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60c741184c89199118ad2234 | 10.26434/chemrxiv.7926869.v1 | Towards a Design of Active Oxygen Evolution Catalysts: Insights from Automated Density Functional Theory Calculations and Machine Learning | <div>
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<div><p>Developing active and stable oxygen evolution catalysts is a key to enabling various future energy technologies and the state-of-the-art catalyst is Ir-containing oxide materials. Understanding oxygen chemistry on oxide materials is significantly more complicated than studying transition metal catalysts for two reasons: the most stable surface coverage under reaction conditions is extremely important but difficult to understand without many detailed calculations, and there are many possible active sites and configurations on O* or OH* covered surfaces. We have developed an automated and high-throughput approach to solve this problem and predict OER overpotentials for arbitrary oxide surfaces. We demonstrate this for a number of previously-unstudied IrO2 and IrO3 polymorphs and their facets. We discovered that low index surfaces of IrO2 other than rutile (110) are more active than the most stable rutile (110), and we identified promising active sites of IrO2 and IrO3 that outperform rutile (110) by 0.2 V in theoretical overpotential. Based on findings from DFT calculations, we pro- vide catalyst design strategies to improve catalytic activity of Ir based catalysts and demonstrate a machine learning model capable of predicting surface coverages and site activity. This work highlights the importance of investigating unexplored chemical space to design promising catalysts.<br /></p></div></div></div></div><div><div><div>
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</div> | Seoin Back; Kevin Tran; Zachary Ulissi | Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741184c89199118ad2234/original/towards-a-design-of-active-oxygen-evolution-catalysts-insights-from-automated-density-functional-theory-calculations-and-machine-learning.pdf |
60c745dd469df40918f4358a | 10.26434/chemrxiv.10277783.v1 | Spatially Resolving Anharmonic Lattice Dynamics in Molecular Crystals With X-Ray Diffraction and Terahertz Spectroscopy | <div><div><div><div><p>The combination of X-ray diffraction and low-frequency vibrational spectroscopy has proven to be a powerful method for understanding the relationship between molecular and crystalline structures, dynamics, and the properties of materials. In this work, we show how information obtained from terahertz time-domain spectroscopy (THz-TDS) measurements, coupled with first-principles simulations including anharmonic effects, is able to reconcile specific vibrational motions to the experimentally observed large- amplitude thermal displacements in a pair of isomeric molecular crystals. In particular, we show that a single terahertz mode is responsible for the observed structural data, and provide a framework for predicting and interpreting the origins of related phenomena.</p></div></div></div></div> | Martin Hutereau; Peter Banks; Ben Slater; J. Axel Zeitler; Andrew Bond; Michael Ruggiero | Spectroscopy (Physical Chem.); Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745dd469df40918f4358a/original/spatially-resolving-anharmonic-lattice-dynamics-in-molecular-crystals-with-x-ray-diffraction-and-terahertz-spectroscopy.pdf |
6292428e6209e07fbd54e817 | 10.26434/chemrxiv-2022-1sx92 | In situ Time-Resolved Spectroelectrochemistry Reveals Limitations of Biohybrid Photoelectrode Performance | Photosynthetic reaction centres catalyse the majority of solar energy conversion on Earth. These pigment proteins achieve this goal with a near-unity quantum efficiency, transducing the energy of almost every absorbed photon into that of a charge separated state. Capturing the high efficiency of these natural proteins with man-made electrodes is the goal of biohybrid technologies such as biophotovoltaics, biofuel cells and biosensors. However, the removal of reaction centres from their natural cellular environment and their integration into an abiotic biohybrid architecture invariably introduces loss channels that compromise energy conversion efficiency. Here, we developed the combined use of spectroscopy and analytical electrochemistry to identify electron transfer bottlenecks, back-reactions and short-circuits that affect the performance of a bacterial reaction centre-based biophotoelectrode. We determined that the system was over 90% efficient under low intensity light but dropped to ~10% efficiency under intense continuous illumination. Limitations and loss processes included bottlenecks in electron transfer that rendered 62% of reaction centres inactive, as well as a short-circuiting of 73% of the photochemical product from active reaction centres. These findings will help shape rational design strategies for improving the performance of biohybrid devices and may be more broadly applied to other donor-acceptor type photocatalysts. | Wojciech J. Nawrocki; Michael R. Jones; Raoul N. Frese; Roberta Croce; Vincent M. Friebe | Catalysis; Analytical Chemistry; Energy; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6292428e6209e07fbd54e817/original/in-situ-time-resolved-spectroelectrochemistry-reveals-limitations-of-biohybrid-photoelectrode-performance.pdf |
6192a4f447f47dd10ea29882 | 10.26434/chemrxiv-2021-42fvb | Amantadine Variant - Aryl Conjugates that Inhibit Multiple Amantadine Resistant M2 Mutant Influenza A Viruses | One challenge facing anti-influenza drug development is the heterogeneity of the circulating influenza A viruses, which comprise several strains with variable susceptibility to antiviral drugs. Viruses bearing the S31N mutant of the M2, such as the pandemic 2009 H1N1 and seasonal H3N2, as well as other mutants (L26F, V27A, A30T, G34E) are resistant to amantadine class of drugs. Here, we synthesized and tested many of the second generation amantadine - aryl conjugates, against the WT M2 and all the M2 amantadine resistant strains, i.e. L26F, V27A, S31N, A30T, G34E generated from WSN/33 (S31N) virus. We identified many compounds that are dual in vitro M2 WT and L26F virus inhibitors. Furthermore, few of them (21, 32, 33), having a rimantadine or diamantadine or 4-(1-adamantyl)aniline instead of amantadine in the conjugate, were in vitro inhibitors against M2 WT, L26F and S31N while one of them inhibited also the A30T virus. The electrophysiology (EP) experiments showed that these compounds blocked significantly M2 WT, L26F or even M2 V27A channels but not the M2 S31N. The observation that adamantane variants and derivatives inhibit multiple M2 mutant virus replication in cell culture, without blocking M2 channel-mediated proton current in EP is not uncommon, underlying a mechanism of antiviral activity that has not been identified. | Christina Tzitzoglaki; Anja Hoffmann; Andreea Turcu; Christos Liolios; Patrick Schmerer; Chunlong Ma; Jun Wang; Santiago Vázquez; Michaela Schmidtke; Antonios Kolocouris | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6192a4f447f47dd10ea29882/original/amantadine-variant-aryl-conjugates-that-inhibit-multiple-amantadine-resistant-m2-mutant-influenza-a-viruses.pdf |
6335534e0e3c6ac0692cc677 | 10.26434/chemrxiv-2022-2h4g1 | Anhydrous Superprotonic Conductivity in the Zirconium Acid Triphosphate ZrH5(PO4)3 | The development of solid-state proton conductors with high proton conductivity at low temperature is crucial for the implementation of hydrogen-based technologies for portable and automotive applications. Here, we report on the discovery of a new crystalline tetravalent metal acid triphosphate, ZrH5(PO4)3 (ZP3), which exhibits record-high proton conductivity of 3.0 x 10-2 S cm-1 at 110 °C in anhydrous conditions. Structural characterization and bond-valence sum energy (BVSE) calculations reveal the pathways and mechanism of proton transport. Extended defective hydrogen bond chains, where the protons are dynamically disordered over two oxygen centers, enable fast ionic diffusion with minimal activation energy for proton hopping. | Sacha Fop; Riccardo Vivani; Silvia Masci; Mario Casciola; Anna Donnadio | Inorganic Chemistry; Energy; Solid State Chemistry; Fuel Cells; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6335534e0e3c6ac0692cc677/original/anhydrous-superprotonic-conductivity-in-the-zirconium-acid-triphosphate-zr-h5-po4-3.pdf |
60c7559b4c891940fead46e5 | 10.26434/chemrxiv.14135645.v1 | Ozone-Mediated Amine Oxidation and Beyond: A Solvent Free, Flow-Chemistry Approach | Ozone is a powerful oxidant, most commonly used for oxidation of alkenes to carbonyls. The synthetic utility of other ozone-mediated reactions is hindered by its high reactivity and propensity to over-oxidize organic molecules, including most solvents. This challenge can largely be mitigated by adsorbing both substrate and ozone onto silica gel, providing a solvent-free oxidation method. In this manuscript, a flow-based packed bed reactor approach is described that provides exceptional control of reaction temperature and time of this reaction to achieve improved control and chemoselectivity over this challenging reaction. A powerful method to oxidize primary amines into nitroalkanes is achieved. Examples of pyridine, C–H bond, and arene oxidations are also demonstrated, confirming the system is generalizable to diverse ozone-mediated processes.<br /> | Eric Skrotzki; Jaya Kishore Vandavasi; Stephen Newman | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7559b4c891940fead46e5/original/ozone-mediated-amine-oxidation-and-beyond-a-solvent-free-flow-chemistry-approach.pdf |
63bebdc9ee6f1827729c949d | 10.26434/chemrxiv-2023-0k7g1 | How the pH controls photoprotection in the
light-harvesting complex of mosses | In response to varying light conditions, light-harvesting complexes (LHCs) switch from a light-harvesting to a quenched state to protect the photosynthetic organism from excessive light irradiation, in a strategy known as nonphotochemical quenching (NPQ). NPQ is activated by an acidification of the thylakoid lumen which is sensed directly or indirectly by the LHC, resulting in a conformational change of the complex that leads to the quenched state. The conformational changes responsible for NPQ activation and their connection to specific quenching mechanisms are still unknown.
Here, we investigate the pH-triggered conformational changes in the light-harvesting complex stress-related (LHCSR) of mosses. By combining constant-pH molecular dynamics and enhanced sampling techniques, we find that the pH sensitivity of the complex is driven by the coupled protonation of three residues modulating the conformation of the short amphipathic helix placed at lumen side of the embedding membrane. Combining these results with quantum mechanics/molecular mechanics calculations, we show that the quenching mechanism sensitive to the pH goes through a charge-transfer between a carotenoid and an excited chlorophyll which is controlled by the protein conformation. | Laura Pedraza-González; Edoardo Cignoni; Jacopo D’Ascenzi; Lorenzo Cupellini; Benedetta Mennucci | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2023-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bebdc9ee6f1827729c949d/original/how-the-p-h-controls-photoprotection-in-the-light-harvesting-complex-of-mosses.pdf |
65fe1b799138d2316110a8c4 | 10.26434/chemrxiv-2024-ncvzn-v2 | Anharmonic vibrational spectroscopy of germanium-containing clusters, Ge(x)C(4−x) and Ge(x)Si(4−x) (x = 0-4), for interstellar detection | An extensive, high-level theoretical study on tetra-atomic germanium carbide/silicide clusters is presented. Accurate harmonic and anharmonic vibrational frequencies and rotational constants are calculated at the CCSD(T)-F12a(b)/cc-pVT(Q)Z-F12 levels of theory. With growing capabilities to discern more of the chemical composition of the interstellar medium (ISM), an accurate database of reference material is required. The presence of carbon is ubiquitous in the ISM, and silicon is known to be present in interstellar dust grains, however germanium-containing molecules remain elusive. To begin understanding the presence and role of germanium in the ISM, we present this study of the vibrational and rotational spectroscopic properties of various germanium- containing molecules to aid in their potential identification in the ISM with modern observational tools such as the James Webb Space Telescope. Structures studied herein include rhomboidal (r-), diamond (d-), and trapezoidal (t-) tetra-atomic molecules of the form Ge(x)C(4−x) and Ge(x)Si(4−x) , where x=0-4. The most promising structure for detection is r-Ge(2)C(2) via the ν4 mode with a frequency of 802.7 cm−1 (12.5 μm) and an intensity of 307.2 km mol−1. Other molecules potentially detectable, i.e., through vibrational modes or rotational transitions, include r-Ge(3)C, r-GeSi(3), d-GeC(3), r-GeC(3), and t-Ge(2)C(2). | Adam Mackenzie Flowers; Alex Brown; Mariusz Klobukowski | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fe1b799138d2316110a8c4/original/anharmonic-vibrational-spectroscopy-of-germanium-containing-clusters-ge-x-c-4-x-and-ge-x-si-4-x-x-0-4-for-interstellar-detection.pdf |
6707da80cec5d6c142c86536 | 10.26434/chemrxiv-2024-8hwr5 | Conformational Dynamics of the Pyrene Excimer | The conformational dynamics of the pyrene excimer play a critical role in its unique fluorescence properties. Yet, the influence of multiple local minima on its excited-state behavior remains underexplored. Using a combination of time-dependent density functional theory (TD-DFT) and unsupervised machine learning analysis, we have identified and characterized a diverse set of stable excimer geometries in the first excited state. Our analysis reveals that rapid structural reorganization towards the most stable stacked-twisted conformer dominates the excimer’s photophysics, outcompeting radiative relaxation. This conformer, which is primarily responsible for the characteristic red-shifted, structureless fluorescence emission, reconciles experimental observations of long fluorescence lifetimes and emission profiles. These findings provide new insights into the excited-state dynamics of excimers. They may inform the design of excimer-based materials in fields ranging from organic electronics to molecular sensing. | Giovanni Parolin; Bidhan Chandra Garain; Saikat Mukherjee; Giovanni Granucci; Stefano Corni; Mario Barbatti | Theoretical and Computational Chemistry; Theory - Computational; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6707da80cec5d6c142c86536/original/conformational-dynamics-of-the-pyrene-excimer.pdf |
64e65c9d79853bbd78469463 | 10.26434/chemrxiv-2023-3g3g8 | DFT and DFT-D3 Studies of Glycerol Adsorption on the Cu(111), Cu(100), and Cu(110) Surfaces | Adsorption of glycerol is the first step in many catalytic reactions to transform glycerol that was formed as biodiesel byproduct into valuable products. Among many feasible catalysts, Cu seems to be a good choice due to its abundance and cost consideration, though extensive studies are needed to evaluate the performance of Cu catalysts on glycerol transformation. Density functional theory (DFT) calculations and van der Waals corrected calculations (DFT-D3) were therefore performed in this work to study the adsorption of glycerol on the three most abundant copper surfaces: Cu(111), Cu(100), and Cu(110). Inclusion of the van der Waals interactions resulted in higher adsorption energies and shorter Cu-O bond distances. The most favorable adsorption location was determined to be the Cu(110) long bridge site. The strongest adsorption is the atop site on the Cu(111) and the hollow site on the Cu(100), though the other adsorption sites are also very favorable. | Frannie Drake; Peshala Jayamaha; Lichang Wang | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Heterogeneous Catalysis; Physical and Chemical Processes; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e65c9d79853bbd78469463/original/dft-and-dft-d3-studies-of-glycerol-adsorption-on-the-cu-111-cu-100-and-cu-110-surfaces.pdf |
60c74eef842e651f2fdb3748 | 10.26434/chemrxiv.12821816.v1 | Trapping an Elusive Fe(IV)-Superoxo Intermediate Inside a Self-Assembled Nanocage at Room Temperature | Natural metalloenzymes stabilize reactive intermediates through specific metal-substrate interactions in protein confinement. Using the structural blueprint of enzyme pockets it is possible to trap elusive intermediates inside molecular cavities. Here we demonstrate room temperature trapping of a rare yet stable Fe(IV)-superoxo [FeIV(O2)-bTAML] intermediate subsequent to dioxygen binding at the Fe(III) site of a (Et4N)2[FeIII(Cl)(bTAML)] catalyst confined inside the hydrophobic interior of a water-soluble Pd6L412+ nanocage.
