, the automotive industry has primarily focussed on utilising a number of extraordinary properties of B2-strengthened Fe-Mn-Al-Ni-C steels, especially high specific strength, and high strain hardening. While reduction in density may be attributed to the addition of Al, high toughness and strain hardening may be ascribed to the precipitation of non- shearable B2 precipitates which suppresses the formation of shearable L’12-κ-carbides ((Fe, Mn)3AlC carbides). Considering the growing interest in these steels, the present review is aimed at highlighting the present state of research and associated challenges (both fundamental and industrial) with a special emphasis on the influence of B2 precipitate distribution and morphology on the strengthening effect in these steels. In addition, the necessity of obtaining both structural and chemical information about ordered B2 precipitates using the newly emerged methodology of correlative microscopy has also been highlighted.
|
Mainak Saha
|
Materials Science; Alloys; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673bede85a82cea2fa9a8730/original/ordered-b2-phase-in-a-disordered-fcc-matrix-current-state-of-research-on-the-development-of-low-density-b2-strengthened-fe-mn-al-ni-c-steels.pdf
|
64197420aad2a62ca11a1f62
|
10.26434/chemrxiv-2023-4fn8j
|
Reinforcement Learning in Crystal Structure Prediction
|
Crystal Structure Prediction (CSP) is a fundamental computational problem in materials science. Basin-hopping is a prominent CSP method that combines global Monte Carlo sampling to search over candidate trial structures with local energy minimisation of these candidates. The sampling uses a stochastic policy to randomly choose which action (such as a swap of atoms) will be used to transform the current structure into the next. Typically hand-tuned for a specific system before the run starts, such a policy is simply a fixed discrete probability distribution of possible actions, which does not depend on the current structure and does not adapt during a CSP run. We show that reinforcement learning (RL) can generate a dynamic policy that both depends on the current structure and improves on the fly during the CSP run. We demonstrate the efficacy of our approach on two CSP codes, FUSE and MC-EMMA. Specifically, we show that, when applied to the autonomous exploration of a phase field to identify the accessible crystal structures, RL can save up to 46% of the computation time.
|
Elena Zamaraeva; Christopher M. Collins; Dmytro Antypov; Vladimir V. Gusev; Rahul Savani; Matthew S. Dyer; George R. Darling; Igor Potapov; Matthew J. Rosseinsky; Paul G. Spirakis
|
Theoretical and Computational Chemistry; Materials Science; Theory - Computational; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2023-03-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64197420aad2a62ca11a1f62/original/reinforcement-learning-in-crystal-structure-prediction.pdf
|
66c2190620ac769e5ffd983a
|
10.26434/chemrxiv-2024-p1txk
|
Rapid Joule Heating-Induced Structural Evolution of Nonstoichiometric Ordered Mesoporous Aluminum-Based Spinel Structures
|
Coupling self-assembly with ultrashort transient heating at high temperatures effectively accelerates reaction kinetics through enhanced transformation pathways. This approach provides precise control over crystalline phase characteristics and enables emergent collective properties and functionalities in mesoporous inorganic materials. Here, we describe the structural evolution and rapid formation of highly crystalline, well-ordered mesoporous magnesium aluminate defect spinel structures with nonstoichiometric compositions, achieved in seconds via block copolymer-directed self-assembly and Joule heating. Isothermal experiments conducted ex situ demonstrated Joule heating-induced acceleration of the amorphous-to-spinel transition. The process aligned with the Johnson-Mehl-Kolmogorov-Avrami model, revealing an instantaneous surface nucleation and diffusion-controlled growth mechanism requiring significantly lower activation energy compared to conventional thermal treatments. Further exploration of the ultrafast approach led to the development of an ordered mesoporous defect spinel-carbon framework decorated with in situ crystallized platinum nanoparticles. This composite structure exhibited enhanced thermal and mechanical stability under high temperature reducing environments, demonstrating its potential for thermal catalytic applications. Understanding Joule heating-induced crystallization kinetics and phase transformations on transient timescales may reveal novel crystalline phases and functionalities inaccessible through conventional heating of nonstoichiometric compositions.
|
Leyan Wang; Qihang Chen; Yong Quan Yeo; Geok Leng Seah; Hossein Akhoundzadeh; Yee Yan Tay; Teddy Salim; Pio Buenconsejo; Edward Corcoran ; Adam Usadi; Jonathan McConnachie; David Moore; Rong Xu; Zhong Chen; Kwan W. Tan
|
Materials Science; Nanoscience; Ceramics; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c2190620ac769e5ffd983a/original/rapid-joule-heating-induced-structural-evolution-of-nonstoichiometric-ordered-mesoporous-aluminum-based-spinel-structures.pdf
|
650b606160c37f4f76262791
|
10.26434/chemrxiv-2023-knbbh
|
Sulfamate Tethered Aza-Wacker Strategy for a Kasugamine Synthon
|
We present our preparation of a kasugamine synthon, which proceeds in 14 steps from a literature epoxide. We expect
that this kasugamine derivative can be used for the total syntheses of kasugamycin, minosaminomycin, and analogue antibiotics. A key step in the synthesis is our laboratory’s sulfamate-tethered aza-Wacker cyclization.
|
Shyam Sathyamoorthi; Gour Mandal
|
Organic Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-09-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650b606160c37f4f76262791/original/sulfamate-tethered-aza-wacker-strategy-for-a-kasugamine-synthon.pdf
|
66defd7612ff75c3a1dd7624
|
10.26434/chemrxiv-2024-kmvvw
|
Surface Coordination Chemistry of Graphitic Carbon Nitride from Ag Molecular Probes
|
Graphitic carbon nitride (g-C3N4) has gained significant attention for its catalytic properties, especially in the development of Single Atom Catalysts (SACs). However, the surface chemistry underlying the formation of these isolated metal sites remains poorly understood. In this study we employ Surface OrganoMetallic Chemistry (SOMC) together with advanced microscopic and spectroscopic techniques for an in-depth analysis of functionalized g-C3N4 materials, where tailored organosilver probe molecules are used to monitor surface processes and characterize resulting surface species. A multi-technique approach – including high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), X-ray absorption spectroscopy (XAS), and multinuclear solid-state Nuclear Magnetic Resonance spectroscopy (ssNMR), coupled with density functional theory (DFT) calculations – identifies three primary surface species in Ag-functionalized g-C3N4: bis-NHC-Ag+, dispersed Ag+ sites, and physisorbed molecular precursor. These findings highlight a dynamic grafting process and provide insights into the surface coordination chemistry of functionalized g-C3N4 materials.
|
Sk Amanullah; Weicheng Cao; Enzo Brack; Milivoj Plodinec; Christophe Copéret
|
Organometallic Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-09-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66defd7612ff75c3a1dd7624/original/surface-coordination-chemistry-of-graphitic-carbon-nitride-from-ag-molecular-probes.pdf
|
60c75267ee301c80a2c7abc6
|
10.26434/chemrxiv.13295987.v1
|
Water Oxidation Kinetics of Nanoporous BiVO4 Photoanodes Functionalised with Nickel/iron Oxyhydroxide Electrocatalysts
|
In this work, spectroelectrochemical techniques are employed to analyse the catalytic water oxidation performance of a series of three nickel/iron oxyhydroxide electrocatalysts deposited on FTO and BiVO<sub>4</sub>, at neutral pH. Similar electrochemical water oxidation performance is observed for each of the FeOOH, Ni(Fe)OOH and FeOOHNiOOH electrocatalysts studied, which is found to result from a balance between degree of charge accumulation and rate of water oxidation. Once added onto BiVO4 photoanodes, a large enhancement in the water oxidation photoelectrochemical performance is observed in comparison to the un-modified BiVO<sub>4</sub>. To understand the origin of this enhancement, the films were evaluated through time-resolved optical spectroscopic techniques, allowing comparisons between electrochemical and photoelectrochemical water oxidation. For all three catalysts, fast hole transfer from BiVO<sub>4</sub> to the catalyst is observed in the transient absorption data. Using operando photoinduced absorption measurements, we find that water oxidation is driven by oxidised states within the catalyst layer, following hole transfer from BiVO<sub>4</sub>. This charge transfer is correlated with a suppression of recombination losses which result in remarkably enhanced water oxidation performance relative to un-modified BiVO<sub>4</sub>. Moreover, despite similar electrocatalytic performance of all three electrocatalysts, we show that variations in water oxidation performance observed among the BiVO<sub>4</sub>/MOOH photoanodes stem from differences in photoelectrochemical and electrochemical charge accumulation in the catalyst layers. Under illumination, the amount of accumulated charge in the catalyst is driven by the injection of photogenerated holes from BiVO<sub>4</sub>, which is further affected by the recombination loss at the BiVO<sub>4</sub>/MOOH interface, and thus leads to deviations from their behaviour as standalone electrocatalysts.
|
Laia Francàs; Shababa Selim; Sacha Corby; Dongho Lee; Camilo Mesa; Ernest Pastor; Kyoung-Shin Choi; James R Durrant
|
Catalysts; Spectroscopy (Anal. Chem.); Electrocatalysis; Heterogeneous Catalysis; Photocatalysis; Redox Catalysis; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-11-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75267ee301c80a2c7abc6/original/water-oxidation-kinetics-of-nanoporous-bi-vo4-photoanodes-functionalised-with-nickel-iron-oxyhydroxide-electrocatalysts.pdf
|
675a37ca7be152b1d0adf5c8
|
10.26434/chemrxiv-2024-9dfqc
|
Organocatalytic Aerobic Oxidative Monodealkylation of tert-Amines to sec-Amines
|
The highly efficient monodealkylation of tertiary amines was achieved using hydroxylamine and NOx catalysts under mildly aerobic conditions. This approach demonstrates high functional group tolerance and a broad substrate scope, including amino acids and alkaloids with complex structures. Mechanistic studies have suggested that the reaction proceeds via aminium radical cations via the one-electron oxidation of tertiary amines.
|
Yusuke Sasano; Haruki Shimabayashi; Shuhei Akutsu; Ryota Sasaki; Yoshiharu Iwabuchi
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675a37ca7be152b1d0adf5c8/original/organocatalytic-aerobic-oxidative-monodealkylation-of-tert-amines-to-sec-amines.pdf
|
664b7089418a5379b0cf872a
|
10.26434/chemrxiv-2024-v4rdx
|
Antimicrobial Potency of Nor-Pyochelin Analogs and Their Cation Complexes Against Multidrug-Resistant Pathogens
|
The Gram-negative, opportunistic pathogen Pseudomonas aeruginosa has become a serious threat to global health, with increasing resistance towards even the most potent antibiotics. Like other bacteria, the pathogen produces a number of virulence factors that promote its pathogenicity. Of these, metallophores constitute an important group, able to scavenge metal ions from the surrounding environment to secure the metabolic functions of the bacterium. Pseudomonads produce the iron-chelating metallophore (siderophore) pyochelin (PCH), which, in addition to its iron scavenging ability, is an effector for the transcriptional regulator PchR in its Feᴵᴵᴵ-bound form (ferripyochelin). In the present study, docking studies predicted a major ferripyochelin binding site in PchR, which prompted the exploration of nor-pyochelin analogs to produce tight binding to PchR, and thereby establish a lasting effector response associated with upregulation of the genes involved in the PCH metabolism. In addition, we investigated the effects of using the analogs to bind the antimicrobial cations Gaᴵᴵᴵ and Inᴵᴵᴵ, leading to enhanced uptake and further disruption of the cell machinery. Selected analogs of nor-pyochelin (nor-PCH) were synthesized and their Gaᴵᴵᴵ and Inᴵᴵᴵ-based complexes were assessed for antimicrobial activity. The results indicate that the Gaᴵᴵᴵ-complexes inhibit the pathogens under iron-limited conditions, while the Inᴵᴵᴵ-based systems are more effective in iron-rich media. Several of the Gaᴵᴵᴵ-complexes were shown to be highly effective against an MDR P. aeruginosa clinical isolate, with minimum inhibitory concentrations (MICs) of ≤1 µg/mL. Similarly, two of the Inᴵᴵᴵ-based systems were particularly effective against the isolate, with an MIC of 8 µg/mL. These results show high promise in comparison with other, traditionally potent antibiotics. Preliminary mechanistic investigations of the antimicrobial activity using pseudomonal transposon mutants suggested that the inhibitory effects of the Inᴵᴵᴵ-based systems could be due to acute iron deficiency as a result of Inᴵᴵᴵ-bound bacterioferritin (BfrB). Cytotoxiticy analysis indicated that the compounds generally show low toxicity toward mammalian cells under the experimental conditions.
