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6548e56ec573f893f1eb19aa | 10.26434/chemrxiv-2023-273lw-v2 | LA-ICP-MS/MS-based Rb-Sr isotope mapping for geochronology | This study introduces a new approach for in-situ Rb-Sr dating that utilizes rapid line scans instead of static spot ablation, enabling the creation of two-dimensional 87Rb/86Sr and 87Sr/86Sr isotope ratio and Rb-Sr age maps. The data acquisition is conducted utilizing an ICP-MS/MS instrument with N2O as the reaction gas, coupled to a 193 nm excimer laser via a low-aerosol-dispersion interface. This configuration allows for high repetition rates (> 100 Hz) and sensitivities, enabling data acquisition at a high scanning speed and small laser beam size (3-4 µm). Notably, this approach requires just about 1/30 of the sample volume typically utilized in conventional spot ablation mode, while achieving similar levels of precision and accuracy. Line scan ablation is tested and compared to spot ablation on age-homogeneous crystalline muscovite and biotite, for which reference Rb-Sr age data is acquired through ID-TIMS. Results show that a key requirement for accurate Rb-Sr ages based on line scan analyses is matrix correction using chemically matched crystalline mica. By presenting Rb-Sr age maps of three naturally deformed mica samples, we highlight the potential of Rb-Sr mapping for extracting age data from rocks that exhibit complex metamorphic-metasomatic histories and microscale dynamic recrystallization. Additionally, we show that quantitative elemental information (Al, Fe, Si, Li) can be collected alongside Rb-Sr isotope data. This advancement offers a distinctly more insightful assessment of isotope mobility in natural systems, the timing of element enrichment processes and enables, in high-Rb/Sr rock systems, highly precise isotopic dating of intricate geological processes at small scales. | Martin Kutzschbach; Johannes Glodny | Earth, Space, and Environmental Chemistry; Geochemistry | CC BY 4.0 | CHEMRXIV | 2023-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6548e56ec573f893f1eb19aa/original/la-icp-ms-ms-based-rb-sr-isotope-mapping-for-geochronology.pdf |
667d1f0fc9c6a5c07a83ad03 | 10.26434/chemrxiv-2024-rvf5l | Synergistic Processes for Enhanced Functionality and Microstructure Engineering in PVDF-based Systems | Vinylidene Fluoride (VDF)-based polymers are renowned for their remarkable electroactive properties, including piezoelectric, pyroelectric, and ferroelectric features. These properties make them highly sought-after in a wide range of applications, such as sensors and energy storage. The modulation of their dielectric characteristics is intricately linked to the crystalline polymorphism, which is contingent upon specific processing conditions. Herein, we delve into the potential for enhancing these dielectric functionalities through modifications of the processing conditions (i.e., solvent casting and evaporation rate). Our findings demonstrate that superior structural characteristics and enhanced dielectric properties are achieved when casting from highly polar solvents followed by vacuum annealing. This simple and efficient method, eliminates the need for extensive processing and excessive energy consumption and it holds promise for streamlining industrial processing on a larger scale by reducing duration, energy, and complexity. | Joulia Housseini; Florian Le Goupil; Kaili Xie; Georges Hadziioannou; Guillaume Fleury | Polymer Science; Fluoropolymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667d1f0fc9c6a5c07a83ad03/original/synergistic-processes-for-enhanced-functionality-and-microstructure-engineering-in-pvdf-based-systems.pdf |
636d6fc5924538e078881f61 | 10.26434/chemrxiv-2022-lk2j4 | Detection of SARS-CoV 2 receptor binding domain using fluorescence probe and DNA flowers enabled by rolling circle amplification | Using rolling circle amplification (RCA) and two different ways of signal readout, we developed analytical methods to detect the receptor binding domain (RBD) of SARS-CoV 2 spike protein (S protein). We modified streptavidin-coated magnetic beads with an aptamer of RBD through a biotin-tagged complementary DNA strand (biotin-cDNA). Binding of RBD caused the aptamer to dissociate from the biotin-cDNA, making the cDNA available to initiate RCA on the magnetic beads. Detection of RBD was achieved using a dual signal output. For fluorescence signaling, the RCA products were mixed with a dsDNA probe labelled with fluorophore and quencher. Hybridization of the RCA products caused the dsDNA to separate to emit fluorescence. To generate easily detectable UV-vis absorbance signal, the RCA amplification was extended to produce DNA flower to encapsulate horseradish peroxidase (HRP). The HRP-encapsulated DNA flower catalyzed a colorimetric reaction between H2O2 and 3,3′,5,5′-tetramethylbenzidine (TMB) to generate an optical signal. The fluorescence and colorimetric assays for RBD have low detection limits (0.11 pg/mL and 0.904 pg/mL) and a wide linear range (0.001-100 ng/mL). For detection of RBD in human saliva, the recovery was 93.0-100% for the fluorescence assay and 87.2-107% for the colorimetric assay. By combining fluorescence and colorimetric detection with RCA, detection of the target RBD in human saliva was achieved with high sensitivity and selectivity. | Man Zhang; Lei Ye | Analytical Chemistry; Biochemical Analysis | CC BY 4.0 | CHEMRXIV | 2022-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636d6fc5924538e078881f61/original/detection-of-sars-co-v-2-receptor-binding-domain-using-fluorescence-probe-and-dna-flowers-enabled-by-rolling-circle-amplification.pdf |
62c88d90fb63817f4ed2de68 | 10.26434/chemrxiv-2022-84bz2 | An Interactive Planetary Boundaries Systems Thinking Learning Tool to Integrate Sustainability into Chemistry Curriculum | Sustainability has a molecular basis that suggests a central role for chemistry in addressing today’s challenges to Earth and societal systems, and this role requires educators to see chemical reactions and processes as integral parts of dynamic and interconnected systems. Despite this prospect, few accessible resources are available for students and educators to facilitate systems thinking in chemistry for sustainability. We have developed an interactive digital learning tool (https://planetaryboundaries.kcvs.ca) based on the Planetary Boundaries sustainability framework, that uses interactive visualizations to help users better understand Earth system sustainability challenges and helps chemists and educators connect substances, reactions, and chemistry concepts to sustainability science. The tool highlights the fundamental role that chemistry plays in regulating the individual biophysical Earth system processes and in determining their control variables. It incorporates key features of a systems thinking framework by illustrating the dynamic interconnections among the processes and their control variables and demonstrates change of the Earth system over time. Finally, the interactive tool provides educators with accessible entry points to support the integration of chemistry curriculum content with sustainability considerations. | Robert P. MacDonald; Anna N. Pattison; Sarah E. Cornell; Ashley K. Elgersma; Sarah N. Greidanus; Sydney N. Visser ; Melanie Hoffman; Peter G. Mahaffy | Earth, Space, and Environmental Chemistry; Chemical Education; Chemical Education - General; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c88d90fb63817f4ed2de68/original/an-interactive-planetary-boundaries-systems-thinking-learning-tool-to-integrate-sustainability-into-chemistry-curriculum.pdf |
61dd6f99e7b7514653964a3c | 10.26434/chemrxiv-2021-nlltl-v2 | Electrochemical oscillatory baffled reactors fabricated with additive manufacturing for efficient continuous-flow oxidations | Electrochemical oscillatory baffled reactors fabricated with additive manufacturing for efficient continuous-flow oxidations | Elena Alvarez; Maria Romero-Fernandez; Diego Iglesias; Raul Martinez-Cuenca; Obinna Okafor; Astrid Delorme; Pedro Lozano; Ruth Goodridge; Francesca Paradisi; Darren A. Walsh; Víctor Sans | Chemical Engineering and Industrial Chemistry; Reaction Engineering | CC BY NC 4.0 | CHEMRXIV | 2022-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61dd6f99e7b7514653964a3c/original/electrochemical-oscillatory-baffled-reactors-fabricated-with-additive-manufacturing-for-efficient-continuous-flow-oxidations.pdf |
62a04f7eb749a05c179c16fd | 10.26434/chemrxiv-2022-g9bvt | Elucidating the Impact of Structural Parameters on the Glass Transition Temperatures of Bottlebrush Polymers | The glass transition of branched polymers is determined by multiple structural parameters that dictate their inter- and intramolecular interactions, and ultimately, their molecular packing in the amorphous phase. Here we examined the impact of side chain length, backbone length, molecular weight composition, and topology on the glass transition behavior of bottlebrush polymers. Through examining precision bottlebrush polymer libraries (PBP, ĐSC = 1.0), we find the infinite molecular weight Tg is reached at a specific brush length after which the effect of the side-chain length dominates. Being a factor more dominant than the backbone, side-chain length affects the Tg of bottlebrush polymers across all sizes and topology variations. To demonstrate the versatility of side chain engineering strategies, a broad range of Tg and glass transition behavior was targeted through judicious choice of side chain length, blend ratios, and brush topology. | Michael Dearman; Nduka D. Ogbonna; Chamberlain A Amofa; Andrew J Peters; JIMMY LAWRENCE | Materials Science; Polymer Science; Organic Polymers; Polymer blends; Polymer brushes; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a04f7eb749a05c179c16fd/original/elucidating-the-impact-of-structural-parameters-on-the-glass-transition-temperatures-of-bottlebrush-polymers.pdf |
6108fd830321148575b994b9 | 10.26434/chemrxiv-2021-m7456 | COVID-19: Attacks Immune Cells and Interferences with Antigen Presentation through MHC-Like Decoy System | The high mortality of COVID-19 is related to poor antigen presentation and lymphopenia. In this present study, domain search results showed that many proteins of the SARS-COV-2 virus had MHC-like domains, which were similar to decoys for the human immune system. MHC-like structures could bind to MHC receptors of immune cells, interfering with antigen presentation. Then the oxygen-free radicals generated by E protein destroyed immune cells after MHC-like of S protein could bind to them. Mutations in the MHC-like region of the viral proteins such as S promoted weaker immune resistance and more robust transmission. S 127-194 were the primary reason for the robust transmission of delta variants. The S 144-162 regulated the formation of S trimer. The mutations of RdRP: G671S and N: D63G of delta variant caused high viral load. S 62-80 of alpha, beta, lambda variants were the important factor for fast-spreading. S 616-676 and 1014-1114 were causes of high mortality for gamma variants infections. These sites were in the MHC-like structure regions. | liu wenzhong; li hualan | Biological and Medicinal Chemistry; Biochemistry; Bioinformatics and Computational Biology; Cell and Molecular Biology | CC BY 4.0 | CHEMRXIV | 2021-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6108fd830321148575b994b9/original/covid-19-attacks-immune-cells-and-interferences-with-antigen-presentation-through-mhc-like-decoy-system.pdf |
646b7381ccabde9f6e2e8cf8 | 10.26434/chemrxiv-2023-gsgrw | New ultrahard tetragonal C9 and C12 allotropes with edge- and corner-sharing C4 tetrahedra and diamond-like properties | Stable tetragonal C9 and C12 with original topologies have been devised based on crystal chemistry rationale and unconstrained geometry optimization calculations within the density functional theory (DFT). The two new carbon allotropes are characterized by corner- and edge-sharing tetrahedra, they are mechanically (elastic constants) and dynamically (phonons) stable, and exhibit thermal and mechanical properties close to diamond. The electronic band structures show insulating behavior with band gaps close to 5 eV, similar to diamond. | Samir F. Matar; Vladimir L. Solozhenko | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646b7381ccabde9f6e2e8cf8/original/new-ultrahard-tetragonal-c9-and-c12-allotropes-with-edge-and-corner-sharing-c4-tetrahedra-and-diamond-like-properties.pdf |
659fd440e9ebbb4db9eb23fa | 10.26434/chemrxiv-2024-rlfnp | Modular synthesis of heterobenzylic amines via Carbonyl Azinylative Amination | The synthesis of α-alkyl, α’-2-azinyl amines by addition of 2-heteroaryl-based nucleophiles to alkyl substituted iminium ion is typically a challenging synthetic transformation due to mismatched reactivities and competing deprotonation adja-cent to the carbon-nitrogen double bond. Here, we report a solution to this problem through the development of a multi-component coupling process wherein a putative 2-azinyl indium nucleophile, generated in situ from the corresponding 2-iodo heteroarene and indium powder, adds to an iminium ion that is also formed directly in the reaction. This modular and operationally straightforward carbonyl azinylative amination (CAzA) displays a broad scope, does not require a tran-sition metal catalyst and only a metal reductant is needed to generate a reactive 2-azinyl nucleophile in the reaction. Beyond the addition to iminium ions, the 2-azinylation of polyfluoromethyl ketones to form the corresponding tertiary al-cohols is also disclosed. Together, the products of these reactions possess a high degree of functionality, are typically challenging to synthesize by other methods, and contain motifs recognized as privileged in the context of pharmaceuti-cals and agrochemicals. | Matthew Gaunt; Alex Rafaniello; Roopender Kumar | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659fd440e9ebbb4db9eb23fa/original/modular-synthesis-of-heterobenzylic-amines-via-carbonyl-azinylative-amination.pdf |
66ed41ad12ff75c3a1e7dcd9 | 10.26434/chemrxiv-2024-f384d | Novel O,N,O-coordinated organofluoroboron probe for
amyloid detection: Insight from experiment and theory | This work presents the results of photophysical studies for a newly synthesized BF-based organoboron dye of D-A-D topology. The one- and two-photon properties of the dye are compared with D-A parent compound and commercially available amyloid marker: Methoxy-X04. We demonstrate that the new dye exhibits better optical properties upon binding to amyloids than Methoxy-X04, including emission above 600 nm, higher values of 2PA cross section, broader excitation range and higher increment of emission intensity upon binding to amyloids. All these data demonstrate that the new probe is interesting scaffold for application in
two-photon microscopy and amyloid staining. | Agata Hajda; Elizaveta Petrusevich; Robert Zaleśny; Borys Ośmiałowski; Joanna Olesiak-Bańska | Physical Chemistry; Organic Chemistry; Materials Science; Dyes and Chromophores; Imaging Agents; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ed41ad12ff75c3a1e7dcd9/original/novel-o-n-o-coordinated-organofluoroboron-probe-for-amyloid-detection-insight-from-experiment-and-theory.pdf |
66d85b7b51558a15ef059e1a | 10.26434/chemrxiv-2024-1gxgq | Weighted distribution of relaxation time analysis of
battery impedance spectra using Gaussian process
regression for noise estimation | Electrochemical impedance spectroscopy (EIS) is one of the most widely deployed methods to characterise electrochemical systems such as batteries, fuel cells or electrolyzers. The distribution of relaxation times (DRT) represents a technique to simplify EIS data by deconvolution with a suitable kernel, while with equivalent circuit modelling (ECM) a user-selected function is fitted to characterize the investigated system. Ideally, the residuals of a DRT fit should represent random white noise without systematic residuals, hence no useful data is lost by this analysis step. Thereby DRT can provide the number of distinguishable features based solely on the EIS data, without a priori knowledge of the response of the investigated system. It is demonstrated that such a 'lossless' DRT inversion is possible if the local noise amplitude is considered, which requires a weighted DRT procedure and a method to estimate the frequency dependent noise amplitude. A noise estimate to determine the necessary weights was obtained using multiple EIS acquisitions of the same battery at identical state-of-charge. Alternatively, it is shown that Gaussian process regression (GPR) is capable of estimating an equivalent weighting matrix from a single data set as a prerequisite for automatized weighted DRT inversion without user intervention. The obtained DRT spectrum is then used for the selection of an equivalent circuit model, its initial parametrization, and setting of constraints. The robustness and reliability of this technique is tested numerically using a simple digital twin model. Eventually, by means of the investigated battery it is discussed that using a combination of DRT and ECM, a more physically relevant description of processes in an electrochemical system can be achieved. | Christian Hippolyt Bartsch; Limei Jin; Franz Philipp Bereck; Andreas Mertens; Rüdiger-Albert Eichel; Christoph Scheurer; Josef Granwehr | Theoretical and Computational Chemistry; Energy; Machine Learning; Artificial Intelligence; Energy Storage | CC BY 4.0 | CHEMRXIV | 2024-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d85b7b51558a15ef059e1a/original/weighted-distribution-of-relaxation-time-analysis-of-battery-impedance-spectra-using-gaussian-process-regression-for-noise-estimation.pdf |
638a1c5c04bc661f3604c898 | 10.26434/chemrxiv-2022-dc220 | Native amides as Enabling Vehicles for Forging sp3–sp3 Architectures via Interrupted Deaminative Ni-catalyzed Chain-Walking | Herein, we disclose an interrupted deaminative Ni-catalyzed chain-walking strategy that forges sp3–sp3 architectures at remote, yet previously unfunctionalized, methylene sp3 C–H sites enabled by the presence of native amides. This protocol is characterized by its mild conditions and wide scope, including challenging substrate combinations. Site-selectivity can be dictated by a judicious choice of the ligand, thus offering an opportunity to enable sp3–sp3 bond-formations that are otherwise inaccessible in conventional chain-walking events. | Jesus Rodrigalvarez; Hao Wang; Ruben Martin | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638a1c5c04bc661f3604c898/original/native-amides-as-enabling-vehicles-for-forging-sp3-sp3-architectures-via-interrupted-deaminative-ni-catalyzed-chain-walking.pdf |
60c7426a567dfe19d9ec3f3d | 10.26434/chemrxiv.8089208.v2 | Low Dimensional Representations along Intrinsic Reaction Coordinates and Molecular Dynamics Trajectories Using Interatomic Distance Matrices | Low dimensional representations along reaction pathways were produced using newly created Python software that utilises Principal Component Analysis (PCA) to do dimensionality reduction. Plots of these pathways in reduced dimensional space, as well as the physical meaning of the reduced dimensional axes, are discussed. | Stephanie Hare; Lars Bratholm; David Glowacki; Barry Carpenter | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426a567dfe19d9ec3f3d/original/low-dimensional-representations-along-intrinsic-reaction-coordinates-and-molecular-dynamics-trajectories-using-interatomic-distance-matrices.pdf |
60c74536702a9b393418a983 | 10.26434/chemrxiv.9924692.v2 | Concise Synthesis and Antimicrobial Evaluation of the Guanidinium Alkaloid Batzelladine D | A concise synthesis of the tricyclic guanidinium alkaloid batzelladine D has been accomplished in a sequence of 8 steps from readily available building blocks. Highlights of the synthesis include gram-scale preparation of a late stage intermediate, pinpoint stereocontrol around the tricyclic skeleton and a modular strategy that enables analog generation. A key bicyclic b-lactam intermediate serves to not only control stereochemistry, but also serves as a pre-activated coupling partner to install the ester sidechain. The stereo-controlled synthesis allowed for the investigation of the antimicrobial activity of batzelladine D, demonstrating promising activity that is more potent for non-natural stereoisomers. | You-Chen Lin; Aubert Ribaucourt; Yasamin Moazami; Joshua Pierce | Natural Products; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74536702a9b393418a983/original/concise-synthesis-and-antimicrobial-evaluation-of-the-guanidinium-alkaloid-batzelladine-d.pdf |
60c743f70f50db81a4396014 | 10.26434/chemrxiv.9722348.v1 | Integrating Allyl Electrophiles into Nickel-Catalyzed Conjunctive Cross-Coupling | Allylation and conjunctive cross-coupling represent two useful, yet largely distinct, reactivity paradigms in catalysis. The union of these two processes would offer exciting possibilities in organic synthesis but remains largely unknown. Herein, we report the use of allyl electrophiles in nickel-catalyzed conjunctive cross-coupling with a non-conjugated alkene and dimethylzinc. The transformation is enabled by weakly coordinating, monodentate azaheterocycle directing groups, that useful building blocks in synthesis, including saccharin, pyridones, pyrazoles, and triazoles. The reaction occurs under mild conditions and is compatible with a wide range of allyl electrophiles. High chemoselectivity through substrate directivity is demonstrated in the facile reactivity of the β-γ alkene of the starting material, while the ε-ζ alkene of the product is preserved. The generality of this approach is further illustrated through the development of analogous method with alkyne substrates. Mechanistic studies reveal the importance of the weakly coordinating directing group in dissociating to allow binding of the allyl moiety to facilitate C(sp<sup>3</sup>)–C(sp<sup>3</sup>) reductive elimination. | Van Tran; Zi-Qi Li; Timothy Gallagher; Joseph Derosa; Peng Liu; Keary Engle | Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f70f50db81a4396014/original/integrating-allyl-electrophiles-into-nickel-catalyzed-conjunctive-cross-coupling.pdf |
