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60c7494f4c891978a8ad306e | 10.26434/chemrxiv.10008545.v2 | A Pyridinic Fe-N4 Macrocycle Effectively Models the Active Sites in Fe/N-Doped Carbon Electrocatalysts | Iron- and nitrogen-doped carbon (Fe-N-C) materials are leading candidates to replace platinum in fuel cells, but their active site structures are poorly understood. A leading postulate is that iron active sites in this class of materials exist in an Fe-N<sub>4</sub> pyridinic ligation environment. Yet, molecular Fe-based catalysts for the oxygen reduction reaction (ORR) generally feature pyrrolic coordination and pyridinic Fe-N<sub>4</sub> catalysts are, to the best of our knowledge, non-existent. We report the synthesis and characterization of a molecular pyridinic hexaazacyclophane macrocycle, (phen<sub>2</sub>N<sub>2</sub>)Fe, and compare its spectroscopic, electrochemical, and catalytic properties for oxygen reduction to a prototypical Fe-N-C material, as well as iron phthalocyanine, (Pc)Fe, and iron octaethylporphyrin, (OEP)Fe, prototypical pyrrolic iron macrocycles. N 1s XPS signatures for coordinated N atoms in (phen<sub>2</sub>N<sub>2</sub>)Fe are positively shifted relative to (Pc)Fe and (OEP)Fe, and overlay with those of Fe-N-C. Likewise, spectroscopic XAS signatures of (phen<sub>2</sub>N<sub>2</sub>)Fe are distinct from those of both (Pc)Fe and (OEP)Fe, and are remarkably similar to those of Fe-N-C with compressed Fe–N bond lengths of 1.97 Å in (phen<sub>2</sub>N<sub>2</sub>)Fe that are close to the average 1.94 Å length in Fe-N-C. Electrochemical studies establish that both (Pc)Fe and (phen<sub>2</sub>N<sub>2</sub>)Fe have relatively high Fe(III/II) potentials at ~0.6 V, ~300 mV positive of (OEP)Fe. The ORR onset potential is found to directly correlate with the Fe(III/II) potential leading to a ~300 mV positive shift in the onset of ORR for (Pc)Fe and (phen<sub>2</sub>N<sub>2</sub>)Fe relative to (OEP)Fe. Consequently, the ORR onset for (phen<sub>2</sub>N<sub>2</sub>)Fe and (Pc)Fe is within 150 mV of Fe-N-C. Unlike (OEP)Fe and (Pc)Fe, (phen<sub>2</sub>N<sub>2</sub>)Fe displays excellent selectivity for 4-electron ORR with <4% maximum H<sub>2</sub>O<sub>2</sub> production, comparable to Fe-N-C materials. The aggregate spectroscopic and electrochemical data establish (phen<sub>2</sub>N<sub>2</sub>)Fe as a pyridinic iron macrocycle that effectively models Fe-N-C active sites, thereby providing a rich molecular platform for understanding this important class of catalytic materials.<p><b></b></p> | Travis Marshall-Roth; Nicole J. Libretto; Alexandra T. Wrobel; Kevin Anderton; Nathan D. Ricke; Troy Van Voorhis; Jeffrey T. Miller; Yogesh Surendranath | Electrocatalysis; Heterogeneous Catalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7494f4c891978a8ad306e/original/a-pyridinic-fe-n4-macrocycle-effectively-models-the-active-sites-in-fe-n-doped-carbon-electrocatalysts.pdf |
645bb5a0f2112b41e9543875 | 10.26434/chemrxiv-2023-25jt9 | Systematic Structural Tuning Yields Hydrazonyl Sultones for Faster Bioorthogonal Protein Modification | We report the synthesis of a series of hydrazonyl sultones (HS) containing an ortho-CF3 group, a five- or six-membered sultone ring, and a varying N-aryl substituent, and characterization of their aqueous stability and reactivity toward bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) in a 1,3-dipolar cycloaddition reaction. To avoid the purification of highly polar intermediates, we employed two protecting groups in our synthetic schemes. Most HS were obtained in moderate to good yields with optimized reaction conditions. The X-ray structure analysis of two HS revealed that the partially negative-charged fluorine atoms in CF3 electrostatically shield the electrophilic nitrile imine (NI) center from a nucleophilic attack, underpinning their extraordinary aqueous stability. In addition, the N-aryl substituents further modulate HS reactivity and stability, with the electron-rich six-membered HS displaying excellent aqueous stability and increased cycloaddition reactivity. The utility of these improved HS reagents was demonstrated through fast and selective modification of a BCNK-encoded nanobody with second-order rate constants as high as 1488 M-1 s-1 in phosphate-buffered saline--ethanol (9:1), representing the fastest HSB--CN ligation reported in the literature. | Ming Fang; Gangam Srikanth Kumar; Qing Lin | Organic Chemistry; Bioorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645bb5a0f2112b41e9543875/original/systematic-structural-tuning-yields-hydrazonyl-sultones-for-faster-bioorthogonal-protein-modification.pdf |
60c75898bdbb897e71a3adbb | 10.26434/chemrxiv.14564508.v1 | On-Chip Fabrication and In-Flow 3D-Printing of Cell-Laden Microgel Constructs: From Chip to Scaffold Materials in One Integral Process | Bioprinting has evolved into a thriving technology for the fabrication of cell-laden scaffolds. Bioinks are the most critical component for bioprinting. Recently, microgels have been introduced as a very promising bioink enabling cell protection and the control of the cellular microenvironment. However, their microfluidic fabrication inherently seemed to be a limitation. Here we introduce a direct coupling of microfluidics and 3D-printing for the microfluidic production of cell-laden microgels with direct in-flow bioprinting into stable scaffolds. The methodology enables the continuous on-chip encapsulation of cells into monodisperse microdroplets with subsequent in-flow cross-linking to produce cell-laden microgels, which after exiting a microtubing are automatically jammed into thin continuous microgel filaments. The integration into a 3D printhead allows direct in-flow printing of the filaments into free-standing three-dimensional scaffolds. The method is demonstrated for different cross-linking methods and cell lines. With this advancement, microfluidics is no longer a bottleneck for biofabrication. <br /> | Stephan Förster; Jürgen Groll; Benjamin Reineke; Stephan Hauschild; Ilona Paulus; Jonas Hazur; Madita Vollmer; Gültekin Tamgüney; Aldo Boccacini | Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75898bdbb897e71a3adbb/original/on-chip-fabrication-and-in-flow-3d-printing-of-cell-laden-microgel-constructs-from-chip-to-scaffold-materials-in-one-integral-process.pdf |
63ce9b2610cb6a6b77e37ce7 | 10.26434/chemrxiv-2023-rf0bz | Synthesis, deprotection, and purification of diphosphorylated RNA oligonucleotides. | In this technical note, we systematically describe the chemical synthesis, deprotection, and purification of diphosphorylated RNA oligonucleotides. This process eliminates the need for an enzymatic step after chemical synthesis of a 5’triphosphate RNA, allowing the user to synthesize the 5’diphosphate RNA directly. This protocol can also be applied to other chemically synthesized nucleic acids, including those with modifications. | Sarah J Fergione; Olga Fedorova; Anna Marie Pyle | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ce9b2610cb6a6b77e37ce7/original/synthesis-deprotection-and-purification-of-diphosphorylated-rna-oligonucleotides.pdf |
6636536221291e5d1d6ba473 | 10.26434/chemrxiv-2024-mdhfl | Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors | Myotonic dystrophy type I (DM1) is the most common form of adult muscular dystrophy and is a severe condition with no treatment currently available. Recently, small-molecule
ligands have been developed that have some selectivity for and covalently inhibit cyclin dependent kinase 12 (CDK12). CDK12 is involved in the transcription of elongated RNA
sections that results in the DM1 condition. The covalent bond is achieved after nucleophilic addition to a Michael acceptor warhead. Previous studies of the conformational preferences of thio-Michael additions have focused on characterizing the reaction profile based on the distance
between the sulfur and β-carbon atoms. Rotamerism, however, has not been investigated extensively and can have a large impact on reaction rates and adduct yields. Here, we use high-level quantum chemistry calculations, up to coupled cluster with single, double, and perturbative
triple excitations [CCSD(T)], to characterize the gas-phase nucleophilic addition of an archetypal nucleophile, methanethiolate, to various nitrogen-containing Michael acceptors which are representative of the small-molecule CDK12 inhibitors. By investigating the structural,
energetic, and electronic properties of the enolate intermediates, we show that synclinal additions are energetically favored over antiperiplanar additions due to the greater magnitude of attractive non-covalent interactions permitted by the conformation. The calculated transition states associated with the addition process indicate that synclinal addition proceeds via lower energetic barriers than antiperiplanar addition and is the preferred reaction pathway. The mechanistic insights from this study will inform the design of new derivatives with faster reaction
rates and higher yields of the adducts required for CDK12 inhibition and treatment of DM1. | Shayantan Chaudhuri; David Rogers; Christopher Hayes; Katherine Inzani; Jonathan Hirst | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6636536221291e5d1d6ba473/original/quantum-chemical-characterization-of-rotamerism-in-thio-michael-additions-for-targeted-covalent-inhibitors.pdf |
666020ee91aefa6ce1d47274 | 10.26434/chemrxiv-2023-6v0hv-v2 | Ultra-fast photochemistry in the strong light-matter coupling regime | Strong coupling between molecules and confined light modes of optical cavities to form polaritons can alter photochemistry, but the origin of this effect remains largely unknown. While theoretical models suggest a suppression of photochemistry due to the formation of new polaritonic potential energy surfaces, many of these models do not account for the energetic disorder among the molecules, which is unavoidable at ambient conditions. Here, we combine simulations and experiments to show that for an ultra-fast photochemical reaction such thermal disorder prevents the modification of the potential energy surface and that suppression is due to radiative decay of the lossy cavity modes. We also show that the excitation spectrum under strong coupling is a product of the excitation spectrum of the “bare” molecules and the absorption spectrum of the molecule-cavity system, suggesting that polaritons can act as gateways for channeling an excitation into a molecule, which then reacts “normally”. Our results therefore imply that strong coupling provides a means to tune the action spectrum of a molecule, rather than to change the reaction. | Arpan Dutta; Ville Tiainen; Luis Duarte; Nemanja Markesevic; Ilia Sokolovskii; Dmitry Morozov; Hassan A. Qureshi; Siim Pikker; Gerrit Groenhof; J. Jussi Toppari | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Plasmonic and Photonic Structures and Devices; Optics; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666020ee91aefa6ce1d47274/original/ultra-fast-photochemistry-in-the-strong-light-matter-coupling-regime.pdf |
67da98eefa469535b9c8b1cd | 10.26434/chemrxiv-2025-fgc4s | C–H functionalization via single atom metathesis of C–H and C–X bonds | Metathesis and reversible catalytic reactions are fundamentally intriguing and powerful tools in modern synthetic chemistry. While most reversible catalytic reactions are predicated on breaking and forming reactive functional groups, the ability to leverage the C–H bond as a functional group into metathesis reactions has proved to be exceptionally challenging. Here, we develop a C–H/C–X metathesis reaction through a radical swapping protocol where a hydrogen and halogen are traded between molecules via reversible hydrogen atom transfer (HAT) and halogen atom transfer (XAT) that allows for mild C–H halogenation. The reversibility of this process allows for selective dehalogenation of polyhalogenated products to form monohalogenated products. Leveraging the reversibility of this process, halogenated organic pollutants can also serve as a halogen source for C–H halogenation. In the broader context, this work establishes that incorporating reversible metathesis logic in C–H bond functionalization can provide complementary advantages in synthetic strategies. | Tanner Jankins; Barnabé Berger; Françoise Aouane; Sergio Barbeira-Arán; Christophe Didier; Bettina Hürlimann; Claudius Zimmer; Bill Morandi | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67da98eefa469535b9c8b1cd/original/c-h-functionalization-via-single-atom-metathesis-of-c-h-and-c-x-bonds.pdf |
64a2d7efba3e99daef72c313 | 10.26434/chemrxiv-2023-kpd8x-v2 | Investigating mass transfer relationships in stereolithography 3D printed electrodes for redox flow batteries | Porous electrodes govern the electrochemical performance and pumping requirements in redox flow batteries, yet conventional carbon-fiber-based porous electrodes have not been tailored to sustain the requirements of liquid-phase electrochemistry. 3D printing is an effective approach to manufacture deterministic architectures, enabling the tuning of electrochemical performance and pressure drop. In this work, model grid structures are manufactured with stereolithography 3D printing followed by carbonization and tested as flow battery electrode materials. Microscopy, tomography, spectroscopy, fluid dynamics, and electrochemical diagnostics are employed to investigate the resulting electrode properties, mass transport, and pressure drop of ordered lattice structures. The influence of the printing direction, pillar geometry, and flow field type on the cell performance is investigated and mass transfer vs. electrode structure correlations are elucidated. It is found that the printing direction impacts the electrode performance through a change in morphology, resulting in enhanced performance for diagonally printed electrodes. Furthermore, mass transfer rates within the electrode are improved by helical or triangular pillar shapes or by using interdigitated flow field designs. This study shows the potential of stereolithography 3D printing to manufacture customized electrode scaffolds, which could enable multiscale structures with superior electrochemical performance and low pumping losses. | Maxime van der Heijden; Marit Kroese; Zandrie Borneman; Antoni Forner-Cuenca | Materials Science; Energy; Carbon-based Materials; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a2d7efba3e99daef72c313/original/investigating-mass-transfer-relationships-in-stereolithography-3d-printed-electrodes-for-redox-flow-batteries.pdf |
60c742ef702a9b684b18a50e | 10.26434/chemrxiv.8856053.v1 | The End of Ice I | <div>
<div>
<div>
<p>The appearance of ice I in the smallest possible clusters and the nature of its phase coexistence with liquid water could not thus far be unravelled. The experimental and theoretical
infrared spectroscopic and free energy results of this work show the emergence of the characteristic hydrogen bonding pattern of ice I in clusters containing only around 90 water
molecules. The onset of crystallization is accompanied by an increase of surface oscillator
intensity with decreasing surface to volume ratio, a new spectral indicator of nanoscale crystallinity of water. In the size range from 90 to 150 water molecules, we observe mixtures of largely crystalline and purely amorphous clusters. Our analysis suggests that the liquid-ice
I transition in clusters loses its sharp first-order character at the end of the crystalline size
regime and occurs over a range of temperatures through heterophasic oscillations in time, a
process without analog in bulk water.</p></div></div></div> | Daniel R. Moberg; Daniel Becker; Christoph W. Dierking; Florian Zurheide; Bernhard Bandow; Udo Buck; Arpa Hudait; Valeria Molinero; Paesani Lab; Thomas Zeuch | Computational Chemistry and Modeling; Theory - Computational; Clusters; Physical and Chemical Processes; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Statistical Mechanics; Structure; Surface; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ef702a9b684b18a50e/original/the-end-of-ice-i.pdf |
61d6f3716be4205f31235398 | 10.26434/chemrxiv-2022-8fs45 | An 'Intermetallic' Molecular Nanomagnet with the Lanthanide Coordinated Only by Transition Metals | The best performing molecular nanomagnets are currently designed by carefully arranging p-element donor atoms (usually carbon, nitrogen and/or oxygen) around the central magnetic ion. Inspired by the structure of the hardest intermetallic magnet SmCo5, we have demonstrated a nanomagnetic molecule where the central lanthanide (Ln) ion Er is coordinated solely by three transition metal (TM) ions in a perfectly trigonal planar fashion. The molecule [Er(ReCp2)3] (ErRe3) constitutes the first example of a molecular nanomagnet (MNM; or single molecule magnet SMM) with unsupported Ln-TM bonds and paves the way towards molecular intermetallics with strong direct magnetic exchange interactions. Such interactions are believed to be crucial for quenching the quantum tunneling of magnetization which limits the application of Ln-SMMs as sub-nanometer magnetic memory units. | Michał Magott; Maria Brzozowska; Stanisław Baran; Veacheslav Vieru; Dawid Pinkowicz | Physical Chemistry; Inorganic Chemistry; Organometallic Chemistry; Lanthanides and Actinides; Ligand Design; Structure | CC BY NC 4.0 | CHEMRXIV | 2022-01-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d6f3716be4205f31235398/original/an-intermetallic-molecular-nanomagnet-with-the-lanthanide-coordinated-only-by-transition-metals.pdf |
662b844e91aefa6ce17e2ac8 | 10.26434/chemrxiv-2024-zxmkq | A paper-based device for on-farm colorimetric detection of soil macronutrients | Testing the quality of soil is essential for appropriate fertilizer use. However, soil testing is currently conducted in dedicated centralized facilities equipped with expensive analytical instruments, not easily accessible to many farmers in lower-income agrarian economies like India. In an attempt to address this gap, we present a prototype for the colorimetric detection and quantification of soil macronutrients – nitrogen (N) and phosphorous (P). For this, we employ a technology previously developed in our laboratory called the barrier-free microfluidic paper analytical device. BF-PADs enable the simultaneous colorimetric detection of multiple analytes without having to pattern paper with hydrophobic barriers for the creation of flow channels. We demonstrate multiplex colorimetric detection of ammonium and nitrate ions for the detection of N, and phosphate ions for the detection of P. The linear quantifiable ranges for ammonium, nitrate, and phosphate ions dissolved in solution were 20-100 mg/L, 20-90 mg/L, and 4-80 mg/L, respectively, with limits of detection of 18 mg/L, 12 mg/L, and 3 mg/L, respectively, which are within the relevant ranges for soil testing. These single-use low-cost paper-based devices promise to increase access to soil testing and reduce dependency on laboratory-based soil testing. | Princekumar Patel; Bhushan Toley | Analytical Chemistry; Analytical Chemistry - General; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662b844e91aefa6ce17e2ac8/original/a-paper-based-device-for-on-farm-colorimetric-detection-of-soil-macronutrients.pdf |
60c73d51842e65e32adb177a | 10.26434/chemrxiv.5743638.v1 | Bulk Contributions Modulate the Sum-Frequency Generation Spectra of Interfacial Water on Model Sea-Spray Aerosols | Vibrational sum-frequency generation (vSFG) spectroscopy is used to determine the molecular structure of water at the interface of palmitic acid monolayers. Both measured and calculated spectra display speci c features due to third-order contributions to the vSFG response which are associated with nite interfacial electric potentials. We demonstrate that theoretical modeling enables to separate the third-order contributions, thus allowing for a systematic analysis of the strictly surface-sensitive, second-order component of the vSFG response. This study provides fundamental, molecular-level insights into the interfacial structure of water in a neutral surfactant system with relevance to single layer bio-membranes and environmentally relevant sea-spray aerosols. These results emphasize the key role that computer simulations can play in interpreting vSFG spectra and revealing microscopic details of water at complex interfaces, which can be difficult to extract from experiments due to the mixing of second-order, surface-sensitive and third-order, bulk-dependent contributions to the vSFG response. | Sandeep K. Reddy; Raphael Thiraux; Bethany A. Wellen Rudd; Lu Lin; Tehseen Adel; Tatsuya Joutsuka; Franz M. Geiger; Heather C. Allen; Akihiro Morita; Paesani Lab | Interfaces; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d51842e65e32adb177a/original/bulk-contributions-modulate-the-sum-frequency-generation-spectra-of-interfacial-water-on-model-sea-spray-aerosols.pdf |
66a7c1c301103d79c52785f9 | 10.26434/chemrxiv-2024-pvttd | Transition State Searching Accelerated by Deep Learning Potential | The exploration and construction of organic chemical reaction networks hold the potential to clarify complex reaction mechanisms. However, this endeavor encounters challenges, particularly in cases requiring computationally intensive quantum mechanical calculations. In recent years, the remarkable advancement of machine learning (ML) technologies has provided a novel approach to address this issue. ML can effectively utilize vast datasets to build and train complex models, enabling prediction and simulation. In this study, we conducted a performance comparison of deep potential for molecular dynamics (DeePMD), recursively embedded atom neural network (REANN), and neural equivariant interatomic potentials (NequIP) based on the Transition1x dataset. The most efficient model, NequIP, was selected for further analysis. Combined with reaction path search methods such as nudged elastic band (NEB) and growing string method (GSM), this model was employed for the identification and exploration of transition states. The results demonstrate that the success ratio of NequIP combined with the NEB method can reach 96.6%, with a mean absolute error (MAE) of 0.32 kcal/mol for barrier prediction. By adding a modest number of data points, NequIP achieves a MAE of 4.01 kcal/mol for barrier prediction in unexplored chemical reaction space. In the future, by combining different reaction network search methods, we anticipate applying this model to swiftly explore reaction pathways and construct more comprehensive reaction networks. We believe that ML will play a significant role in accelerating the elucidation of unknown chemical reaction mechanisms and in revealing complex reaction networks. | Bowen Li; Jin Xiao; Ya Gao; John Zhang; Tong Zhu | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a7c1c301103d79c52785f9/original/transition-state-searching-accelerated-by-deep-learning-potential.pdf |
643d4d3373c6563f1409ddb5 | 10.26434/chemrxiv-2023-s6117 | Substituting fossil-based with bio-based chemicals: The case of limonene as a greener pore expander for micellar templated silica | Porous materials are widely used in applications such as adsorption, catalysis and separation. The use of expander molecules is a versatile route to enlarge the mesopore size in micellar templated mesoporous silica materials. Typical expanders used for this purpose are fossil-based organic molecules such as trimethylbenzene (TMB). In the course of making such syntheses greener and more sustainable, it is highly desirable to substitute such fossil-based chemicals with renewable ones. Here, we show that bio-based limonene can be used as an alternative expander molecule for the synthesis of large-pore templated silica. On the basis of electron microscopy, nitrogen physisorption and small angle X-ray scattering we show that the substitution of TMB by limonene leads to very similar material characteristics, reaching mean mesopore diameters of 17-19 nm. A comparative life-cycle assessment demonstrates the reduced environmental impact of limonene production from citrus peel waste compared to TMB production, supporting the call for more applications of renewable chemicals, ideally from waste-streams, also for the production of porous materials. | Umair Sultan; Katrin Städtke; Andreas Göpfert; Daniel Lemmen; Ezzeldin Metwali; Santanu Maiti; Carola Schlumberger; Tadahiro Yokosawa; Benjamin Apeleo Zubiri; Erdmann Spiecker; Nicolas Vogel; Tobias Unruh; Matthias Thommes; Alexandra Inayat | Chemical Engineering and Industrial Chemistry; Natural Resource Recovery; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643d4d3373c6563f1409ddb5/original/substituting-fossil-based-with-bio-based-chemicals-the-case-of-limonene-as-a-greener-pore-expander-for-micellar-templated-silica.pdf |
60c753cabdbb89752ca3a503 | 10.26434/chemrxiv.13550576.v1 | Simultaneously Achieving High Capacity Storage and Multilevel Anti-Counterfeiting Using Electrochromic and Electrofluorochromic Dual-Functional AIE Polymers | With the advent of the big
data era, information storage and security are becoming increasingly important.