|
Hasitha N.G. Raviranga; Mubarak Ayinla; Harini A. Perera; Yunchuan Qi; Mingdi Yan; Olof Ramstrom
|
Biological and Medicinal Chemistry; Organic Chemistry; Supramolecular Chemistry (Org.); Drug Discovery and Drug Delivery Systems; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664b7089418a5379b0cf872a/original/antimicrobial-potency-of-nor-pyochelin-analogs-and-their-cation-complexes-against-multidrug-resistant-pathogens.pdf
|
63c01844a5c354e209910bed
|
10.26434/chemrxiv-2023-q8484
|
A customized Bayesian algorithm to optimize enzyme-catalyzed reactions
|
Design of experiments (DoE) plays an important role in optimizing the catalytic performance of chemical reactions. The most commonly-used DoE relies on the response surface methodology (RSM) to model the variable space of experimental condi-tions with a minimal number of experiments. However, the RSM leads to an exponential increase in the number of required experiments to be evaluated as the number of variables increases. Herein we describe a Bayesian optimization algorithm (BOA) to optimize the continuous parameters (e.g. temperature, reaction time, reactant and enzyme concentrations etc.) of enzyme-catalyzed reactions with the aim of maximizing performance. Compared to existing Bayesian optimization methods, we propose an improved algorithm that leads to better results under limited resources and time for experiments. To validate the versatility of BOA for the optimization of the turnover number in enzyme-catalyzed reactions, we benchmarked its per-formance for a biocatalytic C-C bond-forming reaction as well as an amination reaction. Gratifyingly, up to 80% improvement compared to RSM and up to 360% improvement vs. previous Bayesian optimization algorithms was obtained. Importantly, this strategy enabled the simultaneous optimization of both the enzyme’s activity and chemoselectivity for a cross-benzoin condensation.
|
Ryo Tachibana; Kailin Zhang; Zhi Zou; Simon Burgener; Thomas R. Ward
|
Catalysis; Chemical Engineering and Industrial Chemistry; Process Control; Heterogeneous Catalysis; Redox Catalysis
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-01-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c01844a5c354e209910bed/original/a-customized-bayesian-algorithm-to-optimize-enzyme-catalyzed-reactions.pdf
|
663679c791aefa6ce1274b6a
|
10.26434/chemrxiv-2024-p6rl3
|
New Carbene Donor for Biocatalysis: Stereodivergent Synthesis of Pyridyl Cyclopropanes via Enzymatic Activation of Pyridyltriazoles
|
Hemoproteins have recently emerged as powerful biocatalysts for new-to-nature carbene transfer reactions. Despite this progress, these strategies have remained largely limited to diazo-based carbene precursor reagents. Here, we report the development of a biocatalytic strategy for the stereoselective construction of pyridine-functionalized cyclopropanes via hemoprotein-mediated activation of pyridyl triazoles (PyTz) as stable and readily accessible carbene sources. This method enables the asymmetric cyclopropanation of a variety of olefins, including electronrich and electrodeficient ones, with high activity, high stereoselectivity, and enantiodivergent selectivity, providing access mono- and diaryl-cyclopropanes that incorporate a pyridine moiety, and thus two structural motifs of high value in medicinal chemistry. Mechanistic studies reveal a multifaceted role of 7-halogen substitution in the pyridyltriazole reagent toward favoring multiple catalytic steps in the transformation. This work provides a first example of asymmetric olefin cyclopropanation with pyridotriazoles, paving the way to the exploitation of these attractive and versatile reagents for enzyme-catalyzed carbene-mediated reactions.
|
Satyajit Roy; Yining Wang; Xinyi Zhao; Thakshila Dayananda; Jia-Min Chu; Yong Zhang; Rudi Fasan
|
Catalysis; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663679c791aefa6ce1274b6a/original/new-carbene-donor-for-biocatalysis-stereodivergent-synthesis-of-pyridyl-cyclopropanes-via-enzymatic-activation-of-pyridyltriazoles.pdf
|
62fd44b94d86694be4d50088
|
10.26434/chemrxiv-2022-864dg-v2
|
Charge transport across dynamic covalent chemical bridges
|
Relationships between chemical structure and conductivity in ordered polymers (OPs) are difficult to probe using bulk samples. We propose that conductance measurements of appropriate molecular-scale models can reveal trends in electronic coupling(s) between repeat units that may help inform OP design. Here we apply the scanning tunneling microscope-based break junction (STM-BJ) method to study transport through single-molecules comprising OP-relevant imine, imidazole, diazaborole, and boronate ester dynamic covalent chemical bridges. Notably, solution-stable boron-based compounds hydrolyze in situ unless measured under a rigorously inert glovebox atmosphere. We find that junction conductance correlates with the electronegativity difference between bridge atoms, and corroborative first-principles calculations further reveal a different nodal structure in the transmission eigenchannels of boronate ester junctions. This work reaffirms expectations that highly polarized bridge motifs represent poor choices for the construction of OPs with high through-bond conductivity and underscores the utility of glovebox STM-BJ instrumentation for studies of air-sensitive materials.
|
Zelin Miao; Timothy Quainoo; Thomas Czyszczon-Burton; Nils Rotthowe; Joseph Parr; Zhen-Fei Liu; Michael Inkpen
|
Physical Chemistry; Nanoscience; Nanodevices; Transport phenomena (Physical Chem.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fd44b94d86694be4d50088/original/charge-transport-across-dynamic-covalent-chemical-bridges.pdf
|
60c74cfbbb8c1a94f33db4f7
|
10.26434/chemrxiv.12581075.v1
|
Artificial Intelligence Guided De Novo Molecular Design Targeting COVID-19
|
An extensive search for active therapeutic agents against the SARS-CoV-2 is being conducted across the globe. Computational docking simulations have traditionally been used for <i>in silico</i> ligand design and remain popular method of choice for high-throughput screening of therapeutic agents in the fight against COVID-19. Despite the vast chemical space (millions to billions of biomolecules) that can be potentially explored as therapeutic agents, we remain severely limited in the search of candidate compounds owing to the high computational cost of these ensemble docking simulations employed in traditional <i>in silico</i> ligand design. Here, we present a <i>de novo</i> molecular design strategy that leverages artificial intelligence to discover new therapeutic biomolecules against SARS-CoV-2. A Monte Carlo Tree Search algorithm combined with a multi-task neural network (MTNN) surrogate model for expensive docking simulations and recurrent neural networks (RNN) for rollouts, is used to sample the exhaustive SMILES space of candidate biomolecules. Using Vina scores as target objective to measure binding of therapeutic molecules to either the isolated spike protein (S-protein) of SARS-CoV-2 at its host receptor region or to the S-protein:Angiotensin converting enzyme 2 (ACE2) receptor interface, we generate several (~100's) new biomolecules that outperform FDA (~1000’s) and non-FDA biomolecules (~million) from existing databases. A transfer learning strategy is deployed to retrain the MTNN surrogate as new candidate molecules are identified - this iterative search and retrain strategy is shown to accelerate the discovery of desired candidates. We perform detailed analysis using Lipinski's rules and also analyze the structural similarities between the various top performing candidates. We spilt the molecules using a molecular fragmenting algorithm and identify the common chemical fragments and patterns – such information is important to identify moieties that are responsible for improved performance. Although we focus on therapeutic biomolecules, our AI strategy is broadly applicable for accelerated design and discovery of any chemical molecules with user-desired functionality.
|
Srilok Srinivasan; Rohit Batra; Henry Chan; Ganesh Kamath; Mathew J. Cherukara; Subramanian Sankaranarayanan
|
Theory - Computational; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Ligand Design
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cfbbb8c1a94f33db4f7/original/artificial-intelligence-guided-de-novo-molecular-design-targeting-covid-19.pdf
|
65e60cb49138d23161a7f044
|
10.26434/chemrxiv-2024-pqr4n
|
Pretreatment Methods for Accelerated PFAS Degradation in Wastewater
|
This study explored different pretreatment methods to enhance photochemical degradation of PFAS in still-bottom (SB) brine. The brine contained concentrated natural organic matter and inorganic salts, which severely inhibited PFAS destruction by prevailing technologies. Pretreatment methods evaluated included flocculation, Fenton oxidation, and Soxhlet extraction. Soxhlet extraction works by repeatedly passing a small volume of solvent through the solid from drying the SB, resulting in efficient extraction of most PFAS. The extract reduced 73% of organic content and 84-98% of inorganic salts in the original SB. The redissolved extract in water (equivalent to 10x dilution of the original SB) yielded 100% PFAS removal and 80% defluorination within 24 hours by UV/sulfite/iodide treatment. In comparison, only 20% defluorination was achieved in 10x diluted SB without pretreatment, 56% with Fenton pretreatment, and 24% with flocculation pretreatment. These findings underscore the importance of removing co-existing components in challenging water matrices to enable efficient PFAS destruction.
|
Dandan Rao; Jinyong Liu
|
Earth, Space, and Environmental Chemistry; Environmental Science; Hydrology and Water Chemistry; Wastes
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e60cb49138d23161a7f044/original/pretreatment-methods-for-accelerated-pfas-degradation-in-wastewater.pdf
|
662fbd42418a5379b008668e
|
10.26434/chemrxiv-2024-zv92k
|
AI-driven discovery of synergistic drug combinations against pancreatic cancer
|
Treatment regimens, especially in cancer, often include more than one medicine in order to achieve durable outcomes. Identifying the optimal combination of treatments has historically been done through clinical trial and error. And for many conditions, such as pancreatic cancer, an optimal treatment protocol has remained elusive, and the best available treatment combinations provide only modest benefit. Recent developments have led to the application of both experimental screening approaches and in silico modeling methods to identify synergistic drug combinations and expand the therapeutic options for multiple diseases. Here we conduct a study to compare different predictive approaches for identifying new treatment combinations for pancreatic cancer using cell line growth as an initial proxy for clinical utility. NCATS performed screening involving 496 pairwise combinations of 32 antineoplastic drugs, tested against the PANC-1 human pancreatic carcinoma cell line in duplicates using a 10 × 10 matrix format. This dataset served as the basis for generating and training advanced AI/ML models focused on pancreatic cancer. Next, three independent groups (NCATS, UNC and MIT), though in a collaborative manner, utilized three different workflows with AL/ML approaches to discover new perspective drug combinations against pancreatic cancer among over 1.5 million drug combinations. As a result of this collaboration, 88 proposed combinations were tested in a cell-based assay; 53 of them were synergistic (hit rate ~60%). While all machine learning approaches demonstrate advances in the direction of predicting synergistic drug combinations, graph convolutional networks resulted in the best performance with a hit rate ~83%, and Random Forest delivered the highest precision of 65%. Interestingly, all utilized AL/ML methods among the three groups proposed different drug combinations with a small overlap of only two combos from 90. This study demonstrates the potential of a collaborative modeling approach for prioritizing drug combinations in large-scale screening campaigns, particularly when focusing on maximizing the efficacy of drugs known to exhibit synergy.
