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60c7543f0f50db1da9397ce6 | 10.26434/chemrxiv.13634849.v1 | Balancing Data on Proteochemometrics Activity Classification | <div>In silico analysis of biological activity data has become an essential technique in pharmaceutical development. </div><div>Specifically, the so-called proteochemometric models aim to share information between targets in machine learning ligand-target activity prediction models. </div><div>However, bioactivity datasets used in proteochemometrics modeling are usually imbalanced, which could potentially affect the performance of the models. In this work, we explored the effect of different balancing strategies in deep learning proteochemometric target-compound activity classification models while controlling for the compound series bias through clustering. These strategies were: (1) no_resampling, (2) resampling_after_clustering, (3) resampling_before_clustering and (4) semi_resampling. </div><div>These schemas were evaluated in kinases and GPCRs from BindingDB. </div><div>We observed that the predicted proportion of positives was driven by the actual data balance in the test set. </div><div>Additionally, it was confirmed that data balance had an impact on the performance estimates of the proteochemometrics model. </div><div>We recommend a combination of data augmentation and clustering in the training set (semi_resampling) in order to mitigate the data imbalance effect in a realistic scenario. </div><div>The code of this analysis is publicly available at https://github.com/b2slab/imbalance_pcm_benchmark.</div> | Angela Lopez-del Rio; Sergio Picart; Alexandre Perera-Lluna | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2021-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7543f0f50db1da9397ce6/original/balancing-data-on-proteochemometrics-activity-classification.pdf |
6235b85f5c8dae7e9eef098c | 10.26434/chemrxiv-2021-01dfq-v2 | On the Role of Solvent in the Formation of
Vacancies on Ibuprofen Crystal Facets | Surface defects play a crucial role in the process of crystal growth, as the incorporation of growth units generally takes place on under-coordinated sites on the growing crystal facet.
In this work, we use molecular dynamics simulations to obtain information on the role of the solvent in the roughening of three morphologically-relevant crystal faces of form I of racemic ibuprofen. To this aim, we devise a computational strategy based on combining independent Well Tempered Metadynamics with Mean Force Integration. This approach enables us to evaluate the energetic cost associated with the formation of a surface vacancy for a set of ten solvents, covering a range of polarities and hydrogen-bonding ability.
We find that both the mechanism of defect formation on these facets and the work associated with the process are indeed markedly solvent-dependent. The methodology developed in this work has been designed with the aim of capturing solvent effects at the atomistic scale while maintaining the computational efficiency necessary for implementation in high-throughput computational screenings of crystallization solvents. | Veselina Marinova; Geoffrey P. F. Wood; Ivan Marziano; Matteo Salvalaglio | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Interfaces; Physical and Chemical Processes; Surface | CC BY 4.0 | CHEMRXIV | 2022-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6235b85f5c8dae7e9eef098c/original/on-the-role-of-solvent-in-the-formation-of-vacancies-on-ibuprofen-crystal-facets.pdf |
61546f14aade364b06c66a1c | 10.26434/chemrxiv-2021-51rbh | Absolute Configuration of Bromofluoroiodomethane after Preparative Gas Chromatographic Separation | The enantiomers of bromofluoroiodomethane (CHBrFI) were separated on a preparative scale using gas chromatography (GC). The collected single enantiomers were analysed by vibrational circular dichroism spectroscopy and polarimetry in combination with ab initio calculations to determine the respective absolute configuration. | Benjamin Spenger; Stefan Näf; Stole Manov; Jürgen Stohner | Physical Chemistry; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61546f14aade364b06c66a1c/original/absolute-configuration-of-bromofluoroiodomethane-after-preparative-gas-chromatographic-separation.pdf |
60c748740f50db6d57396794 | 10.26434/chemrxiv.11912073.v1 | Metal-Free Photoinduced Hydroalkylation Cascade Enabled by an Electron-Donor-Acceptor Complex | A metal- and catalyst-free photoinduced radical
cascade hydroalkylation of 1,7-enynes has been
disclosed. The process is triggered by a SET event involving a photoexcited
electron-donor-aceptor complex between NHPI ester and Hantzsch ester, which
decomposes to afford a tertiary radical that is readily trapped by the enyne. <a>The method provides an operationally simple, robust and
step-economical approach to the construction of diversely functionalized
dihydroquinolinones bearing quaternary-centers. A sequential one-pot hydroalkylation-isomerization
approach is also allowed giving access
to a family of quinolinones. A wide substrate scope and high functional group tolerance was observed in both approaches</a>. | José Tiago Menezes Correia; Gustavo Piva da Silva; Camila Menezes Kisukuri; Elias André; Bruno Pires; Pablo Silva Carneiro; Marcio Weber Paixão | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.); Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748740f50db6d57396794/original/metal-free-photoinduced-hydroalkylation-cascade-enabled-by-an-electron-donor-acceptor-complex.pdf |
67043dad51558a15ef6775ef | 10.26434/chemrxiv-2024-vd8j0 | Proton Donors Influence Nitrogen Adsorption in Lithium-Mediated Electrochemical Ammonia Synthesis | Lithium-mediated electrochemical ammonia synthesis (LiMEAS) has recently shown promise towards efficient electrochemical ammonia production. This process relies on the formation of a lithium nitride film which is sub- sequently protonated to release ammonia. Designing the electrolyte for this technology requires the selection of a proton donor. In this work, we perform a first-principles analysis to investigate the initial step of nitride formation considering 30 different proton donors (PD). As a baseline, modeling nitrogen on a lithium surface without a PD, we observe that N2 does not spontaneously dissociate on the lithium surface. However, explicitly introducing a PD into the system results in five unique recurring nitrogen config- urations on the lithium slab: (1) embedded, (2) adsorbed, (3) standing, (4) buried, and (5) transferred states. We show that these PD-induced states possess an elongated N-N bond and adsorb more strongly on lithium. Using charge analysis, we show that the charge transferred onto these states strongly correlates with the change in their bond length, a crucial parameter for nitrogen dissociation. These results suggest a more involved role of the PD in the initial stages of nitride formation, and motivate greater consideration for their impact on the LiMEAS pathway. | Victor Azumah; Lance Kavalsky; Venkatasubramanian Viswanathan | Theoretical and Computational Chemistry; Catalysis; Energy; Computational Chemistry and Modeling; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2024-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67043dad51558a15ef6775ef/original/proton-donors-influence-nitrogen-adsorption-in-lithium-mediated-electrochemical-ammonia-synthesis.pdf |
60c73cbf337d6cd27ee26059 | 10.26434/chemrxiv.14731779.v1 | A Tale of Two Bioconjugations: pH Controlled Divergent Reactivity of Protein A-Oxo Aldehydes in Competing A-Oxo-Mannich and Catalyst-Free Aldol Ligations | <div><div><div><p>Site-selective chemical methods for protein bioconjugation have revolutionised the fields of cell and chemical biology through the development of novel protein/enzyme probes bearing fluorescent, spectroscopic or even toxic cargos. Herein we report two new methods for the bioconjugation of a-oxo aldehyde handles within proteins using small molecule aniline and/or phenol probes. The ‘a-oxo-Mannich’ and ‘catalyst-free aldol’ ligations both compete for the electrophilic a-oxo aldehyde which displays pH divergent reactivity proceeding through the “Mannich” pathway at acidic pH to afford bifunctionalised bioconjugates, and the “catalyst-free aldol” pathway at neutral pH to afford monofunctionalised bioconjugates. We explore the substrate scope and utility of both these bioconjugations in the construction of neoglycoproteins, in the process formulating a mechanistic rationale for how both pathways intersect with each other at different reaction pH.</p></div></div></div> | Tessa Keenan; Richard Spears; Saeed Akkad; Clare Mahon; Natasha E. Hatton; Julia Walton; Amanda Noble; Nick Yates; Christoph G. Baumann; Alison Parkin; Nathalie Signoret; Martin Fascione | Bioorganic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cbf337d6cd27ee26059/original/a-tale-of-two-bioconjugations-p-h-controlled-divergent-reactivity-of-protein-a-oxo-aldehydes-in-competing-a-oxo-mannich-and-catalyst-free-aldol-ligations.pdf |
6410baaab5d5dbe9e84177f8 | 10.26434/chemrxiv-2023-nk1c0 | Synthesis of Polyethyleneimines from the Manganese Catalyzed Coupling of Ethylene Glycol and Ethylenediamine | Polyethyleneimines find many applications in products such as detergents, adhesives, cosmetics, and for processes such as tissue culture, gene therapy, and CO2 capture. The current state-of-the-art technology for the production of the branched polyethyleneimines involves aziridine feedstock which is a highly toxic, volatile and mutagenic chemical and raises significant concern to human health and environment. We report here a novel method for the synthesis of branched polyethyleneimines from ethylene glycol and ethylenediamine feedstock which are much safer, environmentally benign, commercially available and potentially renewable feedstock. The polymerisation reaction is catalysed by a complex of an earth-abundant metal, manganese and liberates H2O as the only by-product. Our mechanistic studies using DFT computation suggests that the reaction proceeds by the formation and subsequent hydrogenation of imine intermediates. | Claire Brodie; Aniekan Owen; Julian Kolb; Michael Buehl; Amit Kumar | Catalysis; Organometallic Chemistry; Polymer Science; Homogeneous Catalysis; Polymerization (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6410baaab5d5dbe9e84177f8/original/synthesis-of-polyethyleneimines-from-the-manganese-catalyzed-coupling-of-ethylene-glycol-and-ethylenediamine.pdf |
64668855f2112b41e9c54298 | 10.26434/chemrxiv-2022-cdl0z-v2 | Switching nitrofurantoin polymorphic outcome in solvent mediated phase transformation and crystallization using solvent and additives | We demonstrate that several additives and solvents allow switching the polymorphic outcome of solvent mediated phase transformation experiments and crystallization of the antibacterial drug nitrofurantoin. Polymorph β is obtained from most of the solvents, whereas selection of alcohols as solvents or use of crystallization additives provides formation of polymorph α. We also demonstrate that this can be linked to reversed apparent relative solubility of nitrofurantoin polymorphs in these solvents or in presence of the respective additives. We propose that this could be caused by different surface-additive and surface-solvent interactions formed by each of the nitrofurantoin polymorphs, which would change the relative surface energy of polymorphs. | Agris Bērziņš; Aija Trimdale-Deksne; Sergey Belyakov; Joop H. ter Horst | Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64668855f2112b41e9c54298/original/switching-nitrofurantoin-polymorphic-outcome-in-solvent-mediated-phase-transformation-and-crystallization-using-solvent-and-additives.pdf |
65f8527266c13817293ec803 | 10.26434/chemrxiv-2024-qkjr8 | Structural, Ionic, and Electronic Properties of Solid-State Phthalimide-Containing Polymers for All-Organic Batteries | Redox-active polymers serving as the active materials in solid-state electrodes offer a promising path towards realizing all-organic batteries. While both cathodic and an- odic redox-active polymers are needed, the diversity of the available anodic materials is limited. Here, we predict solid-state structural, ionic, and electronic properties of anodic, phthalimide-containing polymers using a multiscale approach that combines atomistic molecular dynamics, electronic structure calculations, and machine learning surrogate models. Importantly, by combining information from each of these scales, we are able to bridge the gap between bottom-up molecular characteristics and macro- scopic properties such as apparent diffusion coefficients of electron transport ($D_{app}$). We investigate the impact of different polymer backbones and of two critical factors during battery operation: state of charge and polymer swelling. Our findings reveal that the state of charge significantly influences solid-state packing and the thermophys- ical properties of the polymers, which, in turn, affect ionic and electronic transport. A combination of molecular-level properties (such as the reorganization energy) and condensed-phase properties (such as effective electron hopping distances) determine the predicted ranking of electron transport capabilities of the polymers. We predict Dapp for the phthalimide-based polymers and for a reference nitroxide radical-based polymer, finding a three orders of magnitude increase in $D_{app}$ ($\approx 10^{−6}$ cm$^2$ s$^{−1}$) with respect to the reference. This study underscores the promise of phthalimide-containing polymers as highly capable redox-active polymers for anodic materials in all-organic batteries, due to their exceptional predicted electron transport capabilities. | Riccardo Alessandri; Cheng-Han Li; Sheila Keating; Khirabdhi T. Mohanty; Aaron Peng; Jodie L. Lutkenhaus; Stuart J. Rowan; Daniel P. Tabor; Juan J. de Pablo | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Machine Learning; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f8527266c13817293ec803/original/structural-ionic-and-electronic-properties-of-solid-state-phthalimide-containing-polymers-for-all-organic-batteries.pdf |
67ac52806dde43c90888b669 | 10.26434/chemrxiv-2025-8dblf-v2 | Development of Ethyl Hydrazide-Based Selective Histone Deacetylase 6 (HDAC6) PROTACs | Histone deacetylases (HDACs) are promising targets for epigenetic drug discovery. Additionally, targeted degradation of HDACs has emerged as a novel approach in medicinal chemistry and chemical biology. However, most inhibitors and degraders rely on the potentially genotoxic hydroxamate as a zinc-binding group (ZBG). In this study, we present the development of HDAC6-directed proteolysis-targeting chimeras (PROTACs) featuring an ethyl hydrazide moiety as an alternative ZBG. This approach avoids the genotoxicity concerns of hydroxamates while maintaining potent HDAC6 degradation. We synthesized a series of CRBN- and VHL-recruiting PROTACs and identified several potent HDAC6 degraders (HDAC6 Dmax > 80%). Among these, 17c was the most effective, achieving an HDAC6 degradation of 91% and a DC50 value of 14 nM. Further characterization proved that 17c acts via the ubiquitin-proteasome system and chemoproteomics confirmed selective HDAC6 degradation over other HDAC isoforms. | Daniel Stopper; Irina Honin; Felix Feller; Finn Kristian Hansen | Biological and Medicinal Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ac52806dde43c90888b669/original/development-of-ethyl-hydrazide-based-selective-histone-deacetylase-6-hdac6-prota-cs.pdf |
639122d504bc6649580bf8cf | 10.26434/chemrxiv-2022-n0mjp | Reducing Exact Two-Component Theory for NMR Couplings to a One-Component Approach: Efficiency and Accuracy | The self-consistent and complex spin-orbit exact two component (X2C) formalism for NMR spin-spin coupling constants [J. Chem. Theory Comput. 17, 3974-3994 (2021)] is reduced to a scalar one-component ansatz. This way, the first-order response term can be partitioned into the Fermi-contact (FC) and spin-dipole (SD) interactions as well as the paramagnetic spin-orbit (PSO) contribution. The FC+SD terms are real and symmetric, while the PSO term is purely imaginary and antisymmetric. The relativistic one-component approach is combined with a modern density functional treatment up to local hybrid functionals including the response of the current density. Computational demands are reduced by factors of 8-24 as shown for a
large tin compound consisting of 137 atoms. Limitations of the current ansatz are critically assessed, i.e. the one-component treatment is not sufficient for tin compounds featuring a few heavy halogen atoms. | Yannick J. Franzke | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639122d504bc6649580bf8cf/original/reducing-exact-two-component-theory-for-nmr-couplings-to-a-one-component-approach-efficiency-and-accuracy.pdf |
64b2d1e0ae3d1a7b0dc2d056 | 10.26434/chemrxiv-2023-t39wm | Exploring reproducible non-aqueous scanning droplet cell electrochemistry in model battery chemistries | The discovery and optimization of new materials for energy storage is essential for a sustainable future. High-throughput experimentation (HTE) using a scanning droplet cell (SDC) is suitable for the rapid screening of prospective material candidates and effective variation of investigated parameters over a millimeter-scale area. Herein, we explore the transition and challenges for SDC electrochemistry from aqueous towards aprotic electrolytes and address pitfalls related to reproducibility in such high-throughput systems. Specifically, we explore whether comparable reproducibilities are achievable on the millimeter half-cell level than for full cells. To study reproducibility in half-cells as a first screening step this study explores the selection of appropriate cell components, such as reference electrodes (REs) and the use of masking techniques for working electrodes (WEs) to achieve consistent wetted areas. Experimental results on a Li-Au model anode system show that SDC, coupled with a masking approach and subsequent optical microscopy, can mitigate issues related to electrolyte leakage and yields good reproducibility. The proposed methodologies and insights contribute to the advancement of high-throughput battery research, enabling the discovery and optimization of future battery materials with improved efficiency and efficacy. | Alexey Sanin; Helge Sören Stein | Materials Science; Analytical Chemistry; Energy; Electrochemical Analysis; High-throughput Screening | CC BY 4.0 | CHEMRXIV | 2023-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b2d1e0ae3d1a7b0dc2d056/original/exploring-reproducible-non-aqueous-scanning-droplet-cell-electrochemistry-in-model-battery-chemistries.pdf |
65de4ca59138d231612e3a80 | 10.26434/chemrxiv-2024-2zvl8 | A green approach for the synthesis of π conjugated phosphonium salts under visible-light irradiation using air as oxidant | We have developed a strategy for synthesizing π-conjugated phosphonium salts through visible-light-induced cyclization of aryl phosphines in the presence of air and protonic acid. The mechanism study revealed that this C−H bond activation/cyclization of aryl phosphine reaction was initiated from the homolysis of P-H bond of phosphonium salts, which is induced by visible light. This reaction is transition metal free, exhibits good chemo-selectivity and has a high atomic economy. | Mengna Wu; Mengyuan Zhu; Yinsheng Miao; Lili Wang; Zheng Duan | Organic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65de4ca59138d231612e3a80/original/a-green-approach-for-the-synthesis-of-conjugated-phosphonium-salts-under-visible-light-irradiation-using-air-as-oxidant.pdf |
60c757d34c8919576bad4aab | 10.26434/chemrxiv.14471244.v1 | Exponential Amplification Using Photoredox Autocatalysis | Exponential molecular amplification such as the polymerase chain reaction is a powerful tool that allows ultrasensitive biodetection. Here we report a new exponential amplification strategy based on photoredox autocatalysis,
where eosin Y, a photocatalyst, amplifies itself by activating a non-fluorescent eosin Y derivative (EYH2) under green light.