<br /> | Rahul Gera; Kundan K. Singh; Sayam SenGupta; Jyotishman Dasgupta | Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Reaction (Inorg.); Small Molecule Activation (Inorg.); Spectroscopy (Inorg.); Supramolecular Chemistry (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eef842e651f2fdb3748/original/trapping-an-elusive-fe-iv-superoxo-intermediate-inside-a-self-assembled-nanocage-at-room-temperature.pdf |
661e98eb91aefa6ce1af6b91 | 10.26434/chemrxiv-2024-bm6vb | A Configurationally Stable Indenofluorene-Based Helical Diradicaloid | The synthesis and the optoelectronic, magnetic and chiroptical properties of a helically chiral diradicaloid have been reported. Dibenzoindeno[2,1-c]fluorene, the simplest configurationally stable chiral derivative of the family of the indenofluorenes, shows a low HOMO-LUMO gap and a moderate singlet-triplet gap. Enantiomers have been isolated and are configurationally stable. Electronic circular dichroism has been measured and dissymmetry factor calculated. Our experimental findings are supported by DFT calculations. | Álvaro Martínez-Pinel; Luis Lezama; Juan M. Cuerva; Raquel Casares; Víctor Blanco; Carlos M. Cruz; Alba Millán | Organic Chemistry; Materials Science; Magnetic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661e98eb91aefa6ce1af6b91/original/a-configurationally-stable-indenofluorene-based-helical-diradicaloid.pdf |
650c0ffced7d0eccc3f32d7f | 10.26434/chemrxiv-2023-685jv | Do Chemformers dream of organic matter? Evaluating a transformer model for multi-step retrosynthesis | Synthesis planning of new pharmaceutical compounds is a well-known bottleneck in modern drug design. Template-free methods, such as transformers, have recently been proposed as an alternative to template-based methods for single-step retrosynthetic predictions. Here, we trained and evaluated a transformer model, called Chemformer, for retrosynthesis predictions within drug discovery. The proprietary dataset used for training comprised ~18M reactions from literature, patents, and electronic lab notebooks. Chemformer was evaluated for the purpose of both single-step and multi-step retrosynthesis. We found that the single-step performance of Chemformer was especially good on reaction classes common in drug discovery, with most reaction classes showing a top-10 round-trip accuracy above 0.97. Moreover, Chemformer reached a higher round-trip accuracy compared to a template-based model. By analyzing multi-step retrosynthesis experiments, we observed that Chemformer found synthetic routes leading to commercial starting materials for 95% of the target compounds, an increase by more than 20% compared to the template-based model. In addition to this, we discovered that Chemformer suggested novel disconnections corresponding to reaction templates which are not included in the template-based model. The conclusions drawn from this work allow for designing a synthesis planning tool where template-based and template-free models work in harmony to optimize retrosynthetic recommendations. | Annie M. Westerlund; Siva Manohar Koki; Supriya Kancharla; Alessandro Tibo; Lakshidaa Saigiridharan; Rocío Mercado; Samuel Genheden | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650c0ffced7d0eccc3f32d7f/original/do-chemformers-dream-of-organic-matter-evaluating-a-transformer-model-for-multi-step-retrosynthesis.pdf |
60c743f19abda28c5ef8c276 | 10.26434/chemrxiv.9699863.v1 | Novel Hierarchical Copper-Based Metal-Organic Frameworks for Improved Catalytic Performance | <p>Introducing
additional meso- or macroporosity into traditionally microporous metal-organic
frameworks (MOFs) is a very promising way to improve the catalytic performance
of these materials, mostly due to the resultant reductions of diffusional
barriers during liquid-phase or gas-phase reactions. Here we show that HKUST-1
can be successfully synthesised either via post-synthetic treatment (etching
prepared HKUST-1 samples in phosphoric acid, here called HKUST AE) or via <i>in situ</i> crystallisation (exposing the MOF
precursor solution to supercritical CO<sub>2</sub>, here called HKUST CO<sub>2</sub>)
to produce hierarchically porous structures that are highly beneficial for
catalysis. These hierarchical MOFs were characterised by powder X-ray
diffraction (PXRD), scanning electron microscopy (SEM) and gas sorption to
confirm the preservation of the microscopic structure and the appearance of
macropores in the crystallites. More importantly, the benefits of introducing these
hierarchical porous structures into this MOF for improving the diffusion
accessibility of reagents to the sample in catalysed liquid- and gas-phase
reactions were quantified for the first time. It was found that the
hierarchical pore structure helped to increase the reaction conversion of
styrene oxide methanolysis (by ~65 % using either HKUST AE and HKUST CO<sub>2</sub>,
at 40 <sup>o</sup>C in 25 min) and CO oxidation (by 55 % using HKUST CO<sub>2</sub>
at 260 <sup>o</sup>C). These findings demonstrate the advantage of using
hierarchical porous MOFs in catalysis.</p> | Huan Doan; Srinivasan Madapusi; Ken Chiang; Samuel Pattisson; Stuart H. Taylor; Valeska Ting | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f19abda28c5ef8c276/original/novel-hierarchical-copper-based-metal-organic-frameworks-for-improved-catalytic-performance.pdf |
6595fe7b66c1381729ab301d | 10.26434/chemrxiv-2024-t9h5w | Achieving Highly Efficient Deep-blue OLEDs by Introducing Intramolecular Hydrogen Bonds to Tune the Properties of Multiple Resonance Emitters | Multi-resonance thermally activated delayed fluorescence (MR-TADF) materials are considered a class of organic materials with exceptional electronic and optical properties, which make them promising for the applications in organic light-emitting diodes (OLEDs). However, the steric repulsion from the spatially-close hydrogens would twist the multi-resonance skeletons to cause the potential spectral broadening issues. Herein, pyridine and pyrimidine as aromatic-heterocyclic-core are introduced to stiffen the MR framework and minimize the emission spectral broadening by an intramolecular locking strategy. Planarizing the molecular skeleton is achieved due to enhancement of intramolecular interactions (hydrogen bonds) and alleviating the hydrogen steric repulsion. In addition, as a first multiple resonance material with heteroatoms-core, the introduction of pyridine and pyrimidine not only maintains the conventional MR properties of the emitters, but also endows the emitters with tunable emission spectra. Thanks to the overall superior properties brought by the hydrogen‐bonds promoted molecular rigidity, our proof-of-concept molecules, Py-BN and Pm-BN, exhibit deep-blue TADF emission with ultra-narrow full width at half maximum (FWHM) of 14 and 13 nm and Commission Internationale de L’Eclairage (CIE) coordinates of (0.16, 0.03) and (0.16, 0.04), respectively. The OLED developed using them as the emitters demonstrate electroluminescence FWHM of 21 and 24 nm and achieve a high external quantum efficiencies (EQEs) of 15.8% and 5.8%, respectively. | xinliang cai; pan yue; chenglong li; yexuan pu; yue wang | Materials Science; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6595fe7b66c1381729ab301d/original/achieving-highly-efficient-deep-blue-ole-ds-by-introducing-intramolecular-hydrogen-bonds-to-tune-the-properties-of-multiple-resonance-emitters.pdf |
60c758d0469df45f4cf4574c | 10.26434/chemrxiv.14588997.v1 | Phase Diagram and Cation Dynamics of Mixed MA1-xFAxPbBr3 Hybrid Perovskites | <p>We use a multi-technique approach
to determine the phase diagram and molecular cation dynamics of mixed
methylammonium-formamidinium MA1-xFAxPbBr3 (0 ≤ x ≤ 1) hybrid perovskites. The
calorimetric, ultrasonic and X-ray diffraction experiments show a substantial
suppression of the structural phase transitions and stabilization of the cubic
phase upon mixing. We use the broadband dielectric and Raman spectroscopies to
study the MA and FA cations dynamics in these compounds. The broadband dielectric
spectroscopy indicates absence of the MA cation ordering and a gradual increase
of the rotation barrier upon mixing. The room-temperature dielectric
permittivity substantially decreases as the fraction of the FA cations is
increased. No significant changes of the permittivity are detected at
temperatures where the dielectric relaxations are absent. We also observe weak
signatures of a dipolar glass phase for the highest mixing level (x = 0.5). The
Raman spectroscopy supports the dielectric results and reveals additional
subtle information about the FA cation dynamics.</p><br /> | Mantas Simenas; Sergejus Balčiūnas; Sarunas Svirskas; Martynas Kinka; Maciej Ptak; Vidmantas Kalendra; Anna Gągor; Daria Szewczyk; Adam Sieradzki; Robertas Grigalaitis; Aron Walsh; Mirosław Mączka; Jūras Banys | Hybrid Organic-Inorganic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758d0469df45f4cf4574c/original/phase-diagram-and-cation-dynamics-of-mixed-ma1-x-f-ax-pb-br3-hybrid-perovskites.pdf |
6732aace5a82cea2fad5c02c | 10.26434/chemrxiv-2024-43vjq | Enhanced Near-Infrared Photogenerated Carrier Transfer via Doublet-State Excitation in D-π-A Structures for Biosensing | The feedback mechanisms of living systems to external signals are vital for survival, particularly through the conversion of light into bioelectric signals by photosensitive molecules, that regulate biological behavior and physiological processes. Nonetheless, the application of materials that rely on near-infrared (NIR) responses for in vivo or opaque sample analysis has been limited. Here, we report the preparation of a C3N2-based doublet-state system for developing novel NIR-responsive materials. Photogenerated carriers are generated from doublet-state dangling bonds in C3N2 and transferred to the highly conductive graphitic materials via donor-π-acceptor conjugated structures, leading to nearly 700-fold enhancement in NIR photoelectric conversion. These materials were further applied for real-time detection of tetracycline in a single drop of whole blood, demonstrating better sensitivity in NIR photoelectrochemical biosensing, which paves the way for broader applications of in vivo biofeedback. | Hong Yang; Chaofeng Huang; Wang Li; Yongji Wang; Kaiyuan Wang; Zhuang Wang; Ying Wang; Songqin Liu; Yanfei Shen; Yuanjian Zhang | Physical Chemistry; Analytical Chemistry; Electrochemical Analysis; Interfaces; Structure; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6732aace5a82cea2fad5c02c/original/enhanced-near-infrared-photogenerated-carrier-transfer-via-doublet-state-excitation-in-d-a-structures-for-biosensing.pdf |
666c794dc9c6a5c07a7c2749 | 10.26434/chemrxiv-2024-3rvk6 | Counterion Exchange Enhances the Brightness and Photostability of a Fluorous Cyanine Dye | We leveraged the low dielectric constant of the fluorous phase to improve the photophysical properties of a fluorous pentamethine dye (FCy5) via counterion exchange. We found that larger aryl borate counterions promote charge delocalization across the polymethine chain and increase the photostability (55-fold) and brightness (6-fold) of FCy5. | Helen Lin ; Irene Lim; Ellen Sletten | Physical Chemistry; Organic Chemistry; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666c794dc9c6a5c07a7c2749/original/counterion-exchange-enhances-the-brightness-and-photostability-of-a-fluorous-cyanine-dye.pdf |
60c74f474c89196117ad3ba2 | 10.26434/chemrxiv.12886919.v1 | Iodine Adsorption in Tetrathiafulvalene-Based Covalent Organic Frameworks | <p>To safeguard the development of nuclear energy, practical
techniques for capture and storage of radioiodine are of critical importance
but remains a significant challenge. Here
we report the synergistic effect of physical and chemical adsorption of iodine
in tetrathiafulvalene-based covalent organic frameworks (COFs), which can markedly
improve both iodine adsorption capacity and adsorption kinetics due to their strong interaction. These functionalized
architectures are designed to have high specific surface areas (up to 2359 m<sup>2</sup> g<sup>−</sup><sup>1</sup>) for efficient physisorption
of iodine, and abundant tetrathiafulvalene functional groups for strong chemisorption
of iodine. We demonstrate that these frameworks achieve excellent iodine
adsorption capacity (~ 8.15 g g<sup>-1</sup>)
and adsorption kinetics (~ 0.69 g g<sup>-1</sup> h<sup>-1</sup>), which are much higher than other materials
reported so far, including silver-doped adsorbents, inorganic porous materials,<sup> </sup>metal−organic
frameworks, porous organic frameworks, and other COFs. Furthermore, a combined theoretical and experimental study<b>, </b>including DFT calculations, electron paramagnetic resonance spectroscopy, X-ray
photoelectron spectroscopy, and Raman spectroscopy, reveals the strong chemical
interaction between iodine and framework of material. Our study thus opens an
avenue to construct functional COFs for a critical environment-related application. <b></b></p> | Jianhong Chang; Hui Li; Xinyu Guan; Cuimei Li; Guangtao Yu; Valentin Valtchev; Yushan Yan; Shilun Qiu; Qianrong Fang | Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f474c89196117ad3ba2/original/iodine-adsorption-in-tetrathiafulvalene-based-covalent-organic-frameworks.pdf |
660579289138d231618cb117 | 10.26434/chemrxiv-2024-9v8dw | Geospatial Life Cycle Analysis of Greenhouse Gas Emissions from US Liquefied Natural Gas Supply Chains | Growth in US liquefied natural gas (LNG) exports have increased concerns about the climate impacts of methane leakage along LNG supply chains. Current life cycle analysis (LCA) models of US LNG supply chains are based on emissions estimates in national inventories that have been demonstrated to significantly underestimate emissions. In addition, recent top-down measurements of methane emissions exhibit significant sub-national spatial and temporal variation across oil and gas (O&G) basins. In this study, we develop a geospatial, measurement informed LCA model that incorporates recent top-down methane measurements to examine regional differences in greenhouse gas (GHG) emissions intensity of US LNG supply chains for delivery to Europe and Asia. For every megajoule of LNG shipped from the US, the energy allocated GHG emissions intensity of the Permian-UK LNG supply chain is 42% higher compared to the Marcellus-UK LNG supply chain. Disparities in LNG emissions intensity across source basins can be directly attributed to higher measured methane emissions compared to inventory estimates. Developing measurement informed, supply-chain specific lifecycle GHG emissions assessments is critical to enabling a global market for differentiated natural gas. | Yuanrui Zhu; David Allen; Arvind Ravikumar | Energy; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660579289138d231618cb117/original/geospatial-life-cycle-analysis-of-greenhouse-gas-emissions-from-us-liquefied-natural-gas-supply-chains.pdf |
674f280d7be152b1d0ceb4f0 | 10.26434/chemrxiv-2024-fb0jm-v2 | Practical Synthesis of Chiral Ferrocenenylphosphino-Gold(I) Cata-lysts and NEST Analysis of the Enantioinduction | The concise modular synthesis of a family of monodentate 1,2-disubstituted ferrocene ligands containing a diaryl phosphine and a 2-aryl indole is described. Their gold(I) complexes were applied to the enantioselective gold(I)-catalyzed formal [4+2] cycloaddition of 1,6-arylenynes, the enyne cyclization/nucleophile addition of N-tethered 1,6-enynes, and the methoxycyclization of 1,6-arylenyne with high levels of enantioselectivity in all cases. Crystallographic and computational studies highlight the relevant role of non-covalent interactions within the ligand scaffold and between ligand-substrate in the modes of enantioinduction in the cyclization of unsaturated substrates. Our recently developed open-source tool NEST was applied to analyze the chiral pockets of the new catalysts, which in combination with RDKit allowed to understand the enantioselectivity in these reactions, paving the way for a predictive-based approach towards the rational development of chiral ligands for enantioselective Au(I) catalysis. | Pablo Mora; Imma Escofet; Maria Besora; Federica Cester Bonati; Antonio Echavarren | Organic Chemistry; Catalysis; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674f280d7be152b1d0ceb4f0/original/practical-synthesis-of-chiral-ferrocenenylphosphino-gold-i-cata-lysts-and-nest-analysis-of-the-enantioinduction.pdf |
676d385afa469535b9d959b6 | 10.26434/chemrxiv-2024-j5wcs | Water-soluble Bioisosteres of meta-Benzenes | Water-soluble bioisosteres of meta-benzenes have been synthesized, characterized, and validated biologically. | Dmitry Dibchak; Pavel Mykhailiuk | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676d385afa469535b9d959b6/original/water-soluble-bioisosteres-of-meta-benzenes.pdf |
67b5cb7cfa469535b90440fa | 10.26434/chemrxiv-2024-jd2bq-v2 | Room-temperature H2 splitting and N2-hydrogenation induced by a neutral Lu(II) complex | The direct splitting of the H2 and N2 molecules are challenging reactions that are closely related to the Haber–Bosch ammonia synthesis process. Until now, such reactivity has never been observed in the case of molecular lanthanide species. Here, we show that careful selection of the ligand scaffold allows the isolation and characterization of a kinetically stable but highly reactive Lu(II) complex. This divalent lanthanide species enables direct H2 splitting at room temperature, an unknown reactivity in lanthanide chemistry, which has been fully corroborated by DFT calculations. In addition, the Lu(II) complex readily binds N2, leading to an end-on coordinated diazenido (N2)2– lanthanide complex. The latter can be hydrogenated under very smooth conditions (ca. 1.2 bar H2, ambient temperature) to form a unique Lu(III)–NH2 complex. Direct N2 hydrogenation and cleavage are thus accessible using low-valent molecular rare-earth metal complexes. | Evangelos Papangelis; Luca Demonti; Iker del Rosal; Angus Shephard; Laurent Maron; Grégory Nocton; Thomas SIMLER | Organometallic Chemistry; Ligands (Organomet.); Small Molecule Activation (Organomet.) | CC BY 4.0 | CHEMRXIV | 2025-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b5cb7cfa469535b90440fa/original/room-temperature-h2-splitting-and-n2-hydrogenation-induced-by-a-neutral-lu-ii-complex.pdf |
62ab4cf2f5524a6b8414948d | 10.26434/chemrxiv-2022-bfl2z | Impact of the current density on paramagnetic NMR
properties | Meta-generalized gradient approximations (meta-GGAs) and local hybrid functionals generally depend on the kinetic
energy density τ. For magnetic properties, this necessitates generalizations to ensure gauge invariance. In most implementations, τ is generalized by incorporating the external magnetic field. However, this introduces artifacts in the response of the density matrix and does not satisfy the iso-orbital constraint. Here, we extend previous approaches
based on the current density to paramagnetic NMR shieldings and EPR g-tensors. The impact is assessed for main-group compounds and transition-metal complexes considering 25 density functional approximations. It is shown that the current density leads to substantial improvements—especially for the popular Minnesota and SCAN functional families. Thus, we strongly recommend to use the current density generalized τ in paramagnetic NMR and EPR calculations with meta-GGAs. | Yannick J. Franzke; Christof Holzer | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ab4cf2f5524a6b8414948d/original/impact-of-the-current-density-on-paramagnetic-nmr-properties.pdf |
631025e9d147b20ac3c05c9d | 10.26434/chemrxiv-2022-dcqc3 | Reductive Activation of N2 using a Calcium/Potassium Bimetallic System Supported by an Extremely Bulky Diamide Ligand | An extremely bulky xanthene bridged diamide ligand (TCHPNON = 4,5-bis(2,4,6-tricyclohexylanilido)-2,7-diethyl-9,9-dimethyl-xanthene) has been developed and used to prepare two monomeric diamido-calcium complexes [(TCHPNON)Ca(D)n] (D = THF, n = 2, 3; D = toluene, n = 1, 4). Reduction of 4 with 5% w/w K/KI under an N2 atmosphere gave the first well-defined, anionic s-block complex of activated dinitrogen, [{K(TCHPNON)Ca}2(-2:2-N2)] 5, presumably via a transient calcium(I) intermediate. | Rahul Mondal; Yuvaraj Kuppusamy; Thayalan Rajeshkumar; Laurent Maron; Cameron Jones | Inorganic Chemistry; Organometallic Chemistry; Main Group Chemistry (Inorg.); Small Molecule Activation (Inorg.); Theory - Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631025e9d147b20ac3c05c9d/original/reductive-activation-of-n2-using-a-calcium-potassium-bimetallic-system-supported-by-an-extremely-bulky-diamide-ligand.pdf |
6233d0ce13d478a50592892b | 10.26434/chemrxiv-2022-n4bsw | Ir-Catalyzed Asymmetric Allylic Alkylation of Dialkyl Malo-nates Enabling the Construction of Enantioenriched All-Carbon Quaternary Centers | ABSTRACT: An enantioselective iridium-catalyzed allylic alkylation of malonates with trisubstituted allylic electro-philes to form all-carbon quaternary stereocenters is reported. This cross-coupling reaction features unprecedented reactivity at ambient temperature, particularly for challenging fully alkyl-substituted allylic electrophiles, and ena-bles the preparation of a wide range of enantioenriched products in up to 93% yield and 97% ee. The products of this transformation can be readily converted to a number of valuable building blocks including vicinal quaternary stereodiads and β-quaternary acids. This method was also used to prepare an enantioenriched intermediate facilitat-ing the asymmetric formal synthesis of the sporochnol family of natural products. | Farbod Moghadam; Elliot Hicks; Zachary Sercel; Alexander Cusumano ; Michael Bartberger ; Brian Stoltz | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry | CC BY NC 4.0 | CHEMRXIV | 2022-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6233d0ce13d478a50592892b/original/ir-catalyzed-asymmetric-allylic-alkylation-of-dialkyl-malo-nates-enabling-the-construction-of-enantioenriched-all-carbon-quaternary-centers.pdf |
