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636a64e9c4c879f1712152b2 | 10.26434/chemrxiv-2022-3wxh7 | Dipolar field effects in a solid-state NMR maser pumped by Dynamic Nuclear Polarization | We report the observation of pulsed solid state MASER from hyperpolarized proton spin system using Dynamic Nuclear Polarization (DNP) at cryogenic temperature.
Induction decays exhibiting multiple asymmetric maser pulses and persistent for tens of second were observed in DNP experiments performed on negatively polarized water samples at cryogenic.
These experiments a qualitatively reproduced by simulations of this non-linear spin dynamics by combining the Bloch-Maxwell equations for radiation damping that further incorporate dipolar interactions, on the one hand, and a simplified model of DNP, on the other hand. | Daniel Abergel; Vineeth Francis Thalakottoor Jose Chacko | Physical Chemistry; Analytical Chemistry; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636a64e9c4c879f1712152b2/original/dipolar-field-effects-in-a-solid-state-nmr-maser-pumped-by-dynamic-nuclear-polarization.pdf |
66f63ede51558a15ef47b0a3 | 10.26434/chemrxiv-2024-3t2lk | Ruthenium, copper and ruthenium-copper complexes of an unsymmetrical phosphino pyridyl 1,8-naphthyridine PNNN ligand | A new unsymmetrical dinucleating phosphino pyridyl 1,8-naphthyridine ligand PNNN is reported. Reaction with CuCl gave the dicopper complex [Cu2(µ-Cl)2(PNNN)] (1). In contrast, complexation of [RuCl2(cymene)]2 yielded a monometallic species [RuCl(cymene)(PNNN)]Cl ([2]Cl) in which the Ru is bound to the κ2-N,N, rather than κ2-P,N, binding pocket. The selective formation of the monoruthenium complex [2]Cl enabled synthesis of heterobimetallic complexes [RuCuCl3(cymene)(PNNN)] (3) and [RuCuCl2(cymene)(PNNN)]2[PF6]2 ([4]2[PF6]2), which both exhibit κ1-P coordination of Cu. Complexes 1 and [4]2[PF6]2 exhibit reversible dearomatisation-aromatisation behaviour at the metal-ligand cooperative methylene site upon sequential treatment with base (KOtBu) and acid (HCl). Notably, deprotonation of [4]2[PF6]2 induces a shift in the coordination mode of Cu to κ2-P,N. | Jingyun Wu; Michael Stevens; Michael Gardiner; Annie Colebatch | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Organometallic Compounds; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f63ede51558a15ef47b0a3/original/ruthenium-copper-and-ruthenium-copper-complexes-of-an-unsymmetrical-phosphino-pyridyl-1-8-naphthyridine-pnnn-ligand.pdf |
62964db86057b1f4598bfd4c | 10.26434/chemrxiv-2022-kwwwd | Synthesis and styrene copolymerization of novel octyl 2-cyano-3-phenyl-2- propenoates | Novel octyl 2-cyano-3-phenyl-2-propenoates, RPhCH=C(CN)CO2CH2(CH2)6CH3 (where R is 2-acetyl, 2,3,4-trimethoxy, 2,4,5-trimethoxy, 2,4,6-trifluoro, 3,4,5-trifluoro, 2,3,5,6-tetrafluoro, 2,3,4,5,6-pentafluoro, 3-bromo-4,5-dimethoxy, 5-bromo-2,3-dimethoxy, 3-chloro-2,6-difluoro) were prepared and copolymerized with styrene. The propenoates were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-substituted benzaldehydes and octyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. The propenoates were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis.
| Hannah A. Adekale; Amy L. Alessi; Mohammed A. Arsalanuddin; Alexander M. Avak; Daniel R. Buechner; Jason A. Hebblethwaite; Sabrina J. Nagy; Giovanny Sanchez; Natalie J. Wiser; Monica Zygula; Sara M. Rocus; William S. Schjerven; Gregory B. Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62964db86057b1f4598bfd4c/original/synthesis-and-styrene-copolymerization-of-novel-octyl-2-cyano-3-phenyl-2-propenoates.pdf |
675ad939085116a1332b3820 | 10.26434/chemrxiv-2024-g61n4 | Diastereo- and Enantioselective Allylation of α-Hydroxy Ketones Enabled by Palladium/Borinic acid Dual Catalysis | Asymmetric allylation reaction between unsymmetrical allyl carbonates and α-hydroxy ketones synergistically catalyzed by a palladium/borinic acid catalytic platform has been developed. The reaction proceeds through nucleophilic activation of α-hydroxy ketone by an achiral borinic acid to form a tetracoordinated enediol boronate complex and its subsequent interception of electrophilic π-allyl palladium complex generated from a chiral Pd catalyst and an allyl component. A broad scope of substrates was suitable in this reaction, providing a series of allyl-substituted α-hydroxy ketones bearing vicinal stereocenters with excellent enantioselectivities (up to 99% ee) and diastereoselectivities (up to 24:1 dr). The methodology also achieved effective kinetic resolution of 1,3-disubstituted allylic carbonates, with the unreacted substrates being recovered with high ee values. A plausible mechanism and model for chiral induction in this reaction are proposed. The utility of this method was demonstrated by a gram scale reaction and subsequent elaboration of the allylation products. | Fan Wu; Kai Huang; Zhihe Cen; Changwen Yan; Yuhe Kan; Xiaoyu Wu | Organic Chemistry; Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675ad939085116a1332b3820/original/diastereo-and-enantioselective-allylation-of-hydroxy-ketones-enabled-by-palladium-borinic-acid-dual-catalysis.pdf |
63ffddda32cd591f12b38dc0 | 10.26434/chemrxiv-2023-qmfjq-v2 | Multi-domain Automated Patterning of DNA-Functionalized Hydrogels | DNA-functionalized hydrogels are capable of sensing oligonucleotides, proteins, and small molecules, and specific DNA sequences sensed in the hydrogels environment can induce changes in these hydrogels shape and fluorescence. Fabricating DNA-functionalized hydrogel architectures with multiple domains could make it possible to sense multiple molecules and undergo more complicated macroscopic changes, such as changing fluorescence or changing the shapes of regions of the hydrogel architecture. However, automatically fabricating multi-domain DNA-functionalized hydrogel architectures, which could enable the construction of hydrogel architectures with tens to hundreds of different domains. We describe a platform for fabricating multi-domain DNA-functionalized hydrogels automatically at the micron scale, where reaction and diffusion processes can be coupled to program material behavior. Using this platform, the hydrogels material properties, such as shape and fluorescence, can be programmed, and the fabricated hydrogels can sense their environment. DNA-functionalized hydrogel architectures with domain sizes as small as 10 microns and with up to 4 different types of domains can be automatically fabricated using ink volumes as low as 50 microliters. We also demonstrate that hydrogels fabricated using this platform exhibit responses similar to those of DNA-functionalized gels fabricated using other methods by demonstrating that DNA sequences can hybridize within them and that they can undergo DNA sequence-induced shape change. | Moshe Rubanov; Joshua Cole; Heon-Joon Lee; Elia Gonzalez; Zachary Chen; Rebecca Schulman | Materials Science; Polymer Science; Chemical Engineering and Industrial Chemistry; Biocompatible Materials; Biopolymers; Hydrogels | CC BY NC 4.0 | CHEMRXIV | 2023-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ffddda32cd591f12b38dc0/original/multi-domain-automated-patterning-of-dna-functionalized-hydrogels.pdf |
66421031418a5379b0255d8a | 10.26434/chemrxiv-2024-zs5xp | Metis - A Python-Based User Interface to Collect Expert Feedback for Generative
Chemistry Models | Current de novo drug design models face one crucial challenge: a disparity between the user’s expectations and the actual output of the model in practical applications. Tailoring models to better align with chemists’ preferences is key to overcoming this obstacle effectively. While interest in preference-based and human-in-the-loop machine learning in chemistry is continuously increasing, no tool currently exists that enables the collection of standardized and chemistry-specific feedback. Metis is a Python-based open-source graphical user interface (GUI), designed to solve this and enable the collection of chemists’ detailed feedback on molecular structures. The GUI enables chemists to explore and evaluate molecules, offering a user-friendly interface for annotating preferences and specifying desired or undesired structural features. By providing chemists the opportunity to give detailed feedback, allows researchers to capture more efficiently the chemist’s implicit knowledge and preferences. This knowledge is crucial to align the chemist’s idea with the de novo design agents. The GUI aims to enhance this collaboration between the human and the "machine" by providing an intuitive platform where chemists can interactively provide feedback on molecular structures, aiding in preference learning and refining de novo design strategies. Metis integrates with the existing de novo framework REINVENT, creating a closed-loop system where human expertise can continuously inform and refine the generative models. | Janosch Menke; Yasmine Nahal; Esben Jannik Bjerrum; Mikhail Kabeshov; Samuel Kaski; Ola Engkvist | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66421031418a5379b0255d8a/original/metis-a-python-based-user-interface-to-collect-expert-feedback-for-generative-chemistry-models.pdf |
60c758ae337d6c50c3e292b8 | 10.26434/chemrxiv.14572935.v1 | Teaching and Learning Materials on the Quasi-Steady-State Approximation and the Partial-Equilibrium Approximation | Starting from simple examples of chemical schemes for which a concentration or an extent of reaction can be eliminated, we highlight the common features of the quasi-steady-state approximation and the partial-equilibrium approximation. General conditions to apply either of these adiabatic eliminations are mentioned.<br /> | Agnès Pellissier-Tanon; Gabriel Morgado; Ludovic Jullien; Annie Lemarchand | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758ae337d6c50c3e292b8/original/teaching-and-learning-materials-on-the-quasi-steady-state-approximation-and-the-partial-equilibrium-approximation.pdf |
67aa9e6881d2151a02e878c2 | 10.26434/chemrxiv-2025-2xsvw | Circularly Polarized Stimulated Emission from a Chiral Cavity Based on Apparent Circular Dichroism Organic Thin-Films | The lack of intrinsic mirror symmetry in cavity mirrors poses a significant challenge for most organic chiral materials in generating circularly polarized (CP) lasers. How ever, nonreciprocal chiroptical materials, such as the recently developed organic thin films exhibiting Apparent Circular Dichroism (ACD), provide a promising approach to CPlight generation. In this work, we integrate an ACD-based thin film into a free-space dye laser cavity, achieving direct CP laser emission with a degree of circular polarization (DOCP) up to 0.6, corresponding to a dissymmetry factor (glum) of 1.2, a new record for organic chiral lasers. The degree of polarization (DOP) is close to 0.8, and the observed ellipticity in the emitted light originates from the ACD effect in the thin film, leading to asymmetric cavity losses for right- and left-circularly polarized light.
This breakthrough demonstrates the potential of ACD-based materials to overcome the limitations of conventional chiral laser systems, marking a significant advancement
in the field and paving the way for next-generation chiral photonic devices. | Li-Zhi Lin; Ling-Qi Huang; Shi-Wei You; Yi-Jan Huang; Francesco Zinna; Andrew Salij; Lorenzo Di Bari; Randall H. Goldsmith; Roel Tempelaar; Chia-Yen Huang; TzuLing Chen | Physical Chemistry; Nanoscience; Chemical Engineering and Industrial Chemistry; Optics; Radiation; Self-Assembly | CC BY 4.0 | CHEMRXIV | 2025-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67aa9e6881d2151a02e878c2/original/circularly-polarized-stimulated-emission-from-a-chiral-cavity-based-on-apparent-circular-dichroism-organic-thin-films.pdf |
6643138021291e5d1d336085 | 10.26434/chemrxiv-2024-69jc4 | Chemoselective Hydrogenolysis of Urethanes to Formamides and Alcohols in the Presence of More Electrophilic Carbonyl Compounds | The development of methods for the chemical recycling of polyurethanes is recognized as an urgent issue. Herein, we report the Ir-catalyzed hydrogenolysis of the urethane C–O bond to produce formamides and alcohols, where both formamides and ester and amide functionalities are tolerated. The chemoselectivity observed is counterintuitive to the generally accepted electrophilicity order of carbonyl compounds. Hydrogenolysis of urea and isocyanurate, potential byproducts in the polycondensation process of polyurethanes, is achieved alongside the selective degradation of polyurethanes themselves, which affords diformamides and diols. The present catalysis offers a novel method for the recycling of polyurethane-containing polymer waste. | Takanori Iwasaki; Yuto Yamada; Naoki Naito; Kyoko Nozaki | Organic Chemistry; Catalysis; Polymer Science; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6643138021291e5d1d336085/original/chemoselective-hydrogenolysis-of-urethanes-to-formamides-and-alcohols-in-the-presence-of-more-electrophilic-carbonyl-compounds.pdf |
6784fdd181d2151a02e86775 | 10.26434/chemrxiv-2024-l40ch-v2 | Compositional and functional diversity of minimal primitive coacervates in a nucleic acid-peptide world | The RNA-peptide world hypothesis postulates the early co-evolution of RNA and peptides, leading to the emergence of non-enzymatic RNA replication and peptide synthesis. Although nucleotides and amino acids were shown to form and polymerise under prebiotic conditions, the origin of their synergy, ubiquitously preserved in the central dogma of modern biology, remains unclear. We propose that the cooperation between DNA, RNA and peptides might have stemmed from their co-localisation in early compartments. Here we show that heterogeneous mixtures of prebiotic oligonucleotides and peptides spontaneously assemble into primitive coacervates. Experimental and computational studies reveal that peptide/nucleic acid coacervates are more robust and form over a broader range of conditions than peptide/peptide analogues. Notably, RNA-based coacervates exhibit exceptional stability and, in the presence of DNA, minimal viscosity, facilitating the diffusion of reactive oligonucleotides and supporting prebiotic RNA chemistry. Our findings suggest that coacervation may have occurred in the early on the evolutionary timeline, fostering the emergence of a nucleic acid-peptide world. This study provides new insights into the prebiotic role of coacervates, reconsidering their significance in the origins of life and the emergence of primitive replication and translation systems. | Karina Kinuyo Nakashima; Fatma Zohra Mihoubi; Jagandeep Saraya; Kieran Russell; Fidan Rahmatova; James Robinson; Maria Julia Maristany; Jan Huertas; Roger Rubio-Sánchez; Rosana Collepardo-Guevara; Derek O'Flaherty; Claudia Bonfio | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling; Self-Assembly | CC BY NC 4.0 | CHEMRXIV | 2025-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6784fdd181d2151a02e86775/original/compositional-and-functional-diversity-of-minimal-primitive-coacervates-in-a-nucleic-acid-peptide-world.pdf |
60c7548e0f50db9e5c397d44 | 10.26434/chemrxiv.13681792.v1 | Study on Interface Reaction of BN-Al Composite Materials-ChemRxiv.pdf | <p>Ceramic-metal
composite materials prepared by the metal infiltration process have become the
topic of intense research. The interface reaction between ceramic and metal has
an important impact on the mechanical properties of composite materials. This
article, for the first time, studies the interface reaction between BN and Al. Scanning electron microscopy (SEM) and transmission electron
microscopy (TEM) were both employed to study interface reaction. Studies have
shown that there is an intermediate transition interface between metal and
ceramic. The interface reaction between Al and BN produces AlN, and there is no
close connection among AlN particles. The grain size of AlN is about 1~2μm. The
rate order is: Al element > B element > N element.</p> | Chao Wang; Mengge Dong; Lu Zhang; Xiaozhou Cao; Xiangxin Xue | Composites | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7548e0f50db9e5c397d44/original/study-on-interface-reaction-of-bn-al-composite-materials-chem-rxiv-pdf.pdf |
60c741f6469df47e93f42f19 | 10.26434/chemrxiv.8109143.v2 | Clickable Cellulosic Surfaces for Peptide-Based Bioassays | The use of peptides in paper-based analytics is a highly appealing field, yet it suffers from severe limitations. This is mostly due to the loss of effective target recognition properties of this relatively small bioprobes upon nonspecific adsorption onto cellulose substrates. Here, we address this issue by introducing a simple polymer-based strategy to obtain clickable cellulosic surfaces, that we exploited for the chemoselective bioconjugation of peptide bioprobes. Our method largely outperformed standard adsorption-based immobilization strategy in a challenging, real-case immunoassay, namely the diagnostic discrimination of Zika+ individuals from healthy controls. Of note, the clickable polymeric coating not only allows efficient peptides bioconjugation, but it provides favorable anti-fouling properties to the cellulosic support. We envisage our strategy to broaden the repertoire of cellulosic materials manipulation and promote a renewed interest in peptide-based paper bioassays. | Maria Teresa Odinolfi; Alessandro Romanato; Greta Bergamaschi; Alessandro Strada; Laura Sola; Alessandro Girella; Chiara Milanese; Marcella Chiari; Alessandro Gori; Marina Cretich | Coating Materials; Analytical Chemistry - General; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741f6469df47e93f42f19/original/clickable-cellulosic-surfaces-for-peptide-based-bioassays.pdf |
65f20dc5e9ebbb4db9a553bb | 10.26434/chemrxiv-2024-sjl0x | Characterization of Indoor Atmospheric
Nitrogenous Chemicals in Poultry Farms | Indoor air pollution is seen in poultry and many other animal husbandry industries. Small airborne nitrogenous chemicals (ANCs), such as ammonia and small amines, are common air pollutants in poultry farms. Elevated ANC concentration in poultry farms can significantly worsen the indoor air quality (IAQ) of the farm, which will affect animal productivity, animal welfare, and occupational health of producers. Re- cent studies have identified ammonia and small volatile organic pollutants in the farm. On the other hand, characterization of large ANCs, such as uric acid (UA) and large amines have rarely been reported, despite they are proposed as the major source of biological nitrogen waste. Our goal is to project a novel insight into nitrogen cycles in poultry farms. This project includes on-site time-resolved collections of ANCs using a particle-into-liquid-sampler (PILS), followed by chemical characterization by liquid chromatography-mass spectrometry (LC-MS) with a novel derivatization method. Over quantitative assessment of ANCs in the poultry farm, we discovered UA and suspended particles are correlated with changing animal behaviors. Phase partition- ing of UA, ammoniacal species, and large amines were discovered among air, particle, and litter materials. The discovery of these indoor pollutants can be associated with the formation of dust particles and ammonia, and the results can benefit the poultry industry in solving persisting IAQ problems. | Xinyang Guo; Rowshon Afroz; Shuang Wu; Kimberly Wong; Valerie Carney; Martin Zuidhof; Joey Saharchuk; Hans Osthoff; Ran Zhao | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Analysis; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f20dc5e9ebbb4db9a553bb/original/characterization-of-indoor-atmospheric-nitrogenous-chemicals-in-poultry-farms.pdf |