The deactivated photocatalyst is stable and rapidly activated under low intensity light, making the eosin Y amplification
suitable for resource-limited settings. Through steady-state kinetic studies and reaction modeling, we found that EYH2 is
either oxidized to eosin Y via one-electron oxidation by triplet eosin Y and subsequent 1e─/H+ transfer, or activated by
singlet oxygen with the risk of degradation. By reducing the rate of the EYH2 degradation, we successfully improved EYH2-
to-eosin Y recovery, achieving efficient autocatalytic eosin Y amplification. Additionally, to demonstrate its flexibility in
output signals, we coupled the eosin Y amplification with photo-induced chromogenic polymerization, enabling sensitive
visual detection of analytes. Finally, we applied the exponential amplification methods in developing bioassays for detection
of biomarkers including SARS-CoV-2 nucleocapsid protein, an antigen used in the diagnosis of COVID-19<br /> | Seunghyeon Kim; Alejandra Martinez Dibildox; Alan Aguirre-Soto; Hadley Sikes | Dyes and Chromophores; Organic Polymers; Polymerization catalysts; Biochemical Analysis; Reaction Engineering; Photocatalysis; Redox Catalysis; Chemical Kinetics; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757d34c8919576bad4aab/original/exponential-amplification-using-photoredox-autocatalysis.pdf |
6225e925daa4fb4328829135 | 10.26434/chemrxiv-2022-k4nbr | Unveiling the Structure-Activity Relationships at the Orthosteric Binding Site of P2X Ion Channels: The Route to Selectivity. | The orthosteric ATP-binding site of the P2X receptors is poorly understood. Only a few compounds were well characterized for their P2X receptor functional activity and subtype selectivity. This study represents the first fully functional characterization of various ATP derivatives combined with in silico studies to advance the understanding of SARs at the orthosteric binding sites of P2X receptors leading to the identification of several subtype-selective P2X receptor agonists and compounds with agonistic as well as antagonistic profiles. | Andreas Isaak; Clemens Dobelmann; Friederike Theresa Füsser; Katharina Sophie Erlitz; Oliver Koch; Anna Junker | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6225e925daa4fb4328829135/original/unveiling-the-structure-activity-relationships-at-the-orthosteric-binding-site-of-p2x-ion-channels-the-route-to-selectivity.pdf |
6774bb16fa469535b969c4f2 | 10.26434/chemrxiv-2025-z6zfd | Exploiting Transformer-Based Networks and Boosting Algorithms for Ultralow Compressible Boride Design | Ultralow compressible materials, which have high bulk modulus (K), are invaluable in extreme conditions due to their ability to undergo significant compression without structural failure. As large number of borides can be found with high K, this study develop a computational framework to scan the vast chemical space to identify the ultralow compressible borides. Transformer-based networks are helpful to generate new chemical compositions due to their self-attention mechanism, scalability, and ability to capture long-range dependencies. First, we developed a transformer-based network to generate new binary and ternary boride compositions based on the known boride compositions. Next, we trained a hybrid model based on AdaBoost and Gradient Boosting algorithms with mean absolute error (MAE) of 14.1 GPa to scan the high K borides. The CALYPSO code was used to find the possible structures for those materials. After predicting K for broad chemical domain, we found that Re-B and W-B systems are promising ultralow compressible materials. We then performed density functional theory (DFT) calculations to investigate the stability of high K materials. Our computations suggest that Re3B2, Re2B3, W5VB4, and Re5CrB4 materials exhibit K > 300 GPa with negative formation energy and energy-above-hull less than 40 meV. Those materials are mechanically and dynamically stable based on the elastic constant calculations and the phonon dispersion. | Edirisuriya Siriwardane; Rongzhi Dong; Jianjun Hu; Deniz Cakir | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6774bb16fa469535b969c4f2/original/exploiting-transformer-based-networks-and-boosting-algorithms-for-ultralow-compressible-boride-design.pdf |
621dcc80daa4fb84e37b773e | 10.26434/chemrxiv-2022-9nf2m | Stable acceptor-donor-acceptor type open-shell diradical with ultra-narrow bandgap and efficient photothermal conversion | It has been reported recently that open-shell diradical character could exist in narrow bandgap donor-acceptor (D-A) organic semiconductors in our previous work. The A-D-A type molecules play as important role in the organic electronic such as donors and acceptors (ITIC and Y6) in organic solar cells. However, their relatively poor chemical and photostability prevent their industrial application. In this work, we reported a stable A-D-A type open-shell diradical, named LY1-4Cl, by replacing the 2-(3-oxo-2,3-dihydro-1H-inden-1-yli-dene)malononitrile (IC)-series end group of typical closed-shell non-fullerene acceptor IT-4Cl. The new electron-withdrawing building block could give LY1-4Cl the redshift near-infrared (NIR) absorption, the smaller bandgap and highly enhanced photostability comparing with IT-4Cl. The open-shell diradical character of LY1-4Cl originates from the formation of quinoid diradical form. Moreover, benefiting from the broad NIR absorption and radical-promoted nonradiative transition, LY1-4Cl displayed high photothermal properties that an increasing temperature of 188℃ was recorded within 60 s under 808 nm laser irradiation of 0.8 W cm-2. This research provides a new strategy to design IC-free A-D-A type open-shell quinoid diradical with ultra-narrow bandgap, good photostability and efficient photothermal conversion. | Liang Weixuan; Wang Zejun; Huang Jiaxing; Tao XIngyang; Li Yuan | Organic Chemistry; Materials Science; Organic Synthesis and Reactions; Optical Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621dcc80daa4fb84e37b773e/original/stable-acceptor-donor-acceptor-type-open-shell-diradical-with-ultra-narrow-bandgap-and-efficient-photothermal-conversion.pdf |
60c74ceeee301c3b9ec7a186 | 10.26434/chemrxiv.12562391.v1 | Novel Multifunctional Porous Liquid Composite for Recyclable Sequestration, Storage and In-situ Catalytic Conversion of Carbon Dioxide | <div><b>Novel Multifunctional Porous Liquid Composite for Recyclable Sequestration, Storage and In-situ Catalytic Conversion of Carbon Dioxide</b> <br /></div><div><br /></div><div>Archita Bhattacharjee, Raj Kumar and Prof. K. P. Sharma* Department of Chemistry, IIT Bombay, Powai, India <br /></div><div>* E-mail: [email protected] <br /></div><div><br /></div><div>Keywords: Porous liquid composite, mesoporous liquid, hollow silica nanorods, CO<sub>2</sub> capture, CO<sub>2</sub> catalytic conversion<br /></div><div><br /></div><div>Abstract: Permanent pores combined with fluidity renders flow processability to porous liquids otherwise not seen in porous solids. Although, sequestration of different gases has recently been shown in porous liquids, there is still adearth of studies for deploying in-situ chemical reactionsto convert adsorbed gases into utility chemicals in this phase. Here, a facile method for the design and development of a new class of solvent-less porous liquid composite which, as shown for the first time, can catalyze the conversion of adsorbed gaseous molecules into industrially relevant product, is shown. The recyclable porous liquid composite comprising polymer-surfactant modified hollow silica nanorods and carbonic anhydrase enzyme not onlysequesters (5.5 ccg<sup>-1</sup> at 273 K and 1 atm) and stores CO<sub>2</sub>,but is also capable of driving an in-situ enzymatic reaction for hydration of CO<sub>2</sub> to HCO<sub>3</sub><sup>-</sup> ion, subsequently converting it CaCO<sub>3</sub> due to reaction with pre-dissolved Ca<sup>2+</sup>. Light and electron microscopy combined with x-ray diffraction reveals the nucleation and growth of calcite and aragonite crystals. Moreover, the liquid-like property of the porous composite material can be harnessed by executing the same reaction via diffusion ofcomplimentary Ca<sup>2+</sup> and HCO<sub>3</sub><sup>-</sup> ions through different compartments separated by an interfacial channel.<br /></div><div></div> | Archita Bhattacharjee; Raj Kumar; KAMENDRA SHARMA | Nanostructured Materials - Materials | CC BY NC 4.0 | CHEMRXIV | 2020-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ceeee301c3b9ec7a186/original/novel-multifunctional-porous-liquid-composite-for-recyclable-sequestration-storage-and-in-situ-catalytic-conversion-of-carbon-dioxide.pdf |
615022a218be85a62530b445 | 10.26434/chemrxiv-2021-ft2zr | Molecular Rotor based on an Oxidized Resorcinarene | Molecular single stator-double rotor activity of an oxidized resorcinarene (fuchsonarene) macrocycle containing unsaturated hemiquinonoid groups at its meso positions was investigated. Fuchsonarenes containing two hemiquinonoid substituents at diagonally-opposed meso-positions with two electron rich phenol groups at the remaining meso-positions between the hemiquinonoid groups. All meso-substituents are in proximity at one side of the resorcinarene macrocycle (so-called rccc-type isomer) with rotational activity of the phenol meso-substituents. Rotation rates of the phenol moieties can be controlled by varying temperature, solvent polarity and acidity of the medium of study with rotation being thermally activated in neutral and acidic media and tunable in the range from 2 s-1 to 20,000 s-1. Experimental and computational data indicate that rotation of the mobile phenol meso-substituents is remotely affected by interactions with acidic solvents at the carbonyl C=O groups of macrocyclic acetyloxy groups, which occurs with the emergence of a lower energy electronic absorption band whose intensity is correlated with both the acidity of the medium and the rotation rate of the phenol substituents. Time-dependent DFT calculations suggest that the low energy band is due to a molecular conformational adjustment affecting electronic conjugation caused by strong interaction of macrocyclic acetyloxy carbonyl groups with the acid medium. The work presents a molecular mechanical model for estimating solution acidity and also gives insight into a possible method for modulating rotor activity in molecular machines. | Daniel T. Payne; Jan Labuta; Zdenĕk Futera; Václav Březina; Lenka Hanyková; Mandeep K. Chahal; Jonathan P. Hill | Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615022a218be85a62530b445/original/molecular-rotor-based-on-an-oxidized-resorcinarene.pdf |
647a1d42be16ad5c575bc2ca | 10.26434/chemrxiv-2023-8c62c | Improved Environmental Chemistry Property Prediction of Molecules with Graph Machine Learning | Rapid prediction of environmental chemistry properties is critical towards the green and sustainable development of chemical industry and drug discovery. Machine learning methods can be applied to learn the relations between chemical structures and their environmental impact. Graph machine learning, by learning the representations directly from molecular graphs, may enable better predictive power than conventional feature-based models. In this work, we leveraged graph neural networks to predict environmental chemistry properties of molecules. To systematically evaluate the model performance, we selected a representative list of datasets, ranging from solubility to reactivity, and compare directly to commonly used methods. We found that the graph model achieved near state-of-the-art accuracy for all tasks and, for several, improved the accuracy by a large margin over conventional models that rely on human-designed chemical features. This demonstrates that graph machine learning can be a powerful tool to do representation learning for environmental chemistry. Further, we compared the data efficiency of conventional feature-based models and graph neural networks, providing guidance for model selection dependent on the size of datasets and feature requirements. | Shang Zhu; Bichlien H. Nguyen; Yingce Xia; Kali Frost; Shufang Xie; Venkatasubramanian Viswanathan; Jake A. Smith | Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647a1d42be16ad5c575bc2ca/original/improved-environmental-chemistry-property-prediction-of-molecules-with-graph-machine-learning.pdf |
6706aa6412ff75c3a1f8d67b | 10.26434/chemrxiv-2024-gnhn7 | Molecule/quantum dot orbital hybridisation harnesses endothermic singlet exciton fission | Singlet exciton fission (SF) is one of the limited options for exceeding the theoretical limit of solar energy utilisation, the so-called Shockley–Queisser limit. Thus, improving endothermic SF efficiency will significantly contribute to the efficient utilisation of solar energy beyond the existing technology. In this regard, combining SF molecules with quantum dots (QDs) has achieved excellent results. However, the factors underlying the enhanced SF efficiency remain poorly understood. Herein, we discovered that inter-material orbital hybridisation between SF molecules and QDs harnesses endothermic SF. Theoretical calculations and transient absorption measurements of tetracene (Tc)–CdX (X = Te, Se, S) QD composites showed that multiple orbital hybrid levels formed by orbital hybridisation act as intermediate levels to facilitate SF. This result sheds light on alternative factors affecting SF efficiency beyond the molecular packing of SF molecules on the QD surface. The synergy effect on the zero-dimensional molecular assembly on QDs will provide guidance for the development of organic-inorganic hybrid solar cells, which overcome the Shockley–Queisser limit. | Jie Zhang; Hayato Sakai; Katsuaki Suzuki; Ramsha Khan; Taku Hasobe; I-Ya Chang ; Kim Hyeon-Deuk; Hironori Kaji; Masanori Sakamoto | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Photochemistry (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6706aa6412ff75c3a1f8d67b/original/molecule-quantum-dot-orbital-hybridisation-harnesses-endothermic-singlet-exciton-fission.pdf |
60c74689ee301c1a5ec79553 | 10.26434/chemrxiv.11348051.v1 | CO2 Solubility in Organophosphate Physical Solvents Wherein Alkyl Groups Are Replaced with Poly(Ethylene Glycol) Groups | Previous success in improving the CO2 capacity of physical solvents for pre-combustion carbon capture by imparting poly(ethylene glycol) (PEG) functionality led us to compare tributyl phosphate (TBP), tri-isobutyl phosphate (TiBP) and three analogous organophosphate solvents in which the length of PEG-substitution was varied. The PEG-substituted solvents proved to have acceptable densities and viscosities for the application of interest, but all three solvents showed poorer CO2 absorption than TBP or TiBP. Inclusion of hydrophilic PEG groups in solvents (1) – (3) also led to the undesired absorption of larger amounts of water from humidified N2 compared to TBP and TiBP. Computational studies of the analogous organophosphate solvents revealed that all solvents had the lowest partial negative charges, closest CO2 interaction, and largest CO2 interaction energy at the double bonded phosphoryl O atom. The fractional free volumes were computed and was found to be largest for TiBP and grew progressively smaller as the length of the PEG group grew longer in solvents (1) – (3). Although introducing PEG groups to these molecules increased the number of interaction sites with CO2, solvents (1) – (3) showed poorer CO2 absorption than TBP and TiBP due to their decreased solvent fractional free volume. | Robert Thompson; Jeffrey T. Culp; Surya Prakash Tiwari; Wei Shi; Nicholas Siefert; David P. Hopkinson | Fuels - Energy Science | CC BY 4.0 | CHEMRXIV | 2019-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74689ee301c1a5ec79553/original/co2-solubility-in-organophosphate-physical-solvents-wherein-alkyl-groups-are-replaced-with-poly-ethylene-glycol-groups.pdf |
674ab142f9980725cf8fb45a | 10.26434/chemrxiv-2024-xqjj1 | Molecular All-Mortise-and-Tenon Frameworks towards Luban Lock | Stacking interactions between molecules are central to the field of crystalline molecular materials. To precisely investigate the impact of structural variations on their properties, the most rational approach involves controlling the stacking of molecules with diverse substituents in an identical geometric configuration. However, this idealized scenario encounters formidable obstacles in practical synthesis. Thus, a central question revolves around the feasibility of discovering novel non-covalent or non-coordinated interactions that possess fixed connection modes, maintaining the directional assembly of molecules into identical geometric configurations. Inspired by the traditional wooden mortise and tenon structure, which combines the features of directional precision allowing for intricate wooden pieces to intertwine seamlessly and forming connections that endure rigorous use, we report the first series of crystalline and stable molecular frameworks entirely constructed by mortise-and-tenon joints (MTF-1, MTF-2, and MTF-3). Despite functional group diversity, the supramolecular assembly of MTFs remains unchanged, demonstrating their robust capability for directed assembly. A surprising revelation emerged: the ethyl groups imparted a more intricate and intriguing mortise-and-tenon joint to MTF-3. Since the ethyl groups are not coplanar with the benzene groups, they effectively introduce additional "tenons" to MTF-3. Consequently, the ethyl groups on type II mortise-and-tenon joints act as "locking pins", preventing the easy disengagement of type I mortise-and-tenon joints. This intricate structure endows MTF-3 with a fascinating Luban lock-like construction and exceptional mechanical stiffness. Additionally, ethyl groups in MTF-3 enhance intermolecular interactions, facilitating the separation and transport of photogenerated charge carriers. Ultimately, MTF-3 demonstrates superior photocatalytic H2O2 activity compared to its counterpart, MTF-2 and MTF-1. This groundbreaking discovery pioneers the molecular all mortise-and-tenon frameworks, vastly enriching the crystalline molecular material portfolio. | Xi Fan; Yifan Wu; Shengchang Xiang; Zhangjing Zhang; Jian Zhang | Inorganic Chemistry; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674ab142f9980725cf8fb45a/original/molecular-all-mortise-and-tenon-frameworks-towards-luban-lock.pdf |
60c75728567dfe294dec661b | 10.26434/chemrxiv.14376866.v1 | Biosynthetic Crossover of 5-Lipoxygenase and Cyclooxygenase-2 Yields 5-Hydroxy-PGE2 and 5-Hydroxy-PGD2 | <p>Biosynthetic crossover of 5-lipoxygenase (5-LOX) and
cyclooxygenase-2 (COX-2) enzymatic activities is a productive pathway to convert
arachidonic acid into unique eicosanoids. Here we show that COX-2 catalysis
with 5-LOX derived 5-hydroxy-eicosatetraenoic acid yields the endoperoxide
5-hydroxy-PGH<sub>2</sub> that spontaneously rearranges to 5-OH-PGE<sub>2</sub>
and 5-OH-PGD<sub>2</sub>, the 5-hydroxy analogs of arachidonic acid derived PGE<sub>2</sub>
and PGD<sub>2</sub>. The endoperoxide was identified via its predicted degradation
product, 5,12-dihydroxy-heptadecatri-6<i>E</i>,8<i>E</i>,10<i>E</i>-enoic
acid, and by SnCl<sub>2</sub>-mediated reduction to 5-OH-PGF<sub>2</sub><sub>a</sub>.