However, high capacity information storage and multilevel anti-counterfeiting
are typically difficult to simultaneously achieve. To
address this challenge, herein, two electrochromic and electrofluorochromic
dual-functional polymers with aggregation-induced emission (AIE) features are
skillfully designed. Upon application of voltage, the absorption and
fluorescence spectra of the two polymers can undergo reversible changes,
accompanying with the variation of appearance color and emission. By utilizing the controllable
characteristics of polymers, the dual-mode display devices are
fabricated via a simple spraying method. More interestingly, the color code
device was elaborately constructed by adding color change multiplexing to two-dimensional space,
thereby achieving high capacity information storage. Moreover, the color code
device can also be applied in the multilevel anti-counterfeiting areas. The encrypted
information can be dynamically converted under different voltages. The AIE
polymers show great promise in the applications of
multidimensional information storage and dynamic anti-counterfeiting and the
design strategy may
provide a new path for advanced information storage and high security
technology.<br /><div><br /></div> | Lin Lu; Kaojin Wang; Haozhong Wu; Anjun Qin; Ben Zhong Tang | Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753cabdbb89752ca3a503/original/simultaneously-achieving-high-capacity-storage-and-multilevel-anti-counterfeiting-using-electrochromic-and-electrofluorochromic-dual-functional-aie-polymers.pdf |
674c7c04f9980725cfafeee7 | 10.26434/chemrxiv-2024-tfdm6-v2 | A New Methodology for Preparing Benzylated Aminopyridines Yields Unprecedented Site-Selective Organocatalysts | While developing site-selective alcohol-modifying catalysts, we found that Lewis acid-promoted benzylation or cyclative dibenzylation of aminopyridines with alcohols effectively overcomes the synthetic challenges typically thwarting access to new aminopyridines, a key family of nucleophilic organocatalysts. Using this innovative approach, we successfully prepared unprecedented (2,5-diarylpyrrolidino)pyridines and new (N-benzyl-N-methylamino)pyridines with expanded ortho-alkoxy tails on the aryls. The new catalysts, with their bulky outer sphere, exhibit remarkable activity and site-selectivity in the phosphorylation of a model diol amphiphile. | Mikhail Kozlov; Fatma Saady; Or Fleischer; Shai Ben Sasson; Ibrahim Amer; Scott J. Miller; Moshe Portnoy | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674c7c04f9980725cfafeee7/original/a-new-methodology-for-preparing-benzylated-aminopyridines-yields-unprecedented-site-selective-organocatalysts.pdf |
65f962f69138d23161c7477a | 10.26434/chemrxiv-2024-g6r6n | Dynamic Supra-MOF self-assembly of ZIF-7 | Supra-MOF assemblies are the assemblies within the assembly. Metal-organic frameworks are nothing but the molecular self-assemblies of metal cations and organic linker anions, which may transition via the initial weak interaction assembly. A part of the molecular self-assembly may further develop into the islands of polycrystalline MOF particles surrounded by weakly interacting assembly. This has been evident from the previous reports on the supra-MOFs. Here in this report, we represent the dynamics of supra-MOF assembly constituting Zn(II) and Benzimidazole (BIm) that eventually results into the crystalline ZIF-7 compound. Results obtained in this work manifests the potential synthetic strategy for generating functional materials serving applications from different realms. | Sreevidhya K B; Abhijeet Chaudhari | Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f962f69138d23161c7477a/original/dynamic-supra-mof-self-assembly-of-zif-7.pdf |
64946146a2c387fa9ac3fc1c | 10.26434/chemrxiv-2023-j1qt8 | Electron spin polarization in supramolecular polymers with complex pathways | Mastering the manipulation of the electron spin plays a crucial role in comprehending the behavior of organic materials in various practical applications, such as asymmetric catalysis, chiroptical switches, and electronic devices. A promising avenue for achieving precise such control lies in the Chiral Induced Spin Selectivity (CISS) effect, where electrons with a favored spin exhibit preferential transport through chiral assemblies of specific handedness. Chiral supramolecular polymers emerge as excellent candidates for exploring the CISS effect due to their ability to modulate their helical structure through noncovalent interactions. Chiral supramolecular polymers capable of responding to external stimuli are particularly intriguing, sometimes even displaying chirality inversion. This study unveils spin selectivity in chiral supramolecular polymers, derived from single enantiomers, through scanning tunneling microscopy (STM) conducted in scanning tunneling spectroscopy (STS) mode. Following two distinct sample preparation protocols for each enantiomer, we generate supramolecular polymers with opposite handedness and specific spin transport characteristics. Our primary focus centers on chiral -conjugated building blocks, with the aim of advancing novel systems that can inspire the organic spintronics community from a supramolecular chemistry level | Kyeong-Im Hong; Abhinandan Kumar; Ana M. Garcia; Subrata Majumder; Amparo Carretero | Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64946146a2c387fa9ac3fc1c/original/electron-spin-polarization-in-supramolecular-polymers-with-complex-pathways.pdf |
64638c9ffb40f6b3eeaf455b | 10.26434/chemrxiv-2023-btbqz-v2 | The 228 valence electron rule for onion-like inorganic fullerenes X1@Y12@Z20 of Ih and Th symmetry | Based on an analysis of the experimentally known 228e- valence electron systems AsNi12As203-, SbNi12Sb203-, SbPd12Sb203-, and SnCu12Sn2012- of Ih symmetry, the new species GeZn12Ge20, KrNi12As20, BrNi12As201-, SeNi12As202-, GeMn12Br20, SeCo12Se206+, and SeFe12Se206- have been designed according to the 228 electron rule introduced in this study for onion-like inorganic fullerenes composed of late main group and transition metal elements. Of these GeZn12Ge20, KrNi12As20, BrNi12As201-, SeNi12As202-, and GeMn12Br20 together with the known AsNi12As203- and its neutral counterpart were investigated at the DFT B3LYP/6-31G(d) level of theory. With one exception they show, in fact, two stable energetic minima of Ih and Th symmetry. Relaxing the symmetry constraints further, e.g. Y12 = {Q6,R6}, additional new neutral species of the general composition Z@Q6R6@Z20 of C5v and C2v symmetry can be formulated, i.e. Z = Se, Q = Fe, R = Mn, following this new building principle, therefore, supporting and inspiring the development of new materials of icosahedral and tetrahedral symmetry.
Dedicated to Professor Helmut Schwarz on the occasion of his 80th birthday | A.B.C. Patzer; Christian Chang; Hans Bauer; Detlev Sülzle | Theoretical and Computational Chemistry; Inorganic Chemistry; Nanoscience | CC BY NC 4.0 | CHEMRXIV | 2023-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64638c9ffb40f6b3eeaf455b/original/the-228-valence-electron-rule-for-onion-like-inorganic-fullerenes-x1-y12-z20-of-ih-and-th-symmetry.pdf |
644bd9376ee8e6b5ed4124e1 | 10.26434/chemrxiv-2023-bgs62 | Formation of MnO2-based electrodes with high catalytic activity on the surface of ITO for glucose detection | In this paper, we report on the formation of MnO2-based electrodes for the determination of hydrogen peroxide. We apply thin films of manganese dioxide on the surface of indium tin oxide-coated glass (ITO) using electrochemical deposition under different conditions. MnO2 is a selective catalyst for the decomposition of hydrogen peroxide. Of all methods of sediment formation, we settled on anodic electrodeposition in sulphate electrolytes. By changing the conditions of the process, we can form an electrode material MnO2/ITO with maximum catalytic performance. The electrodes were characterized by SEM, electrochemical impedance spectroscopy, and XPS. The MnO2/ITO and GOx/MnO2/ITO (modified with glucose oxidase enzymes (GOx)) electrodes’ sensing properties were studied by chronoamperometry at an applied potential and by cyclic voltammetry. The film of manganese dioxide with the best catalytic characteristics is formed by electrochemical deposition on the surface of the ITO in electrolyte with pH 1 by CV method during 30 cycles at the range of potentials 0.65 V – 2.1 V vs Ag/AgCl/3M KCl and after this drying at 60°C. the MnO2 films form branching networks which provide an extra-large surface area and show high conductivity. As a proof-of-principle, we developed a GOx/MnO2/ITO working electrode for biosensors for the detection of glucose based on the electrocatalytic determination of hydrogen peroxide generated in the process of enzymatic glucose oxidation. The calibration curve of the GOx/MnO2/ITO electrode shows a linear relationship with the concentration of glucose from 0.1 mM to 3 mM with a correlation coefficient of 0.9938. The sensitivity of such an electrode is 117.8 μA/mmol cm2. The developed electrode can be used in glucose biosensors or similar systems based on other oxidases. | Veronika Poltavets; Mirosław Krawczyk; Ganna Maslak; Olga Abraimova; Martin Jönsson-Niedziółka | Physical Chemistry; Catalysis; Analytical Chemistry; Electrochemical Analysis; Biocatalysis; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2023-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644bd9376ee8e6b5ed4124e1/original/formation-of-mn-o2-based-electrodes-with-high-catalytic-activity-on-the-surface-of-ito-for-glucose-detection.pdf |
6629fcd121291e5d1da7d034 | 10.26434/chemrxiv-2024-7lkvp | Hyper-crosslinked polyphosphines as microporous macroligands for catalytic CO2 hydrogenation – a systematic study on structure-activity relations | Hyper-crosslinked polymers (HCPs) enable the tailored synthesis of functionalized materials and open up a versatile design strategy for porous macroligands. Based on the prototypical triphenylphosphine (PPh3) monomer, we investigate the roles of the involved crosslinking reagents on the formation of polyphosphines and evaluate structure-activity-relations for application in the catalytic CO2 hydrogenation: namely by varying the Friedel-Crafts catalyst, the crosslinker unit and the degree of crosslinking. The examination of the monomeric reactivities states the insufficient activation of the phosphine through iron chloride catalyzed crosslinking and the requirement for the stronger aluminum chloride to ensure PPh3 incorporation. Applying aromatic crosslinker units introduces porosity and promotes the accessibility of ligating centers for the immobilized ruthenium species. The thus formed solid catalysts exhibit excellent performances in the hydrogenation of CO2 to formic acid in the aqueous phase and are studied over consecutive recycling runs. The partial structural degradation of the frameworks during catalysis is addressed by adjusting higher degrees of crosslinking, leading to an improved stabilization of the catalyst. Overall, this study highlights crosslinking strategies for the tailored crafting of phosphine-based HCPs and the design of stable macroligands under catalytic conditions. | Arne Nisters; Steffen Schleuning; Gerd Buntkowsky; Torsten Gutmann; Marcus Rose | Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6629fcd121291e5d1da7d034/original/hyper-crosslinked-polyphosphines-as-microporous-macroligands-for-catalytic-co2-hydrogenation-a-systematic-study-on-structure-activity-relations.pdf |
61a9d845704d055f7b3e7884 | 10.26434/chemrxiv-2021-bwhp6 | Tuning the magnetic properties of NiPS3 through organic-ion intercalation | Atomically thin van der Waals magnetic crystals are characterized by tunable magnetic properties related to their low dimensionality. While electrostatic gating has been used to tailor their magnetic response, chemical approaches like intercalation remain largely unexplored. Here, we demonstrate the manipulation of the magnetism in the van der Waals antiferromagnet NiPS3 through the intercalation of different organic cations, inserted using an engineered two-step process. First, the electrochemical intercalation of tetrabutylammonium cations (TBA+) results in a ferrimagnetic hybrid compound displaying a transition temperature of 78 K, and characterized by a hysteretic behavior with finite remanence and coercivity. Then, TBA+ cations are replaced by cobaltocenium via an ion-exchange process, yielding a ferrimagnetic phase with higher transition temperature (98 K) and higher remanent magnetization. Importantly, we demonstrate that the intercalation and cation exchange processes can be carried out in bulk crystals and few-layer flakes, opening the way to the integration of intercalated magnetic materials in devices. | Daniel Tezze; José M. Pereira; Yaiza Asensio; Mihail Ipatov; Francesco Calavalle; Fèlix Casanova; Alexander M. Bittner; Maider Ormaza; Beatriz Martín-García; Luis E. Hueso; Marco Gobbi | Materials Science; Hybrid Organic-Inorganic Materials; Magnetic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a9d845704d055f7b3e7884/original/tuning-the-magnetic-properties-of-ni-ps3-through-organic-ion-intercalation.pdf |
655cdd1b6e0ec7777f66d685 | 10.26434/chemrxiv-2023-d0mbc | Application of enzyme-like MnO2 nanoparticles as cathode materials for Li-ion batteries | In this study, the enzyme-like manganese dioxide nanoparticles with high peroxidase-like activity were synthesized and then characterized. The experimental studies proved the high Li-electroactivity of the as-prepared nanoparticles which makes these nanozymes for applying as cathode materials for Li-ion batteries. To determine the redox peaks of Mn4+/Mn3+ against Li anode, the cyclic voltammetry was used, revealed that the enzyme-like manganese dioxide nanoparticles as cathode materials can receive the Li(I) ions and then give it back to the anode. The charge-discharge tests were performed for several successive operational cycles. The results showed that the capacity of enzyme-like manganese dioxide nanoparticles is as high as 164.9 mAhg−1 at 30 mAg−1 while at 1000 mAg−1 the capacity was found to be about 46 mAhg−1. | Saeed Reza Hormozi Jangi | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655cdd1b6e0ec7777f66d685/original/application-of-enzyme-like-mn-o2-nanoparticles-as-cathode-materials-for-li-ion-batteries.pdf |
60c75069567dfe3944ec5853 | 10.26434/chemrxiv.12799922.v2 | The Interplay of Open-Shell Spin-Coupling and Jahn-Teller Distortion in Benzene Radical Cation Probed by X-ray Spectroscopy | We report a theoretical investigation and elucidation of the x-ray absorption spectra of neutral benzene and of the benzene cation. The generation of the cation by multiphoton ultraviolet (UV) ionization as well as the measurement of<br />the carbon K-edge spectra of both species using a table-top high-harmonic generation (HHG) source are described in the companion experimental paper [M. Epshtein et al., J. Phys.<br />Chem. A., submitted. Available on ChemRxiv]. We show that the 1sC -> pi transition serves as a sensitive signature of the transient cation formation, as it occurs outside of the spectral window of the parent neutral species. Moreover, the presence<br />of the unpaired (spectator) electron in the pi-subshell of the cation and the high symmetry of the system result in significant differences relative to neutral benzene in the spectral features associated with the 1sC ->pi* transitions. High-level calculations using equation-of-motion coupled-cluster theory provide the interpretation of the experimental spectra and insight into the electronic structure of benzene and its cation.<br />The prominent split structure of the 1sC -> pi* band of the cation is attributed to the interplay between the coupling of the core -> pi* excitation with the unpaired electron<br />in the pi-subshell and the Jahn-Teller distortion. The calculations attribute most of<br />the splitting (~1-1.2 eV) to the spin coupling, which is visible already at the Franck-Condon structure, and estimate the additional splitting due to structural relaxation to<br />be around ~0.1-0.2 eV. These results suggest that x-ray absorption with increased resolution might be able to disentangle electronic and structural aspects of the Jahn-Teller<br />effect in benzene cation.<br /> | Marta L. Vidal; Michael Epshtein; Valeriu Scutelnic; Zheyue Yang; Tian Xue; Stephen Leone; Anna I. Krylov; Sonia Coriani | Theory - Computational; Photochemistry (Physical Chem.); Physical and Chemical Processes; Physical and Chemical Properties; Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75069567dfe3944ec5853/original/the-interplay-of-open-shell-spin-coupling-and-jahn-teller-distortion-in-benzene-radical-cation-probed-by-x-ray-spectroscopy.pdf |
60c748d0ee301ccb87c7996e | 10.26434/chemrxiv.11882547.v2 | A Universal Platform for Selective Phase Growth and Precise-Layer Control in MoTe2 | Minor structural changes in transition metal dichalcogenides can have dramatic effects on their electronic properties. This makes the quest for key parameters that can enable a selective choice between the competing metallic and semiconducting phases in the 2D MoTe<sub>2</sub> system compelling. Herein, we report the optimal conditions at which the choice of the initial seed layer dictates the type of crystal structure of atomically-thin MoTe<sub>2</sub> films grown by chemical vapour deposition (CVD). When Mo metal is used as a seed layer, phase-pure semiconducting 2H-MoTe<sub>2</sub> is the only product. Conversely, MoO<sub>3</sub> leads to the preferential growth of phase-pure metallic 1Tꞌ-MoTe<sub>2</sub>. The control over phase growth allows for simultaneous deposition of both 2H-MoTe<sub>2</sub> and 1Tꞌ-MoTe<sub>2</sub> phases on a single substrate during one CVD reaction. Furthermore, Rhodamine 6G dye can be detected using few-layered 1Tꞌ-MoTe<sub>2</sub> films down to 5 nM concentration which is several orders of magnitude higher than the value observed for bulk 1Tꞌ-MoTe<sub>2</sub>. | James P. Fraser; Liudvika Masaityte; Jingyi Zhang; Stacey Laing; Juan Carlos Moreno-López; Adam McKenzie; Jessica McGlynn; Vishal Panchal; Duncan Graham; Olga Kazakova; Thomas Pichler; Donald A. MacLaren; David A.J. Moran; Alexey Y. Ganin | Thin Films; Nanostructured Materials - Nanoscience; Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748d0ee301ccb87c7996e/original/a-universal-platform-for-selective-phase-growth-and-precise-layer-control-in-mo-te2.pdf |
623497af13d4787e8992f7fb | 10.26434/chemrxiv-2021-0gpz8-v2 | Non-Hermitian Cavity Quantum Electrodynamics - Configuration Interaction Singles Approach for Polaritonic Structure with ab initio Molecular Hamiltonians | We combine ab initio molecular electronic Hamiltonians with a cavity quantum electrodynamics model for dissipative photonic modes and apply mean-field theories to the ground- and excited-states of resulting polaritonic systems. In particular, we develop a non-Hermitian configuration interaction singles theory for mean-field ground- and excited-states of the molecular system strongly interacting with a photonic mode, and apply these methods to elucidating the phenomenology of paradigmatic polaritonic systems. We leverage the Psi4Numpy framework to yield open-source and accessible reference implementations of these methods. | Jonathan McTague; Jonathan Foley | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Plasmonic and Photonic Structures and Devices; Theory - Computational; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2022-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623497af13d4787e8992f7fb/original/non-hermitian-cavity-quantum-electrodynamics-configuration-interaction-singles-approach-for-polaritonic-structure-with-ab-initio-molecular-hamiltonians.pdf |
645e46ddfb40f6b3ee77a9db | 10.26434/chemrxiv-2023-zb599-v2 | Accuracy Assessment for Equilibrium Dissociation Constant Using a Single Binding Isotherm | The equilibrium dissociation constant (Kd) characterizes stability of non-covalent molecular complexes. Determining Kd for highly stable complexes may be extremely inaccurate if the ratio between the concentration of the limiting component (L0) and the a priori unknown value of Kd exceeds an unknown threshold value (aka threshold ratio). The only known approach to reveal this kind of inaccuracy in Kd requires building multiple experimental binding isotherms; it is resource intensive and, therefore, used very rarely. Here we introduce a single-isotherm approach for assessing Kd accuracy via determining the value of L0/Kd, estimating the threshold ratio, and comparing L0/Kd to the threshold ratio. In this proof-of-concept work, we present the theoretical basis and develop a step-by-step algorithm for our single-isotherm approach. We also demonstrate the experimental use of the developed algorithm. | Tong Ye Wang; Jean-Luc Rukundo; Svetlana Krylova; Sergey Krylov | Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645e46ddfb40f6b3ee77a9db/original/accuracy-assessment-for-equilibrium-dissociation-constant-using-a-single-binding-isotherm.pdf |
6671b33b5101a2ffa8e14ab9 | 10.26434/chemrxiv-2024-lpwfp | Single molecule identification and quantification of whole proteins without purification, proteolysis, or labeling: a computational model | A recent report shows that with a suitably designed buffer solution proteins can be unfolded and translocated through a nanopore unidirectionally and uniformly, with residues exiting the pore in sequence order at a roughly constant rate of 1/µs (Nature Biotechnology 41, 1130–1139, 2023). The present work shows in theory that by sampling the signal of pore exclusion volume (a proxy for the measured blockade current) at a low frequency of 10-20 KHz and digitizing the sampled signal at a volume precision of 70 Å3 a substantial majority of the proteins in a proteome can be identified and counted without labeling. Computations on the full set of sequences in the human proteome (Uniprot id UP000005640_9606) show that ~70% of the proteins can be identified; the result generally holds even when post-translational modifications (PTMs) are present. The identification rate can be increased to better than 95% with modified algorithms; with an array of 100 pores ~109 proteins can be identified/counted in about 1.5 hours. This is a minimalist non-destructive single molecule label-free approach that is based on unmodified nanopores; it serves as a potential alternative to mass spectrometry while overcoming many of the limitations of the latter. In principle it can work with whole proteins in mixtures over the full dynamic range of a proteome without purification/separation, proteolytic degradation, or enzymes for translocation control.