6762c53cfa469535b9fb1afc | 10.26434/chemrxiv-2024-qq119-v2 | Atomic Layer Deposition of TixFe2-xO3 Photoanodes and Photocurrent Response Optimization by using Response Surface Methodology | Hematite (Fe2O3) is a promising visible-light-active semiconductor material for photoelectrocatalytic applications; however, it has yet to achieve its theoretical maximum efficiency. Researchers globally are making significant efforts to enhance its performance and surpass the current efficiency limitations. Here we report the photoelectrocatalytic performance of TixFe2-xO3 films deposited by atomic layer deposition (ALD) using FeCp2 and Ti(OMe)4 as precursors. Response Surface Methodology (RSM) with a face-centered central composite design (FC-CCD) was used to model and optimize the photocurrent response of TixFe2-xO3 thin film photoanodes. Deposition parameters, including the cycle ratio of TiO2 to Fe2O3, total number of ALD cycles and deposition temperature, were selected as independent variables, while the photocurrent density (PCD) at 1.23 V and 1.70 V vs RHE was used as the response variable. Thin film depositions were carried out according to FC-CCD design matrix, followed by post-annealing at 500oC for 1 hour in air. The films were then evaluated for their photocurrent response using a photoelectrochemical cell under standard AM 1.5G illumination, 100 mW/cm2. The experimental photocurrent responses were fitted to a second-order polynomial equation, resulting in the development of a mathematical model that establishes a relationship between the deposition parameters and PCD of TixFe2-xO3 photoanode. Analysis of model parameters revealed that film thickness and dopant concentration are the most significant factors influencing the PCD of TixFe2-xO3 photoanode. This study confirms that RSM based FC-CCD can be efficiently applied for the modeling and optimization of photocurrent response of TixFe2-xO3 photoanodes. | Anjan Deb; Anton Vihervaara; Georgi Popov; Mykhailo Chundak; Ahmed O. Abdelaal; Hugo L. S. Santos; Mikko J. Heikkilä; Marianna Kemell; Pedro H. C. Camargo; Mikko Ritala; Matti Putkonen | Catalysis; Nanoscience; Nanostructured Materials - Nanoscience; Heterogeneous Catalysis; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6762c53cfa469535b9fb1afc/original/atomic-layer-deposition-of-tix-fe2-x-o3-photoanodes-and-photocurrent-response-optimization-by-using-response-surface-methodology.pdf |
668418f45101a2ffa82a83fa | 10.26434/chemrxiv-2024-dmq5l | Promiscuity guided evolution of a decarboxylative aldolase for synthesis of chiral tertiary alcohols | Enzymes play an increasingly important role in synthetic biology and organic synthesis. Many potential applications benefit from promiscuous activity with a diverse array of substrates. Here, we show how to intentionally guide an enzyme towards generality through multi-generational directed evolution using substrate-multiplexed screening (SUMS). We demonstrate the advantages of promiscuity-guided evolution in a challenging context, engineering the decarboxylative aldolase UstD to perform a C-C bond forming reaction with ketone electrophiles. Mutations outside of the active site that impact catalytic function were immediately revealed by shifts in promiscuity, even when the overall activity was lower. By re-targeting these distal residues that couple to the active site with saturation mutagenesis, broadly activating mutations were readily identified. When analyzing active site mutants, SUMS identified both specialist enzymes that would have more limited utility as well as generalist enzymes with complementary activity on diverse substrates. These new UstD enzymes catalyze convergent synthesis of non-canonical amino acids bearing tertiary alcohol side chains. This methodology is easy to implement and enables the rapid and effective evolution of enzymes to catalyze desirable new functions. | Meghan Campbell; Amanda Ohler; Matthew McGill; Andrew Buller | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Bioengineering and Biotechnology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668418f45101a2ffa82a83fa/original/promiscuity-guided-evolution-of-a-decarboxylative-aldolase-for-synthesis-of-chiral-tertiary-alcohols.pdf |
66583be291aefa6ce15584e0 | 10.26434/chemrxiv-2024-199dr | Mg2+-driven selection of natural phosphatidic acids in primitive membranes | Biological membranes are composed of phospholipids comprising exclusively glycerol-1-phosphate or glycerol-3- phosphate. By contrast, primitive membranes would have been composed of heterogeneous mixtures of phospholipids, including non-natural analogues comprising glycerol-2-phosphate, as delivered by prebiotic synthesis. Thus, it is not clear how the selection of natural phospholipids could have come about. Here we show how differences in membrane properties, but not molecular proper- ties, could have been harnessed to drive the selection of natural phosphatidic acids (the biological precursors of all complex phos- pholipids) within primitive membranes. First, we demonstrate that at the molecular level, no prebiotic synthesis or hydrolysis path- way would have enabled the selection of natural phosphatidic acids. Second, we report that at the supramolecular level, natural phospholipids display a greater tendency to self-assemble in more packed and rigid membranes than non-natural analogues of the same chain length. Finally, taking advantage of these differences, we highlight that Mg2+, but not Ca2+, drives the selective precipi- tation of non-natural phosphatidic acids from heterogeneous mixtures obtained by prebiotic synthesis, leaving membranes propor- tionally enriched in natural phosphatidic acids. Our findings delineate a plausible pathway by which the transition towards biologi- cal membranes could have occurred under conditions compatible with prebiotic metal-driven processes, such as non-enzymatic RNA polymerization. | Krishnakavya Thaipurayil Madanan; Yuhan Li; Valeria J. Boide-Trujillo; David A. Russell; Claudia Bonfio | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Supramolecular Chemistry (Org.); Biochemistry | CC BY NC 4.0 | CHEMRXIV | 2024-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66583be291aefa6ce15584e0/original/mg2-driven-selection-of-natural-phosphatidic-acids-in-primitive-membranes.pdf |
647f8329e64f843f416d098b | 10.26434/chemrxiv-2023-jfgcl | Opening the Density-Functional Theory Black Box: a Collection of Pedagogic Jupyter Notebooks | Density-Functional Theory (DFT) is indubitably the most popular and among the most successful approaches for approximately solving the many-electron Schrödinger equation. The level of understanding on the part of both researchers and students using DFT, however, is lacking given the availability of black box software. The present work addresses this knowledge gap by providing three Jupyter notebooks, easily accessible through the Google Colaboratory (GitHub repository: https://github.com/tjz21/DFT_PIB_Code), that provide a short skirmish with the fundamentals of DFT through a particle in a box-type model system. These notebooks were tested in conjunction with a problem worksheet in a graduate-level quantum chemistry course; pre- and post-activity survey results reveal largely positive reactions to this implementation and sustained enthusiasm for the subject. | Jacob S. Hirschi; Dayana Bashirova; Tim J. Zuehlsdorff | Theoretical and Computational Chemistry; Chemical Education; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647f8329e64f843f416d098b/original/opening-the-density-functional-theory-black-box-a-collection-of-pedagogic-jupyter-notebooks.pdf |
65001ff499918fe537d00b3b | 10.26434/chemrxiv-2023-l6k4m | Acid-Catalyzed Highly Enantioselective Synthesis of alpha-Amino Acid Derivatives from Sulfinamides and Alkynes | An acid-catalyzed enantioselective difunctionalization of activated alkynes using chiral sulfinamide reagents is developed. It is an atom-economic functional groups and chirality transfer process that allows modular synthesis of optically active alpha-amino acid derivatives under mild conditions. The reaction proceeds through a [2,3]-sigmatropic rearrangement mechanism with predictable stereochemistry and broad scope. | Herui Liu; Guangwu Sun; Yuchao Zhang; Yongxi Li; Baobiao Dong; BING GAO | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65001ff499918fe537d00b3b/original/acid-catalyzed-highly-enantioselective-synthesis-of-alpha-amino-acid-derivatives-from-sulfinamides-and-alkynes.pdf |
67a1257bfa469535b9f4e0e6 | 10.26434/chemrxiv-2025-m4ml8 | Multicolor Digital Light Processing 3D Printing Enables Dissolvable Supports for Freestanding and Non-Assembly Structures | The limited diversity in photocurable resin chemistries has precluded access to certain geometries using digital light processing (DLP) 3D printing, a rapid, precise, economical, and low-waste manufacturing technology. Specifically, freestanding structures with floating overhangs (e.g., hooks) and mobile non-assembly structures that cannot be physically separated (e.g., joints) represent two such geometries that are difficult or impossible to access with contemporary DLP 3D printing. Herein, we disclose novel resins comprising photosystems that selectively react with different colors of light to form soluble thermoplastics and insoluble thermosetscs. Systematic characterization of the acrylate- and epoxy-based resins and corresponding polymers from simultaneous UV and visible (violet or blue) light exposure revealed a rapid multimaterial 3D printing process (~0.75 mm/min) capable of providing supports that dissolve in ethyl acetate, a “green” solvent, within 10 minutes at room temperature. Relative to manual support removal, the present process provides comparable or improved surface finishes and higher throughput. Finally, several proof-of-concept structures requiring dissolvable supports were 3D printed, including hooks, chains, and joints, which were scanned using computed tomography to showcase the processes geometric versatility and high fidelity. This work provides fundamental design principles for multimaterial resin chemistry and lays a foundation for automating next generation additive manufacturing. | Keldy Mason; Ji-Won Kim; Elizabeth Recker; Jenna Nymick; Mingyu Shi; Franz Stolpen; Jaechul Ju; Zachariah Page | Polymer Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a1257bfa469535b9f4e0e6/original/multicolor-digital-light-processing-3d-printing-enables-dissolvable-supports-for-freestanding-and-non-assembly-structures.pdf |
66b091e5c9c6a5c07a0ba6af | 10.26434/chemrxiv-2024-h5wx5 | Investigating the substrate oxidation mechanism in lytic polysaccharide monooxygenase: H2O2- versus O2-activation | Lytic polysaccharide monooxygenases (LPMOs) form a copper-dependent family of enzymes classified under the auxiliary activity (AA) superfamily. The LPMOs are known for their boosting of polysaccharide degradation through oxidation of the glycosidic bonds that link the monosaccharide subunits. This oxidation has been proposed to be dependent on either O2 or H2O2 as co-substrate. Theoretical investigations have previously supported both mechanisms, although this contrasts with recent experiments. A possible explanation is that the theoretical results critically depend on how the Cu active site is modeled, i.e., which second-sphere residues were included in the QM region. This has also led to different results even when employing only H2O2 as co-substrate. In this paper, we investigate both the O2- and H2O2-driven pathways, employing LsAA9 as the underlying LPMO and a theoretical model based on a quantum mechanics/molecular mechanics (QM/MM) framework. We ensure to consistently include all residues known to be important by using extensive QM regions. We also investigate several conformers that can partly explain the differences seen in previous studies. We find that the O2-driven reaction is unfeasible, in contrast to our previous QM/MM calculations with smaller QM regions. Meanwhile, the H2O2-driven pathway is feasible showing that for LsAA9, only H2O2 is a viable co-substrate as proposed experimentally. | Marlisa M. Hagemann; Erna K. Wieduwilt; Ulf Ryde ; Erik D. Hedegård | Theoretical and Computational Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b091e5c9c6a5c07a0ba6af/original/investigating-the-substrate-oxidation-mechanism-in-lytic-polysaccharide-monooxygenase-h2o2-versus-o2-activation.pdf |
673dd9055a82cea2fae53d3b | 10.26434/chemrxiv-2024-wnzpf | Full non-isocyanate polyurethane self-blown foams prepared at room temperature by utilizing Exo-Vinylene Cyclic Carbonates | Though widely used, commercial polyurethane foams raise health concerns stemming from their isocyanate precursors, and environmental issues due their difficult recycling. Non-isocyanate polyurethane foams made via cyclic carbonate aminolysis, thus polyhydroxyurethanes foams (PHUFs), appear to be potential alternatives, but achieving room-temperature self-blowing PHUFs, predominantly through 5-membered cyclic carbonate and amine chemistry remains challenging without involving epoxides in the formulation. In this research, we demonstrate a new concept that makes the production of full PHUFs possible through the incorporation of exo-vinylene cyclic carbonate (αCC) into the formulation. This approach incorporates hydroxyoxazolidone groups, i.e. cyclic hydroxyurethanes, as pending groups of the polyhydroxyurethane backbone. We investigate the reactions occurring in this foaming system and identify optimal foaming formulations to rapidly produce PHUFs, within 1-5 minutes, with a high gel content. The study explores monomer variations as amine mixtures and different αCCs, demonstrating the potential for future optimization. Compression tests reveal the influence of foam formulation on the thermo-mechanical foam’s properties, particularly under varying humidity conditions. This concept paves the way for the rapid preparation of the next-generation of isocyanate-free polyurethane foams with modular properties, from flexible to rigid foams. | Maksim Makarov; Maxime Bourguignon; Bruno Grignard; Christophe Detrembleur | Polymer Science; Organic Polymers; Polymerization (Polymers); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673dd9055a82cea2fae53d3b/original/full-non-isocyanate-polyurethane-self-blown-foams-prepared-at-room-temperature-by-utilizing-exo-vinylene-cyclic-carbonates.pdf |
653442d487198ede07fb649b | 10.26434/chemrxiv-2023-9w7gf | Circular olefin copolymers made de novo from ethylene and α-olefins | Polyethylene (PE)-based materials, including ethylene homopolymers and its random or block copolymers with α-olefins, are the most produced synthetic materials globally, but current practices in their production, use, and after-use that follow the linear materials economy framework have taken a huge toll on both the environment and society. 1,2 Although several notable advances have been made in PE chemical re/upcycling, 3-10 energy-efficient and selective catalytic processes are still lacking due to the inherent chemical inertness of C-C and C-H bonds in PE. 11 Ideally, PE materials should be made de novo to have a circular, closed-loop lifecycle. 12-15 Recently, several circular polymers with closed-loop lifecycles were developed, 16-22 including recyclable high-density PE (HDPE)-like polymers. 23-25 However, production of circular ethylene/α-olefin copolymers, including high-volume, linear low-density PE (LLDPE) as well as high-value olefin elastomers and block copolymers at scale, presents a particular challenge due to difficulties in introducing branches while simultaneously installing chemical recyclability and also directly using industrial ethylene and α-olefin feedstocks. Here we show that coupling of industrial coordination copolymerization of ethylene and α-olefins with a designer functionalized chain-transfer reagent, followed by modular assembly of the resulting AB telechelic polyolefin building blocks by polycondensation, affords a series of ester-linked LLDPE and PE-based copolymers. These new materials not only retain thermomechanical properties of PE-based materials but also exhibit full chemical circularity via simple transesterification and markedly enhanced adhesion to polar surfaces. | Xing-Wang Han; Xun Zhang; Youyun Zhou; Aizezi Maimaitiming; Xiu-Li Sun; Yanshan Gao; Peizhi Li; Boyu Zhu; Eugene Y.-X. Chen; Xiaokang Kuang; Yong Tang | Catalysis; Organometallic Chemistry; Polymer Science; Polymerization (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2023-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653442d487198ede07fb649b/original/circular-olefin-copolymers-made-de-novo-from-ethylene-and-olefins.pdf |
67ac6230fa469535b9ffc7a6 | 10.26434/chemrxiv-2025-cq53z | Reaction network analysis of organochloride mediated oxidation induced by ionizing radiation | The generation of organoperoxy radical by irradiating aqueous solutions of organochlorides depends on the concentration of organochloride, where low concentration results in low yield of reactive oxygen species (ROS). The need of high concentration of organochloride limits the application in cancer therapy as most small molecule organochlorides show liver toxicity at elevated concentrations. To study if the oxidation is feasible at low concentration of organochloride, we proposed a reaction network where the effect of molecular oxygen is included. We hypothesized that oxygen competes with the organochloride to react with aqueous electrons, thereby causing a low yield of ROS at low organochloride concentrations. However, oxygen is necessary in the ROS formation pathway, which complicates straightforward prediction of reaction outcome. We developed a mathematic model to simulate the yield of ROS depending on organochloride and oxygen concentrations. The simulated results indicate that at low organochloride concentration, decreasing oxygen concentration leads to higher yield of ROS, with a peak at approximately 2% partial pressure of oxygen, and oxygen lower than 2% results in a sharp yield drop of ROS. Experiments using a thioether as reductant to quantify the ROS formation show good agreement with simulated data, verifying the proposed network. After irradiation in phosphate buffer saline/organochloride, a thioether caged drug showed efficient uncaging yield, demonstrating the viability of using thioether as a radiation-sensitive group. | Juncheng Liu; Bing Xu; Evgeny Uslamin; Evgeny Pidko; Antonia Denkova; Rienk Eelkema | Physical Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Physical Organic Chemistry; Chemical Kinetics; Radiation | CC BY 4.0 | CHEMRXIV | 2025-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ac6230fa469535b9ffc7a6/original/reaction-network-analysis-of-organochloride-mediated-oxidation-induced-by-ionizing-radiation.pdf |
63613ba5aca1980bc3ee0c25 | 10.26434/chemrxiv-2022-43d4b | Effects of artificial weathering in NR/SBR elastomer blends | Degradation of polymer blends occurs by the constituent phases undergoing distinct chemical changes that depend on their unique chemical structures. This makes predicting and establishing a structure-property relationship for each phase necessary as well as challenging. In this work, the molecular and physical changes occurring in sulfur-cross-linked natural rubber (NR), styrene-butadiene rubber (SBR), and their 50/50 blend subjected to accelerated weathering are analyzed by 1H nuclear magnetic resonance (NMR) spectroscopy, Fourier-transform infrared (FTIR) spectroscopy, atomic-force microscopy (AFM), and dynamic mechanical thermal analysis (DMTA). NMR transverse relaxation time (T2) studies suggest the formation of rigid components due to weathering. FTIR and AFM reveal that this is related to the formation of a stiff surface due to chemical modifications, which shows up as an additional thermal transition in the DMTA curves. Low-field double-quantum (DQ) NMR studies of the cross-link density, by the residual dipolar coupling constant (Dres), of SBR show a continuous increase in its cross-link density over the weathering duration (988 h). In contrast, NR exhibits dominant chain scission reactions resulting in defects, with both materials demonstrating the formation of different chain lengths. During the first 168 h, NR also undergoes modification of sulfur bond lengths, which is also observed in the blend. The blend largely follows an intermediate trend of cross-link densities compared to the two polymers but shows signs of lesser chain modifications than a weighted average of the two polymers. This is confirmed by phase-resolved DQ magic-angle spinning (MAS) NMR experiments whereby the peak-specific Dres of the blend was measured to be lesser than that of the individual vulcanizates, thus proving that the blend is more resistant to weathering than its constituent elastomers. | Akshay Karekar; Carsten Schicktanz; Muhammad Tariq; Katja Oßwald; Katrin Reincke; Valentin Cepus; Beate Langer; Kay Saalwächter | Materials Science; Polymer Science; Elastic Materials; Polymer blends; Polymer chains | CC BY 4.0 | CHEMRXIV | 2022-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63613ba5aca1980bc3ee0c25/original/effects-of-artificial-weathering-in-nr-sbr-elastomer-blends.pdf |
