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63a09f52963bf330279f534d | 10.26434/chemrxiv-2022-zn2th | O-Methyl-N-Nitroisourea as a NCO Surrogate in Cu-Catalyzed Alkane C-H isocyanation. A Masked Isocyanate Strategy. | The Cu-catalyzed C-H activation of alkanes in the presence of O-methyl-N-nitroisourea affords a facile entry to O-methyl-N-alkylnitroisoureas, shelf stable and benign isocyanate precursors. The latter is then readily converted into carbamates and ureas via an uncommon chloride-mediated demethylation process. O-methyl-N-nitroisourea is available in two steps and large-scale from urea and constitutes an easy to handle NCO surrogate. The methodology has also been applied to the synthesis of a methylisocyanate (MIC) precursor, a valuable synthon for pharmaceutical and agrochemical purposes and for the post-functionalization of a low density polyethylene. | Yannick LANDAIS; Jonathan Lusseau; Frédéric Robert | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Bond Activation; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a09f52963bf330279f534d/original/o-methyl-n-nitroisourea-as-a-nco-surrogate-in-cu-catalyzed-alkane-c-h-isocyanation-a-masked-isocyanate-strategy.pdf |
63f0bb1cfcfb27a31ffe61c0 | 10.26434/chemrxiv-2023-qs2w0 | iEdgeDTA: integrated edge information and 1D graph convolutional neural networks for binding affinity prediction | Drug repurposing, where an existing low-risk drug is applied for new indications, becomes more attractive in drug development as drug discovery is very costly and time-consuming. However, the wet-lab testing process to find a drug candidate for a new purpose from its possible binding to a protein is still expensive and laborious due to the available vast quantity of drugs and target proteins. This study aims to leverage artificial intelligence to aid drug repurposing by utilizing drug-protein interaction data and estimating their binding affinity. In this work, we propose an estimation approach that employs a graph-based deep learning technique and enhances prediction accuracy by incorporating the compound's edge information as a multi-dimensional feature. In addition, we used a pre-trained model for protein embedding and graph operation over a 1D protein sequence to overcome a fixed-length problem in the language model task and also incorporated the global feature of the protein. We evaluated the performance of our model in the same benchmark datasets using a variety
of matrices, and the results show that our model can achieve the best prediction result compared to
other state-of-the-art models while at the same time requiring no contact-map information compared
to recent graph-based works
Availability: https://github.com/cucpbioinfo/iEdgeDTA | Natchanon suviriyapaisal; Duangdao wichadakul | Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f0bb1cfcfb27a31ffe61c0/original/i-edge-dta-integrated-edge-information-and-1d-graph-convolutional-neural-networks-for-binding-affinity-prediction.pdf |
657c2df566c13817293c9746 | 10.26434/chemrxiv-2023-s7m48 | Incommensurate Modulations and Perovskite Growth in LaxSr2-xMnO4−δ Affecting Solid Oxide Fuel Cell Conductivity | Ruddlesden-Popper LaxSr2−xMnO4−δ materials are interesting symmetric solid oxide fuel cell electrodes due to their good redox stability, mixed ionic and electronic conducting behavior and thermal expansion that matches well with common electrolytes. In reducing environments - as at a solid oxide fuel cell anode - the x = 0.5 member, i.e.
La0.5Sr1.5MnO4−δ, has a much higher total conductivity than compounds with a different La/Sr ratio, although all those compositions have the same K2NiF4-type I4/mmm
structure. The origin for this conductivity difference is not yet known in literature. Now, a combination of in-situ and ex-situ 3D electron diffraction, high-resolution imaging, energy-dispersive X-ray analysis and electron energy-loss spectroscopy uncovered clear differences between x=0.25 and x=0.5 in the pristine structure, as well as in the
transformations upon high-temperature reduction. In La0.5Sr1.5MnO4−δ, Ruddlesden-Popper n=2 layer defects and an amorphous surface layer are present, but not in
La0.25Sr1.75MnO4−δ. After annealing at 700°C in 5% H2/Ar, La0.25Sr1.75MnO4−δ transforms to a tetragonal 2D incommensurately modulated structure with modulation vectors q1 = 0.2848(1) · (a* +b*) and q2 =0.2848(1) · (a* -b*), whereas La0.5Sr1.5MnO4−δ only partially transforms to an orthorhombic 1D incommensurately modulated structure, with q = 0.318(2) · (a* - b*). Perovskite domains grow at the crystal edge at 700°C in 5% H2 or vacuum, due to the higher La concentration on the surface compared to the bulk, which leads to a different thermodynamic equilibrium. Since it is known that a lower degree of oxygen vacancy ordering and a higher amount of perovskite blocks enhance oxygen mobility, those differences in defect structure and structural transformation upon reduction, might all contribute to the higher conductivity of La0.5Sr1.5MnO4−δ in solid oxide fuel cell anode conditions compared to other La/Sr ratios. | Daphne Vandemeulebroucke; Maria Batuk; Amirhossein Hajizadeh; Myriam Wastiaux; Pascal Roussel; Joke Hadermann | Inorganic Chemistry; Energy; Solid State Chemistry; Fuel Cells; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657c2df566c13817293c9746/original/incommensurate-modulations-and-perovskite-growth-in-lax-sr2-x-mn-o4-affecting-solid-oxide-fuel-cell-conductivity.pdf |
60c73e994c8919d320ad1e16 | 10.26434/chemrxiv.6453302.v2 | Facile Synthesis of a Diverse Library of Mono-3-substituted β-Cyclodextrin Analogues | We have described simple, high-yield, protocols, which require only commonly accessible equipment, to synthesize a wide range of β-CD derivatives mono-substituted at the secondary face. These derivatives may be useful in their own right, and they are also scaffolds for further modification, and examples of the far broader array of derivatives that may be accessed by these procedures. | Kathryn Kellett; Brendan M. Duggan; Michael Gilson | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Supramolecular Chemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2018-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e994c8919d320ad1e16/original/facile-synthesis-of-a-diverse-library-of-mono-3-substituted-cyclodextrin-analogues.pdf |
660e992821291e5d1d0ae9c3 | 10.26434/chemrxiv-2024-dm4r1-v2 | Electrochemical Regioselective C(sp2)-H Bond Chalcogenation of Pyrazolo[1,5-a]pyrimidines via Radical Cross Coupling at Room Temperature | In this report, we disclose an electrochemical approach for the C(sp2)-H chalcogenation of pyrazolo[1,5-a]pyrimidines at room temperature via radical cross-coupling reaction. The reaction takes place within an undivided cell employing graphite electrodes, with TBABF4 acting as the supporting electrolyte. This technique offers a rapid, oxidant-free, and environmentally conscious protocol for achieving regioselective chalcogenation specifically at the C3 position of pyrazolo[1,5-a]pyrimidines. Furthermore, the procedure uses only 0.5 equivalents of diaryl chalcogenides which underscores the atom economy of the protocol. Key attributes of this methodology include mild reaction conditions, short reaction time, utilization of cost-effective electrode materials, and reliable achievement of yields ranging from good to excellent and environmentally friendly reaction conditions. Cyclic voltammetry studies and radical quenching experiments suggest a radical pathway for the reaction mechanism. | Abhinay Chillal; Rajesh Bhawale; Siddharth Sharma; Umesh Kshirsagar | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660e992821291e5d1d0ae9c3/original/electrochemical-regioselective-c-sp2-h-bond-chalcogenation-of-pyrazolo-1-5-a-pyrimidines-via-radical-cross-coupling-at-room-temperature.pdf |
