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634d52f2339972ddef8df796 | 10.26434/chemrxiv-2022-7fkj9 | Testing the Limits of Imbalanced CPET Reactivity: Mechanistic Crossover in H-atom Abstraction by Co(III)-oxo Complexes | Transition metal-oxo complexes are key intermediates in a variety of oxidative transformations, notably C–H bond activation. The rela-tive rate of C–H bond activation mediated by transition metal-oxo complexes is typically predicated on substrate bond dissociation free energy in cases with a concerted proton-electron transfer (CPET). However, recent work has demonstrated that alternative stepwise thermodynamic contributions such as acidity/basicity or redox po-tentials of the substrate/metal-oxo may dominate in some cases. In this context we have found basicity-governed concerted activation of C–H bonds with the terminal CoIII-oxo complex PhB(tBuIm)CoIIIO. We have been interested in testing the limits of such basicity-dependent reactivity and have synthesized an analo-gous, more basic complex, PhB(AdIm)CoIIIO, and studied its reactiv-ity with H-atom donors. This complex displays a higher degree of imbalanced CPET reactivity than PhB(tBuIm)CoIIIO with C–H substrates and O–H activation of phenol substrates displays mechanistic crossover to stepwise PTET reactivity. Analysis of the thermodynamics of PT and ET reveal a distinct thermodynamic crossing point between concerted and stepwise reactivity. Further-more, the relative rates of stepwise and concerted reactivity suggest that maximally imbalanced systems provide the fastest CPET rates up to the point of mechanistic crossover which results in slower prod-uct formation. | Norman Zhao; McKenna Goetz; Joseph Schneider; John Anderson | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Bond Activation | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634d52f2339972ddef8df796/original/testing-the-limits-of-imbalanced-cpet-reactivity-mechanistic-crossover-in-h-atom-abstraction-by-co-iii-oxo-complexes.pdf |
66f585c812ff75c3a19062c8 | 10.26434/chemrxiv-2024-d7bj8 | Late-stage Minimal Labeling of Peptides and Proteins for Real-time Imaging of Cellular Trafficking | The cellular uptake routes of peptides and proteins are complex and diverse, often handicapping therapeutic success. Understanding their mechanisms of internalization requires chemical derivatization with approaches that are compatible with wash-free and real-time imaging. In this work, we developed a new late-stage labeling strategy for unprotected peptides and proteins, which retains their biological activity while enabling live-cell imaging of uptake and intracellular trafficking. S-bridged nitrobenzodiazoles were selectively incorporated into Cys residues of both linear and cyclic peptides via Pd-mediated arylation with good yields and high purities. The resulting labeled peptides are chemically stable under physiological conditions and display strong fluorogenic character for wash-free imaging studies. We utilized this approach to prepare native-like analogues of cell-penetrating peptides and performed time-course analysis of their internalization routes in live cells by fluorescence lifetime imaging. Furthermore, we applied our strategy to label the chemokine protein mCCL2 and monitor its internalization via receptor-mediated endocytosis in live macrophages. This study provides a straightforward strategy for late-stage fluorogenic labeling of intact peptides and small proteins and direct visualization of dynamic intracellular events. | Ferran Nadal-Bufi; Raj V. Nithun; Fabio de Moliner; Xiaoxi Lin; Shaimaa Habiballah; Muhammad Jbara; Marc Vendrell | Biological and Medicinal Chemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2024-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f585c812ff75c3a19062c8/original/late-stage-minimal-labeling-of-peptides-and-proteins-for-real-time-imaging-of-cellular-trafficking.pdf |
662f9ff321291e5d1d04736d | 10.26434/chemrxiv-2024-6q8nf | Photopatternable, Degradable, and Performant Polyimide Network Substrates for E-Waste Mitigation | The continuous accumulation of electronic waste is reaching alarming levels necessitating sustainable solutions to mitigate environmental impact. Fabrication of the commercial electronic substrates also requires high heat. As an alternative, we propose a series of reprocessible electronic substrates based on photopolymerizable polyimides containing degradable ester linkages. We synthesize imide-containing diallyl monomers derived from readily available chemical feedstocks to produce high-quality substrates via rapid photopolymerization. Such materials possess exceptional thermal properties (thermal conductivity, K = 0.37-0.54 WmK-1; degradation temperature, Td > 300 °C), dielectric (dielectric constant, Dk = 2.81-3.05; dielectric loss, Df < 0.024) and mechanical properties (Strength ~ 50 MPa ; ultimate elongation, dL/L0 > 5%) needed in flex electronic applications. When utilized as electronic substrates, we demonstrate mild depolymerization via transesterification reactions to recover and reuse the functional components. Moreover, these photopolymer resins remain compatible with commercial workflows and enable fabrication of next-generation, dense multilayered circuits. | Caleb Reese; Grant Musgrave; Jenn Wong; Wenyang Pan; John Uehlin; Mason Zadan; Omar Awartani; Thomas Wallin; Chen Wang | Materials Science; Polymer Science; Multilayers; Thin Films | CC BY 4.0 | CHEMRXIV | 2024-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662f9ff321291e5d1d04736d/original/photopatternable-degradable-and-performant-polyimide-network-substrates-for-e-waste-mitigation.pdf |
60c74234842e65e7b7db2036 | 10.26434/chemrxiv.7904450.v3 | AMOEBA+ Classical Potential for Modeling Molecular Interactions | <p>Classical potentials
based on isotropic and additive atomic charges have been widely used to model
molecules in computers for the past few decades. The crude approximations in
the underlying physics are hindering both their accuracy and transferability
across chemical and physical environments. Here we present a new classical potential,
AMOEBA+, to capture essential
intermolecular forces, including permanent electrostatics, repulsion, dispersion,
many-body polarization, short-range
charge penetration and charge transfer, by extending the polarizable
multipole-based AMOEBA (Atomic Multipole Optimized
Energetics for Biomolecular Applications) model. For a set of common
organic molecules, we show that AMOEBA+ with general parameters can reproduce
both quantum mechanical interactions and energy decompositions according to the
Symmetry-Adapted Perturbation Theory (SAPT). Additionally,
a new water model developed based on the AMOEBA+ framework captures various
liquid phase properties in molecular dynamics simulations while remains
consistent with SAPT energy decompositions, utilizing both <i>ab initio</i> data and experimental liquid properties. Our results demonstrate
that it is possible to improve the physical basis of classical force fields to
advance their accuracy and general applicability.</p> | Chengwen Liu; Jean-Philip Piquemal; Pengyu Ren | Computational Chemistry and Modeling; Physical and Chemical Properties; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74234842e65e7b7db2036/original/amoeba-classical-potential-for-modeling-molecular-interactions.pdf |
65fdaa2f66c13817298ff476 | 10.26434/chemrxiv-2023-l0lwk-v2 | Cavity Quantum Electrodynamics Enables para- and ortho- Bromination of Nitrobenzene | Coupling molecules to a quantized radiation field inside an optical cavity has shown great promise to modify chemical reactivity. In this work, we show that the ground state selectivity of the electrophilic bromination of nitrobenzene can be fundamentally changed by strongly coupling the reaction to the cavity, generating the \textit{ortho}- or \textit{para}-substituted products instead of the \textit{meta} product. Importantly, these are products that are not obtained from the same reaction outside the cavity. A recently developed \textit{ab initio} approach was used to theoretically compute the relative energies of the cationic Wheland intermediates, which indicate the kinetically preferred bromination site for all products. Performing an analysis of the ground state electron density for the Wheland intermediates inside and outside the cavity, we demonstrate how strong coupling induces reorganization of the molecular charge distribution, which in turn leads to different bromination sites directly dependent on the cavity conditions. Overall, the results presented here can be used to understand cavity-induced changes to ground state chemical reactivity, from a mechanistic perspective, as well as to directly connect frontier theoretical simulation to state-of-the-art, but realistic, experimental cavity conditions. | Braden Weight; Daniel Weix; Zachary Tonzetich; Todd Krauss; Pengfei Huo | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Theory - Computational; Chemical Kinetics; Physical and Chemical Processes | CC BY 4.0 | CHEMRXIV | 2024-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fdaa2f66c13817298ff476/original/cavity-quantum-electrodynamics-enables-para-and-ortho-bromination-of-nitrobenzene.pdf |
60c7532d337d6c78b9e2880f | 10.26434/chemrxiv.13415918.v1 | Native Separation and Metallation Analysis of SOD1 Protein from the Human Central Nervous System: A Methodological Workflow | We developed a methodological workflow combining size exclusion chromatography, native isoelectric focusing, and high sensitivity X-ray-based metal detection within electrophoresis gels to analyze the metal content of single proteins purified from minimal amounts (<20 mg) of post-mortem human brain and spinal cord tissue. An important metalloprotein in the human central nervous system is copper-zinc superoxide dismutase (SOD1), an antioxidant enzyme linked to the aetiology of both amyotrophic lateral sclerosis and Parkinson’s disease. Abnormal SOD1 metallation is suspected to play a role in the pathogenic aggregation of SOD1 in both disorders, although data describing SOD1 metal occupancy in human tissues has not previously been reported. Validating our novel approach we demonstrated step-by-step metal preservation, preserved SOD1 activity, and substantial enrichment of SOD1 protein vs confounding metalloproteins. We found Cu and Zn were bound to SOD1 in a ratio of 1.12 ± 0.28 in human central nervous system tissues from healthy individuals, a ratio close to the expected value of 1. Our methodological workflow can be adapted to study a range of metalloproteins from human tissues and other sources.<br /> | Stéphane Roudeau; Benjamin G. Trist; Asuncion Carmona; Katherine M. Davies; Glenda M. Halliday; Yann Rufin; Stéphane Claverol; Stijn J.M. Van Malderen; Gerald Falkenberg; Kay L. Double; Richard Ortega | Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7532d337d6c78b9e2880f/original/native-separation-and-metallation-analysis-of-sod1-protein-from-the-human-central-nervous-system-a-methodological-workflow.pdf |
619e5e64c481c3713af73c13 | 10.26434/chemrxiv-2021-0g6f0 | Tunable aziridinium ylide reactivity: non-covalent interactions enable divergent product outcomes | Methods for rapid preparation of densely functionalized and stereochemically complex N-heterocyclic scaffolds are in demand for exploring potential new bioactive chemical space. This work describes experimental and computational studies to better understand the features of aziridinium ylides as intermediates for the synthesis of highly substituted dehydromorpholines. The development of this chemistry has enabled the extension of aziridinium ylide chemistry to the concomitant formation of both a C–N and a C–O bond in a manner that preserves the stereochemical information embedded in the substrate. The chemistry is tolerant of a wide range of functionalities that can be employed for DNA-encoded library (DEL) synthesis to prepare diverse libraries of heterocycles with potential bioactivity. In addition, we have uncovered several key insights that describe the importance of steric effects, rotational barriers around the C–N bond of the aziridinium ylide, and non-covalent interactions (NCIs) on the ultimate reaction outcome. These critical insights will assist in the further development of this chemistry to generate novel and complex N-heterocycles that will further expand complex amine chemical space. | Kate Nicastri; Soren Zappia; Jared Pratt; Julia Duncan; Ilia Guzei; Isra Fernandez; Jennifer Schomaker | Catalysis; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2021-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619e5e64c481c3713af73c13/original/tunable-aziridinium-ylide-reactivity-non-covalent-interactions-enable-divergent-product-outcomes.pdf |
625dc2c588636c7d5f16f463 | 10.26434/chemrxiv-2022-cnz4t | Endocytosis of coacervates into liposomes | Recent studies have shown that the interactions between condensates and biological membranes is of functional importance. Here, we study how the interaction between complex coacervates and liposomes as model systems can lead to membrane deformation and endocytosis. Depending on the interaction strength between coacervates and liposomes, the wetting behavior ranged from non-wetting, to partial wetting (adhesion), engulfment (endocytosis), and finally complete wetting. Endocytosis of coacervates was found to be a general phenomenon: coacervates made from a wide range of components could be taken up by liposomes. A simple theory that takes into account surface energies and coacervate sizes can explain the observed coacervate-liposome interactions. Our findings can help to better understand condensate-membrane interactions in cellular systems and provide new avenues for intracellular delivery using coacervates. | Tiemei Lu; Susanne Liese; Ludo Schoenmakers; Christoph Weber; Hiroaki Suzuki; Wilhelm Huck; Evan Spruijt | Physical Chemistry; Biological and Medicinal Chemistry; Polymer Science; Biophysics; Interfaces; Self-Assembly | CC BY NC 4.0 | CHEMRXIV | 2022-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625dc2c588636c7d5f16f463/original/endocytosis-of-coacervates-into-liposomes.pdf |
629a59ee4f43d6b0e92eccc4 | 10.26434/chemrxiv-2022-00xd7 | Solvent-Free Synthesis of Metal-Organic Frameworks Using Low-Melting Metal Salts | Metal-organic frameworks (MOFs) are porous, crystalline materials constructed from organic linkers and inorganic nodes with myriad potential applications in chemical separations, catalysis, drug delivery, and beyond. However, a major barrier to the application of MOFs in industry is their scalable synthesis, as most frameworks are prepared under highly dilute (≤0.01 M) solvothermal conditions using toxic organic solvents. Herein, we demonstrate that directly combining a range of salicylate and azolate linkers with low-melting metal halide (hydrate) salts above the melting point of the metal salt leads directly to high-quality MOFs without added solvent. Frameworks prepared under these ionothermal condi-tions possess high 77 K N2 surface areas and crystallinities comparable to frameworks prepared under traditional sol-vothermal conditions, as confirmed by powder X-ray diffraction (PXRD) and scanning electron microscopy (SEM). In ad-dition, we report the ionothermal syntheses of two frameworks that cannot be prepared directly under solvothermal con-ditions, namely, Fe2X2(dobdc) (dobdc4− = 2,5-dioxido-1,4-benzenedicarboxylate) and Fe2X2(m-dobdc) (m-dobdc4− = 4,6-dioxido-1,3-benzenedicarboxylate) (X = Cl, OH). These air-stable and porous Fe(III) members of the MOF-74 family pos-sess pressed-pellet conductivities comparable to or higher than those of highly air-sensitive Fe(II) congeners. Overall, the simple solvent-free method reported herein should be broadly applicable to the discovery and sustainable synthesis of metal-organic materials. | Tyler Azbell; Tristan Pitt; Melissa Bollmeyer; Christina Cong; Kyle Lancaster; Phillip Milner | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629a59ee4f43d6b0e92eccc4/original/solvent-free-synthesis-of-metal-organic-frameworks-using-low-melting-metal-salts.pdf |
6320ae0303e27ddb10d370f6 | 10.26434/chemrxiv-2022-w9n02 | Nickel-Catalyzed Double Bond Transposition under Kinetic Control | Taming the reactivity of nickel catalysts is a never-ending inspiration to discover new complexes, ligands, and reaction protocols. Here, we report that a simple combination of Ni(COD)2 and Lewis acids allows activation of allylic CH bonds. Their synergism eases oxidative addition and 1,3-hydrogen atom relocation to yield unprecedented double bond monotransposition. Unique features of this work include polar inner-sphere mechanism, kinetically favored double bond transposition, ligand-controlled stereoselective E or Z isomer distribution, mechanistic insights by control experiments and NMR monitoring. | Eduardo José Carvalho-Junior; Caio Oliveira | Organic Chemistry; Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6320ae0303e27ddb10d370f6/original/nickel-catalyzed-double-bond-transposition-under-kinetic-control.pdf |
65f02afae9ebbb4db98ae3e9 | 10.26434/chemrxiv-2024-59vrz | Characterization of Complex Proteoform Mixtures by
Online Nanoflow Ion-Exchange Chromatography - Native
Mass Spectrometry | The characterization of proteins and complexes in biological systems is essential to
establish their critical properties and to understand their unique functions in a
plethora of bioprocesses. However, it is highly difficult to analyze low levels of intact
proteins in their native states (especially those exceeding 30 kDa) with liquid
chromatography (LC) - mass spectrometry (MS). Herein, we describe for the first
time the use of nanoflow ion-exchange chromatography directly coupled with native
MS to resolve mixtures of intact proteins. Reference proteins and protein complexes
with molecular weight between 10 and 150 kDa and a model cell lysate were
separated using a salt-mediated pH gradient method using volatile additives. The
method allowed for low detection limits (0.22 pmol of monoclonal antibodies) while
proteins presented non-denatured MS (low number of charges and limited charge
state distributions) and the oligomeric state of the complexes analyzed was mostly
kept. Excellent chromatographic separations including the resolution of different
proteoforms of large proteins (> 140 kDa) and a peak capacity of 82 in a 30-minute
gradient, were obtained. The proposed setup and workflows show great potential for
analyzing diverse proteoforms in native top-down proteomics, opening
unprecedented opportunities for clinical studies and other sample-limited
applications. | Ziran Zhai; Despoina Mavridou; Matteo Damian; Francesco G. Mutti; Peter J. Schoenmakers; Andrea F.G. Gargano | Analytical Chemistry; Analytical Chemistry - General; Biochemical Analysis; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f02afae9ebbb4db98ae3e9/original/characterization-of-complex-proteoform-mixtures-by-online-nanoflow-ion-exchange-chromatography-native-mass-spectrometry.pdf |
60c743b8469df43af4f4326b | 10.26434/chemrxiv.9632036.v1 | Tetranuclear Copper and Mononuclear Nickel Complex of the Schiff Base of (3Z)-3-Hydrazonobutan-2-One Oxime with Different Aromatic Carbonyl Compounds: Synthesis, Single Crystal X-Ray Structure, Catecholase Activity, Phenoxazinone Synthase Activity, Catalytic Study for the Homocoupling of Benzyl Amines | Synthesis
and characterisation of one trinuclear copper complex, ([Cu<sub>3</sub>L<sub>3</sub>O]ClO<sub>4</sub>)
(<b>1</b>) and one nickel complex ([Ni(L'H)<sub>2</sub>(dmso)<sub>2</sub>](ClO<sub>4</sub>)<sub>2</sub>)
(<b>2</b>) with Schiff base ligands: (3Z)-3-((Z)-(1-(thiophen-2-yl)ethylidene)hydrazono)butan-2-one
oxime (LH) and 1-(pyridin-2-yl)ethylidene)hydrazono)butan-2-one
oxime (L<sup>'</sup>H). <b>1</b> shows high catecholase activity and has also been tested as a
catalyst for the synthesis of benzylimine. <b>2 </b> shows phenoxazinone synthase activity. | Swaraj Sengupta; Sahanwaj Khan; Shyamal K. Chattopadhyay; Indrani Banerjee; Tarun
K. Panda; Subhendu Naskar | Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b8469df43af4f4326b/original/tetranuclear-copper-and-mononuclear-nickel-complex-of-the-schiff-base-of-3z-3-hydrazonobutan-2-one-oxime-with-different-aromatic-carbonyl-compounds-synthesis-single-crystal-x-ray-structure-catecholase-activity-phenoxazinone-synthase-activity-catalytic-stu.pdf |
65b80fa39138d23161fef522 | 10.26434/chemrxiv-2024-tjwhm | Enantioselective Synthesis of Tetra-substituted 3-Hydroxyphthalide Esters by Isothiourea-Catalysed Acylative Dynamic Kinetic Resolution | A general and highly enantioselective method for the preparation of tetra-substituted 3-hydroxyphthalide esters via isothiourea-catalysed acylative dynamic kinetic resolution (DKR) is reported. Using (2S,3R)-HyperBTM (5 mol%) as the catalyst, the scope and limitations of this methodology have been extensively probed, with high enantioselectivity and good to excellent yields observed (>40 examples, up to 99%, 99:1 er). Substitution of the aromatic core within the 3-hydroxyphthalide skeleton, as well as aliphatic and aromatic substitution at C(3)-, is readily tolerated. A diverse range of anhydrides, including those from bioactive and pharmaceutically relevant acids, can also be used. The high enantioselectivity observed in this DKR process has been probed computation, with a key substrate heteroatom donor O•••acyl-isothiouronium interaction identified through DFT analysis as necessary for enantiodiscrimination | Shubham Agrawal; Pankaj Majhi; Alister Goodfellow; Raj Tak; David Cordes; Aidan McKay; Kevin Kasten; Michael Buehl; Andrew Smith | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Organocatalysis | CC BY 4.0 | CHEMRXIV | 2024-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b80fa39138d23161fef522/original/enantioselective-synthesis-of-tetra-substituted-3-hydroxyphthalide-esters-by-isothiourea-catalysed-acylative-dynamic-kinetic-resolution.pdf |