64470521df78ec5015558696 | 10.26434/chemrxiv-2023-st339 | Hetero-Diels-Alder Reaction between Singlet Oxygen and Anthracene Drives Integrative Cage Self-Sorting | A ZnII8L6 pseudo-cube containing anthracene-centered ligands, a ZnII4L’4 tetrahedron with similar side length as the cube, and a trigonal prism ZnII6L3L’2 formed in equilibrium from a common set of subcomponents. Hetero-Diels-Alder reaction with photogenerated singlet oxygen transformed the anthracene-containing “L” ligands into endoperoxide “LO” ones, ultimately driving the integrative self-sorting to form trigonal prismatic cage ZnII6LO3L’2 exclusively. This ZnII6LO3L’2 structure lost dioxygen in a retro-Diels-Alder reaction after heating, resulting in reversion to the initial ZnII8L6 + ZnII4L’4 ⇌ 2 × ZnII6L3L’2 equilibrating system. Whereas the ZnII8L6 pseudo-cube had a cavity too small for guest encapsulation, the ZnII6L3L’2 and ZnII6LO3L’2 trigonal prisms possessed peanut-shaped internal cavities, with two isolated compartments divided by bulky anthracene panels. Guest binding was also observed to drive the equilibrating system towards exclusive formation of the ZnII6L3L’2 structure, even in the absence of reaction with singlet oxygen. | Yuchong Yang; Tanya Ronson; Dingyu Hou; Jieyu Zheng; Ilma Jahović; Kai Luo; Jonathan Nitschke | Physical Chemistry; Inorganic Chemistry; Organometallic Chemistry; Supramolecular Chemistry (Inorg.); Coordination Chemistry (Organomet.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64470521df78ec5015558696/original/hetero-diels-alder-reaction-between-singlet-oxygen-and-anthra-cene-drives-integrative-cage-self-sorting.pdf |
677d1b79fa469535b912a885 | 10.26434/chemrxiv-2025-5dqdt | On Water Quality of Nagaland, North-eastern India: A Short Review and Statistical Analyses | Water is an integral part for human survival but around 2.1 billion people do not have excess to safe drinking water and 4.5 billion people lack proper sanitation. The human needs and demands have built up the rapid growth of industrialization which alternatively has severely affected the stability of water. In the case of Nagaland, there is a mass knowledge gap on water related problems and its ill effects among locals which have not been identified to this extent. Dimapur district of Nagaland being the fastest developing city of Nagaland has severely affected major sources of water bodies but monitoring and documentation on the water bodies is very scanty. In this article we have presented some articles from neighboring northeastern states of India as Nagaland shares its boundary to these states and have similar geographical features. Then secondary data from research articles of Nagaland was examined to understand the contamination level in the region. Further statistical methods such as descriptive statistics, Correlation, regression, factor analysis was analyzed on the secondary data to give a better understanding on the behavior of water pollutants within the region. | Akito I Sema; Sanjay Chaudhuri; T. Tiakaba Jamir; Jhimli Bhattacharyya | Earth, Space, and Environmental Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677d1b79fa469535b912a885/original/on-water-quality-of-nagaland-north-eastern-india-a-short-review-and-statistical-analyses.pdf |
60ee837b9ab06e02dc4e6ed1 | 10.26434/chemrxiv-2021-sfwj7 | Singlet and triplet excited-state dynamics of a nonfullerene electron acceptor Y6 | Understanding the excited-state dynamics of nonfullerene electron acceptors is essential for further improvement of organic solar cells. Herein, we investigated the singlet and triplet excited-state dynamics in Y6, a novel nonfullerene acceptor, using transient absorption spectroscopy. We found that pristine Y6 films show biphasic singlet exciton decay kinetics with decay constants of ~220 ps and ~1200 ps, which is the origin of the large discrepancies in the previously reported exciton lifetimes in the solid state. The majority of the Y6 singlet excitons decayed with the faster (~220 ps) component, whereas a clear photoluminescence with the slower (~1200 ps) component was observed. Y6 singlet excitons undergo fast diffusion in the crystalline domains, resulting in fast singlet–singlet exciton annihilation, after which ultrafast triplet formation, assigned to singlet fission from higher excited singlet states, is observed. | Shin-ichiro Natsuda; Yuji Sakamoto; Taiki Takeyama; Rei Shirouchi; Toshiharu Saito; Yasunari Tamai; Hideo Ohkita | Physical Chemistry; Materials Science; Energy; Photovoltaics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ee837b9ab06e02dc4e6ed1/original/singlet-and-triplet-excited-state-dynamics-of-a-nonfullerene-electron-acceptor-y6.pdf |
60c74c3af96a003ab3287752 | 10.26434/chemrxiv.12445586.v1 | Violet-Blue Aggregation-Induced Emission Emitters for Non-Doped OLEDs with CIEy Smaller than 0.046 | <p>High emission efficiency and finite molecular
conjugation in aggregate state are two desirable features in violet-blue
emitters. Aggregation-induced emission luminogens (AIEgens) have surfaced as
promising luminescent materials that possess both features. Herein, we report the
design and synthesis of a group of violet-blue emissive AIEgens with photoluminescence
quantum yield higher than 98% in their film states. When utilizing these
AIEgens as non-doped emitting layers, the fabricated organic light-emitting
diode exhibit a maximum external quantum efficiency of 4.34% with Commission
Internationale de L’Eclairage (CIE) coordinates of (0.159, 0.035), which are amenable
to next generation Ultra-high Definition Television (UHDTV) display standard.</p> | Pengbo Han; Chengwei Lin; Dongge Ma; Anjun Qin; Ben Zhong Tang | Dyes and Chromophores; Optical Materials; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c3af96a003ab3287752/original/violet-blue-aggregation-induced-emission-emitters-for-non-doped-ole-ds-with-ci-ey-smaller-than-0-046.pdf |
61b2a60b689c8713b2dcff6e | 10.26434/chemrxiv-2021-g3gbd | Hydrogenolysis cleavage of Csp2-Csp3 bond over a metal-free NbOPO4 catalyst | Ru/NbOx catalysts, which combine the merits of facile hydrogen activation, strong binding to benzene ring and the presence of Brønsted acid sites, were well investigated toward Csp2-Csp3 bond cleavage. Herein, we unlock the ability of bare NbOx catalyst in the dissociation and activation of hydrogen molecule and further hydrogenolysis of the Csp2-Csp3 model compounds including polystyrene (PS). In-situ Drift and density functional theory (DFT) calculations reveal that H2 can be dissociated and surface hydride species can be produced over Nb2O5 through heterolytic and homolytic cleavages of H2. We also find that the existence of surface oxygen vacancies plays a key role in stabilizing hydride species. Further, the NbOPO4 catalyst not only allows the conversion of phenylcyclohexane to monocyclic compounds by cleaving Csp2-Csp3 bond, but also enables the conversion of PS to arenes with a high selectivity. This study provides and proves for the first time, the unique ability of metal oxides (phosphates) in the hydrogenolysis of compounds and plastics containing Csp2-Csp3 bonds. | Hao Zhou; Lu Chen; Yong Guo; Xiaohui Liu; Xin-Ping Wu; Xue-Qing Gong; Yanqin Wang | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b2a60b689c8713b2dcff6e/original/hydrogenolysis-cleavage-of-csp2-csp3-bond-over-a-metal-free-nb-opo4-catalyst.pdf |
6286df4843d1f085eb3261a4 | 10.26434/chemrxiv-2022-jz75v-v2 | Towards the development of machine learning models to predict protein-protein interaction modulators | Protein-protein interaction (PPI) inhibitors have a continued and increasing role in drug discovery. It is hypothesized that machine learning (ML) algorithms are able to classify or identify PPI inhibitors. In this work, we describe the performance of different algorithms broadly used in chemoinformatics to develop a classification model able to identify PPI inhibitors based on structural and physicochemical descriptors. We found that the classification algorithms have different performance according to different features employed in the training process: random forest (RF) models with the extended connectivity fingerprint radius 4 (ECFP4) had the best classification performance as compared to those models trained with ECFP6 o MACCS keys (166-bits). In general, logistic regression models had lower performance metrics than RF models, but ECFP4 was the representation most appropriate for linear regression. ECFP4 also yielded models with high performance metrics, in particular, with support vector machine (SVM). As part of this work, we constructed ensemble models based on the top-performing models. The pipeline code developed in this work and all results are freely available at https://github.com/BarbaraDiazE/PPI_ML. | Bárbara I. Díaz-Eufracio; José L. Medina-Franco | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6286df4843d1f085eb3261a4/original/towards-the-development-of-machine-learning-models-to-predict-protein-protein-interaction-modulators.pdf |
6304649f58843ba8aa99cde3 | 10.26434/chemrxiv-2022-tqvbw | Thirteen-Step Chemoenzymatic Synthesis of Gedunin | The limonoids have attracted significant attention from the synthetic community owing to their striking structural complexity and medicinal potential. Recent efforts notwithstanding, synthetic access to many intact or ring-D seco limonoids still remains elusive. Here, we report the first de novo synthesis of gedunin, a ring-D seco limonoid with HSP90 inhibitory ac-tivity, that proceeds in thirteen steps. Two enabling features in our strategy are the application of modern catalytic transformations to set the key quaternary centers in the carbocyclic core and the application of site- and chemoselective enzymatic oxidation to establish the requisite oxidation pattern on the A ring. This work lays the foundation for efficient synthetic access to other limonoids and unnatural analogs to facilitate further pharmacological investigation of the family. | Jian Li; Fang Chen; Hans Renata | Organic Chemistry; Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6304649f58843ba8aa99cde3/original/thirteen-step-chemoenzymatic-synthesis-of-gedunin.pdf |
672a0ae5f9980725cf29a3ff | 10.26434/chemrxiv-2024-f5kzt | Orthogonal click chemistry methods for preparing amphiphilic polyproline block copolymers: Synthesis and self-assembly | Polyproline-based homo- and diblock copolymers featuring clickable side chains-specifically, alkyne and allyl-have been successfully synthesized using water-assisted controlled ring-opening polymerization. These precursor polymers were then quantitatively modified through azide-alkyne and thiol-ene click chemistry. Sequentially, triethylene glycol monomethyl ether azide (a hydrophilic component) and octane thiol (a hydrophobic component) were grafted onto the pre-cursor block copolymer via orthogonal click reactions. The resulting side-chain-modified polyproline (PLP) amphiphilic co-polymers maintain a PPII helical conformation similar to native polyproline in aqueous environments. Additionally, the self-assembly behaviour of these amphiphilic block copolymers was examined using various analytical techniques, including dynamic light scattering (DLS), transmission electron microscopy (TEM), fluorescence spectroscopy, and confocal microscopy. Imaging through TEM and fluorescence studies indicated that the self-assembled amphiphilic polyprolines display a vesicular morphology. Moreover, incorporating side-chain functionalities into the polyproline backbone enhances the fine-tuning and control of material properties, opening the door to potential applications. | Raj Kumar Roy; Arjun Singh Bisht; Ankita Kumari; Prabir Maiti | Organic Chemistry; Polymer Science; Biopolymers; Organic Polymers; Polymer morphology; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672a0ae5f9980725cf29a3ff/original/orthogonal-click-chemistry-methods-for-preparing-amphiphilic-polyproline-block-copolymers-synthesis-and-self-assembly.pdf |
65f85cb366c13817293f44a2 | 10.26434/chemrxiv-2024-qv9fr | Finishing treatment processes for micropollutant degradation at the outlet of WWTP: Bibliometric analysis and QSPR/QSAR modeling | Micropollutants are substances, both synthetic and natural, that are discharged into the
environment from point and non-point sources, which typically come from wastewater treatment
plants (WWTP), enter the environment with treated wastewater and may be harmful to
ecosystems, wildlife, and human health. The conventional water treatment techniques find it
challenging to degrade these compounds due to their high stability. Despite advanced water
treatment methods, some compounds remain unremovable. The decontamination of water from
non-biodegradable micropollutants has encountered obstacles, necessitating the development of
advanced technologies for follow-up processing. In this review, we focus the micropollutant
removal using adsorption and photocatalysis technologies, we present a bibliometric analysis on
nano-adsorbents, photocatalysts, and photoelectrocatalysis (PEC) technology.
The chemical and degradation pathway diversity of micropollutants in real wastewater,
experimentally determining the effectiveness of micropollutant degradation is an expensive and
complex process. We propose the use nanocatatlysts to understand the quantitative relationship
between the structural characteristics of micropollutants and their degradability, such as
quantitative structure-property/ activity relationship (QSPR/QSAR) models. E.g., phenolic
compounds with different substituents, according to the multiple linear regression (MLR)
equation of the QSPR model, the degradation of phenolic compounds is greatly influenced by
electronic, hydrophobic, topological, and steric properties. These QSPR models underwent strict
internal and external statistical validation procedures and were trained to accurately predict the
experimental degradation rate constants of the test set. We explore the potential benefits and
limitations of various technologies and models for use in water treatment facilities. | Yunzhi Li; Julien G.Mahy; Stéphanie D. Lambert | Catalysis; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Water Purification; Electrocatalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f85cb366c13817293f44a2/original/finishing-treatment-processes-for-micropollutant-degradation-at-the-outlet-of-wwtp-bibliometric-analysis-and-qspr-qsar-modeling.pdf |
6172e5a9ff3ba9c5369d7d6c | 10.26434/chemrxiv-2022-8fhnh | Changes in chemical composition and copepod toxicity during petroleum photooxidation | Photoproducts can be formed rapidly in the initial phase of a marine oil spill. However, their toxicity is not well understood. In this study, oil was irradiated, chemically characterized, and tested for toxicity in three copepod species (A. tonsa, T. longicornis, C.finmarchicus). Irradiation led to a depletion of polycyclic aromatic hydrocarbons (PAHs) and n-alkanes in oil residues, along with an enrichment in aromatic and aliphatic oil photoproducts. Target lipid model-based calculations of PAH toxic units (TU-PAH) predicted that PAH toxicities were lower in water accommodated fractions (WAFs) of irradiated oil residues (“irradiated WAFs”) than in WAFs of dark-control samples (“dark WAFs”). In contrast, biomimetic extraction (BE) measurements showed increased bioaccumulation potential of irradiated WAFs compared to dark WAFs, mainly driven by photoproducts present in irradiated oil. In line with the BE results, copepod mortality increased in response to irradiated WAFs compared to dark WAFs. Low copepod toxicities were observed for WAFs produced with photooxidized oil slicks collected during the Deepwater Horizon oil spill. The results of this study suggest that while oil photoproducts have the potential to be a significant source of copepod toxicity, the water solubility of these products might mitigate their toxicity at sea. | Samuel Katz; Haining Chen; David Fields; Erin Beirne; Phoebe Keyes; Greg Drozd; Christoph Aeppli | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6172e5a9ff3ba9c5369d7d6c/original/changes-in-chemical-composition-and-copepod-toxicity-during-petroleum-photooxidation.pdf |
676bb9b46dde43c908428d05 | 10.26434/chemrxiv-2024-hdq5m | Improved Direct Bioelectrochemical Fructose Oxidation with Surfactant-Free Heterotrimeric Fructose Dehydrogenase Variant Truncating Heme 1c and C-Terminal Hydrophobic Regions | Direct electron transfer (DET)-type bioelectrocatalysis is a coupled redox reaction between enzymatic and electrode reactions. Such mediatorless reactions are an environmentally safe approach that can be applied to various bioelectrochemical devices. We focused on fructose dehydrogenase (FDH), a membrane-bound heterotrimeric enzyme that catalyzes DET-type D-fructose oxidation. Although the overall structure was recently elucidated, its membrane-bound region has not been completely identified. Therefore, this study assumed that the heme 1c region and C-terminal hydrophobic region (CHR) were bound to the membrane. A constructed double variant (Δ1cΔCHR_FDH) was soluble without any surfactants; additionally, cryo-electron microscopy confirmed that this variant was downsized. Δ1cΔCHR_FDH exhibited a 14-fold higher catalytic current density (11 ± 1 mA cm–2) than that of the wild-type recombinant FDH (rFDH) at multi-walled carbon nanotube electrodes. Kinetic analysis of the voltammograms suggested that downsizing of the enzyme and the removal of surfactants increased the surface concentration of enzymes at the electrode. This study elucidates the membrane-binding mechanism of proteins and efficient bioelectrocatalysis overcoming the interference of surfactants. | Taiki Adachi; Konatsu Ichikawa; Tomoko Miyata; Fumiaki Makino; Hideaki Tanaka; Keiichi Namba; Keisei Sowa | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676bb9b46dde43c908428d05/original/improved-direct-bioelectrochemical-fructose-oxidation-with-surfactant-free-heterotrimeric-fructose-dehydrogenase-variant-truncating-heme-1c-and-c-terminal-hydrophobic-regions.pdf |
6593fc1a66c13817298a5d1f | 10.26434/chemrxiv-2024-4bj6m | Unique Reactivity of Cyclic (Alkyl)(Amino)Carbene Stabilized Acyclic Imino Olefin (AIO) Towards Dinitrogen Transfer Reagent | N-Heterocyclic olefins (NHOs) represent a class of zwitterionic compounds known for their effective electron donor properties, often surpassing those of N-heterocyclic carbenes (NHCs). The properties of NHOs can be significantly fine-tuned by altering both the steric and electronic characteristics around the NHO framework. Parallel to NHOs, N-heterocyclic imines (NHIs) also exhibit exceptional donor properties and act as super-nucleophiles due to the strong ylidic nature of their exocyclic imine moiety. In this study, we employed the cyclic alkyl amino carbene (CAAC)-stabilized NHI to isolate a robust electron-donating acyclic olefin system and showcase its unique reactivity in comparison to traditional NHOs. Moreover, compound 2 shows air and moisture stability. In addition, compound 2 shows thermal stability up to 306 °C under an inert atmosphere. Furthermore, the calculated proton affinity of this compound is 269.9 kcal/mol, akin to the high proton affinities of NHOs reported in the literature. The reactivity of compound 2 with highly nucleophilic dinitrogen transfer azide resulted in four different compounds 3-6 by varying the stoichiometric ratios. Compound 3 is an azo-bridged AIO dimer, while compound 5 features a tetrazolium moiety. Compounds 4 and 6 contain unprecedented nitrogen-containing heterocycles. | Subrata Kundu; Bindusagar Das; Dhananjay Gupta; Aryan Chauhan; Ritu Yadav; Tarak Karmakar | Inorganic Chemistry; Ligands (Inorg.); Main Group Chemistry (Inorg.); Organometallic Compounds | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6593fc1a66c13817298a5d1f/original/unique-reactivity-of-cyclic-alkyl-amino-carbene-stabilized-acyclic-imino-olefin-aio-towards-dinitrogen-transfer-reagent.pdf |
637bd8790821294f97ffc3ab | 10.26434/chemrxiv-2022-5wfm6 | Engaging a Non-Catalytic Cysteine Residue Drives Unprecedented Selectivity of Caspase Inhibition | The caspases are a family of cysteine dependent proteases with important cellular functions in inflammation and apoptosis, while also implicated in human disease. Classical chemical tools to study caspase function lack selectivity for specific caspase family members due to highly conserved active sites and catalytic machinery. To overcome this limitation, we tar-geted a non-catalytic cysteine residue (C264) unique to Caspase-6, an enigmatic and understudied caspase isoform. Starting from disulfide ligands identified in a cysteine trapping screen, we used structure-informed covalent ligand design to produce potent, irreversible inhibitors (e.g., 3a) and chemoproteomic probes (e.g., 13-t) of Caspase-6 that exhibit unprecedented se-lectivity over other caspase family members and high proteomic selectivity. This approach and the new tools described will enable rigorous interrogation of the role of Caspase-6 in developmental biology and in inflammatory and neurodegenerative diseases | Kurt Van Horn; Dongju Wang; Daniel Medina-Cleghorn; Peter Lee; Clifford Bryant; Chad Altobelli; Priyadarshini Jaishankar; Kevin Leung; Raymond Ng; Andrew Ambrose; Yinyan Tang; Michelle Arkin; Adam Renslo | Biological and Medicinal Chemistry; Biochemistry; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637bd8790821294f97ffc3ab/original/engaging-a-non-catalytic-cysteine-residue-drives-unprecedented-selectivity-of-caspase-inhibition.pdf |
65cdd68ce9ebbb4db9683b36 | 10.26434/chemrxiv-2024-k36mr | Cyclodehydrogenation catalyzed by atomic hydrogen | Atomically precise synthesis of nanographenes and graphene nanoribbons on semiconductors and insulators has been a formidable challenge. In particular, the metallic substrates needed to catalyze cyclodehydrogenative planarization reactions of precursor molecules limit subsequent applications that exploit the electronic structure of nanographenes. We demonstrate that, counterintuitively, atomic hydrogen can play the role of a catalyst in the cyclodehydrogenative planarization reaction regardless of the substrate type. The high efficiency of the method was demonstrated by the nanographene synthesis on metallic Au, semiconducting TiO2, as well as on inert and insulating Si/SiO2 and thin NaCl layers. | Rafal Zuzak; Pawel Dabczynski; Jesús Castro-Esteban; José Ignacio Martínez; Mads Engelund; Dolores Pérez; Diego Peña; Szymon Godlewski | Physical Chemistry; Organic Chemistry; Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cdd68ce9ebbb4db9683b36/original/cyclodehydrogenation-catalyzed-by-atomic-hydrogen.pdf |