| G Sampath | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Bioengineering and Biotechnology; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6671b33b5101a2ffa8e14ab9/original/single-molecule-identification-and-quantification-of-whole-proteins-without-purification-proteolysis-or-labeling-a-computational-model.pdf |
62e80c87ab605052d2eeb49f | 10.26434/chemrxiv-2022-t319t | Understanding activity trends in furfural hydrogenation on transition metal surfaces | Furfural hydrogenation to furfuryl alcohol is an industrially significant reaction for biomass valorization. The hydrogenation process has been mainly catalyzed by chromite-based materials that are notorious for their toxicity, thereby highlighting the need to find alternate catalyst materials. In addition, there is a gap in the mechanistic understanding of furfural hydrogenation on transition metal surfaces. Herein, we combine density functional theory calculations and microkinetic modeling to study the reaction mechanism of furfural hydrogenation to furfuryl alcohol on terrace (111/0001) and stepped (211) transition metal surfaces. We find the rate- determining steps for furfural hydrogenation to depend on the identity of the metal, where the strong binding metals are limited by desorption of the product (furfuryl alcohol) while the moderate and weak binding metals are limited by steps involving surface hydrogenation or H2 activation. We show that the binding energy of furfural is a good descriptor to rationalize and predict the activity trends for the production of furfuryl alcohol. Among the metal and bulk/single atom alloy surfaces investigated in this work, we find Cu-based alloys to be the most active catalysts, with CuNi alloys predicted to be promising candidates for furfural hydrogenation. | Sihang Liu; Nitish Govindarajan; Karen Chan | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e80c87ab605052d2eeb49f/original/understanding-activity-trends-in-furfural-hydrogenation-on-transition-metal-surfaces.pdf |
632b5a13e61502e09921413d | 10.26434/chemrxiv-2022-wp18w-v2 | An Open-Source Environmental Chamber for Materials-Stability Testing Using an Optical Proxy | This study is motivated by the desire to disseminate a low-cost, high-precision, high-throughput environmental chamber to test materials and devices under elevated humidity, temperature, and light. This paper documents the creation of an open-source tool with a bill of materials as low as US$2,000, and the subsequent evolution of three second-generation tools installed at three different universities spanning thin films, bulk crystals, and thin-film solar-cell devices. We introduce an optical proxy measurement to detect real-time phase changes in materials. We present correlations between this optical proxy and standard X-ray diffraction measurements, describe some edge cases where the proxy measurement fails, and report key learnings from the technology-translation process. By sharing lessons learned, we hope that future open-hardware development and translation efforts can proceed with reduced friction. Throughout the paper, we provide examples of scientific impact, wherein participating laboratories used their environmental chambers to study and improve the stabilities of halide-perovskite materials. All generations of hardware bills of materials, assembly instructions, and operating codes are available in open-source repositories. | Rodolfo Keesey; Armi Tiihonen; Alexander E. Siemenn; Thomas W. Colburn; Shijing Sun; Noor Titan Putri Hartono; James Serdy; Margaret Zeile; Keqing He; Cole A. Gurtner; Austin C. Flick; Clio Batali; Alex Encinas; Richa R. Naik; Zhe Liu; Felipe Oviedo; I. Marius Peters; Janak Thapa; Siyu Isaac Parker Tian; Reinhold H. Dauskardt; Alexander J. Norquist; Tonio Buonassisi | Materials Science; Analytical Chemistry; Hybrid Organic-Inorganic Materials; Analytical Apparatus; Environmental Analysis | CC BY 4.0 | CHEMRXIV | 2022-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632b5a13e61502e09921413d/original/an-open-source-environmental-chamber-for-materials-stability-testing-using-an-optical-proxy.pdf |
60c7472fbb8c1ab2c13da9e7 | 10.26434/chemrxiv.11556300.v1 | A Neutral Porous Organic Polymer Host for the Recognition of Anionic Dyes in Water | Neutral hosts for the recognition of anionic guests in water remain underdeveloped due to the inherent thermodynamic barrier for desolvation. As a new strategy to address this challenge, we have repurposed crosslinked porous organic polymers (POPs) as hosts. This polymer architecture affords a hydrophobic environment with a densely packed array of urea hydrogen bond donors to cooperatively promote anion desolvation and recognition in water. As a proof-of-concept, we demonstrate through adsorption assays that the resulting Urea-POP-1 can discriminate between structurally different dyes containing phosphonate, sulfonate, and carboxylate anions. Moreover, when compared to Methyl-POP-1, a control POP lacking hydrogen bond donors, we find that recognition is not exclusively driven by the hydrophobicity of the dyes but through selective hydrogen bonding interactions of the urea sidechains with the anionic functional groups. This starting point sets the stage to exploit the modularity of our design to build a family of neutral polymer hosts with tunable pore sizes and anion preferences for fundamental investigations and targeted applications. | Whitney Ong; Ron Smaldone; Sheel Dodani | Supramolecular Chemistry (Org.); Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7472fbb8c1ab2c13da9e7/original/a-neutral-porous-organic-polymer-host-for-the-recognition-of-anionic-dyes-in-water.pdf |
60c759404c8919f19ead4d2f | 10.26434/chemrxiv.14675829.v1 | Kinetics of Alkaline Hydrolysis of Synthetic Organic Esters | Manuscript with supporting information describing novel experimental data on the alkaline hydrolysis of synthetic esters, relevant to chemistry in the indoor environment | Do Young Maeng; V. Faye McNeill | Atmospheric Chemistry; Hydrology and Water Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759404c8919f19ead4d2f/original/kinetics-of-alkaline-hydrolysis-of-synthetic-organic-esters.pdf |
60c743f2bdbb89963ca386f5 | 10.26434/chemrxiv.9701468.v1 | Identifying Eigen-Like Hydrated Protons at Negatively Charged Interfaces | Despite the
importance of the hydrogen ion in a wide range of biological, chemical, and
physical processes, its molecular structure in solution remains lively debated.
Progress has been primarily hampered by the extreme diffuse nature of the
vibrational signatures of hydrated protons in bulk solution. Using the
inherently surface-specific vibrational sum frequency spectroscopy, we show
that at selected negatively charged interfaces, a resolved spectral feature
directly linked to the H<sub>3</sub>O<sup>+</sup> core in an Eigen-like species
can be readily identified in a biologically compatible pH range. The results offer
a new molecular perspective for tracking and understanding the behaviour of
hydrated protons at interfaces. | Eric Tyrode; Sanghamitra Sengupta; Adrien Sthoer | Biophysical Chemistry; Interfaces; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Structure; Surface; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f2bdbb89963ca386f5/original/identifying-eigen-like-hydrated-protons-at-negatively-charged-interfaces.pdf |
676eb5befa469535b9fb001a | 10.26434/chemrxiv-2025-rwgt8 | Augmented and Programmatically Optimized LLM Prompts Reduce Chemical Hallucinations | Utilizing Large Language Models (LLMs) for handling scientific information comes with risk of the outputs not matching expectations, commonly called hallucinations. To fully utilize LLMs in research requires improving their accuracy, avoiding hallucinations, and extending their scope to research topics outside their direct training. There is also a benefit to getting the most accurate information from an LLM at the time of inference without having to create and train custom new models for each application. Here, augmented generation and machine learning driven prompt optimization are combined to extract performance improvements over base LLM function on a common chemical research task. Specifically, an LLM was used to predict the topological polar surface area (TPSA) of molecules. By using augmented generation and machine learning optimized prompts, the error in the prediction was reduced to 7.44 root mean squared error (RMSE) from 59.41 RMSE with direct calls to the same LLM. | Scott Reed | Theoretical and Computational Chemistry; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676eb5befa469535b9fb001a/original/augmented-and-programmatically-optimized-llm-prompts-reduce-chemical-hallucinations.pdf |
67725f3d6dde43c908c3ec4b | 10.26434/chemrxiv-2025-6qdbr | Feasibility of Targeted Alpha Therapy for Alzheimer's Disease Using 211At-labeled Agent Targeting Amyloid-β Aggregates | Amyloid-β (Aβ) aggregates are one of the pathological hallmarks and also an important therapeutic target of Alzheimer's disease (AD). Although targeted alpha therapy (TAT) has been established primarily for cancer treatments, it has potential application as a novel treatment approach for AD by reducing Aβ aggregates. However, no TAT agents targeting Aβ aggregates have demonstrated usefulness in vivo. In this study, we newly synthesized and evaluated [211At]APBF-2, a pyridyl benzofuran (PBF) derivative labeled with astatine-211 (211At, t1/2 = 7.2 h), as a small molecule-based TAT agent targeting Aβ aggregates. In an in vitro thioflavin T (ThT) assay, [211At]APBF-2 significantly reduced the quantity of Aβ1-42 aggregates. Additionally, in an in vivo biodistribution study using normal mice, [211At]APBF-2 demonstrated favorable blood-brain barrier (BBB) permeability (2.95% injected dose (ID)/g at 2 min after intravenous injection). These results suggest that [211At]APBF-2 may be a TAT agent demonstrating therapeutic efficacy against AD in vivo. | Rikuto Kashiyama; Hiroyuki Watanabe; Takahiro Akasaka; Hiroyuki Fujimoto; Masashi Murakami; Kazuhiro Ooe; Atsushi Toyoshima; Kazuma Nakashima; Masahiro Ono | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67725f3d6dde43c908c3ec4b/original/feasibility-of-targeted-alpha-therapy-for-alzheimer-s-disease-using-211at-labeled-agent-targeting-amyloid-aggregates.pdf |
60c74bf69abda22820f8d1a7 | 10.26434/chemrxiv.12407117.v1 | Interactions between Ultrastable Na4Ag44(SR)30 Nanoclusters and Coordinating Solvents: Uncovering the Atomic-scale Mechanism | We report the mechanism on the ultrahigh stability of Na<sub>4</sub>Ag<sub>44</sub>(SR)<sub>30</sub>
by uncovering how coordinating solvents interact with the Na<sub>4</sub>Ag<sub>44</sub>(SR)<sub>30</sub>
nanocluster at the atomic scale. Through synchrotron X-ray experiments and theoretical
calculations, it was found that strongly coordinating aprotic solvents interact
with surface Ag atoms, particularly between ligand bundles, which compresses
the Ag core and relaxes surface metal-ligand interactions. Furthermore, water
was used as a cosolvent to demonstrate that semi-aqueous conditions play an
important role in protecting exposed surface regions and can further influence
the local structure of the silver nanocluster itself. Notably, under
semi-aqueous conditions, aprotic coordinating solvent molecules preferentially
remain on the metal surface while water molecules interact with ligands, and
ligand bundling persisted across the varied solvation conditions. | Daniel M. Chevrier; Brian
E. Conn; Bo Li; De-En Jiang; Terry P. Bigioni; Amares Chatt; Peng Zhang | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bf69abda22820f8d1a7/original/interactions-between-ultrastable-na4ag44-sr-30-nanoclusters-and-coordinating-solvents-uncovering-the-atomic-scale-mechanism.pdf |
6551f6386e0ec7777fd92fc3 | 10.26434/chemrxiv-2023-fcf2w-v2 | Process Intensification of the Continuous Synthesis of Bio-derived Monomers for Sustainable Coatings using a Taylor Vortex Flow Reactor | We describe the optimization and scale-up of two consecutive reaction steps in the synthesis of bio-derived alkoxybutenolide monomers that have been reported as potential replacements for acrylate-based coatings (Sci. Adv., 2020, 6, eabe0026). These monomers are synthesized by (i) oxidation of furfural with photo-generated singlet oxygen followed by (ii) thermal condensation of the desired 5-hydroxyfuranone intermediate product with an alcohol, a step which until now has involved a lengthy batch reaction. The two steps have been successfully telescoped into a single kilogram-scale process without any need to isolate the 5-hydroxyfuranone between the steps. Our process development involved FTIR reaction monitoring, FTIR data analysis via 2D-visualization and two different photo-reactors (i) a semi-continuous photo-reactor based on a modified rotary evaporator where FTIR and 2D-correlation spectroscopy (2D-COS) revealed the loss of the methyl formate co-product and (ii) our fully continuous Taylor Vortex photo-reactor which enhanced the mass transfer and permitted the use of near-stoichiometric equivalents of O2. The use of inline FTIR monitoring and modelling greatly accelerated process optimization in the Vortex reactor. This led to scale up of the photo-oxidation with an 85% yield and a projected productivity of 1.3 kg day-1, with a space time yield of 0.06 mol day-1 mL-1. Higher productivities could be achieved whilst sacrificing yield; e.g. 4 kg day-1 at 40% yield. The second step, the thermal condensation of 5-hydroxyfuranone, was transformed from a 20 h batch reflux reaction to a < 1 minute thermal flow reaction in a reactor only 3 mL in volume operating at 200 oC with projected productivities of >700 g day-1. Proof of concept for telescoping the two steps was established with an overall two-step yield of 67%, producing a process with projected productivity of 1.1 kg day-1 of the methoxybutenolide monomer without any purification of the 5-hydroxyfuranone intermediate. | Matthew D. Edwards; Matthew T. Pratley; Charles M. Gordon; Rodolfo I. Teixeira; Hamza Ali; Irfhan Mahmood; Reece Lester; Ashley Love; Johannes G. H. Hermens; Thomas Freese; Ben L. Feringa; Martyn Poliakoff ; Michael W. George | Catalysis; Chemical Engineering and Industrial Chemistry; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6551f6386e0ec7777fd92fc3/original/process-intensification-of-the-continuous-synthesis-of-bio-derived-monomers-for-sustainable-coatings-using-a-taylor-vortex-flow-reactor.pdf |
66682d9fe7ccf7753a80221c | 10.26434/chemrxiv-2024-v4h15 | Molybdenum Sulfide Clusters as Molecular Co-Catalyst on Antimony Selenide Photocathodes for Photoelectrochemical Hydrogen Evolution | Molybdenum sulfide serves as an effective non-precious metal catalyst for hydrogen evolution, primarily active at edge sites with unsaturated molybdenum sites or terminal disulphides. To improve the activity at low loading density, two molybdenum sulfide clusters, [Mo3S4]4+ and [Mo3S13]2–, were investigated. The Mo3Sx molecular catalysts were heterogenized on Sb2Se3 with a simple soaking treatment, resulting in a thin catalyst layer of only a few nanometers that gave up to 20 mA cm–2 under one sun illumination. Both [Mo3S4]4+ and [Mo3S13]2– exhibit catalytic activities on Sb2Se3 through a simple soaking process, with [Mo3S13]2– emerging as the superior catalyst, demonstrating enhanced photovoltage and average faradaic efficiency of 100% for hydrogen evolution. This superiority is attributed to the effective loading and higher catalytic activity of [Mo3S13]2– on the Sb2Se3 surface, validated by X-ray photoelectron and Raman spectroscopy. | Pardis Adams; Jan Bühler; Iva Walz; Thomas Moehl; Helena Roithmeyer; Olivier Blacque; Nicolò Comini; Trey Diulus; Roger Alberto; Sebastian Siol; Mirjana Dimitrievska; Zbynek Novotny; David Tilley | Catalysis; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2024-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66682d9fe7ccf7753a80221c/original/molybdenum-sulfide-clusters-as-molecular-co-catalyst-on-antimony-selenide-photocathodes-for-photoelectrochemical-hydrogen-evolution.pdf |
62c413cc13b85b01b33f3b77 | 10.26434/chemrxiv-2022-l5zk8-v2 | Enantioselective fullerene functionalization via traceless stereochemical information transfer from a self-assembled cage | Metal-organic cages have served as masks to effect the regioselective functionalization of C60. The enantioselective functionalization of C60 remains challenging, however, requiring complex chiral tethers or challenging chromatography. We report a means of defining up to six stereocentres on C60, achieving both enantioselective and regioselective fullerene functionalisation. This method involves stereochemical information transfer from a chiral formylpyridine, through the framework of an enantiopure cage incorporating it, to a series of regio- and stereochemically defined C60 adducts. The surrounding cage is then opened with retention of fullerene stereochemistry. The chiral formylpyridine thus ultimately dictates the stereochemistry of these chiral fullerene adducts without being incorporated into them. The cage acts both as the substrate and “blueprint” for the chiral information imprinted into the fullerene adducts, which form stereoselectively with a distance of up to 6 carbon atoms between stereocentres. Such chiral fullerene adducts may become useful in devices requiring circularly-polarized light manipulation. | Zifei Lu; Tanya Ronson; Andrew Heard; Sascha Feldmann; Nicolas Vanthuyne; Alexandre Martinez; Jonathan Nitschke | Inorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c413cc13b85b01b33f3b77/original/enantioselective-fullerene-functionalization-via-traceless-stereochemical-information-transfer-from-a-self-assembled-cage.pdf |
66ad059c01103d79c5957342 | 10.26434/chemrxiv-2024-x8vt1 | Robust Computation and Analysis of Vibrational Spectra of Layered Framework Materials including Host-Guest Interactions | Layered framework materials, a rapidly advancing class of porous materials, are composed of molecular components stitched together via covalent bonds and are usually synthesized through wet-chemical methods. Computational infrared (IR) and Raman spectra are among the most important characterization tools for this materials class. Besides the a priori known spectra of the molecular building blocks and the solvent, they allow for in situ monitoring of the framework formation during synthesis. Therefore, they need to capture the additional peaks from host-guest interactions and the bands from emerging bonds between the molecular building blocks, verifying the successful synthesis of the desired material. In this work, we propose a robust computational framework based on ab initio molecular dynamics (AIMD), where we compute IR and Raman spectra from the time-correlation functions of dipole moments and polarizability tensors, respectively. As a case study, we apply our methodology to a covalent organic framework (COF) material, COF-1, and present its AIMD-computed IR and Raman spectra with and without 1,4-dioxane solvent molecules in its pores. To determine robust settings, we meticulously validate our model and explore how stacking disorder and different methods for computing dipole moments and polarizabilities affect IR and Raman intensities. Using our robust computational protocol, we achieve excellent agreement with experimental data. Furthermore, we illustrate how the computed spectra can be dissected into individual contributions from the solvent molecules, the molecular building blocks of COF-1, and the bonds connecting them. | Ekin Esme Bas; Karen Marlenne Garcia Alvarez; Andreas Schneemann; Thomas Heine; Dorothea Golze | Theoretical and Computational Chemistry; Materials Science; Carbon-based Materials; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ad059c01103d79c5957342/original/robust-computation-and-analysis-of-vibrational-spectra-of-layered-framework-materials-including-host-guest-interactions.pdf |