623d94122c501022208804cf | 10.26434/chemrxiv-2022-0ps7t | A donor-acceptor Stenhouse adduct displaying reversible
photoswitching in water and neuronal activity | The interest in the photochromism and functional applications of donor-acceptor Stenhouse adducts (DASAs) soared in recent years, owing to their outstanding advantages and flexible design. However, their low solubility and irreversible conversion in aqueous solutions hampered exploring DASAs for biology and medicine. It is notably unknown whether the barbiturate electron acceptor group retains the pharmacological activity of drugs like phenobarbital, which targets γ-aminobutyric acid (GABA) type A receptors (GABAARs) in the brain. Here, we have developed the model compound DASA-barbital based on a scaffold of red-switching second-generation DASAs and we demonstrate that it is active in GABAARs and alters the neuronal firing rate in a physiological medium at neutral pH. DASA-barbital can also be reversibly photoswitched in acidic aqueous solutions using cyclodextrin, an approved ingredient of drug formulations. These findings clear the path towards the biological applications of DASAs and to exploit the versatility displayed in polymers and materials science. | Rossella Castagna; Galyna Maleeva; Deborah Pirovano; Carlo Matera; Pau Gorostiza | Biological and Medicinal Chemistry; Organic Chemistry; Photochemistry (Org.); Chemical Biology; Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623d94122c501022208804cf/original/a-donor-acceptor-stenhouse-adduct-displaying-reversible-photoswitching-in-water-and-neuronal-activity.pdf |
61548212093c9a5dd76d062c | 10.26434/chemrxiv-2021-9htkb | Photophysical Properties of Benzophenone Based TADF Emitters in Relation to Their Molecular Structure | Thermally activated delayed fluorescence (TADF) materials are commonly used in various apparatus, including organic light emitting device (OLED)-based displays, as they remarkably improve the internal quantum efficiencies (IQE). Alt-hough there is a wide range of donor-acceptor based compounds possessing TADF properties, in this computational study we investigated TADF and some non-TADF chromophores, containing benzophenone or its structural derivatives as the acceptor core, together with various donor moieties. Following the computational modeling of the emitters, several excited state properties, such as the absorption spectra, singlet-triplet energy gaps (∆EST), natural transition orbitals (NTO) and the topological ΦS indices, have been computed. Along with the donor-acceptor torsion angles and spin-orbit coupling (SOC) values, these descriptors have been utilized to investigate potential TADF efficiency. Our study has shown that on the one hand, our photophysical/structural descriptors and computational methodologies predict the experi-mental results quite well, on the other hand, our extensive benchmark can be useful to pinpoint the most promising func-tionals and descriptors for the study of benzophenone based TADF emitters. | Ekin Esme Bas; Pelin Ulukan; Antonio Monari; Viktorya Aviyente; Saron Catak | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Quantum Mechanics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61548212093c9a5dd76d062c/original/photophysical-properties-of-benzophenone-based-tadf-emitters-in-relation-to-their-molecular-structure.pdf |
624fd94402f7017713db2ae3 | 10.26434/chemrxiv-2022-0v30j-v2 | A Single Site Mutation Induces a Water-Mediated
Promiscuity in Lignin Breaking Cytochrome P450GcoA | Cytochrome P450 GcoA is an enzyme that catalyses the guaiacol unit of lignin during the lignin breakdown via aryl-O-demethylation reaction. This reaction is intriguing and is of commercial importance for its potential application in the production of biofuel and plastic from biomass feedstock. Recently, the F169A mutation in the P450 GcoA elicits a promiscuous activity for syringol while maintaining the native activity for guaiacol. Using comprehensive MD simulations and hybrid QM/MM calculations we address, herein, the origin of promiscuity in P450 GcoA and its relevance to the specific activity toward lignin-derived substrates. Our study shows a crucial role of an aromatic dyad, F169, and F395 through regulating the water access
to the catalytic center. The F169A mutation opens a water aqueduct and hence increases the native activity for the G-lignin. We show that syringol binds very tightly in the WT enzyme which blocks the conformational rearrangement needed for the second step of O-demethylation. The F169A creates an extra room favoring the conformational rearrangement in the demethylated syringol (3MC) and second dose of the dioxygen insertion. Therefore, using MD simulations and complemented by thorough QM/MM calculations, our study shows how does a single site mutation re-architect active site engineering for promiscuous syringol activity. | Warispreet Singh; Sonia Santos; Paul James; Gary Black; Meilan Huang ; Kshatresh Dubey | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Biocatalysis; Bioorganometallic Chemistry; Catalysis | CC BY 4.0 | CHEMRXIV | 2022-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624fd94402f7017713db2ae3/original/a-single-site-mutation-induces-a-water-mediated-promiscuity-in-lignin-breaking-cytochrome-p450gco-a.pdf |
636fc4e6bef5d41287535b50 | 10.26434/chemrxiv-2022-s16mm | Optofluidic Convection around Au Nanorods and Nanospheres by Photothermal Heating: Effect of Nanoparticle Geometry and Boundary Conditions | Laser mediated heat transfer and optofluidic nano-scale convection can be exploited in the photothermal applications of plamonic nanoparticles in different micro-environment. In this work, heat transfer and fluid flow around Au nanospheres and nanorods in water medium under continuous and pulsed wave laser irradiance was investigated using an FEM based numerical framework. Au nanospheres of a wide range of diameter: 40 nm ≤ Diameter (D) ≤ 180 nm and nanorods with varying aspect ratio (1 ≤ Aspect ratio (A) ≤ 5) and orientation (0o ≤ θ ≤ 90o, ϕ = 0o, 90o) with respect to the incident EM radiation were investigated for continuous wave (CW) and pulsed wave laser. Relatively large Au nanorods dimensions similar to the models were also synthesized. The numerical results were validated by comparison with the experimental optical cross-section of the synthesized nanorods. It was found that although nanorods can attain much higher temperature than nanospheres, orientation of a nanorod is an important factor to be carefully considered in applications. In micro-scale spherical and hemispherical confinements (diameter < 14.4 μm) convective velocity fields around nanoparticles were determined for slip and no-slip condition on the confining walls. It was found that slip boundary condition on the confining walls has a moderate effect on the strength of the flow field. While, the effect of the proximity of the nanoparticle from the walls is considerable. | Rituraj Borah; Millen Samantaray; Ashish Kumar; Anusha Desai; Fan-Gang Tseng | Materials Science; Nanoscience; Nanofluidics; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY 4.0 | CHEMRXIV | 2022-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636fc4e6bef5d41287535b50/original/optofluidic-convection-around-au-nanorods-and-nanospheres-by-photothermal-heating-effect-of-nanoparticle-geometry-and-boundary-conditions.pdf |
