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66fd266d12ff75c3a1278cec | 10.26434/chemrxiv-2024-72hfg | Multi-scale Modeling and Experimental Investigation of Oxidation Behavior in Platinum Nanoparticles | Understanding the oxidation behavior of Pt nanoparticles (NPs) is crucial for developing durable and efficient catalysts. In this study, we investigate the oxidation of a realistic Pt NP, retrieved from scanning transmission electron microscopy (STEM) images. We use a multistep approach combining ReaxFF and MACE-MP-0 forcefields with Density Functional Theory (DFT) calculations. Our Monte Carlo simulations reveal high oxidation of the nanoparticle, with oxygen penetrating deep into the core. We explore the plausibility of these configurations by carrying out XRD, TEM and EXAFS measurements on samples of various average particle sizes. Progressing in our workflow, we find that 100 ns of thermostated dynamics at 350 K using the ReaxFF forcefield leads to the formation of detached Pt$_6$O$_8$ species. To explore the validity of this small platinum-oxide cluster, we first optimize the geometries using the recent MACE-MP-0 forcefield resulting in structures without the species. We then compare both forcefields to DFT calculations showing closer agreement for MACE-MP-0 compared to ReaxFF. Finally, we discuss the electronic structure of our oxidized nanoparticles spanning a whole range of oxygen coverages, finding substantial changes in the Pt-5$d$ and O-2$p$ projected density of states of the platinum structure as the coverage increases. Our findings emphasize the importance of accurately describing the potential energy surface and explicitly modeling oxygen coverage to predict catalytically relevant properties at high potentials. This study aims to provide a foundation for understanding the complex interplay between nanoparticle structure, oxidation state, and catalytic performance, aiming to guide the rational design of advanced catalytic materials. | Tom Demeyere; Husn-Ubayda Islam; Tom Ellaby; Misbah Sarwar; David Thompsett; Chris-Kriton Skylaris | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis; Physical and Chemical Properties | CC BY 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fd266d12ff75c3a1278cec/original/multi-scale-modeling-and-experimental-investigation-of-oxidation-behavior-in-platinum-nanoparticles.pdf |
62f64180a014473626b4fab2 | 10.26434/chemrxiv-2022-dh03b-v2 | Progress Towards the Syntheses of Bactobolin A and C4-epi-Bactobolin A Using a Sulfamate-Tethered Aza-Wacker Cyclization Strategy | We present a progress report towards Bactobolin A and C4-epi-Bactobolin A. Sulfamate-tethered aza-Wacker cyclization followed by a Tsuji-Wacker ketone synthesis furnishes a key tricyclic intermediate which we hypothesize can be elaborated into C4-epi-Bactobolin A. Epimerization of one of the stereocenters of this compound furnishes an intermediate which we hypothesize can be elaborated into
Bactobolin A. | SHYAM SATHYAMOORTHI; Someshwar Nagamalla; Joel Mague | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2022-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f64180a014473626b4fab2/original/progress-towards-the-syntheses-of-bactobolin-a-and-c4-epi-bactobolin-a-using-a-sulfamate-tethered-aza-wacker-cyclization-strategy.pdf |
63120dd0bc257bd04ed8be51 | 10.26434/chemrxiv-2022-grgrd | Brokering between tenants for an international materials acceleration platform | The future of materials science is borderless, cooperative, and distributed across the globe. This necessitates flexible, reconfigurable software defined research workflows, which we herein demonstrate by integrating multiple disciplines and modalities. Our brokering approach to research orchestration exposes entire laboratories in a cooperative multi-tenancy platform that is asynchronous, modular, and resilient. To the best of our knowledge, this constitutes the first international materials acceleration platform (MAP) which is herein demonstrated through a battery electrolyte workflow that ran in five countries over two weeks. We discuss the lessons learned from multi-tenancy and fault tolerance and chart a way to a universal battery MAP with fully ontology- based schemas and cost-aware orchestration. | Monika Vogler; Jonas Busk; Hamidreza Hajiyani; Peter Bjørn Jørgensen; Nehzat Safaei; Ivano Castelli; Francisco Fernando Ramírez; Johan Carlsson; Giovanni Pizzi; Simon Clark; Felix Hanke; Arghya Bhowmik; Helge Sören Stein | Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63120dd0bc257bd04ed8be51/original/brokering-between-tenants-for-an-international-materials-acceleration-platform.pdf |
66e99a5451558a15ef42149c | 10.26434/chemrxiv-2024-nkrd8-v2 | [1,n]-Metal migrations for directional translational motion at the molecular level | The controlled translational motion displayed by nature’s motor proteins underpins a wealth of processes integral to life, from organelle transport to muscle contraction. The motor proteins move along one dimensional cytoskeletal tracks, with their motion characterised by high association of the enzyme to the biopolymer combined with highly dynamic motion along the track. Efforts to mimic this dynamic association and control translational motion in fully synthetic systems have been dominated by rotaxane-based systems, where the properties of the mechanical bond ensure complete association between the moving component (the macrocycle) and the track it encircles, while allowing high rates of translation through shuttling of the moving component under Brownian motion. In addition to the dynamic association displayed by many rotaxane systems, by careful design of the track and macrocyclic component, elegant strategies have been employed to further control the motion in these mechanically interlocked systems, with both energy and information ratchet mechanisms allowing directional translational motion to be achieved. Other than mechanical bonds, alternative platforms for achieving controlled translational motion in fully synthetic systems have had more limited success, with bipedal walker systems that exhibit dynamic association lacking mechanisms to achieve inherent directionality, and bipedal systems that do display high levels of directionality requiring stepwise intervention of an experimentalist (i.e., they lack the dynamic autonomous behaviour that underpins nature’s walkers). Here we introduce carbon-to-carbon metal migration as a new platform for dynamic association and show how such migrations, in combination with the incorporation of a simple hydrocarbon fuel, can be harnessed to achieve autonomous directional translational motion of a metal centre along the length of a polyaromatic thread. | Beatrice Collins; Emma Hollis; Michael Chronias; Carlijn van Beek; Paul Gates | Organic Chemistry; Catalysis; Supramolecular Chemistry (Org.); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e99a5451558a15ef42149c/original/1-n-metal-migrations-for-directional-translational-motion-at-the-molecular-level.pdf |
619d9bcd7c891627584275e1 | 10.26434/chemrxiv-2021-r69b0-v2 | Surface Stability and Morphology of Calcium Phosphate Tuned by pH Values and Lactic Acid Additives: Theoretical and Experimental Study | The ubiquitous mineralization of calcium phosphate (CaP) facilitates biological organisms to produce hierarchically structured minerals. The coordination number and strength of Ca2+ ions with phosphate species, oxygen-containing additives, and solvent molecules played a crucial role in tuning nucleation processes and surface stability of CaP under the simulated body fluid (SBF) or aqueous solutions upon the addition of oligomeric lactic acid (LACn, n=1, 8) and changing pH values. As revealed by ab initio molecular dynamics (AIMD), density functional theory (DFT), and molecular dynamics (MD) simulations as well as high-throughput experimentation (HTE), the binding of LAC molecules with Ca2+ ions and phosphate species could stabilize both pre-nucleation clusters and brushite (DCPD, CaHPO4·2H2O) surface through intermolecular electrostatic and hydrogen bonding interactions. When the concentration of Ca2+ ions ([Ca2+]) is very low, the amount of the formed precipitation decreased with the addition of LAC based on UV-Vis spectroscopic analysis due to the reduced chance for the LAC capped Ca2+ ions to coordinate with phosphates and the increased solubility in acid solution. With the increasing [Ca2+] concentration, the kinetically stable DCPD precipitation was obtained with high Ca2+ coordination number and low surface energy. Morphologies of DCPD precipitation are in plate, needle, or rod, depending on the initial pH values that tuned by adding NH3·H2O, HCl, or CH3COOH. The prepared samples at pH ≈ 7.4 with different Ca/P ratios exhibited negative zeta potential values, which were correlated with the surface electrostatic potential distributions and potential biological applications. | Hongwei Chen; Changchang Lv; Lin Guo; Ming Ma; Xiangfeng Li; Zhengyi Lan; Jun Huo; Hao Dong; Xiangdong Zhu; Qiang Zhu; Yuming Gu; Ziteng Liu; Jianjun Liu; Hangrong Chen; Xuefeng Guo; Jing Ma | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619d9bcd7c891627584275e1/original/surface-stability-and-morphology-of-calcium-phosphate-tuned-by-p-h-values-and-lactic-acid-additives-theoretical-and-experimental-study.pdf |
61e4d1a380719d7f6f1223a3 | 10.26434/chemrxiv-2022-jz11p | Steered Molecular Dynamics Study of the Age-related Stiffening of the Crystalline Lens
| αA-crystallin is a key component of the glassy solution of proteins that constitutes the mammalian
lens. It contributes to the refractive and mechanical properties of the lens, and as a member of
the small heat shock protein (sHSP) family of chaperones, plays a role in aggregate prevention.
Age-dependent L- to D- racemization of amino acids in the sequence of the protein has been
implicated in lens stiffening and cataract, and is suspected to interfere with the protein’s basic
chaperone activity and structural features. This communication investigates the mechanical
properties of bovine αA-crystallin and several of its (point) D-isomerized derivatives by way of
Steered Molecular Dynamics simulation. In a series of induced unfolding experiments, an external
pulling force is applied to the native protein and, independently, to three D-amino acid variants.
A principal component-based technique is applied to extract dominant structural and mechanical
features from the system variants. The D-isomerization of a single residue in the structure of
αA-crystallin alters the protein’s unfolding pathway, and changes the mechanical properties of its
inherent elements of (secondary) protein structure. The location of the D- substituted residue is
critical to defining the extent and nature of the observed effects. The latter are expressed as
divergence from the typical native induced unfolding pathway and altered structural element
stiffnesses.
| Ewa Golas; Leslie Glasser; Harold A. Scheraga | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e4d1a380719d7f6f1223a3/original/steered-molecular-dynamics-study-of-the-age-related-stiffening-of-the-crystalline-lens.pdf |
6278e0c770876770864bceac | 10.26434/chemrxiv-2022-w5260 | Calculation of mass spectra with the QCxMS method for negatively and multiply charged molecules | Detailed information about the structural composition of an unknown chemical analyte can be obtained routinely and reliably by using mass spectrometry (MS).
Analysis and validation of an MS experiment are usually performed by comparison to reference spectra, which are stored in databases that contain a large number of entries for common molecules.
This procedure relies on the quality and completeness of the entries and if structures (classes) are missing, measured spectra cannot be properly matched.
To close this gap, and to enable detailed mechanistic analysis, the Quantum Chemical Mass Spectrometry (QCxMS) program has been developed.
It enables fully automatic calculations of electron ionization (EI), dissociative electron attachment (DEA), and positive ion collision induced dissociation (CID) mass spectra of singly charged molecular ions.
In this work, the extension to negative and multiple ion charge for the CID run mode is presented.
QCxMS is now capable of calculating structures carrying any charge, without the need for pre-tabulated fragmentation pathways or machine-learning of database spectra.
Mass spectra of four single negatively charged, as well as two multiple positively charged organic ions with molecular sizes ranging from 12 to 92 atoms were computed and compared to reference spectra taken from the literature.
The underlying Born-Oppenheimer molecular dynamics (MD) calculations were conducted using the extended tight-binding semi-empirical quantum mechanical GFN2-xTB method while for some small molecules, ab-initio DFT-based MD simulations were performed.
Detailed insights into the fragmentation pathways were gained and the effects of the computed charge assignments on the resulting spectrum are discussed.
Especially for the negative ion mode, the influence of the deprotonation site to create the anion was found to be substantial.
Doubly charged fragments could successfully be calculated for the first time while higher charged structures introduced severe assignment problems.
Overall, this extension of the QCxMS program further enhances its applicability and underlines its value as a sophisticated toolkit for CID-based tandem MS structure elucidation. | Jeroen Koopman; Stefan Grimme | Theoretical and Computational Chemistry; Analytical Chemistry; Mass Spectrometry; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6278e0c770876770864bceac/original/calculation-of-mass-spectra-with-the-q-cx-ms-method-for-negatively-and-multiply-charged-molecules.pdf |
6762bd0181d2151a021ba452 | 10.26434/chemrxiv-2024-g7h8g | Enhanced Characterization of Lignin Nanoparticles by Asymmetric Flow-Field Flow Fractionation | The unique properties of lignin nanoparticles (LNPs)—uniform shape, surface properties and nanoscale—carry great potential for the desired material utilization of technical lignins. Especially, the particle size distribution and dispersity of LNPs are the key for their successful valorization. However, characterization of LNPs usually require a combination of light scattering and microscopy techniques which provide only average values, are often limited in sampling size and require tedious sample preparation. Here we introduce a method based on asymmetric flow field-flow fractionation (AF4) coupled with multi angle laser light scattering (MALLS), dynamic light scattering (DLS) and refractive index (RI) detection for the analysis of size and shape of LNPs. Exploiting the separation power of AF4 in combination with MALLS, DLS, and RI allowed to obtain more enhanced particle size distributions of LNP that are comparable to batch DLS and AFM measurements. Moreover, we discuss the influence of the particle size on the MALLS and DLS signal and determination of the shape factor of LNP. | Nadine Kohlhuber; Irina Sulaeva; Tao Zou; Oliver Musl; Robert Mildner; Scott Renneckar; Monika Österberg; Thomas Rosenau; Antje Potthast | Analytical Chemistry; Polymer Science; Nanoscience; Separation Science | CC BY 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6762bd0181d2151a021ba452/original/enhanced-characterization-of-lignin-nanoparticles-by-asymmetric-flow-field-flow-fractionation.pdf |
657856227acf130c320f6ad3 | 10.26434/chemrxiv-2023-5j129-v2 | Acylphosphates as versatile transient species in reaction networks and optical catalyst screenings | Chemically-driven reaction cycles are prevalent in nature, yet artificial examples are still rare and often lack robustness or versatility. In this study, we introduce acylphosphate steady states that can be accessed from a wide range of organophosphates using either carboxylic anhydride or carbodiimide fuels. The combination of carboxylic anhydride fuel and pyridine catalysis makes this chemistry sufficiently robust to allow for 25 fueling cycles without generation of observable quantities of detrimental side products such as pyrophosphates. We demonstrate that the acylation of organophosphates gives rise to transient aggregates, and we harness the transient fluorescence of acylphosphate-bridged excimers in rapid screenings of more than 50 catalysts in a single well plate experiment. Due to its versatility and robustness, we anticipate that the organophosphate / acylphosphate reaction cycle will prove useful for the creation of chemically-driven molecular machines and transient self-assemblies. | Andreas Englert; Felix Majer; Jannik Schiessl; Alexander Kuehne; Max von Delius | Physical Chemistry; Organic Chemistry; Catalysis; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657856227acf130c320f6ad3/original/acylphosphates-as-versatile-transient-species-in-reaction-networks-and-optical-catalyst-screenings.pdf |
60c74f04f96a00599d287bb2 | 10.26434/chemrxiv.12839177.v1 | Radical Enzymes Control the Chemistry of Their Highly Reactive Intermediates Using the Quantum Coulombic Effect | Here, we report an exquisite strategy that the B12 enzymes exploit to manipulate the reactivity of their radical intermediate (Adenosyl radical). Based on the quantum-mechanic calculations, these enzymes utilize a little known long-ranged through space quantum Coulombic effect (QCE). The QCE causes the radical to acquire an electronic structure that contradicts the Aufbau Principle: The singly-occupied molecular orbital (SOMO) is no longer the highest-occupied molecular orbital (HOMO) and the radical is unable to react with neighbouring substrates. The dynamic nature of the enzyme and its structure is expected to be such that the reactivity of the radical is not restored until it is moved into close proximity of the target substrate. We found that the hydrogen bonding interaction between the nearby conserved glutamate residue and the ribose ring of Adenosyl radical plays a crucial role in manipulating the orbital ordering | Hossein Khalilian; Gino A. DiLabio | Biochemistry; Computational Chemistry and Modeling; Theory - Computational; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f04f96a00599d287bb2/original/radical-enzymes-control-the-chemistry-of-their-highly-reactive-intermediates-using-the-quantum-coulombic-effect.pdf |
61420a05b817b426b71e2ec3 | 10.26434/chemrxiv-2021-qn8wb | Conjugation of proapoptotic peptides with folate and cyanine dyes for enhanced potency and selectivity towards tumor cell lines | Despite continuous advances, anticancer therapy still faces several technical hurdles such as selectivity on cellular and subcellular targets of therapeutics. Toward addressing these limitations, we have combined the use of proapoptotic peptides, cyanine dyes and folate to target the mitochondria of tumor cells. Hence, a series of proapoptotic peptides and their conjugates with a cyanine dye and/or a folate were prepared via solid-phase peptide synthesis (SPPS) and their activity tested in different mammalian cell lines. Compounds bearing either a cyanine dye or folate were found to be more cytotoxic than the parent peptides or more selective towards cells overexpressing the folate receptor α, which is commonly found on the surface of tumor cells. Nevertheless, constructs containing both components showed diminished potency and selectivity. | Davide Cardella; Louis Yu Pan Luk; Yu-Hsuan Tsai | Biological and Medicinal Chemistry; Organic Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2021-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61420a05b817b426b71e2ec3/original/conjugation-of-proapoptotic-peptides-with-folate-and-cyanine-dyes-for-enhanced-potency-and-selectivity-towards-tumor-cell-lines.pdf |
60c73f61842e65a823db1ab8 | 10.26434/chemrxiv.7368299.v1 | EOM-CC Guide for Fock-Space Travel: The C2 Edition | Despite their small size, C<sub>2</sub> species pose a big challenge to electronic structure owing to extensive electronic degeneracies and multi-configurational wave functions leading to a dense manifold of electronic states. We present detailed electronic structure calculations of C<sub>2</sub>, C<sub>2</sub><sup>-</sup>, and C<sub>2</sub><sup>2-</sup> emphasizing spectroscopically relevant properties. We employ double ionization potential (DIP) and ionization potential (IP) variants of equation-of-motion coupled-cluster method with single and double substitutions (EOM-CCSD) and a dianionic reference state. We show that EOM-CCSD is capable of describing multiple interacting states in C<sub>2</sub> and C<sub>2</sub><sup>-</sup> in an accurate, robust, and effective way. We also characterize the electronic structure of C<sub>2</sub><sup>2-</sup>, which is metastable with respect to electron detachment. | Sahil Gulania; Thomas-C. Jagau; Anna I. Krylov | Theory - Computational; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f61842e65a823db1ab8/original/eom-cc-guide-for-fock-space-travel-the-c2-edition.pdf |