661d651b91aefa6ce19ed528 | 10.26434/chemrxiv-2024-h02wc | Alkene Dicarbofunctionalisation via High-Valent Nickel Catalysis | Great advances have been made by leveraging high-valent Pd(II)/Pd(IV) catalysis in the areas of C–H activation and alkene difunctionalisation, thus representing a powerful approach for the construction of carbon-carbon and carbon-heteroatom bond. However, the catalytic reactions involving high-valent Ni(II)/Ni(IV) catalysis are largely underdeveloped. Here we report a Ni(II)-catalysed dicarbofunctionalisation of unactivated alkenes via high-valent Ni(II)/Ni(IV) catalysis. This dicarbofunctionalisation protocol provides a highly efficient and direct route towards vicinal substituted alkanes using primary, secondary, and tertiary amides, as well as secondary and tertiary amines as the native directing group under redox-neutral conditions that are challenging to access through conventional methods. The key to the success of this reaction is the use of a bulky β-diketone ligand, which could enable the insertion of alkene to aryl-Ni(II) species, stabilize the alkyl-Ni(II) species and inhibit the homolytic alkyl-Ni(II) cleavage. This dicarbofunctionalisation reaction features the use of native directing group, a broad substrate scope, and excellent scalability. The resulting Weinreb amide-derived products can be readily derivatized to a variety of ketones and aldehyde, which are fundamentally useful in synthetic chemistry. In addition, this protocol has been employed for the efficient preparation of several bioactive compounds, showcasing the significant synthetic values of our current method. | Dao-Ming Wang; Li-Qin She; Yu-Qing He; Yichen Wu; Yong Tang; Peng Wang | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661d651b91aefa6ce19ed528/original/alkene-dicarbofunctionalisation-via-high-valent-nickel-catalysis.pdf |
66b9d760c9c6a5c07afce407 | 10.26434/chemrxiv-2024-hrnb5 | Probing the Breathing of Reactive Electrical Double Layer | Fundamental understanding of the electrical double layer (EDL) under reactive conditions remains limited, hindering progress in electrocatalysis and energy conversion technologies. Herein, microscopic dynamics of the EDL during the hydrogen evolution reaction (HER) is probed using in-situ surface-enhanced infrared adsorption spectroscopy (SEIRAS). We demonstrate that the inner layer of the EDL contracts and then expands back in a positive-negative-positive potential cycle, a process we term “EDL breathing”. Challenging the classical static picture of the EDL, the contraction of inner layer significantly amplifies the strength of local electric field, revealing a nonlinear relationship between the local electric field and electrode potential. This work deepens our understanding of reactive electrocatalytic interfaces and provides novel insights into EDL dynamics, crucial for leveraging the EDL to advance green technologies. | Li Xiao-Yu; Yu-Chen Cai; Zhao-Dong Meng; Ze-Tong Jia; Jin-Yu Ye; Na Tian; Zhi-You Zhou; Jun Huang; Shi-Gang Sun; Tao Wang | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b9d760c9c6a5c07afce407/original/probing-the-breathing-of-reactive-electrical-double-layer.pdf |
60c740a1337d6c0188e26720 | 10.26434/chemrxiv.7764638.v1 | Expedited Mapping of the Ligandable Proteome Using Fully Functionalized Enantiomeric Probe Pairs | <div>A fundamental challenge in chemical biology and medicine is to understand and expand the fraction of the human proteome that can be targeted by small molecules. We recently described a strategy that integrates fragment-based ligand discovery with chemical proteomics to furnish global portraits of reversible small molecule-protein interactions in human cells.</div><div>Excavating clear structure-activity relationships from these “ligandability” maps, however, was confounded by the distinct physicochemical properties and corresponding overall protein-binding potential of individual fragments. Here, we describe a compelling solution to this problem by introducing a next-generation set of fully functionalized fragments (FFFs) differing only in absolute stereochemistry. Using these enantiomeric probe pairs, or “enantioprobes”, we identify numerous stereoselective protein-fragment interactions in cells and show that these interactions occur at functional sites on proteins from diverse classes. Our findings thus indicate that incorporating chirality into FFF libraries provides a robust and streamlined method to discover ligandable proteins in cells.</div> | Benjamin Cravatt; Yujia Wang; melissa dix; jarrett remsberg; hsin-yu lee; marian kalocsay; steven gygi; gregory vite; michael lawrence; Christopher Parker | Chemoinformatics; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a1337d6c0188e26720/original/expedited-mapping-of-the-ligandable-proteome-using-fully-functionalized-enantiomeric-probe-pairs.pdf |
610936ae8804439fdde55e7b | 10.26434/chemrxiv-2021-kgd0h | MOF Synthesis Prediction Enabled by Automatic Data Mining and Machine Learning | Despite rapid progress in the field of metal-organic frameworks (MOFs), the potential of using machine learning (ML) methods to predict MOF synthesis parameters is still untapped. Here, we show how ML can be used for rationalization and acceleration of the MOF discovery process by directly predicting the synthesis conditions of a MOF based on its crystal structure. Our approach is based on: (i) establishing the first MOF synthesis database via automatic extraction of synthesis parameters from the literature, (ii) training and optimizing ML models by employing the MOF database, and (iii) predicting the synthesis conditions for new MOF structures. The ML models even at an initial stage exhibit a good prediction performance, outperforming human expert predictions, obtained through a synthesis survey. | Yi Luo; Saientan Bag; Orysia Zaremba; Jacopo Andreo; Stefan Wuttke; Manuel Tsotsalas; Pascal Friederich | Theoretical and Computational Chemistry; Organometallic Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry; Reaction (Organomet.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610936ae8804439fdde55e7b/original/mof-synthesis-prediction-enabled-by-automatic-data-mining-and-machine-learning.pdf |
60c74f95337d6cc411e2818a | 10.26434/chemrxiv.12887183.v2 | Rigorous Quantification of the statistical significance of COVID-19 lockdown effect on air quality: The case from ground-based measurements in Ontario, Canada | Preliminary analysis of satellite measurements from around the world showed drops in nitrogen dioxide (NO<sub>2</sub>) with lockdowns due to the COVID-19 pandemic. A number of studies have found these drops to be correlated with local decreases in transportation and/or industry. None of these studies, however, has rigorously quantified the statistical significance of these drops relative to natural meteorological variability and other factors that influence pollutant levels during similar time periods in previous years. Here, we develop a novel statistical testing framework that accounts for seasonal variability, transboundary influences, and new factors such as COVID-19 restrictions in explaining trends in several pollutant levels at 16 ground-based measurement sites in Southern Ontario, Canada. We find statistically significant and temporary drops in NO<sub>2</sub> (11 out 16 sites) and CO (all 4 sites) in April-June 2020, with pollutant levels 20% lower than in the previous three years. Much fewer sites (2-3 out of 16) experienced statistically significant drops in O<sub>3</sub> and PM2.5.<b> </b>The statistical testing framework developed here is the first of its kind applied to air quality data, and highlights the need for rigorous assessment of statistical significance, should analyses of pollutant level changes post COVID-19 lockdowns be used to inform policy decisions in Ontario, Canada. See Methods section in the manuscript. | Hind A. Al-Abadleh; Martin Lysy; Lucas Neil; Priyesh Patel; Wisam Mohammed; Yara Khalaf | Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f95337d6cc411e2818a/original/rigorous-quantification-of-the-statistical-significance-of-covid-19-lockdown-effect-on-air-quality-the-case-from-ground-based-measurements-in-ontario-canada.pdf |
62ebcf4f3b834eb683e4d284 | 10.26434/chemrxiv-2022-dz3j4 | Solvent-induced Inversion of Colloidal Aggregation During Electrophoretic Deposition | Electrophoretic deposition of colloidal particles is a practical system for the study of crystallization and related physical phenomena. The aggregation is driven by the electroosmotic flow fields generated by the polarization of the electrode-particle-electrolyte interface. Here, we report on the electrochemical control of aggregation and repulsion in the electrophoretic deposition of colloidal microspheres. The nature of this transition depends solely on the composition of the solvent. The observed behavior switches between electrical field-driven aggregation in water to electrical field-driven repulsion in ethanol for otherwise identical systems of colloidal microspheres. This work uses optical microscopy-derived particle and a recently developed particle insertion method-approach to extract the effective interparticle potentials as a function of the solvent and electrode potential at the electrode interface. This approach can be used to understand the phase behavior of these systems based on the observable particle positions rather than a detailed understanding of the electrode-electrolyte microphysics. | Justin DeMoulpied; Jessica Killenbeck; Zebulon Schichtl; Babloo Sharma; Susanne Striegler; Robert Coridan | Physical Chemistry; Materials Science; Granular Materials; Materials Processing; Self-Assembly; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ebcf4f3b834eb683e4d284/original/solvent-induced-inversion-of-colloidal-aggregation-during-electrophoretic-deposition.pdf |
6619bdc8418a5379b0ba6c69 | 10.26434/chemrxiv-2024-cllgm | Plant-derived biopolymers initiate heterogeneous ice nucleation via particulate interfaces immersed in supercooled droplets | Organic matter can initiate heterogeneous ice nucleation in supercooled water droplets, thereby influencing atmospheric cloud glaciation. Atmospheric organic matter includes biopolymers, which are emitted as primary bioaerosols, biomass burning aerosols, soil dust and sea spray aerosols and can nucleate ice in the absence of a solid surface like mineral dust. There is evidence that biopolymers could form aggregates in solution, thereby creating ice-nucleating sites. However, the submicron size and heterogeneity of these aggregates creates challenges in studying and predicting their ice-nucleating ability. Here, we characterized self-assembled nanoparticles of cellulose and lignin and of two newly identified ice-nucleating biopolymers, namely xylan and laminarin. Our freezing ice nuclei counter (FINC) instrument measured the median ice nucleation temperatures of aqueous cellulose, lignin, xylan and laminarin samples to be –22.9 °C, –22.0 °C, –14.2 °C, and –20.0 °C, respectively. Furthermore, a nanoparticle tracking technique detected and quantified particles in the biopolymer solutions, with mean diameters between 132 nm and 267 nm. A positive trend between size and nucleation temperatures suggests that the biopolymers initiate freezing via particulate interfaces immersed in the supercooled droplets. Finally, we determined ice-active site densities normalized to quantitatively measured surface area and mass of the nanoparticles, to demonstrate how the biopolymers self-assemble in solution and subsequently nucleate ice in supercooled droplets. The mechanism by which biopolymers nucleate ice leads to improved predictive capabilities to estimate the impact of organic aerosols on climate. | Paul Bieber; Ghinwa H. Darwish; W. Russ Algar; Nadine Borduas-Dedekind | Physical Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6619bdc8418a5379b0ba6c69/original/plant-derived-biopolymers-initiate-heterogeneous-ice-nucleation-via-particulate-interfaces-immersed-in-supercooled-droplets.pdf |
60c7573ff96a003afb288c24 | 10.26434/chemrxiv.14386550.v1 | Correlating the Structural Evolution of ZnO/Al2O3 to Spinel Zinc Aluminate with its Catalytic Performance in Propane Dehydrogenation | Zn-based Al<sub>2</sub>O<sub>3</sub>-suported materials have been proposed as inexpensive and environmentally friendly catalysts for the direct dehydrogenation of propane (PDH), however, our understanding of these catalysts’ structure and deactivation routes is still limited. Here, we correlate the catalytic activity for PDH of a series of Zn-based Al<sub>2</sub>O<sub>3</sub> catalysts with their structure and structural evolution. To this end, three model catalysts are investigated. (i) ZnO/Al<sub>2</sub>O<sub>3</sub> prepared by atomic layer deposition (ALD) of ZnO onto γ-Al<sub>2</sub>O<sub>3 </sub>followed by calcination at 700 °C, which yields a core-shell spinel zinc aluminate/γ-Al<sub>2</sub>O<sub>3</sub> structure. (ii) Zinc aluminate spinel nanoparticles (Zn<sub>x</sub>Al<sub>y</sub>O<sub>4</sub> NPs) prepared via a hydrothermal method. (iii) A reference core-shell ZnO/SiO<sub>2</sub> catalyst prepared by ALD of ZnO on SiO<sub>2</sub>. The catalysts are characterized in detail by synchrotron X-ray powder diffraction (XRD), Zn K-edge X-ray absorption spectroscopy (XAS), and <sup>27</sup>Al solid state nuclear magnetic resonance (ssNMR). These experiments allowed us to identify tetrahedral Zn sites in close proximity to Al sites of a zinc aluminate spinel phase (Zn<sub>IV</sub>–O–Al<sub>IV/VI</sub> linkages) as notably more active and selective in PDH relative to the supported ZnO wurtzite phase (Zn<sub>IV</sub>–O– Zn<sub>IV</sub> linkages) in ZnO/SiO<sub>2</sub>. The best performing catalyst, 50ZnO/Al<sub>2</sub>O<sub>3</sub> gives 77% selectivity to propene (gaseous products based) at 9 mmol C<sub>3</sub>H<sub>6</sub> gcat−1 h<sup>−1</sup> space time yield (STY) after 3 min of reaction at 600 °C. On the other hand, the core-shell ZnO/Al<sub>2</sub>O<sub>3</sub> catalyst shows an irreversible loss of activity over repeated PDH and air-regeneration cycles, explained by Zn depletion on the surface due to its diffusion into subsurface layers or the bulk. ZnxAlyO<sub>4</sub> NPs gave a comparable initial selectivity and catalytic activity as 50ZnO/Al<sub>2</sub>O<sub>3</sub>. With time on stream, Zn<sub>x</sub>Al<sub>y</sub>O<sub>4</sub> NPs deactivate due to the formation of coke at the catalyst surface, yet the extend of coke deposition is lower than for the ZnO/Al<sub>2</sub>O<sub>3</sub> catalysts, and the activity of Zn<sub>x</sub>Al<sub>y</sub>O<sub>4</sub> NPs can be regenerated almost fully using calcination in air.<br /> | Manouchehr Nadjafi; Agnieszka M. Kierzkowska; Andac Armutlulu; Rene Verel; Alexey Fedorov; Paula M. Abdala; Christoph Müller | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7573ff96a003afb288c24/original/correlating-the-structural-evolution-of-zn-o-al2o3-to-spinel-zinc-aluminate-with-its-catalytic-performance-in-propane-dehydrogenation.pdf |
6670d486c9c6a5c07ab0ccc7 | 10.26434/chemrxiv-2024-6nlx1 |
Near-quantitative Removal of Oxalate and Terephthalate from Water by Precipitation with a Rigid Bis-amidinium Compound
| A simple, readily-prepared precipitant (1.Cl2) precipitates oxalate or terephthalate from water with very high efficacy, removing these anions at sub-millimolar concentrations using only one equivalent of precipitant. A simple aqueous base/acid cycle can be used to regenerate 1.Cl2 after use. The resulting precipitates, 1.oxalate and 1.terephthalate, are anhydrous and closely-packed, with each anion receiving eight charge-assisted hydrogen bonds from amidinium N–H donors. Precipitation of oxalate and terephthalate occurs at much lower concentrations than other dicarboxylates, and direct competition experiments with the biologically/environmentally relevant divalent anions CO32–, HPO42– and SO42– reveal very high selectivity for oxalate or terephthalate over these competitors. | Rosemary Goodwin; Phonlakrit Muang-Non; Nikki Tzioumis; Kate Jolliffe; Nicholas White | Physical Chemistry; Organic Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.); Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6670d486c9c6a5c07ab0ccc7/original/near-quantitative-removal-of-oxalate-and-terephthalate-from-water-by-precipitation-with-a-rigid-bis-amidinium-compound.pdf |
656762e3cf8b3c3cd7676b4b | 10.26434/chemrxiv-2023-p7w4n | Enhanced Photocatalytic Water Splitting with Two-Dimensional van der Waals Heterostructures of BAs/WTeSe | The photocatalytic efficiency of monolayer materials can be significantly enhanced by constructing two-dimensional van der Waals heterostructures. This study presents first principles calculations based on density functional theory to investigate the electronic properties and photocatalytic mechanism of van der Walls heterostructures of boron arsenide (BAs) with the Janus MXY (M=W; X/Y=Se, Te) monolayers, with and without Se vacancies. Results from binding energies, phonon spectra, and ab initio molecular dynamics simulations indicate that the heterostructures are stable from all respects. Moreover, all the heterostructures exhibit direct bandgaps with valence band maxima and conduction band minima suitable for water splitting. Additionally, these heterostructures possess high optical absorption coefficients in the visible and ultraviolet regions. In particular, our calculations predict BAs/WTeSe, with and without Se vacancies, as promising candidates for photocatalytic water splitting applications. | Hanifa BiBi; Abdul Jalil; Syed Zafar Illyas; Azeem Ghulam Nabi; Devis Di Tommaso | Physical Chemistry; Catalysis; Photocatalysis; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656762e3cf8b3c3cd7676b4b/original/enhanced-photocatalytic-water-splitting-with-two-dimensional-van-der-waals-heterostructures-of-b-as-w-te-se.pdf |
656c8ccb5bc9fcb5c9f2d2e4 | 10.26434/chemrxiv-2023-l6l27-v2 | Relation between double layer structure, capacitance and surface tension in electrowetting of graphene and aqueous electrolytes | Deciphering the mechanisms of charge storage on carbon-based materials is pivotal for the development of next generation electrochemical energy storage systems. Graphene, the building block of graphitic electrodes, is an ideal model for probing such processes on a fundamental level. Herein, we investigate the thermodynamics of the graphene/aqueous electrolyte interface by utilizing a multiscale quantum mechanics – classical molecular dynamics (QM/MD) approach to provide insights into the effect of alkali metal ion (Li+) concentration on the interfacial tension (γSL) of the charged graphene/electrolyte interface. We demonstrate that the dependence of γSL on the applied surface charge exhibits an asymmetric behaviour relative to the neutral surface. At the positively charged graphene sheet, the electrowetting response is amplified by electrolyte concentration, resulting in a strongly hydrophilic surface. On the contrary, at negative potential bias, γSL shows a weaker response to the charging of the electrode. Changes in γSL greatly affect the total areal capacitance predicted by the Young-Lippmann equation but have negligible impact on the simulated total areal capacitance indicating that the EDL structure is not directly correlated with the wettability of the surface and different interfacial mechanisms drive the two phenomena. The proposed model is validated experimentally by studying the electrowetting response of highly oriented pyrolytic graphite over a wide range of electrolyte concentrations. Our work presents the first combined theoretical and experimental study on electrowetting using carbon surfaces, introducing new conceptual routes for the investigation of wetting phenomena under potential bias. | Zixuan Wei; Joshua Elliott; Athanasios Papaderakis; Robert Dryfe; Paola Carbone | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Computing | CC BY 4.0 | CHEMRXIV | 2023-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656c8ccb5bc9fcb5c9f2d2e4/original/relation-between-double-layer-structure-capacitance-and-surface-tension-in-electrowetting-of-graphene-and-aqueous-electrolytes.pdf |
60c754b4f96a0037e32886c4 | 10.26434/chemrxiv.13424117.v2 | The Stabilizing Effect of Pre-Equilibria: A Trifluoromethyl Complex as CF2 Reservoir in Catalytic Olefin Difluorocarbenation | A new, efficient, catalytic
difluorocarbenation of olefins to give 1,1-difluorocyclopropanes is presented.
