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64c358c4ce23211b20af30ba | 10.26434/chemrxiv-2023-k5zfq-v2 | Synergistic Insights into Pyrazinophenazine based Hybrid Materials for Advancing Optoelectronics | We have synthesized a two novel hybrid molecules 3-(4-(9,9-dimethylacridin-10(9H)-yl)phenyl)-12,13-diphenyldibenzo[a,c]pyrazino[2,3-i]phenazine (Ac-DibzPyrQx) and 3-(4-(3,6-di-tert-butyl-9H-carbazol-9-yl)phenyl)-12,13 diphenyldibenzo[a,c]pyrazino [2,3-i]phenazine (tCz-DibzPyrQx), comprising electron-donating (9,9-dimethyl-9,10-dihydroacridine, 3,6-di-tert-butyl-9H-carbazole) and electron accepting Pyrazinophenazine groups. The two different electron-donating groups with pyrazinophenazine were synthesized with the view to tune the photophysical and electrochemical properties of the hybrids. The photophysical study displayed absorption maxima in the range of 320-340 nm and 400-500 nm whereas emission maxima at 602 and 540 nm in toluene for these emitters respectively. These compounds showed high thermal and morphological stability, as well as appropriate frontier molecular orbital (FMO) energy levels. These synthesized molecules show very high decomposition temperatures (3000C and 3800C) and exhibited good glass transition temperatures (3280C and 3000C), indicating their significant stability and potential utility as a bipolar host material for efficient phosphorescent organic light-emitting diodes (PhOLEDs) and TADF molecules. | Atul Chaskar; Sunil Madagyal; Pratima Yadav; Gokul Ganeshan; Prabhakar Chetti | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c358c4ce23211b20af30ba/original/synergistic-insights-into-pyrazinophenazine-based-hybrid-materials-for-advancing-optoelectronics.pdf |
63a31b07e9d0fd58db252b26 | 10.26434/chemrxiv-2022-4q2pd | Systemic anti-tumor immunity mediated by photodynamic therapy using injectable chitosan hydrogels for intra-tumoral and sustained drug delivery | Photodynamic therapy (PDT) is an anti-cancer therapy with proven efficacy; however, its application is often limited by prolonged skin photosensitivity and solubility issues associated with the phototherapeutic agents. Injectable hydrogels that can effectively provide intra-tumoral delivery of photosensitizers with sustained release is attracting increased interest for photodynamic cancer therapies. However, most of the hydrogels for PDT applications are based on systems with high complexity and often, pre-clinical validation is not provided. Herein, we provide a simple and reliable pH-sensitive hydrogel formulation that presents proper rheological properties for intra-tumoral injection. For this, Temoporfin (m-THPC), which is one of the most potent clinical photosensitizers, was chemically modified to introduce functional groups that act as cross-linkers in the formation of chitosan-based hydrogels. The introduction of -COOH groups gave rise to a water-soluble derivative, named as PS 2, that was the most promising candidate. Although PS 2 was not internalized by the target cells, its extracellular activation cause effective damage of the cancer cells which was likely mediated by lipid peroxidation. The injection of the hydrogel containing PS 2 in the tumors was monitored by high frequency ultrasounds and in vivo fluorescence imaging which confirmed the sustained release of PS 2 for at least 72 h. Following local administration, light exposure was conducted one (single irradiation protocol) or three (multiple irradiation protocol) times. The latter deliver the best therapeutic outcomes which included complete tumor regression and systemic anti-cancer immune responses. Immunological memory was developed as ~ 75% of the mice cured with our strategy rejected a second rechallenge with live cancer cells. Additionally, failure of PDT to treat immunocompromised mice bearing tumors reinforces the relevance of the host immune system. Finally, our strategy promotes anti-cancer immune responses that lead to the abscopal protection against distant metastases. | Piotr Gierlich; Claire Donohoe; Kevin Behan; Daniel J. Kelly; Mathias Senge; Ligia C. Gomes-da-Silva | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a31b07e9d0fd58db252b26/original/systemic-anti-tumor-immunity-mediated-by-photodynamic-therapy-using-injectable-chitosan-hydrogels-for-intra-tumoral-and-sustained-drug-delivery.pdf |
64fa115bb338ec988a10230b | 10.26434/chemrxiv-2023-44qm1-v2 | Collision Induced Unfolding Reveals Disease-Associated Stability Shifts in Mitochondrial tRNAs | Ribonucleic acids (RNAs) remain challenging targets for structural biology, creating barriers to understanding their vast functions in cellular biology and fully realizing their applications in biotechnology. The inherent dynamism of RNAs creates numerous obstacles in capturing their biologically relevant higher-order structures (HOSs), and as a result, many RNA functions remain unknown. In this report, we describe the development of native ion mobility-mass spectrometry (IM-MS) and collision induced unfolding (CIU) for the structural characterization of a variety of RNAs. We evaluate the ability of these techniques to preserve native structural features into the gas-phase across a wide range of functional RNAs. Finally, we apply these tools to study the elusive mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS)-associated A3243G mutation. Our data demonstrate that our experimentally determined conditions preserve some solution-state memory of RNA via the increasing complexity of CIU fingerprints by RNA HOS and the retention of predicted magnesium binding events. Relating to the role of MELAS-inducing mutations in mitochondrial trans-fer RNA (mt-tRNAs), significant differences in collision cross-section (CCS) and stability are observed as a function of the A3243G mutation across a subset of the mitochondrial transfer RNA (tRNA) maturation pathway. We conclude by discussing the potential application of CIU for the development of RNA-based biotherapeutics and, more broadly, transcriptomic characterization. | Anna Anders; Elizabeth Tidwell; Varun Gadkari; Markos Koutmos; Brandon Ruotolo | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Mass Spectrometry; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fa115bb338ec988a10230b/original/collision-induced-unfolding-reveals-disease-associated-stability-shifts-in-mitochondrial-t-rn-as.pdf |
669804b95101a2ffa8a6041d | 10.26434/chemrxiv-2024-kt165 | Exploring Quantum Active Learning for Materials Design and Discovery | The meeting of artificial intelligence (AI) and quantum computing is already a reality; quantum machine learning (QML) promises the design of better regression models. In this work, we extend our previous studies of materials discovery using classical active learning (AL), which showed remarkable economy of data, to explore the use of quantum algorithms within the AL framework (QAL) as implemented in the MLChem4D and QMLMaterials codes. The proposed QAL uses quantum support vector regressor (QSVR) or a quantum Gaussian process regressor (QGPR) with various quantum kernels and different feature maps. Data sets include perovskite properties (piezoelectric coefficient, band gap, energy storage) and the structure optimization of a doped nanoparticle (3Al@Si11) chosen to compare with classical AL results. Our results revealed that the QAL method improved the searches in most cases, but not all, seemingly correlated with the “roughness” of the data. QAL has the potential of finding optimum solutions, within chemical space, in materials science and elsewhere in chemistry. | Maicon Lourenço; Hadi Zadeh-Haghighi; Jiří Hostaš; Mosayeb Naseri; Daya Gaur; Christoph Simon; Dennis Salahub | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669804b95101a2ffa8a6041d/original/exploring-quantum-active-learning-for-materials-design-and-discovery.pdf |
64a40d6cba3e99daef7eaace | 10.26434/chemrxiv-2023-qn9gj | Engineering Biocatalysts for the C-H Activation of Fatty Acids using Ancestral Sequence Reconstruction | Selective, one-step C-H activation of fatty acids from biomass is an attractive concept in sustainable chemistry. Biocatalysis has shown promise for generating high-value hydroxy acids but to date enzyme discovery has relied on laborious screening and produced limited hits, which predominantly oxidise the sub-terminal positions of fatty acids. Here we show that ancestral sequence reconstruction (ASR) is an effective tool to explore the sequence-activity landscape of a family of multi-domain, self-sufficient P450 monooxygenases. We resurrected eleven catalytically active CYP116B ancestors, each with a unique regioselectivity fingerprint that varied from sub-terminal in the older ancestors to mid-chain in the lineage leading to the extant, P450-TT. In lineages leading to extant enzymes in thermophiles, thermostability increased from ancestral to extant forms, as expected if thermophily had arisen de novo. Our studies show that ASR can be applied to multi-domain enzymes to develop active, self- sufficient monooxygenases as regioselective biocatalysts for fatty acid hydroxylation. | Bethan S. Jones; Connie M. Ross; Gabriel Foley; Nico Kress; Raine E. S. Thomson; Yosephine Gumulya ; Martin A. Hayes; Elizabeth M. J. Gillam; Sabine L. Flitsch | Biological and Medicinal Chemistry; Catalysis; Biochemistry; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2023-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a40d6cba3e99daef7eaace/original/engineering-biocatalysts-for-the-c-h-activation-of-fatty-acids-using-ancestral-sequence-reconstruction.pdf |
6463f4d1a32ceeff2dc23675 | 10.26434/chemrxiv-2023-f29mr | A Simple and Flexible Infusion Platform for Automated Native Mass Spectrometry Analysis | High throughput native mass spectrometry analysis of proteins and protein complexes has been enabled by recent development of infusion and liquid chromatography (LC) systems, which often include complete LC pumps without fully utilizing their gra-dient flows. We demonstrated a lower-cost infusion cart for native mass spectrometry applications using a single isocratic solvent pump that can operate at both nano- and high-flow configurations (0.05-150 µL/min) for both infusion and online buffer exchange experiments. The platform is controlled via open-source software and can potentially be expanded for customized experimental designs, offering a lower cost alternative to labs with limited budget and/or needs in student training. | Stephanie Thibert; Carter Bracken; Daniel Orton; Bryson Gibbons; Mowei Zhou | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Apparatus; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6463f4d1a32ceeff2dc23675/original/a-simple-and-flexible-infusion-platform-for-automated-native-mass-spectrometry-analysis.pdf |
64dc064d4a3f7d0c0d3c0ea8 | 10.26434/chemrxiv-2023-vtc6f | Regioselective Fluoroalkylarylation of Enamides Enabled by an Iron-Catalyzed Multicomponent Radical Cross-Coupling Strategy | Fluoroalkylated compounds are important entities in agrochemicals, pharmaceuticals, and materials. The catalytic dicarbofunctionalization of alkenes represents a powerful strategy for the rapid construction and diversification of compounds. In this vein, multicomponent cross-coupling reactions (MC-CCR) can provide an efficient synthetic route to build molecular complexity. In this work, we report the first iron-catalyzed three-component fluoroalkylarylation of enamides via selective formation and trapping of alpha-amide radicals under mild conditions and fast reaction times. The reaction tolerates a variety of commercially available aryl Grignard reagents and fluoroalkyl halides. Finally, the use of a removable phthalimido group provides an efficient strategy to prepare highly valuable difluoroalkylated amines. | Ángel Rentería-Gómez; Macayla Guerrero; Mireya Ramirez-Lopez; osvaldo gutierrez | Organic Chemistry; Catalysis; Organometallic Chemistry; Catalysis; Reaction (Organomet.) | CC BY 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dc064d4a3f7d0c0d3c0ea8/original/regioselective-fluoroalkylarylation-of-enamides-enabled-by-an-iron-catalyzed-multicomponent-radical-cross-coupling-strategy.pdf |
663b9bf891aefa6ce17fba03 | 10.26434/chemrxiv-2024-vgzvh | An Atomically Dispersed Photocatalyst for para-Selective C-H bond Functionalization of Electron-Poor Arenes | Regioselective C-H bond functionalization is pivotal in modern scientific exploration, offering solutions for achieving novel synthetic methodologies and pharmaceutical development. In this aspect, achieving alternative regioselective functionalization, like para-selective products in electron-poor aromatics, diverges from traditional methods. Leveraging the advantages of atomically dispersed photocatalysts, we designed a robust photocatalyst for an unconventional regioselective aromatic C–H bond functionalization. This innovation enabled para-selective trifluoromethylations of electron-deficient meta-directing aromatics (-NO2, -CF3, -CN, etc.), which is entirely orthogonal to the traditional approaches. Mechanistic experiments and DFT analysis confirmed the interaction between Cu-metal and the aromatic substrate, alongside the photocatalyst's molecular arrangement, driving selective exposure of the para-selective functionalization. This strategic approach elucidated pathways for precise molecular transformations, advancing the frontier of regioselective C–H bond functionalization by using atomically dispersed photocatalysts in organic synthesis. | Suman Pradhan; Jun Hu; Peng Ren; Yuman Qin; Noopur Jain; Susanna Monti; Giovanni Barcaro; Aleksander Jaworski; Xingchao Dai; Jabor Rabeah; Joaquin Silvestre-Albero; Veronica Celorrio; Anna Rokicińska; Piotr Kuśtrowski; Sandra Van Aert; Sara Bals; Shoubhik Das | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Heterogeneous Catalysis; Photocatalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663b9bf891aefa6ce17fba03/original/an-atomically-dispersed-photocatalyst-for-para-selective-c-h-bond-functionalization-of-electron-poor-arenes.pdf |
6399b07214d92dcff7ae84a2 | 10.26434/chemrxiv-2022-zc2vv | The winning team reached the terra incognita: Enantioselective synthesis of ferrocene 1,3-derivatives via distal C-H activation by Pd(II)/norbornene cooperative catalysis | Together they solved the cold case! Activation of the distal C-H bonds of ferrocene and its stereoselective functionalization is not a dream anymore. Here we report, regio-and stereo selective catalytic distal C-H functionalization of ferrocenes actualizing the synthesis of ferrocene-1,3-derivatives by a Catellani-type reaction. The winning Pd/norbornene catalyst combination is able to reach hitherto inaccessible reaction site of ferrocene and accomplishes the regio-and stereoselective arylation of ferrocenylmethylamine. The ligand controlled synergistic Pd/norbornene metal-organic cooperative catalysis under aerobic conditions successfully achieves the synthesis of 30 ferrocene-1,3 derivatives in moderate to good yields and with high enantioselectivity in the substrates scanned. | Princi Gupta; Prakash Chandra Tiwari; Suchithra Madhavan; Manmohan Kapur | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Bond Activation; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6399b07214d92dcff7ae84a2/original/the-winning-team-reached-the-terra-incognita-enantioselective-synthesis-of-ferrocene-1-3-derivatives-via-distal-c-h-activation-by-pd-ii-norbornene-cooperative-catalysis.pdf |
6748b06b7be152b1d03f19ea | 10.26434/chemrxiv-2024-1jxhk | Selective Recovery of Gold from Electronic Circuit Board Waste with Pyrogallol-Formaldehyde Polymer | Electrical and electronic waste (e-waste) has become one of the largest solid waste problems today, as it contains valuable recyclable materials like gold, platinum, and silver. Recycling of precious metals is important in terms of re-using the high precious metal content wastes. In this study, pyrogallol-formaldehyde polymer (PGNR) material was synthesized as an adsorbent. The obtained PGNR was characterized by Brunauer-Emmett-Teller (BET), Fourier Transform Infrared Spectroscopy (FTIR), thermogravimetry analysis (TGA) and nuclear magnetic resonance (NMR) analyses. The adsorption performance of solutions containing gold (III) ions was evaluated under variables such as different pH values, adsorbent amounts, initial concentrations, time and temperature. Data obtained from the experiments were used to perform adsorption isotherm, kinetic, and thermodynamic calculations. The results indicated that the "Pseudo Second Order Equation" provided the best fit for the kinetic data, while the "Langmuir Equation" was the most suitable for the isotherm data. The Langmuir isotherm revealed that the monolayer saturation capacity for Au(III) ions on the PGNR polymer was found to be 2456.78 mg/g at a temperature of 328 K. The FTIR analysis conducted after adsorption revealed that polyphenolic groups played a key role in the adsorption of Au(III) species. XRD and XPS characterization studies showed that nearly all of the Au(III) ions were reduced to metallic gold following adsorption. It was found that the PGNR polymer chosen as the adsorbent exhibited a high efficiency in adsorbing Au(III) from the actual leach solution derived from electronic waste. PGNR polymer particles are a potential adsorbent for the selective recovery of gold metal in leach solutions of electronic waste containing high concentrations of base metals. | Engin Deniz Parlar; Mücahit Abdullah Sarı; Mustafa CAN | Physical Chemistry; Polymer Science; Chemical Engineering and Industrial Chemistry; Polymerization (Polymers); Physical and Chemical Processes; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6748b06b7be152b1d03f19ea/original/selective-recovery-of-gold-from-electronic-circuit-board-waste-with-pyrogallol-formaldehyde-polymer.pdf |
60c74563567dfe1bfcec4467 | 10.26434/chemrxiv.10009013.v1 | Reaction Cycling for Efficient Kinetic Analysis in Flow | A reactor capable of efficiently collecting kinetic data in flow is presented. Conversion over time data is obtained by passing a discrete reaction slug back-and-forth between two residence coils, with analysis performed each time the solution is passed from one coil to the other. In combination with minimal material consumption, this represents an improvement in efficiency for typical kinetic experimentation in batch as well. Application to kinetic analysis of a wide variety of transformations is demonstrated, highlighting both the versatility of the reactor and the benefits of performing kinetic analysis as a routine part of reaction optimization/development. Extension to the monitoring of multiple reactions simultaneously is also realized by operating the reactor with multiple reaction slugs at the same time.<br /> | Ryan Sullivan; Stephen Newman | Organic Synthesis and Reactions; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74563567dfe1bfcec4467/original/reaction-cycling-for-efficient-kinetic-analysis-in-flow.pdf |
6397271f9e687b4b4f487aab | 10.26434/chemrxiv-2022-4rxz5-v2 | Synthetic access to a framework-stabilized and fully sulfided analogue of an Anderson polyoxometalate that is catalytically competent for reduction reactions | Polyoxometalates (POMs) featuring 7, 12, 18, or more, redox-accessible transition-metal ions are ubiquitous as
selective catalysts, electrocatalysts, and sensitized photocatalysts, especially for oxidation reactions. The corresponding synthetic and catalytic chemistry of stable, discrete, and capping-ligand-free polythiometalates (PTMs), which could be especially attractive for reduction reactions, is much less well developed. Among the challenges is the propensity of PTMs to agglomerate and form larger clusters of indeterminate size, as well as the tendency for agglomeration to block access of candidate reactants to potential catalyst active-sites. Nevertheless, the pervasive presence of transition-metal sulfur clusters metalloenzymes or cofactors that catalyze reduction reactions, and the justifiable proliferation of studies of 2D metalchalcogenides, and especially their edge sites, as reduction catalysts, point to the promise of well-defined and controllable PTMs as catalysts for reduction reactions, including complex, bond-forming, many-electron reactions. Here we report the fabrication of agglomeration-immune, reactant-accessible, capping-ligand-free CoIIMoIV6S24n- clusters as periodic arrays in a water-stable, hierarchically porous Zr-metal-organic-framework (MOF; NU1K) by first preparing and installing a disk-like Anderson polyoxometalate, CoIIMoVI6O24m(-), in size-matched (<1 nm) micropores termed c-pores, where the siting is established via DED (difference electron density) X-ray diffraction experiments. Prolonged treatment with flowing H2S while heating, uniformly reduces the six molybdenum(VI) ions to Mo(IV) and quantitatively replaces oxygen anions with similarly ligating sulfur anions in the form S(2-), HS(-), and S2(2-). Further DED measurements show that the templated POM-to-PTM conversion leaves the clusters individually isolated in open-channel-connected c-pores. The structure of the immobilized cluster as determined, in part, by XPS, XAFS, and PDF (pair-distribution function) analysis of total X-ray scattering agrees very well with the theoretically simulated structure. Preliminary, proof-of-concept experiments show that electrode-supported thin-films of CoMo6S24@NU1K are electrocatalytically competent for hydrogen evolution in aqueous acid (e.g. 10 mA·cm-2 of current density at an overpotential of 100 mV). Suspensions of CoMo6S24@NU1K in acetonitrile + triethanolamine, are