|
Mohsen Pourmousa; Sankalp Jain; Elena Barnaeva; Wengong Jin; Joshua Hochuli; Zina Itkin; Travis Maxfield; Cleber Melo-Filho; Andrew Thieme; Kelli Wilson; Carleen Klumpp-Thomas; Sam Michael; Noel Southall; Tommi Jaakkola; Eugene Muratov; Regina Barzilay; Alexander Tropsha; Marc Ferrer; Alexey Zakharov
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-04-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662fbd42418a5379b008668e/original/ai-driven-discovery-of-synergistic-drug-combinations-against-pancreatic-cancer.pdf
|
647afc92be16ad5c5764ab1d
|
10.26434/chemrxiv-2023-2qqt5
|
Water Oil Emulsions Studied by Vibrational Sum Frequency Generation
|
Interfacial interactions between water and oil phases are present in various fields, in which other additives, such as surfactants, are utilized to minimize the surface stress between these phases to form an emulsion. However, the consequence of adding additives is not always easy to understand or to control, due to the plethora of parameters that control the production of an emulsion phase. There are several macroscopic techniques to study the properties of emulsions. Nevertheless, these techniques cannot describe the mechanistic steps at molecular level for interfaces with nanometer thicknesses. Among surface sensitive techniques, VSFG (vibrational sum frequency generation) has been utilized to study various parameters that control the formation of surfactant monolayers at water-oil interfaces. In this brief-review, basics about utilization of VSFG along with recent advances for studying the water-oil interfaces will be presented, aiming at familiarizing other scientists with the current understanding of the water-oil interfaces as studied by VSFG
|
Ahmed El-Zohry; Theis Solling
|
Physical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647afc92be16ad5c5764ab1d/original/water-oil-emulsions-studied-by-vibrational-sum-frequency-generation.pdf
|
629cfe4bdd18094c8ef6cbdd
|
10.26434/chemrxiv-2022-vpq0t-v2
|
Polycrystalline Diamond Coating on Orthopaedic Implants: Realization, and Role of Surface Topology and Chemistry in Adsorption of Proteins and Cell Proliferation
|
Polycrystalline diamond has the potential to improve the osseointegration of orthopaedic implants compared to conventional materials such as titanium. However, despite the excellent biocompatibility and superior mechanical properties, the major challenge of using diamond for implants, such as those used for hip arthroplasty, is the limitations of microwave plasma chemical vapor deposition (CVD) techniques to synthesize diamond on complex-shaped objects. Here, for the first time we demonstrate diamond growth on titanium acetabular shells using surface wave plasma CVD method. Polycrystalline diamond coatings were synthesized at low temperatures (~400 °C) on three types of acetabular shells with different surface structure and porosity. We achieved the growth of diamond on highly porous surfaces designed to mimic the structure of the trabecular bone and improve osseointegration. Biocompatibility was investigated on nanocrystalline diamond (NCD) and ultrananocrystalline diamond (UNCD) coatings terminated either with hydrogen or oxygen. To understand the role of diamond surface topology and chemistry in the attachment and proliferation of mammalian cells, we investigated the adsorption of extracellular matrix (ECM) proteins, and monitored the metabolic activity of fibroblasts, osteoblasts, and bone marrow-derived mesenchymal stem cells (MSCs). The interaction of bovine serum albumin (BSA) and Type I collagen with the diamond surfaces was investigated by confocal fluorescence lifetime imaging microscopy (FLIM). We found that the proliferation of osteogenic cells was better on hydrogen terminated UNCD than on the oxygen terminated counterpart. These findings correlated with the behaviour of collagen on diamond substrates observed by FLIM. Hydrogen terminated UNCD provided better adhesion and proliferation of osteogenic cells, compared to titanium, while growth of fibroblasts was poorest on hydrogen terminated NCD and MSCs behaved similarly on all tested surfaces. These results open new opportunities for application of diamond coatings on orthopaedic implants.
|
Justas Zalieckas; Ivan Rios Mondragon; Paulius Pobedinskas; Arne Skodvin Kristoffersen; Samih Mohamed-Ahmed; Cecilie Gjerde; Paul Johan Høl; Geir Hallan; Ove Nord Furnes; Mihaela-Roxana Cimpan; Ken Haenen; Bodil Holst; Martin Møller Greve
|
Materials Science; Nanoscience; Biocompatible Materials; Carbon-based Materials; Coating Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-06-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629cfe4bdd18094c8ef6cbdd/original/polycrystalline-diamond-coating-on-orthopaedic-implants-realization-and-role-of-surface-topology-and-chemistry-in-adsorption-of-proteins-and-cell-proliferation.pdf
|
671a8c2798c8527d9e3c6a80
|
10.26434/chemrxiv-2024-f8wp4
|
easyPARM: Automated, Versatile, and Reliable Force Field Parameters for Metal-Containing Molecules with Unique Labeling of Coordinating Atoms
|
The dynamics of metal centers are challenging to describe due to the vast variety of ligands, metals, and coordination spheres, hampering the existence of transferable force field parameters for classical molecular dynamics simulations. Here we present easyPARM, a python-based tool able to calculate force field parameters for a wide range of metal complexes from routine frequency calculations with electronic structure methods. The approach is based on the unique labeling strategy, in which each ligand atom that coordinates the metal receives a unique atom type. This design prevents parameters shortage, labeling duplication, and the necessity to post-process output files even for very complicated coordination spheres, whose parameterization process remain automatic. The program requires the Cartesian Hessian matrix, the geometry xyz file, and the atomic charges to provide reliable force field parameters extensively benchmarked against density functional theory dynamics both in the gas and condensed phases. The procedure allows the classical description of metal complexes at a low computational cost, with an accuracy as good as the quality of the Hessian matrix obtained by quantum chemistry methods. The tool is available free of charge in the GitHub platform (https://github.com/Abdelazim-Abdelgawwad/easyPARM.git).
|
Abdelazim M. A. Abdelgawwad; Antonio Francés-Monerris
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-10-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671a8c2798c8527d9e3c6a80/original/easy-parm-automated-versatile-and-reliable-force-field-parameters-for-metal-containing-molecules-with-unique-labeling-of-coordinating-atoms.pdf
|
60c750b8bdbb89233ca39f83
|
10.26434/chemrxiv.13076039.v1
|
Investigation of the Reactivity of 1-Azido-3-Iodobicyclo[1.1.1]pentane under “Click” Reaction Conditions
|
The bicyclo[1.1.1]pentane (BCP) unit exhibits special physical and chemical properties and is under scrutiny as a bioisostere in drug molecules. We employed methodologies for the synthesis of different BCP triazole building blocks from one precursor, 1-azido-3-iodobicyclo[1.1.1]pentane, by Cu(I)-catalyzed 1,3-dipolar cycloaddition (“click”) reactions and integrated cycloaddition-Sonogashira coupling reactions. Thereby, we accessed three classes of substituted BCP derivatives: 1,4-disubstituted triazoles, 5-iodo-1,4,5-trisubstituted triazoles and 5-alkynylated 1,4,5-trisubstituted triazoles. This gives entry to the synthesis of multiply substituted BCP triazoles either on a modular or a one-pot basis. These methodologies were further utilized for appending large chromophoric porphyrin moieties onto the BCP core.
|
Elisabeth Sitte; Brendan Twamley; nitika grover; Mathias O.. Senge
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Crystallography – Organic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750b8bdbb89233ca39f83/original/investigation-of-the-reactivity-of-1-azido-3-iodobicyclo-1-1-1-pentane-under-click-reaction-conditions.pdf
|
60c75867337d6c4febe29223
|
10.26434/chemrxiv.14544639.v1
|
Activating Room-Temperature Phosphorescence of Organic Luminophores via External Heavy-Atom Effect and Rigidity of Ionic Polymer Matrix
|
Pure
organic room-temperature phosphorescence (RTP) materials have attracted wide
attention for their easy preparation, low toxicity and applications in professional
fields such as bioimaging and anti-counterfeiting. Developing phosphorescent
systems with more universality and less difficulty in synthesis has long been
the pursuit of materials scientists. By employing polymeric quaternary ammonium
salt with an ionic bonding matrix and heavy atoms, commercial fluorescent dyes
are directly endowed with phosphorescence emission. In a single amorphous
polymer, the external heavy-atom effect generates excited triplet states, which
are further stabilized by the rigid polymer matrix. This study proposed a new
general strategy to design and develop pure organic RTP materials starting from
the vast library of organic dyes without complicated chemical synthesis.
|
Xiang Ma; Zi-Ang Yan; Xiaohan Lin; Siyu Sun; He Tian
|
Photochemistry (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75867337d6c4febe29223/original/activating-room-temperature-phosphorescence-of-organic-luminophores-via-external-heavy-atom-effect-and-rigidity-of-ionic-polymer-matrix.pdf
|
667c83555101a2ffa895f7b5
|
10.26434/chemrxiv-2023-v95p8-v2
|
Synthesis and Post-Assembly Modifications of Dynamic Covalent Boronic Ester [2]Rotaxanes
|
We report on the synthesis of [2]rotaxanes from vicinal diols through dynamic covalent boronic ester templates, as well as the use of the boronic ester for post-assembly modifications. A boronic acid pincer ligand with two alkene-appended arms was condensed with a linear diol-containing thread, and ring-closing metathesis then established a quasi[1]rotaxane architecture along with a non-entangled isomer. Advanced NMR spectroscopy and mass spectrometry unambiguously assigned the isomers and revealed that the quasi[1]rotaxane was in equilibrium with its hydrolyzed free [2]rotaxane form. The boronic ester handle in the quasi[1]rotaxane could also be synthetically addressed in a multitude of ways to obtain different [2]rotaxanes, including direct oxidation, protodeboronation, functional group interconversions and Pd-catalysed cross-couplings.
|
Jingjing Yu; Marius Gaedke; Satyajit Das; Daniel L. Stares; Christoph A. Schalley; Fredrik Schaufelberger
|
Organic Chemistry; Nanoscience; Organic Compounds and Functional Groups; Supramolecular Chemistry (Org.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-06-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667c83555101a2ffa895f7b5/original/synthesis-and-post-assembly-modifications-of-dynamic-covalent-boronic-ester-2-rotaxanes.pdf
|
656773775bc9fcb5c9aa2666
|
10.26434/chemrxiv-2023-t5wrn
|
Organocatalytic Enantioselective Nucleophilic Addition of Indole Imine 5-Methides
|
Despite the enormous developments in the asymmetric transformations of indole imine methides (IIMs), the remote asymmetric induction involving IIMs remains challenging due to the spatial interaction requirement between the substrate and catalyst. Herein we report the first catalytic asymmetric nucleophilic addition to indole imine 5-methide (5-IIM), the only topological isomer of IIMs whose asymmetric addition remains unknown. Considering the challenging remote stereocontrol, high efficiency and respectable enantioselectivity were achieved, providing access to a range of enantioenriched indole-containing triarylmethanes.
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Yuxuan Li; Jing Huang; Zhengyu Han; Hai Huang; Biqiong Hong; Jianwei Sun
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Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Organocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
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2023-12-01
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656773775bc9fcb5c9aa2666/original/organocatalytic-enantioselective-nucleophilic-addition-of-indole-imine-5-methides.pdf
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6509a0fbb927619fe76d09cd
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10.26434/chemrxiv-2023-sd11m
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Quantitative, precise and multi-wavelength evaluation of the light-to-heat conversion efficiency for nanoparticular photothermal agents with calibrated photoacoustic spectroscopy
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Biomedical photothermal therapy with optical nanoparticles is based on the conversion of optical energy into heat through three steps : optical absorption, thermal conversion of the absorbed energy and heat transfer to the surrounding medium. The light-to-heat conversion efficiency (LHCE) has become one of the main metric to quantitatively characterize the last two steps and evaluate the merit of nanoparticules for photothermal therapy. The estimation of the LHCE is mostly performed by monitoring the temperature evolution of a solution under laser irradiation. However, this estimation strongly depends on the experimental set-up and the heat balance model used. We demonstrate here, theoretically and experimentally, that the LHCE at multiple wavelengths can be efficiently and directly determined, without the use of models, by calibrated photoacoustic spectroscopy. The method was validated using already characterized colloïdal suspensions of silver sulfide nanoparticles and maghemite nanoflowers and an uncertainty of 3 to 7% was estimated for the LHCE determination. Photoacoustic spectroscopy provides a new, precise and robust method of analysis of the photothermal capabilities of aqueous solutions of nanoagents
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Théotim Lucas; Clément Linger; Thomas Naillon; Mahshid Hashemkhani; Lise Abiven; Bruno Viana; Corinne Chaneac; Gautier Laurent; Rana Bazzi; Stephane Roux; Sonia Becharef; Giulio Avveduto; Florence Gazeau; Jérôme Gateau
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Physical Chemistry; Biological and Medicinal Chemistry; Nanoscience; Bioengineering and Biotechnology; Optics; Spectroscopy (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
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2023-09-20
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6509a0fbb927619fe76d09cd/original/quantitative-precise-and-multi-wavelength-evaluation-of-the-light-to-heat-conversion-efficiency-for-nanoparticular-photothermal-agents-with-calibrated-photoacoustic-spectroscopy.pdf
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674dd68e5a82cea2fabb5187
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10.26434/chemrxiv-2024-bt323
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Discovering CO Adsorption and Desorption Pathways from Chemical Reaction Neural Networks Modeling of Transient Kinetics Spectroscopy
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We demonstrate a data-driven approach to interpret surface reactions by combining time-resolved gas-pulsing infrared spectroscopy with Chemical Reaction Neural Networks (CRNN). Using CO adsorption and desorption on Pd(111) at 460K-490K as a model system, we show how transient kinetic data can reveal detailed reaction mechanisms. Starting with a simple one-species model, we systematically evaluate increasingly complex mechanisms involving hollow- and bridge-site adsorption. Despite similar goodness of fit to the same experimental absorbance data, our models predict distinct coverage dynamics for different adsorption sites. Through analysis of spectral peak stability and predicted dynamics, we identify a mechanism where CO primarily adsorbs on bridge sites followed by rapid conversion to hollow sites as the most physically consistent with experimental observations. This work provides a framework for extracting mechanistic insights from limited experimental data, demonstrating how machine learning can bridge the gap between transient kinetic measurements and molecular-level understanding of surface reactions.