6167a17d8b620d1a974ecd69 | 10.26434/chemrxiv-2021-6d2bp | Multi-fidelity prediction of molecular optical peaks with deep learning | Optical properties are central to molecular design for many applications, including solar cells and biomedical imaging. A variety of ab initio and statistical methods have been developed for their prediction, each with a trade-off between accuracy, generality, and cost. Existing theoretical methods such as time-dependent density functional theory (TD-DFT) are generalizable across chemical space because of their robust physics-based foundations but still exhibit random and systematic errors with respect to experiment despite their high computational cost. Statistical methods can achieve high accuracy at a lower cost, but data sparsity and unoptimized molecule and solvent representations often limit their ability to generalize. Here, we utilize directed message passing neural networks (D-MPNNs) to represent both dye molecules and solvents for predictions of molecular absorption peaks in solution. Additionally, we demonstrate a multi-fidelity approach based on an auxiliary model trained on over 28,000 TD-DFT calculations that further improves accuracy and generalizability, as shown through rigorous splitting strategies. Combining several openly-available experimental datasets, we benchmark these methods against a state-of-the-art regression tree algorithm and compare the D-MPNN solvent representation to several alternatives. Finally, we explore the interpretability of the learned representations using dimensionality reduction and evaluate the use of ensemble variance as an estimator of the epistemic uncertainty in our predictions of molecular peak absorption in solution. The prediction methods proposed herein can be integrated with active learning, generative modeling, and experimental workflows to enable the more rapid design of molecules with targeted optical properties. | Kevin Greenman; William Green; Rafael Gómez-Bombarelli | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2021-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6167a17d8b620d1a974ecd69/original/multi-fidelity-prediction-of-molecular-optical-peaks-with-deep-learning.pdf |
673f02a57be152b1d019c196 | 10.26434/chemrxiv-2024-t6zqq | Molecular rotors are loud, highly photostable, NIR/SWIR-active molecular optoacoustic contrast agents | Optoacoustic or photoacoustic imaging (PA) combines optical excitation with acoustic readout, for non-invasive in vivo imaging at up to several centimetres' penetration depth, and down to micron resolution. Conceptually, many chromophore types can be used for simple anatomical PA, where signal generation is the only requirement: but few can perform the more complex task of molecular imaging of enzyme activity in practice, for which the many requirements include enzymatic signal switch-on. Here, we leverage molecular rotors to give a rational blueprint for high-performance small molecule PA contrast agents in the NIR/SWIR biotransparency window that offer straightforward adaptation for molecular imaging. According to our hypothesis, the ultrafast nonradiative S1→S0 kinetics (knr) of triphenylmethane rotors would be the chemical key to their PA signal (loudness) being strong, linear against imaging intensity, and outstandingly photostable. After we identified a route to shift typically the green/red absorbance of triarylmethanes into the NIR/SWIR, we showed that they are indeed >1000-fold more photostable as well as >5-fold louder than typical reference chromophores for PA. Pioneering femtosecond transient absorption spectroscopy results in live cells, as a bridge from spectroscopy to biology, supported our conceptual approach of maximising knr to optimise the several key practical aspects of PA performance. Much like molecular switches, molecular rotors had only been used in a limited scope of imaging modalities to date. This approach now shows the potential of rotors for quantitative longitudinal PA; and more broadly, the results will guide the future of mechanism-based design in rationally improving dye performance in a range of basic and translational imaging methods. | Markus Müller; Abha Valavalkar; Vipul Gujrati; Jan P. Prohaska; Divyesh Shelar; Michaela Kaltenegger; Benjamin Dietzek- Ivanšić; Vasilis Ntziachristos; Oliver Thorn-Seshold | Physical Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Photochemistry (Org.); Chemical Biology; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673f02a57be152b1d019c196/original/molecular-rotors-are-loud-highly-photostable-nir-swir-active-molecular-optoacoustic-contrast-agents.pdf |
649a172aba3e99daef175951 | 10.26434/chemrxiv-2023-gjjzs | Thermally Activated Delayed Fluorescence and High-contrast Mechanochromism of Anthrone-Based Donor-Acceptor Systems | The development of materials that emit in the deep red to near-infrared region of the spectrum has attracted significant attention on account of their potential as optical sensing and imaging reagents in biology. We report herein the synthesis and optoelectronic characterization of four anthraquinone-based emitters T-tBuCz-AQ, T-MeOCz-AQ, C-tBuCz-AQ, and C-MeOCz-AQ, and two pyrazoloanthrone-based emitters tBuCz-PA and DMAC-PA. Depending on the donor, these compounds emit between 640-750 nm in the neat film, while the emission of the 10 wt% doped films in PMMA are blue-shifted to between 600-700 nm and have low photoluminescence quantum yields of between 2.6-6.6%. Of these compounds, T-tBuCz-AQ, T-MeOCz-AQ, and C-tBuCz-AQ exhibited thermally activated delayed fluorescence in 10 wt% doped films in PMMA, while the crystals of T-tBuCz-AQ also showed TADF. Compound tBuCz-PA showed high-contrast and reversible PL response upon mechanical grinding and hexane fuming. | Sudhakar Pagidi; Alexandra Slawin; Eli Zysman-Colman | Organic Chemistry; Physical Organic Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649a172aba3e99daef175951/original/thermally-activated-delayed-fluorescence-and-high-contrast-mechanochromism-of-anthrone-based-donor-acceptor-systems.pdf |
64ad80176e1c4c986b3527bc | 10.26434/chemrxiv-2023-1823h | Determining and controlling conformational information from orientationally selective Light-Induced Triplet–Triplet Electron Resonance spectroscopy for a set of bis-porphyrin rulers | We recently reported a new technique, light-induced triplet–triplet electron resonance spectroscopy (LITTER), which allows quantification of the dipolar interaction between the photogenerated triplet states of two chromophores. Here we carry out a systematic LITTER study, considering orientation selection by the detection pulses, of a series of bis-porphyrin model peptides with different porphyrin–porphyrin distances and relative orientations. Orientation-dependent analysis of the dipolar datasets yields conformational information of the molecules in frozen solution which is in good agreement with density functional theory predictions. Additionally, a fast partial orientational-averaging treatment produces distance distributions with minimized orientational artefacts. Finally, by direct comparison of LITTER data to double electron–electron resonance (DEER) measured on a system with Cu(II) coordinated into the porphyrins, we demonstrate the advantages of the LITTER technique over the standard DEER methodology. This is due to the remarkable spectroscopic properties of the photogenerated porphyrin triplet state. This work sets the basis for the use of LITTER in structural investigations of unmodified complex biological macromolecules, which could be combined with Förster resonance energy transfer and microscopy inside cells. | Arnau Bertran; Marta De Zotti; Christiane Timmel; Marilena Di Valentin; Alice Bowen | Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ad80176e1c4c986b3527bc/original/determining-and-controlling-conformational-information-from-orientationally-selective-light-induced-triplet-triplet-electron-resonance-spectroscopy-for-a-set-of-bis-porphyrin-rulers.pdf |
60c74c7eee301c7f38c7a0ae | 10.26434/chemrxiv.12413411.v2 | Ultrathin Carbon Nanosheets for Highly-efficient Capacitive K-ion and Zn-ion Storage | <p></p><p>Porous
carbon has attracted extensive attentions as the electrode material for various
energy storage devices considering its advantages like high theoretical
capacitance/capacity, high conductivity, low cost and earth abundant inherence.
However, there still exists some disadvantages limiting its further
applications, such as the tedious fabrication process, limited metal-ion
transport kinetics and undesired structure deformation at harsh electrochemical
conditions. Herein, we report a facile strategy, with calcium gluconate firstly
reported as the carbon source, to fabricate ultrathin porous carbon nanosheets.
<a>The as-prepared Ca-900 electrode delivers excellent K-ion
storage performance including high reversible capacity (430.7 mAh g<sup>-1</sup>),
superior rate capability (154.8 mAh g<sup>-1</sup> at an ultrahigh current
density of 5.0 A g<sup>-1</sup>) and ultra-stable long-term cycling stability
(a high capacity retention ratio of ~81.2% after 4000 cycles at 1.0 A g<sup>-1</sup>).
</a>Similarly, when being applied in Zn-ion capacitors, the Ca-900 electrode
also exhibits an ultra-stable cycling performance with ~90.9% capacity retention
after 4000 cycles at 1.0 A g<sup>-1</sup>, illuminating the applicable potentials.
Moreover, the origin of the fast and smooth metal-ion storage is also revealed
by carefully designed consecutive CV measurements. Overall, considering the
facile preparation strategy, unique structure, application flexibility and
in-depth mechanism investigations, this work will deepen the fundamental
understandings and boost the commercialization of high-efficient energy storage
devices like potassium-ion/sodium-ion batteries, zinc-ion batteries/capacitors and
aluminum-ion batteries.</p><br /><p></p> | Yamin Zhang; Zhongpu Wang; Deping Li; Qing Sun; Kangrong Lai; kaikai Li; Qunhui Yuan; Xingjun Liu; Lijie Ci | Carbon-based Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c7eee301c7f38c7a0ae/original/ultrathin-carbon-nanosheets-for-highly-efficient-capacitive-k-ion-and-zn-ion-storage.pdf |
60c7507e702a9b585c18bdb3 | 10.26434/chemrxiv.13023164.v1 | Comment on “Boosted Molecular Mobility During Common Chemical Reactions" | The apparent “boosted mobility” observed by nuclear magnetic resonance (NMR) diffusion measurements is the result of a known artefact. When signal intensities are changing during an NMR diffusion measurement for reasons other than diffusion, the use of monotonically increasing gradient amplitudes produces erroneous diffusion coefficient values. We show that no boosted molecular mobility is observed when shuffled gradient amplitudes are applied. | Jan-Philipp Günther; Lucy Fillbrook; Thomas MacDonald; Günter Majer; William S. Price; Peer Fischer; Jonathon Beves | Chemical Kinetics; Physical and Chemical Processes; Solution Chemistry; Spectroscopy (Physical Chem.); Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7507e702a9b585c18bdb3/original/comment-on-boosted-molecular-mobility-during-common-chemical-reactions.pdf |
668fe9e4c9c6a5c07af9f9c7 | 10.26434/chemrxiv-2024-8wvw0 | The influence of the crystal sponge framework on guest molecule conformation | The crystalline sponge (CS) method has become an important technique for structural elucidation of compounds that are challenging to crystallise. However, the impact of the CS environment on guest molecule conformations has not been systematically studied. We present a computational investigation of the conformations of organic molecules of varying flexibility in a set of experimentally determined CS structures, comparing them to gas phase conformers and, where available, pure and co-crystal structures. Via solid state and molecular density functional theory calculations, we quantify the total relative energy, conformational energy, and intramolecular strain of guest molecules, as well as framework strain. Our results show that while CS structures induce some distortion in guest geometries (total relative energies up to 41 kJ/mol), they generally adopt low-energy conformations, often within 2 kJ/mol of the global energy minimum. Intramolecular strain in CS structures is often lower than in conventional crystal structures, suggesting a more neutral packing environment where molecules are closer to their favoured isolated-molecule geometries. We also observe that multiple guests can influence each other's geometries, even in the absence of direct guest-guest interactions. These findings provide a quantification of conformational distortion that can form the basis for interpreting molecular geometries obtained from CS structures. | Eleanor Soper; Simon Coles; Graeme Day | Theoretical and Computational Chemistry; Analytical Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668fe9e4c9c6a5c07af9f9c7/original/the-influence-of-the-crystal-sponge-framework-on-guest-molecule-conformation.pdf |
65b9e73a66c1381729a0932d | 10.26434/chemrxiv-2024-q2784 | Highly Efficient Circularly Polarized Near-infrared Phosphorescence in Both Solution and Aggregate | Circularly polarized phosphorescence (CPP) is a spin-forbidden radiative process with chiroptical activity. The CPP mechanism is far from comprehensively understood, mainly due to the limited examples of efficient triplet emission from small chiral organic molecules with well-defined structures. Herein, a pair of chiral enantiomers R/S-BBTI is reported, featuring the highly distorted spiral ring-locked heteroaromatics with heavy iodine atoms. These chiral molecules emit NIR phosphorescence and exhibit considerable high dissymmetry factors up to 0.013 with an efficiency of 4.2% and a lifetime of 119 μs in dimethyl sulfoxide (DMSO) solution after ultraviolet irradiation. Their crystals show efficient CPP with 7.0% quantum efficiency and a lifetime of 166 μs. Extensive experimental chiroptical investigations combined with theoretical calculations reveal an efficient spin-flip process that modulates the electron and magnetic transition dipole moments to enhance CPP performance. Moreover, the phosphorescence of R/S-BBTI is oxygen-sensitive and photoactivated in DMSO. Therefore, R/S-BBTI can be applied for hypoxia imaging in cells and tumors, expanding the scope of CPP applications. | Dan Liu; Wenjin Wang; Parvej Alam; Zhan Yang; Kaiwen Wu; Lixun Zhu; Yu Xiong; Shuai Chang; Yong Liu; Bo Wu; Qian Wu; Zijie Qiu; Zheng Zhao; Ben Zhong Tang | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b9e73a66c1381729a0932d/original/highly-efficient-circularly-polarized-near-infrared-phosphorescence-in-both-solution-and-aggregate.pdf |
60c73ed5337d6c3a43e263e0 | 10.26434/chemrxiv.7096331.v1 | On the Charging of Carboxylic Acid Monolayers with Monovalent Ions at Low Ionic Strengths: Molecular Insight Revealed by Vibrational Sum Frequency Spectroscopy | The charging of arachidic acid Langmuir monolayers as a function of subphase pH and monovalent ion concentration below 100 mM was investigated using vibrational sum frequency spectroscopy. Molecular information was obtained by targeting the vibrational modes of the carboxylic acid headgroups, alkyl chains, and water molecules in the immediate surface and diffuse double layers. The surface charge in the monolayer was experimentally determined by monitoring the hydrated carboxylate stretching modes. The charging behaviour was found to be in excellent agreement with that predicted by Gouy-Chapman theory using a thermodynamic pKa of 5.1 ± 0.2. This resulted in an apparent pKa of ~10.8 when the only ions present in solution were those associated with adjusting the pH. Water molecules with a preferred orientation in the immediate surface region were found to primarily interact with the uncharged carboxylic acid moiety, decreasing in number as the monolayer further deprotonated. Contributions from water molecules in the diffuse double layer, partly aligned by the exponentially decaying surface electric field, closely followed the predictions of a recently proposed theoretical framework that accounts for interference and screening effects. Finally, the charging of the monolayer was experimentally found to be independent of the identity of either the monovalent cation (i.e., Li+, Na+, Rb+) or anion (i.e., F-, Cl-, I-) at low salt concentrations. | Eric Tyrode; Robert W. Corkery | Interfaces; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Surface; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed5337d6c3a43e263e0/original/on-the-charging-of-carboxylic-acid-monolayers-with-monovalent-ions-at-low-ionic-strengths-molecular-insight-revealed-by-vibrational-sum-frequency-spectroscopy.pdf |
653f3a0ca8b423585a8d0b0d | 10.26434/chemrxiv-2023-t5r6n | Structural hysteresis of dilute fluorine salt aqueous solutions | In contrast with the generally accepted picture for most of the dilute salt aqueous solutions, which defaults that only one structural state/form exists at the given values of system/thermodynamic parameters, in this work, combining characterization of 19F nuclear magnetic resonance, ultraviolet-visible spectroscopies with theoretical calculations, we found that the F−-bearing aqueous solutions with identical component, but prepared by both different pathways, one of which is by mixing subsaturated MF2 solutions and Na//ClO4−(SO42−) solutions (path 1) and another is by mixing concentrated M2+//ClO4−(SO42−) solutions (M = Zn, Cd, Co and Cu) and NaF solution (path 2), can long-termly exist spectrographic distinguishable different thermodynamic steady states, in which the F− in the former preferentially exists in the form of more M2+-F− contact ion pairs (CIP), whereas in the form of more, even all M2+-F− solvent-separated/shared ion pairs (SIP) for the latter. This results from the different solution initial states, where path 1 solutions contain certain amounts of CIPs, whereas there is no CIPs initially in path 2 solutions, the high energy barrier of conversion between SIP and CIP, coupling with the low concentration gradient and thereby small conversion driving force. This makes the solutions exhibit an unusual “apparent” structural hysteresis. Due to the universality of the causes, present findings can expand to other sparingly soluble salts and enhance the significance of solution preparation bias on the thermodynamic studies in solution chemistry domain of sparingly soluble salts. | Ning Zhang; Shaoheng Wang; Qiongqiong Luo; Jianfeng Tang; Dewen Zeng | Physical Chemistry; Chemical Kinetics; Solution Chemistry; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653f3a0ca8b423585a8d0b0d/original/structural-hysteresis-of-dilute-fluorine-salt-aqueous-solutions.pdf |
67451012f9980725cfee32ad | 10.26434/chemrxiv-2024-nhcl8 | Photo-Induced Electron-Nuclear Dynamics of Fullerene and Its Monolayer Networks in Solvated Environments | The recently-synthesized monolayer fullerene network in a quasi-hexagonal phase (qHP-C60) exhibits superior electron mobility and optoelectronic properties compared to molecular fullerene (C60), making it highly promising for a variety of applications. However, the microscopic carrier dynamics of qHP-C60 remain unclear, particularly in realistic environments, which are of significant importance for applications in optoelectronic devices. Unfortunately, traditional $ab~initio$ methods are prohibitive for capturing the real-time carrier dynamics of such large systems due to their high computational cost. In this work, we present the first real-time electron-nuclear dynamics study of qHP-C60 using velocity-gauge density functional tight binding, which enables us to perform several picoseconds of excited-state electron-nuclear dynamics simulations for nanoscale systems with periodic boundary conditions. When applied to C60, qHP-C60, and their solvated counterparts, we demonstrate that water/moisture significantly increases the electron-hole recombination time in C60 but has little impact on qHP-C60. Our excited-state electron-nuclear dynamics calculations show that qHP-C60 is extremely unique and enable an exploration of time-resolved dynamics for understanding excited-state processes of large systems in complex, solvated environments. | Qiang Xu; Daniel Weinberg; Mahmut Okyay; Min Choi; Mauro Del Ben; Bryan Wong | Theoretical and Computational Chemistry; Materials Science; Nanoscience; Carbon-based Materials; Nanostructured Materials - Nanoscience; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67451012f9980725cfee32ad/original/photo-induced-electron-nuclear-dynamics-of-fullerene-and-its-monolayer-networks-in-solvated-environments.pdf |
60c73e57ee301c2602c786ee | 10.26434/chemrxiv.6870830.v1 | Boehmite Nanofiber-Reinforced Resorcinol-Formaldehyde Macroporous Monoliths for Heat/Flame Protection | By distributing boehmite nanofibers (BNFs) to a resorcinol-formaldehyde (RF) skeletal phase formed by phase separation in an aqueous sol, composite macroporous monoliths have been produced. The nanofiber reinforced monoliths have a skeleton in which BNF is arranged in parallel within the RF structure, and showed high Young's modulus against uniaxial compression for their bulk density. These materials can be expected to be applied to heat/flame protection materials using heat insulating properties and high flame resistance.<br /> | Gen Hayase | Fire-Resistant Materials; Hybrid Organic-Inorganic Materials; Thermal Conductors and Insulators | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e57ee301c2602c786ee/original/boehmite-nanofiber-reinforced-resorcinol-formaldehyde-macroporous-monoliths-for-heat-flame-protection.pdf |
663e068e418a5379b0ee28b6 | 10.26434/chemrxiv-2024-qsvv5 | Cavitation as a zero-waste circular economy process to convert citrus processing waste into biopolymers in high demand | Acoustic cavitation applied to untreated citrus processing waste converts it in one pot in highly bioactive “IntegroPectin” pectin and highly micronized cellulose “CytroCell” of low crystallinity. Starting from pigmented sweet orange (Citrus sinensis) biowaste, we use an industrial sonicator to demonstrate the general viability of cavitation carried out in water only as a zero-waste circular economy process to convert an abundant agro-industrial waste in two biopolymers in high and increasing demand for multiple applications. | Rosaria Ciriminna; Giuseppe Angellotti; Giovanna Li Petri; Francesco Meneguzzo; Cristina Riccucci; Gabriella Di Carlo; Mario Pagliaro | Materials Science; Agriculture and Food Chemistry; Biological Materials; Nanostructured Materials - Materials | CC BY NC 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663e068e418a5379b0ee28b6/original/cavitation-as-a-zero-waste-circular-economy-process-to-convert-citrus-processing-waste-into-biopolymers-in-high-demand.pdf |