The catalyst, an organobismuth complex, uses TMSCF<sub>3</sub> as a stoichiometric
difluorocarbene source. We demonstrate both the viability and robustness of this
reaction over a wide range of alkenes and alkynes, including electron-poor alkenes,
to generate the corresponding 1,1-difluorocyclopropanes and
1,1-difluorocyclopropenes. Ease of catalyst recovery from the reaction mixture
is another attractive feature of this method. In depth experimental and
theoretical studies showed that the key difluorocarbene-generating step
proceeds through a bismuth non-redox synchronous mechanism generating a highly
reactive free CF<sub>2</sub> in an endergonic pre-equilibrium. It is the reversibility
when generating the difluorocarbene that accounts for the high selectivity,
while minimizing CF<sub>2</sub>-recombination side-reactions. | Thomas Louis-Goff; Huu Vinh Trinh; Eileen Chen; Arnold L. Rheingold; Christian Ehm; Jakub Hyvl | Organic Synthesis and Reactions; Homogeneous Catalysis; Catalysis; Main Group Chemistry (Organomet.); Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754b4f96a0037e32886c4/original/the-stabilizing-effect-of-pre-equilibria-a-trifluoromethyl-complex-as-cf2-reservoir-in-catalytic-olefin-difluorocarbenation.pdf |
645cc013f2112b41e95ec92f | 10.26434/chemrxiv-2023-lrw82 | Nature-inspired Depolymerization of Soda Lignin by Light-induced Free Radical Promoted Cleavage Using Organic Photocatalyst | The development of sustainable valorization methods for lignin is a challenging task, because the vast majority of the reported methods require either harsh conditions or the use of expensive transition metal catalysts. Inspired from the natural-sunlight degradation of lignin, known as lignin yellowing, we report here the use of a commercially available cheap organic photocatalyst, namely, phenacyl bromide (PAB), for the efficient cleavage of lignin model compound 2-phenoxyacetophenone (2-PAP), and the depolymerization of soda pulped lignin (SL) under UV-A irradiation under ambient conditions. Real-time NMR investigations of the photoreaction between the model compound and PAB shed light on the possible reaction mechanisms involving different radical species, HBr, and molecular oxygen. Interestingly, combined spectral, chromatographic, powder X-ray diffraction and thermal studies of the photocatalytic reaction between PAB and SL indicated the formation of guaiacyl alcohol. The unprecedented catalytic performance of such a simple organic photocatalyst is attributed to the generation of phenacyl radicals, photolabile brominated species and HBr playing key roles in the cleavage of β-O-4 linkages. This study represents a new edge for lignin valorization under mild reaction conditions and offers the opportunity for large-scale environment-neutral production of valuable aromatics using technical lignins as feedstock. | Kerem Kaya; Armagan Atsay; Hande Gunduz; Adam Slabon; Yusuf Yagci | Catalysis; Energy; Earth, Space, and Environmental Chemistry; Wastes; Organocatalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2023-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645cc013f2112b41e95ec92f/original/nature-inspired-depolymerization-of-soda-lignin-by-light-induced-free-radical-promoted-cleavage-using-organic-photocatalyst.pdf |
66bfc83020ac769e5fd8a747 | 10.26434/chemrxiv-2024-fh8j5 | Fluorogenic Coumarins Activated via Bioorthogonal Reaction | Fluorogenic bioorthogonal reagents enable facile detection in complex environments. While useful for real-time imaging, few such probes are available. Existing tools also exploit similar mechanisms for signal turn-on, precluding multiplexed applications. To address these gaps, we developed a palette of cyclopropenone (CpO) scaffolds that are activated by bioorthogonal phosphines to provide coumarins. The top CpO-phosphine pairs show strong fluorescent enhancements (up to 760-fold) and high quantum yields, and are stable in aqueous environments. The CpO fluorogens also exhibit unique reaction profiles, setting the stage for multi-component labeling studies. | Jennifer Prescher; Halley Lin-Jones; Sharon Chen; Yeonseong Seo; Kelly Pham | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bfc83020ac769e5fd8a747/original/fluorogenic-coumarins-activated-via-bioorthogonal-reaction.pdf |
61550e79b19c7e361ce46c90 | 10.26434/chemrxiv-2021-x5mkp | Mechanism and Origin of Remote Stereocontrol in the Organocatalytic C(sp2)-H Alkylation using Nitroalkanes as Alkylating Agents | ABSTRACT: Experimental 13C kinetic isotope effects (KIEs) and DFT calculations are used to evaluate the mecha-nism and the origin of enantioselectivity in the C(sp2)‒H alkylative desymmetrization of cyclopentene-1,3-diones using nitroalkanes as the alkylating agent. An unusual combination of an inverse (~0.980) and a normal (~1.030) KIE is observed on the bond-forming carbon atoms of the cyclopentene-1,3-dione and nitroalkane, respectively. These data provide strong support for a mechanism involving reversible carbon-carbon bond-formation followed by rate- and enantioselectivity-determining nitro-group elimination. The theoretical free energy profile and predicted KIEs indicate that this elimination event occurs via an E1cB pathway. The origin of remote stereocontrol is evaluated by distortion-interaction and SAPT0 analyses of the enantiomeric E1cB transition states. | Sharath Chandra Mallojjala; Rahul Sakar; Rachael W. Karugu; Madhu Sudan Manna; Santanu Mukherjee; Jennifer S. Hirschi | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Physical Organic Chemistry; Organocatalysis | CC BY NC 4.0 | CHEMRXIV | 2021-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61550e79b19c7e361ce46c90/original/mechanism-and-origin-of-remote-stereocontrol-in-the-organocatalytic-c-sp2-h-alkylation-using-nitroalkanes-as-alkylating-agents.pdf |
6361c8a855a081728fce7526 | 10.26434/chemrxiv-2022-23tgm | Customizable metal-phenolic supraparticles based on rationally designed building blocks | Metal-phenolic networks (MPNs) as a versatile platform for particle engineering have been well developed due to their integrated benefits of both metal ions and phenolic molecules. However, the approaches to broaden their applications are limited due to the single-driving force from the coordination of these two components. Herein, we developed a universal approach to introducing programmable assembles into MPNs to form metal-phenolic supraparticles based on the rationally designed phenolic building blocks. These as-prepared building blocks can first assemble into primary nanoparticles driven by various controllable intermolecular interactions (i.e., metal-organic coordination, host-guest interaction, and hydrophobic interaction), followed by particle assembly with metal ions to coat on different templates. The introduction of multiple assembly modalities into phenolic building blocks enriches the functionalities of these metal-phenolic supraparticles, such as dual-pH responsibility, light-controllable permeability, and rapid fluorescence labeling of living cells. Our work provides a conceptual and practical paradigm for customizing MPNs with hierarchical structures by importing various assembly strategies via rationally designed phenolic building blocks. | Yajing Zhang; Jin Wang; Yunxiang He; Jiezhou Pan; Xue Liao; Xin Jin; Jiaojiao Shang; Guidong Gong; Joseph J Richardson; Junling Guo | Materials Science; Nanoscience; Aggregates and Assemblies; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6361c8a855a081728fce7526/original/customizable-metal-phenolic-supraparticles-based-on-rationally-designed-building-blocks.pdf |
66b3afe501103d79c51448ba | 10.26434/chemrxiv-2024-mzq5g | Internal reference for determining orientation of alignment in liquid crystal cells by confocal polarised Raman microscopy | The phase adopted by liquid crystals, in applications such as displays, is controlled by alignment layers. Typically this phase originates from a layer of unidirectionally rubbed polymer on a solid support. The extent to which the alignment layer orders the liquid crystal can be determined by the transmission of polarised light, however this quantifies the net effect of the alignment over the entire depth of the LC layer. The polarisation dependence of the
Raman scattering of liquid crystal molecules, e.g., 5CB, can allow for molecular anisotropic ordering (alignment) at the interface to be characterised directly by polarised Raman microspectroscopy. However, the optical properties of the oriented LC phases and ITO on glass electrodes impacts the depth resolution achievable. Here we introduce a resonance
Raman active component, [Fe(bpy)3](BArF)2, into a PMMA alignment layer as an isotropic reference for Raman scattering. The Raman scattering from this complex is insensitive to the directing of polarisation of the excitation laser and enables estimation of the confocal depth probed in complete liquid crystal cells. The Raman scattering of [Fe(bpy)3](BArF)2 in the PMMA allows for changes in LC orientation near the interface to be followed and compared with changes to the orientation of molecules in the bulk of the liquid crystal. This approach provides spatial resolution (depth) when studying the realignment of LC molecules by electric fields and enables the balance in orientational control by the alignment layer and the electric field to be assessed. | Ruben Feringa; J. M. Bas Klement; Jasmine Sears; Pieter J. van der Zaag; Wesley R. Browne | Physical Chemistry; Interfaces; Spectroscopy (Physical Chem.); Surface; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b3afe501103d79c51448ba/original/internal-reference-for-determining-orientation-of-alignment-in-liquid-crystal-cells-by-confocal-polarised-raman-microscopy.pdf |
60c74a67702a9b62be18b281 | 10.26434/chemrxiv.12197886.v1 | Reduced Density Matrix Cumulants: The Combinatorics of Size-Consistency and Generalized Normal Ordering | Reduced density matrix cumulants play key roles in the theory of both reduced density matrices and multiconfigurational normal ordering, but the underlying formalism has remained mysterious. We present a new, simpler generating function for reduced density matrix cumulants that is formally identical to equating the coupled cluster and configuration interaction ansätze. This is shown to be a general mechanism to convert between a multiplicatively separable quantity and an additively separable quantity, as defined by a set of axioms. It is shown that both the cumulants of probability theory and reduced density matrices are entirely combinatorial constructions, where the differences can be associated to changes in the notion of "multiplicative separability'' for expectation values of random variables compared to reduced density matrices. We compare our generating function to that of previous works and criticize previous claims of probabilistic significance of the reduced density matrix cumulants. Finally, we present the simplest proof to date of the Generalized Normal Ordering formalism to explore the role of reduced density matrix cumulants therein. | Jonathon Misiewicz; Justin Turney; Henry Schaefer | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a67702a9b62be18b281/original/reduced-density-matrix-cumulants-the-combinatorics-of-size-consistency-and-generalized-normal-ordering.pdf |
642050a491074bccd04fa1b6 | 10.26434/chemrxiv-2023-8xmhm | A guideline to mitigate interfacial degradation processes in solid-state batteries caused by cross diffusion | Interdiffusion of transition metals across the cathode-electrolyte interface is identified as a key challenge for the practical realization of solid-state batteries. This is related to the formation of highly resistive interphases impeding the charge transport across the materials thus limiting the battery performance. Herein, we investigate the hypothesis that formation of interphases is associated with the incorporation of Co into the LLZO lattice representing the starting point of a cascade of degradation processes. It is shown that Co incorporates into the garnet structure preferably four-fold coordinated as Co2+ or Co3+ depending on oxygen fugacity. The solubility limit of Co is determined to be around 0.16 pfu, whereby concentrations beyond this limit causes a cubic-to-tetragonal phase transition. Moreover, the temperature-dependent Co diffusion coefficient is determined, e.g., D700 °C = 9.46 × 10-14 cm2/s and an activation energy Ea = 1.65 eV, suggesting that detrimental cross diffusion will take place at any relevant process condition. Additionally, the optimal protective Al2O3 coating thickness for relevant temperatures is studied, which allows to create a process diagram to mitigate any degradation with a minimum compromise on electrochemical performance. This study provides a tool to optimize processing conditions toward developing high energy density solid-state batteries. | Mir Mehraj Ud Din; Lukas Ladenstein; Joseph Ring; Daniel Knez; Stefan Smetaczek; Markus Kubicek; Mohsen Sadeqi-Moqadam; Steffen Ganschow; Elena Salagre; Enrique Garcia Michel; Stefanie Lode; Gerald Kothleitner; Iulian Dugulan; Jeffrey Smith; Andreas Limbeck; Jürgen Fleig; Donald Siegel; Günther Redhammer; Daniel Rettenwander | Materials Science; Inorganic Chemistry; Energy; Materials Processing; Electrochemistry; Energy Storage | CC BY 4.0 | CHEMRXIV | 2023-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642050a491074bccd04fa1b6/original/a-guideline-to-mitigate-interfacial-degradation-processes-in-solid-state-batteries-caused-by-cross-diffusion.pdf |
61e4c7bc7110e630c766d90e | 10.26434/chemrxiv-2022-sgxr4 | Are Vanadium Intermediates Suitable Mimics in Non-Heme Iron Enzymes? An Electronic Structure Analysis | Vanadyl intermediates are frequently used as mimics for the fleeting Fe(IV)=O intermediate in non-heme iron enzymes that catalyze C–H activation. Using density functional theory and correlated wavefunction theory, we investigate the degree to which vanadium mimic electronic structure is comparable to catalytic iron intermediates. Our calculations reveal crucial structural and energetic differences between vanadyl and ferryl intermediates primarily due to differences in ground spin states of low spin and high spin, respectively. This difference in spin state leads to differences in energetics for accessing isomers that confer activity in non-heme hydroxylase and halogenase enzymes. While interconversion between monodentate and bidentate succinate isomers of the key metal-oxo/hydroxo intermediates is energetically favorable for Fe, it is strongly unfavorable in V mimics. Additionally, isomerization of a terminal metal-oxo between an axial and equatorial position is energetically unfavorable for Fe but favorable for V. Electronic structure analyses to quantify differences in binding strength of Fe and V intermediates to –ketoglutarate and succinate cosubstrates reveal that both cosubstrates bind more strongly to V than Fe. Our work highlights the limits of using low- or intermediate-spin V-based intermediates as mimics in studies of fleeting high-spin Fe intermediates in non-heme iron enzymes. | Vyshnavi Vennelakanti; Rimsha Mehmood; Heather Kulik | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biochemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2022-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e4c7bc7110e630c766d90e/original/are-vanadium-intermediates-suitable-mimics-in-non-heme-iron-enzymes-an-electronic-structure-analysis.pdf |
64b6376eb053dad33a7209e6 | 10.26434/chemrxiv-2023-xdwlb | Description of solvatochromism of peak broadening in absorption spectra in solution using the reference interaction site model self-consistent fields spatial electron density distribution | We quantified and subsequently analyzed bandwidth of ultraviolet and visible photoabsorption spectral lines in solution by applying time-dependent first-order perturbation theory using the Born-Oppenheimer adiabatic potential calculated using the multi-state extended-multiconfigurational quasidegenerated second-order perturbation theory (MS-XMCQDPT2) coupled with the reference interaction site model self-consistent field spatial electron density distribution (RISM-SCF-cSED). The proposed method was implemented for 2-thiocytosine in solution, and solvatochromism of the bandwidth of the πSπ∗ transition was clearly observed. The standard deviation of a characteristic electronic excitation was decomposed into the contributions of the characteristic vibrational mode of 2-thiocytosine. The main vibrational modes 1 contributing to peak broadening were found to be for acetonitrile, methanol, and the aqueous phase. We concluded that the mechanism for peak broadening is qualitatively different for phases of protic and aprotic solvents because of the structural variation in 2-thiocytosine driven by breakage of the resonance structures. | Naoki Negishi; Daisuke Yokogawa | Theoretical and Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b6376eb053dad33a7209e6/original/description-of-solvatochromism-of-peak-broadening-in-absorption-spectra-in-solution-using-the-reference-interaction-site-model-self-consistent-fields-spatial-electron-density-distribution.pdf |
6224e47a91a2e6792ee70adb | 10.26434/chemrxiv-2022-gj54j | Quantum effects in photosensitization: The case of singlet oxygen generation by thiothymines | Photosensitization is the indirect electronic excitation of a molecule with the aid of a photosensitizer and is a bimolecular nonradiative energy transfer. In this study, we have attempted to elucidate its mechanism, and we do this by calculating rate constants of photosensitization of oxygen by thiothymines (2-thiothymine, 4-thiothymine and 2,4 dithiothymine). The rate constants have been calculated using two approaches: (a) a classical limit of Fermi's Golden Rule (FGR), and (b) a time-dependent variant of FGR, where the treatment is purely quantum mechanical. The former approach has previously been developed for bimolecular systems and has been applied to the photosensitization reactions studied here. The latter approach, however, has so far only been used for unimolecular reactions, and in this work, we describe how it can be adapted for bimolecular reactions. Experimentally, all three thiothymines are known to have significant singlet oxygen yields, which are indicative of similar rates. Rate constants calculated using the time-dependent variant of FGR are comparable across all three thiothymines and with experiment. While the classical approximation gives reasonable rate constants for 2-thiothymine, it severely underestimates them for 4-thiothymine and 2,4 dithiothymine, by several orders of magnitude. This work indicates the importance of quantum effects in driving photosensitization. | Meghna Manae; Anirban Hazra | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2022-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6224e47a91a2e6792ee70adb/original/quantum-effects-in-photosensitization-the-case-of-singlet-oxygen-generation-by-thiothymines.pdf |
614b2e4518be851f2c2c2699 | 10.26434/chemrxiv-2021-0pq98 | Chemoinformatic Characterization of Synthetic Screening Libraries Focused on Epigenetic Targets | The importance of epigenetic drug and probe discovery is on the rise. This is not only paramount to identify and develop therapeutic treatments associated with epigenetic processes but also to understand the underlying epigenetic mechanisms involved in biological processes. To this end, chemical vendors have been developing synthetic compound libraries focused on epigenetic targets to increase the probabilities of identifying promising starting points for drug or probe candidates. However, the chemical contents of these data sets, the distribution of their physicochemical properties, and diversity remain unknown. To fill this gap and make this information available to the scientific community, we report a comprehensive analysis of eleven libraries focused on epigenetic targets containing more than 50,000 compounds. We used well-validated chemoinformatics approaches to characterize these sets, including novel methods such as automated detection of analog series and visual representations of the chemical space based on Constellation Plots and Extended Chemical Space Networks. This work will guide the efforts of experimental groups working on high-throughput and medium-throughput screening of epigenetic-focused libraries. The outcome of this work can also be used as a reference to design and describe novel focused epigenetic libraries. | E. Alexis Flores-Padilla; K. Eurídice Juárez-Mercado; José J. Naveja; Taewon D. Kim; Ramón Alain Miranda-Quintana; José L. Medina-Franco | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2021-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614b2e4518be851f2c2c2699/original/chemoinformatic-characterization-of-synthetic-screening-libraries-focused-on-epigenetic-targets.pdf |
60c751d74c89196c78ad4028 | 10.26434/chemrxiv.13216196.v1 | Redesigned Silk: A New Macroporous Biomaterial Platform for Antimicrobial Dermal Patches with Unique Exudate Wicking Ability | Silk is one of the most important materials in the history of medical practice. Owing to its excellent
strength, biocompatibility and degradability, silk from Bombyx mori – which is structured as a
concentric assembly of silk fibroin (SF) coated by a sheath of sericin (SS) – has long been used
for wound treatment. Here, we recapitulate for the first time the topology of native silk fibers using
a radically new materials design-oriented approach to achieve unprecedented porous dermal
patches suitable for controlled drug delivery. The method implies four steps: (1) removing SS; (2)
creating anisotropic macroporosity in SF via ice templating; (3) stabilizing the SF foam with a
methanolic solution of Rifamycin (Rif) antibiotic; and (4) coating Rif-loaded redesigned SF foams
with a SS sheath. The core-shell SS@SF foams exhibit water wicking properties accommodate up
to ~20% lateral deformation. Moreover, monitoring of antibacterial activity against
Staphylococcus aureus revealed that the SS@SF foams’ Rif release extended up to 9 days. We
anticipate that reverse-engineering of silk foams opens exciting new avenues towards the
fabrication of advanced drug eluting silk-based biomaterial platforms with improved performance.