Both 5-OH-PGE<sub>2</sub> and 5-OH-PGD<sub>2</sub> were unstable and degraded rapidly
upon treatment with weak base. The instability hampered detection in biologic
samples which was overcome by in situ reduction using NaBH<sub>4</sub> to yield
the corresponding stable 5-OH-PGF<sub>2</sub> diastereomers and enabled
detection of 5-OH-PGF<sub>2</sub><sub>a</sub> in activated primary
human leukocytes. 5-OH-PGE<sub>2</sub> and 5-OH-PGD<sub>2</sub> were unable to
activate EP and DP prostanoid receptors suggesting their bioactivity is
distinct from PGE<sub>2</sub> and PGD<sub>2</sub>. </p> | Fumie Nakashima; Takashi Suzuki; Odaine
N. Gordon; Dominic Golding; Toshiaki Okuno; Juan Antonio Gimenez-Bastida; Takehiko Yokomizo; Claus Schneider | Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75728567dfe294dec661b/original/biosynthetic-crossover-of-5-lipoxygenase-and-cyclooxygenase-2-yields-5-hydroxy-pge2-and-5-hydroxy-pgd2.pdf |
623b979113d4780d4199ba6d | 10.26434/chemrxiv-2022-cwmkk | Synthesis and styrene copolymerization of novel bromo, chloro, and fluoro ring-substituted isobutyl phenylcyanoacrylates | Novel bromo, chloro, and fluoro ring-substituted isobutyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2CH(CH3)2 , where R is 5-bromo-2,4-dimethoxy, 2-bromo-3-hydroxy-4-methoxy, 3-chloro-2,6-difluoro, 4-chloro-2,6-difluoro, 2,3,5-trichloro, 2,3,6-trichloro, 2,3,4-trifluoro, 2,3,5-trifluoro, 2,4,5-trifluoro, 2,4,6-trifluoro, 3,4,5-trifluoro, 2,3,5,6-tetrafluoro, 2,3,4,5,6-pentafluoro were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-substituted benzaldehydes and isobutyl cyanoacetate and characterized by CHN analysis, IR, 1H and 13C NMR. The acrylates were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis. | Gabrielle Escalante; Victoria Escalante; Amanda A. Hartoun; Cynhia B. Hsu; Yousef A. Ibrahim; Will R. Jones; Charles Y. Jun; Madeleine M. Karpiuk; Eghe S. Obaseki; Phillip A. Osak; Jessica R. Schwartzwald; Ryan W. Sloan; Sara M. Rocus; William Schjerven; Gregory B. Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623b979113d4780d4199ba6d/original/synthesis-and-styrene-copolymerization-of-novel-bromo-chloro-and-fluoro-ring-substituted-isobutyl-phenylcyanoacrylates.pdf |
662fce9e21291e5d1d07dea8 | 10.26434/chemrxiv-2024-cpspw | Cooperative Phosphine-Photoredox Catalysis Enables N–H Activation of Azoles for Intermolecular Olefin Hydroamination | Catalytic intermolecular olefin hydroamination is an enabling synthetic strategy that offers direct and atom-economical access to a variety of nitrogen-containing compounds from abundant feedstocks. However, despite numerous advances in catalyst design and reaction development, hydroamination of N–H azoles with unactivated olefins remains an unsolved problem in synthesis. We report a dual phosphine and photoredox catalytic protocol for the hydroamination of numerous structurally diverse and medicinally relevant N–H azoles with unactivated olefins. Hydroamination proceeds with high anti-Markovnikov regioselectivity and N-site selectivity. The mild conditions and high functional group tolerance of the reaction permit the rapid construction of molecular complexity and late-stage functionalization of bioactive compounds. N–H bond activation is proposed to proceed via polar addition of the N–H heterocycle to a phosphine radical cation, followed by P–N α-scission from a phosphoranyl radical intermediate. Reac-tivity and N-site selectivity are classified by heterocycle N–H BDFE and nitrogen-centered radical (NCR) spin density, respectively, which can serve as a useful predictive aid in extending the reaction to unseen azoles. | Kassandra Sedillo; Flora Fan; Robert Knowles; Abigail Doyle | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662fce9e21291e5d1d07dea8/original/cooperative-phosphine-photoredox-catalysis-enables-n-h-activation-of-azoles-for-intermolecular-olefin-hydroamination.pdf |
61832f7e9b583aba02ead00f | 10.26434/chemrxiv-2021-dvnlb | Asymmetric Addition of Allylsilanes to Aldehydes – A Cr/Photoredox Dual Catalytic Approach Complementing the Hosomi–Sakurai Reaction | The allylation of aldehydes is a fundamental transformation in synthetic organic chemistry. Among the multitude of available reagents, especially allylsilanes have been established as preferred allyl source. As initially reported by Hosomi & Sakurai, these non-toxic and highly stable reagents add to carbonyls via an open transition state upon Lewis acid activation.
Herein, we report a general strategy to access a variety of valuable homoallylic alcohols in opposite chemo- and diastereoselectivity to the established Hosomi–Sakurai conditions by switching to photocatalytic activation in combination with a closed transition state (Chromium catalysis). Moreover, this dual catalytic approach displays a straightforward way to introduce excellent levels of enantioselectivity and its mild conditions allow for a broad substrate scope including chiral boron-substituted products as a highlight.
To emphasize the synthetic utility, our method was applied as the key step in the synthesis of a bioactive compound and in the late-stage functionalization of steroid derivatives. Detailed mechanistic studies and DFT calculations hint towards an unprecedented photo-initiated chain being operative.
| Felix Schäfers; Subhabrata Dutta; Roman Kleinmans; Christian Mück-Lichtenfeld; Frank Glorius | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61832f7e9b583aba02ead00f/original/asymmetric-addition-of-allylsilanes-to-aldehydes-a-cr-photoredox-dual-catalytic-approach-complementing-the-hosomi-sakurai-reaction.pdf |
65b5110f9138d23161dc0ea2 | 10.26434/chemrxiv-2024-p3dx2 | Exploring Regioselectivity and Stereoselectivity via GC Analysis of the Product of the Hydroboration-Oxidation of 1-Methylcyclohexene | Hydroboration-Oxidation reaction is both regioselective and diastereoselective. It is regioselective because it places the alcohol at the anti-Markovnikov position, and it is diastereoselective because the reaction proceeds via syn-addition of the -H and -OH groups across the two alkene carbons. By the hydroboration/oxidation of 1-methylcyclohexene and analyzing the product using an appropriate chiral gas chromatographic method, students were able to determine the ratio of Markovnikov to anti-Markovnikov products and also calculate the ratio of trans diastereomer to cis diastereomer, thus confirming the regioselectivity and stereoselectivity of the reaction. The GC provided an additional visual experience towards understanding the concepts. | Annaliese Franklin; Barnabas Otoo | Chemical Education | CC BY 4.0 | CHEMRXIV | 2024-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b5110f9138d23161dc0ea2/original/exploring-regioselectivity-and-stereoselectivity-via-gc-analysis-of-the-product-of-the-hydroboration-oxidation-of-1-methylcyclohexene.pdf |
618911367a002152604aea34 | 10.26434/chemrxiv-2021-5c1cs | Boosting the in situ encapsulation of proteins with MIL-100(Fe): the role of strong Lewis
acid centers | Encapsulation of biomolecules using Metal-Organic Frameworks (MOFs) to form stable
biocomposites has been demonstrated a valuable strategy for their preservation and controlled
release, which has been however restricted to specific electrostatic surface conditions. We
present a general in situ strategy that promotes the spontaneous MOF growth onto a broad
variety of proteins, for the first time, regardless of their surface nature. We demonstrate that
MOFs based on cations exhibiting considerable inherent acidity such as MIL-100(Fe) enable
biomolecule encapsulation, including alkaline proteins previously inaccesible by the welldeveloped
in situ encapsulation with azolate-based MOFs. In particular, MIL-100(Fe)
scaffold permits effective encapsulation of proteins with very distinct surface nature, retaining
their activity and allowing triggered release under biocompatible conditions. This general
strategy will enable an ample use of biomolecules in desired biolotechnological applications. | Jesús Cases; Mónica Giménez-Marqués | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618911367a002152604aea34/original/boosting-the-in-situ-encapsulation-of-proteins-with-mil-100-fe-the-role-of-strong-lewis-acid-centers.pdf |
60c7422aee301cd4c0c78dd5 | 10.26434/chemrxiv.8224292.v1 | Time Dependent Density Functional Theory Calculations of 4-Thiothymidine-containing DNA Dinucleotides | Preliminary research report.<br /> | Dawn Luong; Luis A. Ortiz-Rodríguez; Carlos Crespo-Hernández | Theory - Computational; Biophysical Chemistry; Photochemistry (Physical Chem.); Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7422aee301cd4c0c78dd5/original/time-dependent-density-functional-theory-calculations-of-4-thiothymidine-containing-dna-dinucleotides.pdf |
66a94baec9c6a5c07a8a1487 | 10.26434/chemrxiv-2024-mlczt | A Streamlined Workflow for Microscopy-Driven MALDI Imaging Mass Spectrometry Data Collection | Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a rapidly advancing technology for biomedical research. As spatial resolution increases, however, so does acquisition time, file size, and experimental cost, which increases the need to perform precise sampling of targeted tissue regions to optimize the biological information gleaned from an experiment and minimize wasted resources. The ability to define instrument measurement regions based on key tissue features and automatically sample these specific regions of interest (ROIs) addresses this challenge. Herein, we demonstrate a workflow using standard software that allows for direct sampling of microscopy-defined regions by MALDI IMS. Three case studies were included, highlighting different methods for defining features from common sample types – manual annotation of vasculature in human brain tissue, automated segmentation of renal functional tissue units across whole slide images using custom segmentation algorithms, and automated segmentation of dispersed HeLa cells using open-source software. Each case minimizes data acquisition from unnecessary sample regions and dramatically increases throughput while uncovering molecular heterogeneity within targeted ROIs. This workflow provides an approachable method for spatially targeted MALDI IMS driven by microscopy as part of multimodal molecular imaging studies. | Allison B. Esselman; Megan S. Ward; Cody R. Marshall; Ellie L. Pingry; Martin Dufresne; Melissa A. Farrow; Matthew Schrag; Jeffrey M. Spraggins | Analytical Chemistry; Imaging; Mass Spectrometry; Microscopy | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a94baec9c6a5c07a8a1487/original/a-streamlined-workflow-for-microscopy-driven-maldi-imaging-mass-spectrometry-data-collection.pdf |
66e020b412ff75c3a1efa02f | 10.26434/chemrxiv-2024-xdp9p | Excited-State Reaction Dynamics of the Radical Anions Revealed by the Novel Time-Resolved Photofragment Depletion Spectroscopy | Excited-state reaction dynamics of the radical anions have been investigated by a newly-developed time-resolved photofragment depletion (TRPD) spectroscopy where the different photodetachment cross-sections of the various anionic species during the reaction process were utilized to unravel their overall temporal evolutions. The otherwise formidable interrogation of the excited-state reaction dynamics of the radical anions, primarily due to the fact that their excited-states are often located above the electron detachment threshold, could be realized here. The shape of the excited-state potential energy surface of I2- has been clearly manifested in the TRPD transients taken at several different probe wavelengths, whereas the ultrafast internal conversion from the optically-excited nonvalence-bound state into the ground or excited valence-bound states of CH3NO2- or (CH3NO2)2-, which is followed by the fast chemical bond dissociation or the rather slow cluster decomposition, has been experimentally investigated for the first time to uncover the overall mechanism of the electron transfer dynamics among different (non)valence orbitals. | Sejun An; Sang Kyu Kim | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e020b412ff75c3a1efa02f/original/excited-state-reaction-dynamics-of-the-radical-anions-revealed-by-the-novel-time-resolved-photofragment-depletion-spectroscopy.pdf |
60c74234702a9bab2118a3ee | 10.26434/chemrxiv.7251686.v3 | The fate of altertoxin II during tomato processing steps at a laboratory scale | The emerging <i>Alternaria </i>mycotoxin altertoxin II demonstrated substantial genotoxicity <i>in vitro</i>. Ubiquitous <i>Alternaria ssp</i>. frequently infest various agricultural crops, leading to economic losses and also potential food safety issues caused by associated mycotoxin contaminations. Due to the lack of commercially available reference standards, data on the general chemical behavior, the occurrence and the biological/toxicological effects of altertoxin II are scarce. Since tomatoes are particularly prone to <i>Alternaria </i>infestations, we simulated the storage and food processing of intact tomatoes and purees after altertoxin II-addition. We observed significant decrease in altertoxin II concentrations during storage at room temperature and particularly under thermal stress, by employing a validated LC-MS/MS method. Moreover, the reduction to the compound’s epoxide group to the alcohol, i.e. the formation of altertoxin I, was determined at considerable ratios in intact tomato fruits suggesting effective enzymatic xenobiotic metabolism.<br /> | Hannes Puntscher; Doris Marko; Benedikt Warth | Natural Products; Food; Plant Biology | CC BY NC 4.0 | CHEMRXIV | 2019-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74234702a9bab2118a3ee/original/the-fate-of-altertoxin-ii-during-tomato-processing-steps-at-a-laboratory-scale.pdf |
60c741d0842e65d905db1f82 | 10.26434/chemrxiv.8141789.v1 | Energy Threshold for Chiral Symmetry Breaking in Molecular Self-Replication | We have determined the energy required for symmetry breaking and chiral amplification in the Soai autocatalytic reaction. This work examines the likelihood that parity violation energy difference of enantiomers is implicated in the origin of chiral symmetry breaking and highlights the challenges inherent in a search for a prebiotically plausible version of Soai autocatalysis. | Neil Hawbaker; Donna Blackmond | Stereochemistry; Computational Chemistry and Modeling; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741d0842e65d905db1f82/original/energy-threshold-for-chiral-symmetry-breaking-in-molecular-self-replication.pdf |
650469e4b338ec988a869851 | 10.26434/chemrxiv-2023-jg9vn | Rapid building block-economic synthesis of long, multi-O-GalNAcylated MUC5AC tandem repeat peptides | The study of mucin function requires access to highly O-glycosylated peptides with multiple tandem repeats. Solid-phase synthesis would be a suitable method, however, the central problem in the synthesis of mucin glycopeptides is the need to use precious and potentially vulnerable glycoamino acid building blocks in excess. In this article, we report the development of a method based on SPPS and native chemical ligation/desulfurization chemistry that allows the rapid, reliable, and glyco-economical synthesis of long multi-O-GalNAcylated peptides. To facilitate access to the glycosyl donor required for the preparation of Fmoc-Ser/Thr(Ac3GalNAc)-OH we used an easily scalable azidophenylselenylation of galactal instead of azidonitration. The problem of low yield when coupling glycoamino acids in small excess was solved by carrying out the reactions in 2-MeTHF instead of DMF and using DIC/Oxyma. Remarkably, quantitative coupling was achieved within 10 minutes using only 1.5 equivalents of glycoamino acid. The method does not require (microwave) heating, thus avoiding side reactions such as acetyl transfer to the N-terminal amino acid. This method also improved the difficult coupling of glycoamino acid to the hydrazine-resin and furnished peptides carrying 10 GalNAc units in high purities (>95%) of crude products. Combined with a one-pot method involving native chemical ligation at a glycoamino acid junction and superfast desulfurization, the method yielded highly pure MUC5AC glycopeptides comprising 10 octapeptide tandem repeats with 20 -O-linked GalNAc residues within a week. | Arseniy Galashov; Ekaterina Kazakova; Christian Stieger; Christian Hackenberger; Oliver Seitz | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650469e4b338ec988a869851/original/rapid-building-block-economic-synthesis-of-long-multi-o-gal-n-acylated-muc5ac-tandem-repeat-peptides.pdf |
60c753a5702a9b113118c3c1 | 10.26434/chemrxiv.13368902.v2 | The Role of Methyl Groups in the Early Stage of Thermal Polymerization of Polycyclic Aromatic Hydrocarbons Revealed by Molecular Imaging | The initial thermal reactions of aromatic hydrocarbons are relevant to many industrial applications. However, tracking the growing number of heavy polycyclic aromatic hydrocarbon (PAH) products is extremely challenging because many reactions are unfolding in parallel from a mixture of molecules. Herein, we studied the reactions of 2,7-dimethylpyrene (DMPY) to decipher the roles of methyl substituents during mild thermal treatment. We found that the presence of methyl substituents is key for reducing the thermal severity required to initiate chemical reactions in natural molecular mixtures. A complex mixture of thermal products including monomers, dimers, and trimers were characterized by NMR, mass spectrometry and non-contact atomic force microscopy (nc-AFM). A wide range of structural transformations including methyl transfer and polymerization reactions were identified. A detailed mechanistic understanding was obtained on the roles of H radicals during the polymerization of polycyclic aromatic hydrocarbons. | Pengcheng Chen; Shadi Fatayer; Bruno Schuler; Jordan N. Metz; Leo Gross; Nan Yao; Yunlong Zhang | Carbon-based Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753a5702a9b113118c3c1/original/the-role-of-methyl-groups-in-the-early-stage-of-thermal-polymerization-of-polycyclic-aromatic-hydrocarbons-revealed-by-molecular-imaging.pdf |
650186beb6ab98a41c5e7070 | 10.26434/chemrxiv-2023-rpg9l | Deoxygenative Coupling of CO with a Tetrametallic Magnesium Hydride Complex
| Addition of CO to a tetrametallic magnesium hydride cluster results in both carbon–carbon bond formation and deoxygenation to generate an acetylaldehyde enolate [C2OH3]– which remains coordinated to the cluster. To the best of our knowledge, this is the first example of formation of an isolable complex containing an [C2OH3]– fragment from reaction of CO with a metal hydride, and the first example of CO homologation and deoxygenation at a main group metal. DFT studies suggest that key steps in the mechanism involve nucleophilic attack of an oxymethylene on a formyl ligand to generate an unstable [C2O2H3]3– fragment, which undergoes subsequent deoxygenation. | Wenbang Yang; Andrew White; Mark Crimmin | Inorganic Chemistry; Organometallic Chemistry; Bond Activation; Main Group Chemistry (Organomet.); Small Molecule Activation (Organomet.) | CC BY 4.0 | CHEMRXIV | 2023-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650186beb6ab98a41c5e7070/original/deoxygenative-coupling-of-co-with-a-tetrametallic-magnesium-hydride-complex.pdf |
6612e08491aefa6ce10c08e3 | 10.26434/chemrxiv-2024-z8725 | General Graph Neural Network Based Implicit Solvation Model for Organic Molecules in Water | The dynamical behavior of small molecules in their environment can be studied with molecular dynamics (MD) simulations to gain deeper insight on an atomic level and thus complement and rationalize the interpretation of experimental findings. Such approaches are of great value in various areas of research, e.g., in the development of new therapeutics. The accurate description of solvation effects in such simulations is thereby key and has in consequence been an active field of research since the introduction of MD. Until today the most accurate approaches involve computationally expensive explicit solvent simulations, while widely applied models using an implicit solvent description suffer from reduced accuracy. Recently, machine learning (ML) approaches that provide a probabilistic representation of solvation effects have been proposed as potential alternatives. However, the associated computational costs and minimal or lacking transferability used to render them unusable in practice. Here, we report the first example of a transferable ML-based implicit solvent model trained on a diverse set of 3’000’000 molecular structures that can be applied to organic small molecules for simulations in water. Extensive testing against reference calculations demonstrated that the model delivers on par accuracy with explicit solvent simulations while providing up to 18-fold increase in sampling rate. | Paul Katzberger; Sereina Riniker | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6612e08491aefa6ce10c08e3/original/general-graph-neural-network-based-implicit-solvation-model-for-organic-molecules-in-water.pdf |