6422de0c647e3dca99a645ce | 10.26434/chemrxiv-2023-0bf2c | Voltage imaging with engineered proton-pumping Rhodopsins: Insights from the proton transfer pathway | Voltage imaging using genetically encoded voltage indicators (GEVI) has taken the field of neuroscience by storm in the past decade. Its ability to create subcellular and network level readouts of electrical dynamics depends critically on the kinetics of the response to voltage of the indicator used. Engineered Microbial Rhodopsins form a GEVI sub-class known for their high voltage sensitivity and fast response kinetics. Here we review the essential aspects of mi-crobial rhodopsin photocycles that are critical to understanding the mechanisms of voltage sensitivity in these pro-teins and link them to insights from efforts to create faster, brighter and more sensitive Microbial Rhodopsin-based GEVIs. | Xin Meng; Srividya Ganapathy; Lars van Roemburg; Marco Post; Daan Brinks | Physical Chemistry; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6422de0c647e3dca99a645ce/original/voltage-imaging-with-engineered-proton-pumping-rhodopsins-insights-from-the-proton-transfer-pathway.pdf |
673c7bbc5a82cea2faa78a56 | 10.26434/chemrxiv-2024-t6nqn | Green-LED (Auto)Photocatalysis Initiated by a Transient Charge-Transfer Complex of N-Bromoacetamide and Mes-Acr-MeClO4 | Mes-Acr-MeClO4, a well-known blue-LED visible light photocatalyst, formed a dark red charge-transfer (CT) complex with N-bromoacetamide (NBA) in the presence of K2CO3. This complex enabled the absorption of green light, leading to the generation of an N-centered radical from N-bromoacetamide. This radical underwent anti-Markovnikov and anti-periplanar addition to phenylacetylene, resulting in 100% Z-selective (Z)-N-(2-bromo-2-phenylvinyl)acetamide. The (Z)-N-(2-bromo-2-phenylvinyl)acetamide (λem ~ 518 nm, τ ~ 10 ns) proved to be an effective green and red-LED (auto)photocatalyst, facilitating the synthesis of (Z)-N-(2-bromo-2-phenylvinyl)acetamide from phenylacetylene and NBA within the same reaction system. The process was found to be 100% atom-economical. | Tarun Dinda; Prasenjit Mal | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673c7bbc5a82cea2faa78a56/original/green-led-auto-photocatalysis-initiated-by-a-transient-charge-transfer-complex-of-n-bromoacetamide-and-mes-acr-me-cl-o4.pdf |
67bdb4ccfa469535b9dcdeed | 10.26434/chemrxiv-2025-lwh8m | Realizing the magneto-structural correlation of a highly anisotropic Fe(III) porphyrin complex through ab-initio approaches | A mononuclear pentacoordinate Fe(III)-porphyrin-NCS complex has been synthesized and characterized by single-crystal X-ray diffraction, magnetic, electrochemical, spectroscopic, and theoretical studies. Single crystal X-ray diffraction studies show a planar porphyrin moiety with an axial NCS coordinated to the Fe(III) centre. Electrochemical and spectroelectrochemical studies in solution depict clear changes in the system during oxidation and reduction processes. Mössbauer spectroscopic analysis at different temperatures also supported the observation of a high-spin state of the Fe(III)-porphyrin complex that was further backed by DFT calculations. Attempts to understand the origin of high magnetic anisotropy in the ground state as determined by DC magnetic measurements was undertaken by detailed CASSCF/QD-NEVPT2 calculations. | Mayurika Das; Sujit Kamilya; Subhankar Mandal; Sher Singh Meena; Jiri Pechousek; Radovan Herchel; Abhishake Mondal | Theoretical and Computational Chemistry; Inorganic Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bdb4ccfa469535b9dcdeed/original/realizing-the-magneto-structural-correlation-of-a-highly-anisotropic-fe-iii-porphyrin-complex-through-ab-initio-approaches.pdf |
663d2a7091aefa6ce198bc18 | 10.26434/chemrxiv-2024-3wsx8 | Self-Limiting Electrospray Deposition (SLED) of Porous Polyimide Coatings as Effective Lithium-Ion Battery Separator Membranes | Electrospray deposition (ESD) is employed to produce separator membranes for coin-cell lithium-ion batteries (LIBs) using off-the-shelf polyimide (PI). The PI coatings are deposited directly onto planar NMC electrodes via self-limiting electrospray deposition (SLED). Scanning electron microscopy (SEM), optical microscopy, and spectroscopic microreflectometry are implemented in combination to evaluate the porosity, thickness, and morphology of sprayed PI films. Electrochemical performance of the PI separators are analyzed via charge/discharge cycle rate tests. Discharge capacities of cells with the unoptimized SLED PI separators are within 83-99.8% of those with commercial Celgard 2325 PP/PE/PP separators. Furthermore, ultraviolet-visual wavelength spectroscopy (UV-vis) is utilized to qualitatively assess variation in film porosity within a prescribed temperature range of 20-400oC. UV-vis results underscore the ability of the SLED PI separator to maintain its porous microstructure up to ~350oC. This study points to the unique possibility of SLED as a separator manufacturing technique for geometrically complex energy storage systems. Further research is needed to optimize the polymer-solvent system to enhance control of porosity, pore size, and coating thickness. This can lead to significant improvement in rate and cycle life performance in more advanced energy storage devices. | Robert Green-Warren; Andrew Fassler; Abigail Juhl; Noah McAllister; Andrew Huth; Michael Grzenda; S. Rahman Pejman; Maxim Arkhipov; Michael Durstock; Jonathan Singer | Materials Science; Polymer Science; Energy; Coating Materials; Nanostructured Materials - Materials; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663d2a7091aefa6ce198bc18/original/self-limiting-electrospray-deposition-sled-of-porous-polyimide-coatings-as-effective-lithium-ion-battery-separator-membranes.pdf |
6471afb3e64f843f41d94860 | 10.26434/chemrxiv-2023-pw7l8-v2 | Study on ordered anode in proton exchange membrane water electrolysers | Acidic oxygen evolution reaction is crucial for proton exchange membrane water electrolysers, which have been hindered by the high catalytic overpotential and high loading of noble metal catalysts and high mass transfer resistance. Here we present an ordered anode with ultra low precious metal loading. Ordered TiO2 nanotubes were grown on a titanium substrate by elec-tro-oxidation, then treated at high temperature in H2/Ar to enhance the electrical conductivity of the substrate, and finally loaded with IrO2 by electrodeposition. This ordered anode exhibits a low overpotential of 224 mV at 10 mA cm-2 towards oxygen evolution reaction in 0.5 M H2SO4. A proton exchange membrane electrolyser using the ordered anode with a low mass loading of 59.27 μg cm-2 can operate stably at 500 mA cm-2 for 1000 hours. The contact resistance of the ordered membrane electrode assembly is lower than that of the conventional second generation membrane electrode by the equiva-lent circuit fitting analysis of electrochemical impedance spectra. | Zijin Zhang; Hongmei Gao; Jiaqi Liu; Tianyu Wu; Mengyi Qiu; Jinbo Wang; Ru Chen | Physical Chemistry; Catalysis; Acid Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6471afb3e64f843f41d94860/original/study-on-ordered-anode-in-proton-exchange-membrane-water-electrolysers.pdf |
674de4177be152b1d0b3771c | 10.26434/chemrxiv-2024-g23tk | Understanding the Role of Energy Transfer Processes in Chemical Reactions at Plasma-Liquid Interfaces | Electrochemistry can enable sustainable chemical manufacturing but is limited by the reactions possible with conventional metal electrodes. Plasma electrochemistry, which replaces a conventional solid electrode with plasma in electrochemical cells, offers new avenues for chemical synthesis by combining charge transfer with alternative energy transfer processes at the plasma-liquid interface. To understand how plasma electrochemistry differs from conventional electrochemistry, we investigated plasma reactions with acrylonitrile, an industrially relevant molecule used as the precursor in the well-characterized electrosynthesis of adiponitrile. We demonstrate that non-charge transfer processes dominate plasma-driven chemistry through systematic variation of plasma polarity, current, and reactant concentration, combined with comprehensive quantitative analysis of solid, liquid, and gas products. Most notably, we observed no adiponitrile formation (the desired electrochemical product) while total product yields exceeded the theoretical charge-transfer maximum by up to 32-fold. Substantial polyacrylonitrile formation occurred under all conditions, a product not typically seen in conventional electrochemistry. The plasma anode yielded consistently higher products than the plasma cathode, producing hydrogen and propionitrile at 21 and 2 times the charge-transfer maximum, respectively. Electron scavenger experiments confirmed these transformations occurred primarily through non-Faradaic processes rather than charge transfer. These results demonstrate that plasma electrochemistry is primarily driven by energy transfer at plasma-electrolyte interfaces, providing fundamental insights for harnessing these interactions in chemical synthesis. | Casey Bloomquist; Daniel Naumov; Ahrin Yang; Ricardo Mathison; Benjamin Herzog; William Tenn; Miguel Modestino; Eray Aydil | Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674de4177be152b1d0b3771c/original/understanding-the-role-of-energy-transfer-processes-in-chemical-reactions-at-plasma-liquid-interfaces.pdf |
65938b1fe9ebbb4db939a631 | 10.26434/chemrxiv-2024-sllvn | Solid-state 183W NMR spectroscopy as a high-resolution probe of polyoxotungstate structures and dynamics | Polyoxometalates such as ammonium paratungstate (APT) are an important class of metal oxides with applications for catalysis, (opto)electronics, and functional materials. Structural analyses of solid polyoxometalates mostly rely on X-ray or neutron diffraction techniques, which are limited to compounds that can be isolated with long-range crystallographic order. While 183W NMR has been shown to probe polyoxotungstate structures and dynamics in solution, its application to solids has been extremely limited. Here, state-of-the-art methods for the detection of solid-state 183W NMR spectra are tested and compared for APT in different hydration states. The highly resolved solid-state spectra distinguish each crystallographically distinct site in the tungstate structure. Furthermore, the 183W chemical shifts are shown to be highly sensitive to the local structure, dynamics, and symmetry of APT, establishing solid-state 183W NMR spectroscopy as a potent probe for analysis of polyoxotungstates and other tungsten-derived materials to complement solution NMR and diffraction-based techniques. | Zachariah Berkson; Moritz Bernhardt; Christophe Copéret | Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Spectroscopy (Inorg.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65938b1fe9ebbb4db939a631/original/solid-state-183w-nmr-spectroscopy-as-a-high-resolution-probe-of-polyoxotungstate-structures-and-dynamics.pdf |
60c73d7c469df43b9df42702 | 10.26434/chemrxiv.5836059.v1 | The challenge of determining the crystal structure of epitaxial 0001 oriented sp2-BN films | <p>Boron nitride (BN) as a thin film is promising for many future
electronic applications. On technologically important substrates, 0001 α-Al<sub>2</sub>O<sub>3</sub>
and 0001 4H/6H-SiC, chemical vapor deposition yields epitaxial sp<sup>2</sup>-BN
films oriented around the c-axis. Here, we seek to point out that sp<sup>2</sup>-BN
can form two different polytypes; hexagonal BN (h-BN) and rhombohedral BN
(r-BN), only differing in the stacking of the basal planes but with identical
distance between the basal planes and in-plane lattice parameters. This makes
structural identification challenging in c-axis oriented films. We suggest the
use of a combination of high-resolution electron microscopy with careful sample
preparation and thin film X-ray diffraction techniques like pole figure
measurements and glancing incidence (in-plane) diffraction to fully distinguish
h-BN from r-BN.</p> | Mikhail Chubarov; Hans Högberg; Anne Henry; Henrik Pedersen | Ceramics; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2018-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d7c469df43b9df42702/original/the-challenge-of-determining-the-crystal-structure-of-epitaxial-0001-oriented-sp2-bn-films.pdf |
60c740e3567dfe3347ec3c89 | 10.26434/chemrxiv.7853414.v1 | pH Swing Cycle for CO2 Capture Electrochemically Driven through Proton-Coupled Electron Transfer | We propose and
perform a thermodynamic analysis of the energetic costs of CO<sub>2</sub>
separation from flue gas using a pH swing created by electrochemical
redox reactions involving
proton-coupled electron transfer from molecular species in aqueous
electrolyte. Electrochemical reduction of these molecules results in the
formation of alkaline solution, into which CO<sub>2</sub> is absorbed;
subsequent electrochemical oxidation of the reduced molecules results in the
acidification of the solution, triggering the release of pure CO<sub>2</sub>
gas. We examined the effect of buffering from the CO<sub>2</sub>-carbonate
system on the solution pH during this pH swing cycle, and thus on the
open-circuit potential of a hypothetical electrochemical cell in a 4-step CO<sub>2</sub>
capture-release cycle. The thermodynamic minimum work input varies from 16 to
75 kJ/mol<sub>CO2 </sub>as throughput increases, for both flue gas and direct
air capture, with the potential to go substantially lower if CO<sub>2</sub>
capture or release is performed simultaneously with electrochemical reduction
or oxidation. These values are compared with those for other separation methods. We discuss the properties
required of molecules that would be suitable for such a cycle. | Michael Aziz; David G. Kwabi | Atmospheric Chemistry; Separation Science; Electrochemistry; Thermodynamics (Chem. Eng.); Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e3567dfe3347ec3c89/original/p-h-swing-cycle-for-co2-capture-electrochemically-driven-through-proton-coupled-electron-transfer.pdf |
64f3aadc3fdae147fa57fe17 | 10.26434/chemrxiv-2023-qpf2x | Rapid Automated Iterative Small Molecule Synthesis | Automated iterative small molecule synthesis has the potential to advance and democratize the discovery
of new medicines, materials, and many other classes of functional chemical matter. But to date this approach
has been limited by a requirement of about one day of time per C-C bond forming step. Here, we report a nextgeneration small molecule synthesizer which operates at an order of magnitude faster than prior systems through
improvements in both chemistry and engineering. These findings move the field of small molecule synthesis a
step closer to democratizing its core discovery engine.
| Wesley Wang; Nicholas Angello; Daniel Blair; Kameron Medine; Theodore Tyrikos-Ergas; Antonio Laporte; Martin Burke | Organic Chemistry; Catalysis; Natural Products; Organic Synthesis and Reactions; Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f3aadc3fdae147fa57fe17/original/rapid-automated-iterative-small-molecule-synthesis.pdf |
615ca8c335b40624af09fc6b | 10.26434/chemrxiv-2021-vjzll | An Easily Prepared Monomeric Cobalt(II) Tetrapyrrole Complex that Efficiently Promotes the 4e–/4H+ Peractivation of O2 to Water
| The selective 4e–/4H+ reduction of dioxygen to water is an important reaction that takes place at the cathode of fuel cells. Monomeric aromatic tetrapyrroles (such as porphyrins, phthalocyanines, and corroles) coordinated to Co(II) have been considered as oxygen reduction catalysts due to their low cost and relative ease of synthesis. How- ever, these systems have been repeatedly shown to be selective for O2 reduction by the less desired 2e –/2H+ pathway to yield hydrogen peroxide. Herein, we report the initial synthesis and study of a Co(II) tetrapyrrole complex based upon a non-aromatic isocorrole scaffold that is competent for 4e–/4H+ ORR. This Co(II) 10,10-dimethyl isocorrole (Co[10- DMIC]) is obtained in a just four simple steps and excellent yield from a known dipyrromethane synthon. Evaluation of the steady state spectroscopic and redox properties of Co[10-DMIC] against those of Co(II) porphyrin ([Co(TPFPP)]) and corrole ([Co(TPFPC)(PPh3)]) homologs demonstrated that the light harvesting and electrochemical properties of the isocorrole are distinct from those displayed by more traditional aromatic tetrapyrroles. Further, investigation of the ORR activity of Co[10-DMIC] using a combination of electrochemical and chemical reduction studies revealed that this simple, unadorned monomeric Co(II) tetrapyrrole is ~85% selective for the 4e–/4H+ reduction of O2 to H2O over the more kinetically facile 2e–/2H+ process that delivers H2O2. By contrast, the same ORR evaluations conducted for the Co(II) porphyrin and corrole homologs demonstrated that these traditional aromatic systems catalyze the 2e–/2H+ conversion of O2 to H2O2 with near complete selectivity. Despite being a simple, easily prepared, monomeric tetrapyrrole platform, Co[10-DMIC] supports an ORR catalysis that has historically only been achieved using elaborate porphyrinoid-based architectures that incorporate pendant proton-transfer groups, ditopic molecular clefts, or which impose cofacially ori- ented O2 binding sites. Accordingly, Co[10-DMIC] represents the first simple, unadorned, monomeric metalloisocorrole complex that can be easily prepared and which shows a privileged performance for the 4e–/4H+ peractivation of O2 to water as compared to other simple Co(II) tetrapyrroles. | Qiuqi Cai; Linh Tran; Tian Qiu; Jennifer Eddy; Glenn Yap; Joel Rosenthal | Inorganic Chemistry; Catalysis; Energy; Electrochemistry; Ligands (Inorg.); Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615ca8c335b40624af09fc6b/original/an-easily-prepared-monomeric-cobalt-ii-tetrapyrrole-complex-that-efficiently-promotes-the-4e-4h-peractivation-of-o2-to-water.pdf |
6650738c418a5379b02a09a1 | 10.26434/chemrxiv-2024-jk23r | Improvement of Inhibitors of the Macrophage Infectivity Potentiator Protein from Trypanosoma cruzi, Burkholderia pseudomallei, and Legionella pneumophila – a Comparison | The treatment of Chagas disease and infections with Gram-negative bacteria is limited to a low number of antibiotics. Due to the development of resistance and partially severe side effects, there is an urgent need for new treatment strategies and virulence factors such as the macrophage infectivity potentiator (MIP) protein have emerged as a promising new therapeutic target. Inhibition of microbial MIP proteins leads to reduced viability and proliferation in pathogens such as Legionella pneumophila and Burkholderia pseudomallei. The parasitic pathogen of Chagas disease, Trypanosoma cruzi, also expresses a MIP protein, presumably involved in host cell invasion. Here, we took advantage of a compound library initially designed to inhibit MIPs of Burkholderia (BpMIP) and Legionella (LpMIP), to screen compounds against the Trypanosoma-MIP (TcMIP). Using a fluorescence polarization assay (FPA), the first qualitative structure-activity relationships could be derived. Further compound development led to highly active inhibitors of all tested MIPs from pathogenic microorganisms. Docking studies, molecular dynamics simulations and quantum mechanical calculations suggest an extended σ-hole of the meta-halogenated phenyl sulfonamide to be responsible for the high affinity. | Theresa Lohr; Carina Herbst; Nicole Bzdyl; Christopher Jenkins; Nicolas Scheuplein; Wisely Oki Sugiarto; Jacob Whittaker; Albert Guskov; Isobel Norville; Ute Hellmich; Felix Hausch; Mitali Sakar-Tyson; Christoph Sotriffer; Ulrike Holzgrabe | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6650738c418a5379b02a09a1/original/improvement-of-inhibitors-of-the-macrophage-infectivity-potentiator-protein-from-trypanosoma-cruzi-burkholderia-pseudomallei-and-legionella-pneumophila-a-comparison.pdf |
629ecbb41959596234c3e1d8 | 10.26434/chemrxiv-2022-g5v90 | ColorLab: Visualizing Color from Absorbance Spectra | We present here the first public release of ColorLab, a Python-based program that can convert absorbance spectra into color images. It was designed for use with organic photovoltaic (OPV) materials and blends, which represent a myriad of colors based on molecular design and material blending that can exhibit persistent color or evolve over time via degradation or morphology changes. However, ColorLab is not limited to this application, and can generate color images from a single spectrum or an evolving color bar on a time axis from multiple time-stamped spectra. Using internationally defined illuminants, ColorLab can display colors that are representative of a variety of lighting situations, from indoor to outdoor. The development of this program aims to aid with the visualization of semitransparent materials and to connect researchers with designers, through conversion of spectra to color. | Spencer M. Yeager; Michael A. Anderson; Priscilla Babiak; Bryon W. Larson; Erin L. Ratcliff | Materials Science | CC BY NC 4.0 | CHEMRXIV | 2022-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629ecbb41959596234c3e1d8/original/color-lab-visualizing-color-from-absorbance-spectra.pdf |
60c7426c702a9b3a7c18a472 | 10.26434/chemrxiv.8282258.v1 | A Metal-Free Facile Construction of C(sp3) –CF3 Bond: Trifluoromethylation of Hydrazones with Togni’s Reagent under Mild Conditions | A metal-free trifluoromethylation of hydrazones with