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Jay Shukla; Xiaohui Qu; Zubin Darbari; Marija Iloska; Jorge Anibal Boscoboinik; Qin Wu
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Physical Chemistry; Chemical Kinetics
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CC BY NC ND 4.0
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CHEMRXIV
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2024-12-11
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674dd68e5a82cea2fabb5187/original/discovering-co-adsorption-and-desorption-pathways-from-chemical-reaction-neural-networks-modeling-of-transient-kinetics-spectroscopy.pdf
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660533ebe9ebbb4db9c16064
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10.26434/chemrxiv-2024-m8drx
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C3-Chiral truxenes showing high circularly polarized fluorescence and phosphorescence properties based on symmetry-forbidden transition
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Significant effort has been devoted to creating new molecules that show circularly polarized luminescence (CPL) and can be used in devices from both experimental and theoretical approaches. Here we show a new design strategy to achieve a large dissymmetric factor (g value) for CPL based on the symmetry-forbidden transition of π-conjugated molecules. This approach was successfully demonstrated by simple syn-5,10,15-trisubstituted truxenes exhibiting excellent g value for CPL on the order of 10–2. A Herzberg-Teller vibronic analysis and variable-temperature CPL measurements revealed that molecular vibrations dramatically lower the intensity of CPL. Furthermore, at low temperatures, syn-5,10,15-trimethyltruxene exhibits prolonged and strong phosphorescent CPL, which can be analyzed by calculating transition dipole moments using molecular orbitals in the triplet excited state. Leveraged on these findings, a conformationally rigid double-decker-type truxene with robust CPL properties at high temperatures was applied as an emitter in electroluminescence devices exhibiting CPL with a high g value.
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Takuya Omine; Fumitaka Ishiwari; Taehyun Won; Naoya Aizawa; Youhei Takeda; Yumi Yakiyama; Tadashi Mori; Takashi Hirose; Ken-ichi Nakayama; Akinori Saeki
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Organic Chemistry; Photochemistry (Org.)
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CC BY NC ND 4.0
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CHEMRXIV
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2024-03-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660533ebe9ebbb4db9c16064/original/c3-chiral-truxenes-showing-high-circularly-polarized-fluorescence-and-phosphorescence-properties-based-on-symmetry-forbidden-transition.pdf
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67b65febfa469535b9152923
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10.26434/chemrxiv-2025-r4408
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Defluorinative Coupling of (NH)-Heteroarenes and Unactivated Vinyl Fluorides Enabled by Metal–Organic Frameworks
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N-vinyl azoles are prevalent moieties in pharmaceuticals, and fluorovinyl groups are widely recognized as carbonyl bi-oisosteres in drug design. Thus, N-fluorovinylated heteroarenes represent highly desirable functional groups in medicinal chemistry. To streamline the development of novel N-fluorovinylation and N-pentafluoropropenylation reactions, herein we safely handle fluorinated gases, such as vinylidene fluoride (VDF) and hexafluoropropene (HFP), as solid reagents using a metal–organic framework (MOF), Mg2(dobdc) (dobdc4− = 2,5-dioxidobenzene-1,4-dicarboxylate). Free (NH)-heteroarenes react directly with VDF via a defluorinative pathway under mild conditions, yielding terminal N-fluorovinylated products. Various complex, biologically active molecules smoothly undergo N-fluorovinylation under these conditions in much higher yields than with the gas alone. Mechanistic investigations, including deuterium incorpo-ration experiments and density functional theory calculations, suggest that this transformation represents a rare example of a concerted nucleophilic vinylic substitution (SNV) process. This protocol can be performed on gram scale, and the resulting N-fluorovinyl moieties can be further diversified to yield valuable motifs, such as N-fluorocyclopropyl groups. Finally, this defluorinative coupling can be generalized to other fluorinated alkene gases, such as HFP. Overall, this robust defluorinative coupling offers a straightforward strategy for synthesizing diverse fluorinated heteroarenes from readily available starting materials, providing broad access to these valuable motifs for the first time.
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Kaitlyn Keasler; Jaehwan Kim; Julia Pitolaj; Phillip Milner
|
Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Materials Chemistry
|
CC BY NC ND 4.0
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CHEMRXIV
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2025-02-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b65febfa469535b9152923/original/defluorinative-coupling-of-nh-heteroarenes-and-unactivated-vinyl-fluorides-enabled-by-metal-organic-frameworks.pdf
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66228a4321291e5d1d2fce03
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10.26434/chemrxiv-2024-n7grl
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In situ crosslinkable small molecule organic cathode with self-nanostructuring property for stable and fast-rechargeable batteries
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Redox-active organic materials (ROMs) for energy storage devices are emerging as sustainable alternatives to inorganic cathode materials. However, the development of high-performance organic cathodes has been challenged by the incompatibility between the insolubilization of ROMs for high stability and the fabrication of electrodes with high surface area for high-rate capability. Herein, we present a small-molecule organic cathode material, 1,3,5-tris(3-vinyl-10H-phenoxazin-10-yl)benzene (V3PXZ), that overcomes this limitation by in situ electrochemical crosslinking in the cell after electrode fabrication using soluble small-molecule. V3PXZ is designed to form a non-conjugated polymer without byproducts through in situ electrochemical crosslinking to ensure the coupling reaction does not degrade cell performance. This method not only yields an insoluble network of V3PXZ, but also forms nanostructures with high surface area in the electrode. Utilizing self-nanostructuring, we demonstrate an aqueous-processed V3PXZ cathode operating at a voltage of 3.87 V vs. Li/Li+, comparable to inorganic cathodes. Notably, V3PXZ simultaneously achieves the highest cycling stability (capacity retention of 99.995% per cycle over 10,000 cycles) and rate capability (charging 56% of total capacity in 36 seconds) with the highest active content (70 wt%) among the small molecule organic p-type cathodes reported to date.
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Kyunam Lee; Illia E. Serdiuk; Jihyeon Kim; Dong Joo Min; Hyunji Park; Kisuk Kang; Soo Young Park; Ji Eon Kwon
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Materials Science; Energy; Energy Storage; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2024-04-22
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66228a4321291e5d1d2fce03/original/in-situ-crosslinkable-small-molecule-organic-cathode-with-self-nanostructuring-property-for-stable-and-fast-rechargeable-batteries.pdf
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60c759320f50db64fd3985b3
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10.26434/chemrxiv.14518038.v2
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Radical Chain Monoalkylation of Pyridines
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<p>The monoalkylation of N-methoxypyridinium salts with alkyl
radicals generated from alkenes (via hydroboration with
catecholborane), alkyl iodides (via iodine atom transfer) and
xanthates is reported. The reaction proceeds under neutral conditions
since no acid is needed to activate the heterocycle and does not
require the use of an external oxidant. A rate constant for the addition
of a primary radical to N-methoxylepidinium >107 M–1 s–1 was
experimentally determined. This rate constant is more than one order
of magnitude larger than the one measured for the addition of primary
alkyl radical to protonated lepidine demonstrating the remarkable
reactivity of methoxypyridinium salts towards radicals. The reaction
could be extended to a three component carbopyridinylation of
electron rich alkenes including enol esters, enol ethers and enamides.</p>
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Samuel Rieder; Camilo Meléndez; Kleni Mulliri; Philippe Renaud
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Organic Synthesis and Reactions
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CC BY NC ND 4.0
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CHEMRXIV
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2021-05-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759320f50db64fd3985b3/original/radical-chain-monoalkylation-of-pyridines.pdf
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65c3ff4ae9ebbb4db9e10c8f
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10.26434/chemrxiv-2024-l3wwz
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Electrospray ionization tandem mass spectrometry of 4-aryl-3,4-dihydrocoumarins
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We have investigated the gas-phase fragmentation reactions of eleven synthetic 4-aryl-3,4-dihydrocoumarins by electrospray ionization tandem mass spectrometry (ESI-MS/MS) on a quadrupole-time-of flight (Q-TOF) hybrid mass spectrometer. We have also estimated thermochemical data for the protonated coumarins (precursor ion A) and product ion structures by computational chemistry at a B3LYP level of theory to establish the ion structures and to rationalize the fragmentation pathways. The most intense peaks in the product ion spectra of coumarins 1–11 resulted from C8H8O2, CO2, C4H4O3, C8H10O3, C8H8O2, and CH3OH eliminations through retro-Diels-Alder (RDA) reactions, remote hydrogen rearrangements (β-eliminations), and β-lactone ring contraction. Although the investigated coumarins shared most of the fragmentation pathways, formation of a benzylic product ion and its corresponding tropylium ion was diagnostic of the substituents at ring C. The thermochemical data revealed that the nature and position of the substituents at ring C played a key role in the formation of this product ion and determined the relative intensity of its peak in the product ion spectrum. The results of this study contribute to knowledge of the gas-phase ion chemistry of this important class of organic compounds.
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Herbert Dias; William Santos; Luiz Carlos Silva-Filho; Eduardo Crevelin; J. Scott McIndoe; Ricardo Vessecchi; Antônio Crotti
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Theoretical and Computational Chemistry; Organic Chemistry; Analytical Chemistry; Organic Synthesis and Reactions; Mass Spectrometry; Computational Chemistry and Modeling
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CC BY NC ND 4.0
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CHEMRXIV
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2024-02-09
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c3ff4ae9ebbb4db9e10c8f/original/electrospray-ionization-tandem-mass-spectrometry-of-4-aryl-3-4-dihydrocoumarins.pdf
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60c73dd54c891943bfad1c8d
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10.26434/chemrxiv.6194747.v1
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Defect-Free Chemical Functionalization of Magnetic Monolayers Based on Coordination Polymers
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<p>Chemical functionalization has demonstrated to be a powerful approach to tailor the physical and chemical properties of two-dimensional (2D) materials, to increase their processability and</p>
<p>stability, to add new functionalities and, even, to create new 2D materials. However, this post synthetic method – which involves the anchoring of molecules on the surface of an exfoliated 2D crystal – inevitably leads to defective materials, which lack long-range structural order. If defect-free functionalized monolayers are required, a radically new approach needs to be developed. Here we present a pre-synthetic method based on coordination chemistry that affords the isolation of crystalline functionalized monolayers. This involves functionalization of the ligand prior to the formation of the 2D material. The concept is illustrated using layered coordination polymers formed by reacting various benzimidazole derivatives with ferrocene. This surface tuneability, together with the robust magnetic and mechanical properties of these 2D materials, make them exceptional candidates for studying the magnetism in the 2D limit, as well as for developing membranes for selective molecular sensing.</p>
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Javier López-Cabrelles; Samuel Mañas-Valero; Iñigo J. Vitórica-Yrezábal; Pablo J. Bereciartúa; J. Alberto Rodríguez-Velamazán; João Carlos Waerenborgh; Bruno J. C. Vieira; Dejan Davidovikj; Peter G. Steeneken; Herre S. J. van
der Zant; Guillermo Minguez Espallargas; Eugenio Coronado
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Hybrid Organic-Inorganic Materials; Magnetic Materials; Nanostructured Materials - Materials; Coordination Chemistry (Inorg.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2018-04-30
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd54c891943bfad1c8d/original/defect-free-chemical-functionalization-of-magnetic-monolayers-based-on-coordination-polymers.pdf
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65fb9f9b9138d23161e880fd
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10.26434/chemrxiv-2024-p63jh
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Topological optimization for tailored designs of advection-diffusion-reaction porous reactors based on pore scale modeling and simulation
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Reactive transport within porous reactors is crucial to many diverse applications, and the efficacy of these reactors hinges on their microstructure. Mathematical modeling and optimization play a pivotal role in the exploration of efficient designs, enabling the generation of structures that may not be achievable through random realizations of packings. In this study, we propose a framework for high-resolution topological optimization of porous flow-through reactors based on pore-scale simulations using a non-dominated sorting genetic algorithm II. A pore network model for an advection-diffusion-reaction system is developed to simulate reactor performance. This model is integrated with a mathematical optimization algorithm, incorporating a background grid and Delaunay tessellation. The optimization framework generates enhanced porous structures, simultaneously maximizing conversion rates while minimizing pumping costs. Striking a balance between permeability and reactive surface area, the final designs yield a set of Pareto optimal solutions, encompassing diverse non-dominated designs with varying reaction rates and hydraulic requirements. The results demonstrate that optimal pore configurations lead to a 280% increase in conversion rates and a 6% reduction in pumping costs at one end, while on the opposite end of the Pareto front, a 15.2% increase in reaction rates and an 11.3% reduction in pumping costs are observed.
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Mehrzad Alizadeh ; Jeff Gostick; Takahiro Suzuki; Shohji Tsushima
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Chemical Engineering and Industrial Chemistry; Transport Phenomena (Chem. Eng.)