6699766801103d79c55cc41f | 10.26434/chemrxiv-2024-5fm7t | Comparative analysis of continuous similarity measures for compound identification in mass spectrometry-based metabolomics | In mass spectrometry (MS)-based metabolomics, compound identification relies on Liquid Chromatography-MS (LC-MS) and Gas Chromatography-MS (GC-MS). The most popular and efficient approach for this purpose is the comparison of similarity scores between experimental spectra and reference spectra. Among the various single and composite similarity measures, the Cosine Correlation is widely favored due to its simplicity, efficiency, and effectiveness. Recently, the Shannon Entropy Correlation has shown superior performance over several other measures, including the Cosine Correlation, in LC-MS-based metabolomics, particularly concerning receiver operating characteristic (ROC) curves and false discovery rates. However, previous comparisons did not consider the weight factor transformation, which is critical for achieving higher accuracy with the cosine correlation. This study conducted a comparative analysis of the Cosine Correlation and Shannon Entropy Correlation, incorporating the weight factor transformation during preprocessing. Additionally, we developed a novel entropy correlation measure, the Tsallis Entropy Correlation, which offers greater versatility than the Shannon Entropy Correlation. Our results indicate that the weight factor transformation is essential for achieving higher accuracy in both LC-MS and GC-MS-based compound identification. While the Tsallis Entropy Correlation outperforms the Shannon Entropy Correlation, it is also more computationally expensive. The Cosine Correlation, when combined with the weight factor transformation, achieves the highest accuracy and the lowest computational expense, demonstrating its robustness and efficiency in MS-based compound identification. | Hunter Dlugas; Xiang Zhang; Seongho Kim | Analytical Chemistry; Chemoinformatics; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2024-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6699766801103d79c55cc41f/original/comparative-analysis-of-continuous-similarity-measures-for-compound-identification-in-mass-spectrometry-based-metabolomics.pdf |
627c0aaa59f0d682ea8d5231 | 10.26434/chemrxiv-2022-7j4pd | Untethered unidirectionally crawling gels driven by an asymmetry in contact forces | The development of untethered soft robots capable of locomotion in response to environmental stimuli is important for biomimetics, drug delivery, and non-minimally invasive surgery. Reversible thermoresponsive hydrogels, which swell and shrink in the temperature range of (30-60 °C), provide an attractive material class for operating such untethered soft robots in human physiological and ambient conditions. Crawling has been demonstrated previously with thermoresponsive hydrogels but needs a patterned or ratcheted surface to break symmetry for unidirectional motion. Here, we demonstrate a new locomotor mechanism for unidirectionally crawling gels driven by spontaneous asymmetries in contact forces during swelling and deswelling of segmented active thermoresponsive poly (N-isopropyl acrylamide) (pNIPAM) and passive polyacrylamide (pAAM) bilayers with suspended linkers. Experiments demonstrate consistent unidirectional movement of hydrogel crawlers across multiple thermal cycles on flat, unpatterned surfaces. We explain the mechanism using finite element simulations and varying experimental parameters such as the number of segments, linker size, and design. We compare and validate experiments, image analysis, and models to elucidate design and engineering principles. We anticipate that this mechanism could be widely applied and adapted to create a variety of shape-changing and smart locomotors. | Aishwarya Pantula; Bibekananda Datta; Yupin Shi; Margaret Wang; Jiayu LIu; Siming Deng; Noah Cowan; Thao Nguyen; David Gracias | Materials Science; Polymer Science; Chemical Engineering and Industrial Chemistry; Materials Processing; Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627c0aaa59f0d682ea8d5231/original/untethered-unidirectionally-crawling-gels-driven-by-an-asymmetry-in-contact-forces.pdf |
66ffec1acec5d6c1422377f8 | 10.26434/chemrxiv-2024-w17ws-v2 | First Principles Assessment of ZnTe and CdSe as Prospective Tunnel Barriers at the InAs/Al Interface | Majorana zero modes are predicted to emerge in superconductor/semiconductor interfaces, such as Al/InAs. Majorana modes could be utilized for fault tolerant topological qubits. However, their realization is hindered by materials challenges. The coupling between the superconductor and the semiconductor may be too strong for Majorana modes to emerge, due to effective doping of the semiconductor by the metallic contact. This could be mediated by adding a tunnel barrier of controlled thickness. We use density functional theory (DFT) with Hubbard U corrections, whose values are machine-learned via Bayesian optimization (BO) to assess ZnTe and CdSe as prospective tunnel barriers for the InAs/Al interface. The results of DFT+U(BO) for ZnTe are validated by comparison to angle resolved photoemission spectroscopy (ARPES). We then study bilayer interfaces of the three semiconductors with each other and with Al, as well as tri-layer interfaces with a varying number of ZnTe or CdSe layers inserted between InAs and Al. We find that 16 atomic layers of either material completely insulate the InAs from metal induced gap states (MIGS). However, ZnTe and CdSe differ significantly in their band alignment, such that ZnTe forms an effective barrier for electrons, whereas CdSe forms a barrier for holes. Because of Fermi level pinning in the conduction band at the surface, only electron transport is possible in InAs-based devices. Therefore, ZnTe is the better choice. Based on the results of our simulations, we suggest conducting experiments with ZnTe barriers in the thickness range of 6-18 atomic layers. | Malcolm Jardine; Derek Dardzinski; Zefeng Cai; Vladimir Strocov; Moïra Hocevar; Chris Palmstrøm; Noa Marom | Materials Science; Core-Shell Materials; Nanostructured Materials - Materials | CC BY 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ffec1acec5d6c1422377f8/original/first-principles-assessment-of-zn-te-and-cd-se-as-prospective-tunnel-barriers-at-the-in-as-al-interface.pdf |
620e16a60c0bf04a07ec9b84 | 10.26434/chemrxiv-2022-5m2t5 | Access to Fluoroalkylated Azoles and 2-Acylaminoketones via Anhydride-Mediated Cleavage of NH-1,2,3-Triazoles | NH-1,2,3-Triazoles undergo a ring cleavage in reactions with fluorinated acid anhydrides (trifluoroacetic, difluoroacetic
chlorodifluoroacetic and pentafluoropropionic anhydrides) by nitrogen acylation and acid-mediated triazole ring opening. Structurally diverse fluoroalkylated oxazoles were prepared from 4,5-disubstituted-1,2,3-triazoles. Efficient synthesis of 2-acylaminoketones was achieved from 4-substituted-1,2,3-triazoles. Finally, easy access to fluoroalkylated imidazoles and 1,2,4-tetrazines was
developed by one-pot two step routes from fluorinated anhydrides and NH-triazoles. | Vladimir Motornov; Petr Beier | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620e16a60c0bf04a07ec9b84/original/access-to-fluoroalkylated-azoles-and-2-acylaminoketones-via-anhydride-mediated-cleavage-of-nh-1-2-3-triazoles.pdf |
63b6c5ef74e09535e80f226e | 10.26434/chemrxiv-2023-rst23 | How to deal with future possible coronavirus: hints from the analysis of the interaction between potential inhibitors with 3C-Like protease via molecular docking | The COVID-19 pandemic has resulted in millions of infections and deaths. However, there is still a lack of broad-spectrum effective and safe anti-CoV drugs. 3CL protease is one of the promising targets for the development of anti-CoV drugs. In this study, we explored the binding effects of 36 potential inhibitors with five hu-man coronavirus 3CL proteases (SARS-CoV-2, MERS-CoV, SARS-CoV, HCoV-HKU1 and HCoV-229E) via molecular docking using SwissDock. The correlation study demonstrated that small molecule inhibitors with higher molecular weight were likely to be more effective. Based on the fact that SARS-CoV-2 3CLpro had the poorest binding tendency and affinity with ligands, we predicted that the CoVs will become more and more difficult to overcome as they evolve. The interaction analysis showed that the lethal human coronavirus 3CL proteases had higher hydrogen bonding interaction propensity on Glu16X. These findings offer interesting perspectives for future drug design strategies against human coronavirus. | Tao Meng; Yinong Qiu; Fangya Li; Jianyu Zhang | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b6c5ef74e09535e80f226e/original/how-to-deal-with-future-possible-coronavirus-hints-from-the-analysis-of-the-interaction-between-potential-inhibitors-with-3c-like-protease-via-molecular-docking.pdf |
60c755efee301c067fc7b270 | 10.26434/chemrxiv.14185742.v1 | Non-Covalent Bonding Caught in Action: From Amorphous-to-Cocrystalline Molecular Thin Films | <p>We demonstrate the solvent-free amorphous-to-cocrystalline transformations of nanoscale molecular films. Exposing amorphous films to vapors of a haloarene results in the formation of a cocrystalline coating. This transformation proceeds by gradual strengthening of halogen-bonding interactions as a result of the crystallization process. The gas-solid diffusion mechanism involves formation of an amorphous metastable phase prior to crystallization of the films. <i>In-situ </i>optical microscopy shows mass transport during this process, which is confirmed by cross-section analysis of the final structures using focused ion beam (FIB) milling combined with scanning electron microscopy (SEM). Nanomechanical measurements support the role of rigidity of the amorphous films influences the crystallization process. This surface transformation results in molecular arrangements that are not readily obtained through other means. Whereas cocrystals grown in solution crystallize in a monoclinic centrosymmetric space group, whereas the on-surface halogen-bonded assembly crystallizes into a noncentrosymmetric material with a bulk second-order non-linear optical (NLO) response.<br /></p> | Olga Chovnik; Sidney Cohen; Iddo Pinkas; Lothar Houben; Tatiana E. Gorelik; Yishay Feldman; linda shimon; Mark Iron; Michal Lahav; Milko van der Boom | Supramolecular Chemistry (Org.); Thin Films; Microscopy; Spectroscopy (Anal. Chem.); Self-Assembly; Spectroscopy (Physical Chem.); Structure; Surface; Materials Chemistry; Crystallography; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755efee301c067fc7b270/original/non-covalent-bonding-caught-in-action-from-amorphous-to-cocrystalline-molecular-thin-films.pdf |
61b338f9dcbea25ce09dd440 | 10.26434/chemrxiv-2021-k6hqt-v3 | Ultrafast intersystem crossing in xanthone from wavepacket dynamics | Most aromatic ketones containing first-row elements undergo unexpectedly fast intersystem crossing in few tens of picoseconds and a quantum yield close to unity. Among them, xanthone (9H-xanthen-9-one) possesses one of the fastest singlet-triplet rates of ~1.5 ps. The exact mechanism of this unusually fast transition is still under debate. Here, we perform the wavepacket dynamics of the photochemistry of xanthone in the gas phase and in polar solvents. We show that xanthone follows El-Sayed's rule for intersystem crossing. From the second singlet excited state, the mechanism is sequential: (i) an internal conversion between singlets 1pipi*-1npi* (85 fs), (ii) an intersystem crossing 1npi*-3pipi* (2.0 ps), and (iii) an internal conversion between triplets 3pipi*-3npi* (602 fs). Each transfer finds its origin in a barrierless access to electronic state intersections. These intersections are close to minimum energy structures, allowing for efficient transitions from the initial singlet state to the triplets.
| Marc Alías Rodríguez; Coen De Graaf; Miquel Huix-Rotllant | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b338f9dcbea25ce09dd440/original/ultrafast-intersystem-crossing-in-xanthone-from-wavepacket-dynamics.pdf |
61fa02aa71868d546ac6e929 | 10.26434/chemrxiv-2022-3xq29 | Stereocontrolled Acyclic Diene Metathesis Polymerization | The cis/trans geometry of olefins is known to dramatically influence the thermal and mechanical properties of polyalkenamers. Yet, polymerization methods that allow the practitioner to efficiently control this parameter are scarce. Herein, we report the development of a stereoretentive acyclic diene metathesis (ADMET) polymerization that capitalizes on the unique reactivity of dithiolate Ru carbenes combined with cis monomers. These Ru catalysts exhibit exquisite retention of the cis geometry and tolerate many polar functional groups, enabling the synthesis of all-cis polyesters, polycarbonates, polyethers, and polysulfites. Additionally, the stereoretentive ADMET is characterized by low catalyst loadings and tolerance toward trans impurities in the monomer batch, which should lend to ready implementation at large-scale. Remarkably, modulation of the reaction conditions including temperature and reaction time leads to an erosion of stereoretention, thereby permitting a stereocontrolled synthesis of polyalkenamers with predictable cis:trans ratios. The impact of the cis:trans alkene content within the polymer backbone on the thermal properties was clearly demonstrated through differential scanning calorimetry and thermogravimetric analysis. Stereocontrolled ADMET provides a unique synthetic approach toward materials with precise structures and tailored properties. | Ting-Wei Hsu; Samuel Kempel; Alyssa Felix Thayne; Quentin Michaudel | Organic Chemistry; Polymer Science; Stereochemistry; Polymerization (Polymers); Polymerization catalysts | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fa02aa71868d546ac6e929/original/stereocontrolled-acyclic-diene-metathesis-polymerization.pdf |
60c7472af96a000934286e93 | 10.26434/chemrxiv.11550057.v1 | Discovery of a Difluoroglycine Synthesis Method through Quantum Chemical Calculations | The systematic exploration of synthetic pathways to afford a desired product through quantum chemical calculations remains a considerable challenge. In 2013, Maeda et al. introduced ‘quantum chemistry aided retrosynthetic analysis’ (QCaRA), which uses quantum chemical calculations to search systematically for decomposition paths of the target product and propose a synthesis method. However, until now, no new reactions suggested by QCaRA have been reported to lead to experimental discoveries. Using a difluoroglycine derivative as a target, this study investigated the ability of QCaRA to suggest various synthetic paths to the target without relying on previous data or the knowledge and experience of chemists. Furthermore, experimental verification of the seemingly most promising path led to the discovery of a synthesis method for the difluoroglycine derivative. The extent of the hands-on expertise of chemists required during the verification process was also evaluated. These insights are expected to advance the applicability of QCaRA to the discovery of viable experimental synthetic routes. | Tsuyoshi Mita; Yu Harabuchi; Satoshi Maeda | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7472af96a000934286e93/original/discovery-of-a-difluoroglycine-synthesis-method-through-quantum-chemical-calculations.pdf |
61daf7b1e7b751b1b8934f98 | 10.26434/chemrxiv-2022-l355m | Breaking The Monotony: Cobalt and Maleimide as a New Entrant to the Catellani Reaction | A catalytic system was discovered for the intramolecular C-H amidation of N-phenoxy acetamide derivatives. For the first time, a cobalt catalyst was employed for the Catellani reaction. Additionally, a monocyclic olefin, maleimide, was used as a transient mediator in place of bicyclic norbornenes. Maleimide promotes a Co(III) intermediate to undergo oxidative addition into the O–N bond to form a Co(V) nitrene species and subsequently directs nitrene addition to the ortho position. A plausible mechanism for the transformation is proposed, supported by experimental and density functional theory (DFT) computational studies. Further, the synthetic utility of this methodology was demonstrated via the ortho-amidation of estrone. | Tanmayee Nanda; Shyam Kumar Banjare; Supreeth Prasad; Pragati Biswal; Lokesh Gupta; Bedadyuti Vedvyas Pati; Smruti Ranjan Mohanty; Dean J Tantillo; Ponneri C. Ravikumar | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Bond Activation; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61daf7b1e7b751b1b8934f98/original/breaking-the-monotony-cobalt-and-maleimide-as-a-new-entrant-to-the-catellani-reaction.pdf |
60c753fdee301ca26bc7aed6 | 10.26434/chemrxiv.13591313.v1 | Preparation of AlB12 Powder by Self-Propagating High-Temperature Synthesis (SHS) | <p>Self-propagating high-temperature synthesis (SHS) process
is used to prepare AlB<sub>12</sub>. The phase analysis results of preparing
AlB<sub>12</sub> with Al and B<sub>2</sub>O<sub>3</sub> as raw materials show
that: under air and argon conditions, the self-propagating and acid-washed self-propagating
powders all have α-Al<sub>2</sub>O<sub>3</sub> impurities; Mg, Al and B<sub>2</sub>O<sub>3</sub>
are used as raw materials. The phase analysis results of the preparation of AlB<sub>12</sub>
show that under argon conditions, the self-propagating and acid-washed
self-propagating powder has unremovable MgAl<sub>2</sub>O<sub>4</sub>
impurities; the root cause of the low purity of AlB<sub>12</sub> prepared by
the self-propagating method is that there are unremovable impurities exist.</p> | Chao Wang; Xiaoming Cao; Mengge Dong; Lu Zhang; Jianxing Liu; Xiaozhou Cao; Xiangxin Xue | Ceramics | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753fdee301ca26bc7aed6/original/preparation-of-al-b12-powder-by-self-propagating-high-temperature-synthesis-shs.pdf |
6532b8b82431cc1dac2c6bf8 | 10.26434/chemrxiv-2023-v1nqv | Elucidating Ultranarrow 2F7/2 to 2F5/2 Absorption in Ytterbium(III) Complexes | Achieving ultranarrow absorption linewidths in the condensed phase could enable optical state preparation of specific non-thermal states, a prerequisite for quantum-enabled technologies. The 4f orbitals of lanthanide(III) complexes are often referred to as “atom-like”, reflecting their isolated nature, and are promising substrates for the optical preparation of specific quantum states. To better understand the photophysical properties of 4f states and assess their promise for quantum applications, theoretical building blocks are required for rapid screening. In this study, an atomic-level perturbative calculation (spin-orbit crystal field, SOCF) is applied to various Yb(III) complexes to investigate their linear absorption and emission through a fitting mechanism of their experimentally determined transition energies and oscillator strengths. In particular, the optical properties of (thiolfan)YbCl(THF) (thiolfan = 1,1′-bis(2,4-di-tert-butyl-6-thiomethylenephenoxy)ferrocene), a recently reported complex with a ultranarrow optical linewidth, are computed and compared to those of other Yb(III) compounds. Through a symmetry descent procedure and a transition energy sampling study, major contributors to the optical linewidth are identified. We find that low-symmetry crystal fields, combined with the ultra-high similarity of states resulting from an anisotropic crystal field, create particularly isolated f-f transitions and narrow linewidths. Simultaneously, we find that these atom-like transitions have highly correlated excited-ground energy fluctuations that serve to greatly suppress inhomogeneous line-broadening. This article illustrates how SOCF can be used as a low-cost method to probe the influence of symmetry and ligands on the optical properties of Yb(III) complexes to assist the development of novel lanthanide series quantum materials. | Barry Y. Li; Claire E. Dickerson; Ashley J. Shin; Changling Zhao; Yi Shen; Yongjia He; Paula L. Diaconescu; Anastassia N. Alexandrova; Justin R. Caram | Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Lanthanides and Actinides; Spectroscopy (Inorg.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6532b8b82431cc1dac2c6bf8/original/elucidating-ultranarrow-2f7-2-to-2f5-2-absorption-in-ytterbium-iii-complexes.pdf |
61a6579f568d33caaa4bff69 | 10.26434/chemrxiv-2021-crpd0 | ChemInformatics Model Explorer (CIME): Exploratory analysis of chemical model explanations | The introduction of machine learning to small molecule research – an inherently multidisciplinary field in which chemists and data scientists combine their expertise and collaborate – has been vital to making screening processes more efficient.