631b5fea5351a30f1ef491fe | 10.26434/chemrxiv-2022-vw8nv | Optimization of headspace solid-phase microextraction of volatile organic compounds from dry soil samples by porous coatings using COMSOL Multiphysics | Headspace solid-phase microextraction (HSSPME) is one of the simplest and cost-efficient sample preparation approaches for determination of volatile organic compounds (VOCs) in soil. This study was aimed at the development of the model for numerical optimization of HSSPME of volatile organic compounds from dry soil samples by porous coatings using COMSOL Multiphysics (CMP). ‘Transport of Diluted Species in Porous Medium’ physics was used for modeling. Effect of sample mass, pressure, fiber-headspace and soil-headspace distribution constants on extraction profiles and time of 95% equilibrium has been studied using the developed model. Equilibrium extraction under atmospheric pressure (1 atm) can take up to 97 min, while under vacuum (0.0313 atm) – 2.3 min. Equilibration time under vacuum was 42-43 times lower than under 1 atm at all studied distribution constants and sample masses. The developed model was modified for optimization of pre-incubation time using ‘Transport of Diluted Species’ physics. According to the obtained plots, 95% equilibration time can reach 13.3 min and depends on both sample mass and soil-headspace distribution constant of the analyte. The developed model can be recommended for optimization of pressure, preincubation and extraction time when fiber-headspace and soil-headspace distribution constants, soil porosity and density are known. | Bulat Kenessov; Anel Kapar | Analytical Chemistry; Environmental Analysis; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631b5fea5351a30f1ef491fe/original/optimization-of-headspace-solid-phase-microextraction-of-volatile-organic-compounds-from-dry-soil-samples-by-porous-coatings-using-comsol-multiphysics.pdf |
60c753b0bb8c1a468a3dc0cb | 10.26434/chemrxiv.13488177.v1 | Deciphering Aspartyl Peptide Sweeteners Using the Ultimate Molecular Theory of Sweet Taste | More than thirty years ago, I proposed a theory about sweet and bitter molecules’ recognition by protein helical structures. Unfortunately the papers<br />could not go to public platform until now. The sweet and bitter taste theory is updated and presented in separated papers. 1,2 Under the guidance of the sweet<br />receptor helix recognition theory 1, aspartyl/aminomalonyl peptide sweeteners are deciphered. Here it demonstrates that, this series of sweeteners has a<br />hydrogen-bond type hydrogen donor - hydrogen acceptor DH-B moiety and their DH-B is very special. Their B of the DH-B moiety is an oxygen of the carboxylic<br />group, which is widely accepted one. The DH of the DH-B moiety however is the NH of the aspartyl/aminomalonyl peptide, which is a selection for the first time to<br />the best of my knowledge. Even more unusual, their dynamic action acts through<br />the hydrogen on alpha carbon of aspartyl/aminomalonyl group. The receptor main and side grooves have different space characteristics in accepting sweet<br />molecules’ groups, which is elaborated in this paper. This unprecedented elucidation well explains the aspartyl/aminomalonyl peptide sweeteners’<br />phenomenon and, in return, strongly supports this sweet receptor helix recognition theory. | Huazhong He | Bioorganic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Stereochemistry; Food; Biochemistry; Biophysics; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753b0bb8c1a468a3dc0cb/original/deciphering-aspartyl-peptide-sweeteners-using-the-ultimate-molecular-theory-of-sweet-taste.pdf |
65260d6d8bab5d2055157be6 | 10.26434/chemrxiv-2023-5kl9x | Molecular origins of the ultrafast relaxation of a photoexcited hydrated electron | Recent experiments have shown conclusively that the photoexcited hydrated electron has a non-radiative lifetime of ~50 fs. However, theoretical studies have been unable to rationalize such an ultrafast timescale and a molecular mechanism has remained elusive. To address this, we simulated the excited-state dynamics of this species with our recently developed quantum-mechanics/molecular-mechanics technology. Analyzing the evolution of the hydrated electron's ground and excited-state wavefunctions within a charge-transfer picture reveals that the lobes of the excited p state undergo a rapid separation which closes the energy gap to the ground state and promotes internal conversion on an ultrafast timescale. The lobe separation is seen to correlate with hydrogen bond rearrangements in the first few solvation shells of the electron. | Amiel Paz; William Glover | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Chemical Kinetics; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65260d6d8bab5d2055157be6/original/molecular-origins-of-the-ultrafast-relaxation-of-a-photoexcited-hydrated-electron.pdf |
60c74a544c89194b32ad3206 | 10.26434/chemrxiv.11302301.v2 | NWPEsSe: an Adaptive-Learning Global Optimization Algorithm for Nanosized Cluster Systems | Global optimization constitutes an important and fundamental problem in theoretical studies in many chemical fields, such as catalysis, materials or separations problems. In this paper, a novel algorithm has been developed for the global optimization of large systems including neat and ligated clusters in gas phase, and supported clusters in periodic boundary conditions. The method is based on an updated artificial bee colony (ABC) algorithm method, that allows for adaptive-learning during the search process. The new algorithm is tested against four classes of systems of diverse chemical nature: gas phase Au<sub>55</sub>, ligated Au<sub>8</sub><sup>2+</sup>, Au<sub>8</sub> supported on graphene oxide and defected rutile, and a large cluster assembly [Co<sub>6</sub>Te<sub>8</sub>(PEt<sub>3</sub>)<sub>6</sub>][C<sub>60</sub>]<sub>𝑛</sub>, with sizes ranging between 1 to 3 nm and containing up to 1300 atoms. Reliable global minima (GMs) are obtained for all cases, either confirming published data or reporting new lower energy structures. The algorithm and interface to other codes in the form of an independent program, Northwest Potential Energy Search Engine (NWPEsSe), is freely available and it provides a powerful and efficient approach for global optimization of nanosized cluster systems. | Jun Zhang; Vassiliki-Alexandra Glezakou; Roger Rousseau; Manh-Thuong Nguyen | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a544c89194b32ad3206/original/nwp-es-se-an-adaptive-learning-global-optimization-algorithm-for-nanosized-cluster-systems.pdf |
60c7511abb8c1a85d63dbc05 | 10.26434/chemrxiv.13118642.v1 | Deconvolution of Intermixed Redox Processes in Ni-based Cation-Disordered Li-Excess Cathodes | Cation-disordered
rock-salt transition-metal oxides or oxyfluorides (DRX) have emerged as
promising cathode materials for Li-ion batteries due to their potential to
reach high energy densities and accommodate diverse, lower cost transition-metal
chemistries compared to conventional layered oxide materials. However, the
intricate local coordination environment in DRX also results in complex
electrochemical electron transfer involving parallel mechanisms of
transition-metal (TM) redox and oxygen (anionic) redox. Without decoupled and
quantitative information of these intermixed redox processes, the origin of
irreversibility, voltage hysteresis, and capacity fading is obscured, which
impedes the development of strategies to address these issues. Here we
deconvolute the mixed redox processes in a Ni-based DRX, Li<sub>1.15</sub>Ni<sub>0.45</sub>Ti<sub>0.3</sub>Mo<sub>0.1</sub>O<sub>1.85</sub>F<sub>0.15</sub>,
by combining <sup>18</sup>O isotopic enrichment, differential electrochemical
mass spectrometry (DEMS), and <i>ex-situ </i>acid
titration. The summation of TM-redox and oxygen-redox capacities measured
through our approach agrees with the net electron transfer measured by the
potentiostat. This study reveals much less Ni oxidation efficiency (59<i>.</i>5%) than its initially designed
efficiency (100%) due to competition of oxygen redox, which can occur at
potentials as low as 4.1 V (vs. Li/Li<sup>+</sup>). We propose that the
chemical approach presented in this work and its future extension can resolve
and quantify various mixed redox processes in different DRX, which allows clear
correlations among material design, deconvoluted redox capacities, and battery
performance. | Tzu-Yang Huang; Matthew Crafton; Yuan Yue; Wei Tong; Bryan D. McCloskey | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7511abb8c1a85d63dbc05/original/deconvolution-of-intermixed-redox-processes-in-ni-based-cation-disordered-li-excess-cathodes.pdf |
625762c9bdc9c2451cd3d150 | 10.26434/chemrxiv-2022-9s40c | Control of dual emission behaviour of μ-oxo-bridged Si(IV) corrole dimers by substituent bulkiness | The μ-oxo-bridged dimer of Si(IV) corrole has been recently reported to exhibit dual emissive properties depending on the solvent-viscosity. Here we examined the control of the excited-state dynamics and dual emission by meso-aryl substituents. Less hindered 10-unsubstituted and 10-phenyl-5,15-bis(pentafluorophenyl)-Si(IV) corrole dimers and more hindered 5,15-bis(pentafluorophenyl)-10-(2,4,6-trimethoxy)phenyl-Si(IV) corrole dimer were newly prepared and characterised. Interestingly, their solid-state structures are different; parallel, anti-parallel or orthogonal. In contrast, the energy-minimized structures in the excited-state have been suggested to be parallel in all cases owing to the significant excimer-like stabilization. As a result, different emission behaviours and viscosity dependence were observed. | Kyo Yamagata; Kento Ueta; Akito Nakai; Atsuhiro Osuka; Takayuki Tanaka | Organic Chemistry; Photochemistry (Org.); Physical Organic Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625762c9bdc9c2451cd3d150/original/control-of-dual-emission-behaviour-of-oxo-bridged-si-iv-corrole-dimers-by-substituent-bulkiness.pdf |
65c3207ae9ebbb4db9d49502 | 10.26434/chemrxiv-2024-svj8b | Formal 1,2-Diketone Decarbonylation Enabled by Synergistic Catalysis of Lewis Acid-Base Pairs and Redox Properties in CeO2 | Various decarbonylation reactions via oxidative addition of carbonyl compounds to metal catalysts can be applied to late-stage modification and have been actively studied to date; however, several inherent problems derived from the oxidative addition are difficult to be solved, such as toxic CO production, deactivation of catalysts by CO adsorption, intolerance of some functional groups, or air-sensitivity of catalysts. In this context, formal decarbonylation, which eliminates CO as other compounds without involving oxidative addition, is attractive but hardly reported, especially using heterogeneous catalysts. Herein, formal decarbonylation of diaryl 1,2-diketones to afford monoketones using CeO2 as a reusable heterogeneous catalyst and O2 in air as the terminal oxidant was developed, generating CO2 as the only byproduct. The results revealed that the reaction was enabled by the synergistic catalytic effect of the Lewis acid–base pairs and redox properties in CeO2. | Takehiro Matsuyama; Takafumi Yatabe; Kazuya Yamaguchi | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c3207ae9ebbb4db9d49502/original/formal-1-2-diketone-decarbonylation-enabled-by-synergistic-catalysis-of-lewis-acid-base-pairs-and-redox-properties-in-ce-o2.pdf |
6446c459df78ec501553f511 | 10.26434/chemrxiv-2023-v8gqj | New star-shaped ligands generated by evolutionary fitting the Omicron spike inner-cavity | Predictions generated by evolutionary docking of star-shaped ligands targeting the prefusion state of Omicron variants are described here. For this, one selected star-shaped molecule previously identified with the seeSAR program, was used as parent to randomly generate made-on-demand large children libraries evolutionary selected for best fitting to the Omicron spike top-to-bottom inner-cavity with the DataWarrior subprogram. The generated children docking-scores were consensed by AutoDockVina ranks normalized by molecular size and hydrophobicity. These explorations identified one new main chemotype and variants with improved specificity and exceptional nanomolar affinities, predicting aqueous soluble molecules targeting the prefusion state of Omicron spike inner-cavity of trimeric alpha-helices.
| julio coll | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY 4.0 | CHEMRXIV | 2023-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6446c459df78ec501553f511/original/new-star-shaped-ligands-generated-by-evolutionary-fitting-the-omicron-spike-inner-cavity.pdf |
63c824f00cc4333d44d66bc4 | 10.26434/chemrxiv-2022-41xlq-v2 | Hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry method for quantification of five phospholipid classes in various matrices | Hydrophilic interaction liquid chromatography (HILIC), coupled to tandem mass spectrometry, can be used to separate and determine various polar lipid classes. The development of an HILIC chromatographic separation of several molecular species among five phospholipid classes (PC, PE, PG, PI and PS) is reported here. In this method, a gradient with acetonitrile and 40 mM ammonium acetate buffer was employed. The initial composition was 95 % of acetonitrile, then this proportion was decreased to 70 % in order to elute all the compounds of interest for a total running time of 11 mins. Furthermore, mobile phase pH can affect the ionizable character of the compounds, according to their pKa values, and also the stationary phase charge state. The influence of such a parameter on both retention times and resolution was evaluated. Besides, the response of different kinds of internal standards (post-extraction standard addition) was evaluated in four different biological matrices, two microalgae extracts and two marine fish extracts. This study found that the recovery rates were between 70-140 % of the expected value, with relative standard deviations between 10 and 35 %, and then limited matrix effects. | Nicolas Mazzella; Aurélie Moreira; Mélissa Eon; Arthur Médina; Débora Millan-Navarro; Nicolas Creusot | Analytical Chemistry; Separation Science | CC BY NC 4.0 | CHEMRXIV | 2023-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c824f00cc4333d44d66bc4/original/hydrophilic-interaction-liquid-chromatography-coupled-with-tandem-mass-spectrometry-method-for-quantification-of-five-phospholipid-classes-in-various-matrices.pdf |
660221ea9138d2316149eccc | 10.26434/chemrxiv-2024-4vrs0 | Targeted Protein Degradation in the Mitochondrial Matrix and Its Application to Chemical Control of Mitochondrial Morphology | Dysfunction of mitochondria is implicated in various diseases, including cancer and neurodegenerative disorders, but drug discovery targeting mitochondria and mitochondrial proteins has so far made limited progress. Targeted protein degradation (TPD) technologies represented by proteolysis targeting chimeras (PROTACs) are potentially applicable for this purpose, but most existing TPD approaches leverage the ubiquitin-proteasome system or lysosomes, which are absent in mitochondria, and TPD in mitochondria (mitoTPD) remains little explored. Herein, we describe the design and synthesis of a bifunctional molecule comprising TR79, an activator of the mitochondrial protease complex caseinolytic protease P (ClpP), linked to desthiobiotin. This compound successfully induced the degradation of monomeric streptavidin (mSA) and its fusion proteins localized to the mitochondrial matrix. Furthermore, in cells overexpressing mSA fused to short transmembrane protein 1 (mSA-STMP1), which enhances mitochondrial fission, our mitochondrial mSA degrader restored the mitochondrial morphology by reducing the level of mSA-STMP1. A preliminary structure-activity relationship study indicated that a longer linker length enhances the degradation activity towards mSA. These findings highlight the potential of mitoTPD as a tool for drug discovery targeting mitochondria and for research in mitochondrial biology, as well as the utility of mSA as a degradation tag for mitochondrial protein. | Wakana Yamada; Shusuke TOMOSHIGE; Sho Nakamura; Shinichi Sato; Minoru Ishikawa | Biological and Medicinal Chemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2024-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660221ea9138d2316149eccc/original/targeted-protein-degradation-in-the-mitochondrial-matrix-and-its-application-to-chemical-control-of-mitochondrial-morphology.pdf |
60c73fde337d6c099be265d7 | 10.26434/chemrxiv.7527572.v1 | A Semiconducting Material Exhibiting Visible-Light Promoted Photochromism, Photoluminescent and Photocatalytic Activity | Multifunctional materials working under solely visible-light are expected to play a significant role in photo-electronics, in particular photo-switches, photo-optical sensors, smart windows, displays, optical storage memories, and self-cleaning materials.<div>In this work, we have modified the surface of a versatile semiconductor material (TiO<sub>2</sub>) with a noble metal (copper), and simultaneously doped its lattice with a rare-earth element (neodymium). Exploiting the ability of a semiconductor to generate an exciton upon excitation, a multifunctional material working with visible-light and showing photochromic, photoluminescent and photocatalytic activity was engineered. Advanced transmission electron microscopy techniques – aberration-corrected imaging combined with image simulation, statistical analyses and electron energy-loss spectroscopy – were used to characterise thoroughly the structure and local chemical environment as a function of the Nd<sup>3+</sup> content, as well as to link the variation of these aspects to the evolution of the physico-chemical properties. Combined X-ray, spectroscopic and microscopy technique results showed that Nd entered the TiO<sub>2</sub> lattice in a substitutional fashion. When at 1 mol%, neodymium atoms were ultra-dispersed inside the TiO2 (anatase) structure. On the contrary, when the neodymium mol% was higher than 1 mol%, neodymium atoms mostly clustered at the surface of the grains, forming a dense network. Furthermore, the Cu-modified / Nd-doped TiO<sub>2</sub> exhibited faster (two times), as well as a reversible photoswitching that was remarkably more stable compared to standard Cu-TiO<sub>2</sub> photochromic material. The same material also displayed visible-light and solar-light induced photocatalytic activity in the gas-solid phase (degradation of benzene, one of the most hazardous pollutants found indoor) superior to unmodified titania (1.35 and nearly 3.00 times higher, with a LED visible- and solar-light lamps, respectively). It was demonstrated that the optimum amounts of copper and neodymium, for both photochromic and photocatalytic performances, were 1 mol%.</div> | David Maria Tobaldi; Luc Lajaunie; Miguel López‐Haro; Rute Ferreira; Matteo Leoni; Maria Paula Seabra; José Calvino; Luís Carlos; Joao Antonio Labrincha | Nanostructured Materials - Materials; Solid State Chemistry; Photocatalysis; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fde337d6c099be265d7/original/a-semiconducting-material-exhibiting-visible-light-promoted-photochromism-photoluminescent-and-photocatalytic-activity.pdf |
61f3e7460716a873d03eee54 | 10.26434/chemrxiv-2022-wszv7 | Chemical Bonding Origin of Glass Formation in Metal-Organic Frameworks | Glass-forming metal organic frameworks (MOFs) have novel applications, but the origin of their peculiar melting behavior is unclear. Here, we report synchrotron X-ray diffraction electron densities of two zeolitic imidazolate frameworks (ZIFs), the glass-forming Zn-ZIF-zni and the isostructural thermally decomposing Co-ZIF-zni. Electron density analysis shows that the Zn‒N bonds are more ionic than Co‒N bond, which have distinct covalent features. Variable temperature Raman spectra reveal onset of significant imidazolate bond weakening in Co-ZIF-zni above 673 K. Melting can be controlled by tuning the metal–ligand and imidazole bonding strength as shown from nine solid solution structures of CoxZn1-x-ZIF-zni (x = 0.3 to 0.003) were synthesized, and a mere 4% Co-doping into Zn-ZIF-zni results in thermal decomposition instead of melting. These findings advocate significant chemical space for de-signing new MOF glasses either by engineering the chemical bonding with ligand functionalization or by avoiding defects at the metal site in the crystal lattice. | Sounak Sarkar; Thomas Bjørn Egede Grønbech; Aref Mamakhel; Martin Bondesgaard; Kunihisa Sugimoto; Eiji Nishibori; Bo Brummerstedt Iversen | Physical Chemistry; Physical and Chemical Properties; Materials Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f3e7460716a873d03eee54/original/chemical-bonding-origin-of-glass-formation-in-metal-organic-frameworks.pdf |
60c74fad702a9b156918bc14 | 10.26434/chemrxiv.12926807.v1 | Tuning Nitric Oxide Adsorption in Cobalt–Triazolate Frameworks | <p>Nitric oxide (NO) is an important signaling molecule in biological systems, and as such the ability of certain porous materials to reversibly adsorb NO is of interest for medical applications. Metal–organic frameworks have been explored for their ability to reversibly bind NO at coordinatively-unsaturated metal sites, however the influence of metal coordination environment on NO adsorption has yet to be studied in detail. Here, we examine NO adsorption in the frameworks Co<sub>2</sub>Cl<sub>2</sub>(bbta) and Co<sub>2</sub>(OH)<sub>2</sub>(bbta) (H<sub>2</sub>bbta = 1<i>H</i>,5<i>H</i>-benzo(1,2-<i>d</i>:4,5-<i>d</i>′)bistriazole) via gas adsorption, infrared spectroscopy, powder X-ray diffaction, and magnetometry measurements. While NO adsorbs reversibly in Co<sub>2</sub>Cl<sub>2</sub>(bbta) without electron-transfer, adsorption of low pressures of NO in Co<sub>2</sub>(OH)<sub>2</sub>(bbta) is accompanied by charge transfer from the cobalt(II) centers to form a cobalt(III)–NO<sup>−</sup> adduct, as supported by diffraction and infrared spectroscopy data. At higher pressures of NO, characterization data support additional uptake of the gas and disproportionation of the bound NO to form a cobalt(III)–nitro (NO<sub>2</sub><sup>−</sup>) species and N<sub>2</sub>O gas, a transformation that appears to be facilitated in part by stabilizing hydrogen bonding interactions between the bound NO<sub>2</sub><sup>−</sup> and framework hydroxo groups. This reactivity represents a rare example of reductive NO-binding in a metal–organic framework and demonstrates that NO binding can be tuned by changing the coordination environment of the framework metal centers.</p> | Julia Oktawiec; Henry Z. H. Jiang; Ari Turkiewicz; Jeffrey R. Long | Hybrid Organic-Inorganic Materials; Small Molecule Activation (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fad702a9b156918bc14/original/tuning-nitric-oxide-adsorption-in-cobalt-triazolate-frameworks.pdf |