60f6488e8f6bf663216fa81a | 10.26434/chemrxiv-2021-c3w1l-v2 | A Comparative Study of Marginalized Graph Kernel and Message Passing Neural Network | <p>This work proposes a state-of-the-art hybrid kernel to calculate molecular similarity. Combining with Gaussian process models, the performance of the hybrid kernel in predicting molecular properties is comparable to that of the Directed Message Passing Neural Network (D-MPNN). The hybrid kernel consists of a marginalized graph kernel (MGK) and a radial basis function (RBF) kernel that operates on molecular graphs and global molecular features, respectively. Bayesian optimization was used to get the optimal hyperparameters for both models. The comparisons are performed on 11 publicly available data sets. Our results show that the predictions of both models are correlated with similar performance, and the ensemble prediction of both models performs better than either of them. Through principal component analysis, we found that the features extracted by the hybrid kernel are similar to those extracted by D-MPNN. The advantage of D-MPNN lies in computational efficiency, while the advantage of the graph kernel models lies in the inherent uncertainty quantification and accurate uncertainty quantification. All codes for graph kernel machines used in this work can be found at <a href="https://github.com/Xiangyan93/Chem-Graph-Kernel-Machine">https://github.com/Xiangyan93/Chem-Graph-Kernel-Machine</a>.</p> | Yan Xiang; Yu-Hang Tang; Guang Lin; Huai Sun | Theoretical and Computational Chemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f6488e8f6bf663216fa81a/original/a-comparative-study-of-marginalized-graph-kernel-and-message-passing-neural-network.pdf |
67a0b9e76dde43c90874a693 | 10.26434/chemrxiv-2025-g8q8d | [5]Cumulene Bridged Tri(9-anthryl)methyl Dimer | Towards the synthesis and evaluation of stable radical-based 2D frameworks, a diacetylene-bridged tri(9-anthryl)methyl (TAntM) radical dimer was designed and synthesized. X-ray crystallographic analysis revealed a strong spin-spin interaction between TAntM radical units through the diacetylene linker, resulting in a closed-shell [5]cumulene structure as the stable form. Variable-temperature (VT) 1H-NMR measurements at high temperatures showed signal broadening for aromatic protons, indicating an increased population of thermally excited triplet species as a metastable form. To facilitate spin-state modulation by external stimuli, mechanical grinding in the solid state was conducted. Due to its reactivity, mechanical grinding partially induced structural changes to radical species in the solid state. | Tomohiko Nishiuchi; Shino Takeuchi; Takashi Kubo | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a0b9e76dde43c90874a693/original/5-cumulene-bridged-tri-9-anthryl-methyl-dimer.pdf |
67dc6edb6dde43c9089ca6d8 | 10.26434/chemrxiv-2024-f9bv7-v2 | Long Molecular Wires and the Auto-ionization of Water | Water auto-ionization is critical in a wide range of chemical, biological, physical, and industrial processes. In this work, we describe a series of hitherto unknown collective molecular processes leading to auto-ionization. Specifically, by combining machine-learned interatomic potentials and spectral adaptive biasing force techniques, we determine the relevant free energy landscape of water auto-ionization. At ambient conditions, the free energy profile reveals two distinct saddle points, each leading to the formation of three- and four-member water wires. The wires feature an individual Zundel ion and a proton diffusion-like transition state, respectively. At elevated temperatures, the auto-ionization process exhibits a more concerted hydrogen transfer mechanism and reveals an alternative pathway involving the synchronous diffusion of Zundel ion pairs, with the ion pair corresponding to an energetic local minimum on the free energy surface. These findings help resolve long-standing conflicting views of the mechanism of water auto-ionization and provide new avenues for the study of proton behavior in different aqueous environments. | Yinan Xu; Samuel Varner; Yezhi Jin; Gustavo Pérez-Lemus; Joan Montes de Oca; Paul Nealey; Seth Darling; Zhen-Gang Wang; Juan de Pablo | Physical Chemistry; Inorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dc6edb6dde43c9089ca6d8/original/long-molecular-wires-and-the-auto-ionization-of-water.pdf |
64eefd823fdae147fa1fa210 | 10.26434/chemrxiv-2023-w73hw | A simple method for rheological measurements of air sensitive samples | Rheology of air- or moisture sensitive liquids, gels, and glasses requires expensive and complicated rheometer-in-glovebox laboratory setups. Here, we demonstrate the use of a heavy-than-air cover gas, sulfur hexafluoride, and the design of a cheap and simple cover gas container that can attach to the lower geometry plate of any rheometer in order to carry out rheology experiments on air-sensitive liquids and soft solids. Rheological measurements of titanium(IV) propoxide, a moisture-from-air reactive liquid, are shown to demonstrate the effectiveness of the cover-gas method on acquiring correct temperature dependent viscosity data of the sample in the absence of polymeric reaction products. | Ben Russell; Klaas Wynne | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64eefd823fdae147fa1fa210/original/a-simple-method-for-rheological-measurements-of-air-sensitive-samples.pdf |
6776c8d0fa469535b98fada4 | 10.26434/chemrxiv-2025-4n2nb | Design of Partial Agonists of ADAMTS Metalloproteinases as Therapeutics for Neurodegenerative Diseases | Neurodegenerative diseases (NDDs) are characterized by progressive neuronal dysfunction and structural instability, precipitated by aberrations in extracellular matrix (ECM) remodeling and chronic neuroinflammation. The ADAMTS family of metalloproteinases plays a key role in regulating ECM dynamics and neuroinflammatory responses, with dysregulation of specific isoforms contributing to the pathology of NDDs such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis. This article proposes the development of partial agonists targeting ADAMTS enzymes as a novel therapeutic approach for managing NDDs. By selectively modulating enzymatic activity, partial agonists could mitigate pathological ECM degradation while preserving essential protease functions. Structural scaffolds for partial agonist development are discussed, leveraging insights from bioisosteric design and computational methodologies. Additionally, advanced drug delivery platforms and preclinical validation paradigms are explored to address translational challenges. The integration of emerging technologies and modeling strategies is highlighted as a means to overcome current limitations and enhance the precision of ADAMTS-targeting therapies. | David Ferguson, MRSB MRSC | Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Cell and Molecular Biology | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6776c8d0fa469535b98fada4/original/design-of-partial-agonists-of-adamts-metalloproteinases-as-therapeutics-for-neurodegenerative-diseases.pdf |
62aa0c4ce00d4ea1502b9999 | 10.26434/chemrxiv-2022-rc6hb | Bioinspired Intramolecular Diels-Alder Cycloaddition for the Total Synthesis of Ophiorrhine A via Ophiorrhine G and Ophiorrhiside E | We report the first total synthesis of the monoterpene indole alkaloids ophiorrhine A via a late stage bioinspired intramolecular Diels-Alder cycloaddition to form the intricate bridged and spirannic polycyclic system. Several strategies were investigated to construct the indolopyridone moiety of ophiorrhiside E, the postulated biosynthetic precursor of ophiorrhine A. Eventually, the Friedel-Crafts-type coupling of indolyl-acetamide with secologanin-derived acid chloride delivered ophiorrhine G. Cyclode-hydratation of a protected form of the latter was followed by the desired spontaneous intramolecular Diels-Alder cycloaddition of protected ophiorrhiside E leading to ophiorrhine A. | Wei Cao; Yingchao Dou; Cyrille Kouklovsky; GUILLAUME VINCENT | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62aa0c4ce00d4ea1502b9999/original/bioinspired-intramolecular-diels-alder-cycloaddition-for-the-total-synthesis-of-ophiorrhine-a-via-ophiorrhine-g-and-ophiorrhiside-e.pdf |
660c680866c138172981cccd | 10.26434/chemrxiv-2024-sscbn | A modified all-in-one DMSO-activating and base releasing reagent for the Parikh-Doering-type benzylic oxidation reaction | The Parikh-Doering reaction, an example of the series of DMSO-mediated selective oxidation named reaction family, finds ongoing use in natural product synthesis when mild oxidative reaction conditions are required. The original conditions require the use of Py-SO3 and NEt3 along with DMSO and DCM. As part of our ongoing interest in sulfating agents, we recently disclosed the novel structure of tributylsulfoammonium betaine (TBSAB) that has a formal N-S bond (not dative) and may indicate that other N(sp3) amine-SO3 complexes have been misassigned.
Herein, we explore a commercial sulfating agent, triethylamine-sulfur trioxide complex, as an all-in-one sulfation and base releasing reagent for a modified Parikh-Doering reaction. Single crystal X-ray crystallography further confirms our hypothesis than triethylamine-sulfur trioxide complex exists as triethylsulfoammonium betaine (TESAB). Employing TESAB as an all-in-one reagent, a range of primary and secondary alcohols were screened for competency. Reactivity was observed for the first time with 1) a non Py-SO3 sulfating agent and 2) without the need for additional base. Moderate to good yields of aldehydes and ketones can be prepared in an atom-efficient improvement with concomitant removal of toxic pyridine by-products.
| Jiaqian Xie; Louise Male; Alan Jones | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660c680866c138172981cccd/original/a-modified-all-in-one-dmso-activating-and-base-releasing-reagent-for-the-parikh-doering-type-benzylic-oxidation-reaction.pdf |
67d832ad6dde43c9082019ab | 10.26434/chemrxiv-2025-hm2fc | Amino Acid Profile of Selected Arthropod Hemolymph in Zaria, Kaduna State, Nigeria | Arthropods have been studied for their anti-viral ability, anti-parasitic ability and anti-cancer ability. These abilities possessed by arthropods depend on the presence of amino acid in hemolymph to fight and also protect themselves against abilities infection. In this study, arthropods were collected from the field in Zaria using suitable/appropriate trapping and sampling techniques. The hemolymph was collected from scorpion, beetle, grasshopper, butterfly, cricket, cockroach, spider and crab using novel Antennae method of hemolymph sampling that involved ollection of hemolymph was carried out with micropipettes and drops collected was transferred into Eppendorf tubes (on ice) and kept in freezing (-11oC) compartment of ordinary refrigerator prior to use. The amino acid profile of hemolymph was carried out using microkjeldahl method. The results of the study revealed the presence of leucine, lysine, isoleucine, phenylalanine, serine, aspartic acid, valine, methionine, proline, arginine, histidine, cystine, alanine, glutamic acid, glycine and threonine in the arthropod’s hemolymph studied. Glutamic acid was found to be the most abundant in spider (5.08g/100g) while cystine was the least abundant in cricket (0.02 g/100g). | jocelyn Agbanu; Umar Yahaya Abdullahi; Vantsawa Philip Anthony; Dikwa Karderem Bukar; Garba Umaru Musa | Biological and Medicinal Chemistry; Cell and Molecular Biology; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2025-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d832ad6dde43c9082019ab/original/amino-acid-profile-of-selected-arthropod-hemolymph-in-zaria-kaduna-state-nigeria.pdf |
60c745e9567dfe01abec452e | 10.26434/chemrxiv.10288514.v1 | Scalable Approach to High Coverages on Oxides via Iterative Training of a Machine-Learning Algorithm | Understanding the interaction of multiple types of adsorbate molecules on solid surfaces is crucial to establishing the stability of catalysts under various chemical environments. Computational studies on the high coverage and mixed coverages of reaction intermediates are still challenging, especially for transition-metal compounds. In this work, we present a framework to predict differential adsorption energies and identify low-energy structures under high- and mixed-adsorbate coverages on oxide materials. The approach uses Gaussian process machine-learning models with quantified uncertainty in conjunction with an iterative training algorithm to actively identify the training set. The framework is demonstrated for the mixed adsorption of CH<sub>x</sub>, NH<sub>x</sub> and OH<sub>x</sub> species on the oxygen vacancy and pristine rutile TiO<sub>2</sub>(110) surface sites. The results indicate that the proposed algorithm is highly efficient at identifying the most valuable training data, and is able to predict differential adsorption energies with a mean absolute error of ~0.3 eV based on <25% of the total DFT data. The algorithm is also used to identify 76% of the low-energy structures based on <30% of the total DFT data, enabling construction of surface phase diagrams that account for high and mixed coverage as a function of the chemical potential of C, H, O, and N. Furthermore, the computational scaling indicates the algorithm scales nearly linearly (N<sup>1.12</sup>) as the number of adsorbates increases. This framework can be directly extended to metals, metal oxides, and other materials, providing a practical route toward the investigation of the behavior of catalysts under high-coverage conditions. | Andrew Medford; Shengchun Yang; Fuzhu Liu | Catalysts | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745e9567dfe01abec452e/original/scalable-approach-to-high-coverages-on-oxides-via-iterative-training-of-a-machine-learning-algorithm.pdf |
63fd7057897b18336f3a422c | 10.26434/chemrxiv-2023-sc37c | An Integrated Covalent Drug Design Workflow using Site-Identification by Ligand Competitive Saturation | Covalent drug design is an important component in drug discovery. Traditional drugs interact with their target in a reversible equilibrium while irreversible covalent drugs increase the drug-target interaction duration by forming a covalent bond with targeted residues, and thus may offer a more effective therapeutic approach. To facilitate the design of this class of ligands, computational methods can be used to help identify reactive nucleophilic residues, frequently cysteines, on a target protein for covalent binding, to test various warhead groups for their potential reactivity, and to predict non-covalent contributions to binding that can facilitate drug-target interactions that are important for binding specificity. To further aid covalent drug design, we extended a functional group mapping approach based on explicit solvent all-atom molecular simulations (SILCS: Site Identification by Ligand Competitive Saturation) that intrinsically considers protein flexibility, functional group and protein desolvation along with functional group-protein interactions. Through docking of a library of representative warhead fragments using SILCS-Monte Carlo (SILCS-MC), reactive cysteines can be correctly identified for proteins being tested. Furthermore, a machine learning model was trained to quantify the effectiveness of various warhead groups for proteins using metrics from SILCS-MC as well as experimental model compound warhead reactivity data. The ability to rank covalent molecular binders with similar warheads using SILCS ligand grid free energy (LGFE) ranking was also tested for several proteins. Based on these tools, an integrated SILCS based workflow was developed, named SILCS-Covalent, that can both qualitatively and quantitatively inform covalent drug discovery. | Wenbo Yu; David J. Weber; Alexander D. MacKerell | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fd7057897b18336f3a422c/original/an-integrated-covalent-drug-design-workflow-using-site-identification-by-ligand-competitive-saturation.pdf |
644b50bf0d87b493e368ea6a | 10.26434/chemrxiv-2023-h7h38 | A route to potent, selective and biased salvinorin chemical space | The salvinorins serve as templates for next generation analgesics, antipruritics and dissociative hallucinogens via selective and potent agonism of the kappa-opioid receptor (KOR). In contrast to most opioids, the salvinorins lack basic amines and bind with high affinity and selectivity via complex polyoxygenated scaffolds that have frustrated deep-seated modification by synthesis. Here we describe a short asymmetric synthesis that relies on a sterically-confined organocatalyst to dissociate acidity from reactivity and effect Robinson annulation of an unactivated nucleophile / unstable electrophile pair. Combined with a cobalt-catalyzed polarized diene-alkyne cycloaddition, the route allows divergent access to a focused library of salvinorins. We appraise the synthesis by its generation of multiple analogs that exceed the potency, selectivity, stability and functional bias of salvinorin A itself. | Sarah Hill; Nathan Dao; Vuong Dang; Edward Stahl; Laura Bohn; Ryan Shenvi | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644b50bf0d87b493e368ea6a/original/a-route-to-potent-selective-and-biased-salvinorin-chemical-space.pdf |
6543be6148dad23120eff293 | 10.26434/chemrxiv-2023-tcnvf | Reshaping Echinocandin Antifungal Drugs to Circumvent Glucan Synthase Point Mutation-Mediated Resistance | Echinocandins are important antifungal drugs that inhibit the activity of the membrane-bound glucan synthase complex, which is responsible for the synthesis of the fungal cell wall β-(1,3)-glucan. Echinocandin resistance, linked to mutations in Fks, the catalytic subunit of the glucan synthase complex, is on the rise, particularly in Candida species, the most common human fungal pathogens. In this study, we used molecular docking experiments between echinocandins and the recently reported structure of Fks to propose a model in which these drugs form a ternary complex with the enzyme and membrane lipids. We then used site-selective reductive dehydration of alcohols to generate dehydroxylated echinocandin derivatives, which we evaluated against a panel of Candida strains constructed by introducing resistance-conferring mutations. We found that removing the hemiaminal alcohol that drives alterations in the three-dimensional structures of the echinocandin reduced their efficacy. Conversely, eliminating the benzylic alcohol of echinocandins enhanced their efficacy by up to two orders of magnitude, depending on the resistance-conferring mutation. Our findings provide valuable insights into how site-selective modifications of echinocandins can be used to combat resistance to these clinically important antifungal drugs. | Moriah Jospe-Kaufman; Efrat Ben-Zeev; Shmuel Carmeli; Micha Fridman | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2023-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6543be6148dad23120eff293/original/reshaping-echinocandin-antifungal-drugs-to-circumvent-glucan-synthase-point-mutation-mediated-resistance.pdf |
67c0a32efa469535b933bbe1 | 10.26434/chemrxiv-2025-ggjq5 | Electrochemical CO2 valorization pathways and processes toward C2 to C6 products: acetylene, propylene, butadiene, and benzene | CO2 electrolysis on Cu catalysts at near-ambient conditions yields a range of important C1 to C3 products. Despite recent advances, our mechanistic understanding of the CO2 electrolysis reaction network has remained incomplete, with C4 products, in particular long-sought after aromatic C6 product molecules, still being elusive. Here, we use a novel real-time capillary DEMS technique to determine accurate kinetic onset potentials of a wide set of C1-3 CO2 reduction products. Included in our study are rarely and never-before reported reaction products, such as propionaldehyde, propylene, and firstly acetylene. We focus on the formation of acetylene, C2H2, and also investigate its alkyne electro-reduction, the C2H2 reduction reaction (C2H2RR). Acetylene is shown to electro-reduce on Cu catalysts to the C4 compound 1,3-butadiene in a 2e- reduction reaction. In parallel, it revealed a potential-dependent electroless Cu-catalyzed ambient-condition [2+2+2] cycloaddition reaction to C6 benzene. We discuss the mechanistic implications of our experimental kinetic onset potentials and rationalize the potential-dependent valorizations of acetylene on Cu. Finally, we propose a future two-step process concept to valorize captured CO2 into industrially important aromatic C6+ molecules. This process cascade will open up reaction pathways towards sustainable e-aromatics | Jorge Ferreira De Araujo; Jan Rossmeisl; Hanqing Yin; Xingli Wang; Alexander Bagger; Peter Strasser | Physical Chemistry; Materials Science; Catalysis; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c0a32efa469535b933bbe1/original/electrochemical-co2-valorization-pathways-and-processes-toward-c2-to-c6-products-acetylene-propylene-butadiene-and-benzene.pdf |