617efc0ce04a8ebe432287c0 | 10.26434/chemrxiv-2021-z4811 | On-chip Direct Laser Writing of PAN-based Carbon Supercapacitor Electrodes | We report carbonization of polyacrylonitrile by direct laser writing to produce microsupercapacitors directly on-chip. We demonstrate the process by producing interdigitated carbon finger electrodes directly on a printed circuit board, which we then employ to characterize our supercapacitor electrodes. By varying the laser power, we are able to tune the process from carbonization to material ablation. This allows to not only convert pristine polyacrylonitrile films into carbon electrodes, but also to pattern and cut away non-carbonized material to produce completely freestanding carbon electrodes. While the carbon electrodes adhere well to the printed circuit board, non-carbonized polyacrylonitrile is peeled off the substrate. We achieve specific capacities as high as 260 µF/cm2 in a supercapacitor with 16 fingers. | Andreas Hoffmann; Pablo Jiménez-Calvo; Volker Strauss; Alexander Kühne | Polymer Science; Conducting polymers; Organic Polymers; Polymer morphology; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617efc0ce04a8ebe432287c0/original/on-chip-direct-laser-writing-of-pan-based-carbon-supercapacitor-electrodes.pdf |
60c74bddee301c24d6c79f71 | 10.26434/chemrxiv.12385940.v1 | Multiconfigurational Static and Dynamic Calculations Explain Tricyclo[4,2,0,02,5]octa-3,7-diene Photochemistry | <p>Sunlight is a renewable energy source that can be stored in chemical bonds using photochemical reactions. The synthesis of exotic and strained molecules is especially attractive with photochemical techniques because of the associated efficient and mild reaction conditions. We have used complete active space self-consistent field (CASSCF) calculations with an (8,7) active space and the ANO-S-VDZP basis set to understand the photophysics and subsequent photochemistry of a possible cubane precursor tricyclo[4,2,0,0<sup>2,5</sup>]octa-3,7-diene (<b>1</b>). The energies were corrected with a second-order perturbative correction CASPT2(8,7)/ANO-S-VDZP. The S<sub>0</sub>→S<sub>1</sub> vertical excitation energy of <b>1</b> is 6.25 eV, whose nature is π→π<sup>*</sup> excitation. The minimum energy path from the S<sub>1</sub> Franck-Condon point leads directly to a 4π-disrotatory electrocyclic ring-opening reaction to afford bicyclo[4,2,0]octa-2,4,7-triene. The 2D potential energy surface scan located a rhomboidal S<sub>1</sub>/S<sub>0</sub> minimum energy crossing point that connects <b>1</b> and cubane, suggesting that a cycloaddition is theoretically possible. We used the fewest switches surface hopping to study this reaction: 85% of 1,722 trajectories relaxed to 8 products; the major products are bicyclo[4,2,0]octa-2,4,7-triene (30%) and cycloocta-1,3,5,7-tetraene (32%). Only 0.4% of trajectories undergo a [2+2] cycloaddition to form cubane.<i></i></p> | Jingbai Li; Steven Lopez | Photochemistry (Org.); Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bddee301c24d6c79f71/original/multiconfigurational-static-and-dynamic-calculations-explain-tricyclo-4-2-0-02-5-octa-3-7-diene-photochemistry.pdf |
60c74a28702a9b622d18b24a | 10.26434/chemrxiv.12158952.v1 | Detection of Cardiac Biomarker Troponin (cTnI) with Enhanced Immune Sensitivity using a Single Monoclonal Antibody | <p>This work reports on using surface plasmon-enhanced
fluorescence (SPFS) assay for the sensitive detection of cTnI at clinically
relevant concentrations, using only one monoclonal antibody specific for one
epitope. Moreover, it attempts to elucidate the role of the biointerface design
by combined SPR and SPFS study in order to optimize the assay performance
characteristics. This study is supported by protein modelling in order to
visualize the dependence of the epitopes exposure on the protein orientation,
which plays a significant role and it may provide important insights into the
future development of cTnI immunoassays for accurate screening of CVD at early
stage.</p> | Anıl Bozdogan; Reham F. El-kased; Vanessa Jungbluth3; Wolfgang Knoll; Jakub Dostalek; Amal Kasry | Biological Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a28702a9b622d18b24a/original/detection-of-cardiac-biomarker-troponin-c-tn-i-with-enhanced-immune-sensitivity-using-a-single-monoclonal-antibody.pdf |
618a478aad7f7ccde75aa247 | 10.26434/chemrxiv-2021-z5bf4 | An Extended Gate Field Effect Transistor-based (EGFET-based) Urea Microbiosensor Based on Polypyrrole | Here, an extended – gate field effect transistor (EGFET) urea microsensor based on modified polypyrrole (PPy) is reported for the quantitative detection of urea in aqueous solution. the EGFET urea sensor was made by integrating a small and cheap metal oxide semiconductor field - effect transistor (MOSFET) with a Au microelectrode modified with urease and pH sensitive PPy. First, the urease was added to a pyrrole solution and then pyrrole/urease solution was electropolymerized on the surface of gold microelectrode in galvostanic mode to produce a urea sensitive microelectrode. The microsensor was imaged using a stereo microscope to confirm the polymerization of pyrrole/urease. The EGFET urea microsensor was tested in deionized water containing various concentrations of urea. The electrode showed a linear response for a wide concentration range of urea from 10−9 to 10−5 M with a sensitivity of 35.5 mV/decade urea. | Merve Oğuz; İpek Avci; Mustafa SEN | Analytical Chemistry; Analytical Chemistry - General; Biochemical Analysis; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618a478aad7f7ccde75aa247/original/an-extended-gate-field-effect-transistor-based-egfet-based-urea-microbiosensor-based-on-polypyrrole.pdf |
64ec5f2bdd1a73847fb0c199 | 10.26434/chemrxiv-2023-5s80n | Quasi-direct quantum molecular dynamics: The time-dependent adaptive density-guided approach for potential energy surface construction | We present a new quasi-direct quantum molecular dynamics computational method which offer a compromise between quantum dynamics using a pre-computed potential energy surface (PES) and fully direct quantum dynamics. This method is termed the time-dependent adaptive density-guided approach (TD-ADGA) and is a method for constructing a PES on the fly during a dynamics simulation. This is achieved by acquisition of new single point (SP) calculations and refitting of the PES depending on the need of the dynamics. The TD-ADGA is a further development of the adaptive density-guided approach (ADGA) for PES construction where the placement of SPs is guided by the density of the nuclear wave function. In TD-ADGA, the ADGA framework has been integrated into the time-propagation of the time-dependent nuclear wave function and we use the reduced one-mode density of this wave function to guide when and where new SPs are placed. The PES is thus extended or updated if the wave function moves into new areas or if a certain area becomes more important. We here derive equations for the reduced one-mode density for the time-dependent Hartree (TDH) method and for multi configuration time-dependent Hartree (MCTDH) methods, but the TD-ADGA can be used with any time-dependent wave function method as long as a density is available. The TD-ADGA method has been investigated on molecular systems containing single- and double-minimum potentials and on single- and multi-mode systems. We explore different approaches to handle the fact that the TD-ADGA involves a PES that changes during the computation and show how results can be obtained that are in very good agreement with results obtained by using an accurate reference PES. Dynamics with TD-ADGA is essentially a black box procedure, where only the initialization of the system and how to compute SPs must be provided. The TD-ADGA thus makes it easier to carry out quantum molecular dynamics and the quasi-direct framework opens up the possibility to compute quantum dynamics accurately for larger molecular systems. | Nicolai Machholdt Høyer; Ove Christiansen | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2023-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ec5f2bdd1a73847fb0c199/original/quasi-direct-quantum-molecular-dynamics-the-time-dependent-adaptive-density-guided-approach-for-potential-energy-surface-construction.pdf |
66680bc3409abc034523ce7e | 10.26434/chemrxiv-2024-hwkks | Machine learning assisted Raman spectroscopy to
discern the markers associated with colistin
Resistance | Raman spectroscopy (RS) is rapidly becoming a key
analytical tool for a wide range of microbiology applications. In combination with diverse machine learning methods, RS has demonstrated potentials to be translated in form of a culture-free, rapid, and objective tool for identifying antimicrobial resistance (AMR). Colistin is regarded as the final line of defense antibiotic for treating infections caused by gram-negative bacteria. In this
study, we have employed a combinatorial approach of machine learning and RS to identify a novel spectral marker associated with phosphoethanolamine modification in lipid A moiety of colistin resistant gram-negative Escherichia coli. The visible spectral fingerprints of this marker have been validated by partial least square regression and discriminant analysis. The origin of the spectral feature has been confirmed by hyperspectral imaging and K-means clustering of a single bacterial cell. The chemical
structure of the modified lipid A moiety has been verified by gold standard MALDI-TOF mass spectrometry. Our findings support futuristic applicability of this spectroscopic marker in objectively identifying colistin-sensitive and resistant strains. | Dimple Saikia; Cebajel Tanan; Dhananjaya G; Basavraj Hungund; Nilkamal Mahanta; Surya Pratap Singh | Biological and Medicinal Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Bioengineering and Biotechnology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66680bc3409abc034523ce7e/original/machine-learning-assisted-raman-spectroscopy-to-discern-the-markers-associated-with-colistin-resistance.pdf |
627df022809e3201648e335f | 10.26434/chemrxiv-2022-2swtc-v3 | Hydrazide-Linked Covalent Organic Frameworks for Water Harvesting | We report a postsynthetic strategy and its implementation to make covalent organic frameworks (COFs) with irreversible hydrazide linkages. This involved the synthesis of three 2D and 3D hydrazine-linked frameworks and their
oxidation. The linkage synthesis and functional group transformation—hydrazine and hydrazide—was evidenced by 15N multi-CP-MAS NMR. In addition, the isothermal water uptake profiles of these frameworks were studied, leading to the discovery of one hydrazide-linked COF suitable for water harvesting from air in arid conditions. This COF displayed characteristic S-shaped water sorption profiles, a steep pore-filling step below 18% relative humidity at 25 °C, and a total uptake capacity of 0.45 g g-1. We found that even small changes made on the molecular level can lead to major differences in the water isotherm profiles, therefore pointing to the utility of water sorption analysis as a complementary analytical tool to study linkage transformations. | Ha Nguyen; Cornelius Gropp; Nikita Hanikel; Anna Möckel; Alicia Lund; Omar Yaghi | Organic Chemistry; Energy; Organic Synthesis and Reactions; Fuels - Energy Science; Materials Chemistry; Crystallography – Organic | CC BY NC 4.0 | CHEMRXIV | 2022-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627df022809e3201648e335f/original/hydrazide-linked-covalent-organic-frameworks-for-water-harvesting.pdf |
64f0799f3fdae147fa3072e0 | 10.26434/chemrxiv-2023-hkmsn-v3 | Off-stoichiometry, Vacancy Trapping and Pseudo-irreversible First-cycle Capacity in LiNiO2 | We demonstrate that the ubiquitous off-stoichiometry of LiNiO2 in the form of Li_{1-z}Ni_{1+z}O2 slows the kinetics of the material both by diminishing the number of charge carriers and increasing the length of diffusion paths. Excess Ni in the Li layer, Ni_{Li}, exerts an attractive potential on Li vacancies, lowering their energy with respect to defect-free regions. This attractive field extends over a radius of two lattice sites and also considerably lowers the barrier for a Li vacancy to approach the defect, effectively making Ni_{Li} a sink for lithium vacancies. A similar argument can be made for divacancies, which are split by Ni_{Li} and pinned in the form of single vacancies. In addition to pinning effects, which could vary depending on the state of charge, Ni_{Li} also constitutes an obstacle to Li migration, because it is rather immobile and does not undergo site-exchange with an adjacent Li vacancy. | Sabrina Sicolo; Marcel Sadowski; Kilian Vettori; Matteo Bianchini; Juergen Janek; Karsten Albe | Theoretical and Computational Chemistry; Materials Science; Energy; Computational Chemistry and Modeling; Theory - Computational; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f0799f3fdae147fa3072e0/original/off-stoichiometry-vacancy-trapping-and-pseudo-irreversible-first-cycle-capacity-in-li-ni-o2.pdf |
652da604bda59ceb9ab83596 | 10.26434/chemrxiv-2023-m5s0w-v2 | Characterising conical intersections in DNA/RNA nucleobases with multiconfigurational wave functions of varying active space size | We characterise the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space selfconsistent field (CASSCF) algorithms. We benchmark two different basis set contractions and several active spaces for each nucleobase and conical intersection type, measuring for the first time how active space size affects conical intersection topographies in these systems, and the potential implications these may have towards their description of photoinduced phenomena. Our results show conical intersection topographies are highly sensitive to the electron correlation included in the model: by changing the amount (and type) of correlated orbitals, conical intersection topographies vastly change, and the changes
observed do not follow any converging pattern towards the topographies obtained with the largest and most correlated active spaces. Comparison across systems shows anal-
ogous topographies for almost all intersections mediating population transfer to the dark ¹nO/Nπ* states, while no similarities are observed for the “ethylene-like” conical
intersection ascribed to mediate the ultrafast decay component to the ground state in all DNA/RNA nucleobases. Basis set size seems to have a minor effect, appearing to be only relevant for purine-based derivatives. We rule out structural changes as a key factor in classifying the different conical intersections, which display almost identical geometries across active space and basis set change, and highlight instead the importance of correctly describing the electronic states involved at these crossing points.
Our work shows careful active space selection is essential to accurately describe conical intersection topographies, and therefore to adequately account for their active role in
molecular photochemistry. | Juliana Cuéllar-Zuquin; Ana Julieta Pepino; Ignacio Fernández Galván; Ivan Rivalta; Francesco Aquilante; Marco Garavelli; Roland Lindh; Javier Segarra-Martí | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652da604bda59ceb9ab83596/original/characterising-conical-intersections-in-dna-rna-nucleobases-with-multiconfigurational-wave-functions-of-varying-active-space-size.pdf |
63bfc7d33af973429c65cff7 | 10.26434/chemrxiv-2023-fcnwg | Influence of the fluorophore mobility on distance measurements by gas phase FRET. | Gas-phase Förster resonance energy transfer (FRET) combines the advantages of mass spectrometry and fluorescence spectroscopy for the conformational analysis of mass-selected biomolecules. While this implementation of FRET in the gas phase promises detailed insights for fundamental and applied studies, the gas-phase environment also poses great challenges. For FRET, fluorophore pairs are typically covalently attached to strategic binding sites in the backbone of a biomolecule, using short linkers. The linker further increases the mobility of the dye, contributing to rotational averaging of the relative orientation of the transition dipole moments of donor and acceptor. However, little is known about the fluorophore’s degrees of freedom in the gas phase and how it may be influenced by intramolecular interactions. In this study, we test the influence of a fluorophore’s linker length on the measured FRET efficiencies in the gas phase to probe the mobility of the fluorophore. An increased FRET efficiency was observed with increasing linker length, ranging from 5.3 % for a linker consisting of 2 atoms to 27.7 % for a linker length of 13 atoms. To rationalize this trend, we profiled the conformational landscape of each model system with MD simulations. Employing state-of-the-art enhanced sampling techniques, we captured intramolecular interactions that promote a population shift towards smaller donor-acceptor separation for longer linker lengths and induce a significant increase in their acceptor dipole. The presented methodology is a first step towards the explicit consideration of a fluoruophore’s range of motion in the interpretation of gas-phase FRET experiments. | Jonas B. Metternich; Paul Katzberger; Anna S. Kamenik; Prince Tiwari; Ri Wu; Sereina Riniker; Renato Zenobi | Physical Chemistry; Analytical Chemistry; Mass Spectrometry; Spectroscopy (Anal. Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bfc7d33af973429c65cff7/original/influence-of-the-fluorophore-mobility-on-distance-measurements-by-gas-phase-fret.pdf |
60c73d0dbb8c1a70fe3d969c | 10.26434/chemrxiv.5355997.v1 | What are the ranges and basis of auxeticity in the phases of cellulose microfibrils? | <p>One sample of 1D bundle of cellulose microfibrils in the form of lignified flax fibre (0.10526 mm x 10 mm), and one 2D networks of cellulose microfibrils in the form of tunicate cellulose (0.07 mm x 5 mm x 10 mm), bacterial cellulose (0.135 mm x 5 mm x 10 mm) and microfibrillated cellulose (0.08 mm x 5 mm x 10 mm) were put on a glass slide parallel to the principal spectrometer axis. Raman spectra were measured all round in-plane under both half (in 5° steps) polarisation from 0° to 360° in extended mode between 100 cm<sup>-1</sup> and 1150 cm<sup>-1</sup> in 3 accumulations at 10s exposure and 100% laser power. The cursor was placed at the peak of the 1095 cm<sup>-1</sup> band, and intensity read.</p> | Akwasi Asamoah | Biocompatible Materials; Carbon-based Materials; Composites; Elastic Materials; Fibers; Oligomers; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2017-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0dbb8c1a70fe3d969c/original/what-are-the-ranges-and-basis-of-auxeticity-in-the-phases-of-cellulose-microfibrils.pdf |