65dad8bee9ebbb4db9300790 | 10.26434/chemrxiv-2024-vll5v-v2 | Accurate first-principles simulation for the response of 2D chemiresistive gas sensors | The realm of chemiresistive gas sensors has witnessed a notable surge in interest in two-dimensional (2D) materials. The advancement of high-performance 2D gas sensing materials necessitates a quantitative theoretical method capable of accurately predicting their response. In this context, we present our first-principles framework for calculating the response of 2D materials, incorporating both carrier concentration and mobility. We showcase our method by applying it to prototype NH3 sensing on 2D MoS2 and comparing the results with prior experiments in the literatures. Our approach offers a thorough solution for carrier concentration, taking into account the electronic structure around the Fermi level. In conjunction with the mobility calculation, this enables us, for the first time, to provide a quantitative prediction of the response profile and limit of detection (LOD), yielding a notably improved alignment with prior experimental findings. Further analysis quantifies the contributions of carrier concentration and mobility to the overall response of 2D MoS2 to NH3. We identify that discrepancies in the charge-transfer-based method primarily stem from overestimating carrier concentrations. Our method opens exciting opportunities to explore carrier mobility-dominated sensing materials, facilitates efficient screening of promising gas sensing materials, and quantitative understanding of the sensing mechanism. | Li Shuwei; Liang Zhang | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Theory - Computational; Thermodynamics (Physical Chem.); Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65dad8bee9ebbb4db9300790/original/accurate-first-principles-simulation-for-the-response-of-2d-chemiresistive-gas-sensors.pdf |
668d884101103d79c5841e05 | 10.26434/chemrxiv-2024-q2v5h | 31P NMR chemical shift anisotropy in paramagnetic lanthanide phosphide complexes | Lanthanide (Ln) magnetic resonance imaging and chiral shift reagents generally exploit 1H NMR shifts, as paramagnetic broadening tends to preclude the use of heavier, less sensitive nuclei. Here we report the solution and solid-state 31P NMR shifts of an isostructural series of distorted trigonal bipyramidal Ln(III) tris-silylphosphide complexes, [Ln{P(SiMe3)2}3(THF)2] (1-Ln; Ln = La, Ce, Pr, Nd, Sm); 1-Ln were also characterized by elemental analysis, single crystal and powder X-ray diffraction, multinuclear NMR, EPR, ATR-IR, and UV-Vis-NIR spectroscopy, and SQUID magnetometry. Breaking assumptions, we observed paramagnetically broadened 31P NMR spectra for the Ln-bound P atoms for the 1-Ln family; in solution, 1-Nd showed the most downfield chemical shift (δ{31P} = 2570.14 ppm) and 1-Sm the most upfield value (δ{31P} = –259.21 ppm). We determined the span of the chemical shift anisotropies (CSA) for solid 1-Ln using magic angle spinning NMR spectroscopy; the CSA was largest for 1-Pr (Ω{31P} ≈ 2000 ppm), consistent with a combination of paramagnetism and the relatively large differences in pyramidalization of the three P atoms in the solid-state. Density functional theory calculations for 1-La were in excellent agreement with the experimentally-determined 31P NMR parameters. We find good agreement of experimental 1H NMR chemical shifts with ab initio-calculated values for paramagnetic 1-Ln, whilst the shifts of heavier 13C, 29Si and 31P nuclei are not well-reproduced due to the current limitations of paramagnetic NMR calculations for nuclei with large contact shifts. | Jack Baldwin; Katherine Bonham; Toby Thompson; Gemma Gransbury; George Whitehead; Inigo Vitorica-Yrezabal; Daniel Lee; Nicholas Chilton; David Mills | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Magnetism; Spectroscopy (Inorg.) | CC BY 4.0 | CHEMRXIV | 2024-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668d884101103d79c5841e05/original/31p-nmr-chemical-shift-anisotropy-in-paramagnetic-lanthanide-phosphide-complexes.pdf |
60c7487fbb8c1a31053dac91 | 10.26434/chemrxiv.11848422.v2 | Multiplexed Online-Monitoring of Microfluidic Free-Flow Electrophoresis via Mass Spectrometry | Free-flow electrophoresis is
a tool for the continuous fractionation of electrically charged
analytes. In this study we introduce a novel method to couple
microchip-based free-flow electrophoresis with mass spectrometry. The
successive connection of multiple microchip outlets to the electrospray
ionization source of a mass spectrometer is automated using a
multiposition valve. With this novel setup it is possible to
continuously fractionate and collect compounds while simultaneously
monitoring the process online with mass spectrometry. The functionality
of the method is demonstrated by the successful separation and
identification of the biomolecules AMP, ATP and CoA, which are
fundamental for numerous biochemical processes in every organism. | Matthias Jender; Pedro Novo; Dominic Maehler; Ute Münchberg; Dirk Janasek; Erik Freier | Mass Spectrometry; Separation Science; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7487fbb8c1a31053dac91/original/multiplexed-online-monitoring-of-microfluidic-free-flow-electrophoresis-via-mass-spectrometry.pdf |
60c7453a702a9b36f818a98f | 10.26434/chemrxiv.9976913.v1 | In-Situ Formation of H-Bonding Imidazole Chains in Break-Junction Experiments | As a small molecule possessing both strong H-bond donor and acceptor functions, 1H-imidazole can participate in extensive homo- or heteromolecular H-bonding networks. These properties are important in Nature, as imidazole moieties are incorporated in many biologically-relevant compounds. Imidazole also finds applications ranging from corrosion inhibition to fire retardants and photography. We have found a peculiar behaviour of imidazole during scanning tunnelling microscopy-break junction (STM-BJ) experiments, in which oligomeric chains connect the two electrodes and allow efficient charge transport. We attributed this behaviour to the formation of hydrogen-bonding networks, as no evidence of such behaviour was found in 1-methylimidazole (incapable of participating in intramolecular hydrogen bonding). The results are supported by DFT calculations, which confirmed our hypothesis. These findings pave the road to the use of hydrogen-bonding networks for the fabrication of dynamic junctions based on supramolecular interactions. | Chuanli Wu; Aminah Alqahtani; Sara Sangtarash; Andrea Vezzoli; Hatef Sadeghi; Craig M. Robertson; Chenxin Cai; Colin Lambert; Simon Higgins; Richard Nichols | Physical Organic Chemistry; Nanodevices; Interfaces; Quantum Mechanics; Self-Assembly; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453a702a9b36f818a98f/original/in-situ-formation-of-h-bonding-imidazole-chains-in-break-junction-experiments.pdf |
61571ff4cc53d9264cb91815 | 10.26434/chemrxiv-2021-r9g8r | Conformation and supramolecular arrangement of 1,3:2,4-dibenzyli-dene-D-sorbitol in solution and in single crystals | The X-ray crystal structure of the gelator 1,3:2,4-dibenzylidene-D-sorbitol (DBS) is reported here. DBS is an important gelating molecule known for nearly 130 years, that has eluded crystallization until now. The crystal obtained presents an axial stacking of DBS molecules stabilized by both Van der Waals interactions and intermolecular hydrogen bonds of the side chain hydroxyl groups with either neighboring DBS or water molecules. The crystal structure shows definitive evidence for the frequently assumed “butterfly” type aggregation mode and experimentally proves the equatorial placement of the phenyl rings. The conformation of DBS has been analyzed in the crystal structure and compared with that determined in solution through NMR spectroscopy. | Fernán Berride; Victor M. Sánchez-Pedregal; Bruno Dacuña; Eurico Cabrita; Armando Navarro-Vázquez; Richard G. Weiss; María Magdalena Cid | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61571ff4cc53d9264cb91815/original/conformation-and-supramolecular-arrangement-of-1-3-2-4-dibenzyli-dene-d-sorbitol-in-solution-and-in-single-crystals.pdf |
60c74ba1469df4f0e7f43f60 | 10.26434/chemrxiv.12366584.v1 | SARS-CoV-2 Main Protease: A Molecular Dynamic Study | We provide results from a molecular dynamics simulation of the SARS-CoV-2 main protease in the monomer and dimer states of the native enzyme and also bound to a peptide substrate.<br /> | Dimas Suárez; Natalia Díaz | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ba1469df4f0e7f43f60/original/sars-co-v-2-main-protease-a-molecular-dynamic-study.pdf |
654f3cacdbd7c8b54b0f4d49 | 10.26434/chemrxiv-2023-tf4gb | Design, Synthesis and Biological Evaluation of Chalcone Acetamide Derivatives against Triple Negative Breast Cancer | Breast Cancer (BC) incidence rates increased (0.5%) annually in recent decades with moderate mortality. Triple-negative breast cancer (TNBC) poses molecularly diversified tumor aggressiveness, heterogeneous illness, recurrence, and high risk of metastasis. TNBC patients have poor prognosis due to later-stage diagnosis and fewer treatment options than other subtypes. Chalcones are chemical scaffolds found in natural products, especially in plants, considered diverse and structurally privileged in medicinal chemistry for drug development. Herein, we designed and synthesized novel acetamide derivatives of chalcone to evaluate against TNBC, and characterized them using 1H NMR, 13C NMR, HRMS and IR spectroscopic methods. The derivatives were screened against human cancer cells for their cytotoxicity using SRB assay. Among the derivatives, 8h with the pyrrolidine group exhibited better cell growth inhibitor activity against both TNBC (MDA-MB-231 and MDA-MB-468) cells. SRB, Colony formation and fluorescent dye-based screening assays demonstrated that 8h significantly inhibited MDA-MB-231 cell proliferation. Furthermore, 8h promoted apoptosis via upregulation of the cellular reactive oxygen species (ROS) levels and loss of mitochondrial membrane potential. 8h increased the pro-apoptotic proteins (Bax and caspase-3) and Bax/Bcl-2 ratio, inhibiting the anti-apoptotic (Bcl-2) protein levels in TNBC cells. The above results suggest that 8h can promote cellular death through apoptotic mechanisms in TNBC cells, and this hypothesis confirms that chalcones can be designed with potential cytotoxicity against TNBC. | Puneet Kumar; Ruhi Singh; Deepak Sharma; Qazi Parvaiz Hassan; Boobalan Gopu; Jasha Momo H. Anal | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654f3cacdbd7c8b54b0f4d49/original/design-synthesis-and-biological-evaluation-of-chalcone-acetamide-derivatives-against-triple-negative-breast-cancer.pdf |
646689f6f2112b41e9c54e9b | 10.26434/chemrxiv-2023-qswf5-v2 | UV-Driven Self-Repair of Cyclobutane Pyrimidine Dimers in RNA | Nucleic acids can be damaged by ultraviolet (UV) irradiation, forming structural photolesions such as cyclobutane-pyrimidine-dimers (CPD). In modern organisms, sophisticated enzymes repair CPD lesions in DNA, but to our knowledge, no RNA-specific enzymes exist for CPD repair. Here, we show for the first time that RNA can protect itself from photole-sions by an intrinsic UV-induced self-repair mechanism. This mechanism, prior to this study, has exclusively been ob-served in DNA and is based on charge transfer from CPD-adjacent bases. In a comparative study, we determined the quantum yields of the self-repair of the CPD-containing RNA sequence, GAU=U to GAUU (0.23%), and DNA sequence, d(GAT=T) to d(GATT) (0.44%), upon 285 nm irradiation via UV / Vis spectroscopy and HPLC analysis. After several hours of irradiation, a maximum conversion yield of 16% for GAU=U and 33% for d(GAT=T) was reached. We examined the dynamics of the intermediate charge transfer (CT) state responsible for the self-repair with ultrafast UV pump – IR probe spectroscopy. In the dinucleotides GA and d(GA), we found comparable quantum yields of the CT state of ~50% and lifetimes on the order of several hundred picoseconds. Charge transfer in RNA strands might lead to reactions cur-rently not considered in RNA photochemistry and may help understanding RNA damage formation and repair in modern organisms and viruses. On the UV-rich surface of the early Earth, these self-stabilizing mechanisms likely affected the se-lection of the earliest nucleotide sequences from which the first organisms may have developed. | Sarah Crucilla; Dian Ding; Gabriella Lozano; Jack Szostak; Dimitar Sasselov; Corinna Kufner | Physical Chemistry; Biological and Medicinal Chemistry; Biochemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646689f6f2112b41e9c54e9b/original/uv-driven-self-repair-of-cyclobutane-pyrimidine-dimers-in-rna.pdf |
626834bdef2ade6f1a3e4493 | 10.26434/chemrxiv-2022-7m5vp | Understanding the effect of an amorphous surface on the ultrafast dynamics of a heterogeneous photoinduced reaction: CD3I photoinduced reaction on amorphous cerium oxide films | In this work, to understand how an amorphous surface influence the dynamics of surface photoinduced reactions, pump-probe spectroscopy in conjunction with mass spectrometry is employed to track the ultrafast evolution of intermediates and final products with time, mass, and energy resolution. As a model system, the photoinduced reaction of CD3I adsorbed on amorphous cerium oxide films is investigated. A fraction of the first intermediates produced on a freshly prepared surface are trapped to passivate the surface. After the A-band excitation, the minimum dissociation time of CD3I, indicate that CD3I adsorption geometries with either CD3 or I facing the gas-phase exist, however the transient data suggest that most molecules are adsorbed with the I atom facing the surface. CD3 and I are consumed to form I2 and reform CD3I, which are produced with a steady rate only after the intermediates are losing the excess translational energy released from photodissociation. | Md Afjal Khan Pathan; Aakash Gupta; Mihai E. Vaida | Physical Chemistry; Materials Science; Thin Films; Photochemistry (Physical Chem.); Surface | CC BY NC 4.0 | CHEMRXIV | 2022-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626834bdef2ade6f1a3e4493/original/understanding-the-effect-of-an-amorphous-surface-on-the-ultrafast-dynamics-of-a-heterogeneous-photoinduced-reaction-cd3i-photoinduced-reaction-on-amorphous-cerium-oxide-films.pdf |
6532792587198ede07e1b7c3 | 10.26434/chemrxiv-2022-x2cml-v2 | High Pressure Homogenization – An Update on its Usage and Understanding | Despite being a technology of several decades, high pressure homogenization (HPH) remains widely used in food and pharmaceutical industries, often as an essential unit operation in liquid product processing. Continual advances in the technology are made on multiple fronts, on equipment innovations by the manufacturers, new applications by users, and advances in process understanding by multidisciplinary scientists alongside subject matter experts amongst industry practitioners. While HPH is comparatively simple conceptually, the homogenization process involves complex engineering physics which is influenced by the varied processing conditions and highly diverse inputs with each use-case requiring its own treatment. The successful application of a HPH process indubitably requires practitioners to draw upon insights from multiple domains and the optimization for each case. Thus, this timely review aims to outline the more recent trends and advancements in HPH process understanding and novel applications involving HPH from both academic and industrial perspectives. | Pavan Inguva; Silvia Grasselli; Paul W.S. Heng | Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Industrial Manufacturing; Pharmaceutical Industry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6532792587198ede07e1b7c3/original/high-pressure-homogenization-an-update-on-its-usage-and-understanding.pdf |
62a3ab0d99b7831562fc154e | 10.26434/chemrxiv-2022-hcnfk | Computationally aided design of defect-appended aliphatic amines for CO2 activation within UiO-66 | We report CO2 adsorption and subsequent formation of carbamic acid within defective UiO-66 functionalised with aliphatic amines. Periodic Density Functional Theory (DFT) calculations confirm the activation of CO2 with the aliphatic amines and the mechanism followed to obtain the final carbamic acid, the key point in this process is the formation of hydrogen bonding between the aliphatic amines. | Gerard Pareras; Marco Taddei; Davide Tiana | Theoretical and Computational Chemistry; Inorganic Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a3ab0d99b7831562fc154e/original/computationally-aided-design-of-defect-appended-aliphatic-amines-for-co2-activation-within-ui-o-66.pdf |
66deae51cec5d6c14294404b | 10.26434/chemrxiv-2024-l65kd | Multiple Reaction Pathways for Oxygen Evolution as Key Factor for the Catalytic Activity of Nickel-Iron (Oxy)Hydroxides | We present the results of a comprehensive theoretical investigation, based on state-of-the-art density functional theory simulations, of the structural and electrochemical properties of amorphous pristine and iron-doped nickel-(oxy)hydroxide catalyst films for water oxidation in alkaline solution, hereafter referred to as NiCat and Fe:NiCat. In the case of the structural properties, our simulations accurately reproduce the structural changes occurring in locally ordered units, reported by X-ray absorption spectroscopy measurements when the catalyst films are activated by exposition to a positive potential. We have highlighted the crucial role in this process of a series of proton- coupled electron transfer events in the reversible oxidation of Ni(II) to Ni(III). Once assessed structural models of NiCat and Fe:NiCat in close agreement with experimental results, we used them to investigate the oxygen evolution reaction (OER) atomistic mechanism, activated when the applied potential exceeds the overpotential required to oxidize water and produce molecular oxygen. We have quantitatively compared seven different pathways for the OER enrolled on both the proposed families of reaction mechanisms, namely the adsorbate evolution mechanism (AEM) and the lattice-oxygen mediate mechanism (LOM), and we have rationalized the effect of iron in the huge enhancement of catalytic activity of Fe:NiCat with respect to NiCat. Regarding the competition between AEM and LOM mechanisms, our results support the idea that simple metal- oxygen-metal atomistic motifs, ubiquitous on the surface of all kinds of crystalline and amorphous metal (oxy)hydroxide catalyst films, are able to promote different mechanisms of both types, all compatible with the application of an external positive potential in the range of those used in real electrochemical devices performing the OER. Finally, our results suggest that the elusive role of iron is related to the significant difference between Ni(IV)-O and Fe(IV)-O bonds in two crucial reaction intermediates immediately preceding the formation of the O-O bond, with Fe ions able to lower the potential required to form such intermediates along most of the investigated reaction paths. | Giuseppe Mattioli; Leonardo Guidoni | Theoretical and Computational Chemistry; Catalysis; Energy; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66deae51cec5d6c14294404b/original/multiple-reaction-pathways-for-oxygen-evolution-as-key-factor-for-the-catalytic-activity-of-nickel-iron-oxy-hydroxides.pdf |
60c75186702a9bf97518bf72 | 10.26434/chemrxiv.13175207.v1 | In Silico Exploration of Efficacious Inhibitors for SARS-CoV-2’s Papain-like Protease | We applied the flexible docking method to rank-order all FDA-approved drugs as inhibitors for the papain-like protease (PLpro) of SRAS-CoV-2. We also evaluated these results using molecular dynamics (MD) simulations. From MD simulations, we unveiled the molecular mechanism for a known inhibitor rac5c's binding with PLpro. <br /> | Tien Huynh; Wendy Cornell; Binquan Luan | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75186702a9bf97518bf72/original/in-silico-exploration-of-efficacious-inhibitors-for-sars-co-v-2-s-papain-like-protease.pdf |