60c73f59ee301c7633c7888c | 10.26434/chemrxiv.7301951.v1 | Engineering New Defective Phases of UiO Family Metal-Organic Frameworks with Water | As defects significantly affect the properties of metal-organic frameworks (MOFs)–from changing their mechanical properties to enhancing their catalytic ability–obtaining synthetic control over defects is essential to tuning the effects on the properties of the MOF. Previous work has shown that synthesis temperature and the identity and concentration of modulating acid are critical factors in determining the nature and distribution of defects in the UiO family of MOFs. In this paper we demonstrate that the amount of water in the reaction mixture in the synthesis of UiO family MOFs is an equally important factor, as it controls the phase which forms for both UiO-67(Hf)<br />and UiO-66(Hf) (F4BDC). We use this new understanding of the importance of water to develop a new route to the stable defect-ordered <b>hcp</b> UiO-66(Hf) phase, demonstrating the effectiveness of this method of defect-engineering in the rational design of MOFs. The insights provided by this<br />investigation open up the possibility of harnessing defects to produce new phases and dimensionalities of other MOFs, including nanosheets, for a variety of applications such as MOF-based membranes. | Francesca Firth; Matthew Cliffe; Diana Vulpe; Peyman Moghadam; David Fairen-jimenez; ben slater; Clare P. Grey | Nanostructured Materials - Materials; Coordination Chemistry (Inorg.); Organometallic Compounds; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f59ee301c7633c7888c/original/engineering-new-defective-phases-of-ui-o-family-metal-organic-frameworks-with-water.pdf |
65d6a95766c13817293501a7 | 10.26434/chemrxiv-2024-prhbg-v3 | Understanding the Adiabatic Evolution of Surface States in Tetradymite Topological Insulators under Electrochemical Conditions | Nontrivial surface states in topological materials have emerged as exciting targets for surface chemistry research. In particular, topological insulators have been utilized as electrodes in electrocatalytic reactions. Herein, we investigate the robustness of topological surface states and band topology under electrochemical conditions, specifically in the presence of an electric double layer. First-principles band structure calculations are performed on the electrified (001) surfaces of Bi2Te3, Bi2Se3, and Sb2Te3 using an implicit electrolyte model. Our results demonstrate the adiabatic evolution of the surface states upon surface charging. Under oxidizing potentials, the surface states are shifted upward in energy, preserving the Dirac point on the surface and the band inversion in the bulk. Conversely, under reducing potentials, hybridization is observed between the surface and bulk states, suggesting a likely breakdown of topological protection. The position of the Fermi level, which dictates the working states in catalytic reactions, should ideally be confined within the bulk bandgap. This requirement defines a potential window for the effective application of topological electrocatalysis. | Guorong Weng; William Laderer; Anastassia N. Alexandrova | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d6a95766c13817293501a7/original/understanding-the-adiabatic-evolution-of-surface-states-in-tetradymite-topological-insulators-under-electrochemical-conditions.pdf |
60c74292ee301cd38ec78e78 | 10.26434/chemrxiv.8312120.v1 | Cyclophospholipids Increase Protocellular Stability to Metal Ions | <p>Model protocells have long been constructed with fatty acids, because these lipids are prebiotically plausible and can, at least theoretically, support a protocell life cycle. However, fatty acid protocells are stable only within a narrow range of pH and metal ion concentration. This instability is particularly problematic as the early Earth would have had a range of conditions, and life as we know it is completely reliant on metal ions for catalysis and the folding and activity of biological polymers. Here we show that prebiotically plausible monoacyl cyclophospholipids form robust vesicles that survive a broad range of pH and high concentrations of Mg2+, Ca2+, and Na+. Importantly, stability to Mg2+ and Ca2+ is improved by the presence of environmental concentrations of Na+. These results suggest that cyclophospholipids, or lipids with similar characteristics, may have played a central role during the emergence of Darwinian evolution.</p> | Ö. Duhan Toparlak; Megha Karki; Veronica Egas Ortuno; Ramanarayanan Krishnamurthy; Sheref Mansy | Biochemistry; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74292ee301cd38ec78e78/original/cyclophospholipids-increase-protocellular-stability-to-metal-ions.pdf |
62e941d000ed9c1d7b1f3497 | 10.26434/chemrxiv-2021-p3d4s-v4 | Mechanism for acetate formation in electrochemical CO(2) reduction on Cu: Selectivity with potential, pH, and nanostructuring | Nanostructured Cu catalysts have increased the selectivities and geometric activities for high value C-C coupled (C2) products (ethylene, acetate, and ethanol) in the electrochemical CO(2) reduction reaction (CO(2)RR). The selectivity among the high-value C2 products is also altered, where for instance the yield of acetate increases with alkalinity and is dependent on the catalyst morphology. The reaction mechanisms behind the selectivity towards acetate vs. other C2 products remain controversial. In this work, we elucidate the reaction mechanism towards acetate by using ab-initio simulations, a coupled kinetic-transport model, and loading experiments. We find that trends in acetate selectivity can be rationalized from variations in electrolyte pH and the local mass transport properties of the catalyst and not from changes of Cu's intrinsic activity. The selectivity mechanism originates in the transport of ketene, a stable (closed shell) intermediate, away from the
catalyst surface into solution where it reacts to acetate. While such a mechanism has not yet been discussed in CO(2)RR, variants of it may explain similar selectivity fluctuations observed for other stable intermediates like CO and acetaldehyde. Our proposed mechanism suggests that acetate selectivity increases with increasing pH, decreasing catalyst roughness and significantly varies with applied potential. | Hendrik H. Heenen; Haeun Shin; Georg Kastlunger; Sean Overa; Joseph A. Gauthier; Feng Jiao; Karen Chan | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e941d000ed9c1d7b1f3497/original/mechanism-for-acetate-formation-in-electrochemical-co-2-reduction-on-cu-selectivity-with-potential-p-h-and-nanostructuring.pdf |
61107e8503182f70791c3083 | 10.26434/chemrxiv-2021-vsd4j-v3 | Virtual computational chemistry teaching laboratories – hands-on at a distance | The COVID-19 pandemic disrupted chemistry teaching practices globally as many courses were forced online necessitating adaptation to the digital platform. The biggest impact was to the practical component of the chemistry curriculum – the so-called wet lab. Naively, it would be thought that computer-based teaching labs would have little problem in making the move. However, this is not the case as there are many unrecognised differences between delivering computer-based teaching in-person and virtually: software issues, technology and classroom management. Consequently, relatively few “hands-on” computational chemistry teaching laboratories are delivered online. In this paper we describe these issues in more detail and how they can be addressed, drawing on our experience in delivering a third-year computational chemistry course as well as remote hands-on workshops for the Virtual Winter School on Computational Chemistry and the European BIG-MAP project. | Rika Kobayashi; Theodorus P. M. Goumans; N. Ole Carstensen; Thomas M. Soini; Nicola Marzari; Iurii Timrov; Samuel Poncé; Edward B. Linscott; Christopher J. Sewell; Giovanni Pizzi; Francisco Ramirez; Marnik Bercx; Sebastiaan P. Huber; Carl S. Adorf; Leopold Talirz | Theoretical and Computational Chemistry; Materials Science; Chemical Education; Chemical Education - General; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2021-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61107e8503182f70791c3083/original/virtual-computational-chemistry-teaching-laboratories-hands-on-at-a-distance.pdf |
62bbb0729ca5bb5321eaab12 | 10.26434/chemrxiv-2022-6ndj0 | Theoretical studies on the effects of π-bridge engineering on the photoelectric performance of Y6 | Molecular engineering of high performance non-fullerene acceptors (NFAs) is critical to enhance the power conversion efficiencies (PCEs) of bulk heterojunction organic solar cells (BHJ OSCs). In this work, the density functional theory (DFT) and time-dependent DFT are employed to investigate the effects of π-bridge engineering on the photoelectric performance of high-performance NFA Y6. This π-bridge engineering principally involves 1) inserting different types of π-bridge units between the fused-ring core and the terminal unit of Y6, and then the π-bridge unit with better performance is screened for the next study, 2) inserting different numbers of screened π-bridge units between the fused-ring core and the terminal unit of Y6, and 3) modifying the side chains of the screened π-bridge unit with halogen atoms. Theoretical results predict that the selenophene π-bridge has superior properties in terms of dipole moment, exciton binding energy, and light absorption compared with other π-bridge units. In addition, studies on different numbers of selenophene π-bridges suggest that increasing the number of selenophene π-bridges has significant advantages in enhancing light absorption and electron transport capabilities for enhancing the short circuit current density (JSC). Meanwhile, the study of π-bridged side chains substituted with different halogen atoms indicates that the substitution of halogen atoms can play a significant role in reducing the exciton binding energy and raising the transferred charge amounts. The results obtained in this work are expected to be used to design new Y6 derivatives. | meizhen tao; liang peng; fenglong gu | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bbb0729ca5bb5321eaab12/original/theoretical-studies-on-the-effects-of-bridge-engineering-on-the-photoelectric-performance-of-y6.pdf |
631a22f8173b5da209f62453 | 10.26434/chemrxiv-2022-2ln30 | Reaction Environment Impacts Charge Transfer But Not Chemical Reaction Steps in Hydrogen Evolution Catalysis | Heterogeneous electrocatalysis involves elementary chemical and charge transfer reaction steps, with the kinetics of each step contributing to the overpotential requirement at a given reaction rate. Typical experiments report on the aggregate rate-overpotential profile with no information about the relative contributions from charge transfer and chemical steps. For the hydrogen evolution reaction (HER), the applied overpotential can be partitioned into a charge transfer overpotential, the overpotential necessary to drive proton-coupled electron transfer (PCET) to and from the surface, and a chemical overpotential, corresponding to a change in surface H activity. Reaction conditions can affect either or both the charge transfer and chemical components. Herein, we employ a Pd membrane double cell to spatially separate the charge transfer and chemical reactions steps of HER catalysis, enabling quantification of the chemical and charge transfer overpotential. We further analyze how each depend on pH, and the introduction of HER poisons and promoters. We find that for a given rate of H2 release, the chemical overpotential is constant across diverse reaction environments whereas the charge transfer overpotential is strongly sensitive to reaction conditions. These findings suggest that reaction condition dependent-HER efficiencies are driven predominantly by changes to the kinetics of charge transfer rather than the chemical reactivity of surface H. | Bryan Y. Tang; Ryan P. Bisbey; Kunal M. Lodaya; Wei Lun Toh; Yogesh Surendranath | Catalysis; Energy; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631a22f8173b5da209f62453/original/reaction-environment-impacts-charge-transfer-but-not-chemical-reaction-steps-in-hydrogen-evolution-catalysis.pdf |
665d7e3691aefa6ce1ad224a | 10.26434/chemrxiv-2024-6x59r-v2 | Handheld Methanol Detector for Beverage Analysis: Interlaboratory Validation | Methanol is a toxic alcohol contained in alcoholic beverages as a natural byproduct of fermentation or added intentionally to counterfeits to increase profit. To ensure consumer safety, many countries and the EU have established strict legislation limits for methanol content. Methanol concentration is mostly detected by laboratory instrumentation since mobile devices for routine on-site testing of beverages in distilleries, at border stations or even at home are not available. Here, we validated a handheld methanol detector for beverage analysis in an ISO 5725 interlaboratory trial: A total of 119 measurements were performed by 17 independent participants (distilleries, universities, authorities, and competence centers) from six countries on samples with relevant methanol (0.1, 1.5 vol%). The detector was based on a microporous separation filter and a nanostructured gas sensor allowing on-site measurement of methanol down to 0.01 vol% (in the liquid) within only 2 min by laymen. The detector showed excellent repeatability (<5.4%), reproducibility (<9.5%) and small bias (<0.012 vol%). Additional measurements on various methanol-spiked alcoholic beverages (whisky, rum, gin, vodka, tequila, port, sherry, liqueur) indicated that the detector is not interfered by environmental temperature and spirit composition, featuring excellent linearity (Pearson’s R²>0.99) down to methanol concentrations of 0.01 vol%. This device has been recently commercialized (Alivion Spark M-20) with comparable accuracy to the gold-standard gas chromatography and can be readily applied for final product inspection, intake control of raw materials or to identify toxic counterfeit products. | Jan van den Broek; Sebastian Keller; Ian Goodall; Katie Parish-Virtue; Claudia Bauer-Christoph; Johannes Fuchs; Despina Tsipi; Andreas Güntner; Thomas Blum; Jean-Charles Mathurin; Matthias Steiger; Roghayeh Shirvani; Manfred Gössinger; Monika Graf; Peter Anderhub; Daniel Z'graggen; Claudio Hüsser; Benjamin Faigle; Agapiou Agapios | Analytical Chemistry; Chemical Engineering and Industrial Chemistry; Analytical Apparatus; High-throughput Screening; Quality Control | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665d7e3691aefa6ce1ad224a/original/handheld-methanol-detector-for-beverage-analysis-interlaboratory-validation.pdf |
62df6f3fcf6612a262b50868 | 10.26434/chemrxiv-2022-vbczc | Growth Synchronization and Size Control in Magic-Sized Semiconductor Nanocrystals | “Magic-sized” nanocrystals (MSNCs) grow in discrete jumps between a series of specific sizes. Consequently, MSNCs have been explored as an alternative route to uniform semiconductor particles, potentially with atomic precision. However, because the growth mechanism has been poorly understood, the best strategies to control MSNC syntheses and obtain desired sizes are unknown. Experiments have found that common parameters such as growth time and temperature have limited utility. Here, we theoretically and experimentally investigate reactant supersaturation as a tool to control MSNC growth. We compare direct synthesis of CdSe MSNCs with ripening of isolated MSNCs or their mixtures. Surprisingly, we find that MSNCs readily synchronize to the same growth trajectory, even starting from distinct initial conditions, explaining the robustness of MSNC growth. Further, by understanding the synchronization mechanism, we demonstrate methods to control the final MSNC size. These results deepen our knowledge of MSNCs and indicate strategies to tailor their growth. | Sergio Mazzotti; Aniket S. Mule; Andrew B. Pun; Jacob T. Held; David J. Norris | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Clusters; Thermodynamics (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62df6f3fcf6612a262b50868/original/growth-synchronization-and-size-control-in-magic-sized-semiconductor-nanocrystals.pdf |
646b91ecccabde9f6e2fc4b5 | 10.26434/chemrxiv-2023-p8qcv | openOCHEM consensus model wins Kaggle First EUOS/SLAS Joint Compound Solubility Challenge | The EUOS/SLAS challenge has its goal to develop reliable algorithms to predict solubility of small molecules experimentally measured aqueous solubility of 100k compounds. In total, hundred teams took part in the challenge to predict low, medium and highly soluble compounds as measured by nephelometry assay. This article describes the winning Top I rank model which was developed using the publicly available Online CHEmical database and Modeling environment (OCHEM) and which is publicly available at https://ochem.eu/article/27. We describe in detail the assumptions and steps used to select methods, descriptors and strategy which contributed to the winning solution. | Andrea Kopp; Peter Hartog; Martin Šícho; Guillaume Godin; Igor Tetko | Theoretical and Computational Chemistry; Physical Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry; Physical and Chemical Properties | CC BY 4.0 | CHEMRXIV | 2023-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646b91ecccabde9f6e2fc4b5/original/open-ochem-consensus-model-wins-kaggle-first-euos-slas-joint-compound-solubility-challenge.pdf |
60c74d9e842e6561a9db34cf | 10.26434/chemrxiv.12639974.v1 | A New Release of MOPAC Incorporating the INDO/S Semiempirical Model with CI Excited States | We have incorporated the semiempirical INDO/S Hamiltonian into a new release of MOPAC2016, which has long been at the forefront of semiempirical quantum chemical methods (SEQMs). Our new code enables the calculation of excited states using the INDO/S Hamiltonian combined with a configuration interaction approach using single excitations (CIS), single and double excitations (CISD), or multiple reference determinants (MRCI) where reference determinants are generated using a complete active space (CAS) approach. The capacity to perform excited-state calculations beyond the CIS level makes INDO/CI one of the few low-cost computational methods capable of accurately modeling states with substantial double-excitation character. Solvent corrections to the ground-state and excited-state energies can be computed using the COSMO implicit solvent model, incorporating state-specific corrections to the excited states based on the solvent refractive index. We demonstrate that this code produces physically reasonable electronic structures, absorption spectra, and solvatochromic shifts at low computational costs for systems up to hundreds of atoms, and for both organic molecules and metal clusters. | Rebecca Gieseking | Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY NC 4.0 | CHEMRXIV | 2020-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d9e842e6561a9db34cf/original/a-new-release-of-mopac-incorporating-the-indo-s-semiempirical-model-with-ci-excited-states.pdf |
66586a8921291e5d1da3797a | 10.26434/chemrxiv-2023-z7cnv-v3 | On the thermodynamic stability of polycations | We present a simple approximation to estimate the largest charge that a given molecule can hold until fragmentation into smaller charged species becomes more energetically favorable. This approximation solely relies on the ionization potentials, electron affinities of the parent and fragment species, and also on the neutral parent's dissociation energy. By parametrizing these quantities, it is possible to obtain analytical phase diagrams of polycationic stability. We demonstrate the applicability of this approach by discussing maximal charge dependence on the size of the molecular system. A numerical demonstration for linear polyenes, monocyclic annulenes, and helium clusters is provided. | Denis S. Tikhonov; Jason W.L. Lee; Melanie Schnell | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Processes | CC BY 4.0 | CHEMRXIV | 2024-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66586a8921291e5d1da3797a/original/on-the-thermodynamic-stability-of-polycations.pdf |
60c75636567dfe4e16ec63fc | 10.26434/chemrxiv.14207348.v1 | Ultrafast Energy Transfer Between Lipid-Linked Chromophores and Plant Light-Harvesting Complex II | Light-Harvesting Complex II
(LHCII) is a membrane protein found in plant chloroplasts that has the crucial
role of absorbing solar energy and subsequently performing excitation energy
transfer to the reaction centre subunits of Photosystem II. LHCII provides
strong absorption of blue and red light, however, it has minimal absorption in
the green spectral region where solar irradiance is maximal. In a recent
proof-of-principle study, we enhanced the absorption in this spectral range by
developing a biohybrid system where LHCII proteins together with lipid-linked
Texas Red (TR) chromophores were assembled into lipid membrane vesicles. The
utility of these systems was limited by significant LHCII quenching due to
protein-protein interactions and heterogeneous lipid structures. Here, we
organise TR and LHCII into a lipid nanodisc, which provides a homogeneous, well-controlled
platform to study the interactions between TR molecules and single LHCII complexes.