The present approach can be generalizable to re-build multicomponent biological materials with
tunable porosity.<br /> | Kankan Qin; Rui F.P. Pereira; Thibaud Coradin; Verónica de Zea Bermudez; Francisco Fernandes | Biocompatible Materials; Biological Materials; Biopolymers | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751d74c89196c78ad4028/original/redesigned-silk-a-new-macroporous-biomaterial-platform-for-antimicrobial-dermal-patches-with-unique-exudate-wicking-ability.pdf |
6386a0730949e18c2f5b1b75 | 10.26434/chemrxiv-2022-kxcg8-v2 | Divergent Mechanistic Pathways for Copper(I) Hydrophosphination Catalysis: Understanding that Allows for Diastereoselective Hydrophosphination of a Tri-substituted Styrene | Readily available and bench-stable Cu(acac)2 (1) addresses many challenges in exploratory hydrophosphination catalysis. Mechanistic investigations were performed to answer questions that remain about the reactivity of 1, the role of light in the catalysis, and to provide direction for further study. A divergent Hammett plot indicates differing mechanisms based on electron density at the alkene substrate. A radical process was eliminated based on trapping reactions and in-situ EPR experiments. Isotopic labeling experiments, a zwitterionic trapping experiment, stoichiometric model reactions, and catalytic reactions using proxy intermediates indicate that both conjugate addition and insertion-based mechanistic pathways occur with this system, depending on the unsaturated substrate. Computational analysis indicates that the lowest energy transition is a ligand-to-metal charge transfer (LMCT) from the phosphido ligand where the LUMO has significant Cu–P antibonding character, suggesting that a weakened Cu–P bond accelerates insertion under photocatalytic conditions. This hypothesis explains the greater activity of 1 compared to copper-catalyzed hydrophosphination reports and appears to be a general phenomenon for copper(I) catalysts. These results have been leveraged to achieve heretofore unknown catalytic hydrophosphination reactivity, namely the diastereoselective hydrophosphination of a tri-substituted styrene substrate. | Steven Dannenberg; Dennis Seth; Emma Finfer; Rory Waterman | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Main Group Chemistry (Inorg.); Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6386a0730949e18c2f5b1b75/original/divergent-mechanistic-pathways-for-copper-i-hydrophosphination-catalysis-understanding-that-allows-for-diastereoselective-hydrophosphination-of-a-tri-substituted-styrene.pdf |
63e5d86f9da0bc6b33a974ea | 10.26434/chemrxiv-2023-q24pc | Oxidation of Thiols with IBX or DMP: One-pot Access to Thiosulfonates or 2-Iodobenzoates and Applications in Functional Group Transformations | Thiosulfonates are accessed by oxidation of feed-stock thiols using either DMP in DCM or IBX in MeCN at rt (~30 degree C). The protocol gives access to a variety of thiosulfonates in good to excellent yields from both aromatic and aliphatic thiols. The reaction with DMP is found to be better than IBX in terms of reaction rate and conversion, whereas the oxidation with DMP requires lower equivalent than IBX. Benzyl thiols are however found to follow a different reaction pathway when treated with DMP; O-benzyl esters of o-iodobenzoates were isolated. The 1H NMR spectroscopic monitoring studies for the IBX-mediated oxidation of thiol found disulfide as an initial intermediate, which is proposed to undergoes a cascade of oxidations to produce thiosulfonate | Ajeet Chandra; Navin R. Yadav; Soumen Payra; Keshaba N. Parida | Organic Chemistry; Chemical Education; Agriculture and Food Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Process Chemistry | CC BY 4.0 | CHEMRXIV | 2023-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e5d86f9da0bc6b33a974ea/original/oxidation-of-thiols-with-ibx-or-dmp-one-pot-access-to-thiosulfonates-or-2-iodobenzoates-and-applications-in-functional-group-transformations.pdf |
60c750c20f50db4186397607 | 10.26434/chemrxiv.13073231.v1 | Masked Alkyne Equivalents for the Synthesis of Mechanically Interlocked Polyynes | Polyyne polyrotaxanes, encapsulated cyclocarbon
catenanes and other fascinating mechanically interlocked carbonrich architectures should become accessible if masked alkyne
equivalents (MAEs) can be developed that are large enough to
prevent unthreading of a macrocycle, and that can be cleanly
unmasked under mild conditions. Here we report the synthesis of a
new bulky MAE based on a t-butylbicyclo[4.3.1]decatriene. This
MAE was used to synthesize a polyyne [2]rotaxane and a maskedpolyyne [3]rotaxane by Cadiot-Chodkiewicz coupling. Glaser cyclooligomerization of the [2]rotaxane gave masked cyclocarbon
catenanes. The unmasking behavior of the catenanes and rotaxanes
was tested by photolysis at a range of UV wavelengths.
Photochemical unmasking did not proceed cleanly enough to
prepare extended encapsulated polyyne polyrotaxanes. We highlight
the scope and challenges involved with this approach to interlocked
carbon-rich architectures. | Przemyslaw Gawel; Steffen Woltering; Yaoyao Xiong; Kirsten Christensen; Harry Anderson | Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750c20f50db4186397607/original/masked-alkyne-equivalents-for-the-synthesis-of-mechanically-interlocked-polyynes.pdf |
66a8c11bc9c6a5c07a7a59c0 | 10.26434/chemrxiv-2024-w953h-v2 | A multi-agent-driven robotic AI chemist enabling autonomous chemical research on demand | The successful integration of large language models (LLMs) into laboratory workflows has demonstrated robust capabilities in natural language processing, autonomous task execution, and collaborative problem-solving. This offers an exciting opportunity to realize the dream of autonomous chemical research on demand. Here, we report a robotic AI chemist powered by a hierarchical multi-agent system, ChemAgents, based on an on-board Llama-3-70B LLM, capable of executing complex, multi-step experiments with minimal human intervention. It operates through a Task Manager agent that interacts with human researchers and coordinates four role-specific agents—Literature Reader, Experiment Designer, Computation Performer, and Robot Operator—each leveraging one of four foundational resources: a comprehensive Literature Database, an extensive Protocol Library, a versatile Model Library, and a state-of-the-art Automated Lab. We demonstrate its versatility and efficacy through six experimental tasks of varying complexity, ranging from straightforward synthesis and characterization to more complex exploration and screening of experimental parameters, culminating in the discovery and optimization of functional materials. Our multi-agent-driven robotic AI chemist showcases the potential of on-demand autonomous chemical research to drive unprecedented efficiencies, accelerate discovery, and democratize access to advanced experimental capabilities across academic disciplines and industries. | Tao Song; Man Luo; Linjiang Chen; Yan Huang; Qing Zhu; Daobin Liu; Baicheng Zhang; Gang Zou; Fei Zhang; Weiwei Shang; Jun Jiang; Yi Luo | Theoretical and Computational Chemistry; Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a8c11bc9c6a5c07a7a59c0/original/a-multi-agent-driven-robotic-ai-chemist-enabling-autonomous-chemical-research-on-demand.pdf |
60c741a50f50db0e57395b5b | 10.26434/chemrxiv.8072378.v1 | Membrane Disruption by Very Long Chain Fatty Acids During Necroptosis | In this work we investigate the mechanisms by which very long chain fatty acids (VLCFA) contribute to membrane permeabilization during necroptosis, a form of highly regulated necrotic cell death. We show that inactivating fatty acid elongase ELOVL7 prevents VLCFA accumulation and necroptotic cell death, while it's overexpression causes membrane permeabilization. We show that VLCFA can directly permeabilize lipid bilayers and investigate the basis of these effects by molecular dynamics simulations. Finally, we show that VLCFA can be used as substrates for protein fatty acylation during necroptosis, suggesting another potential mechanism by which VLCFA may mediate membrane permeabilization. | Laura Parisi; Shahin Sowlati-Hashjin; Ilyas Berhane; Kevin Carter; Jonathan Lovell; Sherry Chemler; Mikko Karttunen; G. Ekin Atilla-Gokcumen | Cell and Molecular Biology; Chemical Biology; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a50f50db0e57395b5b/original/membrane-disruption-by-very-long-chain-fatty-acids-during-necroptosis.pdf |
60c753f14c89192508ad43d8 | 10.26434/chemrxiv.13580348.v1 | The Structural Changes in the Signaling Mechanism of Bacteriophytochromes in Solution Revealed by a Multiscale Computational Investigation | <pre>Phytochromes are red-light sensing proteins, with important light-regulatory roles in different organisms, which are capturing an increasing interest in bioimaging and optogenetics. Upon absorption of light by the embedded bilin chromophore, they undergo structural changes that extend from the chomophore to the protein and finally drive the biological function. Up to now, the underlying mechanism still has to be characterized fully. </pre>
<pre>Here we investigate the Pfr activated form of a bacterial phytochrome, by combining extensive Molecular Dynamics simulations with a polarizable QM/MM description of the spectroscopic properties, revealing a large structure relaxation in solution, compared to the crystal structure, both in the chromophore-binding pocket and in the overall structure of the phytochrome. Our results indicate that the final opening of the dimeric structure is preceded by an important internal reorganization of the phytochrome specific (PHY) domain involving a bend of the helical spine connecting the PHY domain with the chromophore-binding domain, opening the way to a new understanding of the activation pathway. </pre> | Veronica Macaluso; Giacomo Salvadori; Lorenzo Cupellini; Benedetta Mennucci | Computational Chemistry and Modeling; Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753f14c89192508ad43d8/original/the-structural-changes-in-the-signaling-mechanism-of-bacteriophytochromes-in-solution-revealed-by-a-multiscale-computational-investigation.pdf |
60c7554ebb8c1a0b183dc397 | 10.26434/chemrxiv.14068763.v1 | On-Demand Transformation of Carbon Dioxide into Polymers Enabled by Comb Shaped Metallic Oligomer Catalyst | Quantitative transformation of CO2 can greatly elevate the sustainability impact of CO2 chemical utilization, but it is formidably challenging due to the sluggish kinetics requiring overwhelmingly excess usage of CO2. Here, we report an on demand CO2 transformation by a switch polymerization method, that is, all reactants including CO2 are fully converted without any by-product, generating tailor-made poly(ether carbonate) polyols (CO2-polyols) whose composition and chain length exactly correspond to the feed of CO2, epoxide and diacid. This is the first time for CO2 as a countable monomer which is in most cases obscurely considered as “pressure condition”. Studies on the kinetics rate law and the activation parameters of key intermediates disclose that it is the multisite cooperativity from metallic oligomer catalyst that facilitates quantitative insertion of CO2 into polymer backbone without adverse backbiting throughout the polymerization. Hence, this work not only introduces the conception of quantitative CO2 transformation, but engineers exquisite CO2-based polymer which is rarely achieved.<br /> | Han Cao; Ruoyu Zhang; zhou zhou; Shunjie Liu; Youhua Tao; Fosong Wang; Xianhong Wang | Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7554ebb8c1a0b183dc397/original/on-demand-transformation-of-carbon-dioxide-into-polymers-enabled-by-comb-shaped-metallic-oligomer-catalyst.pdf |
66a0f52cc9c6a5c07ac34ca1 | 10.26434/chemrxiv-2024-mf7t6 | High Throughput Approaches to Engineer Fluorescent Nanosensors | Optical sensors/probes are powerful tools to identify and image (biological) molecules. Because of their optoelectronic properties, nanomaterials are often used as building blocks. Such nanosensors are assembled from an optically sensitive nanomaterial, a (biological) recognition unit, and linker chemistry that connects them. To transduce the chemical interaction with the analyte into an optical signal, the interplay between surface chemistry and nanomaterial photophysics has to be optimized. Understanding these aspects promises major opportunities for tailored sensors with optimal performance. However, this requires methods to create and explore the wide range of possible chemical permutations. Indeed, many current approaches are limited in throughput. This affects the chemical design space that can be studied, the application of machine learning approaches as well as fundamental mechanistic understanding. Here, we provide an overview of selection-limited and synthesis-limited approaches to create and identify molecular nanosensors. We discuss bottlenecks and highlight opportunities of non-classical recognition strategies such as corona phase molecular recognition as well as the requirements for high throughput and scalability. Fluorescent carbon nanotubes are powerful building blocks for sensors and their huge chemical design space makes them an ideal platform for high throughput approaches. Therefore, they are the focus of this article, but the insights are transferable to any nanosensor system. Overall, this perspective aims to provide a fresh perspective to overcome current challenges in the nanosensor field. | Justus T. Metternich; Sujit K. Patjoshi; Tanuja Kistwal; Sebastian Kruss | Biological and Medicinal Chemistry; Materials Science; Analytical Chemistry; Optical Materials; Biochemical Analysis; High-throughput Screening | CC BY 4.0 | CHEMRXIV | 2024-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a0f52cc9c6a5c07ac34ca1/original/high-throughput-approaches-to-engineer-fluorescent-nanosensors.pdf |
67bf080bfa469535b9057879 | 10.26434/chemrxiv-2025-kxk6r | X-ray Absorption Spectroscopy Probing of Gold Electrooxidation Reveals Intermediate Surficial Au(I) | While Au electrooxidation in acidic aqueous media on a phenomenological level proceeds directly from Au(0) to Au(III), it has previously been suggested that Au(I) states are intermediate species of the oxidation mechanism. Here we add to the evidence for the transient Au(I) by probing Au oxidation operando in a pH=3 HClO4 electrolyte by high energy resolution fluorescence detected X-ray absorption near-edge structure (HERFD-XANES) at potentials up to 1.8 V vs the reversible hydrogen electrode. The perchlorate ions in the electrolyte are used as sacrificial oxidizing agents. The reduced perchlorate compounds in turn produces chlorine ions which reacts with Au ions to form chlorinated Au-Cl compounds. The operando HERFD-XANES detects the chlorinated compounds yielding separate peaks based on the oxidation state of Au. Through this methodology, we observe the formation of Au(I) during the early stages of Au oxidation, and we further infer that Au(I) is accessed by the electrolyte These observations are consistent with the previously hypothesized route for Au electrooxidation involving charge transfer after a dipole induced place-exchange step. | David Degerman; Sara Boscolo Bibi; Bernadette Davies; Vladimir Grigorev; Aleksandr Kalinko; Tony Hansson; Sergey Koroidov | Physical Chemistry; Catalysis; Electrocatalysis; Heterogeneous Catalysis; Interfaces; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bf080bfa469535b9057879/original/x-ray-absorption-spectroscopy-probing-of-gold-electrooxidation-reveals-intermediate-surficial-au-i.pdf |
63f9bf6f937392db3d0869b3 | 10.26434/chemrxiv-2023-p693m | Direct Synthesis of Eco-friendly Construction Material from Low-quality Sand via Sol-gel Method | A strong, eco-friendly construction material was synthesised directly from low-quality sand via the sol-gel method with ethanol as the solvent. Appropriate KOH content and ethanol concentration further promoted the compressive strength (> 25 MPa). The high strength was attributed to microcline and tetraethoxysilane formation. The carbon emission of the sand-based material in the construction phase was 4281% of those of concrete from four types of buildings based on lifecycle cost analysis. Therefore, a green and tough construction material was synthesised, which can partially substitute concrete, thus addressing the problem of insufficient concrete raw materials and high CO2 emissions. | Pengcheng Qiu; Yuya Sakai; Naoki Ogiwara; Sayaka Uchida; Yuki Tamura | Materials Science; Aggregates and Assemblies; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f9bf6f937392db3d0869b3/original/direct-synthesis-of-eco-friendly-construction-material-from-low-quality-sand-via-sol-gel-method.pdf |
60c74603567dfed780ec4556 | 10.26434/chemrxiv.10317578.v1 | First-Principles Study of the Electrochemical Sodiation of Rutile-Type Vanadium Dioxide | <p>We
investigate, from first principles, the electrochemical sodiation mechanism of
rutile-type vanadium dioxide as a possible electrode material for sodium-ion
batteries. The computed voltages are small in comparison to current
state-of-the-art sodium-ion battery cathodes, which we can relate to the large
space demand of sodium ions in the compact rutile structure and the resulting
severe lattice deformations compared to other working metals. Due to the same
reason large anisotropic unit cell volume changes are predicted during cycling.