663e497f21291e5d1df0e1f5 | 10.26434/chemrxiv-2024-dwtg3 | Harmonic scale factors of fundamental transitions for dispersion-corrected quantum chemical methods | This work provides a procedure and database for obtaining the vibrational frequency scale factors that align quantum chemically computed harmonic frequencies with experimental vibrational spectroscopic data. The database comprises 441 molecules of various sizes, from diatomics to the buckminsterfullerene C60. We provide scale factors for 27 dispersion-corrected methods, 24 of which are DF-Dn/B with DF=BLYP, PBE, B3LYP,~PBE0, Dn=D3(BJ), D4, and B=6-31G, def2-SVP, def2-TZVP, and three of them are the 3c-family composite methods (HF-3c, PBEh-3c, and r2SCAN-3c). The two scale factors are derived for each method: the absolute scaling, minimizing the absolute deviation of the scaled harmonic frequency from the experimental value, and the relative scaling, which minimizes an analogous relative deviation. The absolute type of scaling is recommended for frequencies above 2000 cm-1, while the relative scaling is optimal for frequencies below 2000 cm-1. | Denis Tikhonov; Igor Gordiy; Danila A. Iakovlev; Alisa A. Gorislav; Mikhail A. Kalinin; Sergei A. Nikolenko; Ksenia M. Malaskeevich; Karina Yureva; Nikita A. Matsokin; Melanie Schnell | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663e497f21291e5d1df0e1f5/original/harmonic-scale-factors-of-fundamental-transitions-for-dispersion-corrected-quantum-chemical-methods.pdf |
6491ff06853d501c0037f4ed | 10.26434/chemrxiv-2023-rhvw4 | Plasma radicals as kinetics-controlling species during plasma-assisted catalytic NH3 formation: support from microkinetic modeling | About 1% of the world’s CO2 emissions are tied to the standard method to produce NH3 (i.e., Haber-Bosch process), hence there is a need to decarbonize the production this chemical. To this end, plasma-assisted catalysis is emerging as a “green” alternative to synthesize NH3. However, insufficient mechanistic understanding of this process has hindered significant improvements in its cost-effectiveness. Here we leverage “minimal plasma” microkinetic models and select experiments in a dielectric-barrier discharge (DBD) plasma reactor to look for missing mechanistic insights. Relatively robust to model assumptions, we find that our modeling supports the thesis that plasma N and H radicals are the kinetics controlling plasma species for reactions involving the catalyst. This support stems from the realization that only the inclusion of N and H radicals in our models can readily explain key experimental observations for plasma assisted NH3 synthesis such as: i) similar catalytic activity for Fe and Ag (two metals at the opposite ends of N2 dissociation capabilities), ii) activity increase in Fe (a metal that readily dissociates N2) relative to thermal catalysis, and iii) detection of catalyst bound N2HY species. We also find the N radicals (a source of surface bound N*) to be more important in nitrophobic metals and H radicals (a hydrogenating agent via Eley-Rideal reactions) to be more important in nitrophilic metals. On the other hand, other mechanistic aspects such as the kinetic relevance of N2HY-forming pathways and dissolution reactions are discussed as a function of model assumptions. Our modeling suggests that some of these assumptions could be potentially clarified through in situ compositional analysis of catalyst adlayers (e.g., the fraction of radicals from the plasma bulk that reach the catalyst surface), as the adlayer composition seems to be rather sensitive to the plasma environment assumed to be “seen” by the catalyst. | Tsung-Wei Liu; Fnu Gorky; Maria Carreon; Diego Gomez-Gualdron | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6491ff06853d501c0037f4ed/original/plasma-radicals-as-kinetics-controlling-species-during-plasma-assisted-catalytic-nh3-formation-support-from-microkinetic-modeling.pdf |
6279def1d5555033e594a26b | 10.26434/chemrxiv-2022-bt457 | Oxidative coupling for facile, stable carbon modification with DNA and proteins | Modification of electrodes with biomolecules is an essential first step for the development of biosensors. Conventionally, gold electrodes are used because of their ease of modification with thiolated biomolecules. However, carbon screen-printed electrodes (SPEs) are gaining popularity for the development of cost-effective platforms, as they do not require precious metals for the work-ing electrode and are more consistent than most equivalent gold screen-printed electrodes. However, their universal modification with biomolecules remains a challenge; the majority of work to-date relies on non-specific amide bond formation to chemical handles on the electrode surface. By combining facile and consistent electrochemical modification to add an aniline handle to elec-trodes with a specific and biocompatible bioorthogonal oxidative coupling reaction, we can attach DNA and proteins to carbon electrodes. Importantly, for both proteins and DNA, the biomolecules maintain activity following coupling, ensuring that the DNA is in a biologically-relevant conformation and that proteins remain folded following coupling. We have further demonstrated the ability to generate self-assembled whole-cell films on these electrodes using DNA-directed immobilization to DNA-modified elec-trodes. This work provides an important platform for the modification of inexpensive carbon SPEs and is anticipated to be appli-cable to any carbon-based electrode material. | Amruta Karbelkar; Rachel Ahlmark; Gang Fan; Victoria Yang; Ariel Furst | Analytical Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6279def1d5555033e594a26b/original/oxidative-coupling-for-facile-stable-carbon-modification-with-dna-and-proteins.pdf |
677e93576dde43c908bb2b80 | 10.26434/chemrxiv-2024-s8zql-v2 | Altmetrics in Chemistry: Alternative Metrics for Research Impact in Chemistry | Evaluation of research chemists worldwide for retention, tenure, and promotion is based on research impact generally measured by citation-based metrics such as the overall number of citations or the Hirsch index. The research impact of published research, however, is measured not only by citations in other academic research papers and books, but also by alternative metrics indicators such as news in newspapers and magazines, posts in social media, mentions in patents, policy documents, online encyclopedias, blogs, and research websites. The analysis of alternative metrics in chemistry-related disciplines fifteen years after its introduction to complement citation-based metrics for assessing research impact suggests three main outcomes. Said insight may further inform undergraduate and graduate chemistry education on scholarly communication in the digital era. | Rosaria Ciriminna; Cristina Della Pina; Rafael Luque; Mario Pagliaro | Chemical Education | CC BY NC 4.0 | CHEMRXIV | 2025-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677e93576dde43c908bb2b80/original/altmetrics-in-chemistry-alternative-metrics-for-research-impact-in-chemistry.pdf |
655ed8645bc9fcb5c92c4786 | 10.26434/chemrxiv-2023-h00ht | Atmospheric pressure continuous flow methane oxidation to methanol and acetic acid using H2O2 over Au-Fe catalyst | An enormous value proposition exists when molecules like acetic acid and methanol are derived from natural gas. With abundant worldwide resources, methane to methanol (M2M) by partial oxidation or acetic acid through C-insertion is considered one of the catalysis's most enterprising chemical transformations. In this work, significant catalytic challenges successfully tackled are the continuous partial oxidation of methane to methanol and acetic acid at atmospheric pressure. In continuous flow and at atmospheric pressure, a modified silica-supported bimetallic (AuFeHS) catalyzed methane to methanol using H2O2 with an impressive yield of 224 mmol/gFe+Au. Co-feeding CO in the stream produces acetic acid, demonstrating a selectivity switch from methanol with an overall yield of 92 mmol/gFe+Au. | Anuradha Jagtap; Pawan Kumar; Sharad Gupta; Abharana N; Shambu Jha; Dibyendu Bhattacharyya; Thalasseril Ajithkumar; Vinod Prabhakaran | Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655ed8645bc9fcb5c92c4786/original/atmospheric-pressure-continuous-flow-methane-oxidation-to-methanol-and-acetic-acid-using-h2o2-over-au-fe-catalyst.pdf |
67a0b31d81d2151a0207e2f2 | 10.26434/chemrxiv-2025-2zrpp | Measuring Zn Transference with Precision: Insights for Dendrite-Free Zinc Metal Anodes | Electrolyte engineering in Zn-metal batteries frequently explores the use of alkaline metal supporting salts to enhance conductivity and reduce overpotential for Zn plating and stripping. While these additives improve conductivity, the presence of more mobile alkali cations can negatively affect the Zn2+ transference number. Optimizing the Zn2+ transference number is crucial for high-rate performance, efficiency, and safety, as a high Zn2+ transference number minimizes concentration polarization and dendrite formation during high-current cycling. However, reliably measuring the transference number of Zn ions in non-binary electrolytes presents significant experimental challenges due to the dynamic nature of Zn metal interfaces, rendering traditional methods ineffective. Here, we introduce a modified Hittorf-type method to reliably measure Zn2+ transference numbers in complex electrolytes. Supported by MD simulations, we apply this method to accurately obtain transport numbers of Zn2+, K+ and acetate ions in Zn-K acetate electrolytes. By varying the Zn2+ fraction, we study the impact of co-electrolytes on transport properties and correlate these with the Zn solvation environment using X-ray absorption spectroscopy. We reveal that while overall ionic conductivity notably increases with the addition of KOAc co-salt, the Zn2+ transference number dramatically decreases. Electrolytes with higher Zn2+ transference numbers enable longer high-rate cycling, underscoring the importance of optimizing Zn2+ transference for improved performance and stability of Zn-metal anodes. | Dario Gomez Vazquez; Travis P. Pollard; Oleg Borodin; Maria R. Lukatskaya | Physical Chemistry; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a0b31d81d2151a0207e2f2/original/measuring-zn-transference-with-precision-insights-for-dendrite-free-zinc-metal-anodes.pdf |
60c73f9dbb8c1a00d53d9bbc | 10.26434/chemrxiv.7422683.v1 | How Much Aromatic Naphthalene and Graphene Are? | <p>Naphthalene, (Aromatic stabilization Energy;
ASE, 50-60 kcal/mol) polyacenes and graphene are considered aromatic. Existing models for polyacenes predict a
linearly increasing ASE and give little insights into their high reactivity and
decreasing stability. Graphene’s
aromaticity has been studied earlier qualitatively suggesting alternate Clar’s
sextet and two-electrons per ring, but ASE estimates have not been reported yet. In this paper, various Heat of Hydrogenation
(HoH) and isodesmic schemes have been proposed and compared for the estimation
of naphthalene ASE. Results show that HoH
schemes are simple to design, are equivalent to isodesmic schemes, and unconjugated
unsaturated reference systems predict ASE values in agreement with literature
reports. Partially aromatic reference systems
underestimate ASE. HoH schemes require
calculations for a smaller number of structures, and offer scope for
experimental validation, and involve enthalpy differences. Polyacene (X-axis extensions of benzene) ASE estimates
(using HoH scheme) correlate well with experimental instability data and offer new
physical insights explaining the absence of arbitrarily larger polyacenes. ASEs extrapolated from quadratic and
logarithmic regression models have been used to estimate the largest polyacene
with limiting ASE values. ASE values for
Pyrene (Y-axis extension of benzene) and higher analogues (here called
pyrene-vertacenes) are estimated using HoH schemes. Further truncated graphene models and
graphene are approximated as combinations of polyacene and pyrene-vertacene units. First ever ASE and molecular sizes (22-255
nM) estimates predict nanometer size ranges for flat graphene in agreement with
recent experiments and offer new physical insights. These ASE and size estimates for graphene may
prove useful in the design of novel energy (hydrogen) storage, electronic and
material science applications.</p> | Vaibhav Dixit; Yashita Y. Singh | Physical Organic Chemistry; Carbon-based Materials; Theory - Computational; Physical and Chemical Processes; Structure; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9dbb8c1a00d53d9bbc/original/how-much-aromatic-naphthalene-and-graphene-are.pdf |
60c74115337d6c839ae267f0 | 10.26434/chemrxiv.7440227.v2 | Efficient Charge Transfer at a Homogeneously Distributed (NH4)2Mo3S13 / WSe2 Heterojunction for Solar Hydrogen Evolution | <p></p><p>In the present work we demonstrate a record photocurrent
density of 5.6 mA cm<sup>-2</sup> at 0 V<sub>RHE</sub> for WSe<sub>2</sub> photocathodes coated with an effective/earth abundant catalyst
- ammonium thiomolybdate (NH<sub>4</sub>)<sub>2</sub>Mo<sub>3</sub>S<sub>13</sub>
(ATM). The photocurrent density can be tuned by optimizing the WSe<sub>2</sub>
film thickness. The features of this new combination (NH<sub>4</sub>)<sub>2</sub>Mo<sub>3</sub>S<sub>13</sub>
/ WSe<sub>2</sub> and its performance for solar hydrogen evolution is discussed
in the manuscript. Our new finding is that the ATM can be used as a
photocatalyst, not only as an electrocatalyst known up to date. The results
further expand and develop the field of the transition metal dichalcogenides
especially in the context of the solar hydrogen evolution. This work is an
important milestone towards large scale photocathodes using earth abundant
elements.</p><p></p> | Farabi Bozheyev; Fanxing Xi; Paul Plate; Thomas Dittrich; Sebastian Fiechter; Klaus Ellmer | Thin Films; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Photocatalysis; Energy Storage; Fuels - Energy Science | CC BY 4.0 | CHEMRXIV | 2019-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74115337d6c839ae267f0/original/efficient-charge-transfer-at-a-homogeneously-distributed-nh4-2mo3s13-w-se2-heterojunction-for-solar-hydrogen-evolution.pdf |
6260152bbdc9c225f0dc5da4 | 10.26434/chemrxiv-2022-hmbjr | Selective hydrodeoxygenation of lignin-derived phenols to aromatics catalyzed by Nb2O5-supported iridium | Here we report the first heterogeneous iridium-based catalyst (Ir@Nb2O5) able to combine full conversion in hydrodeoxygenation (HDO) of lignin-derived phenols to hydrocarbons with appreciable selectivity for aromatics. With temperature and pressure optimization, and coking inhibition by selective removal of acid sites, the aromatic yields reach 69% under mild conditions. | Gabriel Jeantelot; Simen P. Følkner; Johanna I. S. Manegold; Morten G. Ingebrigtsen; Vidar R. Jensen; Erwan Le Roux | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6260152bbdc9c225f0dc5da4/original/selective-hydrodeoxygenation-of-lignin-derived-phenols-to-aromatics-catalyzed-by-nb2o5-supported-iridium.pdf |
65ed87f166c1381729ac281c | 10.26434/chemrxiv-2024-lfr2x | Effect of Microhydration in Tuning the Photophysical Behavior of a Luminescent DNA Probe Revealed by Non-Adiabatic Dynamics | We report the non-adiabatic dynamics, performed in the surface hopping formalism, of an environment-dependent luminescent organic DNA probe. In particular we have shown that the first shell solvent water molecules undergo a rather complex reorganization upon light excitation. This involves also the triggering of a water-mediated proton transfer process which leads to the formation of the tautomeric structure. The presence of this solvent-mediated transfer mechanism globally diminishes the intersystem crossing efficiency, and hence the population of the triplet state manifold, as compared to the non-solvated systems. Our results also point out the non-innocent role of solvent networks in tuning complex photophysical processes, while opening competitive relaxation channels. | Elise Lognon; Alain Burger; Elise Dumont; Antonio Monari | Physical Chemistry; Photochemistry (Physical Chem.); Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2024-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ed87f166c1381729ac281c/original/effect-of-microhydration-in-tuning-the-photophysical-behavior-of-a-luminescent-dna-probe-revealed-by-non-adiabatic-dynamics.pdf |
60c742a64c8919fe65ad24b3 | 10.26434/chemrxiv.8320583.v1 | Chemoselective Peptide Cyclization and Bicyclization Directly on Unprotected Peptides | Herein, we report a highly chemoselective and
operation-simple method directly cyclizing unprotected peptides, in which <i>ortho</i>-phthalaldehyde (OPA) is found to
react with the lysine/N-terminus and cysteine within one unprotected peptide
sequence effectively to form the isoindole-bridged cyclic peptides. This
reaction is carried out in the aqueous buffer and features tolerance of diverse
functionalities, rapid and clean transformation and operational simplicity. | Yue Zhang; Qing Zhang; Clarence Wong; Xuechen Li | Bioorganic Chemistry; Organic Synthesis and Reactions; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742a64c8919fe65ad24b3/original/chemoselective-peptide-cyclization-and-bicyclization-directly-on-unprotected-peptides.pdf |
6799224c81d2151a02515c0a | 10.26434/chemrxiv-2025-xlt1q | Identifying organic co-solvents via machine learning solubility predictions in organic solvents and water | Developing predictive models of solubility is useful for accelerating solvent selection for applications ranging from electrochemical conversion of organics to pharmaceutical drug development. Herein, we report the development of a machine learning (ML) workflow for identifying organic co-solvents to increase the concentration of hydrophobic molecules in aqueous mixtures. This task is of particular interest for the electrocatalytic conversion of biomass and bio-oils into sustainable fuels, which faces challenges due to the low aqueous solubility of the feedstock. First, we predict the miscibility of potential co-solvents in water, and we only consider co-solvents that are miscible. Second, we rank the co-solvents based on their ability to solubilize the molecules of interest. As such, we train two ML models on the AqSolDB and the BigSolDB datasets to predict the aqueous solubility (S) and the organic solubility (x), respectively. We select the Light Gradient Boosting Machine model architecture for aqueous solubility (test R2 = 0.864, RMSE = 0.851 log(S / (mol/dm3)) and organic solubility (test R2 = 0.805, RMSE = 0.511 log(x)) predictions based on comparing different ML models and features. We examine the generalizability of the organic solubility model on unseen solutes both quantitatively and qualitatively. We evaluate the utility of this ML workflow by identifying co-solvents for benzaldehyde and limonene—two hydrophobic molecules that are relevant for sustainable fuel production—and validate our predictions via experimental solubility measurements. | Maurycy Krzyzanowski; Sirazam Munira Aishee; Nirala Singh; Bryan R. Goldsmith | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Machine Learning; Physical and Chemical Properties; Solution Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6799224c81d2151a02515c0a/original/identifying-organic-co-solvents-via-machine-learning-solubility-predictions-in-organic-solvents-and-water.pdf |
6673f039c9c6a5c07aeb0fc8 | 10.26434/chemrxiv-2024-w1s7f | Ring Contracted 16π Tetrathia Core-Modified Isophlorin | Ethylene bridged 16π [2.2.2.2] tetrathiaisophlorin represents a novel example for the ring contracted isophlorin, where all the thiophenes are connected only through α, β position, along with E-form of ethylene bridge. It was synthesized through McMurry coupling of appropriate dialdehydes. Single Crystal X-ray diffraction studies displayed the planar con-formation of the macrocycle along with all thiophene and ethylene protons. 1H NMR studies confirms the paratropic ring current of the macrocycle, where all the ethylene protons resonate in downfield. Two 8π cyclooctatetraenes, were isolated as racemic mixture having the puckered 4nπ ring. | Venkataramanarao Anand; Ramesh Hiremath; Hosahalli Udaya | Organic Chemistry; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6673f039c9c6a5c07aeb0fc8/original/ring-contracted-16-tetrathia-core-modified-isophlorin.pdf |
62d95bceb464fa424b6ce2cd | 10.26434/chemrxiv-2022-r1hd3 | Conformational control of ortho-phenylenes by terminal amides | Control over the folding of oligomers, be it broad induction of a preferred helical handedness or subtle changes in the orientations of individual functional groups, is important for applications ranging from molecular recognition to long-range conformational communication. Here, we report a series of ortho-phenylene hexamers functionalized with achiral and chiral amides at their termini. NMR spectroscopy, taking advantage of F-19 labeling, allows multiple conformers to be detected for each compound. In combination with CD spectroscopy and DFT calculations, specific geometries corresponding to each conformer have been identified and quantified. General conclusions about the effect of sterics and the amide linker on conformational behavior have been drawn, revealing some similarities and key differences with previously reported imines. A model for twist sense control has been developed that is supported by computational models. | Govinda Prasad Devkota; William P. Carson; C. Scott Hartley | Organic Chemistry; Physical Organic Chemistry; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d95bceb464fa424b6ce2cd/original/conformational-control-of-ortho-phenylenes-by-terminal-amides.pdf |
6319a9c049042a1cc7cfe0ae | 10.26434/chemrxiv-2022-609ck | Amplified EQCM-D Detection of Extracellular Vesicles using 2D Gold Nanostructure Arrays Fabricated by Block Copolymer Self-assembly | Extracellular vesicles (EVs) are routinely released from nearly all cell types as transport vehicles and for cell communication. Crucially, they contain biomolecular content for the identification of health and disease states that can be detected from readily accessible physiological fluids, including urine, plasma, or saliva. Despite their clinical utility within noninvasive diagnostic platforms such as liquid biopsies, the currently available portfolio of analytical approaches are challenged by EV heterogeneity in size and composition, as well as the complexity of native biofluids. Quartz crystal microbalance with dissipation monitoring (QCM-D) has recently emerged as a powerful alternative for the phenotypic detection of EVs, offering multiple modes of analyte discrimination by frequency and dissipation. While providing rich data for sensor development, further progress is required to reduce detection limits and fully exploit the technique’s potential within biosensing.