63ca9de207308ae2e7a093fa | 10.26434/chemrxiv-2023-8l10w | The Rational Design of Highly Potent and Selective Covalent MAP2K7 Inhibitors | The mitogen-activated protein kinase signaling cascade is conserved across eukaryotes from yeast to humans, where it plays a central role regulating activities including proliferation, differentiation, and stress responses. This pathway propagates external stimuli through a series of phosphorylation events, allowing external signals to influence metabolic and transcriptional activities. Within the cascade, MEK, or MAP2K, enzymes occupy a molecular crossroads situated immediately upstream to significant signal divergence and cross-talk. One such kinase, MAP2K7, also known as MEK7 and MKK7, is a protein of great interest in the molecular pathophysiology underlying pediatric T-cell acute lymphoblastic leukemia. Herein, we describe the rational design, synthesis, evaluation, and optimization of a novel class of irre-versible MAP2K7 inhibitors. With a streamlined one-pot synthesis, favorable in vitro potency and selectivity, as well as promising cellular activity, this novel class of compounds wields promise as a powerful tool in the study of pediatric T-ALL | Karl Scheidt; Dalton Kim; Meghan Orr; Ada Kwong; Kristine Deibler; Hasan Munshi; Cory Bridges; Taylor Chen; Xiaoyu Zhang; Daniel Lacorazza | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ca9de207308ae2e7a093fa/original/the-rational-design-of-highly-potent-and-selective-covalent-map2k7-inhibitors.pdf |
628be10c5d94858181cc1536 | 10.26434/chemrxiv-2022-krng1 | Interpretable Deep-Learning Unveils Structure-Property Relationships in Polybenzenoid Hydrocarbons | In this work, interpretable deep learning was used to identify structure-property relationships governing the HOMO-LUMO gap and relative stability of polybenzenoid hydrocarbons (PBHs). To this end, a ring-based graph representation was used. In addition to affording reduced training times and excellent predictive ability, this representation could be combined with a subunit-based perception of PBHs, allowing chemical insights to be presented in terms of intuitive and simple structural motifs. The resulting insights agree with conventional organic chemistry knowledge and electronic structure-based analyses, and also reveal new behaviors and identify influential structural motifs. In particular, we evaluated and compared the effects of linear, angular, and branching motifs on these two molecular properties, as well as explored the role of dispersion in mitigating torsional strain inherent in non-planar PBHs. Hence, the observed regularities and the proposed analysis contribute to a deeper understanding of the behavior of PBHs and form the foundation for design strategies for new functional PBHs. | Tomer Weiss; Alexandra Wahab; Alex M. Bronstein; Renana Gershoni-Poranne | Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628be10c5d94858181cc1536/original/interpretable-deep-learning-unveils-structure-property-relationships-in-polybenzenoid-hydrocarbons.pdf |
60c745a8bdbb8934a0a38a7f | 10.26434/chemrxiv.9808355.v2 | Catalytic Asymmetric Radical-Polar Crossover Hydroalkoxylation | Asymmetric intramolecular hydrofunctionalization of tertiary allylic alcohols is described. This metal hydride-mediated catalytic radical-polar crossover reaction delivers corresponding epoxides in good to high enantioselectivity and constitutes the first example of asymmetric hydrogen atom transfer-initiated process. A series of modified cobalt salen complexes has proven optimal for achieving good efficiency and asymmetric induction. Experimental data suggest that cationic cobalt complexes are involved in enantio-determining step, where cation–π interactions in the catalyst contribute to the asymmetric induction. | Christopher Discolo; Eric Touney; Sergey Pronin | Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745a8bdbb8934a0a38a7f/original/catalytic-asymmetric-radical-polar-crossover-hydroalkoxylation.pdf |
66504fa721291e5d1d25b8fd | 10.26434/chemrxiv-2024-vpw8x-v2 | Efficient Parahydrogen Induced 13C Hyperpolarization on a Microfluidic Device | We show the direct production and detection of 13C-hyperpolarized fumarate by parahydrogen-induced polarization (PHIP) in a microfluidic Lab-on-a-Chip (LoC) device and achieve 8.5% 13C polarization. This is the first demonstration of 13C-hyperpolarization of a metabolite by PHIP in a microfluidic device. LoC technology allows the culture of mammalian cells in a highly controlled environment, providing an important tool for the life sciences. In-situ preparation of hyperpolarized metabolites greatly enhances the ability to quantify metabolic processes in such systems by microfluidic NMR. PHIP of 1H nuclei has been successfully implemented in microfluidic systems, with mass sensitivities in the range of pmol √s. However, metabolic NMR requires high-yield production of hyperpolarized metabolites with longer spin life times than is possible with 1H. This can be achieved by transfer of the polarization onto 13C nuclei, which exhibit much longer T1 relaxation times. We report an improved microfluidic PHIP device, optimised using a finite element model, that enables the direct and efficient production of 13C hyperpolarized fumarate. | Sylwia Barker; Laurynas Dagys; Malcolm Levitt; Marcel Utz | Physical Chemistry; Analytical Chemistry; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66504fa721291e5d1d25b8fd/original/efficient-parahydrogen-induced-13c-hyperpolarization-on-a-microfluidic-device.pdf |
62f265d51ea5f6c0096e3c96 | 10.26434/chemrxiv-2022-jbzc5 | Probing the Separation Distance between Biological Nanoparticles and Cell Membranes Mimics Using Neutron Reflectometry with Sub-Nanometer Accuracy | Nanoparticle interactions with cellular membranes are controlled by molecular recognition reactions and regulate a multitude of biological processes, including virus infections, biological nanoparticle-mediated cellular communication, and drug delivery applications. Aided by the design of various supported cell membrane mimics, multiple methods have been employed to investigate these types of interactions, revealing information on nanoparticle coverage, interaction kinetics as well as binding strength; however, precise quantification of the separation distance across which these delicate interactions occur remains elusive. Here we demonstrate that carefully designed neutron reflectometry experiments combined with intricate theoretical modeling offer a means to quantify the distance separating biological nanoparticles from a supporting lipid bilayer (SLB) with sub-nanometer precision. The distance between the nanoparticles and SLBs was tuned by exploiting either direct adsorption or specific binding using DNA tethers with different conformations, revealing separation distances of around 1, 3, and 7 nm with nanometric accuracy. We also show that NR provides precise information on nanoparticle coverage, size distribution, material composition, and potential structural changes in the underlying planar SLB induced upon nanoparticle binding. The precision with which these parameters could be quantified should pave an attractive path for investigations of the interactions between nanoparticles and interfaces at length scales and resolutions that were previously inaccessible, but crucial for gaining in-depth understanding of the molecular recognition reactions responsible for the interactions between inorganic and biological nanoparticles with cellular membranes. | Antonius Armanious; Yuri Gerelli; Samantha Micciulla; Hudson Pace; Rebecca Welbourn; Mattias Sjöberg; Björn Agnarsson; Fredrik Höök | Physical Chemistry; Analytical Chemistry; Nanoscience; Biophysical Chemistry; Interfaces; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f265d51ea5f6c0096e3c96/original/probing-the-separation-distance-between-biological-nanoparticles-and-cell-membranes-mimics-using-neutron-reflectometry-with-sub-nanometer-accuracy.pdf |
