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672864edf9980725cf062079 | 10.26434/chemrxiv-2024-1hpjr | Insights into the microphase separation of polystyrene-b-polyproline: Role of polyprolines' secondary structure | Understanding the role of polymers' secondary structure on self-assembly provides a deeper insight into structure-property relationships and is also imperative for designing functional materials. This study investigates the self-assembly of a multi-structured rod-coil diblock copolymer consisting of poly(L-proline) and polystyrene (PS) segments. The unique feature of these diblock copolymers is that the secondary structure of polyproline (PLP) blocks can independently be tuned into two distinct conformations (PPI and PPII). Furthermore, a high energy barrier (81 KJ/mole) associated with the conformational transition between PPI and PPII structures makes it attractive to study the influence of the secondary structure on self-assembly under thermodynamic equilibrium. Thus, the self-assembly of this block copolymer was investigated in terms of the molecular weight and composition of the individual blocks and their secondary structures. A pair of diblock copolymers (PSm-b-PLPn) with differing polyproline block lengths have been synthesized. It has been found that irrespective of the length of the PLP block studied here, the diblock copolymer with trans-polyproline (PPII) self-assembled and microphase separated into a lamellar morphology. However, the diblock copolymer with a cis-polyproline (PPI) segment does not exhibit a well-defined microphase-separated structure despite having identical compositions and molecular weights. As a result, secondary structures are shown to play a role in self-assembly. | Raj Kumar Roy; Arjun Singh Bisht; Subhendu Samanta; Sneha C; Shiv Kumar Alwera | Polymer Science; Nanoscience; Organic Polymers; Polymer morphology; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672864edf9980725cf062079/original/insights-into-the-microphase-separation-of-polystyrene-b-polyproline-role-of-polyprolines-secondary-structure.pdf |
652f837d2431cc1daccbd5ff | 10.26434/chemrxiv-2023-xxcfb | Synthesis of Stereocontrolled Polyurethanes with Defined Monomer Order by Step-economy Approach | Polyurethanes are valuable materials in the industrial sector due to their broad scope of various applications. Traditional synthesis methods rely on step-growth polymerization, which inherently lacks precise molecular weight and structure control. Consequently, pursuing a synthetic strategy for stereocontrolled, sequence-defined polyurethanes represent a substantial challenge in soft material design. This study demonstrates an approach to synthesising discrete, stereo-regulated polyurethanes with defined monomer order by combining the one-pot synthesis method with iterative exponential growth. This work presents a methodology to fabricate non-biological polymers with structural precision characteristics for biomacromolecules. By varying the composition of different monomers and gradually increasing the chiral monomer content or altering its position within the polymer chain, we can influence the secondary structures of polyurethanes and, consequently, their properties and functions. Furthermore, we demonstrated the production of polymers with non-symmetrical sequences, showcasing the feasibility of tailoring polymer chains to specific requirements and preserving complete sequence control. This synthetic strategy paves the way for the facile fabrication of abiotic polymers that could emulate the characteristics of artificial proteins. | Anuj Sharma; Pawel Cwynar; Vijaj Gupta; Róża Szweda | Polymer Science; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652f837d2431cc1daccbd5ff/original/synthesis-of-stereocontrolled-polyurethanes-with-defined-monomer-order-by-step-economy-approach.pdf |
60e536ce609d0dff39d8428b | 10.26434/chemrxiv-2021-zcn1p | Molecular Design and Synthesis of Dicarbazolophane-Based Cen-trosymmetric through-Space Donors for Solution-Processed TADF OLEDs | Conjugation-extended carbazolophane donors, dicarbazolophanes (DCCP), were designed and synthesized by a multi-fold stepwise Pd-catalyzed Buchwald-Hartwig amination/ring cyclization process. Further, elaboration of the DCCP core is possible with introduction of pendant carbazole derivative groups. This provided a way of tuning the optoelectronic properties of the thermally activated delayed fluorescence (TADF) compounds DCCPTRZtBu2, dtBuCzDCCPTRZtBu2, and dMeOCzDCCPTRZtBu2. Solution-processed OLEDs were fabricated and achieved maxi-mum external quantum efficiencies (EQEmax) of 8.2% and EQE of 7.9% at 100 cd/m2. | Zhen Zhang; Stefan Diesing; Ettore Crovini; Abhishek Kumar Gupta; Eduard Spuling; Xuemin Gan; Olaf Fuhr; Martin Nieger; Zahid Hassan; Ifor Samuel; Stefan Bräse; Eli Zysman-Colman | Organic Chemistry; Materials Science; Organic Compounds and Functional Groups; Dyes and Chromophores; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e536ce609d0dff39d8428b/original/molecular-design-and-synthesis-of-dicarbazolophane-based-cen-trosymmetric-through-space-donors-for-solution-processed-tadf-ole-ds.pdf |
60c750804c89195448ad3dad | 10.26434/chemrxiv.13049531.v1 | Evidence of Nanostructure Development from the Molecular Dynamics of Poly(pentamethylene 2,5- Furanoate) | <div><div><div><p>We report on the molecular origin of poly(pentamethylene 2,5-furanoate) particular physical properties. From the structural point of view we found this polymer can develop crystallinity when stored at room conditions for months. On the other hand, we used broadband dielectric spectroscopy (BDS) measurements, to analyze in very detail the local and segmental molecular dynamics of the material subjected to several thermal treatments. In this way we evidenced that the molecular dynamics are sensitive to thermal history over a broad temperature range. This behavior has been attributed to possible inter-chain interactions detected via infrared spectroscopy and rheology measurements in the non-crystallized polymer.</p></div></div></div> | Daniel E Martínez-Tong; Michelina Soccio; Beatriz Robles-Hernández; Giulia Guidotti; Massimo Gazzano; Nadia Lotti; Angel Alegria | Biocompatible Materials; Biodegradable Materials; Carbon-based Materials; Nanostructured Materials - Materials; Biopolymers; Physical and Chemical Properties; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750804c89195448ad3dad/original/evidence-of-nanostructure-development-from-the-molecular-dynamics-of-poly-pentamethylene-2-5-furanoate.pdf |
66dfb873cec5d6c142a47bba | 10.26434/chemrxiv-2024-31x2z | Smooth dispersion is physically appropriate: Assessing and amending the D4 dispersion model | The addition of dispersion corrections to density functionals is essential for accurate energy and geometry predictions. Among them, the D4 scheme is popular due to low computational cost and high accuracy. However, due to its design, the D4 correction can occasionally lead to anomalies, such as un-physical curvature and bumps in the potential energy surface. We find these anomalies are common in the D4 model, although observable consequences are rarer than in the D3 model for reasons we explain. Nevertheless we uncover instances of unphysical local minima and stationary points with the D4 scheme, and propose two solutions that yield smoother dispersion energy as a function of nuclear position. One is trivial to implement, based on a smoother re-parametrization of gaussian weighting (D4S) to find the effective coordination number. The other replaces gaussian weighting with soft linear interpolation (D4SL). These new approaches usually remove artificial extremum points, while maintaining accuracy. | Nikolay V. Tkachenko; Linus Bjarne Dittmer; Rebecca Tomann; Martin Head-Gordon | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66dfb873cec5d6c142a47bba/original/smooth-dispersion-is-physically-appropriate-assessing-and-amending-the-d4-dispersion-model.pdf |
60c74fdbbdbb891b12a39e36 | 10.26434/chemrxiv.12951089.v1 | The Potential of JAK/STAT Pathway Inhibition as a New Treatment Strategy to Control Cytokine Release Syndrome in COVID-19 | COVID-19, a pandemic affecting virus, which is caused by the current SARS-CoV2 coronavirus.
The present research is performed on anti virus and immune-modulating therapies. Cytokine
storms are the toxic drivers and mortality caused by various human viral infections. In addition,
the intensity was linked to an elevated risk of acute respiratory failure, myocardial injury, and
mortality in SARS-CoV-2-infected patients. The Janus kinase (JAK) therapeutic inhibitor class
showed significant clinical benefits in anti-inflammatory and anti-viral effects. Among them,
filgotinib has been approved as an active JAK inhibitor by decreasing biomarkers with main
immune reaction functions and markers supporting matrix-degradation, angiogenesis, leukocyte
adhesion, and recruitment in both research trials. In this study, we tried to get an insight into the
choice of this drug in controlling the jack, to treat Covid 19 using drug design methods will be
discussed.<br /><b></b> | Mohammad Seyedhamzeh; Hazha Omar Othman; Ali aghajani Sharivar; Fatemeh Aliabadi; Mehdi Shafiee Ardestani; Hamidreza Pazoki-Toroudi | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fdbbdbb891b12a39e36/original/the-potential-of-jak-stat-pathway-inhibition-as-a-new-treatment-strategy-to-control-cytokine-release-syndrome-in-covid-19.pdf |
647cf04d4f8b1884b7d770c0 | 10.26434/chemrxiv-2023-l1dtg-v2 | Chemical and Electrocatalytic Ammonia Oxidation by Ferrocenium | Recognizing the potential of ammonia to serve as a carbon-free fuel, we describe an electrocatalytic system for the oxidation of ammonia based on ferrocene (Cp2Fe), an inexpensive, robust catalyst utilizing Earth-abundant iron. Ferrocenium (Cp2Fe+), the 1-electron oxidized form of ferrocene, cleanly oxidizes ammonia to generate nitrogen gas (N2) and protons captured by excess ammonia as NH4+ with electrons reducing ferrocenium to ferrocene. This process occurs under electrocatalytic condi-tions to generate N2 with sustained current. Simple modification of ferrocene through sulfonation allows for solubility in liquid ammonia to enable electrocatalysis in highly concentrated, energy dense solutions of ammonia. Kinetic analysis pro-vides mechanistic clues into the oxidation of ammonia by ferrocenium. | Mahdi Raghibi Boroujeni; Christine Greene; Jeffery A. Bertke; Thomas Cundari; Timothy H. Warren | Inorganic Chemistry; Catalysis; Small Molecule Activation (Inorg.); Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647cf04d4f8b1884b7d770c0/original/chemical-and-electrocatalytic-ammonia-oxidation-by-ferrocenium.pdf |
6601812f9138d2316140646d | 10.26434/chemrxiv-2024-s31dq | In vitro and in vivo Evaluation of Chemically Synthesized,
Receptor-Biased Interleukin-4 and Photocaged Variants
| Interleukin-4 (IL-4) is a cytokine that plays a central role in type 2 immune responses and is involved in regulating pleiotropic actions in our body by engaging multiple different IL-4 receptor (IL-4R) complexes. Targeting the IL-4R system has a high potential for therapeutic intervention for allergic and autoimmune diseases. A challenge in developing this pleiotropic cytokine for clinical application is the construction of variants tailored for engagement with specific receptor IL-4R subunits, which are necessary for selective activation of specific signaling pathways to treat disease with minimum side effects. To establish a platform for preparation of tailored IL-4 variants, we developed a modular and flexible chemical synthesis of IL-4 and applied this approach to the preparation of (i) IL-4 variants that act as receptor antagonist due to presence of unnatural residues that block specific interactions, and (ii) photocaged and in vivo half-life extended IL-4 variants that can be conditionally activated using UV light, achieved by the incorporation of a photocaged Gln116 residue. We were able to show that these different cytokine variants elicit differential STAT5 or STAT6 phosphorylation in lymphocytes or neutrophils in vitro with just one amino acid substitution. Furthermore, we demonstrated that the photocaged IL-4 can be activated by UV light and effectively suppresses neutrophils in an inflammation model in vivo. Collectively, this work demonstrated the flexibility and applicability of chemical protein synthesis by allowing us to broaden the scope of protein variants that can be accessed for the preparation and evaluation of therapeutically valuable proteins. | Mamiko Ninomiya; Cecilie Egholm; Daniel Breu; Onur Boyman; Jeffrey Bode | Biological and Medicinal Chemistry; Organic Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6601812f9138d2316140646d/original/in-vitro-and-in-vivo-evaluation-of-chemically-synthesized-receptor-biased-interleukin-4-and-photocaged-variants.pdf |
60c7453c0f50db67e0396214 | 10.26434/chemrxiv.9936623.v2 | Reductive Electrophotocatalysis: Merging Electricity and Light to Achieve Extreme Reduction Potentials | We describe a new electrophotocatalytic strategy that harnesses the power of light and electricity to generate an excited radical anion with a reducing potential of –3.2 V vs. SCE, which can be used to activate substrates with very high reduction potentials (<i>E</i><sub>red</sub> ~ –1.9 to –2.9 V). The resultant aryl radicals can be engaged in various synthetically useful transformations to furnish arylboronate, arylstannane, and biaryl products.<br /> | Hyunwoo Kim; Hyungjun Kim; Tristan Lambert; Song Lin | Organic Synthesis and Reactions; Electrocatalysis; Organocatalysis; Photocatalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453c0f50db67e0396214/original/reductive-electrophotocatalysis-merging-electricity-and-light-to-achieve-extreme-reduction-potentials.pdf |
60c74b88ee301c0f37c79e97 | 10.26434/chemrxiv.12229232.v2 | A Quantum-Inspired Approach to De-Novo Drug Design | Design and optimization of targeted drug-like compounds is an important part of the early stage drug discovery process. In this paper, we describe the use of a novel technique for rapid design of lead-like compounds for the Dengue viral RNA-dependent-RNA polymerase (RdRp). Initially, a large (>billions) fragment-based chemical library is designed by mapping relevant pharmacophores to the target binding pocket. The de-novo synthesis of molecules from fragments is formulated as a quadratic unconstrained binary optimization problem that can be solved using the quantum-inspired Digital Annealer (DA), providing an opportunity to take advantage of this fledgling, groundbreaking technology. The DA constrains the search space of molecules with drug-like properties that match the binding pocket and then optimizes for synthetic feasibility and novelty, thus offering significant commercial advantages over existing techniques. | David Snelling; Ganesh Shahane; William Shipman; Alexander Balaeff; Mark Pearce; Shahar Keinan | Computational Chemistry and Modeling; Quantum Computing; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b88ee301c0f37c79e97/original/a-quantum-inspired-approach-to-de-novo-drug-design.pdf |
60c755e3702a9b354d18c7d1 | 10.26434/chemrxiv.14178485.v1 | Purely Organic Phosphor Sensitization Based Highly Efficient Electrofluorescence Material | Pure organic room temperature phosphorescence (RTP) materials are considered as potential
candidates for replacing precious metal-based complexes to fabricate highly efficient organic light
emitting devices (OLEDs). However, for reported RTP materials, low photoluminescence quantum
yields (PLQYs) in thin film state seriously impede their applications in OLEDs. On the other hand, how
using normal organic fluorescence materials to fabricate OLEDs with an internal quantum efficiency
(IQE) over 25% remains a great unaddressed issue beyond the thermally activated delayed fluorescence
(TADF) sensitization approach. Here, we establish a strategy to construct highly efficient OLEDs based
on pure organic RTP material sensitized fluorescence emitter. The key point for our strategy is that
benzimidazole-triazine molecules (PIM-TRZ), 2,6-di(phenothiazinyl)naphthalene (β-DPTZN) and
5,6,11,12-tetraphenylnaphthacene (rubrene) were screened as host, phosphor sensitizer and fluorescent
emitter, respectively. Detail photophysical characterizations demonstrate that the host material PIMTRZ with unique RTP nature is critical for achieving phosphor sensitizing process. As an organic RTP
compound, the singlet and triplet state energy levels of β-DPTZN perfectly match with those of PIMTRZ, resulting in the formation and lasting existence of phosphor’s excitons in emitting layer. The large
overlap between the absorption spectrum of rubrene and PL spectrum of PIM-TRZ:10% β-DPTZN film
can facilitate the Förster energy transfer from the triplet β-DPTZN to the singlet rubrene and the finally
displayed fluorescence is derived from singlet excited states of rubrene. The perfect collocation of host,
phosphorescent sensitizer and fluorescent emitter in the emitting layer promise the predominant
performance of the devices with external quantum efficiency (EQE) of 15.7%. The PLQY of emitting
layer is 60.3%, and therefore about 90% carrier injection induced excitons are harvested for light
emission. We present a new strategy to fabricate efficient fluorescent devices by employing ingenious
combination of host, phosphorescent sensitizer and fluorescent emitter, which is significant to the
development of OLEDs.<br /> | Jiaxuan Wang; Baoyan Liang; Jinbei Wei; Yincai Xu; Zhiqiang Li; Tong Yang; Chenglong Li; Yue Wang | Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755e3702a9b354d18c7d1/original/purely-organic-phosphor-sensitization-based-highly-efficient-electrofluorescence-material.pdf |
677436edfa469535b962e499 | 10.26434/chemrxiv-2025-lph6p | A novel bottom-up approach to find lead-compounds in billion-sized libraries | Drug discovery starts with the identification of a ‘hit’ compound that, following a long and expensive optimization process, evolves into a drug candidate. Bigger screening collections increase the odds of finding more and better hits. For this reason, large pharmaceutical companies have invested heavily in high-throughput screening (HTS) collections that can contain several million compounds. However, this figure pales in comparison with the emergent on-demand chemical collections, which have recently reached the trillion scale. These chemical collections are potentially transformative for drug discovery, as they could deliver many diverse and high-quality hits, even reaching lead-like starting points. But, first, it will be necessary to develop computational tools capable of efficiently navigating such massive virtual collections. To address this challenge, we have conceived a novel strategy that explores the chemical universe from the bottom up, performing a systematic search on the fragment space (exploration phase), to then mine the most promising areas of on-demand collections (exploitation phase). Using a hierarchy of increasingly sophisticated computational methods to remove false positives, we maximize the success probability and minimize the overall computational cost. A basic implementation of the concept has enabled us to validate the strategy prospectively, allowing the identification of new BRD4 (BD1) binders with potencies comparable to stablished drug candidates. | Álvaro Serrano-Morrás; Andrea Bertran-Mostazo; Marina Miñarro-Lleonar; Arnau Comajuncosa-Creus; Adrià Cabello; Carme Labranya; Carmen Escudero; Tian Tian; Inna Khutorianska; Dmytro S. Radchenko; Yurii S. Moroz; Lucas Defelipe; David Ruiz-Carrillo; Maria Garcia-Alai; Robert Schmidt; Matthias Rarey; Patrick Aloy; Carles Galdeano; Jordi Juárez-Jiménez; Xavier Barril | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677436edfa469535b962e499/original/a-novel-bottom-up-approach-to-find-lead-compounds-in-billion-sized-libraries.pdf |
67d02e0a6dde43c908694072 | 10.26434/chemrxiv-2025-72vft | Solvent-Free Photochemical Formation of Cubane-type Ru Complexes from Organometallic Ionic Liquids with Cyanoborate Anions | Coordination compounds, including cage compounds, are typically synthesized via solution reactions. Here, we report the solvent-free, quantitative conversion of organometallic ionic liquids (ILs) containing alkyltricyanoborate anions into solid tetraalkyl cubane-type tetranuclear Ru complexes upon ultraviolet irradiation. Furthermore, we elucidated the diverse packing structures of the octyl derivative. | Haruka Koshino; Zi Lang Goo; Sugimoto Kunihisa ; Tomoyuki Mochida | Inorganic Chemistry; Organometallic Compounds | CC BY 4.0 | CHEMRXIV | 2025-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d02e0a6dde43c908694072/original/solvent-free-photochemical-formation-of-cubane-type-ru-complexes-from-organometallic-ionic-liquids-with-cyanoborate-anions.pdf |
675254845a82cea2fa21c28a | 10.26434/chemrxiv-2024-7p4ws | Autoparty: Machine Learning-Guided Visual Inspection of Molecular Docking Results | Human inspection of potential drug compounds is crucial in the virtual drug screening pipeline. However, there is a pressing need to accelerate this process, as the number of molecules humans can realistically examine is extremely limited relative to the scale of virtual screens. Furthermore, computational medicinal chemists can evaluate different poses inconsistently, and there is no standard way of recording annotations. We propose Autoparty, a containerized tool to address these challenges. Autoparty leverages on-premises active learning for drug discovery to facilitate human-in-the-loop training of models that extrapolate human intuition. We leverage multiple uncertainty quantification metrics to query the user with informative examples for model training, limiting the number of human expert training labels. The collected annotations populate a persistent and exportable local database for broad downstream uses. Incorporating Autoparty doubled the hit rate among 193 experimentally tested compounds in a real-world case study. | Laura Shub; Magdalena Korczynska; Duncan F. Muir; Fang-Yu Lin; Alan M. Mathiowetz; Michael J. Keiser | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675254845a82cea2fa21c28a/original/autoparty-machine-learning-guided-visual-inspection-of-molecular-docking-results.pdf |
652d622ebda59ceb9ab4e6c6 | 10.26434/chemrxiv-2023-zmb05 | Toward a General Glycosylation Strategy: Exploring the Dual Functions of Acyl Group Direction in Various Nucleophilic Environments | A universal glycosylation strategy could significantly simplify glycoside synthesis. One approach to achieving this goal is through acyl group stereodirecting participation for the corresponding 1,2-, 1,3-, 1,4-, or 1,6-trans glycosylation; how-ever, this approach had been challenging for glycosidic bonds that require distal equatorial-acyl group direction. We have developed an approach in weakly nucleophilic environments for selective 1,4-trans glycosylation directed by the equato-rial-4-O-acyl group. Here, we explored this condition in other distal acyl groups and found, besides stereodirecting partic-ipation, acyl groups also mediated hydrogen bonding between acyl groups and alcohols. The latter showed a diverse ef-fect and classified the acyl group direction into axial and equatorial categories. Corresponding glycosylation conditions were distinguished as guidance for acyl group direction from either category. Hence, the acyl group direction may serve as a general glycosylation strategy. | Yongtao Gao; Wenjie Chen; Juan Zhao; Min Yang; Yongliang Zhang; Changsheng Chen; Linbin Yao; Jiayuan Xu; Fei Wang; Bangzhi Zhang; Guofeng Gu; Bencan Tang; Feng Cai | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652d622ebda59ceb9ab4e6c6/original/toward-a-general-glycosylation-strategy-exploring-the-dual-functions-of-acyl-group-direction-in-various-nucleophilic-environments.pdf |
6220f20ac6bb55a3927b406d | 10.26434/chemrxiv-2022-22ts5 | Density Functional Tight Binding Calculations for Probing Electronic-Excited States of Large Systems | This review focuses on the application of Density Functional Tight Binding (DFTB) to electronic-excited states, which has attracted significant attention for extending the computationally efficient approach to the time domain. The chapter highlights the use of real-time time-dependent-DFTB to probe the electron dynamics of large systems in external electric fields where the nuclei are held fixed. Surface hopping is a general mixed quantum-classical nonadiabatic dynamics methodology with many variants, such as fewest-switches surface-hopping, decoherence induced surface hopping, independent electron surface hopping, and others. The nuclei are propagated according to classical mechanics, and the forces on the nuclei, at any given instant of time, arise from a single adiabatic potential energy surfaces. The review illustrates the charge transfer dynamics of Phenyl-C61-butyric acid methyl ester/polythiophene, which is a model system for understanding photo-induced charge transfer dynamics in organic photovoltaics. | Sharma Yamijala; M. Belen Oviedo; Bryan Wong | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2022-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6220f20ac6bb55a3927b406d/original/density-functional-tight-binding-calculations-for-probing-electronic-excited-states-of-large-systems.pdf |
60c74dbd337d6ced21e27e34 | 10.26434/chemrxiv.12248561.v2 | Drug Repurposing for Candidate SARS-CoV-2 Main Protease Inhibitors by a Novel in Silico Method | <p>The SARS-CoV-2 outbreak caused an
unprecedented global public health threat, having a high transmission rate with
currently no drugs or vaccines approved. An alternative powerful additional
approach to counteract COVID-19 is <em>in silico</em> drug repurposing. The
SARS-CoV-2 main protease is essential for viral replication and an attractive
drug target. In this study, we used the virtual screening (VS) protocol with
both long-range and short-range interactions to select candidate SARS-CoV-2
main protease inhibitors. First, the ISM applied for Small Molecules was used
for searching the Drugbank database and further followed by molecular docking.