In recent years, numerous models that predict pharmacokinetic properties or bioactivity have been published, and these are used on a daily basis by chemists to make decisions and prioritize ideas. The emerging field of explainable artificial intelligence is opening up new possibilities for understanding the reasoning that underlies a model. In small molecule research, this means relating contributions of substructures of compounds to their predicted properties, which in turn also allows the areas of the compounds that have the greatest influence on the outcome to be identified. However, there is no interactive visualization tool that facilitates such interdisciplinary collaborations towards interpretability of machine learning models for small molecules.
To fill this gap, we present CIME (ChemInformatics Model Explorer), an interactive web-based system that allows users to inspect chemical data sets, visualize model explanations, compare interpretability techniques, and explore subgroups of compounds. The tool is model-agnostic and can be run on a server or a workstation. | Christina Humer; Henry Heberle; Floriane Montanari; Thomas Wolf; Florian Huber; Ryan Henderson; Julian Heinrich; Marc Streit | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2021-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a6579f568d33caaa4bff69/original/chem-informatics-model-explorer-cime-exploratory-analysis-of-chemical-model-explanations.pdf |
60c748f2567dfe2534ec4ad7 | 10.26434/chemrxiv.11336975.v3 | Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein (NCp7) using Extensive Polarizable Force Field Free-Energy Simulations | Using polarizable (AMOEBA) and non-polarizable (CHARMM) force fields, we compare the relative free-energy stability of two extreme conformations of the HIV-1 NCp7 nucleocapsid that had been previously experimentally advocated to prevail in solution. Using accelerated sampling techniques, we show that they differ in stability by no more than 0.75-1.9 kcal/mol depending on the reference protein sequence. While the extended form appears to be the most probable structure, both forms should thus coexist in water explaining the differing NMR findings.<br /> | Léa El Khoury; Frédéric Célerse; Louis Lagardere; Luc-Henri Jolly; Étienne Derat; Zeina Hobaika; Richard G. Maroun; Pengyu Ren; Serge Bouaziz; Nohad Gresh; Jean-Philip Piquemal | Biophysics; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748f2567dfe2534ec4ad7/original/reconciling-nmr-structures-of-the-hiv-1-nucleocapsid-protein-n-cp7-using-extensive-polarizable-force-field-free-energy-simulations.pdf |
60c74e3b469df45f29f44429 | 10.26434/chemrxiv.12727796.v1 | Triboluminescence of a New Family of CuI-NHC Complexes in Crystalline Solid and in Amorphous Polymer Films | Triboluminescent compounds that generate emission of light in response to mechanical stimulus are promising targets in the development of “smart materials” and damage sensors. Among triboluminescent metal complexes, rare-earth europium and terbium complexes are most widely used, while there is no systematic data on more readily available and inexpensive Cu complexes. We report a new family of photoluminescent Cu-NHC complexes that show bright triboluminescence (TL) in the crystal state visible in ambient indoor light under air. Moreover, when these complexes are blended into amorphous polymer films even at small concentrations, TL is easily observed. Observation of TL in polymer films overcomes the limitation of using crystals and opens up possibilities for the development of mechanoresponsive coatings and materials based on inexpensive metals such as Cu. Our results may also have implications for the understanding of the TL effect’s origin in polymer films. | Ayumu Karimata; Pradnya Patil; Robert R. Fayzullin; Eugene Khaskin; Sébastien Lapointe; Julia Khusnutdinova | Organic Polymers; Organometallic Compounds; Polymers; Sensors; Transition Metal Complexes (Inorg.); Coordination Chemistry (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e3b469df45f29f44429/original/triboluminescence-of-a-new-family-of-cu-i-nhc-complexes-in-crystalline-solid-and-in-amorphous-polymer-films.pdf |
658a85f2e9ebbb4db9c54b43 | 10.26434/chemrxiv-2023-jh93v | Hydroxyl-Diazomethylation of Alkenes via Photoredox Catalysis | α-Diazoesters belong to significantly important carbenoid precursors in synthetic chemistry, diazomethylation-based difunctionalization of alkenes is highly valuable but remain nontrivial. Herein, we reported a general and modular approach for the direct 1,2-hydroxyl-diazomethylation of alkenes through visible-light photoredox catalysis. This process exploits photocatalyzed strategy to convert alkenes to γ-hydroxyl-α-diazoesters using α-diazo iodonium salts as carbyne precursors, featuring wide substrate tolerance and broad late-stage diversifications. Mechanistic studies suggest that the formation of γ-carbocation-tethered α-diazoesters plays a crucial role in trapping H2O to allow for this transformation. | Ying Zeng; Xiaochan Zheng; Shaoyong Chen; Zhongfeng Luo; Haisheng Xie; Junshan Liu; Huanfeng Jiang; Wei Zeng | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2023-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658a85f2e9ebbb4db9c54b43/original/hydroxyl-diazomethylation-of-alkenes-via-photoredox-catalysis.pdf |
65856d2766c1381729c9064c | 10.26434/chemrxiv-2023-m1x1r | Highly modular PDMS microwave-microfluidic chip reactor for MAOS applications | In this work, we introduce a microfluidic chip reactor based on a Complementary Split Ring Resonator (CSRR) for conducting microscale microwave-assisted organic synthesis (MAOS). This microwave-microfluidic chip reactor (µw-µf-CR) is easy to assemble and highly customizable, featuring interchangeable flow cells fabricated on inexpensive PDMS, providing high levels of versatility in
terms of manufacturing and design. Various flow cells were designed and explored, offering internal volumes ranging from 2.82 to 6.48 μL and accommodating flow rates between 5 to 8 μL/min. This allows the reaction to be irradiated within a timeframe spanning from seconds to minutes. Remarkably, our setup design bears the
potential to operate across a broad range of frequencies (around 2 or 6-12 GHz). Moreover, it provides controllable and efficient heating, reaching temperatures up to 120°C within seconds with a maximum low input power of 4.4 W. Simulations showed an excellent homogeneous heat distribution throughout the flow cell. The applicability of the µw-µf-CR was demonstrated in several organic reactions, where good yields and short reaction times were observed.
| Laura Y. Vázquez-Amaya; Matko Martinic; Bart Nauwelaers; Erik V. Van der Eycken; Tomislav Markovic; Upendra K. Sharma | Organic Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Reaction Engineering; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65856d2766c1381729c9064c/original/highly-modular-pdms-microwave-microfluidic-chip-reactor-for-maos-applications.pdf |
63c518a3cac318a5b3a28539 | 10.26434/chemrxiv-2023-l11xx-v3 | Size-Dependent Errors in Real-Time Electron Density Propagation | Real-time (RT) electron density propagation with time-dependent density functional theory (TDDFT) or
Hartree-Fock (TDHF) is one of the most popular methods to model the charge transfer in molecules and
materials. However, both RT-TDHF and RT-TDDFT within the adiabatic approximation are known to
produce inaccurate evolution of the electron density away from the ground state in model systems, leading
to large errors in charge transfer and erroneous shifting of peaks in absorption spectra. Given the poor
performance of these methods with small model systems and the widespread use of the methods with larger
molecular and materials systems, here we bridge the gap in our understanding of these methods and examine
the size-dependence of errors in real-time density propagation. We analyze the performance of real-time
density propagation for systems of increasing size during the application of a continuous resonant field to
induce Rabi-like oscillations, during charge-transfer dynamics, and for peak shifting in simulated absorption
spectra. We find that the errors in the electron dynamics are indeed size dependent for these phenomena,
with the largest system producing the results most aligned with those expected from linear response theory.
The results suggest that although RT-TDHF and RT-TDDFT methods may produce severe errors for model
systems, the errors in charge transfer and resonantly driven electron dynamics may be much less significant
for more realistic, large-scale molecules and materials. | Karnamohit Ranka; Christine M. Isborn | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c518a3cac318a5b3a28539/original/size-dependent-errors-in-real-time-electron-density-propagation.pdf |
66c8883aa4e53c48765c8a66 | 10.26434/chemrxiv-2024-b7sxm | Understanding and Quantifying Molecular Flexibility: Torsion Angular Bin Strings | Molecular flexibility is a commonly used, but not easily quantified term. It is at the core of understanding composition and size of a conformational ensemble and contributes to many molecular properties. For many computational workflows, it is necessary to reduce a conformational ensemble to meaningful representatives, however defining them and guaranteeing the ensemble’s completeness is difficult. We introduce the concepts of torsion angular bin strings (TABS) as a discrete vector representation of a conformer’s dihedral angles and the number of possible TABS (nTABS) as an estimation for the ensemble size of a molecule, respectively. Here, we show that nTABS corresponds to an upper limit for the size of the conformational space of small molecules and compare the classification of conformer ensembles by TABS with classifications by RMSD. Overcoming known drawbacks like the molecular size dependency and threshold picking of the RMSD measure, TABS is shown to meaningfully discretize the conformational space and hence allows e.g. for fast checks of the coverage of the conformational space. The current proof-of-concept implementation is based on the ETKDGv3sr conformer generator as implemented in the RDKit and known torsion preferences extracted from small-molecule crystallographic data. | Jessica Braun; Paul Katzberger; Gregory A. Landrum; Sereina Riniker | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c8883aa4e53c48765c8a66/original/understanding-and-quantifying-molecular-flexibility-torsion-angular-bin-strings.pdf |
60c75104842e650426db3b04 | 10.26434/chemrxiv.13089353.v1 | Spontaneous Emergence of Membrane-Forming Protoamphiphiles from a Lipid-Amino Acid Mixture Under Wet-Dry Cycles | <p>The
prelude to the origin of cellular life on Earth would have involved a fundamental
step, that of protocell formation. This involves the coming together of two
crucial processes; abiotic synthesis of informational and catalytic polymers,
and the assembly of membrane compartments. Mutual interactions between these
processes would have likely affected the emergence and early stages of
protocell evolution. Previous investigations have predominantly focused on
cooperative interactions, often neglecting any competitive behavior that might
ensue as ‘counterproductive cross-talk’. However, in a realistic scenario, both
cooperative and competitive reactions would have occurred simultaneously in a
complex prebiotic soup, generating a plethora of
chemical species with their own prebiotic implications. In this study, we followed
a systematic and unbiased approach to explore this interdependence. We
used a lipid-amino acid system to demonstrate the above-mentioned phenomenon
wherein we investigated the effect of a membrane-forming amphiphile on peptide
synthesis, under prebiotically plausible conditions. </p><p><br /></p>
<p>Interestingly, our study shows the formation of a hitherto unobserved reaction
product that could have played a significant role during the emergence of life
on the early Earth. We do show that peptide synthesis occurs but with a
decrease in the yield. This is due to another concurrent and competing
reaction, wherein an amino acid covalently interacts with a phospholipid to
generate new amphiphilic species called N-acyl amino acids (NAAs) via an
ester-amide exchange process. These NAAs are thermostable and, hence, persistent
even at high temperatures. Furthermore, this protoamphiphile is also able to
self-assemble into vesicles at acidic pH. <i>Au
contraire</i>, fatty acids, a widely accepted constituent of prebiotic
compartments, have been shown to generate vesicles only at neutral to alkaline
pH. Thus, NAAs could have had a selective advantage over fatty acids to form
thermostable protocell compartments under acidic geothermal pool-like
conditions, a niche that has gained prominence as one of the important
geological settings where life could have originated. Our study underlines the
importance of an unbiased exploration of the complex interactions between
prebiotic processes, which could potentially open new avenues to solving the
origin of life conundrum. </p>
<p> </p> | Manesh Joshi; Anupam Sawant; Sudha Rajamani | Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75104842e650426db3b04/original/spontaneous-emergence-of-membrane-forming-protoamphiphiles-from-a-lipid-amino-acid-mixture-under-wet-dry-cycles.pdf |
60c741ec9abda2394ef8bf59 | 10.26434/chemrxiv.8187608.v1 | Steric Protection of Rhodium-Nitridyl Radical Species | In an attempt to synthesize a mononuclear rhodium nitridyl complex with a reduced tendency to undergo nitridyl radical N-N coupling we synthesized a bulky analog of Milstein’s bipyridine-based PNNH ligand, bearing a tert-butyl group at the 6’ position of the bipyridine moiety. A three-step synthetic route toward this new bulky tBu<sub>3</sub>PNNH ligand was developed, involving a selective nucleophilic substitution step, followed by a Stille coupling and a final hydrophosphination step to afford the desired 6-(tert-butyl)-6'-((di-tert-butylphosphino)methyl)-2,2'-bipyridine (tBu<sub>3</sub>PNNH) ligand. This newly developed tBu<sub>3</sub>PNNH ligand was incorporated in the synthesis of the sterically protected azide complex [Rh(N<sub>3</sub>)(tBu<sub>3</sub>PNNH)]. We explored N<sub>2</sub> elimination form this species using photolysis and thermolysis, hoping to synthesize a mononuclear rhodium complex with a terminal nitrido moiety. Characterization of the reaction product(s) using NMR, coldspray HR-ESI-MS and EPR spectroscopy shows that the material is both EPR and NMR silent, and data obtained by MS spectrometry revealed masses corresponding with both monomeric and dimeric nitrido/nitridyl complexes. The combined data point to formation of a paramagnetic [(tBu<sub>3</sub>PNN)Rh(µ-N)Rh(tBu<sub>3</sub>PNN)] species. It thus seems that despite its three tBu groups the new ligand is not bulky enough to prevent formation of Rh-N-Rh bridged species. However, the increased steric environment does prevent further reaction with carbon monoxide, which is unable to coordinate to rhodium.<br /> | Christophe Rebreyend; Valentinos Mouarrawis; Jarl Ivar van der Vlugt; Bas de Bruin | Bond Activation; Coordination Chemistry (Organomet.); Ligand Design; Small Molecule Activation (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741ec9abda2394ef8bf59/original/steric-protection-of-rhodium-nitridyl-radical-species.pdf |
60c753c1702a9b045a18c3e4 | 10.26434/chemrxiv.13029359.v2 | Triplet State Baird-Aromaticity in Macrocycles: Scope, Limitations and Complications | <p>The aromaticity of cyclic 4<i>n</i>p-electron molecules
in their first pp* triplet state (T<sub>1</sub>),
labelled Baird-aromaticity, has gained growing attention in the last decade.