66ac8dde01103d79c58bd9a1 | 10.26434/chemrxiv-2024-zhswk-v2 | When metal complexes evolve, and a minor species is the most active: the case of bis(phenanthroline)copper in the catalysis of glutathione oxidation and hydroxyl radical generation | Several copper-ligands, including 1,10-phenanthroline (Phen), have been investigated for anticancer purposes based on their capacity to bind excess Cu in cancer tissues and form redox active complexes able to catalyse the formation of reactive oxygen species (ROS), ultimately leading to oxidative stress and cell death. Glutathione (GSH) is a critical compound as it is highly concentrated intracellularly and can reduce and dissociate copper(II) from the ligand forming poorly redox-active copper(I)-thiolate clusters. Here we report that Cu-Phen2 speciation evolves in physiologically relevant GSH concentrations. Experimental and computational experiments suggest that at pH 7.4 mostly copper(I)-GSH clusters are formed, but a minor species of copper(I) bound to one Phen and forming ternary complexes with GSH (GS-Cu-Phen) is the redox active species, oxidizing quite efficiently GSH to GSSG and forming HO• radicals. This minor active species becomes more populated at lower pH, such as typical lysosomal pH 5, resulting in faster GSH oxidation and HO• production. Consistently, cell culture studies showed lower toxicity of Cu-Phen2 upon inhibition of lysosomal acidification. Overall, this study underscores that sub-cellular localisation can considerably influence the speciation of Cu-based drugs and that minor species can be the most redox- and biologically- active. | Enrico Falcone; Vincenzo Vigna; Hemma Schueffl; Francesco Stellato; Bertrand Vileno; Merwan Bouraguba; Gloria Mazzone; Olivier Proux; Silvia Morante; Petra Heffeter; Emilia Sicilia; Peter Faller | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ac8dde01103d79c58bd9a1/original/when-metal-complexes-evolve-and-a-minor-species-is-the-most-active-the-case-of-bis-phenanthroline-copper-in-the-catalysis-of-glutathione-oxidation-and-hydroxyl-radical-generation.pdf |
649266c4853d501c003d2267 | 10.26434/chemrxiv-2023-0616f | Lethal weapon IL: a nano-copper/tetraalkylphosphonium ionic liq-uid composite material with potent antibacterial activity | Ionic liquid (IL) based composite materials have shown great promise as antimicrobial coatings, owing to their inherent germicidal properties, as well as their ability to stabilize metal nanoparticles (NPs), which may serve as a secondary antimicrobial reservoir. Here, we show that tetraalkylphosphonium ILs (TAPILs) on their own can annihilate pathogens by interfering with their cell membranes; however, the nature of the alkyl substituents on the central P atom and the nature of the anion play decisive roles in determining their antimicrobial activities. Con-comitantly, TAPILs can stabilize copper nanoparticles (Cu NPs) generated directly within the IL matrices without the addition of any second-ary stabilizers. The composites thus generated were thoroughly characterized and shown to be far more lethal to E. coli than just the TAPILs. The antibacterial effect demonstrated by the composite created from P[6,6,6,8]Cl (TAPIL-2) was orders of magnitude more lethal to microbes in comparison with P[6,6,6,8]Cl or copper nanoparticles alone. Neither the parent TAPIL-2 nor composite-2 were compromised by ambient storage conditions over a period of months with regards to their bactericidal effects. The composite with the best performance (composite-2) also proved to be effective against a panel of selected microbes. SEM studies were conducted to image E. coli after exposure to the TAPILs or composite-2; with the latter, only bacterial debris were noticed post-exposure, indicating total bacterial annihilation. The killing kinetic assay and regression analyses for time-dependent bactericidal activity of composite-2 against E. coli and S. aureus demonstrated increase in log re-duction values over time, indicating the effectiveness of composite-2 in reducing the viable cell counts for both bacterial strains. Finally, Cu K-edge XANES was used to investigate the fate of Cu NPs within the composites, revealing oxidative disintegration of the Cu NPs within the TAPIL matrices over time, releasing charged copper ions and/or small copper clusters which interfere with the integrity and the permeability of E. coli cell membranes, inducing cell death. This was confirmed by SEM of bacterial preparations before and after exposure to both the TAPILs themselves as well as to the composites. Exposing E. coli to composite-2 causes complete cellular destruction, leaving behind cellular debris as the only visible organic matter. Thus, these TAPIL-based composites containing ‘ion reservoir’ metal NPs are potent antimicrobial materials, deserving additional research. | Abhinandan Banerjee; Bukola R. Aremu; Sima Dehghandokht; Rayan Salama; Hao Zhou; Sharon Lackie; Moutasem Seifi; Pierre Kennepohl; John Trant | Biological and Medicinal Chemistry; Chemical Engineering and Industrial Chemistry; Microbiology; Water Purification; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649266c4853d501c003d2267/original/lethal-weapon-il-a-nano-copper-tetraalkylphosphonium-ionic-liq-uid-composite-material-with-potent-antibacterial-activity.pdf |
676baaf9fa469535b9b7eb33 | 10.26434/chemrxiv-2024-jtfwd | LASSO for CALPHAD model selection enables data-efficient thermodynamic modeling: an application in thermochemical hydrogen production materials | Phenomenological CALPHAD (CALculation of PHAse Diagrams) models, widely used for multicomponent materials, often contain a considerable number of parameters and require fitting using data from a relatively small number of experimental measurements or theoretical calculations. Sometimes these parameters are introduced for the purpose of improving model fits but without clear physical justification, which leads to over-parameterized models with poor generalization performance. Automated approaches for optimal model selection based on the available data therefore become critical. In this work, a least absolute shrinkage and selection operator (LASSO)-based approach is developed for model selection by leveraging the linearity of the CALPHAD model with
respect to its parameters to convert the model selection and fitting to a LASSO minimization problem. We demonstrate its utility for thermodynamic modeling of thermochemical hydrogen (TCH) production materials, using lanthanum strontium manganite (LSM) as an example. Various TCH relevant properties, including oxygen stoichiometry as function of oxygen partial pressure, enthalpy of reduction, and entropy of reduction, are successfully predicted with reasonable accuracy using a minimal set of model parameters. Importantly, the model selection and fitting involve minimal human decision; it can therefore be applied to high-throughput DFT defect calculations and yield efficient workflows for TCH materials modeling and optimization. | Pinwen Guan; Bert Debusschere; Sean R. Bishop; Matthew Witman; Anthony H. McDaniel | Physical Chemistry; Energy; Fuels - Energy Science; Physical and Chemical Properties; Thermodynamics (Physical Chem.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676baaf9fa469535b9b7eb33/original/lasso-for-calphad-model-selection-enables-data-efficient-thermodynamic-modeling-an-application-in-thermochemical-hydrogen-production-materials.pdf |