photocatalytically competent for hydrogen evolution via sensitization with chromophoric MOF linkers. Nevertheless, the initially installed PTM appears to be a pre-catalyst, as hydrogen evolution is observed only after four hours of photolysis. Reduction-assisted loss of ~3-to-6 sulfurs, as H2S, likely is responsible for pre-catalyst-to-catalyst conversion, as the loss opens coordination sites on multiple cluster-sited metal ions, perhaps enabling hydrogen evolution via a Mo-hydride intermediate. Given the great variety of sizes and compositions available for both POMs and Zr-MOFs, we suggest that the approach described here can be adapted for the synthesis and stabilization of periodic arrays of other non-agglomerating, capping-ligand-free PTMs of well-defined metal-nuclearity, presumably including catalytically functional PTMs. | Jiaxin Duan; Hafeera Shabbir; Zhihengyu Chen; Wentuan Bi; Qin Liu; Jingyi Sui; Luka Dordević; Samuel I. Stupp; Karena Chapman; Alex B. F. Martinson; Alice Li; Subhadip Goswami; Richard D. Schaller; Rachel Getman; Joseph T. Hupp | Theoretical and Computational Chemistry; Catalysis; Electrocatalysis; Heterogeneous Catalysis; Photocatalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6397271f9e687b4b4f487aab/original/synthetic-access-to-a-framework-stabilized-and-fully-sulfided-analogue-of-an-anderson-polyoxometalate-that-is-catalytically-competent-for-reduction-reactions.pdf |
60c7420bbdbb893f00a38438 | 10.26434/chemrxiv.8206214.v1 | Production Prediction of Hydraulically Fractured Reservoirs Based on Material Balances | Transient flow is dominant during most of the productive life of unconventional wells in ultra-low permeabilities resources such as shales. As a result, traditional reservoir performance analysis such as the conventional material balance have been rendered inapplicable. A new novel semi-analytical production predictive tool based on application of material balance on a transient linear flow system is developed. | Raul Velasco; Palash Panja; Milind Deo | Geological Materials; Geochemistry; Natural Resource Recovery | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7420bbdbb893f00a38438/original/production-prediction-of-hydraulically-fractured-reservoirs-based-on-material-balances.pdf |
623e01928ab373eeb971e07c | 10.26434/chemrxiv-2022-tdx0v | The Kasi Learning System – Providing Blind and Low Vision Students Independence in Studying Diagrams | Usable accommodations for students who rely on senses other than vision have not kept pace with the rapid evolution of educational materials to digital format. This trend poses the risk of deselecting Blind and Low Vision (BLV) students from studying fields, such as chemistry, that rely heavily on the use of visuals for communication of ideas and concepts. Practices of adding in accessibility afterwards, by either the producer or school support staff, are generally resource intensive, often do not provide a comparable experience, and are not amenable to dynamic interactive visuals. The Kasi Learning System was built with accessibility at the forefront to provide equitable experiences to students regardless of their visual level. Kasi combines digital interactives with tactile manipulatives and audio-based Augmented Reality to provide a multisensory learning experience. Reported are the design principles and findings from a usability and feasibility study of a prototype of Kasi with ten BLV high school students. Findings from the study indicate that students who used Kasi felt more independent and able to study chemistry. The study also revealed that students who do not regularly rely on their auditory channel for accessing information took longer to become proficient with using the system. | Sarah Wegwerth; Gianna Manchester; Julia Winter | Chemical Education; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623e01928ab373eeb971e07c/original/the-kasi-learning-system-providing-blind-and-low-vision-students-independence-in-studying-diagrams.pdf |
6335595e975e943a0d8d09e4 | 10.26434/chemrxiv-2022-9pslv | What the Heck? – Automated regioselectivity calculations of palladium-catalyzed Heckreactions using quantum chemistry | We present a quantum chemistry (QM)-based method that computes the relative energies of intermediates in the Heck reaction that relate to the regioselective reaction
outcome: branched (α), linear (β), or a mix of the two. The calculations are done for two different reaction pathways (neutral and cationic) and are based on r2SCAN-3c single point calculations on GFN2-xTB geometries that, in turn, derive from a GFNFFxTB conformational search. The method is completely automated and is sufficiently efficient to allow for the calculation on thousands of reaction outcomes. The method can mostly reproduce systematic experimental studies where the ratios of regioisomers are carefully determined. For a larger dataset extracted from Reaxys the results are somewhat worse with accuracies of 63 % for β-selectivity using the neutral pathway and 29 % for α-selectivity using the cationic pathway. Our analysis of the dataset suggests that only the major or desired regioisomer is reported in the literature in many cases, which makes accurate comparisons difficult. The code is freely available on GitHub under the MIT open source license: https://github.com/jensengroup/HeckQM | Nicolai Ree; Andreas H. Göller; Jan H. Jensen | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6335595e975e943a0d8d09e4/original/what-the-heck-automated-regioselectivity-calculations-of-palladium-catalyzed-heckreactions-using-quantum-chemistry.pdf |
626e4f981033882b100198f2 | 10.26434/chemrxiv-2022-05mbp-v2 | Dimensionless parameters and numbers controlling PFAS transport in unsaturated porous media | Per- and polyfluoroalkyl substances (PFAS) is the emerging contaminants of critical concern. Comprehensive understanding of the transport and fate of PFAS in the vadose-zone, a type of water-unsaturated porous media, is key to determination of the risks of the PFAS contamination in the subsurface and to the development of the effective remediation strategies. PFAS transport in the unsaturated porous media is a complex process. In order to disclose the main factors controlling the PFAS transport in unsaturated porous media, we develop the theoretical model based on the dimensionless governing equations for the transient water flow and PFAS transport. The effects of the dimensionless parameters and numbers on the PFAS transport in 2D unsaturated porous media are uncovered based on the second order accurate finite volume method. We find that the retardation numbers and the dimensionless parameters relevant to the properties of porous media as well as the relation between the surface tension and the PFAS concentration play an important role in the PFAS transport in the unsaturated porous media. The effects of the Péclet numbe, Damköhler numbers, and fraction of instantaneous sorption are not significant, however. These findings provide a better understanding of the PFAS transport in vadose zone. | Wentao Jiao; Xiaoxing Li; Mingxiu Zhan; Rui Wu; Yongping Shan; Chenchen Zhang; Yongguang Yin; John Giesy | Earth, Space, and Environmental Chemistry; Environmental Science; Hydrology and Water Chemistry; Soil Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626e4f981033882b100198f2/original/dimensionless-parameters-and-numbers-controlling-pfas-transport-in-unsaturated-porous-media.pdf |
60c7426f469df4215ef42fc2 | 10.26434/chemrxiv.8126912.v1 | Cost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments | <div>The fragment-based polarizable embedding model combined with an appropriate electronic-structure method constitutes a highly efficient and accurate multiscale approach for computing spectroscopic properties of a central moiety including effects from its molecular environment through an embedding potential. There is, however, a comparatively high computational overhead associated with the computation of the embedding potential which is derived from first principles calculations on individual fragments of the environment. To reduce the computational cost associated with the calculation of embedding-potential parameters, we developed a set of amino-acid-specific transferable parameters tailored for large-scale polarizable embedding calculations that include proteins. The amino-acid-based parameters are obtained by simultaneously fitting to a set of reference electric potentials based on structures derived from a backbone-dependent rotamer library. The developed cost-effective polarizable protein potential (CP<sup>3</sup>) consists of atom-centered charges and isotropic dipole-dipole polarizabilities of the standard amino acids. In terms of reproduction of electric potentials, the CP<sup>3</sup> is shown to perform consistently and with acceptable accuracy across both small tripeptide test systems and larger proteins. We show, through applications on realistic protein systems, that acceptable accuracy can be obtained by using a pure CP<sup>3</sup> representation of the protein environment, thus altogether omitting the cost associated with the calculation of embedding-potential parameters. High accuracy comparable to the full fragment-based approach can be achieved through a mixed description where the CP<sup>3</sup> is used only to describe amino acids beyond a threshold distance from the central quantum part.</div> | Peter Reinholdt; Erik Kjellgren; Casper Steinmann; Jógvan Magnus Haugaard Olsen | Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2019-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426f469df4215ef42fc2/original/cost-effective-potential-for-accurate-polarizable-embedding-calculations-in-protein-environments.pdf |
623b586e74104f4a20af659a | 10.26434/chemrxiv-2022-fsq05 | Recombination Between ¹³C and ²H to Form Acetylide (¹³C₂²H‾) Probes Nanoscale Interactions in Lipid Bilayers Via Dynamic Secondary Ion Mass Spectrometry: Cholesterol and GM₁ Clustering | Although it is thought that there is lateral heterogeneity of lipid and protein components within biological membranes, probing this heterogeneity has proven challenging. The difficulty in such experiments is due to both the small length scale over which such heterogeneity can occur, and the significant perturbation resulting from fluorescent or spin labeling on the delicate interactions within bilayers. Atomic recombination during dynamic nanoscale secondary ion imaging mass spectrometry (NanoSIMS) is a non-perturbative method for examining nanoscale bilayer interactions. Atomic recombination is a variation on conventional NanoSIMS imaging whereby an isotope on one molecule combines with a different isotope on another molecule during the ionization process, forming an isotopically enriched polyatomic ion in a distance-dependent manner. We show that the recombinant ion, ¹³C₂²H‾, is formed in high yield from ¹³C- and ²H-labeled lipids. The low natural abundance of triply labeled acetylide has makes it an ideal ion to probe GM₁ clusters in model membranes and the effects of cholesterol on lipid-lipid interactions. We find evidence supporting the cholesterol condensation effect as well as the presence of nanoscale GM₁ clusters in model membranes. | Dashiel Grusky; Frank Moss; Steven Boxer | Physical Chemistry; Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623b586e74104f4a20af659a/original/recombination-between-13c-and-2h-to-form-acetylide-13c22h-probes-nanoscale-interactions-in-lipid-bilayers-via-dynamic-secondary-ion-mass-spectrometry-cholesterol-and-gm1-clustering.pdf |
60c742af0f50dbbd09395d77 | 10.26434/chemrxiv.8397731.v1 | A Short Synthesis of (+)-Brefeldin C via Enantioselective Radical Hydroalkynylation | <div><div><div><div><p>A very concise total synthesis of (+)-brefeldin C starting from 2-furanylcyclopentene is described. This approach is based on an unprecedented enantioselective radical hydroalkynylation process to introduce the two cyclopentane stereocenters in a single step. The use of a furan substituent allows to achieve a high trans diastereoselectivity during the radical process and it contains the four carbon atoms C1–C4 of the natural product in an oxidation state closely related to the one of the target molecule. The eight-step synthesis require six product purifications and it provides (+)-brefeldin C in 18% overall yield.</p></div></div></div></div> | Lars Gnägi; Severin Vital Martz; Daniel Meyer; Robin Marc Schärer; Philippe Renaud | Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742af0f50dbbd09395d77/original/a-short-synthesis-of-brefeldin-c-via-enantioselective-radical-hydroalkynylation.pdf |
6251e80588636c7ce20cd6ca | 10.26434/chemrxiv-2022-7lrps-v2 | The Absorption of Phosphonium Cations and Dications into a Hydrated POPC Phospholipid Bilayer: a Computational Study | Molecular dynamics (MD) based on an empirical force field is applied to investigate the effect of phosphonium cations ([P 6,6,6,6 ] + ) and geminal dications ([DxC10] 2+ ) inserted at T = 300 K into the hydration layer separating planar POPC phospholipid bilayers. Up to high concentration, nearly every added cation and dication becomes absorbed into the lipid phase. Absorption takes place during several µs and is virtually irreversible. The neutralising counterions ([Cl] − , in the present simulation) remain dissolved in water, giving origin to charge separation and strong electrostatic double layer at the water/lipid interface. Incorporation of cations and dications changes properties of the lipid bilayer such as diffusion, viscosity and electrostatic pattern. At high ionic concentration, the bilayer acquires a long-wavelength standing undulation, corresponding to a change of phase
from fluid planar to ripple. All these changes are potentially able to affect processes relevant in the context of cell biology. The major difference between cations and dications concerns the kinetics of absorption, that takes place nearly two times faster in the [P 6,6,6,6 ] + case, and for [DxC10] 2+ dications displays a marked separation into two-stages, corresponding to the easy absorption of the first phosphonium head of the dication, and the somewhat more activated absorption of the second phosphonium head of each dication. | Visakh Pillai; Pallavi Kumari; Antonio Benedetto; Dorothea Gobbo; Pietro Ballone | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling; Interfaces | CC BY NC 4.0 | CHEMRXIV | 2022-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6251e80588636c7ce20cd6ca/original/the-absorption-of-phosphonium-cations-and-dications-into-a-hydrated-popc-phospholipid-bilayer-a-computational-study.pdf |
61b08a730e35ebca34991c8f | 10.26434/chemrxiv-2021-mfkh0 | Role of Central Atom on the Pressure Response of 2D Perovskites Containing a Long Alkyl Chain (Decylammonium, DA): DA2PbI4 and DA2GeI4 | The application of an external pressure on Metal Halide Perovskite (MHPs) has become a fascinating way of tuning their optical properties, achieving also novel features. Here, the pressure response of 2D MHPs including a long alkyl chain made of ten carbon atoms, namely decylammonium (DA), has been investigated as a function of the central atom in DA2PbI4 and DA2GeI4. The two systems share a common trend in the phase stability, displaying a transition from an orthorhombic to a monoclinic phase around 2 GPa, followed by a phase separation in two monoclinic phases characterized by different c-axis. The optical properties show rather different behavior due to the presence of Pb or Ge. DA2PbI4 shows a progressive red shift of the band gap from 2.28 eV at ambient conditions, to 1.64 eV at 11.5 GPa, with a narrow PL emission composed by two components, with the second one appearing in concomitance with the phase separation and significantly shifted to lower energy. On the other hand, DA2GeI4, changes from a non-PL system at ambient pressure, to a clear broadband emitter centered around 730 nm (FWHM ~ 170 nm), with a large stoke shift, and an intensity maximum at about 3.7 GPa. This work sheds light on the structural stability of 2D perovskites characterized by extended alkyl chains, to date limited to four carbon atoms, and shows the pressure-induced emergence of broad emission in a novel lead-free perovskite, DA2GeI4. The evidence of wide emission by a moderate pressure in a germanium-based 2D MHP represents a novel result which may open the design, by chemical pressure, of efficient wide or even white lead-free emitters. | Lorenzo Malavasi; Marta Morana; Boby Joseph; Mauro Coduri; Ausonio Tuissi; Thomas B. Shiell; Timothy A. Strobel; Gianluca Accorsi; Rossella Chiara | Inorganic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b08a730e35ebca34991c8f/original/role-of-central-atom-on-the-pressure-response-of-2d-perovskites-containing-a-long-alkyl-chain-decylammonium-da-da2pb-i4-and-da2ge-i4.pdf |
62db30f0a7d17e34206889cc | 10.26434/chemrxiv-2021-8f6mc-v2 | Insights into the Importance of WPD-Loop Sequence for Activity and Structure in Protein Tyrosine Phosphatases | Protein tyrosine phosphatases (PTPs) possess a conserved mobile catalytic loop, the WPD-loop, which brings an aspartic acid into the active site where it acts as an acid/base catalyst. Prior experimental and computational studies, focused on the human enzyme PTP1B and the PTP from Yersinia pestis, YopH, suggested that loop conformational dynamics are important in regulating both catalysis and evolvability. We have generated a chimeric protein in which the WPD-loop of YopH is transposed into PTP1B, and eight chimeras that systematically restored the loop sequence back to native PTP1B. Of these, four chimeras were soluble and were subjected to detailed biochemical and structural characterization, and a computational analysis of their WPD-loop dynamics. The chimeras maintain backbone structural integrity, with somewhat slower rates than either wild-type parent, and show differences in the pH dependency of catalysis, and changes in the effect of Mg2+. The chimeric proteins’ WPD-loops differ significantly in their relative stability and rigidity. The time required for interconversion, coupled with electrostatic effects revealed by simulations, likely accounts for the activity differences between chimeras, and relative to the native enzymes. Our results further the understanding of connections between enzyme activity and the dynamics of catalytically important groups, particularly the effects of non-catalytic residues on key conformational equilibria. | Ruidan Shen; Rory M. Crean; Keith J. Olsen; Marina Corbella; Ana Rita Calixto; Teisha Richan; Tiago A. S. Brandão; Ryan D. Berry; Alex Tolman; J. Patrick Loria; Sean J. Johnson; Shina Caroline Lynn Kamerlin; Alvan C. Hengge | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62db30f0a7d17e34206889cc/original/insights-into-the-importance-of-wpd-loop-sequence-for-activity-and-structure-in-protein-tyrosine-phosphatases.pdf |
653a624548dad2312066755a | 10.26434/chemrxiv-2023-lpf8m | Synthesis of C3-Substituted N1-tert-Butyl 1,2,4-Triazinium Salts via the Liebeskind–Srogl Reaction for Fluorogenic Labeling of Live Cells | We recently described the development and application of new bioorthogonal conjugation, the triazinium ligation. To explore the wider application of this reaction, in this work we introduce a general method for synthesizing C3-substituted triazinium salts based on the Liebeskind–Srogl cross-coupling reaction and catalytic thioether reduction. These methods enabled the synthesis of triazinium derivatives for investigating the effect of different substituents on the ligation kinetics and stability of the compounds under biologically relevant conditions. Finally, we demonstrate that the combination of coumarin fluorophore attached to position C3 with a C5-(4-methoxyphenyl) substituent, yields a fluorogenic triazinium probes suitable for no-wash, live-cell labeling. The developed methodology represents a promising synthetic approach to the late-stage modification of triazinium salts, potentially widening their application in bioorthogonal reactions. | Veronika Šlachtová; Simona Bellová; Milan Vrabel | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653a624548dad2312066755a/original/synthesis-of-c3-substituted-n1-tert-butyl-1-2-4-triazinium-salts-via-the-liebeskind-srogl-reaction-for-fluorogenic-labeling-of-live-cells.pdf |
60c74d38bdbb8971bea39941 | 10.26434/chemrxiv.12318689.v2 | An in-silico evaluation of COVID-19 main protease with clinically approved drugs | <p></p><p>A novel strain
of coronavirus, namely, SARS-CoV-2 identified in Wuhan city of China in
December 2019, continues to spread at a rapid rate worldwide. There are no
specific therapies available and investigations regarding the treatment of this
disease are still lacking. In order to identify a novel potent inhibitor, we
performed blind docking studies on the main virus protease M<sup>pro</sup> with
eight approved drugs belonging to four pharmacological classes such as:
anti-malarial, anti-bacterial, anti-infective and anti-histamine. Among the
eight studied compounds, Lymecycline and Mizolastine appear as potential
inhibitors of this protease. When docked against M<sup>pro </sup>crystal
structure, these two compounds revealed a minimum binding energy of -8.87 and
-8.71 kcal/mol with 168 and 256 binding modes detected in the binding substrate
pocket, respectively. Further, to study the interaction mechanism and
conformational dynamics of protein-ligand complexes, Molecular dynamic
simulation and MM/PBSA
binding free calculations were performed. Our results showed that both Lymecycline and
Mizolastine bind in the active site. And exhibited good binding affinities
towards target protein. Moreover, the ADMET analysis also indicated
drug-likeness properties. Thus it is suggested that the identified compounds
can inhibit Chymotrypsin-like protease (3CL<sup>pro</sup>) of SARS-CoV-2. </p><br /><p></p> | TACHOUA Wafa; KABRINE Mohamed; Mamona Mushtaq; Zaheer Ul-Haq | Biochemistry; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d38bdbb8971bea39941/original/an-in-silico-evaluation-of-covid-19-main-protease-with-clinically-approved-drugs.pdf |
64305eb7736114c9631720de | 10.26434/chemrxiv-2023-ns82p | Rate Equations for Reversible Disproportionation Reactions and Fitting to Timecourse Data | Integrated rate equations are straightforward to fit to experimental data to verify a proposed mechanism and extract kinetic parameters. Such equations are derived for reversible disproportionation/comproportionation reactions with any set of initial concentrations. Extraction of forward and reverse rate constants from experimental data by fitting the rate law to the data are demonstrated for the disproportionation of TEMPO (2,2,6,6-tetramethyl-1-piperidinyl-N-oxyl) under acidic conditions where the approach to equilibrium is observed. | James Gerken; Alexios Stamoulis; Shannon Stahl | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Chemical Kinetics | CC BY NC 4.0 | CHEMRXIV | 2023-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64305eb7736114c9631720de/original/rate-equations-for-reversible-disproportionation-reactions-and-fitting-to-timecourse-data.pdf |