Herein, we investigate the impact of nanostructuring the sensor electrode surface for enhancing its detection capabilities. We employ self-assembly of the block copolymer polystyrene-block-poly(4-vinylpyridine) to create well defined 2D gold islands via selective impregnation of the pyridine domain with gold precursors and subsequent removal of the template. When matched to the EV length scale, we find a 4-fold improvement in sensitivity despite a 4-fold reduction in area for analyte and ligand anchoring in comparison to a flat sensor surface. Creation of tailored and confined sensing regions interspersed by non-binding silica provides optimal spatial orientation for EV capture with reduced steric effects and negative cooperativity of grafted antibodies, offering a promising route for enhanced binding efficiency and performance of sensor platforms. | Jugal Suthar; Alberto Alvarez-Fernandez; Gareth R. Williams; Stefan Guldin | Materials Science; Analytical Chemistry; Nanoscience; Nanostructured Materials - Materials; Biochemical Analysis; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6319a9c049042a1cc7cfe0ae/original/amplified-eqcm-d-detection-of-extracellular-vesicles-using-2d-gold-nanostructure-arrays-fabricated-by-block-copolymer-self-assembly.pdf |
610d3e8c7117506008e3daac | 10.26434/chemrxiv-2021-fxw2c-v2 | Reproducible Untargeted Metabolomics Data Analysis Workflow for Exhaustive MS/MS Annotation | Motivation
Unknown features in untargeted metabolomics and non-targeted analysis (NTA) are identified using fragment ions from MS/MS spectra to predict the structures of the unknown compounds. The precursor ion selected for fragmentation is commonly performed using data dependent acquisition (DDA) strategies or following statistical analysis using targeted MS/MS approaches. However, the selected precursor ions from DDA only cover a biased subset of the peaks or features found in full scan data. In addition, different statistical analysis can select different precursor ions for MS/MS analysis, which make the post-hoc validation of ions selected by new statistical methods impossible for precursor ions selected by the original statistical method. By removing redundant peaks and performing pseudo-targeted MS/MS analysis on independent peaks, we can comprehensively cover unknown compounds found in full scan analysis using a “one peak for one compound” workflow without a priori redundant peak information. Here we propose an reproducible, automated, exhaustive, statistical model-free workflow: paired mass distance-dependent analysis (PMDDA), for untargeted mass spectrometry identification of unknown compounds found in MS1 full scan.
Results
More annotated compounds/molecular networks/spectrum were found using PMDDA compared with CAMERA and RAMClustR. Meanwhile, PMDDA can generate the preferred ions list for iterative DDA to cover more compounds when instruments support such functions.
Availability and implementation
The whole workflow is fully reproducible as a docker image xcmsrocker with both the original data and the data processing template. https://hub.docker.com/r/yufree/xcmsrocker A related R package is developed and released online: https://github.com/yufree/rmwf. R script, data files and links of GNPS annotation results including MS1 peaks list and MS2 MGF files were provided in supplementary information. | Miao Yu; Georgia Dolios; Lauren Petrick | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610d3e8c7117506008e3daac/original/reproducible-untargeted-metabolomics-data-analysis-workflow-for-exhaustive-ms-ms-annotation.pdf |
6700766151558a15ef1955c4 | 10.26434/chemrxiv-2024-cpwfd | Toxicity of Haloacetonitrile Mixtures in a Normal Tissue-Derived Human Cell Line: Are they additive, synergistic, or antagonistic? | Haloacetonitriles (HANs), a class of nitrogen-containing disinfection by-products found in treated drinking water, are cytotoxic and genotoxic to mammalian cells. However, most cell toxicity data has been ascertained using transformed or cancer-derived animal and human cell lines with an ambiguous relevance to human health. In this study, we evaluated the cytotoxicity of individual chloro-, bromo-, and iodo-acetonitrile (ClCH2CN, BrCH2CN, and ICH2CN) and their mixtures using normal tissue-derived human epithelium-derived RPE-1hTERT cells. The order for individual HAN cytotoxicity from most to least toxic was ICH2CN>BrCH2CN>>ClCH2CN with the inhibitory concentration that reduced the cell viability by 50% of the untreated cells (IC50) of 3.0, 8.7, and 219.8 µM, respectively. For HAN mixtures cytotoxicity from most to least toxic was BrCH2CN+ICH2CN>ICH2CN+ClCH2CN>ClCH2CN+BrCH2CN+ICH2CN>ClCH2CN+BrCH2CN with IC50 of 8.9, 9.9, 10.1 and 17.8 µM, respectively. The cytotoxicity of ClCH2CN+BrCH2CN was well predicted by both concentration addition (CA) and independent action (IA) models. The CA model overestimated the toxicity of the other three mixtures which indicates an antagonistic effect with a model deviation ratio of less than 2. The IA model predicted the cytotoxicity of BrCH2CN+ICH2CN and ClCH2CN+BrCH2CN+ICH2CN slightly better than the CA model. According to the Chou-Talalay method, all binary mixtures showed strong antagonistic cytotoxic effects, particularly at low concentrations. However, binary mixtures with ClCH2CN had a slight synergistic effect at high concentrations. | Thilina Jayawardana; Aaron A. Goodarzi; Ebba U. Kurz; Tatek Temesgen; Susana Y. Kimura | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6700766151558a15ef1955c4/original/toxicity-of-haloacetonitrile-mixtures-in-a-normal-tissue-derived-human-cell-line-are-they-additive-synergistic-or-antagonistic.pdf |
65e27d3d66c1381729fd5af5 | 10.26434/chemrxiv-2024-lmg7f | Mechanism of Ni-catalyzed Photochemical Halogen Atom-Mediated C(sp3)–H Arylation | Within the context of Ni photoredox catalysis, halogen atom photoelimination from Ni has emerged as a fruitful strategy for enabling hydrogen atom transfer (HAT)-mediated C(sp3)-H functionalization within the context of Ni photoredox catalysis. Despite the numerous synthetic transformations invoking this paradigm, a unified mechanistic hypothesis that is consistent with experimental findings on the catalytic systems and accounts for halogen radical formation and facile C(sp2)–C(sp3) bond formation remains elusive. We employ kinetic analysis, organometallic synthesis, and computational investigations to deci-pher the mechanism of a prototypical Ni-catalyzed photochemical C(sp3)–H arylation reaction. Our findings revise the previ-ous mechanistic proposals, first by examining the relevance of SET and EnT processes from Ni intermediates relevant to the HAT-based arylation reaction. Our investigation highlights the ability for blue light to promote efficient Ni–C(sp2) bond homolysis from cationic NiIII and C(sp2)–C(sp3) reductive elimination from bipyridyl NiII complexes. However interesting, the rates and selectivities of these processes do not account for the productive catalytic pathway. Instead, our studies support a mechanism that involves halogen atom evolution from in situ generated NiII dihalide intermediates, radical capture by a NiII(aryl)(halide) resting state, and a key C–C bond formation from NiIII. Oxidative addition to NiI, as opposed to Ni0, and rapid NiIII/NiI comproportionation play key roles in this process. The findings presented herein offer fundamental insight into the reactivity of Ni in the broader context of catalysis. | Alex Cusumano; Braden Chaffin; Abigail Doyle | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Photocatalysis; Kinetics and Mechanism - Organometallic Reactions; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e27d3d66c1381729fd5af5/original/mechanism-of-ni-catalyzed-photochemical-halogen-atom-mediated-c-sp3-h-arylation.pdf |
6793b1196dde43c90835b4fe | 10.26434/chemrxiv-2025-rbcfg | Probing Substrate Binding and Release Events in Iridium-Catalysed Hydrogen Isotope Exchange Reactions | Directed, metal-catalysed C-H activation reactions rely on the binding of a Lewis basic functional group to the metal centre to ensure precise control of regioselectivity. However, groups that bind the metal centre too strongly have the potential to decrease turnover frequency and inhibit productive catalysis. Herein, we have used kinetic studies of iridium-catalysed hydrogen isotope exchange reactions, with NMR spectroscopy and mass spectrometry as the analytical techniques, to investigate the binding and release behaviour of a representative series of mono-subsituted aromatic systems bearing a Lewis basic directing group. It was found that pyridine and pyrimidine exhibit anomalous behaviour, with a singlebinding/dual labelling process dominating, or at least being competitive with, a binding/labelling/dissociation pathway. In contrast, with other directing groups (e.g. ketone, nitro, ester), initial formation of an appreciable population of d1- isotopologue is observed, and this is subsequently converted to the corresponding d2-isotopologue, suggesting a mainly binding/labelling/dissociation pathway. These data reveal three classes of substrate with rather different behaviour and for which reaction design and optimisation needs to be approached rather differently. | Daria Timofeeva; William Kerr; David Lindsay; David Nelson | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Bond Activation; Kinetics and Mechanism - Organometallic Reactions | CC BY 4.0 | CHEMRXIV | 2025-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6793b1196dde43c90835b4fe/original/probing-substrate-binding-and-release-events-in-iridium-catalysed-hydrogen-isotope-exchange-reactions.pdf |
67ab5b2781d2151a02f89053 | 10.26434/chemrxiv-2025-wz11n | Room Temperature Ruthenium-Catalyzed Coupling of Cyclopropanols and α-Diazo-β-Ketoesters to α-Ester-δ-Diketones | Organic synthesis in the conventional descriptor wisdom of reactivity chemistry scheme asserts functional group as the originator of reactivity in reactive site, leading to ill-informed reaction development from a static, local perspective. We report herein the proposal of reactivity transduction chemistry scheme, a descriptor system highlighting reactivity and reactive fragment flow as the source for emergence of reactivity, showcasing a well-informed, dynamic, global perspective for reaction development. Through the lens of this descriptor system, the reactivity flow of zinc carbenoid and azide promises the differentiation of ineffective ketone–β-ketoester cross coupling reactivity into competent cyclopropanol–α-diazo carbene cross coupling reactivity. Correspondingly, a room temperature ruthenium catalytic protocol has been developed for the coupling of cyclopropanols and α-diazo-β-ketoesters to α-ester-δ-diketones, featuring a broad substrate scope. The two-carbonyl, one-ester molecular architecture in α-ester-δ-diketones presents an ideal combinatorial synthetic handle for further elaboration into a diversified pool of linear and cyclic structures. The ubiquity of reactivity flow in reaction chains promises reactivity transduction chemistry as a powerful conceptual tool for the productive establishment of most efficient global reactivity network. | Lili Fang; Renpeng Zhou; Jin Zhu | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ab5b2781d2151a02f89053/original/room-temperature-ruthenium-catalyzed-coupling-of-cyclopropanols-and-diazo-ketoesters-to-ester-diketones.pdf |
6319f64fbada38bf34bdbc07 | 10.26434/chemrxiv-2022-w0d5g-v3 | Extension of Generic Amyloid Hypothesis to Metabolites of Urea Cycle and Uric Acid pathway | Herein, we report the aggregation properties of metabolites of urea cycle and uric acid pathway. The aggregation/ self-assembly properties of these metabolites were studied extensively via microscopic techniques. In this context the self-assembling properties of citrulline, ornithine, xanthine, hypoxanthine, cytosine and uracil were studied by assessing its aggregation under varying ageing time from fresh to day 15 of incubation. Interestingly, the metabolites exhibited tendency to aggregate and form soft fibril assembly during the course of ageing and gradually changes to crystalline structures on prolonged incubation. The results presented in this manuscript may have important implications in the pathogenesis of diseasescause urea and uric acid pathway metabolic dysfunction like HHH syndrome, Citrullinemia, Xanthinuria, Lesh Nyahn syndrome and Gout caused by accumulation of these metabolites. | Monisha Patel; Shilpi Gupta; Aayushi Joshi; Basil Wilson; Manoj Pandey; Nidhi Gour | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6319f64fbada38bf34bdbc07/original/extension-of-generic-amyloid-hypothesis-to-metabolites-of-urea-cycle-and-uric-acid-pathway.pdf |
64e77e8379853bbd7856815d | 10.26434/chemrxiv-2023-4ssgd | Peptide stereochemistry effects from pKa-shift to gold nanoparticle templating in a supramolecular hydrogel. | The divergent supramolecular behavior of a series of tripeptide stereoisomers was elucidated through spectroscopic, microscopic, crystallographic and computational techniques. Only two epimers were able to effectively self-organize into amphipathic structures, leading to supramolecular hydrogels or crystals, respectively. Despite the similarity between the two peptides’ turn conformations, stereoconfiguration led to different abilities to engage in intramolecular hydrogen bonding. Self-assembly further shifted the pKa of the C-terminal side chain. As a result, across the pH range 4-6, only one epimer predominated sufficiently as a zwitterion to reach the critical molar fraction allowing gelation. By contrast, the differing pKa values and higher dipole moment of the other epimer favored crystallization. The four stereoisomers were further tested for gold nanoparticle (Au NP) formation, with the supramolecular hydrogel being key to control and stabilize Au NPs, yielding a nanocomposite that catalyzed the photodegradation of a dye. Importantly, the Au NP formation occurred without the use of reductants other than the peptide, and the redox chemistry was investigated by LC-MS and NMR. This study provides important insights for the rational design of simple peptides as minimalistic and green building blocks for functional nanocomposites. | Simone Adorinni; Serena Gentile; Ottavia Bellotto; Slavko Kralj; Evelina Parisi; Maria Cringoli; Caterina Deganutti; Giuliano Malloci; Federica Piccirilli; Paolo Pengo; Lisa Vaccari; Silvano Geremia; Attilio Vargiu; Rita De Zorzi; Silvia Marchesan | Organic Chemistry; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e77e8379853bbd7856815d/original/peptide-stereochemistry-effects-from-p-ka-shift-to-gold-nanoparticle-templating-in-a-supramolecular-hydrogel.pdf |
60c74e26ee301c56dfc7a457 | 10.26434/chemrxiv.12706574.v1 | Molecular and Supported Ti(III)–Alkyls: Efficient Ethylene Polymerization Driven by π-Character of Metal-Carbon Bonds and Back Donation from a Singly Occupied Molecular Orbital | <div>Manuscript on a study on a homogeneous polymerization catalyst, its conversion to a heterogeneous catalyst by reaction with a support, an improvement of catalytic properties by this step, characterization of the structure of both catalysts, and insight into the mechanism of ethylene polymerization and its relation to electronic structure of intermediates. <br /></div><div><br /></div><div>All important information for interpreting and reproducing the findings is contained in the main text and the supplementary information appended within the same PDF document.</div> | Anton Ashuiev; Florian Allouche; Nino Wili; Keith Searles; Daniel Klose; Christophe Copéret; Gunnar Jeschke | Heterogeneous Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e26ee301c56dfc7a457/original/molecular-and-supported-ti-iii-alkyls-efficient-ethylene-polymerization-driven-by-character-of-metal-carbon-bonds-and-back-donation-from-a-singly-occupied-molecular-orbital.pdf |
64a2fa0cba3e99daef73fa6a | 10.26434/chemrxiv-2023-2dd4c | Supporting Sustainability of Chemistry by Linking Research Data with Physically Preserved Research Materials | Results of scientific work in chemistry can usually be obtained in the form of materials and data. A big step towards transparency and reproducibility of the scientific work can be gained if scientists publish their data in a FAIR (Findable, Accessible, Interoperable, Reusable) manner in research data repositories. Nevertheless, in order to make chemistry as a discipline sustainable, obtaining FAIR data is insufficient and a comprehensive concept including the preservation of materials is needed. We describe in this article how we combined two infrastructures, a repository for research data (Chemotion repository) and an archive for chemical compounds (Molecule Archive), in order to offer a comprehensive infrastructure to find and access data and materials that were generated in chemistry projects. Samples play a key role in this concept: we describe how FAIR metadata of a virtual sample representation can be used to refer to the physically available sample stored in a materials’ archive and to link FAIR research data gained with the sample. We further describe the measures to make the physically available samples not only FAIR through the sample’s metadata but also accessible and reusable in the form of their material for others. | Chia-Lin Lin; Pei-Chi Huang; Simone Graessle; Christoph Grathwol; Pierre Tremouilhac; Sylvia Vanderheiden; Patrick Hodapp; Sonja Herres-Pawlis; Alexander Hoffmann; Fabian Fink; Georg Manolikakes; Till Opatz; Andreas Link; M. Manuel B. Marques; Lena J. Daumann; Manuel Tsotsalas; Frank Biedermann; Hatice Mutlu; Eric Täuscher; Felix Bach; Tim Drees; Steffen Neumann; Nicole Jung; Stefan Bräse | Biological and Medicinal Chemistry; Organic Chemistry; Inorganic Chemistry; Organic Synthesis and Reactions; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2023-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a2fa0cba3e99daef73fa6a/original/supporting-sustainability-of-chemistry-by-linking-research-data-with-physically-preserved-research-materials.pdf |
60f6bb77171fc7201eb786de | 10.26434/chemrxiv-2021-g5g40 | Electronic coherences steer the strong isotope effect in the ultrafast Jahn-Teller structural rearrangement of methane cation upon tunnel ionization | We report on fully quantum electronic-nuclear dynamics following sudden ionization from the neutral in the three lowest electronic states of the CH4+ and CD4+ cations. There is a strong Jahn-Teller effect in the Franck-Condon region and we employ two nuclear degrees of freedom that span the internal coordinates involved in the Jahn-Teller coupling. The initial state results from tunneling ionization by a strong IR field which coherently pumps the three lowest states of the cation, D0, D1 and D2. The quantum dynamical simulations show that a strong isotope effect occurs when the ionization accesses significantly the D2 state of the cation in the Franck-Condon region. The computed isotope effect is larger than expected on the basis of the effective mass ratio. The strong effect is due to fast oscillations of the electronic coherences between the D2 and the D1 and D0 electronic states and their modulation by the non adiabatic couplings before a significant onset of nuclear motion. The magnitude of the effect is similar to the one that we previously reported for a sudden photoionization process. A strong isotope effect has been observed in high harmonic spectroscopy studies of the very short time dynamics Jahn-Teller structural rearrangement of the methane cation upon sudden ionization. | Martin Blavier; Ksenia Komarova; Cayo Goncalves; Raphael Levine; Francoise Remacle | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f6bb77171fc7201eb786de/original/electronic-coherences-steer-the-strong-isotope-effect-in-the-ultrafast-jahn-teller-structural-rearrangement-of-methane-cation-upon-tunnel-ionization.pdf |
6522f6c7bda59ceb9a215d43 | 10.26434/chemrxiv-2023-dcwqr | Tailored Functional Monolayers Made from Mesoionic Carbenes | Significant progress has been made over the last decades in surface functionalization of coinage metals using thiols and more recently N-heterocyclic carbenes. As shown in this work, mesoionic carbenes (MICs) provide straightforward access to a novel class of surface ligands and thus materials. Importantly, MICs are easily accessed from triazolium salts (TS) onto which functional groups may be attached with little synthetic effort. Here, we present a library of TS that were further converted into MICs, in situ, and grafted to gold surfaces. The modified surfaces were thoroughly characterized by advanced spectroscopic methods and electrochemistry for MICs bearing electroactive moieties. We also prepared mixed MIC/thiol self-assembled monolayers, which opens the route to multifunctional surfaces. | Emmanuel Maisonhaute; Omar Sadek; Jad Rabah; Dimitri Mercier; Philippe Marcus; Clément Chauvier; François Ribot; Louis Fensterbank | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6522f6c7bda59ceb9a215d43/original/tailored-functional-monolayers-made-from-mesoionic-carbenes.pdf |
60c758e1f96a00e506288ef0 | 10.26434/chemrxiv.14601264.v1 | Development of the First Covalent Monopolar Spindle Kinase 1 (MPS1/TTK) Inhibitor | Monopolar spindle kinase 1 (MPS1/TTK) is a key element
of the mitotic checkpoint securing proper chromosome segregation. It is being
evaluated as a target in the treatment of aggressive tumors such as triple-negative
breast cancer with several reversible inhibitors currently undergoing clinical
trials. While long drug–target residence times have been suggested to be
beneficial in the context of therapeutic MPS1 inhibition, no irreversible
inhibitors are known. Here we present the design and characterization of the
first irreversible covalent MPS1 inhibitor <b>RMS-07</b>
targeting a cysteine (Cys604) in the kinase's hinge region present only in few
other protein kinases. The compound showed excellent MPS1 inhibitory potency
and high selectivity against all protein kinases harboring an equivalent
cysteine as well as in a larger differential scanning fluorimetry-based
screening panel. Covalent binding was confirmed by mass spectrometry and X-ray crystal
structure. We expect this tool compound to open new avenues for the design of
MPS1-specific covalent chemical probes or drugs. | Ricardo Serafim; André Santiago; Caio dos Reis; Jessica Takarada; Priscila Mezzomo; Katlin Massirer; Martin P. Schwalm; Mark Kudolo; Stefan Gerstenecker; Apirat Chaikuad; Stefan Knapp; Stefan Laufer; Rafael Counago; Matthias Gehringer | Organic Synthesis and Reactions; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758e1f96a00e506288ef0/original/development-of-the-first-covalent-monopolar-spindle-kinase-1-mps1-ttk-inhibitor.pdf |