60c73d2bbdbb892891a37c0d | 10.26434/chemrxiv.5480422.v1 | Unexpected dimeric form of 17 - hydroxylupanine - MS and crystallographic studies | The bis-quinolizidine alkaloids such as sparteine, lupanine and their derivatives are produced by the plants of Leguminoseae family. 17-Hydroksylupanine can be obtained both: naturally (in reaction catalysed by enzyme) and synthetically. Our data demonstrate that 17-hydroxylupanine can exists in dimeric form. It is the first time that one of bisquinolisidine alkaloids exists in the dimeric form in a solid state. A structure of dimeric form was confirmed by EI MS mass spectra and X-ray analysis. | Joanna Kurek; Beata Jasiewicz; Anrdzej Katrusiak | Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2017-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d2bbdbb892891a37c0d/original/unexpected-dimeric-form-of-17-hydroxylupanine-ms-and-crystallographic-studies.pdf |
6415c1abaad2a62ca1f681b4 | 10.26434/chemrxiv-2023-7nsmz | Nature of Interactions between Boron Clusters: Extended Delocalization and Retention of Aromaticity post Oxidation | Polyhedral boron clusters are lauded as 3D-aromatic that frequently form interconnected periodic networks in boron-rich borides with metal and non-metals having high thermodynamic stability and hardness. This leads to the question of whether the spherical delocalization of electrons in these clusters is extended across the network as in organic aromatic networks. These borides also frequently show partial oxidation, having fewer electrons than that is mandated by electron counting rules, whose impact on their aromatic stability and geometry remains mysterious. Understanding the nature of electronic communication between polyhedra in polyhedral borides is largely unknown though it is crucial for the rational design of advanced materials with desirable mechanical, electronic and optical properties. Here we show that electronic delocalization across polyhedral clusters has a significant impact on their structure and stability. Our computational inquiry on closo borane dimers shows substantial variation in conjugation with the ideal electron count. Upon two-electron oxidation, instead of forming exohedral multiple bonding that disrupts the aromaticity, it undergoes subtle geometric transformations that conserve aromaticity. The nature of geometric transformation depends on the HOMO that is decided locally on the polyhedral degree of the interacting vertices. The prevalence of π-type interactions as HOMO in tetravalent vertices encourage conjugation across clusters and turn into a macropolyhedral system hosting a rhombic linkage between clusters upon oxidation. In contrast, the σ-type interactions dominate the HOMO of pentavalent vertices that prefers to confine aromaticity within the polyhedra by separating them with localized 3c-2e bonds. Our findings expose the fundamental bonding principles that govern the interaction between boron clusters and will provide chemical guidance for the design and analysis of polyhedral boride networks with desired properties. | SOHAIL HAMID DAR; Pattath D. Pancharatna; Musiri M. Balakrishnarajan | Theoretical and Computational Chemistry; Inorganic Chemistry; Bonding; Main Group Chemistry (Inorg.); Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6415c1abaad2a62ca1f681b4/original/nature-of-interactions-between-boron-clusters-extended-delocalization-and-retention-of-aromaticity-post-oxidation.pdf |
6423e1e962fecd2a839d9ef1 | 10.26434/chemrxiv-2023-v5gll | Bulk, one step generation of single-core double emulsions from polymer-osmose-induced aqueous phase separation in polar oil droplets | Double water-in-oil-in-water (W/O/W) emulsions are aqueous droplet(s) embedded within oil droplets dispersed in a continuous water phase. They are exploited for many applications from cosmetic to food science since both hydrosoluble and liposoluble cargos can be encapsulated within. They are generally prepared using a one-step or a two-step method, phase inversion and also via spontaneous emulsification. Here, we describe a general and simple one-step method based on hydrophilic polymers dispersed in polar oils to generate osmose-induced diffusion of water into oil droplets, forming polymer-rich aqueous droplet within. Polyethylene glycol (PEG), but also other hydrophilic polymers (branched polyethylene imine, bPEI, or polyvinyl pyrrolidone, PVPone) were successfully dispersed in 1-octanol or other polar oils (oleic acid or tributyrin) to produce an O/W emulsion that spontaneously transformed into a W1/O/W2 emulsion, with the inner aqueous droplet (W1) enriched with the hydrophilic polymer (PEG, bPEI or PVPone). Dispersion of hydrosoluble dyes in the oil/polymer mixture in the form of a W/O microemulsion further allowed their encapsulation within the internal W1 aqueous droplet of the double emulsion. Single drop experiments, as well as macroscopic viscosity measurements, confirm that the double emulsion is actually the result of water diffusion, which amplitude can be adjusted by the polymer concentration. Production of high internal phase emulsions (HIPE) was also achieved together with a pH-induced transition from multiple to single core double emulsion. We expect this new method for producing double emulsions to find applications in domains of microencapsulation and materials chemistry. | Jean-Paul Douliez; Arnaud Saint Jalmes | Materials Science; Chemical Engineering and Industrial Chemistry; Aggregates and Assemblies; Controlled-Release Systems; Core-Shell Materials; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6423e1e962fecd2a839d9ef1/original/bulk-one-step-generation-of-single-core-double-emulsions-from-polymer-osmose-induced-aqueous-phase-separation-in-polar-oil-droplets.pdf |
62d5748381efd03957b0a3a4 | 10.26434/chemrxiv-2022-4pv1z | Chirality Analysis for Nanostructured Microparticles Using Deep Learning | Chirality of helical objects, exemplified by nanostructured inorganic particles, has unifying importance for many scientific fields. Their handedness can be determined visually, but its identification by analysis of electron microscopy images is fundamentally difficult because (1) image features differentiating left- and right-handed particles can be ambiguous and ancillary, and (2) three-dimensional particle structure essential for chirality is 'flattened' into two-dimensional projections. Here we show that deep learning algorithms can reliably identify and classify twisted bowtie-shaped microparticles in scanning electron microscopy images with accuracy as high as 94.4% having been trained on as few as 180 images. Furthermore, after training on bowtie particles with complex nanostructured features, the model can recognize other chiral shapes with different geometries without re-training. These findings indicate that deep learning can potentially replicate the visual analysis of chiral objects by humans and enable automated analysis of microscopy data for the accelerated discovery of chiral materials. | Anastasia Visheratina; Alexander Visheratin; Prashant Kumar; Michael Veksler; Nicholas Kotov | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC 4.0 | CHEMRXIV | 2022-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d5748381efd03957b0a3a4/original/chirality-analysis-for-nanostructured-microparticles-using-deep-learning.pdf |
60c74167ee301c5045c78c44 | 10.26434/chemrxiv.8044607.v1 | Towards Higher Alcohol Formation using a single-layer MoS2 activated Au on Silica: Methanol Carbonylation to Acetaldehyde | <p>We demonstrate that a fused silica substrate can be
rendered active for acetaldehyde (CH<sub>3</sub>CHO) synthesis from a gas
mixture of carbon monoxide (CO) and methanol (CH<sub>3</sub>OH) under mild
process conditions (308 kPa and 393 K) by deposition first of a homogenous
single-layer MoS<sub>2</sub> film and subsequently of a sub-mnonolayer (1
Angstrom) loading of gold. <i>In operando</i>
monitoring of the catalyst performance in a flow reactor reveals uncompromised
activity even after 2 hours on stream. The carbonylation of methanol to a C<sub>2</sub>
species represents a crucial step toward the formation of higher alcohols from
syngas derived from methane or biomass.
Characterization of the film by imaging and spectroscopy reveals that
the single-layer MoS<sub>2</sub> film disperses the gold loading into nanoscale
islands; density functional theory (DFT) calculations identify low-coordinated
edge sites on these islands as active centers for the carbon-carbon coupling at
barriers significantly below 1 eV. </p> | Kortney Almeida; Katerina L. Chagoya; Alan Felix; Tao Jiang; Duy Le; Takat B. Rawal; Prescott E. Evans; Michelle Wurch; Koichi Yamaguchi; Peter A. Dowben; Ludwig Bartels; Talat
S. Rahman; Richard G. Blair | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74167ee301c5045c78c44/original/towards-higher-alcohol-formation-using-a-single-layer-mo-s2-activated-au-on-silica-methanol-carbonylation-to-acetaldehyde.pdf |
61bfe14c7f367e288e5974a8 | 10.26434/chemrxiv-2021-cdpf5 | Zeolitic Imidazolate Framework Nanoencapsulation of CpG for Stabilization and Enhancement of Immunoadjuvancy | Metal-organic frameworks (MOFs) have been used to improve vaccine formulations by stabilizing proteins and protecting them against thermal degradation. This has led to increased
2
immunogenicity of these proteinaceous therapeutics. In this work we show that MOFs can also be used to protect the ssDNA oligomer, CpG, to increase its immunoadjuvancy. By encapsulating phosphodiester CpG in the zinc-based MOF, ZIF-8, the DNA oligomer is protected from nuclease degradation and exhibits improved cellular uptake. As a result, we have been able to achieve drastically enhanced B-cell activation in splenocyte cultures comparable to the current state-of-the-art, phosphorothioate CpG. Furthermore, we have made a direct comparison of micro- and nano-sized MOF for the optimization of particulate delivery of immunoadjuvants to maximize immune activation. | Olivia R. Brohlin; Ryanne E. Ehrman; Fabian C. Herbert; Yalini H. Wijesundara; Arun Raja; Arezoo Shahrivarkevishahi; Shashini D. Diwakara; Ronald A. Smaldone; Jeremiah Gassensmith | Materials Science; Nanoscience; Biocompatible Materials; Biodegradable Materials; Controlled-Release Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61bfe14c7f367e288e5974a8/original/zeolitic-imidazolate-framework-nanoencapsulation-of-cp-g-for-stabilization-and-enhancement-of-immunoadjuvancy.pdf |
6756f3aff9980725cf84456e | 10.26434/chemrxiv-2024-r98bn | The Piancatelli rearrangement of AMF (5-azidomethylfurfural) derivatives: a biobased opportunity for the synthesis of nitrogenous cyclopentenones | In the field of renewable material to substitute petroleum-based products, one of the main areas of research is the study and transformation of small molecules derived from biomass into high added-value compounds. In this context, we report the preparation of 4-(azidomethyl)-cyclopentenones starting from AMF (5-azidomethylfurfural) derivatives, directly obtained from the well-known biosourced renewable material CMF (5-chloromethylfurfural). The Piancatelli rearrangement of these AMF derivatives, catalyzed by Dy(OTf)3 and under microwave activation affords substituted cyclopentenones with two contiguous stereogenic centres, one of which is quaternary, with high diastereoselectivities. We were able to exploit the azidomethyl side chain to produce cyclopentenones with other nitrogenous functionalities, such as amine or triazole moities. Moreover, these 4-(azidomethyl)-cyclopentenones exhibited relevant cytotoxic activities against HCT116 and HL60 cancer cell lines with nanomolar IC50 values. | Clementine MAYET; Jerome BIGNON; JEAN-FRANCOIS BETZER | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6756f3aff9980725cf84456e/original/the-piancatelli-rearrangement-of-amf-5-azidomethylfurfural-derivatives-a-biobased-opportunity-for-the-synthesis-of-nitrogenous-cyclopentenones.pdf |
616342102aca5305bc5f61e4 | 10.26434/chemrxiv-2021-k7k1w | Vinylcyclopropane [3+2] Cycloaddition with Acetylenic Sulfones Based on Visible Light Photocatalysis | We describe the first intermolecular visible light [3+2] cycloaddition reaction being performed on a meta photocycloadduct employing acetylenic sulfones. The developed methodology exploits the advantages of combining UV and Visible light in a two-step sequence that provides a photogenerated cyclopropane which, through a strain-release process, generates a new cyclopentane ring while increasing significally the molecular complexity. This strategy could be extended to simpler vinylcyclopropanes. | Adriana Luque; Jonathan Groß; Till Opatz | Organic Chemistry; Catalysis; Photochemistry (Org.); Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616342102aca5305bc5f61e4/original/vinylcyclopropane-3-2-cycloaddition-with-acetylenic-sulfones-based-on-visible-light-photocatalysis.pdf |
624e0e183b5f99e2efd04fe6 | 10.26434/chemrxiv-2022-pzs6m | Catalytic, Undirected Borylation of Tertiary C–H Bonds in Bicyclo[1.1.1]pentanes and Bicyclo[2.1.1]hexanes | Catalytic borylations of sp3 C–H bonds occur with high selectivities for primary C–H bonds or secondary C–H bonds that are activated by nearby electron-withdrawing substituents. The catalytic borylation at tertiary C–H bonds has not been observed. We describe a broadly applicable method for the synthesis of boron-substituted bicyclo[1.1.1]pentanes (BCPs) and (hetero)bicyclo[2.1.1]hexanes (BCHs) by an iridium-catalyzed borylation of the bridgehead tertiary C–H bond. This reaction is highly selective for the formation of bridgehead boronic esters and is compatible with a broad range of functional groups (>35 examples). The method is applicable to the late-stage modification of pharmaceuticals containing this substructure and the synthesis of novel bicyclic building blocks. Kinetic and computational studies suggest that C–H bond cleavage occurs with a modest barrier and that the turnover-limiting step of this reaction is an isomerization that occurs prior to reductive elimination that forms the C–B bond. | Isaac F. Yu; Jenna L. Manske; Alejandro Diéguez-vázquez; Antonio Misale; Alexander E. Pashenko; Sergey V. Ryabukhin; Dmitriy M. Volochnyuk; John F. Hartwig | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Bond Activation; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624e0e183b5f99e2efd04fe6/original/catalytic-undirected-borylation-of-tertiary-c-h-bonds-in-bicyclo-1-1-1-pentanes-and-bicyclo-2-1-1-hexanes.pdf |
67bc9bf6fa469535b9bb872e | 10.26434/chemrxiv-2025-jggvw | Open-Source Generation of Sigma Profiles: Impact of Quantum Chemistry and Solvation Treatment on Machine Learning Performance | The combination of machine learning (ML) models with chemistry-related tasks requires the description of molecular structures in a machine-readable way. The nature of these so-called molecular descriptors has a direct and major impact on the performance of ML models and remains an open problem in the field. Structural descriptors like SMILES strings or molecular graphs lack size-independence and can be memory intensive. Machine-learned descriptors can be of low dimensionality and constant size but lack physical significance and human interpretability. Sigma profiles, which are unnormalized histograms of the surface charge distributions of solvated molecules, combine physical significance with low dimensionality and size-independence, making them a suitable candidate for a universal molecular descriptor. However, their widespread adoption in ML applications requires open access to sigma profile generation, which is currently not available. This work details the development of an open-source software for generating sigma profiles. Also presented are studies on the effect of different settings on the efficacy of the generated sigma profiles at predicting thermophysical material properties when used as inputs to a Gaussian Process as a simple surrogate ML model. We find that a higher level of theory does not translate to more accurate results. We also provide further recommendations for sigma profile calculation and use in ML models. | Fathya Salih; Dinis Abranches; Edward Maginn; Yamil Colón | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bc9bf6fa469535b9bb872e/original/open-source-generation-of-sigma-profiles-impact-of-quantum-chemistry-and-solvation-treatment-on-machine-learning-performance.pdf |
60c75867469df44585f4565a | 10.26434/chemrxiv.14178113.v2 | Exact Solution of Kinetic Analysis for Thermally Activated Delayed Fluorescence Materials | The photophysical analysis of thermally activated delayed fluorescence (TADF) materials has become instrumental to providing insight into their stability and performance, which is not only relevant for organic light-emitting diodes (OLED), but also for other applications such as sensing, imaging and photocatalysis. Thus, a deeper understanding of the photophysics underpinning the TADF mechanism is required to push materials design further. Previously reported analyses in the literature of the kinetics of the various processes occurring in a TADF material rely on several a priori assumptions to estimate the rate constants for forward and reverse intersystem crossing (ISC and RISC, respectively). In this report, we demonstrate a method to determine these rate constants using a three-state model together with a steady-state approximation and, importantly, no additional assumptions. Further, we derive the exact rate equations, greatly facilitating a comparison of the TADF properties of structurally diverse emitters and providing a comprehensive understanding of the photophysics of these systems. | Youichi Tsuchiya; Stefan Diesing; Fatima Bencheikh; Yoshimasa Wada; Paloma dos Santos; Hironori Kaji; Eli Zysman-Colman; Ifor Samuel; Chihaya Adachi | Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75867469df44585f4565a/original/exact-solution-of-kinetic-analysis-for-thermally-activated-delayed-fluorescence-materials.pdf |
61ae8fc49e56b85989b0c42e | 10.26434/chemrxiv-2021-x7z1v | Chemical Decomposition of the TFSI Anion Under Aqueous Basic Conditions | Understanding the interfacial reactivity of aqueous electrolytes is crucial for their use in future batteries. We investigate the reactivity of the bis(trifluoromethane)sulfonimide (TFSI) anion when exposed to a strong alkaline medium, by means of ab initio molecular dynamics and enhanced sampling techniques. In particular, we study the nucleophilic attack by the hydroxide anion, which was proposed as a mechanism for the formation of the solid electrolyte interphase at the negative electrode with water-in-salt electrolytes. While in the gas phase we recover a stable gaseous product, namely fluoroform, we observe the formation of trifluoromethanol in strong basic conditions, which then rapidly deprotonates to form CF3O-. This anion was suggested recently as a key compound leading to the formation of a solid electrolyte interphase on an Si-C anode. Such an approach could be leveraged to discover convenient additives leading to the formation of a stable interphase. | Arthur France-Lanord; Fabio Pietrucci; A. Marco Saitta; Jean-Marie Tarascon; Alexis Grimaud; Mathieu Salanne | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Computational Chemistry and Modeling; Energy Storage; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ae8fc49e56b85989b0c42e/original/chemical-decomposition-of-the-tfsi-anion-under-aqueous-basic-conditions.pdf |
61fe899fe0f529422ba863b1 | 10.26434/chemrxiv-2022-jmm26 | Concise Total Synthesis and Stereochemical Assignment of (–)-Psychotridine. | We report the first enantioselective total synthesis and stereochemical assignment of (–)-psychotridine. Application of our diazene-directed assembly of enantiomerically enriched cyclotryptamines afforded a highly convergent synthesis of the pentameric alkaloid, allowing its detailed structural assignment. Highlights of the synthesis include introduction of four quaternary stereocenters with complete stereochemical control in a single step via photoextrusion of three molecules of dinitrogen from an advanced intermediate and metal-catalyzed C–H amination in complex settings. | Tony Scott; Vinicius Armelin; Mohammad Movassaghi | Organic Chemistry; Natural Products; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fe899fe0f529422ba863b1/original/concise-total-synthesis-and-stereochemical-assignment-of-psychotridine.pdf |
64377b9f1d262d40ea59b3a1 | 10.26434/chemrxiv-2023-2w25b-v2 | Adjustable Positive-Negative Signal in Self-Driven Photodetector based on Cubic CH3NH3PbI3 Large Single Crystal | <p><b>In this study, for
the first time, self-driven photodetector based on cubic CH<sub>3</sub>NH<sub>3</sub>PbI<sub>3</sub>
large single crystal </b><b>(C-MAPbI<sub>3