64f0deffdd1a73847fe81e98 | 10.26434/chemrxiv-2023-3vsls-v2 | EFFICIENT ORGANIC MOLECULAR CRYSTAL STRUCTURE PREDICTION USING THE DENSITY FUNCTIONAL TIGHT-BINDING METHOD | Over the years, crystal structure prediction (CSP) has thrived as an area of research, spanning various scientific disciplines, and having significant applications in industries such as pharmaceuticals and agrochemicals. Within the field of batteries, redox-active organic materials (ROMs) such as quinones have received increased attention as promising electrode materials for rechargeable batteries. However, experimental determination of the crystal structure of intermediate species formed during the discharge/charge cycle can often be challenging. Incomplete X-ray diffraction patterns can also lead to difficulties in crystal structure determination for ROMs used in batteries. Use of a semiempirical electronic structure method for CSP helps to avoid force field reparameterization for different species, sometimes with complex electronic structure, formed during battery operation. It also helps to significantly lower the computational cost compared to the widely used density functional theory (DFT). The goal of this study is to systematically investigate the ability of a DFT-based semiempirical method, third-order density functional tight-binding (DFTB3), to predict the most stable crystal structures of organic molecules with different kinds of intermolecular interactions ranging from hydrogen bonding to -stacking. Here, DFTB3 in conjunction with the particle swarm optimization (PSO) algorithm, as implemented in the CALYPSO software, is also used to predict the most stable crystal structures of selected quinones relevant to organic batteries. Our findings emphasize the potential of CALYPSO/DFTB as a promising approach for CSP of different classes of organic molecules, including quinones. Additionally, they establish the foundation for future CSP studies of other organic molecules utilized in rechargeable batteries. | Maureen Kitheka; Yan Jing; Yan Yao; Puja Goyal | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Materials Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f0deffdd1a73847fe81e98/original/efficient-organic-molecular-crystal-structure-prediction-using-the-density-functional-tight-binding-method.pdf |
6501320499918fe537db9426 | 10.26434/chemrxiv-2023-slnrf | ArI(NTf)2: The boundary of oxidative capacity for ArIL2? | Crystallographic characterization of NO2-C6H4-I(NTf)2 (NTF = bistriflimide) is reported. Experimental results find that this compound can perform oxidation reactions that ArI(OTf)2 is unable to and theoretical analysis indicates Ar-I(NTf)2 is the most oxidizing in the ArIL2 class of compound known and may also be the most oxidizing compound in the class practically possible. | Lachlan Barwise; Jason Bennetts; Jason Dutton | Inorganic Chemistry; Main Group Chemistry (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2023-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6501320499918fe537db9426/original/ar-i-n-tf-2-the-boundary-of-oxidative-capacity-for-ar-il2.pdf |
60c74029f96a001c3a28624d | 10.26434/chemrxiv.7565822.v2 | Ultrafast Photodissociation Dynamics of Pyrazole, Imidazole and their Deuterated Derivatives using Ab Initio Multiple Cloning | <div>Using the ab initio multiple cloning (AIMC) method, fully quantum dynamics were simulated for imidazole and its structural isomer pyrazole along with their selectively deuterated species, focussing on the ultrafast dissociation of the N-H/D bond for these molecules. Our results gave evidence for a two-stage dissociation of the N-H/D bond on the sub-50~fs regime for all molecules, and gave further evidence for the importance of the repulsive <sup>1</sup>πσ* state along the N-H/D bond coordinate for the relaxation of both imidazole and pyrazole.<br /></div> | Christopher Symonds; Dmitry Makhov; Neil C. Cole-Filipiak; James Green; Vasilios G. Stavros; Dmitry Shalashilin | Computational Chemistry and Modeling; Theory - Computational; Photochemistry (Physical Chem.); Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74029f96a001c3a28624d/original/ultrafast-photodissociation-dynamics-of-pyrazole-imidazole-and-their-deuterated-derivatives-using-ab-initio-multiple-cloning.pdf |
64b0a880ae3d1a7b0da82eb6 | 10.26434/chemrxiv-2023-4cbwb-v2 | AutoParams: An Automated Web-Based Tool To Generate Force Field Parameters for Molecular Dynamics Simulations | The growth of machine learning as a predictive tool in biochemical research has led to an increased need for large-scale datasets. Certain research questions benefit from molecular dynamics simulations to observe the motions and conformations of molecules over time, however contemporary methods rely on forcefields which describe sets of common biomolecules. Unusual molecules, such as nucleotide analogues, functionalized carbohydrates, and modified amino acids are often ill-described in standard forcefields, requiring the development of custom parameters for each unique molecule. While these parameters may be created by individual users, the process is time-consuming and can introduce errors that may not be immediately apparent. We present an open-source automated parameter generation service, AutoParams, which requires minimal input from the user and creates useful forcefield parameter sets for most molecules, particularly those that combine molecular types (ex: a carbohydrate functionalized with a benzene). It can be straightforwardly linked to any charge generation program, and currently has interfaces to PsiRESP and TeraChem, and is available via GitHub and as a Docker container. It includes error checking and testing protocols to ensure the parameters will be sufficient for subsequent molecular dynamics simulations, and streamlines the creation of force field databases. | Mark A. Hix; Alice R. Walker | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b0a880ae3d1a7b0da82eb6/original/auto-params-an-automated-web-based-tool-to-generate-force-field-parameters-for-molecular-dynamics-simulations.pdf |
651c9170bda59ceb9acd55e0 | 10.26434/chemrxiv-2023-3p8jv | Insight into Dehydrogenation of C2HX Species in Ethane Steam Reforming on Ir(100): A DFT Study | The reaction barrier and heat of formation of various dehydrogenation reactions involved in the steam reforming of ethane (SRE) are critical parameters in the understanding and improving the technology of SRE. Focusing on Ir-based catalyst, we report a comprehensive reaction network of dehydrogenation of ethane on Ir(100) based on extensive density functional theory (DFT) calculations on 10 C-H bond cleavage reactions. The geometric and electronic structures of the adsorption of C2Hx species with corresponding transition-state and product structures are reported. We found that the C-H bond in CH3C required the most energy to activate, due to the most stable four-fold hollow configuration of the adsorption site. Ethane can easily dissociate to CH3CH and CH2CH2 on Ir(100). By using the degree of dehydrogenation of the reactant species as a variable to correlate the C-H bond cleavage barrier as well as reaction energy, DFT results reveal that the Ir(100) surface to a great extent promotes ethane dehydrogenation when compared to other surfaces. | Rotimi Ore; Ruitao Wu; Lichang Wang | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Heterogeneous Catalysis; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651c9170bda59ceb9acd55e0/original/insight-into-dehydrogenation-of-c2hx-species-in-ethane-steam-reforming-on-ir-100-a-dft-study.pdf |
60c745014c891998f0ad28fb | 10.26434/chemrxiv.9956069.v1 | Elucidating the Molecular Basis of Avibactam Mediated Inhibition of Class A β-Lactamases | Disseminating antibiotic resistance rendered by bacteria against the widely used β-lactam antibiotics is a serious concern in the public health care. Development of inhibitors for drug-resistant β-lactamase enzymes is vital to combat this rapidly escalating problem. Recently, the Food and Drug Administration has approved a non-β-lactam inhibitor called avibactam for the treatment of complicated intra-abdominal and urinary tract infections caused by drug-resistant Gram-negative bacteria. This work sheds light on the molecular origin of the inhibitory effect of avibactam against drug resistant CTX-M variant of Class-A β-lactamase. Especially, we probed the structural evolution, dynamical features and energetics along the acylation and the deacylation reaction pathways through reliable enhanced sampling molecular dynamics methods and free energy calculations. We scrutinize the roles of active site residues, the nature of the carbonyl linkage formed in the inhibitor–enzyme covalent intermediate and other structural features of the inhibitor molecule. While unraveling the reasons behind the inhibition of all the deacylation routes, this study explains various experimental structural and kinetics data, and paves the way to design new inhibitors based on the β-lactam framework.<br /> | Chandan Kumar Das; Nisanth
N. Nair | Computational Chemistry and Modeling; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745014c891998f0ad28fb/original/elucidating-the-molecular-basis-of-avibactam-mediated-inhibition-of-class-a-lactamases.pdf |
67cfbb1c81d2151a02f4efc6 | 10.26434/chemrxiv-2024-pf3ph-v2 | Conformal Selection for Efficient and Accurate Compound Screening in Drug Discovery | In drug discovery, the reliability of compound screening based on manual assessments is compromised by potential bias, while existing methods lack robust risk control measures. To address these challenges, we introduced conformal selection as an enhanced approach to optimize the compound screening process with balanced risks and benefits. Leveraging conformal inference, our approach constructs p-values for each candidate molecule to quantify statistical evidence for selection. The final selection of molecules is determined by comparing these p-values against thresholds derived from multiple testing principles. Our approach offers rigorous control over the false discovery rate, ensuring validity independent of dataset size and requiring minimal assumptions. By avoiding the estimation of prediction errors required in previous approaches, our method achieves higher accuracy (power), thereby improving the ability to identify promising candidates. Furthermore, our method demonstrates superior computational efficiency. We validate these advantages through numerical simulations on real-world datasets. | Tian Bai; Peng Tang; Yuting Xu; Vladimir Svetnik; Bingjia Yang; Abbas Khalili; Xiang Yu; Archer Yang | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cfbb1c81d2151a02f4efc6/original/conformal-selection-for-efficient-and-accurate-compound-screening-in-drug-discovery.pdf |
66c9bf8f20ac769e5fb3b36a | 10.26434/chemrxiv-2024-jp0vj | Knowles Partitioning at the Multi-reference Level | A multi-reference generalization of the partitioning introduced recently by Knowles (J. Chem. Phys. 2022 156, 011101) is presented with the aim to study electronic systems at a medium level of correlation. The multi-reference formalism applied is the general framework of multi-configuration perturbation theory (MCPT). | Ágnes Szabados; András Gombás; Péter Surján | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c9bf8f20ac769e5fb3b36a/original/knowles-partitioning-at-the-multi-reference-level.pdf |
65baa07b9138d2316124f224 | 10.26434/chemrxiv-2023-k7ct5-v2 | Fine-tuning Large Language Models for Chemical Text Mining | Extracting knowledge from complex and diverse chemical texts is a pivotal task for both experimental and computational chemists. The task is still considered to be extremely challenging due to the complexity of the chemical language and scientific literature. This study explored the power of fine-tuned large language models (LLMs) on five intricate chemical text mining tasks: compound entity recognition, reaction role labelling, metal-organic framework (MOF) synthesis information extraction, nuclear magnetic resonance spectroscopy (NMR) data extraction, and the conversion of reaction paragraph to action sequence. The fine-tuned LLMs models demonstrated impressive performance, significantly reducing the need for repetitive and extensive prompt engineering experiments. For comparison, we guided GPT-3.5 and GPT-4 with prompt engineering and fine-tuned GPT-3.5 as well as other open-source LLMs such as Llama2, T5, and BART. The results showed that the fine-tuned GPT models excelled in all tasks. It achieved exact accuracy levels ranging from 69% to 95% on these tasks with minimal annotated data. It even outperformed those task-adaptive pre-training and fine-tuning models that were based on a significantly larger amount of in-domain data. Given its versatility, robustness, and low-code capability, leveraging fine-tuned LLMs as flexible and effective toolkits for automated data acquisition could revolutionize chemical knowledge extraction. | Wei Zhang; Qinggong Wang; Xiangtai Kong; Jiacheng Xiong; Shengkun Ni; Duanhua Cao; Buying Niu; Mingan Chen; Runze Zhang; Yitian Wang; Lehan Zhang; Xutong Li; Zhaoping Xiong; Qian Shi; Ziming Huang; Zunyun Fu; Mingyue Zheng | Theoretical and Computational Chemistry; Organic Chemistry; Materials Science; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65baa07b9138d2316124f224/original/fine-tuning-large-language-models-for-chemical-text-mining.pdf |
6641291791aefa6ce1d032d4 | 10.26434/chemrxiv-2024-wsjwh | Interfacial Water Structural Entropy as the Descriptor for pH-dependent HOR/HER Activity on Pt | The transition to renewable energy and variability in solar and wind production rates necessitates the use of an energy intermediary, well suited to acid based electrolyzer and fuel cell devices in an idealized hydrogen economy. However, high material costs have motivated a transition to alkaline based devices, exposing pH dependent performance losses on traditionally ideal catalysts. Understanding reduced hydrogen oxidation and evolution (HOR/HER) activity on platinum with increasing pH is essential from both a fundamental electrocatalysis perspective to the engineering of electrochemical interfaces. Here we show that reducing electrolyte water structural entropy (SStr) to promote hydrogen bonding with benzyl tri-alkylammonium cations and dibenzo crown ethers improves HOR/HER kinetics in 0.1 M KOH by 25%. In situ surface enhanced infrared spectroscopy verifies strengthened water hydrogen bonding through increased ν(O-H) stretching bands between 3000 and 3200 cm-1. Hydrogen bonding allows for facile transfer of H+/OH- between the electrolyte bulk and interface through the Grotthuss mechanism. Our results show that SStr is the descriptor for HOR/HER kinetics and engineering it through substitution and conversion of structure breakers or incorporation of structure makers, can increase HOR/HER kinetics. | Nicholas Oliveira; Yushan Yan | Materials Science; Catalysis; Energy; Electrocatalysis; Energy Storage; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6641291791aefa6ce1d032d4/original/interfacial-water-structural-entropy-as-the-descriptor-for-p-h-dependent-hor-her-activity-on-pt.pdf |
67cf4fb281d2151a02e8e0b7 | 10.26434/chemrxiv-2025-18qfh | Monitoring Confined Inorganic-Polyepoxy-Inorganic Adhesive Interfacial Changes during Curing
at Various Environmental Conditions
| Polyepoxides are becoming a preferred alternative to heavier materials in structural applications, functioning as bonding agents and matrices for high-performance composites. The durability of polyepoxy-inorganic substrate interfaces depends on surface treatments (physical and chemical) and environmental curing conditions such as temperature, humidity, and mechanical stress. Detecting real-time changes at these interfaces is crucial to prevent failures. This study used a Surface Forces Apparatus (SFA) with multiple beam interferometry to investigate interface degradation during curing and aging. A stoichiometric mixture of bisphenol-A diglycidyl ether (BADGE) and amine-terminated polyoxypropylene glycol (JeffAmine D-230) was confined between smooth alumina substrates under varying humidity. The SFA and fringes of equal chromatic order (FECO) technique enabled real-time imaging and refractive index measurements of the confined polyepoxy. Curing strains and stresses were monitored over 48 hours. Key findings include: (1) low tensile forces promote complete curing across different humidity levels, dominated by molecular interactions; (2) high tensile forces prevent full curing unless compressive forces are applied; (3) high humidity rapidly induces water diffusion, increasing plasticization and preventing cure. Additional micro-tensile tests and failure analysis imaging revealed primarily cohesive (polymer-polymer) rather than adhesive (polymer-substrate) failure modes. This study introduces a novel method for assessing interface quality in polyepoxy-inorganic substrate systems, which has implications for various technological applications requiring durable bonding and adhesion performance. | Roberto Andresen Eguiluz; Jeffrey Scott; Kai Kristiansen; Howard Dobbs; Thomas Cristiani; George Degen; Szu-Ying Chen; Jacob Israelachvili | Materials Science; Polymer Science | CC BY 4.0 | CHEMRXIV | 2025-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cf4fb281d2151a02e8e0b7/original/monitoring-confined-inorganic-polyepoxy-inorganic-adhesive-interfacial-changes-during-curing-at-various-environmental-conditions.pdf |
6505caa999918fe5370e1dfd | 10.26434/chemrxiv-2023-8kc5t-v2 | Aromaticity Reversal Induced by Vibrations in Cyclo[16]carbon | Aromaticity is typically regarded as an in-trinsic property of a molecule. It is often correlated with electron delocalization, stability, and other properties. Small variations in the molecular geometry usually result in small changes in aromaticity, in line with Hammond’s postu-late: for example, introducing bond-length alternation in benzene and square cyclobutadiene gradually decreases the magnitude of their ring currents, making them less aromatic and less antiaromatic, respectively. A sign change in the ring current, corresponding to a reversal of aromaticity, typically requires a gross perturbation such as electronic excitation, addition or removal of two electrons, or a dramatic change in the molecular geometry. Here, we use multireference calculations to show how small changes in bond-length alternation induce a sudden reversal in the ring current of cyclo[16]carbon, C16. This reversal occurs when the two orthogonal π systems of C16 sustain opposing currents. These results are rationalized by a Hückel model which includes bond-length alternation combined with a minimal model accounting for orbital contributions to the ring current. Finally, we successfully describe the electron-ic structure of C16 with a divide-and-conquer approach suitable for execution on a quantum computer. | Igor Rončević; Freddie J. Leslie; Max Rossmannek; Ivano Tavernelli; Leo Gross; Harry L. Anderson | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6505caa999918fe5370e1dfd/original/aromaticity-reversal-induced-by-vibrations-in-cyclo-16-carbon.pdf |
626b4fb8368ab605a6913fe3 | 10.26434/chemrxiv-2022-hvf9g | The importance of a charge transfer descriptor for the screening of electrocatalysts at the example of CO2 reduction. | It has been over twenty years, since the linear scaling of reaction intermediate adsorption energies has started to coin the fields of heterogeneous and electrocatalysis as a blessing and a curse at the same time. It has established the possibility to construct activity volcano plots as a function of a single or two readily accessible adsorption energies as descriptors, but also limited the maximal catalytic conversion rate. In this work, we find that these established adsorption energy-based descriptor spaces are not applicable to electrochemistry, because they are lacking an important additional dimension, the potential of zero charge (PZC). The PZC-dependence arises from the interaction of the electric double layer with reaction intermediates which does not scale with adsorption energies. At the example of the electrochemical reduction of CO2, we show that the PZC descriptor breaks the scaling relations, opening up a huge chemical space which is readily accessible via PZC-based material design. The PZC dependence also reveals intriguing material trends in close agreement with reported experimental data highlighting the importance of the PZC for electrocatalyst design. | Stefan Ringe | Theoretical and Computational Chemistry; Catalysis; Energy; Theory - Computational; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2022-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626b4fb8368ab605a6913fe3/original/the-importance-of-a-charge-transfer-descriptor-for-the-screening-of-electrocatalysts-at-the-example-of-co2-reduction.pdf |
64916165853d501c002eff51 | 10.26434/chemrxiv-2023-kccqn | Photoinduced dearomatization of (hetero)arenes catalyzed by polysulfide anions | The facile construction of C(sp3)-rich carbo- and heterocyclic compounds is a pivotal synthetic strategy to foster contemporary drug discovery programs. The downstream dearomatization of readily accessible two-dimensional (2D) planar arenes represents a direct pathway towards accessing three-dimensional (3D) aliphatic scaffolds. Here, we demonstrate that polysulfide anions are capable of catalyzing a dearomatization process of substituted naphthalenes, indoles, and other related heteroaromatic compounds in the presence of potassium formate and methanol under visible light irradiation. The developed protocol exhibits broad functional group tolerance, operational simplicity, scalability, and cost-effectiveness, representing a practical and sustainable alternative synthetic tool for the arene dearomatization. | Eugene Yew Kun Tan; Amirah S. Mat Lani; Wayne Sow; Yuliang Liu; Haoyu Li; Shunsuke Chiba | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64916165853d501c002eff51/original/photoinduced-dearomatization-of-hetero-arenes-catalyzed-by-polysulfide-anions.pdf |