61673b33fb8619187cf77af2 | 10.26434/chemrxiv-2021-qxsr4 | Biophysical and in silico characterization of NrtA: A protein-based host for aqueous nitrate and nitrite recognition | Nitrate and nitrite are key components of the global nitrogen cycle. As such, Nature has evolved proteins as biological supramolecular hosts for the recognition, translocation, and transformation of both nitrate and nitrite. To understand the supramolecular principles that govern these anion-protein interactions, here, we employ a hybrid biophysical and in silico approach to characterize the thermodynamic properties and protein dynamics of NrtA from the cyanobacterium Synechocystis sp. PCC 6803 for the recognition of nitrate and nitrite. | Ke Ji; Kiheon Baek; Weicheng Peng; Kevin Alberto; Hedieh Torabifard; Steven Nielsen; Sheel Dodani | Biological and Medicinal Chemistry; Biochemistry; Bioinformatics and Computational Biology; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61673b33fb8619187cf77af2/original/biophysical-and-in-silico-characterization-of-nrt-a-a-protein-based-host-for-aqueous-nitrate-and-nitrite-recognition.pdf |
60c75964bdbb8923c1a3af69 | 10.26434/chemrxiv.14687601.v1 | Copper(II) Ketimides in sp3 C-H Amination | <p>Commercialy available benzphenone imine (HN=CPh<sub>2</sub>) reacts with b-diketiminato copper(II) <i>tert</i>-butoxide complexes [Cu<sup>II</sup>]-O<i><sup>t</sup></i>Bu to form isolable copper(II) ketimides [Cu<sup>II</sup>]-N=CPh<sub>2</sub>. Structural characterization of the three coordinate copper(II) ketimide [Me<sub>3</sub>NN]Cu-N=CPh<sub>2</sub> reveals a short Cu-N<sub>ketimide</sub> distance (1.700(2) Å) with a nearly linear Cu-N-C linkage (178.9(2)°). Copper(II) ketimides [Cu<sup>II</sup>]-N=CPh<sub>2</sub> readily capture alkyl radicals R• (PhCH(•)Me and Cy•) to form the corresponding R-N=CPh<sub>2</sub> products that competes with N-N coupling of copper(II) ketimides [Cu<sup>II</sup>]-N=CPh<sub>2</sub> to form the azine Ph<sub>2</sub>C=N-N=CPh<sub>2</sub>. Copper(II) ketimides [Cu<sup>II</sup>]-N=CAr<sub>2</sub> serve as intermediates in catalytic sp<sup>3</sup> C-H amination of substrates R-H with ketimines HN=CAr<sub>2</sub> and <i><sup>t</sup></i>BuOO<i><sup>t</sup></i>Bu as oxidant to form <i>N</i>-alkyl ketimines R-N=CAr<sub>2</sub>. This protocol enables the use of unactivated sp<sup>3</sup> C-H bonds to give R-N=CAr<sub>2</sub> products easily converted to primary amines R-NH<sub>2</sub> via simple acidic deprotection.</p> | Isuri Jayasooriya; Abolghasem (Gus) Bakhoda; Rachel Palmer; Kristi Ng; Nour Khachemoune; Jeffery A. Bertke; Timothy H. Warren | Organometallic Compounds; Transition Metal Complexes (Inorg.); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75964bdbb8923c1a3af69/original/copper-ii-ketimides-in-sp3-c-h-amination.pdf |
64a301fbba3e99daef744b88 | 10.26434/chemrxiv-2023-m261p | High-Fidelity Templated Ligation of RNA via 2′,3′-cyclic Phosphate | The templated ligation of oligonucleotides offers a mode of replication in an RNA world. The 2′,3′-cyclic phosphate (>P) is a prebiotically available activation group for RNA and the product of backbone hydrolysis. Using gel electrophoresis and liquid chromatography, we found that the templated ligation of RNA with >P activation proceeds in alkaline (pH 9-11) low-salt aqueous solutions with 1 mM MgCl2 in temperatures ranging from 20 to 25 °C within a few days. Under the optimum conditions of pH 10 and 5 °C, the ligation yielded 40% after 7 days. No additional catalysts were required. In contrast to previous reports, we found an equimolar mixture of 2′-5′ and 3′-5′ linked oligomers in the used conditions. We probed the nucleotide specificity at the ligation site and found that one mutation reduced the ligation yield by 82-92%. We extrapolated these results to a per-nucleotide replication fidelity of 95-98% when ligating 4- to 6-mers. With splinted oligomers, five ligations created a 96 mer strand, demonstrating a possible assembly pathway for long ribozymes. With the low salt requirements, strand separation will be compatible with the ligation conditions using non-equilibrium settings. The findings suggest that templated ligation mediated by 2′,3′-cyclic phosphate in alkaline conditions offer a slow, but precise replication and elongation reaction for RNA on early Earth. | Adriana Calaça Serrão; Sreekar Wunnava; Avinash Vicholous Dass; Lennard Ufer; Philipp Schwintek; Christof B. Mast; Dieter Braun | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a301fbba3e99daef744b88/original/high-fidelity-templated-ligation-of-rna-via-2-3-cyclic-phosphate.pdf |
674d4c1af9980725cfbf4a65 | 10.26434/chemrxiv-2024-cc5vg | A Simple Scalable Production Route for Superparamagnetic Ferrite Nanoparticles with Size and Shape Tuneability | Ferrites can be considered as special cases of magnetite where Fe2+ cations are replaced with other divalent metal cations. The synthetic protocols for the production of ferrite nanoparticles also bear striking similarities to the preparation of magnetite. Synthetic methods followed for the preparation of the ferrite nanoparticles are known to alter magnetic, catalytic, and optoelectronic properties drastically. Thus, optimizing the synthetic protocol for the fine-tuning of dimension and morphology-dependent properties is of primary importance. In this work, the use of simple metal nitrate salts as precursor materials for the preparation of ferrite nanoparticles is described. The alcoholic hydrolysis of the metal nitrates in isopropanol produces corresponding hydroxides, which, in addition to oleic acid, result in metal-oleate complexes. Thermal decomposition of the precursor oleate complex produces highly monodispersed ferrite nanoparticles. | Sohel Reja; Sukumaran Vasudevan | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674d4c1af9980725cfbf4a65/original/a-simple-scalable-production-route-for-superparamagnetic-ferrite-nanoparticles-with-size-and-shape-tuneability.pdf |
60c7488b9abda27132f8cac1 | 10.26434/chemrxiv.11920947.v1 | Catalytic Enantioselective Synthesis of Heterocyclic Vicinal Fluoroamines Using Asymmetric Protonation: A Method Development and Mechanistic Study | <div>
<div>
<div>
<p>A catalytic enantioselective synthesis of heterocyclic vicinal fluoroamines is reported. A chiral Brønsted acid promotes aza-Michael addition to fluoroalkenyl heterocycles to give a
prochiral enamine intermediate, which undergoes asymmetric protonation upon rearomatization. The reaction accommodates a range
of azaheterocycles and nucleophiles, generating the C–F stereocenter in high enantioselectivity, and is also amenable to stereogenic
C–CF3 bonds. Extensive DFT calculations have provided insight
into the reaction mechanism and the origin of catalyst selectivity.
Crystal structure data shows the dominance of non-covalent interactions in the core structure conformation, enabling modulation of
the conformational landscape. Ramachandran-type analysis of conformer distribution and protein data bank mining has indicated benzylic fluorination using this approach has potential for improved
potency in several marketed drugs.