</sub>LSC) </b><b>with adjustable
positive-negative signal is fabricated. </b><b>The preparation of MAPbI<sub>3 </sub>large single crystal (MAPbI<sub>3 </sub>LSC)
is realized by the method of growth-drop-growth (GDG). </b><b>The band gap of </b><b>MAPbI<sub>3 </sub></b><b>single crystals </b><b>with Pm-3m (221) space group (6.134×6.134×6.134
Å, 90.00 x 90.00 x 90.00) </b><b>is 1.58 eV.</b> <b>CH<sub>3</sub>NH<sub>3</sub><sup>+</sup> cation
is orientation-disorder </b><b>within the perovskite cubo-octahedral cavity.</b><b> The photocurrent density at 803 nm of the</b><b> C-MAPbI<sub>3 </sub>LSC</b><b> photodetector under different bias voltages
is the highest under different wavelength. The </b><b>responsivities (R),
response time, external quantum efficiencies (EQE) and the detectivity (D) for </b><b>C-MAPbI<sub>3 </sub>LSC</b><b> photodetector at 803 nm wavelength with 1 W
m<sup>-2</sup></b><b>, respectively, is </b><b>508.7 µA/mW, 0.1338 ms, 79.6% and 8.64*10<sup>11</sup> Jones. Notably, </b><b>the C-MAPbI<sub>3 </sub>LSC photodetector
can be self-driven under 0 V bias voltage, in particular, the positive and
negative values of the photocurrent can be adjusted. The proposed mechanism of
poling inducing built-in potential is explained adjustable positive-negative
signal in self-driven photodetector based on cubic CH<sub>3</sub>NH<sub>3</sub>PbI<sub>3</sub>
large single crystal.</b><b></b></p> | Huawei Zhou; Jingxuan Tan; Xuewei Fu; Yunying Wang; Yan Chen; Chen Wang; Xingchen Hu; Yi Wang; Jie Yin; Xianxi Zhang | Organometallic Chemistry; Electrochemistry - Organometallic | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64377b9f1d262d40ea59b3a1/original/adjustable-positive-negative-signal-in-self-driven-photodetector-based-on-cubic-ch3nh3pb-i3-large-single-crystal.pdf |
647072744f8b1884b7507020 | 10.26434/chemrxiv-2023-9pxq1 | Fast and accurate excited states predictions: Machine learning and diabatization | The efficiency of machine learning algorithms for electronically excited states is far behind ground-state applications. One of the underlying problems is the insufficient smoothness of the fitted potential energy surfaces and other properties in the vicinity of state crossings and conical intersections, which is a prerequisite for an efficient regression. Smooth surfaces can be obtained by switching to the diabatic basis. However, diabatization itself is still an outstanding problem. We overcome these limitations by solving both problems at once. We use a machine learning approach combining clustering and regression techniques to correct for the deficiencies of property-based diabatization which, in return, provides us with smooth surfaces that can be easily fitted. Our approach extends the applicability of property-based diabatization to multidimensional systems. We show the performance of the proposed methodology by reconstructing global potential energy surfaces of excited states of nitrosyl fluoride and formaldehyde. While the proposed methodology is independent of the specific property-based diabatization and regression algorithm, we show its performance for kernel ridge regression and a very simple diabatization based on transition multipoles. Compared to most other algorithms based on machine learning, our approach needs only a small amount of training data. | Štěpán Sršeň; O. Anatole von Lilienfeld; Petr Slavicek | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647072744f8b1884b7507020/original/fast-and-accurate-excited-states-predictions-machine-learning-and-diabatization.pdf |
60d1e9fee2113370bee03aca | 10.26434/chemrxiv-2021-75pmp | Computational studies of a DNA-based aptasensor: toward theory-driven transduction improvement. | Aptamers are a class of bioreceptors used in analytical tools dedicated to molecular diagnostics due to their ability to perform structural reorganization upon target binding. However, there is a lack of methodologies allowing to rationalize their structure in order to improve their transduction efficiency. We chose here, a three-strand DNA structure as probe anchored on a gold surface and partially hybridized with an aptamer sequence sensitive to Ampicillin (AMP). Using a set of computational techniques, we investigated the structure change upon analyte binding, taking into account the grafting on the surface. Original analyses unveil a distinct pattern between both states which can be related to changes in capacitance of the interface between these states. To our knowledge, this work demonstrates for the first time the ability of computational investigations to drive, in-silico, the design of aptasensors. | Mario Araujo-Rocha; Benoît Piro; Vincent Noël; Florent Barbault | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanodevices; Computational Chemistry and Modeling; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d1e9fee2113370bee03aca/original/computational-studies-of-a-dna-based-aptasensor-toward-theory-driven-transduction-improvement.pdf |
66d0610020ac769e5f383eb8 | 10.26434/chemrxiv-2023-c0svs-v2 | Selection or removal of compounds from complex samples by peak isolation using an enhanced GCxGC configuration | We developed a novel approach to isolate and recollect or remove nearly any compound from complex GCxGC chromatograms. This was achieved by modifying a thermal desorption-GCxGC-Q-TOF system with a Deans switch, a passive splitter, and careful optimization of flows and capillary dimensions. The setup was evaluated with 106 standard chemicals covering a wide range of volatility (boiling points: 56 – 343 ⁰C) and polarity (log P: -0.2 – 9.4). We found that the recovery from tube to tube can become highly efficient if a custom-made adapter is attached directly on the flame ionization detector port (average recovery rate of 76 ± 7%). Furthermore, we were able to isolate peaks separated by a minimum distance of 50 milliseconds from each other at the base throughout the whole chromatographic run. In addition, the setup was designed for easy adaptation by repurposing existing instrument control software to define the isolation windows for the compounds of interest (first and second column retention time windows). We expect this novel development to allow several new applications, e.g., the isolation and selective enrichment or removal of molecules in food and flavour analysis; the investigation of suspect chemicals (incl. unknowns) for effect directed analysis (e.g., bioassays), and the isolation of compounds in the high-ng range (upon multiple isolation iterations) to be subjected to further chemical analyses (e.g. chemical ionization tandem mass spectrometry). | Matyas Ripszam; Tobias Bruderer; Federico Vivaldi; Serena Reale; Fabio Di Francesco | Analytical Chemistry; Analytical Apparatus; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d0610020ac769e5f383eb8/original/selection-or-removal-of-compounds-from-complex-samples-by-peak-isolation-using-an-enhanced-g-cx-gc-configuration.pdf |
62c5fd7e14201f3bbe287333 | 10.26434/chemrxiv-2022-nq47c | Metabolites of Cannabigerol (CBG) Generated by Human Cytochrome P450s are Bioactive | The phytocannabinoid cannabigerol (CBG) is the central biosynthetic precursor to many cannabinoids, including Δ9-tetrahydrocannabinol (THC) and cannabidiol (CBD). Though the use of CBG has recently witnessed a widespread surge because of its beneficial health effects and lack of psychoactivity, its metabolism by human cytochrome P450s is largely unknown. Herein, we describe comprehensive in vitro and in vivo cytochrome P450 (CYP)-mediated metabolic studies of CBG, ranging from LC-MS/MS-based primary metabolic site determination, synthetic validation, and kinetic behavior using targeted mass spectrometry. These investigations revealed that cyclo-CBG, a recently isolated phytocannabinoid, is the major metabolite that is rapidly formed by selected human cytochrome P450s (CYP2J2, CYP3A4, CYP2D6, CYP2C8, and CYP2C9). Additionally, in vivo studies with mice administered with CBG, supported these studies, where cyclo-CBG is the major metabolite as well. Spectroscopic binding studies along with docking and modeling of CBG molecule near the heme in the active site of P450s confirmed these observations, pointing at the preferred site-selectivity of CBG metabolism at the prenyl chain over other positions. Importantly, we found out that CBG and its oxidized CBG metabolites reduced inflammation in BV2 microglial cells stimulated with LPS. Overall, combining enzymological studies, mass spectrometry, and chemical synthesis, we showcase that CBG is rapidly metabolized by human P450s to form oxidized metabolites that are bioactive. The study reveals the structure-activity relationship of CBG metabolites and analogs to their anti-inflammatory activity. | Pritam Roy; David G. Dennis; Mark D. Eschbach; Shravanthi D. Anand; Fengyun Xu; Jonathan Maturano; Judith Hellman; David Sarlah; Aditi Das | Biological and Medicinal Chemistry; Biochemistry; Biophysics; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2022-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c5fd7e14201f3bbe287333/original/metabolites-of-cannabigerol-cbg-generated-by-human-cytochrome-p450s-are-bioactive.pdf |
60c74b7d567dfe6f0fec4f59 | 10.26434/chemrxiv.12296180.v2 | SGC-CK2-1: The First Selective Chemical Probe for the Pleiotropic Kinase CK2 | Building upon a wealth of published knowledge surrounding the pyrazolopyrimidine scaffold, we designed a small library around the most selective small molecule CK2 inhibitors reported. Through extensive evaluation of this library we identified inhibitor 24 (SGC-CK2-1) as a potent, selective, and cell-active CK2 chemical probe. Remarkably, despite years of research pointing to CK2 as a key driver in cancer, our probe did not elicit an antiproliferative phenotype in cell lines tested. While many publications have attempted tocharacterize CK2 function, CK2 biology is complex and a high-quality chemical tool like SGC-CK2-1 will aid in connecting CK2 functions to phenotypes. | Carrow Wells; David Drewry; Julie E. Pickett; Alison D. Axtman | Bioorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b7d567dfe6f0fec4f59/original/sgc-ck2-1-the-first-selective-chemical-probe-for-the-pleiotropic-kinase-ck2.pdf |
60c747bdf96a006aac286f8a | 10.26434/chemrxiv.11777322.v1 | Negligible Voltage Hysteresis with Strong Anionic Redox in Conventional Battery Electrode | <div>Lattice oxygen redox reactions (ORR) offers opportunities for developing highcapacity batteries, however, suffers the notoriously high voltage hysteresis and low initial coulombic efficiency, which hinder its practical applications. Particularly, ORR was widely considered inherent to these kinetic issues. In this paper, unambiguous evidence of strong and reversible ORR is found in Na<sub>2/3</sub>Ni<sub>1/3</sub>Mn<sub>2/3</sub>O<sub>2</sub>, which displays negligible voltage hysteresis (0.1 V) and high initial coulombic efficiency with a highly stable electrochemical profile. Our independent and quantitative analysis of all the Ni, Mn and O states consistently interpret the redox mechanism of Na<sub>2/3</sub>Ni<sub>1/3</sub>Mn<sub>2/3</sub>O<sub>2</sub>, which reveals, for the first time, a conventional 3d transition-metal ORR system with facile kinetics and highly stable electrochemical profile that previously found only in cationic redox systems.</div> | Kehua Dai; Jing Mao; Zengqing Zhuo; Guo Ai; Wenfeng Mao; Yan Feng; Feng Pan; Yi-de Chuang; Gao Liu; Wanli Yang | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747bdf96a006aac286f8a/original/negligible-voltage-hysteresis-with-strong-anionic-redox-in-conventional-battery-electrode.pdf |
60c75032337d6c3cc2e2825e | 10.26434/chemrxiv.13006382.v1 | Prediction and Validation of a Druggable Site on Virulence Factor of Drug Resistant Burkholderia Cenocepacia | <br /><p> </p>
<p>We use a virtual screening approach
to explore the binding pocket close to the fucose binding site in a lectin from
opportunistic pathogen. This is a novel approach for designing anti-adhesive
drugs, and it has been very successful since we were able to obtain leads with
sub millimolar affinity. Furthermore, the crystal structure of the target
protein complexed with the fragment validated the existence of this secondary
binding site, opening route for new design of inhibitors</p> | Kanhaya Lal; Rafael Bermo; Jonathan Cramer; Francesca Vasile; Beat Ernst; Anne Imberty; Anna Bernardi; Annabelle Varrot; Laura Belvisi | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75032337d6c3cc2e2825e/original/prediction-and-validation-of-a-druggable-site-on-virulence-factor-of-drug-resistant-burkholderia-cenocepacia.pdf |
61517db7d9c9560d99e1f927 | 10.26434/chemrxiv-2021-rxxbb-v2 | Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design | The recent advances in relative protein-ligand binding free energy calculations have shown the value of alchemical methods in drug discovery. Accurately assessing absolute binding free energies, although highly desired, remains a challenging endeavour, mostly limited to small model cases. Here, we demonstrate accurate first principles based absolute binding free energy estimates for 128 pharmaceutically relevant targets. We use a novel rigorous method to generate protein-ligand ensembles for the ligand in its decoupled state. Not only do the calculations deliver accurate protein-ligand binding affinity estimates, but they also provide detailed physical insight into the structural determinants of binding. We identify subtle rotamer rearrangements between apo and holo states of a protein that are crucial for binding. When compared to relative binding free energy calculations, obtaining absolute binding free energies is considerably more challenging in large part due to the need to explicitly account for the protein in its apo state. In this work we present several approaches to obtain apo state ensembles for accurate absolute ΔG calculations, thus outlining protocols for prospective application of the methods for drug discovery. | Yuriy Khalak; Gary Tresadern; Matteo Aldeghi; Hannah Magdalena Baumann; David L. Mobley; Bert L. de Groot; Vytautas Gapsys | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2021-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61517db7d9c9560d99e1f927/original/alchemical-absolute-protein-ligand-binding-free-energies-for-drug-design.pdf |
678d71ee6dde43c9083ab2e2 | 10.26434/chemrxiv-2025-vp17h | Analyzing Spectral Distributions of Charge Transfer Character in Ensembles: A Case Study on the Reaction Center of Photosystem II | Understanding the primary charge separation events in Nature's photosynthetic reaction centers is a key step toward harnessing the microscopic processes of light conversion into chemical energy. Despite intense research efforts employing state-of-the-art spectroscopic and theoretical techniques, the precise nature of energy transfer and charge separation events in these systems are still insufficiently understood. Herein, we present a computational approach that enables analysis of the charge transfer character in excited electronic states with inclusion of thermal effects in ensembles. We showcase an application of this approach to the reaction center of Photosystem II, focusing on the Chl[D1]Pheo[D1] and P[D1]P[D2] pairs of pigments. We find that the Chl[D1]Pheo[D1] pair is a more likely candidate for the primary charge separation than P[D1]P[D2] pair. Our computational approach is transferable to other biological and man-made charge separation and charge transfer systems. | Adam Šrut; Sinjini Bhattacharjee; Dimitrios A. Pantazis; Vera Krewald | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2025-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678d71ee6dde43c9083ab2e2/original/analyzing-spectral-distributions-of-charge-transfer-character-in-ensembles-a-case-study-on-the-reaction-center-of-photosystem-ii.pdf |
6720008083f22e42147a06f7 | 10.26434/chemrxiv-2024-khsfs | Guidelines for evaluating the antioxidant activity of lignin via the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay | The most widespread procedure to measure the antioxidant activity of lignin is via the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. So far, different experimental procedures (i.e., different solvent, time, etc.) have been used to implement the DPPH methodology without estimating the effect of such modifications on the experimental procedure. To overcome this issue, the impact of the solvent, the time, and the type of substrate on the evaluation of the antioxidant activity (AoA) of lignin via the DPPH assay was investigated in this work. We found that multiple different parameters affect the evaluation of the AoA of lignin: i) the stability of the DPPH radical and the lignin solubility in a given solvent; ii) the importance of reaching steady state (the effect of time); iii) the background noise associated with lignin absorbance at λ = 515 nm (used to monitor the DPPH radical scavenging); iv) lignin structure; v) providing a normalized radical scavenging index (nRSI); vi) comparing nRSI vs. inhibition percentage (IP) values. Overall, our investigation allowed us to provide guidelines on how to perform the DPPH assay for a more reliable evaluation of lignin AoA. | Daryna Diment; Oliver Musl; Mikhail Balakshin; Davide RIGO | Organic Chemistry; Earth, Space, and Environmental Chemistry; Agriculture and Food Chemistry; Natural Products; Organic Compounds and Functional Groups; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6720008083f22e42147a06f7/original/guidelines-for-evaluating-the-antioxidant-activity-of-lignin-via-the-2-2-diphenyl-1-picrylhydrazyl-dpph-assay.pdf |
60c741249abda201daf8bdee | 10.26434/chemrxiv.7956248.v1 | Assessing the Role of Inter-Molecular Interactions in a Perylene-Based Nanowire Using First-Principles Many-Body Perturbation Theory | <div>
<div>
<div>
<div>
<p>We present a first-principles many-body perturbation theory study of the role of inter-molecular
coupling on the optoelectronic properties of a one-dimensional p-stacked nanowire composed of perylene-3,4,9,10-tetracarboxylic diimide (PTCDI) molecules on a DNA-like backbone. We
determine that strong inter-molecular electronic coupling results in large bandwidths and low
carrier effective masses, suggesting a high electron mobility material. Additionally, by including
the role of finite temperature phonons on optical absorption via a newly presented approach, we
predict that the optical absorption spectrum at room temperature is significantly altered from
room temperature due to allowed indirect transitions, while the exciton delocalization and
binding energy, a measure of inter-molecular electronic interactions, remains constant. Overall,
our studies indicate that strong inter-molecular coupling can dominate the optoelectronic
properties of π-conjugated 1D systems even at room temperature.</p>
</div>
</div>
</div>
</div> | Tianlun Huang; D. Kirk Lewis; Sahar Sharifzadeh | Physical Organic Chemistry; Optical Materials; Computational Chemistry and Modeling; Quasiparticles and Excitations | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741249abda201daf8bdee/original/assessing-the-role-of-inter-molecular-interactions-in-a-perylene-based-nanowire-using-first-principles-many-body-perturbation-theory.pdf |
65fca7d566c13817297fd137 | 10.26434/chemrxiv-2024-lbtb0 | Advancing Organic Photoredox Catalysis: Mechanistic Insight through Time-Resolved Spectroscopy | The rapid development of light-activated organic photoredox catalysts has led to the proliferation of powerful synthetic chemical strategies with industrial and pharmaceutical applications. Despite the advancement in synthetic approaches, a detailed understanding of the mechanisms governing these reactions has lagged. Time-resolved optical spectroscopy provides a method to track organic photoredox catalysis processes and reveal the energy pathways that drive reaction mechanisms. These measurements are sensitive to key processes in organic photoredox catalysis such as charge or energy transfer, lifetimes of singlet or triplet states and solvation dynamics. The sensitivity and specificity of ultrafast spectroscopic measurements can provide a new perspective on the mechanisms of these reactions, including electron-transfer events, the role of solvent, and the short lifetimes of radical intermediates. | Vanessa Huxter | Physical Chemistry; Catalysis; Photocatalysis; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fca7d566c13817297fd137/original/advancing-organic-photoredox-catalysis-mechanistic-insight-through-time-resolved-spectroscopy.pdf |