65b39bf19138d23161c949ad | 10.26434/chemrxiv-2024-gmjgr | Organic Dye Photocatalyzed Synthesis of Functionalized Lactones and Lactams via a Cyclization-Alkynylation Cascade | An organic dye photocatalyzed lactonization-alkynylation of easily accessible homoallylic cesium oxalates using ethynylbenziodoxolones (EBXs) reagents has been developed. The reaction gave access to valuable functionalized lactones and lactams in up to 88% yield via the formation of two new C-C bonds. The transformation was carried out on primary, secondary and tertiary homoallylic alcohols and primary homoallylic amines and could be applied to the synthesis of spirocyclic compounds, as well as fused and bridged bicyclic lactones. | Diana Cavalli; Jerome Waser | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2024-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b39bf19138d23161c949ad/original/organic-dye-photocatalyzed-synthesis-of-functionalized-lactones-and-lactams-via-a-cyclization-alkynylation-cascade.pdf |
60c74f3dbdbb8983a6a39d32 | 10.26434/chemrxiv.12869900.v1 | Surface Chemical Trapping of Optical Cycling Centers | <div>Quantum information processors based on trapped atoms utilize laser-induced optical cycling transitions for state preparation and measurement. These transitions consist of an electronic excitation from the ground to an excited state and a decay back to the initial ground state, associated with a photon emission. While this technique has been used primarily with atoms, it has also recently been shown to work for some divalent metal hydroxides (e.g. SrOH) and alkoxides (e.g. SrOCH3). This extension to molecules is possible because these molecules feature nearly isolated, atomic-like ground and first-excited electronic states centered on the radical metal atom. We theoretically investigate the extension of this idea to a larger scale by growing the alkyl group, R, beyond the initial methyl group, CH3, while preserving the isolated and highly vertical character of the electronic excitation on the radical metal atom, M. Theory suggests that in the limit as the size of the ligand carbon chain increases, it can be considered a functionalized diamond (or cubic boron nitride) surface. Several requirements must be observed for the cycling centers to function when bound to the surface. First, the surface must have a significant band gap that fully encapsulates both the ground and excited states of the cycling center. Second, while the surface lattice imposes strict limits on the achievable spacing between the SrO- groups, at high coverage, SrO- centers can interact, and show geometric changes and/or electronic state mixing. We show that the coverage of the diamond surface with SrO- cycling centers needs to be significantly submonolayer for the functionality of the cycling center to be preserved. Having the lattice-imposed spatial control of SrO- placements will allow nanometer-scale proximity between qubits and will eliminate the need for atom traps for localized cycling emitters. Our results also imply that a functionalization could be done on a scanning microscope tip for local quantum sensing or on photonic structures for optically-mediated quantum information processing. </div> | Han Guo; Claire E. Dickerson; Ashley Shin; Changling Zhao; Timothy Atallah; Justin Caram; Wesley C. Campbell; Anastassia N. Alexandrova | Computational Chemistry and Modeling; Theory - Computational; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f3dbdbb8983a6a39d32/original/surface-chemical-trapping-of-optical-cycling-centers.pdf |
62a06add70f8a71131fb3b63 | 10.26434/chemrxiv-2022-dgvgt-v2 | Investigation of the Effectiveness of Aquatic Plants in Filtering Contaminated Water | Population increase and rapid urbanization are two major factors for scarcity of clean water in 21st century societies across the world. Modern sewage water treatment plants and filtration systems require a lot of economic and land resources which many “lesser developed countries” do not have, leading to large amounts of raw sewage water being released into the enviornment and a lack of clean water for millions. To fulfil such water demand, the use of aquatic plants, also known as macrophytes, have been used in a constructed wetland which allows for the filtration of contaminated water using natural processes involving wetland vegetation, soils, and their associated microbial assemblages. In the present study, Typha (cattail) and Pontederia crassipes (water hyacinth) have been tested in a simulated constructed wetland to study their effect on pollutants removal efficiency (nitrates, ammonium, pH, and Dissolved oxygen). Results show that both the Typha and Pontederia crassipes were effective in filtering out the aforementioned contaminants through the process of phytoaccumulation. However, there was no clear correlation between Dissolved oxygen levels and time in contact with the macrophyte roots possibly due to environmental factors. A better quantitative understanding of the phytoaccumulation process, such as the limits and plateau points of contaminant uptake is needed to optimize the usage and application of Typha and Pontederia crassipes in practical constructed wetlands. | Andrew Lee; Jude Clapper | Biological and Medicinal Chemistry; Earth, Space, and Environmental Chemistry; Agriculture and Food Chemistry; Environmental Science; Environmental biology; Plant Biology | CC BY 4.0 | CHEMRXIV | 2022-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a06add70f8a71131fb3b63/original/investigation-of-the-effectiveness-of-aquatic-plants-in-filtering-contaminated-water.pdf |
67ddd86481d2151a025e2d59 | 10.26434/chemrxiv-2025-26vjz-v2 | High and Ultra-High Temperature Reaction Kinetics by Single Nanoparticle Mass Spectrometry | Methodology is presented for non-destructive, optically-detected single nanoparticle (NP) mass
spectrometry, with the goal of extracting surface reaction kinetics for single NPs at high temperatures.
Methods for determining the NP charge, mass, and temperature as a function of time are discussed, and
the data are used to extract both the absolute kinetics for mass change, as well as the efficiencies of the
surface processes that cause them. Factors that contribute to the uncertainties in absolute and relative
mass determination, and in the resulting kinetic parameters, are discussed. The method allows the NP-to-
NP variations in initial reactivity to be measured directly, along with the time evolution of reactivity
resulting from NP structural/compositional changes that occur under reaction conditions.
The strengths and limitations of single nanoparticle mass spectrometry as a high temperature surface
kinetics tool are discussed in the context of sublimation and O2 oxidation kinetics experiments for single
hafnium (Hf) NPs at temperatures ranging above 2400 K. The Hf oxidation kinetics are compared to
analogous oxidation experiments for silicon, graphite, and carbon black NPs. In all four cases, the
oxidation chemistry was dominated by processes that result in net mass loss, and the distinct mechanisms
responsible are discussed. All four NPs also eventually passivated, i.e., the efficiencies for oxidative
etching decreased by at least two orders of magnitude, relative to the initial efficiencies. The passivation
mechanisms, which are quite different for carbon, compared to silicon or hafnium, are discussed. Carbon
NP passivation is attributed to structural isomerization leading to fully coordinated, fullerene-like NP
surfaces, while for silicon and hafnium, passivation results from delayed formation of an oxide layer,
triggered by accumulation of oxygen in the NP sub-surface region. | Abigail Friese; Audrey Burrows; Scott Anderson | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Chemical Kinetics; Surface; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ddd86481d2151a025e2d59/original/high-and-ultra-high-temperature-reaction-kinetics-by-single-nanoparticle-mass-spectrometry.pdf |
60c741e69abda2c721f8bf26 | 10.26434/chemrxiv.8038973.v2 | Controlling Thermal Stability and Volatility of Organogold(I) Compounds for Vapor Deposition with Complementary Ligand Design | We compare and contrast the volatility and thermal stability of a family of twelve organometallic gold(I) compounds using a combination of X-ray crystallography, thermogravimetric analysis (TGA), and density functional theory (DFT) techniques. Pentafluorophenyl is used as a new ligand for vapor deposition which produces rather low volatility, but very thermally stable compounds when combined with PMe<sub>3</sub> and <i>N</i>,<i>N</i>'-di-<i>tert</i>-butylimidazolidin-2-ylidene. We introduce a precursor figure of merit that can be used to rank precursor usefulness. Using DFT, we find a linear correlation between Au-L bond strength and thermal stability, which demonstrates the power of computational techniques to predict successful synthetic targets for future precursor design studies. | Matthew Griffiths; Zachary Dubrawski; Goran Bačić; Jason Masuda; Achini Japahuge; Tao Zeng; Sean Barry | Bonding; Coordination Chemistry (Inorg.); Ligands (Inorg.); Organometallic Compounds; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e69abda2c721f8bf26/original/controlling-thermal-stability-and-volatility-of-organogold-i-compounds-for-vapor-deposition-with-complementary-ligand-design.pdf |
64ddb0724a3f7d0c0d4cd530 | 10.26434/chemrxiv-2023-nc64t | Balance between physical interpretability and energetic predictability in widely used dispersion-corrected density functionals | We assess the performance of different dispersion models for several popular density functionals across a diverse set of non-covalent systems, ranging from the benzene dimer to molecular crystals. By analyzing the interaction energies and their individual components, we demonstrate that there exists variability across different systems for empirical dispersion models, which are calibrated for reproducing the interaction energies of specific systems. Thus, parameter fitting may undermine the underlying physics, as dispersion models rely on error compensation among the different components of the interaction energy. Energy decomposition analyses reveal that, the accuracy of revPBE-D3 for some aqueous systems originates from significant compensation between dispersion and charge transfer energies. However, revPBE-D3 is less accurate in describing systems where error compensation is incomplete, such as the benzene dimer. Such cases highlight the propensity for unpredictable behavior in various dispersion-corrected density functionals across a wide range of molecular systems, akin to the behavior of force fields. On the other hand, we find that SCAN-rVV10, a targeted-dispersion approach, affords significant reductions in errors associated with the lattice energies of molecular crystals, whilst it has limited accuracy in reproducing structural properties. Given the ubiquitous nature of non-covalent interactions and the key role of density functional theory in computational sciences, the future development of dispersion models should prioritize the faithful description of the dispersion energy, a shift that promises greater accuracy in capturing the underlying physics across diverse molecular and extended systems. | Saswata Dasgupta; Etienne Palos; Yuanhui Pan; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Quantum Mechanics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ddb0724a3f7d0c0d4cd530/original/balance-between-physical-interpretability-and-energetic-predictability-in-widely-used-dispersion-corrected-density-functionals.pdf |
643d315608c86922ff289ddb | 10.26434/chemrxiv-2023-5l0sj | Assessing Utilization Boundaries for Pt-based Catalysts in an Operating PEMFC | Octahedra (oh) PtNiX/C catalysts have attracted attention as cathode catalysts for proton-exchange membrane fuel cells (PEMFCs) due to their exceptional catalytic activities toward the oxygen reduction reaction. Here, we investigate the degradation dynamics of oh-PtNiIr in fuel cell conditions by operando X-ray diffraction (XRD). Two XRD-coupled square-wave accelerated stress tests (0.6 to 0.95) V and (0.7 to 0.95) V (where V is the cell voltage) confirm that, when fixing the upper limit, the dissolution and overall degradation strongly depend on the lower potential limit. By directly observing the extent of metal oxidation during potential cycling, we link the alloy redox dynamics to the stability. The studied catalysts' stability is proportional to both the extent of metal oxidation and, more interestingly, the degree of reduction. Comparing a benchmark Pt catalyst with oh-PtNiIr allows for associating the differences between oxidation and reduction potentials and the optimal usage window for each class of catalysts. This relatively simple method can be employed to find the operation boundaries of the PEMFC to minimize the degradation of a large class of Pt-based catalysts without time-consuming stress tests. | Michal Ronovský; Lujin Pan; Malte Klingenhof; Isaac Martens; Raphael Chattot; Lukáš Fusek; Peter Kúš; Marta Mirolo; Fabio Dionigi; Harriet Burdett; Jonathan Sharman; Peter Strasser; Alex Martinez Bonastre; Jakub Drnec | Catalysis; Energy; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms; Fuel Cells; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643d315608c86922ff289ddb/original/assessing-utilization-boundaries-for-pt-based-catalysts-in-an-operating-pemfc.pdf |
634e7cc34b0af36129c9be2b | 10.26434/chemrxiv-2022-9l5gq | Denitrative hydroxylation of unactivated nitroarenes | A one-step method for the conversion of nitroarenes into phenols under operationally simple, transition-metal-free conditions is described. This denitrative functionalisation protocol provides a concise and economical alternative to conventional three-step synthetic sequences. Experimental and computational studies suggest that unactivated nitroarenes may be substituted via an electron-catalysed radical-nucleophilic substitution (SRN1) chain mechanism. | Lee Duff; Harry Meakin; Adam Richardson; Andrew Greener; George Smith; Ivan Ocaña; Victor Chechik; Michael James | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634e7cc34b0af36129c9be2b/original/denitrative-hydroxylation-of-unactivated-nitroarenes.pdf |
6718440912ff75c3a13d759e | 10.26434/chemrxiv-2024-7xklv | Decoupling First-Cycle Capacity Loss Mechanisms in Sulfide Solid-State Batteries | Solid-state batteries (SSBs) promise more energy-dense storage than liquid electrolyte lithium ion batteries (LIBs). However, first-cycle capacity loss is higher in SSBs than in LIBs due to interfacial reactions. The chemical evolution of key interfaces in SSBs has been extensively characterized. Electrochemically, however, we lack a versatile strategy for quantifying the reversibility of solid electrolyte (SE) redox for established and next-generation SSB electrolytes. In this work, we perform tailored electrochemical tests and operando X-ray diffraction to disentangle reversible and irreversible sources of capacity loss in positive electrodes composed of Li6PS5Cl SE, Li(Ni0.5Mn0.3Co0.2)O2 (NMC), and carbon conductive additives. We leverage an atypically low voltage cutoff (2.0 V vs. Li/Li+) to quantify the reversibility of SE redox. Using slow (5.5 mA g−1 NMC) cycling paired with > 100 h low-voltage holds, our cells achieve a surprising 96.2% first-cycle Coulombic efficiency, which is higher than previously reported (mean: 72%, maximum: 91.6% across surveyed literature). We clarify that sluggish NMC relithiation kinetics have been historically mistaken for permanently irreversible capacity loss. Through systematic decoupling of loss mechanisms, we uncover the unexpected reversibility of SE redox and isolate the major contributors to capacity loss, outlining a strategy for an accurate assessment of next-generation SE materials and interface modifications. | Emma Kaeli; Zhelong Jiang; Xiaomian Yang; Emma Choy; Nicolas Liang; Edward Barks; Sunny Wang; Stephen Kang; William Chueh | Materials Science | CC BY NC 4.0 | CHEMRXIV | 2024-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6718440912ff75c3a13d759e/original/decoupling-first-cycle-capacity-loss-mechanisms-in-sulfide-solid-state-batteries.pdf |
60c74003469df4653ef42bb0 | 10.26434/chemrxiv.7581590.v1 | Instructed-Assembly as Context-Dependent Nanoscale Signals for Death and Morphogenesis of Cells | Context-dependent signaling, as a ubiquitous phenomenon in nature, is a dynamic molecular process at nano- and microscales, but how to mimic its essence using non-covalent synthesis in cellular environment has yet to be developed. Here we show a dynamic continuum of non-covalent filaments formed by instructed-assembly (iA) of a supramolecular phosphoglycopeptide (sPGP) as context-dependent signals for controlling death and morphogenesis of cells. Specifically, while enzymes (i.e., ectophosphatases) on cancer cells catalyze the formation of the filaments of the sPGP to result in cell death, damping the enzyme activity induces 3D cell spheroids. Similarly, relying on the ratio of stromal and cancer cells in a co-culture to modulate the expression of the ectophosphatase, the iA process enables cell spheroids. The spheroids act as a mimic of tumor microenvironment for drug screening. As the first demonstration of iA as multifunctional processes according to local enzyme activity for controlling cell behavior, this work illustrates context-dependent biological functions of non-covalent synthesis in cellular environment. | Huaimin Wang; Zhaoqianqi Feng; Bing Xu | Supramolecular Chemistry (Org.); Nanostructured Materials - Materials; Imaging; Biochemistry; Cell and Molecular Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74003469df4653ef42bb0/original/instructed-assembly-as-context-dependent-nanoscale-signals-for-death-and-morphogenesis-of-cells.pdf |
63576b40aa278413a54b3462 | 10.26434/chemrxiv-2022-vtnkq-v2 | Protein Cargo Encapsulation by Virus-Like Particles: Strategies and Applications | Viruses and the recombinant protein cages assembled from their structural proteins, known as virus-like particles (VLPs), have gained wide interest as tools in biotechnology and nanotechnology. Detailed structural information and their amenability to genetic and chemical modification make them attractive systems for further engineering. This review describes the range of non-enveloped viruses that have been co-opted for heterologous protein cargo encapsulation and the strategies that have been developed to drive encapsulation. Spherical capsids of a range of sizes have been used as platforms for protein cargo encapsulation. Various approaches, based on native and non-native interactions between the cargo proteins and inner surface of VLP capsids, have been devised to drive encapsulation. Here we outline the evolution of these approaches, discussing their benefits and limitations. Like the viruses from which they are derived, VLPs are of interest in both biomedical and materials applications. The encapsulation of protein cargo inside VLPs leads to numerous uses in both fundamental and applied biocatalysis and biomedicine, some of which are discussed herein. The applied science of protein encapsulating VLPs is emerging as a research field with great potential. Developments in loading control, higher order assembly, and capsid optimization are poised to realize this potential in the near future. | Donna McNeale; Noor Dashti; Li Chen Cheah; Frank Sainsbury | Biological and Medicinal Chemistry; Catalysis; Nanoscience; Bioengineering and Biotechnology; Chemical Biology; Biocatalysis | CC BY NC 4.0 | CHEMRXIV | 2022-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63576b40aa278413a54b3462/original/protein-cargo-encapsulation-by-virus-like-particles-strategies-and-applications.pdf |
64ce07a769bfb8925a679c3c | 10.26434/chemrxiv-2023-zbssm-v3 | 18F-Fluorination of 2-methyl-6-nitrobenzenesulfonate ester and its application to the synthesis of a 18F-labeled amino acid. | In the development of an efficient 18F-labeling method for the synthesis of PET tracers, it is essential not only to improve the efficiency of [18F]fluorine incorporation into a carrier but also to minimize non-radioactive side products from the precursor. Highly reactive sulfonate esters are promising precursors for 18F-nucleophilic fluorination under mild conditions. However, the expected labeling efficiency from the precursor is often hampered by its competitive degradation due to coexisting bases during 18F-fluorination. In this report, we designed a 2-methyl-6-nitrobenzenesulfonate (2-MeNs) ester as a precursor for 18F-fluorination, in which the methyl group suppresses hydrolysis of the sulfonate ester via steric hindrance. An increase in labeling efficiency in the 18F-labeling of a neopentyl labeling group was observed for the neopentyl 2-MeNs ester compared with that of the 2-nitrobenzenesulfonate ester. Ultimately, we achieved the automated synthesis of an 18F-labeled amino acid using a neopentyl labeling group by using a 2-MeNs ester as a precursor. | Shogo Iida; Tetsuro Tago; Masatoshi Tada; Jun Toyohara; Hiroshi Tanaka | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ce07a769bfb8925a679c3c/original/18f-fluorination-of-2-methyl-6-nitrobenzenesulfonate-ester-and-its-application-to-the-synthesis-of-a-18f-labeled-amino-acid.pdf |