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CC BY NC ND 4.0
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CHEMRXIV
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2024-03-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fb9f9b9138d23161e880fd/original/topological-optimization-for-tailored-designs-of-advection-diffusion-reaction-porous-reactors-based-on-pore-scale-modeling-and-simulation.pdf
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60c74648702a9b620418aba9
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10.26434/chemrxiv.11298896.v1
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Experimental Determination of Octanol-Water Partition Coefficients of Selected Natural Toxins
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Natural toxins are ubiquitously occurring highly diverse organic compounds produced by e.g., plants or fungi. In predictive environmental fate and risk assessment of organic chemicals for regulatory purposes, the octanol-water partition coefficient (Kow) remains one of the key parameters. However, experimental data for natural toxins is largely missing and current estimation models for Kow show limited applicability for multifunctional, ionizable compounds. Thus, log Kow data was first experimentally derived for a diverse set of 45 largely ionizable natural toxins and then compared to predicted values from three different models (KOWWIN, ACD/Percepta, Chemicalize). Both approaches were critically evaluated with regards to their applicability for multifunctional, ionizable compounds. The miniaturized shake-flask approach allowed reliable quantification of pH dependent partitioning behavior for neutral, acidic and basic ionizable natural toxins. All analyzed toxins are rather polar with an average log Kow < 1 and an observed maximum log Kow of 2.7. Furthermore, the comparison of experimental data to those of commonly used prediction models showed that the latter match the former with only minorly increased errors. The Chemicalize tool gave overall best predictions with a mean absolute error of 0.49 and thus should be preferred in comparison to ACD/Percepta and KOWWIN.
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Carina Schoensee; Thomas Bucheli
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Physical and Chemical Properties
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CC BY NC ND 4.0
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CHEMRXIV
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2019-12-09
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74648702a9b620418aba9/original/experimental-determination-of-octanol-water-partition-coefficients-of-selected-natural-toxins.pdf
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66896dbb01103d79c531eb46
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10.26434/chemrxiv-2024-g3q0w-v3
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Effects of Ligand Chemistry on Ion Transport in Two-Dimensional Hybrid Organic-Inorganic Perovskites
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Two-dimensional (2D) hybrid organic-inorganic perovskites are potentially promising materials as passivation layers that can enhance the efficiency and stability of perovskite photovoltaics. The ability to suppress ion transport has been proposed as a stabilization mechanism, yet effective characterization of relevant modes of halide diffusion in 2D perovskites is nascent. In light of this knowledge gap, we combine molecular dynamics simulations with enhanced sampling and experimental validation to systematically characterize how ligand chemistry in seven (R-NH3)2PbI4 systems impacts halide diffusion, particularly in the out-of-plane direction. We find that increasing stiffness and length of ligands generally inhibits ion transport, while increasing ligand polarization generally enhances it. Structural and energetic analyses of the migration pathways provide quantitative explanations for these trends, which reflect aspects of the disorder of the organic layer. Overall, this mechanistic analysis greatly enhances the current understanding of halide migration in 2D hybrid organic-inorganic perovskites and yields insights that can inform the design of future passivation materials.
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Grace Wei; Alan Kaplan; Hang Zhang; Yueh-Lin Loo; Michael Webb
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Theoretical and Computational Chemistry; Materials Science; Energy; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Computational Chemistry and Modeling
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CC BY NC 4.0
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CHEMRXIV
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2024-07-08
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66896dbb01103d79c531eb46/original/effects-of-ligand-chemistry-on-ion-transport-in-two-dimensional-hybrid-organic-inorganic-perovskites.pdf
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6402039f63e8d44e594e7521
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10.26434/chemrxiv-2023-bhl82
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Oxidative Two-State Photoreactivity of a Manganese(IV) Complex using NIR Light
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Highly reducing or oxidizing photocatalysts are a fundamental challenge in the field of inorganic and organic photochemistry. Only a few transition metal complexes with earth-abundant metal ions have so far advanced to excited state oxidants, including chromium, iron and cobalt. All these photocatalysts require high energy light for excitation and their oxidizing power has not been fully exploited due to significant energy dissipation before reaching the photoactive state. Herein we demonstrate that the complex [Mn(dgpy)2]4+ based on earth-abundant manganese can be excited with low-energy NIR light (850 nm, 1.46 eV) to yield a luminescent mixed 2LMCT/2MC excited state (1435 nm, 0.86 eV) with a lifetime of 1.6 ns. The dissipated energy amounts to 0.60 eV. In spite of this energy loss, *[Mn(dgpy)2]4+ with its excited state redox potential Ered* of 1.80 V vs SCE outcompetes the strongest reported precious metal photooxidant (iridium(III)). *[Mn(dgpy)2]4+ oxidizes naphthalene (Eox 1.31 1.54 V vs. SCE) to its radical cation giving the manganese(III) complex [Mn(dgpy)2]3+ in a clean outer-sphere electron transfer process. Unexpectedly, mesitylene, toluene, benzene and nitriles with even extremely high oxidation potentials up to Eox = 2.4 V provoke the [Mn(dgpy)2]4+/3+ reduction under photolysis. A higher energy short-lived 4LMCT excited state with a lifetime of 0.78 ps is made responsible for these demanding oxidations, which proceed by static rather than dynamic quenching. This dual excited state reactivity from 2LMCT/2MC and 4LMCT states is linked to the 4LMCT 2LMCT/2MC intersystem crossing process. These unique findings demonstrate how the design of manganese complexes (i) expands the absorption cross section to 400 850 nm, (ii) increases the 2LMCT/2MC state lifetime to the nanosecond range allowing luminescence and classical dynamic photoredox processes and (iii) enables non-classical static quenching of an extremely oxidizing 4LMCT excited state by the solvent. This conceptually novel approach of static quenching by the solvent minimizes free energy losses, harnesses the full photooxidizing power and thus allows even oxidation of nitriles and benzene using earth-abundant elements and low-energy light.
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Nathan East; Robert Naumann; Christoph Förster; Charusheela Ramanan; Gregor Diezemann; Katja Heinze
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Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Photochemistry (Physical Chem.)
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CC BY NC 4.0
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CHEMRXIV
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2023-03-07
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6402039f63e8d44e594e7521/original/oxidative-two-state-photoreactivity-of-a-manganese-iv-complex-using-nir-light.pdf
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66daf1c1cec5d6c142505199
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10.26434/chemrxiv-2024-5sfvf
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High-resolution in-situ photo-irradiation MAS NMR: Application to the UV-polymerization of n-butyl acrylate
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Light plays a pivotal role in many solid-state materials technologies. Solid-state nuclear magnetic resonance (NMR) is a key tool for characterizing atomic-scale structure and dynamics in solid materials, but requisite magic angle spinning (MAS) of the sample-containing rotors limit the measurement of these systems in their irradiated states. Here we report on a bespoke methodology for performing solid-state NMR of a sample irradiated with visible/ultraviolet (vis/UV) light, while undergoing MAS at frequencies ≤ 15 kHz. A fiber optic insert guides vis/UV light to the spinning NMR rotor, where a glass end cap and dispersion rod acts to illuminate the sample inside the rotor. This methodology was used to follow the photopolymerization reaction of n-butyl acrylate, providing well-resolved 1H and 13C NMR assignments of the formation of a semi-solid polymer gel.
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Thomas Hooper; Rodrigo de Oliveira Silva; Dimitrios Sakellariou
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Materials Science; Analytical Chemistry; Polymer Science; Polymerization kinetics; Spectroscopy (Anal. Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-09-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66daf1c1cec5d6c142505199/original/high-resolution-in-situ-photo-irradiation-mas-nmr-application-to-the-uv-polymerization-of-n-butyl-acrylate.pdf
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663b397491aefa6ce17285c1
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10.26434/chemrxiv-2024-m3g5r
|
Scaling Laws for Optimal Power-Law Fluid Flow within Converging-Diverging Dendritic Networks of Tubes and Rectangular Channels
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Power-law fluid flows in the converging-diverging tubes and rectangular channel are prevalent in engineered microfluidic devices, many industrial processes and heat transfer applications. We analyzed optimal flow conditions and network structures for power-law fluids in linear, parabolic, hyperbolic, hyperbolic cosine and sinusoidal converging-diverging dendritic networks of tubes and rectangular channels, and aiming to maximize flow conductance under volume and surface-area constraints. This model shed light on strategies to achieve efficient fluid transport within these complex dendritic networks. Our study focused on steady, incompressible, 2D planar and axisymmetric laminar flow without considering network losses. We found that the flow conductance is highly sensitive to network geometry. The maximum conductance occurs when a specific radius/channel-height ratio $\beta$ is achieved. This value depends on the constraint as well as on the vessel geometry such as tube or rectangular channel. However independent of the kind of the converging-diverging profile along the length of the vessel. We found that the scaling, i.e., $\beta_{\max}^* = \beta_{\min}^* = N^{-1/3}$ for constrained tube volume and $\beta_{\max}^* = \beta_{\min}^*= N^{-(n+1)/(3n+2)}$ for constrained surface area for all converging-diverging tube-networks profile remains the same as found by \citet{garg2024scaling} for the power-law fluid flow in a uniform tube. Here, $\beta_{\max}^*,~ \beta_{\min}^*$ are the radius ratios of daughter-parent pair at the maximum divergent part or minimum convergent part of the vessel. $N$ represents the number of branches splitting at each junction, and $n$ is the power-law index of the fluid. Further, we found that the optimal flow scaling for the height ratio in the rectangular channel, i.e., $\beta_{\max}^* = \beta_{\min}^* = N^{-1/2} \alpha^{-1/2}$ for constrained tube volume and $\beta_{\max}^* = \beta_{\min}^*= N^{-1/2} \alpha^{-n/(2n+2)}$ for constrained surface area for all converging-diverging channel-networks, respectively, where $\alpha$ is the channel-width ratio between parent and daughter branches. We validated our results with experiments, existing theory for limiting conditions, and extended Hess-Murray's law to encompass shear-thinning and shear-thickening fluids for any branching number $N$.
|
Ashish Garg
|
Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Transport Phenomena (Chem. Eng.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-05-09
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663b397491aefa6ce17285c1/original/scaling-laws-for-optimal-power-law-fluid-flow-within-converging-diverging-dendritic-networks-of-tubes-and-rectangular-channels.pdf
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60c7565d9abda20119f8e4f0
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10.26434/chemrxiv.14233103.v1
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The Price is Right: Predicting Reagent Prices
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<div>
<p>We present a model for estimating the price of a reagent
from its chemical structure. It is intended to be useful when doing reagent
selection for library design. The model is a Random Forest regressor which is trained
on the MolPort catalog of 302K reagents and the log of their price. For descriptors
we use topological fingerprints from RDKit: chiral Morgan fingerprints, its medicinal
chemistry descriptors, and counts of undetermined chiral centers. The model has
an out-of-bag performance of 34% variance explained in log Price. When
predicting on known reagents, the model explains 91% of the variance in log Price.