60e5ab958825827a46a5dc92 | 10.26434/chemrxiv-2021-cdzx4 | Catalyzed Reaction of Isocyanates (RNCO) with Water | The reactions between substituted isocyanates (RNCO) and other small molecules (e.g. water, alcohols, and amines) are of significant industrial importance, particularly for the development of novel polyurethanes and other useful polymers. We present very high-level ab initio computations on the HNCO + H2O reaction, with results targeting the CCSDT(Q)/CBS//CCSD(T)/cc-pVQZ level of theory. Our results affirm that hydrolysis can occur across both the N=C and C=O bonds of HNCO via concerted mechanisms to form carbamate or imidic acid with 0 K enthalpy barrier heights of 38.5 and 47.5 kcal mol^-1 A total of 24 substituted RNCO + H2O reactions were studied. Geometries obtained with a composite method and refined with CCSD(T)/CBS single point energies determine that substituted RNCO species have a significant influence on these barrier heights, with an extreme case like fluorine lowering both barriers by close to 20 kcal mol^-1 and most common alkyl substituents lowering both by approximately 4 kcal mol^-1. Natural Bond Orbital (NBO) analysis provides evidence that the predicted barrier heights are strongly associated with the occupation of the in-plane C-O* orbital of the RNCO reactant. Key autocatalytic mechanisms are considered in the presence of excess water and RNCO species. Additional waters (one or two) are predicted to lower both barriers significantly at the CCSD(T)/aug-cc-pV(T+d)Z level of theory with strongly electron withdrawing RNCO substituents also increasing these effects, similar to the uncatalyzed case. The 298 K Gibbs energies are only marginally lowered by a second catalyst water molecule, indicating that the decreasing 0 K enthalpy barriers are offset by the loss of translational entropy with more than one catalyst water. Two-step 2RNCO + H2O mechanisms are characterized for the formation of carbamate and imidic acid. The second step of these two pathways exhibits the largest barrier and presents no clear pattern with respect to substituent choice. Our results indicate that an additional RNCO molecule might catalyze imidic acid formation but have less influence on the efficiency of carbamate formation. We expect that these results lay a firm foundation for the experimental study of substituted isocyanates and their relationship to the energetic pathways of related systems. | Mark Wolf; Jonathon Vandezande; Henry Schaefer | Theoretical and Computational Chemistry; Polymer Science; Organic Polymers; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e5ab958825827a46a5dc92/original/catalyzed-reaction-of-isocyanates-rnco-with-water.pdf |
66b97b4f5101a2ffa80a3baf | 10.26434/chemrxiv-2024-3kk6v | Integrating of Nickel Hexacyanoferrate with Hollow Mesoporous Carbon Spheres (HMCSs) for Highly Efficient Capacitive Deionization | Capacitive deionization (CDI) is a promising technology for seawater desalination, offering a green, low-cost, and low-energy alternative to traditional methods. However, its widespread adoption relies on the development of high-performance electrode materials. Prussian blue analogs (PBAs), such as NiHCF, are attractive candidates due to their high theoretical ion storage capacity but often suffer from poor conductivity and structural integrity. To address these limitations, we designed a group of hierarchical composite materials (i.e., PBA@HMCS) by integrating NiHCF with hollow mesoporous carbon spheres (HMCS) using a stepwise "ship-in-the-boat" approach. This composite combines the protective and conductive roles of carbon materials with the high ion storage capacity of PBAs. The resulting PBA@HMCS electrodes demonstrated exceptional CDI performance, with a maximum salt adsorption capacity of 80.5 mg g−1 in 500 mg L−1 NaCl solution at 1.2 V. Notably, the core-shell PBA@HMCS-1 electrode exhibited enhanced cycling stability, while the unwrapped PBA micropellets showed reduced performance. Furthermore, our investigation revealed the high affinity of PBA@HMCS electrodes for Na+ over other ions in synthetic brine, and particularly, the yolk-shell PBA@HMCS-3 electrode demonstrated high repulsion to K+, highlighting its potential for selectively extracting specific ions from dicationic brines with K+ ions. This study highlights the vast potential of hierarchical yolk-shell PBA@HMCS as a promising CDI electrode design and underscores the need for continued exploration into hierarchical structured PBA-based materials with tunable features to further enhance their CDI performance. | Shu Zhang; Feihu Li | Chemical Engineering and Industrial Chemistry; Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b97b4f5101a2ffa80a3baf/original/integrating-of-nickel-hexacyanoferrate-with-hollow-mesoporous-carbon-spheres-hmc-ss-for-highly-efficient-capacitive-deionization.pdf |
63851cfd28c164845a5b6611 | 10.26434/chemrxiv-2022-49s4d-v2 | Off Detailed Balance: Non-Equilibrium Steady States in Catalysis, Molecular Motors and Supramolecular Materials | All chemists are familiar with the idea that, at equilibrium steady state, the relative concentrations of species present in a system are predicted by the corresponding equilibrium constants, which are in turn related to the relative free energy difference of the system components. There is also no net flux between species, no matter how complicated the reaction network. Achieving and harnessing non-equilibrium steady states, by coupling a reaction network to a second spontaneous chemical process, has been the subject of work in a number of disciplines including the autonomous operation of molecular motors, the assembly of supramolecular materials, and strategies in enantioselective catalysis. Here we juxtapose these linked fields to highlight their common features, the similar issues that must be overcome, and some common misconceptions that may be serving to stymie progress. | Stephen Goldup; Ivan Aprahamian | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Supramolecular Chemistry (Org.); Heterogeneous Catalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63851cfd28c164845a5b6611/original/off-detailed-balance-non-equilibrium-steady-states-in-catalysis-molecular-motors-and-supramolecular-materials.pdf |
62e00a6eed926e6544a6d4c9 | 10.26434/chemrxiv-2022-xj26g | A Novel Instrumented Technique for Measuring Cutting Resistance of Plastics : Comparison with Rodent Bite Resistance Test and Other Mechanical Properties of the Material | This paper discusses a new mechanical test, to study the resilience of cutting of specimens, using a heavy-duty cable cutter, with an aim to mimic rodent damage of materials. Various mechanical properties of the composites; like tensile modulus, tensile strength, toughness and roughness have been studied, and corroborated with resilience and toughness of cutting. Performance of 3 compositions; consisting of certain Blends of Polyamide 12 : HDPE, Hytrel : Polytrimethylene Terephthalate (PTT), and Wollastonite reinforced Hytrel : HDPE Blends, selected from a pool of earlier studied blends and composites, displaying high Shore D and Scratch hardness, have been compared to the popular choice for cable jacketing i.e., High Density Polyethylene (HDPE). These 4 types of materials have also been exposed to rodents, to compare the results with the newly developed cutting test. These results help in understanding the properties that are essential in a material to prevent rodent damage. | Manoj Praharaj Bhatnagar | Materials Science; Polymer Science; Elastic Materials; Materials Processing; Polymer blends | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e00a6eed926e6544a6d4c9/original/a-novel-instrumented-technique-for-measuring-cutting-resistance-of-plastics-comparison-with-rodent-bite-resistance-test-and-other-mechanical-properties-of-the-material.pdf |
60c75626f96a00472e2889f8 | 10.26434/chemrxiv.13611140.v2 | Ensemble Effects of Explicit Solvation on Allylic Oxidation | Umbrella-sampling density functional theory molecular dynamics (DFT-MD) has been employed to study the full catalytic cycle of the allylic oxidation of cyclohexene using a Cu(II) 7-amino-6-((2-hydroxybenzylidene)amino)quinoxalin-2-ol complex in acetonitrile to create cyclohexenone and H$_2$O as products. In comparison to gas-phase DFT, the solvent effect is observed as the rate determining allylic H-atom abstraction step has a free energy barrier of 12.1 $\pm$ 0.2 kcal/mol in solution. During the cycle, the explicit solvation and ensemble sampling of solvent configurations reveals important dehydrogenation and re-hydrogenation steps of the -NH$_2$ group bound to the Cu-site that are essential to catalyst recovery. This work illustrates the importance of ensemble solvent configurational sampling to reveal the breadth of processes that underpin the full catalytic cycle.<br /> | Hung Le; Mariano Guagliardo; Anne Gorden; Aurora Clark | Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75626f96a00472e2889f8/original/ensemble-effects-of-explicit-solvation-on-allylic-oxidation.pdf |
63885f6debc1c741aed9bf03 | 10.26434/chemrxiv-2022-g2jf3 | Photochemistry of thymine in solution and DNA revealed by an electrostatic embedding QM/MM combined with mixed-reference spin-flip TDDFT | The photochemistry of nucleobases, important for their role as building blocks of DNA, is largely affected by the electrostatic environment in which they are soaked. For example, despite the numerous studies of thymine in solution and DNA, there is still a debate on the photochemical deactivation pathways after UV absorption. Many theoretical models are oversimplified due to the lack of computationally accurate and efficient electronic structure methodologies that capture excited state electron correlation effects when nucleobases are embedded in large electrostatic media. Here, we combine mixed-reference spin-flip time-dependent density-functional theory (MRSF-TDDFT) with electrostatic embedding QM/MM using electrostatic potential fitting (ESPF) atomic charges, as a strategy to accurately and efficiently describe the electronic structure of chromophores polarized by an electrostatic medium. In particular, we develop analytic expressions for the energy and gradient of MRSF/MM based on the ESPF coupling using atom-centered grids and total charge conservation. We apply this methodology to the study of solvation effects on thymine photochemistry in water and thymine dimers in DNA. In the former, the combination of trajectory surface hopping (TSH) non-adiabatic molecular dynamics (NAMD) with MRSF/MM remarkably revealed the accelerated deactivation decay pathways, which is consistent with the experimental decay time of ~ 400 fs. The enhanced hopping rate can be explained by the preferential stabilization of corresponding conical interactions due to their increased dipole moments. Structurally, it is a consequence of characteristic methyl puckered geometries near the conical intersection region. For the thymine dimer in B-DNA, we found new photochemical pathways through conical intersections that could explain the formation of cyclobutadiene dimers and 6-4 photoproducts. | Miquel Huix-Rotllant; Karno Schwinn; Vladimir Pomogaev; Maryam Farmani; Nicolas Ferre; Seunghoon Lee; Cheol Ho Choi | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63885f6debc1c741aed9bf03/original/photochemistry-of-thymine-in-solution-and-dna-revealed-by-an-electrostatic-embedding-qm-mm-combined-with-mixed-reference-spin-flip-tddft.pdf |
67af839dfa469535b954a74b | 10.26434/chemrxiv-2025-96kzg | Integrating Machine Learning-Based Pose Sampling with Established Scoring Functions for Virtual Screening | Abstract Classical docking methods have dominated the field of structure-based virtual screening (VS) for decades. Recently, several machine learning (ML)-based docking approaches have been introduced, presenting a promising avenue for advancing VS technologies. In this work, we report on the integration of DiffDock-L, one of the most promising ML-based pose sampling methods, into VS workflows by combining it with the established Vina and Gnina scoring functions. We assess the integrated approach regarding its VS effectiveness, pose sampling quality, and complementarity to classical docking methods, represented by AutoDock Vina. Our results on the DUD-Z benchmark data set show that pose sampling with DiffDock-L and AutoDock Vina yields comparable performance. In contrast, the choice of the scoring function has a decisive impact on VS success. In general, DiffDock-L generates physically plausible and biologically relevant poses in most cases, confirming it as a viable alternative to classical docking algorithms. | Thi Ngoc Lan Vu; Hosein Fooladi; Johannes Kirchmair | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67af839dfa469535b954a74b/original/integrating-machine-learning-based-pose-sampling-with-established-scoring-functions-for-virtual-screening.pdf |
615e158df718df8d43d5f919 | 10.26434/chemrxiv-2021-wt095 | Red-Light Triggered Photouncaging from Dicyanomethylene-4H-pyran Phototrigger in Aqueous Solution: Applied as a Single Component Nano-Drug Delivery System for Cancer Therapy | The development of Photoremovable protecting groups (PRPGs), which can be activated in the ʽphototherapeutic windowʼ for biological applications, is highly challenging. Only PRPGs based on BODIPY dye have been developed so far, which can be excited ≥600 nm. Herein, we developed for the first time NIR dye hydroxystyryl dicyanomethylene-4H-pyran (DCM) as a PRPG that can be operated in the phototherapeutic window. Ours easily synthesized DCM photocages efficiently released aromatic and aliphatic carboxylic acids in an aqueous solution on irradiation using the light of wavelength ≥600 nm and 650 nm, separately. As an application, we used our DCM-PRPG as a single component nanocarrier drug delivery system (DDS) to uncage valproic acid (a known histone deacetylase inhibitor) for cancer treatment. In vitro studies revealed that our DDS, hydroxystyryl dicyanomethylene-4H-pyran valproic acid conjugate nanoparticles (DCM-VPA-NPs) exhibited good cellular internalization, biocompatibility, and enhanced cytotoxicity upon irradiation.
| Biswajit Roy; Rakesh Mengji; Moumita Kundu; Sujit Ghosh; Mahitosh Mondal; Avijit Jana; N. D. Pradeep Singh | Biological and Medicinal Chemistry; Organic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615e158df718df8d43d5f919/original/red-light-triggered-photouncaging-from-dicyanomethylene-4h-pyran-phototrigger-in-aqueous-solution-applied-as-a-single-component-nano-drug-delivery-system-for-cancer-therapy.pdf |
63845d130949e1fd5f589527 | 10.26434/chemrxiv-2022-lvckb | The most common linkers in bioactive molecules and their bioisosteric replacement network | Structures of the large majority of bioactive molecules are composed of several rings that are decorated by substituents and connected by linkers. While numerous cheminformatics studies focusing on rings and substituents are available, practically nothing has been published about the third important structural constituent of bioactive molecules - the linkers. The current study attempts to fill this gap. The most common linkers present in bioactive molecules are identified, their properties analyzed and a method for linker similarity search introduced. The bioisosteric replacement network of linkers is generated based on a large corpus of structure-activity data from medicinal chemistry literature.The results are presented in a graphical form and the underlying data are also made available for download. This analysis is intended to help medicinal chemists to better understand the role of linkers in bioactive molecules and to select an optimal set of linkers in their future project. | Peter Ertl; Eva Altmann; Sophie Racine | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63845d130949e1fd5f589527/original/the-most-common-linkers-in-bioactive-molecules-and-their-bioisosteric-replacement-network.pdf |
67db680ffa469535b9dedf7a | 10.26434/chemrxiv-2025-0wkrd | A Minimalistic Deep Graph Learning Approach for Protein-Ligand Binding Affinity: One Step Towards Generalization | Predicting protein-ligand binding affinity is a fundamental challenge in structure-based drug design. While deep learning models have significantly improved affinity predictions, many state-of-the-art approaches rely on complex architectures with tens or hundreds of thousands of trainable parameters, which may lead to overfitting and reduced generalizability. In this study, we introduce ECIF-GCN, a minimalist deep graph learning model that extends the Extended Connectivity Interaction Features (ECIF) framework by incorporating a fully connected graph representation and leveraging Graph Convolutional Networks (GCNs) to process molecular interactions. ECIF-GCN was trained and evaluated on LP-PDBbind, a benchmark specifically designed to minimize protein and ligand similarity across dataset splits, providing a rigorous assessment of model generalization. Despite having significantly fewer trainable parameters compared to more complex architectures, ECIF-GCN achieved the lowest RMSE (1.52) in the test set of LP-PDBbind, outperforming models such as InteractionGraphNet and RF-Score, which contain a substantially larger number of parameters. These results demonstrate that high predictive accuracy in binding affinity estimation does not require highly overparameterized deep learning models. These results highlight the potential of minimalist deep learning architectures in protein-ligand binding affinity prediction, providing a balance between predictive power, computational efficiency, and generalization ability, and suggest that a carefully designed low-parameter model can achieve state-of-the-art performance, reinforcing the idea that overparameterization is not a prerequisite for robust molecular modeling. | Ulises Rojas-Castañeda; Gabriel A. Argüelles-Arjona; Víctor H. Ramón-Cetina; Norberto Sánchez-Cruz | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67db680ffa469535b9dedf7a/original/a-minimalistic-deep-graph-learning-approach-for-protein-ligand-binding-affinity-one-step-towards-generalization.pdf |
60c746babdbb89e790a38c5c | 10.26434/chemrxiv.11371086.v1 | Carbon-11 Carboxylation of Trialkoxysilane and Trimethylsilane Derivatives Using [¹¹C]CO2 | A novel carbon-11 carboxylation radiosynthesis methodology is described with the potential to be used to produce in vivo molecular imaging radiotracers for positron emission tomography. This is a simple and rapid method for incorporating carbon-11 labelling precursors such as [<sup>11</sup>C]carbon dioxide and [<sup>11</sup>C]methyl iodide into fluoride-activated silanes. | Salvatore Bongarzone; Nicola Raucci; Igor Fontana; Federico Luzi; Antony Gee | Nuclear Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746babdbb89e790a38c5c/original/carbon-11-carboxylation-of-trialkoxysilane-and-trimethylsilane-derivatives-using-11c-co2.pdf |
60c73f9c567dfe4973ec3a43 | 10.26434/chemrxiv.7410908.v1 | The Effect of Particle-Size Distribution on the Electrochemical Performance of a Red Phosphorus-Carbon Composite Anode for Sodium-Ion Batteries | Sodium-ion batteries will have an important role as a complement to lithium-ion in a future where lithium or cobalt, two critical elements for lithium-ion batteries, become scarce or prohibitively expensive. Red phosphorus (RP) is a promising candidate as an anode for sodium-ion batteries because of its low potential and high specific capacity. Its main disadvantage is its 490% volumetric expansion during sodiation. This leads to particle pulverization and substantial reduction of the cycle life. Furthermore, RP has an extremely low electronic conductivity of 10<sup>-14</sup> S cm<sup>-1</sup>. Both issues have been previously addressed by ball milling RP with a carbon matrix. This decreases the RP particle size and also forms a more electronically conductive composite. However, it is challenging to determine the RP particle size independent of the size of the composite particles. Consequently, little is known about how much the RP particle size must be reduced to improve anode performance. Here we quantify the relationship between the RP particle-size distribution and its cycle life for the first time by separating the ball milling process into two steps. An initial wet ball milling is used to control the RP particle-size distribution, which is measured via dynamic light scattering. This is followed by a dry milling step to produce RP-graphite composites. We found that wet milling breaks apart the largest RP particles in the range of 2 to 10 µm decreases the Dv90 from 1.85 to 1.26 µm and significantly increases the cycle life of the RP. Furthermore, we determined that the length of time of the second milling step affects the uniformity of the carbon distribution in the composite. Photoelectron spectroscopy and transmission electron microscopy confirms the successful formation of a carbon coating, thus improving the performance of the resulting material. The RP with a Dv90 of 0.79 µm mixed with graphite for 48h delivered 1,354 mA h g<sup>-1</sup> with high coulombic efficiency (>99%) and cyclability (88% capacity retention after 100 cycles). These results are an important step in the development of cyclable, high-capacity anodes for sodium-ion batteries. | Isaac Capone; Kevin Hurlbutt; Andrew Naylor; Albert Xiao; Mauro Pasta | Electrochemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9c567dfe4973ec3a43/original/the-effect-of-particle-size-distribution-on-the-electrochemical-performance-of-a-red-phosphorus-carbon-composite-anode-for-sodium-ion-batteries.pdf |