63ca6068f604d165095dab57 | 10.26434/chemrxiv-2023-9rkjf | Triplet Dynamic Nuclear Polarization of Pyruvate via Supramolecular Chemistry | Dynamic nuclear polarization (DNP) significantly improves the sensitivity of magnetic resonance imaging, and its most important medical application is cancer diagnosis via hyperpolarized 13C-labeled pyruvate. Unlike cryogenic DNP, triplet-DNP uses photoexcited triplet electrons under mild conditions. However, triplet-DNP of pyruvate has not been observed because of incompatibility of the hydrophobic polarizing agent with hydrophilic pyruvate. This work demonstrates that supramolecular complexation with β-cyclodextrin can disperse 4,4′-(pentacene-6,13-diyl)dibenzoate (NaPDBA), a pentacene derivative with hydrophilic substituents, even in the presence of high sodium pyruvate concentrations. The polarization of photoexcited triplet electron spins in NaPDBA was transferred to the 13C spins of sodium pyruvate via triplet-DNP of 1H spins in water and 1H-to-13C cross-polarization. This provides an important step toward the widespread use of ultra-sensitive MRI for cancer diagnosis. | Tomoyuki Hamachi; Koki Nishimura; Keita Sakamoto; Yusuke Kawashima; Hironori Kouno; Shunsuke Sato; Go Watanabe; Kenichiro Tateishi; Tomohiro Uesaka; Nobuhiro Yanai | Physical Chemistry; Biological and Medicinal Chemistry; Photochemistry (Physical Chem.); Self-Assembly; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ca6068f604d165095dab57/original/triplet-dynamic-nuclear-polarization-of-pyruvate-via-supramolecular-chemistry.pdf |
61937f0678db4ef7520feeca | 10.26434/chemrxiv-2021-8q72j-v2 | Studies into exfoliation and coating of Egyptian blue in methanol for application to the detection of latent fingermarks | We have recently demonstrated that coated exfoliated Egyptian blue powder is effective for detecting latent fingermarks on a range of highly-patterned non-porous and semi-porous surfaces. In this extension of that work, we present our studies into an alternative approach to prepare exfoliated Egyptian blue coated with cetrimonium bromide and Tween® 20 using a simpler technique. The quality of the latent fingermarks developed with these exfoliated powders and the commercial powder were compared in a comprehensive study. Depletion series of natural fingermarks from a wide range of donors (12 males and females) deposited on non-porous (glass slides) and semi-porous (Australian banknotes) surfaces were used in this study. Enhancement in the performance of the coated exfoliated particles compared to the commercial powder was observed, particularly in the case of aged fingermarks and polymer banknotes as challenging substrates. | Sorour Shahbazi; John Goodpaster; Gregory Smith; Thomas Becker; Simon W. Lewis | Materials Science; Analytical Chemistry; Nanoscience; Nanostructured Materials - Materials; Analytical Chemistry - General; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61937f0678db4ef7520feeca/original/studies-into-exfoliation-and-coating-of-egyptian-blue-in-methanol-for-application-to-the-detection-of-latent-fingermarks.pdf |
67ab126f6dde43c908602309 | 10.26434/chemrxiv-2025-pzlfx | Mild and Scalable C4-Alkylation of Pyridine Derivatives: Enhanced Regioselectivity via Silane-Assisted Electroreduction | Pyridine derivatives are valuable components of biologically active compounds, materials, and ligands; however, traditional methods for site-selective direct functionalization are often hindered by multistep procedures and harsh conditions. Herein, we report a streamlined approach for the selective C4-alkylation of pyridine derivatives under electroreductive conditions using alkyl bromides. The addition of chlorotrimethylsilane significantly enhanced the yield and regioselectivity, and mechanistic studies revealed that the reaction involves a temporary dearomatization step, yielding a 1,4-difunctionalized intermediate, which then re-aromatizes upon air exposure. This method is scalable, mild, and highly selective, and demonstrates a broad substrate scope and good functional-group tolerance. In addition, C4-alkylated pyridines can undergo a subsequent electroreductive ortho-alkylation under standard conditions. This stepwise strategy allows the sequential incorporation of distinct alkyl groups through the selective use of different alkyl bromides at each stage, providing a versatile strategy for accessing structurally diverse di- and trifunctionalized pyridines. | Zhihao Yang; Xuan Liu; Yi-Xuan Chen; Yuting Gao; Hirofumi Maekawa; Tianyuan Zhang; Xin-Qi Hao; Mao-Ping Song | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ab126f6dde43c908602309/original/mild-and-scalable-c4-alkylation-of-pyridine-derivatives-enhanced-regioselectivity-via-silane-assisted-electroreduction.pdf |
6126a041656369c4fe19deff | 10.26434/chemrxiv-2021-zxtmf | Taming Phosphorus Mononitride (PN) | Phosphorus mononitride (PN) only has a fleeting existence on Earth and molecular precursors for a mild release of the molecule to enable chemical synthesis in solution do not exist. Here we report the synthesis of an anthracene (A) based molecular precursor (N3PA) that dissociates into dinitrogen (N2), A and PN in solution with a first order half-life of roughly t 1/2 = 30 min at room temperature associated with an activation enthalpy of ΔH ⧧ = 19.5 ± 1.7 kcal mol –1 and an activation entropy of ΔS ⧧ = −8.8 ± 0.8 cal mol –1 K –1 . Heated under vacuum N3PA decomposes in an explosive fashion at around 42 °C as demonstrated in a molecular beam mass spectrometry (MBMS) study. N3PA serves as a PN transfer reagent as demonstrated in the synthesis of [(dppe)Fe(Cp*)(NP)][BArF24]. Surprisingly, the terminal N-bonded linkage isomer is energetically preferred due to significant covalent iron pnictogen bond character and associated less unfavorable Pauli repulsion in the metal-ligand interaction. | Andre Eckhardt; Martin-Louis Riu; Mengshan Ye; Peter Mueller; Giovanni Bistoni; Christopher Cummins | Physical Chemistry; Inorganic Chemistry; Earth, Space, and Environmental Chemistry; Main Group Chemistry (Inorg.); Small Molecule Activation (Inorg.); Transition Metal Complexes (Inorg.) | CC BY 4.0 | CHEMRXIV | 2021-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6126a041656369c4fe19deff/original/taming-phosphorus-mononitride-pn.pdf |
62499979739db1575821e6a7 | 10.26434/chemrxiv-2022-vklw0 | Photocatalytic degradation of methanol-water in presence of g-C3N4 and graphene/g-C3N4. | Photocatalytic production of H2 from the decomposition of water has attracted increased attention, as the environmental damages caused by the rapid evolution of industry are threatening the development of human society. This energy production is considered a green and eco-friendly resource. It has the potential to replace the carbon component of fuelling the society; on the other hand allows for the limitation of greenhouse gas emissions, thereby mitigating the worsening of climate change. While titanium dioxide is widely used in the photocatalytic field, its yield is still low due to the fast recombination of the photo-generated charge carriers. Graphitic carbon nitride (g-C3N4) possessing high thermal and chemical stability, non-toxicity and low band gap energy is a promising candidate for photocatalytic applications. In this study the exfoliation of the bulk g-C3N4 made with melamine was synthesised via a chemical approach using nitric acid at room temperature, in order to get prolonged carrier lifetime. Moreover the surface of bulk g-C3N4 made with melamine and urea and the exfoliated g-C3N4 made with melamine was modified with graphene (0.5 wt% and 1 wt%). Hydrogen generation from methanol/water mix proved that only hydrogen was produced in the unmodified bulk and exfoliated g-C3N4 , while H2, CH4 and CO have been generated in the modified specimens with graphene. This was assigned to the increased spatial charge carrier separation conducted by graphene. | Wassila TOUATI; Ahmed Bekka; Mohamed Karmaoui; Clarisse Furgeaud; Chakib Alaoui; Imene Kadi allah; Miroslava Filip Edelmannová; Bruno Figueiredo; João António Labrincha; Raul Arenal; Kamila Koci; David Maria Tobaldi | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62499979739db1575821e6a7/original/photocatalytic-degradation-of-methanol-water-in-presence-of-g-c3n4-and-graphene-g-c3n4.pdf |
65968c8ee9ebbb4db9684b77 | 10.26434/chemrxiv-2024-4t3n9 | NMR Spectroscopic Signatures of Cationic Surface Sites from Supported Coinage Metals Interacting with N-Heterocyclic Carbenes | N-heterocyclic carbenes (NHCs) have been extensively studied to modulate the reactivity of molecular catalysts, colloids and their supported analogues, being isolated sites, clusters or nanoparticles. While the interaction of NHCs on metal surfaces has been discussed in great details, showing specific coordination chemistry depending on the type of NHC ligands, much less is known when the metal is dispersed on oxide supports as in heterogeneous catalysts. Herein, we study the interaction of NHC ligands with Au surface sites dispersed on silica, a non-reducible oxide support. We identify the easy formation of bis-NHC ligated Au(I) surface sites paralleling what is found on metallic Au surfaces. These species display a specific 13C NMR spectroscopic signature that clearly distinguishes them from the mono-NHC Au(I) surface sites or supported imidazoliums. We find that bis-ligated surface species are not unique to supported Au(I) species and are found for the corresponding Ag(I) and Cu(I) species as well as for the isolobal surface silanols. Furthermore, the interaction of NHC ligand with silica-supported Au nanoparticles also yields bis-NHC ligated Au(I) surface sites, indicating that metal atoms can also be easily extracted from nanoparticles, further illustrating the dynamics of these systems and the overall favorable formation of such bis-ligated species across a range of systems, besides what has been found on crystalline metal facets. | Shahar Dery; Weicheng Cao; Chengbo Yao; Christophe Copéret | Physical Chemistry; Inorganic Chemistry; Catalysis; Spectroscopy (Inorg.); Heterogeneous Catalysis; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65968c8ee9ebbb4db9684b77/original/nmr-spectroscopic-signatures-of-cationic-surface-sites-from-supported-coinage-metals-interacting-with-n-heterocyclic-carbenes.pdf |
60c73e964c89196dacad1dce | 10.26434/chemrxiv.6189617.v2 | A Bayesian Approach to Predict Solubility Parameters | Solubility is a ubiquitous phenomenon in many aspects of material science. While solubility can be determined by considering the cohesive forces in a liquid via the Hansen solubility parameters (HSP), quantitative structure-property relationship models are often used for prediction, notably due to their low computational cost. Herein, we report gpHSP, an interpretable and versatile probabilistic approach to determining HSP. Our model is based on Gaussian processes (GP), a Bayesian machine learning approach that provides uncertainty bounds to prediction. gpHSP achieves its flexibility by leveraging a variety of input data, such as SMILES strings, COSMOtherm simulations, and quantum chemistry calculations. gpHSP is built on experimentally determined HSP, including a general solvents set aggregated from literature, and a polymer set experimentally characterized by this group of authors. In all sets, we obtained a high degree of agreement, surpassing well-established machine learning methods. We demonstrate the general applicability of gpHSP to miscibility of organic semiconductors, drug compounds and in general solvents, which can be further extended to other domains. gpHSP is a fast and accurate toolbox, which could be applied to molecular design for solution processing technologies.<br /> | Benjamin Sanchez-Lengeling; Loic Roch; Jose Dario Perea; Stefan Langner; Christoph J. Brabec; Alan Aspuru-Guzik | Materials Processing; Organic Polymers; Computational Chemistry and Modeling; Machine Learning; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e964c89196dacad1dce/original/a-bayesian-approach-to-predict-solubility-parameters.pdf |
651d2bd0bda59ceb9ad8b216 | 10.26434/chemrxiv-2023-34g53 | ELEMENTAL ANALYSIS OF PARTICULATE MATTER BY X-RAY FLUORESCENCE METHODS: A GREEN APPROACH TO AIR QUALITY MONITORING | This review explores X-ray fluorescence (XRF) for elemental analysis of particulate matter (PM) for air quality monitoring. The introduction presents PM classification based on size and composition, covering various elemental analysis methods while highlighting the increasing interest in XRF due to its non-destructive, rapid, and green features. The fundamental concepts of XRF and the experimental configurations commonly used are discussed, focusing on Energy Dispersive X-Ray Fluorescence (EDXRF) and Total Reflection X-Ray Fluorescence (TXRF). PM sampling devices and substrate are described, with a specific emphasis on filtering membranes for EDXRF and reflecting substrates for TXRF. Sample preparation strategies and procedures are presented. Qualitative and quantitative analysis is described, with a particular focus on the calibration approaches implemented for PM. Finally, the challenges faced by XRF in becoming a recognized reliable analytical technique for PM analysis, comparable to other standardized techniques for PM filters analysis, while capitalizing on its green advantages. | Fabjola Bilo; Paola Cirelli; Laura Borgese | Analytical Chemistry; Environmental Analysis; Spectroscopy (Anal. Chem.) | CC BY 4.0 | CHEMRXIV | 2023-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651d2bd0bda59ceb9ad8b216/original/elemental-analysis-of-particulate-matter-by-x-ray-fluorescence-methods-a-green-approach-to-air-quality-monitoring.pdf |
60c74729ee301cfd52c79667 | 10.26434/chemrxiv.11547036.v1 | Electrochemical C2 Production from CO2 via Self-Assembled Nanoparticles of Cuprous Coordination Polymer | Copper (Cu) metal electrocatalysts activate the CO2 reduction reaction to produce multi electron reductants; however, the instability of the copper active species causes a change in reaction selectivity. Molecular catalysts can be designed as CO2 reduction catalysts with high selectivity, although the production of multi-electron reductants (>2e-) while maintaining the catalyst structure remains difficult. Here we present self-assembled nanoparticles of a cuprous coordination polymer (Cu-SCP) that can catalyze CO2 electrochemical reduction to C2 products, such as ethylene and ethanol, with a total faradaic efficiency of 55%. Cu-SCP maintains its metal complex structure and the Cu (I) oxidation state throughout the reaction. The Cu-SCP catalyst has advantages of being both a molecular and metal catalyst, which should open up new possibilities for CO2 reduction catalysts. <br /> | Naonari Sakamoto; Yusaku F. Nishimura; Takamasa Nonaka; Masataka Ohashi; Nobuhiro Ishida; Kosuke Kitazumi; Yuichi Kato; Takeo Arai | Catalysts; Nanostructured Materials - Materials; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74729ee301cfd52c79667/original/electrochemical-c2-production-from-co2-via-self-assembled-nanoparticles-of-cuprous-coordination-polymer.pdf |
646b938eccabde9f6e2fd280 | 10.26434/chemrxiv-2023-djhp2 | Room-temperature monitoring of CH4 and CO2 using a metal-organic framework-based QCM sensor showing inherent analyte discrimination | The detection of methane and carbon dioxide is of growing importance due to their negative impact on global warming. This is true both for environmental monitoring, as well as leak detection in industrial processes. Although solid-state sensors are technologically mature, they have limitations that prohibit their use in certain situations, e.g., explosive atmospheres. Thus, there is a need to develop new types of sensor materials. Herein, we demonstrate a simple, low-cost metal-organic framework-based gas leak detection sensor. The system is based on gravimetric sensing using a quartz crystal microbalance. The quartz crystal is functionalized by layer-by-layer growth of a thin metal-organic framework film. This film shows selective uptake of methane or carbon dioxide under atmospheric conditions. The hardware has low cost, simple operation, and theoretically high sensitivity. Overall, the sensor is characterized by simplicity and high robustness. Furthermore, by exploiting the different adsorption kinetics as measured by multiple harmonics analyses, it is possible to discriminate whether the response is due to methane or carbon dioxide. In summary, we demonstrate data relevant towards new applications of metal-organic frameworks and microporous hybrid materials in sensing applications. | Jaskaran Singh Malhotra; Mariusz Kubus; Kasper Steen Pedersen; Simon Ivar Andersen; Jonas Sundberg | Inorganic Chemistry; Nanoscience; Nanodevices; Coordination Chemistry (Inorg.); Sensors; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646b938eccabde9f6e2fd280/original/room-temperature-monitoring-of-ch4-and-co2-using-a-metal-organic-framework-based-qcm-sensor-showing-inherent-analyte-discrimination.pdf |
633c4a18cf382907febcebdd | 10.26434/chemrxiv-2022-h91bz | Photocatalytic Deoxygenative Alkylation of C(sp3)−H Bonds Using Sulfonylhydrazones | The ability to construct C(sp3)–C(sp3) bonds from easily accessible reagents is a crucial, yet challenging endeavor for synthetic organic chemists. Herein, we report the realization of such a cross-coupling reaction, which combines N-sulfonyl hydrazones and C(sp3)–H donors through a diarylketone-enabled photocatalytic Hydrogen Atom Transfer and a subsequent fragmentation of the obtained alkylated hydrazide. This mild and metal-free protocol was employed to prepare a wide array of alkyl-alkyl cross-coupled products and is tolerant of a variety of functional groups. The application of this chemistry further provides a preparatively useful route to various medicinally-relevant compounds, such as homobenzylic ethers, aryl ethyl amines, β-amino acids and other moieties which are commonly encountered in approved pharmaceuticals, agrochemicals and natural products. | Antonio Pulcinella; Stefano Bonciolini; Florian Lukas; Andrea Sorato; Timothy Noel | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2022-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633c4a18cf382907febcebdd/original/photocatalytic-deoxygenative-alkylation-of-c-sp3-h-bonds-using-sulfonylhydrazones.pdf |
62bbff70253021428f82b724 | 10.26434/chemrxiv-2022-5mk8z | Direct Analysis of Biotransformations with Mass Spectrometry – DiBT-MS | Ambient ionization coupled to mass spectrometry has the advantages of minimal requirements for sample preparation prior to analysis which renders it suitable for high throughput screening. We present a protocol that permits the application of this method in routine biotechnology and chemical biology laboratories which are using engineered enzymes to produce target compounds from substrates. We show how DESI-MS can be used to directly analyse the activity of biotransformations from crude cell lysate which we term DiBT-MS, this method is 10-1000 times faster than LC-MS and uses far less solvent. This protocol demonstrates the impact of solvent spray composition on ionization efficiency of the target analyte, the benefits of a nylon membrane slide and the reusability of sample slides in multiple experiments.