We analyzed the model to understand the errors that the model makes. We show
that the compounds with the highest errors have only a subtly different
structure from similar molecules, but very different in price. </p>
</div>
|
Kwabena Ofori-Atta; Clayton Springer
|
Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7565d9abda20119f8e4f0/original/the-price-is-right-predicting-reagent-prices.pdf
|
631a01e55351a3ebe2f33cd7
|
10.26434/chemrxiv-2022-lcnkp
|
Side-chain torsional dynamics strongly influence charge transport in organic semiconductors
|
The role of low-frequency (terahertz) vibrational motions on charge carrier dynamics in organic semiconductors (OSCs) is becoming well-known, and efforts are underway to rationally design new materials to mitigate these detrimental effects. However, most efforts have focused on stabilizing the fused-ring semiconducting `core', often by functionalizing with various side-groups, yet questions regarding the role of such modifications on electron-phonon couplings are still outstanding. In this work, the influence of thiophene rings sigma-bonded directly to the pi-conjugated cores is explored. The manner in which these groups alter low-frequency vibrational, and resulting electronic, dynamics is quantified using a theoretical approach employing fully-periodic density functional theory (DFT) simulations. Ultimately, these results showcase how the equilibrium geometry and corresponding electronic structure are directly related to detrimental electron-phonon coupling, which have important implications for the design of improved organic optoelectronic materials.
|
Peter Banks; Adam Dyer; Adam Whalley; Michael Ruggiero
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Theory - Computational; Spectroscopy (Physical Chem.); Crystallography
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-09-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631a01e55351a3ebe2f33cd7/original/side-chain-torsional-dynamics-strongly-influence-charge-transport-in-organic-semiconductors.pdf
|
66e69301cec5d6c1421e4cd5
|
10.26434/chemrxiv-2024-54kfj
|
Chitosan Nanoparticles in Oral Drug Delivery: A comprehensive and equivocal review
|
Oral medications are prevalent within modern-day society because of their convenience for patients and their cost-effectiveness. However, challenges such as poor solubility and gastrointestinal degradation decrease their effectiveness. Recently, advancements in nanotechnology have improved the efficiency of drug delivery, with specialized nanocarriers being developed and synthesized for different functions. This review is concentrated on chitosan nanoparticles (CSNPs), which are derived from chitosan, a polysaccharide that is biodegradable and offers a promising solution for overcoming certain challenges associated with drug delivery. CSNPs have been synthesized using a variety of methods such as emulsion cross-linking, ionic gelation, and biosynthesis and more novel methods such as incorporation of a magnetic core. These methods have shown improvements in particle stability, CSNP solubility, and targeted drug delivery, however, challenges like aggregation remain, and must be addressed to optimize the performance of CSNPs. Overall, CSNPs offer a promising advancement in the usage of nanoparticles in medicine with important implications for improving oral drug delivery systems and creating innovative solutions within healthcare.
|
Ronith Lahoti; Aidan Weaver; Taehoon Kim
|
Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Drug Discovery and Drug Delivery Systems
|
CC BY 4.0
|
CHEMRXIV
|
2024-09-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e69301cec5d6c1421e4cd5/original/chitosan-nanoparticles-in-oral-drug-delivery-a-comprehensive-and-equivocal-review.pdf
|
629e682397e76a6befc8a634
|
10.26434/chemrxiv-2022-c1hcf
|
Combining Iminium and Supramolecular Catalysis for the [4 + 2] Cycloaddition of E-Cinnamaldehydes
|
Herein we describe a method for combining supramolecular catalysis with imininum-based organocatalysis in the Diels–Alder cycloaddition reaction. Notably, both cage and L-proline are required for the reaction to occur, implying that encap-sulation of the substrates and co-catalyst are necessary for the reaction to occur. We explore the substrate scope for a va-riety of E-cinnamaldehydes and dienes. Finally, we probe the supramolecular assembly processes responsible for the observed catalysis using NMR spectroscopic methods, determining that the reaction is negative order in the cinnamalde-hyde substrate and experiences product inhibition.
|
Kendra Shrestha; Michael Hilyard; Indunil Alahakoon; Michael Young
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Supramolecular Chemistry (Org.); Organocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-06-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629e682397e76a6befc8a634/original/combining-iminium-and-supramolecular-catalysis-for-the-4-2-cycloaddition-of-e-cinnamaldehydes.pdf
|
60c74b51567dfe8b60ec4f05
|
10.26434/chemrxiv.12317465.v1
|
Active Learning and Neural Network Potentials Accelerate Molecular Screening of Ether-based Solvate Ionic Liquids
|
Solvate Ionic Liquids (SIL) have promising applications as electrolyte materials. Despite the broad design space of oligoether ligands, most reported SILs are based on simple tri- and tetraglyme. Here, we describe a computational search for complex ethers that can better stabilize SILs. Through active learning, a neural network interatomic potential is trained from density functional theory data. The learned potential fulfills two key requirements: transferability across composition space, and high speed and accuracy to find low-energy ligand-ion poses across configurational space. Candidate ether ligands for Li<sup>+</sup>, Mg<sup>+2</sup> and Na<sup>+</sup> SILs with higher binding affinity and electrochemical stability than the reference compounds are identified. Lastly, their properties are related to the geometry of the coordination sphere.
|
Wujie Wang; Tzuhsiung Yang; William Harris; Rafael Gomez-Bombarelli
|
Computational Chemistry and Modeling; Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b51567dfe8b60ec4f05/original/active-learning-and-neural-network-potentials-accelerate-molecular-screening-of-ether-based-solvate-ionic-liquids.pdf
|
60c740a3337d6c198ae26735
|
10.26434/chemrxiv.7795664.v1
|
Selecting Between Two Transition States by Which Water Oxidation Intermediates on an Oxide Surface Decay
|
<p>While catalytic mechanisms on electrode
surfaces have been proposed for decades, the pathways by which the product’s chemical
bonds evolve from the initial charge-trapping intermediates have not been
resolved in time. Here, we discover a
reactive population of charge-trapping intermediates with states in the middle
of a semiconductor’s band-gap to reveal the dynamics of two parallel transition
state pathways for their decay. Upon photo-triggering the water oxidation
reaction from the n-SrTiO<sub>3</sub> surface with band-gap, pulsed excitation,
the intermediates’ microsecond decay reflects transition state theory (TST)
through: (1) two distinct and reaction dependent (pH, T, Ionic Strength, and
H/D exchange) time constants, (2) a primary kinetic salt effect on each activation
barrier and an H/D kinetic isotope effect on one, and (3) realistic activation
barrier heights (~0.4-0.5 eV) and TST pre-factors
(~10<sup>11</sup> -10<sup>12</sup> Hz). A photoluminescence
from mid-gap states in n-SrTiO<sub>3</sub> reveals the reaction dependent
decay; the same spectrum was previously assigned by us to hole-trapping at
parallel Ti-O<sup>·</sup>-Ti (bridge) and perpendicular Ti-O<sup>·</sup> (oxyl) O-sites using <i>in-situ</i>
ultrafast vibrational and optical spectroscopy. Therefore, the two transition
states are naturally associated with the decay of these respective
intermediates. Furthermore, we show that
reaction conditions select between the two pathways, one of which reflects a
labile intermediate facing the electrolyte (the oxyl) and the other a lattice
oxygen (the bridge). Altogether, we
experimentally isolate an important activation barrier necessary for water oxidation,
which is necessary for designing water oxidation catalysts for high O<sub>2</sub>
turn-over. Moreover, in isolating it,
we identify competing mechanisms for O<sub>2</sub> evolution at surfaces and
show how to use reaction conditions to select between them.<b></b></p>
|
Xihan Chen; Daniel J. Aschaffenburg; Tanja Cuk
|
Electrocatalysis; Heterogeneous Catalysis; Physical and Chemical Processes; Spectroscopy (Physical Chem.); Surface
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a3337d6c198ae26735/original/selecting-between-two-transition-states-by-which-water-oxidation-intermediates-on-an-oxide-surface-decay.pdf
|
62ce2a51b464fa07a35e0a24
|
10.26434/chemrxiv-2022-btvk9
|
LassoHTP: a High-throughput Computational Tool for Lasso Peptide Structure Construction and Modeling
|
Lasso peptides are a sub-class of ribosomally synthesized and post-translationally modified peptides with a slipknot conformation. Often with superior thermal stability, protease resistance, and antimicrobial activity, lasso peptides are promising candidates for bioengineering and pharmseutical applications. To enable high-throughput computational prediction and design of lasso peptides, we developed software, LassoHTP, for automatic lasso peptide structure construction and modeling. LassoHTP consists of three modules, including: scaffold constructor, mutant generator, and molecular dynamics (MD) simulator. Based on a user-provided sequence and conformational annotation, LassoHTP can either generate the structure and conformational ensemble as is or conduct random mutagenesis. We used LassoHTP to construct eight known lasso peptide structures de novo and to simulate their conformational ensembles from 100 ns MD simulations. For benchmarking, we calculated the root mean square deviation (RMSD) of these ensembles with reference to their experimental crystal or NMR PDB structures; we also compared these RMSD values against those of the MD ensembles that are initiated from the PDB structures. The results show that the RMSD values of the LassoHTP-initiated ensembles are highly similar to those of the PDB-initiated ensembles with the ∆RMSD ranging from 0.0 to 1.2 Å and averaging at 0.5 Å. LassoHTP offers a computational platform to develop strategies for lasso peptide prediction and design.
|
Reecan J. Juarez; Matthew Tremblay; Yaoyukun Jiang; Qianzhen Shao; A. James Link; Zhongyue Yang
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ce2a51b464fa07a35e0a24/original/lasso-htp-a-high-throughput-computational-tool-for-lasso-peptide-structure-construction-and-modeling.pdf
|
611534d018911d675edf20e2
|
10.26434/chemrxiv-2021-hzrls
|
Aliovalent doping response and impact on ionic conductivity in the antiperovskite solid electrolyte Li3OCl
|
Aliovalent doping of solid electrolytes with the intention of increase the concentration of charge carrying mobile defects is a common strategy for enhancing their ionic conductivities. For the antiperovskite lithium-ion solid electrolyte Li3OCl, both supervalent (donor) and subvalent (acceptor) doping schemes have previously been proposed. The effectiveness of these doping schemes depends on two conditions: first, that aliovalent doping promotes the formation of mobile lithium vacancies or interstitials rather than competing immobile defects; and second, that any increase in lithium defect concentration gives a corresponding increase in ionic conductivity. To evaluate the effectiveness of aliovalent doping in Li3OCl, we have performed a hybrid density-functional theory study of the defect chemistry of Li3OCl and the response to supervalent and subvalent doping. In nominally stoichiometric Li3OCl the dominant native defects are predicted to be VLi, OCl, and VCl. Supervalent doping increases VLi and OCl concentrations, with the preferentially formed defect species dependent on synthesis conditions. Subvalent doping increases the concentration of VCl more than the concentration of Lii under all accessible synthesis conditions. While supervalent doping is predicted to be effective at increasing ionic conductivity, particularly under Li-poor synthesis conditions, subvalent doping is predicted to decrease room-temperature ionic conductivities at low-to-moderate doping levels. This effect is due to a reduction in the number of lithium vacancies formed during synthesis, and increased [VLi + Lii] Frenkel-pair recombination upon cooling to room temperature. The strongly asymmetric doping response of Li3OCl with respect to supervalent versus subvalent doping is explained as a consequence of the low [VLi + VCl] Schottky pair formation energy, suggesting analogous behaviour should be expected in other Schottky-disordered solid electrolytes.
|
Alex Squires; Jacob M. Dean; Benjamin J. Morgan
|
Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Theory - Computational; Energy Storage; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2021-08-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611534d018911d675edf20e2/original/aliovalent-doping-response-and-impact-on-ionic-conductivity-in-the-antiperovskite-solid-electrolyte-li3o-cl.pdf
|
67daa8ab81d2151a02fd1a89
|
10.26434/chemrxiv-2025-rvz03
|
Calix[4]arene-supported trigonal and square prisms of Mn and Na
|
The heterometallic tricapped trigonal prism [MnIII3Na6(TBC[4])3(CO3)(Cl)(dmso)7]·5MeCN ([Mn3Na6]; 1·5MeCN) and the related heterometallic tetracapped square prism [MnIII4MnII2Na6(bisTBC[4])2(CO3)2(Cl)2(dmf)8(MeOH)1.2(H2O)0.8]·6MeCN ([Mn6Na6]; 2·6MeCN), are isolated using p-tBu-calix[4]arene (H4TBC[4]) and 2,2’-bis-p-tBu-calix[4]arene (H8-bisTBC[4]), respectively. In the former the MnIII ions sit in the TBC[4] polyphenolic pockets, forming three Mn-(TBC[4]) metalloligands that cap the square faces of the prism, whose vertices contain the six Na ions. Introduction of the bis-calix[4]arene enables expansion of the main building block from three Mn-TBC[4] metalloligands in 1 to four Mn-TBC[4] metalloligands in 2. The result is the formation of a square prism of Na/MnII ions, with four of the square faces capped with MnIII ions. Dc magnetic susceptibility and magnetisation measurements reveal paramagnetism in 1 and weak antiferromagnetic exchange interactions in 2.
|
Euan Brechin; Lucinda Wilson; Gary Nichol; Scott Dalgarno
|
Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism; Transition Metal Complexes (Inorg.)
|
CC BY 4.0
|
CHEMRXIV
|
2025-03-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67daa8ab81d2151a02fd1a89/original/calix-4-arene-supported-trigonal-and-square-prisms-of-mn-and-na.pdf
|
624203f7d09df0d9f1fead64
|
10.26434/chemrxiv-2022-nskrq
|
Dual Capillary-based Vibrating Sharp-edge Spray Ionization (cVSSI) with On-line Solution-phase Hydrogen/Deuterium Exchange for Distinguishing Carbohydrates Isomers
|
In-droplet hydrogen-deuterium exchange (HDX) combined with mass spectrometry (MS) has been used to characterize the reactivities of monosaccharide (3 pairs), disaccharide (4 pairs), and glycan (1 pair) isomer compounds. To accomplish in-droplet HDX, capillary vibrating sharp-edge spray ionization (cVSSI) employing a dual emitter tip setup is utilized. The solution-phase HDX technique is shown to be extremely reproducible for these measurements such that several different isomer sets can be distinguished by their unique isotopic distributions in the mass spectrum. The results are discussed in light of their applicability toward identifying metabolite compounds in complex metabolomics mixtures.