We furthermore find a change of the preferred reaction mechanism during
discharge, with a switching between insertion- and conversion-type reaction at
higher degrees of sodiation. The predicted capacities on the other hand are
appreciable, making a further consideration of this material as anode in
combination with sodium working metal interesting.</p> | Daniel Koch; Sergei Manzhos | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74603567dfed780ec4556/original/first-principles-study-of-the-electrochemical-sodiation-of-rutile-type-vanadium-dioxide.pdf |
658933d9e9ebbb4db9b34df3 | 10.26434/chemrxiv-2023-8s8zw | Enabling Uniform and Accurate Control of Cycling Pressure for All-Solid-State Batteries | All-solid-state batteries are emerging as potential successors in energy storage technologies due to their increased safety, stemming from replacing organic liquid electrolytes in conventional Li-ion batteries with less flammable solid-state electrolytes. However, All-solid-state batteries require precise control over cycling pressure to maintain effective interfacial contacts between materials. Traditional uniaxial cell holders, often used in battery research, face challenges in accommodating electrode volume changes, providing uniform pressure distribution, and maintaining consistent pressure over time. This study introduces isostatic pouch cell holders utilizing air as pressurizing media to achieve uniform and accurately regulated cycling pressure. LiNi0.8Co0.1Mn0.1O2 | Li6PS5Cl | Si pouch cells were fabricated and tested under 1 to 5 MPa pressures, revealing improved electrochemical performance with higher cycling pressures, with 2 MPa as the minimum for optimal operation. A bilayer pouch cell with a theoretical capacity of 100 mAh, cycled with an isostatic pouch cell holder, demonstrated a first-cycle Coulombic efficiency of 76.9% and a discharge capacity of 173.6 mAh g-1 (88.1 mAh), maintaining 83.6% capacity after 100 cycles. These findings underscore the effectiveness of isostatic pouch cell holders in enhancing the performance and practical application of All-solid-state batteries. | Yu-Ting Chen; Jihyun Jang; Jin An Sam Oh; So-Yeon Ham; Hedi Yang; Dong-Ju Lee; Marta Vicencio; Jeong Beom Lee; Darren H. S. Tan; Mehdi Chouchane; Ashley Cronk; Min-Sang Song; Yijie Yin; Jianting Qian; Zheng Chen; Ying Shirley Meng | Energy | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658933d9e9ebbb4db9b34df3/original/enabling-uniform-and-accurate-control-of-cycling-pressure-for-all-solid-state-batteries.pdf |
65d8c60ae9ebbb4db90f6276 | 10.26434/chemrxiv-2024-hk34t | COMPAS-3: a Data Set of peri-Condensed
Polybenzenoid Hydrocarbons | We introduce the third installment of the COMPAS Project – a COMputational database of Polycyclic Aromatic Systems, focused on peri-condensed polybenzenoid hydrocarbons. In
this installement, we develop two data sets containing the optimized ground-state structures and a selection of molecular properties of ∼39k and ∼9k peri -condensed polybenzenoid hydrocarbons (at the GFN2-xTB and
CAM-B3LYP-D3BJ/cc-pvdz//CAM-B3LYP-D3BJ/def2-SVP levels, respectively). The manuscript details the enumeration and data generation processes and describes the information available within the data sets. An in-depth comparison between the two types of computation is performed, and it is found that the geometric disagreement is maximal for slightly-distorted molecules. In addition, a data-driven analysis of the structure-property trends of peri-condensed PBHs is performed, highlighting the effect of the size of peri-condensed islands and linearly annulated
rings on the HOMO-LUMO gap. The insights described herein are important for rational design of novel functional aromatic molecules for use in, e.g., organic electronics. The generated data sets provide a basis for additional data-
driven machine- and deep-learning studies in chemistry | Alexandra Wahab; Renana Gershoni-Poranne | Theoretical and Computational Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d8c60ae9ebbb4db90f6276/original/compas-3-a-data-set-of-peri-condensed-polybenzenoid-hydrocarbons.pdf |
60c74a31337d6c00b0e27820 | 10.26434/chemrxiv.12156018.v1 | Unraveling Minimum Active Units and Substrate Activation for Carbon Nitride in Photocatalytic Oxidation Reactions | <p>Covalent bonded carbon nitride (CN) has stimulated
extensive attentions from photosynthesis to optoelectronics. However, the
acquisition of correct numbers beyond stoichiometry and composition remains
indefinable. Moreover, the electronic coupling by the substrates to the photoexcitation
processes in value-added oxidation reactions is essential, but still poorly
understood. Herein,
we report by far the minimum active structure
of CN by
constructing fragments consisting of melem (M1) and its
incomplete condensed form with cyanide termination (M2). Surprisingly, such
configuration endowed a boosted activity of 11 times of traditional bulk CN in
photocatalytic oxidation of tetracycline
as a showcase application of water cleaning and sanitation. The mechanism studies
disclosed that M1 and M2 were primarily responsible for light absorption and
charge separation, respectively;<a></a><a> meanwhile the electronic coupling by the O<sub>2</sub>
substrate participated the photoexcited processes thus synergistically enhanced
the photocatalytic reactions.</a></p> | Chaofeng Huang; Yaping Wen; Dandan Dong; Yanfei Shen; Songqin Liu; Haibo Ma; Yuanjian Zhang | Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a31337d6c00b0e27820/original/unraveling-minimum-active-units-and-substrate-activation-for-carbon-nitride-in-photocatalytic-oxidation-reactions.pdf |
636b284cdeff976061dcf376 | 10.26434/chemrxiv-2022-6jkg0-v2 | Invisible Bactericidal Coatings on Generic Surfaces through A Convenient Hand Spray | Robust antimicrobial coatings featuring high transparency, strong bactericidal activity, and easy application procedure on generic surfaces can be widely accepted by the public to prevent pandemics. In this work, we demonstrated the hand sprayer-based approach to deposit complex oxide coatings composed of Co-Mn-Cu-Zn-Ag on screen protectors of smartphones through acidic redox-assisted deposition (ARD). The as-obtained coatings possess high transparency (99.74% transmittance at 550 nm) and long-lasting durability against swiping (for 135 days of average use) or wet cleaning (for 33 days of thrice-a-day routine). The spray coating enabling 3.14% E. coli viability can further be reduced to 0.21% through a consistent elemental composition achieved via the immersion method. The high intake of Cu2+ in the coating is majorly responsible for bactericidal activity, and the presence of Ag+ and Zn2+ is necessary to achieve almost complete eradication. The success of extending the bactericidal coatings on other typical hand-touched surfaces (e.g. stainless steel railings, rubber handrails, and plastic switches) in public areas has been demonstrated. | Joey Andrew A. Valinton; Alfin Kurniawan; Ren-Huai Jhang; Christian R. Pangilinan; Che-Hsin Lee; Chun-Hu Chen | Materials Science; Coating Materials; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636b284cdeff976061dcf376/original/invisible-bactericidal-coatings-on-generic-surfaces-through-a-convenient-hand-spray.pdf |
60c74fc70f50db0104397467 | 10.26434/chemrxiv.9874550.v2 | Exploiting In-Situ NMR to Monitor the Formation of a Metal-Organic Framework | The formation processes of metal-organic frameworks are
becoming more widely researched using in-situ techniques, although there
remains a scarcity of NMR studies in this field. In this work, the synthesis of
framework MFM-500(Ni) has been investigated using an in‑situ NMR strategy that provides information on the time-evolution of the reaction
and crystallization process. In our in‑situ NMR study of MFM-500(Ni)
formation, liquid-phase 1H NMR
data recorded as a function of time at 5 fixed temperatures afford qualitative information on the solution-phase processes and
quantitative information on the kinetics of crystallization, allowing the activation
energies for nucleation and
growth to be determined. Ex-situ SAXS studies provide complementary nanoscale information on the rapid self-assembly
prior to MOF crystallization and in-situ powder X-ray diffraction confirms
that the only crystalline phase present during the reaction is phase-pure
MFM-500(Ni). | Corey Jones; Colan Hughes; Hamish Yeung; Alison Paul; Kenneth D. M. Harris; Timothy Easun | Analytical Chemistry - General; Coordination Chemistry (Inorg.); Solid State Chemistry; Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fc70f50db0104397467/original/exploiting-in-situ-nmr-to-monitor-the-formation-of-a-metal-organic-framework.pdf |
6625baa721291e5d1d56d292 | 10.26434/chemrxiv-2024-6lwb3-v2 | Modifications of the Charge-Discharge Behaviour of Fe2(MoO4)3 in All-Solid-State Lithium-Ion Batteries | The solidification of lithium-ion batteries (LIBs) by replacing liquid electrolytes with solid electrolytes enables the development of new-class LIBs, namely all-solid-state lithium-ion batteries (ASSLIBs), with improved safety and energy density. Such battery solidification can greatly influence the properties of battery components, as exemplified by a recent report suggesting that the (dis)charge behaviour of Fe2(MoO4)3 (FMO), a promising two-phase electrode material, differs on solid electrolytes compared to liquid electrolytes. However, its underlying mechanism remains unclear. Here we examined the (de)lithiation behaviour of FMO thin films on solid electrolytes using operando synchrotron X-ray diffraction (XRD) to gain insights into the influence of the solidification on the (dis)charge mechanism of electrode materials. The XRD results revealed that FMO on solid electrolytes exhibits a monotonic peak shift over a wide capacity range, accompanied by a temporary peak broadening. This suggests that FMO possesses an expanded solid-solution reaction region and a narrower two-phase reaction region in solidified batteries compared to liquid-based LIBs. The altered (dis)charge behavior was suggested to be thermodynamically driven, as it remained largely unchanged with varying rates and under open circuit conditions. Qualitative analysis considering stress-induced variations in Gibbs free energy curves demonstrated that external stress, potentially caused by the constraint of chemo-mechanical expansion, can thermodynamically narrow the two-phase region when the chemical expansion coefficients of the two phases of FMO differ. These findings highlight the significant impact of the battery solidification on electrode material properties, emphasizing the importance of considering these unique issues in the design of ASSLIBs. | Yuta Kimura; Shintaro Kobayashi; Shogo Kawaguchi; Koji Ohara; Yasuhiro Suzuki; Takashi Nakamura; Yasutoshi Iriyama; Koji Amezawa | Energy; Energy Storage | CC BY 4.0 | CHEMRXIV | 2024-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6625baa721291e5d1d56d292/original/modifications-of-the-charge-discharge-behaviour-of-fe2-mo-o4-3-in-all-solid-state-lithium-ion-batteries.pdf |
642e421ea41dec1a568c99ea | 10.26434/chemrxiv-2023-w8c40 | Lipidic drug delivery systems: is the microbiome a cause for concern? | The formulation of ‘smart’ therapeutics has sparked an explosion of interest in lipidic nanomaterials. In vitro and in vivo tests for therapeutic agents have traditionally been run in sterile environments, but many target areas for drug delivery such as the gastrointestinal (GI) tract and skin are home to thousands of microbial species. Here, we examine the behaviour of lipidic nanomaterials after exposure to representative strains of four bacterial species found in several human microbiomes. Small angle x-ray scattering (SAXS) measurements show that the nanostructure of monoolein cubic and inverse hexagonal phases are transformed, respectively, into inverse hexagonal and inverse micellar cubic phase upon exposure to a strain of live Staphylococcus aureus often present on skin. Further investigations support that these transitions are due to enzymatic hydrolysis of constituent lipids. The structural transformations induced by S. aureus are shown to take place within a timeframe relevant to the therapeutic application of these materials, and significantly reduced the rate of drug release from monoolein-based nanomaterials. Interestingly, the representative strains of bacteria investigated from the GI tract (E. coli, L. rhamnosus) and in disease states (P. aeruginosa) had no effect on liquid crystal structure. These findings are the first to demonstrate how the live human microbiome can trigger changes in the structure and consequent drug release properties of lipidic nanomaterials. The effect appears to be strain specific, and varies from patient to patient, body region to body region, and is anticipated to affect the bioapplication of monoglyceride-based formulations. | Jonathan Caukwell ; Salvatore Assenza; Karl Hassan; Brett Neilan; Livia Salvati Manni; Wye-Khay Fong | Nanoscience; Nanostructured Materials - Nanoscience | CC BY 4.0 | CHEMRXIV | 2023-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642e421ea41dec1a568c99ea/original/lipidic-drug-delivery-systems-is-the-microbiome-a-cause-for-concern.pdf |
634f825ee79b3f8696eedd8e | 10.26434/chemrxiv-2022-8z976-v2 | Molecular screening for solid–solid phase transition by machine learning | Solid–solid phase transition is a mechanism manifesting and regulating functionalities in molecular crystals. The phase transitions are generally found by chance empirically, and screening molecules theoretically to predict their existence is challenging. In this study, we screened for the possibility of solid–solid phase transitions by positive-unlabeled learning using molecular descriptors and verified the inference by finding new substances exhibiting solid–solid phase transitions in the solid state. We also found that the molecular structure of a substance is weakly related to the transition temperature but not the transition enthalpy. The findings of this study are useful for designing functional molecular crystals. | Daisuke Takagi; Kazuki Ishizaki; Toru Asahi; Takuya Taniguchi | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634f825ee79b3f8696eedd8e/original/molecular-screening-for-solid-solid-phase-transition-by-machine-learning.pdf |
634323f0e615027a1738a2c5 | 10.26434/chemrxiv-2022-090pf-v2 | Src kinase app: valid inhibitor generation and prediction with explanation using predictive model and selfies | Dealing with a small Experimental dataset using a generative model produces a model with underfitting and reduces its ability to generate a new valid compound. Even in the presence of free available chemical databases SMILES string has to use a complex and computationally intensive model to solve validation problems. SELFIES solve all validation problems but further activity optimization is needed with the absence of an app that records molecules generated. In this study, the author uses a predictive model to provide a dataset by a virtual screen of 3 million compounds from a chemical online database in addition to experimental active dataset. Data feed to a different model of one layer Recurrent Neural Network model using both SELFIES and SMILES for about 2-4 epochs. Structure-based drug design was used and Src Kinase as a target to validate both the predictive model and compounds produced by Recurrent Neural Network and further filtration happens using Molecular Dynamics Simulation. SELFIES outperform SMILES in producing valid molecules in all types of Recurrent Neural Network simple structures. Recurrent Neural Network can produce active compounds using the GRU layer without any activity optimization from just 4 runs 100 molecules each. The novelty of the result can be compared to the result coming from predictive model virtual screen data. Recurrent Neural Network can produce novel compounds with key interaction residue with the target protein. All Predictive Models were deployed and ExplainableAI is used to guide generated molecules. MERN stack app SaveMol is used to save molecules produced with substructure research ability and apps links provide here(https://github.com/phalem/Src). | Mohamed Abd Elaleem | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634323f0e615027a1738a2c5/original/src-kinase-app-valid-inhibitor-generation-and-prediction-with-explanation-using-predictive-model-and-selfies.pdf |
60c7523f702a9b547018c0c2 | 10.26434/chemrxiv.13269617.v1 | A Biocompatible Dual-AIEgen System without Spectral Overlap for Quantitation of Microbial Viability and Monitoring of Biofilm Formation | <p>Lacking
rapid and reliable microbial detection and sensing platforms, insufficient understanding
towards microbial behaviors may generated or delayed precautions could be made,
which greatly threatens human life and increase heavy financial burdens to the
society. In this contribution, a dual-aggregation-induced emission luminogen (AIEgen)
system is successfully developed for microbial imaging and metabolic status sensing.
This system consists of two AIEgens (DCQA and TPE-2BA) that bear positive
charged groups or boric acid groups, providing universal microbial staining
ability and specific affinity to dead microbes, respectively. On the basis of
the distinctive fluorescence response produced by the diverse interaction of
AIEgens with live or dead microbes, this dual-AIEgen system can detect all the
microbe and identify their viabilities. Furthermore, the morphology and
metabolic status of a sessile biofilm can also be imaged and monitored. The system
exhibits rapid labelling, suitable for various microbes, and good
biocompatibilities.</p> | Wei He; Zheng Zheng; Haotian Bai; Ling-Hong Xiong; Lei Wang; Yinghui Li; Ryan Tsz Kin Kwok; Jacky W. Y. Lam; Qinghua Hu; Jinquan Cheng; Ben Zhong Tang | Aggregates and Assemblies; Biological Materials; Dyes and Chromophores; Imaging Agents | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7523f702a9b547018c0c2/original/a-biocompatible-dual-ai-egen-system-without-spectral-overlap-for-quantitation-of-microbial-viability-and-monitoring-of-biofilm-formation.pdf |
60c742d2ee301ca6b9c78ef6 | 10.26434/chemrxiv.8791442.v1 | Hypervalent Iodine(III)-Mediated Cyclization of Unsaturated N-Alkoxyureas: Cationic Oxybromination vs. Radical Aminobromination and Aminooxyamination | <div>In this study we describe the reactivity of unsaturated N-alkoxyureas in the presence of different combinations of a hypervalent iodine(III) reagent and a bromide source or TEMPO. Three complementary cyclizations can be achieved depending on the reaction conditions. On the one hand, PIFA with pyridinium bromide leads to an oxybromination reaction. On the other hand, bis(tert-butylcarbonyloxy)iodobenzene with tetrabutylammonium bromide or TEMPO triggers aminobromination or aminooxyamination reactions, respectively. Control experiments showed that while the first process is ionic, the other two follow a radical manifold.</div> | Laure Peilleron; Pascal Retailleau; Kevin Cariou | Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742d2ee301ca6b9c78ef6/original/hypervalent-iodine-iii-mediated-cyclization-of-unsaturated-n-alkoxyureas-cationic-oxybromination-vs-radical-aminobromination-and-aminooxyamination.pdf |
667342c401103d79c59db0a5 | 10.26434/chemrxiv-2024-x59gl | Small Basis Set Density Functional Theory Method for Cost-efficient, Large-scale Condensed Matter Simulations | We present an efficient first-principles based method geared towards reliably predicting the structures of solid materials across the periodic table. To this end, we use a density functional theory (DFT) baseline with a compact, near-minimal \emph{min+s} basis set, yielding low computational costs and memory demands. Since the use of such small basis set leads to systematic errors in chemical bond lengths, we develop a linear pairwise correction (LPC), available for elements $Z$ = 1-86 (excluding the lanthanide series), parameterized for use with the PBE exchange-correlation functional. We demonstrate the reliability of this corrected approach for equilibrium volumes across the periodic table and the transferability to differently coordinated environments and multi-elemental crystals. We examine relative energies, forces and stresses in geometry optimizations and MD simulations. | Elisabeth Keller; Jack Morgenstein; Karsten Reuter; Johannes T. Margraf | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2024-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667342c401103d79c59db0a5/original/small-basis-set-density-functional-theory-method-for-cost-efficient-large-scale-condensed-matter-simulations.pdf |
6202792be0f529f7ccab90cc | 10.26434/chemrxiv-2022-kk74h | Virtual data augmentation method for reaction prediction in small dataset scenario | To improve the performance of data-driven reaction prediction models, a new data augmentation method for augmenting data volumes is presented that aims to add fake data in training dataset. This method is only pay attention to small-scale reactions, and manually generates fake data which is chemical and credible molecules by replacing functional groups in reaction sites. And we call this method as virtual data augmentation. Additionally, the transformer model is introduced to explore the effectiveness of virtual data augmentation method in the task of reaction prediction based on small data sets. We apply our method to five classic coupling reactions, the results show that the overall performance of the transformer-baseline model and transformer-transfer learning model combined with virtual data augmentation method is obviously improved, compared to raw datasets. Especially for Suzuki reaction, combining transfer learning strategy and virtual data augmentation method, reaches top-1 accuracy of 97.8%. To sum up, virtual data augmentation can be used as a measure to face up the problem of insufficient data and significantly improves the performance of reaction prediction.