60c74548469df43eacf434a6 | 10.26434/chemrxiv.9890141.v1 | Fundamental Design Rules for Turning on Fluorescence in Ionic Molecular Crystals | <p>Fluorescence is critical to many advanced materials including OLEDs and bioimaging. While molecular fluorophores that show bright emission in solution are potential sources of these materials, their emission is frequently lost in the solid state preventing their direct translation to optical applications. Unpredictable packing and coupling of dyes leads to uncontrolled spectral shifts and quenched emission. No universal solution has been found since Perkin made the first synthetic dye 150 years ago. We report the serendipitous discovery of a new type of material that we call <i>small-molecule ionic isolation lattices</i>(SMILES) tackling this long-standing problem. SMILES are easily prepared by adding two equivalents of the anion receptor cyanostar to cationic dyes binding the counter anions and inducing alternating packing of dyes and cyanostar-anion complexes. SMILES materials reinstate solution-like spectral properties and bright fluorescence to thin films and crystals. These positive outcomes derive from the cyanostar. Its wide 3.45-eV band gap allows the HOMO and LUMO levels of the dye to nest inside those of the complex as verified by electrochemistry. This feature simultaneously enables spatial and electronic isolation to decouple the fluorophores from each other and from the cyanostar-anion lattice. Representative dyes from major families of fluorophores, viz, xanthenes, oxazines, styryls, cyanines, and trianguleniums, all crystalize in the characteristic structure and regain their attractive fluorescence. SMILES crystals of rhodamine and cyanine display unsurpassed brightness per volume pointing to uses in demanding applications such as bioimaging. SMILES materials enable predictable fluorophore crystallization to fulfil the promise of optical materials by design.</p> | Christopher R. Benson; Laura Kacenauskaite; Katherine L. VanDenburgh; Wei Zhao; Bo Qiao; Tumpa Sadhukhan; Maren Pink; Junsheng Chen; Sina Borgi; Chun-Hsing Chen; Krishnan Raghavachari; Bo W. Laursen; Amar Flood | Organic Compounds and Functional Groups; Photochemistry (Org.); Physical Organic Chemistry; Supramolecular Chemistry (Org.); Dyes and Chromophores; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74548469df43eacf434a6/original/fundamental-design-rules-for-turning-on-fluorescence-in-ionic-molecular-crystals.pdf |
675a25c4f9980725cfc5f313 | 10.26434/chemrxiv-2024-qb5wr | Rapid, Scalable Buchwald-Hartwig Amination by Resonant Acoustic Mixing (RAM): Establishing Parameters for RAM Reaction Design | We outline the systematic development of Resonant Acoustic Mixing (RAM) for rapid, scalable Buchwald-Hartwig amination in the absence of bulk solvent. While RAM is rapidly emerging as a scalable methodology for media-free mechanochemical synthesis, the design parameters for reaction control, optimization, and scale-up remain poorly understood. This study establishes the filling ratio (φ), acceleration, and amount of liquid additive (η) as three critical parameters that can be used to design scalable Buchwald-Hartwig coupling reactions under RAM conditions. Systematic investigation of several model reactions reveals a relationship between reaction conversion and φ, providing a simple means to maximize conversion. The simultaneous real-time in situ monitoring of a model reaction through infrared thermography, fingerprint Raman, as well as low-frequency Raman (THz-Raman) spectroscopy enabled correlation of the reaction progress with the evolution of temperature during RAM, and established the RAM acceleration as a parameter that can be used to tune the reaction kinetic behavior. At high accelerations the reactions can proceed under sigmoidal kinetics, enabling multi-gram syntheses within 5 minutes, while lower accelerations can be used to switch the reactions to a more linear kinetic profile, associated with longer reaction times and milder temperature profiles. Following the reaction progress in the THz-Raman region is a reaction monitoring strategy that enables the detection of crystalline and non-crystalline phases in the reaction, permitting the observation of a non-crystalline intermediate whose evolution and replacement with the crystalline product could be tracked through non-negative least-squares fitting algorithm of the real-time spectroscopic data. This study establishes key parameters for manipulating the course and stoichiometric selectivity of a metal-catalyzed reaction in RAM and illustrates the scalability to at least 100 mmol without any protocol changes, except the volume of the vessel. | Lori Gonnet; Cameron Lennox; Tristan Borchers; Mohammad Askari; Alexander Wahrhaftig-Lewis; Stefan Koenig; Karthik Nagapudi; Tomislav Friscic | Organic Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675a25c4f9980725cfc5f313/original/rapid-scalable-buchwald-hartwig-amination-by-resonant-acoustic-mixing-ram-establishing-parameters-for-ram-reaction-design.pdf |
63d01e7d66069413153cc1f7 | 10.26434/chemrxiv-2023-2shgz | Copper-Catalyzed, Aerobic Aminooxygenation of N-Alkoxycinnamyl Carbamates via Substrate-Promoted Catalyst Activation | We report a method for a ligand-enabled, copper-catalyzed, aerobic aminooxygenation of internal alkenes. The synergistic combination of a phenanthroline-based ligand and substrate coordination promotes reduction of Cu(II) to Cu(I), resulting in a cyclization that proceeds via an amidyl radical pathway rather than a previously-established aminocupration path-way. The complementary reactivity enabled by this switch in reaction mechanism provides access to new substrate classes and a considerably broadened scope for this transformation. Experimental evidence supports a free radical mechanism involving substrate-promoted reduction to Cu(I) as well as the role of O2 as both oxidant and functionalizing agent. | Caitlyn P. McNichol; Ethan M. DeCicco; Amanda M. Canfield; Daniel P. Carstairs; Shauna M. Paradine | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d01e7d66069413153cc1f7/original/copper-catalyzed-aerobic-aminooxygenation-of-n-alkoxycinnamyl-carbamates-via-substrate-promoted-catalyst-activation.pdf |
6723b9fd7be152b1d09865eb | 10.26434/chemrxiv-2024-n178z | Core-extended Naphthalene Diimide dyads as light-up probes with targeted cytotoxicity toward tumor cells | In the frame of rational drug design this study introduces a novel approach to enhance the specificity of small molecules in targeting cancer cells. The approach starts from the use of dyads merging into a single entity a naphthalene diimide (NDI) and core-extended NDI (ceNDIs), both known as G-quadruplex (G4) ligands and fluorescent probes. The strategy aims to leverage the unique diagnostic strenghts of the ceNDI moiety featuring red emission by improving binding affinity and target selectivity through inclusion in dyads built with different linkers. A flexible and more rigid linker were used for this scope. The newly developed NDI-ceNDI dyads are promising probes as they exhibit both fluorescence turn-on upon DNA recognition and induced circular dichroism signals dependent on DNA conformation. Both dyads are endowed with excellent affinity for hybrid G4 with binding constants two orders of magnitude higher than those for ds DNA. The high cytotoxicity on cancer cell lines further demostrates their potential as therapeutic agents, highlighting the role of the linker in the target selectivity. Specifically, only the dyad with the rigid triazole linker exhibits selectively induces DNA damage in transformed cells, compared to normal cells primarily targeting telomeric regions. Our findings shed light on the DIPAC potential as a promising theranostic agent, offering insights for future development in precision medicine | Ilse Gert Julia Manet; Filippo Doria; Valentina Pirota; Mauro Freccero; Erica Salvati; Francesco Manoli; Carla Risoldi; Pasquale Zizza; Annamaria Biroccio; Angela Rizzo | Physical Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Cell and Molecular Biology; Photochemistry (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6723b9fd7be152b1d09865eb/original/core-extended-naphthalene-diimide-dyads-as-light-up-probes-with-targeted-cytotoxicity-toward-tumor-cells.pdf |
63507c40a2c79080d54e9923 | 10.26434/chemrxiv-2022-3tvnb | Room-temperature photodeposited amorphous VOx hole-transport layers for organic devices | Hole-transport layers (HTL) are an integral part of optoelectronic devices such as organic photovoltaic cells (OPVs) and organic light-emitting diodes (OLEDs). A class of materials commonly used as HTLs are metal oxides because they have high transparency and stability. These metal oxides are, however, often made using techniques that are not conducive to large-scale fabrication, a challenge thatmust be resolved for thewidespread adoption
of these devices. In this work, we demonstrate the use of a room-temperature, ambient photochemical deposition route to formvanadium oxide films. We show, using a combination of X-ray absorption and X-ray photoemission spectroscopies, that the VOx film consist of V2O5, but with significant amount of V4+ present. These films are initially created amorphous and become nanocrystalline after annealing in air at a temperature of 250 ◦C. After incorporating these VOx thin films as HTLs in both OPV and OLED devices, we surprisingly find this increase in crystallinity does not translate in improvement in device performance. All devices performsimilarly to – or better – than control devices using PEDOT:PSS as an HTL.We furthermore demonstrate that these films are not affected by the operation of these devices, and that the technique can be employed in combination with slot-die coating printing techniques. This work provides an easily upscaled, low-temperature method for depositing metal-oxide HTL layers. | Renaud Miclette Lamarche; Akpeko Gasonoo; Anderson Hoff; Gregory Welch; Roman Chernikov; Simon Trudel | Physical Chemistry; Energy; Photovoltaics; Optics; Structure; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63507c40a2c79080d54e9923/original/room-temperature-photodeposited-amorphous-v-ox-hole-transport-layers-for-organic-devices.pdf |
644036f971383d0921f8ca9d | 10.26434/chemrxiv-2023-clcrj | High-Spin Blatter’s Triradicals | Robust organic triradicals with high-spin quartet ground-state provide promising applications in molecular magnets, spintronics, etc. In this context, a triradical based on Blatter’s radical has been synthesized recently possessing two doublet-quartet energy gaps with 70% occupation of quartet ground state at room temperature. The traditional broken-symmetry (BS)-DFT computed energy gaps are reported to be somewhat overestimated in comparison to the experimentally observed values. In this work, we have employed different ab initio methods on this prototypical system to obtain more accurate doublet-quartet energy gaps for this triradical. The spin constraint broken symmetry (CBS)-DFT method has been used to reduce the overestimation of energy gaps from BS-DFT. To address the issues of spin-contamination and multi-reference nature of low-spin states affecting the DFT methods, we have computed the energy gaps using appropriately state-averaged CASSCF and NEVPT2 computations. Using a series of active spaces, our calculations are shown to provide quite accurate values in concordance with the experimentally observed results. Further, we have proposed
and modeled another three triradicals based on Blatter’s radical which are of interest for experimental synthesis and characterization. Our computations show that all these triradicals also have quartet ground state with similar energy difference between the excited doublet states. | Rishu Khurana; Ashima Bajaj; K.R. Shamasundar; Md. Ehesan Ali | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644036f971383d0921f8ca9d/original/high-spin-blatter-s-triradicals.pdf |
65b3182266c13817294a1af0 | 10.26434/chemrxiv-2023-njhwz-v2 | Modular Synthesis of Templated Bimetallic Sites in Metal–Organic Framework Pores | Binuclear metal active sites are found throughout all subfields of catalysis, from homogeneous and heterogeneous systems to enzymes. Here, we report a synthetic route to install well-defined bimetallic sites in metal–organic frameworks that offers independent control over the ligand environment, metal identity, metal–metal distance, active site flexibility, and pore environment. Our approach uses thermolabile tertiary carbamate crosslinkers to template pairs of amine functional groups within framework pores. The templated amine pairs can be quantitatively converted into diverse chelating sites, such as iminopyridine and bis(2-pyridylmethyl)amine ligands, and metalated with a variety of metal cations (M = Mn(II), Fe(II), Co(II), Ni(II), Cu(I), and Cu(II)). A combination of density functional theory, extended X-ray absorption fine structure spectroscopy, and electron paramagnetic resonance spectroscopy is used to confirm the local coordination environment and support the proximal nature of the templated bimetallic sites. The templating strategy described here will enable the exploration of new bimetallic motifs in heterogeneous catalysis. | Jackson Geary; Jonathan P. Aalto; Dianne J. Xiao | Organic Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Organometallic Compounds; Solid State Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b3182266c13817294a1af0/original/modular-synthesis-of-templated-bimetallic-sites-in-metal-organic-framework-pores.pdf |
63be4d83cac318aa609c4525 | 10.26434/chemrxiv-2022-swmc2-v3 | Artificial Neural Network Encoding of Molecular Wavefunction for Quantum Computing | Artificial neural networks (ANNs) for material modeling have received significant interest. We recently reported an adaptation of ANNs based on Boltzmann machine (BM) architectures to an ansatz of the multiconfigurational many-electron wavefunction, designated neural-network quantum state (NQS), for quantum chemistry calculations [Yang et al., J. Chem. Theory Comput., 2020, 16, 3513--3529]. Here, this study presents its extended formalism to a quantum algorithm that enables the preparation of the NQS through quantum gates. The descriptors of the ANN model, which are chosen as the occupancies of electronic configurations, are quantum-mechanically represented by qubits. Our algorithm may thus bring potential advantages over classical sampling-based computation employed in the previous studies. The NQS can be accurately formed using quantum-native procedures. Still, the training of the model in terms of energy minimization is efficiently performed on a classical computer; thus, our approach is a class of variational quantum eigensolver. The BM models are related to the Gibbs distribution, and our preparation procedures exploit techniques of quantum phase estimation but with no Hamiltonian evolution. The proposed algorithm is assessed by implementing it on a quantum computer simulator. Illustrative molecular calculations at the complete-active-space configuration interaction level of theory are displayed, confirming consistency with the accuracy of our previous classical approaches. | Masaya Hagai; Mahito Sugiyama; Koji Tsuda; Takeshi Yanai | Theoretical and Computational Chemistry; Theory - Computational; Artificial Intelligence; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63be4d83cac318aa609c4525/original/artificial-neural-network-encoding-of-molecular-wavefunction-for-quantum-computing.pdf |
60c753a40f50db81fd397bdf | 10.26434/chemrxiv.13379948.v2 | Equation-of-Motion Coupled-Cluster Method with Double Electron-Attaching Operators: Theory, Implementation, and Benchmarks | <div>
<div>
<div>
<p>We report a production-level implementation of equation-of-motion coupled-cluster method with double electron-
attaching EOM operators of 2p and 3p1h types, EOM-DEA-CCSD. This ansatz, suitable for treating electronic structure patterns that can be described as two-electrons-in-many orbitals, represents a useful addition to EOM-CC family
of methods. We analyze the performance of EOM-DEA-CCSD for energy differences and molecular properties. By
considering reduced quantities, such as state and transition one-particle density matrices, we can compare EOM-DEA-
CCSD wave-functions with wave-functions computed by other EOM-CCSD methods. The benchmarks illustrate that
EOM-DEA-CCSD capable of treating diradicals, bond-breaking, and some types of conical intersection.
</p>
</div>
</div>
</div> | Sahil Gulania; Eirik Fadum Kjønstad; John F. Stanton; Henrik Koch; Anna Krylov | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753a40f50db81fd397bdf/original/equation-of-motion-coupled-cluster-method-with-double-electron-attaching-operators-theory-implementation-and-benchmarks.pdf |
60c74640337d6c21e1e2711a | 10.26434/chemrxiv.11284007.v1 | Aggregation-induced Radical and Room-Temperature Ferromagnets of Diketopyrrolopyrrole Derivatives | It is extremely challenging to prepare room-temperature ferromagnet
(RTF) semiconductors as it is of great importance for development of electronic
and <a>spintronic devices in future</a>. Herein, we report that
significant radical signals were detected in three low bandgap small molecules
based on diketopyrrolopyrrole <a></a><a>derivatives</a>, since these molecules have an open-shell singlet
diradical ground state. A new mechanism of aggregation-induced radical (AIR) was
proposed to interpret the origin of radical signals and the transformation from
the aromatic structure to the quinoid-diradical (Q-D) structure in D-A type low bandgap organic
semiconductors. More importantly, the molecule Py-TTDPP exhibited obvious ferromagnetism
at room temperature, which also showed extensive radical signals due to the
thermally-excited triplet state in aggregation state. It was the first report
on the RTF based on neutral organic small
molecule semiconductors. Our findings unambitiously indicate the coming of the
room-temperature magnets based on organic small molecule radicals in future. | Wenqiang Li; Weiya Zhu; Miao Zeng; Jiawen Zhou; Yuan Li | Magnetic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74640337d6c21e1e2711a/original/aggregation-induced-radical-and-room-temperature-ferromagnets-of-diketopyrrolopyrrole-derivatives.pdf |
6528e68b8bab5d205541b324 | 10.26434/chemrxiv-2023-ptff7 | Sodium Carbonate ion complexes modify water structure at electrode interfaces | Water structure near electrode interfaces may play an important role in controlling CO2 electroreduction. Using plasmon-enhanced vibrational sum frequency generation spectroscopy, we demonstrate the emergence of an interfacial water subpopulation with large electric fields along their OH bonds, when Na2CO3 ions are present near the electrode under applied potential. With molecular dynamics simulations, we show that the approach of aqueous Na2CO3 to electrodes is coupled to the formation of structured and oriented ion complexes, and that the emergent water population is associated with the first solvation shell of these complexes. This water subpopulation is seen even when the sole source of CO3 is its in-situ generation from CO2, indicating that the interfacial species investigated here are likely ubiquitous in CO2 electroreduction contexts. | Amro Dodin; Gang-Hua Deng; Jaclyn A. Rebstock; Quansong Zhu; David T. Limmer; L. Robert Baker | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Electrochemistry - Mechanisms, Theory & Study; Interfaces | CC BY 4.0 | CHEMRXIV | 2023-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6528e68b8bab5d205541b324/original/sodium-carbonate-ion-complexes-modify-water-structure-at-electrode-interfaces.pdf |
660c5ccae9ebbb4db9378cc1 | 10.26434/chemrxiv-2024-l7gf5 | rNets: A standalone package to visualize reaction networks. | In the study of chemical reactions, visualizing reaction networks is pivotal for identifying crucial compounds and reactions. Traditional methods, such as network schematics and reaction path linear plots, often struggle to effectively represent complex reaction networks due to their size and intricate connectivity. Alternatives capable of leading with complexity include graph methods, but they are not user-friendly, lacking simplicity and modularity, which hinders their integration with widely-used research software. This work introduces rNets an innovative tool designed for the efficient visualization of reaction networks with a user-friendly interface, modularity, and seamless integration with existing software packages. The effectiveness of rNets is demonstrated through its application in analyzing three catalytic reactions, showcasing its potential to significantly enhance research both in homogeneous and heterogeneous catalysis fields. This tool not only simplifies the visualization process but also opens new avenues for exploring complex reaction networks in diverse research contexts. | Sergio Pablo-García; Raúl Pérez-Soto; Albert Sabadell-Rendón; Diego Garay-Ruiz; Vladyslav Nosylevskyi; Nuria López | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660c5ccae9ebbb4db9378cc1/original/r-nets-a-standalone-package-to-visualize-reaction-networks.pdf |
60c73dd4702a9b03f8189c52 | 10.26434/chemrxiv.5954518.v2 | Endgroup and Sidechain Functionalization of Surface-Initiated ROMP Thin Films: Progress Towards ROMP-Based Molecular Wires | A set of experiments in surface-initiated ring-opening metathesis polymerization, including end-functionalization of growing brushes and contact angle/cyclic voltammetry measurements. We report preparation and CV of two different conjugated polymer films, and several endgroup and sidechain functionalization experiments using cross-metathesis and active ester substitution.<br /> | Nicholas Marshall | Organic Polymers; Polymer brushes; Polymerization (Polymers); Electrochemical Analysis | CC BY 4.0 | CHEMRXIV | 2018-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd4702a9b03f8189c52/original/endgroup-and-sidechain-functionalization-of-surface-initiated-romp-thin-films-progress-towards-romp-based-molecular-wires.pdf |
60c75789469df48608f454d9 | 10.26434/chemrxiv.14414027.v1 | Labeling and Probing the Silica Surface Using Mechanochemistry and 17O NMR Spectroscopy | In
recent years, there has been increasing interest in developing cost-efficient,
fast, and user-friendly <sup>17</sup>O enrichment protocols to help understand
the structure and reactivity of materials using <sup>17</sup>O NMR. Here, we
show for the first time how ball milling (BM) can be used to selectively and
efficiently enrich the surface of fumed silica, which is widely used at the
industrial scale. Short milling times (up to 15 min) allowed modulation of the
enrichment level (up to ca. 5%) without significantly changing the nature of
the material. High-precision <sup>17</sup>O-compositions were measured at
different milling times using LG-SIMS. High-resolution <sup>17</sup>O NMR
analyses (including at 35.2 T) allowed clear identification of the signals from
siloxane (Si-O-Si) and silanols (Si-OH), while DNP analyses, performed using
direct <sup>17</sup>O polarization and indirect <sup>17</sup>O{<sup>1</sup>H}
CP excitation, agreed with selective<sup> </sup>labeling of the surface.