Togni’s reagent under mild conditions was developed. Various functional groups including ester, methoxy, dimethoxy, nitro, halogen and heterocyclic compounds were tolerated. This
simple and green strategy provides a practical tool to construct C(sp<sup>3</sup>) –CF<sub>3</sub>
bonds | Zhen Luo; Xinlong Han; Huiying Zeng; Chao-Jun Li | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426c702a9b3a7c18a472/original/a-metal-free-facile-construction-of-c-sp3-cf3-bond-trifluoromethylation-of-hydrazones-with-togni-s-reagent-under-mild-conditions.pdf |
60c753c8567dfe6b0dec5f81 | 10.26434/chemrxiv.12925238.v2 | O-Mesityl(sulfonyl)hydroxylamine: A Novel Reagent for Reduction of Electron Deficient α,β-Unsaturated Carbonyl Derivatives | <div>Hydrogenation of electron deficient ,-unsaturated carbonyl derivatives</div><div>using O-mesityl(sulfonyl)hydroxylamine in the presence of catalytic amount of ytterbium</div><div>triflate to obtain good to excellent is described.</div> | Sudershan Reddy Gondi | Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2020-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753c8567dfe6b0dec5f81/original/o-mesityl-sulfonyl-hydroxylamine-a-novel-reagent-for-reduction-of-electron-deficient-unsaturated-carbonyl-derivatives.pdf |
670846f212ff75c3a1160d86 | 10.26434/chemrxiv-2024-8jwjg | An Electrochemical Pipette for the Study of Drug Metabolite | Electrochemistry offers an effective means of mimicking enzymatic metabolite pathways, particularly the oxidative pathways catalyzed by the cytochrome P450 superfamily. The electrochemical generation and identification of metabolites are time-sensitive, necessitating adjustable cell designs for accurate mechanistic interpretation. We present a thin-layer electrode (TLE) that addresses the needs of both analytical and synthetic electrochemical generation of drug metabolites. The TLE’s ability to conduct experiments on a minute-to-hour timescale allows for detailed observation of reaction mechanisms for metabolites not easily identified by traditional methods. The utility of the TLE for drug metabolite was benchmarked for electrochemical oxidation of acetaminophen, acebutolol, and 2-acetyl-4-butyramidophenol, known to produce quinone imine metabolites, i.e., NAPQI, upon oxidation. When combined with a microelectrode (µE), the TLE enables probing the concentration pro-files for metabolic oxidation of these drugs. The micromole scale and pipette-type structure of the TLE facilitate comprehen-sive structural elucidation of intermediates and products using chromatographic and spectroscopic techniques. | Nastaran Nikzad; Buwanila T. Punchihewa; Vidit Minda; William G. Gutheil; Mohammad Rafiee | Analytical Chemistry; Electrochemical Analysis | CC BY NC 4.0 | CHEMRXIV | 2024-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670846f212ff75c3a1160d86/original/an-electrochemical-pipette-for-the-study-of-drug-metabolite.pdf |
60c73e5f337d6cf630e2632a | 10.26434/chemrxiv.6652955.v2 | Boehmite Nanofibers as a Dispersant for Nanotubes in an Aqueous Sol | By exploiting the dispersibility and rigidity of boehmite nanofibers (BNFs) with a high aspect ratio of 4 nm in diameter and several micrometers in length, multiwall-carbon nanotubes (MWCNTs) were successfully dispersed in aqueous solutions. In these sols, the MWCNTs were dispersed at a ratio of about 5–8% relative to BNFs. Self-standing BNF–nanotube films were also obtained by filtering these dispersions and showing their functionality. These films can be expected to be applied to sensing materials. | Gen Hayase | Composites; Fibers; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2018-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e5f337d6cf630e2632a/original/boehmite-nanofibers-as-a-dispersant-for-nanotubes-in-an-aqueous-sol.pdf |
62b34fc558b3d6faef5a7e06 | 10.26434/chemrxiv-2022-0mzxq | Hydrogen bond donors in drug design | In medicinal chemistry, hydrogen bond donors are seen to cause more problems than hydrogen bond acceptors and this study examines hydrogen bond donor-acceptor asymmetries in the context of drug design. Hydrogen bond acidity is reviewed and it is shown how polarity can be estimated for individual hydrogen bond donors and acceptors from alkane/water partition coefficient measurements. Hydrogen bond donors are generally less polar than hydrogen bond acceptors and desolvation penalty is therefore an implausible explanation for deleterious effects of hydrogen bond donors. Generally, the number of hydrogen bond acceptors in organic compounds exceeds the number of hydrogen bond donors and the apparently greater restrictiveness of the Rule of 5 for hydrogen bond donors may simply be a reflection of this imbalance. The weaker hydration of hydrogen bond donors implies that attempts to address polarity surfeit in optimization of permeability should be focused on hydrogen bond acceptors. Elimination of redundant hydrogen bond donors can potentially reduce active efflux and destabilize the solid state without resulting in unacceptable increases in lipophilicity. The key hydrogen bond donor-acceptor asymmetry in the context of target recognition is that the presence of a hydrogen bond donor usually implies that a hydrogen bond acceptor is also present. Target-ligand hydrogen bonds form in aqueous media and design opportunities presented by frustrated hydration and secondary interactions are discussed. Hydrogen bond donors based on oxygen, nitrogen and carbon are compared as target recognition elements and potential benefits of halogen and chalcogen bond donors as replacements for hydrogen bond donors are discussed. | Peter Kenny | Physical Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b34fc558b3d6faef5a7e06/original/hydrogen-bond-donors-in-drug-design.pdf |
60c73f9eee301c3813c78950 | 10.26434/chemrxiv.7453223.v1 | Strong Bases and Weak Anions in Catalytic C–H Insertion Reactions of Vinyl Carbocations | <p>Here we report the surprising discovery that high-energy vinyl carbocations can be generated under strongly basic conditions, and that they engage in intramolecular sp3 C–H insertion reactions through the catalysis of commercially available weakly coordinating anion salts. This approach relies on the unconventional combination of lithium hexamethyldisilazide base and the commercially available catalyst, triphenylmethylium tetrakis(pentafluorophenyl)borate. These reagents form a catalytically active lithium species that enables the application of vinyl cation C–H insertion reactions to heteroatomcontaining substrates.</p> | Benjamin Wigman; Stasik Popov; Alex L. Bagdasarian; Brian Shao; Tyler R. Benton; Chloé G. Williams; Steven P. Fisher; Vincent LaVallo; Kendall N. Houk; Hosea Nelson | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Main Group Chemistry (Inorg.); Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9eee301c3813c78950/original/strong-bases-and-weak-anions-in-catalytic-c-h-insertion-reactions-of-vinyl-carbocations.pdf |
673fb1005a82cea2fa4b3dcc | 10.26434/chemrxiv-2024-pdv44 | A Spectrochemical Series for Electron Spin Relaxation | Controlling the rate of electron spin relaxation in paramagnetic molecules is essential for contemporary applications in molecular magnetism and quantum information science. However, the physical mechanisms of spin relaxation remain incompletely understood, and new spectroscopic observables play an important role in evaluating spin dynamics mechanisms and structure-property relationships. Here, we use cryogenic magnetic circular dichroism (MCD) spectroscopy and pulse electron paramagnetic resonance (EPR) in tandem to examine the impact of ligand field (d-d) excited states on spin relaxation rates. We employ a broad scope of square-planar Cu(II) compounds with varying ligand field strength, including CuS4, CuN4, CuN2O2, and CuO4 first coordination spheres. An unexpectedly strong correlation exists between spin relaxation rates and the average d-d energy (R2 = 0.97). The relaxation rate trends as the inverse eleventh power of the excited-state energies, whereas simplified theoretical models predict only an inverse second power dependence. These experimental results directly implicate ligand field excited states as playing a critical role in the ground state spin relaxation mechanism. Furthermore, ligand field strength is revealed to be a particularly powerful design principle for spin dynamics, enabling formation of a spectrochemical series for spin relaxation. | Nathanael Kazmierczak; Kay Xia; Erica Sutcliffe; Jonathan Aalto; Ryan Hadt | Physical Chemistry; Inorganic Chemistry; Magnetism; Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673fb1005a82cea2fa4b3dcc/original/a-spectrochemical-series-for-electron-spin-relaxation.pdf |
663cfabb418a5379b0dfc4a5 | 10.26434/chemrxiv-2024-4bznl | The OrbiTOF Mass Analyzer: Time-of-Flight Analysis via an Orbitrap Quadro-Logarithmic Field with Periodic Drift Focusing. | Thermo Scientific™ Orbitrap™ analyzers represent prominent class of high-resolution mass analyzer commonly used in life sciences, and for interrogation of complex samples. Injected ions, trapped within a quadro-logarithmic field, orbit a central electrode and oscillate up and down the axis. A new class of multi-reflection time-of-flight mass analyzer has been developed based on the Orbitrap field structure plus an additional series of periodic lenses wrapped around the central axis to constrain beam dispersion. The axial and angular velocity of the injected ions was balanced so that with each axial oscillation, the ions passed through the next lens in the series, to form a tightly folded 25-metre long, 3-dimensional ion path, ending with ions striking a detector surface.
Performance was interrogated via experiment and simulation. 70k resolving power was observed within the relatively compact analyzer, albeit at cost to transmission. A larger design with an integrated extraction trap and greater flight energy is discussed. | Anastassios Giannakopulos; Hamish Stewart; Dmitry Grinfeld; Christian Hock; Wilko Balschun; Matthias Biel; Alexander Makarov | Physical Chemistry; Analytical Chemistry; Analytical Apparatus; Biochemical Analysis; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2024-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663cfabb418a5379b0dfc4a5/original/the-orbi-tof-mass-analyzer-time-of-flight-analysis-via-an-orbitrap-quadro-logarithmic-field-with-periodic-drift-focusing.pdf |
623dce0574104f6d14b1cd29 | 10.26434/chemrxiv-2022-brsxc | Volcanic ash as multi-nutrient mineral fertilizer: science and early applications | Volcanic ash is a multi-nutrient mineral fertilizer whose catalytic mechanism of action, replenishing trace metals necessary to soil bacterial enzymes for the efficient biogenochemical cycling of key elements such as N, C, P and S, ensures use of relatively small amounts to fertilize large soil surfaces. Chiefly demonstrated in the course of the 2010s in Russia’s Kamchatka and in Indonesia, two world’s areas hosting highly active volcanoes, these findings remain poorly known. Fulfilling the principles of the emerging circular economy, the large-scale use of readily available and overabundant tephra as agricultural fertilizer is a significant economic opportunity for both farmers and populations living near active volcanoes, affording also important environmental advantages. Providing a unified picture, this study will hopefully accelerate such progress. | Rosaria Ciriminna; Antonino Scurria; Giuseppe Tizza; Mario Pagliaro | Agriculture and Food Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623dce0574104f6d14b1cd29/original/volcanic-ash-as-multi-nutrient-mineral-fertilizer-science-and-early-applications.pdf |
62f2487f1ea5f6ba6e6e1b94 | 10.26434/chemrxiv-2022-9jb6k-v2 | Perturbative expansion of non-orthogonal
product approach for charge-transfer states
| Modeling of the excited states of multichromophoric systems is crucial for the understanding of photosynthesis functioning. The excitonic Hamiltonian method is widely
used for such calculations. Excited states of the combined system are constructed from
the wave functions of individual chromophores while their interactions are described by
excitonic couplings. In the current study we enhance earlier proposed non-orthogonal
product approach to incorporate dynamic correlation effects accounted for by the multireference perturbation theory. We discuss the problems of constructing the excitonic
Hamiltonian including charge-transfer states for the molecular systems where the overlap contribution to the excitonic couplings is non-negligible. The benchmark calculations were performed for a model system. It was shown that the overlap component
of the excitonic coupling is of great importance. The enhanced method provides an
accurate description of the excited states energies and other properties.
| Ilya Glebov; Vladimir Poddubnyy; Daniil Khokhlov | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f2487f1ea5f6ba6e6e1b94/original/perturbative-expansion-of-non-orthogonal-product-approach-for-charge-transfer-states.pdf |
610d4e8003182f2d1d1aaa7f | 10.26434/chemrxiv-2021-m1x3t | All-Red-Light Photoswitching of Indirubin Controlled by Supramolecular Interactions
| Red light responsiveness of photoswitches is a highly desired property for many important application areas such as biology or material sciences. The main approach to elicit this property uses strategic substitution of long known photoswitch motives such as azobenzenes or diarylethenes. Only very few photoswitches possess inherent red-light absorption of their core chromophore structures. Here we present a strategy to convert the long known purple indirubin dye into a prolific red light responsive photoswitch. In a supramolecular approach its photochromism can be changed from a negative to a positive one while at the same time significantly higher yields of the metastable E isomer are obtained. E to Z photoisomerization can then also be induced by red light of longer wavelengths. Indirubin therefore represents a unique example of reversible photoswitching using entirely red light for both switching directions. | Stefan Thumser; Laura Köttner; Nadine Hoffmann; Peter Mayer; Henry Dube | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Photochemistry (Org.); Supramolecular Chemistry (Org.); Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610d4e8003182f2d1d1aaa7f/original/all-red-light-photoswitching-of-indirubin-controlled-by-supramolecular-interactions.pdf |
6418c73fdab08ad68f6e8c1e | 10.26434/chemrxiv-2023-cwr53 | PepFun 2.0: improved protocols for the analysis of natural and modified peptides | The role of peptides is nowadays relevant in fields such as drug discovery and biotechnology. Computational analyses are required to study their properties and gain insights into rational design strategies. Both natural and modified peptides containing non-natural amino acids require customized tools to run sequence and structure-based studies. PepFun 2.0 is a new version of the python package for the study of natural and modified peptides using a set of modules to analyze the sequence and structure of the molecules. PepFun 2.0 comprises five main modules for different tasks such as sequence alignments, prediction of properties, generation of conformers, modification of structures, detection of protein-peptide interactions, and extra functions to include peptides containing non-natural amino acids. The code and tutorial are available at: https://github.com/rochoa85/PepFun2 | Rodrigo Ochoa | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6418c73fdab08ad68f6e8c1e/original/pep-fun-2-0-improved-protocols-for-the-analysis-of-natural-and-modified-peptides.pdf |
64ca9d5369bfb8925a3f9bcc | 10.26434/chemrxiv-2023-5k2q9 | Direct synthesis of ultrasmall PbS nanocrystals passivated with a metal-halide-perovskite monolayer | Inorganic shelling is a key strategy to address unwanted, surface-mediated non-radiative pathways in semiconductor nanocrystals. Improved passivation particularly advances the use of the smallest nanocrystals, because complex photophysics arise as nanomaterials approach the molecular limit. However, shelling strategies developed for larger/more-robust nanocrystals are not always applicable in this size regime. Herein we introduce the direct synthesis of ultrasmall (ø<2 nm) PbS nanocrystals shelled with a range of metal-halide perovskite monolayers by employing the appropriate two-dimensional perovskite as a precursor at the point of nanocrystal growth. These passivated nanocrystals possess improved photoluminescence quantum yields; reduced dynamic spectral red-shifting after photoexcitation; and longer, more-monoexponential photoluminescence dynamics—consistent with a reduction in defect-mediated exciton-phonon coupling. We then apply these shelled, ultrasmall PbS nanocrystals as sensitizers in a triplet-fusion upconversion architecture and observe two-fold improved triplet yields. This demonstration emphasizes the photophysical benefits realized via our 2D perovskite shelling strategy, which can be applied to other nanocrystals—especially to small particles that are similarly vulnerable to existing strategies for post-synthetic modifications. | Christian Imperiale; Francisco Villanueva; Ehsan Nikbin; Jane Howe; Mark Wilson | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ca9d5369bfb8925a3f9bcc/original/direct-synthesis-of-ultrasmall-pb-s-nanocrystals-passivated-with-a-metal-halide-perovskite-monolayer.pdf |
630c53621945adb4d1eabd2c | 10.26434/chemrxiv-2022-v4drk | Pd(II)-Catalyzed Annulative Difunctionalization of Two Inert C(sp3)-H Bonds by a Bifunctional Reagent | Illustrated herein is a Pd(II) catalyzed one-pot direct difunc-tionalization of two distinct C(sp3)-H bonds [gem-ʹ-di-Me groups bearing aliphatic carboxylic acid] with bifunctional reagent (BFR) 2-iodo benzoic acid. The methyl 2-pyridyl sul-foximine (MPyS) bidentate directing group (DG), 2-chloro-5-trifluoromethyl ligand, and NaBrO3 co-oxidant combination helps the concerted metalation deprotonation (CMD) of inert C(sp3)-H bond as well reductive elimination steps; density functional theory (DFT) studies validate such insights. This process makes two [CC and CO] bonds of gem-ʹ-di-Me groups of DG-enabled aliphatic carboxylic acids in a single operation offering access to unusual benzo-fused peripheral substituted ω-membered lactones. This concept is uncovered for the first time. The transformation tolerates labile functional groups featuring broad scope with the construction of wide range of novel molecules of structural diversity. Ki-netic and control experiments study reveal the participation of monomeric-Pd-species on the catalytic cycle. Synthetic versatility of the complex molecular entities is also presented. | Arghadip Ghosh; Nicolas Grimblat; Somratan Sau; Arijit Saha; Vincent Gandon; Akhila K Sahoo | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis; Ligands (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630c53621945adb4d1eabd2c/original/pd-ii-catalyzed-annulative-difunctionalization-of-two-inert-c-sp3-h-bonds-by-a-bifunctional-reagent.pdf |
64fc0d4ab338ec988a27bc08 | 10.26434/chemrxiv-2023-0lsf4 | Selective and Biocompatible Detection of Acetylcholine with a Fluorous Potentiometric Laser-Induced Graphene Sensor | Acetylcholine (ACh) appears in the brain and body of mammalians and functions both as a neuromuscular transmitter and neuromodulator. Tools with high spatial and temporal resolution to study ACh are in high demand due to the diverse function of ACh and its implications in neurodegenerative diseases. This work presents a highly promising sensor for a selective and biocompatible recording of ACh with a fluorous-phase potentiometric sensor. Fluorous compounds are nonpolar and not miscible with water and hydrocarbons, making them bio-orthogonal and biocompatible. This work presents the first proof-of-concept detection of ACh using a fluorous sensing phase. We show drastic improvement in selectivity for the fluorous phase ion-exchanger electrode compared to a conventional ion-exchanger potentiometric sensor with a lipophilic sensing membrane. As a result, we observed more than an order of magnitude improvement in the limit of detection, and two orders of magnitude increase in the electrode linear range during measurement of ACh in artificial cerebrospinal fluid. To enable the development of flexible and compact ACh sensing neural probes, this work combines the unique advantages of the fluorous phase with a flexible laser-induced porous graphitic carbon (LIG) to create the first flexible solid-contact fluorous-phase potentiometric sensor. The fluorous-phase solid-contact LIG ion exchanger electrode showed a near Nernstian slope of 54.9 ±0.8 and a 42 nM limit of detection. | Farbod Amirghasemi; Abdulrahman Al-Shami; Kara Ushijima; Maral P. S. Mousavi | Biological and Medicinal Chemistry; Materials Science; Analytical Chemistry; Electrochemical Analysis; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fc0d4ab338ec988a27bc08/original/selective-and-biocompatible-detection-of-acetylcholine-with-a-fluorous-potentiometric-laser-induced-graphene-sensor.pdf |