After <em>in silico</em> screening of drug space, we identified 57 drugs as
potential SARS-CoV-2 main protease inhibitors that we propose for further
experimental testing.</p> | Milan Sencanski; Vladimir Perovic; Snezana Pajovic; Miroslav Adzic; Slobodan Paessler; Sanja Glisic | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dbd337d6ced21e27e34/original/drug-repurposing-for-candidate-sars-co-v-2-main-protease-inhibitors-by-a-novel-in-silico-method.pdf |
62f506c76948b9f73fb4816b | 10.26434/chemrxiv-2022-p9nht | Nanoscale chemical imaging of human cell membrane using Tip-enhanced Raman spectroscopy | The lack of an appropriate tool for visualizing cell membrane molecules at the nanoscale in a non-invasive and label free fashion limits our understanding of many vital cellular processes. Herein, we demonstrate that tip-enhanced Raman spectroscopy (TERS) is capable of visualizing the molecular distribution in pancreatic cancer cell (BxPC-3) membranes in ambient conditions without labelling with a spatial resolution down to ca. 2.5 nm. TERS imaging successfully reveals segregation of phenylalanine-rich and histidine-rich, phosphatidylcholine (PC) lipid-rich and protein-rich, as well as cholesterol-rich BxPC-3 cell membrane domains at the nanometer length-scale. Additionally, TERS imaging also showed a BxPC-3 cell membrane region where cholesterol is mixed with protein. Interestingly, the higher resolution TERS imaging revealed that the molecular domains observed on the BxPC-3 cell membrane are not chemically “pure” but also contain other biomolecules. These results demonstrate the potential of TERS for non-destructive and label-free imaging of biological cell membranes with nanoscale resolution. | Dušan Mrđenović; Wenjie Ge; Naresh Kumar; Renato Zenobi | Physical Chemistry; Analytical Chemistry; Nanoscience; Analytical Chemistry - General; Imaging; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f506c76948b9f73fb4816b/original/nanoscale-chemical-imaging-of-human-cell-membrane-using-tip-enhanced-raman-spectroscopy.pdf |
66bdb55ba4e53c48767278a7 | 10.26434/chemrxiv-2024-flsz3 | Europium Doping Effects on the Properties of CsPbBr3 Nanocrystals: In-situ vs. Ex-situ Synthetic Path Analysis | Metal halide perovskites (MHPs), particularly CsPbBr3 nanocrystals (NCs), attract significant interest due to their remarkable optoelectronic properties. These properties make them ideally suited for applications such as photovoltaics and ionizing radiation detectors. However, CsPbBr3 NCs suffer from poor luminescence efficiency and short service life. Doping with rare earth (RE) elements, especially europium (Eu), has emerged as a viable method for solving these problems because of their unique electronic structure. Doping with RE improves luminescence efficiency and extends the service life of the MHPs, enhancing their optoelectronic properties and catalytic capabilities. This study examines the effects of in-situ and ex-situ europium doping on the structural, optical, and photocatalytic properties of CsPbBr3 NCs. In-situ doping was achieved by introducing the dopant during the NC synthesis, while ex-situ doping involved adding the dopant to pre-prepared NCs via sonochemical synthesis with an ultrasonic bath. The doped NCs exhibit enhanced emission and boosted photocatalytic activity, showcasing the multifaceted benefits of Eu ions doping. The study concludes that in-situ europium doping, particularly at 5 wt%, significantly enhances the structural and functional characteristics of CsPbBr3 NCs, offering a promising approach for improving their performance in optoelectronic and photocatalytic applications. | Hila Shalom; Raanan Carmieli; Pini Shekhter; Lena Yadgarov | Materials Science; Catalysis; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bdb55ba4e53c48767278a7/original/europium-doping-effects-on-the-properties-of-cs-pb-br3-nanocrystals-in-situ-vs-ex-situ-synthetic-path-analysis.pdf |
6229a9b6011b584c14c45060 | 10.26434/chemrxiv-2022-5ztvt | On the potential intermediacy of PhIBr2 as a brominating agent | PhIBr2, first purported 100 years ago, has been subject of few reports due to its low stability. However, a recent publication proposes a reaction of PIFA (PhI(OC(O)-CF3)2) with TMSBr to form PhIBr2 in-situ and demonstrated its efficacy in aryl brominations. Our report investigates this synthesis by replicating bromination reactions claiming to use in-situ PhIBr2 as described. The spectroscopical and computational results indicate formation of PhI and Br2 where Br2 is responsible for bromination and no supporting evidence for invoking PhIBr2 as an intermediate is found. | Jason Dutton; David Wilson; Tania _; Andrew Molino | Organic Chemistry; Inorganic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Main Group Chemistry (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2022-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6229a9b6011b584c14c45060/original/on-the-potential-intermediacy-of-ph-i-br2-as-a-brominating-agent.pdf |
62dfd1bf5be0419ad69bf06e | 10.26434/chemrxiv-2022-mrfmx | Investigation on the relationship between lipid composition and structure in model membranes composed of extracted natural phospholipids | Unravelling the structural diversity of cellular membranes is a paramount challenge in life sciences. In particular, lipid composition affects the membrane collective behaviour, and its interactions with other biological molecules.
Here, the relationship between membrane composition and resultant structural features was investigated by surface pressure-area isotherms, Brewster angle microscopy and neutron reflectometry on in vitro membrane models of the mammalian plasma and endoplasmic-reticulum-Golgi intermediate compartment membranes in the form of Langmuir monolayers. Natural extracted yeast lipids were used because, unlike synthetic lipids, the acyl chain saturation pattern of yeast and mammalian lipids are similar.
The structure of the model membranes, orthogonal to the plane of the membrane, as well as their lateral packing, was found to depend strongly on their specific composition, with cholesterol having a major influence on the in-plane morphology, yielding a coexistence of liquid-order and liquid-disorder phases.
| Andreas Santamaria; Krishna C. Batchu; Giovanna Fragneto; Valerie Laux; Michael Haertlein; Tamim A. Darwish; Robert A. Russell; Eduardo Guzman; Nathan Zaccai; Armando Maestro | Biological and Medicinal Chemistry; Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62dfd1bf5be0419ad69bf06e/original/investigation-on-the-relationship-between-lipid-composition-and-structure-in-model-membranes-composed-of-extracted-natural-phospholipids.pdf |
62b26b1c1278ae5d7dea8c5f | 10.26434/chemrxiv-2022-2q2xp | Origins of the Selective C−S Bond Formation by the Non-Heme Iron EgtB | The nonheme iron EgtB and OvoA are sulfoxide synthases that catalyze oxidative C−S bond formation in the synthesis of ergothioneine and ovothiol. Despite the extensively experimental and computational studies of the catalytic mecha-nisms of these enzymes, the root causes for the selective C−S bond formation remains elusive. Using combined molecu-lar dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) method, we show here that coordination dynamics of the sulfoxide intermediate is involved in the catalysis of nonheme iron EgtB. Such coordina-tion switch from S to O atom is driven by the S/ electrostatic interactions, which promotes efficiently the observed stereoselective C-S bond formation while bypassing cysteine dioxygenation. As such, the present mechanism high-lights the critical role of coordination dynamics in catalysis, and it is in agreement with all available experimental data, including regioselectivity, stereoselectivity and KIE results. | Peng Wu; Yang Gu; Langxing Liao; Yanfei Wu; JiaoYu Jin; Zhanfeng Wang; Jiahai Zhou; Sason Shaik; Binju Wang | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b26b1c1278ae5d7dea8c5f/original/origins-of-the-selective-c-s-bond-formation-by-the-non-heme-iron-egt-b.pdf |
6728f5b57be152b1d0f6db25 | 10.26434/chemrxiv-2024-7fg0w | Modern organophotocatalysts: a new inspiration source for Symmetrical Organic Redox Flow Batteries | Redox flow batteries (RFBs) have emerged as significant energy storage systems amid the growing adoption of renewable energy. However, the advancement of all-organic RFBs is hindered by material crossover, limited energy density, and the time-consuming selection of suitable electrolyte partners. To address these challenges, bipolar redox-active organic molecules (BRMs) show promise for charge storage in symmetric organic redox flow batteries (SORFBs), although their development can be complex and tedious. In this study, we report an approach aimed at streamlining the identification of suitable compounds through an examination of the organophotocatalyst literature, illustrated through six acridinium compounds exhibiting stable redox states. These compounds were thoroughly characterized in electrochemical cells and subjected to cycling tests in fully symmetric flow batteries. Notably, a trisubstituted electron-rich acridinium compound emerged as a potential candidate, demonstrating over 20 days of cycling stability. Given the extensive library of organic catalysts and the advantages of SORFB designs, this approach will prove to be essential for developing an innovative electrochemical storage system. | Jules Moutet; Mubarak Md Hossain; Ramandeep Kaur; Tarek H. El-Assaad; Waleed K. Yual; Janelle M. Amegatse; Thomas L. Gianetti | Organic Chemistry; Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6728f5b57be152b1d0f6db25/original/modern-organophotocatalysts-a-new-inspiration-source-for-symmetrical-organic-redox-flow-batteries.pdf |
6634f02021291e5d1d58702c | 10.26434/chemrxiv-2024-6wmg4 | Accelerated end-to-end chemical synthesis development with large language models | The rapid emergence of large language model (LLM) technology presents significant opportunities to facilitate the development of synthetic reactions. In this work, we leveraged the power of GPT-4 to build a multi-agent system to handle fundamental tasks involved throughout the chemical synthesis development process. The multi-agent system comprises six specialized LLM-based agents, including Literature Scouter, Experiment Designer, Hardware Executor, Spectrum Analyzer, Separation Instructor, and Result Interpreter, which are pre-prompted to accomplish the designated tasks. A web application was built with the multi-agent system as the backend to allow chemist users to interact with experimental platforms and analyze results via natural language, thus, requiring zero-coding skills to allow easy access for all chemists. We demonstrated this multi-agent system on the development of a recently developed copper/TEMPO catalyzed aerobic alcohol oxidation to aldehyde reaction, and this LLM multi-agent copiloted end-to-end reaction development process includes: literature search and information extraction, substrate scope and condition screening, reaction kinetics study, reaction condition optimization, reaction scale-up and product purification. This work showcases the trilogy among chemist users, LLM-based agents, and automated experimental platforms to reform the traditional expert-centric and labor-intensive reaction development workflow. | Yixiang Ruan; Chenyin Lu; Ning Xu; Jian Zhang; Jun Xuan; Jianzhang Pan; Qun Fang; Hanyu Gao; Xiaodong Shen; Ning Ye; Qiang Zhang; Yiming Mo | Organic Chemistry; Organic Synthesis and Reactions; Process Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6634f02021291e5d1d58702c/original/accelerated-end-to-end-chemical-synthesis-development-with-large-language-models.pdf |
67c8228e81d2151a02276c23 | 10.26434/chemrxiv-2025-1nxwg | The Bond Capacity Electronegativity Equilibration Charge Model (EEQBC) for the Elements Z=1–103 | The accurate and efficient assignment of atomic partial charges is crucial for many applications in theoretical and computational chemistry, including polarizable force fields, dispersion corrections, and charge-dependent basis sets. Classical charge models struggle to distinguish between neutral and zwitterionic fragments because, unlike quantum mechanical methods, there are no discrete electronic states. This limitation can lead to either reduced or additional artificial charge transfer (CT) at different interfragment distances. To address this issue, we propose a new version of a bond capacity electronegativity equilibration (EEQBC) model, which limits artificial CT between distant fragments in the simple EEQ framework. EEQBC offers excellent agreement with DFT-based reference charges for elements up to lawrencium (Z = 103) with mean absolute errors as low as 0.02 and 0.07 e− for random PubChem molecules and "mindless" molecules (MLMs), respectively. Thanks to its computational efficiency for both atomic charges and their analytical nuclear gradients, EEQBC is highly suitable as an initial charge guess for next-generation tight-binding methods. For seamless accessibility, EEQBC is implemented in the freely available multicharge program at: github.com/thfroitzheim/multicharge/tree/eeq-bc. | Thomas Froitzheim; Marcel Müller; Andreas Hansen; Stefan Grimme | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c8228e81d2151a02276c23/original/the-bond-capacity-electronegativity-equilibration-charge-model-eeqbc-for-the-elements-z-1-103.pdf |
60c74714ee301c2924c7963a | 10.26434/chemrxiv.11494428.v1 | Combining Automated Microfluidic Experimentation with Machine Learning for Efficient Polymerization Design | <div><div><div><p>Understanding polymerization reactions has challenges relating to the complexity of the systems, hazards associated with the reagents, environmental footprint of the operations, and the highly non-linear topologies of reaction spaces. In this work, we aim to present a new methodology for studying such complex reactions using machine-learning-assisted automated microchemical reactors. A custom-designed rapidly prototyped microreactor is used in conjunction with in situ infrared thermography and efficient, high-speed experimentation to map the reaction space for a zirconocene polymerization catalyst. Chemical waste was decreased by two orders of magnitude and catalytic discovery was performed in one hour. Here we show that efficient microfluidic technology can be coupled with machine learning algorithms to obtain high-fidelity datasets on a complex chemical reaction.</p></div></div></div> | Benjamin Rizkin; Albert Shkolnik; Neil Ferraro; Ryan L. Hartman | Organic Synthesis and Reactions; Process Chemistry; Organic Polymers; Polymerization (Polymers); Polymerization catalysts; Polymerization kinetics; Analytical Apparatus; Chemoinformatics; Spectroscopy (Anal. Chem.); High-throughput Screening; Theory - Computational; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Industrial Manufacturing; Process Control; Reaction Engineering; Homogeneous Catalysis; Organocatalysis; Catalysis; Polymerization (Organomet.); Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74714ee301c2924c7963a/original/combining-automated-microfluidic-experimentation-with-machine-learning-for-efficient-polymerization-design.pdf |
674e4013f9980725cfd6b75c | 10.26434/chemrxiv-2024-cfz3l | Redox, Spectroscopic and Magnetic Properties of C3-Symmetry Rare Earth Complexes Featuring Atypical Ortho-Dioxolene Binding | The molecular symmetry in rare earth (RE) coordination chemistry is critically important for controlling the electronic structure of the RE ion and resulting magnetic and photophysical properties. Here we report a family with unusual C3 point symmetry, [REIII(Br4catH)3(tpa)] (Br4catH− = tetrabromocatecholate, tpa = tris(2-pyridylmethyl)amine). The synthesis and solid-state characterisation of eleven analogues (RE = Y, Sm to Lu) were performed, enabling a systematic investigation of the effect of symmetry on various physical properties across the RE series. The crystal structures reveal a unique cooperative coordination motif, featuring a cyclic hydrogen-bonding network between the atypical monodentate monoprotonated Br4catH− ligands. Electrochemistry reveals a single oxidation process that suggests a concerted three-electron oxidation of all tetrabromocatecholate ligands to semiquinonate. Furthermore, single-molecule magnet (SMM) behaviour was investigated, revealing unexpected in-field slow magnetic relaxation for both Dy and Yb analogues, which can be rationalised by the effect of C3-symmetry. Finally, luminescence measurements were performed to probe the CF splitting of the Yb analogue and quantify the error in the overall CF splitting suggested by ab initio calculations. The governing effects of C3-symmetry are consistent observations in all RE3+ metals studied in this work, manifesting in the concerted three-electron oxidation, SMM behaviour, ground state composition, and luminescence properties. | Stanley Bagio; Jonay Gonzalez; Robert Gable; Colette Boskovic; Christopher Hall; Marcus Giansiracusa | Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Magnetism | CC BY 4.0 | CHEMRXIV | 2024-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674e4013f9980725cfd6b75c/original/redox-spectroscopic-and-magnetic-properties-of-c3-symmetry-rare-earth-complexes-featuring-atypical-ortho-dioxolene-binding.pdf |
610286830321141768b89462 | 10.26434/chemrxiv-2021-l2svh | Chemical Synthesis and Immunological Evaluation of Cancer Vaccines Based on Ganglioside Antigens and α-Galactosylceramide | iNKT cells – often referred as the “Swiss Army knife” of the immune system ‒ have emerged as central players in cancer vaccine therapies. Glycolipids activating iNKT cells, such as α-galactosylceramide (αGalCer), can enhance the immune response against co-delivered cancer antigens and have been applied in the design of self-adjuvanting anti-tumor vaccines. In this context, this work focuses on the chemical synthesis of ganglioside tumor-associated carbohydrate antigens (TACAs), namely GM3 and (Neu5Gc)GM3 antigens, their conjugation to αGalCer, and their formulation into liposomes as an efficient platform for their in vivo delivery. Liposomes containing GM3‒αGalCer, (Neu5Gc)GM3‒αGalCer, and equimolar amounts of the two conjugates have been fully characterized and their ability to activate iNKT cell has been confirmed in vitro. Finally, the candidates were tested in in vivo immunization studies, demonstrating an ability to induce both Th1 and Th2 cytokines further leading to the production of all subclasses of IgG antibodies. Notably, the study also demonstrated that serum antibodies raised against the two TACAs alone and in combination were cross-reactive. This finding has consequences for future vaccine designs – even if a highly tumor-selective antigen is chosen, the resulting antibody response may be broader than anticipated. | Cecilia Romanò; Hao Jiang; Sahar Tahvili; Peng Wei; Ulrik Bering Keiding; Gael Clergeaud; Jonas Rosager Henriksen; Thomas Lars Andresen; Anders Elias Hansen; Dennis Christensen; Mads Hartvig Clausen | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610286830321141768b89462/original/chemical-synthesis-and-immunological-evaluation-of-cancer-vaccines-based-on-ganglioside-antigens-and-galactosylceramide.pdf |
60c74d800f50db7e8e39704f | 10.26434/chemrxiv.12324188.v2 | Valuing Economic Impact Reductions of Nutrient Pollution from Livestock Waste | Nutrient pollution from livestock waste impacts both fresh and marine coastal waters. Harmful algae blooms (HABs) are a common ecosystem-level response to such pollution that is detrimental to both aquatic life and human health and that generates economic losses (e.g., property values and lost tourism). Waste treatment and management technologies are not well established practices due, in part, to the difficulty to attribute economic value to associated social and environmental impacts of nutrient pollution. In this work, we propose a computational framework to quantify the economic impacts of HABs. We demonstrate the advantage of quantifying these impacts through a case study on livestock waste management in the Upper Yahara watershed region (in the state of Wisconsin, USA). Our analysis reveals that every excess kilogram of phosphorus runoff from livestock waste results in total economic losses of 74.5 USD. Furthermore, we use a coordinated market analysis to demonstrate that this economic impact provides a strong enough incentive to activate a nutrient management and valorization market that can help balance phosphorus within the study area. The proposed framework can help state, tribes, and federal regulatory agencies develop regulatory and non-regulatory policies to mitigate the impacts of nutrient pollution. | Apoorva Sampat; Andrea Hicks; Gerardo Ruiz-Mercado; Victor M. Zavala | Environmental Science; Wastes | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d800f50db7e8e39704f/original/valuing-economic-impact-reductions-of-nutrient-pollution-from-livestock-waste.pdf |
6797589afa469535b9073248 | 10.26434/chemrxiv-2025-5v2bj | Global Kinetic-Thermodynamic Responses: Derivation of a General Non-Linear Equation and Demonstrations on Chemical Reactions | How to accelerate a reaction has been a critical question in physical organic chemistry, eliciting multiple models describing the interplay between kinetics and thermodynamic driving forces. However, existing models often come with inevitable limitations: valid only within finite thermodynamic ranges, rely on heavy physical assumptions, or treat specific observed reactivity as isolated occurrences. We present the derivation of the non-linear relationship that generalises the relationship between activation energies with respect to reaction energies in chemical reactions, providing a broader and more overarching model than the classical Bell-Evans-Polanyi relationships, Leffler equation, and Marcus equation. This formulation is reached with minimal assumptions, stemming from the principle of microscopic reversibility. In contrast to the commonly observed Brønsted slopes and intrinsic barriers which represent the local approximation of the kinetic-thermodynamic response of a family of reactions only within a small range of reaction energies, we introduce a new set of thermodynamic-independent parameters (Emin, Eeq and θ) that capture the global kinetic-thermodynamic relationship across the entire thermodynamic range. We showcase the applicability of this model and the insights it provides from a set of 1,2-hydride shifts and Beckmann rearrangements, identifying the origin of differences in activation barriers across substrates and enabling the rational evaluation of reactivity trends. The findings demonstrate the chemical significance of the three parameters in the non-linear model inherently affording information about the reaction unattainable through simple data fitting. The equation governing the non-linear relationship provides new paths for the rational modulation of energy barriers, new perspectives towards developing reaction methodology. Our global non-linear relationship can still be applied to a linear approximation within finite thermodynamic ranges, while also enabling the examination and improvement of its reliability, providing straightforward practical guidance for reaction analysis and optimisation. | Eduardo Garcia-Padilla; Guanqi Qiu | Theoretical and Computational Chemistry; Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6797589afa469535b9073248/original/global-kinetic-thermodynamic-responses-derivation-of-a-general-non-linear-equation-and-demonstrations-on-chemical-reactions.pdf |