61cb210ed6dcc26d12484422 | 10.26434/chemrxiv-2021-l4d67 | Preliminary Study of Using Colloidal SiO2@ZrO2 Particles in Recovering Actinides from Water and Immobilizing them in a Glass-Ceramic | Actinides, which are toxic for humans, increased their presence in the hydrosphere over the last 80 years. Though actinide recovery from water and immobilization for safe storage is technically feasible, it remains a complex process. Herein, we preliminary studied SiO2@ZrO2 in recovering actinides from water and trapping them in a glass-ceramic upon thermal treatment. To simplify our experimental work, we surrogated radioactive actinides with stable cerium. In the first part of the work, we tested SiO2@ZrO2's ability to recover Ce from water in batch systems. Then, we thermally treated SiO2@ZrO2 with Ce to form a glass-ceramic. All batch experiments showed that SiO2@ZrO2 removes Ce from water. Moreover, all experiments show that SiO2@ZrO2 with Ce converts into a glass-ceramic upon thermal treatment. When heated up to 1000 °C, particles remained spherical, and Ce remained trapped within the structure of crystalline spheroids located between the outer surface and a 50 nm depth. When heated up to 1450 °C, sintering produced bigger particles than the original colloid, and Ce remained trapped within the structure of crystalline spheroids having a broad size distribution located everywhere in the particles. | Pablo Arnal; Ariana Salvia | Nanoscience; Earth, Space, and Environmental Chemistry; Environmental Science; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61cb210ed6dcc26d12484422/original/preliminary-study-of-using-colloidal-si-o2-zr-o2-particles-in-recovering-actinides-from-water-and-immobilizing-them-in-a-glass-ceramic.pdf |
632227b4faf4a4f5891262dc | 10.26434/chemrxiv-2022-0sqnf | Order Versus Disorder in 1,2,3- and 1,2,6- Trimethylpyridinium Chlorocuprate(II) Salts | The vicinal trimethypyridinium (TMP) cations with 1,2,3- or 1,2,6- substitution form distinct compounds when crystallized from aqueous solution. (1,2,6-TMP)2CuCl4 forms asdark green crystals, in which the 1,2,6-TMP cation is ordered, that exhibit a thermochromic transition to a yellow phase above 60 degrees C. (1,2,3-TMP)CuCl3(H2O) forms as emerald green crystals, in which the 1,2,3-TMP cations are two-fold disordered by symmetry, that are non-thermochromic. In order to study the effect of disorder on the choice of compound, a successful attempt was made to prepare mixed cation crystals by slow evaporation of a solution containing a 1:1:1 ratio of 1,2,3-tmP:1,2,6-TMP:CuCl2. Dark green crystals with the characteristic color of the CuCl4 dianion compound were the only ones obtained. Structure determination on on of these crystals verified the presence of the CuCl4 dianion, but now with a mix of 1,2,3-TMP and !,2,6-TMP with occupancies of 0.85 and 0.15 respectively. Thus it appears that a small reduction of the positional disorder of the 1,2,3-TMP cation favors formation of the CuCl4 compound over the CuCl3(H2O) compound. Further, the presence of disorder now in the CuCl4 compound appears to stabilize the low temperature phase. Observation of thermal response of several different crystal to increasing temperature found the transition temperature dramatically higher than in pure (1,2,6-TMP)2CuCl4 or completely absent. The variation of thermal response by different crystal suggest the mixed cation crystals form as a solid solution rather than as a compound with a defined composition. These results suggest several different directions for future work. | Habeeb Al-Mashala; Brendan MacAinsh; Marcus Bond | Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632227b4faf4a4f5891262dc/original/order-versus-disorder-in-1-2-3-and-1-2-6-trimethylpyridinium-chlorocuprate-ii-salts.pdf |
65f285c39138d231616bbedc | 10.26434/chemrxiv-2024-5c76p | Chirality Sensing in Coordination-driven Supramolecular Assemblies | Chirality is a widespread structural characteristic found in nature and plays a vital role in the structure and functioning of almost all biological systems. Nevertheless, the translation of chirality into synthetic systems is highly intricate, yet captivating, as it not only applies fundamental understanding but also has the potential to tackle significant difficulties in biochemistry and medicine. Structurally, the process of coordination-driven self-assembly involves the organization of basic molecular components into well-defined porous homochiral metal-organic cages (MOCs). This allows for a systematic investigation of the enantioselective processes occurring within the nanocavities, which have limited space and specific chiral microenvironments. This article aims to provide a comprehensive summary of the recent advancements in supramolecular chirality generated in the fascinating class of porous MOCs. It will cover the synthesis and characterization of these materials, as well as the implications of their stereochemical information in terms of chiral recognition and enantio-separation. Subsequently, a subjective viewpoint will be presented regarding the potential, possibilities, and significant challenges in the future advancement of this domain, aiming to expand the progress in creating novel chiral functional materials in the realm of chemistry and beyond. | ABHIK PAUL; Subhadip Roy | Organic Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Org.); Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.) | CC BY 4.0 | CHEMRXIV | 2024-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f285c39138d231616bbedc/original/chirality-sensing-in-coordination-driven-supramolecular-assemblies.pdf |
66aa22a5c9c6a5c07a98962a | 10.26434/chemrxiv-2024-bnpbf | Combined Photopolymerization and Localized Photochromism Generation by Aza-Diarylethene and Hemiindigo Synergy | Molecular photoswitches produce light-controlled changes at the nanometer scale and can therefore be used to alter states and behavior of materials in a truly bottom-up fashion. Here we show an escalating photonic complexity of material property control with light using a recently developed aza-diarylethene in combination with hemiindigo (HI) photoswitches. First, the aza-diarylethene can be used as a photoswitch in polystyrene (PS) and to inscribe relief-type 3D structures reversibly into PS. Second, aza- diarylethene can further be used as a photoinitiator for light-induced polymerization of acrylates, demonstrating for the first time light-controlled chemical reactivity control with its zwitterionic switching state. Third, aza-diarylethene and HIs are implemented into aza-diarylethene polymerized PMA, generating photochromic polymers. At the fourth level, the binary mixture allows to synergize aza-diarylethene induced photopolymerization with localized photochromism changes of the simultaneously entrapped functional HI. With such multi-level light response, the utility of this particular photoswitch combination for applications in advanced photonic materials is demonstrated. | Maximilian Sacherer; Henry Dube | Physical Chemistry; Organic Chemistry; Polymer Science; Photochemistry (Org.); Organic Polymers; Polymerization (Polymers) | CC BY 4.0 | CHEMRXIV | 2024-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66aa22a5c9c6a5c07a98962a/original/combined-photopolymerization-and-localized-photochromism-generation-by-aza-diarylethene-and-hemiindigo-synergy.pdf |
6455426007c3f02937447236 | 10.26434/chemrxiv-2023-k4vl8 | Interfacing Whole Cell Biocatalysis with a Biocompatible Pictet-Spengler Reaction for One-Pot Syntheses of Tetrahydroisoquinolines and Tryptolines | Biocatalytic processes are highly selective and specific. However, their utility is limited by the comparatively narrow scope of enzyme-catalysed transformations. To expand product scope, we are developing biocompatible processes that combine biocatalytic reactions with chemo-catalysis in single-flask processes. Here, we show that a chemocatalysed Pictet-Spengler annulation can be interfaced with biocatalysed alcohol oxidation. This two-step, one-pot cascade reaction converts tyramine and aliphatic alcohols to tetrahydroquinoline alkaloids in aqueous buffer at mild pH. Tryptamine derivatives are also efficiently converted to tryptolines. Optimization of stoichiometry, pH, reaction time, and whole-cell catalyst deliver the tetrahydroisoquinolines and tryptolines in >90% and >40% isolated yield, respectively, with excellent regioselectivity. | Campbell Andersen; Dylan W. Domaille | Organic Chemistry; Catalysis; Bioorganic Chemistry; Organic Synthesis and Reactions; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6455426007c3f02937447236/original/interfacing-whole-cell-biocatalysis-with-a-biocompatible-pictet-spengler-reaction-for-one-pot-syntheses-of-tetrahydroisoquinolines-and-tryptolines.pdf |
6643840c21291e5d1d403826 | 10.26434/chemrxiv-2024-nt5f2 | The gallophosphate cloverite – A promising adsorbent for environmental remediation…? | Several recent molecular simulation studies proposed the gallophosphate zeotype cloverite, or cloverite-type materials, as promising adsorbents for the removal of various contaminants from water. This comment presents evidence that the cloverite models used in the simulations presented in those articles were most likely not charge-neutral. Use of such physically unrealistic adsorbent models is expected to have a negative impact on the meaningfulness of the simulation results. To provide a potential starting point for future simulation studies, a neutral model of guest-free cloverite is constructed and optimised with density functional theory calculations. | Michael Fischer | Theoretical and Computational Chemistry; Materials Science; Earth, Space, and Environmental Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6643840c21291e5d1d403826/original/the-gallophosphate-cloverite-a-promising-adsorbent-for-environmental-remediation.pdf |
60c74291337d6c291fe26a96 | 10.26434/chemrxiv.8311481.v1 | Preliminary Observations on the Interactions Between Chlorogenic Acid and Select Amino Acids | This report presents our preliminary observations
regarding the interactions between chlorogenic acid and select amino acids or
tyramine. In most cases, these interactions resulted in the formation of a
green pigment in line with published reports. However, in the case of
tryptophan a green or red pigment was generated depending on the concentration
of tryptophan that was present. In the cases of serine or threonine the green
pigment that was generated in the first minutes of the reactions disappeared
entirely when the mixtures were kept reacting for longer periods of time. Published
reports indicate that the formation of the green pigment between chlorogenic
acid and amino acids involves a covalent interaction between both. In our
experiments we did observe the disappearance of chlorogenic acid during the
reactions but in the cases of tryptophan or tyrosine no decline in the
concentration of both amino acids could be observed. This was in contrast to
the reaction between chlorogenic acid and tyramine where the concentration of
both compounds declined while producing a green pigment. | Koen Vercruysse | Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74291337d6c291fe26a96/original/preliminary-observations-on-the-interactions-between-chlorogenic-acid-and-select-amino-acids.pdf |
60c73efd337d6c0d0be26460 | 10.26434/chemrxiv.5746065.v3 | A kinetic analysis of coupled (or auxiliary) enzyme reactions | <div>As a case study, we consider a coupled (or auxiliary) enzyme assay of two reactions obeying the Michaelis-Menten mechanism. The coupled reaction consists of a single-substrate, single-enzyme non-observable reaction followed by another single-substrate, single-enzyme observable reaction (indicator reaction). In this assay, the product of the non-observable reaction is the substrate of the indicator reaction. A mathematical analysis of the reaction kinetics is performed, and it is found that after an initial fast transient, the coupled reaction is described by a pair of interacting Michaelis-Menten equations. Moreover, we show that when the indicator reaction is slow, the quasi-steady-state dynamics are governed by two fast variables and two slow variables, and when the indicator reaction is fast, the dynamics are governed by three fast variables and one slow variable. Timescales that approximate the respective lengths of the indicator and non-observable reactions, as well as conditions for the validity of the Michaelis-Menten equations are derived. The theory can be extended to deal with more complex sequences of enzyme catalyzed reactions.</div> | Justin Eilertsen; Santiago Schnell | Biochemical Analysis; Biophysical Chemistry; Chemical Kinetics; Solution Chemistry | CC BY 4.0 | CHEMRXIV | 2018-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73efd337d6c0d0be26460/original/a-kinetic-analysis-of-coupled-or-auxiliary-enzyme-reactions.pdf |
6490a904a2c387fa9a947669 | 10.26434/chemrxiv-2023-f7ms7 | Open Circuit Potential Decay Transients Quantify Non-Equilibrium Local pH During Electrocatalysis | Many key energy conversion reactions are proton-coupled electron transfer (PCET) reactions that consume or generate protons at electrode surfaces. Thus, catalytic turnover can generate non-equilibrium local pH environments at the surface that differ substantially from that of the bulk. Quantitative insight into the magnitude of this interfacial pH swing is a prerequisite for understanding and designing efficient systems for energy conversion, but is difficult to measure, particularly under high current density operation; with complex gas diffusion electrodes (GDEs); and with membrane-decorated surfaces employed in functional devices. Herein, we develop and validate a general methodology for experimentally quantifying interfacial pH swings using open circuit potential (OCP) decay transients. Using this method, we quantify the impact of buffer strength, supporting electrolyte composition, and the presence of cation exchange polymer overlayers on the polarization-induced pH swing on Pt GDEs. We find that modest current densities of −30 mA cm−2 are sufficient to sustain pH swings of > 2 pH units, even for strongly buffered solutions. Meanwhile, the addition of alkali supporting electrolyte to unbuffered, acidic electrolyte can induce pH swings so large that the polarized electrode environment becomes strongly alkaline. The presence of a Nafion polymer overlayer containing fixed anionic charges serves to further augment the interfacial pH swing, resulting in a similar pH swing at half the applied current density. The transport characteristics of these systems were analytically modelled, enabling direct calculation of boundary layer thickness and quantitative prediction of the OCP decay transient. These studies establish methods for quantifying local pH swings and highlight the dramatic variation in local pH relative to the bulk under many electrolyte conditions. | Yogesh Surendranath; Ethan Richard Sauvé; Bryan Yuk-Wah Tang; Neil Kanth Razdan; Wei Lun Toh; Sophia Weng | Inorganic Chemistry; Catalysis; Energy; Electrochemistry; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6490a904a2c387fa9a947669/original/open-circuit-potential-decay-transients-quantify-non-equilibrium-local-p-h-during-electrocatalysis.pdf |
60c74777469df4a2bdf43813 | 10.26434/chemrxiv.11665728.v1 | Design of Boradecarboxylation Reaction | For mechanism of
decarboxylation reaction, all textbooks show that the electron moves from the pi<sub>C=O</sub> bond. However, the most donating bond orbital
in the carbonyl group should be the lone pair(s) on the oxygen. Thus, a picture of orbital theory with delocalization from a lone pair should be
more appropriate than that from the pi<sub>C=O</sub> orbital. We confirmed our idea by theoretical
calculation. In the TS, if we use 2-substituted b-ketoacids,
the boat-form conformation should result in exclusively preferred generation of
<i>E</i>-enolates. Normally, decarboxylation
reaction performs in polar solvent, so that the resulting enols should be
transformed to the corresponding ketones by tautomerization. Suppose we use the
heteroatoms to obtain the enolate or enol ethers without tautomerization, it
would offer a diastereoselective enol(ate) synthesis with regioselectivity, since the C=C
double bond should always be introduced between two carbonyl groups. After
screening the heteroatoms by the theoretical
calculations, we found that boron is suitable for this purpose. We confirmed
our idea by theoretical calculations, offering a new boradecarboxylation
reaction to produce enolates diastereoselecitively and regioselectively. | Yuji Naruse; Atsushi Takamori; Kenji Oda | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74777469df4a2bdf43813/original/design-of-boradecarboxylation-reaction.pdf |
62a8d8f4eb1f0c336488e1c0 | 10.26434/chemrxiv-2022-n5wb1 | Covalent functionalization of CdSe quantum dot films with molecular [FeFe] hydrogenase mimics for light-driven hydrogen evolution | CdSe quantum dots combined with [FeFe] hydrogenase mimics as molecular catalytic reaction centers based on earth abundant elements have demonstrated promising activity for photocatalytic hydrogen generation. Direct linking of the [FeFe] hydrogenase mimics to the quantum dots surface is expected to enhance the activity of the system by establishing close contact between the [FeFe] hydrogenase mimics and the light harvesting quantum dots supporting the transfer and accumulation of several electrons which are needed to drive hydrogen evolution. To circumvent the problem of limited colloidal stability upon covalent functionalization of the quantum dots under optimal pH conditions for hydrogen evolution, in this work, we report on the functionalization of quantum dots immobilized in a thin film architecture on a substrate with [FeFe] hydrogenase mimics by covalent linking via carboxylate groups as anchoring functionality to bind to the QD surface. The functionalization was monitored via UV/Vis absorption, photoluminescence, infrared (ATR-FTIR) and X-ray photoelectron spectroscopy (XPS) and quantified via micro X-ray fluorescence spectrometry (μXRF). The activity of the molecularly functionalized thin film was demonstrated and in dependence on the linker length TONs in the range of 360-580 (short linker) and 130-160 (long linker) were achieved. This work presents a proof of concept study showing the potential of thin film architectures of immobilized quantum dots as platform for light-driven hydrogen evolution and beyond. | Stefan Benndorf; Alexander Schleusener; Riccarda Müller; Mathias Micheel; Raktim Baruah; Jan Dellith; Andreas Undisz; Christof Neumann; Andrey Turchanin; Kerstin Leopold; Wolfgang Weigand; Maria Wächtler | Catalysis; Nanoscience; Energy; Nanocatalysis - Catalysts & Materials; Photocatalysis; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a8d8f4eb1f0c336488e1c0/original/covalent-functionalization-of-cd-se-quantum-dot-films-with-molecular-fe-fe-hydrogenase-mimics-for-light-driven-hydrogen-evolution.pdf |
60c73e16567dfe48b4ec3787 | 10.26434/chemrxiv.6474038.v1 | A simple model for halogen bonds | In this article we develop a simple statistical model for the prediction of halogen bond interaction energies at equilibrium geometries. The model is based on explicitly correlated coupled cluster results and produces root-mean-squared deviations of 0.14 and 0.28 kcal mol<sup>–1</sup> over separate fitting and validation sets, respectively. We also show how the model can be used to highlight cases where induction or dispersion significantly affect the underlying nature of the interaction.<br /> | Robert A. Shaw; Grant Hill | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e16567dfe48b4ec3787/original/a-simple-model-for-halogen-bonds.pdf |
60c75521842e65a163db42ad | 10.26434/chemrxiv.14044205.v1 | A Revised Relationship Between Fracture Toughness and Y2O3 Content in Modern Dental Zirconias | <p>The relationship between fracture toughness and Yttria content in modern zirconia ceramics was revised. For that purpose, we evaluated here 10 modern Y<sub>2</sub>O<sub>3</sub>-stabilized zirconia (YSZ) materials currently used in biomedical applications, namely prosthetic and implant dentistry. The most relevant range between 2-5 mol% Y<sub>2</sub>O<sub>3</sub> was addressed by selecting from conventional opaque 3 mol% YSZ up to more translucent compositions (4-5 mol% YSZs). A technical 2YSZ was used to extend the range of our evaluation. The bulk mol% Y<sub>2</sub>O<sub>3</sub> concentration was measured by X-Ray Fluorescence Spectroscopy. Phase quantification by Rietveld refinement are supplied by considering only two tetragonal phases or an additional improbable cubic phase. A first-account of the fracture toughness (<i>K</i><sub>Ic</sub>) of the partly-sintered materials is given, which amounted to 0.4 – 0.7 MPaÖm. In the fully-densified state, an inverse power-law behavior was obtained between <i>K</i><sub>Ic</sub> and bulk mol% Y<sub>2</sub>O<sub>3</sub> content, whether using only our measurements or including literature data, challenging some established relationships.</p> | Renan Belli; Katrin Hurle; Jana Schürrlein; Anselm Petschelt; Katharina Werbach; Herwig Peterlik; Torsten Rabe; Björn Mieller; Ulrich LOHBAUER | Ceramics | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75521842e65a163db42ad/original/a-revised-relationship-between-fracture-toughness-and-y2o3-content-in-modern-dental-zirconias.pdf |
60c74a9fbb8c1a9ee33db04e | 10.26434/chemrxiv.12221717.v1 | Towards Reversible and Moisture Tolerant Aprotic Lithium-Air Batteries | <b>The development of moisture-tolerant,
LiOH-based non-aqueous Li-O<sub>2</sub> batteries is a promising route to bypassing
the inherent limitations caused by the instability of their typical discharge
products, LiO<sub>2</sub> and Li<sub>2</sub>O<sub>2</sub>. The use of the I<sup>-</sup>/I<sub>3</sub><sup>-</sup>
redox couple to mediate the LiOH-based oxygen reduction and oxidation reactions
has proven challenging to develop due to the multiple reaction paths induced by
the oxidation of I<sup>-</sup> on cell charging. In this work we demonstrate a
reversible LiOH-based Li-O<sub>2</sub> battery cycling through a 4 e<sup>-</sup>/O<sub>2</sub>
process with low charging overpotential (below 3.5 V vs Li/Li<sup>+</sup>) by
introducing an ionic liquid to a glyme-based electrolyte containing LiI and water.