| Ruth Knox; Emily Kempa; Reynard Spiess; Christian Schnepel; Sabine Flitsch; Perdita Barran; Nicholas Turner | Biological and Medicinal Chemistry; Catalysis; Analytical Chemistry; Mass Spectrometry; High-throughput Screening; Bioengineering and Biotechnology | CC BY NC 4.0 | CHEMRXIV | 2022-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bbff70253021428f82b724/original/direct-analysis-of-biotransformations-with-mass-spectrometry-di-bt-ms.pdf |
623e41add6d3ed48af9f509f | 10.26434/chemrxiv-2022-qqt8x | Synthesis and styrene copolymerization of alkoxy ring-substituted 2-methoxyethyl phenylcyanoacrylates | Novel trisubstituted ethylenes, alkoxy ring-substituted 2-methoxyethyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2CH2OCH3 (where R is 2-methoxy, 3-methoxy, 4-methoxy, 2-ethoxy, 3-ethoxy, 4-ethoxy, 4-propoxy, 4-butoxy, 4-hexyloxy) were prepared and copolymerized with styrene. The ethylenes were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-substituted benzaldehydes and 2-methoxyethyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. All the ethylenes were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis. | Christian Lopez; Monica A. Martinez; Emma L. Melendez-Scherer; Alyssa Nunez; Kyle J. Ochwat; Presley O’Neil; Michal P. Papierz; Limariz Rebolledo; Alyssa D. Spires; Sara Rocus; William Schjerven; Gregory B. Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623e41add6d3ed48af9f509f/original/synthesis-and-styrene-copolymerization-of-alkoxy-ring-substituted-2-methoxyethyl-phenylcyanoacrylates.pdf |
60c757c99abda251fdf8e7cb | 10.26434/chemrxiv.14461962.v1 | Evaluation of Log P, pKa and Log D Predictions from the SAMPL7 Blind Challenge | <div>The Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenges focuses the computational modeling community on areas in need of improvement for rational drug design. The SAMPL7 physical property challenge dealt with prediction of octanol-water partition coefficients and pKa for 22 compounds. </div><div>The dataset was composed of a series of N-acylsulfonamides and related bioisosteres.</div><div>17 research groups participated in the logP challenge, submitting 33 blind submissions total. For the pKa challenge, 7 different groups participated, submitting 9 blind submissions in total. Overall, the accuracy of octanol-water logP predictions in the SAMPL7 challenge was lower than octanol-water logP predictions in SAMPL6, likely due to a more diverse dataset. Compared to the SAMPL6 pKa challenge, accuracy remains unchanged in SAMPL7.</div><div>Interestingly, here, though macroscopic pKa values were often predicted with reasonable accuracy, there was dramatically more disagreement among participants as to which microscopic transitions produced these values (with methods often disagreeing even as to the sign of the free energy change associated with certain transitions), indicating far more work needs to be done on pKa prediction methods.</div> | Teresa Danielle Bergazin; Nicolas Tielker; Yingying Zhang; Junjun Mao; Marilyn R. Gunner; karol francisco; Carlo Ballatore; Stefan Kast; David Mobley | Computational Chemistry and Modeling; Machine Learning; Quantum Computing; Physical and Chemical Properties; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2021-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757c99abda251fdf8e7cb/original/evaluation-of-log-p-p-ka-and-log-d-predictions-from-the-sampl7-blind-challenge.pdf |
60c74b2eee301c2d46c79db9 | 10.26434/chemrxiv.12292544.v1 | Reaction Landscape and Bioconjugation Profile of Tyrosinase Generated Quinones | <p>We describe a class of bioconjugation reactions that</p><p>enables site-specific modification of proteins through</p><p>enzymatic generation of o-quinone from either tyrosine</p><p>residues or phenol reagents. The enzymatically generated</p><p>o-quinone rapidly reacts chemically with numerous</p><p>common nucleophiles and dienophiles, including thiols,</p><p>anilines, alkoxyamines, cyclooctynes, and cyclooctenes.</p><p>Nucleophilic chemoenzymatic reaction with engineered</p><p>tyrosine residues creates a hydroxytyrosine (HOT)</p><p>bridge; a similar reaction with phenols creates a hydroxyphenol</p><p>(HOP). Diels-alder cycloaddition following</p><p>o-quinone generation results in an arylbicyclodiketone (ABCD). The stability of each conjugate against</p><p>physiological pH and temperature varies from less than one day to multiple months in vitro.</p> | Patrick Holder; Adel M. ElSohly | Bioorganic Chemistry; Biochemistry; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b2eee301c2d46c79db9/original/reaction-landscape-and-bioconjugation-profile-of-tyrosinase-generated-quinones.pdf |
65aa7b7b66c1381729cf9bf8 | 10.26434/chemrxiv-2024-5ppgz | Pre-analytical (mis)handling of plasma investigated by 1H-NMR metabolomics | The pre-analytical handling of plasma, how it is drawn, processed, and stored, influences its composition. Samples in e.g. biobanks often lack this information and consequently important information about their quality. Especially metabolite concentrations are affected by pre-analytical handling making conclusions from metabolomics studies particularly sensitive to misinterpretations. The perturbed metabolite profile, however, also offers an attractive choice for assessing the pre-analytical history from the measured data. Here we show that it is possible using Orthogonal Projections to Latent Structures Discriminative Analysis to divide plasma NMR data into a multivariate 'original sample space' suitable for further less biased metabolomics analysis and an orthogonal 'pre-analytical handling space' describing the changes occurring from pre-analytical mishandling. Apart from confirming established pre-analytical effects on glucose metabolization and the consequent increase in e.g. lactate and pyruvate, the sample preparation protocol involved methanol precipitation which allowed the observation of reversible changes in short-chain fatty acid concentrations as a function of temperature. | Daniel Malmodin; Anders Bay Nord; Huma Zafar; Linda Paulson; Göran Karlsson; Åsa Torinsson Naluai | Analytical Chemistry; Analytical Chemistry - General; Chemoinformatics; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65aa7b7b66c1381729cf9bf8/original/pre-analytical-mis-handling-of-plasma-investigated-by-1h-nmr-metabolomics.pdf |
63b54452dadddc8a99a65bdb | 10.26434/chemrxiv-2022-dqnwf-v4 | Electrochemical Synthesis of Urea:
Co-reduction of Nitric Oxide and Carbon Monoxide | Electrocatalytic conversion is a promising technology for storing renewable electricity in the chemical form. Substantial efforts have been made on the multi-carbon
feedstock production,while producing nitrogen-containing chemicals like urea via C-N coupling little is known. Here, we elucidate the possible urea production on metals
through co-reduction of nitric oxide (NO) and carbon oxide (CO). Based on adsorption energies calculated by DFT, we find that Cu is able to bind both *NO and *CO while not binding *H. During NO + CO co-reduction, we identify two kinetically and thermodynamically possible C-N couplings via *CO + *N and *CONH + *N, and further hydrogenation leads to urea formation. A 2-D activity heatmap has been constructed for describing nitrogen conversion to urea. This work provides a clear example of using computational simulations to predict selective and active materials for urea production. | Hao Wan; Xingli Wang; Lei Tan; Michael Filippi; Peter Strasser; Jan Rossmeisl; Alexander Bagger | Theoretical and Computational Chemistry; Catalysis; Energy; Computational Chemistry and Modeling; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b54452dadddc8a99a65bdb/original/electrochemical-synthesis-of-urea-co-reduction-of-nitric-oxide-and-carbon-monoxide.pdf |
60c75681702a9b4ea318c903 | 10.26434/chemrxiv.14252666.v1 | Stable Boron-Containing Blue-Photoluminescent Radicals | <div>It is highly urgent to develop synthetic strategies to make new category of stable luminescent radicals with desired emission wavelength. In this study, we have isolated two dioxoborocyclic radicals ( <b>3</b> and <b>4</b> ) by a direct sy nthetic rou te. They were charac terized by UV, EPR spectroscopy and SQUID measurements. Their structures were obtained by single crystal X ray diffraction. Both radicals produce blue photoluminescence (458 nm for <b>3</b> and 478 nm for <b>4</b> ) by radiative decay from higher excited states (D<sub>2</sub>/D<sub>3</sub>) to the ground state (D<sub>0</sub>) based on theoretical calculation, breaking Kasha rule. The work records a new kind of radical emitters and the first stable radicals with blue emission bands.</div> | Zhongtao Feng; Yuanyuan Chong; Shuxuan Tang; Huapeng Ruan; Yong Fang; Yue Zhao; Jun Jiang; Xinping Wang | Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75681702a9b4ea318c903/original/stable-boron-containing-blue-photoluminescent-radicals.pdf |
60c748c9ee301c4de8c7994c | 10.26434/chemrxiv.11972031.v1 | Resonance-Promoted Formic Acid Oxidation via Dynamic Electrocatalytic Modulation | It is a truth
universally acknowledged that faster catalysts enable the more efficient
transformation of molecules to useful products and enhance the sustainable
utilization of natural resources.
However, the limit of <i>static</i>
catalyst performance defined by the Sabatier principle has motivated a new
approach to <i>dynamic</i> catalyst design, whereby
catalysts oscillate with time between varying energetic states at sufficiently
high resonant frequencies to overcome the Sabatier ‘volcano peak’. In this work, the concept of dynamic
catalytic resonance was experimentally demonstrated via the electro-catalytic
oxidation of formic acid in water on a Pt working electrode within a
semi-continuous multi-phase flow reactor.
Steady-state electro-oxidation of formic acid at 0.6 V (NHE) exhibited a
maximum turnover frequency (TOF) of CO<sub>2</sub> formation of ~1.0 s<sup>-1</sup>
at room temperature. However,
oscillation of the electrodynamic potential between 0.8 V and open circuit via
a square waveform at varying frequency (10<sup>-3</sup> < <i>f</i> < 10<sup>3</sup> Hz) increased the
optimal TOF to ~5 s<sup>-1</sup> at 0.5 Hz.
An even higher TOF of ~20 s<sup>-1</sup> was observed at a resonant
frequency of 100 Hz for a square waveform oscillating between zero and 0.8
V. The rate increase in formic acid
electro-oxidation via catalytic resonance of more than an order of magnitude
(20x) above potentiostatic conditions was interpreted to occur by non-faradaic
formic acid dehydration to surface-bound carbon monoxide at low potentials, followed
by surface oxidation and desorption to carbon dioxide at high potentials. | Joshua Gopeesingh; Matthew Ardagh; Manish Shetty; Sean Burke; Paul Dauenhauer; Omar Abdelrahman | Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748c9ee301c4de8c7994c/original/resonance-promoted-formic-acid-oxidation-via-dynamic-electrocatalytic-modulation.pdf |
62aaabed04a3a9015c48a07f | 10.26434/chemrxiv-2022-6h3l7-v2 | Taming highly unstable radical anions and 1,4-organodilithiums by flow microreactors: controlled reductive dimerization of styrenes | Reduction of styrenes with lithium arenide in a flow microreactor leads to the instantaneous generation of the radical anion of styrenes and subsequent dimerization by fast mixing to yield the corresponding 1,4-dilithium species. The efficiency and selectivity of this reductive dimerization are low in a batch reactor. A series of styrenes undergo the dimerization and the resulting 1,4-dilithium species are trapped with various electrophiles. Trapping with divalent electrophiles such as dichlorosilanes affords precursors for useful yet less accessible cyclic structures such as siloles. Single electron reduction of unsaturated compounds in flow microreactors has thus proved to be a powerful protocol in organic synthesis. | Yiyuan Jiang; Hideki Yorimitsu | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2022-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62aaabed04a3a9015c48a07f/original/taming-highly-unstable-radical-anions-and-1-4-organodilithiums-by-flow-microreactors-controlled-reductive-dimerization-of-styrenes.pdf |
60c753bd4c8919326fad438f | 10.26434/chemrxiv.13546823.v1 | An Efficient Nickel Hydrogen Oxidation Catalyst for Hydroxide Exchange Membrane Fuel Cells | The hydroxide exchange membrane fuel cell (HEMFC) is a promising energy conversion technology, but it is limited by the need of platinum-group-metal (PGM) electrocatalysts, especially for the hydrogen oxidation reaction (HOR). Here we report a Ni-based HOR catalyst that exhibits an electrochemical surface area-normalized exchange current density of 70 μA/cm2, the highest among PGM-free catalysts. The catalyst comprises of Ni nanoparticles embedded in a nitrogen-doped carbon support. According to X-ray and ultraviolet photoelectron spectroscopy as well as H2 chemisorption, the electronic interaction between the Ni nanoparticles and its support leads to an optimal hydrogen binding energy, which is the likely origin of its high activity. PGM-free HEMFCs employing this Ni HOR catalyst give a peak power density of 450 mW/cm2, up to 6 times higher than previous best-performing analogous. This work demonstrates the feasibility of efficient PGM-free HEMFCs.<br /> | Weiyan Ni; Teng Wang; Florent Heroguel; Anna Krammer; seunghwa lee; Liang Yao; Andreas Scheeler; Jeremy Luterbacher; Yushan Yan; Xile Hu | Electrocatalysis; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753bd4c8919326fad438f/original/an-efficient-nickel-hydrogen-oxidation-catalyst-for-hydroxide-exchange-membrane-fuel-cells.pdf |
661d2a5221291e5d1de1a7b1 | 10.26434/chemrxiv-2024-2q612 | Modulators of the Hop-HSP90 Protein-Protein Interaction Disrupt Early-Stage of KSHV Lytic Replication | The central role of the chaperome in maintaining cellular proteostasis has seen numerous viral families evolve to parasitically exploit host chaperones in their life cycle. The HSP90 chaperone protein and its co-chaperone Hop, have both individually been shown to be essential factors for KSHV lytic replication. Given the fundamental regulatory role that PPIs play in cellular biology, we reasoned that disrupting the Hop-HSP90 PPI may provide a new host-based target for inhibiting KSHV lytic replication. This study expands upon a previous report of non-natural peptides, which disrupted the association between the HopTPR2A and its interacting HSP90CTD. Here, in addition to demonstrating disruption of the full-length Hop-HSP90PPI, and selective engagement with the HopTPR2A domain in cell lysates, we showed that a cell-penetrating peptide modified analogue, inhibited intracellular HSP90 and acted as a non-cytotoxic inhibitor of early-stage KSHV lytic replication. Importantly, this activity resulted from inhibition of specific KSHV lytic genes, rather than a global reduction in viral DNA transcription. In addition to tentative evidence for the Hop-HSP90 PPI as a much-needed target for KSHV drug discovery, this study represents an important step in understanding host HSP90 – viral interactions. | Clinton Veale; Michael Okpara; Michaelone Vaaltyn; Alhassan Mahama; Fernando Albericio; Beatriz de la Torre; David Clarke; Adrienne Edkins | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661d2a5221291e5d1de1a7b1/original/modulators-of-the-hop-hsp90-protein-protein-interaction-disrupt-early-stage-of-kshv-lytic-replication.pdf |
675aec64f9980725cfd816cc | 10.26434/chemrxiv-2024-t24pz | A Cobotic, digitally-controlled Schlenk line unlocks access to elusive Copper(II) bis-disilylamides | Bis(trimethylsilyl)amide ligands are ubiquitous in coordination chemistry for their ability to stabilize low-coordination numbers and provide soluble, and even volatile, metal complexes. Bis-silylamide complexes are known for the divalent ions of all first-row transition metals except for copper, which has been shown to be unstable to reduction. Herein, we demonstrate the stabilization and isolation of (DMAP)CuII(N{SiMe3}2)2 and investigate the role of the DMAP ligand and silylamide transfer reagent in the kinetics of this reaction. To undertake these studies we have utilized our newly developed ‘Cobotic’ Schlenk line which allows for digital control of the atmosphere under which we conduct our highly reac-tive syntheses. By digitizing Schlenk-line handling, we have improved synthetic productivity by creating protocols for automated inertization, solvent evaporation, liquid handling and crystallization all while capturing reaction log data. Importantly our Cu silylamide synthesis provides a case study showing that our cobotics approach allows for the discovery and isolation of unstable species which may remain elusive by traditional manual or fully autonomous methodologies. | Nicola L. Bell; Marina Gladkikh; Cameron Fraser; Mostafa Elsayed; Richard Drummond-Turnbull | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Organomet.); Kinetics and Mechanism - Organometallic Reactions; Transition Metal Complexes (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2024-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675aec64f9980725cfd816cc/original/a-cobotic-digitally-controlled-schlenk-line-unlocks-access-to-elusive-copper-ii-bis-disilylamides.pdf |
66ba735001103d79c5c59396 | 10.26434/chemrxiv-2024-bgf8b | Continuous structure modification of metal- organic framework glasses via halide salts | Melting and glass formation of metal-organic frameworks (MOFs) allow them to be processed into bulk materials. However, two major challenges remain: only a small fraction of MOF crystals undergo melting and glass-formation, and no well-established strategies exist for tuning MOF glass structures and properties. Here, we address both challenges through co-melting of zeolitic imidazole frameworks (ZIFs), a subset of MOFs, with heterocycle-based halide salts. The salt acts as a chemical “modifier”, akin to the role of alkali modifiers in traditional silicate glasses, allowing the melting of ZIF-8 that otherwise decomposes prior to melting. Through experimental and computational analyses, we show that the salts depolymerize the ZIFs, enabling continuous tuning of the fraction of bridging to non-bridging imidazolate linkers and, thereby, the thermal and mechanical properties. The proposed strategy enables diversification of MOF glass chemistry, tunable structures and properties, and ultimately an increased number of glass-forming MOFs with new functionalities. | Fengming Cao; Søren Strandskov Sørensen; Anders K. R. Christensen; Samraj Mollick; Xuan Ge; Daming Sun; Anders B. Nielsen; Niels Christian Nielsen; Peter K. Kristensen; Lars R. Jensen; Francesco Dallari; Jacopo Baglioni; Giulio Monaco; Martin A. Karlsen; Volodymyr Baran; Morten M. Smedskjaer | Materials Science; Hybrid Organic-Inorganic Materials; Materials Processing; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ba735001103d79c5c59396/original/continuous-structure-modification-of-metal-organic-framework-glasses-via-halide-salts.pdf |
617de6bbf4bd35ffa2a44fa5 | 10.26434/chemrxiv-2021-d4pf8 | Hydrophobic association and solvation of neopentane in Urea, TMAO and Urea-TMAO solution | A detailed knowledge on hydrophobic association and solvation is crucial in understanding the con-formational stability of proteins and polymers in osmolyte solutions. Using Molecular Dynamics simulations, we found the hydrophobic association using neopentane molecules is greater in mixed urea-TMAO-water solution in comparison to that in 8 M urea solution, in 4 M TMAO solution and in neat water. The neopentane association in urea solution is greater than that in TMAO solution or neat water. We find the association is even less in TMAO solution than pure water. From free ener-gy calculations, it is revealed that the neopentane sized cavity creation in mixed urea-TMAO-water is most unfavorable and that causes the highest hydrophobic association. The cavity formation in urea solution is either more unfavorable or comparable to that in TMAO solution. Importantly, it is found that the population of neopentane-neopentane contact pair and the free energy contribution for cavity formation step in TMAO solution are very sensitive towards the choice of TMAO force-fields. A careful construction of TMAO force-fields is important for studying hydrophobic associa-tion. Interestingly it is observed that the total solute-solvent dispersion interaction energy contribu-tion is always most favorable in mixed urea-TMAO-water. The magnitude of this interaction energy is greater in urea solution relative to TMAO solution for two different force-fields of TMAO, whereas the lowest value is obtained in pure water. It is revealed that the extent of the overall hy-drophobic association in osmolyte solutions is mainly governed by the cavity creation step and it nullifies the contribution comes from the solute-solvent interaction contribution. | Timir Hajari; Mayank Dixit; Hari O. S. Yadav | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Self-Assembly; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2021-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617de6bbf4bd35ffa2a44fa5/original/hydrophobic-association-and-solvation-of-neopentane-in-urea-tmao-and-urea-tmao-solution.pdf |
66f67a7d51558a15ef4d273a | 10.26434/chemrxiv-2024-mxvlp | First Principles Optoelectronic Calculations of BeSeO3 | Using a first principles approach the optoelectronic properties of monoclinic BeSeO3 is investigated with Density Function Theory (DFT) for application in photonics with a calculated band gap of 4.34 eV, refractive index of 2.16 and absorption coefficient of approximately zero within the visible light range (400-700 nm) such that BeSeO3 is characterized to be a wide bandgap semiconductor with stable optical transmission | Abdullahi isse | Materials Science; Inorganic Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f67a7d51558a15ef4d273a/original/first-principles-optoelectronic-calculations-of-be-se-o3.pdf |