6646b23191aefa6ce134773c | 10.26434/chemrxiv-2024-n73xg | Liquid Crystalline Pressure-Sensitive Adhesive based on a
Shape-Assisted Molecular Assembly with Electron-Deficient Twofold Columnar π-Stacking | Recently, the chemistry of supramolecular adhesives has rapidly progressed in materials science and tissue engineering. Many structural motifs with a variety of non-covalent interactions have been proposed for advanced adhesive properties. Here, we propose a new materials class of liquid crystalline pressure-sensitive adhesive (LC-PSA). Without the aid of hydrogen bonding or Coulomb force, a cyclooctatetraene(COT)-fused electron-deficient dipyridophenazine dimer (dppz-FLAP) forms a tight twofold columnar-stacking based on its V-shaped molecular structure (π-π distance: 3.32 Å). With the dppz-FLAP core as a mesogen of liquid crystal, a high shear LC-PSA bearing a well-defined packing structure in a hexagonal columnar phase has been developed. Both hydrophobic and hydrophilic glass substrates can be easily bonded at room temperature by simply pressing a flake sample of the molecular adhesive between the substrates. Tensile shear strengths reached approximately 1 MPa for glass, SUS and Fe substrates based on dispersion interaction with significant ductility, while the easy peelability on a PET tape was confirmed. The rigid columnar structure formed by the shape-assisted assembly results in the high cohesive force of the material, while the soft liquid crystalline properties provide sufficient fluidity as a PSA. Viscoelastic analysis revealed a unique position of the LC-PSA (G′~10^7 Pa, G′′~10^6 Pa) compared with conventional PSAs. The concept of LC-PSA based on the rigid/soft hybridization and hydrogen-bond-free molecular engineering extends the potential of supramolecular adhesives and functional small-molecule materials. | Kota Ono; Kensuke Suga; Mitsuo Hara; Katsuki Miyokawa; Tsubasa Honda; Kazuya Otsubo; Shohei Saito | Organic Chemistry; Materials Science; Supramolecular Chemistry (Org.); Liquid Crystals; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6646b23191aefa6ce134773c/original/liquid-crystalline-pressure-sensitive-adhesive-based-on-a-shape-assisted-molecular-assembly-with-electron-deficient-twofold-columnar-stacking.pdf |
60c74888469df435cbf43a4b | 10.26434/chemrxiv.11919039.v1 | Spin–Phonon Coupling and Dynamic Zero-Field Splitting Contributions to Spin Conversion Processes in Iron(II) Complexes | Magnetization dynamics of transition metal complexes manifest in properties and phenomena of fundamental and applied interest (e.g., slow magnetic relaxation in single molecule magnets (SMMs), quantum coherence in quantum bits (qubits), and intersystem crossing (ISC) rates in photophysics). While spin–phonon coupling is recognized as an important determinant of these dynamics, additional fundamental studies are required to unravel the nature of the coupling and thus leverage it in molecular engineering approaches. To this end, we describe here a combined ligand field theory and multireference <i>ab initio</i> model to define spin–phonon coupling terms in S = 2 transition metal complexes and demonstrate how couplings originate from both the static and dynamic properties of ground and excited states. By extending concepts to spin conversion processes, ligand field dynamics manifest in the evolution of the excited state origins of zero-field splitting (ZFS) along specific normal mode potential energy surfaces. Dynamic ZFSs provide a powerful means to independently evaluate contributions from spin-allowed and/or -forbidden excited states to spin–phonon coupling terms. Furthermore, ratios between various intramolecular coupling terms for a given mode drive spin conversion processes in transition metal complexes and can be used to analyze mechanisms of ISC. Variations in geometric structure strongly influence the relative intramolecular linear spin–phonon coupling terms and will thus define the overall spin state dynamics. While of general importance for understanding magnetization dynamics, this study links the phenomenon of spin–phonon coupling across fields of single molecule magnetism, quantum materials/qubits, and transition metal photophysics. | Nicholas Higdon; Alexandra Barth; Patryk Kozlowski; Ryan Hadt | Magnetism; Spectroscopy (Inorg.); Theory - Inorganic; Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling; Theory - Computational; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74888469df435cbf43a4b/original/spin-phonon-coupling-and-dynamic-zero-field-splitting-contributions-to-spin-conversion-processes-in-iron-ii-complexes.pdf |
65c244c6e9ebbb4db9c9446e | 10.26434/chemrxiv-2023-dj4m0-v3 | Monovalent Ion - Graphene Oxide Interactions are Controlled by Carboxylic Acid Groups: Sum Frequency Generation Spectroscopy Studies | Graphene oxide (GO) is a two dimensional, mechanically strong, and chemically tunable material for separations. Elucidating GO-ion-water interactions at the molecular scale is highly important for predictive understanding of separation systems. However, direct observations of the nanometer region by the GO surfaces under operando conditions is not trivial. Therefore, thin films of GO at the air/water interface can be used as model systems. With this approach, we study the effects of alkali metal ions on water organization near graphene oxide films at the air/water interface using vibrational sum frequency generation (SFG) spectroscopy. We also use an arachidic acid Langmuir monolayer as a benchmark for a pure carboxylic acid surface. Theoretical modeling of the concentration-dependent sum frequency signal from graphene oxide and arachidic acid surfaces reveals that the adsorption of monovalent ions is mainly controlled by the carboxylic acid groups on graphene oxide. An in-depth analysis of sum frequency spectra reveals at least three distinct water populations with different hydrogen bonding strengths. The origin of each population can be identified from the concentration dependent variations of their SFG signal. Interestingly, interfacial water structure seemed mostly insensitive to the character of the alkali cation, in contrast to similar studies conducted at the silica/water interface. However, we observed an ion-specific effect with lithium, whose strong hydration prevented direct interactions with the graphene oxide film. | Seung Eun Lee; Amanda J. Carr; Raju R. Kumal; Ahmet Uysal | Physical Chemistry; Interfaces; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c244c6e9ebbb4db9c9446e/original/monovalent-ion-graphene-oxide-interactions-are-controlled-by-carboxylic-acid-groups-sum-frequency-generation-spectroscopy-studies.pdf |
60c7445e842e65101fdb2438 | 10.26434/chemrxiv.9783791.v1 | Towards an Artificial Carbohydrates Supply on Earth | How to feed a growing global population in a secure and sustainable way? The conventional, biogenic agriculture has yet failed to provide a reliable concept which circumvents its severe environmental externalities—such as the massive use of land area, water for irrigation, fertiliser, pesticides, herbicides, and fossil fuel. In contrast, the artificial synthesis of carbohydrates from atmospheric carbon dioxide, water, and renewable energy would allow not only for a highly reliable production without those 10 externalities, but would also allow to increase the agricultural capacities of our planet by several orders of magnitude. All required technology is either commercially available or at least developed on a lab-scale. No directed research has, however, yet been conducted to wards an industry-scale carbohydrate synthesis because the biogenic carbohydrate production was economically more competitive. Taking the environmental and socioeconomic externalities of the conventional sugar production into account, this economical narrative has to be questioned. We estimate the production costs of artificial sugar at 1 C/kg. While the today’s spot market price for conventional sugar is about 0.3 C/kg, we estimate its total costs (including external costs) at 0.9 C/kg in humid regions and 2 C/kg in semi-arid regions. Accordingly, artificial sugar appears already today to be the less expensive way of production. The artificial sugar production allows in principle also for a subsequent synthesis of other carbohydrates such as starch and cellulose as well as fats. This manuscript aims at rising research interest and at enhancing awareness for a transition to a nonagricultural and more resource conserving way to supply carbohydrates for food.<br /> | Florian Dinger; Ulrich Platt | Feed; Food | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7445e842e65101fdb2438/original/towards-an-artificial-carbohydrates-supply-on-earth.pdf |
66753e9401103d79c5c250e7 | 10.26434/chemrxiv-2024-rrvb6-v2 | FRETting about CRISPR-Cas assays: Dual-channel reporting lowers detection limits and times-to-result | CRISPR-Cas systems have evolved several mechanisms to specifically target foreign DNA. These properties have made them attractive as biosensors. The primary drawback associated with contemporary CRISPR-Cas biosensors is their weak signaling capacity, which is typically compensated for by coupling the CRISPR-Cas systems to nucleic acid amplification. This adds time and complexity to the diagnostic process, limiting the practicality of these assays for many clinical applications. An alternative strategy to improve signaling capacity is to engineer the reporter, i.e., design new signal-generating substrates for Cas proteins. Unfortunately, due to their reliance on custom synthesis or specialized analytical equipment, most of these engineered reporter substrates are inaccessible to many researchers. Herein, we present a substrate for Cas12a that functions as a seamless “drop-in” replacement for existing reporters, without the need to change any other aspect of a CRISPR-Cas12a-based assay. The reporter is readily available and employs a FRET pair to produce two signals upon cleavage by Cas12a. Use of both signals in a ratiometric manner provides for improved assay performance and a decreased time-to-result for several CRISPR-Cas12a assays. We comprehensively characterize this reporter to better understand the reasons for the improved signaling capacity and benchmark it against the current standard CRISPR-Cas reporter. Finally, to showcase the real-world utility of our reporter, we apply it to the analysis of Human papillomavirus in clinical samples | Jacob Lesinski; Nathan Khosla; Carolina Paganini; Bo Verberckmoes; Heleen Vermandere; Andrew deMello; Daniel Ashley Richards | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66753e9401103d79c5c250e7/original/fre-tting-about-crispr-cas-assays-dual-channel-reporting-lowers-detection-limits-and-times-to-result.pdf |
64a507626e1c4c986bd365c9 | 10.26434/chemrxiv-2023-tphcd | Use of Emerging C–H Functionalization Methods to Implement Strategies for the Divergent Total Syntheses of Bridged Polycyclic Natural Products | Carbon–hydrogen (C–H) bonds are ubiquitous in complex natural products. Over the past three decades, many methods to convert C–H bonds distal from functional groups, which were generally considered inert, have been developed. These advances now enable selective peripheral functionalizations at a late-stage. The direct engagement of traditionally unreactive C–H bonds in reactions expands chemical space by reducing functional group interconversions. As such, C–H functionalization serves as a powerful tool in medicinal and agrochemical chemistry as well as in the total synthesis of natural products where diversification to a broad array of compounds from a common intermediate is often desired. In this Account, we detail the thought processes and design principles that relied on emerging methods for C–H functionalization to prepare a wide range of bridged, polycyclic, natural products in the cephalotane and longibornane families from a common intermediate in each case. | Goh Sennari; Richmond Sarpong | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a507626e1c4c986bd365c9/original/use-of-emerging-c-h-functionalization-methods-to-implement-strategies-for-the-divergent-total-syntheses-of-bridged-polycyclic-natural-products.pdf |
60c74857567dfef14dec49cf | 10.26434/chemrxiv.11898126.v1 | Electrochemical Detection of Free-Chlorine in Water Samples Facilitated by In-Situ pH Control Using Interdigitated Microelectrodes | Residual free-chlorine concentration in water supplies is a key metric studied to ensure disinfection. High residual chlorine concentrations lead to unpleasant odours and tastes, while low concentrations may lead to inadequate disinfection. The concentration is most commonly monitored using colorimetric techniques which require additional reagents. Electrochemical analysis offers the possibility for in-line analysis without the need for additional reagents. Electrochemical-based detection of chlorine is influenced by the solution pH, which defines the particular chlorine ionic species present in solution. As such, controlling the pH is essential to enable electrochemical based detection of residual chlorine in water. To this end, we explore the application of solid state interdigitated electrodes to tailor the in-situ pH of a solution while simultaneously detecting free-chlorine. Finite element simulations and subsequent electrochemical characterization, using gold interdigitated microelectrode arrays, were employed to explore the feasibility of an in-situ pH control approach. In practice, the approach converted residual chlorine from an initial mixture of two species (hypochlorous acid and hypochlorite ion), to one species (hypochlorous acid). Chlorine detection was shown in water samples using this exploratory method, resulting in a two-fold increase in signal response, compared to measurements without pH control. Finally, tap water samples were measured using the in-situ pH control method and the results showed excellent correlation (within experimental error) with a commercial instrument, demonstrating the efficacy of the developed technique. This work establishes the possibility of deploying an electrochemical based reagent-free, in-line chlorine sensor required for water distribution networks. | Alan O'Riordan; Benjamin O'sullivan; Pierre Lovera; Ian Seymour; James Rohan | Electrochemical Analysis; Environmental Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74857567dfef14dec49cf/original/electrochemical-detection-of-free-chlorine-in-water-samples-facilitated-by-in-situ-p-h-control-using-interdigitated-microelectrodes.pdf |
66bb0911a4e53c48763ac057 | 10.26434/chemrxiv-2024-2qgpb-v3 | How good are current pocket based 3D generative models? : The benchmark set and evaluation of protein pocket based 3D molecular generative models | The development of three-dimensional (3D) molecular generative model based on protein pockets has recently attracted a lot of attentions. This type of model aims to achieve the simultaneous generation of molecular graph and 3D binding conformation under the constraint of protein binding. Various pocket based generative models have been proposed, however, currently there is a lack of systematic and objective evaluation metrics for these models. To address this issue, a comprehensive benchmark dataset, named as POKMOL-3D, is proposed to evaluate protein pocket based 3D molecular generative models. It includes 32 protein targets together with their known active compounds as a test set to evaluate the versatility of generation models to mimick the real-world scenario. Additionally, a series of 2D and 3D evaluation metrics was integrated to assess the quality of generated molecular structures and their binding conformations. It is expected that this work can enhance our comprehension of the effectiveness and weakness of current 3D generative models, and stimulate the discussion on challenges and useful guidance for developing next wave of molecular generative models. | Haoyang Liu; Yifei Qin; Zhangming Niu; Mingyuan Xu; Jiaqiang Wu; Xianglu Xiao; Jinping Lei; Ting Ran; Hongming Chen | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bb0911a4e53c48763ac057/original/how-good-are-current-pocket-based-3d-generative-models-the-benchmark-set-and-evaluation-of-protein-pocket-based-3d-molecular-generative-models.pdf |
60c75882bb8c1abb9c3dca45 | 10.26434/chemrxiv.14558121.v1 | The Transcriptional Repressor Orphan Nuclear Receptor TLX Is Responsive to Caffeine and Istradefylline | The orphan nuclear receptor TLX is expressed almost exclusively in neural stem cells. TLX acts as an essential factor for neural stem cell survival and is hence considered as a promising drug target in neurodegeneration. However, few studies have characterized the roles of TLX due to a lack of ligands and limited functional understanding. Here, we identify caffeine and istradefylline as TLX ligands that counteract the receptor’s intrinsic repressor activity in reporter gene assays and modulate TLX regulated SIRT1 and p21 expression. Mutagenesis of residues lining a cavity within the TLX ligand binding domain altered activity of these ligands suggesting direct interactions with helix 5. Using istradefylline as a tool compound, we observed ligand-sensitive recruitment of the co-repressor SMRT and heterodimerization of TLX with RXR. Both protein-protein complexes evolve as factors that modulate TLX function and suggest an unprecedented role of TLX in directly repressing other nuclear receptors.<br /> | Giuseppe Faudone; Whitney Kilu; Xiaomin Ni; Apirat Chaikuad; Sridhar Sreeramulu; Pascal Heitel; Harald Schwalbe; Stefan Knapp; Manfred Schubert-Zsilavecz; Jan Heering; Daniel Merk | Bioorganic Chemistry; Natural Products; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2021-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75882bb8c1abb9c3dca45/original/the-transcriptional-repressor-orphan-nuclear-receptor-tlx-is-responsive-to-caffeine-and-istradefylline.pdf |
678e399ffa469535b9c87908 | 10.26434/chemrxiv-2025-cljhb | Isolation and bioinspired synthesis of lauenones A and B, skeleton-rearranged diterpenoids with antiadipogenic activity from Croton laui | Skeleton-rearranged diterpenoids have attracted burgeoning interest. Chemical investigation into an ethnomedicinal plant, Croton laui, resulted in the isolation of two highly rearranged labdane diterpenoids, lauenones A (1) and B (2), featuring an unprecedented carbon skeleton with six contiguous stereogenic centers. To validate the proposed biosynthetic origin and obtain sufficient materials for biological studies, chemical syntheses of lauenones A and B were achieved without using any protecting groups in 10 and 11 steps, respectively. The key features of the current synthesis include a semipinacol rearrangement to construct the contracted B-ring and a substrate-controlled one-pot reaction cascade involving photooxidation and aldol condensation to forge the sterically congested 4-hydroxy-2-cyclopentenone moiety. Our synthetic attempts suggested that the semipinacol rearrangement step likely occurred prior to the aldol condensation step in the biosynthetic pathway. This study underscores the importance of arranging the sequence of crucial reactions in achieving a successful synthesis process. Furthermore, both lauenones A and B exhibited antiadipogenic effects in 3T3-L1 adipocytes by downregulating the differentiation factors (PPARγ and C/EBPα) and liposynthesis enzymes (FASN and ACC) at both mRNA transcription and protein expression levels. | Zong-Yi Zhang; Yu-Han Chen; Cheng-Yu Zheng; Yuan Gao; Yao-Yue Fan; Jian-Min Yue; Jin-Xin Zhao | Organic Chemistry; Bioorganic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678e399ffa469535b9c87908/original/isolation-and-bioinspired-synthesis-of-lauenones-a-and-b-skeleton-rearranged-diterpenoids-with-antiadipogenic-activity-from-croton-laui.pdf |
60c7447d567dfec7a0ec42cb | 10.26434/chemrxiv.8316815.v3 | Ewald-Based Methods for Gaussian Integral Evaluation: Application to a New Parametrization of GEM* | Our manuscript describes the implementation and performance of Ewald-based approaches for the calculation of Gaussian integrals in the pmemd.gem code as released in the AMBER18 suite, as well as a new parametrization of our density-based Gaussian Electrostatic Model* (GEM*) force field using CCSD(T)/CBS//SAPT2+3/aug-cc-pVTZ data for the fit. | Robert E. Duke; G. Andres Cisneros | Theory - Computational; Quantum Mechanics; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7447d567dfec7a0ec42cb/original/ewald-based-methods-for-gaussian-integral-evaluation-application-to-a-new-parametrization-of-gem.pdf |
62fc6cab1d6a997c1206cd0d | 10.26434/chemrxiv-2022-hjbwg | Facial Access to 2,2-Difluoro-2,3-dihydrofuran Skeleton without Extra Additive: DMF-Promoted Difluorocarbene Formation of ClCF2CO2Na | The practical and facile difluorocarbene-triggered cycloaddition reaction of enaminones was developed, that delivered 2,2-difluoro-2,3-dihydrofurans with broad substrates scope. Notably, the reaction proceeded smoothly without any extra additive. The readily available sodium chlorodifluoroacetate (ClCF2CO2Na, SCDA) played as difluorocarbene precursor in this transformation through DMF-promotion. Moreover, it is proved that the 2,2-difluoro- 2,3-dihydrofuran derivatives exposed potential antiproliferative activity against human tumour cells HeLa, MCF7 and HepG2. | Zunsheng Chen; Xin Xie; Weiming Chen; Nianhua Luo; Xiaoning Li; Fuchao Yu; Jiuzhong Huang | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fc6cab1d6a997c1206cd0d/original/facial-access-to-2-2-difluoro-2-3-dihydrofuran-skeleton-without-extra-additive-dmf-promoted-difluorocarbene-formation-of-cl-cf2co2na.pdf |
6697668dc9c6a5c07a8252cb | 10.26434/chemrxiv-2024-1sqhr | Novelty and Coverage: An Integrated Metric Addressing Quality Trade-offs in AI-Generated Compounds for Drug Discovery | Introduction: Generative AI models have been introduced to find novel chemical compounds for drug discovery. To evaluate different generative AI models quantitatively, computational metrics such as rule of five, validity, novelty, uniqueness and FCD are needed. However, conventional metrics still have limitations in terms of comprehensive evaluation including drug-likeness, diversity, and novelty.