Fluorescence spectroscopy determined that TR-to-LHCII energy transfer has an
efficiency of at least 60%, resulting in a 255% enhancement of LHCII fluorescence,
two-fold greater than in the previous system. Ultrafast transient absorption
spectroscopy revealed two time constants of 3.7 and 128 ps for TR-to-LHCII
energy transfer. Structural modelling and theoretical calculations indicate
that these timescales correspond to TR-lipids that are loosely- or
tightly-associated with the protein, respectively, with estimated TR-to-LHCII
separations of ~3.5 nm and ~1
nm. Overall, we demonstrate that a nanodisc-based biohybrid system provides an
idealised platform to explore the photophysical interactions between extrinsic
chromophores and membrane proteins with potential applications in understanding
more complex natural or artificial photosynthetic systems. | Ashley M. Hancock; Minjung Son; Muath Nairat; Tiejun Wei; Lars J. C. Jeuken; Christopher D. P. Duffy; Gabriela S. Schlau-Cohen; Peter G. Adams | Biophysics; Plant Biology; Biophysical Chemistry; Photochemistry (Physical Chem.); Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75636567dfe4e16ec63fc/original/ultrafast-energy-transfer-between-lipid-linked-chromophores-and-plant-light-harvesting-complex-ii.pdf |
625f9c17d048ed5fd54a5380 | 10.26434/chemrxiv-2022-141p3 | Aluminum Catalyzed Selective Reduction of Heteroallenes via Hy-droboration: Amide/Thioamide/Selenoamide Bonds Construction and C=X (X= O, S, Se) Bond Activation | An unprecedented conjugated bis-guanidinate (CBG) stabilized aluminum dihydride, [LAlH2; (L = {(ArNH)(ArN)–C=N–C=(NAr)(NHAr)}; Ar = 2,6- Et2-C6H3)] (I) catalyzed chemoselective hydroboration of heteroallenes such as carbodiimide (CDI)s, isocyanates, isothiocyanates, and isoselenocyanates is reported. A wide range of heteroallenes, including electron-donating and withdrawing groups, experience hydroboration to obtain selectively N-boryl amide, N-borylaminal, and N-boryl methyl amine products. More importantly, a single sustainable molecular aluminum-based catalyst effectively catalyzes CDIs, isocyanates, isothiocyanates, and isoselenocyanates into formamidines, formamides, thioformamides, and selenoformamides, respectively. Fur-ther, heteroallene substrates undergo hydrodeoxygenation (HDO), hydrodesulfurization (HDS), and hydrodeselenization (HDSe) reactions leading to N-boryl methyl amines. In addition, a series of control and kinetic experiments indicate that the aluminum hydride species are essential for all partial and complete reduction steps and breaking the C=X (X = O, S, and Se) bonds in het-eroallenes. | Nabin Sarkar; Rajata Sahoo; Sharanappa Nembenna | Catalysis; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2022-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625f9c17d048ed5fd54a5380/original/aluminum-catalyzed-selective-reduction-of-heteroallenes-via-hy-droboration-amide-thioamide-selenoamide-bonds-construction-and-c-x-x-o-s-se-bond-activation.pdf |
6196b87ae0ea8401d79ccf45 | 10.26434/chemrxiv-2021-z1b7f | Electrical conductivity of Self-assembling Peptide-semiconducting dye Conjugate nanofibre networks | Conjugates comprising a semiconducting dye (Thiophene-diketopyrrolopyrrole, TDPP-dye) attached to a self-assembling peptide (HEFISTAH) assemble into long nanofibers. Well-ordered Langmuir-Blodgett films of these materials can be prepared. Networks of these nanofibres can be deposited to bridge electrodes. Although similar systems have been proposed as organic semiconductors, in this case, no electronic conductivity was observed. Instead, the fibres behaved as ionic (probably proton) conductors as a consequence of adsorbed water. A strong dependence of electrical conductivity on relative humidity and fibre network density was demonstrated. The system of nanofibers bridging gold electrodes behaved as an electrolytic cell, with oxygen reduction as a limiting electrode reaction. | Zainab Makinde; Aakanksha Rani; Taniela Lolohea ; Laura Domigan; Duncan McGillivray ; Margaret Brimble; David Williams | Materials Science; Biocompatible Materials; Nanostructured Materials - Materials; Thin Films | CC BY NC 4.0 | CHEMRXIV | 2021-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6196b87ae0ea8401d79ccf45/original/electrical-conductivity-of-self-assembling-peptide-semiconducting-dye-conjugate-nanofibre-networks.pdf |
60c74a8c0f50db1609396aa3 | 10.26434/chemrxiv.12217814.v1 | Photodissociation Dynamics of the Tert-Butyl Perthiyl Radical | <p>The photodissociation dynamics of the <i>tert</i>-butyl perthiyl (<i>t</i>-BuSS) radical are investigated by fast-beam coincidence translational spectroscopy. A fast (6-8 keV) beam of neutral <i>t</i>-BuSS radicals is produced via photodetachment of the corresponding anion, followed by photodissociation at 248 nm (5.00 eV) or 193 nm (6.42 eV) and coincident detection of the neutral products. Photofragment mass and translational energy distributions are obtained at both wavelengths. At 248 nm, the dominant product channel (90%) is found to be S loss, with a product translational energy distribution that peaks close to the maximum available energy and an anisotropic photofragment angular distribution, indicating dissociation along a repulsive excited state. A minor channel (10%) leading to the formation of S<sub>2</sub> + <i>t</i>-Bu is also observed. At 193 nm, both two- and three-body dissociation are observed. Formation of S<sub>2</sub> + <i>t</i>-Bu is the dominant two-body product channel, with multiple electronic states of the S<sub>2</sub> molecule produced via excited state dissociation processes. Formation of S + <i>t</i>-BuS is a minor two-body channel at this dissociation energy. The three-body channels are S<sub>2</sub> + H + isobutene, S<sub>2</sub> + CH<sub>3</sub> + propene, and S + SH + isobutene. The first two of these channels result from a sequential dissociation process in which loss of S<sub>2</sub> from <i>t</i>-BuSS results in ground state <i>t</i>-Bu with sufficient internal energy to undergo secondary fragmentation. The third three-body channel, S + SH + isobutene, is attributed to loss of internally excited HS<sub>2</sub> from <i>t</i>-BuSS, which then rapidly dissociates to form S + SH in an asynchronous concerted dissociation process. </p> | Bethan Nichols; Erin Sullivan; Daniel Neumark | Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a8c0f50db1609396aa3/original/photodissociation-dynamics-of-the-tert-butyl-perthiyl-radical.pdf |
63a23f6116e9a872d32f81ef | 10.26434/chemrxiv-2022-2t0dq-v3 | Enhancing hit discovery in virtual screening through accurate calculation of absolute protein-ligand binding free energies | In the hit identification stage of drug discovery, a diverse chemical space needs to be explored to identify initial hits. Contrary to empirical scoring functions, absolute protein-ligand binding free energy perturbation (ABFEP) provides a theoretically more rigorous and accurate description of protein-ligand binding thermodynamics and could in principle greatly improve the hit rates in virtual screening. In this work, we describe an implementation of an accurate and reliable ABFEP method in FEP+. We validated the ABFEP method on eight congeneric compound series binding to eight protein receptors including both neutral and charged ligands. For ligands with net charges, the alchemical ion approach is adopted to avoid artifacts in electrostatic potential energy calculations. The calculated binding free energies are highly correlated with experimental results with the weighted average of R2 of 0.55 for the entire dataset and an overall RMSE of 1.1 kcal/mol when protein reorganization effect upon ligand binding was accounted for. Through ABFEP calculations using apo versus holo protein structures, we demonstrated that the protein conformational and protonation state changes between the apo and holo proteins are the main physical factors contributing to the protein reorganization free energy manifested by the overestimation of raw ABFEP calculated binding free energies using the holo structures of the proteins. Furthermore, we performed ABFEP calculations in three virtual screening applications for hit enrichment. ABFEP greatly improves the hit rates as compared to docking scores or other methods like metadynamics. The highly accurate ABFEP results demonstrated in this work position it as a useful tool to improve the hit rates in virtual screening, thus facilitate hit discovery. | Wei Chen; Di Cui; Steven V. Jerome; Mayako Michino; Eelke B. Lenselink; David Huggins; Alexandre Beautrait; Jeremie Vendome; Robert Abel; Richard A. Friesner; Lingle Wang | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a23f6116e9a872d32f81ef/original/enhancing-hit-discovery-in-virtual-screening-through-accurate-calculation-of-absolute-protein-ligand-binding-free-energies.pdf |
60da22b3b912f81bd95c0590 | 10.26434/chemrxiv-2021-3nqv9 | Evaluating the Performance of a Transformer-based Organic Reaction Prediction Model | Forward and retrosynthetic organic reaction prediction are challenging applications of artificial intelligence (AI) research in chemistry. IBM’s freely available RXN for Chemistry (https://rxn.res.ibm.com) treats reaction prediction as a translation problem, by using transformer-based machine learning models trained on patent data to convert reactant SMILES string sequences into product strings. Here we characterize the performance of transformer models on 100 undergraduate text-book problems to expose reaction classes where the fundamentals of organic chemistry are violated. The forward prediction model is generally successful in predicting outcomes for substitution reactions and unsuccessful for elimination and organocopper reactions. For the retrosynthesis model, we found characteristic examples of a lack of atom conservation and nonsensical chemical transformations. We also compared the dif- ferences in molecular complexity and synthetic accessibility between predicted and literature reactions to probe how AI plans reactions compared to humans. Forward predictions replicated a similar distribution of differences in molecular complexity as the human reactions from the literature, whereas retrosynthetic predictions resulted in both positive and negative deviations from literature complexity. Finally, we analyzed the atom mapping in test reactions to expose errors in how the model identifies reactive atoms and species. | William Borrelli; Joshua Schrier | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2021-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60da22b3b912f81bd95c0590/original/evaluating-the-performance-of-a-transformer-based-organic-reaction-prediction-model.pdf |
64f5eefc3fdae147fa7d5d55 | 10.26434/chemrxiv-2023-zncbf | Selective and potent PROTAC degraders of c-Src kinase | Using dasatinib linked to E3 ligase ligands, we identified a potent and selective dual Csk/c-Src PROTAC degrader. We then replaced dasatinib the c-Src directed ligand with a conformation-selective analog that stabilizes the aC-helix out conformation of c-Src. Using the C-helix out ligand, we identified a PROTAC that is potent and selective for c-Src. Using our c-Src PROTACs, we identified pharmacological advantages to c-Src degradation compared to inhibition with respect to cancer cell proliferation. | Wuxiang Mao; Nathalie Vandecan; Christopher Bingham; Pui Ki Tsang; Peter Ulintz; Rachel Sexton; Daniel Bochar; Sofia Merajver; Matthew Soellner | Biological and Medicinal Chemistry; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f5eefc3fdae147fa7d5d55/original/selective-and-potent-protac-degraders-of-c-src-kinase.pdf |
65f007e966c1381729d18fc5 | 10.26434/chemrxiv-2024-nxtpf | Effect of H+ Exchange & Surface Impurities on Bulk & Interfacial Electrochemistry of Garnet Solid Electrolytes | Contact loss and current constriction pose significant challenges at the Li metal interface of solid-state batteries. For garnet-structured Li7La3Zr2O12 (LLZO), these effects are amplified by Li+/H+ exchange and surface contamination reactions, which lead to conductivity losses and poor Li wetting. In this study, we utilize a variety of surface treatment processes across 37 cells to selectively induce proton exchange and contamination reactions in LLZO. The resulting bulk and surface chemistry is systematically characterized and correlated to changes in electrochemical properties. Additionally, we combine impedance analysis and finite element method modeling to deconvolute sources of impedance contributions at the Li metal interface. Specifically, we show that constriction impedance at the Li metal interface arises not solely from voids, but also from ionically-resistive surface contaminants. These findings emphasize the connection between ionic conductivity and constriction, demonstrating that micron-scale ionically-resistive components increase constriction even with identical contact geometries. Finally, we leverage our comprehensive dataset to highlight unstable overpotential growth as a failure mechanism, additionally showing that the phase of a cell’s impedance is a sensitive indicator for the onset of interfacial instability. Overall, this study clarifies the impacts of proton exchange and surface contamination on electrochemical properties at the Li|solid electrolyte interface and elucidates insights that are generalizable to other solid-state battery systems. | Sunny Wang; Edward Barks; Po-Ting Lin; Xin Xu; Celeste Melamed; Geoff McConohy; Slavomir Nemsak; William Chueh | Materials Science; Energy; Ceramics; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f007e966c1381729d18fc5/original/effect-of-h-exchange-surface-impurities-on-bulk-interfacial-electrochemistry-of-garnet-solid-electrolytes.pdf |
60c7590cee301c5c63c7b829 | 10.26434/chemrxiv.13514467.v2 | A Transition State Theory Perspective on the Relation of Reversible Metal Hydride First-Order Kinetics to Equilibrium Thermodynamics | In the event of hydrogen desorption from reversible metal hydrides, equilibrium thermodynamics exert a rate-limiting effect: if system pressure reaches equilibrium pressure, the reaction rate becomes zero. This is usually dealt with by an empiric term of either polynomial or logarithmic nature to first-order kinetics. This paper approaches the matter from a transition state theory perspective, combining the classic Eyring-Polanyi equation with insights on reversible metal hydride chemical overpotential for scrutinizing the relation of Arrhenius first-order kinetics to van’t Hoff equilibrium pressure. The outcome, tested for the example of 4 mol % Ti-doped NaAlH<sub>4</sub>, suggests theoretical coherency and provides a method for identifying the factor by which an experiment deviates from ideal first-order kinetics. Adopting Arrhenius-Eyring-Polanyi first-order kinetics as baseline for modelling kinetic behaviour of metal hydride sorption reactions not only covers a blind spot in the Arrhenius approach but creates a standard for result comparability. | Roland Hermann Pawelke | Catalysts; Fuels - Materials; Hydrogen Storage Materials; Chemical Education - General; Nanocatalysis - Catalysts & Materials; Kinetics and Mechanism - Inorganic Reactions; Main Group Chemistry (Inorg.); Reaction (Inorg.); Small Molecule Activation (Inorg.); Solid State Chemistry; Theory - Inorganic; Transition Metal Complexes (Inorg.); Reaction Engineering; Thermodynamics (Chem. Eng.); Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Catalysis; Energy Storage; Fuels - Energy Science; Fuel Cells; Chemical Kinetics; Physical and Chemical Processes; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7590cee301c5c63c7b829/original/a-transition-state-theory-perspective-on-the-relation-of-reversible-metal-hydride-first-order-kinetics-to-equilibrium-thermodynamics.pdf |
61a9df4aa02d16431de242e6 | 10.26434/chemrxiv-2021-1qb7z | Co/Ba/La2O3 catalyst for ammonia synthesis under mild reaction conditions | Ruthenium catalysts may allow realization of renewable energy–based ammonia synthesis processes using mild reaction conditions (<400 °C, <10 MPa). However, ruthenium is relatively rare and therefore expensive. Here, we report a Co nanoparticle catalyst loaded on a basic Ba/La2O3 support and pre-reduced at 700 °C (Co/Ba/La2O3_700red) that showed higher ammonia synthesis activity at 350 °C and 1.0–3.0 MPa than two benchmark Ru catalysts, Cs+/Ru/MgO and Ru/CeO2. The synthesis rate of the catalyst at 350 °C and 1.0 MPa (19.3 mmol h−1g−1) was 8.0 times that of Co/Ba/La2O3_500red and 6.9 times that of Co/La2O3_700red. The catalyst showed activity at temperatures down to 200 °C. High-temperature reduction induced formation of a BaO-La2O3 nano-fraction around the Co nanoparticles, which increased turnover frequency, inhibited Co nanoparticle sintering, and suppressed ammonia poisoning. These strategies may also be appliable to nickel catalysts. | Katsutoshi Nagaoka; Shin-ichiro Miyahara; Katsutoshi Sato; Yuta Ogura; Kotoko Tsujimaru; Yuichiro Wada; Takaaki Toriyama; Tomokazu Yamamoto; Syo Matsumura; Koji Inazu | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a9df4aa02d16431de242e6/original/co-ba-la2o3-catalyst-for-ammonia-synthesis-under-mild-reaction-conditions.pdf |
6305248ef9e99c60f5873634 | 10.26434/chemrxiv-2022-gl2gt | A universal synthesis protocol for tuneable metal-organic framework nanohybrid | Metal-organic frameworks (MOFs) with encapsulated functional nanoparticles (NPs) enjoy a vastly expanded application potential in catalysis, filtration, and sensing. In general, diffusion-controlled infiltration and metal ion-based strategies that force heterogeneous nucleation have yielded piecemeal, partial successes in overcoming the lattice mismatch between the MOF-shells and NP-cores. To this date, however, no universally applicable synthesis for MOF-nanohybrids emerged that covers the full diversity of all possible core-shell combinations. Here, we show a versatile, general synthesis protocol using a representative set of seven MOF-shells (ZIF-zni, ZIF-8, ZIF-67, FJU-30, MIL-88(Fe), HKUST-1, and MOF-74(Co)) and six NP-cores (Ag, Au, NaYF4, β-FeOOH, Fe2O3 and Ni3[Fe(CN)6]2) that are fine-tuned to incorporate from single to hundreds of cores in mono-, bi-, tri- and quaternary composites. Our key strategy is to regulate the rate of diffusion of alkaline vapours that deprotonate the organic building blocks and trigger the controlled MOF-growth and encapsulation of NP-cores. This strategy is expected to pave the way for the exploration of sophisticated MOF-nanohybrids that draws from the full range of hitherto known MOF-architectures and core-compositions. | Wei Zhang; Michael Bojdys; Nicola Pinna | Inorganic Chemistry; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6305248ef9e99c60f5873634/original/a-universal-synthesis-protocol-for-tuneable-metal-organic-framework-nanohybrid.pdf |
65095c9c60c37f4f760aea31 | 10.26434/chemrxiv-2023-rcjv5-v2 | Long-term continuous degradation of carbon nanotubes by a bacteria-driven Fenton reaction | Very few bacteria are known that can degrade carbon nanotubes (CNTs), and the only known degradation mechanism is a Fenton reaction driven by Labrys sp. WJW with siderophores, which only occurs under iron-deficient conditions. No useful information is available on the degradation rates or long-term stability and continuity of the degradation reaction although several months or more are needed for CNT degradation. In this study, we investigated long-term continuous degradation of oxidized (carboxylated) single-walled CNTs (O-SWCNTs) using bacteria of the genus Shewanella. These bacteria are widely present in the environment and can drive the Fenton reaction by alternating anaerobic-aerobic growth conditions under more general environmental conditions. We first examined the effect of O-SWCNTs on the growth of S. oneidensis MR-1, and it was revealed that O-SWCNTs promote growth up to 30 μg/mL but inhibit growth at 40 μg/mL and above. Then, S. oneidensis MR-1 was subjected to incubation cycles consisting of 21-h anaerobic and 3-h aerobic periods in the presence of 30 μg/mL O-SWCNTs and 10 mM Fe(III) citrate. We determined key factors that help prolong the bacteria-driven Fenton reaction and finally achieved long-term continuous degradation of O-SWCNTs over 90 d. By maintaining a near neutral pH and replenishing Fe(III) citrate at 60 d, a degraded fraction of 56.3% was reached. S. oneidensis MR-1 produces Fe(II) from Fe(III) citrate, a final electron acceptor for anaerobic respiration during the anaerobic period. Then, ·OH is generated through the Fenton reaction by Fe(II) and H2O2 produced by MR-1 during the aerobic period. ·OH was responsible for O-SWCNT degradation, which was inhibited by scavengers of H2O2 and ·OH. Raman spectroscopy and X-ray photoelectron spectroscopy showed that the graphitic structure in O-SWCNTs was oxidized, and electron microscopy showed that long CNT fibers initially aggregated and became short and isolated during degradation. Since Shewanella spp. and iron are ubiquitous in the environment, this study suggests that a Fenton reaction driven by this genus is applicable to the degradation of CNTs under a wide range of conditions and will help researchers develop novel methods for waste treatment and environmental bioremediation against CNTs. | Seira Takahashi; Katsutoshi Hori | Earth, Space, and Environmental Chemistry; Environmental Science; Wastes | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65095c9c60c37f4f760aea31/original/long-term-continuous-degradation-of-carbon-nanotubes-by-a-bacteria-driven-fenton-reaction.pdf |