65cf63e166c1381729ca0c81 | 10.26434/chemrxiv-2024-m5j49 | Development of Ribityllumazine Analogs as Mucosal-associated Invariant T Cell Activators | Mucosal-associated invariant T (MAIT) cells are a subset of innate-like T cells abundant in human tissues that play a significant role in defense against bacterial and viral infections and in tissue repair. MAIT cells are activated by recognizing microbial-derived small-molecule ligands presented by the MHC class I related-1 protein. Although several MAIT cell modulators have been identified in the last decade, potent and chemically stable ligands remain limited. Herein, we carried out a structure-activity relationship study of ribityllumazine derivatives and found chemically stable MAIT cell activators with a pteridine core and a 2-oxopropyl group as the Lys-reactive group. The activators showed high potency toward a co-cultivation assay using model cell lines of antigen-presenting cells and MAIT cells (EC50 = 20 nM). The X-ray crystallographic analysis revealed the binding mode of the activator to MR1 and T cell receptor, indicating that it forms a covalent bond with MR1 via Shiff base formation. Furthermore, we found that one activator stimulated proliferation of human MAIT cells in human peripheral blood mononuclear cells and showed an adjuvant effect in mice. Our developed activator is one of the most potent among chemically stable MAIT cell activators, contributing to accelerating therapeutic applications of MAIT cells. | Ryosuke Takasaki; Masamichi Nagae; Yuki Takahashi; Emi Ito; Takuro Matsuoka; Wakana Yasue; Norihito Arichi; Hiroaki Ohno; Sho Yamasaki; Shinsuke Inuki | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cf63e166c1381729ca0c81/original/development-of-ribityllumazine-analogs-as-mucosal-associated-invariant-t-cell-activators.pdf |
612cedeed5f0809897b674e4 | 10.26434/chemrxiv-2021-d7fq2 | Multivariate sodalite Zeolitic Imidazolate frameworks: a direct solvent-free synthesis | Different mixed-ligand Zeolitic Imidazolate Frameworks (ZIFs) with sodalite topology, i.e. isoreticular to ZIF-8, unachievable by conventional synthetic routes, have been prepared using a solvent-free methodology. In particular, the versatility of this method is demonstrated with three different metal centres (Zn, Co and Fe) and binary combinations of three different ligands (2-methylimidazole, 2-ethylimidazole and 2-methylbenzimidazole). One combination of ligands, 2-ethylimidazole and 2-methylbenzimidazole, results in the formation of SOD frameworks for the three metal centres despite this topology not being obtained for the individual ligands. Theoretical calculations confirm that this topology is the lowest in energy upon ligand mixing. | Javier López-Cabrelles; Eugenia Miguel-Casañ; Maria Esteve-Rochina; Eduardo Andres-Garcia; Iñigo Vitórica-Yrezábal; Joaquin Calbo; Guillermo Minguez Espallargas | Materials Science; Inorganic Chemistry; Hybrid Organic-Inorganic Materials; Coordination Chemistry (Inorg.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-08-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612cedeed5f0809897b674e4/original/multivariate-sodalite-zeolitic-imidazolate-frameworks-a-direct-solvent-free-synthesis.pdf |
6495cbc72e632767b0abcf58 | 10.26434/chemrxiv-2023-bztxr | Ligand Control of Regioselectivity in Palladium-Catalyzed Heteroannulation Reactions of 1,3-Dienes | Olefin carbofunctionalization reactions are indispensable tools for constructing diverse, functionalized scaffolds from simple starting materials. However, achieving precise control over regioselectivity in intermolecular reactions remains a formidable challenge. By using PAd2nBu as a ligand, we have achieved regioselective heteroannulation of o-bromoanilines with branched 1,3-dienes through ligand control. This enables regiodivergent access to 3-substituted indolines, showcasing excellent regioselectivity and reactivity across a range of functionalized substrates. To gain further insights into the origin of selectivity control, we employed a data-driven strategy, developing a linear regression model using calculated parameters for phosphorus ligands. This model identified four key parameters governing regioselectivity in this transformation, paving the way for future methodology development. Additionally, density functional theory calculations elucidated key selectivity-determining transition structures along the reaction pathway, corroborating our experimental observations and establishing a solid foundation for future advancements in regioselective olefin difunctionalization reactions. | Dasha Rodina; Jakub Vaith; Shauna Paradine | Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6495cbc72e632767b0abcf58/original/ligand-control-of-regioselectivity-in-palladium-catalyzed-heteroannulation-reactions-of-1-3-dienes.pdf |
60c740649abda214d1f8bcc1 | 10.26434/chemrxiv.7732472.v1 | Molecular Engineering of an Alkaline Naphthoquinone Flow Battery | <p>Aqueous organic redox flow batteries (AORFBs) have recently gained significant attention as a potential candidate for grid-scale electrical energy storage. Successful implementation of this technology will require redox-active organic molecules with many desired properties. Here we introduce a naphthoquinone dimer, bislawsone, as the redox-active material in a negative potential electrolyte (negolyte) for an AORFB. This novel dimerization strategy substantially improves the performance of the electrolyte vs. that of the lawsone monomer in terms of solubility, stability, reversible capacity, permeability and cell voltage. An AORFB pairing bislawsone with a ferri/ferrocyanide positive electrolyte delivers an open-circuit voltage of 1.05 V and cycles at a current density of 300 mA/cm<sup>2</sup> with a negolyte concentration of 2 M electrons in alkaline solution. We determined the degradation mechanism for the naphthoquinone-based electrolyte using chemical analysis, and predict theoretically electrolytes based on naphthoquinones that will be even more stable.</p> | Liuchuan Tong; Marc-Antoni Goulet; Daniel P. Tabor; Emily F. Kerr; Diana De Porcellinis; Eric M. Fell; Alan Aspuru-Guzik; Roy G. Gordon; Michael J. Aziz | Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740649abda214d1f8bcc1/original/molecular-engineering-of-an-alkaline-naphthoquinone-flow-battery.pdf |
642e80ed736114c96300604a | 10.26434/chemrxiv-2023-hqppl | Bubble Detection on the Cathode and Anode of a High-Performing Capillary-Fed Water Electrolysis Cell | The cathode and anode of a ‘bubble-free’ ‘capillary-fed’ water electrolysis cell that was previously reported to consume only 40.4 kWh kg-1 hydrogen under standard commercial operating conditions, have been separately investigated for the incidence of gas bubble formation during operation. Adaptions of a voltage fluctuation and an acoustic emission technique were applied in combination, to detect and analyze bubble formation at current densities up to 1 A cm-2. The two techniques produced very similar results, showing little bubble formation up to 0.17-0.20 A cm-2. Thereafter, bubbles were formed predominantly at
the cathode up to ~0.6 A cm2. At higher current densities, the cathode and anode produced bubbles at similar rates, that were substantially lower than in conventional, ‘bubbled’
electrolysis cells. In the course of this work, the previously reported high electrochemical performance of the capillary-fed cell was independently confirmed. | Gerhard Swiegers; Anh Linh Hoang; Rhodri E. Owen; George Tsekouras; Dan J. L. Brett | Catalysis; Energy; Base Catalysis; Electrocatalysis; Fuels - Energy Science; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642e80ed736114c96300604a/original/bubble-detection-on-the-cathode-and-anode-of-a-high-performing-capillary-fed-water-electrolysis-cell.pdf |
65ef72bd66c1381729c67bd7 | 10.26434/chemrxiv-2024-n0hbh-v2 | Stability and Structure of Potentially Atmospherically Relevant Glycine Ammonium Bisulfate Clusters | New particle formation (NPF) is the process by which trace atmospheric acids and bases cluster and grow into particles that ultimately impact climate. Sulfuric acid concentration drives NPF, but nitrogen-containing bases promote the formation of more stable clusters via salt bridge formation. Recent computational efforts have suggested that amino acids can enhance NPF, predicting that they can stabilize new particles via multiple protonation sites, but there has yet to be experimental validation of these predictions. We used mass spectrometry and infrared spectroscopy to study the structure and stability of cationic clusters composed of glycine, sulfuric acid, and ammonia. When collisionally activated, clusters were significantly more likely to eliminate ammonia or sulfuric acid than glycine, while quantum chemical calculations predicted lower binding free energies for ammonia but similar binding free energies for glycine and sulfuric acid. These calculations predicted several low-energy structures, so we compared experimental and computed vibrational spectra to attempt to validate the computationally-predicted minimum energy structure. Unambiguous identification of the experimental structure by comparison to these calculations was made difficult by the complexity of the experimental spectra and the fact that the identity of the computed lowest-energy structure depended strongly on temperature. If their vapors are present, amino acids are likely to be enriched in new particles by displacing more weakly-bound ammonia, similar to the behavior of other atmospheric amines. The carboxylic acid groups were found to preferentially interact with other carboxylic acids, suggesting incipient organic/inorganic phase separation even at these small sizes. | Annapoorani Hariharan; Conor J. Bready; Jack G. Ajello; Samantha H. Black; George C. Shields ; Christopher J. Johnson | Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Clusters; Structure | CC BY 4.0 | CHEMRXIV | 2024-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ef72bd66c1381729c67bd7/original/stability-and-structure-of-potentially-atmospherically-relevant-glycine-ammonium-bisulfate-clusters.pdf |
63bbd940ded31e4531828fce | 10.26434/chemrxiv-2022-kdz2g-v2 | Anion vacancy regulated sodium/potassium intercalation in potassium Prussian blue analogue cathodes for hybrid sodium ion batteries | Fe-based potassium Prussian blue analogues (K-PBAs) are traditionally used as K-ion battery cathodes. Interestingly, K-PBAs are appealing cathodes for Na-ion batteries (NIBs), due to the increased cation intercalation voltage compared to Na-PBAs. In such a hybrid NIB cell, where Na+ is in the electrolyte and K+ is in the PBA cathode, cation intercalation and electrochemical performance of the cathode can be significantly affected by [Fe(CN)6]4- anion vacancy. This work studies the effect of [Fe(CN)6]4- anion vacancy in K-PBAs on regulating K+/Na+ intercalation mechanism in hybrid NIB cells, by comparing two K-PBA cathodes with different vacancy contents. Experimental and computational results demonstrate that introducing a level of anion vacancy can maximize the number of K+ intercalation sites and enhance K+ diffusion in the PBA framework. This facilitates K+ intercalation and suppresses Na+ intercalation, resulting in a K+-dominated and high-discharge-voltage ion storage process in the hybrid NIB cell. The K-PBA cathode with 20% anion vacancy delivers 127 mAh g-1 at 50 mA g-1 and 63 mAh g-1 at 500 mA g-1, as well as retains 87% and 77% capacity after 100 and 300 cycles, respectively. It completely outperforms the counterpart with 7% anion vacancy, which exhibits increased Na+ intercalation but overall deteriorated ion storage. Our results show the promise of hybrid battery systems and the crucial role of vacancy regulation in designing electrode materials for these systems. | Runzhe Wei; Xingwu Zhai; Henry Tinker; Charlie Nason; Yupei Han; Veronica Celorrio; Diego Gianolio; Gopinathan Sankar; Min Zhou; Yang Xu | Materials Science; Energy; Nanostructured Materials - Materials; Energy Storage | CC BY 4.0 | CHEMRXIV | 2023-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bbd940ded31e4531828fce/original/anion-vacancy-regulated-sodium-potassium-intercalation-in-potassium-prussian-blue-analogue-cathodes-for-hybrid-sodium-ion-batteries.pdf |
645a2ce6f2112b41e941a2aa | 10.26434/chemrxiv-2022-2s6hm-v2 | Aggregation-Induced Emission Artificial Enzyme (AIEzyme) with DNase-Like Activity: Imaging and Matrix Cleavage for Combating Bacterial Biofilm | DNase-catalyzed hydrolysis of extracellular DNA (eDNA) have been widely employed to eradicate intractable biofilms. Although aggregation-induced emission (AIE) has become the ideal tool for killing planktonic bacteria, AIE luminogens (AIEgens) often lack DNase-mimetic activity, in order to suffer from poor anti-biofilm capacity. Here, an “AIEzyme”, a kind of AIE nanomaterial with enzyme-like activity, is designed and synthesized, where the AIEgens are used as the ligands of Zr-based coordination polymer nanoparticles. Not only do AIEzyme have enduring DNase-mimetic activity with high substrate affinity and low activation energy, but also structural rigidity-stabilized fluorescence. Due to the long-acting hydrolysis for eDNA in biofilm, AIEzyme can efficiently disorganize the established biofilms with good penetrability and realize the healing of superbugs-infected wound for at least seven days under only one dose of AIEzyme. Moreover, AIEzymes can be observed by virtue of their own AIE character, facilitating the study on self-positioning and residual amount of AIEzymes in wound. On the support of AIEzyme, we expect to explore an idea for the application development of AIEgen. | Lei Han; Yucui Zhang; Baojian Huang; Xuhui Bian | Biological and Medicinal Chemistry; Catalysis; Bioengineering and Biotechnology; Biophysics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645a2ce6f2112b41e941a2aa/original/aggregation-induced-emission-artificial-enzyme-ai-ezyme-with-d-nase-like-activity-imaging-and-matrix-cleavage-for-combating-bacterial-biofilm.pdf |
60d0c6a4c62295b40f1a50d9 | 10.26434/chemrxiv-2021-xkzzr | Local perturbations of periodic systems. Chemisorption and point defects by GoGreenGo. | We present a software package GoGreenGo -- aimed
to model local perturbations of periodic systems due to either chemisorption or point defects. The electronic structure of an ideal crystal is obtained by worldwide distributed standard quantum physics/chemistry
codes, then processed by various tools performing projection to atomic orbital basis sets. Starting from this, the perturbation is addressed by GoGreenGo with use of the Green's functions formalism, which allows to evaluate its effect on the electronic structure, density matrix and energy of the system. In the present contribution the main
accent is made on processes of chemical nature such as chemisorption or doping. We address a general theory and its computational implementation supported by a series of test calculations for benchmark model solids: simple, face-centered and body-centered cubium systems. In addition,
more realistic problems of local perturbations in graphene lattice such as lattice substitution, vacancy and "on-top"
chemisorption are considered. | Andrei L. Tchougreeff; Timofey Kuhsnir; Ilya Popov | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d0c6a4c62295b40f1a50d9/original/local-perturbations-of-periodic-systems-chemisorption-and-point-defects-by-go-green-go.pdf |
6720ade3f9980725cf3f51c3 | 10.26434/chemrxiv-2024-w1qd6-v2 | The Direct Pd-Catalyzed γ-Lactonization of Aliphatic Carboxylic Acids | A direct palladium-catalyzed γ-lactonization of free carboxylic acids via C–O reductive elimination as a key step is described. Notable aspects of this protocol include the use of convenient and easily available sodium percarbonate as an oxidant and the development of a new beta-alanine derived ligand. The reported method enables the functionalization of a wide range of aliphatic acids including previously inaccessible β-non-quaternary acids. The regioselectivity and consequently substrate scope of this protocol proved complementary to established routes for the direct lactonization of aliphatic carboxylic acids. A modification of this method furthermore enables a direct β-C(sp3)–H hydroxylation of challenging α-non-quaternary carboxylic acids with considerable functional group tolerance. Through this report valuable compound libraries of γ-lactones and β-hydroxy acids with potential applications in various fields become available. | Tianxiao Xu; Sourjya Mal; Manuel van Gemmeren | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6720ade3f9980725cf3f51c3/original/the-direct-pd-catalyzed-lactonization-of-aliphatic-carboxylic-acids.pdf |
64d3b7064a3f7d0c0de25921 | 10.26434/chemrxiv-2023-1fg86 | Characterization of 2,4-dianilinopyrimidines Against Five P. falciparum Kinases PfARK1, PfARK3, PfNEK3, PfPK9 and PfPKB | Plasmodium kinases are increasingly recognized as potential novel antiplasmodial targets for the treatment of malaria, but only a small subset of these kinases have had structure-activity-relationship (SAR) campaigns reported. Herein we report the discovery of CZC-54252 (1) as an inhibitor of five P. falciparum kinases PfARK1, PfARK3, PfNEK3, PfPK9 and PfPKB. 39 analogues were evaluated against all five kinases to establish SAR at three regions of the kinase active site. Nanomolar inhibitors of each kinase are discovered. We identify common and divergent SAR trends across all five kinases, highlighting substituents at each region that improve potency and selectivity for each kinase. Potent analogues were evaluated against the P. falciparum blood stage. Eight submicromolar inhibitors were discovered, of which 37 demonstrated potent antiplasmodial activity (EC50 = 0.16 μM). Our results provide an understanding of features needed to inhibit each individual kinase and lay groundwork for future optimization efforts towards novel antimalarials. | Han Wee Ong; Chandi de Silva; Krisha Avalani ; Frank Kwarcinski ; Christopher Mansfield ; Michael Chirgwin ; Anna Truong ; Emily Derbyshire ; Reena Zutshi ; David Drewry | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d3b7064a3f7d0c0de25921/original/characterization-of-2-4-dianilinopyrimidines-against-five-p-falciparum-kinases-pf-ark1-pf-ark3-pf-nek3-pf-pk9-and-pf-pkb.pdf |
60c74c1a702a9b85d318b5bd | 10.26434/chemrxiv.12425372.v1 | A Computational Protocol to Predict Anti-Kasha Emissions: The Case of Azulene Derivatives | <p>In this contribution we present a computational protocol to predict anti-Kasha photoluminescence. The herein developed protocol is based on state-of-the-art quantum chemical calculations and excited state decay rate theories (i.e., thermal vibration correlation function formalism), along with appropriate kinetic models which include all relevant electronic states. This protocol is validated for a series of azulene derivatives. For this series, we have computed absorption and emission spectra for both their first and second excited states, their radiative and non-radiative rates as well as fluorescence yields from the two different excited states. All the studied azulene derivatives are predicted to exclusively display anomalous anti-Kasha S<sub>2 </sub>emission. A quantitative agreement for the herein computed excited state spectra, lifetimes and fluorescence quantum yieldsis obtained with respect to the experimental values. Given the increasing interest on anti-Kasha emitters, we foresee that the herein developed computational protocol can be used to pre-screen dyes with the desired aforementioned anomalous photoluminescence properties.</p> | Koen Veys; Daniel Escudero | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c1a702a9b85d318b5bd/original/a-computational-protocol-to-predict-anti-kasha-emissions-the-case-of-azulene-derivatives.pdf |
65491d71c573f893f1eecf6e | 10.26434/chemrxiv-2023-k7q5l | A Golden Touch in the Design of Porphyrin Metallacages as Multifaceted Anticancer Agents | The use of three-dimensional self-assembled metallacages (MCgs) as theranostic platforms holds great promise. This work reports on the integration of a gold(III) porphyrin scaffold into a prismatic metallacage structure and explores its application for photodynamic therapy (PDT) of cancer in vitro. Not only the new metallacage retains the photosensitizing properties of the gold porphyrin, but unexpectedly, it also shows remarkable selective stabilization of guanine-quadruplexes (G4) structures as validated anticancer drug targets. | Tamara Rodríguez-Prieto; Darren Wragg; Nicole Heiduk; Mihyun Park; Nicole Strittmatter; Roland A. Fischer; Angela Casini; Guillermo Moreno-Alcántar | Biological and Medicinal Chemistry; Inorganic Chemistry; Organometallic Chemistry; Bioinorganic Chemistry; Supramolecular Chemistry (Inorg.); Coordination Chemistry (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2023-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65491d71c573f893f1eecf6e/original/a-golden-touch-in-the-design-of-porphyrin-metallacages-as-multifaceted-anticancer-agents.pdf |
61cf117b7f367e074365fb7d | 10.26434/chemrxiv-2021-nccgc-v3 | Complex Energies and Transition-Dipoles for the Uracil anion Shape-type Resonances from stabilization curves via Padé | Absorption of slow moving electrons by neutral ground state nucleobases have been known to produce resonance, metastable, states. There are indications that such metastable states may play a key-role in DNA/RNA damage. Therefore, herein, we present an ab-initio, non-Hermitian investigation of the resonance positions and decay rates of the low lying shape-type states of the uracil anion. In addition, we calculate the complex transition dipoles between these resonance states. We employ the resonance via Padé (RVP) method to calculate these complex properties from real stabilization curves by analytical dilation into the complex plane. This method has al-ready been successfully applied to many small molecular systems and herein we present the first application of RVP to a medium-size system. The presented resonance energies are converged with respect to the size of the basis set and compared with previous theoretical works and experimental findings. Complex transition dipoles between the shape-type resonances are computed using the energy-converged basis set. The ability to calculate ab-initio energies and lifetimes of biologically relevant systems opens the door for studying reactions of such systems in which autoionization takes place. While the ability to also calculate their complex transition dipoles open the door for studying photo induced dynamics of such biological molecules. | Gal Bouskila; Arie Landau; Idan Haritan; Nimrod Moiseyev; Debarati Bhattacharya | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Physical and Chemical Processes; Physical and Chemical Properties | CC BY NC 4.0 | CHEMRXIV | 2022-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61cf117b7f367e074365fb7d/original/complex-energies-and-transition-dipoles-for-the-uracil-anion-shape-type-resonances-from-stabilization-curves-via-pade.pdf |
61400bf68e38a349cb525743 | 10.26434/chemrxiv-2021-cdzlk | Proton Transfer from a Photoacid to Water: First Principles Simulations and Fast Fluorescence Spectroscopy | Proton transfer reactions are ubiquitous in chemistry, especially in aqueous solutions. We
investigate photo-induced proton transfer between the photoacid 8-hydroxypyrene-1,3,6-
trisulfonate (HPTS) and water using fast fluorescence spectroscopy and ab initio molecular
dynamics simulations. Photo-excitation causes rapid proton release from the HPTS hydroxyl.