</p>
</div>
</div>
</div> | Matthew Ashford; Chao Xu; john molloy; Cameron Carpenter-Warren; Alexandra Slawin; Andrew Leach; Allan Watson | Acid Catalysis; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7488b9abda27132f8cac1/original/catalytic-enantioselective-synthesis-of-heterocyclic-vicinal-fluoroamines-using-asymmetric-protonation-a-method-development-and-mechanistic-study.pdf |
60c7575f0f50dbc367398267 | 10.26434/chemrxiv.14394746.v1 | Electrodeposition of Atmosphere-Sensitive Ternary Sodium Transition Metal Oxide Films for Sodium-Based Electrochemical Energy Storage | <p>Layered sodium transition metal oxides constitute an important class of materials with applications including electrochemical energy storage, high temperature superconductivity and electrocatalysis. However, electrodeposition of these compounds, an approach commonly used to grow other oxides, has been elusive due to their atmosphere instability and intrinsic incompatibility with aqueous electrolytes. Through use of a dry molten sodium hydroxide electrolyte, we demonstrate the high throughput electrodeposition of O3 (O’3) and P2 type layered sodium transition metal oxides across multiple transition metal chemistries, and apply these electrodeposits as high areal capacity cathodes in sodium-ion batteries. The electrodeposits are microns thick, polycrystalline, and structurally similar to materials synthesized classically at high temperature. This work enables fabrication of a wide group of previously inaccessible alkali and alkaline earth ion intercalated, higher valent transition group oxides in important thick film form factors.</p> | Arghya Patra; Jerome Davis III; Saran Pidaparthy; Manohar H. Karigerasi; Beniamin Zahiri; Ashish A. Kulkarni; Michael A. Caple; Daniel P. Shoemaker; Jian-min Zuo; Paul V. Braun | Electrochemistry; Kinetics and Mechanism - Inorganic Reactions; Theory - Inorganic; Transition Metal Complexes (Inorg.); Energy Storage; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7575f0f50dbc367398267/original/electrodeposition-of-atmosphere-sensitive-ternary-sodium-transition-metal-oxide-films-for-sodium-based-electrochemical-energy-storage.pdf |
66c71e2bf3f4b05290b9118a | 10.26434/chemrxiv-2024-ql0fx | Liquid Crystals: Unlocking the Quantum Revolution in Computing | Quantum computing promises exponential advances in information processing, necessitating the development of appropriate materials for implementing quantum qubits and gates. Liquid crystals, known for their electro-optical characteristics and use in displays, have recently received attention as prospective candidates for quantum computing applications.
This review delves into the role of liquid crystals in quantum information science, starting with an overview of their characteristics, classification and phase transition mechanisms. It then directs focus to their quantum attributes, their ability to display quantum coherence and entanglement. The review also showcases validations of quantum phenomena in liquid crystals, highlighting their suitability for use in quantum systems.
Recent advances are discussed, including the development of liquid crystal qubits, quantum gates, and circuits. The review also explores the integration of liquid crystals with quantum photonic devices, emphasizing their role in enhancing quantum communication and information processing. Potential room temperature operation applications such as quantum sensing and quantum cryptocurrency are illustrated through case studies.
Challenges such as material synthesis, decoherence, stability, and compatibility with existing technologies are addressed, with proposed solutions including hybrid systems and novel fabrication techniques. Future research directions focus on innovative liquid crystal materials, interdisciplinary collaboration, and their use in emerging quantum technologies.
| Edward Otieno; Katarzyna Matczyszyn; Nelson Mokaya | Theoretical and Computational Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Liquid Crystals; Optical Materials; Quantum Computing | CC BY 4.0 | CHEMRXIV | 2024-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c71e2bf3f4b05290b9118a/original/liquid-crystals-unlocking-the-quantum-revolution-in-computing.pdf |
640edd767290f69f8ee7b696 | 10.26434/chemrxiv-2023-d44rr | Reactivity of Aryl Pinacol Boronates Towards Disulfide Bonds | Aryl pinacol boronates are important synthons in organic synthesis. Radical reactions of alkyl catechol boronates offer the possibility to synthesize N-, S-, O- and F-alkyls, while Suzuki- Miyaura reaction has been explored for bioorthogonal protein labelling and drug synthesis in living cells. Here, we show an intriguing reactivity of aryl pinacol boronates with peptides and protein disulfide bonds under aqueous conditions. The reaction can be carried out by N,N- dimethylacetamide (DMA) or ammonium persulfate (APS) and allows a proteome-wide, protein and peptide derivatization. We show the efficient reaction of various disulfides, using different aryl pinacol boronates. This approach opens up a new possibility for protein derivatization, covalent drug designs and organic synthesis. | Haoyu Chen; Pavel Kielkowski | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640edd767290f69f8ee7b696/original/reactivity-of-aryl-pinacol-boronates-towards-disulfide-bonds.pdf |
6666d44e12188379d8c3ad22 | 10.26434/chemrxiv-2024-lrhrg | Accurate measurement of sequential Ar desorption energies from the dispersion-dominated Ar1-3 complexes of 1-naphthol | We devise a unique experimental methodology to accurately measure the sequential desorption of Ar atoms from the aromatic surface of 1-naphthol (NpOH). The dispersion-dominated NpOH·Ar1-3 complexes were characterized using resonant two-photon ionization (R2PI) spectroscopy in the gas phase. The band origins 〖(0〗_0^0) for S1←S0 transition in the NpOH·Ar, NpOH·Ar2 and NpOH·Ar3 complexes were observed at 31440, 31425 and 31415 cm-1, respectively. The above values were red-shifted by 15, 30 and 40 cm-1 () compared to that of the NpOH (0_0^0 at 31455 cm-1) molecule. The disappearance of Franck-Condon active vibrational bands in the R2PI spectrum was utilized to determine the D0(S1) values of non-covalently bound molecular complexes. The single Ar desorption energies from the NpOH·Ar, NpOH·Ar2 and NpOH·Ar3 complexes were measured as 487 5, 471 21 and 442 24 cm-1, respectively. The corresponding dissociation energies D0(S1) were measured as 487 5, 958 26 and 1400 50 cm-1. The D0(S0) values were determined by subtracting the shift of the origin band, and the respective values are 472 5, 928 26 and 1360 50 cm-1. The preferable orientation for the efficient desorption was obtained with the first Ar atom positioned on the top face of the NpOH ring. A second Ar atom was bound to the bottom face of the NpOH ring. The docking of third Ar atom could be on the NpOH face above OH (I1), CH (I2) or π (I3), as all these structures are isoenergetic to each other. The best correlation of the experimental and calculated dissociation energies of NpOH·Ar1-3 (I1) complexes is obtained at the B-LYP-D4/def2-TZVPP level of theory, with an accuracy of 3-5%. The current study provides an inexpensive laser spectroscopic method to precisely determine the dissociation energies of the dispersively bound complexes of biorelevant aromatic molecules based on their Franck-Condon activity | Simran Baweja; Bhavika Kalal; Surajit Maity | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6666d44e12188379d8c3ad22/original/accurate-measurement-of-sequential-ar-desorption-energies-from-the-dispersion-dominated-ar1-3-complexes-of-1-naphthol.pdf |