Method: In this paper, we propose a metric, novelty, and coverage (NC), which measures the structural similarity between the generated set and the actual ligand set. Novelty and coverage filters the generated set by comparing molecular properties with known drugs, and then calculates structural similarity and diversity, allowing a comprehensive evaluation based on the trade-off relationship between them. For the comparison of conventional metrics and NC, we used models from the MOSES platform in addition to the latest deep learning models. We built the two representative sets for the comparison of molecular properties (ChEMBL) and structural similarity (ZINC).
Result: The results show that conventional metrics can be grouped into three clusters (drug-likeness, external diversity, internal diversity) and point out their limitations. We compared the results of conventional metrics and NC, and then verified that NC explained conventional metrics. NC explained comprehensive evaluation in drug discovery with harmonic mean between contrasting features in chemical generative models.
Availability and implementation: Codes are freely available to non-commercial users at https://github.com/KyoungYeulLee/drug_novelty_and_coverage.
| suhyeon Jin; Boram Lee; Kyoungyeul Lee; Dongsup Kim | Analytical Chemistry; Chemoinformatics | CC BY NC 4.0 | CHEMRXIV | 2024-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6697668dc9c6a5c07a8252cb/original/novelty-and-coverage-an-integrated-metric-addressing-quality-trade-offs-in-ai-generated-compounds-for-drug-discovery.pdf |
610037227bf0c9e6c6613ad8 | 10.26434/chemrxiv-2021-48jvm | Questioning the orbital picture of magnetic spin coupling: a real space alternative | The prevailing magnetic spin coupling paradigm is based on a one-electron picture, thus being orbital dependent and unsatisfactory from a physical point of view. We examine it under a truly invariant real space perspective, focusing on the role of electron delocalization. We show that this view, compatible with orbital thinking, overcomes its limitations. By examining simple model systems we show that it is electron delocalization that drives any singlet-triplet gap, and that delocalization and ionic mixing are two sides of the same reality. It is in the end delocalization, fostered or hindered by the specific structure of a system, that lies behind its preferred magnetic coupling mode. In the case of superexchange-mediated coupling through atomic bridges, we also point out the non-essential role of the bridge's electrons in setting up singlet-triplet preferences. We show that the use of real space thinking allows for tuning singlet-triplet gaps using knobs that are not easily grasped from the orbital standpoing, opening new avenues in the design and control of molecular
magnets. | Ángel Martín Pendás; Evelio Francisco | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610037227bf0c9e6c6613ad8/original/questioning-the-orbital-picture-of-magnetic-spin-coupling-a-real-space-alternative.pdf |
60c7464dbb8c1a66003da86b | 10.26434/chemrxiv.11301725.v1 | Aggregation-Induced Improvement of Catalytic Activity of Metalfullerene-Based Surfactants Used in Water Splitting Reaction | An inherent paradigm of molecular compounds used in homogeneous catalysis is that maximum performance requires maximum dispersion, and that any form of aggregation results in a loss of activity. We here present a new concept based on surfactants with functional heads, which become better catalysts when they aggregate. The head group of the surfactants is composed of a diethylenetriamine-functionalized fullerene, which coordinates Co II ions. This system is applied as an electrocatalyst for the water-splitting reaction. Detailed electrochemistry studies were performed at concentrations below and above the critical aggregation concentration (cac), when 150 nm sized vesicles are formed. While isolated surfactant molecules represent only moderately active catalysts, drastic improvement in the hydrogen evolution (HER) as well as in the oxygen evolution reactions (OER) were detected for the vesicular structures. Self-organization of the surfactants leads to an increase in turnover frequencies of up to 1300% (HER). We show that the strongly beneficial effect of aggregation arises from the favorable alignment of individual molecules, thus facilitating intermolecular charge transfer processes in the vesicles. | Marius Kunkel; Stefan Bitter; Frank Sailer; Rainer
F. Winter; Sebastian Polarz | Nanocatalysis - Catalysts & Materials; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7464dbb8c1a66003da86b/original/aggregation-induced-improvement-of-catalytic-activity-of-metalfullerene-based-surfactants-used-in-water-splitting-reaction.pdf |
60c753819abda207f2f8dfce | 10.26434/chemrxiv.13501668.v1 | Non-adiabatic Matsubara Dynamics and Non-adiabatic Ring Polymer Molecular Dynamics | We present the non-adiabatic Matsubara dynamics, a general framework for computing the time-correlation function (TCF) of electronically non-adiabatic systems. This new formalism is derived based on the generalized Kubo-transformed time-correlation function, using the Wigner representation for both the nuclear degrees of freedom (DOF) and the electronic mapping variables. By dropping the non-Matsubara nuclear normal modes in the quantum Liouvillian and explicitly integrate these modes out of the TCF, we derived the non-adiabatic Matsubara dynamics approach. Further making the approximation to drop the imaginary part of the Matsubara Liouvillian and enforce the nuclear momentum integral to be real, we arrived at the non-adiabatic ring-polymer molecular dynamics (NRPMD) approach. We have further justified the capability of NRPMD for simulating the non-equilibrium time-correlation function. This work provides the rigorous theoretical foundation for several recently proposed state-dependent RPMD approaches and offers a general framework for developing new non-adiabatic quantum dynamics approaches in the future. | Sutirtha N. Chowdhury; Pengfei Huo | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753819abda207f2f8dfce/original/non-adiabatic-matsubara-dynamics-and-non-adiabatic-ring-polymer-molecular-dynamics.pdf |
65842cbf66c1381729b7a603 | 10.26434/chemrxiv-2023-h2cb8 | On the Valorisation of Chitin-Derived Furans by Ball Milling. | Aromatic compounds containing nitrogen atoms in their structure are currently obtained from non-renewable sources with the incorporation of nitrogen from ammonia, which is industrially produced by the highly energy demanding Haber process. To minimize the carbon footprint of nitrogen containing chemicals and drive the production of nitrogenated aromatic compounds in a Haber-independent manner, the use of furans derived from chitin has become an affordable and promising source for nitrogen fixation in compounds with high added-value. Herein, we address the challenge of using two chitin-derived furans, 3-acetamido-5-acetylfuran (3A5AF) and 3-acetamido-5-furfural aldehyde (3A5F), to favor the formation of exo Diels–Alder adducts and 4-acetylaminophthalimides using Mechanochemistry, as a more sustainable and cleaner synthesis compared to the classical methods in solution-phase. The Mechanochemistry activation is explored through the synthesis of novel 7-oxa-norbornene backbones and it showed an improvement in both yield and exo:endo selectivity when compared to solution-phase, with yields reaching up to 77% and selectivity >19:1. We also investigated the use of a less toxic and commercially available hydrazine in order to promote the synthesis of 4-acetylaminophthalimides from 3A5F in yields ranging 20–79%. | Renan Mattioli; Camila Santos; Bruna De Souza; Pedro Branco; Robert Bolt; Sarah Raby-Buck; Tadeu Cabral; Claúdio Tormena; Duncan Browne; Julio Pastre | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65842cbf66c1381729b7a603/original/on-the-valorisation-of-chitin-derived-furans-by-ball-milling.pdf |
60c75111bb8c1a30933dbbf0 | 10.26434/chemrxiv.12623840.v2 | Two-Field Transverse Relaxation-Optimized Spectroscopy for the Study of Large Biomolecules – an in Silico Investigation | <div>
<div>
<div>
<p>Biomolecular NMR spectroscopy has greatly benefited from the development of TROSY-type
pulse sequences, in pair with specific labeling. The selection of spin operators with favorable
relaxation properties has led to an increase in the resolution and sensitivity of spectra of large
biomolecules. However, nuclei with a large chemical shift anisotropy (CSA) contribution to
relaxation can still suffer from large linewidths at conventional magnetic fields (higher than 9
T). Here, we introduce the concept of two-field TROSY (2F-TROSY) where the chemical shifts
of nuclei with large CSA is labeled at low fields (ca. 2 T) dramatically reducing the contribution
of CSA to relaxation. Signal detection is performed at high field (> 9 T) on a nucleus with
efficient TROSY interference to yield high-resolution and sensitivity. We use comprehensive
numerical simulations to demonstrate the power of this approach on aromatic 13C-19F spin pairs
for which a TROSY pulse sequence has recently been published. We predict that the 2F-
TROSY experiment shall yield good quality spectra for large proteins (global tumbling
correlation times as high as 100 ns) with one order of magnitude higher sensitivity than the
single-field experiment.
</p>
</div>
</div>
</div> | Nicolas Bolik-Coulon; Philippe Pelupessy; Guillaume Bouvignies; Fabien Ferrage | Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75111bb8c1a30933dbbf0/original/two-field-transverse-relaxation-optimized-spectroscopy-for-the-study-of-large-biomolecules-an-in-silico-investigation.pdf |
64b0f322b053dad33a3768a9 | 10.26434/chemrxiv-2023-6181f | Unified roadmap for ZIF-8 Nucleation and Growth: Machine Learning Analysis of Synthetic Variables and their Impact on Particle Size and Morphology | Metal-Organic Frameworks (MOFs) have settled in the scientific community over the last decades as versatile materials with several applications. Among those, Zeolitic Imidazolate Framework 8 (ZIF-8) is a well-known MOF that has been applied in various and diverse fields, from drug-delivery platforms to microelectronics. However, the complex role played by the reaction parameters in controlling the size and morphology of ZIF-8 particles is still not fully understood. Even further, many individual reports propose different nucleation and growth mechanisms for ZIF-8, thus creating a fragmented view of the system's behavior. To provide a unified view, we have generated a comprehensive dataset of synthetic conditions and their final outputs and applied Machine Learning techniques to analyze the data. Our approach has enabled us to identify the nucleation and growth mechanisms operating for ZIF-8 in a given portion of the chemical space and to reveal the underlying impact of synthetic variables on the final particle size and morphology. By doing so, we draw connections between the role of each synthetic variable over ZIF-8 synthesis and provided with a rule of thumb to control the final particle size. Our results provide a unified roadmap for the nucleation and growth mechanisms of ZIF-8 in agreement with mainstream trends, which can guide the rational design of ZIF-8 particles with specific sizes and morphology, determining their suitability for any targeted application. Altogether, our work represents a step forward in seeking control of the properties of MOFs through a deeper understanding of the rationale behind synthesis procedures employed for their synthesis. | Juan A Allegretto; Diego Onna; Laura Acion; Sara A Bilmes; Omar Azzaroni; Matías Rafti | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Structure; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b0f322b053dad33a3768a9/original/unified-roadmap-for-zif-8-nucleation-and-growth-machine-learning-analysis-of-synthetic-variables-and-their-impact-on-particle-size-and-morphology.pdf |
65170469a69febde9eef3bbc | 10.26434/chemrxiv-2023-l9dt9-v2 | Nuclear Quantum Effects in Gas-Phase 2-Fluoroethanol | Torsional motions along the FCCO and HOCC dihedrals lead to the five unique conformations of 2-fluoroethanol, of which the gauche conformer along both dihedrals has the lowest energy. In this work, we explore how nuclear quantum effects (NQEs) are manifest in the structural parameters of the lowest energy conformer, in the intramolecular free energy landscape along the FCCO and HOCC dihedrals, and also in the infrared spectrum of the title molecule, through the use of path integral simulations. We have first developed a full dimensional potential energy surface using the reaction surface Hamiltonian framework. On this potential, we have carried out path integral molecular dynamics simulations at several temperatures starting from the minimum energy well to explore structural influences of NQEs including geometrical markers of the interaction between the OH and F groups. From the computed free energy landscapes, significant reduction of the torsional barrier is found at low temperature near the cis region of the dihedrals, which can be understood through the trends in the radii of gyration of the atomic ring polymers. We find that the inclusion of NQEs in the computation of infrared spectrum is important to obtain good agreement with the experimental band positions. | Mrinal Arandhara; Sai G. Ramesh | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65170469a69febde9eef3bbc/original/nuclear-quantum-effects-in-gas-phase-2-fluoroethanol.pdf |
6446a426df78ec501552183a | 10.26434/chemrxiv-2023-hd568 | A Robust Framework for Generating Adsorption Isotherms to Screen Materials for Carbon Capture | To rank the performance of materials for a given carbon capture process, we rely on pure component isotherms from which we predict the mixture isotherms. For screening a large number of materials we also increasingly rely on isotherms predicted from molecular simulations. In particular, for such screening studies, it is important that the procedures to generate the data are accurate, reliable, and robust. In this work, we develop an efficient and automated workflow for a meticulous sampling of pure component isotherms. The workflow was tested on a set of metal-organic frameworks (MOFs) and proved to be reliable given different guest molecules. We show that the coupling of our workflow with the Clausius-Clapeyron relation saves CPU time, yet enables us to accurately predict pure component isotherms at the temperatures of interest, starting from a reference isotherm at a given temperature. We also show that one can accurately predict the CO2 and N2 mixture isotherms using Ideal Adsorbed Solution Theory (IAST). In particular, we show that IAST is a more reliable numerical tool to predict binary adsorption uptakes for a range of pressures, temperatures, and compositions, as it does not rely on the fitting of experimental data, which typically needs to be done with analytical models such as dual-site Langmuir (DSL). This makes IAST a more suitable and general technique to bridge the gap between adsorption (raw) data and process modelling. To demonstrate this point, we show that the ranking of materials, for a standard 3-step Temperature Swing Adsorption (TSA) process, can be significantly different depending on the thermodynamic method used to predict binary adsorption data. We show that for the design of processes that capture CO2 from low concentration (0.4%) streams, the commonly used methodology to predict mixture isotherms incorrectly assigns up to 33% of the materials as top-performing. | Elias Moubarak; Seyed Mohamad Moosavi; Charithea Charalambous; Susana Garcia; Berend Smit | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Thermodynamics (Chem. Eng.) | CC BY 4.0 | CHEMRXIV | 2023-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6446a426df78ec501552183a/original/a-robust-framework-for-generating-adsorption-isotherms-to-screen-materials-for-carbon-capture.pdf |
60c758d7702a9b3edd18cde3 | 10.26434/chemrxiv.14582484.v1 | Key Interacting Residues Between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamic Simulation and Density Functional Calculation | <p>The
spike protein of SARS-CoV-2 binds to ACE2 receptor <i>via</i> its receptor-binding domain (RBD), with the RBD-ACE2 complex presenting
an essential molecular target for vaccine development to stall the virus
infection proliferation. The computational analysis at molecular, amino acid
(AA) and atomic levels have been performed systematically to identify the key
interacting AAs in the formation of the RBD-ACE2 complex, including the MD
simulations with molecular mechanics generalized Born surface area (MM-GBSA)
method to predict binding free energy (BFE) and to determine the actual
interacting AAs, as well as two <i>ab initio</i> quantum chemical protocols
based on the density functional theory (DFT) implementation. Based on MD
results, Q<sup>493</sup>, Y<sup>505</sup>, Q<sup>498</sup>, N<sup>501</sup>,
T<sup>500</sup>, N<sup>487</sup>, Y<sup>449</sup>, F<sup>486</sup>, K<sup>417</sup>,
Y<sup>489</sup>, F<sup>456</sup>, Y<sup>495</sup>, and L<sup>455</sup> have
been identified as hotspots in RBD, while those in ACE2 are K<sup>353</sup>, K<sup>31</sup>,
D<sup>30</sup>, D<sup>355</sup>, H<sup>34</sup>, D<sup>38</sup>, Q<sup>24</sup>,
T<sup>27</sup>, Y<sup>83</sup>, Y<sup>41</sup>, E<sup>35</sup>, and E<sup>37</sup>.