Previous experiments on HPTS/water described the progress from photoexcitation to proton
diffusion using kinetic equations with two time constants. The shortest time constant has been
interpreted as protonated and photoexcited HPTS evolving into an “associated” state, where the
proton is “shared” between the HPTS hydroxyl and an originally hydrogen bonded water. The
longer time constant has been interpreted as indicating evolution to a “solvent separated” state
where the shared proton undergoes long distance diffusion. In this work, we refine the previous
experimental results using very pure HPTS. We then use excited state ab initio molecular dynamics
to elucidate the detailed molecular mechanism of aqueous excited state proton transfer in HPTS.
We find that the initial excitation results in rapid rearrangement of water, forming a strong
hydrogen bonded network (a “water wire”) around HPTS. HPTS then deprotonates in ≤3 ps,
resulting in a proton that migrates back and forth along the wire before localizing on a single water
molecule. We find a near linear relationship between emission wavelength and proton-HPTS
distance over the simulated time scale, suggesting that emission wavelength can be used as a ruler
for proton distance. Our simulations reveal that the “associated” state corresponds to a water wire
with a mobile proton and that the diffusion of the proton away from this water wire (to a
generalized “solvent-separated” state) corresponds to the longest experimental time constant. | Alice R. Walker; Boning Wu; Jan Meisner; Michael D. Fayer; Todd J. Martinez | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61400bf68e38a349cb525743/original/proton-transfer-from-a-photoacid-to-water-first-principles-simulations-and-fast-fluorescence-spectroscopy.pdf |
60c756dcee301cd2cec7b436 | 10.26434/chemrxiv.14339708.v1 | A Step Towards Change: A Green Alternative for the Synthesis of Metal–Organic Frameworks | Metal–organic frameworks (MOFs) are
traditionally synthesized using formamide solvents that are hazardous to human
health and the environment. In order to alleviate the environmental impact of
MOF synthesis in both academic and industrial settings, safer and greener
solvent alternatives are desired. Herein, STEPOSOL® MET-10U (<i>N,N</i>-dimethyl-9-decenamide),
a bioderived solvent produced <i>via</i> olefin metathesis using renewable
feedstocks, such as plant oils, is explored as a solvent for the synthesis of a
series of structurally diverse MOFs. | Paola Marino; P. Rafael Donnarumma; Hudson de Aguiar Bicalho; Victor Quezada-Novoa; Hatem M. Titi; Ashlee J Howarth | Coordination Chemistry (Inorg.); Solid State Chemistry; Supramolecular Chemistry (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756dcee301cd2cec7b436/original/a-step-towards-change-a-green-alternative-for-the-synthesis-of-metal-organic-frameworks.pdf |
60c74b9b702a9be0d518b48b | 10.26434/chemrxiv.12362222.v1 | Intermolecular Interaction Among Remdesivir, RNA and RNA-Dependent RNA Polymerase of SARS-CoV-2 Analyzed by Fragment Molecular Orbital Calculation | <p>COVID-19,
a disease caused by a new strain of coronavirus (SARS-CoV-2) originating from
Wuhan, China, has now spread around the world, triggering a global pandemic,
leaving the public eagerly awaiting the development of a specific medicine and
vaccine. In response, aggressive efforts are underway around the world to
overcome COVID-19. In this study, referencing the data published on the Protein
Data Bank (PDB ID: 7BV2) on April 22, we conducted a detailed analysis of the
interaction between the complex structures of the RNA-dependent RNA polymerase
(RdRp) of SARS-CoV-2 and Remdesivir, an antiviral drug, from the quantum
chemical perspective based on the fragment molecular orbital (FMO) method. In
addition to the hydrogen bonding and intra-strand stacking between
complementary strands as seen in normal base pairs, Remdesivir bound to the
terminus of an primer-RNA strand was further stabilized by diagonal π-π stacking
with the -1A base of the complementary strand and an additional hydrogen bond
with an intra-strand base, due to the effect of chemically modified functional
group. Moreover, stable OH/π interaction is also formed with Thr687 of the
RdRp. We quantitatively revealed the exhaustive interaction within the complex among
Remdesivir, template-primer-RNA, RdRp and co-factors, and published the results
in the FMODB database.</p> | Koichiro Kato; Teruki Honma; Kaori Fukuzawa | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b9b702a9be0d518b48b/original/intermolecular-interaction-among-remdesivir-rna-and-rna-dependent-rna-polymerase-of-sars-co-v-2-analyzed-by-fragment-molecular-orbital-calculation.pdf |
65969020e9ebbb4db9688e80 | 10.26434/chemrxiv-2024-bjv8s | A fluorogenic pseudo-infection assay to probe transfer and distribution of influenza viral contents to target vesicles | Fusion of enveloped viruses with endosomal membranes and subsequent release of viral genome into the cytoplasm is crucial to the viral infection cycle. It is often modelled by carrying out fusion between virus particles and target lipid vesicles. We utilized fluorescence microscopy to characterize the kinetic and spatial aspects of the transfer of influenza viral ribonucleoprotein (vRNP) complexes to target vesicles and their distribution within the fused volumes to gain deeper insight into the mechanistic aspects of endosomal escape. The fluorogenic RNA-binding dye QuantiFluor® (Promega) was found to be well-suited for direct and sensitive microscopic observation of vRNPs which facilitated background-free detection and kinetic analysis of fusion events on a single particle level. To determine the extent to which the viral contents are transferred to the target vesicles through the fusion pore, we carried out virus-vesicle fusion in a side-by-side fashion. Measurement of the Euclidean distances between the centroids of super-localized membrane and content dye signals within the fused volumes allowed determination of any symmetry (or the lack thereof) between them as expected in the event of transfer (or the lack thereof) of vRNPs, respectively. We found that in case of fusion between viruses and 100 nm target vesicles, ~39% of the events led to transfer of viral contents to the target vesicles. This methodology provides a rapid, generic and cell-free method to assess the inhibitory effects of anti-viral drugs and therapeutics on the endosomal escape behavior of enveloped viruses. | Ahanjit Bhattacharya; Nahal Bagheri; Steven G. Boxer | Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Biophysical Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65969020e9ebbb4db9688e80/original/a-fluorogenic-pseudo-infection-assay-to-probe-transfer-and-distribution-of-influenza-viral-contents-to-target-vesicles.pdf |
67658671fa469535b94292fc | 10.26434/chemrxiv-2024-k00zf | Mechanism behind oxidase activity of cellulose-active AA10 lytic polysaccharide monooxygenases | Lytic polysaccharide monooxygenases (LPMOs) are unique mono-copper enzymes that boost the degradation of different polysaccharides and play important roles in the sustainable production of biofuels, in human and plant pathogens and potentially also in plastic degradation. Their activity depends on a co-substrate, where recent results show that hydrogen peroxide is the preferred co-substrate. Under typical experimental conditions, no hydrogen peroxide is added and it is instead produced in situ by LPMOs themselves, which could possibly be the rate-limiting step. Previous theoretical investigations of the oxidase reaction have been highly inhomogeneous, and focused on different aspects of LPMO reactivity. In this paper, we systematically investigate how LPMOs generate hydrogen peroxide using accurate quantum mechanics/molecular mechanics (QM/MM) hybrid methods with extended QM regions. We find that protonation of a generated superoxide intermediate at the active-site is most likely, but that this requires further reduction of the superoxide. | Erna Katharina Wieduwilt; Marlisa Muriel Hagemann; Ulf Ryde; Erik Donovan Hedegård | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67658671fa469535b94292fc/original/mechanism-behind-oxidase-activity-of-cellulose-active-aa10-lytic-polysaccharide-monooxygenases.pdf |
65f6d2cd9138d23161a37ed6 | 10.26434/chemrxiv-2024-zxzfw | Theoretical Investigation of Transient Species following Photodissociation of Ironpentacarbonyl in Ethanol Solution | Photodissociation of ironpentacarbonyl in solution generates transient species in different electronic states, which we have studied theoretically. From ab initio molecular dynamics simulations in ethanol solution, the closed-shell parent compound Fe(CO)5 is found to interact weakly with the solvent, whereas the irontetracarbonyl (Fe(CO)4) species, formed after photodissociation, has a strongly spin-dependent behavior. It coordinates a solvent molecule tightly in the singlet state and weakly in the triplet state. From the simulations, we have gained insight into intersystem crossing in solvated irontetracarbonyl, based on the distinct structural differences induced by the change in multiplitity. Alternative forms of coordination between Fe(CO)4 and functional groups of the ethanol molecule are simulated and a quantum chemical investigation of the energy landscape for the coordinated irontetracarbonyl give information about the interconversion of different transient species in solution. Furthermore, insights from the simulations, in which we find evidence of a solvent exchange mechanism, challenge the previously proposed mechanism of chain walking for undercoordinated metal carbonyls in solution. | Michael R. Coates; Ambar Banerjee; Raphael M. Jay; Philippe Wernet; Michael Odelius | Inorganic Chemistry; Transition Metal Complexes (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f6d2cd9138d23161a37ed6/original/theoretical-investigation-of-transient-species-following-photodissociation-of-ironpentacarbonyl-in-ethanol-solution.pdf |
60c75444469df44c68f44ef3 | 10.26434/chemrxiv.13635206.v1 | Phosphorus-Mediated sp2-sp3 Couplings for Selective C–H Fluoroalkylation of Complex Azines | Fluoroalkyl groups profoundly affect the physical properties of pharmaceuticals and influence virtually all metrics associated with their pharmacokinetic and pharmacodynamic profile.<sup>1-4</sup> Drug candidates increasingly contain CF<sub>3</sub> and CF<sub>2</sub>H groups, and the same trend in agrochemical development shows that the effect of fluoroalkylation translates across human, insect, and plant life.<sup>5,6</sup> New fluoroalkylation reactions have undoubtedly stimulated this uptake; however, methods that directly convert C–H bonds into C–CF<sub>2</sub>X (X = F or H) groups in complex drug-like molecules are rare.<sup>7-13</sup> For pyridine, the most common aromatic heterocycle in pharmaceuticals,<sup>14</sup> only one approach, via fluoroalkyl radicals, is viable for pyridyl C–H fluoroalkylation in the elaborate structures encountered during drug development.<sup>15-17</sup> Here, we have developed a new set of bench-stable fluoroalkylphosphines that directly convert the C–H bonds in pyridine building blocks, drug-like fragments, and pharmaceuticals into fluoroalkyl derivatives. No pre-installed functional groups or directing groups are required; the reaction tolerates a variety of sterically and electronically distinct pyridines and is exclusively selective for the 4-position in most cases. The reaction proceeds via initial phosphonium salt formation followed by <i>sp</i><sup>2</sup>-<i>sp</i><sup>3</sup> phosphorus ligand-coupling, an underdeveloped manifold for C–C bond formation. | Xuan Zhang; Kyle G. Nottingham; Chirag Patel; Juan V. Alegre-Requena; Jeffrey N. Levy; Robert S. Paton; Andrew McNally | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75444469df44c68f44ef3/original/phosphorus-mediated-sp2-sp3-couplings-for-selective-c-h-fluoroalkylation-of-complex-azines.pdf |
674f0c785a82cea2fad63834 | 10.26434/chemrxiv-2024-vm2dc | Genipin-Crosslinked Gelatin Hydrogel for the Detection and Treatment of Active Metalloprotease Releasing Pseudomonas aeruginosa. | We report a genipin-crosslinked gelatin hydrogel for the detection of the pathogenic strains of Pseudomonas aeruginosa releasing active metalloproteases. Enzymatic degradation of the blue gel gives a clear visual signal that indicates the presence of P. aeruginosa. A total of 36 strains of both Gram-positive and Gram-negative bacteria were tested and only P. aeruginosa strains caused degradation of the gels within 24 h. Gene sequencing revealed that P. aeruginosa strains with mutations in their quorum sensing operon were not able to degrade the hydrogels even though the genes coding for metalloproteases were present. Finally, we created a gel multilayer that can both detect and treat active strains of P. aeruginosa through the release of bacteriophage. Our system provides a simple and reproducible assay for P. aeruginosa metalloproteases and showcases the feasibility of responsive wound dressings able to both detect and treat P. aeruginosa infection. | Céline Feuilloley; Khanzadi Nazneen Manzoor; Naing Tun Thet; Maciej Kopeć; Toby Jenkins; Mark Sutton; Charlotte Hind; Patrick Grossmann; Kilian Vogele; Maisem Laabei; Matthew Wand; P.J. Cameron | Biological and Medicinal Chemistry; Microbiology; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674f0c785a82cea2fad63834/original/genipin-crosslinked-gelatin-hydrogel-for-the-detection-and-treatment-of-active-metalloprotease-releasing-pseudomonas-aeruginosa.pdf |
65b7916de9ebbb4db934cb57 | 10.26434/chemrxiv-2024-w671q | Liposomes to cubosomes: The evolution of lipidic nanocarriers and their cutting-edge biomedical applications | Lipidic nanoparticles have undergone extensive research towards the exploration of their diversely ranging therapeutic applications. Although several liposomal formulations are in the clinics (e.g., DOXIL) for cancer therapy there are many challenges associated with the traditional liposomes. To address these issues, modifications in liposomal structure and further functionalization are desirable, leading to the emergence of solid lipid nanoparticles and the more recent liquid lipid nanoparticles. In this context, ‘cubosomes’, third-generation lipidic nanocarriers, have attracted significant attention due to their numerous advantages, including their porous structure, structural adaptability, high encapsulation efficiency resulting from their extensive internal surface area, enhanced stability, and biocompatibility. Cubosomes offer the potential for both enhanced cellular uptake and controlled release of encapsulated payloads. Beyond cancer therapy, cubosomes have demonstrated effectiveness in wound healing, antibacterial treatments, and various dermatological applications. In the article, the authors provide an overview of the evolution of lipidic nanocarriers, spanning from conventional liposomes to solid lipid nanoparticles, with a special emphasis on the development and applications of cubosomes. Additionally, it delves into recent applications and pre-clinical trials associated with cubosome formulations, which could be of significant interest to readers from backgrounds in nanomedicine and clinicians. | Nishtha Attri; Swarnali Das; Jhimli Banerjee; Shazana H. Shamsuddin; Sandeep Kumar Dash; ARINDAM PRAMANIK | Biological and Medicinal Chemistry; Materials Science; Nanoscience; Biocompatible Materials; Nanostructured Materials - Nanoscience; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b7916de9ebbb4db934cb57/original/liposomes-to-cubosomes-the-evolution-of-lipidic-nanocarriers-and-their-cutting-edge-biomedical-applications.pdf |
60c74cd6567dfe662fec5210 | 10.26434/chemrxiv.11573427.v3 | Denoising DNA Encoded Library Screens with Sparse Learning | <div><div>DNA-encoded libraries (DELs) are large, pooled collections of compounds in which every library member is attached to a stretch of DNA encoding its complete synthetic history. DEL-based hit discovery involves affinity selection of the library against a protein of interest, whereby compounds retained by the target are subsequently identified by next-generation sequencing of the corresponding DNA tags. When analyzing the resulting data, one typically assumes that sequencing output (i.e. read counts) is proportional to the binding affinity of a given compound, thus enabling hit prioritization and elucidation of any underlying structure-activity relationships (SAR). This assumption, though, tends to be severely confounded by a number of factors, including variable reaction yields, presence of incomplete products masquerading as their intended counterparts, and sequencing noise. In practice, these confounders are often ignored, potentially contributing to low hit validation rates, and universally leading to loss of valuable information. To address this issue, we have developed a method for comprehensively denoising DEL selection outputs. Our method, dubbed "deldenoiser", is based on sparse learning and leverages inputs that are commonly available within a DEL generation and screening workflow. Using simulated and publicly available DEL affinity selection data, we show that "deldenoiser" is not only able to recover and rank true binders much more robustly than read count-based approaches, but also that it yields scores which accurately capture the underlying SAR. The proposed method can, thus, be of significant utility in hit prioritization following DEL screens.</div></div> | Peter Komar; Marko Kalinic | Combinatorial Chemistry; High-throughput Screening; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cd6567dfe662fec5210/original/denoising-dna-encoded-library-screens-with-sparse-learning.pdf |
62f3868ee78f70347d3666a8 | 10.26434/chemrxiv-2022-b61sx-v3 | Understanding water transport through graphene-based nanochannels via experimental control of slip length | The water transport along graphene-based nanochannels has gained significant interest. However, experimental access to the influence of defects and impurities on transport poses a critical knowledge gap. Here, we investigate the water transport of cation intercalated graphene oxide membranes. The cations act as water-attracting impurities on the channel walls. Via water transport experiments, we show that the slip length of the nanochannels decay exponentially with the hydrated diameter of the intercalated cations, confirming that water transport is governed by the interaction between water molecules and the impurities on the channel wall. The exponential decay of slip length approximates non-slip conditions. This offers experimental support for the use of the Hagen-Poiseuille equation in graphene-based nanochannels, which was previously only confirmed by simulations. Our study gives valuable feedback to theoretical predictions of the water transport along graphene-based channels with water-attracting impurities. | Xinyue Wen; Tobias Foller; Xiaoheng Jin; Tiziana Musso; Priyank Kumar; Rakesh Joshi | Physical Chemistry; Materials Science; Nanoscience; Carbon-based Materials; Nanofluidics; Physical and Chemical Processes | CC BY 4.0 | CHEMRXIV | 2022-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f3868ee78f70347d3666a8/original/understanding-water-transport-through-graphene-based-nanochannels-via-experimental-control-of-slip-length.pdf |
6210cf7f0aec1ae3e6230e86 | 10.26434/chemrxiv-2021-zk549-v2 | Inherent Promotion of Ionic Conductivity via Coherent Vibrational Strong Coupling of Water | Hydrogen bonding interactions among water molecules play a critical role in chemical reactivity, dynamic proton mobility, static dielectric behavior, and thermodynamic properties of water. In this study, we demonstrate the modification of ionic conductivity of water via hybridization with vacuum electromagnetic field by strongly coupling O–H stretching mode of H2O to a Fabry–Perot cavity mode. This leads to formation of collective vibro-polaritonic states which, as experiments show, enhances the proton conductivity does increase by an order of magnitude at resonance. In addition, an increase of dielectric constants is observed at resonance in the coupled state. Our finding illustrates that the potential of engineering a vacuum electromagnetic environment to control the ground-state properties of water. | Tomohiro Fukushima; Soushi Yoshimitsu; Kei Murakoshi | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study; Photochemistry (Physical Chem.); Transport phenomena (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6210cf7f0aec1ae3e6230e86/original/inherent-promotion-of-ionic-conductivity-via-coherent-vibrational-strong-coupling-of-water.pdf |