Here we explore computationally the limitations of T<sub>1</sub> state
Baird-aromaticity in macrocyclic compounds, <b>[<i>n</i>]CM</b>’s, which are cyclic
oligomers of four different monocycles (M = <i>para</i>-phenylene
(PP), 2,5-linked furan (FU), 1,4-linked cyclohexa-1,3-diene (CHD), and 1,4-linked
cyclopentadiene (CPD)). We strive for conclusions that are general for various DFT
functionals, although for macrocycles with up to 20 p-electrons in their main conjugation paths we find
that for their T<sub>1</sub> states single-point energies at both canonical
UCCSD(T) and approximative DLPNO-UCCSD(T) levels are lowest when based on
UB3LYP over UM06-2X and UCAM-B3LYP geometries. This finding is in contrast to
what has earlier been observed for the electronic ground state of expanded
porphyrins. Yet, irrespective of functional, macrocycles with 2,5-linked furans
(<b>[<i>n</i>]CFU</b>’s)
retain Baird-aromaticity until larger <i>n</i>
than those composed of the other three monocycles. Also, when based on
geometric, electronic and energetic aspects of aromaticity, a <b><sup>3</sup>[<i>n</i>]CFU</b> with a specific <i>n</i>
is more strongly Baird-aromatic than the analogous <b><sup>3</sup>[<i>n</i>]CPP</b> while
the magnetic indices tell the opposite. To construct large T<sub>1</sub> state
Baird-aromatic <b>[<i>n</i>]CM</b>’s the design should be such that the T<sub>1</sub> state
Baird-aromaticity of the macrocyclic perimeter dominates over a situation with local
closed-shell Hückel-aromaticity of one or a few monocycles and semi-localized
triplet diradical character. Monomers with lower Hückel-aromaticity in S<sub>0</sub>
than benzene (<i>e.g.</i>, furan) that do
not impose steric congestion are preferred. Structural confinement imposed by, <i>e.g.</i>, methylene bridges is also an approach
to larger Baird-aromatic macrocycles. Finally, by using the Zilberg-Haas description
of T<sub>1</sub> state aromaticity we reveal the analogy to the
Hückel-aromaticity of the corresponding closed-shell dications, yet, observe
stronger Hückel-aromaticity in the macrocyclic dications than Baird-aromaticity
in the T<sub>1</sub> states of the neutral macrocycles. </p> | Rabia Ayub; Ouissam El Bakouri; Joshua R. Smith; Kjell Jorner; Henrik Ottosson | Photochemistry (Org.); Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753c1702a9b045a18c3e4/original/triplet-state-baird-aromaticity-in-macrocycles-scope-limitations-and-complications.pdf |
673f839a5a82cea2fa46b483 | 10.26434/chemrxiv-2024-f1znb | Assessing the Performance of Emerging and Existing Continuous Monitoring Solutions under a Single-blind Controlled Testing Protocol | Continuous Monitoring (CM) solutions have been identified as one method to address methane emissions at oil and gas (O&G) facilities, as these solutions may facilitate faster emission detection and repair than traditional survey methods. This study tested 13 CM solutions over 12 weeks using single-blind controlled testing. Controlled release rates ranged from 0.08 to 6.75 kg CH4/hr and lasted 18 minutes to 8 hours. Six solutions demonstrated 90% detection limits (DLs) within the range of controlled releases, 0.5 [0.3, 0.6] kg CH4/hr to 6.8 [5.9, 8.0] kg CH4/hr. Of the six solutions, 4 had False Positive (FP) rates of 7.8-14%, and four had False Negative rates (FN) of 8-34.1%. Compared with Ilonze et al., these results show retested solutions balancing method sensitivity and FP and FN rates. All scanning/imaging solutions had high localization (≥ 40%) precision and accuracy to the equipment unit. Eleven of 13 solutions were tested for quantification; three had a mean relative quantification error ranging from 33.4 [0.85, 66.0] % to 96.1 [63.4, 128.9] %, 95% CI for leaks between 0.1 – 1 kg CH4/hr. For larger emissions (> 1 kg CH4/hr), nine solutions had a mean relative quantification error ranging from 2.8 [-20.3, 25.9] % to 32.8 [17.2, 48.5] %, 95% CI. Relative to previous studies, uncertainties in quantification estimates decreased, as did FN and FP rates, with improved detection limits for 2 of the four retested solutions. These findings highlight that continuous, rigorous testing enhances solution performance, with notable improvements observed across multiple test programs using the same test protocol. | Fancy Cheptonui; Ethan Emerson; Chiemezie Ilonze; Rachel Day; Ezra Levin; Daniel Fleischmann; Ryan Brouwer; Daniel Zimmerle | Energy; Earth, Space, and Environmental Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673f839a5a82cea2fa46b483/original/assessing-the-performance-of-emerging-and-existing-continuous-monitoring-solutions-under-a-single-blind-controlled-testing-protocol.pdf |
64ace81aba3e99daefe30beb | 10.26434/chemrxiv-2023-z157s | Computational study on the action of saturated, monounsaturated and polyunsaturated fatty acids against Echinococcus granulosus EgFABP1 | The zoonotic infection caused by tapeworms Echinococcus is a neglected tropical disease in poor regions with limited access to suitable sanitary conditions. Hydatid cysts produced by Echinococcus granulosus use fatty-acid-binding proteins (FABP) to obtain the fatty acids and cholesterol necessary for their survival from the host. In this work, we analyzed the behaviour of saturated, monounsaturated, and polyunsaturated fatty acids against EgFABP1. To achieve this goal, we used quantum mechanical analysis by density functional theory, molecular dynamics simulations, and binding free energy estimations by MM/GBSA. This study has allowed to elucidate, among a variety of fatty acids, the promising action of docosahexaenoic acid and eicosapentaenoic acid against EgFABP1. Hence, these results suggest that the action of polyunsaturated fatty acids could play an interesting role in detecting early Echinococcus granulosus | Margot Paco-Chipana; Karel Mena-Ulecia; Yoan Hidalgo Rosa; Maria Isabel Herrera; Luis Daniel Goyzueta-Mamani; Berly Cárdenas-Pillco; Miguel Angel Chavez-Fumagalli; Haruna L. Barazorda-Ccahuana | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ace81aba3e99daefe30beb/original/computational-study-on-the-action-of-saturated-monounsaturated-and-polyunsaturated-fatty-acids-against-echinococcus-granulosus-eg-fabp1.pdf |
67115cdd51558a15ef5e8319 | 10.26434/chemrxiv-2024-k0svz | Characterizing the Stability of Ultra-Thin Metal Oxide Catalyst Films in Non-thermal Plasma CO2 Reduction Reactions | The use of metal oxide catalysts to enhance plasma CO2 reduction has seen significant recent development towards processes to reduce greenhouse gas emissions and produce renewable chemical feedstocks. While plasma reactors are effective at producing the intended chemical transformations, the conditions can result in catalyst degradation. Atomic layer deposition (ALD) can be used to synthesize complex, hierarchically structured metal oxide plasma catalysts that, while active for plasma CO2 reduction, are particularly vulnerable to degradation due to their high surface area and nanoscopic thickness. In this work, we characterized the effects of extended non-thermal, glow-discharge plasma exposure on ALD synthesized, ultra-thin film (< 30 nm) TiO2 and ZnO catalysts. We used x-ray diffraction, reflectivity, and spectroscopy to compare films exposed to a CO2 plasma to ones exposed to an Ar plasma and to ones annealed in air. We found that the CO2 plasma exposure generated some surface reduction in TiO2 and increased surface roughening by a small amount, but did not initiate any phase changes or crystallite growth. The results suggest that ALD-deposited metal oxide films are robust to low pressure CO2 plasma exposure and are suitable as catalysts or catalyst supports in extended reactions. | Samuel Conlin; Joseph Joel Muhanga; David Parette; Robert Coridan | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67115cdd51558a15ef5e8319/original/characterizing-the-stability-of-ultra-thin-metal-oxide-catalyst-films-in-non-thermal-plasma-co2-reduction-reactions.pdf |
616461328b620db66f4bd541 | 10.26434/chemrxiv-2021-ttdr9 | Self-organization at air-water interfaces emerging from
Marangoni and elastocapillary effects
directed by amphiphile filament connections. | Marangoni and elastocapillary effects are well-known as driving forces in the self-organization of floating objects at air-water interfaces. The release of surface active compounds generates Marangoni flows that cause repulsion, whereas capillary forces drive attraction. Typically, these interactions are non-directional and mechanisms to establish directional connections between the self-organizing elements are lacking. In this work, we unravel the mechanisms involved in the self-organization of a linear amphiphile into millimeter-long filaments that form connections between floating droplets. First, we show how the release of the amphiphile tetra(ethylene glycol) monododecyl ether from a floating source droplet onto the air-water interface generates a Marangoni flow. This flow extrudes self-assembled amphiphile filaments which grow from the source droplet, and concomitantly repels floating droplets in the surroundings. A hydrophobic drain droplet that depletes the amphiphiles from the air-water interface directs the Marangoni flow and thereby the growing filaments. We show how these filaments, upon tethering to the drain, potentially facilitate internal Marangoni convection and elastocapillary effects, which attract the drain back towards the source droplet. Furthermore, this concept establishes connections that are selective to the composition of the drain droplets – which influences the rate at which they deplete the amphiphile – such that repulsive and attractive forces can be balanced. Thereby, we provide a novel method through which directional attraction can be established in synthetic self-organizing systems, and advance our understanding of how complexity arises from simple building blocks. | Mitch Winkens; Peter A. Korevaar | Physical Chemistry; Interfaces; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616461328b620db66f4bd541/original/self-organization-at-air-water-interfaces-emerging-from-marangoni-and-elastocapillary-effects-directed-by-amphiphile-filament-connections.pdf |
60c747eebb8c1aa0c63dab93 | 10.26434/chemrxiv.11821731.v1 | Modulation of Metal-Azolate Frameworks for the Tunable Release of Encapsulated Glycosaminoglycans | In this work, selected GAG-based biotherapeutics, including one proteoglycan, were successfully encapsulated with high efficiency in three different pH-responsive metal-azolate frameworks (ZIF-8, ZIF-90, and MAF-7). The GAG@MOF biocomposites obtained present significant differences in terms of crystallinity, particle size, and spatial distribution of the cargo, which enables to modulate their performance as drug delivery systems. | Miriam Velasquez; Efwita Astria; Sarah Winkler; Weibin Liang; Heinz Amenitsch; Arpita Poddar; Ravi Shukla; Glenn Prestwich; John Paderi; Christian Doonan; paolo falcaro | Biocompatible Materials; Composites; Controlled-Release Systems; Core-Shell Materials; Hybrid Organic-Inorganic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747eebb8c1aa0c63dab93/original/modulation-of-metal-azolate-frameworks-for-the-tunable-release-of-encapsulated-glycosaminoglycans.pdf |
656f1bc029a13c4d47b3a2bb | 10.26434/chemrxiv-2023-1r389 | Robust Mechanism Discovery with Atom Conserving Chemical Reaction Neural Networks | Chemical reaction neural networks (CRNNs) established as the state-of-the-art tool for autonomous mechanism discovery. While they encode some fundamental physical laws, mass- and atom conservation are still violated. We enforce atom conservation by adding a dedicated neural network layer which can be interpreted as constraining the model to physically realizable stoichiometries. Using the standard test cases of the original CRNN paper, we show that the resulting atom conserving chemical reaction neural networks improve training stability and speed, offer robustness against noisy and missing data, and require less data overall. As a result, we anticipate increased model reliability and greater utilization of the potential of real-world data sets. We also discuss the potential of the new atom balance layer for other applications in combustion modeling and beyond, such as mechanism reduction and kinetic surrogate models for reactive flow simulations. | Felix Döppel; Martin Votsmeier | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656f1bc029a13c4d47b3a2bb/original/robust-mechanism-discovery-with-atom-conserving-chemical-reaction-neural-networks.pdf |
671fe8eb1fb27ce124def4de | 10.26434/chemrxiv-2024-74zr6 | Identification of orthosteric inhibitors of MutSbeta ATPase function | Orthosteric inhibitors of the human heterodimeric DNA mismatch repair complex MutSbeta were identified by high-throughput screening. Following extensive hit confirmation to remove false positives, two series were found to give consistent activity free of likely artefactual effects. Extensive hit profiling confirmed an ATP-competitive mode of action, and X-ray crystallography showed the inhibitors occupying the ATP-binding site of MSH3. | Gareth Brace; Karsten Tillack; Peter Johnson; Markus Ritzefeld; Sabine Schaertl; Elizabeth Frush; Becka Warfield; George Ballantyne; Jung-Hoon Lee; Gabriel Thieulin-Pardo; Stefan Steinbacher; Maren Thomsen; David Witte; Michael Finley; Brinda Prasad; Edith Monteagudo; Nikolay Plotnikov; Robert Pacifici; Michel Maillard; Hilary Wilkinson; Ravi Iyer; Celia Dominguez; Thomas Vogt; Dan Felsenfeld; Tasir Haque | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671fe8eb1fb27ce124def4de/original/identification-of-orthosteric-inhibitors-of-mut-sbeta-at-pase-function.pdf |
60c7540c4c8919c97aad440e | 10.26434/chemrxiv.13604450.v1 | Irreversible Inhibition of BoNT/A Protease: Unique Warhead Reactivity and Function Contingent upon a Bifunctional Approach | We describe a comprehensive screening campaign of warheads, linked to a hydroxamate chelating anchor, for the modification of Cys165 within the BoNT/A protease. <div>Engaging thorough enzyme kinetics, we detail a remarkable proximity-driven
covalent bond with an epoxide warhead, a weak electrophile; yet, one that possessed
superior irreversible inhibition, and pharmacological properties, when compared
to intrinsically higher reactive warheads. This directed, selective covalent
bond was contingent upon the crucial hydroxamate-Zn<sup>2+ </sup>chelating
interaction as exemplified by examining non-chelating compounds. </div><div>We discuss previous approaches using non-target selective cysteine-reactive
warheads to modify the BoNT/A protease of which none present any therapeutic
potential – our bifunctional strategy allows the use of intrinsically less
reactive warheads to intercept the cysteine, which will allow for less
off-target modifications of such inhibitors. Moreover, we also broach that this
bifunctional approach is not a one-off strategy that we believe can be broadly
translated to other metalloproteases that possess non-catalytic, yet, nucleophilic
residues within the enzymes catalytic sphere. </div> | Lewis Turner; Alexander Lund Nielsen; Lucy Lin; Sabine Pellett; Takashi Sugane; Margaret Olsen; Eric Johnson; Kim janda | Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7540c4c8919c97aad440e/original/irreversible-inhibition-of-bo-nt-a-protease-unique-warhead-reactivity-and-function-contingent-upon-a-bifunctional-approach.pdf |
60c75226702a9b08e918c097 | 10.26434/chemrxiv.13251344.v1 | A Chemical Definition of Efficiency | The term <i>efficient </i>has gained great popularity in the chemical literature, despite the lack of an applicable and relatable definition. In this perspective, a chemical definition of efficiency is discussed building on the concept of non-wasteful resource usage. It is proposed than an efficient method, synthesis or protocol is one which requires less resources in the form of money, time and materials than comparable approaches which accomplish the same task.<br /> | Felix Kaspar | Chemical Education - General | CC BY 4.0 | CHEMRXIV | 2020-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75226702a9b08e918c097/original/a-chemical-definition-of-efficiency.pdf |
63fd6d4a32cd591f1295c834 | 10.26434/chemrxiv-2023-lt9vb | A Convergent Total Synthesis of (+)-Ineleganolide | ABSTRACT: We report the total synthesis of the furanobutenolide-derived diterpenoid (+)-ineleganolide. The synthetic approach relies on a convergent strategy, based on the coupling of two enantioenriched fragments which are derived from (-)-linalool and (+)-norcarvone respectively. A high-yielding, one-step Michael addition and aldol cascade furnishes a pentacyclic framework as a single diastereomer, overcoming previous challenges in controlling stereochemistry. The endgame features an O2 facilitated C-H oxidation and a samarium diiodide induced semi-pinacol rearrangement to furnish the highly rigid central seven membered ring. | Benjamin Gross; Seojung Han; Scott Virgil ; Brian Stoltz | Organic Chemistry; Natural Products; Organic Synthesis and Reactions; Stereochemistry | CC BY NC 4.0 | CHEMRXIV | 2023-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fd6d4a32cd591f1295c834/original/a-convergent-total-synthesis-of-ineleganolide.pdf |
627139b1d048edfa005a9308 | 10.26434/chemrxiv-2022-1c73h-v2 | Enhancing the capacity of supercapacitive swing adsorption CO2 capture by tuning charging protocols | Supercapacitive swing adsorption (SSA) is a recently discovered electrochemically driven CO2 capture technology that promises significant efficiency improvements over traditional methods. A limitation of this approach is the relatively low CO2 adsorption capacity, and the underlying molecular mechanisms of SSA remain poorly understood, hindering optimization. Here we present a new device architecture for simultaneous electrochemical and gas adsorption measurements, and use it to investigate the effects of charging protocols on SSA performance. We show that altering the voltage applied to charge the SSA device can significantly improve performance. Charging the gas-exposed electrode positively rather than negatively increases CO2 adsorption capacity and causes CO2 desorption rather than adsorption with charging. We also show that switching the voltage between positive and negative values further increases CO2 capacity. Previously proposed mechanisms of the SSA effect fail to explain these phenomena, so we present a new mechanism based on movement of CO2-derived species into and out of electrode micropores. Overall, this work advances our knowledge of electrochemical CO2 adsorption by supercapacitors, potentially leading to devices with increased uptake capacity and efficiency. | Trevor Binford; Grace Mapstone; Israel Temprano; Alexander Forse | Physical Chemistry; Materials Science; Energy; Carbon-based Materials; Energy Storage | CC BY 4.0 | CHEMRXIV | 2022-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627139b1d048edfa005a9308/original/enhancing-the-capacity-of-supercapacitive-swing-adsorption-co2-capture-by-tuning-charging-protocols.pdf |
618bdc722bf8a939c3d6e78c | 10.26434/chemrxiv-2021-zqptw-v2 | Modular Terpene Synthesis Enabled by Mild Electrocatalytic Couplings | The synthesis of terpenes is a large field of research that is woven deeply into the history of chemistry. Terpene biosynthesis is a case-study of how the logic of a modular design can lead to diverse structures with unparalleled efficiency. This work mimics Nature by leveraging modern Ni-catalyzed electrochemical sp2–sp3 decarboxylative coupling reactions—enabled by Ag-nanoparticle modified electrodes—to intuitively assemble terpene natural products and complex polyenes. The step-change in efficiency of this approach is exemplified through the scalable preparation of 13 complex terpenes, which minimized protecting group manipulations, functional group interconversions, and redox fluctuations. Finally, the mechanistic aspects of the essential functionalized electrodes are studied in depth through a variety of spectroscopic and analytical techniques. | Stephen Harwood; Maximilian Palkowitz; Cara Gannett; Paulo Perez; Zhen Yao; Lijie Sun; Hector Abruña; Scott Anderson; phil baran | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2021-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618bdc722bf8a939c3d6e78c/original/modular-terpene-synthesis-enabled-by-mild-electrocatalytic-couplings.pdf |
60c747ba702a9bd0f718ae3d | 10.26434/chemrxiv.11770443.v1 | High Performance and Flexible Aqueous Zinc Batteries Using N-Containing Organic Cathodes | Aqueous zinc batteries are considered as one of
the most promising energy storage systems for large-scale energy storage and
wearable electronics, owing to their low cost and intrinsic safety. However, cathode materials that can reversibly host Zn<sup>2+</sup>
are still less. Here, we demonstrate that two N-containing organic compounds, hexamethoxy
hexaazatrinaphthylene (HMHATN) and hexaazatrinaphthylene (HATN), used as
cathodes can exhibit excellent reversible Zn<sup>2+</sup> storage capability
with fast kinetics and the high capacity of 542 and 963 mA h g<sup>-1</sup>,
respectively. The Zn//HMHATN and Zn//HATN full batteries display the high
energy density of 160 and 221.6 W h kg<sup>-1</sup>, respectively, and
long-term cycling stability. Further, we investigate the mechanism of Zn<sup>2+</sup>
storage in the cathodes. More importantly, the flexible aqueous Zn//HMHATN and Zn//HATN
batteries fabricated also have high capacity, long-term cycling life and impressive
energy density, displaying its application prospect in wearable electronics. Our
work opens a new system for finding organic cathode materials used in aqueous
zinc batteries. | Guangchi Sun; Baozhu Yang; Gui Yin; Hanping Zhang; Qi Liu | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747ba702a9bd0f718ae3d/original/high-performance-and-flexible-aqueous-zinc-batteries-using-n-containing-organic-cathodes.pdf |
60c75770567dfe42abec66a1 | 10.26434/chemrxiv.14402387.v1 | The Effects on Lipophilicity of Replacing Oxygenated Functionality with Their Fluorinated Bioisosteres | The replacement of oxygenated
functionality (hydroxy, alkoxy) with a fluorine atom is a very commonly used
bioisosteric replacement in medicinal chemistry. In this paper we use a
Molecular Matched Pair Analysis approach to better understand the effects of
this bioisosteric replacement on the physicochemical properties of compounds,
particularly in terms of lipophilicity. We observe that the presence of
electron-donating groups on an aromatic ring generally increase the difference
in lipophilicity between an oxygenated compound and its fluorinated analogue. | Richard J. Glyn; Graham Pattison | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75770567dfe42abec66a1/original/the-effects-on-lipophilicity-of-replacing-oxygenated-functionality-with-their-fluorinated-bioisosteres.pdf |
60c75449bb8c1ae12a3dc1d2 | 10.26434/chemrxiv.13638347.v1 | Deep Generative Models Enable Navigation in Sparsely Populated Chemical Space | Deep generative models are powerful tools for the exploration of chemical space, enabling the on-demand gener- ation of molecules with desired physical, chemical, or biological properties. However, these models are typically thought to require training datasets comprising hundreds of thousands, or even millions, of molecules. This per- ception limits the application of deep generative models in regions of chemical space populated by only a small number of examples. Here, we systematically evaluate and optimize generative models of molecules for low-data settings. We carry out a series of systematic benchmarks, training more than 5,000 deep generative models and evaluating over 2.6 billion generated molecules. We find that robust models can be learned from far fewer examples than has been widely assumed. We further identify strategies that dramatically reduce the number of molecules required to learn a model of equivalent quality, and demonstrate the application of these principles by learning models of chemical structures found in bacterial, plant, and fungal metabolomes. The structure of our experiments also allows us to benchmark the metrics used to evaluate generative models themselves. We find that many of the most widely used metrics in the field fail to capture model quality, but identify a subset of well-behaved metrics that provide a sound basis for model development. Collectively, our work provides a foundation for directly learning generative models in sparsely populated regions of chemical space. | Michael A. Skinnider; R. Greg Stacey; David
S. Wishart; Leonard J. Foster | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75449bb8c1ae12a3dc1d2/original/deep-generative-models-enable-navigation-in-sparsely-populated-chemical-space.pdf |
64dd9db7dfabaf06ff664a6c | 10.26434/chemrxiv-2023-05hdm-v2 | A Visible Light Driven Direct synthesis of Industrially Relevant Glutaric Acid Diesters from Aldehydes | Alpha-substituted glutaric diesters are synthesized directly from acrylates and aldehydes under visible light. This process provides a direct access to alpha-substituted glutaric diesters by exploring the HAT property of Eosin Y followed by the consecutive Giese type addition. We have performed the reaction under sunlight as a sustainable alternative light source. As an application of this protocol, the biologically potent and industrially relevant substituted 4,5-dihydro-2H-pyridazinones have also been directly synthesized from alpha-substituted glutaric diesters. A detailed and systematic control experiments have been carried out to investigate the plausible mechanistic pathway. | Anindita Bhowmick; Abhijit Chatterjee; Sidharth S. Pathak ; Dr. Ramakrishna G. Bhat | Organic Chemistry; Catalysis; Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dd9db7dfabaf06ff664a6c/original/a-visible-light-driven-direct-synthesis-of-industrially-relevant-glutaric-acid-diesters-from-aldehydes.pdf |
60c752494c891948fdad40de | 10.26434/chemrxiv.13140011.v2 | Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory | Grid Inhomogeneous Solvation Theory (GIST) maps out solvation thermodynamic properties on a
fine meshed grid and provides a statistical mechanical formalism for thermodynamic end-state
calculations. However, differences in how long-range non-bonded interactions are calculated in
molecular dynamics engines and in the current implementation of GIST have prevented precise
comparisons between free energies estimated using GIST and those from other free energy methods
such as thermodynamic integration (TI). Here, we address this by presenting PME-GIST, a
formalism by which particle mesh Ewald (PME) based electrostatic energies and long-range
Lennard-Jones (LJ) energies are decomposed and assigned to individual atoms and the
corresponding voxels they occupy in a manner consistent with the GIST approach. PME-GIST yields
potential energy calculations that are precisely consistent with modern simulation engines and
performs these calculations at a dramatically faster speed than prior implementations. Here, we
apply PME-GIST end-states analyses to 32 small molecules whose solvation free energies are close
to evenly distributed from 2 kcal/mol to -17 kcal/mol and obtain solvation energies consistent with TI
calculations (R2 = 0.99, mean unsigned difference 0.8 kcal/mol). We also estimate the entropy
contribution from the 2nd and higher order entropy terms that are truncated in GIST by the differences
between entropies calculated in TI and GIST. With a simple correction for the high order entropy
terms, PME-GIST obtains solvation free energies that are highly consistent with TI calculations (R2
= 0.99, mean unsigned difference = 0.4 kcal/mol) and experimental results (R2 = 0.88, mean
unsigned difference = 1.4 kcal/mol). The precision of PME-GIST also enables us to show that the
solvation free energy of small hydrophobic and hydrophilic molecules can be largely understood
based on perturbations of the solvent in a region extending a few solvation shells from the solute.