Both
the electrostatic and hydrophobic interactions are the main driving force to
form the AA-AA binding pairs. We confirm that Q<sup>493</sup>,
N<sup>501</sup>, F<sup>486</sup>, K<sup>417</sup>, and
F<sup>456</sup> in
RBD are the key residues responsible for the tight binding of SARS-CoV-2 with
ACE2 compared to SARS-CoV. The DFT results reveal that N<sup>487</sup>, Q<sup>493</sup>, Y<sup>449</sup>, T<sup>500</sup>, G<sup>496</sup>, G<sup>446</sup> and G<sup>502</sup> in
RBD form pairs <i>via</i> specific hydrogen bonding with Q<sup>24</sup>, H<sup>34</sup>,
E<sup>35</sup>, D<sup>38</sup>, Y<sup>41</sup>, Q<sup>42</sup> and K<sup>353</sup>
in ACE2. </p> | Bahaa Jawad; Puja Adhikari; Rudolf Podgornik; Wai-Yim Ching | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758d7702a9b3edd18cde3/original/key-interacting-residues-between-rbd-of-sars-co-v-2-and-ace2-receptor-combination-of-molecular-dynamic-simulation-and-density-functional-calculation.pdf |
60c73e99702a9b8cef189dd3 | 10.26434/chemrxiv.7040324.v1 | The Synthesis of 1,4-anhydro-α-D-Mannopyranose | Manuscript describing efforts, ultimately successful, to synthesize 1,4-anhydromannose. Full experimental details and spectroscopic characterization. | Spencer Williams; PHILLIP VAN DER PEET | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e99702a9b8cef189dd3/original/the-synthesis-of-1-4-anhydro-d-mannopyranose.pdf |
64d8b4c0dfabaf06ff3467da | 10.26434/chemrxiv-2023-619nj | Doubly Tuned Exchange-Correlation Functionals for Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory | It is demonstrated that significant accuracy improvements of MRSF-TDDFT can be achieved by introducing two different XC functionals for the reference Kohn-Sham DFT and the response part of calculations, respectively. Accordingly, two new exchange-correlation (XC) functionals of DTCAM-VEE and DTCAM-AEE were developed on the basis of the "adaptive exact exchange (AEE)" concept in the framework of the Coulomb-attenuating XC functionals. The values by DTCAM-VEE are in excellent agreement with those of Thiel's set (mean absolute error (MAE) and interquartile range (IQR) of 0.218 and 0.327 eV, respectively). On the other hand, DTCAM-AEE faithfully reproduced the qualitative aspects of conical intersections of trans-butadiene and thymine, and the NAMD simulations on thymine. The latter functional also remarkably exhibited the exact 1/R asymptotic behavior of the charge-transfer state of an ethylene-tetrafluoroethylene dimer, and the accurate potential energy surfaces along the two torsional angles of retinal protonated Schiff base model with six double bonds (rPSB6). The current idea can be also applied to other XC functionals as well as other variants of linear response theories, opening a new way of developing XC functionals. | Konstantin Komarov; Woojin Park; Seunghoon Lee; Miquel Huix-Rotllant; Cheol Ho Choi | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d8b4c0dfabaf06ff3467da/original/doubly-tuned-exchange-correlation-functionals-for-mixed-reference-spin-flip-time-dependent-density-functional-theory.pdf |
6625c9a391aefa6ce10ee646 | 10.26434/chemrxiv-2024-3c9cq | Method and mechanism for efficient radium isolation from bulk thorium based on anion exchange | In recent years, targeted-α-nuclide therapy (TAT) has been widely concerned in the world. As one of the few representative TAT nuclides, 212Pb has shown good efficacy in cancer treatment; however, the amount remains scarce. Separating 228Ra and 224Ra from 232Th is expected to fundamentally solve this issue. In this work, a novel and effective method for trace radium isolation from bulk thorium was proposed and verified through a systematic investigation of the adsorption behaviors of an anion exchanger denoted IRA900 toward thorium and barium/radium. Batch experiments suggested that IRA900 had unique selectivity for thorium in nitric acid solution, with almost no barium adsorbed. The thorium adsorption performance kept improving with increasing concentration of nitric acid and decreasing temperature. The IRA900 resin required about 8 h to reach adsorption equilibrium, and the estimated maximum adsorption capacity toward thorium was about 254 mg/g. The adsorption kinetics and adsorption isotherm could be well fitted by the pseudo-second-order kinetic model and the Langmuir model, respectively. Column experiments suggested that thorium could be effectively immobilized by a column packed with IRA900, while barium was directly penetrated. For desorbing the fixed thorium, 0.1 M HNO3 was optimal. A final hot test demonstrated the successful radium isolation from bulk thorium, with high chemical yield and purity. The selective separation mechanism was attributed to the formation of an anionic [Th(NO3)5]− complex, while barium or radium existed in the cationic form in any nitric acid concentration. This work provides a promising method for separating trace radium from natural thorium, which will be significant for promoting the large-scale utilization of 212Pb. | Xuexiang He; Jing Tang; Zhuo Wang; Wannian Feng; Qingqing Yan; Yuezhou Wei; Hiroshi Watabe; Wenlong Li; Shunyan Ning; Lifeng Chen | Chemical Engineering and Industrial Chemistry; Natural Resource Recovery | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6625c9a391aefa6ce10ee646/original/method-and-mechanism-for-efficient-radium-isolation-from-bulk-thorium-based-on-anion-exchange.pdf |
665e6fb9418a5379b0075bf6 | 10.26434/chemrxiv-2024-n8145 | Multistep Enzymatic Low-density Polyethylene Degradation via Phenylalanine Monooxygenase and Isocitrate Lyase in Pseudomonas aeruginosa | Plastics have become indispensable in modern industries; however, their resistance to natural degradation poses environmental challenges. Biological degradation technologies employing microorganisms offer promising solutions. Here, we analyzed the transcriptome and proteome of Pseudomonas aeruginosa, a plastic-degrading microorganism found in the gut of superworms, to identify the genes and enzymes upregulated during polyethylene degradation. Functional analyses of these upregulated genes and enzymes using the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology databases revealed an increase in lipid and hydrophobic amino acid metabolism, suggesting their involvement in polyethylene degradation. Based on these analyses, we identified phenylalanine monooxygenase, which is capable of oxidizing plastics, and isocitrate lyase, which is involved in C-C bond cleavage. To investigate the involvement of these enzymes in polyethylene degradation, phhA and aceA were transformed into Escherichia coli, and the enzymes were produced and purified. The purified enzymes were then reacted with polyethylene and analyzed. The results revealed the formation of hydroxyl (-OH) and C-O groups on the polyethylene surface after treatment with phenylalanine monooxygenase, confirming its ability to oxidize polyethylene. Isocitrate lyase alone did not affect polyethylene production; however, when combined with phenylalanine monooxygenase, it contributed to a reduction in molecular weight. This suggests a two-stage process of polyethylene degradation involving oxidation and depolymerization that requires sequential action of multiple enzymes. Thus, we identified the enzymes involved in each stage and demonstrated the degradation ability of polyethylene using purified enzymes. | Hong Rae Kim; Ye Eun Lee; Dong-Eun Suh; Donggeun Choi; Sukkyoo Lee | Biological and Medicinal Chemistry; Polymer Science; Earth, Space, and Environmental Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665e6fb9418a5379b0075bf6/original/multistep-enzymatic-low-density-polyethylene-degradation-via-phenylalanine-monooxygenase-and-isocitrate-lyase-in-pseudomonas-aeruginosa.pdf |
6453e8f107c3f0293737695a | 10.26434/chemrxiv-2023-p4rn7 | Low-valent main group catalysis under ambient conditions | Low-valent main group element compounds are typically air and moisture sensitive. Using these compounds as organic transfor-mation catalysts needs that the reactions be carried out under inert conditions. Given the growing demand for simple chemical pro-cesses, we looked for strategies that could be used to carry out these reactions simply under ambient lab conditions. We were able to accomplish this by employing an air and water stable germylene cation ([DPMGe][(HO)B(C6F5)3] (2). The dipyrrinate (DPM) ligand stabilized compound 2 catalyzes aldehyde and ketone hydrosilylations under ambient conditions. | Hemant Kumar; Pritam Mahawar; Vivek Kumar Singh; Pratima Shukla; Prakash Chandra Joshi; Nagendran Selvarajan | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Main Group Chemistry (Inorg.); Main Group Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6453e8f107c3f0293737695a/original/low-valent-main-group-catalysis-under-ambient-conditions.pdf |
634056f2084700a75998d35a | 10.26434/chemrxiv-2022-pc12b | Long term phase separation dynamics in liquid crystal-enriched microdroplets obtained from binary fluid mixtures | The dynamics of long term phase separation in binary liquid mixtures remains a subject of fundamental interest. Here, we study a binary liquid mixture, where the minority phase is confined to a liquid crystal (LC)-rich droplet, by investigating the evolution of size, defect and mesogen alignment over time. We track the binary liquid mixture evolving towards equilibrium by visualising the configuration of the liquid crystal droplet through polarisation microscopy. We compare our experimental findings with computational simulations and elucidate the bulk vs microdroplet difference based on the thermodynamics of phase separation. Our work provides insights on how phase transitions on the microscale can deviate from bulk ph | Mehzabin Patel; Seishi Shimizu; Martin Bates; Alberto Fernandez-Nieves; Stefan Guldin | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Interfaces; Physical and Chemical Processes; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634056f2084700a75998d35a/original/long-term-phase-separation-dynamics-in-liquid-crystal-enriched-microdroplets-obtained-from-binary-fluid-mixtures.pdf |
60c747ce9abda22e30f8c9a4 | 10.26434/chemrxiv.9831536.v2 | NCIPLOT4: A New Step Towards a Fast Quantification of Noncovalent Interactions | <br />The quantification of noncovalent interactions in big systems is of crucial importance for understanding the structure and function of biosystems. The NCI method [J. Am. Chem. Soc. 132 , 6498 (2010)] enables to identify attractive and repulsive noncovalent interactions from promolecular densities in a fast manner. However, the approach remained up to now visual/qualitative, the relationship with energetics was conspicuously missing. We present a new version of NCIPLOT which allows quantifying the properties of the NonCovalent Interaction (NCI) regions in a fast manner. In order to do so, the definition of NCI volumes is introduced, which allows quantification of intra and intermolecular NCI properties in big systems where wavefunctions are not available. The connection between these integrals and energetics is reviewed for benchmark systems (S668), showing that our simple approach can lead to GGAquality energies while scaling with the number of atoms involved in the interaction (not the total number of atoms). The new implementation also includes an adaptive grid which allows the computation in a fast, parallelizable and efficient computational environment. The relationship with energetics derived from force fields is highlighted<br />and the faster algorithm exploited to analyze the evolution of interactions along MD trajectories. Through machine learning algorithms we characterize the relevance of NCI integrals in understanding the energetics of big systems, which is then applied in revealing the energetic changes along conformational changes, as well as identifying the atoms involved. This simple approach enables to identify the driving forces in biomolecular structural changes both at the spatial and energetic levels, while going beyond a mere parametrized-distances analysis.<br /> | Roberto Boto; Francesca Peccati; Rubén Laplaza; chaoyu quan; Alessandra Carbone; Jean-Philip Piquemal; Yvon Maday; Julia Contreras-García | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747ce9abda22e30f8c9a4/original/nciplot4-a-new-step-towards-a-fast-quantification-of-noncovalent-interactions.pdf |
643027ca0784a63aeeb333ca | 10.26434/chemrxiv-2022-35bt7-v2 | Reimagining Hair Science:
A New Approach to Classify Curly Hair Phenotypes via New Quantitative Geometrical & Structural Mechanical Parameters | Hair is one of the key characteristics that classify us as mammals. It is a natural polymeric composite that is primarily composed of tight macro-bundles of keratin proteins, which are highly responsive to external stimuli, including pH, temperature, and ionic solvent content. The external responsive behavior displayed by hair is similar to the behavior displayed by hydrogels and other natural fibrous gel systems like collagen and fibrin. Hair and its appearance play a significant role in human society. It is a highly complex biocomposite system, which has been traditionally challenging to characterize and thus develop functional personal care products for consumers. Over the last few decades, a significant societal paradigm shift occurred among those with curly hair. They began to accept the natural morphological shape of their curls and style their hair according to its innate, distinct, and unique material properties. These societal and cultural shifts have given rise the development of new hair classification systems, beyond the traditional and highly limited ethnicity-based distinction between Caucasian, Mongolian, and African. L’Oréal developed a hair typing taxonomy based on quantitative geometric parameters displayed among the four key curl patterns – straight, wavy, curly, and coily (kinky). However, the system fails to capture the complex diversity of curly and kinky/coily hair. Acclaimed celebrity hair stylist, Andre Walker, developed a classification system that is the existing gold standard for classifying curly and kinky/coily hair, however the system relies upon qualitative classification measures, making the system vague and ambiguous to the full diversity of phenotypic differences. The goal of this research is to use quantitative methods to identify new geometric parameters, which will be more representative of curly and kinky/coily hair curl patterns. These new parameters will therefore provide more information on the kinds of personal care product ingredients that will resonate best with these curl patterns, and thus maximize desired appearance and overall hair health. The goal is also to correlate these new parameters with its mechanical properties. This was accomplished by identifying new geometric and mechanical parameters from several types of human hair samples. Geometric properties were measured using scanning electron microscopy (SEM), photogrammetry, and optical microscopy. Mechanical properties were measured under tensile extension using a texture analyzer (TA) and a dynamic mechanical analyzer (DMA), which bears similarity to the common act of brushing or combing. Both instruments measure force as a function of applied displacement, thus allowing the relationship between stress and applied stretch ratio to be measured as a hair strand uncurls and stretches to the point of fracture. From the resulting data, correlations were made between fiber geometry and mechanical performance. This data will be used to draw more conclusions on the contribution that fiber morphology has on hair fiber mechanics and will promote cultural inclusion among researchers and consumers possessing curly and kinky/coily hair. | Michelle Gaines; Imani Page; Nolan Miller; Benjamin Greenvall; Josh Medina; Duncan Irschick; Adeline Southard; Alexander Ribbe; Gregory Grason; Alfred Crosby | Biological and Medicinal Chemistry; Materials Science; Polymer Science; Biological Materials; Elastic Materials; Fibers | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643027ca0784a63aeeb333ca/original/reimagining-hair-science-a-new-approach-to-classify-curly-hair-phenotypes-via-new-quantitative-geometrical-structural-mechanical-parameters.pdf |
6662c25b91aefa6ce1fc36d9 | 10.26434/chemrxiv-2024-6wgbl | Deep Learning-Driven Prediction of Chemical Addition Patterns for Carboncones and Fullerenes | Carboncones and fullerenes are exemplary π-conjugated carbon nanomaterials with unsaturated, positively curved surfaces, enabling the attachment of atoms or functional groups to enhance their physicochemical properties. However, predicting and understanding the addition patterns in functionalized carboncones and fullerenes are extremely challenging due to the formidable complexity of the regioselectivity exhibited in the adducts. Existing predictive models fall short in systems where the carbon molecular framework undergoes severe distortion upon high degrees of addition. Here, we propose an incremental deep learning approach to predict regioselectivity in the hydrogenation of carboncones and chlorination of fullerenes. Utilizing exclusively graph-based features, our deep neural network (DNN) models rely solely on atomic connectivity, without requiring 3D molecular coordinates as input or iterative optimization of them. This advantage inherently avoids the risk of obtaining chemically unreasonable optimized structures, enabling the handling of highly distorted adducts. The DNN models allow us to study regioselectivity in hydrogenated carboncones of C70H20 and C62H16, accommodating up to at least, 40 and 30 additional H atoms, respectively. Our approach also correctly predicts experimental addition patterns in C50Cl10 and C76Cln (n = 18, 24, and 28), whereas in the latter cases all other known methods have proven unsuccessful. Compared to our previously developed topology-based models, the DNN’s superior predictive power and generalization ability make it a promising tool for investigating complex addition patterns in similar chemical systems. | Zhengda Li; Xuyang Chen; Yang Wang | Theoretical and Computational Chemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6662c25b91aefa6ce1fc36d9/original/deep-learning-driven-prediction-of-chemical-addition-patterns-for-carboncones-and-fullerenes.pdf |
642d88300784a63aee94ca46 | 10.26434/chemrxiv-2023-rg552 | The Catcher in the Water: Magnetic Biochar for the Treatment of Wastewater | Magnetic biochar (MBC) is obtained from the same raw materials used to have biochar. With inclusion of iron or addition of magnetic precursors, biochar turns into a material which has magnetic separation capabilities. Defined as a win-win material for the treatment of wastewater pollution, here we consider MBC for those specific applications where it is acting as a ''catcher in the water''. | Amelia Carolina Sparavigna | Materials Science; Carbon-based Materials | CC BY NC 4.0 | CHEMRXIV | 2023-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642d88300784a63aee94ca46/original/the-catcher-in-the-water-magnetic-biochar-for-the-treatment-of-wastewater.pdf |
6250848c88636c50090bd8a5 | 10.26434/chemrxiv-2022-6ncg6 | Medium-density amorphous ice | The amorphous ices govern a wide range of cosmological processes and are potentially key materials for explaining the anomalies of liquid water. A substantial density gap between low-density amorphous (LDA) and the high-density amorphous ices (HDA) with liquid water in the middle is a cornerstone of our current understanding of water. However, here we show that ball milling ‘ordinary’ ice Ih at low temperature gives a structurally distinct medium-density amorphous ice (MDA) within this density gap. These results raise the possibility that MDA is the true glassy state of liquid water or alternatively a heavily sheared crystalline state. Remarkably, the compression of MDA at low temperature leads to a sharp increase of its recrystallization enthalpy highlighting that H2O can be a high-energy geophysical material. | Alexander Rosu-Finsen; Michael Davies; Alfred Amon; Andrea Sella; Angelos Michaelides; Christoph Salzmann | Physical Chemistry; Materials Science; Structure; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6250848c88636c50090bd8a5/original/medium-density-amorphous-ice.pdf |