6392fd1a0fd992e5773ebdea | 10.26434/chemrxiv-2022-tpf8w-v2 | Enantioselective molecular recognition in a flexible self-folding cavitand | We report a chiral deep cavitand receptor based on calix[5]arene stabilized by a cooperative network of hydrogen bonds and having a highly flexible structure. The dynamic features of the host have been studied by 1H NMR spectroscopy, revealing a bowl inversion motion that is slow in the NMR time scale. The cavitand displays enantioselective molecular recognition with a series of chiral quaternary ammonium salts, providing unprecedented stability ratios between the corresponding diasteromeric host-guest complexes. Molecular dynamics simulations corroborate the higher flexibility of the new host and the emergence of superior induced fit behavior with regards to resorcin[4]arene derived self-folding cavitands. | Rubén Álvarez-Yebra; Ricard López-Coll; Pere Galán-Masferrer; Agustí Lledó | Organic Chemistry; Stereochemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6392fd1a0fd992e5773ebdea/original/enantioselective-molecular-recognition-in-a-flexible-self-folding-cavitand.pdf |
6648dd0921291e5d1da49dec | 10.26434/chemrxiv-2024-bqr88 | Assessment of Radioactive Cesium Contamination in Concrete Structures near Fukushima Daiichi Nuclear Power Plant | This study investigates the contamination of concrete by radioactive cesium released by the Tokyo Electric Power Company Fukushima Daiichi Nuclear Power Plant accident using samples from various sites in the town of Okuma, Japan. Concrete contamination was effectively evaluated through surface dose rate measurements using Geiger-Müller tubes with shielding. Corresponding radioactivity concentrations were evaluated using an NaI scintillator in a low background environment. The contamination levels were considerably lower in areas shielded from rain compared with outdoor areas exposed to rain. Contamination within concrete can be primarily attributed to radioactive Cs enrichment in specific concrete aggregates and further influenced by carbonation of the cement paste. In non-carbonated sections, radioactive Cs was concentrated in aggregates near the surface, hindering the penetration of detection into the cement paste. Concrete samples subjected to rain exhibited reduced contamination over time. Thus, rain exposure, aggregate properties, and the degree of carbonation emerged as pivotal in predicting concrete contamination. Therefore, this study yields insights into on-site measurement methods, temporal contamination trends in the environment, and the distribution of contamination within concrete structures. | Kazuo yamada; Hiroyuki Arai; Ippei Maruyama; Kazutoshi Shibuya; Kazuto Endo | Materials Science; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6648dd0921291e5d1da49dec/original/assessment-of-radioactive-cesium-contamination-in-concrete-structures-near-fukushima-daiichi-nuclear-power-plant.pdf |
60c74945bdbb897f52a3912a | 10.26434/chemrxiv.7663112.v2 | Divergent Synthesis of Complex ent-Kauranes, ent-Atisanes and ent-Trachylobanes via a Hybrid Oxidative Approach | Nine complex diterpenes were synthesized using a hybrid oxidative approach that combines chemical and enzymatic C–H oxidation methods. | Xiao Zhang; Emma King-Smith; Liao-Bin Dong; Li-Cheng Yang; Jeffrey D. Rudolf; Ben Shen; Hans Renata | Bioorganic Chemistry; Natural Products; Organic Synthesis and Reactions; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74945bdbb897f52a3912a/original/divergent-synthesis-of-complex-ent-kauranes-ent-atisanes-and-ent-trachylobanes-via-a-hybrid-oxidative-approach.pdf |
62e43a8ccf6612831dbacd55 | 10.26434/chemrxiv-2022-rjc20 | Iminologous Epoxide Ring-Closure | Herein, we apply the principle of iminology to the well-established epoxide ring-closure reaction. The synthesis of tetrasubstituted, nitrile-tethered epoxides can be achieved via activation of iminologous diols followed by fragmentation. Mechanistic study reveals the transformation to be stereoretentive, which is consistent with the concerted nature of the epoxide ring-closure. | Andrei Yudin; Chieh-Hung Tien; Alan Lough | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e43a8ccf6612831dbacd55/original/iminologous-epoxide-ring-closure.pdf |
65e7505a9138d23161b9c22a | 10.26434/chemrxiv-2024-j819s | H and CO Co-induced Adatom Formation on Cu in CO2 Electroreduction Conditions | Dynamic restructuring of Cu electrode has been observed under electrochemical conditions, and it has been hypothesized to underly the unique reactivity of Cu towards CO2 electroreduction. Surface roughening is one of the key surface phenomena to Cu activation, in which the surface forms numerous atomic vacancies and adatoms. However, the atomic structure of such surface motifs, in the presence of relevant adsorbates has remained elusive. Here, we explore the chemical space of Cu surface restructuring under coverage of CO and H in realistic electroreduction conditions, by a combination of grand canonical density functional theory and global optimization techniques, from which we construct a potential-dependent grand canonical ensemble representation of the surface. Significant vertical displacement of surface Cu atoms is observed in the regime of intermediate and mixed CO and H coverage. This regime, while predicted to be thermodynamically inaccessible, is kinetically controlled, presenting a tough challenge for theory. To investigate the kinetic trapping effects, we develop a quasi-kinetic Monte Carlo simulation to track the evolution of the system during a simulated cathodic scan. The simulation reveals the path that the system takes across the coverage space and the metastable structures that the system evolves into along the way. Chemical bonding analysis is performed on the metastable structures with elevated Cu*CO species to understand its formation mechanism. By molecular dynamics simulations and free energy calculations, the surface chemistry of the Cu*CO species is explored, and we identifies potential mechanisms via which the Cu*CO species may diffuse or dimerize. This work provides rich atomistic insights into the surface roughening phenomenon and the structure of the involved species. It also features generalizable methods to explore the chemical space of restructuring surfaces with mixed adsorbates, and its evolution in non-equilibrium. | Zisheng Zhang; Wiston Gee; Philippe Sautet; Anastassia N. Alexandrova | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e7505a9138d23161b9c22a/original/h-and-co-co-induced-adatom-formation-on-cu-in-co2-electroreduction-conditions.pdf |
60c757cdbb8c1ac54e3dc8f2 | 10.26434/chemrxiv.14464710.v1 | Polymer-Stretching-Regulated Microscopic Photoluminescence of Vibration-Induced Emission (VIE) Molecules | Photoluminescence
materials play an inseparable role in the
application of polymer systems. However, intrinsic
polymer systems have rarely been intuitively interpreted based on
photoluminescence regulation. A novel photoluminescence mechanism called
vibration-induced emission (VIE) has recently drawn great attention due to its multicolor fluorescence from a single molecular entity. Based on the unique
fluorescent properties of VIE molecules, we doped
9,14-diphenyl-9,14-dihydrodibenzo[a,c]-phenazine (DPAC) and its derivative
DPAC-CN in two stretchable polymers, <a></a><a>poly(ε-caprolactone)</a> and ethylene
vinyl acetate (EVA) copolymer, to explore the important relationship between luminophores and polymer systems. This
research focused on the multicolor photoluminescence of the obtained blend
films that resulted from stretching exertions and temperature responses.
The successive conformational alterations of VIE molecules endowed
continuous photoluminescent changes. Meanwhile, the multicolor variations also provided
specific visual evidence regarding the amplified tensile stresses and
microstructural changes in the
polymer. This demonstration
will therefore provide advantageous insights into the development of
functional optical materials. | Fan Gu; Yuanhao Li; Tao Jiang; Jianhua Su; Xiang Ma; He Tian | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757cdbb8c1ac54e3dc8f2/original/polymer-stretching-regulated-microscopic-photoluminescence-of-vibration-induced-emission-vie-molecules.pdf |
61ec67a4e4d9b85106f4ccd8 | 10.26434/chemrxiv-2021-gsq6s-v3 | Photoredox α-Arylation of cyclic ketones | The direct α-arylation of unactivated carbonyl compounds using aryl halides represents a powerful method to synthesize criti-cal building blocks for diverse useful compounds. Numerous synthetic methods exist to forge C(sp2)-C(sp3) bonds, albeit metal free direct α-arylation of unactivated cyclic ketones has long been an elusive transformation. Herein, we report a green-light-mediated α-arylation of unactivated ketones from readily available aryl halides via activation of a C(sp2)-X bond (X=I, Br, Cl) and an α-carbonyl C(sp3)-H bond in a single photocatalytic cycle. This approach is characterized by its mild reaction conditions, operational simplicity, and wide functional group tolerance. Importantly, the impressive outcome from multi-gram photocatalytic reaction underpins the strength of this method as a potentially practical and attractive approach for scale-up industrial purposes. The utility and scope of this reaction were further demonstrated by new syntheses of several feedstock chemicals that are commercially expensive but critical for synthesizing numerous pharmaceutical agents. | MdMubarak Hossain; Aslam Shaikh; Jules Moutet; thomas Gianetti | Organic Chemistry; Catalysis; Photochemistry (Org.); Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ec67a4e4d9b85106f4ccd8/original/photoredox-arylation-of-cyclic-ketones.pdf |
6619c28b418a5379b0baaeec | 10.26434/chemrxiv-2024-85kfq | Unnatural Thiamine Radical Enzymes for Photobiocatalytic
Asymmetric Alkylation of Benzaldehydes and a-Ketoacids | Despite substantial progress made toward elucidating the
elegant natural radical enzymology with thiamine pyrophosphate (TPP)-dependent pyruvate:ferredoxin oxidoreductases (PFORs) and pyruvate oxidases (POXs), repurposing naturally occurring two electron TPP-dependent enzymes to catalyze single-electron transformations with significant synthetic value remains a daunting task. Enabled by the synergistic use of visible-light photocatalyst fluorescein and a set of engineered TPP-dependent enzymes derived from benzoylformate decarboxylase (BFD) and benzaldehyde lyase (BAL), we developed an asymmetric photobiocatalytic decarboxylative alkylation of benzaldehydes and a-keto acids to produce highly enantioenriched a-branched ketones. Mechanistically,
this dual catalytic radical alkylation involves single-electron oxidation of the enzyme-bound Breslow intermediate and subsequent interception of the photoredox-generated transient alkyl radical. In conjunction with visible light photoredox catalysis, thiamine radical biocatalysis represents a new platform to discover and optimize new
asymmetric radical transformations which are unknown to biological systems and not amenable to small-molecule catalysis. | Yang Yang; Xin Liu; Sheng Xu; Heyu Chen | Catalysis | CC BY 4.0 | CHEMRXIV | 2024-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6619c28b418a5379b0baaeec/original/unnatural-thiamine-radical-enzymes-for-photobiocatalytic-asymmetric-alkylation-of-benzaldehydes-and-a-ketoacids.pdf |
64e50861dd1a73847f5020a1 | 10.26434/chemrxiv-2023-tkqqk | Pitfalls and considerations in determining the potency and mutant selectivity of covalent epidermal growth factor receptor inhibitors | Pursuing enzyme inhibitors with molecules that form covalent bonds with the desired target is an attractive focus in drug development that is increasing in prevalence. However, challenges arise when carrying out assessments of their time-dependent inhibitory properties as well as making correlations with values reported in the literature. Given the prominent focus on the Epidermal Growth Factor Receptor (EGFR) tyrosine kinase in oncology, and the diverse structures and binding modes of covalent EGFR inhibitors, this perspective seeks to explore various broadly relevant factors that arise in the measurement of kinetic parameters within this class of drugs. A review of several studies indicates that variable literature potency values require investigators to include appropriate reference molecules and consistent substrate conditions for experimental consistency and proper benchmarks. The impact on covalent inhibitor potency with respect to common buffer conditions and compound liquid handling is surveyed highlighting the importance of multiple experimental variables when conducting these assays. Additionally, when assessing the potency for inhibitor selectivity in targeting EGFR mutants over wild-type (WT), it is ideal to consider ratios of true potency due to the variable ATP substrate binding affinities. The overview presented here, although most directly applicable to the tyrosine kinase inhibitor field, serves inhibitor assessments broadly by providing guided insights into conducting biochemical assays for designing and validating next-generation covalent inhibitors. | Kristopher W Hoyt; Daniel A Urul; Blessing C Ogboo; Florian Wittlinger; Stefan A Laufer; Erik M Schaefer; Earl W May; David E Heppner | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e50861dd1a73847f5020a1/original/pitfalls-and-considerations-in-determining-the-potency-and-mutant-selectivity-of-covalent-epidermal-growth-factor-receptor-inhibitors.pdf |
60c750640f50db7096397574 | 10.26434/chemrxiv.13028105.v1 | A Chemically Consistent Graph Architecture for Massive Reaction Networks Applied to Solid-Electrolyte Interphase Formation | Modeling reactivity with chemical reaction networks could yield fundamental mechanistic understanding that would expedite the development of processes and technologies for energy storage, medicine, catalysis, and more. Thus far, reaction networks have been limited in size by chemically inconsistent graph representations of multi-reactant reactions (e.g. A + B reacts to C) that cannot enforce stoichiometric constraints, precluding the use of optimized shortest-path algorithms. Here, we report a chemically consistent graph architecture that overcomes these limitations using a novel multi-reactant representation and iterative cost-solving procedure. Our approach enables the identification of all low-cost pathways to desired products in massive reaction networks containing reactions of any stoichiometry, allowing for the investigation of vastly more complex systems than previously possible. Leveraging our architecture, we construct the first ever electrochemical reaction network from first-principles thermodynamic calculations to describe the formation of the Li-ion solid electrolyte interphase (SEI), which is critical for passivation of the negative electrode. Using this network comprised of nearly 6,000 species and 4.5 million reactions, we interrogate the formation of a key SEI component, lithium ethylene dicarbonate. We automatically identify previously proposed mechanisms as well as multiple novel pathways containing counter-intuitive reactions that have not, to our knowledge, been reported in the literature. We envision that our framework and data-driven methodology will facilitate efforts to engineer the composition-related properties of the SEI - or of any complex chemical process - through selective control of reactivity. | Samuel Blau; Hetal Patel; Evan Spotte-Smith; Xiaowei Xie; Shyam Dwaraknath; Kristin Persson | Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry; Coordination Chemistry (Organomet.); Electrochemistry - Organometallic; Reaction (Organomet.); Theory - Organometallic; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Processes; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750640f50db7096397574/original/a-chemically-consistent-graph-architecture-for-massive-reaction-networks-applied-to-solid-electrolyte-interphase-formation.pdf |
67024b7951558a15ef3e9796 | 10.26434/chemrxiv-2023-1zplz-v2 | Site-specific effects of acetylation within the histone H3 tail on liquid-liquid phase separation with DNA | Post-translational modifications (PTMs) of histone proteins play a pivotal role in the regulation of chromatin condensation, with evidence increasingly pointing to the involvement of liquid–liquid phase separation (LLPS). Here, we report the significant impact of the acetylation site of the N-terminal histone H3 peptide on LLPS with nucleosomal-linker DNA. In our model system, which mimics a part of the structure of chromatin, non-acetylated H3 peptide and DNA undergo LLPS, driven primarily by electrostatic interactions. Acetylation of the H3 peptide significantly inhibits LLPS, with the inhibitory effects varying markedly depending on the acetylation site. Specifically, acetylation near the ends of the 20-residue H3 peptide (i.e., H3K4ac and H3K18ac) results in stronger inhibition of LLPS compared to acetylation near the center (i.e., H3K9ac and H3K14ac). Through experiments (circular dichroism and interaction assays using salts and 1,6-hexanediol) and molecular-dynamics (MD) simulations, it was revealed that differences in the DNA thermal stability, hydrophobic effects, and charge distribution of the H3 peptides/DNA complexes underlie this phenomenon. Our findings provide fundamental insights that link LLPS-mediated chromatin condensation to various biological phenomena depending on the acetylation sites on the histone proteins, thus shedding light on the mechanisms of gene regulation. | Masahiro Mimura; Hiroka Sugai; Tomoshi Kameda; Ryo Kitahara; Soichiro Kitazawa; Yoichi Shinkai; Ryoji Kurita; Shunsuke Tomita | Physical Chemistry; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67024b7951558a15ef3e9796/original/site-specific-effects-of-acetylation-within-the-histone-h3-tail-on-liquid-liquid-phase-separation-with-dna.pdf |
60c7544f567dfe5d21ec604e | 10.26434/chemrxiv.13643570.v1 | PQQ-Aza-Crown Ether Complexes as Biomimetics for Lanthanide and Calcium Dependent Alcohol Dehydrogenases | <div>Understanding the role of metal ions in biology can lead to the development of new catalysts for</div><div>several industrially important transformations. Lanthanides are the most recent group of metal ions</div><div>that have been shown to be important in biology i.e. - in quinone-dependent methanol</div><div>dehydrogenases (MDH). Here we evaluate a pyrroloquinoline quinone and 1-aza-15-crown-5 based</div><div>ligand platform as scaffold for Ca2+ , Ba2+ , La3+ and Lu3+ biomimetics of MDH and we evaluate the</div><div>importance of ligand design, charge, size, counterions and base for the alcohol oxidation reaction</div><div>using NMR spectroscopy. In addition, we report a new straightforward synthetic route (3 steps</div><div>instead of 11 and 33% instead of 0.6% yield) for biomimetic ligands based on PQQ. We show that</div><div>when studying biomimetics for MDH, larger metal ions and those with lower charge in this case</div><div>promote the dehydrogenation reaction more effectively and that this is likely an effect of the ligand</div><div>design which must be considered when studying biomimetics. To gain more information on the</div><div>structures and impact of counterions of the complexes, we performed collision induced dissociation</div><div>(CID) experiments and observe that the nitrates are more tightly bound than the triflates. To resolve</div><div>the structure of the complexes in the gas phase we combined DFT-calculations and ion mobility</div><div>measurements (IMS). Furthermore, we characterized the obtained complexes and reaction mixtures</div><div>using Electron Paramagnetic Resonance (EPR) spectroscopy and show the emergence of a quinone-</div><div>based radical during the reaction with substrate and base.</div> | Violeta A. Vetsova; Katherine R. Fisher; Henning Lumpe; Alexander Schäfer; Erik K. Schneider; Patrick Weis; Lena Daumann | Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7544f567dfe5d21ec604e/original/pqq-aza-crown-ether-complexes-as-biomimetics-for-lanthanide-and-calcium-dependent-alcohol-dehydrogenases.pdf |
67c9c16a6dde43c908c21683 | 10.26434/chemrxiv-2025-n1t1c | Supramolecular complexes of PNIPAAM-co-MA and imogolite to obtain thermo-responsive clay nanotubes | In this study, we investigate the colloidal properties of hybrids formed by imogolite nanotubes (INTs) and poly(N-isopropylacrylamide)-co-methacrylic (PNIPAAM-co-MA), which is a thermo-sensitive copolymer suitable for drug delivery applications. The selective adsorption of anionic PNIPAAM-co-MA onto the positively charged external surface of imogolite is driven by electrostatic attractions as evidenced by both ζ-potential and Dynamic Light Scattering (DLS) experiments. According to polarized optical microscopy (POM) and Small-angle X-ray scattering (SAXS) measurements, the specific interactions with PNIPAAM-co-MA affect the structural organization of imogolite nanotubes destabilizing the nematic phase. On the other hand, the formation of PNIPAAM-co-MA/INTs complex alters the thermo-responsive characteristics of the copolymer due to variations on the thermodynamics of the coil-to-globule transition of PNIPAAM-co-MA. Thermodynamic characterizations (Differential Scanning Calorimetry, Density and Speed of sound experiments) reveal that the lower crystalline solution temperature (LCST) of PNIPAAM-co-MA is reduced in the presence of imogolite nanotubes.