Information on the distribution of Si-OH environments at the surface was
obtained from 2D <sup>1</sup>H-<sup>17</sup>O D-HMQC correlations. Finally, the
surface-labeled silica was reacted with titania and using <sup>17</sup>O DNP,
their common interface was probed and Si-O-Ti bonds identified. | Chia-Hsin Chen; Frederic Mentink-Vigier; Julien Trébosc; Ieva Goldberga; Philippe Gaveau; Emilie Thomassot; Dinu Iuga; Mark E. Smith; Kuizhi Chen; Zhehong Gan; Nicolas Fabrègue; Thomas-Xavier Métro; Bruno Alonso; Danielle Laurencin | Interfaces; Spectroscopy (Physical Chem.); Structure; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75789469df48608f454d9/original/labeling-and-probing-the-silica-surface-using-mechanochemistry-and-17o-nmr-spectroscopy.pdf |
60c747c50f50db2769396666 | 10.26434/chemrxiv.8081924.v2 | Spectral Deep Learning for Prediction and Prospective Validation of Functional Groups | <p>State-of-the-art identification of the functional groups present in an unknown chemical entity requires expertise of a skilled spectroscopist to analyse and interpret Fourier Transform Infra-Red (FTIR), Mass Spectroscopy (MS) and/or Nuclear Magnetic Resonance (NMR) data. This process can be time-consuming and error-prone, especially for complex chemical entities that poorly characterized in the literature, or inefficient to use with synthetic robots producing molecules at an accelerated rate. Herein, we introduce a fast, multi-label deep neural network for accurately identifying all the functional groups of unknown compounds using a combination of FTIR and MS spectra. We do not use any database, pre-established rules, procedures, or peak-matching methods. Our trained neural network reveals patterns typically used by human chemists to identify standard groups. Finally, we experimentally validated our neural network, trained on single compounds, to predict functional groups in compound mixtures. Our methodology showcases practical utility for future use in autonomous analytical detection.</p> | Jonathan Fine; Anand Rasjashekar; Krupal P. Jethava; Gaurav Chopra | Chemoinformatics; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Spectroscopy (Physical Chem.); Robotics | CC BY 4.0 | CHEMRXIV | 2020-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747c50f50db2769396666/original/spectral-deep-learning-for-prediction-and-prospective-validation-of-functional-groups.pdf |
6549195ca8b423585a11fc5d | 10.26434/chemrxiv-2023-k7mws | Modelling of enhanced water flow in deformable carbon nanotubes using a linear pressure-diameter relationship | Numerous researchers have documented a notable enhancement in water flow through nanotubes While modelling, these researchers typically treated the CNTs with rigid walls. The flow rates of water within carbon nanotubes (CNTs) are significantly influenced by the nanoconfined density, viscosity and the slip length. Despite considering substantial slip effects, there are unresolved findings of massive enhancements in flow rates. Recently, using a linear pressure-area relationship for the deformable tube walls, Garg (2023) derived a model for the flow rates. In contrast to that, this paper takes a different approach, utilizing a small displacement structural mechanics framework with a linear pressure-diameter relationship, to incorporate the deformable nature of carbon nanotubes and derive another deformable model. We compare predicted flow rates with previous findings. The rigid-wall model with slips accurately predicted the outcomes of numerous studies. Nonetheless, we observed that in many studies featuring high porosity and thin-walled tubes, the inclusion of tube elasticity or deformability is crucial for accurate modeling. In such cases, our deformable-wall model with slips performed exceptionally well in predictions. We also compare and contrast the flow physics and flow rate scaling of the current model with the predictions from the Garg (2023) deformable model. We also find that as the deformability $1/\beta$ increases, the flow rate also increases. Although the scaling for how the flow rate and flow physics varies are different than reported by Garg (2023) with pressure-area model. We find that the flow rate in deformable tubes scales as $\dot{m}_{\text{deformable}}\sim 1/\beta^0 $ for $\Big ( \Delta p/\beta \sqrt{A_o} \Big ) \ll 1$, $\dot{m}_{\text{deformable}}\sim 1/\beta $ for $\Big ( \Delta p/\beta \sqrt{A_o} \Big ) \sim O(10^{-1})$ and $\dot{m}_{\text{deformable}}\sim 1/ \beta^4 $ for $\Big ( \Delta p/\beta \sqrt{A_o} \Big ) \sim O(1)$. Further, for a given deformability factor $\beta$, the flow rate in the smaller diameter of the tube is much larger than the larger diameter where the flow rate increases with $D_o^{-1}$ followed by $D_o^{-4}$ as diameter decreases. We also find that for the rigid tube, the mass flow rate varies linearly with pressure, whereas for the deformable tubes, the flow rate scales as $\dot{m}_{\text{deformable}}\sim \Delta p^2 $ for $ \Big ( \Delta p/\beta \sqrt{A_o} \Big ) \sim O(10^{-1})$ during transition from $\dot{m}_{\text{rigid}} \sim \Delta p $ to $\sim \Delta p^5 $, and finally to $\dot{m}_{\text{deformable}}\sim \Delta p^5 $ for $ \Big ( \Delta p/\beta \sqrt{A_o} \Big ) \sim O(1)$. On the otherhand, the scaling reported by Garg (2023) was $\dot{m}_{\text{deformable}}\sim \Delta p^3 $ for $ \Big ( \Delta p/\alpha A_o \Big ) \sim O(1)$. | Ashish Garg | Nanoscience; Nanodevices; Nanofluidics; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6549195ca8b423585a11fc5d/original/modelling-of-enhanced-water-flow-in-deformable-carbon-nanotubes-using-a-linear-pressure-diameter-relationship.pdf |
6727b8fa5a82cea2faea7e16 | 10.26434/chemrxiv-2024-zmq13 | MOSAEC-DB: A comprehensive database of experimental metal-organic frameworks with verified chemical accuracy suitable for molecular simulations | Ongoing developments in computational databases seek to improve the accessibility and breadth of high-throughput screening and materials discovery efforts. Their reliance on experimental crystal structures necessitates significant processing prior to computation in order to resolve any crystallographic disorder or partial occupancies and remove any residual solvent molecules in the case of activated porous materials. Contemporary investigations revealed that deficiencies in the experimental characterization and computational preprocessing methods generated considerable occurrence of structural errors in metal-organic framework (MOF) databases. The MOSAEC MOF database (MOSAEC-DB) tackles these structural reliability concerns through utilization of innovative preprocessing and error analysis protocols applying the concepts of oxidation states and formal charge to exclude erroneous MOF crystal structures. Comprising more than 124k crystal structures, this work maintains the largest and most accurate dataset of experimental MOFs ready for immediate deployment in molecular simulations. The databases’ comparative diversity is demonstrated through its enhanced coverage of the periodic table, expansive quantity of structures, and balance of chemical properties relative to existing MOF databases. Chemical and geometric descriptors, as well as DFT electrostatic potential-fitted charges, are included to facilitate subsequent atomistic simulation and machine-learning (ML) studies. Curated subsets—sampled according to their chemical properties and structural uniqueness—are also provided to further enable ML studies in recognition of the strict demand for duplicate elimination and dataset diversity in such applications. | Marco Gibaldi; Anna Kapeliukha; Andrew White; Jun Luo; R. Alex Mayo; Jake Burner; Tom Woo | Theoretical and Computational Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Machine Learning; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6727b8fa5a82cea2faea7e16/original/mosaec-db-a-comprehensive-database-of-experimental-metal-organic-frameworks-with-verified-chemical-accuracy-suitable-for-molecular-simulations.pdf |
652cc4ae8bab5d20557017ca | 10.26434/chemrxiv-2023-thjhj | Understanding the Dynamic Aggregation in Single Atom Catalysis | The dynamic response of single atom catalysts to a reactive environment is an increasingly significant topic for understanding the reaction mechanism at the molecular level. In particular, single atoms may experience dynamic aggregation into clusters or nanoparticles driven by thermodynamic and kinetic factors. Herein, we will uncover the inherent mechanistic nuances that determine the dynamic profile during the reaction, including the intrinsic stability and site-migration barrier of single atoms, external stimuli (temperature, voltage, and adsorbates), and the influence of catalyst support. Such dynamic aggregation can have beneficial or deleterious effects on the catalytic performance depending on the optimal initial state. We will highlight those examples where in situ formed clusters, rather than single atoms, serve as catalytically active sites for improved catalytic performance. This is followed by the introduction of typical operando techniques to understand the structural evolution. Finally, we will briefly discuss the emerging strategies via confinement and defect-engineering to regulate dynamic aggregation. | Laihao Liu; Tiankai Chen; Zhongxin Chen | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Nanocatalysis - Reactions & Mechanisms | CC BY 4.0 | CHEMRXIV | 2023-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652cc4ae8bab5d20557017ca/original/understanding-the-dynamic-aggregation-in-single-atom-catalysis.pdf |
611b5c65711750b602eb03f6 | 10.26434/chemrxiv-2021-1w08t | Rational design of Two-dimensional Binary Polymers from Hetero Triangulenes for Photocatalytic Water Splitting | Based on first principles calculations, we report the design of three two-dimensional (2D) binary honeycomb-kagome polymers composed of B- and N-centered heterotriangulenes with a periodically alternate arrangement as in hexagonal boron nitride. The 2D binary polymers with donor-acceptor characteristics, are semiconductors with a direct band gap of 1.98-2.28 eV. The enhanced in-plane electron conjugation contributes to high charge carrier mobilities for both electrons and holes, about 6.70 and 0.24 × 103 cm2 V-1 s-1, respectively, for the 2D binary polymer with carbonyl bridges (2D CTPAB). With appropriate band edge alignment to match the water redox potentials and pronounced light adsorption for the ultraviolet and visible range of spectra, 2D CTPAB is predicted to be an effective photocatalyst/photoelectrocatalyst to promote overall water splitting. | Zhenpei Zhou; Maximilian Springer; Weixiang Geng; Xinyue Zhu; Tianchun Li; Manman Li; Yu Jing; Thomas Heine | Theoretical and Computational Chemistry; Catalysis | CC BY 4.0 | CHEMRXIV | 2021-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611b5c65711750b602eb03f6/original/rational-design-of-two-dimensional-binary-polymers-from-hetero-triangulenes-for-photocatalytic-water-splitting.pdf |
60c741e2ee301ce797c78d29 | 10.26434/chemrxiv.8144075.v1 | The Principle of Conservation of Structural Aspect: Facilitating Visual Communication and Learning in Organic Chemistry Instruction | <p>An effective pedagogical
method is presented for the visual communication of chemical reactions learned
in organic chemistry undergraduate courses. The basis for the method is the
preservation of the visual aspect of reactant and product structures so that
the tracking of cleaved and formed chemical bonds is made self-evident. This
consequently leads to improved clarity of presentation and a better
understanding and grasp of proposed reaction mechanisms to explain product
outcomes. The method is demonstrated for a variety of individual reaction types
and synthesis plans. Various visual training exercises are also presented using
ChemDraw Ultra 7.0 software and literature table of contents (TOC) graphics
appearing in journal articles.</p><br /> | john andraos | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e2ee301ce797c78d29/original/the-principle-of-conservation-of-structural-aspect-facilitating-visual-communication-and-learning-in-organic-chemistry-instruction.pdf |
60c74744337d6c31e2e27311 | 10.26434/chemrxiv.11585601.v1 | Thermal Conductivity of Polyelectrolytes with Different Counterions | <div>
<div>
<div>
<p>Polyelectrolytes are important to many applications, such as electronics and batteries. In this
work, we study the thermal conductivity of polyelectrolytes with different counterions using
molecular dynamics (MD) simulations. Both anionic and cationic polyelectrolytes, including
poly(acrylic acid) and poly(allylamine hydrogen halide), are investigated. We have simulated a
total number of 17 polyelectrolytes with different counterions and we find that all of them have
thermal conductivity values between 0.2 and 0.7 W/(m.K). By analyzing thermal conductivity
against different counterion descriptors (atomic mass, atomic radius, van der Waals radius and
ionic radius), we find a strong negative relationship between thermal conductivity and the ionic
radii of counterions. We rationalize such a discovery through analyzing the heat flux at
molecular level and find that thermal conductivity shows a general increasing trend with respect
to the interatomic non-bonding forces and atomic velocities. We have also found a positive
correlation between the MD-calculated thermal conductivity and that from the minimum thermal
conductivity model, and this correlation can also be traced back to the same molecular level
origin. Our study provides new insights to the heat transfer physics in polymers and may help
scientists develop polyelectrolytes with desirable thermal conductivity.