60c742b00f50dbcac3395d80 | 10.26434/chemrxiv.8428904.v1 | Docking Flexible Cyclic Peptides with AutoDock CrankPep | While a new therapeutic cyclic peptide is approved nearly every year, docking large macrocycles has remained challenging. Here, we present a new version of our peptide docking software<i> AutoDock CrankPep </i>(<i>ADCP</i>), extended to dock peptides cyclized through their backbone and/or sidechain disulfide bonds. We show that within the top 10 solutions, <i>ADCP</i> identifies the proper interactions<i> </i>for 71% of a dataset of 38 complexes, thus making it a useful tool for rational peptide-based drug design. | Yuqi Zhang; Michel Sanner | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742b00f50dbcac3395d80/original/docking-flexible-cyclic-peptides-with-auto-dock-crank-pep.pdf |
663e9dd0418a5379b0f72abc | 10.26434/chemrxiv-2024-6xq70 | An Investigation into Transition States of Cyclic
Tetra-Atomic Silicon and Germanium Interstellar
Dust Compounds: Si(x)C(4−x), Ge(x)C(4−x), and
Ge(x)Si(4−x) (x ∈ {1, 2, 3}) | Presented in this work is a thorough determination of the transition states between the different isomers of cyclic tetra-atomic silicon-carbide, germanium-carbide, and germanium-silicide clusters. Through use of density functional theory (B3LYP-D3BJ, M06-2X, ωB97X-D4, and B2GP-PLYP) in conjunction with the aug-cc-pVTZ basis set, transition state structures and their barrier heights are determined for the interconversions between the various isomers for the family of tetra-atomic SiC, GeC, and GeSi compounds. SiC dust grains are known to be prevalent in interstellar dust, and among this group, so far only diamond-shaped (d-)SiC(3) has been detected in the interstellar medium (ISM). Determining which other structures might be detectable not only depends on their intrinsic spectroscopic features, but whether or not they are likely to exist as isomers in interstellar environments. By examining the energy barrier heights for transitions between isomers, we determined that many of these structures are unlikely to exhibit interconversion in the ISM, outside of hotter circumstellar environments. Although Boltzmann population ratios at approximate circumstellar temperatures suggest the presence of higher energy minima, it is likely that once interconversion happens, as molecules travel away from a star and cool, they will get kinetically trapped in the potential energy well they inhabit, making how the ratios freeze out dependent on the time and pathways the molecules take to cool down. As such, many of these higher energy minima may still be good candidates for detection including (rhomboidal) r-SiC(3), r-GeC(3), r-GeSi(3), (trapezoidal) t-Si(2)C(2), r-Ge(2)C(2), and d-Si(3)C. | Adam Mackenzie Flowers; Alex Brown; Mariusz Klobukowski | Theoretical and Computational Chemistry; Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663e9dd0418a5379b0f72abc/original/an-investigation-into-transition-states-of-cyclic-tetra-atomic-silicon-and-germanium-interstellar-dust-compounds-si-x-c-4-x-ge-x-c-4-x-and-ge-x-si-4-x-x-1-2-3.pdf |
67be992a81d2151a021ab88e | 10.26434/chemrxiv-2025-dkw14-v2 | Chemical Vapor Deposited Si:P Epitaxial Growth for DRAM Bit Contact | Next generation DRAM series will rely on the ability
to obtain low resistance contact junctions in very tight spaces and narrow trenches. Current DRAM technology uses a polycrystalline plug, followed by silicidation with Ti metal to obtain a low resistance interface. The upcoming generations of DRAM series requires us to narrow the bit contact (BC) CD down to ~10 nm and further decrease the BC resistance. This requires the use of a highly doped epitaxial plug to obtain low resistance BC. In this paper, we
study the growth mechanisms and physics of SiP epitaxy. We explain the process optimizations that were undertaken to obtain an epitaxial plug close to our device specifications. We also explore the fundamental limitations of epitaxial growth, referred in this paper as Epitaxy trilemma. TEM/STEM and fundamental material characterizations showed the fundamental mechanisms
behind the growth of SiP epi. Furthermore, we also characterized the effects of post-processing on the structural integrity of the BC. | Protyush Sahu; Jay Brown; Silvia Borsari; Jeff Hull | Materials Science; Thin Films | CC BY 4.0 | CHEMRXIV | 2025-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67be992a81d2151a021ab88e/original/chemical-vapor-deposited-si-p-epitaxial-growth-for-dram-bit-contact.pdf |
60c73e97f96a00267a285f40 | 10.26434/chemrxiv.6005279.v2 | Testing for Physical Validity in Molecular Simulations | <p>Advances in recent years have made molecular dynamics (MD) and Monte Carlo (MC) simulations powerful tools in molecular-level research, allowing the prediction of experimental observables in the study of systems such as proteins, membranes, and polymeric materials. However, the quality of any prediction based on molecular dynamics results will strongly depend on the validity of underlying physical assumptions.</p>
<p>Unphysical behavior of simulations can have significant influence on the results and reproducibility of these simulations, such as folding of proteins and DNA or properties of lipid bilayers determined by cutoff treatment, dynamics of peptides and polymers affected by the choice of thermostat, or liquid properties depending on the simulation time step. Motivated by such examples, we propose a two-fold approach to increase the robustness of molecular simulations. The first part of this approach involves tests which can be performed by the users of MD programs on their respective systems and setups. We present a number of tests of different complexity, ranging from simple post-processing analysis to more involved tests requiring additional simulations. These tests are shown to significantly increase the reliability of MD simulations by catching a number of common simulation errors violating physical assumptions, such as non-conservative integrators, deviations from the Boltzmann ensemble, and lack of ergodicity between degrees of freedom. To make the usage as easy as possible, we have developed an open-source and platform-independent Python library (https://physical-validation.readthedocs.io) implementing these tests.</p>
<p>The second part of the approach involves testing for code correctness. While unphysical behavior can be due to poor or incompatible choices of parameters by the user, it can just as well originate in coding errors within the program. We therefore propose to include physical validation tests in the code-checking mechanism of MD software packages. We have implemented such a validation for the GROMACS software package, ensuring that every major releases passes a number of physical sanity checks performed on selected representative systems before shipping. It is, to our knowledge, the first major molecular mechanics software package to run such validation routinely. The tests are, as the rest of the package, open source software, and can be adapted for other software packages.</p> | Pascal T. Merz; Michael R. Shirts | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2018-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e97f96a00267a285f40/original/testing-for-physical-validity-in-molecular-simulations.pdf |
60c7480fbdbb891677a38f1c | 10.26434/chemrxiv.11763426.v2 | A Chemically Soldered Polyoxometalate Single-Molecule Transistor | Polyoxometalates have been proposed in the literature as promising components for nanoelectronic applications, where they could offer key advantages with their structural versatility and rich electrochemistry. Apart from a few studies on their ensemble behaviour (for instance, as monolayers or thin films) this potential remains largely unexplored. We synthesised a pyridyl-capped Anderson-Evans polyoxometalate and used it to fabricate single-molecule junctions, by using the organic termini to chemically “solder” a single metal oxide cluster to two nanoelectrodes through coordination bonds. Operating the device in an electrochemical environment allowed us to probe charge transport through different oxidation states of the polyoxometalate, and we report here an efficient three-state transistor behaviour. Conductance data fits a quantum tunnelling transport mechanism, with charge having different tunnelling probabilities through different oxidation states of the polyoxometalate. Our results show the promise of such compounds in nanoelectronics, and are, to our best knowledge, the first report on the single-entity electrochemical behaviour of polyoxometalates.<p></p> | Chuanli Wu; Xiaohang Qiao; Craig M. Robertson; Simon Higgins; Chenxin Cai; Richard Nichols; Andrea Vezzoli | Nanodevices; Organometallic Compounds; Electrochemistry - Organometallic; Clusters; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7480fbdbb891677a38f1c/original/a-chemically-soldered-polyoxometalate-single-molecule-transistor.pdf |