66a8b15cc9c6a5c07a792487 | 10.26434/chemrxiv-2024-nwbqd | Performance of Quantum Chemistry Methods for Benchmark Set of Spin–State Energetics Derived from Experimental Data of 17 Transition Metal Complexes (SSE17) | Reliable prediction of spin-state energetics for transition metal (TM) complexes is recognized as a challenging and compelling problem in quantum chemistry, with implications for modeling catalytic reaction mechanisms and computational discovery of materials. The computed spin–state energetics are highly variable with the choice of method and credible reference data are scarce, making it difficult to conduct conclusive computational studies of open-shell TM systems. Here, we present a novel benchmark set of first-row TM spin–state energetics, which is derived from curated experimental data of 17 representative complexes containing Fe(II), Fe(III), Co(II), Co(III), Mn(II), and Ni(II) with chemically diverse ligands. The reference values of adiabatic or vertical energy differences are derived from spin-crossover enthalpies (9 complexes) or energies of spin-forbidden absorption bands in reflectance spectra (8 complexes). These are carefully back-corrected for relevant vibrational and environmental effects (due to solvation or crystal lattice) in order to provide the reference values directly comparable with computed electronic energy differences. The new benchmark set makes it possible to assess the accuracy of spin–state energetics from approximate density functional theory (DFT) and wave function methods with a level of statistical reliability not attained in earlier studies. The lowest mean absolute error (MAE) of 1.5 kcal/mol and maximum error of −3.5 kcal/mol are found for the coupled-cluster CCSD(T) method, which outperforms all tested multireference methods: CASPT2, MRCI+Q, CASPT2/CC and CASPT2+δMRCI. Contrary to earlier claims in the literature, the use of Kohn–Sham instead of Hartree–Fock orbitals in the reference determinant is not found to consistently improve the accuracy of the CCSD(T) spin–state energetics. The best performing DFT methods are double-hybrids (PWPB95-D3(BJ), B2PLYP-D3(BJ)) with the MAEs below 3 kcal/mol and maximum errors within 6 kcal/mol, whereas DFT methods traditionally recommended for spin states (e.g., B3LYP*-D3(BJ) and TPSSh-D3(BJ)) are found to perform much worse with the MAEs of 5–7 kcal/mol and maximum errors beyond 10 kcal/mol. The results of this work are relevant for the proper choice of methods to characterize TM systems in computational catalysis and (bio)inorganic chemistry, and may also stimulate new developments in quantum-chemical or machine learning approaches. | Mariusz Radon; Gabriela Drabik; Maciej Hodorowicz; Janusz Szklarzewicz | Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a8b15cc9c6a5c07a792487/original/performance-of-quantum-chemistry-methods-for-benchmark-set-of-spin-state-energetics-derived-from-experimental-data-of-17-transition-metal-complexes-sse17.pdf |
62eec2e4d131b727610f2265 | 10.26434/chemrxiv-2022-k32j0 | Synthesis and Calculations of Wurtzite Al1−xGdxN Heterostructural Alloys | Al1−xGdxN is one of a series of novel heterostructural alloys involving rare earth cations with potentially interesting properties for (opto)electronic, magnetic and neutron detector applications. Using alloy models in conjunction with density functional theory, we explored the full composition range for Al1−xGdxN and found that wurtzite is the ground state structure up to a critical composition of x = 0.82. The calculated temperature-composition phase diagram reveals a large miscibility gap inducing spinodal decomposition at equilibrium conditions, with higher Gd substitution (meta)stabilized at higher temperatures. By depositing combinatorial thin films at
high effective temperatures using radio frequency co-sputtering, we have achieved the highest Gd3+ incorporation into the wurtzite phase reported to date, with single-phase compositions at least up to x ≈ 0.25 confirmed by high resolution synchrotron grazing incidence wide angle X-ray scattering. High resolution transmission electron microscopy on material with x ≈ 0.13 confirmed a uniform composition polycrystalline film with uniform columnar grains having the wurtzite structure. Expanding our calculations to other rare earth cations (Pr and Tb) reveals similar thermodynamic stability and solubility behavior to Gd. From this and previous studies on Al1−xScxN, we elucidate that both smaller ionic radius and higher bond ionicity promote increased incorporation of group IIIB cations into wurtzite AlN. This work furthers the development of design rules for new alloys in this materials family. | Rebecca W. Smaha; Keisuke Yazawa; Andrew Norman; John S. Mangum; Geoff L. Brennecka; Andriy Zakutayev; Sage R. Bauers; Prashun Gorai; Nancy Haegel | Theoretical and Computational Chemistry; Materials Science; Alloys; Thin Films; Theory - Computational; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62eec2e4d131b727610f2265/original/synthesis-and-calculations-of-wurtzite-al1-x-gdx-n-heterostructural-alloys.pdf |
6682f21ac9c6a5c07aee087f | 10.26434/chemrxiv-2024-gw7g1 | Plasmon Modulation in Copper Phosphide Nanocrystals | We present the modulation of surface plasmon resonance in non-stoichiometric copper phosphide nanocrystals. This was achieved through control over the carrier concentration by an applied electrochemical potential. Application of anodic potential
resulted in the blueshift of the plasmon resonance and increment in its extinction. Under cathodic potential, the plasmon redshifted and reduced the extinction. Further,
these changes were reversible over multiple cycles of anodic and cathodic potential
steps. We also discuss how the post synthetic ligand treatment can impact the plasmon peak and structure of Cu3−xP nanocrystals . Specifically, the treatment of thiols
resulted in the decomposition of the nanocrystal. This work demonstrates how plasmon peak in Cu3−xP can be used as a probe to visualize the changes in the structure
and carrier density of these nanocrystals in various applications. | Jiyuan Yu; Zifei Chen; Heyou Zhang; James Hutchison; Paul Mulvaney; Arun Ashokan | Physical Chemistry; Nanoscience; Plasmonic and Photonic Structures and Devices; Quasiparticles and Excitations; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6682f21ac9c6a5c07aee087f/original/plasmon-modulation-in-copper-phosphide-nanocrystals.pdf |
669a7b3fc9c6a5c07adb7b7b | 10.26434/chemrxiv-2024-x2dlc | Uranium(III) and uranium(IV) meta-terphenyl thiolate complexes | We report the synthesis and characterization of crystalline uranium(IV) and uranium(III) complexes supported by the bulky hexa-iso-propyl-m-terphenylthiolate ligand system, SAriPr6 (SAriPr6 = {SC6H3-2,6-(Tripp)2}; Tripp = 2,4,6-iPr-C6H2). These constitute the first examples of m-terphenylthiolate complexes of uranium in any oxidation state and highlight the supporting role of U···arene interactions in the isolation of heteroleptic complexes with this ligand set, and demonstrate the diverse reactivity of [UIV(BH4)4]. Treatment of UIVCl4 with two equivalents of KSAriPr6 in Et2O afforded [UIV(SAriPr6)2(Cl)2] (1) in poor yield along with several crystals of the Et2O adduct, [UIV(SAriPr6)2(Cl)2(Et2O)2] (1·Et2O). While the reaction between [UIV(BH4)4] and one equivalent of KSAriPr6 in toluene gave several crystals of the poorly soluble double salt, [UIV(μ-SAriPr6)(BH4)2(μ-BH4)(μ3-BH4)K]2 (2), exposing the crude reaction mixture to Et2O gave the oxidized disulfide ligand dimer, (SAriPr6)2 as the sole identifiable product. The reaction between [UIV(BH4)4] and one equivalent of HSAriPr6 in hot toluene gave [UIII(H3B·SAriPr6 κS,H,H)(BH4)2] (3) – the net product of thermolytic reduction of the uranium and deprotonation of the arylthiol. Complex 3 proved resistant to further substitution using either HSAriPr6 or KSAriPr6. Both U(III) mono-arylthiolates, [UIII(SAriPr6)(BH4)2] (4a) and [{UIII(SAriPr6)(BH4)}2{μ-B2H6}] (4b) were isolated as a mixture from the reaction between [UIII(BH3)3(toluene)] and one equivalent of KSAriPr6. Complex 4b is a rare example of a nido-mettaloborane. When two equivalents of KSAriPr6 were reacted with [UIII(BH3)3(toluene)], the bis-arylthiolate complex [UIII(SAriPr6)2(BH4)] (5) was isolated in good yield. Complexes 1–5 have been characterized variously by single-crystal X-ray diffraction, multi-nuclear NMR spectroscopy, infra-red spectroscopy, UV-Vis-NIR spectroscopy, SQUID magnetometry, elemental analyses as appropriate. Quantum chemical calculations have been employed to interpret the nature of the U–S bonding interactions across these U(III) and U(IV) complexes. | Benjamin Réant; John Seed; George Whitehead; Conrad Goodwin | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669a7b3fc9c6a5c07adb7b7b/original/uranium-iii-and-uranium-iv-meta-terphenyl-thiolate-complexes.pdf |
60c75465ee301c6570c7af67 | 10.26434/chemrxiv.12782456.v2 | Using Atomic Charges to Describe the pKa of Carboxylic Acids | <div>In this study, we present an accurate protocol for the fast prediction of pKa's of carboxylic acids based on the linear relationship between computed atomic charges of the anionic form of the carboxylate fragment and their experimental pKa values. Five charge descriptors, three charge models, three solvent models, gas phase calculations and several DFT methods (combination of eight DFT functionals and fifteen basis sets) were tested. Among those, the best combination to reproduce experimental pKa's is to compute NPA atomic charge using the SMD model at the M06L/6-311G(d,p) level of theory and selecting the maximum atomic charge on carboxylic oxygen atoms (R^2 = 0.955). The applicability of the suggested protocol and its stability along geometrical changes are verified by molecular dynamics simulations performed for a set of aspartate, glutamate and alanine peptides. By reporting the calculated atomic charge of the carboxylate form into the linear relationship derived in this work, it will be possible to estimate accurately the amino acid’s pKa's in protein environment.</div><div><br /></div> | Zeynep Pinar Haslak; Sabrina Zareb; Ilknur Dogan; Viktorya Aviyente; Gerald Monard | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75465ee301c6570c7af67/original/using-atomic-charges-to-describe-the-p-ka-of-carboxylic-acids.pdf |
60c74c03337d6c55ece27b8a | 10.26434/chemrxiv.11916015.v2 | Extending Scaled-Interaction Adaptive-Partitioning QM/MM to Covalently Bonded Systems | Quantum mechanics/molecular mechanics (QM/MM) is the method of choice for atomistic simulations of large systems that can be partitioned into active and environmental regions. Adaptive-partitioning (AP) methods extend the applicability of QM/MM, allowing active zones to change during the simulation. AP methods achieve continuous potential energy surface (PES) by introducing buffer regions in which atoms have both QM and MM characters. Most of the existing AP-QM/MM methods require multiple QM calculations per time step, which can be expensive for systems with many atoms in buffer regions. Although one can lower the computational cost by grouping atoms into fragments, this may not be possible for all systems, especially for applications in covalent solids. The SISPA method [J. Chem. Theory Comput. 2017, 13, 2342] differs from other AP-QM/MM methods by only requiring one QM calculation per time step, but it has the flaw that the QM charge density and wavefunction near the buffer/MM boundary tend to those of isolated atoms/fragments. Besides, regular QM/MM methods for treating covalent bonds cut by the QM/MM boundary are incompatible with SISPA. Due to these flaws, SISPA in its original form cannot treat covalently bonded systems properly. In this work, I show that a simple modification to the SISPA method improves the treatment of covalently bonded systems. I also study the effect of correcting the charge density in SISPA by developing a density-corrected pre-scaled algorithm. I demonstrate the methods with simple molecules and bulk solids. | Zenghui Yang | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c03337d6c55ece27b8a/original/extending-scaled-interaction-adaptive-partitioning-qm-mm-to-covalently-bonded-systems.pdf |
64d8c99a4a3f7d0c0d19a747 | 10.26434/chemrxiv-2023-sx9lr | Highly Transparent, Yet Photoluminescent: 2D CdSe/CdS Nanoplatelet-Zeolitic Imidazolate Framework Composites Sensitive to Gas Adsorption | In this work, thin composite films of zeolitic imidazolate frameworks (ZIFs) and colloidal two-dimensional (2D) CdSe/CdS nanoplatelet emitters with minimal scattering are formed by cycled growth and yield highly transparent coatings while retaining the strong and narrow photoluminescence of the nanoplatelets at 546 nm (FWHM: 25 nm) in a solid-state composite structure. The porous ZIF matrix acts as functional encapsulation for the nanoplatelet emitters which is shown by the adsorption of the guest molecules water and ethanol by the ZIF and sensed by a reversable change in the photoluminescence of the embedded nanoplatelets. Additionally, the transmittance of the composite films surpasses the values of uncoated glass substrates at UV-Vis wavelengths where the nanoplatelets show no absorption, rendering it a photoluminescent antireflective coating. The fast formation of smooth films without pre-polymerizing the colloidal nanoplatelet emitters provides a powerful tool for application-oriented photoluminescence-based gas sensing in the composites. | Lars F. Klepzig; Nils C. Keppler; Dominik Rudolph; Andreas Schaate; Peter Behrens; Jannika Lauth | Physical Chemistry; Inorganic Chemistry; Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d8c99a4a3f7d0c0d19a747/original/highly-transparent-yet-photoluminescent-2d-cd-se-cd-s-nanoplatelet-zeolitic-imidazolate-framework-composites-sensitive-to-gas-adsorption.pdf |
60c75115469df4086af44975 | 10.26434/chemrxiv.13118423.v1 | Inferring Experimental Procedures from Text-Based Representations of Chemical Reactions | The experimental execution of chemical reactions is a context-dependent and time-consuming process, often solved using the experience collected over multiple decades of laboratory work or searching similar, already executed, experimental protocols. Although data-driven schemes, such as retrosynthetic models, are becoming established technologies in synthetic organic chemistry, the conversion of proposed synthetic routes to experimental procedures remains a burden on the shoulder of domain experts. In this work, we present, for the first time, data-driven models for predicting the entire sequence of synthesis steps starting from a textual representation of a chemical equation. We generated a data set of 693,517 chemical equations and associated action sequences by extracting and processing experimental procedure text from patents, using state-of-the-art natural language models. We used the attained data set to train three different models: a nearest-neighbor model based on recently-introduced reaction fingerprints, and two deep-learning sequence-to-sequence models based on the Transformer and BART architectures. When evaluated on the ground truth data, the best performing model (transformer) achieves an accuracy of 72.7% for single action predictions, and a 100% match of the full action sequence for 3.6% of experimental procedures. An analysis by a trained chemist revealed that the predicted action sequences are adequate for execution without human intervention in more than 50% of the cases.<br /> | Alain C. Vaucher; Philippe Schwaller; Joppe Geluykens; Vishnu H Nair; Anna Iuliano; Teodoro Laino | Organic Synthesis and Reactions; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75115469df4086af44975/original/inferring-experimental-procedures-from-text-based-representations-of-chemical-reactions.pdf |
629617f8dd1809d81af0123e | 10.26434/chemrxiv-2022-x1cbd | Cobalt Homeostatic Catalysis for Coupling of Enaminones and Oxadiazolones to Quinazolinones | Transition metal catalysis has revolutionized modern synthetic chemistry for its diverse modes of coordination reactivity. However, this versatility in reactivity is also the predominant cause of catalyst deactivation, a persisting issue that can significantly compromise its synthetic value. Homeostatic catalysis, a catalytic process that can sustain its productive catalytic cycle even when chemically disturbed, is proposed herein as an effective tactic to address the challenge. In particular, a cobalt homeostatic catalysis process has been developed for water-tolerant coupling of enaminones and oxadiazolones to quinazolinones. Dynamic covalent bonding serves as a mechanistic handle for preferred buffering of water onto enaminone and reverse exchange back by released secondary amine, thus securing reversible entry into cobalt dormant and active states for productive catalysis. Through this homeostatic catalysis mode, a broad structural scope has been achieved for quinazolinones, enabling further elaboration into distinct pharmaceutically active agents. | Weiping Wu; Shuaixin Fan; Xuan Wu; Lili Fang; Jin Zhu | Catalysis; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2022-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629617f8dd1809d81af0123e/original/cobalt-homeostatic-catalysis-for-coupling-of-enaminones-and-oxadiazolones-to-quinazolinones.pdf |
60c73f1b567dfedbf2ec391f | 10.26434/chemrxiv.7235411.v1 | Optimizing Single Slater Determinant for Electronic Hamiltonian with Lagrange Multipliers and Newton-Raphson Methods as an Alternative to Ground State Calculations via Hartree-Fock Self Consistent Field | Considering the emblematic Hartree-Fock (HF) energy expression with single Slater determinant and the ortho-normal molecular orbits (MO) in it, expressed as a linear combination (LC) of atomic orbits (LCAO) basis set functions, the HF energy expression is in fact a 4th order polynomial of the LCAO coefficients, which is relatively easy to handle. The energy optimization via the Variation Principle can be made with a Lagrange multiplier method to keep the ortho-normal property and the Newton-Raphson (NR) method to find the function minimum. It is an alternative to the widely applied HF self consistent field (HF-SCF) method which is based on unitary transformations and eigensolver during the SCF, and seems to have more convenient convergence property. This method is demonstrated for closed shell (even number of electrons and all MO are occupied with both, alpha and beta spin electrons) and restricted (all MOs have single individual spatial orbital), but the extension of the method to open shell and/or unrestricted cases is straightforward. | Sandor Kristyan | Computational Chemistry and Modeling; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1b567dfedbf2ec391f/original/optimizing-single-slater-determinant-for-electronic-hamiltonian-with-lagrange-multipliers-and-newton-raphson-methods-as-an-alternative-to-ground-state-calculations-via-hartree-fock-self-consistent-field.pdf |
6166f583b564b66361760e98 | 10.26434/chemrxiv-2021-s6k4c | From Appendage to Crosslinker – Unusual Swelling Behavior in Spiropyran-Modified Hydrogels | Stimuli-responsive materials typically contain responsive molecular units that couple an external trigger to a defined macroscale response. Ongoing efforts to boost the versatility and complexity of these responses increasingly focus on multi-stimuli-responsive molecular units and crosslinkers, as these bear the potential to impart self-regulatory behaviors building on cooperative effects and feedback mechanisms. Herein, we study a stimuli-responsive platform consisting of polyacrylamide-based hydrogels with well-known multi-responsive spiropyrans covalently bound as pendant groups or ´non-innocent´ crosslinkers. Surprisingly, as compared to their appended counterparts, spiropyran crosslinkers cause up to two-fold larger hydrogel swelling in methylenebisacrylamide-crosslinked poly(acrylamide-co-acrylic acid) hydrogels, despite their increased relative crosslinking density. We seek the origin of this unexpected behavior by employing nanoindentation, swelling studies, and UV-vis spectroscopy to study changes in mechanical properties and in spiropyran isomer distribution as a function of solution pH, co-monomer chemistry, and swelling-induced polymer strain. We then estimate the osmotic counterion pressures as a function of spiropyran isomer distribution but find that such pressures alone are insufficient to explain the observed behavior. Charge complexation, cooperative effects between the hydrogel´s mechanics and chemistry, and aggregate formation may all be invoked to explain features of the observed ´non-innocence´ of spiropyran crosslinkers. Taken together, these insights will aid rational implementation of such responsive crosslinkers in materials design and extend the functionality of existing polymeric materials towards more complex and better tunable behaviors. | Michael M. Lerch; Ankita Shastri; Thomas B.H. Schroeder; Amos Meeks; Shucong Li; Anna V. Shneidman; Michael Aizenberg; Joanna Aizenberg | Physical Chemistry; Materials Science; Dyes and Chromophores; Polyelectrolytes - Materials; Physical and Chemical Properties; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6166f583b564b66361760e98/original/from-appendage-to-crosslinker-unusual-swelling-behavior-in-spiropyran-modified-hydrogels.pdf |