</p>
</div>
</div>
</div> | xingfei wei; RUIMIN MA; Tengfei Luo | Polyelectrolytes - Polymers | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74744337d6c31e2e27311/original/thermal-conductivity-of-polyelectrolytes-with-different-counterions.pdf |
60c74781567dfeb46fec481c | 10.26434/chemrxiv.11688795.v1 | Conditional Copper-Catalyzed Azide Alkyne Cycloaddition by Catalyst Encapsulation | Supramolecular encapsulation is known to alter chemical properties of guest molecules. Here we apply this strategy of molecular encapsulation to temporally control the catalytic activity of a stable Cu(I)-carbene catalyst. Encapsulation of the Cu(I)-carbene catalyst by supramolecular host cucurbit[7]uril (CB[7]) resulted in the complete inactivation of a copper catalyzed alkyne-azide cycloaddition (CuAAC) reaction. The addition of a chemical signal achieved the near instantaneous activation of the catalyst, by releasing the catalyst from the inhibited CB[7] catalyst complex. To broaden the scope of our on demand CuAAC reaction, we demonstrated the protein labelling of Vinculin using the Cu(I)-carbene catalyst, to inhibit its activity by encapsulation with CB[7], and to initiate labelling at any moment by adding a specific signal molecule. <br /> | Tobias Brevé; Mike Filius; Can Araman; Michelle van der Helm; Peter-Leon Hagedoorn; Chirlmin Joo; Sander I. van Kasteren; Rienk Eelkema | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74781567dfeb46fec481c/original/conditional-copper-catalyzed-azide-alkyne-cycloaddition-by-catalyst-encapsulation.pdf |
60c757040f50db5ead3981bb | 10.26434/chemrxiv.14356796.v1 | Polyethylene Materials with In-Chain Ketones from Catalytic Copolymerization | The world’s most important plastic, polyethylene, consists of inert hydrocarbon chains. An introduction of reactive polar groups in these chains is much sought-after, to overcome the problematic environmental persistency and enhance compatibility with other materials. However, with state of the art catalytic polymerization processes this has not been possible. Here, we show how a low density of individual in-chain keto groups can be generated in the high molecular weight polyethylene chains by catalytic copolymerization with carbon monoxide. Most importantly, the desirable materials’ properties of high density polyethylene (HDPE) are retained. Processing can be performed by common injection molding and mechanical characteristics are on a par.<br /><br /> | Maximilian Baur; Fei Lin; Tobias Morgen; Lukas Odenwald; Stefan Mecking | Inorganic Polymers; Polymerization (Polymers); Polymerization catalysts | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757040f50db5ead3981bb/original/polyethylene-materials-with-in-chain-ketones-from-catalytic-copolymerization.pdf |
663d1d6b91aefa6ce1981405 | 10.26434/chemrxiv-2024-86stv-v2 | Graphene and Graphene Oxide (Raman Spectroscopy) | In previous discussions we have considered the Raman spectra of specific carbon-based materials, such as diamond, graphite, and the biochar resulting from pyrolysis of biomass. We have shown how the spectra can be decomposed, according to the intended number of components and the considered line shapes. Here, we approach the Raman spectra of graphene and graphene oxide, to understand how many components are required to interpret the related fingerprints. | Amelia Carolina Sparavigna | Materials Science | CC BY 4.0 | CHEMRXIV | 2024-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663d1d6b91aefa6ce1981405/original/graphene-and-graphene-oxide-raman-spectroscopy.pdf |
63ea3d7f1d2d1840636c1ba8 | 10.26434/chemrxiv-2023-sxw2w | N-Terminal-selective Cu-catalyzed [3+2] cycloaddition for irreversible assembly of two modules with a peptide | Site-selective introduction of multiple components into peptides is greatly needed for the preparation of densely functionalized peptides with uniform quality. In particular, N-terminal-selective peptide modification has attracted considerable attention in recent years for the purpose of single-site modification. In this work, an N-terminal selective [3+2] cycloaddition of peptide-based azomethine ylides with maleimides was developed. This reaction was catalyzed by Cu/Xantphos complex under mild conditions to afford the cycloadduct in excellent yield and with complete exo-diastereoselectivity, leaving the alkyl amine of a lysine residue untouched. Furthermore, the reaction forms an irreversible C–C bond, preventing the elimination of the introduced modules, which has been a major concern in previous methods. The reaction was applied to a convenient three-component assembly by a one-pot procedure using a peptide with aldehyde and maleimide. Furthermore, this method was efficiently applied to a single-site modification of oligopeptides. These results showcase the utility of this method for the single-site bi-functionalization of complex peptides. | Haruka Machida; Kazuya Kanemoto; Haruhiko Fuwa | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ea3d7f1d2d1840636c1ba8/original/n-terminal-selective-cu-catalyzed-3-2-cycloaddition-for-irreversible-assembly-of-two-modules-with-a-peptide.pdf |
67cf322a81d2151a02e23884 | 10.26434/chemrxiv-2024-p8fz6-v2 | Droplet deformation in steady fluidic flows enables robust, accessible, high-throughput surface tension measurements | Impressive improvements in the ability of microfluidic devices to reliably fabricate a wide variety of droplet, capsule, and particle architectures necessitate comparable improvements in techniques to measure and characterize these materials in line with fabrication. Measurement and control of droplet surface tension are needed to ensure droplet stability while minimizing excess use of surfactants. Standard techniques to measure surface tension typically measure one droplet at a time, off-chip. Fluidics can be leveraged to measure surface tension in-line with droplet formation. Typically, this requires channel geometries that enable extensional flow. Transient relaxation of deformed droplets is then measured at the exit of a constriction. We propose an alternative approach, in which a single value of steady deformation within a constriction is used to measure surface tension. We flow emulsion droplets through a series of increasingly narrow constrictions and measure steady deformation. We measure surface tension over a wide range of surfactant concentrations. We use nonionic surfactant Span 80 to pinch-off and stabilize water drops in mineral oil and anionic surfactant SDS to stabilize mineral oil drops in water. In a subset of experiments, water droplets contain varying concentrations of polyethylene glycol diacrylate, a common blank-slate hydrogel polymer. We calculate surface tension using Taylor's small deformation theory, which describes the relationship between steady deformation in shear flows and the Capillary number, the ratio of the applied viscous stress to restoring surface tension stress. Validation using both the transient deformation fluidic approach and pendant drop measurements on individual droplets demonstrates the viability of our approach. The use of multiple constrictions allows measurement of hundreds of droplets at several distinct shear rates without the need to vary control parameters. Importantly, our results suggest that steady state measurements of deformation in pressure driven flows provide accurate assessments of surface tension, even when droplets are slightly confined. This steady deformation approach represents a readily-accessible option for measuring surface tension of micro-scale droplets in pressure driven flow through rectangular channels, without requiring specialized channel geometries. | Evyatar Shaulsky; Sabrina Marnoto; Avi J. Patel; Sara M. Hashmi | Materials Science; Chemical Engineering and Industrial Chemistry; Surfactants; Fluid Mechanics; Transport Phenomena (Chem. Eng.) | CC BY NC 4.0 | CHEMRXIV | 2025-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cf322a81d2151a02e23884/original/droplet-deformation-in-steady-fluidic-flows-enables-robust-accessible-high-throughput-surface-tension-measurements.pdf |
66ffe65a51558a15ef0d1c81 | 10.26434/chemrxiv-2024-4rk8f | Chemically fueled active transport. | Biology uses chemical potential differences from molecules like ATP to drive membrane pumps, transporting molecules across mem-branes even against concentration gradients. Here, we report a synthetic system that transports small molecules from an aqueous phase (the sender) to an aqueous receiver across a centimeter-sized immiscible solvent at the expense of chemical energy. Molecules with high chemical potential (fuels) in the sender phase transiently activate the transporter molecule to enter the immiscible solvent and exit on the receiver phase side, thus allowing transport from sender to receiver against a concentration gradient. Importantly, we show this active transport mechanism transports molecules across a hydrophobic barrier without complex pumping machinery. Using a reaction-diffusion model, we determined the critical parameters that determine the efficiency of the active transport. Selective transport enables the sorting of a mixture of different molecules. In future work, we will use these design criteria to actively transport molecules across membranes, e.g., of vesicles, at the expense of chemical fuel, thereby mimicking biological processes and enabling the feeding of synthetic cells. | Christine Kriebisch; Brigitte Kriebisch; Gregor Häfner; Yanyan Fei; Marcus Müller; Job Boekhoven | Organic Chemistry; Materials Science; Nanoscience; Combinatorial Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ffe65a51558a15ef0d1c81/original/chemically-fueled-active-transport.pdf |
666b13365101a2ffa88206b6 | 10.26434/chemrxiv-2024-dv0pj | DNA-based AND logic gate as a molecular precision tool: selective recognition of protein pairs in lipid nanodiscs and subsequent binding of gold nanorods | The specificity of target recognition is paramount in fields such as cellular biology, diagnostics, and therapy. Traditional antibody-based methods focus on recognizing single antigens; however, the next level of specificity involves targeting pairs of antigens simultaneously. This study introduces a DNA-based molecular logic AND gate designed to recognize the two membrane proteins PD-L1 and CD3 as antigens via the corresponding antibody-oligonucleotide conjugates. The two membrane proteins are embedded in lipid nanodiscs that serve as a model system for cell membranes. By utilizing antibody-oligonucleotide conjugates as input signals, the DNA logic gate operates sequentially, becoming fully activated only upon binding both target proteins. The output signal facilitates subsequent actions, such as target isolation via magnetic bead extraction and functionalization with DNA-tagged gold nanorods for potential photothermal therapy. Our proof of concept for a molecular precision tool that processes two input signals in an AND operation and converts them to an output signal offers new avenues for high-specificity diagnostics and therapeutic interventions. | Sayantan De; Michelle Hechler; Mingpan Cheng; Helene Giesler; Sven Brandau; Barbara Saccà; Sebastian Schlücker | Biological and Medicinal Chemistry; Nanoscience; Nanodevices; Nanostructured Materials - Nanoscience; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666b13365101a2ffa88206b6/original/dna-based-and-logic-gate-as-a-molecular-precision-tool-selective-recognition-of-protein-pairs-in-lipid-nanodiscs-and-subsequent-binding-of-gold-nanorods.pdf |
640d731a7290f69f8ed88a99 | 10.26434/chemrxiv-2023-nwgg8 | Eliminating Fragment Group Orbital (eFGO) Analysis for Deciphering Chemical Bonding in Complex Systems | The delocalized nature of canonical molecular orbitals in quantum chemistry calculations is always in conflict with the localized nature of orbital interactions and derived chemical concepts. Localization of molecular orbitals has been achieved in many approaches, but sometimes they could be over-localized for complex systems, especially those with multicenter bonding. A fragment-based approach is thus proposed to eliminate the electron density contribution from substituents, ligands and other peripheral moieties such that the skeletal bonding is clearly revealed. To be specific, fragment group orbitals, as in analogy with ligand group orbitals in coordination chemistry, are eliminated from the space spanned by occupied molecular orbitals. Via this approach, the skeletal bonding orbitals of complex systems including but not limited to pi-delocalized systems and cluster compounds are recovered with a minimal contribution from surrounding moieties, making this method the ideal choice to analyze the electronic structure of complex systems and separate skeletal bonding contribution against peripheral moieties from various sum-over-orbital properties. | Jing-Xuan Zhang; Fu Kit Sheong; Yun-Shu Cui; Jun Li; Zhenyang Lin | Theoretical and Computational Chemistry; Inorganic Chemistry; Bonding; Theory - Inorganic; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640d731a7290f69f8ed88a99/original/eliminating-fragment-group-orbital-e-fgo-analysis-for-deciphering-chemical-bonding-in-complex-systems.pdf |
639c731e04902aa697054955 | 10.26434/chemrxiv-2022-800px | Quantitative, room‐temperature, solvent-free mechanochemical oxidation of elemental gold into organosoluble gold salts | Gold is highly valued for its wide-ranging commercial and technological use and is currently almost exclusively processed via aggressive reaction conditions that produce water soluble salts. Oxidative mechanochemistry has previously been shown as a rapid, mild, and room-temperature alternative for chemically activating and transforming gold into water soluble species in the presence of potassium and ammonium halides. Demonstrated here is the extension of this strategy in the presence of tetraalkylammonium halides to directly and efficiently produce salts soluble in pure organic solvents and aqueous alcoholic media. This method affords gold salts that are rapidly and easily purified from byproducts using benign and easily recycled solvents and can be readily used for subsequent materials synthesis such as Au(I) salts and gold nanoparticles. | Jean-Louis Do; Thomas Auvray; Cameron Lennox; Hatem Titi; Louis Cuccia; Tomislav Friscic | Inorganic Chemistry; Coordination Chemistry (Inorg.); Solid State Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639c731e04902aa697054955/original/quantitative-room-temperature-solvent-free-mechanochemical-oxidation-of-elemental-gold-into-organosoluble-gold-salts.pdf |
60c7526c702a9b8aa918c13a | 10.26434/chemrxiv.13297694.v1 | Capturing The Dynamic Association Between A Tris-Dipicolinate Lanthanide Complex And A Decapeptide: A Combined Paramagnetic NMR And Molecular Dynamics Exploration. | <div><div><div><div><p>Our study sheds new light on the highly dynamic structural interplay between a tris-dipicolinate lanthanide probe and a test decapeptide SASYKTLPRG. Whereas a rather monotous, electrostatically-driven association may have been expected, the combination of paramagnetic NMR and molecular dynamics simulations extensively captures interaction sites and their occupancy. This study reveals the importance of a large conformational sampling to reconcilate characteristic time in NMR with molecular dynamics simulations, where sampling at the microsecond range is needed. This study opens the door for a detailed mechanistic elucidation of the early steps of lanthanide complexe-peptide or lanthanide complexe-protein interaction or self-assembly processses.</p></div></div></div></div> | Sandrine Denis-Quanquin; Alessio Bartocci; florence szczepaniak; François Riobé; Olivier MAURY; Elise Dumont; nicolas giraud | Computational Chemistry and Modeling; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7526c702a9b8aa918c13a/original/capturing-the-dynamic-association-between-a-tris-dipicolinate-lanthanide-complex-and-a-decapeptide-a-combined-paramagnetic-nmr-and-molecular-dynamics-exploration.pdf |
620c207c7a054a925b0ee729 | 10.26434/chemrxiv-2022-rgs0n | THE OPTIMIZATION OF HYDRATED LIME PUTTIES AND LIME MORTARS USING NOPAL PECTIN | Considered the base material of millenary building systems in Mexico, hydrated lime has been traditionally produced since pre-Hispanic times. This implies intangible heritage that is currently at risk of being lost due to the high costs involved in its manufacture, especially during its hydration stage, which involves a resting time of several months before it develops the mechanical and rheological properties that make it useful in construction and works of restoration. Multidisciplinary research was carried out to reduce the cost of manufacture and to revitalize an ancient technique. It involved several experimental phases of physicochemical, architectural and constructive analysis that resulted in the discovery of a key substance contained in the nopal mucilage. This substance not only enabled a good chemical interaction with lime, but also managed to function as a catalyst in the hydration and aging process of lime putties from its crystallographic modification. Moreover, it had a significant impact on the optimization of the mechanical and rheological properties of the mortars prepared with them, as well as on their behavior during the carbonation process and their ability to absorb moisture. The results that allowed to conclude this optimization were obtained from the characterization and comparison of the behavior of the new lime putties with pectin and the mortars prepared with them through analysis in SEM, XRD, as well as the adaptation of some established methods of analysis and many others proposed in the research for this binder and its by-products. The theories produced from this research open the door to new lines of exploration that involve further research about the interference that mortar dosage has and the interaction with pectin compared to other fruits. | Angélica Pérez Ramos; José Luz González Chávez; Luis Fernando Guerrero Baca; Anaí Chiken Soriano; Miguel Ángel Sánchez Espinosa | Materials Science; Coating Materials; Core-Shell Materials; Hybrid Organic-Inorganic Materials | CC BY NC 4.0 | CHEMRXIV | 2022-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620c207c7a054a925b0ee729/original/the-optimization-of-hydrated-lime-putties-and-lime-mortars-using-nopal-pectin.pdf |
61b6f8379e56b899c3ba6a7e | 10.26434/chemrxiv-2021-rlm8t-v3 | Mechanically axially chiral catenanes and noncanonical chiral rotaxanes | Chirality, the property of objects that are distinct from their own mirror image, is important in many scientific areas but particularly chemistry, where the appearance of molecular chirality because of rigid arrangements of atoms in space famously influences a molecule’s biological properties. Less generally appreciated is that two molecular rings with chemically distinct faces combined like links in a chain results in a chiral structure even when the rings are achiral. To date, no enantiopure examples of such mechanically axially chiral catenanes has been reported. We re-examined the symmetry properties of the mechanically axially chiral motif and identified a straightforward route to such molecules from simple building blocks. We also identify that common representations of axially chiral catenanes obscure that a previously overlooked stereogenic unit arises when a ring is threaded onto a dumbbell-shaped molecule to generate a rotaxane. These insights allowed us to demonstrate the first stereoselective syntheses of an axially chiral catenane and a noncanonical axially chiral rotaxane motif. With methods to access these structures in hand, the process of exploring their properties and applications can now begin. | John Maynard; Peter Gallagher; David Lozano; Patrick Butler; Steve Goldup | Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry; Supramolecular Chemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2021-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b6f8379e56b899c3ba6a7e/original/mechanically-axially-chiral-catenanes-and-noncanonical-chiral-rotaxanes.pdf |
60c73e9abb8c1a7fc93d994e | 10.26434/chemrxiv.7066622.v1 | Cyclopentannulation and Cyclodehydrogenation of Isomerically Pure 5,11-Dibromo-Anthradithiophenes Leading to Contorted Aromatics | Isomerically pure 5,11-dibromo-2,8-dihexylanthra[2,3-b:7,6-b']dithiophene, a brominated analog of anthracenedithiophene (ADT), was prepared and utilized for a palladium catalyzed cyclopentannulation reaction with 3,3’-dimethoxyphenylacetylene. The resulting cyclopentannulated-ADT (CP-ADT) was found to be more photo-oxidatively stable than isoelectronic CP-pentacene analogs previously prepared. In addition, the CP-ADT was able to undergo an additional Scholl cyclodehydrogenation reaction to create a contorted aromatic, an incapable feat for previous CP-pentacene analogs. The resulting compound, 4-dihexyl-5,10,17,22-tetramethoxytetrabenzo[4,5:6,7:11,12:13,14]rubiceno[2,3-b:10,9-b']dithiophene, was significantly contorted out of planarity owing to four [5]helicene-like arrangements. The density functional theory (DFT) energy minimized structures suggests splay angles of 41.80 and 40.90 for the cove regions, which are significantly larger than previously published anthracene cyclopentannulated analogs. The contorted aromatic possessed a moderately low optical gap (1.50 eV) and relatively low Lowest Occupied Molecular Orbital energy (-3.70 eV).<br /> | Sambasiva Bheemireddy; Waseem A. Hussain; Ain Uddin; Yachu Du; Matthew Hautzinger; Paul Kevorkian; Frankie Petrie; Kyle Plunkett | Organic Synthesis and Reactions; Physical Organic Chemistry; Theory - Computational; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e9abb8c1a7fc93d994e/original/cyclopentannulation-and-cyclodehydrogenation-of-isomerically-pure-5-11-dibromo-anthradithiophenes-leading-to-contorted-aromatics.pdf |
6335ac8dba8a6de5fc616f0d | 10.26434/chemrxiv-2022-wjw9j | Biological studies with comprehensive GCxGC-HRMS screening: Exploring the human sweat volatilome | A key issue in GCxGC-HRMS data analysis is how to approach large-sample studies in an efficient and comprehensive way. We have developed a semi-automated data-driven workflow from identification to suspect screening, which allows highly selective monitoring of each identified chemical in a large-sample dataset. The example dataset used to illustrate the potential of the approach consisted of human sweat samples from 40 participants, including field blanks (80 samples). These samples have been collected in a Horizon 2020 project to investigate the capacity of body odour to communicate emotion and influence social behaviour. We used dynamic headspace extraction, which allows comprehensive extraction with high preconcentration capability, and has to date only been used for a few biological applications. We found 325 sweat volatiles compared to 581 known skin volatiles, 107 of which matched perfectly with the literature, and 218 compounds (67%) novel sweat volatiles. Unlike partitioning-based extraction methods, the developed method detects semi-polar (log P < 2) nitrogen and oxygen-containing compounds. However, it is unable to detect certain acids due to the pH conditions of unmodified sweat samples. Using a single analytical method, our coverage of the boiling point and polarity space was comparable to the cumulative coverage of all the available 35 studies investigating skin volatiles with different analytical methods. We believe that our framework will open up the possibility of efficiently using GCxGC-HRMS for large-sample studies in a wide range of applications such as biological and environmental studies. | Matyas Ripszam; Tobias Bruderer; Denise Biagini; Silvia Ghimenti; Tommaso Lomonaco; Fabio Di Francesco | Analytical Chemistry; Analytical Chemistry - General; Analytical Apparatus; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2022-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6335ac8dba8a6de5fc616f0d/original/biological-studies-with-comprehensive-g-cx-gc-hrms-screening-exploring-the-human-sweat-volatilome.pdf |
60c744f9567dfe80d0ec4394 | 10.26434/chemrxiv.9936614.v1 | How DNA Base Pairs Escape From the Excited-State: Antiaromaticity Relief in the Picoseconds | <p>Before the development of an ozone
layer in the Archean atmosphere, the flux of UV radiation reaching Earth was
suggested to be several orders of magnitude higher than it is today. For the
emerging biomolecules, constant exposure to strong UV irradiation meant that