We have integrated PME-GIST into the open-source molecular dynamics analysis software
CPPTRAJ. | Lieyang Chen; Anthony Cruz; Daniel R. Roe; Andrew Simmonett; Lauren Wickstrom; Nanjie Deng; Tom Kurtzman | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752494c891948fdad40de/original/thermodynamic-decomposition-of-solvation-free-energies-with-particle-mesh-ewald-and-long-range-lennard-jones-interactions-in-grid-inhomogeneous-solvation-theory.pdf |
63ea5f1f1d2d1840636d53ec | 10.26434/chemrxiv-2023-0dq9g | Continuous Hydrothermal Liquefaction of Sargassum seaweed | Hydrothermal liquefaction (HTL) is often mooted as a promising and sustainable processing methodology for conversion of biomass into usable products, including bio-oils, which have the potential to alleviate humanitys reliance on fossil fuels. To date, the majority of HTL development work with novel biomasses has been undertaken at laboratory scale in batch processes and the results extrapolated to theoretical continuous flow processes required for industrial uptake. Here, we assess the use of a novel continuous flow HTL system, applying it to Sargassum (seaweed) material and generating a bio-oil which is assessed against typical crude oil fractions. | Michael (Mike) Allen; Matthew Pearce | Energy; Chemical Engineering and Industrial Chemistry; Natural Resource Recovery; Petrochemicals; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ea5f1f1d2d1840636d53ec/original/continuous-hydrothermal-liquefaction-of-sargassum-seaweed.pdf |
661d33f991aefa6ce19b3d1f | 10.26434/chemrxiv-2024-f0g5q | Dedenser: a Python command line tool for clustering and downsampling chemical libraries | The screening of chemical libraries is an essential starting point in the drug discovery process. While some researchers desire a more thorough screening of drug targets against a narrower scope of molecules, it is not uncommon for diverse screening sets to be favored during early stages of drug discovery. However, a cost burden is associated with the screening of molecules, with potential drawbacks if particular areas of chemical space are needlessly over represented. To facilitate triaged sampling of chemical libraries and other collections of molecules, we have developed Dedenser, a tool for the downsampling of chemical clusters. Dedenser functions by reducing the membership of clusters within chemical point clouds while maintaining the initial topology, or distribution, in chemical space. Dedenser is a Python package that utilizes Hierarchical Density-Based Spatial Clustering of Applications with Noise to first identify clusters present in 3D chemical point clouds, and then downsamples by applying Poisson disk sampling to clusters based on either their volume or density in chemical space. A command line interface tool is available with Dedenser, which allows for generation of chemical point clouds, using Mordred for QSAR descriptor calculations and uniform manifold approximation and projection for 3D embedding, as well as visualization. We hope that Dedenser will serve the community by enabling quick access to reduced collections of molecules that are representative of larger sets, selecting even distributions of molecules within clusters rather than single representative molecules. | Armen G. Beck; Jonathan Fine; Yu-hong Lam; Edward C. Sherer; Erik L. Regalado; Pankaj Aggarwal | Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661d33f991aefa6ce19b3d1f/original/dedenser-a-python-command-line-tool-for-clustering-and-downsampling-chemical-libraries.pdf |
60c758d0bb8c1aea543dcad9 | 10.26434/chemrxiv.14595606.v1 | Molecular Mechanisms of Aroma Persistence: From Noncovalent Interactions Between Aroma Compounds and Oral Mucosa to Metabolization of Aroma Compounds by Saliva and Oral Cells | <p>Aroma
persistence plays a major role in the liking and wanting of orally consumed products
(food, dental toiletries, tobacco, drugs, etc.). Here, we use an integral
approach including <i>ex vivo</i>
experiments using a novel model of oral mucosa and saliva in well controlled
conditions as well as <i>in vivo</i> dynamic
instrumental and sensory experiments. <i>Ex
vivo</i> experiments show the ability of the mucosal pellicle, the thin layer
of salivary proteins covering the oral mucosa, to interact with aroma compounds,
as well as the ability of oral cells and saliva to metabolize carbonyl aroma compounds.
<i>In vivo</i> evaluation of the exhaled air
and perception of individuals after aroma sample consumption confirm <i>ex vivo</i> findings in a more real context.
Thus, aroma compounds susceptible to be
metabolized by saliva and oral cells show a lower aroma persistence than non
metabolized compounds, for which other mechanisms such as the adsorption at the
surface of the oral mucosa (mucosal pellicle) as a function of their
hydrophobicity are involved. Thus, we argue that the physiological aspects
occurring during the oral processing, and especially, metabolization of aroma
compounds, have to be considered when studying the phenomenon of aroma
persistence.</p> | Carolina Muñoz-Gonzalez; Marine Brulé; Christophe Martin; Gilles Feron; Francis Canon; CAROLINA MUNOZ | Analytical Chemistry - General; Mass Spectrometry; Food | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758d0bb8c1aea543dcad9/original/molecular-mechanisms-of-aroma-persistence-from-noncovalent-interactions-between-aroma-compounds-and-oral-mucosa-to-metabolization-of-aroma-compounds-by-saliva-and-oral-cells.pdf |
6179d9cc913a7458886d678a | 10.26434/chemrxiv-2021-8w6fx | Nonadiabatic Dynamics Algorithms with Only Potential Energies and Gradients: Curvature-Driven Coherent Switching with Decay of Mixing and Curvature-Driven Trajectory Surface Hopping | Direct dynamics by mixed quantum–classical nonadiabatic methods is an important tool for understanding processes involving multiple electronic states. Very often, the computational bottleneck of such direct simulation comes from electronic structure theory. For example, at every time step of a trajectory, nonadiabatic dynamics requires potential energy surfaces, their gradients, and the matrix elements coupling the surfaces. The need for the couplings can be alleviated by employing the time derivatives of the wave functions, which can be evaluated from overlaps of electronic wave functions at successive timesteps. However, evaluation of overlap integrals is still expensive for large systems. In addition, for electronic structure methods for which the wave functions or the coupling matrix elements are not available, nonadiabatic dynamics algorithms become inapplicable. In this work, building on recent work by Baeck and An, we propose new nonadiabatic dynamics algorithms that only require adiabatic potential energies and their gradients. The new methods are named curvature- driven coherent switching with decay of mixing (κCSDM) and curvature-driven trajectory surface hopping (κTSH). We show how powerful these new methods are in terms of computer time and good agreement with methods employing nonadiabatic coupling vectors computed in conventional ways. The lowering of the computational cost will allow longer nonadiabatic trajectories and greater ensemble averaging to be affordable, and the ability to calculate the dynamics without electronic structure coupling matrix elements extends the dynamics capability to new classes of electronic structure methods. | Yinan Shu; Linyao Zhang; Shaozeng Sun; Yudong Huang; Donald Truhlar; Xiye Chen | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2021-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6179d9cc913a7458886d678a/original/nonadiabatic-dynamics-algorithms-with-only-potential-energies-and-gradients-curvature-driven-coherent-switching-with-decay-of-mixing-and-curvature-driven-trajectory-surface-hopping.pdf |
635156a4ee3186060a6ae126 | 10.26434/chemrxiv-2022-96hx8 | Aerosol-assisted sol-gel synthesis of mesoporous Ag-Ta-SiO2 catalysts for the direct upgrading of ethanol to butadiene | The Lebedev process, or the direct catalytic conversion of bioethanol to butadiene, offers an up-and-coming sustainable alternative to the petrochemical route toward this high-demand C4 hydrocarbon. Since the reaction mechanism involves a cascade of dehydrogenation, hydrogen transfer and dehydration steps, a bifunctional catalyst is required, combining both redox (for the dehydrogenation reaction) and acid (for hydrogen transfer and dehydration reactions) functionalities. Multi-step preparation methods are typically implemented to obtain tailored bifunctional catalysts, and a challenge is to balance the two functions to maximize the BD yield. Here, we disclose a straightforward, one-step, and continuous preparation of Ta-doped SiO2 loaded with Ag nanoparticles by coupling sol-gel chemistry with aerosol processing. Combining tantalum ethoxide, silver nitrate, hydrolysed tetraethyl orthosilicate and Pluronic F127 as templating agent in the aerosol process leads to mesoporous bifunctional catalysts featuring a specific surface area between 310–370 m2 g–1, a pore volume of ca. 0.5 mL g–1 and an average pore diameter of 5 nm. As attested by a variety of characterization techniques, the method leads to the homogeneous incorporation of highly dispersed tantalum species in the silica matrix, thereby creating the required acidic sites. These new catalysts have higher dehydration activity, as compared to the corresponding reference catalysts prepared by classical impregnation. Concomitantly, relatively small silver nanoparticles are stabilized (~15 nm). The relative Ta and Ag loading can be tuned easily. In the ethanol to butadiene reaction, these aerosol-made catalysts achieve a butadiene yield of ca. 25 % by optimizing the relative loadings of Ta and Ag, outcompeting the corresponding formulations prepared by impregnation. | Denis Dochain; Antoine Van Den Daelen; Ales Styskalik; Vit Vykoukal; Damien Debecker | Catalysis; Acid Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC 4.0 | CHEMRXIV | 2022-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635156a4ee3186060a6ae126/original/aerosol-assisted-sol-gel-synthesis-of-mesoporous-ag-ta-si-o2-catalysts-for-the-direct-upgrading-of-ethanol-to-butadiene.pdf |
637b62dd74b7b6472f062ceb | 10.26434/chemrxiv-2022-4rrb6-v2 | Accurate quantum-chemical fragmentation calculations for ion-water clusters with the density-based many-body expansion | The many-body expansion (MBE) provides an attractive fragmentation method for the efficient quantum-chemical treatment of molecular clusters. However, its convergence with the many-body order is generally slow for molecular clusters that exhibit large intermolecular polarization effects. Ion--water clusters are thus a particularly challenging test case for quantum-chemical fragmentation methods based on the MBE. Here, we assess the accuracy of both the conventional, energy-based MBE and the recently developed density-based MBE [Schmitt-Monreal and Jacob, Int. J. Quantum Chem, 120, e26228 (2020)] for ion--water clusters. As test cases, we consider hydrated Ca^2+, F^-, OH^-, and H3O^+, and compare both total interaction energies and the relative interaction energies of different structural isomers. We show that an embedded density-based two-body expansion yields highly accurate results compared to supermolecular calculations. Already at the two-body level, the density-based MBE clearly outperforms a conventional, energy-based embedded three-body expansion. We compare different embedding schemes and find that a relaxed frozen-density embedding potential yields the most accurate results. This opens the door to accurate and efficient quantum-chemical calculations for large ion--water clusters as well as condensed-phase systems.
| Stefanie Schürmann; Johannes R. Vornweg; Mario Wolter; Christoph R. Jacob | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637b62dd74b7b6472f062ceb/original/accurate-quantum-chemical-fragmentation-calculations-for-ion-water-clusters-with-the-density-based-many-body-expansion.pdf |
60c7539e4c891969ebad435b | 10.26434/chemrxiv.12599951.v3 | Thermochromic AIE Dual Phosphorescence via Temperature-Dependent sp3-Linked Donor-Acceptor Electronic Coupling | <p>Aggregation-induced emission (AIE) has proven to be a viable strategy to achieve highly efficient RTP in bulk by restricting molecular motions. Here we show that by utilizing triphenylamine (TPA) as an electronic donor which connects to an acceptor via an sp3 linker, six TPA-based AIE-active RTP luminophores were obtained. Both the TPA AIE-gen and the <i>sp</i><sup>3</sup>-linkage can suppress aggregation-caused quenching. Consequently, dual phosphorescence bands emitting from localized donor and acceptor triplet states, respectively, could be recorded at lowered temperatures; at room temperature, only a single RTP band corresponding to the lowest triplet state is present, presumably due to thermally assisted electronic coupling between the two states. The reported molecular construct serves as an “intermediary case” between a fully conjugated donor-acceptor system and a do-nor/acceptor binary mix, which may provide important clues on the design and control of molecular systems with complex excited-state dynamics.<br /></p> | Tao Wang; Zhubin Hu; Xiancheng Nie; Linkun Huang; Hui Miao; Xiang Sun; Guoqing Zhang | Physical Organic Chemistry; Aggregates and Assemblies; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7539e4c891969ebad435b/original/thermochromic-aie-dual-phosphorescence-via-temperature-dependent-sp3-linked-donor-acceptor-electronic-coupling.pdf |
60c7483d4c89194900ad2e93 | 10.26434/chemrxiv.11866062.v1 | Functional Gradient Transparent Conducting Oxide Nanowire Arrays as Monophasic Schottky-Barrier Free Memristors for Bipolar Linear Switching | <div><div><div><p>One of the fascinating properties of metal-semiconductor Schottky-barriers, which has been observed for some material combinations, is memristive behavior. Memristors are smart, since they can reversibly switch between a low resistance state and a high resistance state. The devices offer a great potential for advanced computing and data storage, including neuromorphic networks and resistive random-access memory. However, as for many other cases, the presence of a real interface (metal - metal oxide) has numerous disadvantages. The realization of interface-free, respectively Schottky-barrier free memristors is highly desirable. The aim of the current paper is the generation of nanowire arrays with each nanorod possessing the same crystal phase (Rutile) and segments only differing in composition. The electric conductivity is realized by segments made of highly-doped antimony tin oxide (ATO) transitioning into pure tin oxide (TO). Complex nanoarchitectures are presented, which include ATO-TO, ATO-TO-ATO nanowires either with a stepwise distribution of antimony or as a graded functional material. The electrical characterization of the materials reveals that the introduction of memristive properties in such structures is possible. The special features observed in voltage-current (IV) curves are correlated to the behavior of mobile oxygen vacancies (VO..) at different values of applied electrical potential.</p></div></div></div> | Thomas Herzog; Naomi Weitzel; Sebastian Polarz | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7483d4c89194900ad2e93/original/functional-gradient-transparent-conducting-oxide-nanowire-arrays-as-monophasic-schottky-barrier-free-memristors-for-bipolar-linear-switching.pdf |
61124e0b30231ab5dd07347a | 10.26434/chemrxiv-2021-kjh23-v3 | High Resolution Photoelectron Spectroscopy of Vibrationally Excited OHˉ | The effect of vibrational pre-excitation of anions on their photoelectron spectra is explored, combining slow photoelectron velocity-map imaging of cryogenically cooled anions (cryo-SEVI) with tunable IR radiation to pre-excite the anions. This new IR cryo-SEVI method is applied to OHˉ as a test system, where the R(0) transition of the hydroxyl anion (3591.53 cm-1) is pumped. Vibrational excitation induces a 30% depletion in photodetachment signal from the v = 0, J = 0 ground state of the anion and the appearance of all five allowed photodetachment transitions from the v = 1, J = 1 rovibrational level, each with peak widths between 1-2 cm-1. By scanning the IR laser, IR cryo-SEVI can also serve as a novel action technique to obtain the vibrational spectrum of OHˉ, giving an experimental value for the R(0) transition of 3591(1.2) cm-1. | Marty DeWitt; Mark Babin; Daniel Neumark | Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61124e0b30231ab5dd07347a/original/high-resolution-photoelectron-spectroscopy-of-vibrationally-excited-oh.pdf |
6555f034dbd7c8b54b60e072 | 10.26434/chemrxiv-2023-25548-v2 | Electrochemical C–H/C–C Bond Oxygenation: A Potential Technology for Plastic Depolymerization | Herein, we provide eco-friendly and safely operated electrocatalytic methods for the selective oxidation directly or with water, air, light, metal catalyst or other mediators serving as the only oxygen supply. Heavy metals, stoichiometric chemical oxidants, or harsh conditions were drawbacks of earlier oxidative cleavage techniques. It has recently come to light that a crucial stage in the deconstruction of plastic waste and the utilization of biomass is the selective activation of inert C(sp3)–C/H(sp3) bonds, which continues to be a significant obstacle in the chemical upcycling of resistant polyolefin waste. An appealing alternative to chemical oxidations using oxygen and catalystsis direct or indirect electrochemical conversion. An essential transition in the chemical and pharmaceutical industries is the electrochemical oxidation of C–H/C–C bonds. In this review, we discuss cutting-edge approaches to chemically recycle commercial plastics and feasible C–C/C–H bondsoxygenation routes for industrial scale-up. | Sadia Rani; Samina Aslam; Kiran Lal; Sobia Noreen; Khadeeja Ali Mohammed Alsader; Riaz Hussain; Bahareh Shirinfar; Nisar Ahmed | Organic Chemistry; Catalysis; Electrocatalysis; Heterogeneous Catalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6555f034dbd7c8b54b60e072/original/electrochemical-c-h-c-c-bond-oxygenation-a-potential-technology-for-plastic-depolymerization.pdf |
66841dae5101a2ffa82aebbb | 10.26434/chemrxiv-2024-n10m0 | Catalytic Resonance Theory: Forecasting the Flow of Programmable Catalytic Loops | Chemical transformations on catalyst surfaces occur through series and parallel reaction pathways. These complex networks and their behavior can be most simply evaluated through a three-species surface reaction loop (A* to B* to C* to A*) that is internal to the overall chemical reaction. Application of an oscillating dynamic catalyst to this reactive loop has been shown to exhibit one of three types of behavior: (1) a positive net flux of molecules about the loop in the clockwise direction, (2) a negative net flux of molecules about the loop in the counterclockwise direction, or (3) negligible flux of molecules about the loop at the limit cycle of reaction. Three-species surface loops were simulated with microkinetic modeling to assess the reaction loop behavior resulting from a catalytic surface oscillating between two or more catalyst surface energy states. Selected input parameters for the simulations spanned 11-dimensional parameter space using 127,688 different parameter combinations. Their converged limit cycle solutions were analyzed for their loop turnover frequencies, the majority of which were found to be approximately zero. Classification and regression machine learning models were trained to predict the sign and magnitude of the loop turnover frequency and successfully performed above accessible baselines. Notably, the classification models exhibited a baseline weighted F1 score of 0.48, whereas trained models achieved weighted F1 scores of 0.91 and 0.96 when trained on the parameters used to define the simulations and derived rate constants, respectively. The trained models successfully predicted catalytic loop behavior, and interpretation of these models revealed all input parameters to be important for the prediction and performance of each model. | Madeline Murphy; Kyle Noordhoek; Sallye Gathmann; Paul Dauenhauer; Christopher Bartel | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66841dae5101a2ffa82aebbb/original/catalytic-resonance-theory-forecasting-the-flow-of-programmable-catalytic-loops.pdf |
60c74459337d6c44b5e26d97 | 10.26434/chemrxiv.9782375.v1 | Visualization Tool for Atomic Models (VITAL): A Simple Visualization Tool for Materials Predictions | This preprint describes the first version of VITAL, a tool used to visual materials predictions. Instructions for use are outlined and a few basic examples are shown. The code for this tool is included as a zip file and archived version is linked in the text. A GitHub repository is also linked for the most up-to-date version of VITAL. | Steven Kauwe; Yucheng Yang; Taylor Sparks | Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74459337d6c44b5e26d97/original/visualization-tool-for-atomic-models-vital-a-simple-visualization-tool-for-materials-predictions.pdf |