66ab68c9c9c6a5c07ab0d1e9 | 10.26434/chemrxiv-2023-d3p80-v2 | Bench-stable 2-halopyridinium ketene hemiaminals as new reagents for the synthesis of 2-aminopyridine derivatives | 2-Chloro-1-(1-ethoxyvinyl)pyridinium triflate and several other bench-stable N-(1-alkoxyvinyl) 2-halopyridinium triflates have been developed as reagents for the synthesis of valuable 2-aminopyridine scaffolds via unusually mild SNAr substitu-tions with amine nucleophiles. Advantages of this approach include an operationally simple mix-and-stir procedure at room temperature or mild heat, ambient atmosphere, and without the need of transition metal catalysts, coupling reagents, or high-boiling solvents. The stable N-(1-ethoxyvinyl) moiety serves as a dual SNAr-activating group and pyridine N-protecting group that can be cleaved under thermal, acidic, or oxidative conditions. Preliminary results of other nucleophilic substitu-tions using oxygen, sulfur, and carbon-based nucleophiles are also demonstrated. | Isabelle Bote; Zoe Krevlin; Maria Christina Crespo; Sudchananya Udomphan; Carolyn Levin; Christie Lam; Amy Glanzer; Holly Hutchinson; Alisha Blades; Danielle McConnell; Crystal Lin; John Frank; William Strutton; Jordan Merklin; Beau Sinardo; Khady Gueye; Karly Leiman; Ashley Thayaparan; Joel Adade; Nestor Martinez; Wesley Kramer; Max Majireck | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ab68c9c9c6a5c07ab0d1e9/original/bench-stable-2-halopyridinium-ketene-hemiaminals-as-new-reagents-for-the-synthesis-of-2-aminopyridine-derivatives.pdf |
671a4b3398c8527d9e356fa7 | 10.26434/chemrxiv-2024-247jv | Synthesising Lead Oxide and Oxychloride Minerals from Spent Lead Acid Battery Waste using a Choline-Chloride based Deep Eutectic Solvent | Lead acid batteries have been successfully recycled with pyrometallurgy for many years. However, this process has historically been associated with mass lead poisonings and continues to contribute significantly to disease burden in developing nations. In this paper a cleaner alternative to pyrometallurgical processing is proposed using deep eutectic solvents (DES) based on choline chloride and oxalic acid to dissolve and convert lead materials into pure lead oxalate which can then be calcined at low temperatures into lead oxide products that can be used for the synthesis of new batteries. We also show that lead oxychlorides can be formed at lower calcination temperatures due to the presence of residual chlorine from the DES. | Enrico Manfredi-Haylock; Gwilherm Kerherve; David Payne | Energy; Chemical Engineering and Industrial Chemistry; Natural Resource Recovery; Reaction Engineering; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671a4b3398c8527d9e356fa7/original/synthesising-lead-oxide-and-oxychloride-minerals-from-spent-lead-acid-battery-waste-using-a-choline-chloride-based-deep-eutectic-solvent.pdf |
67307a8b7be152b1d09c106e | 10.26434/chemrxiv-2024-dqlqf | Boron, Aluminium, and Gallium Fluorides as Catalysts for the Defluorofunctionalisation of Electron-Deficient Arenes: The Role of NaBArF4 Promoters | A series of molecular boron, aluminium, and gallium difluoride complexes [{(ArNCMe)2CH}MF2] (M = B, Al, Ga) are reported as catalysts for the defluorofunctionalisation of electron-deficient arenes. Thiodefluorination reactions between TMS–SPh and poly(fluorinated aromatics) proceed with group 13 catalysis under forcing conditions. Evidence is presented for the fluoride entering the catalytic cyclic through a metathesis reaction with TMS–SPh to form metal thiolate intermediates, e.g. [{(ArNCMe)2CH}MF(SPh)], that are then competent nucleophiles for addition to the aromatic substrate, likely through a cSNAr mechanism. Attempts to expand the scope of reactivity to include the hydrodefluorination of electron-deficient arenes with the same group 13 difluoride catalysts met with limited success. Activity could, however, be recovered through addition of NaBArF4 as a catalytic additive (ArF = 3,5-C6H3(CF3)2). NMR titrations suggest that NaBArF4 is capable of coordinating to aluminium and gallium fluoride complexes, most likely through weak M–F---Na interactions (M = Al, Ga) and can play a role in lowering the barrier of metathesis between [{(ArNCMe)2CH}MF2] and Et3SiH to form the group 13 hydrido fluoride [{(ArNCMe)2CH}M(H)F], facilitating catalytic turnover. DFT calculations indicate this weak interaction, leads to a polarization of the M–F bond. The discovery of this additive effect has potentially broad implications in developing new reactivity and applications of thermodynamically stable metal–fluorides. | Wenbang Yang; Andrew White; Mark Crimmin | Organic Chemistry; Inorganic Chemistry; Catalysis; Organic Synthesis and Reactions; Main Group Chemistry (Inorg.); Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67307a8b7be152b1d09c106e/original/boron-aluminium-and-gallium-fluorides-as-catalysts-for-the-defluorofunctionalisation-of-electron-deficient-arenes-the-role-of-na-b-ar-f4-promoters.pdf |
60c753b0bb8c1a90523dc0bb | 10.26434/chemrxiv.13526597.v1 | Drastic Enhancement of Carbon Dioxide Adsorption in Fluoroalkyl-Modified Poly(allylamine) | Polyamine-based carbon dioxide sorbents suffer from a seesaw relationship between amine content
and amine efficiency. High polyamine loadings equate to increased amine contents, but often at
the expense of amine efficiency. Carbon dioxide mass transport in compact polymers is severely
limited, especially at ambient temperature. High polymer contents curtail diffusion pathways,
hindering CO2 from reaching and reacting with the numerous amine functions. Here, we overcome
this issue using poly(allylamine) (PAA) grafted with short fluoroalkyl chains and then cross-linked
with C60. As experimentally evidenced by positron annihilation lifetime spectroscopy, the
incorporation of fluoroalkyl chains generates free volume elements that act as additional diffusion
pathways within the material. The inclusion of void volume in fluoroalkyl-functionalized PAA
sorbents results in radically increased CO2 uptakes and amine efficiencies in diluted gas streams
at room temperature, including simulated air. We speculate that the hydrophobic fluorinated
functions interfere with the strong amine hydrogen bonding network disrupting and consequently
altering the packing and conformation of the polymer chains. The evidence presented here is a
blueprint for the development of more efficient amine-based CO2 sorbents | Athanasios Koutsianos; Louise B. Hamdy; Chun-Jae Yoo; Jason J. Lee; Marco Taddei; Jagoda M. Urban-Klaehn; Jerzy Dryzek; Christopher W. Jones; Andrew R. Barron; Enrico Andreoli | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753b0bb8c1a90523dc0bb/original/drastic-enhancement-of-carbon-dioxide-adsorption-in-fluoroalkyl-modified-poly-allylamine.pdf |
66fff04451558a15ef0e4c8d | 10.26434/chemrxiv-2024-g85dm | Rational discovery of molecular glues for the glucocorticoid receptor – 14-3-3 protein-protein interaction starting with application of traditional hit-finding methods | Given the importance of glucocorticoid receptor (GR) agonists in medicine, despite their numerous adverse side effects, it is of great interest to fully delineate the regulatory network of GR. Post-translational modifications form part of this regulatory network including phosphorylation. After phosphorylation GR interacts with 14-3-3, adding another layer of regulation beyond the ligand-driven activation. Here, we use a screening strategy inspired from traditional hit-finding methods for prospective identification of the first de novo molecular glues of the GR–14-3-3 protein-protein interactions (PPI). Screening 8,000 compounds led to the discovery of one hit. To foster confidence in its stabilisation activity, this hit was further investigated in an array of experiments using biophysical assays, 1D and 2D NMR spectroscopy, and analysis of near neighbours outlined initial structure activity relationships. In addition, those early chemical probes provide starting points for future development into potent tool compounds which could contribute to answer the long-standing question of the physiological role of the GR–14-3-3 PPI. | Matthew Perry; Claire Munier; Joao Neves; Anders Gunnarsson; Fredrik Edfeldt; Isabelle Landrieu; Christian Ottmann | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fff04451558a15ef0e4c8d/original/rational-discovery-of-molecular-glues-for-the-glucocorticoid-receptor-14-3-3-protein-protein-interaction-starting-with-application-of-traditional-hit-finding-methods.pdf |
60c74c21bdbb89baf0a39702 | 10.26434/chemrxiv.11926293.v2 | Tuning the Water Reduction Through Controlled Nanoconfinement Within an Organic Liquid Matrix | <p>The growing hydrogen-economy
requires accelerating the hydrogen evolution reaction. The water dissociation
step (Volmer step) has been proposed as a main kinetic limitation, but the
mechanisms at play in the electrochemical double-layer are poorly understood.
This is due to the ambivalent role of water: it acts both as a reactant and as
a solvent. Here we propose to confine water inside an organic liquid matrix in
order to isolate the sole role of water as a reactant. We observe the formation
of aqueous-rich nanodomains, which size can be tuned by changing the supporting
electrolyte, and found that the reactivity of the system significantly varies
with its nanostructure. Depending on the conditions, it is dominated by either
the strength of short-range cation-water interactions or the formation of long
chains of water molecules. This understanding paves the way toward the
development of more efficient and selective electrocatalysts for the water, CO<sub>2</sub>,
O<sub>2</sub> or N<sub>2</sub> reduction.</p> | Nicolas Dubouis; Alessandra Serva; Roxanne Berthin; Guillaume Jeanmairet; Benjamin Porcheron; Elodie Salager; Mathieu Salanne; Alexis Grimaud | Electrocatalysis; Energy Storage; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c21bdbb89baf0a39702/original/tuning-the-water-reduction-through-controlled-nanoconfinement-within-an-organic-liquid-matrix.pdf |
61109a10abc9e2a3c96988c4 | 10.26434/chemrxiv-2021-x05x1 | Electrochemical Regeneration of Anthraquinones for Lifetime Extension in Flow Batteries | Aqueous organic redox flow batteries (AORFBs) offer a safe and potentially inexpensive solution to the problem of storing massive amounts of electricity produced from intermittent renewables. However, molecular decomposition is the major barrier preventing AORFBs from being commercialized. Structural modifications can improve molecular stability at the expense of increased synthetic cost and molecular weight. Utilizing 2,6-dihydroxy-anthraquinone (DHAQ), without further structural modification, we demonstrate that electrochemical regeneration could be a viable route to achieve low-cost, long-lifetime AORFBs. In situ (online) NMR and EPR and complementary electrochemical analyses reveal that decomposition compounds i.e., 2,6-dihydroxy-anthrone (DHA) and its tautomer, 2,6-dihydroxy-anthranol (DHAL), can be converted back to DHAQ in two steps: first DHA(L)2− are oxidized to the dimer (DHA)24− at − 0.32 V vs. SHE by one-electron transfer; subsequently, the (DHA)24− is oxidized to DHAQ2− at +0.57 V vs. SHE by three-electron transfer. Electrochemical regeneration rejuvenates not only DHAQ2−, but also the positive electrolyte – rebalancing the states of charge of both electrolytes without introducing extra ions. We demonstrate the repeated capacity recovery with DHAQ | potassium ferro-/ferricyanide flow battery in basic conditions, and show the approach is also effective for anthraquinone-2,7-disulfonate in acid. Electrochemical regeneration strategies may extend the useful lifetime of many water-soluble organic molecules with anthraquinone core structures in electrochemical cells. | Yan Jing; Evan Wenbo Zhao; Marc-Antoni Goulet; Meisam Bahari; Eric Fell; Shijian Jin; Ali Davoodi; Erlendur Jónsson; Min Wu; Clare Grey; Roy Gordon; Michael Aziz | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61109a10abc9e2a3c96988c4/original/electrochemical-regeneration-of-anthraquinones-for-lifetime-extension-in-flow-batteries.pdf |
648a981de64f843f41cda54b | 10.26434/chemrxiv-2023-mt7tz-v2 | Synthesis of Nickel(I)–Bromide Complexes via Oxidation and Ligand Displacement: Evaluation of Ligand Effects on Speciation and Reactivity | Nickel’s +1 oxidation state has received much interest due to its varied and often enigmatic behavior in increasingly popular catalytic methods. In part, the lack of understanding about Ni(I) results from common synthetic strategies limiting the breadth of complexes that are accessible for mechanistic study and catalyst design. We report an oxidative approach using tribromide salts that allows for the generation of a well-defined precursor, [Ni(I)(COD)Br]2, as well as several new NiI complexes. Included among them are complexes bearing bulky monophosphines, for which structure–speciation relationships are established and catalytic reactivity in a Suzuki-Miyaura coupling (SMC) is investigated. Notably, these routes also allow for the synthesis of well-defined monomeric t-Bu-bpy-bound Ni(I) complexes, which has not previously been achieved. These complexes, which react with aryl halides, can enable previously challenging mechanistic investigations and present new opportunities for catalysis and synthesis. | Samuel Newman-Stonebraker; T. Judah Raab; Hootan Roshandel; Abigail Doyle | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Organometallic Compounds; Coordination Chemistry (Organomet.); Kinetics and Mechanism - Organometallic Reactions | CC BY NC 4.0 | CHEMRXIV | 2023-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648a981de64f843f41cda54b/original/synthesis-of-nickel-i-bromide-complexes-via-oxidation-and-ligand-displacement-evaluation-of-ligand-effects-on-speciation-and-reactivity.pdf |
6560a8b2cf8b3c3cd705e1af | 10.26434/chemrxiv-2023-8n92m | Redox behaviour of Cu-Aβ(4-16) complexes related to Alzheimer's Disease | The development of Alzheimer’s Disease (AD) has been linked to abnormal quantities of β-amyloid peptides in the brain. The majority of studies have focussed on Aβ(1-40/42) amyloids and their Cu(II)-Aβ(1-40/42) complexes which are responsible for production of reactive oxygen and nitrogen species (ROS and RNS), which are highly toxic to neurons. According to recent studies on amyloid plaques, Aβ(4-42), which is an N-truncated version of Aβ(1-42), is as prevalent as Aβ(1-42) in the brain. Although Cu(II) ions, bounded by Aβ(4-42), can be oxidized to highly reactive Cu(III) ions, its Cu(II) complexes do not appear to contribute to ROS/RNS formation. In this paper, the pH-dependent voltammetric response of Aβ(4-16)-Cu(II) complexes is investigated to understand the influence of the deprotonation of tyrosine within the complex towards the Cu(II)/Cu(III) reaction. The results will help to better understand the scavenging role of tyrosine in quenching highly reactive Cu(III) ions not only in Aβ(4-x)-Cu(II) complexes but also provide clues to the reactive properties of other tyrosine-containing amyloid-metal complexes. | Magdalena Wiloch; Steven Linfield; Natalia Baran; Wojciech Nogala; Martin Jönsson-Niedziółka | Physical Chemistry; Biological and Medicinal Chemistry; Electrochemistry - Mechanisms, Theory & Study | CC BY 4.0 | CHEMRXIV | 2023-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6560a8b2cf8b3c3cd705e1af/original/redox-behaviour-of-cu-a-4-16-complexes-related-to-alzheimer-s-disease.pdf |
644850b5df78ec5015627c47 | 10.26434/chemrxiv-2023-zms13 | Quantum Zeno Effect: Irreversible and Quantum Thermodynamic considerations | The Quantum Zeno Effect slows down the quantum system's time evolution under frequent measurements. This paper aims to study this quantum effect by introducing the definition of time based on an irreversible thermodynamic analysis of quantum systems. Consequently, the Quantum Zeno Effect requires (i) high values of the electromagnetic entropy generation rate related to the spontaneously down-converted light and (ii) a decrease in the quantum system's entropy value. So, the Quantum Zeno Effect is a quantum process related to the interaction between a quantum system and the electromagnetic waves of the measurement device, causing a quantum thermodynamic stationary state. Last, the fundamental role of irreversibility emerges. | Umberto Lucia | Theoretical and Computational Chemistry; Physical Chemistry; Quantum Computing; Quantum Mechanics; Thermodynamics (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644850b5df78ec5015627c47/original/quantum-zeno-effect-irreversible-and-quantum-thermodynamic-considerations.pdf |
60c75553f96a001c14288850 | 10.26434/chemrxiv.13536950.v2 | DECIMER Segmentation - Automated Extraction of Chemical Structure Depictions from Scientific Literature | <p>Chemistry looks back at many decades of publications on chemical compounds, their structures and properties, in scientific articles. Liberating this knowledge (semi-)automatically and making it available to the world in open-access databases is a current challenge. Apart from mining textual information, Optical Chemical Structure Recognition (OCSR), the translation of an image of a chemical structure into a machine-readable representation, is part of this workflow. As the OCSR process requires an image containing a chemical structure, there is a need for a publicly available tool that automatically recognizes and segments chemical structure depictions from scientific publications. This is especially important for older documents which are only available as scanned pages. Here, we present DECIMER (Deep lEarning for Chemical IMagE Recognition) Segmentation, the first open-source, deep learning-based tool for automated recognition and segmentation of chemical structures from the scientific literature.</p><br /><p>The workflow is divided into two main stages. During the detection step, a deep learning model recognizes chemical structure depictions and creates masks which define their positions on the input page. Subsequently, potentially incomplete masks are expanded in a post-processing workflow. The performance of DECIMER Segmentation has been manually evaluated on three sets of publications from different publishers. The approach operates on bitmap images of journal pages to be applicable also to older articles before the introduction of vector images in PDFs. </p><br /><p>By making the source code and the trained model publicly available, we hope to contribute to the development of comprehensive chemical data extraction workflows. In order to facilitate access to DECIMER Segmentation, we also developed a web application. The web application, available at <a href="https://decimer.ai">https://decimer.ai</a>, lets the user upload a pdf file and retrieve the segmented structure depictions.</p><div><br /></div> | Kohulan Rajan; Henning Otto brinkhaus; Maria Sorokina; Achim Zielesny; Christoph Steinbeck | Chemoinformatics; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75553f96a001c14288850/original/decimer-segmentation-automated-extraction-of-chemical-structure-depictions-from-scientific-literature.pdf |
60c74d264c8919abbead3780 | 10.26434/chemrxiv.12592286.v1 | In Silico Exploration of Small-Molecule α-Helix Mimetics as Inhibitors of SARS-COV-2 Attachment to ACE2 | The novel coronavirus, SARS-CoV-2, has infected more than 10 million people and caused more than 502,539 deaths worldwide as of June 2020. The explosive spread of the virus and the rapid increase in the number of cases require the immediate development of effective therapies and vaccines as well as accurate diagnosis tools. The pathogenesis of the disease is triggered by the entry of SARS-CoV-2 via its spike protein into ACE2-bearing host cells, particularly pneumocytes, resulting in overactivation of the immune system, which attacks the infected cells and damages the lung tissue. The interaction of the SARS-CoV-2 receptor binding domain (RBD) with host cells is primarily mediated by the N-terminal helix of the ACE2; thus, inhibition of the spike-ACE2 interaction may be a promising therapeutic strategy for blocking the entry of the virus into host cells. In this paper, we used an in-silico approach to explore small-molecule α-helix mimetics as inhibitors that may disrupt the attachment of SARS-CoV-2 to ACE2. First, the RBD-ACE2 interface in the 6M0J structure was studied by the MM-GBSA decomposition module of the HawkDock server, which led to the identification of two critical target regions in the RBD. Next, two virtual screening experiments of 7236 α-helix mimetics from ASINEX were conducted on the above regions using the iDock tool, which resulted in 10 candidates with favorable binding affinities. Finally, the stability of RBD complexes with the top-two ranked compounds was further validated by 40 ns MD simulations using Desmond package of Schrodinger.<br /> | Mohammed Hakmi; El Mehdi Bouricha; Jihane Akachar; Badreddine Lmimouni; Jaouad EL Harti; Lahcen Belyamani; Azeddine Ibrahimi | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d264c8919abbead3780/original/in-silico-exploration-of-small-molecule-helix-mimetics-as-inhibitors-of-sars-cov-2-attachment-to-ace2.pdf |
60c750c70f50db9351397625 | 10.26434/chemrxiv.13082138.v1 | Fluorinated Mannosides Inhibit Cellular Fucosylation. | Fucose sugars are expressed on mammalian cell
membranes as part of glycoconjugates and mediates essential physiological processes.