The addition to the ionic liquid increases the oxidizing power of I<sub>3</sub><sup>-</sup>,
shifting the
charging mechanism from IO<sup>-</sup>/IO<sub>3</sub><sup>- </sup>formation to
O<sub>2</sub> evolution</b> | Israel Temprano; Tao Liu; Enrico Petrucco; James H. J. Ellison; Gunwoo Kim; Erlendur Jónsson; Clare P. Grey | Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2020-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a9fbb8c1a9ee33db04e/original/towards-reversible-and-moisture-tolerant-aprotic-lithium-air-batteries.pdf |
617287b9ff3ba904509d14dd | 10.26434/chemrxiv-2021-08md1 | Discovery of novel orexin receptor antagonists using a 1,3,5-trioxazatriquinans bearing multiple effective residues (TriMER) library
| Structurally diverse small compounds are utilized to obtain hit compounds that have suitable pharmacophores in appropriate three-dimensional conformations for the target drug receptors. We have focused on the 1,3,5-trioxazatriquinane skeleton, which has a high degree of three-dimensional properties, leading to a novel small-scale focused library based on 1,3,5- trioxazatriquinane. In the library screening for the orexin receptor, some of the compounds showed orexin receptor antagonistic activity with a high hit rate of 7%. By optimizing the hit compounds, we discovered a potent dual orexin receptor antagonist, 38b, and a selective orexin 1 receptor antagonist, 41b carrying the same plane structure. Both compounds showed reasonable brain permeability and beneficial effects when administered intraperitoneally to wild-type mice. Docking simulations of their eutomers, (–)-38b and (+)-41b, with orexin receptors suggested that the interaction between the 1,3,5-trioxazatriquinane core structure and the hydrophobic subpocket in orexin receptors enables a U-shape structure, which causes tight van der Waals interactions with the receptors similar to SB-334867, a selective orexin 1 receptor antagonist. These results indicate that the 1,3,5-trioxazatriquinanes bearing multiple effective residues (TriMERs) could serve as a privileged structure for G-protein coupled receptors (GPCRs) and the TriMER library approach might be useful for the hit discovery process targeting other GPCRs not only opioid and orexin receptors. | Tsuyoshi Saitoh; Mao Amezawa; Jumpei Horiuchi; Yasuyuki Nagumo; Naoshi Yamamoto; Noriki Kutsumura; Ryuichiro Oshita; Akihisa Tokuda; Yoko Irukayama-Tomobe; Yasuhiro Ogawa; Yukiko Ishikawa; Emi Hasegawa; Takeshi Sakurai; Yasuo Uchida; Tetsu Sato; Hiroaki Gouda; Ryuji Tanimura; Masashi Yanagisawa; Hiroshi Nagase | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617287b9ff3ba904509d14dd/original/discovery-of-novel-orexin-receptor-antagonists-using-a-1-3-5-trioxazatriquinans-bearing-multiple-effective-residues-tri-mer-library.pdf |
60c758b39abda25651f8e96d | 10.26434/chemrxiv.14579232.v1 | Cross Sphere Electrode Reaction: the Case of Hydroxyl Desorption during the Oxygen Reduction Reaction on Pt(111) in Alkaline Media | Hydroxide ion is a common electrolyte when electrode reactions take place in alkaline media. In the case of oxygen reduction reaction on Pt(111), we demonstrate by ab initio molecular dynamics calculations, that the desorption of hydroxyl (OH*) from the electrode surface to form a solvated OH<sup>−</sup> is a cross sphere process, with the reactant OH* in the inner sphere and the product OH<sup>−</sup> directly generated in the aqueous outer sphere. Such a mechanism is distinct from the typical inner sphere and outer sphere reactions. It is dictated by the strong hydrogen bonding interactions between a hydroxide ion and water molecules and facilitated by proton transfer through solvation layers. It should play a significant role whenever OH* desorption, or its reverse, OH<sup>−</sup> adsorption, is involved in an electrochemical reaction | Yuke Li; Zhi-Feng Liu | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758b39abda25651f8e96d/original/cross-sphere-electrode-reaction-the-case-of-hydroxyl-desorption-during-the-oxygen-reduction-reaction-on-pt-111-in-alkaline-media.pdf |
60c74f699abda28a1ff8d847 | 10.26434/chemrxiv.12897095.v1 | Biosynthesis of Mycotoxin Fusaric Acid and Application of a PLP-Dependent Enzyme for Chemoenzymatic Synthesis of Substituted L-Pipecolic Acids | <div><p>Fusaric acid (FA) is a well-known mycotoxin that plays an important role in plant pathology. The biosynthetic gene cluster for FA has been identified but the biosynthetic pathway remains unclarified. Here, we elucidated the biosynthesis of FA, which features a two-enzyme catalytic cascade, a pyridoxal 5’-phosphate (PLP)-dependent enzyme (Fub7) and a flavin mononucleotide (FMN)-dependent oxidase (Fub9) in synthesizing the picolinic acid scaffold. FA biosynthesis also involves an off-line collaboration between a highly reducing polyketide synthase (HRPKS, Fub1) and a nonribosomal peptide synthetase (NRPS)-like carboxylic acid reductase (Fub8) in making an aliphatic alpha,beta-unsaturated aldehyde. By harnessing the stereoselective C-C bond forming activity of Fub7, we established a chemoenzymatic route for stereoconvergent synthesis of a series of 5-alkyl, 5,5-dialkyl, and 5,5,6-trialkyl-L-pipecolic acids of high diastereomeric ratio. </p></div> | Yang Hai; Mengbin Chen; Arthur Huang; Yi Tang | Biochemistry; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f699abda28a1ff8d847/original/biosynthesis-of-mycotoxin-fusaric-acid-and-application-of-a-plp-dependent-enzyme-for-chemoenzymatic-synthesis-of-substituted-l-pipecolic-acids.pdf |
6182a8878ac7a249ac66635f | 10.26434/chemrxiv-2021-dhggv | Interrogation of the Selectivity and Electrokinetics of CO2 Reduction by AgSn Films in the Presence of Protic Organic [DBU–H]+ Cations as judged by Impedance Spectroscopy and Distribution of Relaxation Times Analysis | The use of renewable electricity to synthesize high energy and high value chemicals via reduction of CO2 is an attractive strategy for renewable energy storage. Improving our understanding of how heterogeneous CO2 reduction electrocatalysts function is important to designing efficient systems for conversion of CO2 into commodity chemicals such as CO and HCO2H. Both Ag- and Sn-based materials have been previously considered as CO2 reduction catalysts and offer distinct CO2RR selectivities. In this work, we have considered electrodeposited composite film electrodes prepared from electroplating baths with varying ratios of Ag+ and Sn2+ triflates to understand how the performance of such composite materials varies as a function of composition. XPS analysis confirms that for each composite film electrodes, Ag existed in the metallic (Ag0) state, while the Sn was mainly oxidized (Sn2+/4+). The AgSn composite film electrodes studied herein are therefore best considered as AgSnOx cathodes with varying ratios of Ag0:Sn2+/4+. These systems were assessed as CO2RR electrocatalysts and were found to promote the 2e–/2H+ reductions to deliver CO and HCOOH with fast kinetics and high efficiencies from electrolyte solutions containing the protic organic cation [DBU–H]+. While Sn-rich composite films showed poor selectivities for CO versus HCO2H, a significant increase in CO versus HCO2H selectivity (up to 99%) is achieved for composite film electrodes in which the Ag content ranged from 25 - 75%. By tuning the ratio of Ag0 to SnOx we prepared composite film cathode materials that support quantitative current efficiencies for generation of CO with geometric current densities approaching 30 mA/cm2 at applied overpotentials that are less than 750 mV were realized. Additionally, electrochemical impedance spectroscopy (EIS) coupled with analysis of the distribution of relaxation times (DRT) was used to better understand factors important to the composites’ activity under CO2RR conditions. Probing the dynamics with DRT analysis revealed that multiple processes relating to both adsorption and diffusion-controlled events are important to the activity of the electrocatalysts considered in this work. The collection of electroanalytical investigations suggest that synergistic interactions between Ag and SnOx give rise to porous films that support enhanced CO2RR kinetics and that mixing of Ag with SnOx enhances the efficacy of adsorption and stabilization of reduced CO2 intermediates and [DBU–H]+ cations to facilitate CO evolution at the cathode/electrolyte interface. | Thabiso Kunene; Abderrahman Atifi; Joel Rosenthal | Inorganic Chemistry; Catalysis; Energy; Electrochemistry; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6182a8878ac7a249ac66635f/original/interrogation-of-the-selectivity-and-electrokinetics-of-co2-reduction-by-ag-sn-films-in-the-presence-of-protic-organic-dbu-h-cations-as-judged-by-impedance-spectroscopy-and-distribution-of-relaxation-times-analysis.pdf |
67c1d96381d2151a02742d9c | 10.26434/chemrxiv-2025-1pj9b | Standard-free Quantitative Mass Spectrometry of RNA Modifications | The coupling of liquid chromatography (LC) to mass spectrometry (MS) is an accurate and proven technique for identifying different types of RNA modifications. However, due to the lack of standards and analytical biases, epitranscriptome-wide quantitative MS analysis of RNA modifications is challenging. Here, we report the development of a standard-free quantitative mass spectrometry (SqMS) method for measuring multiple RNA modifications. Starting from the extraction of total RNA to the LC-MS analysis of digested RNA, the commonly used approach is used in SqMS. To eliminate the biases that resulted from MS ionization efficiency, the SqMS method adjusts the MS signal of each ribonucleoside with a corresponding factor. Each adjustment factor is derived from measuring a serially diluted control sample, which contains a comparable set of RNA modifications as in our samples of interest. By using a post-column UV detector and the information on molar absorptivity, the ribonucleoside concentration in each diluted control sample is determined and plotted against the corresponding MS signal. The resulting dilution curve of each detectable ribonucleoside is equivalent to the standard curve, thus no ribonucleoside standard is required. After normalizing the adjusted MS signals, the accuracy of SqMS in the quantitation of multiple RNA modifications within the same sample is as good as performing the absolute quantitation. By using SqMS, the epitranscriptomic variations in glioblastoma cells were accurately differentiated.
| Jennifer Simpson; Renata Fleming; Hongzhou Wang; Daniel Todd; Jian Teng; Bakhos Tannous; Norman Chiu | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c1d96381d2151a02742d9c/original/standard-free-quantitative-mass-spectrometry-of-rna-modifications.pdf |
667fb135c9c6a5c07abab704 | 10.26434/chemrxiv-2024-nbdtj | Dissecting Errors in Machine Learning for Retrosynthesis: A Granular Metric Framework and Transformer-Based Model for More Informative Predictions | Chemical reaction prediction, encompassing forward synthesis and retrosynthesis, stands as a fundamental challenge in organic synthesis. A widely adopted computational approach frames synthesis prediction as a sequence-to-sequence translation task, using the common SMILES representation for molecules. Current evaluation of machine learning methods for retrosynthesis assume perfect training data, overlooking imperfections in reaction equations in popular datasets, such as missing reactants, products, other physical and practical constraints such as temperature and cost, primarily driven by a focus on the target molecule. This limitation leads to an incomplete representation of viable synthetic routes, especially when multiple sets of reactants can yield a given desired product. In response to these shortcomings, this study examines the prevailing evaluation methods and introduces comprehensive metrics designed to address imperfections in the dataset. Our novel metrics not only assess absolute accuracy by comparing predicted outputs with ground truth but also introduce a nuanced evaluation approach. We provide scores for partial correctness and compute adjusted accuracy through graph matching, acknowledging the inherent complexities of retrosynthetic pathways. Additionally, we explore the impact of small molecular augmentations while preserving chemical properties and employ similarity matching to enhance the assessment of prediction quality. We introduce SynFormer, a sequence-to-sequence model tailored for SMILES representation. It incorporates architectural enhancements to the original transformer, effectively tackling the challenges of chemical reaction prediction. SynFormer achieves a top-1 accuracy of 53.2% on the USPTO-50k dataset, demonstrating an improvement over previous state-of-the-art language models while being more efficient and eliminating the need for pre-training. | Arihanth Srikar Tadanki; H. Surya Prakash Rao; U. Deva Priyakumar | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667fb135c9c6a5c07abab704/original/dissecting-errors-in-machine-learning-for-retrosynthesis-a-granular-metric-framework-and-transformer-based-model-for-more-informative-predictions.pdf |
67ddc259fa469535b920f4b5 | 10.26434/chemrxiv-2025-s7925 | High Oxygen Barrier Packaging Materials from Protein-rich Single-Celled Organisms | Fossil-based plastics pose significant environmental challenges due to their persistence and carbon footprint, resulting in pollution and long-term climate change. In the present study innovative bioplastic films and trays for packaging applications were developed from protein-rich microbial biomass with glycerol as the plasticizer. The microbial biomass demonstrated excellent film-forming properties through compression molding, and the final materials exhibited good mechanical properties and excellent gas barrier properties - an average oxygen permeability coefficient of 0.33 cm3 mm m-2 day-1 atm-1 at 50% relative humidity and 23 °C. The oxygen barrier properties highlight these microbial biomass materials as a promising, sustainable alternative to fossil-based synthetic films like EVOH, which are widely used in multilayer food packaging. Beyond offering a microplastic-free solution, the protein-rich materials present an opportunity to mitigate microplastic pollution at the end of their lifecycle. The current results position bioplastics based on microbial biomass as a critical step forward in addressing environmental sustainability challenges with current commercial packaging materials. | Kiran Reddy Baddigam; Bor Shin Chee; Elodie Guilloud; Chaitra Venkatesh; Helena Koninckx; Kim Windey; Margaret Brennan Fournet; Mikael Hedenqvist; Anna J. Svagan | Materials Science; Polymer Science; Biodegradable Materials; Biopolymers | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ddc259fa469535b920f4b5/original/high-oxygen-barrier-packaging-materials-from-protein-rich-single-celled-organisms.pdf |
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