The attained knowledge represents a starting point to develop thermo-responsive clay nanotubes useful for biomedical purposes by exploiting the selective coating of imogolite with PNIPAAM-co-MA.
| Claire Hotton; Lorenzo Lisuzzo; Giuseppe Cavallaro; Erwan Paineau; Thomas Bizien; Giuseppe Lazzara | Physical Chemistry; Polymer Science; Nanoscience; Self-Assembly; Structure; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c9c16a6dde43c908c21683/original/supramolecular-complexes-of-pnipaam-co-ma-and-imogolite-to-obtain-thermo-responsive-clay-nanotubes.pdf |
60c74885bdbb89ce81a38fcd | 10.26434/chemrxiv.11911209.v1 | Ceramic Ultrafiltration and Nanofiltration Membrane for Removal of Black Carbon Ink, Blue Dye Ink, Fe3+ and Cu2+ Ions from Water | This paper reports on performance of ceramic ultrafiltration and nanofiltration membrane to remove carbon ink particles, blue ink dye, Fe3+ and Cu2+ ions from water. The ceramic filters have α-Al2O3 flat-sheet supporter, with TiO2 nanoparticles sintered membrane on the surface of supporter. Carbon ink particles, blue ink dye, FeCl3 and CuSO4 water solution were used to test their filtration performance. The results show that the ceramic ultrafilter can 100% decolored the black carbon solution. The nanomembrane can 100% decolored blue ink dye, FeCl3 and CuSO4 solution. Electrical conductivity rate of ironflocculated dye waste water from a textile company can be reduced by the nanomembrane from 4000 μs/cm to 1000 μs/cm. It assumed that the ultramembrane pore size is about 10 nm, and the nanomembrane pore size might be 1 nm. The performance can fulfill the requirements for removal of heavy metal ions, materials with molecule bigger than 250 Dalton and salts retention from water, air filtration of novel corona virus defending mask and negative pressure patient room. | Zhiqiang Wang; Tian Cheng Wang | Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74885bdbb89ce81a38fcd/original/ceramic-ultrafiltration-and-nanofiltration-membrane-for-removal-of-black-carbon-ink-blue-dye-ink-fe3-and-cu2-ions-from-water.pdf |
60c74b20469df4a6f2f43e78 | 10.26434/chemrxiv.12287504.v1 | Electrofuels from Excess Renewable Electricity at High Variable Renewable Shares: Cost, Greenhouse Gas Abatement, Carbon Use and Competition | Increasing shares of variable renewable electricity (VRE) generation are necessary for achieving high renewable shares in all energy sectors. This results in increased excess renewable electricity (ERE) at times when supply exceeds demand. ERE can be utilized as a low-emission energy source for sectorcouplingthroughhydrogenproductionviaelectrolysis, whichcanbeuseddirectlyorcombined with a carbon source to produce electrofuels. Such fuels are crucial for the transport sector, where renewable alternatives are scarce. However, while ERE increases with raising VRE shares, carbon emissions decrease and may become a limited resource with several usage options, including carbon storage (CCS). These counteracting effects for the electrofuel production have not been analysed before. Here we perform a model based analysis for the German case until 2050, with a general analysis for regions with a high VRE reliance. Results indicate that ERE-based electrofuels can achieveagreenhousegas(GHG)abatementof74MtCO2eqyearly(46%ofcurrentGermantransport emissions) by displacing fossil fuels, at high fuel-cell electric vehicle (FCEV) shares, at a cost of 250320 € t CO2eq−1. The capital expenditure of electrolysers was found not to be crucial for the cost, despitelowcapacityfactorsduetovariableEREpatterns. Carbonwilllikelybecomealimitingfactor when aiming for stringent climate targets and renewable electricity-based hydrocarbon electrofuels replacing fossil fuels achieve up to 70% more GHG abatement than CCS. Given (1) an unsaturated demandforrenewablehydrocarbonfuels,(2)asaturatedrenewablehydrogendemandand(3)unused ERE capacities which would otherwise be curtailed, we find that carbon is better used for renewable fuel production than being stored.<br /> | Markus Millinger; Philip Tafarte; Matthias Jordan; Alena Hahn; Kathleen Meisel; Daniela Thrän | Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b20469df4a6f2f43e78/original/electrofuels-from-excess-renewable-electricity-at-high-variable-renewable-shares-cost-greenhouse-gas-abatement-carbon-use-and-competition.pdf |
646687befb40f6b3eecc72e1 | 10.26434/chemrxiv-2023-12gkw | Suppressing Co-ion Generation via Cationic Proton Donors to Amplify Driving Forces for Electrochemical CO2 Reduction | Interfacial microenvironments critically define reaction pathways for electrocatalytic processes through a combination of electric field gradients and proton activity. Non-aqueous ionic liquid electrolytes have been shown to sustain enhanced interfacial electric field gradients at intermediate ion concentration regimes of around 1 M, creating local environments that promote CO2 electroreduction. Notably, water at low concentrations absorbed by non-aqueous electrolytes is usually assumed to be the proton donor for CO2 reduction. Consumption of protons causes proton donors to become more negative by one unit charge, which significantly modifies the local concentration of charged species and hence should strongly impact local electric fields. Yet, how the coupling between proton donation and changing interfacial electric fields influences electrocatalytic processes in non-aqueous electrolytes remains largely unexplored. In this work, we show that the high activity of 1,3-dialkylimidazolium ionic liquids for CO2 reduction in acetonitrile-based electrolytes stems from the ability to act as cationic proton donors that release neutral conjugate bases. Using in situ electrochemical surface-enhanced Raman spectroscopy, we find that the formation of neutral conjugate bases from imidazolium cations preserves local electric field strengths at electrode-electrolyte interfaces, providing a powerful strategy to maintain an active local microenvironment for CO2 reduction. In contrast, conditions where water behaves as the primary proton donor generates [OH]- anions as negative “co-ions” in the electric double layer, which weakens the interfacial electric field and significantly compromises the steady-state CO2 reduction activity. Our study highlights that electrochemical driving forces are highly sensitive to the charge state of both reactant and product species and highlights the fact that the generation of interfacial co-ions plays a key role in determining electrochemical driving forces. | Wenxiao Guo; Beichen Liu; Matthew Gebbie | Catalysis; Chemical Engineering and Industrial Chemistry; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646687befb40f6b3eecc72e1/original/suppressing-co-ion-generation-via-cationic-proton-donors-to-amplify-driving-forces-for-electrochemical-co2-reduction.pdf |
60c756b4f96a0048b9288b54 | 10.26434/chemrxiv.14308421.v1 | A Platform for Alkene Carbofunctionalization with Diverse Nucleophiles | A general system achieving three-component intermolecular carbofunctionalization of alkenes is presented. A range of substituted alkenes are functionalized with α-bromo carbonyl electrophiles and nitrogen, oxygen, and carbon nucleophiles. Mechanistic findings support the intermediacy of a cyclic oxocarbenium ion. | Travis Buchanan; Samuel Gockel; Alexander Veatch; Ya-Nong Wang; Kami Hull | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756b4f96a0048b9288b54/original/a-platform-for-alkene-carbofunctionalization-with-diverse-nucleophiles.pdf |
663cd3eb21291e5d1dd9e450 | 10.26434/chemrxiv-2024-kh4qm | Surface-Enhanced Infrared Spectroscopy by Resonant Vibrational Coupling with Plasmonic Metal Oxide Nanocrystals | Coupling between plasmonic resonances and molecular vibrations in nanocrystals (NCs) offers a promising approach for detecting molecules at low concentrations and discerning their chemical identities. Metallic NC superlattices can enhance vibrational signals under far-field detection by generating a myriad of intensified electric field hot spots between the NCs. Yet, their effectiveness is limited by the fixed electron concentration dictated by the metal composition and inefficient hot spot creation due to the large mode volume. Doped metal oxide NCs, such as tin-doped indium oxide (ITO), could overcome these limitations by enabling broad tunability of resonance frequencies in the mid-infrared range through independent variation of size and doping concentration. This study investigates the potential of close-packed ITO NC monolayers for surface enhanced infrared absorption by quantifying trends in the coupling between their plasmon modes and various molecular vibrations. We show that maximum vibrational
signal intensity occurs in monolayers composed of larger, more highly doped NCs, where the plasmon resonance peak lies at higher frequency than the molecular vibration. Using finite element and mutual polarization methods, we establish that near-field enhancement is stronger on the low-frequency side of the plasmon resonance and for more strongly coupled plasmonic NCs, thus rationalizing the design rules we experimentally uncovered. Our results can guide the development of optimal metal oxide NC-based superstructures for sensing target molecules or modifying their chemical properties through vibrational coupling. | Woo Je Chang; Benjamin Roman; Allison Green; Thomas Truskett; Delia Milliron | Physical Chemistry; Nanoscience; Plasmonic and Photonic Structures and Devices; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663cd3eb21291e5d1dd9e450/original/surface-enhanced-infrared-spectroscopy-by-resonant-vibrational-coupling-with-plasmonic-metal-oxide-nanocrystals.pdf |
61a7ac1a7ce056304e8512f0 | 10.26434/chemrxiv-2021-sr171 | Computation-informed optimization of Ni(PyC)₂ functionalization for noble gas separations | Metal-organic frameworks (MOFs) are promising nanoporous materials for the adsorptive capture and separation of noble gases at room temperature. Among the numerous MOFs synthesized and tested for noble gas separations, Ni(PyC)₂ (PyC = pyridine-4-carboxylate) exhibits one of the highest xenon/krypton selectivities at room temperature. Like lead-optimization in drug discovery, here we aim to tune the chemistry of Ni(PyC)₂, by appending a functional group to its PyC ligands, to maximize its Xe/Kr selectivity. To guide experiments in the laboratory, we virtually screen Ni(PyC-X)₂ (X=functional group) structures for noble gas separations by (i) constructing a library of Ni(PyC-X)₂ crystal structure models then (ii) using molecular simulations to predict noble gas (Xe, Kr, Ar) adsorption and selectivity at room temperature in each structure. The virtual screening predicts several Ni(PyC-X)₂ structures to exhibit a higher Xe/Kr, Xe/Ar, and Kr/Ar selectivity than the parent Ni(PyC)₂ MOF, with Ni(PyC-m-NH₂)₂ among them. In the laboratory, we synthesize Ni(PyC-m-NH₂)₂, determine its crystal structure by X-ray powder diffraction, and measure its Xe, Kr, and Ar adsorption isotherms (298 K). In agreement with our molecular simulations, the Xe/Kr, Xe/Ar, and Kr/Ar selectivities of Ni(PyC-m-NH₂)₂ exceed those of the parent Ni(PyC)₂. Particularly, Ni(PyC-m-NH₂)₂ exhibits a [derived from experimental, equilibrium adsorption isotherms] Xe/Kr selectivity of 20 at dilute conditions and 298 K, compared to 17 for Ni(PyC)₂. According to in situ X-ray diffraction, corroborated by molecular models, Ni(PyC-m-NH₂)₂ presents well-defined binding pockets tailored for Xe and organized along its one-dimensional channels. In addition to discovering the new, performant Ni(PyC-m-NH₂)₂ MOF for noble gas separations, our study illustrates the computation-informed optimization of the chemistry of a "lead" MOF to target adsorption of a specific gas. | Nickolas Gantzler; Min-Bum Kim; Alexander Robinson; Maxwell W. Terban; Sanjit Ghose; Robert E. Dinnebier; Arthur Henry York; Davide Tiana; Cory M. Simon; Praveen K. Thallapally | Theoretical and Computational Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a7ac1a7ce056304e8512f0/original/computation-informed-optimization-of-ni-py-c-2-functionalization-for-noble-gas-separations.pdf |
619b1d882bf8a99723e78350 | 10.26434/chemrxiv-2021-3l4zh | Evaluating quantum alchemy of atoms with thermodynamic cycles: Beyond ground electronic states | Due to the sheer size of chemical and materials space, high throughput computational screening thereof will require the development of new computational methods that are accurate, efficient, and transferable. These methods need to be applicable to electron configurations beyond ground states. To this end, we have systematically studied the applicability of quantum alchemy predictions using a Taylor series expansion on quantum mechanics (QM) calculations for single atoms with different electronic structures arising from different net charges and electron spin multiplicities. We first compare QM method accuracy to experimental quantities including first and second ionization energies, electron affinities, and multiplet spin energy gaps for a baseline understanding of QM reference data. We then investigate the intrinsic accuracy of an approach we call "manual" quantum alchemy schemes compared to the same QM reference data, which employ QM calculations where the basis set of a different element is used for an atom as the limit case of quantum alchemy. We then discuss the reliability of quantum alchemy based on Taylor series approximations at different orders of truncation. Overall, we find that the errors from finite basis set treatments in quantum alchemy are significantly reduced when thermodynamic cycles are employed, which points out a route to improve quantum alchemy in explorations of chemical space. This work establishes important technical aspects that impact the accuracy of quantum alchemy predictions using a Taylor series and provides a foundation for further quantum alchemy studies. | Emily Eikey; Alex Maldonado; Charles Griego; Guido Falk von Rudorff; John Keith | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY NC 4.0 | CHEMRXIV | 2021-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619b1d882bf8a99723e78350/original/evaluating-quantum-alchemy-of-atoms-with-thermodynamic-cycles-beyond-ground-electronic-states.pdf |
60c74788bb8c1a3c3f3daac2 | 10.26434/chemrxiv.11708844.v1 | Cooperative and Synchronized Rotation in Motorized Porous Frameworks: Impact on Local and Global Transport Properties of Confined Fluids | <div>Molecules in gas and liquid states, as well as in solution, exhibit significant and random Brownian motion. Molecules in the solid-state, although strongly immobilized, can still exhibit significant intramolecular dynamics. However, in most framework materials, these intramolecular dynamics are driven by temperature, and therefore are neither controlled nor spatially or temporarily aligned. In recent years, several examples of molecular machines that allow for a stimuli-responsive control of dynamical motion, such as rotation, have been reported.</div><div><br /></div><div>In this contribution, we investigate the local and global properties of a Lennard-Jones (LJ) fluid surrounding a molecular motor and consider the influence of cooperative and non-directional rotation for a molecular motor-containing pore system. This study uses classical molecular dynamics simulations to describe a minimal model, which was developed to resemble known molecular motors. The properties of an LJ liquid surrounding an isolated molecular mo-tor remain mostly unaffected by the introduced rotation. We then considered an arrangement of motors within a one-dimensional pore. Changes in diffusivity for pore sizes approaching the length of the rotor were observed, resulting from rotation of the motors. We also considered the influence of cooperative motor directionality on the directional transport properties of this con-fined fluid. Importantly, we discovered that specific unidirectional rotation of altitudinal motors can produce directed diffusion.</div><div><br /></div><div>This study provides an essential insight into molecular machine-containing frameworks, highlighting the specific structural arrangements that can produce directional mass transport.</div> | Jack D. Evans; Simon Krause; Ben L. Feringa | Computational Chemistry and Modeling; Physical and Chemical Properties; Transport phenomena (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2020-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74788bb8c1a3c3f3daac2/original/cooperative-and-synchronized-rotation-in-motorized-porous-frameworks-impact-on-local-and-global-transport-properties-of-confined-fluids.pdf |
60f8e1630b093ee195e2bca0 | 10.26434/chemrxiv-2021-zk477 | Artificial Intelligence-Enhanced Quantum Chemical Method with Broad Applicability | High-level quantum mechanical (QM) calculations are indispensable for accurate explanation of natural phenomena on the atomistic level. Their staggering computational cost, however, poses great limitations, which luckily can be lifted to a great extent by exploiting advances in artificial intelligence (AI). Here we introduce the general-purpose, highly transferable artificial intelligence–quantum mechanical method 1 (AIQM1). It approaches the accuracy of the ‘gold-standard’ coupled cluster QM method with low computational speed of the approximate low-level semiempirical QM methods. AIQM1 can provide accurate ground-state energies for diverse organic compounds as well as geometries for even challenging systems such as large conjugated compounds (fullerene C60) close to experiment. Noteworthy, our method’s accuracy is also good for ions and excited-state properties, although the neural network part of AIQM1 was never fitted to these properties. | Peikun Zheng; Roman Zubatyuk; Wei Wu; Olexandr Isayev; Pavlo O. Dral | Theoretical and Computational Chemistry; Theory - Computational; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f8e1630b093ee195e2bca0/original/artificial-intelligence-enhanced-quantum-chemical-method-with-broad-applicability.pdf |
6605388ae9ebbb4db9c1cd3f | 10.26434/chemrxiv-2024-bgpkn-v2 | Fungal peptidomelanin: a novel biopolymer for the amelioration of soil heavy metal toxicity | Heavy metal contamination of agricultural soils reduces crop yields, contaminates groundwater and disrupts local ecosystems. Here, we describe a novel, water-soluble form of melanin (peptidomelanin) capable of chelating heavy metals in large quantities. Peptidomelanin is composed of an L-DOPA core polymer that is solubilized via short, heterogeneous peptide chains with a mean amino acid length of ∼2.6. It is secreted by the spores of Aspergillus niger melanoliber during germination. It was found to chelate large quantities of lead, mercury, and uranyl. It increased the germination rate, seed mass, and shoot length of wheat planted in substrate contaminated with 100 ppm mercury. Therefore, peptidomelanin may increase crop yields in contaminated agricultural soils treated in situ with the substance. | Rakshita Sukruth Kolipakala; Suranjana Basu; Senjuti Sarkar; Beneta Merin Biju; Daniela Salazar; Likhit Reddy; Harshitha Balaji; Shrijita Nath; Anish Hemanth Samprathi; Aparna Shetye; Deepesh Nagarajan | Polymer Science; Agriculture and Food Chemistry; Biopolymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6605388ae9ebbb4db9c1cd3f/original/fungal-peptidomelanin-a-novel-biopolymer-for-the-amelioration-of-soil-heavy-metal-toxicity.pdf |
66e0b2f112ff75c3a1f8e242 | 10.26434/chemrxiv-2024-rqzh9 | Naphtho[2,3-a]pyrene Thin Films – H,I, or J? Aggregate Alphabet Soup | Photon upconversion within the solid state has the potential to improve existing solar and imaging technologies due to its achievable efficiency at low power thresholds. However, despite considerable advancements in solution-phase upconversion, expanding the library of potential solid-state annihilators and developing a fundamental understanding of their solid-state behaviors remains challenging due to intermolecular couplings affecting the energy landscape. Naphtho[2,3-a]pyrene has shown promise as a suitable solid-state annihilator; however, the origin of the underlying emissive features remains unknown. To this point, here, we investigate NaPy/polymethylmethacrylate thin films at varying concentrations to tune the intermolecular coupling strength to determine its photophysical properties. The results suggest that the multiple emissive features present at room temperature arise from an I-aggregate (520 nm), an excimer (550 nm), and a strongly coupled J-dimer (620 nm). | Colette Sullivan; Adrienn Szucs; Theo Siegrist; Lea Nienhaus | Physical Chemistry; Photochemistry (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e0b2f112ff75c3a1f8e242/original/naphtho-2-3-a-pyrene-thin-films-h-i-or-j-aggregate-alphabet-soup.pdf |
6584fe019138d231613a8a68 | 10.26434/chemrxiv-2023-hfcm5-v2 | Transfer Learning Graph Representations of Molecules for pKa, 13C-NMR, and Solubility | We explore transfer learning models from a pre-trained graph convoluntional neural network representation of molecules, obtained from SchNet, 1 to predict 13 C-NMR, pKa, and logS sol- ubility. SchNet learns a graph representation of a molecule by associating each atom with an “embedding vector” and interacts the atom-embeddings with each other by leveraging graph- convolutional filters on their interatomic distances. We pre-trained SchNet on molecular energy and demonstrate that the pre-trained atomistic embeddings can then be used as a transferable representation for a wide array of properties. On the one hand, for atomic properties such as micro-pK1 and 13 C-NMR, we investigate two models, one linear and one neural net, that inputs pre-trained atom-embeddings of a particular atom (e.g. carbon) and predicts a local property (e.g. 13 C-NMR). On the other hand, for molecular properties such as solubility, a size-extensive graph model is built using the embeddings of all atoms in the molecule as input. For all cases, qualitatively correct predictions are made with relatively little training data (< 1000 training points), showcasing the ease with which pre-trained embeddings pick up on important chemical patterns. The proposed models successfully capture well-understood trends of pK1 and solu- bility. This study advances our understanding of current neural net graph representations and their capacity for transfer learning applications in chemistry. | Amer Marwan El Samman; Stefano De Castro; Brooke Morton; Stijn De Baerdemacker | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6584fe019138d231613a8a68/original/transfer-learning-graph-representations-of-molecules-for-p-ka-13c-nmr-and-solubility.pdf |
60c742abee301c7fe5c78ea4 | 10.26434/chemrxiv.8281469.v2 | Reversible Spatiotemporal Control of Induced Protein Degradation by Bistable photoPROTACs | Off-target effects
are persistent issues of modern inhibition-based therapies. By merging the
strategies of photopharmacology and small molecule degraders, we introduce a
novel concept for persistent spatiotemporal control of induced protein
degradation that potentially prevents off-target toxicity. Building on the
successful principle of bifunctional all-small molecule Proteolysis Targeting
Chimeras (PROTACs), we designed photoswitchable PROTACs (<b>photoPROTACs</b>) by
including <i>ortho-</i>F<sub>4</sub>-azobenzene
linkers between both warhead ligands. This highly bistable yet photoswitchable structural
component leads to reversible control over the topological distance between
both ligands. The <i>azo</i>-<i>cis</i>-isomer is observed to be inactive because
the distance defined by the linker is prohibitively short to permit complex
formation between the protein binding partners. By contrast, the <i>azo</i>-<i>trans</i>-isomer
is active because it can engage both protein partners to form the necessary and
productive ternary complex. Importantly, due to the bistable nature of the <i>ortho</i>-F<sub>4</sub>-azobenzene
moiety employed, the photostationary state of the <b>photoPROTAC</b> is
persistent, with no need for continuous irradiation. This technique offers
reversible on/off switching of protein degradation that is compatible with an
intracellular environment and, therefore, could be vastly useful in experimental
probing of biological signaling pathways – especially those crucial for oncogenic signal transduction.