The aberrant expression of fucosylated glycans has been linked to pathologies such
as cancer, inflammation, infection, and genetic disorders. Tools to modulate
fucose expression on living cells are needed to elucidate the biological role
of fucose sugars and the development of potential therapeutics. Herein, we
report a novel class of fucosylation inhibitors directly targeting de novo GDP-fucose biosynthesis. We demonstrate that cell permeable
fluorinated mannoside 1-phosphate derivatives (Fucotrim I & II) are
metabolic prodrugs that are metabolized to their respective GDP-mannose
derivatives and efficiently inhibit cellular fucosylation. | Johan Pijnenborg; Emiel Rossing; Marek Noga; Willem Titulaer; Raisa Veizaj; Dirk J. Lefeber; Thomas Boltje | Biochemistry; Bioengineering and Biotechnology; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750c70f50db9351397625/original/fluorinated-mannosides-inhibit-cellular-fucosylation.pdf |
636d28d781f223439d941d4c | 10.26434/chemrxiv-2022-dntx4-v4 | Solid-phase synthesis of cereblon-recruiting selective histone deacetylase 6 degraders (HDAC6 PROTACs) with anti-leukemic activity | In this work, we utilized the proteolysis targeting chimera (PROTAC) technology to achieve the chemical knock-down of histone deacetylase 6 (HDAC6). Two series of cereblon-recruiting PROTACs were synthesized via a solid-phase parallel synthesis approach, which allowed the rapid preparation of two HDAC6 degrader mini libraries. The PROTACs were either based on an unselective vorinostat-like HDAC ligand or derived from a selective HDAC6 inhibitor. Notably, both PROTAC series demonstrated selective degradation of HDAC6 in leukemia cell lines. The best degraders from each series (denoted A6 and B4) were capable of degrading HDAC6 via ternary complex formation and the ubiquitin−proteasome pathway, with DC50 values of 3.5 and 19.4 nM, respectively. PROTAC A6 demonstrated promising antiproliferative activity via inducing apoptosis in myeloid leukemia cell lines. These findings highlight the potential of this series of degraders as effective pharmacological tools for the targeted degradation of HDAC6. | Laura Sinatra; Jing Yang; Julian Schliehe-Diecks; Niklas Dienstbier; Melina Vogt; Philip Gebing; Luisa M. Bachmann; Melf Sönnichsen; Thomas Lenz; Kai Stühler; Andrea Schöler; Arndt Borkhardt; Sanil Bhatia; Finn K. Hansen | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636d28d781f223439d941d4c/original/solid-phase-synthesis-of-cereblon-recruiting-selective-histone-deacetylase-6-degraders-hdac6-prota-cs-with-anti-leukemic-activity.pdf |
65977396e9ebbb4db9754d21 | 10.26434/chemrxiv-2024-2zlrs | Lagrangian of extended multiconfigurational self-consistent field second-order quasidegenerate perturbation theory combined with reference interaction site model self-consistent field constraint spatial electron density | Lagrangians of the SA multiconfigurational self-consistent field(SA-MCSCF) and multistate extended second-order quasidegenerate perturbation theory (MS-XMCQDPT2) coupled with the reference interaction site model self-consistent field constraint spatial electron density (RISM-SCF-cSED) are defined. In addition, variational equations were derived to calculate the excitation energies of target molecules dissolved in various solvents. The theory was applied to a phenol molecule in various solutions and the gradients and Hessian matrices were calculated to evaluate the absorption spectral lines including the broadening bandwidth. Numerical calculations revealed fine structures in any solvent surroundings. The main intramolecular vibrational modes related to such fine structures were stretching vibrations of the aromatic ring and the oxygen atom of the phenol molecule. The present theory plays an important role when predicting the structure of potential energy surfaces, such as Hessian matrices for various solvent types, during the photoexcitation process. | Naoki Negishi; Daisuke Yokogawa | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65977396e9ebbb4db9754d21/original/lagrangian-of-extended-multiconfigurational-self-consistent-field-second-order-quasidegenerate-perturbation-theory-combined-with-reference-interaction-site-model-self-consistent-field-constraint-spatial-electron-density.pdf |
64f0be873fdae147fa355a41 | 10.26434/chemrxiv-2023-trrrz | Charge transport in individual short single-stranded RNA molecules | Charge transport in biomolecules is crucial for many biological and technological applications, including biomolecular electronics devices and biosensors. RNA has become the focus of research because of its importance in biomedicine, but its charge transport properties are poorly understood. Here, we use the Scanning Tunneling Microscopy-assisted molecular break junction method to measure, for the first time, the electrical conductance of 5-base and 10-base single-stranded (ss) RNA sequences. These ssRNAs show single-molecule conductance values around 0.001 G0 (G0 = 2e2/h), while equivalent ssDNAs result in featureless conductance histograms. Circular dichroism (CD) spectra and MD simulations reveal the existence of extended ssRNA conformations versus folded ssDNA conformations, consistent with their different electrical behaviors. Computational molecular modeling and Machine Learning-assisted interpretation of CD data helped us to disentangle the structural and electronic factors underlying CT, thus explaining the observed electrical behavior differences. RNA with a measurable conductance corresponds to sequences with overall extended base-stacking stabilized conformations characterized by lower HOMO energy levels delocalized over a base-stacking mediating CT. In contrast, DNA and a control RNA sequence tend to form closed structures and thus are incapable of efficient CT. | Subrata Chandra; Farkhad Maksudov; Evgenii Kliuchnikov; Keshani GG Pattiya Arachchillage; Patrick Piscitelli; Aderlyn castillo; Kenneth Marx; Valeri Barsegov; Juan Manuel Artés Vivancos | Physical Chemistry; Materials Science; Nanoscience; Nanostructured Materials - Nanoscience; Biophysical Chemistry; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f0be873fdae147fa355a41/original/charge-transport-in-individual-short-single-stranded-rna-molecules.pdf |
6627d66991aefa6ce136e633 | 10.26434/chemrxiv-2024-6twmx-v2 | δ-Bonding and Electron Localisation in Crystalline Divalent Rare Earth Arene Complexes | Landmark advances in rare earth (RE) chemistry have shown that formally divalent complexes can be isolated with non-Aufbau 4fn5d(dz2)1 or 4fn{5d/6s}1 electron configurations, which facilitate novel bonding motifs and phenomenal magnetic properties. We report an unprecedented series of divalent bis-tethered arene complexes, [RE(NHAriPr6)2] (2RE; RE = Sc, Y, La, Sm, Eu, Tm, Yb; NHAriPr6 = {N(H)C6H3-2,6-(C6H2-2,4,6-iPr3)2}), where 2Sc, 2Y, and 2La show metal-arene δ-bonding via nd(x2-y2)- and π* orbital mixing, while 2Sm, 2Eu, 2Tm, and 2Yb contain 4fn+1 ions without δ-bonds. Fluid solution EPR spectroscopy gives giso = 1.9995, 1.998, 1.989 for 2Sc, 2Y, and 2La, respectively, consistent with formal nd1 configurations, while metal hyperfine interactions suggest extensive delocalisation. Solution and crystalline phase EPR and UV-Vis-NIR spectroscopy for 2Y show incongruities due to minor structural changes between these phases that markedly alter the metal 4d(x2-y2) character to the SOMO (22% vs 12%, respectively). In contrast to existing 4fn5d(dz2)1 or 4fn{5d/6s}1 complexes where the valence d-based electron resides in a non-bonding orbital, the sensitivity of 2Y to its local environment suggests RE(II) arene δ-bonding represents a hitherto unexplored opportunity to tune the electronic structure properties of nd1 rare earth ions. | Ross MacKenzie; Tomáš Hajdu; John Seed; George Whitehead; Ralph Adams; Nicholas Chilton; David Collison; Eric McInnes; Conrad Goodwin | Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6627d66991aefa6ce136e633/original/bonding-and-electron-localisation-in-crystalline-divalent-rare-earth-arene-complexes.pdf |
676954de6dde43c90814c096 | 10.26434/chemrxiv-2024-79drl-v2 | Assessing Accelerated Reaction Network Exploration with ChemTraYzer-TAD and PESmapping | Developing chemical combustion mechanisms for novel bio- and e-fuels is a challenge, given that many established mechanism analogies originate from fossil fuels. This work studies the ability of two new reaction network exploration methods, ChemTraYzer-TAD and PESmapping, to suggest potentially important reaction paths to combustion mechanisms, highlighting the differences and similarities of the two methods. In the reaction space of the ethyl-2-yl formate radical combustion, all expected important reactions are found, with many additional reactions suggested by one or the other method. This shows that the combination of both methods provides an optimal exploration result, i.e. both expected and novel reaction pathways. | Felix Schmalz; Enia Mudimu; Ilias Chair; Wassja Kopp; Kai Leonhard | Theoretical and Computational Chemistry; Energy; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Reaction Engineering; Fuels - Energy Science | CC BY 4.0 | CHEMRXIV | 2024-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676954de6dde43c90814c096/original/assessing-accelerated-reaction-network-exploration-with-chem-tra-yzer-tad-and-pe-smapping.pdf |
65736ce45bc9fcb5c9652b3b | 10.26434/chemrxiv-2023-6xj3m | Mineralization of Captured Per- and Polyfluoroalkyl Substances (PFAS) at Zero Net Cost Using Flash Joule Heating | Per- and polyfluorinated alkyl substances (PFAS) are persistent and widespread environmental contaminants that have infiltrated freshwater systems. Granular activated carbon (GAC), the most widely used sorbent for PFAS removal from water, becomes a secondary waste when PFAS is sorbed upon it (PFAS-GAC). Current methods for treatment of this contaminated spent carbon, such as incineration, release large amounts of hazardous gaseous fluorocarbons. To address these challenges, here we demonstrate the disposal of PFAS-GAC using an electrothermal mineralization process. Flash Joule heating (FJH) of PFAS-GAC in the presence of sodium or calcium salts yields inert, non-toxic fluoride salts with >96% fluorine conversion efficiency. Simultaneously, the spent carbon is upcycled into high-value flash graphene, offsetting the cost of treatment by $1900 US per tonne. The entire process operates without the need for solvents or expensive catalysts. The life cycle assessment (LCA) shows a reduction in cumulative energy consumption, greenhouse gas emissions, and water usage. The ease of scalability and the production of valuable co-products, as highlighted in the technoeconomic assessment (TEA), showcases this method as an attractive route to mineralize PFAS in ~1 s. | Phelecia Scotland; Kevin Wyss; Lucas Eddy; Yi Cheng; Jacob Beckham; Youngkun Chung; Bo Wang; Chi Choi; Bing Deng; Tengda Si; Yu-Yi Shen; Sarah Zetterholm; Christopher Griggs; Yimo Han; Mason Tomson; Michael Wong; Boris Yakobson; Yufeng Zhao; James Tour | Inorganic Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Hydrology and Water Chemistry; Wastes | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65736ce45bc9fcb5c9652b3b/original/mineralization-of-captured-per-and-polyfluoroalkyl-substances-pfas-at-zero-net-cost-using-flash-joule-heating.pdf |
60c74f81ee301c1d05c7a6ec | 10.26434/chemrxiv.12915383.v1 | Soft Mode Metal-Linker Dynamics in Carboxylate MOFs | <div>
<div>
<div>
<p>Through comprehensive analysis of carboxylate-based metal-organic frameworks
(MOFs), we present general evidence for dynamic metal-linker bonding that challenges the
common perception of MOF structures being static. Structural dynamics in MOFs, however,
typically refers to the “breathing” behavior of pore cavities and the transient binding of guest
molecules, but dynamic bonding would explain important MOF phenomena in catalysis, post-
synthetic exchange, negative thermal expansion, and crystal growth. Here, we demonstrate through
use of variable-temperature diffuse reflectance infrared Fourier transform spectroscopy (VT-
DRIFTS) aided by ab initio plane wave density function theory, that similar evidence for melting
behavior in zeolitic imidazolate frameworks (ZIFs) can be observed for carboxylate MOFs by
monitoring the red-shifts of carboxylate stretches coupled to anharmonic metal-carboxylate
oscillators. To demonstrate the generality of these findings, we investigate a wide class of
carboxylate MOFs that includes iconic examples with diverse structures and metal-linker
chemistry. As the very vibrations invoked in ZIF melting, but heretofore unobserved for
carboxylate MOFs, these metal-linker dynamics resemble the ubiquitous soft modes that trigger
important phase transitions in diverse classes of materials, while offering a fundamentally new
perspective for the design of next-generation metal-organic materials.
</p>
</div>
</div>
</div> | Anastasia Andreeva; Lihaokun Chen; Khoa N. Le; Michael E. Kellman; Christopher
H. Hendon; Carl Brozek | Hybrid Organic-Inorganic Materials; Solid State Chemistry; Self-Assembly; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f81ee301c1d05c7a6ec/original/soft-mode-metal-linker-dynamics-in-carboxylate-mo-fs.pdf |
636c63008e0d35eb1f14f43a | 10.26434/chemrxiv-2022-rvbk0 | Brønsted Base-Catalyzed Domino Annulation of α-oxo-β, γ-Unsaturated Ketones and Malononitrile: Facile Access to Poly-substituted Tetrahydrocyclopenta[b]furanols | An efficient and atom-economical Brϕnsted base-catalyzed domino reaction of α-oxo-β, γ-unsaturated ketone is described. Under the catalysis of 20 mol% K2CO3, both symmetrical cinnamils and unsymmetrical β, γ-unsaturated diketones can react with malononitrile to produce polysubstituted tetrahydrocyclopenta[b]furanols in good to high yields and excellent diastereoselectivity. Three quaternary carbon centers and one tertiary carbon center can be constructed simultaneously, and the reaction can be easily scaled up. | JInyun Luo; Zenan Feng; Zhihua Cai; Guangfen Du; Jichang Liu; Bin Dai; Lin He | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636c63008e0d35eb1f14f43a/original/br-nsted-base-catalyzed-domino-annulation-of-oxo-unsaturated-ketones-and-malononitrile-facile-access-to-poly-substituted-tetrahydrocyclopenta-b-furanols.pdf |
612f4b5eabeb63de21c5a6f6 | 10.26434/chemrxiv-2021-p0fzf | Modular Synthesis of Azabicyclohexanes and Cyclobutenyl Amines | The development of two divergent and complementary Lewis acid catalyzed additions of bicyclobutanes to imines is described. Microscale high-throughput experimentation was integral to the discovery and optimization of both reactions. N-arylimines undergo formal (3+2) cycloaddition with bicyclobutanes to yield azabicyclo[2.1.1]hexanes in a single step; in contrast, N-alkylimines undergo an addition/elimination sequence to generate cyclobutenyl methanamine products with high diastereoselectivity. These new products contain a variety of synthetic handles for further elaboration, including many functional groups relevant to pharmaceutical synthesis. The divergent reactivity observed is attributed to differences in basicity and nucleophilicity of the nitrogen atom in a common carbocation intermediate, leading to either nucleophilic attack (N-aryl) or E1 elimination (N-alkyl). | Kushal Dhake; Kyla Woelk; Joseph Becica; Andy Un; Sarah Jenny; David Leitch | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612f4b5eabeb63de21c5a6f6/original/modular-synthesis-of-azabicyclohexanes-and-cyclobutenyl-amines.pdf |
63f8083c897b18336f06f598 | 10.26434/chemrxiv-2023-hg600 | Fragment-Based Calculations of Enzymatic Thermochemistry Require Dielectric Boundary Conditions | Quantum-chemical calculations of enzymatic thermochemistry require hundreds of atoms to obtain converged results, severely limiting the levels of theory that can be used. Fragment-based approaches offer a means to circumvent this problem, and we present calculations on enzyme models containing 500–600 atoms using the many-body expansion with three- and four-body terms. Results are compared to benchmarks in which the supramolecular enzyme–substrate complex is described at the same level of theory. When the amino acid fragments contain ionic side chains, the many-body expansion oscillates under vacuum boundary conditions, exaggerating the role of many-body effects. Rapid convergence is restored using low-dielectric boundary conditions. This implies that full-system calculations in the gas phase are inappropriate benchmarks for assessing errors introduced by fragment-based approximations. For calculations with dielectric boundary conditions, a three-body protocol with distance cutoffs retains sub-kcal/mol fidelity with respect to a supersystem calculation at the same level of theory, as does a two-body protocol when combined with a full-system correction at a low-cost level of theory. Both calculations dramatically reduce the cost of large-scale enzymatic thermochemistry, paving the way for application of high-level ab initio methods to very large systems. | Paige Bowling; Dustin Broderick; John Herbert | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f8083c897b18336f06f598/original/fragment-based-calculations-of-enzymatic-thermochemistry-require-dielectric-boundary-conditions.pdf |
60c74129bb8c1a904b3d9ee7 | 10.26434/chemrxiv.7987475.v1 | Inverse Design in Porous Materials Using Artificial Neural Networks | Generating optimal nanomaterials using artificial neural networks can potentially lead to a significant revolution in future materials design. Although progress has been made in creating small and simple molecules, complex materials such as crystalline porous materials have yet to be generated using any of the neural networks. In this work, we have for the first time implemented a generative adversarial network that uses a training set of 31,713 known zeolites to produce 14 crystalline porous materials. Our neural network takes in inputs in the form of energy and material dimensions and we show that zeolites with a user-desired range of 4 kJ/mol methane heat of adsorption can be reliably produced using our neural network. The fine-tuning of user-desired capability can potentially accelerate materials development as it demonstrates a successful case of inverse design in porous materials. | Baekjun Kim; Sangwon Lee; Jihan Kim | Minerals; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74129bb8c1a904b3d9ee7/original/inverse-design-in-porous-materials-using-artificial-neural-networks.pdf |
6734965ff9980725cf0cb45a | 10.26434/chemrxiv-2024-gthhs | A consistent set of thermophysical properties of methane curated with machine learning | Accurately predicting thermophysical properties across different states of matter is essential for industrial and scientific applications. However, experimental data often suffer from variability and noise, among other problems, thus necessitating robust modeling approaches to create consistent sets. In this work, we employ machine learning (ML) models to predict multiple thermophysical properties of methane in liquid, vapor, and supercritical phases, including isobaric and isochoric heat capacities, density, volume, Joule-Thomson coefficients, enthalpies, sound speed, and viscosities. We explored different ML algorithms including Adaptive Boosting, Bagging, Decision Trees, Extra Trees, Gradient Boosting, Histogram-based Gradient Boosting Regression Tree, K-Nearest Neighbors, Light Gradient Boosting Machine, Nu-Support Vector Regression, Random Forest, Extreme Gradient Boosting, and Artificial Neural Networks across regions of the phase diagram. Combining ML techniques with previously available raw experimental data shows that ML models provide predictions closer to the statistically treated National Institute of Standards and Technology (NIST) data when compared to the original experimental datasets. Therefore, our approach shows the ML’s potential to identify and generalize complex patterns, smooth inherent data noise, and manage variability. The results indicate that ML models, particularly the Extra Trees and Gradient Boosting models, are a scalable alternative for thermophysical property predictions, offering consistency and efficiency over traditional methods in data processing and curation. | Matheus Maximo-Canadas; Rubens Caio Souza; Julio Cesar Duarte; Jakler Nichele; Leonardo Santos de Brito Alves; Luis Octavio Vieira Pereira; Ligia Gaigher Franco; Itamar Borges Jr | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Engineering and Industrial Chemistry; Artificial Intelligence; Fluid Mechanics; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6734965ff9980725cf0cb45a/original/a-consistent-set-of-thermophysical-properties-of-methane-curated-with-machine-learning.pdf |
60c7593d842e6572acdb49d2 | 10.26434/chemrxiv.14675403.v1 | Complexation of C-Functionalized Cyclams with Copper(II) and Zinc(II): Similarities and Changes When Compared to Parent Cyclam Analogues | Herein, we report a comprehensive coordination
study of the previously reported ligands <b>cyclam</b>,
<b>CB-cyclam TMC</b>, <b>DMC</b>, <b>CB-DMC</b>, and