66cf7863a4e53c4876eae135 | 10.26434/chemrxiv-2024-m2h4h | A comprehensive approach to analyzing environmental data with non-detects | Non-detects—measurements reported as “below the detection limit”—are ubiquitous in environmental science and engineering. They are frequently replaced with a constant, but this biases estimates of means, regression slopes, and correlation coefficients. Omitting non-detects is worse, and has led to serious errors. Simple alternatives are available: rank-based statistics, maximum likelihood estimation, and re-purposed survival analysis routines. But many environmental datasets do not align well with the assumptions these methods make—it is often necessary to account for hierarchy (e.g., measurements nested within lakes), sampling strategy (e.g., measurements collected as time series), heterogeneity (e.g., site-dependent variance), and measurement error. Bayesian methods offer the flexibility to do this; incorporating non-detects is also easy and does not bias model parameter estimates as substitution does. Here we discuss Bayesian implementations of common bivariate and multivariate statistical methods relevant to environmental science. We use a dataset comprising time series of Ag, As, Cd, Ce, Co, Sb, Ti, U, and V concentrations in municipal biosolids that includes many non-detects. The models can be reproduced and extended to new problems using the data and code accompanying this paper. | Benjamin F. Trueman; Madison Gouthro; Amina K. Stoddart; Graham A. Gagnon | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC 4.0 | CHEMRXIV | 2024-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cf7863a4e53c4876eae135/original/a-comprehensive-approach-to-analyzing-environmental-data-with-non-detects.pdf |
60c75475bdbb895425a3a669 | 10.26434/chemrxiv.13665074.v1 | Electrolytic Conversion of Bicarbonate Solutions to CO at >500 mA cm-2 and 2.2 V | Electrolyzers that reduce carbon dioxide (CO2) into chemicals and fuels often use high-purity gaseous CO2 feedstocks that need to be isolated from upstream carbon capture units. If CO2 were to be captured directly from air, the eluent is likely to be an aqueous solution rich in bicarbonate ions (HCO3-). This scenario provides the impetus to electrolytically reduce these bicarbonate-rich carbon capture solutions into the same products as a CO2 electrolyzer. We report here an electrolyzer configuration that couples the conversion of bicarbonate to CO at the cathode with hydrogen oxidation at an anode. This unique system is capable of reaching a commercially-relevant current density of 500 mA cm-2 at merely 2.2 V, which is >0.5 V more efficient than any other reported electrolyzer that reduces HCO3- or CO2 at these current densities. | Zishuai Zhang; Eric W. Lees; Shaoxuan Ren; Aoxue Huang; Curtis P. Berlinguette | Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75475bdbb895425a3a669/original/electrolytic-conversion-of-bicarbonate-solutions-to-co-at-500-m-a-cm-2-and-2-2-v.pdf |
6701913e51558a15ef33301e | 10.26434/chemrxiv-2024-63194 | Unleashing Phosphorus Mononitride: Formation of PN-Multiple Bonded Exemplars [NPS2]2–, [NPCl]–, and [PN4]– | The interstellar diatomic molecule, phosphorus mononitride (P≡N), is highly unstable under conditions typical on Earth, and its utility for constructing elusive P–N multiply-bonded archetypes is essentially uncharted. Herein, we show how Na(OCP) transfers a P atom to an electrophilic osmium nitride complex to form a terminally bound P≡N functionality. Quantum chemical calculations and X-ray absorption spectroscopy unveil a cumulenic [Os(IV)=N=P] electronic structure comprising orthogonal Os=N and N=P π-bonding. The highly reduced P≡N ligand, formally [PN]2–, undergoes two-fold oxidation with elemental sulfur to form a trigonal planar [NPS2]2– group. On reaction with Ph3CCl, the P≡N ligand forms a bent [NPCl]– motif coordinated to Os(III) (S = ½). [3+2] cycloaddition of this radical species with Me3SiN3 forms an aromatic heterocyclic interpnictide, [PN4]–, that is inaccessible from the parent P≡N system. | Simon Edin; Christian Sandoval-Pauker; Nathan Yutronkie; Zoltan Takacs; Fabrice Wilhelm; Andrei Rogalev; Balazs Pinter; Kasper S. Pedersen; Anders Reinholdt | Inorganic Chemistry; Organometallic Chemistry; Earth, Space, and Environmental Chemistry; Small Molecule Activation (Inorg.); Coordination Chemistry (Organomet.); Main Group Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6701913e51558a15ef33301e/original/unleashing-phosphorus-mononitride-formation-of-pn-multiple-bonded-exemplars-nps2-2-np-cl-and-pn4.pdf |
67075628cec5d6c142be0404 | 10.26434/chemrxiv-2024-f03hn | Macrocyclizing DNA-Encoded Peptides via Visible-Light-Mediated Desulfurisation | DNA-encoded library technology (DELT) facilitates the generation of billions of DNA-tagged macrocycles containing noncanonical amino acids, synthesized through diverse cyclization strategies. The varied appended residues and ring conformations expand chemical space, enabling the identification of hit compounds with improved properties such as higher binding affinity, enhanced metabolic stability, and increased oral bioavailability. This study expands the on-DNA chemical toolkit by introducing a DNA-compatible C(sp3)-C(sp3) bond formation method via a visible-light-mediated desulfurative macrocyclization. This reaction proceeds efficiently under mild conditions, exhibiting broad substrate scope and good conversions. Notably, the reaction condition is com-patible with free amines, allowing for late-stage modifications and the preparation of covalent DNA-encoded macrocyclic libraries. | Qingyi Zhao; Hanqing Zhao ; Shijie Zhang; Weiwei Lu; Yujun Zhao; Xiaojie Lu; Xuan wang | Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC 4.0 | CHEMRXIV | 2024-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67075628cec5d6c142be0404/original/macrocyclizing-dna-encoded-peptides-via-visible-light-mediated-desulfurisation.pdf |
669a8b3ec9c6a5c07add20fd | 10.26434/chemrxiv-2024-b4rln | From chemical similarity measures to an unconventional modeling framework: The application of c-RASAR along with dimensionality reduction techniques in a representative hepatotoxicity dataset | With the exponential progress in the field of cheminformatics, the conventional modeling approaches have so far been to employ supervised and unsupervised machine learning (ML) and deep learning models, utilizing the standard molecular descriptors, which represent the structural, physicochemical, and electronic properties of a particular compound. Deviating from the conventional approach, in this investigation, we have employed the classification Read-Across Structure-Activity Relationship (c-RASAR), which involves the amalgamation of the concepts of classification-based quantitative structure-activity relationship (QSAR) and Read-Across to incorporate Read-Across-derived similarity and error-based descriptors into a statistical and machine learning modeling framework. ML models developed from these RASAR descriptors use similarity-based information from the close source neighbors of a particular query compound. We have employed different classification modeling algorithms on the selected QSAR and RASAR descriptors to develop predictive models targeted towards the efficient prediction of hepatotoxicity of query compounds. The predictivity of each of these models was evaluated on a large number of test set compounds. Additionally, the best-performing model was used to screen a true external set of data. The concepts of explainable AI (XAI) coupled with Read-Across were used to interpret the contributions of the RASAR descriptors in the best c-RASAR model and to explain the chemical diversity in the dataset. The application of various unsupervised dimensionality reduction techniques like t-SNE and UMAP, and the supervised ARKA framework showed the usefulness of the RASAR descriptors over the selected QSAR descriptors in their ability to group similar compounds, enhancing the modelability of the dataset and efficiently identifying activity cliffs. Furthermore, the activity cliffs were also identified from Read-Across by observing the nature of compounds constituting the nearest neighbors for a particular query compound. On comparing our simple linear c-RASAR model with the previously reported models developed using the same dataset derived from the US FDA Orange Book (https://www.accessdata.fda.gov/scripts/cder/ob/index.cfm), it was observed that our model is simple, reproducible, transferable, and highly predictive. The performance of the LDA c-RASAR model on the true external set supersedes that of the previously reported work. Therefore, the present simple LDA c-RASAR model can efficiently be used to predict the hepatotoxicity of query chemicals. | Arkaprava Banerjee; Kunal Roy | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669a8b3ec9c6a5c07add20fd/original/from-chemical-similarity-measures-to-an-unconventional-modeling-framework-the-application-of-c-rasar-along-with-dimensionality-reduction-techniques-in-a-representative-hepatotoxicity-dataset.pdf |
60c74e6c567dfe12dbec54fd | 10.26434/chemrxiv.12746561.v1 | Analytical Validation of an ATR-FTIR Based Method for Quantifying the Amount of Polysorbate 80 Adsorbed on the PLGA Nanoparticles | <p>Nanomedicine is envisioned to have a tremendous impact on targeted drug
delivery in future. Coating of nanoparticles with non-ionic surfactants has
been often employed for enhancing targeting in drug delivery systems. Polysorbate
80 is one of the non-ionic surfactants
used often as a coating agent for receptor-mediated endocytosis into the brain.
However, very few studies have been done to investigate the actual amount of
the surfactant adsorbed or the mechanism of adsorption onto the nanoparticles. We
had developed an assay using an ATR-FTIR method for quantiation and adsorption
mechanism of polysorbate 80 on PLGA nanoparticles. Here we show the analytical
validation of this method, for exploring its suitability for its intended purpose in industries. To
comply with regulatory bodies and for standardization, we have followed the ICH
and FDA guidelines for analytical validation and investigated the required
criteria i.e. accuracy, precision, linearity, range ,limit of detection and
quantitation. The method successfully complied with all regulatory criteria and
is therefore suitable for successful use in industry, academia and by regulatory
bodies.</p> | Nabodita Sinha; Abhayraj Shrikrishna Joshi; Ashwani Thakur | Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e6c567dfe12dbec54fd/original/analytical-validation-of-an-atr-ftir-based-method-for-quantifying-the-amount-of-polysorbate-80-adsorbed-on-the-plga-nanoparticles.pdf |
60c7591a9abda2847ff8ea1f | 10.26434/chemrxiv.14643360.v1 | Actively Searching: Inverse Design of Novel Molecules with Simultaneously Optimized Properties | <p>Combining quantum chemistry characterizations with generative machine learning models has the potential to accelerate molecular searches in chemical space. In this paradigm, quantum chemistry acts as a relatively cost-effective oracle for evaluating the properties of particular molecules while generative models provide a means of sampling chemical space based on learned structure-function relationships. For practical applications, multiple potentially orthogonal properties must be optimized in tandem during a discovery workflow. This carries additional difficulties associated with specificity of the targets and the ability for the model to reconcile all properties simultaneously. Here we demonstrate an active learning approach to improve the performance of multi-target generative chemical models. We first demonstrate the effectiveness of a set of baseline models trained on single property prediction tasks in generating novel compounds with various property targets, including both interpolative and extrapolative generation scenarios. For property ranges where accurate targeting proves difficult, the novel compounds suggested by the model are characterized using quantum chemistry to obtain the true values, and these new molecules closest to expressing the desired properties are fed back into the generative model for additional training. This gradually improves the generative models’ understanding of unknown areas of chemical space and shifts the distribution of generated compounds towards the targeted values. We then demonstrate the effectiveness of this active learning approach in generating compounds with multiple chemical constraints, including vertical ionization potential, electron affinity, and dipole moment targets, and validate the results at the B97X-D3/def2-TZVP level. This method requires no modifications to extant generative approaches, but rather utilizes their inherent generative and predictive aspects for self-refinement, and can be applied to situations where any number of properties with varying degrees of correlation must be optimized simultaneously.</p> | Nicolae C. Iovanac; Robert MacKnight; Brett Savoie | Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7591a9abda2847ff8ea1f/original/actively-searching-inverse-design-of-novel-molecules-with-simultaneously-optimized-properties.pdf |
60de2057e7f2bf0c8c809eaa | 10.26434/chemrxiv-2021-mw89q | Unusual Rearrangement-Remercuration Reactions of Allylic Silanols | We present the first examples of rearrangement reactions of allylic silanol substrates into linear ketone and 5-membered cyclic silanediol organomercurial products. Both reactions are mediated by Hg(OTf)2 but differ in the use of base, solvent, and temperature. The substrate scope of both transformations was explored, and the product organomercurials were shown to be valuable synthons. Mechanistic studies suggest that both products are the result of a series of transformations, cascading in one pot. DFT analysis provides a basis for understanding the rearrangement of a 6-endo intermediate into the 5-exo cyclic silanediol product. | Shyam Sathyamoorthi; Someshwar Nagamalla; Ranjeet Dhokale; Frederick Seidl; Joel Mague | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2021-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60de2057e7f2bf0c8c809eaa/original/unusual-rearrangement-remercuration-reactions-of-allylic-silanols.pdf |
623080702c50103d1b7bd171 | 10.26434/chemrxiv-2022-tt41m | Dynamic Architectures on Expanded Heterohelicenes | Expanded heterohelicenes are an emerging class of heteroatom-containing flexible helicenes, empowered by dual modification with doped heteroatom(s) as well as expanded helicity. Owing to the intriguing fusion of unique structural and electronic features, these molecules captured recent research focus, yielding some fascinating fundamental understanding and new insights in the helicene chemistry, as well as valued electronic and optoelectronic applications. However, limited synthetic strategies to access these molecules act as a major bottleneck for a rapid development of this field by uncovering hidden potentials of purposefully designed task-specific expanded heterohelicenes. In this regard, expanded heterohelicenes consisting of backbone-decorated dynamic architectures are promising toward exploring stimuli-switchable physicochemical properties and functions; however, they are yet to be developed. In this work, we reported a convenient and modular synthetic protocol for such a novel class of expanded heterohelicenes containing stimuli-responsive core and peripheral modules in order to unearth the hitherto unexplored dynamic properties of these molecules. The rhodium(III)-catalyzed method employed here, named as “rollover π-expansion (ROPE)”, involves a concurrent linear and angular ring fusions on readily accessible imidazolium-containing pyridines as templates by annulation with alkyne staples, generating a 6-6-5-6-6-6-5-6-6-ring-based expanded polyaza[9]helicene skeleton. The intermediacy of a unique dirhoda-hetero[9]-helicene species generated by quadruple C–H activation-rollover metalation was arrested. Single crystal X-ray crystallographic studies of the dirhoda-hetero[9]-helicene intermediate as well as the expanded polyaza[9]helicenes revealed the origin of the characteristic flexible helical rim and its translation into the organic products. The dynamic behavior of these stimuli-responsive molecules was demonstrated with redox and light triggers, which enabled the molecules to function as reversible hydride-transport and prospective photomechanical molecular spring-like systems. | Pirudhan Karak; Joyanta Choudhury | Organic Chemistry; Organometallic Chemistry; Bond Activation; Catalysis; Transition Metal Complexes (Organomet.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623080702c50103d1b7bd171/original/dynamic-architectures-on-expanded-heterohelicenes.pdf |
65f0a0f4e9ebbb4db991f93c | 10.26434/chemrxiv-2023-k9rvm-v2 | PyJCFit: A Non-Linear Regression Random Search Algorithm for Chemistry Data Fitting | Hyperparameter optimization using non-linear least-square regression is a common fitting method for data analysis in chemistry, physics, biology, and engineering. It is sometimes challenging to balance various factors such as accuracy, computational time cost, and time cost in setting up the optimization. In this report, I introduce a naïve dynamic grid-searching algorithm named Python jump-chain fitting (PyJCFit) to reduce setting up time costs for a beginner in early-stage optimizations, which combines two different methods, grid and stochastic searching algorithms. The idea is to search all parameters heuristically and sequentially (a vector, not a grid matrix) in trusted bounds with an exponential distribution of space paying attention to the neighbor area of the guessed value. The distribution is somewhat random, and the chain does not require differential equations to optimize. PyJCFit is relatively slow but carries significant advantages in compound equations with breaks, peak searching, and global fitting; and various scoring functions beyond square residual, even those poorly behaved are allowed. | Jixin Chen | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Analytical Chemistry - General; Chemical Kinetics | CC BY NC 4.0 | CHEMRXIV | 2024-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f0a0f4e9ebbb4db991f93c/original/py-jc-fit-a-non-linear-regression-random-search-algorithm-for-chemistry-data-fitting.pdf |
60c7456c842e65dac5db2611 | 10.26434/chemrxiv.9991976.v1 | On the Design of Molecular Excitonic Circuits for Quantum Computing: The Universal Quantum Gates | This manuscript presents a theoretical strategy for encoding elementary quantum computing operations into the design of molecular excitonic circuits. Specifically, we show how the action of a unitary transformation of coupled two-level systems can be equivalently represented by the evolution of an exciton in a coupled network of dye molecules. We apply this strategy to identify the geometric parameters for circuits that perform universal quantum logic gate operations. We quantify the design space for these circuits and how their performance is affected by environmental noise. | Maria Castellanos; Amro Dodin; Adam Willard | Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7456c842e65dac5db2611/original/on-the-design-of-molecular-excitonic-circuits-for-quantum-computing-the-universal-quantum-gates.pdf |
61ba43ea7f367e695754e558 | 10.26434/chemrxiv-2021-rp36t | Ultrafast Triplet Generation at the Lead Halide Perovskite/Rubrene Interface | Triplet sensitization of rubrene by bulk lead halide perovskites has recently resulted in efficient infrared-to-visible photon upconversion via triplet-triplet annihilation. Notably, this process occurrs under solar relavant fluxes, potentially paving the way toward integration with photovoltaic devices. In order to further improve the upconversion efficiency, the fundamental photophysical pathways at the perovskite/rubrene interface must be clearly understood to maximize charge extraction. Here, we utilize ultrafast transient absorption spectroscopy to elucidate the processes underlying the triplet generation at the perovskite/rubrene interface. Based on the bleach and photoinduced absorption features of the perovskite and perovskite/rubrene devices obtained at multiple pump wavelengths and fluences, along with their resultant kinetics, our results do not support charge transfer states or long-lived trap states as the underlying mechanism. Instead, the data points towards a triplet sensitization mechanism based on rapid extraction of thermally excited carriers on the picosecond timescale. | Carl Conti; Alexander Bieber; Zachary VanOrman; Gregory Moller; Sarah Wieghold; Richard Schaller; Geoffrey Strouse; Lea Nienhaus | Physical Chemistry; Energy; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ba43ea7f367e695754e558/original/ultrafast-triplet-generation-at-the-lead-halide-perovskite-rubrene-interface.pdf |
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