632314a99cf662028492a1fc | 10.26434/chemrxiv-2022-qh9rq-v2 | Solid-state NMR spectra of protons and quadrupolar nuclei at 28.2 T: resolving signatures of surface sites with fast magic angle spinning | Advances in solid-state nuclear magnetic resonance (NMR) methods and hardware offer expanding opportunities for analysis of materials, interfaces, and surfaces. Here, we demonstrate the application of a very high magnetic field strength of 28.2 T and fast magic-angle-spinning rates (MAS, >40 kHz) to surface species relevant to catalysis. Specifically, we present as case studies the 1D and 2D solid-state NMR spectra of important catalyst and support materials, ranging from a well-defined silica-supported organometallic catalyst to dehydroxylated γ-alumina and zeolite solid acids. The high field and fast-MAS measurement conditions substantially improve spectral resolution and narrow NMR signals, which is particularly beneficial for solid-state 1D and 2D NMR analysis of 1H and quadrupolar nuclei such as 27Al at surfaces. | Zachariah Berkson; Snædís Björgvinsdóttir; Alexander Yakimov; Domenico Gioffrè; Maciej Korzyński; Alexander Barnes; Christophe Copéret | Physical Chemistry; Materials Science; Inorganic Chemistry; Catalysts; Spectroscopy (Inorg.); Surface | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632314a99cf662028492a1fc/original/solid-state-nmr-spectra-of-protons-and-quadrupolar-nuclei-at-28-2-t-resolving-signatures-of-surface-sites-with-fast-magic-angle-spinning.pdf |
60c7484c9abda2cc10f8ca6a | 10.26434/chemrxiv.11886792.v1 | Dewar Heterocycles as Versatile Monomers for Ring-Opening Metathesis Polymerization | We report the utility of readily available heterocycles as precursors to unique ring-opening metathesis polymerization (ROMP) monomers. Photochemical valence isomerization reactions of pyridones, dihydropyridines, and pyrones dearomatize the parent heterocycles to their highly strained Dewar isomers, which readily engage in controlled ROMP reactions using Grubbs catalysts. This strategy is used to access novel polymer backbones that contain strained β-lactam and azetidine cores, which can be further derivatized using post-polymerization chemistries. We demonstrate this through the synthesis of water-soluble β-amino acid polymers and soluble poly(acetylene) derivatives. | Sepand Nistanaki; Hosea Nelson | Organic Synthesis and Reactions; Photochemistry (Org.); Organic Polymers; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7484c9abda2cc10f8ca6a/original/dewar-heterocycles-as-versatile-monomers-for-ring-opening-metathesis-polymerization.pdf |
63a1edeb16e9a878922f41cf | 10.26434/chemrxiv-2022-x4ptf-v2 | Compound specific carbon, hydrogen, and nitrogen isotope
analysis of nitro- and amino-substituted chlorobenzenes in
complex aqueous matrices | Compound specific isotope analysis (CSIA) is an established tool to study the fate of legacy groundwater contaminants but is only emerging for non-conventional contaminants, e.g., nitro- and amino-substituted chlorobenzenes. Both chemical groups are widely used as feedstock for numerous industrial applications and often found as a mixture in contaminated sites. However, major bottlenecks to apply CSIA for these heteroatom-bearing chemicals are analytical complexities requiring special considerations and potential matrix interferences in environmental samples. We validated CSIA methods for δ13C, δ2H, and δ15N of several analytes from these chemical groups and developed a solid phase extraction (SPE) method to minimize matrix interferences during preconcentration of complex aqueous samples. Method quantification limits of SPE-CSIA for δ13C, δ2H, and δ15N were 0.03-0.57, 1.3-2.7, and 3.4-10.2 μM aqueous-phase concentrations, respectively, using 2 L water. The SPE-CSIA procedure showed negligible isotope fractionation for δ13C, δ2H, and δ15N. In addition, solvent evaporation, water sample storage up to 7 months, and SPE extract storage for 1.5 years did not change analytes’ original isotope signatures. However, to avoid significant δ2H and δ15N fractionation of aminoaromatics, cartridge breakthrough should be avoided and SPE preconcentration must be conducted at pH>pKa+2. Finally, the method was applied at a contaminated site and the measured δ13C, δ2H, and δ15N values showed excellent precision. The methods validated here are the first necessary step towards the application of SPE-CSIA to understand the environmental fate of nitro-and amino-substituted chlorobenzenes in complex aqueous samples. | Shamsunnahar Suchana; Langping Wu; Elodie Passeport | Organic Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a1edeb16e9a878922f41cf/original/compound-specific-carbon-hydrogen-and-nitrogen-isotope-analysis-of-nitro-and-amino-substituted-chlorobenzenes-in-complex-aqueous-matrices.pdf |
60c73e14ee301cc72ec78691 | 10.26434/chemrxiv.6349253.v1 | Generation of Phosphoranyl Radicals via Photoredox Catalysis Enables Voltage–Independent Activation of Strong C–O Bonds | Alcohols and carboxylic acids are ubiquitous functional groups found in organic molecules that could serve as radical precursors, but C–O bonds remain difficult to activate. We report a synthetic strategy for direct access to both alkyl and acyl radicals from these ubiquitous functional groups via photoredox catalysis. This method exploits the unique reactivity of phosphoranyl radicals, generated from a polar/SET crossover between a phosphine radical cation and an oxygen centered nucleophile. We first show the desired reactivity in the reduction of benzylic alcohols to the corresponding benzyl radicals with terminal H-atom trapping to afford the deoxygenated product. Using the same method, we demonstrate access to synthetically versatile acyl radicals which enables the reduction of aromatic and aliphatic carboxylic acids to the corresponding aldehydes with exceptional chemoselectivity. This protocol also transforms carboxylic acids to heterocycles and cyclic ketones via intramolecular acyl radical cyclizations to forge new C–O, C–N and C–C bonds in a single step. | Erin Stache; Alyssa B. Ertel; Tomislav Rovis; Abigail G. Doyle | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.); Photocatalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e14ee301cc72ec78691/original/generation-of-phosphoranyl-radicals-via-photoredox-catalysis-enables-voltage-independent-activation-of-strong-c-o-bonds.pdf |
620e755ccbb4f44c2cc448dc | 10.26434/chemrxiv-2022-g6x6n | Synthesis of melazolide B, a degraded limonoid, from a natural terpene precursor | Degraded limonoids are a subclass of limonoid natural products that derive from ring-intact or ring-rearranged limonoids. Establishment of robust synthetic routes to access them could provide valuable materials to identify the simplest active pharmacophore responsible for the observed biological activities of the parent molecules. This communication delineates the development of a divergent strategy to furnish melazolide B and several other related congeners from a common keto-lactone intermediate, which was rapidly assembled from α-ionone. A chemoselective carbonyl α,β-dehydrogenation and a Wharton reduction were key strategic steps in this synthetic pathway.
| Timothy Newhouse; Yannan Liu; Alexander Schuppe; Yizhou Zhao; Jaehoo Lee | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2022-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620e755ccbb4f44c2cc448dc/original/synthesis-of-melazolide-b-a-degraded-limonoid-from-a-natural-terpene-precursor.pdf |
60c749c44c8919c7d3ad3112 | 10.26434/chemrxiv.12102771.v1 | Mechanism of Iodine(III)-Promoted Oxidative Dearomatizing Hydroxylation of Phenols: Evidence for Radical-Chain Pathway | In the recent years, the dearomatization of phenols with the addition of nucleophiles to the aromatic ring, induced by hypervalent iodine(III) reagents and catalysts, has emerged as a highly useful synthetic approach. However, experimental mechanistic studies of this important process have been extremely scarce. As a result, the mechanism of the reaction remained elusive and as of today there exist as many as three distinct mechanistic proposals. In this report, we describe systematic investigations of the dearomatizing hydroxylation of phenols using an array of experimental techniques. Kinetics, EPR spectroscopy, and reactions with radical probes demonstrate that all the previously suggested mechanisms are incorrect, and that the transformation in fact proceeds via a radical-chain mechanism, with the aryloxyl radical being the key chain-carrying intermediate. Moreover, UV and NMR spectroscopy, high-resolution mass spectrometry, and cyclic voltammetry show that before reacting with the aryloxyl radical, water molecule becomes activated by the interaction with the iodine(III) center, causing this formally nucleophilic substrate to act as an electrophile. The C–O bond formation is identified as the rate-determining step of the reaction. This step generates the dearomatized product and an iodanyl(II) species, which is the second chain-carrying radical. The radical-chain mechanism emerging from our investigations allows to rationalize all other existing observations regarding the iodine(III)-promoted oxidative dearomatization of phenols.<br /> | Karol Kraszewski; Ireneusz Tomczyk; Aneta Drabinska; Krzysztof Bienkowski; Renata Solarska; Marcin Kalek | Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749c44c8919c7d3ad3112/original/mechanism-of-iodine-iii-promoted-oxidative-dearomatizing-hydroxylation-of-phenols-evidence-for-radical-chain-pathway.pdf |
647d9d22be16ad5c578018b2 | 10.26434/chemrxiv-2023-kbclp | A chemically self-charging flexible aqueous Zinc battery using a covalent organic framework cathode | The development of novel high performance organic cathode materials is the focus of research in aqueous Zn-organic batteries. Covalent organic framework (COF) is a new type of crystalline porous polymer with the advantages of large capacity, flexible structural design and low solubility in electrolyte. It is considered as a promising cathode material for zinc battery. In this study, a novel nitrogen-heterocyclic covalent organic framework COF material (HTAQ-COF) with abundant redox active sites of C═N and C═O was designed and synthesized, which was successfully applied to the cathode of aqueous Zn battery. The constructed HTAQ-COF cathode exhibits a high discharge specific capacity of 305 mA h g-1 at 0.04 A g-1 with excellent cycle life and high rate-performance, and a high energy density of 135 Wh kg-1. In addition, the fabricated flexible aqueous Zn//HTAQ-COF batteries also exhibited excellent long-cycle stability (about 87% capacity retention after 1000 cycles at 2.0 A g-1). At the same time, the flexible aqueous Zinc battery can be effectively charged by harvesting pervasive energy from the ambient air. After air-charging for 30 h, the discharged flexible Zn//HTAQ-COF battery can be self-charged to 1.2 V around without any external power supply, deliver a considerable discharge capacity of 279 mA h g-1, display a high-rate performance and the higher chemically self-charging stability. More importantly, this air-rechargeable flexible Zn//HTAQ-COF batteries are compatible with different chemical or/and galvanostatic charging hybrid modes. This work provides a new way to develop energy storage systems that are not limited by the power supply environment. | Qi Liu; Xiaojuan Chen; Yanwei Ma; Yiwen Lu; Huimin Zhang; Baozhu Yang | Organic Chemistry; Materials Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647d9d22be16ad5c578018b2/original/a-chemically-self-charging-flexible-aqueous-zinc-battery-using-a-covalent-organic-framework-cathode.pdf |
66a8c1cc5101a2ffa891ed62 | 10.26434/chemrxiv-2024-v77tj | Reductive Addition of a Zn–Zn Bond to Main Group Carbene Analogues | Oxidative Addition involves the addition of a substrate to a metal centre. This reaction is fundamental across synthetic chemistry and underpins numerous catalytic methods. In the textbook description of oxidative addition reactions, charge flow predominately occurs from the metal centre to the substrate, leading to a net increase in the formal oxidation state of the metal; this occurs with simultaneous bond breaking at the substate. The majority of known reactions, however, involve substrates bearing relatively electronegative elements (e.g. H, C, N, O, halogen) and there has been little discussion of how addition processes may fundamentally change if substrates were constructed from more electropositive elements. Here we show that the zinc–zinc bonded complex, Cp*ZnZnCp*, which is isoelectronic with dihydrogen, undergoes facile addition to the metal (or semi-metal) centres of a series of main group carbene analogues based on aluminium, gallium, or silicon. Reactions proceed with complete breaking of the Zn–Zn bond and increase in the coordination number of the central metal from 2 to 4. Based of DFT calculations and reactivity, these addition processes are not oxidative. Rather data suggest that they are better described as a reductive addition, from the perspective of the main group centre. Our findings challenge our preconceptions regarding text-book definitions and hint that when involving electropositive substrates that oxidative addition processes may not always be oxidative. | Wenbang Yang; Andrew White; Mark Crimmin | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Main Group Chemistry (Inorg.); Bond Activation | CC BY 4.0 | CHEMRXIV | 2024-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a8c1cc5101a2ffa891ed62/original/reductive-addition-of-a-zn-zn-bond-to-main-group-carbene-analogues.pdf |
63f6005d937392db3de4b1e1 | 10.26434/chemrxiv-2023-5dbsv-v2 | Nickel-Catalyzed Direct Stereoselective Alpha-Allylation of Ketones with Non-conjugated Dienes | The development of efficient, sustainable methods for the construction of carbon-carbon bonds with the simultaneous stereoselective generation of vicinal stereogenic centers is a longstanding goal in organic chemistry. In this respect, the carbonyl group is a particularly relevant due to its ability reacting either as electrophile or pro-nucleophile at the alpha-carbon in its enolized form. The transition from precious metals to catalysts based on earth-abundant metals made impressive progress, and especially nickel became a powerful tool due to its low-cost and unique reactivity profiles. Low-valent nickel(0) complexes promote reductive couplings carbonyl compounds exploiting the electrophilic nature of the carbonyl group. In stark contrast, complementary alpha-functionalization of carbonyls leveraging its pro-nucleophilic character in conjunction with olefin acceptors are very scarce despite their attractivity. We report a Ni(0)NHC catalyst which promotes the conversion of ketones and non-conjugated dienes that are both cheap and widely accessible starting materials to synthetically highly valuable alpha-allylated products in excellent yields under mild conditions without any additional base or additive. The catalyst directly activates the alpha-hydrogen atom of the carbonyl substrates transferring it the olefin acceptor. The complete process is redox neutral and fully atom-economic. This feature contrasts typical carbonyl -functionalizations with precious metals that require functionalized substrates like a pre-formed enolate nucleophile and allyl electrophile. The transformation creates adjacent quaternary and tertiary stereogenic centers in a highly diastereoselective manner. Moreover, we introduce a chiral bulky designer NHC ligand allowing to conduct the reaction in an enantioselective manner providing the functionalized products with up to 99:1 er and >20:1 dr. Mechanistic and computational studies indicate an initial LLHT process from the ketone substrate to the olefin substrate to set the selectivity of the whole transformation. A beta-hydride elimination chain walking events is triggered until a favorable pi-allyl intermediate is reached leading by reductive elimination to the targeted products. The shown facile and selective functionalization of alpha-C-H bond of carbonyl groups by Ni(0)NHC catalysts opens new opportunities to exploit sustainable 3d-metal catalysis for a stereoselective access to valuable chiral building blocks. | Yi-Xuan Cao; Matthew Wodrich; Nicolai Cramer | Organic Chemistry; Catalysis; Organometallic Chemistry; Stereochemistry; Bond Activation; Ligand Design | CC BY 4.0 | CHEMRXIV | 2023-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f6005d937392db3de4b1e1/original/nickel-catalyzed-direct-stereoselective-alpha-allylation-of-ketones-with-non-conjugated-dienes.pdf |
60c74d0b4c8919e2d3ad374e | 10.26434/chemrxiv.12584822.v1 | New Insights into the Reactivity of 2-Halo-Glycals. Synthesis of Novel Iodinated Oand S-Glycosides | <p><i>This
is the first report on the Ferrier rearrangement of 2-halo-glycals with
S-nucleophiles. We present herein the selective synthesis of new
2-iodo-2,3-unsaturated O- and S-glycosides. We obtained in good yields and high
anomeric selectivity </i><i>a</i><i>-glycosydes. As a particular behaviour, we also
describe heteroaromatic thio sugar derivatives were the C3 addition was
performed in an alternative mechanism. A complete structure and conformation analysis
by NMR was also presented. </i></p> | Agustín Rojas; Leticia Lafuente; Virginia Vetere; Agustin Ponzinibbio | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d0b4c8919e2d3ad374e/original/new-insights-into-the-reactivity-of-2-halo-glycals-synthesis-of-novel-iodinated-oand-s-glycosides.pdf |
619456e39960f33f03af1808 | 10.26434/chemrxiv-2021-c5t48 | Unity of Opposite: Highly Emissive Luminogens in both Solution and Aggregate States toward Room Temperature Phosphorescence and Electroluminescence | Organic light-emitting materials, especially those with two-phase high emission, have attracted considerable attention for applications in bioimaging agents, sensors, optoelectronic devices, etc. Many fluorophores applied in such fields either emit brightly in dilute solution or in aggregate state, with the former often suffering from aggregation-caused quenching effect, and the latter falling dark at low concentrations. Herein, we overcame the dilemma by balancing the planar and distorted structures with various side units and achieved bright emission in both dilute solution (e.g., the absolute quantum yields (ФPL) = 90.2% in THF) and in aggregate states (e.g., ФPL=92.7% in powder state, ФPL = 95.3% in crystal). These luminescent mate-rials are demonstrated as promising guests embedded into host matrix to achieve efficient room temperature phosphores-cence, and these host-guest systems could be applied in the information encryption. Moreover, these luminogens could also be used as single-component emitting layers to construct non-doped organic light-emitting diodes, from which a maximum external quantum efficiency up to 4.75% with Commission International de L’Eclairge (CIE) coordinates of (0.15, 0.05), which is neatest to next generation ultra-high definition television (UHDTV) display standard, was realized. This work pro-vides a feasible strategy of balancing the planar and distorted structure of a luminogen toward highly efficient emission in both solution and solid states. | Pengbo Han; Chengwei Lin; Yejun Yao; Jia Wang; Yanping Qiu; Dongge Ma; Anjun Qin; Ben Zhong Tang | Materials Science; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619456e39960f33f03af1808/original/unity-of-opposite-highly-emissive-luminogens-in-both-solution-and-aggregate-states-toward-room-temperature-phosphorescence-and-electroluminescence.pdf |
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