60c749c5337d6c23b0e2777e | 10.26434/chemrxiv.12102456.v1 | A Simple Molecular Orbital Picture of RIXS Distilled from Many-Body Damped Response Theory | <div>Ab initio calculations of resonant inelastic X-ray scattering (RIXS) rely on the damped response theory, which prevents the divergence of response solutions in the resonant regime. Within the damped response theory formalism, RIXS moments are expressed as sum over all electronic states of the system (SOS expressions). By invoking resonance arguments, these expressions can be reduced to a few terms, an approximation commonly exploited for interpretation of the computed cross sections. We present an alternative approach: a rigorous formalism for deriving a simple molecular orbital picture of the RIXS process from the many-body calculations using damped</div><div>response theory. In practical implementations, the SOS expressions of RIXS moments are recast in terms of matrix elements between the zero-order wave functions and first-order frequency-dependent response wave functions of the initial and final states, such that the RIXS moments can be evaluated using complex response</div><div>one-particle transition density matrices (1PTDMs). Visualization of these 1PTDMs connects the RIXS process with the changes in electronic density. We demonstrate that the real and imaginary components of the response 1PTDMs can be interpreted as contributions of the undamped off-resonance and damped near-resonance SOS terms, respectively. By analyzing these 1PTDMs in terms of natural transition orbitals, we derive a rigorous, black-box mapping of the RIXS process into a molecular orbital picture. We illustrate the utility of the new tool by analyzing RIXS transitions in the OH radical, benzene, para-nitroaniline, and</div><div> 4-amino-4'-nitrostilbene. These examples highlight the significance of both near-resonance and off-resonance channels. </div> | Kaushik Nanda; Anna I. Krylov | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749c5337d6c23b0e2777e/original/a-simple-molecular-orbital-picture-of-rixs-distilled-from-many-body-damped-response-theory.pdf |
61d5c0fbdb4d9f6a128c80c7 | 10.26434/chemrxiv-2022-drsxv | Catalytic Asymmetric β-Oxygen Elimination | A catalytic enantioselective β-O-elimination reaction is reported in the form of a zirconium-catalyzed asymmetric opening of meso-ketene acetals. Furthermore, a regiodivergent β-O-elimination is demonstrated. The reaction proceeds under mild conditions, at low catalyst loadings, and produces chiral monoprotected 1,2-diol building blocks in good yield and enantiomeric excess. The combination with a Mitsunobu reaction then gives access to all 1,2-diol stereoisomers and trans-1,2-aminoalcohols in high enantiomeric purity. A stereochemical analysis supported by DFT calculations reveals that a high selectivity in the hydrozirconation step is also important for achieving high enantioselectivity, although it does not constitute the asymmetric step. This insight is crucial for the future development of related asymmetric β-elimination reactions. | Christof Matt; Andreas Orthaber; Jan Streuff | Organic Chemistry; Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d5c0fbdb4d9f6a128c80c7/original/catalytic-asymmetric-oxygen-elimination.pdf |
66b691aac9c6a5c07aac9b48 | 10.26434/chemrxiv-2024-nm8ks | Thermodynamic stability and diffusion mechanism of LiMXCl4 superionic conductors | LiMXCl4 is a recently discovered lithium superionic conductor reported with a Li conductivity up to 12.4 mS/cm at room temperature. In this work, we explore various types of M-cation and X-anion substitutions in the LiMXCl4 system. We find that fluoro-chlorides may provide promising thermodynamic and electrochemical stability without compromising ionic conductivity. Ab-initio molecular dynamics simulations on seven substitutions and three lithium concentrations for each substitution suggest that even higher conductivity may be achieved in LiMXCl4 than has been reported. A Meyer-Neldel analysis comparing LiMXCl4, close-packed halides, and LaCl3-type systems demonstrates the potential of the LiMXCl4 family due to their high Meyer-Neldel energy, high prefactor, and low activation energy, projecting a range of conductivity of 10-100 mS/cm. An analysis of the correlation between lithium-ion hops and small-angle tilting events finds that LiMXCl4 systems exhibit a strong cradle effect where weakly bound M-octahedra often tilt their orientation in conjunction with a nearby Li-ion hop to flatten the lithium-ion energy landscape. Such an advantage originates from the fact that in the LiMXCl4 structure, one-dimensional M-octahedral chains are bound via weak van der Waals interactions which can accommodate for reduction in free volume via rotational correlation of the octahedra. Our work demonstrates an exciting direction towards further improving this class of materials in terms of ionic conductivity and electrochemical stability and provides a fundamental understanding of the factors that lead to high ionic conductivity in non-close-packed oxyhalide systems. | KyuJung Jun; Grace Wei; Gerbrand Ceder | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b691aac9c6a5c07aac9b48/original/thermodynamic-stability-and-diffusion-mechanism-of-li-mx-cl4-superionic-conductors.pdf |
60c750faf96a00bc54287f2b | 10.26434/chemrxiv.13107236.v1 | Supramolecular Secondary Ion Mass Spectrometry - Revealing Molecular Surroundings and Inter-Molecular Interactions in Organic Matter | <div>While supramolecular chemistry is a firmly established research field in laboratory conditions,
the experimental study of non-covalent interactions, such as hydrogen bonding and piinteractions, between different molecules in chemically rich, non-crystalline matter remains
highly challenging. We demonstrate that soft ion bombardment can trigger the joint desorption of
weakly interacting adjacent molecules, and that this in turn allows molecular interaction probabilities, surroundings, and arrangement in organic matter to be probed. Assemblies of
organic molecules linked by hydrogen bonds or dipole- interactions are extracted here with
preservation of chemistry and structure as single-charged supramolecular secondary ions.
Among the examples shown is the desorption of stable 12-molecular clusters of the amino acid
L-proline, which suggest an icosahedral on-surface self-assembly, and the desorption of supramolecular linear oligomers of 2,5-piperazinedione. The second half of the study lays down
the statistical framework for the reconstruction of a molecular interactome based on the relative
abundances of supramolecular dimers of different compositions within a mass spectrum acquired
on organic matter containing more than one type of molecule.
</div> | Maciej Kawecki; Laetitia Bernard; Daniele Passerone; Rowena Crockett | Supramolecular Chemistry (Org.); Aggregates and Assemblies; Mass Spectrometry; Clusters | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750faf96a00bc54287f2b/original/supramolecular-secondary-ion-mass-spectrometry-revealing-molecular-surroundings-and-inter-molecular-interactions-in-organic-matter.pdf |
62fae2d31d6a99f6c305655c | 10.26434/chemrxiv-2022-vk5lb | Understanding Mechanisms of All-solid-state Lithium-Sulfur Batteries through Operando Raman and Ex-situ XAS Studying | All-solid-state lithium-sulfur batteries (ASLSBs) have been considered a promising next-generation energy storage technology due to their remarkable safety and high energy density. In ASLSBs, the electrochemical pathways are intrinsically different from conventional Li-S batteries using liquid electrolytes. However, the mechanism still lacks clear identification and deep understanding. Herein, for the first time, we investigated the chemistries and explored the electrochemical reaction mechanism and kinetic in ASLSBs through coupling operando Raman spectroscopy and ex-situ X-ray absorption spectroscopy. We proved no long-chain lithium polysulfides (Li2Sn, 4≤n≤8) were formed during the redox reactions, but a short-chain polysulfide (Li2S2) intermediate phase formation was identified in the conversion between active material S8 and reduction product Li2S. The existence of intermediate phase Li2S2 results in low sulfur utilization and poor battery performance. In comparison to liquid cells, ASLSBs exhibit sluggish reaction kinetics due to the higher conversion barrier and slower charger transfer in solid-solid reactions. This study revealed the generation of Li2S2 intermediates in ASLSBs, inspiring future research to further improve the performance of ASLSBs through completing the conversions and promoting reaction kinetics in ASLSBs. | Xiao Sun; Daxian Cao; Seong-Min Bak; Tongtai Ji; Yonghua Du; Michael Geiwitz; Kenneth Burch; Hongli Zhu | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fae2d31d6a99f6c305655c/original/understanding-mechanisms-of-all-solid-state-lithium-sulfur-batteries-through-operando-raman-and-ex-situ-xas-studying.pdf |
6348ee4e1df6884ef18fa087 | 10.26434/chemrxiv-2022-8m2z7 | ZnOS+C adsorbent for the effective removal of Fast Green dye from synthetic and real wastewater | Wastewater treatment is becoming increasingly important due to the potential shortage of pure drinking water in many parts of the world. Adsorption offers a potential technique for the uptake of contaminants and wastewater purification. In the last two decades, several efforts have been made to remove fast green (FG) dye from wastewater via different adsorbent materials. But adsorption capacity shown by these adsorbents is low and is time-consuming. Herein, we have synthesized for the first time a new powdered adsorbent ZnOS+C, modified Zinc peroxide with sulfur and activated carbon to effectively remove FG dye from wastewater. Results of batch adsorption experiments have suggested that ZnOS+C has the maximum adsorption capacity of 238.28 mg/g for FG dye within 120 minutes of adsorption equilibrium for a wide range of pH ranging from 2-10 pH. The adsorption process follows the Freundlich isotherm model, suggesting a multilayered adsorption process that occurs on the surface of ZnOS+C. The adsorption kinetics study indicates that the kinetics of the reaction is the intraparticle diffusion model. Briefly, this study shows the proof of application of ZnOS+C powder as a new eco-friendly adsorbent with extremely high efficiency and high surface area for removing FG dye. | Sachin .; Biplob Kumar Pramanik; Harshit Gupta; Shrawan Kumar; Jai Shankar Tawale; Kalpit Shah; Nahar Singh | Materials Science; Chemical Engineering and Industrial Chemistry; Carbon-based Materials; Dyes and Chromophores; Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6348ee4e1df6884ef18fa087/original/zn-os-c-adsorbent-for-the-effective-removal-of-fast-green-dye-from-synthetic-and-real-wastewater.pdf |
635082b2e79b3fee72f07871 | 10.26434/chemrxiv-2022-jhfgl | Architected Hydrogels for Functional Tissue Engineering Applications | The functionality of many biological tissues relies on their highly sophisticated architecture. Recent advances have enabled in vitro generation of human organoid models through 3D stem cell culture in animal-derived protein hydrogels. However, these oversimplified materials often lack in vivo-like microarchitecture and mechanical stimuli to support in vitro tissue formation. As such, there is an imperative need to develop architected hydrogels that can be integrated with 3D cell culture and microfluidic technologies to provide native-like dynamic 3D environments promoting multicellular self-organization and tissue maturation. In this review article, we provide an overview of the design and properties of architected hydrogels and highlight their integration with other bioengineering tools for functional tissue engineering. Firstly, we discuss the structural and physical properties in natural nanofibrillar hydrogels and synthetic analogues with non-linear elasticity. We then provide a comparative summary of different methods to generate macroporous hydrogels that facilitate mass transport, cell-cell communication, and tissue maturation in 3D. Next, we investigate examples of 3D printed hydrogels with complex tissue-mimicking architectures and discuss emerging applications of architected hydrogels in tissue engineering, organ-on-chip technology and mechanobiology. Lastly, existing challenges and future directions in developing architected hydrogels towards functional tissue engineering are highlighted. | Doris Zauchner; Monica Zippora Müller; Sophie Zengerle; Adam Aleksander Korczak; Muriel Alexandra Holzreuter; Xiao-Hua Qin | Materials Science; Polymer Science; Biocompatible Materials; Fibers; Hydrogels | CC BY NC 4.0 | CHEMRXIV | 2022-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635082b2e79b3fee72f07871/original/architected-hydrogels-for-functional-tissue-engineering-applications.pdf |
67d95a696dde43c9083f7c98 | 10.26434/chemrxiv-2024-46lf6-v3 | Computational evaluation of the binding of activated ribonucleotides in nonenzymatic RNA template copying | Nonenzymatic self-replication is considered as one of the most primordial functions of RNA, which likely preceded the emergence of more complex ribozymes. Among different possible scenarios, nucleotide activation with imidazole derivatives attracted substantial attention over the last years. However, despite the progress in proposing plausible variants of nonezymatic RNA template copying with phosphoroimidazolides, mechanistic aspects of this process still remain obscure. Furthermore, efficient RNA self-replication involving activated uridine and adenosine still remains a challenge. Here, we employed classical molecular dynamics simulations to evaluate the binding specificity of different imidazolium-bridged dinucleotide intermediates, which was suggested to control the yield and fidelity of the reaction. In particular, RMSD-based clustering of the MD trajectories revealed previously unknown structural arrangements of activated dinucleotide indermediates that may play a critical role in non-enzymatic primer extension. Most importantly, our results indicate that yield and fidelity of nonenzymatic RNA template copying cannot be simply associated with the number of Watson-Crick hydrogen bonds between the activated dinucleotides and the templating strand. Instead, efficiency of the reaction correlates with the preference for the formation of canonically stacked form of the activated dinucleotide intermediate, which can then selectively bind to the template and participate in the primer extension reaction. | Barbara Katarzyna Lech; Boluwatife B. Ogunnaiya; Elizaveta F. Petrusevich; Rafał Szabla | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d95a696dde43c9083f7c98/original/computational-evaluation-of-the-binding-of-activated-ribonucleotides-in-nonenzymatic-rna-template-copying.pdf |
6698bf8f01103d79c54ffd8a | 10.26434/chemrxiv-2024-n59fn-v2 | DLP printing of non-modified protein-only compositions | This study explores the utilization of digital light processing (DLP) printing to fabricate complex structures using native gelatin as the sole structural component for applications in biological implants. Unlike approaches relying on synthetic materials or chemically modified biopolymers, this research harnesses the inherent properties of gelatin to create biocompatible structures. The printing process is based on a crosslinking mechanism using a di-tyrosine formation initiated by visible light irradiation. Formulations containing gelatin were found to be printable at the maximum documented concentration of 30 wt.%, thus allowing the fabrication of overhanging objects and open embedded tubes with a compressive modulus akin to soft tissues. Cell adhesion and growth onto and within the gelatin-based 3D constructs were evaluated by examining two implant fabrication techniques: (1) cell seeding onto the printed scaffold and (2) printing compositions that contain cells (cell-laden). The preliminary biological experiments indicate that both the cell-seeding and cell-laden strategies enable making 3D cultures of chondrocytes within the gelatin constructs. This study underscores the potential of utilizing non-modified protein-only bioinks in DLP printing to produce intricate 3D objects with high fidelity, paving the way for advancements in regenerative tissue engineering. | Ayelet Bunin; Orit Harari-Steinberg; Doron Kam; Tatyana Kuperman; Moran Friedman-Gohas; Bruria Shalmon; Liraz Larush; Shay Ithak Duvdevani; Shlomo Magdassi | Biological and Medicinal Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6698bf8f01103d79c54ffd8a/original/dlp-printing-of-non-modified-protein-only-compositions.pdf |
6683377201103d79c5b25624 | 10.26434/chemrxiv-2023-4vb0m-v2 | Discovery of fully synthetic FKBP12-mTOR molecular glues | Molecular glues are a class of drug modalities with the potential to engage otherwise undruggable targets. However, the rational discovery of molecular glues for desired targets is a major challenge and most known molecular glues have been discovered by serendipity. Here we present the first fully synthetic FKBP12-mTOR molecular glues, which were discovered from a FKBP-focused, target-unbiased ligand library. Our biochemical screening of >1000 in-house FKBP ligands yielded one hit that induced dimerization of FKBP12 and the FRB domain of mTOR. The crystal structure of the ternary complex revealed that the hit targeted a similar surface on FRB domain compared to natural product rapamycin but with a radically different interaction pattern. Structure-guided optimization improved potency 500-fold and led to compounds, which initiate FKBP12-FRB complex formation in cells. Our results show that molecular glues targeting flat surfaces can be discovered by focused screening and support the use of FKBP12 as a versatile presenter protein for molecular glues. | Robin C.E. Deutscher; Christian Meyners; Maximilian L. Repity; Wisely Oki Sugiarto; Jürgen Kolos; Edvaldo Maciel; Tim Heymann; Thomas M. Geiger; Stefan Knapp; Frederik Lermyte; Felix Hausch | Biological and Medicinal Chemistry; Biophysics; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2024-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6683377201103d79c5b25624/original/discovery-of-fully-synthetic-fkbp12-m-tor-molecular-glues.pdf |
60c748b84c89195e34ad2f8b | 10.26434/chemrxiv.11961987.v1 | Dearomative Allylation of Aromatic Cyanohydrins by Palladium Catalysis: Catalyst-Enhanced Site-Selectivity | A dearomative allylation of aromatic cyanohydrins with allyl borates and allyl stannanes under palladium catalysis was developed. At the initial stage of this study, the dearomative reaction (C4-substitution of the aromatics) was competing with benzyl substitution. To circumvent this issue, the use of palladium and <i>meta</i>-disubstituted triarylphosphine as the catalyst in a 1:1 ratio was found to enhance the site-selectivity, furnishing the desired dearomatized products. As the products possess an unsaturated nitrile moiety, further derivatizations of products such as conjugate additions and reductions were achieved. | Aika Yanagimoto; Masaaki Komatsuda; Kei Muto; Junichiro Yamaguchi | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748b84c89195e34ad2f8b/original/dearomative-allylation-of-aromatic-cyanohydrins-by-palladium-catalysis-catalyst-enhanced-site-selectivity.pdf |
60c7482f337d6c725be274df | 10.26434/chemrxiv.11861580.v1 | Four Resonance Structures Elucidate Double-Bond Isomerisation of a Biological Chromophore | Photoinduced double-bond isomerisation of the chromophore of photoactive yellow protein (PYP) is highly sensitive to chromophore-protein interactions. On the basis of high-level ab initio calculations, using the XMCQDPT2 method, we scrutinise the effect of the chromophore-protein hydrogen bonds on the photophysical and photochemical properties of the chromophore. We identify four resonance structures – two closed-shell and two biradicaloid – that elucidate the electronic structure of the ground and first excited states involved in the isomerisation process. Changing the relative energies of the resonance structures by hydrogen-bonding interactions tunes all photochemical properties of the chromophore in an interdependent manner. Our study sheds new light on the role of the chromophore electronic structure in tuning in photosensors and fluorescent proteins. | Evgeniy Gromov; Tatiana Domratcheva | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7482f337d6c725be274df/original/four-resonance-structures-elucidate-double-bond-isomerisation-of-a-biological-chromophore.pdf |
6632db7c418a5379b034189d | 10.26434/chemrxiv-2024-ljht5-v2 | The Influence of Electron Donors on the Charge Transfer Dynamics of Carbon Nanodots in Photocatalytic Systems | Carbon nanodots are nanosized light-harvesters emerging as sustainable next-generation photosensitizers in photocatalytic reactions. Despite their ever-increasing potential applications, the intricate details underlying their photoexcited charge carrier dynamics are yet to be elucidated. In this study, nitrogen-doped graphitic carbon nanodots (NgCNDs) are selectively excited in the presence of methyl viologen (MV2+, redox mediator) and different electron donors, namely ascorbic acid (AA) and ethylenediaminetetraacetic acid (EDTA). The consequent formation of the methyl viologen radical cation (MV·+) is investigated, and the excited charge carrier dynamics of the photocatalytic system are understood on a 0.1 ps to 1 ms time range, providing spectroscopic evidence of oxidative or reductive quenching mechanisms experienced by optically excited NgCNDs (NgCNDs*) depending on the electron donor implemented. In the presence of AA, NgCNDs* undergo oxidative quenching by MV2+ to form MV·+, but is short-lived due to dehydroascorbic acid, a product of photoinduced hole quenching of oxidized NgCNDs. The EDTA-mediated reductive quenching of NgCNDs* is observed to be at least two orders of magnitude slower due to screening by EDTA-MV2+ complexes, but the MV·+ population is stable due to the irreversibly oxidized EDTA preventing a back reaction. In general, our methodology provides a distinct solution with which to study charge transfer dynamics in photocatalytic systems on an extended time range spanning 10 orders of magnitude. This approach generates a mechanistic understanding to select and develop suitable electron donors to promote photocatalytic reactions.