| Xinyi Wu; Yun Zhang; Jiahui Yu; Chengyun Zhang; Haoran Qiao; Yejian Wu; Zhipeng Wu; Xinqiao Wang; Hongliang Duan | Theoretical and Computational Chemistry; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6202792be0f529f7ccab90cc/original/virtual-data-augmentation-method-for-reaction-prediction-in-small-dataset-scenario.pdf |
60c73eae469df428bbf428fd | 10.26434/chemrxiv.13735084.v8 | Unimolecular, bimolecular and intramolecular hydrolysis mechanisms of 4-nitrophenyl β-D-glucopyranoside | 1,2-<i>trans</i>-Glycosides hydrolyze through different
mechanisms at different pH values, but systematic studies are lacking. Here we
report the pH-rate constant profile for the hydrolysis of<i> </i>4-nitrophenyl
β-D-glucoside. An inverse kinetic isotope effect of <i>k</i>(H<sub>3</sub>O<sup>+</sup>)/<i>k</i>(D<sub>3</sub>O)<sup>+</sup> = 0.65 in the acidic region indicates that the mechanism requires the
formation of the conjugate acid of the substrate for the reaction to proceed,
with heterolytic cleavage of the glycosidic C-O bond. Reactions in the
pH-independent region exhibit general catalysis with a single proton in flight,
a normal solvent isotope effect of <i>k</i><sub>H</sub>/<i>k</i><sub>D</sub> =
1.5, and when extrapolated to zero buffer concentration show a small solvent
isotope effect <i>k</i>(H<sub>2</sub>O)/<i>k</i>(D<sub>2</sub>O) = 1.1,
consistent with water attack through a dissociative mechanism. In the basic
region, solvolysis in <sup>18</sup>O-labelled water and H<sub>2</sub>O/MeOH
mixtures allowed detection of bimolecular hydrolysis and neighboring group participation,
with a minor contribution of nucleophilic aromatic substitution. Under mildly
basic conditions, a bimolecular concerted mechanism is implicated through an
inverse solvent isotope effect of <i>k</i>(HO<sup>–</sup>)/<i>k</i>(DO<sup>–</sup>)
= 0.5 and a strongly negative entropy of activation (D<i>S</i><sup>‡</sup> = –13.6 cal
mol<sup>–1</sup> K<sup>–1</sup>). Finally, at high pH, an inverse solvent
isotope effect of <i>k</i>(HO<sup>–</sup>)/<i>k</i>(DO<sup>–</sup>) = 0.6 indicates
that the formation of 1,2-anhydrosugar is the rate determining step.<br /> | Amani Alhifthi; Spencer Williams | Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73eae469df428bbf428fd/original/unimolecular-bimolecular-and-intramolecular-hydrolysis-mechanisms-of-4-nitrophenyl-d-glucopyranoside.pdf |
60c747c1bb8c1a40f13daafe | 10.26434/chemrxiv.11768718.v1 | Plasma-Catalytic Ammonia Synthesis Beyond the Equilibrium Limit | We explore the consequences of non-thermal plasma activation on product yields in catalytic ammonia synthesis, a reaction that is equilibrium-limited at elevated temperatures. We employ a minimal microkinetic model that incorporates the influence of plasma activation on N<sub>2</sub> dissociation rates to predict NH<sub>3</sub> yields into and across the equilibrium-limited regime. NH<sub>3</sub> yields are predicted to exceed bulk thermodynamic equilibrium limits on materials that are thermal-rate-limited by N<sub>2</sub> dissociation. In all cases, yields revert to bulk equilibrium at temperatures at which thermal reaction rates exceed plasma-activated ones. Beyond-equilibrium NH<sub>3</sub> yields are observed in a packed bed dielectric-barrier-discharge reactor and exhibit sensitivity to catalytic material choice in a way consistent with model predictions. The approach and results highlight the opportunity to exploit synergies between non-thermal plasmas and catalysts to affect transformations at conditions inaccessible through thermal routes. | Prateek Mehta; Patrick M. Barboun; Yannick Engelmann; David B. Go; Annemie Bogaerts; William
F. Schneider; Jason C. Hicks | Heterogeneous Catalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747c1bb8c1a40f13daafe/original/plasma-catalytic-ammonia-synthesis-beyond-the-equilibrium-limit.pdf |
639c9f7504902a19060580cf | 10.26434/chemrxiv-2022-k31gr | 3D Quantification of Elemental Gradients within Heterostructured Particles of Battery Cathodes | Heterogenous architectures with elemental gradients tailored within particles have been pursued to combat the instabilities limiting Ni-rich cathode materials for lithium-ion batteries. The growth of different compositional layers is accomplished during the synthesis of hydroxide precursors. However, the extent to which these concentration gradients are modified during high-temperature reactions is difficult to establish in their intact, spherical form. Here, we show the entire three-dimensional structure of a secondary particle can be resolved non-destructively with differential X-ray absorption spectroscopy (XAS) through transmission X-ray microscopy (TXM). The relationship between particle location and elemental content was fully quantified, with high statistical significance, for heterostructures possessing different compositional gradients in the precursors with 90:5:5 Ni:Mn:Co core compositions. Reduced elemental heterogeneity was observed after high-temperature synthesis, but gradients remained. The methodology presented should be used to guide synthesis while assuring that gains in electrochemical performance are linked to precise elemental distributions at the nanoscale. | Eva Allen; Youngho Shin; William Judge; Mark Wolfman; Vincent De Andrade; Stephanie Cologna; Jordi Cabana | Materials Science; Energy; Coating Materials; Core-Shell Materials; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639c9f7504902a19060580cf/original/3d-quantification-of-elemental-gradients-within-heterostructured-particles-of-battery-cathodes.pdf |
6569ce0f5bc9fcb5c9d1df5b | 10.26434/chemrxiv-2023-lx3q4 | Bicyclo[2.2.0]hexene (BCH): A Multimodal Mechanophore with Force-Governed Chemoselectivity | The identity of reactive sites in a molecule and the selectivity between them in chemical transformations depends on applied reagents and external drives. Polymer mechanochemistry has been an enabling tool in accessing chemical reactivity and reaction pathways that are distinctive from the thermal counterparts. However, mechanochemical selectivity, i.e., activation of multiple unique reaction pathways from the same mechanophore, remains elusive. Here, we report the design of bicyclo[2.2.0]hexene (BCH) as a multimodal mechanophore to leverage its structural simplicity and relatively low molecular symmetry to demonstrate the idea of force-governed chemoselectivity. Upon changing the attachment points of pendant polymer chains, different C–C bonds in bicyclo[2.2.0]hexene are specifically activated via sonication by externally applied force. Extensive experimental characterization confirms that each mode of activation results in a unique reaction, entailing retro-[2+2] cycloreversion, 1,3-allylic migration, and 4π-electrocyclic ring-opening reactions, respectively. Control experiments with small-molecule analogues reveal that observed chemoselectivity of BCH regioisomers is only possible with mechanical force. Theoretical studies further elucidate that the changes of substitution have minimal impact on the potential energy surface of parent BCH. The mechanochemical bond-specific activation is a result of selective and effective coupling of force to the targeted C–C bonds in each mode. | Shihao Ding; Wenkai Wang; Anne Germann; Yiting Wei; Tianyi Du; Jan Meisner; Rong Zhu; Yun Liu | Physical Chemistry; Organic Chemistry; Polymer Science; Organic Synthesis and Reactions; Physical Organic Chemistry; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6569ce0f5bc9fcb5c9d1df5b/original/bicyclo-2-2-0-hexene-bch-a-multimodal-mechanophore-with-force-governed-chemoselectivity.pdf |
60c754749abda2961ff8e199 | 10.26434/chemrxiv.13665083.v1 | Phosphonofluoresceins: Synthesis, Spectroscopy, and Applications | <p>Xanthene fluorophores, like fluorescein, have been versatile
molecules across diverse fields of chemistry and life sciences. Despite the
ubiquity of 3-carboxy and 3-sulfuonofluorescein for the last 150 years, to
date, no reports of 3-phosphonofluorescein exist. Here, we report the synthesis,
spectroscopic characterization, and applications of 3-phosphonofluoresceins. The
absorption and emission of 3-phosphonofluoresceins remain relatively unaltered
from the parent 3-carboxyfluorescein. 3-phosphonofluoresceins show enhanced
water solubility compared to 3-carboxyfluorescein and persist in an open,
visible light-absorbing state even at low pH and in low dielectric media while
3-carboxyfluoresceins tend to lactonize. In contrast, the spirocyclization
tendency of 3-phosphonofluoresceins can be modulated by esterification of the
phosphonic acid. The bis-acetoxymethyl ester of 3-phosphonofluorescein readily
enters living cells, showing excellent accumulation (>6x) and retention
(>11x), resulting in a nearly 70-fold improvement in cellular brightness
compared to 3-carboxyfluorescein. In a complementary fashion, the free acid
form of 3-phosphonofluorescein does not cross cellular membranes, making it
ideally suited for incorporation into a voltage-sensing scaffold. We develop a
new synthetic route to functionalized 3-phosphonofluoresceins to enable the
synthesis of phosphono-voltage sensitive fluorophores, or phosVF2.1.Cl.
Phosphono-VF2.1.Cl shows excellent membrane localization, cellular brightness,
and voltage sensitivity (26% ΔF/F per 100 mV), rivalling that of sulfono-based
VF dyes. In sum, we develop the first synthesis of 3-phosphonofluoresceins,
characterize the spectroscopic properties of this new class of xanthene dyes,
and utilize these insights to show the utility of 3-phosphonofluoresceins in
intracellular imaging and membrane potential sensing. </p>
<p> </p> | Joshua Turnbull; Brittany Benlian; Ryan Golden; Evan Miller | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754749abda2961ff8e199/original/phosphonofluoresceins-synthesis-spectroscopy-and-applications.pdf |
6459a76307c3f0293770d131 | 10.26434/chemrxiv-2023-qtzzd | Rapid Fluorescence EEM spectra acquisition using super-cycle Hadamard-Transform Multiplexing | Hadamard-transform multiplexing has recently been applied to increasingly complex spectroscopic techniques. It had been shown that the data acquisition time for fluorescence Excitation-Emission-Matrix spectroscopy can be reduced by one or two orders of magnitude using Hadamard-Transform multiplexing of the excitation light using a programmable lightsource. In these previous studies, the data acquisition rate had been limited by the time it took to record an EEM, i.e. to complete one cycle of multiplexed excitation spectra. The extraction of chemical information, such as concentration and chemical identity, is then obtained from parallel factor (PARAFAC) analysis of the sequence of EEM spectra.
In this contribution we increase the data acquisition rate by another order of magnitude, i.e. to the time it takes to record a single excitation spectrum. Our algorithm is entirely based on improved data processing, i.e. it can be applied to previously recorded Hadamard-Transform multiplexed data sets.
The algorithm is based on three previously unexplored approaches: (1) we perform a PARAFAC multivariate analysis on the raw (multiplexed) data set (2) the PARAFAC loading vectors are obtained prior to obtaining the score vectors, (3) when loading vectors are difficult to obtain from the stack of EEM spectra, we instead use a rolling-average approach to considerably increase the number of spectra and the stability of the fit. Analysis of experimental data shows that fluorescence EEM spectra with 7 excitation wavelengths and over 1000 emission wavelengths can be obtained in less than 20 ms. | Travis Ferguson; Hans-Peter Loock | Analytical Chemistry; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6459a76307c3f0293770d131/original/rapid-fluorescence-eem-spectra-acquisition-using-super-cycle-hadamard-transform-multiplexing.pdf |
65e585c266c138172927cb94 | 10.26434/chemrxiv-2024-pjxtj | Hyperlocal Air Pollution in London Part 1: Validating Low-Cost Sensors for Mobile Measurements from Vehicles | This study assesses low-cost sensors (LCS) for mobile monitoring of air quality, which has thus far been scarcely investigated. NO2 and PM2.5 were measured using
LCS and higher-grade instruments while driving across various environments in London (943 km) and northern Europe (2923 km), including urban areas, motorways, and
tunnels. The data was classified according to the environment where the measurements were carried out, and the performance of LCS and higher-grade instruments was compared. Results indicate that the performance of the sensors was influenced by the rate of change in pollutant concentration in different environments, and not by
vehicle speed. Excluding tunnel environments, overall, the particulate matter sensors correlated better with their higher-grade instrument than the electrochemical (EC)
sensors, with R2 values from 0.90−0.96 in the different environments, compared with 0.39−0.72 for the EC sensors. Tunnels presented a unique opportunity to test the time
response of the systems, given the rapid change in concentration upon entering, and all sensors showed limited response times. This is the first time that EC NO2 sensors have been rigorously tested against reference monitors whilst mobile. Their absolute measurements appear unaffected by movement; however, their time resolution may not be high enough for mobile monitoring in highly variable environments. | Hugo S. Russell; Louise B. Frederickson; Martin O. B. Sørensen; Johan A. Schmidt; Ole Hertel; Matthew S. Johnson | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e585c266c138172927cb94/original/hyperlocal-air-pollution-in-london-part-1-validating-low-cost-sensors-for-mobile-measurements-from-vehicles.pdf |
60c749760f50db96f03968f6 | 10.26434/chemrxiv.12067851.v1 | Supramolecular Encapsulation of Small-Ultra Red Fluorescent Proteins in Virus-Like Nanoparticles for Non-Invasive In Vivo Imaging Agents | <div>
<div>
<div>
<p>Icosahedral virus-like particles (VLPs) derived from bacteriophages Qβ and PP7 encapsulating small-ultra red
fluorescent protein (smURFP) were produced using a versatile supramolecualr capsid dissassemble-reassemble approach. The
generated fluorescent VLPs display identical structural properties to their non-fluorescent analogs. Encapsulated smURFP shows
indistinguishable photochemical properties to its unencapsulated counterpart, exhibits outstanding stability towards pH, and
produces bright in vitro images following phagocytosis by macrophages. In vivo imaging allows biodistribution to be imaged at
different time points. Ex vivo imaging of intravenously administered encapsulated smURFP reveleas localization in the liver and
</p>
</div>
</div>
<div>
<div>
<p>kidneys after 2 h blood circulation and substantial elimination
constructs as non-invasive in vivo imaging agents.
</p>
</div>
</div>
</div> | Fabian C. Herbert; Olivia Brohlin; Tyler Galbraith; Candace Benjamin; Cesar A. Reyes; Michael A. Luzuriaga; Arezoo Shahrivarkevishahi; Jeremiah J. Gassensmith | Supramolecular Chemistry (Org.); Nanostructured Materials - Materials; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749760f50db96f03968f6/original/supramolecular-encapsulation-of-small-ultra-red-fluorescent-proteins-in-virus-like-nanoparticles-for-non-invasive-in-vivo-imaging-agents.pdf |
64ca17d869bfb8925a39d5ab | 10.26434/chemrxiv-2022-qr7wt-v2 | Reactant-Induced Dynamics of Lithium Imide Surfaces during the Ammonia Decomposition Process | Ammonia decomposition on lithium imide surfaces has been intensively investigated owing to its potential role in a sustainable hydrogen-based economy. Through advanced molecular dynamics simulations of ab initio accuracy, we show that the surface structure of the catalyst changes upon exposure to the reactants, and a new dynamic state is activated. It is this highly fluctuating state that is responsible for catalysis and not a well defined static catalytic center. In this activated environment, a series of reactions that eventually leads to the release of N2 and H2 molecules become possible. Once the flow of reagent is terminated the imide surface returns to its pristine state. We suggest that by properly engineering this dynamic interfacial state one can design improved catalytic systems. | Manyi Yang ; Umberto Raucci; Michele Parrinello | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Heterogeneous Catalysis; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ca17d869bfb8925a39d5ab/original/reactant-induced-dynamics-of-lithium-imide-surfaces-during-the-ammonia-decomposition-process.pdf |
67629675fa469535b9f7be6c | 10.26434/chemrxiv-2024-wd5j8 | Times are changing but order matters: Transferable prediction of small molecule liquid chromatography retention times | Thousands of publications on the prediction of small molecule retention times were published during the last decades. The ultimate goal is, without doubt, the transferable prediction of retention times: We want to train a model on a certain set of compounds from one dataset and then use the model to predict retention times for a different set of compounds from another dataset. Unfortunately, retention times may change massively, even for nominally identical chromatographic conditions. Retention order is much better retained, yet even the retention order of compounds may change if chromatographic conditions vary. Here, we systematically study what chromatographic conditions result in notable changes in retention order. We then present a machine learning model that can predict retention order or, more precisely, a retention order index, taking into account chromatographic conditions. Finally, we show how to map the retention order index to retention times. Disentangling these two task finally enables retention time prediction across chromatographic conditions and compound classes. | Fleming Kretschmer; Eva-Maria Harrieder; Michael Witting; Sebastian Böcker | Theoretical and Computational Chemistry; Analytical Chemistry; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2024-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67629675fa469535b9f7be6c/original/times-are-changing-but-order-matters-transferable-prediction-of-small-molecule-liquid-chromatography-retention-times.pdf |
671d3cad83f22e42144ad31e | 10.26434/chemrxiv-2024-mhgmj | MoS2 as a Bifunctional Electrocatalyst for Water Splitting | With rising global energy demands and increasing environmental concerns, sustainable energy
technologies are crucial for ensuring a cleaner future. Water splitting has emerged as a key
method for producing clean hydrogen fuel. However, developing efficient bifunctional
electrocatalysts for this process remains a significant challenge. Traditional noble metals like
platinum (Pt) and ruthenium (Ru) offer high performance but are costly and scarce, highlighting
the need for cost-effective alternatives. MoS₂-based electrocatalysts have attracted attention
due to their promising performance and cost-effectiveness compared to noble metals. Despite
their potential, challenges such as optimizing efficiency, reducing overpotential, and enhancing
stability must be addressed. This review explores the MoS₂ as an alternative to noble metals,
focusing on its performance metrics through the lens of materials engineering. A detailed
analysis of the structural and electronic characteristics of MoS2 is provided, examining how
these factors influence its bifunctional electrocatalytic performance. Additionally, the review
delves into the reaction mechanisms, critically evaluating key performance parameters such as
overpotential, Tafel slope, exchange current density, stability, and electrochemically active
surface area. Furthermore, the impact of synthesis and processing methods on MoS₂’s
performance is discussed, including phase and defect engineering, morphology optimization,
and heterostructure construction. By integrating current research and offering insights into the
structure-property-performance relationships, this review aims to guide future developments
in sustainable energy technologies. | Tracy Asamoah; Albert Antwi; Esther Doku; Karim Asare; Martinson Nartey; Kwadwo Mensah-Darkwa | Catalysis; Energy; Electrocatalysis; Redox Catalysis; Fuels - Energy Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671d3cad83f22e42144ad31e/original/mo-s2-as-a-bifunctional-electrocatalyst-for-water-splitting.pdf |
6758e9de085116a133003c60 | 10.26434/chemrxiv-2023-8c9vh-v2 | Persistent Topological Laplacians -- a Survey | Persistent topological Laplacians constitute a new class of tools in topological data analysis (TDA). They are motivated by the necessity to address challenges encountered in persistent homology when handling complex data. These Laplacians combines multiscale analysis with topological techniques to characterize the topological and geometrical features of functions and data. Their kernels fully retrieve the topological invariants of corresponding persistent homology, while their non-harmonic spectra provide supplementary information. Persistent topological Laplacians have demonstrated superior performance over persistent homology in analyzing large-scale protein engineering datasets. In this survey, we offer a pedagogical review of persistent topological Laplacians formulated in various mathematical settings, including simplicial complexes, path complexes, flag complexes, digraphs, hypergraphs, hyperdigraphs, cellular sheaves, as well as $N$-chain complexes. | Xiaoqi Wei; Guo-Wei Wei | Biological and Medicinal Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6758e9de085116a133003c60/original/persistent-topological-laplacians-a-survey.pdf |
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