60c75308bdbb891f4ca3a3c9 | 10.26434/chemrxiv.13381046.v1 | Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field | Computational protein design, ab initio protein/RNA folding, and protein-ligand screening can be too computationally demanding for explicit treatment of solvent. For these applications, implicit solvent offers a compelling alternative, which we describe here for the polarizable atomic multipole AMOEBA force field based on three treatments of continuum electrostatics: numerical solutions to the Poisson-Boltzmann equation (PBE), the domain-decomposition Conductor-like Screening Model (ddCOSMO) approximation to the PBE, and the analytic generalized Kirkwood (GK) approximation. The continuum electrostatic models are combined with a nonpolar estimator based on novel cavitation and dispersion terms. Electrostatic model parameters are numerically optimized using a least squares style target function based on a library of 103 small molecule solvation free energy differences. Mean signed errors for the APBS, ddCOSMO, and GK models are 0.05, 0.00, and 0.00 kcal/mol, respectively, while the mean unsigned errors are 0.70, 0.63, and 0.51 kcal/mol, respectively. Validation of the electrostatic response of the resulting implicit solvents, which are available in the Tinker (or Tinker-HP), OpenMM, and Force Field X software packages, is based on comparisons to explicit solvent simulations for a series of proteins and nucleic acids. Overall, the emergence of performative implicit solvent models for polarizable force fields will open the door to their use for folding and design applications.<br /> | Rae Corrigan; Guowei Qi; Andrew Thiel; Jack Lynn; Brandon Walker; Thomas Casavant; Louis Lagardère; Jean-Philip Piquemal; Jay Ponder; Pengyu Ren; Michael Schnieders | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75308bdbb891f4ca3a3c9/original/implicit-solvents-for-the-polarizable-atomic-multipole-amoeba-force-field.pdf |
64bb582ab053dad33aad1463 | 10.26434/chemrxiv-2023-3h23n | Nickel-based Single-Molecule Catalysts with Synergistic Geometric Transition and Magnetic Field-assisted Spin Selection Outperforms RuO2 for Oxygen Evolution | Overcoming slow kinetics and high overpotential in electrocatalytic oxygen evolution reaction (OER) requires innovative catalysts and approaches that transcend the scaling relationship between binding energies for intermediates and catalyst surfaces. Inorganic complexes provide unique catalyst designs with customizable geometries, which can help enhance their efficiencies. However, they are unstable and susceptible to oxidation under extreme pH conditions. Immobilizing complexes on substrates creates single-molecule catalysts (SMCs) with functional similarities to single-atom catalysts (SACs). Here, an efficient SMC, composed of dichloro(1,3-bis(diphenylphosphino)propane) nickel [NiCl2dppp] anchored to a graphene acid (GA), is presented. This SMC surpasses ruthenium-based OER benchmarks, exhibiting an ultra-low onset and overpotential at 10 mAcm-2 when exposed to a static magnetic field. Comprehensive experimental and theoretical analyses imply that an interfacial charge transfer from the Ni center in NiCl2dppp to GA enhances the OER activity. Spectroscopic investigations reveal an in-situ geometrical transformation of the complex and the formation of a paramagnetic Ni center, which under a magnetic field, enables spin-selective electron transfer, resulting in enhanced OER performance. The results highlight the significance of in-situ geometric transformations in SMCs and underline the potential of an external magnetic field to enhance OER performance at a single-molecule level, pushing the boundaries of volcano limits. | Kavish Saini; Aruna N Nair; Anju Yadav; Lissette Garcia Enriquez; Christopher J. Pollock; Stephen D. House; Shize Yang; Xin Guo; Sreeprasad T. Sreenivasan | Materials Science; Catalysis; Energy; Magnetic Materials; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bb582ab053dad33aad1463/original/nickel-based-single-molecule-catalysts-with-synergistic-geometric-transition-and-magnetic-field-assisted-spin-selection-outperforms-ru-o2-for-oxygen-evolution.pdf |
65b2636766c1381729410746 | 10.26434/chemrxiv-2024-s6hbz | Insights into the First Multi-Transition-Metal Containing Ruddlesden Popper-Type Cathode for all-solid-state Fluoride Ion Batteries | Promising cathode materials for fluoride-ion batteries (FIBs) are 3d transition metal containing oxides with Ruddlesden-Popper-type structure. So far, multi-elemental compositions were not investigated, but could alternate electrochemical performance similar to what had been found for cathode materials for lithium-ion batteries. Within this study, we investigate RP type La2Ni0.75Co0.25O4.08 as an intercalation-based active cathode material for all-solid-state FIBs. We determine the structural changes of La2Ni0.75Co0.25O4.08 during fluoride intercalation / de-intercalation by ex-situ X-ray diffraction, which showed that F- insertion leads to transformation of the parent phase to three different phases. Changes in Ni and Co oxidation states and coordination environment were examined by X-ray absorption spectroscopy and magnetic measurements in order to understand the complex reaction behaviour of the phases in detail, showing that the two transition metals behave differently in the charging and discharging process. Under optimized operating conditions, a cycle life of 120 cycles at a critical cut-off capacity of 40 mAh g-1 against Pb/PbF2 was obtained, which is one of the highest observed for intercalation electrode materials in FIBs so far. The average Coulombic efficiencies ranged from 85% to 90%. Thus, La2Ni0.75Co0.25O4.08 could be a promising candidate for cycling-stable high-energy cathode materials for all-solid-state FIBs | Vanita Vanita; Aamir Iqbal Waidha; Sami Vasala; Pascal Puphal; Roland Schoch; Pieter Glatzel; Matthias Bauer; Oliver Clemens | Materials Science; Inorganic Chemistry; Energy; Electrochemistry; Transition Metal Complexes (Inorg.); Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2024-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b2636766c1381729410746/original/insights-into-the-first-multi-transition-metal-containing-ruddlesden-popper-type-cathode-for-all-solid-state-fluoride-ion-batteries.pdf |
6704e87bcec5d6c1429061dd | 10.26434/chemrxiv-2024-qjz27 | Fisetin as a Blueprint for Senotherapeutic Agents — Elucidating Geroprotective and Senolytic Properties with Molecular Modeling | Targeting senescent cells and the factors that accelerate this pathological state has recently emerged as a novel field in medicinal chemistry. As attention shifts to synthetic substances, studies on natural agents are often overlooked. In this paper, we present a detailed computational modeling study that encompasses quantum mechanics and molecular dynamics to elucidate the senotherapeutic activity of fisetin. The mitochondrial environment, serving as a proxy for senescence, received special attention. Throughout the study, fisetin’s outstanding geroprotective properties—exhibiting significant potential against •OOH, O2•–, and •OH radicals, surpassing those of Trolox or ascorbate—were identified. Furthermore, fisetin demonstrated a high capacity to restore oxidatively damaged biomolecules to their pristine forms, thereby renewing the functionality of proteins and amino acids. The senolytic properties were examined in terms of Bcl–2 and Bcl–xL inhibition. The results indicated that fisetin not only binds effectively to these proteins but also, with appropriate modifications, may exhibit specific selectivity toward either target. This study highlights fisetin’s remarkable activity in these areas and provides a molecular description of the underlying processes, paving the way for future research. | Maciej Spiegel | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Agriculture and Food Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6704e87bcec5d6c1429061dd/original/fisetin-as-a-blueprint-for-senotherapeutic-agents-elucidating-geroprotective-and-senolytic-properties-with-molecular-modeling.pdf |
66aeabbd5101a2ffa809a6fa | 10.26434/chemrxiv-2024-8qcg4 | Palladium Bisphosphine Mono-Oxide Complexes: Synthesis, Scope, Mechanism, and Catalytic Relevance | Recent studies in transition metal catalysis employing chelating phosphines have suggested a role for partial ligand oxidation in formation of the catalytically active species, with potentially widespread relevance in a number of cata-lytic systems. We examine the internal redox reaction of PdII(bisphosphine)X2 (X = Cl, OAc, etc.) complexes to reveal previously underexplored aspects of bisphosphine mono-oxides (BPMOs), including evaluation of ligand structure and development of general reaction conditions to access a collection of structurally diverse BPMO precatalysts based on organopalladium oxidative addition complexes. In particular, a series of PdII(BPMO)(R)(X) (R=Aryl, Alkyl; X=I, Br) oxidative addition complexes bearing 24 different BPMO ligands were characterized by NMR and X-ray crystallog-raphy. Comparison of the catalytic performance of the oxidative addition complexes of phosphine versus bisphos-phine mono-oxides as precatalysts is demonstrated to be an enabling diagnostic tool in Pd catalytic reaction develop-ment. Finally, the differences in catalytic behavior between bisphosphine and bisphosphine mono-oxide complexes were rationalized through solid-state parametrization and stoichiometric experiments. | Shenghua Yang; Min Deng; Ryan Daley; Andrea Darù; William Wolf; David George; Senjie Ma; Bryn Werley; Erika Samolova; Jake Bailey; Milan Gembicky; Jonathan Marshall; Steven Wisniewski; Donna Blackmond; Keary Engle | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66aeabbd5101a2ffa809a6fa/original/palladium-bisphosphine-mono-oxide-complexes-synthesis-scope-mechanism-and-catalytic-relevance.pdf |
60faa347537d100aab7f024c | 10.26434/chemrxiv-2021-zrpzx | Optimal Representation of the Nuclear Ensemble: Application to Electronic Spectroscopy
| Nuclear densities are frequently represented by an ensemble of nuclear configurations or points in the phase space in various contexts of molecular simulations. The size of the ensemble directly affects the accuracy and computational cost of subsequent calculations of observable quantities. In the present work, we address the question of how many configurations do we need and how to select them most efficiently. We focus on the nuclear ensemble method in the context of electronic spectroscopy, where thousands of sampled configurations are usually needed for sufficiently converged spectra. The proposed representative sampling technique allows for a dramatic reduction of the sample size. By using an exploratory method, we model the density from a large sample in the space of transition properties. The representative subset of nuclear configurations is optimized by minimizing its Kullback-Leibler divergence to the full density with simulated annealing. High-level calculations are then performed only for the selected subset of configurations. We tested the algorithm on electronic absorption spectra of three molecules: (E)-azobenzene, the simplest Criegee intermediate, and hydrated nitrate anion. Typically, dozens of nuclear configurations provided sufficiently accurate spectra. A strongly forbidden transition of the nitrate anion presented the most challenging case due to rare geometries with disproportionately high transition intensities. This problematic case was easily diagnosed within the present approach. We also discuss various exploratory methods and a possible extension to dynamical simulations. | Štěpán Sršeň; Petr Slavíček | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60faa347537d100aab7f024c/original/optimal-representation-of-the-nuclear-ensemble-application-to-electronic-spectroscopy.pdf |
60c74abcee301c891fc79cc3 | 10.26434/chemrxiv.12212927.v1 | Tele-Substitution Reactions in the Synthesis of a Promising Class of Antimalarials | <p></p><p>We
have discovered and studied a <i>tele</i>substitution reaction in a
biologically important heterocyclic ring system. Conditions that favour
the <i>tele</i>-substitution pathway were identified: the use of increased
equivalents of the nucleophile or decreased equivalents of base, or the use of
softer nucleophiles, less polar solvents and larger halogens on the
electrophile. Using results from X-ray crystallography and isotope labelling
experiments a mechanism for this unusual transformation is proposed. We focused
on this triazolopyrazine as it is the core structure of the <i>in
vivo </i>active anti-plasmodium compounds of Series 4 of the Open Source
Malaria consortium.</p>
<p> </p>
<p>Archive
of the electronic laboratory notebook with the description of all conducted
experiments and raw NMR data could be accessed via following link <a href="https://ses.library.usyd.edu.au/handle/2123/21890">https://ses.library.usyd.edu.au/handle/2123/21890</a> .
For navigation between entries of laboratory notebook please use file
"Strings for compounds in the article.pdf" that works as a reference
between article codes and notebook codes, also this file contain SMILES for
these compounds. </p><br /><p></p> | Marat Korsik; Edwin Tse; David Smith; William Lewis; Peter J. Rutledge; Matthew Todd | Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74abcee301c891fc79cc3/original/tele-substitution-reactions-in-the-synthesis-of-a-promising-class-of-antimalarials.pdf |
64edd18f79853bbd78ab820d | 10.26434/chemrxiv-2023-tjjb5 | Lifting Hofmeister’s curse: Impact of cations on diffusion, hydrogen bonding and clustering of water | Water plays a role in the stability, reactivity, and dynamics of the solutes it contains. The presence of ions alters this capacity by changing the dynamics and structure of water. However, our understanding of how and to what extent this occurs is still incomplete. Here a study of the low-frequency Raman spectra of aqueous solutions of various cations using optical Kerr-effect spectroscopy is presented. This technique allows for the measurement of the changes that ions cause in both the diffusive dynamics and the vibrations of the hydrogen-bond structure of water. It is found that when salts are added, some of the water molecules become part of the ion solvation layers, while the rest retain the same dif-fusional properties as those of pure water. The slowing down of the dynamics of the water molecules in the solvation shell of each ion was found to depend on its charge density at infinite dilution conditions and on its position in the Hofmeister series at higher concentrations. It is also observed that all cations weaken the hydrogen bond structure of the solution and that this weakening depends only on the size of the cation. Finally, evidence is found that ions tend to form amorphous aggregates even at very dilute concentrations. This work provides a novel approach to water dynamics that can be used to better study the mechanisms of solute nucleation and crystallization, the structural stability of bio-molecules, and the dynamic properties of complex solutions such as water-in-salt electrolytes. | Mario González-Jiménez; Zhiyu Liao; Elen Williams; Klaas Wynne | Physical Chemistry; Materials Science; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64edd18f79853bbd78ab820d/original/lifting-hofmeister-s-curse-impact-of-cations-on-diffusion-hydrogen-bonding-and-clustering-of-water.pdf |
660e45f091aefa6ce1bfc44c | 10.26434/chemrxiv-2024-sb2q2 | Complex network analysis of completely extended chains in rubber elasticity | Rubber elastic theory describes the relationship between the microscopic chain structure and macroscopic mechanical properties of soft network polymers, such as elastomers and gels. When the deformation exceeds a certain threshold, the formation of extended chains induces hardening and failure of the materials, which has been tackled by experiments involving measurement techniques and mechanochemistry. However, the relationship between the network structure as concerns connectivity and the formation behavior of extended chains has hardly been described. Herein, we demonstrate the quantification of chain connectivity based on complex network science to investigate the formation mechanism of completely extended chains in rubber elasticity. Polymer chains in the central position of the network tended to persist in the extended chains as concerns connectivity. Furthermore, the formation of extended chains induces neighboring polymer chains to become extended chains, causing stress concentration at the network scale. Our approach, based on complex network theory, is useful as a bridge between conventional theory and experiments for describing complicated rubber elasticity at the mesoscale. | Yoshifumi Amamoto; Ken Kojio; Atsushi Takahara; Yuichi Masubuchi; Mariko Ito; Takaaki Ohnishi | Polymer Science; Polymer chains; Polymer morphology | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660e45f091aefa6ce1bfc44c/original/complex-network-analysis-of-completely-extended-chains-in-rubber-elasticity.pdf |
60c74357337d6c16bfe26b9e | 10.26434/chemrxiv.9108527.v1 | A Heterogeneous CPU + GPU Algorithm for Variational Two-Electron Reduced-Density Matrix Driven Complete Active Space Self-Consistent Field Theory | <div><div><div><p>We present a heterogeneous CPU+GPU algorithm for the direct variational optimization of the two-electron reduced-density matrix (2RDM) under two-particle N-representability conditions. This variational 2RDM (v2RDM) approach is the driver for a polynomially-scaling approximation to configuration-interaction-driven complete active space self-consistent field (CASSCF) theory. For v2RDM-based CASSCF com- putations involving an active space consisting of 50 electrons in 50 orbitals [denoted (50e,50o)], we observe a speedup of a factor of 3.7 when the code is executed on a combination of an NVIDIA TITAN V GPU and an Intel Core i7-6850k CPU, relative to the case when the code is executed on the CPU alone. We use this GPU-accelerated v2RDM-CASSCF algorithm to explore the electronic structure of the 3,k-circumacene and 3,k-periacene series (k=2–7) and compare indicators of polyradical character in the lowest-energy singlet states to those observed for oligoacene molecules. The singlet states in larger circumacene and periacene molecules display the same polyradical characteristics observed in oligoacenes, with the onset of this behavior occuring at smallest k for periacenes, followed by the circumacenes and then the oligoacenes. However, the unpaired electron density that accumulates along the zig-zag edge of the circumacenes is slightly less than that which accumulates in the oligoacenes, while periacenes clearly exhibit the greatest build-up of unpaired electron density in this region.</p></div></div></div> | J. Wayne Mullinax; Elvis Maradzike; Lauren N. Koulias; Mohammad Mostafanejad; Evgeny Epifanovsky; Gergely Gidofalvi; Eugene DePrince | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74357337d6c16bfe26b9e/original/a-heterogeneous-cpu-gpu-algorithm-for-variational-two-electron-reduced-density-matrix-driven-complete-active-space-self-consistent-field-theory.pdf |
6154b426ef08e6e51d1d0bfc | 10.26434/chemrxiv-2021-65skk | Mechanistic insights of key host proteins and potential repurposed inhibitors regulating SARS-CoV-2 pathway | The emergence of pandemic situations originated from SARS-CoV-2 and its new variants created worldwide medical emergencies. Due to the non-availability of efficient drugs and vaccines, hundreds of thousands of people succumbed to death intoxicated by this virus. At these emergency hours, repurposing existing drugs can effectively treat patients critically infected by SARS-CoV-2. Using a high-throughput screening approach, we validated a list of potential repurposed drugs, like Nafamostat, Camostat, Silmitasertib, Valproic acid, Zotatifin, and essential host target proteins HDAC2, eIF4E2, CSK22, that are essential for viral mechanism. We determined multiple dissociation pathways of repurposed drugs, suggesting the availability of sub pockets within the host target proteins. We showed the preferential residues involved in the (un)binding kinetics of the ligands correlated to the underlying mechanism of the host protein activity. Interestingly, the residues we obtained for HDAC2 and CSK22 target proteins, which we highlighted, are also involved in the catalytic activity. The mechanistic insight presented in this work is envisaged to help use these key host proteins and potential repurposed drugs as a treatment for the SARS-CoV-2 virus. | Debabrata Pramanik; Aiswarya Pawar; Sudip Roy ; Jayant K Singh | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6154b426ef08e6e51d1d0bfc/original/mechanistic-insights-of-key-host-proteins-and-potential-repurposed-inhibitors-regulating-sars-co-v-2-pathway.pdf |
62b96950e84dd18ca70542a8 | 10.26434/chemrxiv-2022-cgqd3-v2 | Pore Topology Analysis in Porous Molecular Systems | Porous molecular materials are constructed from molecules that assemble in the solid-state such
that there are cavities or an interconnected pore network. It is challenging to control the assembly
of these systems, as the interactions between the molecules are generally weak, and subtle changes
in the molecular structure can lead to vastly different intermolecular interactions and subsequently
different crystal packing arrangements. Similarly, the use of different solvents for crystallisation,
or the introduction of solvent vapour, can result in different polymorphs and pore networks being
formed. It is difficult to uniquely describe the pore networks formed, and thus we analysed 1033
crystal structures of porous molecular systems to determine the underlying topology of their void
spaces and potential guest diffusion networks. Material-agnostic topology definitions are applied.