| Stuart Macpherson; Takashi Lawson; Anna Abfalterer; Paolo Andrich; Ava Lage; Erwin Reisner; Tijmen Euser; Samuel Stranks; Alexander Gentleman | Physical Chemistry; Catalysis; Energy; Photocatalysis; Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6632db7c418a5379b034189d/original/the-influence-of-electron-donors-on-the-charge-transfer-dynamics-of-carbon-nanodots-in-photocatalytic-systems.pdf |
60c7549aee301c24a7c7afc5 | 10.26434/chemrxiv.13693540.v1 | Mechanistic Studies of Pd-Catalyzed Fluorination of Cyclic Vinyl Triflates: Evidence for in situ Ligand Modification | <div><div><div><p>Pd-catalyzed nucleophilic fluorination reactions are important methods for the synthesis of fluoroarenes and fluoroalkenes. However, these reactions can generate a mixture of regioisomeric products that are often difficult to separate. While investigating the Pd- catalyzed fluorination of cyclic vinyl triflates, we observed that the addition of a substoichiometric quantity of TESCF3 significantly improves both the efficiency and the regioselectivity of the fluorination process. Herein, we report a combined experimental and computational study on the mechanism of this transformation focused on the role of TESCF3. We found that in the absence of additives such as TESCF3, the transmetalation step produces predominantly the thermodynamically more stable trans isomer of the key LPd(vinyl)F complex (L = biaryl monophosphine ligand). This intermediate, rather than undergoing reductive elimination, preferentially reacts through an intramolecular β-deprotonation to form a Pd-cyclohexyne intermediate. This undesired reactivity is responsible for the low efficiency (11% yield) and poor regioselectivity (1.8:1) of the catalytic reaction. When TESCF3 is added to the reaction mixture, the cis-LPd(vinyl)F complex is instead formed, through a pathway involving an unusual dearomatization of the ligand by nucleophilic attack from a trifluoromethyl anion (CF3–). In contrast to the trans isomer, this cis-LPd(vinyl)F complex readily undergoes reductive elimination to provide the vinyl fluoride product with desired regioselectivity, without the generation of Pd-cyclohexyne intermediates.</p></div></div></div> | Yuxuan Ye; Seoung-Tae Kim; Ryan P. King; Mu-Hyun Baik; Stephen L. Buchwald | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7549aee301c24a7c7afc5/original/mechanistic-studies-of-pd-catalyzed-fluorination-of-cyclic-vinyl-triflates-evidence-for-in-situ-ligand-modification.pdf |
669ac45e01103d79c59c5f6e | 10.26434/chemrxiv-2024-7cqhw | Strategic Fluorination to Achieve a Potent, Selective, Metabolically-Stable, and Orally-Bioavailable Inhibitor of CSNK2. | The host kinase casein kinase 2 (CSNK2) has been proposed to be an antiviral target against β-coronaviral infection. To pharmacologically validate CSNK2 as a drug target in vivo, potent and selective CSNK2 inhibitors with good pharmacokinetic properties are required. Inhibitors based on the pyrazolo[1,5-a]pyrimidine scaffold possess outstanding potency and selectivity for CSNK2, but bioavailability and metabolic stability were often challenging. By strategically installing a fluorine atom on an electron-rich phenyl ring of a previously characterized inhibitor 1, we discovered compound 2 as a promising lead compound with improved in vivo metabolic stability. Compound 2 maintained excellent cellular potency against CSNK2, submicromolar antiviral potency, favorable solubility, and was remarkably selective for CSNK2 when screened against 192 kinases across the human kinome. We additionally present a co-crystal structure to support its on-target binding mode. In vivo, compound 2 was orally bioavailable, and demonstrated modest and transient inhibition of CSNK2, although antiviral activity was not observed, possibly attributed to its lack of prolonged CSNK2 inhibition. | Han Wee Ong; Xuan Yang; Jeffery Smith; Sharon Taft-Benz; Stefanie Howell; Rebekah Dickmander; Tammy Havener; Marcia Sanders; Jason Brown; Rafael Couñago; Edcon Chang; Andreas Krämer; Nathaniel Moorman; Mark Heise; Alison Axtman; David Drewry; Timothy Willson | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669ac45e01103d79c59c5f6e/original/strategic-fluorination-to-achieve-a-potent-selective-metabolically-stable-and-orally-bioavailable-inhibitor-of-csnk2.pdf |
60c74011567dfe6429ec3b01 | 10.26434/chemrxiv.7594646.v1 | The PMI Predictor - a Web App Enabling Green-by-Design Chemical Synthesis | <div>Herein we describe a green-by-design approach to route selection and development, assisted by predictive analytics and historical data. In order to aid the selection of more efficient strategies, we created a user-friendly web application, the “PMI Prediction Calculator,” to foretell the probable efficiencies of proposed synthetic routes, prior to their evaluation in the laboratory. This tool can also be used to benchmark the outcome performance of a developed process. We expect that use of this app will bring greater awareness of sustainability during the ideation phase of route design and will contribute to a reduced environmental impact of pharmaceutical production. The app can be accessed following the link:</div><div>https://acsgcipr-predictpmi.shinyapps.io/pmi_calculator/</div> | Alina Borovika; Jacob Albrecht; Jun Li; Andrew S. Wells; Christiana Briddell; Barry R. Dillon; Louis J. Diorazio; James R. Gage; Fabrice Gallou; Stefan G. Koenig; Michael E. Kopach; David K. Leahy; Isamir Martinez; Martin Olbrich; Jared L. Piper; Frank Roschangar; Edward Sherer; Martin D. Eastgate | Organic Synthesis and Reactions; Process Chemistry; Wastes; Chemoinformatics - Computational Chemistry; Pharmaceutical Industry; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74011567dfe6429ec3b01/original/the-pmi-predictor-a-web-app-enabling-green-by-design-chemical-synthesis.pdf |
616d102b7d3da54556fbadde | 10.26434/chemrxiv-2021-xdbzq-v2 | Structural Basis for the Friedel-Crafts Alkylation in Cylindrocyclophane Biosynthesis | The Lewis acid-catalyzed Friedel-Crafts alkylation of an aromatic ring with an alkyl halide is extensively used in
organic synthesis. However, its biological counterpart was not reported until the elucidation of the cylindrocyclophane biosynthetic pathway in Cylindrospermum licheniforme ATCC 29412 by Balskus and co-workers. CylK is the key enzyme to catalyze the formation of the cylindrocyclophane scaffold through the Friedel-Crafts alkylation reactions with regioselectivity and stereospecificity. Further research demonstrates that CylK can accept other resorcinol rings and secondary alkyl halides as substrates. To date, the
crystal structure of CylK has not been disclosed and the catalytic mechanism remains obscure. Herein we report the crystal structures of CylK in its apo form and its complexes with the analogues of its substrate and reaction intermediate. Combining the crystal structures, free energy simulations and the mutagenesis experiments, we proposed a concerted double-activation mechanism, which could explain the regioselectivity and stereospecificity. This work provides a foundation for engineering CylK as a biocatalyst to expand its substrate scope and applications in organic synthesis. | Hua-Qi Wang; Shu-Bin Mou; Wen Xiao; Huan Zhou; Xu-Dong Hou; Su-Jing Wang; Qian Wang; Jiali Gao; Zhiyi Wei; Lijun Liu; Zheng Xiang | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Natural Products; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616d102b7d3da54556fbadde/original/structural-basis-for-the-friedel-crafts-alkylation-in-cylindrocyclophane-biosynthesis.pdf |
63f0a2571d2d184063b2f27a | 10.26434/chemrxiv-2022-rnqlv-v2 | Can machine learning predict the phase behavior of surfactants? |
We explore the prediction of surfactant phase behavior using state-of-the-art machine learning methods, using a data set for twenty-three non-ionic surfactants in line with Bell, Phil. Trans. R. Soc. A 2016, 374, 20150137. Most machine learning classifiers we tested are capable of filling in missing data in a partially complete data set. However, strong data bias and a lack of chemical space information generally lead to poorer results entire de novo phase diagram prediction. Although some machine learn- ing classifiers perform better than others, these observations are largely robust to the particular choice of algorithm. Finally we explore how de novo phase diagram prediction can be improved by the inclusion of observations from state points sampled by analogy to commonly used experimental protocols. Our results indicate what factors should be considered when preparing for machine learning prediction of surfactant phase behavior in future studies. | Joseph Thacker; David Bray; Patrick Warren; Richard Anderson | Theoretical and Computational Chemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f0a2571d2d184063b2f27a/original/can-machine-learning-predict-the-phase-behavior-of-surfactants.pdf |
67a605996dde43c908ed89c1 | 10.26434/chemrxiv-2025-765rs | Selective Phosphorylation of Phenols and Benzenediols by the Kinase PsiK and Variants Thereof | Phosphorylation plays important roles in biology by modulating the structure, reactivity, and biological function of a broad range of molecules. Biocatalytic phosphorylation has attracted attention from synthetic chemists due to its selectivity and mild reaction conditions using ATP as a phosphate donor. Given the potential synthetic utility of kinases with activity on small molecule substrates, we explored the activity of PsiK, the enzyme responsible for selective 4-O-phosphorylation of 4-hydroxytryptamine or psilocin in psylocybin biosynthesis by Psilocybe cubensis. We find that PsiK has good activity on a range of substituted phenols and benzenediols beyond its native substrate, enabling preparative phosphorylation of different substrates and gram-scale phosphorylation of a representative substrate with a turnover number over 10,000. | Ahram Kim; Nicolás M. Morato; Prabir Saha; Pascal Eyimegwu; Aqeel A. Niyaz; Rui Huang; R. Graham Cooks; Ryan M. Phelan; Jared Lewis | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Bioengineering and Biotechnology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a605996dde43c908ed89c1/original/selective-phosphorylation-of-phenols-and-benzenediols-by-the-kinase-psi-k-and-variants-thereof.pdf |
64d557654a3f7d0c0df5ebbe | 10.26434/chemrxiv-2023-gxqsn-v2 | Complexity-Generating Transformations Enabled by Intramolecular Radical Migration: Alkyl–Arylation of Simple Olefins | A free-radical cascade approach has enabled the develop-ment of a synthetically versatile alkyl–arylation of olefins. This transformation engages an excellent range of olefins, from mono- to tetrasubstituted, without requiring directing or electronically activating groups. Further synthetic advantages, such as the facile generation of quaternary cen-ters and the introduction of heteroaryl groups with Lewis basic nitrogen atoms, also complement transition-metal-catalyzed alkyl–arylation. Vicinal stereoarrays were gener-ated with high levels of diastereoselectivity. The synthetic potential of this transformation was demonstrated by serving as the key step in a concise synthesis of oliceridine, a new painkiller that received FDA approval in 2020. | Dylan J. Babcock; Andrew J. Wolfram; Jaxon L. Barney; Santino M. Servagno; Ayush Sharma; Eric D. Nacsa | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d557654a3f7d0c0df5ebbe/original/complexity-generating-transformations-enabled-by-intramolecular-radical-migration-alkyl-arylation-of-simple-olefins.pdf |
61663114fb86192723f6830b | 10.26434/chemrxiv-2021-5t2lc | A Cocktail Approach Toward Tunable Organic Afterglow Systems | In this work, a cocktail approach toward tunable organic long-lived luminescence materials in solid, solution, and gel states is proposed. The tunable long-lived luminescence (τ > 0.7 s) is realized by controlling the energy transfer via manipulating the photo-induced isomerization of the energy acceptor (5). The afterglow can be regulated between blue and yellow emission upon irradiation of UV or visible light. And the “apparent lifetime” for the long-lived fluorescence is the same as the lifetime of the energy donor. The function is relying on the simple radiative energy transfer (reabsorption) between a long-lived phosphorescence and a highly efficient fluorescent isomer (5b), rather than the complicated communication between the excited state of the molecules such as Förster resonance energy transfer or Dexter energy transfer. The simple working principle endows this strategy with huge universality, flexibility, and operability. This work offers an extremely simple, feasible, and universal way to construct tunable afterglow materials in solid, solution, and gel states. | Xiang Ma; Liangwei Ma; Qiangyang Xu; Bingbing Ding; Zizhao Huang; Siyu Sun; He Tian | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61663114fb86192723f6830b/original/a-cocktail-approach-toward-tunable-organic-afterglow-systems.pdf |
639f6b2adadddc5a0b9315f2 | 10.26434/chemrxiv-2022-5x1fv | Recycling of All-Solid-State Li-ion Batteries: A Case Study of the Separation of Individual Components Within a System Composed of LTO, LLZTO, and NMC | All solid-state lithium-ion batteries (lithium ASSBs) are promising candidates for their use in high energy density applications like electric vehicles (EVs). With the current global projections of over 130 million EVs on road by 2030, there soon will be a need for lithium ASSBs waste management. For lithium ASSBs, various combinations of solid electrolytes and electrode materials could be imagined, e.g., with garnet electrolyte Li6.5La3Zr1.5Ta0.5O12 (LLZTO) and the use of a solid electrolyte might shift focus on recycling strategies. Not only the transition metals of the electrode materials will then be an important target, but also the recovery of La/Zr/Ta.
In this work, we present a recycling approach based on a two-step leaching process with citric acid to separate and recover the individual components of a full model cell comprising of Li4Ti5O12 (LTO) anode, Li6.5La3Zr1.5Ta0.5O12 (LLZTO) garnet electrolyte and LiNi1/3Mn1/3Co1/3O2 (NMC) cathode. By treating the complex mixture of LTO/LLZTO/NMC in this process, we manage to separate the materials from each other without strong mixing of elements between the individual phases. We show that the battery components can maintain their principle performance characteristics, demonstrating that the developed process can serve as a basis to recover functional battery materials. Thus, the process developed has a potential for upscaling and can guide towards considering separation capability for battery components in the development of lithium ASSBs.
| Aamir Iqbal Waidha; Amila Salihovic; Martine Jacob; Vanita Vanita; Burak Aktekin; Kristina Brix; Kerstin Wissel; Ralf Kautenburger; Juergen Janek; Wolfgang Ensinger; Oliver Clemens | Inorganic Chemistry; Energy; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639f6b2adadddc5a0b9315f2/original/recycling-of-all-solid-state-li-ion-batteries-a-case-study-of-the-separation-of-individual-components-within-a-system-composed-of-lto-llzto-and-nmc.pdf |
60c74ee5bdbb8917dfa39c80 | 10.26434/chemrxiv.12818132.v1 | Mechanism to Enhance Visible-light-driven Photocatalysis of Flower-like Composite of AgI Nanoparticle/BiOI Nanosheet | Nanosheet BiOI materials were prepared by using the precipitation-hydrothermal method.