Additionally, this strategy may be suitable for therapeutic implementation in a
wide variety of disease phenotypes. By enabling reversible activation and
deactivation of protein degradation, <b>photoPROTACs</b>
offer advantages over conventional photocaging strategies that irreversibly release
active agents. | Patrick Pfaff; Kusal
T. G. Samarasinghe; Craig M. Crews; Erick Carreira | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.); Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742abee301c7fe5c78ea4/original/reversible-spatiotemporal-control-of-induced-protein-degradation-by-bistable-photo-prota-cs.pdf |
60c73fdf702a9b6fb5189fbc | 10.26434/chemrxiv.6448253.v4 | Lanthanoid Complexes Supported by Retro-Claisen Condensation Products of β-Triketonates | <i>β</i>-Triketonates have been recently used as chelating ligands for lanthanoid ions, presenting unique structures varying from polynuclear assemblies to polymers. In an effort to overcome low solubility of the complexes of tribenzoylmethane, four <i>β</i>-triketones with higher lipophilicity were synthesised. Complexation reactions were performed for each of these molecules using different alkaline bases in alcoholic media. X-ray diffraction studies suggested that the ligands were undergoing decomposition under the reaction conditions. This is proposed to be caused by <i>in situ</i>retro-Claisen condensation reactions, consistent with two examples that have been reported previously. The lability of the lanthanoid cations in the presence of a varying set of potential ligands gave rise to structures where one, two, or three of the molecules involved in the retro-Claisen condensationreaction were linked to the lanthanoid centres. These results, along with measurements of ligand decomposition in the presence of base alone, suggest that using solvents of lower polarity will mimimise the impact of the retro-Claisen condensation in these complexes. <br /> | Laura Abad Galán; Alexandre N. Sobolev; Eli Zysman-Colman; Mark Ogden; Massimiliano Massi | Coordination Chemistry (Inorg.); Lanthanides and Actinides; Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fdf702a9b6fb5189fbc/original/lanthanoid-complexes-supported-by-retro-claisen-condensation-products-of-triketonates.pdf |
60c74ca3ee301c13bcc7a12d | 10.26434/chemrxiv.12478469.v1 | Regio- and Stereo-Specific Chemical Depolymerization of High Molecular Weight Polybutadiene and Polyisoprene for Their Analysis by High Resolution FTICR Mass Spectrometry. Comparison with Py-GCxGC-MS, ASAP&DIP-APCI MS and IMS-MS | Polybutadiene (PB) and Polyisoprene (PI) the two
most common polydienes (PD), are
involved in a large number of materials and used in a wide variety of
applications. The characterization of these polymers by mass spectrometry (MS)
continues to be very challenging due to their high insolubility and the
difficulty to ionize them. In this work, cross-metathesis reaction was used to generate
end-functionalized acetoxy ionizable oligomers for the structural deciphering
of different commercial PB and PI samples. A cross-metathesis reaction was
carried out between polymers and the <i>Z</i>-1,4-diacetoxy-2-butene
as chain transfer agent in dichloromethane using Hoveyda-Grubbs
second-generation catalyst. Well-defined acetoxy telechelic structures were
obtained and analysed by Fourier-Transform ion cyclotron resonance (FTICR) high
resolution MS. However, after depolymerization, low molar mass polyolefins
contained some units with different configurations, suggesting an olefin
isomerization reaction due to the decomposition of the catalyst. The addition
of an electron-deficient reagent such as 2,6-dichloro-1,4-benzoquinone
suppressed this isomerization in the case of both <i>Z</i>- and <i>E-</i> PB and PI.
Ion-mobility spectrometry-mass spectrometry (IMS-MS) and energy resolved tandem
mass spectrometry (ERMS) analyses confirmed a successful isomerization
suppression. For comparing the results obtained by depolymerisation with
classical methods for polymer analysis, pyrolysis-comprehensive two-dimensional
gas chromatography/mass spectrometry (Py-GC×GC-MS), atmospheric solid analysis
probe (ASAP) and DIP-APCI analyses were performed on the same polymers. This
strategy can be applied on a variety of synthetic and natural not yet
characterized polymers. | Christian ROLANDO; Carlos Afonso; Marie Hubert-Roux; ziad mahmoud; michel SABLIER; Fabrice BRAY | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ca3ee301c13bcc7a12d/original/regio-and-stereo-specific-chemical-depolymerization-of-high-molecular-weight-polybutadiene-and-polyisoprene-for-their-analysis-by-high-resolution-fticr-mass-spectrometry-comparison-with-py-g-cx-gc-ms-asap-dip-apci-ms-and-ims-ms.pdf |
60c74ca20f50db6dad396eca | 10.26434/chemrxiv.12501842.v1 | Crystallographic Characterization of the Metal–Organic Framework Fe2(bdp)3 upon Reductive Cation Insertion* | <div><p>Precisely locating extra-framework cations in anionic metal–organic framework compounds remains a long-standing, yet crucial, challenge for elucidating structure-performance relationships in functional materials. Single-crystal X-ray diffraction is one of the most powerful approaches for this task, but single crystals of frameworks often degrade when subjected to post-synthetic metalation or reduction. Here, we demonstrate the growth of sizable single crystals of the robust metal–organic framework Fe<sub>2</sub>(bdp)<sub>3</sub> (bdp<sup>2−</sup> = benzene-1,4-dipyrazolate) and employ single-crystal-to-single-crystal chemical reductions to access the solvated framework materials A<sub>2</sub>Fe<sub>2</sub>(bdp)<sub>3</sub>∙<i>y</i>THF<sub> </sub>(A = Li<sup>+</sup>, Na<sup>+</sup>, K<sup>+</sup>). X-ray diffraction analysis of the sodium and potassium congeners reveals that the cations are located near the center of the triangular framework channels and are stabilized by weak cation–π interactions with the framework ligands. Freeze-drying with benzene enables isolation of activated single crystals of Na<sub>0.5</sub>Fe<sub>2</sub>(bdp)<sub>3 </sub>and Li<sub>2</sub>Fe<sub>2</sub>(bdp)<sub>3</sub> and the first structural characterization of activated metal–organic frameworks wherein extra-framework alkali metal cations are also structurally located. Comparison of the solvated and activated sodium-containing structures reveals that the cation positions differ in the two materials, likely due to cation migration that occurs upon solvent removal to maximize stabilizing cation–π interactions. Hydrogen adsorption data indicate that these cation-framework interactions are sufficient to diminish the effective cationic charge, leading to little or no enhancement in gas uptake relative to Fe<sub>2</sub>(bdp)<sub>3</sub>. In contrast, Mg<sub>0.85</sub>Fe<sub>2</sub>(bdp)<sub>3</sub> exhibits enhanced H<sub>2</sub> affinity and capacity over the non-reduced parent material. This observation shows that increasing the charge density of the pore-residing cation serves to compensate for charge dampening effects resulting from cation–framework interactions and thereby promotes stronger cation–H<sub>2</sub> interactions.</p></div> | Naomi Biggins; Michael Ziebel; Miguel Gonzalez; Jeffrey R. Long | Hybrid Organic-Inorganic Materials; Hydrogen Storage Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ca20f50db6dad396eca/original/crystallographic-characterization-of-the-metal-organic-framework-fe2-bdp-3-upon-reductive-cation-insertion.pdf |
6419ddf42bfb3dc25122fe23 | 10.26434/chemrxiv-2022-xhmzj-v2 | Catalysis at the Origin of Life | The construction of hypothetical environments to produce organic molecules such as metabolic intermediates or amino acids is the subject of ongoing research into the emergence of life. Experiments specifically focused on an anabolic approach typically rely on a mineral catalyst to facilitate the supply of organics that may have produced prebiotic building blocks for life. Alternatively to a true catalytic system, a mineral could be sacrificially oxidized in the production of organics, necessitating the emergent ‘life’ to turn to virgin materials for each iteration of metabolic processes. The aim of this perspective is to view the current ‘metabolism-first’ literature through the lens of materials chemistry to evaluate the need for higher catalytic activity and materials analyses. While many elegant studies have detailed the production of chemical building blocks under geologically plausible and biologically relevant conditions, none appear to do so with sub-stoichiometric amounts of metals or minerals. Moving toward sub-stoichiometric metals with rigorous materials analyses could finally demonstrate the viability of an elusive cornerstone of the ‘metabolism-first’ hypotheses: catalysis. We emphasize that future work should aim to demonstrate decreased catalyst loading, increased productivity, and/or rigorous materials analyses for evidence of true catalysis. | Ruvan de Graaf; Yannick De Decker; Victor Sojo; Reuben Hudson | Catalysis; Earth, Space, and Environmental Chemistry; Geochemistry; Space Chemistry; Electrocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6419ddf42bfb3dc25122fe23/original/catalysis-at-the-origin-of-life.pdf |
633c24ae114b7e034f27fd4d | 10.26434/chemrxiv-2022-2zx46 | Optical Chemical Sensors for Soil Analysis: Possibilities and
Challenges of Visualizing NH3 Concentrations as well as pH and O2 Microscale Heterogeneity | Agricultural nitrogen (N) application to soils is the main source of atmospheric ammonia (NH3) emissions. Ammonia negatively impacts the environment on a large scale. These emissions are affected by spatiotemporal heterogeneities of parameters within the soil on a microscale. Some key parameters controlling processes of the N cycle are soil oxygen (O2) and pH. To better understand biogeochemical soil processes and NH3 emissions we propose the application of optical chemical sensors (optodes) in soils. The use of optodes in soil science is in its infancy. In this study, we investigated the possibilities and challenges of using optodes in non-waterlogged soils with the extended application of a recently developed NH3 optode in combination with pH and O2 optodes in two different soils and with different fertilizers. Our results demonstrated the possibility to visualize reductions of NH3 concentrations by 76 % and 87 % from the incorporation of sludge compared to the surface application of sludge. We showed in 2D how soil pH and fertilizer composition correlate with NH3 volatilization. Our measurements revealed that pH optodes show certain advantages over conventional methods when measuring pH in soils in-situ. Lastly, we investigated spatiotemporal dynamics of O2 at different soil water contents and discussed potential challenges, which can lead to measuring artifacts. | Theresa Merl; Yihuai Hu; Johanna Pedersen; Silvia E. Zieger; Marie Louise Bornø; Azeem Tariq; Sven Gjedde Sommer; Klaus Koren | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Agriculture and Food Chemistry; Environmental Science; Soil Science; Imaging | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633c24ae114b7e034f27fd4d/original/optical-chemical-sensors-for-soil-analysis-possibilities-and-challenges-of-visualizing-nh3-concentrations-as-well-as-p-h-and-o2-microscale-heterogeneity.pdf |
66a8959601103d79c5343eec | 10.26434/chemrxiv-2024-kglxm-v2 | Photo-induced Energy Transfer Polymerization | In conventional photo-induced polymerization strategies, the active species that initiate the reaction tend to be exogenous radical species. Inspired by photo-induced cycloaddition reactions, in this study we investigated photo-induced polymerization from the perspective of energy transfer processes. Utilizing low-energy, highly reactive triplet species of olefin molecules as energy acceptors, a polymerization strategy without the need for exogenous active components was developed. Triplet species from various sources were able to induce polymerization, demonstrating the excellent versatility of this strategy. The reaction mechanism was thoroughly investigated with controlled experiments and spectroscopic methods using thiochromanone as a template. It was clearly established that the key to polymerization is an active triplet species rather than a conventional radical species. As a result, the findings of this study stimulate further discussion on the role of monomers in photo-induced polymerization. | Jian Liu; Yaxiong Wei; Liangwei Ma; Xin Jin; Siyu Sun; Meng Liu; Jun Du; Xinsheng Xu; He Tian; Xiang Ma | Physical Chemistry; Photochemistry (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a8959601103d79c5343eec/original/photo-induced-energy-transfer-polymerization.pdf |
6298ad3482f9564a19cda3c5 | 10.26434/chemrxiv-2022-p1vj9 | A little about Pyrazolo[3,4-d][1,2]diazepine: simple sustainable synthesis, NMR identification and prototropic equilibrium | A simple and sustainable method for the synthesis of pyrazolo [3,4-d] [1,2] diazepin-8-one, the heterocyclic isoster of 2,3-benzodiazepine, has been developed. It was found that the use of acids to cyclization of the pyrazolopyrone hydrazinolysis product leads to the formation of a condensed pyridine ring instead of 1,2-diazepine. Pyrazolodiazepinone in acidic medium also dramatically contracts the seven-membered cycle. The structure of this compound is proved by the hmbc and hsqc 2D NMR heteronuclear correlation in deuterated dimethyl sulfoxide solution in dynamic. Was studied the transformation of its tautomers. It was found that the problem for the pyrazolo [3,4-d] [1,2] diazepin-8-one molecule identification is caused by prototropic isomerization of the pyrazole ring. | Serhii Bohza; Natalia Bohdan; Diana Stepanova; Alexei Nikolaev; Serhii Suikov | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6298ad3482f9564a19cda3c5/original/a-little-about-pyrazolo-3-4-d-1-2-diazepine-simple-sustainable-synthesis-nmr-identification-and-prototropic-equilibrium.pdf |
60dde02ae7f2bffc28808c22 | 10.26434/chemrxiv-2021-zvwhh-v2 | Low Electronic Conductivity of Li7La3Zr2O12 (LLZO) Solid Electrolytes from First Principles | Lithium-rich garnets such as Li7La3Zr2O12(LLZO) are promising solid electrolytes with potential application in all-solid-state batteries that use lithium-metal anodes. The practical use of garnet electrolytes, however, is limited by pervasive lithium-dendrite growth, which leads to short-circuiting and cell failure. One possible mechanism for this lithium-dendrite growth is the direct reduction of lithium ions to lithium metal within the electrolyte, and lithium garnets have suggested to be particularly susceptible to this dendrite-growth mechanism due to high electronic conductivities relative to other solid electrolytes [Hanet al. Nature Ener.4187, 2019]. The electronic conductivities of LLZO and other lithium-garnet solid electrolytes, however, are not yet well characterised. Here, we present a general scheme for calculating the intrinsic electronic conductivity of nominally insulating material under variable synthesis conditions from first principles and apply this to the prototypical lithium-garnet LLZO. Our model predicts that under typical battery operating conditions, electron and hole mobilities are low (<1 cm2V−1s−1), and bulk electron and hole carrier concentrations are negligible, irrespective of initial synthesis conditions or dopant levels. These results suggest that the bulk electronic conductivity of LLZOis not sufficiently high to cause bulk lithium-dendrite growth during cell operation, and that any non-negligible electronic conductivity in lithium garnet samples is likely due to extended defects or surface contributions. | Alex Squires; Daniel Davies; Sunghyun Kim; David Scanlon; Aron Walsh; Benjamin Morgan | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60dde02ae7f2bffc28808c22/original/low-electronic-conductivity-of-li7la3zr2o12-llzo-solid-electrolytes-from-first-principles.pdf |
628267623f1e7c609cbfd948 | 10.26434/chemrxiv-2022-xg6nz | Synthesis and styrene copolymerization of novel methoxy, methyl, halogen and oxy ring-disubstituted octyl phenylcyanoacrylates | Novel methoxy, methyl, halogen, and oxy ring-disubstituted octyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2(CH2)6CH3 (where R is 4-methoxy-2-methyl, 4-methoxy-3-methyl, 3-ethoxy-4-methoxy, 4-ethoxy-3-methoxy, 3-benzyloxy-4-methoxy, 4-benzyloxy-3-methoxy, 2,3-(methylenedioxy), 3-bromo-4-methoxy, 5-bromo-2-methoxy, 2-chloro-3-methoxy, 2-chloro-6-methyl, 3-chloro-4-methyl) were prepared and copolymerized with styrene. The acrylates were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-disubstituted benzaldehydes and octyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. All the acrylates were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis. | Emma J. Clajus; Natalie Cote; Rama Dalloul; Giulia M. DiMarco; Mollie J. Eriksson; Yesenia Garcia; Nathalie A. Gijsbers; Jay H. Kaila; Amina S. Malik; Madeeha I. Mohiuddin; Anaa Mulk; Neil T. Patel; Sara M. Rocus; William S. Schjerven; Gregory B. Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628267623f1e7c609cbfd948/original/synthesis-and-styrene-copolymerization-of-novel-methoxy-methyl-halogen-and-oxy-ring-disubstituted-octyl-phenylcyanoacrylates.pdf |
60c742a4842e65f86bdb20c2 | 10.26434/chemrxiv.8283962.v1 | 2,2’-Dipyridylamine as Heterogeneous Organic Molecular Electrocatalyst for Two-Electron Oxygen Reduction Reaction in Acid Media | Continuous production of hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) through the two-electron oxygen reduction reaction (2e-ORR) in distributed electrochemical cells offers important advantages for point-of-use water treatment and pulp bleaching over the complex industrial anthraquinone process. A low-cost, heterogeneous 2e-ORR electrocatalyst with high activity and selectivity is key to meeting the future needs for distributed production of H<sub>2</sub>O<sub>2</sub> with large capacity. Herein, we demonstrate high activity and selectivity of a new heterogeneous organic molecular electrocatalyst, 2,2’-dipyridylamine, with an H<sub>2</sub>O<sub>2</sub> yield of <i>ca.</i> 80%, and an onset potential of <i>ca.</i> 0.60 V <i>vs.</i> RHE in acidic aqueous electrolyte. We show that this acid-compatible, inexpensive, small organic molecule can catalyze 2e-ORR as efficiently as the state-of-the-art catalysts based on mercury-precious metal alloys. We propose different mechanisms of dioxygen electroreduction based on density functional theory calculations, which correlate activity with calculated standard reduction potential of reaction intermediates. | Xi Yin; Ling Lin; Ulises Martinez; Piotr Zelenay | Catalysts; Theory - Computational; Electrocatalysis; Organocatalysis; Fuel Cells; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742a4842e65f86bdb20c2/original/2-2-dipyridylamine-as-heterogeneous-organic-molecular-electrocatalyst-for-two-electron-oxygen-reduction-reaction-in-acid-media.pdf |
6729dc887be152b1d007c41d | 10.26434/chemrxiv-2024-53jpl | Towards Predictive Models of Acrylates Free Radical Polymerization in Solution: The Key Role of Solvent-induced Cage Effects | The rate constant of poly-butyl acrylate backbiting in the temperature range 310-510 K is investigated through Born Oppenheimer molecular dynamics in the gas phase, in polar and nonpolar solvents. The Arrhenius parameters so determined are introduced in a mechanistic kinetic mechanism of butyl acrylate polymerization in bulk and solution. The results are compared with the experimental data available for bulk and solution polymerization in the temperature range 350-430 K, allowing to explain how polymerization rate is affected by backbiting reactions of poly-butyl acrylate in different solvents. This work opens the possibility of developing detailed kinetic models in the condensed phase by using kinetic parameters determined a priori from molecular-scale simulations, widening their range of applicability beyond the one experimentally accessible. | Francesco Serse; Matteo Salvalaglio; Matteo Pelucchi | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Reaction Engineering; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6729dc887be152b1d007c41d/original/towards-predictive-models-of-acrylates-free-radical-polymerization-in-solution-the-key-role-of-solvent-induced-cage-effects.pdf |