|
Stephen Valentine; Sandra Majuta; Anthony DeBastiani; Sara Macios; Kushani Attanayake; Peng Li
|
Analytical Chemistry; Biochemical Analysis; Mass Spectrometry; Separation Science
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-04-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624203f7d09df0d9f1fead64/original/dual-capillary-based-vibrating-sharp-edge-spray-ionization-c-vssi-with-on-line-solution-phase-hydrogen-deuterium-exchange-for-distinguishing-carbohydrates-isomers.pdf
|
60c741d24c89195096ad2360
|
10.26434/chemrxiv.8143274.v1
|
In the Quest for a Stable Triplet State in Small Polyaromatic Hydrocarbons : An In-Silico Tool for Rational Design and Prediction
|
<div>Combining the roles of spin frustration and geometry of odd and even numbered rings in polyaromatic hydrocarbons (PAHs), we design small molecules that show exceedingly small singlet-triplet gaps and stable triplet ground states. Furthermore, a computationally efficient protocol with a model spin Hamiltonian is shown to be capable of qualitative agreement with respect to high level multireference calculations and therefore, can be used for fast molecular discovery and screening.</div>
|
Madhumita Rano; Sumanta K Ghosh; Debashree Ghosh
|
Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-05-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741d24c89195096ad2360/original/in-the-quest-for-a-stable-triplet-state-in-small-polyaromatic-hydrocarbons-an-in-silico-tool-for-rational-design-and-prediction.pdf
|
639c9de1e9d0fd49a41f6d30
|
10.26434/chemrxiv-2022-gln27
|
Can We Quickly Learn to “Translate” Bioactive Molecules with Transformer Models?
|
Meaningful exploration of the chemical space of druglike molecules in drug design is a highly challenging task due to a combinatorial explosion of possible modifications of molecules. In this work, we address this problem with transformer models, a type of machine learning (ML) model, with recent demonstrated success in applications to machine translation and other tasks. By training transformer models on pairs of similar bioactive molecules from the public ChEMBL dataset, we enable them to learn medicinal-chemistry-meaningful, context-dependent transformations of molecules, including those absent from the training set. Most generated molecules are highly plausible and follow similar distributions of simple properties (molecular weight, polarity, hydrogen bond donor and acceptor numbers) as the training dataset. By retrospective analysis of the performance of transformer models on ChEMBL subsets of ligands binding to COX2, DRD2, or HERG protein targets, we demonstrate that the models can generate structures identical or highly similar to highly active ligands, despite the models having not seen any ligands active against the corresponding protein target during training. Thus, our work demonstrates that transformer models, originally developed to translate texts from one natural language to another, can be easily and quickly extended to “translations” from known molecules active against a given protein target to novel molecules active against the same target, and thereby contribute to hit expansion in drug design.
|
Emma Tysinger; Brajesh Rai; Anton Sinitskiy
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-12-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639c9de1e9d0fd49a41f6d30/original/can-we-quickly-learn-to-translate-bioactive-molecules-with-transformer-models.pdf
|
6512d79d0065940912e9bbd9
|
10.26434/chemrxiv-2023-10vcv
|
Boron Catalysis in a Designer Enzyme
|
The creation of enzymes containing non-biological functionalities with activation modes outside of Nature’s canon paves the way towards fully programmable biocatalysis. Here, we present a fully genetically encoded boronic acid containing designer enzyme with organocatalytic reactivity not achievable with natural or engineered biocatalysts. This boron enzyme catalyzes the kinetic resolution of hydroxyketones by oxime formation where crucial interactions with the protein scaffold assist in the catalysis. A directed evolution campaign lead to a variant with natural enzyme like enantioselectivities for a number of different substrates. The unique activation mode of the boron enzyme was studied via X-ray crystallography, high resolution mass spectrometry and 11B NMR spectroscopy and opens up the possibility for a new class of boron dependent biocatalysts.
|
Lars Longwitz; Reuben B. Leveson-Gower; Henriëtte J. Rozeboom; Andy-Mark W. H. Thunnissen; Gerard Roelfes
|
Biological and Medicinal Chemistry; Catalysis; Biochemistry; Biocatalysis; Organocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6512d79d0065940912e9bbd9/original/boron-catalysis-in-a-designer-enzyme.pdf
|
62d8ccdc5819874a6449a0d6
|
10.26434/chemrxiv-2022-s177n
|
Small-Scale Electrochemical Oxidation of Non-Steroidal Anti-Inflammatory Drugs: Conventional Approaches and Conditions
|
Improper disposal of pharmaceutical wastes, coupled with low pollutant removal efficiency at wastewater treatment plants (WWTPs), has created a disastrous ecological issue. Ecotoxicity reviews have consolidated that low concentrations of pharmaceutical pollutants, specifically non-steroidal anti-inflammatory drugs, impose significant toxicological risks on the aquatic ecosystem. Research solutions have shifted towards electrochemical oxidation for its environmental-friendly, precise, and flexible reduction characteristics over non-electrochemical technologies. However, there isn't significant literature dedicated to finding the conditions for small-scale pretreatment, leaving the environment between the pollutant source and WWTPs at risk. This research explores the optimal conditions to pretreat pharmaceutical wastewater using electrochemical oxidation on a small-scale. A conventional approach, utilizing accessible materials and simple procedures, was selected to ease the implementation of pretreatment outside of WWTPs. Spectrophotometric analysis was performed to identify the concentration changes through absorbance for reagents. Manipulated variables of temperature, pH level, scale, and electrode metal type were analyzed individually per solution and in combination to produce the overall effect. F-Test and Tukey-Kramer post-hoc tests were employed to derive the maximum electrochemical oxidation ability for different variables. Results indicate that at the 95% confidence level, temperatures below 25˚C, pH levels below 4, larger scale, and higher reactivity metal plates produce the highest electrochemical oxidation magnitude. Overall analysis comparing the combined optimal conditions with the control group yielded an approximately 50% greater concentration reduction magnitude. Future directions include the implementation of electrochemical oxidation as a pretreatment appliance in the household using our optimal conditions and exploring other manipulative variables to increase the flexibility and efficiency of such devices.
|
Benjamin Chang; Jeffrey Huang; Jocelyn Ho
|
Physical Chemistry; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Water Purification; Electrochemistry - Mechanisms, Theory & Study
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d8ccdc5819874a6449a0d6/original/small-scale-electrochemical-oxidation-of-non-steroidal-anti-inflammatory-drugs-conventional-approaches-and-conditions.pdf
|
67c993bd6dde43c908bbd2c7
|
10.26434/chemrxiv-2024-2t8hw-v2
|
Near-Infrared-Activated Photocages Made to Order: Late-Stage Caging Protocol
|
Nature has perfected the reversible control over the activity of molecules and biomolecules in the human body. Pho- tocages aim to mimic this control in space and time using light as a trigger, and the field has witnessed many excellent contributions that extend their use to the tissue-penetrating region. Yet little attention has been paid to developing simple caging strategies which are crucial to translating photocages into a widely accepted tool beyond chemical space. Here, we report a robust and user-friendly protocol that enables the installation of complex amine, thiol and phenol pay- loads in a single step under mild conditions and using bench-stable in- termediates. The protocol displays excellent compatibility with a range of payloads, manifested by caging hormones, neurotransmitters, a tripeptide and many highly complex FDA-approved drugs, including antibiotics and anti-cancer agents. As a proof of concept, we applied this strategy to cage the clinically approved CDK4/6 inhibitor palbo- ciclib and evaluated its near-infrared (NIR) light-dependent activation in modulating the tumor-suppressing retinoblastoma protein. We an- ticipate that this user-friendly synthetic approach to accessing NIR- absorbing photocages will accelerate research across various scientific disciplines.
|
Marina Russo; Dominika Zielinska; Katarzyna Hanc; Andrea Ramundo; Delia Meier; Attila Szabo; Peter Stacko
|
Physical Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Cell and Molecular Biology
|
CC BY NC 4.0
|
CHEMRXIV
|
2025-03-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c993bd6dde43c908bbd2c7/original/near-infrared-activated-photocages-made-to-order-late-stage-caging-protocol.pdf
|
61a0855c78480507259b642f
|
10.26434/chemrxiv-2021-2hm77
|
A Triad Photoanode for Visible Light-Driven Water Oxidation via Immobilization of Molecular Polyoxometalate on Polymeric Carbon Nitride
|
Due to their availability, low cost, non-toxicity and tunability, polymeric carbon nitrides (CNx) represent one of the most attractive materials classes for the development of fully sustainable photo(electro)catalytic systems for solar-driven water splitting. However, the development of CNx-based photoanodes for visible light-driven water oxidation to dioxygen is rather challenging, particularly due to issues related to photoelectrode stability and effective coupling of the light absorber with water oxidation catalysts. Herein, a triadic photoanode comprising a porous TiO2 electron collector scaffold sensitized by CNx coupled to a molecular cobalt polyoxometalate (CoPOM = [Co4(H2O)2(PW9O34)2]10─) catalyst is reported. Complete water oxidation to dioxygen under visible (λ > 420 nm) light irradiation is demonstrated, with photocurrents down to relatively low bias potentials (0.2 V vs. RHE). Furthermore, polyethyleneimine (PEI), a cationic polymer is shown to act as an effective and non-sacrificial electrostatic linker for immobilization of the anionic CoPOM onto the negatively charged surface of CNx. The optimized deposition of CoPOM using the PEI linker translates directly into improved efficiency of the transfer of photogenerated holes to water molecules and to enhanced oxygen evolution. This work thus provides important design rules for effective immobilization of POM-based catalysts into soft-matter photoelectrocatalytic architectures for light-driven water oxidation.
|
Ruihao Gong; Dariusz Mitoraj; Dandan Gao; Manuel Mundszinger; Dieter Sorsche; Ute Kaiser; Carsten Streb; Radim Beranek; Sven Rau
|
Physical Chemistry; Catalysis; Photocatalysis; Photochemistry (Physical Chem.); Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2021-11-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a0855c78480507259b642f/original/a-triad-photoanode-for-visible-light-driven-water-oxidation-via-immobilization-of-molecular-polyoxometalate-on-polymeric-carbon-nitride.pdf
|
653610bd2431cc1dac56909e
|
10.26434/chemrxiv-2023-9z796
|
High molecular weight crystalline PEO6 based polymer electrolytes for lithium-ion conduction– Effect of cellulose nano whiskers
|
We explore the crystal structure and ionic conductivity of unfilled and cellulose nanowhisker-filled polymer electrolytes, based on high molecular weight PEO and LiClO4 at a concentration EO: Li = 6:1 (EO=ether oxygen). At this concentration, the polymer electrolyte forms crystalline PEO6 [PEOy - the crystal structure co-crystallizes ‘y’ PEO ether oxygens to one Li-anion pair]. While the diffraction patterns for PEO3 and PEO6 with LiClO4 are available, their structures are not. Thus, we optimize these structures using density functional theory and show agreement between simulated and experimental diffraction patterns. The PEO6 crystal shows insufficient Li-ion conductivity due to a lack of percolated conduction paths, and the crystal structure is unstable following two months after annealing. Cellulose nanowhiskers, with their patterned surface -OH groups, extend the length of PEO6 tunnels, stabilize these tunnels for as long as a year, and result in the percolation of crystals. Although the EO: Li = 6:1 stoichiometry should not favor PEO3 formation, we observe this crystal phase in some unfilled samples. But, with the addition of nanowhiskers, the patterned surface templates PEO6 formation rather than PEO3. Despite these advantages, nanowhiskers do not improve ionic conductivity as hypothesized. The tools developed in this work allow further mechanistic exploration of conduction through crystalline domains.
|
Shankar C.V. Ram; Shyam Deo; Pengfei Zhan; Michael Janik; Janna K. Maranas
|
Materials Science; Polymer Science; Energy; Polyelectrolytes - Materials; Conducting polymers; Energy Storage
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CC BY NC ND 4.0
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CHEMRXIV
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2023-10-25
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653610bd2431cc1dac56909e/original/high-molecular-weight-crystalline-peo6-based-polymer-electrolytes-for-lithium-ion-conduction-effect-of-cellulose-nano-whiskers.pdf
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67c50601fa469535b9abc86d
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10.26434/chemrxiv-2025-1dv97
|
Impact of lipid conjugation on the membrane selectivity of phospholipid sensors
|
Phosphatidylserine is the major anionic phospholipid exposed on the surface of mammalian cells during biological processes such as apoptosis.1 The zinc(II) dipicolylamine (ZnDPA) fluorescent sensors are widely employed tools to detect PS on artificial membranes2, 3 and cellular surfaces.2, 4-7 Introducing diverse lipid anchors to fluorophores influences their cellular uptake8 and sub-cellular localization.9 However, the impact of conjugating ZnDPA fluorescent sensors with lipids on their phosphatidylserine selectivity and cellular uptake remains elusive. In this study, we systematically introduced different lipid anchors to ZnDPA fluorescent sensors and performed liposome- and cell-based experiments to determine the impact of lipid anchors on anionic lipid selectivity, membrane leakage, and permeability. We found that long-chain fatty acid conjugated ZnDPA sensors do not distinguish anionic membranes as effectively. Furthermore, cellular uptake and plasma membrane retention of ZnDPA sensors can be significantly modulated depending on the type of lipid conjugation used. Importantly, surface-exposed phosphatidylserine alters the cellular uptake of medium-chain lipid anchor conjugated ZnDPA sensors. Thus, our study advances our understanding of how to select specific lipid anchors to optimize the design of ZnDPA-based sensors for different research goals.