of their <i>C</i>-functional analogues, <b>cyclam-E</b>, <b>CB-cyclam-E</b>, <b>TMC-E</b>, <b>DMC-E</b> and <b>CB-DMC-E</b>. This group of ligands includes <b>cyclam</b>, cross-bridged
<b>cyclams</b>, their di- or tetramethylated derivatives and the analogues
bearing an additional hydroxyethyl group on one β-N position of the ring. These
Cu(II) and Zn(II) complexes of these macrocycles have been highlighted
previously for the biological interest, but the details of their structures in
the solid state and in solution remained largely unexplored. <br /> | Evan Lelong; Jong-Min Suh; Gunhee Kim; David Esteban-Gómez; Marie Cordier; Mi Hee Lim; Rita Delgado; Guy Royal; Carlos Platas-Iglesias; Hélène Bernard; Raphael Tripier; Tripier Raphael | Coordination Chemistry (Inorg.); Electrochemistry; Ligands (Inorg.); Theory - Inorganic; Transition Metal Complexes (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7593d842e6572acdb49d2/original/complexation-of-c-functionalized-cyclams-with-copper-ii-and-zinc-ii-similarities-and-changes-when-compared-to-parent-cyclam-analogues.pdf |
63d7dd49ab681c2c9d20db9a | 10.26434/chemrxiv-2023-nh571 | Complete active space methods for NISQ devices: The importance of canonical orbital optimization for accuracy and noise resilience | To break the scaling of the number of qubits with the size of the basis set, one can divide the molecular space into active and inactive, also known as complete active space methods. Nevertheless, more than the active space selection is needed for accuracy and effectively describing quantum mechanical effects as correlation. This study highlights the importance of optimizing the active space orbitals to describe correlation and improve the Hartree-Fock energies. We will explore orbital optimization classically and through quantum computation and how, theoretically, a chemically inspired ansatz as the UCCSD compares with a classical full CI (FCI) description of the active space in weakly and strongly correlated molecules. Finally, we will explore the practical implementation of a quantum CASSCF where hardware-efficient circuits need to be used, and noise hinders its accuracy and convergence. Moreover, we explore canonical and non-canonical active orbitals and how those influence the convergence of the quantum CASSCF routine in the presence of noise. | Juan Ángel de Gracia Triviño; Mickael G Delcey; Göran Wendin | Theoretical and Computational Chemistry; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d7dd49ab681c2c9d20db9a/original/complete-active-space-methods-for-nisq-devices-the-importance-of-canonical-orbital-optimization-for-accuracy-and-noise-resilience.pdf |
60c74a1a337d6c9863e27808 | 10.26434/chemrxiv.12152820.v1 | Quantitative Mapping of Molecular Substituents to Macroscopic Properties Enables Predictive Design of Oligoethyleneglycol-Based Lithium Electrolytes | <p>Molecular details often dictate the macroscopic properties of materials, yet, due to their vastly different length scales, relationships between molecular structure and bulk properties are often difficult to predict <i>a priori</i>, requiring Edisonian optimizations and preventing rational design. Here, we introduce an easy-to-execute strategy based on linear free energy relationships (LFERs) that enables quantitative correlation and prediction of how molecular modifications, <i>i.e.</i>, substituents, impact the ensemble properties of materials. First, we developed substituent parameters based on inexpensive, DFT-computed energetics of elementary pairwise interactions between a given substituent and other constant components of the material. These substituent parameters were then used as inputs to regression analyses of experimentally measured bulk properties, generating a predictive statistical model. We applied this approach to a widely studied class of electrolyte materials: oligo-ethylene glycol (OEG)-LiTFSI mixtures; the resulting model enables elucidation of fundamental physical principles that govern the properties of these electrolytes and also enables prediction of the properties of novel, improved OEG-LiTFSI-based electrolytes. The framework presented here for using context-specific substituent parameters will potentially enhance the throughput of screening new molecular designs for next-generation energy storage devices and other materials-oriented contexts where classical substituent parameters (<i>e.g.</i>, Hammett parameters) may not be available or effective.</p> | Bo Qiao; Somesh Mohapatra; Jeffrey Lopez; Graham Leverick; Ryoichi Tatara; Yoshiki Shibuya; Yivan Jiang; Arthur France-Lanord; Jeffrey C. Grossman; Rafael Gomez-Bombarelli; Jeremiah Johnson; Yang Shao-Horn | Organic Compounds and Functional Groups; Physical Organic Chemistry; Computational Chemistry and Modeling; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a1a337d6c9863e27808/original/quantitative-mapping-of-molecular-substituents-to-macroscopic-properties-enables-predictive-design-of-oligoethyleneglycol-based-lithium-electrolytes.pdf |
60c74544702a9b67ef18a9cd | 10.26434/chemrxiv.9901070.v2 | Deep Generative Model for Sparse Graphs using Text-Based Learning with Augmentation in Generative Examination Networks | Graphs and networks are a key research tool for a variety of science fields, most notably chemistry, biology, engineering and social sciences. Modeling and generation of graphs with efficient sampling is a key challenge for graphs. In particular, the non-uniqueness, high dimensionality of the vertices and local dependencies of the edges may render the task challenging. We apply our recently introduced method, Generative Examination Networks (GENs) to create the first text-based generative graph models using one-line text formats as graph representation. In our GEN, a RNN-generative model for a one-line text format learns autonomously to predict the next available character. The training is stopped by an examination mechanism checking validating the percentage of valid graphs generated. We achieved moderate to high validity using dense g6 strings (random 67.8 +/- 0.6, canonical 99.1 +/- 0.2). Based on these results we have adapted the widely used SMILES representation for molecules to a new input format, which we call linear graph input (LGI). Apart from the benefits of a short compressible text-format, a major advantage include the possibility to randomize and augment the format. The generative models are evaluated for overall performance and for reconstruction of the property space. The results show that LGI strings are very well suited for machine-learning and that augmentation is essential for the performance of the model in terms of validity, uniqueness and novelty. Lastly, the format can address smaller and larger dataset of graphs and the format can be easily adapted to define another meaning of the characters used in the LGI-string and can address sparse graph problems in used in other fields of science. | Ruud van Deursen; Guillaume Godin | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74544702a9b67ef18a9cd/original/deep-generative-model-for-sparse-graphs-using-text-based-learning-with-augmentation-in-generative-examination-networks.pdf |
61acf2f557f82740aba82f46 | 10.26434/chemrxiv-2021-013gn-v2 | BiRDS - Binding Residue Detection from Protein Sequences using Deep ResNets |
Protein-drug interactions play important roles in many biological processes and therapeutics. Prediction of the active binding site of a protein helps discover and optimise these interactions leading to the design of better ligand molecules. The tertiary structure of a protein determines the binding sites available to the drug molecule. A quick and accurate prediction of the binding site from sequence alone without utilising the three-dimensional structure is challenging. Deep Learning has been used in a variety of biochemical tasks and has been hugely successful. In this paper, a Residual Neural Network (leveraging skip connections) is implemented to predict a protein's most active binding site. An Annotated Database of Druggable Binding Sites from the Protein DataBank, sc-PDB, is used for training the network. Features extracted from the Multiple Sequence Alignments (MSAs) of the protein generated using DeepMSA, such as Position-Specific Scoring Matrix (PSSM), Secondary Structure (SS3), and Relative Solvent Accessibility (RSA), are provided as input to the network. A weighted binary cross-entropy loss function is used to counter the substantial imbalance in the two classes of binding and non-binding residues. The network performs very well on single-chain proteins, providing a pocket that has good interactions with a ligand. | Vineeth Chelur; U. Deva Priyakumar | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61acf2f557f82740aba82f46/original/bi-rds-binding-residue-detection-from-protein-sequences-using-deep-res-nets.pdf |
60c744b0bdbb894a56a3886f | 10.26434/chemrxiv.9598715.v2 | How to Stay out of Trouble in RIXS Calculations Within Equation-of-Motion Coupled-Cluster Damped Response Theory? Safe Hitchhiking in the Excitation Manifold by Means of Core-Valence Separation | <div>We present a novel approach for computing resonant inelastic X-ray scattering (RIXS) cross sections within the equation-of-motion coupled-cluster (EOM-CC) framework. The approach is based on recasting the sum-over-state expressions for RIXS moments into a compact form by using damped response theory. Damped response formalism allows one to circumvent problems of divergent behavior of the response equation in the resonant regime. However, the convergence of response equations in the X-ray frequency range is often erratic due to the resonant nature of the virtual core-excited states embedded in the valence ionization continuum. We demonstrate that this problematic behavior can be avoided by extending the core-valence separation (CVS) scheme, which decouples the valence-occupied and core-occupied excitation manifolds, into the response domain. The accuracy of the CVS-enabled damped response theory, implemented within the EOM-EE-CCSD (EOM-CC for excitation energies with single and double excitations) framework, is assessed by comparison against damped EOM-EE-CCSD response calculations. The capabilities of the new approach are illustrated by calculations of RIXS cross sections for benzene and benzene radical cation.</div> | Kaushik Nanda; Marta L. Vidal; Rasmus Faber; Sonia Coriani; Anna Krylov | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744b0bdbb894a56a3886f/original/how-to-stay-out-of-trouble-in-rixs-calculations-within-equation-of-motion-coupled-cluster-damped-response-theory-safe-hitchhiking-in-the-excitation-manifold-by-means-of-core-valence-separation.pdf |
63f4d8cd1d2d184063dfcdcd | 10.26434/chemrxiv-2023-p28cb | Versatile triphenylphosphine-containing polymeric catalysts and elucidation of structure-function relationships | Synthetic polymers are a modular solution to bridging the two most common classes of catalysts: proteins and small molecules. Polymers offer the synthetic versatility of small molecule catalysts, while simultaneously having the ability to construct microenvironments mimicking those of natural proteins. We synthesized a panel of polymeric catalysts containing a novel triphenylphosphine acrylamide monomer (TPPAm) and investigated how their properties impact the rate of a model Suzuki-Miyaura cross-coupling reaction. Systematic variation of polymer properties, such as molecular weight, functional density, and comonomer identity, led to tunable reaction rates and solvent compatibility, including full conversion in an aqueous medium. Studies with bulky substrates revealed connections between polymer parameters and reaction conditions that were further elucidated with a regression analysis. Some connections were substrate-specific, highlighting the value of the rapidly tunable polymer catalyst. Collectively, these results aid in building structure-function relationships to guide the development of polymer catalysts with tunable substrate and environment compatibility. | Matthew Sanders; Supraja Chittari; Nicole Sherman; Jack Foley; Abigail Knight | Organic Chemistry; Catalysis; Polymer Science; Polymer scaffolds; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f4d8cd1d2d184063dfcdcd/original/versatile-triphenylphosphine-containing-polymeric-catalysts-and-elucidation-of-structure-function-relationships.pdf |
6793d26f81d2151a02d22369 | 10.26434/chemrxiv-2025-4wbvd | Low-frequency Raman Spectra of Amyloid Fibrils | We report on how low-frequency Raman measurements can be used as a facile tool to investigate the supramolecular
structure of amyloid fibrils. We investigate the low-frequency Raman spectra (< 500 cm−1) of six different amyloid fibrils exhibiting parallel β-sheet structures prepared from amyloid-β1−40, amylin, amyloid-β25−35, and amylin20−29 peptides . We propose band assignments using a combination of semi-empirical tight-binding calculations and insights gleaned from previously published studies on model polypeptides in β-sheet conformations. We discuss how lowfrequency Raman modes can be used to probe the interactions, packing, and ordering of strands and side chains within fibril β-sheets to gain insights into their supramolecular structures. | Madeline Harper; Amanda Dumi; Shiv Upadhyay; Riley J. Workman; Delaney Nelson; Uma Nudurupati; Yangguang Ou; David Punihaole | Physical Chemistry; Biophysical Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6793d26f81d2151a02d22369/original/low-frequency-raman-spectra-of-amyloid-fibrils.pdf |
64f8c1ef3fdae147faa3515d | 10.26434/chemrxiv-2023-7631n | Phenoxythiazoline (FTz)–Cobalt(II) Precatalysts Enable C(sp2)–C(sp3) Bond– Formation for the Key Intermediate in the Synthesis of Afimetoran and Related Toll-like Receptor 7/8 (TLR7/8) Antagonists | Evaluation of the relative rates of the cobalt-catalyzed C(sp2)–C(sp3) Suzuki–Miyaura cross-coupling between the neopentylglycol ester of 4-fluorophenylboronic acid and N-Boc-4- bromopiperidine established that decreasing the size of the N-alkyl substituents on the phenoxyimine (FI) supporting ligand accelerated the overall rate of the reaction. This trend inspired the design of optimal cobalt catalysts with phenoxyoxazoline (FOx) and phenoxythiazoline (FTz) ligands. An air-stable cobalt(II) precatalyst, (FTz)CoBr(py)3 was synthesized and applied to the cross-coupling of an indole-5-boronic ester nucleophile with a piperidine-4-bromide electrophile that is relevant to the synthesis of reported toll-like receptor (TLR) 7/8 antagonist molecules including afimetoran. Addition of excess KOMe•B(OiPr)3 improved catalyst lifetime due to attenuation of alkoxide basicity that otherwise leads to demetallation of the FI chelate. Determination of the experimental rate law established a first- order dependence on the cobalt precatalyst and a saturation regime in heterogeneous potassium aryl boronate (apparent zeroth order), supporting turnover-limiting transmetalation and the origin of the observed trends in N-imine substitution. The optimized cobalt precatalyst and reaction conditions were applied to the multigram-scale synthesis of an intermediate used in both the discovery and process routes for toll-like receptor (TLR) 7/8 antagonist molecules. | L. Reginald Mills; Francesca DiMare; David Gygi; Heejun Lee; Eric M. Simmons; Junho Kim; Steven R. Wisniewski; Paul J. Chirik | Organic Chemistry; Catalysis; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f8c1ef3fdae147faa3515d/original/phenoxythiazoline-f-tz-cobalt-ii-precatalysts-enable-c-sp2-c-sp3-bond-formation-for-the-key-intermediate-in-the-synthesis-of-afimetoran-and-related-toll-like-receptor-7-8-tlr7-8-antagonists.pdf |
67b05051fa469535b96e5c48 | 10.26434/chemrxiv-2025-gqz38 | Electrochemical Synthesis of Size-Tuned Carbon-Coated Stanene Quantum Dots at Room Temperature for High-Performance Lithium-Ion Batteries | Quantum Dots have received extensive attention recently, paving the way for exploring their utility due to their intriguing size-dependent properties, solubility manipulation, and susceptibility to surface modification/doping. Among all types of quantum dots, Stanene is a topological insulator exhibiting enhanced spin-orbit coupling, making it a promising zero-dimensional material with augmented optical and electrical properties. Given these exceptional characteristics, the development of efficient methods to synthesize Stanene quantum dots with precise size distribution is of significant interest. We report the electrochemical transformation of Tin powder to carbon-coated stanene quantum dots at room temperature in a non-aqueous media. Ultraviolet-visible and photoluminescence spectroscopy results confirm the size-dependent properties of stanene quantum dots. Transmission electron micrographs, powder X-ray diffraction, and Fourier transform infrared analysis further supplement the size-dependent properties of these quantum dots, which are potential candidates for applications in catalysis, sensors, energy storage and medical imaging. For example, a Li-ion battery fabricated using the anode reveals a stable capacity of 260 mAh g-1 consistently after coupling with a standard cathode like lithium in an electrolyte of LiPF6 in ethylene carbonate (EC) and dimethyl carbonate (DMC). | Bikash Ranjan Isaac; S. Sreedeep; Sankeerth Satish; Subbiah Alwarappan; Vijayamohanan K. Pillai | Physical Chemistry; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b05051fa469535b96e5c48/original/electrochemical-synthesis-of-size-tuned-carbon-coated-stanene-quantum-dots-at-room-temperature-for-high-performance-lithium-ion-batteries.pdf |
66e74f3951558a15ef13b033 | 10.26434/chemrxiv-2024-kl8mp-v2 | Fluorescence Lifetime Imaging Microscopy (FLIM) as a Tool to Understand Chemical Reactions and Catalysis | Fluorescence lifetime imaging microscopy (FLIM) is an emerging tool to characterize ongoing chemical reactions in synthetic chemistry and catalysis. Initially applied to biological systems, FLIM now reveals spatially resolved chemical reaction species and system-wide physiochemical changes that accompany ongoing reactions. FLIM combines the advantage of environmental sensitivity with high signal sensitivity (as sensitive as single molecules) and has the key ability to operate under synthetic conditions (e.g., high concentrations of reagents, in organic solvents, under ambient temperature and pressure, in opaque mixtures, and in multiphasic systems). Chemical reactions inherently induce changes in the reaction medium, neighboring compounds, surface compositions, and/or the bonding structure of the compounds involved, resulting in environmental changes. The FLIM methods recently developed harness and interpret these changes in ways that lead to characterizing compounds and enhancing mechanistic understanding. Here, current advantages and limitations of FLIM method are considered, common factors influencing fluorescence lifetime in chemical systems are discussed in a tutorial format, and seven research case studies are strategically analyzed—chosen to highlight how FLIM provided complementary information to understand chemical reaction mechanisms, intermediates, product distributions, partitioning, roles of reagents, and catalyst behaviors. These data and insights obtained from FLIM assist the rational design and optimization of synthetic and catalytic methods. | Pia Lopez; Suzanne Blum | Organic Chemistry; Catalysis; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e74f3951558a15ef13b033/original/fluorescence-lifetime-imaging-microscopy-flim-as-a-tool-to-understand-chemical-reactions-and-catalysis.pdf |
6632669191aefa6ce1e3ae02 | 10.26434/chemrxiv-2024-jt6g5 | Total Synthesis Facilitates in vitro Reconstitution of SgvP, the C–S Bond Forming P450 in Griseoviridin Biosynthesis | Griseoviridin is a group A streptogramin natural product from Streptomyces with broad-spectrum antibacterial activity. A hybrid polyketide-non-ribosomal peptide, it comprises a 23-membered macrocycle, an embedded oxazole motif, and a macro-lactone with a unique ene-thiol linkage Recent analysis of the griseoviridin biosynthetic gene cluster implicated SgvP, a cytochrome P450 monooxygenase, in late-stage installation of the critical C–S bond. While genetic and crystallographic experiments provided indirect evidence to support this hypothesis, the exact function of SgvP has never been confirmed bio-chemically. Herein, we report a convergent total synthesis of pre-griseoviridin, the putative substrate of P450 SgvP and precursor to griseoviridin. Our strategy features concise and rapid assembly of two fragments joined via sequential peptide coupling and Stille macrocyclization. Access to pre-griseoviridin then enabled in vitro validation of SgvP as the C–S bond forming P450 during griseoviridin biosynthesis, culminating in a 9-step chemoenzymatic synthesis of griseoviridin. | Carter Stout; Hans Renata | Organic Chemistry; Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6632669191aefa6ce1e3ae02/original/total-synthesis-facilitates-in-vitro-reconstitution-of-sgv-p-the-c-s-bond-forming-p450-in-griseoviridin-biosynthesis.pdf |
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