66bbce81f3f4b05290c86e77 | 10.26434/chemrxiv-2024-kt7xx-v2 | Overcoming Nuclear Spin Diffusion Barrier in DNP via Electron-Electron Flip-Flop | The study introduces a new mechanism of nuclear spin diffusion in the context of Dynamic Nuclear Polarization (DNP) with magic angle spinning (MAS) under high magnetic fields. Electron-electron ($e$-$e$) coupling interactions, particularly the electron spin flip-flop interaction, play a significant role in enhancing nuclear spin diffusion in DNP polarizing agents with substantial hyperfine couplings. Using a four-spin system model, both theoretical analysis and numerical simulations suggest that the $e-e$ interactions eliminate the spin diffusion barrier in the $\alpha\beta\$ and $\beta\alpha$ coupled electron spin manifolds when the electron and nuclear states are degenerate through a concurrent four-spin flip-flop mechanism, known as the Electron-Assisted Spin Diffusion (EASD) mechanism. Experimental DNP buildup curves measured at 14.1 T under MAS conditions validate the EASD model, since a radical system with larger $e-e$ coupling shows faster spin diffusion rates. Our results provide fresh perspectives with the potential to greatly improve DNP transfer under MAS conditions. They elucidate how polarization can be diffused out of polarizing agents that otherwise would not diffuse to the bulk nuclei and lay the groundwork for designing and synthesizing more efficient DNP polarizing agents. In particular, this suggests engineering bis-nitroxides with ideal $e-e$ coupling for the cross-effect and EASD, along with narrow-line bis-BDPA and bis-trityl for solid-effect DNP. | Venkata SubbaRao Redrouthu; Marwa Mannai; Lina Taha; Waqqas Zia; Sajith V Sadasivan; Ribal Jabbour; Asif Equbal | Theoretical and Computational Chemistry; Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bbce81f3f4b05290c86e77/original/overcoming-nuclear-spin-diffusion-barrier-in-dnp-via-electron-electron-flip-flop.pdf |
66cd4318f3f4b05290353022 | 10.26434/chemrxiv-2024-lvzf7 | Unveiling the molecular basis of selective fluorination: computation-guided identification, characterization, and engineering of SAM-dependent fluorinases | S-adenosyl methionine (SAM)-dependent fluorinases have emerged as environmentally friendly alternatives for organofluorine synthesis. However, their use are limited by their rarity; only 16 fluorinases have so far been found in nature, and with limited SAM substrate specificities. Here we report two new fluorinases, FLASbac from Streptosporangiales bacterium and the N-terminal modified FLAAdig_Nter from Actinoplanes digitatis. Through molecular dynamics (MD) simulations, we proposed the critical roles played by the SAM-binding site and an identified ion-egress site (IES) in the fluorinase function such as fluoride ion preference. We confirmed these findings by testing respective mutants of these two new fluorinases, along with the known fluorinase from Streptomyces sp. MA37 (FLAMA37). Specifically, with these identified mutations, for the first time, we have managed to maintain fluorinase activity while also improving specificity towards fluoride ions over chloride ions. Overall, this research advances our fundamental understanding of enzymatic fluorination, paving the way for the rational design of fluorinases. These advancements will aid the pharmaceutical industry in developing fluorine-containing drugs and other fluorine-reliant biotechnologies. | Ravi Kumar Verma; Wan Lin Yeo; Elaine Tiong; Ee Lui Ang; Yee Hwee Lim; Fong Tian Wong; Hao Fan | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cd4318f3f4b05290353022/original/unveiling-the-molecular-basis-of-selective-fluorination-computation-guided-identification-characterization-and-engineering-of-sam-dependent-fluorinases.pdf |
60c742aebb8c1a2d063da191 | 10.26434/chemrxiv.8396954.v1 | Unified Approach to Implicit and Explicit Solvent Simulations of Electrochemical Reaction Energetics | <div>
<div>
<div>
<p>One of the major open challenges in <i>ab initio</i> simulations of the electrochemical
interface is the determination of electrochemical barriers under a constant driving force.
Existing methods to do so include extrapolation techniques based on fully explicit
treatments of the electrolyte, as well as implicit solvent models which allow for a
continuous variation in electrolyte charge. Emerging hybrid continuum models have
the potential to revolutionize the field, since they account for the electrolyte with
little computational cost while retaining some explicit electrolyte, representing a “best
of both worlds” method. In this work, we present a unified approach to determine
reaction energetics from both fully explicit, implicit, and hybrid treatments of the
electrolyte based on a new multi-capacitor model of the electrochemical interface. A given electrode potential can be achieved by a variety of interfacial structures; a crucial
insight from this work is that the <i>effective</i> surface charge gives the true driving force
of electrochemical processes. In contrast, we show that the traditionally considered
work function gives rise to multi-valued functions depending on the simulation cell
size. Furthermore, we show that the reaction energetics are largely insensitive to the
countercharge distribution chosen in hybrid implicit/explicit models, which means that
any of the myriad implicit electrolyte models can be equivalently applied. This work
thus paves the way for the accurate treatment of <i>ab initio</i> reaction energetics of general
surface electrochemical processes using both implicit and explicit electrolyte. </p>
</div>
</div>
</div> | Joseph Gauthier; Colin Dickens; Hendrik H. Heenen; Stefan Ringe; Karen Chan | Theory - Computational; Electrocatalysis; Heterogeneous Catalysis; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742aebb8c1a2d063da191/original/unified-approach-to-implicit-and-explicit-solvent-simulations-of-electrochemical-reaction-energetics.pdf |
6708cb1051558a15efc244a5 | 10.26434/chemrxiv-2024-mj25f | Following Nature’s Lead. Designing a Very Simple yet Effective Ligand System Applicable to Pd-Catalyzed Cross Couplings…in Water | A new ligand design based on Nature’s use of simple elements is described. This relatively uncommon array of atoms is arrived at in a single step leading to “P3N” ligands, such as “(n-Bu2N)3P”, derived from PCl3 and three equivalents of n-Bu2NH. These readily participate in homogeneous, Pd-catalyzed Cu-free Sonogashira and Suzuki-Miyaura couplings. Reliance on low loadings of Pd is documented under aqueous micellar conditions (i.e., in water). Comparisons with several typically used representative ligands, which, by contrast are made in an environmentally egregious fashion, clearly show that this new series of ligands is preferred, cost-wise, synthetically, as well as in terms of their environmental impact. | Bruce Lipshutz; Erfan Oftadeh; Max Baumann; Marco Ortiz; Kirubel Mamo; Eduam Boeira; Sam Nguyen; Donald Aue | Organic Chemistry; Catalysis; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6708cb1051558a15efc244a5/original/following-nature-s-lead-designing-a-very-simple-yet-effective-ligand-system-applicable-to-pd-catalyzed-cross-couplings-in-water.pdf |
67ca06086dde43c908cdc86e | 10.26434/chemrxiv-2025-ft635 | The effect of hydrostatic pressure on g-tensor and hyperfine coupling constants of nitroxide radical characterized by ab initio calculations | We present a computational study characterizing the effect of hydrostatic pressure on magnetic spin parameters, which enter the analysis of the electron paramagnetic resonance (EPR) spectra. Site-directed spin labeling (SDSL) in combination with EPR spectroscopy is a powerful tool for investigating the structures and dynamics of biological molecules. In studies using SDSL-based EPR spectroscopy, it is essential to know the spin parameters, such as the g-factor and the hyperfine constants, precisely. However, the experimental characterization of these spin parameters under extreme conditions is often challenging. We report quantum-chemistry calculations of g-tensors and hyperfine coupling tensors (A-tensors) for the nitroxide radical spin label in the pressure range of 0-15 GPa. The hydrostatic pressure causes structural changes, which, in turn, result in the linear changes of the g- and A-tensors. The observed linear dependence of the g- and A-tensors suggests that these quantities can serve as reporters of a local pressure in complex environments. The corresponding simulated EPR spectra at the 9 GHz and 230 GHz reveal that the changes of EPR spectrum are more pronounced in the former. Our results indicate that the computational approach can address the challenge of determining magnetic spin parameters under extreme conditions, such as under high hydrostatic pressure. | Susumu Takahashi; Ana Gurgenidze; Anna Krylov | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Physical and Chemical Properties | CC BY 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ca06086dde43c908cdc86e/original/the-effect-of-hydrostatic-pressure-on-g-tensor-and-hyperfine-coupling-constants-of-nitroxide-radical-characterized-by-ab-initio-calculations.pdf |
6554fa5adbd7c8b54b544b90 | 10.26434/chemrxiv-2023-63ckv | Streamlining the Automated Discovery of Porous Organic Cages | Self-assembly through dynamic covalent chemistry (DCC) can yield a range of multi-component organic assemblies. The reversibility and dynamic nature of DCC has made prediction of reaction outcome particularly difficult and thus slows the discovery rate of new organic materials. In addition, traditional experimental processes are time-consuming and often rely on serendipity. Here, we present a streamlined hybrid workflow that combines automated high-throughput experimentation, automated data analysis, and computational modelling, to accelerate the discovery process of one particular subclass of molecular organic materials, porous organic cages. We demonstrate how the design and implementation of this workflow aids in the identification of organic cages with desirable properties. The curation of a precursor library of 55 tri- and di-topic aldehyde and amine precursors enabled the experimental screening of 366 imine condensation reactions experimentally, and 1464 hypothetical organic cage outcomes to be computationally modelled. From the screen, 225 cages were identified experimentally using mass spectrometry, 54 of which were cleanly formed as a single topology as determined by both turbidity measurements and 1H NMR spectroscopy. Integration of these characterisation methods into a fully automated Python pipeline, named cagey, led to over a 350-fold decrease in the time required for data analysis. This work highlights the advantages of combining automated synthesis, characterisation, and analysis, for large-scale data curation towards an accessible data-driven materials discovery approach. | Annabel Basford; Steven Bennett; Muye Xiao; Lukas Turcani; Jasmine Allen; Kim Jelfs; Rebecca Greenaway | Theoretical and Computational Chemistry; Organic Chemistry; Supramolecular Chemistry (Org.); Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6554fa5adbd7c8b54b544b90/original/streamlining-the-automated-discovery-of-porous-organic-cages.pdf |
636421961db0bd14a145ae1a | 10.26434/chemrxiv-2022-nr1k3 | Stereodivergent, Multicomponent Metal-Catalyzed Couplings Generating Three Stereocenters: Combining Enantioselective Rh-Catalyzed Conjugate Addition and Ir-Catalyzed Allylic Alkylation | Stereodivergent dual catalysis has emerged as a powerful tool to selectively prepare all four stereoisomers in molecules containing two chiral centers from common starting materials. Most processes involve the use of two substrates, and it remains challenging to use dual catalyst approaches to generate molecules having three newly formed stereocenters with high diastereo- and enantioselectivity. Here we report a multicomponent, stereodivergent method for the synthesis of targets containing three contiguous stereocenters by the combination of enantioselective Rh-catalyzed conjugate addition and Ir-catalyzed allylic alkylation methodologies. Both cyclic and acyclic ,-unsaturated ketones undergo -arylation using aryl boron reagents to form an enolate nucleophile that can be subsequently allylated at the -position. The reactions proceed with generally >95% ee and with >90:10 dr. Epimerization at the -carbonyl center enables the preparation of any of the eight possible stereoisomers from common starting materials, as demonstrated for cyclohexanone products. | Qiqige Qiqige; Rylan Lundgren; Duanyang Kong | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636421961db0bd14a145ae1a/original/stereodivergent-multicomponent-metal-catalyzed-couplings-generating-three-stereocenters-combining-enantioselective-rh-catalyzed-conjugate-addition-and-ir-catalyzed-allylic-alkylation.pdf |
6115b3ccd800ad25f74512e9 | 10.26434/chemrxiv-2021-2s4hl | A Unified Strategy to Access Trans-Syn-Fused Drimane Meroterpe-noids: Chemoenzymatic Total Syntheses of Polysin, N-Acetyl-Polyveoline and the Chrodrimanins | Trans-syn-fused drimane meroterpenoids are unique natural products that arise from contra-thermodynamic polycyclizations of their polyene precursors. Herein we report the first total syntheses of four trans-syn-fused drimane meroterpenoids, namely polysin, N-acetyl-polyveoline, chrodrimanin C and verruculide A in 7–18 steps from sclareolide. The trans-syn-fused drimane unit is accessed through an efficient acid-mediated C9 epimerization of sclareolide. Subsequent applications of enzy-matic C–H oxidation and contemporary annulation methodologies install the requisite C3 hydroxyl group and enable rapid gen-eration of structural complexity to provide concise access to these natural products. | Fuzhuo Li; Hans Renata | Organic Chemistry; Natural Products | CC BY 4.0 | CHEMRXIV | 2021-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6115b3ccd800ad25f74512e9/original/a-unified-strategy-to-access-trans-syn-fused-drimane-meroterpe-noids-chemoenzymatic-total-syntheses-of-polysin-n-acetyl-polyveoline-and-the-chrodrimanins.pdf |
648344a14f8b1884b7105f2c | 10.26434/chemrxiv-2023-mlsp5 | Oxygen-Resistant CO2 Reduction Enabled by Electrolysis of Liquid Feedstocks | Electrolytic CO2 reduction fails in the presence of O2. This failure occurs because the reduction of O2 is thermodynamically favored over the reduction of CO2. Consequently, O2 must be removed from the CO2 feed prior to entering an electrolyzer, which is an expensive process. Here, we show the use of liquid bicarbonate feedstocks (e.g., aqueous 3.0 M KHCO3), rather than gaseous CO2 feedstocks, enables efficient and selective CO2 reduction without additional procedures for removing O2. This advance is made possible because liquid bicarbonate solutions deliver high concentrations of captured CO2 to the cathode, while the low solubility of O2 in aqueous media maintains a low O2 concentration at the same cathode surface. Consequently, electrolyzers fed with liquid bicarbonate feedstocks create an environment at the cathode that favors the reduction of CO2 over O2. We validate this claim by electrochemically converting CO2 into CO with reaction selectivities of ~65% at 100 mA cm-2 using 3.0 M KHCO3 solution bubbled with 100% CO2 or 100% O2. Similar experiments performed with a gaseous CO2 feedstock showed that merely 1% of O2 in the feedstock reduced CO selectivity to 11 ± 3.7%. Our findings demonstrate that a liquid bicarbonate feedstock enables efficient CO2 reduction without the need for expensive O2 removal steps. | Douglas Pimlott; Andrew Jewlal; Yongwook Kim; Curtis Berlinguette | Inorganic Chemistry; Catalysis; Electrochemistry; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648344a14f8b1884b7105f2c/original/oxygen-resistant-co2-reduction-enabled-by-electrolysis-of-liquid-feedstocks.pdf |
622535d2ce899bccbbaec45a | 10.26434/chemrxiv-2022-wgwzj | The dielectric function profile across the water interface through surface-specific vibrational spectroscopy and simulations | The dielectric properties of interfacial water on sub-nanometer length scales govern chemical reactions, carrier transfer, and ion transport at interfaces. Yet, the nature of the interfacial dielectric function has remained debated as it is challenging to access the interfacial dielectric with sub-nanometer resolution. Here, we use the vibrational response of interfacial water molecules probed using surface-specific sum-frequency generation (SFG) spectra to obtain exquisite depth resolution. Different responses originate from water molecules at different depths, and report back on the local interfacial dielectric environment via their spectral amplitudes. From experimental and simulated SFG spectra at the air/water interface, we find that the interfacial dielectric constant changes drastically across a ~1 Å thin interfacial water region. The strong gradient of the interfacial dielectric constant leads, at charged planar interfaces, to the formation of an electric triple layer that goes beyond the standard double-layer model. | Kuo-Yang Chiang; Takakazu Seki; Chun-Chieh Yu; Tatsuhiko Ohto; Johannes Hunger; Mischa Bonn; Yuki Nagata | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Interfaces; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622535d2ce899bccbbaec45a/original/the-dielectric-function-profile-across-the-water-interface-through-surface-specific-vibrational-spectroscopy-and-simulations.pdf |
61e63697deeafa61a020754d | 10.26434/chemrxiv-2022-vq7tt | The relationship between gel mesh and particle size in determining nanoparticle diffusion in hydrogel nanocomposites | The diffusion of poly(ethylene glycol) methyl ether thiol (PEGSH) functionalized gold nanoparticles (NPs) was measured in polyacrylamide gels of various crosslinking densities. The molecular weight of the PEGSH ligand and particle core size were both varied to yield particles with hydrodynamic diameters ranging from 7 to 21 nm. Gel mesh size was varied from approximately 36 to 60 nm by controlling the crosslinking density of the gel. Because high molecular weight ligands are expected to yield more compressible particles, we expected the diffusion constants of the NPs to depend on their hard:soft ratios (where the hard component of the particle consists of the particle core and the soft component of the particle consists of the ligand shell). However, our measurements revealed that NP diffusion coefficients resulted primarily from changes in the overall hydrodynamic diameter and not the ratio of particle core size to ligand size. Across all particles and gels, we found that the diffusion coefficient was well-predicted by the confinement ratio calculated from the diameter of the particle and an estimate of the gel mesh size obtained from the elastic blob model. These results suggest that the elastic blob model provides a reasonable estimate of the mesh size that particles “see” as they diffuse through the gel. This work brings new insights into the factors that dictate how NPs move through polymer gels and will inform development of hydrogel nanocomposites for applications such as drug delivery in heterogeneous, viscoelastic biological materials. | Paige Moncure; Zoe Simon; Jill Millstone; Jennifer Laaser | Polymer Science; Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e63697deeafa61a020754d/original/the-relationship-between-gel-mesh-and-particle-size-in-determining-nanoparticle-diffusion-in-hydrogel-nanocomposites.pdf |
60c73f84842e65f4d5db1ad5 | 10.26434/chemrxiv.6653381.v4 | Primary α-Tertiary Amine Synthesis via α-C–H Functionalization | <i>A quinone-mediated general platform for the
construction of primary α-tertiary amines from abundant primary α-branched amine
starting materials is described. This procedure pivots on the efficient in situ
generation of reactive ketimine intermediates and subsequent reaction with
carbon-centered nucleophiles such as organomagnesium and organolithium
reagents, and TMSCN, creating quaternary centers. Furthermore, extension to
reverse polarity photoredox catalysis enables reactivity with electrophiles.