useful molecules had to be resistant to UV damage and harmful photochemical
reactions. From this prebiotic environment, the Watson–Crick structures of A·T
and G·C base pairs survived to encode genetic information—and the
photostability of these winning pairs in this specific arrangement is
astonishing. Upon UV irradiation, the photoexcited canonical base pairs undergo
proton-coupled electron transfer (PCET), followed by non-radiative decay, and
convert internally to the electronic ground state within picoseconds. But the
underlying reason why this process happens so efficiently has not been
explained. Here we show that efficient photodeactivation in isolated base pairs
are driven by antiaromaticity relief during PCET. According to computed nucleus
independent chemical shifts, the A·T and G·C base pairs are aromatic in the
electronic ground state, but the purines become highly antiaromatic in the
first <sup>1</sup>ππ* state, and PCET relieves this excited-state
antiaromaticity. We found especially pronounced antiaromaticity relief for the
major PCET pathway of isolated Watson–Crick A·T and G·C base pairs, when
compared to alternative proton transfer routes or to PCET reactions in
non-canonical pairs. Our findings suggest that excited-state deactivation of
isolated base pairs are tied to sudden changes in aromaticity and
antiaromaticity within the picoseconds that follow a strike of UV-light.</p> | Lucas Karas; Chia-Hua Wu; Henrik Ottosson; Judy Wu | Photochemistry (Org.); Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744f9567dfe80d0ec4394/original/how-dna-base-pairs-escape-from-the-excited-state-antiaromaticity-relief-in-the-picoseconds.pdf |
6344bb03ea6a22807b119f6e | 10.26434/chemrxiv-2022-9jb69 | A Class of Organic Units Featuring Matrix-controlled Color-tunable Ultralong Organic Room Temperature Phosphorescence | We for the first time report a novel class of organic units (N-1 and N-2) and their derivatives (PNNA-1 and PNNA-2) with excellent property of ultralong organic room temperature phosphorescence (UORTP). In this work, N-1, N-2 and their derivatives function as the guests while organic powders (PNCz, BBP, DBT) and polymethyl methacrylate (PMMA) serve as the host matrixes. Amazingly, the color of ultralong phosphorescence can be tuned in different states or by varying the host matrixes. At 77 K, all the four molecules show green afterglow in the monomer state but yellow afterglow in the aggregated state because strong intermolecular interactions exist in the self-aggregate and induce a redshift of the afterglow. In particular, PNNA-1 and PNNA-2 demonstrate distinctive photo-activated green UORTP in the PMMA film owing to the generation of their cation radicals. Whereas the PNNA-1@PNCz and PNNA-2@PNCz doping powders give out yellow UORTP, showing matrix-controlled color-tunable UORTP. In the matrix PNCz, the cation radicals of PNNA-1 and PNNA-2 can stay stably and form strong intermolecular interactions with PNCz because of their high molecular structure similarity, leading to a redshift of ultralong phosphorescence. Additionally, PNNA-1 and PNNA-2 show green UORTP in other matrixes DBT and BBP probably because they have a low molecular structure similarity with DBT and BBP. It is exciting that N-1, N-2 and their derivatives perform much better than Bd (H-benzo[f]indole) and its derivatives in UORTP. This study provides another example to support that cation radical might be a universal mechanism in organic phosphorescence. We believe that this work will expand the scope of organic phosphorescence. | Xue Zhang; Chen Qian; Zhimin Ma; Xiaohua Fu; Zewei Li; Huiwen Jin; Mingxing Chen; Hong Jiang; Zhiyong Ma | Materials Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6344bb03ea6a22807b119f6e/original/a-class-of-organic-units-featuring-matrix-controlled-color-tunable-ultralong-organic-room-temperature-phosphorescence.pdf |
6667d49512188379d8d1365f | 10.26434/chemrxiv-2024-03mmk | Cooperative Effects Associated with High Electrolyte Concentrations in Driving the Conversion of CO2 to C2H4 on Copper | Increasing the product selectivity and decreasing the cost of product separation is critical for large scale application of electrochemical CO2 reduction (ECO2R). We hypothesize that highly concentrated aqueous electrolytes can tune the microenvironment of the catalyst/electrolyte interface and improve product selectivity. Compared to a conventional electrolyte concentration of 1 M HCOOK, the use of a 7.1 M HCOOK electrolyte increases the FE ratio of C2H4/CO from 2.2 ± 0.3 to 18.3 ± 4.8 at -1.08 V vs RHE on a Cu gas diffusion electrode. Based on electrochemical analysis and AIMD simulation, the identity and concentration of the cation and anion play more important roles in controlling the CO2R reaction pathway than the bulk CO2 solubility and the bulk pH of electrolytes. In-situ ATR-SEIRAS suggests that, unlike 1 M HCOOK, the *CO-bridge binding mode on Cu is dominant in 7.1 M HCOOK electrolyte, which potentially results in less CO release and higher yield of C2H4. This study demonstrates that while we can tailor the electrolyte composition to shift product selectivity, the factors that control the product selectivity are numerous and cannot be distilled down into one correlated property-reactivity relationship. Thus, when CO2R conditions are changed, care must be taken to understand their effects on the bulk electrolyte properties and the electrode-electrolyte interface. | Shaoyang Lin; Yuval Fishler; Soonho Kwon; Annette E. Böhme; Weixuan Nie; Matthias H. Richter; Moon Young Yang; Jesse E. Matthews; Zachery W. B. Iton; Brian C. Lee; Thomas F. Jaramillo; Harry A. Atwater; William A. Goddard III; Wilson A. Smith; Kimberly A. See | Inorganic Chemistry; Catalysis; Electrochemistry; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6667d49512188379d8d1365f/original/cooperative-effects-associated-with-high-electrolyte-concentrations-in-driving-the-conversion-of-co2-to-c2h4-on-copper.pdf |
60c74e399abda28acff8d5bd | 10.26434/chemrxiv.12241784.v3 | NIC-CAGE: An Open-Source Software Package for Predicting Optimal Control Fields in Photo-Excited Chemical Systems | We present an open-source software package, NIC-CAGE (Novel Implementation of Constrained Calculations for Automated Generation of Excitations), for predicting quantum optimal control fields in photo-excited chemical systems. Our approach utilizes newly derived analytic gradients for maximizing the transition probability (based on a norm-conserving Crank-Nicolson propagation scheme) for driving a system from a known initial quantum state to another desired state. The NIC-CAGE code is written in the MATLAB and Python programming environments to aid in its readability and general accessibility to both users and practitioners. Throughout this work, we provide several examples and outputs on a variety of different potentials, propagation times, and user-defined parameters to demonstrate the robustness of the NIC-CAGE software package. As such, the use of this predictive tool by both experimentalists and theorists could lead to further advances in both understanding and controlling the dynamics of photo-excited systems. | Akber Raza; Chengkuan Hong; Xian Wang; Anshuman Kumar; Christian Shelton; Bryan Wong | Computational Chemistry and Modeling; Theory - Computational; Photocatalysis; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e399abda28acff8d5bd/original/nic-cage-an-open-source-software-package-for-predicting-optimal-control-fields-in-photo-excited-chemical-systems.pdf |
62f5ec731803739937a2a558 | 10.26434/chemrxiv-2022-2x0p4 | Three-Dimensional Covalent Organic Frameworks with scu Topology | Three-dimensional (3D) covalent organic frameworks (COFs) exemplify a new generation of crystalline extended solids with intriguing structures and unprecedented porosity. Notwithstanding substantial scope, the reticular synthesis of 3D COFs from pre-designed building units leading to new network topologies yet remains a demanding task owing to the shortage of 3D building units and inadequate reversibility of the linkages between the building units. In this work, by linking a tetragonal prism (8-connected) node with a square planar (4-connected) node, we report the first 3D COF with scu topology. The new COF, namely TUS-84, features a two-fold interpenetrated structure with well-defined porosity and a Brunauer−Emmett−Teller surface area of 679 m2 g-1. In drug delivery applications, TUS-84 shows efficient drug loading and sus-tained release profile. | Saikat Das; Taishu Sekine; Haruna Mabuchi; Tsukasa Irie; Jin Sakai; Yuichi Negishi | Organic Chemistry; Materials Science; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f5ec731803739937a2a558/original/three-dimensional-covalent-organic-frameworks-with-scu-topology.pdf |
67d47d486dde43c908cd8408 | 10.26434/chemrxiv-2025-r8mvz | TuNa-AI: a hybrid kernel machine to design tunable nanoparticles for drug delivery | Artificial intelligence (AI) stands to accelerate the development of nanoparticles for drug delivery, but current methodologies either focus on the identification of materials or adjusting of relative ratios of multi-component systems. Here, we developed a bespoke hybrid kernel machine integrating molecular learning and relative composition inference to engineer nanoparticles with new components and tunable composition. Our approach identified nanoformulations that encapsulate previously inaccessible drugs and can also guide excipient reduction. | Zilu Zhang; Yan Xiang; Joe Laforet Jr.; Ivan Spasojevic; Ping Fan; Ava Heffernan; Christine E. Eyler; Kris C. Wood; Zachary C. Hartman; Daniel Reker | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Drug Discovery and Drug Delivery Systems; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2025-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d47d486dde43c908cd8408/original/tu-na-ai-a-hybrid-kernel-machine-to-design-tunable-nanoparticles-for-drug-delivery.pdf |
60c740e5f96a00ab2b28637a | 10.26434/chemrxiv.7871921.v1 | Electronic Transitions of Molecules: Vibrating Lewis Structures | In this work we demonstrate a simple and intuitive description of electronic resonances in terms of localized electron vibrations. By partitioning the 3N-dimensional space of a many-electron wavefunction into hyper-regions related by permutation symmetry, chemical structures naturally result which correspond closely to Lewis structures, with identifiable single and double bonds, and lone pairs. Here we demonstrate how this picture of electronic structure develops upon the admixture of electronic wavefunctions, in the spirit of coherent electronic transitions. We show that pi-pi* transitions correspond to double-bonding electrons oscillating along the bond axis, and n-pi* transitions reveal lone-pairs vibrating out of plane. In butadiene and hexatriene, the double-bond oscillations combine with in- and out-of-phase combinations, revealing the correspondence between electronic transitions, molecular normal mode vibrations, and molecular plasmonics. This analysis allows electronic excitations to be described by building upon ground state electronic structures, without the need for molecular orbitals. | Yu Liu; Phil Kilby; Terry J. Frankcombe; Timothy Schmidt | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e5f96a00ab2b28637a/original/electronic-transitions-of-molecules-vibrating-lewis-structures.pdf |
673791f6f9980725cf4d7375 | 10.26434/chemrxiv-2024-db406 | A point-of-need framework for illicit drug identification with high-resolution mass spectrometry | The continually evolving drug landscape, with novel synthetic drugs and unique compositions, necessitates the need to advance technologies, data analysis methods, and data accessibility for compound detection and identification. Providing public health, first responder, and law enforcement communities with critical information in near real-time will aid emergency response and public awareness, and direct overdose prevention and interdiction efforts. A major component of this framework is the progression of accurate drug screening and preliminary identifications from a more rigid laboratory-based arrangement to an agile point-of-need paradigm. We investigated drug detection and identification of a field deployable high-resolution time-of-flight mass spectrometer, employing both acetone-assisted vacuum ultraviolet (VUV) photoionization and dielectric barrier discharge ionization (DBDI) schemes. This preliminary fit-for-purpose exploration was conducted under laboratory conditions, building toward deployment in a mobile laboratory setting. The chromatography-free measurements enabled rapid analysis of neat drug solutions and multi-component mixtures. Characterization and optimization of system parameters demonstrated sensitive performance, with limits of detection in the tens to hundreds of picograms for a range of drug classes from multiple-component mixtures. The system’s high mass resolution was calibrated with a polyethylene glycol calibrant, enabling accurate matching with spectral library entries. Integrating compound identification with the NIST DART-MS Forensics Database and NIST/NIJ DART-MS Data Interpretation Tool provided a solid foundation for transition to the point-of-need. The overarching framework seeks to support technology advancement and adoption, as well as the development of novel data analysis tools, processes, and management for public access and utilization. | Thomas P Forbes; Elizabeth L Robinson; Edward Sisco; Abigail Koss | Analytical Chemistry; Analytical Chemistry - General; Analytical Apparatus; Mass Spectrometry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673791f6f9980725cf4d7375/original/a-point-of-need-framework-for-illicit-drug-identification-with-high-resolution-mass-spectrometry.pdf |
673e51a17be152b1d0f96fd9 | 10.26434/chemrxiv-2024-ks4j1 | Uncovering Ion Transport Mechanisms in Ionic Liquids Using Data Science | Batteries play a key role in the energy transition but suffer from safety concerns arising from the electrochemical instability of organic electrolytes. Ionic liquids are emerging as promising, non-flammable electrolytes for next-generation batteries. Yet, designing ionic liquids to facilitate redox ion transport has proven challenging, because ionic liquids are concentrated electrolytes where ion-ion interactions cause pronounced deviation from classical electrolyte scaling theories which assume viscosity governs mobility. Machine learning studies show that ionic liquid transport properties are challenging to predict from molecular descriptors, preventing rational design. Here, we pursue a broader data-centric approach to provide insight into ionic liquid design by merging databases of experimental properties and computational molecular features for 218 ionic liquids across 127 publications. We find that ionic liquids are well-described by a modified Arrhenius model that captures structure-driven ion transport in correlated electrolytes, yielding energy barriers of around 20-30 kJ/mol. This exhibits remarkable agreement with the approximately 25 kJ/mol screened ion pair interaction energy derived from surface forces measurements, suggesting links between mechanisms of ion transport and interfacial screening. We also use machine learning models to find that molecular features can predict some properties, such as density, while failing to predict properties that rely on long-range correlations, such as viscous dissipation. Our study reveals that data science tools can be leveraged to reveal non-classical transport scaling relationships and alternative materials descriptors that promise to be transformative for designing ionic liquids and other correlated electrolytes for next-generation batteries. All data and models are shared as open-source code. | J. E. Umaña; Ryan K. Cashen; Victor M. Zavala; Matthew A. Gebbie | Theoretical and Computational Chemistry; Physical Chemistry; Machine Learning; Transport phenomena (Physical Chem.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673e51a17be152b1d0f96fd9/original/uncovering-ion-transport-mechanisms-in-ionic-liquids-using-data-science.pdf |
60c74680ee301c6a4ec79536 | 10.26434/chemrxiv.11339063.v1 | Ligand-Mediated Phase Control in Colloidal AgInSe2 Nanocrystals | Synthetic studies of colloidal nanoparticles that
crystallize in metastable structures represent an emerging area of interest in
the development of novel functional materials, as metastable nanomaterials may
exhibit unique properties when compared to their counterparts that crystallize
in thermodynamically preferred structures. Herein, we demonstrate how phase
control of colloidal AgInSe<sub>2</sub> nanocrystals can be achieved by
performing reactions in the presence, or absence, of 1-dodecanethiol. The thiol
plays a crucial role in formation of metastable AgInSe<sub>2</sub>
nanocrystals, as it mediates an in-situ topotactic cation exchange from an
orthorhombic Ag<sub>2</sub>Se intermediate to a metastable orthorhombic phase
of AgInSe<sub>2</sub>. We provide a detailed mechanistic description of this cation
exchange process to structurally elucidate how the orthorhombic phase of AgInSe<sub>2</sub>
forms. Density functional theory calculations suggest that the metastable
orthorhombic phase of AgInSe<sub>2</sub> is metastable by a small margin, at 10
meV/atom above the thermodynamic ground state. In the absence of 1-dodecanethiol,
a mixture of Ag<sub>2</sub>Se nanocrystal intermediates form that convert
through kinetically slow, non-topotactic exchange processes to yield the
thermodynamically preferred chalcopyrite structure of AgInSe<sub>2</sub>. Finally,
we offer new insight into the prediction of novel metastable multinary
nanocrystal phases that do not exist on bulk phase diagrams. | Bryce
A. Tappan; Matthew Horton; Richard Brutchey | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74680ee301c6a4ec79536/original/ligand-mediated-phase-control-in-colloidal-ag-in-se2-nanocrystals.pdf |
62c5f55e516311a09813bb11 | 10.26434/chemrxiv-2022-mxq0n | Electron Paramagnetic Resonance for the Detection of Electrochemically Generated Hydroxyl Radicals: Issues Associated with Electrochemical Oxidation of the Spin Trap | For the detection of electrochemically produced hydroxyl radicals (OH˙) from the oxidation of water, electron paramagnetic resonance spectroscopy (EPR) in combination with spin trap labels is a popular technique. Here we show that quantification of the true concentration of OH˙ generated from water oxidation via electrochemical (EC)-EPR is unlikely. This is primarily due to the spin trap oxidising at potentials less positive than water and resulting in the same spin trap adduct as is formed from the solution reaction of OH˙ with the spin trap. We illustrate this through consideration of 5,5-dimethyl-1-pyrroline N-oxide (DMPO) to spin trap OH˙. DMPO oxidation on a boron doped diamond (BDD) electrode in stationary solution occurs at a peak current potential of +1.90 V vs SCE, water oxidation commences at +2.35 V vs SCE. EC-EPR spectra shows signatures due to the hydroxyl spin adduct (DMPO-OH˙) at potentials lower than the thermodynamic standard water/HO˙ potential and in the region for DMPO oxidation. Increasing the potential into the water oxidation region, surprisingly, shows a lower DMPO-OH˙ concentration than when the potential is in the DMPO oxidation region. This behavior is attributed to further oxidation of DMPO-OH˙, production of fouling products on the electrode surface and bubble formation. Radical scavengers (ethanol) and other spin traps, here N-tert-butyl-α-phenylnitrone (PBN), α-(4-pyridyl N-oxide)-N-tert-butylnitrone (POBN) and 2-methyl-2-nitrosopropane dimer (MNP), also show oxidation signals less positive than that of water. However, by monitoring ethanol-DMPO adduct versus DMPO-OH˙ product distributions as a function of applied potential, it is possible to identify the potential at which HO˙ generation via water oxidation starts to dominate. | Emily Braxton; David Fox; Ben Breeze; Joshua Tully; Katherine Levey; Mark Newton; Julie Macpherson | Analytical Chemistry; Electrochemical Analysis; Spectroscopy (Anal. Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c5f55e516311a09813bb11/original/electron-paramagnetic-resonance-for-the-detection-of-electrochemically-generated-hydroxyl-radicals-issues-associated-with-electrochemical-oxidation-of-the-spin-trap.pdf |
612d1a09656369b8901dffce | 10.26434/chemrxiv-2021-7lw6b | Brønsted Acid-Catalyzed Stereospecific Dearomative Spirocyclization of Benzothiophenyl Analogues of Tertiary cis-β-Benzylstyrenes | 3-Substituted benzothiophenyl analogues of tertiary cis-β-benzylstyrenes undergo triflic acid-catalyzed dearomative spirocyclization to afford vicinal quaternary center-containing compounds at room temperature. Hydroarylation of the styrene is a competing process that could be selected for in substrates possessing electron-rich styrenyl alkenes, or an indole in place of the benzothiophene. | Anargul Tohti; Victoria Lerda; Benjamin J. Stokes | Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612d1a09656369b8901dffce/original/br-nsted-acid-catalyzed-stereospecific-dearomative-spirocyclization-of-benzothiophenyl-analogues-of-tertiary-cis-benzylstyrenes.pdf |
618f291a78db4e337b0bf449 | 10.26434/chemrxiv-2021-kthjg-v3 | Direct and indirect role of Fe doping in NiOOH monolayer for water oxidation catalysis | The oxygen evolution reaction (OER) activity of pristine NiOOH is enhanced by doping with Fe. However, the precise role of Fe is still being debated. Here, we use the first-principles DFT+U approach to study three different types of active sites: one on pristine and the other two on Fe-doped NiOOH monolayers to account for the direct and indirect roles of Fe. To compare the activity of the active sites, we consider two mechanisms of OER based on the source of O-O bond formation. Our results show that the mechanism involving the coupling of lattice oxygen is generally more favorable than water nucleophilic attack on lattice oxygen. On doping with Fe, the overpotential of NiOOH is reduced by 0.33 V in excellent agreement with experimental findings. Introducing Fe at active sites results in different potential determining steps (PDS) in the two mechanisms, whereas Ni sites in pristine and Fe-doped NiOOH have the same PDS regardless of the mechanism. The Fe sites not only have the lowest overpotential but also decrease the overpotential for Ni sites. | Manish Kumar; Simone Piccinin; Varadharajan Srinivasan | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618f291a78db4e337b0bf449/original/direct-and-indirect-role-of-fe-doping-in-ni-ooh-monolayer-for-water-oxidation-catalysis.pdf |
655b072f2c3c11ed71c1d780 | 10.26434/chemrxiv-2023-gpxww | Evaluation of acenes as potential acceptors in thermally activated delayed fluorescence emitters and the promise of a phenoxazine-naphthalene emitter for OLEDs | Thermally activated delayed fluorescence (TADF) is one of the most promising technologies for harvesting triplet excitons in all-organic emitters, a property that is essential for achieving high efficiency in devices. Compounds that operate via this mechanism for emission typically rely on a combination of electron donating and accepting moieties separated by an aromatic bridge. Here we demonstrate that although naphthalene is underutilised as an acceptor, it can nonetheless be used in a donor-acceptor TADF emitter when coupled to two phenoxazines in the 1- and 4- positions. The compound 1,4-PXZ-Nap-PXZ emits at 508 nm, has a photoluminescence quantum yield of 48% and a delayed lifetime of 22.7 ms in a 20 wt% doped film in 1,3-bis(N-carbazolyl)benzene (mCP). An organic light-emitting diode (OLED) using this emitter showed a maximum external quantum efficiency (EQEmax) of 11% and green emission at λEL of 505 nm, demonstrating for the first time the potential of naphthalene-acceptor based emitters for devices. Finally, we have demonstrated by way of a density functional theory (DFT) study why naphthalene alone amongst linear acenes is suitable for this role. | Oliver Lee; Nidhi Sharma; Alexanadra Slawin; Yoann Olivier; Ifor Samuel; Malte Gather; Eli Zysman-Colman | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655b072f2c3c11ed71c1d780/original/evaluation-of-acenes-as-potential-acceptors-in-thermally-activated-delayed-fluorescence-emitters-and-the-promise-of-a-phenoxazine-naphthalene-emitter-for-ole-ds.pdf |
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