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Jingyao You; Nian Kee Tan; Bilge Ercan; Katrina A. Jolliffe
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Biological and Medicinal Chemistry; Organic Chemistry; Supramolecular Chemistry (Org.); Chemical Biology
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CC BY NC ND 4.0
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CHEMRXIV
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2025-03-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c50601fa469535b9abc86d/original/impact-of-lipid-conjugation-on-the-membrane-selectivity-of-phospholipid-sensors.pdf
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64db8445dfabaf06ff507b5b
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10.26434/chemrxiv-2023-396mm
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Model selection using replica averaging with Bayesian inference of conformational populations
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Bayesian Inference of Conformational Populations (BICePs) is a reweighting algorithm that reconciles simulated ensembles with sparse and/or noisy observables, by sampling the full posterior distribution of conformational populations in the presence of experimental restraints. By modifying BICePs to use replica-averaging in its forward model, BICePs becomes similar to other MaxEnt approaches, but with the significant advantages of (1) being able to sample over the posterior distribution of uncertainties due to random and systematic error, with improved likelihoods to deal with outliers, and (2) having an objective score for model selection, a free energy-like quantity called the BICePs score. To demonstrate the power of our approach, we used BICePs to reweight conformational ensembles of the mini-protein chignolin simulated in nine different force fields with TIP3P water, using a set of 158 experimental measurements (139 NOE distances, 13 chemical shifts, and 6 vicinal $J$-coupling constants for H$^{\text{N}}$ and H$^{\alpha}$. In all cases, reweighted populations favor the correctly folded conformation. The BICePs score, which reports the free energy of "turning on" conformational populations along with experimental restraints, provides a metric to evaluate each force field. For the nine force fields tested (A14SB, A99SB-ildn, A99, A99SBnmr1-ildn, A99SB, C22star, C27, C36, OPLS-aa), we obtain results consistent with previous work that used a conventional $\chi^{2}$ metric for model selection for small polypeptides and ubiquitin (Beauchamp et al 2012). These results suggest a powerful role for BICePs in future applications requiring ensemble reweighting and model selection.
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Robert M. Raddi; Tim Marshall; Yunhui Ge; Vincent Voelz
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling; Statistical Mechanics
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CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64db8445dfabaf06ff507b5b/original/model-selection-using-replica-averaging-with-bayesian-inference-of-conformational-populations.pdf
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642ef6d5736114c96307ff72
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10.26434/chemrxiv-2023-zmtk4
|
Photoactive yellow protein adsorption at hydrated polyethyleneimine and poly-L-glutamic acid interfaces
|
Chiral and achiral vibrational sum-frequency generation (VSFG) spectroscopy was performed in the 1400-1700 and 2800-3800 cm-1 range to study the interfacial structure of photoactive yellow protein (PYP) adsorbed on polyethyleneimine (PEI) and poly-L-glutamic acid (PGA) surfaces. Nanometer-thick polyelectrolyte layers served as the substrate for PYP adsorption, with 6.5-pair layers providing the most homogeneous surfaces. When the topmost material was PGA, it acquired a random coil structure with a small number of ß2-fibrils. Upon adsorption on oppositely charged surfaces, PYP yielded similar achiral spectra. However, the VSFG signal intensity increased for PGA surfaces with a concomitant redshift of the chiral C-H and N-H stretching bands suggesting increased adsorption for PGA compared to PEI. At low wavenumbers, both the backbone and the side chains of PYP induced drastic changes to all measured chiral and achiral VSFG spectra. Decreasing ambient humidity led to the loss of tertiary structure with a re-orientation of a-helixes, evidenced by a strongly blue-shifted chiral amide I band of the ß-sheet structure with a shoulder at 1654 cm-1. Our observations indicate that chiral VSFG spectroscopy is not only capable of determining the main type of secondary structure of PYP, i.e., ß-scaffold, but is also sensitive to tertiary protein structure.
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Szilvia Krekic; Mark Mero; Michel Kuhl; Kannan Balasubramanian; Andras Der; Zsuzsanna Heiner
|
Physical Chemistry; Interfaces; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642ef6d5736114c96307ff72/original/photoactive-yellow-protein-adsorption-at-hydrated-polyethyleneimine-and-poly-l-glutamic-acid-interfaces.pdf
|
640654476642bf8c8f1458ae
|
10.26434/chemrxiv-2023-fjjk7-v2
|
Materials Science Optimization Benchmark Dataset for Multi-Objective, Multi-Fidelity Optimization of Hard-Sphere Packing Simulations
|
In scientific disciplines, benchmarks play a vital role in driving progress forward. For a benchmark to be effective, it must closely resemble real-world tasks. If the level of difficulty or relevance is inadequate, it can impede progress in the field. Moreover, benchmarks should have low computational overhead to ensure accessibility and repeatability. The objective is to achieve a kind of "Turing test" by creating a surrogate model that is practically indistinguishable from the ground truth observation, at least within the dataset's explored boundaries. This objective necessitates a large quantity of data. This study encompasses numerous features that are characteristic of chemistry and materials science optimization tasks that are relevant to industry. These features include high levels of noise, multiple fidelities, multiple objectives, linear constraints, non-linear correlations, and failure regions. We performed 494498 random hard-sphere packing simulations representing 206 CPU days' worth of computational overhead. Simulations required nine input parameters with linear constraints and two discrete fidelities each with continuous fidelity parameters. The results were logged in a free-tier shared MongoDB Atlas database, producing two core tabular datasets: a failure probability dataset and a regression dataset. The failure probability dataset maps unique input parameter sets to the estimated probabilities that the simulation will fail. The regression dataset maps input parameter sets (including repeats) to particle packing fractions and computational runtimes for each of the two steps. These two datasets were used to create a surrogate model as close as possible to running the actual simulations by incorporating simulation failure and heteroskedastic noise. In the regression dataset, percentile ranks were calculated for each group of identical parameter sets to account for heteroskedastic noise, thereby ensuring reliable and accurate results. This differs from the conventional approach that imposes a-priori assumptions, such as Gaussian noise, by specifying mean and standard deviation. This technique can be extended to other benchmark datasets to bridge the gap between optimization benchmarks with low computational overhead and the complex optimization scenarios encountered in the real world.
|
Sterling G. Baird; Ramsey Issa; Taylor D. Sparks
|
Materials Science; Aggregates and Assemblies; Composites; Materials Processing
|
CC BY 4.0
|
CHEMRXIV
|
2023-03-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640654476642bf8c8f1458ae/original/materials-science-optimization-benchmark-dataset-for-multi-objective-multi-fidelity-optimization-of-hard-sphere-packing-simulations.pdf
|
6715caf6b91c6e9971a2dbc7
|
10.26434/chemrxiv-2024-pn3xw
|
Enhanced photocatalytic conversion of CO2 by H2O over Ag@Cr-cocatalyst-modified ZnTa2O6
|
A zinc tantalate (ZnTa2O6) photocatalyst modified with an Ag cocatalyst via ultrasonic reduction (denoted as Ag(USR)/ZnTa2O6) exhibited higher activity for the photocatalytic conversion of CO2 by H2O than Ag/ZnTa2O6 via other widely used methods. However, the CO formation rate was low. In this study, a photocatalyst was prepared by coating the Ag nanoparticles of Ag(USR)/ZnTa2O6 with Cr(OH)3·xH2O via the photodeposition (PD) method (denoted as Cr(PD)/Ag(USR)/ZnTa2O6) to increase the CO formation rate. Cr(PD)/Ag(USR)/ZnTa2O6 produced CO at the maximum formation rate of ∼600 µmol h1, which was 50 and 8.5 times higher than bare ZnTa2O6 and Ag(USR)/ZnTa2O6, respectively. Furthermore, an induction period was observed during the time course of photocatalytic activity. The scanning electron microscopy results highlighted that Ag nanoparticles migrate to a specific site on the surface of ZnTa2O6 with progression of the photoirradiation time, causing the rearrangement of Ag nanoparticles during this period. This rearrangement caused the separation of the photocatalytic reaction field, achieving high activity toward the photocatalytic conversion of CO2 because of the efficient reduction and oxidation reactions. Moreover, inductively coupled plasma mass spectrometry and ultraviolet-visible absorption spectroscopy revealed that Cr3 in Cr(PD)/Ag(USR)/ZnTa2O6 is oxidized to dissolvable CrO42 during the induction period. These CrO42 anions in solution were found to play a crucial role in maintaining the Cr layer of Cr(PD)/Ag(USR)/ZnTa2O6.
|
Kio Kawata; Shoji Iguchi; Shimpei Naniwa; Masamu Nishimoto; Kentaro Teramura
|
Catalysis; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6715caf6b91c6e9971a2dbc7/original/enhanced-photocatalytic-conversion-of-co2-by-h2o-over-ag-cr-cocatalyst-modified-zn-ta2o6.pdf
|
6477459b4f8b1884b7987a4d
|
10.26434/chemrxiv-2023-hjzvm
|
Efficient Cu-catalyzed intramolecular Heck-borylation of unactivated alkenes to boronated indolines
|
Efficient Cu-catalyzed intramolecular Heck-borylation of alkenes was developed. Racemic and chiral boronated indolines were achieved by borarylation of alkenes with B2pin2 via simultaneous construction of C-C and C-B bonds by Cu/phosphine ligand system. With CuOAc and DPPE ligand, a series of 3-substituted borylated indoline derivatives were concisely synthesized in good to excellent yields in short time under mild conditions. Asymmetric synthesis was investigated by ligand screening, and the chiral 3-substituted borylated indoline was obtained in 80% yield and 80:20 er with (R,R)-MeDuphos. Application of 3-substituted borylated indolines has been demonstrated by a gram scale synthesis and further functionalization.
|
Guodu Liu; Lin Fan; Xinlong Yan; Changjiang Li; Yuxue Cao
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Compounds and Functional Groups; Homogeneous Catalysis; Bond Activation
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6477459b4f8b1884b7987a4d/original/efficient-cu-catalyzed-intramolecular-heck-borylation-of-unactivated-alkenes-to-boronated-indolines.pdf
|
60c755c1337d6c77d2e28cc4
|
10.26434/chemrxiv.14159162.v1
|
Unraveling the Allosteric Cross-Talk Between Coactivator Peptide and Ligand Binding Site in Glucocorticoid Receptor
|
<div>Glucocorticoid receptor (GR) is a nuclear receptor that controls critical biological processes by regulating the</div><div>transcription of specific genes. There is a known allosteric cross-talk between the ligand and coregulator binding</div><div>sites within the GR ligand binding domain that is crucial for the control of the functional response. However, the</div><div>molecular mechanisms underlying such an allosteric control remain elusive. Here, molecular dynamics (MD)</div><div>simulations, bioinformatic analysis and biophysical measurements are integrated to capture the structural and</div><div>dynamic features of the allosteric cross-talk within GR. We identified a network of evolutionarily conserved</div><div>residues that enables the allosteric signal transduction, in agreement with experimental data. MD simulations</div><div>clarify how such network is dynamically interconnected and offer a mechanistic explanation of how the different</div><div>peptides affect the intensity of the allosteric signal. This study provides useful insights to elucidate the GR</div><div>allosteric regulation, ultimately, posing the foundation for designing novel drugs.</div>
|
Giuseppina La Sala; Anders Gunnarsson; karl edman; Christian Tyrchan; anders hogner; Andrey Frolov
|
Bioinformatics and Computational Biology; Biophysics; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755c1337d6c77d2e28cc4/original/unraveling-the-allosteric-cross-talk-between-coactivator-peptide-and-ligand-binding-site-in-glucocorticoid-receptor.pdf
|
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