This efficient, broadly applicable and scalable amine-to-amine synthetic
platform was successfully applied to library and API synthesis and in the late
stage functionalization of drug molecules. </i><br /> | Dhananjayan Vasu; Ángel L. Fuentes de Arriba; Jamie Leitch; Antoine de Gombert; Darren J. Dixon | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f84842e65f4d5db1ad5/original/primary-tertiary-amine-synthesis-via-c-h-functionalization.pdf |
6412e9f1aad2a62ca1d95170 | 10.26434/chemrxiv-2023-z396j | Cascading degradations artificially improving the lifetime of Li-ion full cells using DMC-based highly concentrated electrolyte | The deployment of energy dense Ni-rich NMC (LiNixMnyCozO2 with x > 0.8) in Li-ion batteries is hampered by a poor interfacial stability above 4.2 V. Among the strategies to mitigate this instability, highly concentrated electrolytes (HCE) has shown a promising resilience at high potential. In this work, we demonstrate that although cells using HCE experience low capacity fading compared to conventional carbonate based-electrolyte, HCE does not prevent oxidation of dimethyl carbonate at high potential. Even worse, this phenomenon cannot be fully offset by lithium intercalation at the negative electrode and eventually leads to lithium plating that precipitates the cell end of life. To circumvent lithium plating, cycling at high temperature is shown to build a more passivating solid electrolyte interphase (SEI); while promising at first, the lithium losses associated with the SEI formation trigger a jump of graphite staging. Only replacing DMC by ethyl carbonate (EC) solvent reduces efficiently the parasitic oxidation and prevents capacity rollover. This work, by the use of adapted testing protocols and analysis workflows, provides the necessary understanding to open new routes for tackling parasitic reaction at high voltage in Li-ion batteries, which including mastering of SEI formation conditions and the use of appropriate solvent. | Valentin Meunier; Federico Capone; Rémi Dedryvère; Alexis Grimaud | Materials Science; Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6412e9f1aad2a62ca1d95170/original/cascading-degradations-artificially-improving-the-lifetime-of-li-ion-full-cells-using-dmc-based-highly-concentrated-electrolyte.pdf |
658e21bc9138d23161b75403 | 10.26434/chemrxiv-2023-7m2dn-v2 | Bioisostere-conjugated fluorescent probes for live-cell protein imaging without non-specific organelle accumulation. | Specific labeling of proteins using membrane-permeable fluorescent probes is a powerful technique for bioimaging. Cationic fluorescent dyes with high fluorescence quantum yield, photostability, and water solubility provide highly useful scaffolds for protein-labeling probes. However, cationic probes generally show undesired accumulation in organelles, which causes a false-positive signal in localization analysis. Herein, we report a design strategy for probes that suppress undesired organelle accumulation using a bioisostere for intracellular protein imaging in living cells. Our design allows the protein labeling probes to possess both membrane permeability and suppress non-specific accumulation and has been shown to use several protein labeling systems, such as PYP-tag and Halo tag systems. We further developed a fluorogenic PYP-tag labeling probe for intracellular proteins and used it to visualize multiple localizations of target proteins in the intracellular system. Our strategy offers a versatile design for undesired accumulation-suppressed probes with cationic dye scaffolds and provides a valuable tool for intracellular protein imaging. | Takuya Kamikawa; Akari Hashimoto; Nozomi Yamazaki; Junya Adachi; Kazuya Kikuchi; Yuichiro Hori | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2023-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658e21bc9138d23161b75403/original/bioisostere-conjugated-fluorescent-probes-for-live-cell-protein-imaging-without-non-specific-organelle-accumulation.pdf |
60c743739abda25732f8c1d5 | 10.26434/chemrxiv.6279296.v2 | Quantitative Characterization of Molecular-Stream Separation | Molecular-stream separation (MSS), e.g. by free flow electrophoresis or continuous annular chromatography, has great potential for applications that require continuous downstream separation such continuous flow synthesis. Despite its potential, MSS still needs to be greatly advanced, which requires currently lacking tools for quantitative characterization of streams in MSS. We developed and introduce here an analytical toolbox for this task. The first tool is a method to convolute 3D raw MSS data into a 2D “angulagram” via signal integration over the whole separation zone using a polar coordinate system. The second tool is three quantitative parameters characterizing stream width, linearity, and deflection, which are determined from an angulagram. The third tool is the analysis of the three parameters in relation to physicochemical characteristics of MSS which reveals deficiencies and guides improvements in MSS devices and methods. Examples of toolbox application to validation of previously published MSS data are provided. | Sven Kochmann; Sergey N. Krylov | Analytical Chemistry - General; Chemoinformatics; Imaging; Separation Science; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743739abda25732f8c1d5/original/quantitative-characterization-of-molecular-stream-separation.pdf |
633f60632984c9020d7b1c48 | 10.26434/chemrxiv-2022-ng4g9 | The art of compartment design for organometallic catalysis | Confining organometallic catalysts in nanoscopic compartments has been gaining traction as a method to introduce additional levels of control in catalytic transformations. Running reactions inside of compartments is ubiquitous in biology, and recent attention has turned toward applying the same principles to organometallic systems. This perspective attempts to ellucidate compartment design principles and identify shortcomings of current methodologies. We start by using enzymes as an exemplar model system for biological compartments, extrapolate guiding principles, and apply them to organometallic catalysts. Structure and space are then explored as overarching design principles at work in compartmentalization. Finally, suggestions for future directions are provided. Compartmentalization has the potential to become a powerful synthetic tool, however, more work in understanding the fundamental principles at play is required. | Ashton Davis; Chong Liu; Paula Diaconescu | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Heterogeneous Catalysis; Homogeneous Catalysis; Catalysis | CC BY 4.0 | CHEMRXIV | 2022-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633f60632984c9020d7b1c48/original/the-art-of-compartment-design-for-organometallic-catalysis.pdf |
61e6df8a4a603d6b74343fe7 | 10.26434/chemrxiv-2022-zms0g | Orthogonal DNA barcodes enable the high-throughput screening of sequence-defined polymers | Polymers with sequence definition allow access to programmable morphologies and applications, but directly correlating polymer structure to function currently requires case-by-case analysis: high throughput methods that identify promising species from entire chemical families are required. Here, we show that the discovery of effective protein target-recognition molecules can be achieved using DNA-encoded libraries of chemically diverse sequence-defined oligomers, generated on an automated DNA synthesizer. These structures are ALENOMERs – Aptamer-Like ENcoded OligoMERs – that are read and sequenced using a DNA code that branches from, and corresponds to, the target-binding oligomer. By incorporating nucleosidic and non-nucleosidic components into alenomers at specific locations, we unlock new supramolecular interactions for biomolecule binding, and directly correlate their effectiveness at each site. Our alenomer library screening removes the low throughput bottleneck of analyzing individual sequence-defined polymers, improving the binding efficacies of natural systems and enabling wide chemical spaces to be sampled for biomolecule sensing, therapy, and diagnostics. | Donatien de Rochambeau; Serhii Hirka; Daniel Saliba; Shaun Anderson; Violeta Toader; Michael Dore; Felix Rizzuto; Maureen McKeague; Hanadi Sleiman | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e6df8a4a603d6b74343fe7/original/orthogonal-dna-barcodes-enable-the-high-throughput-screening-of-sequence-defined-polymers.pdf |
64eca19379853bbd789bf951 | 10.26434/chemrxiv-2023-sqb5c | Machine learning-guided high throughput nanoparticle design | Designing nanoparticles with desired properties is a challenging endeavor, due to the large combinatorial space
and complex structure-function relationships. High throughput methodologies and machine learning
approaches are attractive and emergent strategies to accelerate nanoparticle composition design. To date, how
to combine nanoparticle formulation, screening, and computational decision-making into a single effective
workflow is underexplored. In this study, we showcase the integration of three key technologies, namely
microfluidic-based formulation, high content imaging, and active machine learning. As a case study, we apply
our approach for designing PLGA-PEG nanoparticles with high uptake in human breast cancer cells. Starting
from a small set of nanoparticles for model training, our approach led to an increase in uptake from ~5-fold to
~15-fold in only two machine learning guided iterations, taking one week each. To the best of our knowledge,
this is the first time that these three technologies have been successfully integrated to optimize a biological
response through nanoparticle composition. Our results underscore the potential of the proposed platform for
rapid and unbiased nanoparticle optimization. | Ana Ortiz-Perez; Derek van Tilborg; Roy van der Meel; Francesca Grisoni; Lorenzo Albertazzi | Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64eca19379853bbd789bf951/original/machine-learning-guided-high-throughput-nanoparticle-design.pdf |
66ea0ef812ff75c3a1a48e7d | 10.26434/chemrxiv-2024-f5ngq | A simple solution form for triple tube heat exchanger with non-adiabatic condition on the outer wall by analogy with moving bed heat exchanger | Triple tube heat exchangers (TTHEs) are suitable equipment for thick viscosity products, with or without particulates, with various applications in the food and pharmaceutical industries. Of less widespread use than double tube heat exchangers (DTHEs), they generally perform better when compared to the latter. However, in the case of thermal models of "TTHEs with heat loss to the surroundings" (TTHEs-HL), there is no analytical solution in which the character of the roots has been analyzed. - except for the analogous problem of a "tubular moving bed heat exchanger, indirectly heated and with heat loss to the surroundings " (MBHE-HL), but only for certain flow arrangements -. Thus, it is not certain that the known solutions are of general application. Furthermore, regarding the important design parameter for co-current flow TTHEs, the crossover point, very little is known for TTHEs-HL. Also, recently published analogies provide an opportunity to synergistically increase the knowledge of TTHEs and MBHEs, for the case of non-adiabatic external surface. Aware of these needs and opportunities, the present work starts from a known analytical solution for a MBHE-HL thermal model and, by analogy, develops a compact form of an analytical solution for TTHE-HL, suitable for co-current and counter-current flow arrangements. The character analysis of the roots - not trivial for this solution - is performed according to a methodology recently described in the literature, consisting of several mathematical techniques. Approximate expressions for crossover point and temperature equality point between streams are obtained. In the case studies, the values calculated by the analytical solution and by a numerical solution by the finite analytical method (FAM), were shown to be very close. For the flow arrangements analyzed, it was possible to conclude about the generality of the solutions, in addition, the analogies between MBHE and TTHE made it possible to advance in the understanding of the thermal operation of these equipments. For a better understanding of the underlying physics, a scale analysis was performed. | Sávio Bertoli; Jesús Apolinar-Hernández; Natan Padoin; Cíntia Soares | Chemical Engineering and Industrial Chemistry; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ea0ef812ff75c3a1a48e7d/original/a-simple-solution-form-for-triple-tube-heat-exchanger-with-non-adiabatic-condition-on-the-outer-wall-by-analogy-with-moving-bed-heat-exchanger.pdf |
6553d190dbd7c8b54b44b599 | 10.26434/chemrxiv-2023-t9pxs | Separation and Characterization of Synthetic Cannabinoid Metabolite Isomers using SLIM High-Resolution Ion Mobility-Tandem Mass Spectrometry (HRIM-MS/MS) | Synthetic cannabinoids, a subclass of new psychoactive substances (NPS), are lab-made substances that are chemically similar to those found naturally in the cannabis plant. Many of these substances are illicitly manufactured and have been associated with severe health problems, prompting a need to development analytical methods capable of characterizing both known and previously undetected compounds. This work focuses on a novel Structures for Lossless Ion Manipulations (SLIM) IM-MS approach to differentiation and structural characterization of synthetic cannabinoid metabolites, specifically MDA-19/BUTINACA, JWH-018, and JWH-250 isomer groups. These different compound classes are structurally very similar, differing only in the position of one or a few functional groups; this yielded similarity in measured collision cross section (CCS) values. However, the high resolution of SLIM IM provided adequate separation of many of these isomers, such as sodiated JWH-250 metabolites N-4-OH, N-5-OH, and 5-OH which displayed CCS of 187.5, 182.5, and 202.3 Å2, respectively. In challenging cases where baseline separation was precluded due to nearly identical CCS, such as for JWH-018 isomer, simple derivatization by dansyl chloride selectively reacted with the 6-OH compound to provide differentiation of all isomers using a combination of CCS and m/z. Finally, the opportunity to use this method for structural elucidation of unknowns was demonstrated using SLIM IM mobility-aligned MS/MS fragmentation. Different MDA-19/BUTINACA isomers were first mobility separated and then could be individually activated, yielding unique fragments for both targeted identification and structural determination. Overall, the described SLIM IM-MS/MS workflow provides significant potential as a rapid screening tool for characterization of emerging NPS such as synthetic cannabinoids and their metabolites. | Ralph Aderorho; Shadrack Wilson Lucas; Christopher Chouinard | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6553d190dbd7c8b54b44b599/original/separation-and-characterization-of-synthetic-cannabinoid-metabolite-isomers-using-slim-high-resolution-ion-mobility-tandem-mass-spectrometry-hrim-ms-ms.pdf |
60c742acf96a001a29286652 | 10.26434/chemrxiv.8341016.v1 | Cu-Catalyzed Hydroboration of Benzylidenecyclopropanes: Reaction Optimization, (Hetero)Aryl Scope, and Origins of Pathway Selectivity | The copper-catalyzed hydroboration of benzylidenecyclopropanes, conveniently accessed in one step from readily available benzaldehydes, is reported. Under otherwise identical reaction conditions, two distinct phosphine ligands grant access to different products by either suppressing or promoting cyclopropane opening via β-carbon elimination. Computational studies provide insight into how the rigidity and steric environment of these different bis-phosphine ligands influence the relative activation energies of β-carbon elimination versus protodecupration from the key benzylcopper intermediate. The method tolerates a wide variety of heterocycles prevalent in clinical and pre-clinical drug development, giving access to valuable synthetic intermediates. The versatility of the tertiary cyclopropylboronic ester products is demonstrated through several derivatization reactions. | Jose Medina; Taeho Kang; Tuğçe Erbay; Huiling Shao; Gary Gallego; Shouliang Yang; Michelle Tran-Dubé; Paul Richardson; Joseph Derosa; Ryan Helsel; Ryan Patman; Fen Wang; Christopher Ashcroft; John Braganza; Indrawan McAlpine; Peng Liu; Keary Engle | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Computational Chemistry and Modeling; Homogeneous Catalysis; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742acf96a001a29286652/original/cu-catalyzed-hydroboration-of-benzylidenecyclopropanes-reaction-optimization-hetero-aryl-scope-and-origins-of-pathway-selectivity.pdf |
60c74063567dfe53eeec3b8f | 10.26434/chemrxiv.7730654.v1 | Singlet Oxygen Generation in Classical Fenton Chemistry | <div><div><div><p>The Fenton reaction, the Fe-catalyzed conversion of hydrogen peroxide to reactive oxygen species (ROS) was discovered more than a century ago. It occurs widely in nature because of the ubiquity of Fenton reagents, i.e., Fe and H2O2, and ROS in environmental and biological systems; however, its mechanisms and the identity of the ROS generated under varying conditions have remained controversial. The widely accepted mechanism is that of successive oxidation and reduction of Fe2+ and Fe3+ by hydrogen peroxide to form ·OH and O2-·, respectively, where ·OH is implicated as the primary oxidant. However, the formation of high-valent Fe4+=O species has also been implicated. Herein, by systematically dissecting the contributions of various ROS species generated in the classical Fenton reaction by using specific ROS traps and scavengers, we identified that singlet oxygen (1O2) is the main ROS from pH 4–7. In contrast, although ·OH is produced in measurable quantities, it was not a major contributor to the oxidation of organic molecules.</p></div></div></div> | Andrew Carrier; Saher Hamid; David Oakley; Ken Oakes; Xu Zhang | Homogeneous Catalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74063567dfe53eeec3b8f/original/singlet-oxygen-generation-in-classical-fenton-chemistry.pdf |
667bb33a01103d79c526a0c9 | 10.26434/chemrxiv-2024-qm5lh | Enhanced payload localization in antibody-drug conjugates using a middle-down mass spectrometry approach with proton transfer charge reduction | Antibody-drug conjugates (ADCs) represent a novel class of immunoconjugates with growing therapeutic relevance since they combine the efficacy of cytotoxic drugs with the specificity of antibodies. However, by design, ADCs introduce structural features to the mAb scaffold that complicate their analysis. Payload attachment to cysteine or lysine residues can often result in product heterogeneity regarding both the number of attached drug molecules and their conjugation site, necessitating the use of state-of-the-art MS instrumentation to elucidate their complexity. In middle-down mass spectrometry (MD MS), the gas-phase sequencing of ~25 kDa ADC subunits with dif-ferent ion activation techniques generally produces rich fragmentation mass spectra; however, spectral congestion can cause some fragment ions to go undetected, includ-ing those that can pinpoint the exact location of payload conjugation sites. Proton transfer charge reduction (PTCR) can substantially simplify fragment ion spectra, thereby unveiling the presence of product ions whose signals were previously sup-pressed. Herein, we present an MD MS strategy relying on the use of PTCR to investi-gate a cysteine-based ADC mimic with a variable drug-to-antibody ratio, targeting the unambiguous localization of payload conjugation sites. Unlike traditional tandem MS experiments (MS2), which could not provide a full map of conjugation sites, a single PTCR-based experiment (MS3) proved to be sufficient to achieve this goal across all variably modified ADC subunits, including isomeric ones. Combining the results ob-tained from orthogonal ion activation techniques followed by PTCR further strength-ened the confidence in assignments. | Linda Lieu; Cynthia Nagy; Jingjing Huang; Christopher Mullen; Graeme McAlister; Vlad Zabrouskov; Kristina Srzentić; Kenneth Durbin; Rafael Melani; Luca Fornelli | Biological and Medicinal Chemistry; Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667bb33a01103d79c526a0c9/original/enhanced-payload-localization-in-antibody-drug-conjugates-using-a-middle-down-mass-spectrometry-approach-with-proton-transfer-charge-reduction.pdf |
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