We use the underlying topological nets to examine whether it is possible to apply isoreticular design
principles to porous molecular materials. Overall, our automatic analysis of a large data set gives us
the opportunity to gain a general insight into the relationships between molecular topologies and the
topological nets of their pore network. We show that while porous molecular systems tend to pack
similarly to non-porous molecules, the topologies of their pore distributions resemble those of more
prominent porous materials, such as MOFs and COFs. | Verity Anipa; Andrew Tarzia; Kim Jelfs; Eugeny Alexandrov; Matthew Addicoat | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b96950e84dd18ca70542a8/original/pore-topology-analysis-in-porous-molecular-systems.pdf |
6674e73cc9c6a5c07aff53e8 | 10.26434/chemrxiv-2024-vqk19 | Intramolecular C-H Functionalization of alpha-Alkyl-alpha-diazoesters towards the Synthesis of Lactones | Intramolecular C-H functionalization was achieved using rhodium-catalysis with alpha-alkyl-alpha-diazoesters. Dirhodium tetratriphenylacetate (Rh2(TPA)4), a sterically bulky achiral catalyst was found to enable the formation of lactones. Alkyl gamma-lactones were synthesized in excellent yields and diastereoselectivity, and a diverse array of disubstituted lactones (gamma-, delta-, epsilon-) were synthesized with good yields and diastereoselectivity. This chemistry was extended to intramolecular C-H insertion in late-stage functionalization with an excellent regio- and diastereoselectivity. | Bijaya Bagale; Aubree Nolan; Elizabeth Heuser; Jeffrey Mighion | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6674e73cc9c6a5c07aff53e8/original/intramolecular-c-h-functionalization-of-alpha-alkyl-alpha-diazoesters-towards-the-synthesis-of-lactones.pdf |
60c74eaa337d6c7580e27fe9 | 10.26434/chemrxiv.12780044.v1 | Radical Tropolone Biosynthesis | <div>
<div>
<div>
<p>Non-heme iron (NHI) enzymes perform a variety of oxidative rearrangements to advance simple building blocks toward
complex molecular scaffolds within secondary metabolite pathways. Many of these transformations occur with selectivity
that is unprecedented in small molecule catalysis, spurring an interest in the enzymatic processes which lead to a particular
rearrangement. In-depth investigations of NHI mechanisms examine the source of this selectivity and can offer inspiration
for the development of novel synthetic transformations. However, the mechanistic details of many NHI-catalyzed
rearrangements remain underexplored, hindering full characterization of the chemistry accessible to this functionally diverse
class of enzymes. For NHI-catalyzed rearrangements which have been investigated, mechanistic proposals often describe
one-electron processes, followed by single electron oxidation from the substrate to the iron(III)-hydroxyl active site species.
Here, we examine the ring expansion mechanism employed in fungal tropolone biosynthesis. TropC, an α-ketoglutarate-
dependent NHI dioxygenase, catalyzes a ring expansion in the biosynthesis of tropolone natural product stipitatic acid
through an under-studied mechanism. Investigation of both polar and radical mechanistic proposals suggests tropolones
are constructed through a radical ring expansion. This biosynthetic route to tropolones is supported by X-ray crystal structure
data combined with molecular dynamics simulations, alanine-scanning of active site residues, assessed reactivity of putative
biosynthetic intermediates, and quantum mechanical (QM) calculations. These studies support a radical ring expansion in
fungal tropolone biosynthesis.
</p>
</div>
</div>
</div> | Tyler
J. Doyon; Kevin Skinner; Di Yang; Leena Mallik; Troy Wymore; Markos Koutmos; Paul M. Zimmerman; Alison Narayan | Bioorganic Chemistry; Natural Products; Biochemistry; Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eaa337d6c7580e27fe9/original/radical-tropolone-biosynthesis.pdf |
657a1937bec7913d27876ead | 10.26434/chemrxiv-2023-z94lv | 1,4-Dihydropyridine Anions as Potent Single-Electron Photoreductants | Organic anions offer a promising route for promoting difficult single-electron reductions, owing to their strongly reducing excit-ed states that can be accessed under visible light irradiation. This report describes the use of simple 1,4-dihydropyridine anions as a general platform for promoting single-electron photoreductions. In the presence of a mild base, 1,4-dihydropyridines were shown to effectively promote the hydrodechlorination and borylation of aryl chlorides and the photodetosylation of N–Tosyl aromatic amines under visible light irradiation. | Prasadi Gallage; Mary McKee; Spencer Pitre | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657a1937bec7913d27876ead/original/1-4-dihydropyridine-anions-as-potent-single-electron-photoreductants.pdf |
60c74649842e65f4e0db27b4 | 10.26434/chemrxiv.11086460.v1 | N–H Chirality in Folded Peptide LK7β is Governed by the Cα–H Chirality | Recent chiral sum-frequency generation vibrational spectroscopy (cSFG-VS) measurements revealed that the two N-H stretching modes in the 3000-3500 cm-1 range in folded protein and peptide exhibit chiral characteristics. Here we report the first phase-resolved sub-wavenumber high-resolution broadband SFG-VS (HR-BB-SFG-VS) measurement of the LK7β peptide. The results show that this chiral N-H band consists of four, instead of two, distinctive peaks, and they are with two groups of opposite spectral phases. Moreover, the phases of these N-H peaks completely flip from the L-LK7β to the D-LK7β peptide, suggesting that the chirality of the N-H in the folded LK7β peptide is completely governed by the chirality of the Cα–H of the amino acids. This discovery provides clue on why proteins in nature are composed of α-amino acids rather than β- or γ-amino acids, and may help us understand the question on the origin of life. | Xiaohua Hu; Li Fu; jian hou; yuening zhang; Zhen Zhang; Hongfei Wang | Biophysical Chemistry; Interfaces; Spectroscopy (Physical Chem.); Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74649842e65f4e0db27b4/original/n-h-chirality-in-folded-peptide-lk7-is-governed-by-the-c-h-chirality.pdf |
60c747e8702a9b540a18ae84 | 10.26434/chemrxiv.11815935.v1 | Meso-Architecture Block Copolymers with High Surface Area Styrene-Bridged Organosilica Particles as Constituent for the Stimuli-Responsive Remediation of Water | The development of drugs for birth-control has changed society, and they are used by billions of woman on an every day basis. As for every mass product, there are problems associated with the waste it causes. One has found that residues of hormones in the urine of woman cannot be removed sufficiently from waste-water and this, in-turn, has already observable and undesired consequences in the biosphere. Apart from the removal of drugs, one is in general seeking new methods for the removal of hydrophobic impurities from waste-water. An ideal system would quantitatively take up the impurity, entrap it followed by preferably simple separation. Finally, one wants to reuse the absorbent, which implies the possibility for regeneration and recycling. Such as complex set of tasks requires a relatively complex materials architecture. Functional organic polymers with high affinity towards the drug, with stable open porosity and high surface area, stimuli-responsive properties and in the form of colloidal dispersions could do the job. Unfortunately, such a system does not exist. We solved this problem by generating mesoporous organosilica nanoparticles, which are monomers at the same time. Initiation of the polymerization reaction by surface-bound pore-walls leads to the formation of a special type of block-copolymer. The pore-walls are covered by the polymer, which cannot leach. An orthogonal modification was achieved by modification of the external surfaces of the particles with a thermoresponsive polymer by click-chemistry. The final core-shell system was able to remove hydrophobic molecules such as the hormone progesterone from water. A change of temperature induces the collapse of the thermoresponsive polymer, which closes the pores and induces aggregation of the particles. After separation of the particles, and thus also the entrapped impurity, from the solvent, one can re-open the pores, which leads to a release of the adsorbed compound(s). | Dennis Kollofrath; Marcel Geppert; Sebastian Polarz | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747e8702a9b540a18ae84/original/meso-architecture-block-copolymers-with-high-surface-area-styrene-bridged-organosilica-particles-as-constituent-for-the-stimuli-responsive-remediation-of-water.pdf |
6113e2dd4cb47935332cfeb7 | 10.26434/chemrxiv-2021-szmqs | Radical–Anion Coupling Through Reagent Design: Hydroxylation of Aryl Halides | The design and development of an oxime-based hydroxylation reagent, which can chemoselectively convert aryl halides (X = F, Cl, Br, I) into phenols under operationally simple, transition-metal-free conditions is described. Key to the success of this approach was the identification of a reducing oxime anion which can interact and couple with open-shell aryl radicals. Experimental and computational studies support the proposed radical-nucleophilic substitution chain mechanism. | Andrew J. Greener; Patrycja Ubysz; Will Owens-Ward; George Smith; Adrian C. Whitwood; Michael J. James | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6113e2dd4cb47935332cfeb7/original/radical-anion-coupling-through-reagent-design-hydroxylation-of-aryl-halides.pdf |
61975c6d62372e6a65bf7ab0 | 10.26434/chemrxiv-2021-gsq3b | Triplet Dynamic Nuclear Polarization of Guest Molecules through Induced Fit in a Flexible Metal-Organic Framework | Dynamic nuclear polarization utilizing photoexcited triplet electrons (triplet-DNP) has great potential for room-temperature hyperpolarization of nuclear spins. However, the polarization transfer to molecules of interest remains a challenge due to the fast spin relaxation and weak interaction with target molecules at room temperature in conventional host materials. Here, we demonstrate the first example of DNP of guest molecules in a porous material at around room temperature by utilizing the induced-fit-type structural transformation of a crystalline yet flexible metal-organic framework (MOF). In contrast to the usual hosts, 1H spin-lattice relaxation time becomes longer by accommodating a pharmaceutical model target 5-fluorouracil as the flexible MOF changes its structure upon guest accommodation to maximize the host-guest interactions. Combined with triplet-DNP and cross-polarization, this system realizes an enhanced 19F-NMR signal of guest target molecules at around room temperature. | Saiya Fujiwara; Naoto Matsumoto; Koki Nishimura; Nobuo Kimizuka; Kenichiro Tateishi; Tomohiro Uesaka; Nobuhiro Yanai | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61975c6d62372e6a65bf7ab0/original/triplet-dynamic-nuclear-polarization-of-guest-molecules-through-induced-fit-in-a-flexible-metal-organic-framework.pdf |
6229dcb8daa4fb095186d869 | 10.26434/chemrxiv-2022-7nns6 | Unexpected Fluorescent Behavior of Maleimide Based Zwitterionic Molecule: Aggregation Induced Emission | A novel traditional fluorophore free bright blue light emitting small organic molecule with aqueous solubility consisting N-substituted maleimide with zwitterionic side chain was explored. The combined experimental and theoretical studies revealed that the fluorescence originated due to the aggregation of N-substituted maleimide molecules named N-(ethyl sulfobetaine) maleimide (M) in solution. It was also observed that the aggregation induced emission (AIE) was originated after certain threshold concentration which was confirmed by both the experiment and the first principal calculations. The aggregation of the M molecule in solution happens predominantly due to nonbonded electrostatic interaction. This finding may add a new dimension to broad sensing application with a feasible molecular strategy. | Dr. Ishita Mukherjee | Physical Chemistry; Photochemistry (Physical Chem.); Solution Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6229dcb8daa4fb095186d869/original/unexpected-fluorescent-behavior-of-maleimide-based-zwitterionic-molecule-aggregation-induced-emission.pdf |
675b11147be152b1d0c282b2 | 10.26434/chemrxiv-2024-hl427-v4 | Development of an Automated Workflow for Screening the Assembly and Host-Guest Behaviour of Metal-Organic Cages towards Accelerated Discovery | Metal-organic cages (MOCs) are a class of self-assembled materials with promising applications in chemical purifications, sensing, and catalysis. Their potential is, however, hampered by challenges in the targeted design of MOCs with desirable properties. MOC discovery is thus often reliant on trial-and-error approaches and brute-force manual screening, which are time-consuming, costly and material-intensive. Translating the synthesis and property screening of MOCs to an automated workflow is therefore attractive, to both accelerate discovery and provide the datasets crucial for data-led approaches to accelerate MOC discovery and to realize their targeted properties for specific applications. Here, an automated workflow for the streamlined assembly and property screening of MOCs was developed, incorporating automated high-throughput screening of variables pertinent to MOC synthesis, data curation and automated analysis, and development of a host:guest assay to rapidly assess binding behavior. Computational modelling supplemented this automated experimental workflow for post priori rationalization of experimental outcomes. This study lays the groundwork for future large-scale MOC screening: from a relatively modest screen of 24 precursor combinations under one set of reaction conditions, 3 clean MOC species were identified, and subsequent screening of their host:guest behavior highlighted trends in binding and the identification of potential applications in molecular separations. | Annabel Basford; Aaron Hero Bernardino; Paula Teeuwen; Benjamin Egleston; Joshua Humphreys; Kim Jelfs; Jonathan Nitschke; Imogen Riddell; Rebecca Greenaway | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675b11147be152b1d0c282b2/original/development-of-an-automated-workflow-for-screening-the-assembly-and-host-guest-behaviour-of-metal-organic-cages-towards-accelerated-discovery.pdf |
60c74b5b469df48318f43ee4 | 10.26434/chemrxiv.12318398.v1 | Migratory Reductive Cross-Coupling via Dual Nickel Metathesis | <div>Cross-electrophile coupling has been developed into a practical approach for the construction of carbon-</div><div>carbon bonds, wherein nickel catalysis has been widely employed. Mechanistically, a catalytic cycle involving</div><div>sequentially selective oxidative addition or radical chain process is proposed. Although the catalytic cycle of dual nickel metathesis has been discussed in several important works, none thinks this pathway is possible. In this manuscript, we present a thorough mechanistic study by a series of designed experiments toward the nickel-catalyzed migratory reductive cross-coupling. The results suggest that a catalytic cycle involving two organonickel(II) species metathesis as a key step, operates in this reaction. Moreover, we provide a discussion on the difference between the nickel-catalyzed migratory reductive cross-couplings and the classical ones. Additionally, based on the mechanistic finding, a new catalytic system has also been developed, which allows the use of electron-deficient aryl halides as starting materials, affording the migratory cross-coupling products efficiently.</div> | Yuqiang Li; Binzhi Zhao; Long Peng; Guoyin Yin | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b5b469df48318f43ee4/original/migratory-reductive-cross-coupling-via-dual-nickel-metathesis.pdf |
6632941791aefa6ce1e6f2f8 | 10.26434/chemrxiv-2024-lprs0 | Bioorthogonal Polymerization of Coiled-Coil Peptides | Peptides capable of forming homotetrameric coiled-coil bundles are utilized as the monomeric building blocks (“bundlemers”) to synthesize hybrid polymers consisting of covalently linked coiled-coil microdomains with regularly spaced ethylene glycol repeats via tetrazine ligation with trans-cyclooctene. We confirm the formation of long, semiflexible rods with a Kuhn length of 6 - 7 nm and a molecular weight of 100 - 3,000 kDa. Polymerization at tetrazine concentrations > 5 mM results in the formation of mechanically robust hydrogels with defined viscoelastic properties through chain entanglements. Copolymerization of coiled-coil peptides with distinct composition and thermal stability gives rise to hydrogels that are thermally tractable. Solid-to-fluid transition occurs when one of the coiled-coil repeats melts. Upon cooling, solid-like properties are partially recovered through intermolecular association of the helical peptides. Overall, tetrazine ligation has enabled the covalent polymerization of self-assembled coiled-coil motifs for the establishment of protein-like linear polymers with unprecedent molecular weight. | Hanyuan Gao; Tianren Zhang; Matthew Langenstein; Weiran Xie; Samiksha Udan; Zihan Zhang; Jeffery Saven; Shi Bai; Darrin Pochan; Joseph Fox; Xinqiao Jia | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6632941791aefa6ce1e6f2f8/original/bioorthogonal-polymerization-of-coiled-coil-peptides.pdf |
656dd7655bc9fcb5c904bd2e | 10.26434/chemrxiv-2023-n1wv0 | Copper/BINOL-Catalyzed Enantioselective C-H Functionalization towards Planar Chiral Ferrocenes Under Mild Conditions | Copper-catalyzed enantioselective C–H activation proceeds through inner-sphere mechanism remains a huge challenge. Herein, a copper-catalyzed enantioselective C−H alkynylation with terminal alkynes assisted by 8-aminoquinoline using readily available (S)-BINOL as chiral ligand was disclosed. The reaction proceeded under mild conditions with a catalytic amount of copper salt, providing a range of chiral ferrocenes in good yields and enantioselectivities (0 oC, up to 77% yield and 94% ee). The alteration of stoichiometric chemical oxidant with renewable electricity is also feasible at ambient temperature, demonstrating the robustness of this copper/BINOL catalysis. Notably, this is the first enantioselective cupraelectro-catalyzed C-H activation reaction. Gram-scale synthesis, versatile transformations, and application of the resulting oxazoline-olefin ligand in asymmetric synthesis also highlight the utility of the protocols. | Zhuo-Zhuo Zhang; Qi-Jun Yao; Gang Zhou; Qiang Yue; Bing-Feng Shi | Organic Chemistry; Catalysis; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656dd7655bc9fcb5c904bd2e/original/copper-binol-catalyzed-enantioselective-c-h-functionalization-towards-planar-chiral-ferrocenes-under-mild-conditions.pdf |
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