Moreover, nanoparticle AgI/BiOI nanosheet composites were prepared using an ion-exchange
method and by controlling the amount of BiOI. The phase composition, optical morphology, and
absorption properties of the samples were determined using XRD, SEM, XPS, TEM, HRTEM,
and UV-Vis diffuse reflectance. Organic dyes, such as methyl orange (MO) and Coomassie
brilliant blue R-250 (CBB), were used to check the photocatalytic performance of the composites
when undergoing photodegradation in visible light. The prepared composites had high purity, and
the AgI nanoparticles were evenly loaded on the flower-like BiOI nanosheets, and both can absorb
the visible light. The photocatalytic activity of sole BiOI or AgI was poor, whereas that of the
composites was much better. The composite with 50% AgI exhibited the best photocatalytic
activity because of the formation of a p-n heterojunction, which promotes the separation of
photogenerated carriers and makes AgI stable under visible-light irradiation. | Jaafar Hasan; Gaowei Ouyang; Jing Wang; Haidi Li; Guangdong Tian; Chuanguang Qin | Catalysts; Dyes and Chromophores; Nanostructured Materials - Materials; Photosensitizers; Nanostructured Materials - Nanoscience; Solid State Chemistry; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Photocatalysis; Interfaces; Photochemistry (Physical Chem.); Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ee5bdbb8917dfa39c80/original/mechanism-to-enhance-visible-light-driven-photocatalysis-of-flower-like-composite-of-ag-i-nanoparticle-bi-oi-nanosheet.pdf |
60c74bd4469df43a5ef43f88 | 10.26434/chemrxiv.12382265.v1 | Molecular Mechanism of Clinically Oriented Drug Famotidine with the Identified Potential Target of SARS-CoV-2 | <p>Due to the current pandemic nature, severity, and rapid spread of COVID-19, there is eminent need to identify potential therapeutics to inhibit the novel coronavirus. In the quest, scientists from the USA had reported that the use of Famotidine in patients was associated with improved clinical outcomes and a reduced risk of intubation or death from COVID-19. However, the exact mode of action, the binding mechanism, and precise <a>COVID-19 </a>molecular target with which Famotidine interacts are yet to be ascertained. Here, 12 different COVID-19 protein targets have been screened against Famotidine employing molecular docking and molecular dynamics simulation. This reveals, among all the targets, the Papain-like protease (PLpro) as the potential target having the strongest affinity to Famotidine estimated to be of -7.9 kcal/mol with three hydrogen bonds. Tyrosine residue in the 268<sup>th</sup> position in the binding site seems to be very crucial for the stability of the PLpro-Famotidine complex, giving rise to multiple interactions such as hydrogen bonding as well as π-Sulfur. While the post-molecular dynamics (MD) analyses such as the root-mean-square deviation (RMSD) and fluctuation (RMSF), the radius of gyration (R<sub>g</sub>), and the principal component analysis (PCA) affirm the stability of the complex providing an insight into the binding mechanism, the identification of a valid target PLpro of SARS-COV-2 for Famotidine would help understand its action, further development, and experimental exploration.</p> | Parth Sarthi Sen Gupta; Satyaranjan Biswal; Dipankar Singha; Malay Kumar Rana | Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bd4469df43a5ef43f88/original/molecular-mechanism-of-clinically-oriented-drug-famotidine-with-the-identified-potential-target-of-sars-co-v-2.pdf |
60c750900f50db6c523975bd | 10.26434/chemrxiv.13058519.v1 | Reinterpreting π-Stacking | The nature of pi-pi interactions has long been debated. The term "pi-stacking" is considered by some to be a misnomer, in part because overlapping pi-electron densities are thought to incur steric repulsion, and the physical origins of the widely-encountered "slip-stacked" motif have variously been attributed to either sterics or electrostatics, in competition with dispersion. Here, we use quantum-mechanical energy decomposition analysis to investigate pi-pi interactions in supramolecular complexes of polycyclic aromatic hydrocarbons, ranging in size up to realistic models of graphene, and for comparison we perform the same analysis on stacked complexes of polycyclic <i>saturated</i> hydrocarbons, which are cyclohexane-based analogues of graphane. Our results help to explain the short-range structure of liquid hydrocarbons that is inferred from neutron scattering, trends in melting-point data, the interlayer separation of graphene sheets, and finally band gaps and observation of molecular plasmons in graphene nanoribbons. Analysis of intermolecular forces demonstrates that aromatic pi-pi interactions constitute a unique and fundamentally quantum-mechanical form of non-bonded interaction. Not only do stacked pi-pi architectures enhance dispersion, but quadrupolar electrostatic interactions that may be repulsive at long range are rendered attractive at the intermolecular distances that characterize pi-stacking, as a result of charge penetration effects. The planar geometries of aromatic sp<sup>2</sup> carbon networks lead to attractive interactions that are "served up on a molecular pizza peel", and adoption of slip-stacked geometries minimizes steric (rather than electrostatic) repulsion. The slip-stacked motif therefore emerges not as a defect induced by electrostatic repulsion but rather as a natural outcome of a conformation landscape that is dominated by van der Waals interactions (dispersion plus Pauli repulsion), and is therefore fundamentally quantum-mechanical in its origins. This reinterpretation of the forces responsible for pi-stacking has important implications for the manner in which non-bonded interactions are modeled using classical force fields, and for rationalizing the prevalence of the slip-stacked pi-pi motif in protein crystal structures.<br /><br /> | Kevin Carter-Fenk; John Herbert | Physical Organic Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750900f50db6c523975bd/original/reinterpreting-stacking.pdf |
6719156ed433919392f61c03 | 10.26434/chemrxiv-2024-b1lz5 | Borate-Catalysed Direct Amidation Reactions of Coordinating Substrates | The catalytic activity of different classes of boron catalysts was studied in amidation reactions with 4-phenylbutylamine/benzoic acid, and with 2-aminopyridine/phenylacetic acid. Whilst a simple boronic acid catalyst showed high catalytic activity with the former substrates, it was completely inactive in the latter reaction. In contrast, a borate ester catalyst was able to mediate the amidation of both substrate pairs with moderate activity. By screening a range of borate esters we were able to identify a novel borate catalyst that shows high reactivity with a range of challenging carboxylic acids/amine pairs, enabling catalystic amidation reactions to be achieved effectively with these industrially relevant compounds. The reactions can be perfomed on multigram scale with high levels of efficiency and in situ catalyst generation from commercially available reagents renders the process readily accessible for everyday laboratory use. Further experiments showed that the deactivating effect of 2-aminopyridine on boronic acid catalysts was due to its ability to stabilise catalytically inactive boroxines. | Richard Procter; Carla Alamillo-Ferrer; Usman Shabbir; Phyllida Britton; Dejan-Krešimir Bučar; Alexandre Dumon; Henry Rzepa; Jordi Bures; Andrew Whiting; Tom Sheppard | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Organocatalysis | CC BY 4.0 | CHEMRXIV | 2024-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6719156ed433919392f61c03/original/borate-catalysed-direct-amidation-reactions-of-coordinating-substrates.pdf |
60c7471a4c891941a7ad2c45 | 10.26434/chemrxiv.11515596.v1 | Electrochemical Properties and Crystal Structure of Li+/H+ Cation-Exchanged LiNiO2 | LiNiO<sub>2</sub> has high energy density but easily reacts with moisture in the atmosphere and deteriorates. We performed qualitative and quantitative evaluations of the degraded phase of LiNiO<sub>2</sub> and the influence of the structural change on the electrochemical properties of the phase. Li<sub>1-x</sub>H<sub>x</sub>NiO<sub>2</sub> phase with cation exchange between Li<sup>+</sup> and H<sup>+</sup> was confirmed by thermogravimetric analysis and Karl Fischer titration measurement. As the H concentration in LiNiO<sub>2</sub> increased, the rate capability deteriorated, especially in the low-temperature range and under low state of charge. Experimental and density functional theory (DFT) calculation results suggested that this outcome was due to increased activation energy of Li<sup>+</sup> diffusion owing to cation exchange. Rietveld analysis of X-ray diffraction and DFT calculation confirmed that the c lattice parameter and Li-O layer reduced because of the Li<sup>+</sup>/H<sup>+</sup> cation exchange. These results indicate that LiNiO<sub>2</sub> modified in the atmosphere has a narrowed Li-O layer, which is the Li diffusion path, and the rate characteristics are degraded. | Takahiro Toma; Ryo Maezono; Kenta Hongo | Ceramics; Electrochemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7471a4c891941a7ad2c45/original/electrochemical-properties-and-crystal-structure-of-li-h-cation-exchanged-li-ni-o2.pdf |
60c74169ee301ccba6c78c8e | 10.26434/chemrxiv.8051915.v1 | Voltage-Switchable HCl Transporters: The Effect of Lipid Headgroup Binding | Synthetic anion transporters that facilitate transmembrane H<sup>+</sup>/Cl<sup>-</sup>symport (cotransport)have anti-cancer potential due to their ability to neutralize pH gradients and inhibit autophagy in cells. However, compared to the natural product prodigiosin, synthetic anion transporters have low-to-modest H<sup>+</sup>/Cl<sup>-</sup>symportactivity and their mechanism of action remains less well understood. We here report a chloride-selective tetraurea macrocycle that has a record-high H<sup>+</sup>/Cl<sup>-</sup>symportactivity similar to prodigiosin and most importantly demonstrates unprecedented voltage-switchable transport properties that is linked to the lack of uniport activity. By studying anion binding affinity and transport mechanisms of four other anion transporters, we show that the lack of uniport and the voltage-dependent H<sup>+</sup>/Cl<sup>-</sup>symport originate from strong binding to lipid phosphate headgroup that hampers the diffusion of the free transporters through the membranes, leading to an unusual H<sup>+</sup>/Cl<sup>-</sup>symport mechanism that involves only charged species. Our work provides important mechanistic insights into different classes of anion transporters and a new approach to achieve voltage-switchability in artificial membrane transport systems. | Xin Wu; Jennifer Small; Alessio Cataldo; Anne Withecombe; Peter Turner; Philip Gale | Supramolecular Chemistry (Org.); Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74169ee301ccba6c78c8e/original/voltage-switchable-h-cl-transporters-the-effect-of-lipid-headgroup-binding.pdf |
612ef70d656369a3751f0f14 | 10.26434/chemrxiv-2021-gztdd | Actinic Wavelength Action Spectroscopy of the IO− Reaction Intermediate | Iodinate anions are important in the chemistry of the atmosphere where they are implicated in ozone depletion and particle formation. The atmospheric chemistry of iodine is a complex overlay of neutral-neutral, ion-neutral and photochemical processes, where many of the reactions and intermediates remain poorly characterised. This study targets the visible spectroscopy and photostability of the gas-phase hypoiodite anion (IO−), the initial product of the I− + O3 reaction, by mass spectrometry equipped with resonance-enhanced photodissociation and total ion-loss action spectroscopies. It is shown that IO− undergoes photodissociation to I− + O (3P) over 637 – 459 nm (15700 – 21800 cm−1) due to excitation to the bound first singlet excited state. Electron photodetachment competes with photodissociation above the electron detachment threshold of IO− at 521 nm (19200 cm−1) with peaks corresponding to resonant autodetachment involving the singlet excited state and the ground state of neutral IO possibly mediated by a dipole-bound state. | Benjamin McKinnon; Samuel Marlton; Boris Ucur; Evan Bieske; Berwyck Poad; Stephen Blanksby; Adam Trevitt | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2021-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612ef70d656369a3751f0f14/original/actinic-wavelength-action-spectroscopy-of-the-io-reaction-intermediate.pdf |
61dcdf827f1d671c5143de46 | 10.26434/chemrxiv-2021-rbm7n-v3 | Transition Metal Catalyst Free Cross-Coupling Reaction of Tertiary Propargylic Alcohols with Hetero-Areneboronic Acids | We report a perfluorophenylboronic acid catalyzed cross coupling reaction of tertiary propargylic alcohols and hetero-areneboronic acids for valuable benzo[b]thiophene and cyclopenta[a]indene derivates. This coupling reaction proceeds efficiently with a wide array of substrates scope in up to 89% yield and excellent regioselectivity. A significant advantage of our protocol is the transition metal catalyst free and mild conditions needed. This strategy provides direct and facile access to medicinally important benzo[b]thiophene and cyclopenta[a]indene scaffold containing a quaternary carbon center. | Jian-Fei Bai; Jianbo Tang; Xiaolong Gao; Zhi-Jiang Jiang; Jia Chen; Zhanghua Gao | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2022-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61dcdf827f1d671c5143de46/original/transition-metal-catalyst-free-cross-coupling-reaction-of-tertiary-propargylic-alcohols-with-hetero-areneboronic-acids.pdf |
6290092c1df2edd1ac59ea52 | 10.26434/chemrxiv-2022-ntxcl-v2 | Non-adiabatic Mapping Dynamics in the Phase Space of the SU(N) Lie Group | We present the rigorous theoretical framework of the generalized spin mapping representation for non- adiabatic dynamics. This formalism is based on the generators of the su(N) Lie algebra to represent N discrete electronic states, thus preserving the size of the original Hilbert space in the state representation. The Stratonovich-Weyl transform is then used to map an operator in the Hilbert space to a continuous func- tion on the SU(N) Lie Group manifold which is a phase space of continuous variables. Wigner representation is used to describe the nuclear degrees of freedom. Using the above representations, we derived an exact expression of the time-correlation function as well as the exact quantum Liouvillian. Making the linearization approximation, this exact Liouvillian is reduced to the Liouvillian of the several recently proposed meth- ods. These expressions lead to a self-consistent trajectory-based method to simulate non-adiabatic dynamics, which is based entirely on the generalized spin mapping formalism to treat the electronic states without the necessity of converting back to the cartesian Meyer-Miller-Stock-Thoss mapping variables. We envision that the theoretical work presented in this work provides a rigorous and unified framework to formally derive non-adiabatic quantum dynamics approaches with continuous variables. | Duncan Bossion; Wenxiang Ying; Sutirtha Chowdhury; Pengfei Huo | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Physical and Chemical Processes; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2022-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6290092c1df2edd1ac59ea52/original/non-adiabatic-mapping-dynamics-in-the-phase-space-of-the-su-n-lie-group.pdf |
654fb5576e0ec7777fc33e69 | 10.26434/chemrxiv-2023-2hk9l | The nature of carotenoid S* state and its role in the nonphotochemical quenching of plants | Light-harvesting complexes (LHCs) of plants serve as antennas to collect light and transfer the absorbed energy to reaction centers, but also regulate energy transport by dissipating the excitation energy of chlorophylls. This process, known as nonphotochemical quenching (NPQ), seems to be activated by conformational changes within the LHCs, but the identity of the quenching species remains elusive. Recent spectroscopic measurements suggest the so-called S* dark state of the bound carotenoids as the quencher of chlorophyll excitation. Here, we employ excited state nonadiabatic dynamics simulations to investigate lutein embedded in different conformations of a minor LHC of plants, CP29. We reveal that different conformations of the complex differentially stabilize the minor s-trans conformer of lutein with respect to the dominant s-cis one. Our findings also demonstrate that it is the s-trans conformer that presents the spectroscopic signatures of the S* state and rationalize how it is able to accept energy from the closest chlorophyll, providing thus a relationship between LHC conformation and quenching. | Davide Accomasso; Giacomo Londi; Lorenzo Cupellini; Benedetta Mennucci | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654fb5576e0ec7777fc33e69/original/the-nature-of-carotenoid-s-state-and-its-role-in-the-nonphotochemical-quenching-of-plants.pdf |
60c7500e469df4b4a0f447cc | 10.26434/chemrxiv.12988526.v1 | The Steadfast Au@Pt Soldier: Peroxide-Tolerant Nanozyme for Signal Enhancement in Lateral Flow Immunoassay of Peroxidase-Containing Samples | <div>The approach to inhibit endogenous peroxidases by elevated concentrations of hydrogen peroxide while maintaining the high peroxidase-mimicking activity of Au@Pt nanozymes was developed. The approach facilitates selective and highly-sensitive detection of peroxidase-mimicking nanozyme nanozymes in the background of endogenous peroxidases. Au@Pt nanozyme was used as the colorimetric and catalytic label in lateral flow immunoassay of an important plant pathogen – potato virus X. The inhibition of endogenous peroxidases in plant extracts and selective detection of Au@Pt nanozyme provides the lowest limit of detection among immunochemical assays of potato virus X (up to 500 times lower compared to the assay with conventional gold nanoparticles). </div><div>The proposed approach uses the fundamental principle of enzyme inhibition by the substrate. It is universal and applicable to all matrixes with peroxidase activity. </div> | Vasily Panferov; Irina V. Safenkova; Anatoly V. Zherdev; Boris B. Dzantiev | Biochemical Analysis; Environmental Analysis; Nanocatalysis - Catalysts & Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7500e469df4b4a0f447cc/original/the-steadfast-au-pt-soldier-peroxide-tolerant-nanozyme-for-signal-enhancement-in-lateral-flow-immunoassay-of-peroxidase-containing-samples.pdf |
634b550086473a8387149260 | 10.26434/chemrxiv-2022-v5kts-v2 | Electric fields drive bond homolysis | Electric fields have been used to control and direct chemical reactions in biochemistry and enzymatic catalysis, yet directly applying external electric fields to activate reactions in bulk solution and to characterize them ex situ remains a challenge. Here we utilize the scanning tunneling microscope-based break-junction technique to investigate the electric field driven homolytic cleavage of the radical initiator 4-(methylthio)benzoic peroxyanhydride at ambient temperatures in bulk solution, without the use of co-initiators or photochemical activators. Through ex-situ quantification by high performance liquid chromatography and UV-vis analysis as a function of time, we find that the electric field catalyzes the reaction. Importantly, we demonstrate that the reaction rate in a field increases linearly with solvent dielectric constant. Using density functional theory calculations, we show that the applied electric field decreases the dissociation energy of the O-O bond and stabilizes the product relative to the reactant due to their different dipole moments.
| Boyuan Zhang; Cedric Schaack; Claudia Prindle; Ethan Vo; Miriam Aziz; Michael Steigerwald; Timothy Berkelbach; Colin Nuckolls; Latha Venkataraman | Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634b550086473a8387149260/original/electric-fields-drive-bond-homolysis.pdf |
6511be8ced7d0eccc3339980 | 10.26434/chemrxiv-2023-51l4t | Asymmetric Migratory Hydroarylation for the Concise Synthesis of Chiral α-(Hetero)Aryl-Substituted Amines | Complementary to design of a single structurally complex chiral ligand to promote each step in transition-metal catalysis, multiligand relay catalysis through dynamic ligand exchange with each step in the catalytic cycle promoted by its best ligand provides an attractive approach to enhance the whole reaction reactivity and selectivity. Herein, we report a regio- and enantioselective NiH-catalyzed migratory hydroarylation process with a simple combination of a chain-walking ligand and an asymmetric arylation ligand, producing high value chiral α-(hetero)aryl-substituted amines and their derivatives under mild conditions. The potential synthetic applications of this transformation are demonstrated by the concise synthesis of (S)-nicotine and a CDK8 inhibitor. | Junqian Zhou; Yuli He; Zihao Liu; Shaolin Zhu | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6511be8ced7d0eccc3339980/original/asymmetric-migratory-hydroarylation-for-the-concise-synthesis-of-chiral-hetero-aryl-substituted-amines.pdf |
6500c74ab6ab98a41c563b4c | 10.26434/chemrxiv-2023-sdl91-v2 | Ligand-Enforced Geometries and Associated Reactivity in P-Block Compounds | The geometry at an element centre can generally be predicted based on the number of electron pairs around it using valence shell electron pair repulsion (VSEPR) theory. Strategies to distort p-block compounds away from these predicted geometries have gained considerable interest due to the unique structural outcomes, spectroscopic properties or reactivity patterns engendered by such distortion. This review presents an up-to-date group-wise summary of this exciting and rapidly growing field with a focus on understanding how the ligand employed unlocks structural features, which in turn influences the associated reactivity. Relevant geometrically constrained compounds from groups 13-16 are discussed, along with selected stoichiometric and catalytic reactions. Several areas for advancement in this field are also discussed. Collectively, this review advances the notion of geometric tuning as an important lever, alongside electronic and steric tuning, in controlling bonding and reactivity at p-block centres. | Tyler Hannah; Saurabh Chitnis | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Bonding; Coordination Chemistry (Inorg.); Inorganic Acid/Base Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6500c74ab6ab98a41c563b4c/original/ligand-enforced-geometries-and-associated-reactivity-in-p-block-compounds.pdf |
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