66a1a281c9c6a5c07ad671d4 | 10.26434/chemrxiv-2024-hk43q-v2 | Diverse Quantum Interference Regime in Intramolecular Singlet Fission Chromophores with Thiophene-Based Linkers | An array of thiophene-based π-conjugated linkers in covalently-linked pentacene dimers allows us to access diverse quantum interference (QI), modulating nonadiabatic coupling (NAC) in singlet fission (SF) process. Simulations show that structural isomerism in terms of S atom orientation substantially alters NAC with relatively marginal impacts on energies. Extended curly arrow rules (ECARs) reveal sensitive dependence of QI on SF linker topologies and connectivity, categorizing regimes of constructive, destructive, and previously unrealized in SF research, suppressed destructive QI. Drastic NAC changes in terms of S atom orientation are rationalized based on the nature of QI. Our results from nonequilibrium Green’s function calculation using density functional theory corroborates the classification of QI regimes based on ECARs. Moreover, we found that the extent of charge resonance contribution in electronic states relevant to multiexciton formation and the appearance of optically allowed charge transfer excitation strongly depends on the operative QI regime. Notably, the magnitude of NAC effectively captures this influence. Our findings show that QI can rationalize and semi-quantitatively correlate to NAC for multiexciton formation step in SF process. | Jonghwan Lee; Sungsik Eom; Hyungjun Kim | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a1a281c9c6a5c07ad671d4/original/diverse-quantum-interference-regime-in-intramolecular-singlet-fission-chromophores-with-thiophene-based-linkers.pdf |
652e6d4845aaa5fdbb2eae84 | 10.26434/chemrxiv-2023-xbhbf | Design of organic cathode material based on quinone and pyrazine motifs for rechargeable lithium and zinc batteries | Despite the rapid expansion of the organic cathode materials field, there is still a lack of materials obtained through facile synthesis that have stable cycling and high energy density. Herein, we report a two-step synthesis of small organic molecule from commercially available precursors that can be used as a cathode material. Oxidized tetraquinoxalinecatechol (OTQC) was derived from tetraquinoxalinecatechol (TQC) by the introduction of additional quinone redox active centers into the structure. The modification increased the voltage and capacity of the material. The OTQC delivers a high specific capacity of 327 mAhg-1 with an average voltage of 2.63 V vs. Li/Li+ in the Li-ion battery. That corresponds to an energy density of 860 Whkg-1 on the material level. Furthermore, the material demonstrated excellent cycling stability, having a capacity retention of 82 % after 400 cycles. Similarly, the OTQC demonstrates increased average voltage and specific capacity in comparison with TQC in Zn-organic battery using aqueous electrolyte, reaching the specific capacity of 326 mAhg-1 with an average voltage of 0.86 V vs. Zn/Zn2+. Apart from good electrochemical performance, this work provides an additional in-depth analysis of the redox mechanism and degradation mechanism related to capacity fading. | Svit Menart; Olivera Lužanin; Klemen Pirnat; David Pahovnik; Jože Moškon; Robert Dominko | Organic Chemistry; Energy; Organic Synthesis and Reactions; Physical Organic Chemistry; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652e6d4845aaa5fdbb2eae84/original/design-of-organic-cathode-material-based-on-quinone-and-pyrazine-motifs-for-rechargeable-lithium-and-zinc-batteries.pdf |
60c75474ee301c440dc7af7f | 10.26434/chemrxiv.13622417.v2 | Deep Generative Models for Ligand-based de Novo Design Applied to Multi-parametric Optimization | <div>
<div>
<div>
<p>Multi-Parameter Optimization (MPO) is a major challenge in New Chemical Entity (NCE) drug discovery
projects, and the inability to identify molecules meeting all the criteria of lead optimization (LO) is an
important cause of NCE project failure. Several ligand- and structure-based de novo design methods
have been published over the past decades, some of which have proved useful multiobjective
optimization. However, there is still need for improvement to better address the chemical feasibility
of generated compounds as well as increasing the explored chemical space while tackling the MPO
challenge. Recently, promising results have been reported for deep learning generative models applied
to de novo molecular design, but until now, to our knowledge, no report has been made of the value
of this new technology for addressing MPO in an actual drug discovery project. Our objective in this
study was to evaluate the potential of a ligand-based de novo design technology using deep learning
generative models to accelerate the discovery of an optimized lead compound meeting all in vitro late
stage LO criteria.
</p>
</div>
</div>
</div> | Quentin Perron; Olivier Mirguet; Hamza Tajmouati; Adam Skiredj; Anne Rojas; Arnaud Gohier; Pierre Ducrot; Marie-Pierre Bourguignon; Patricia Sansilvestri-Morel; Nicolas Do Huu; Françoise Gellibert; Yann Gaston-Mathé | Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75474ee301c440dc7af7f/original/deep-generative-models-for-ligand-based-de-novo-design-applied-to-multi-parametric-optimization.pdf |
61de35c381f3fe8570a42b25 | 10.26434/chemrxiv-2022-w343k | An Unexpected Dual-Emissive Luminogen: Tunable Aggregation-Induced Emission with Cyan-White-Red Colors, Stable Inherent Chirality, and Enhanced Chiroptical Property | Herein we report a novel chiral bismacrocycle with unexpected dual emission and tunable aggregation-induced emission colors. A facile four-step synthesis strategy is developed to construct this rigid bismacrocycle, (1,4)[8]cycloparaphenylenophane (SCPP[8]), which possesses a 1,2,4,5-tetraphenylbenzene core locked by two intersecting polyphenylene-based macrocycles. The luminescent behavior of SCPP[8] shows the unique characteristics of both aggregation-caused quenching effect and aggrega-tion-induced emission (AIE) effect, inducing remarkable redshift emission including near white-light emission. SCPP[8] is configurationally stable and possesses a novel shape-persistent bismacrocycle scaffold with a high strain energy (up to 127.83 kcal/mol). In addition, SCPP[8] displays enhanced circularly polarized luminescence properties due to AIE effect. | Pingwu Du; Xinyu Zhang; Huiqing Liu; Guilin Zhuang; Shangfeng Yang | Organic Chemistry; Organic Compounds and Functional Groups; Photochemistry (Org.); Physical Organic Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61de35c381f3fe8570a42b25/original/an-unexpected-dual-emissive-luminogen-tunable-aggregation-induced-emission-with-cyan-white-red-colors-stable-inherent-chirality-and-enhanced-chiroptical-property.pdf |
60c9ba19551c4fdef3c4c2e6 | 10.26434/chemrxiv.7726139.v5 | Understanding Beam Induced Electronic Excitations in Materials | A time dependent self consistent field based method for determining the rates of electronic excitations induced in materials by the presence of external point charges is presented. The method utilizes the full scalar potential of the external point charge in the interaction Hamiltonian instead of relying on multipolar expansions thereof. A general method is presented for determining the conditions under which dipole selection rules are adequate to describe the electronic response of the material to perturbation by external point charges. The position dependence of point charge induced transition rates between the ground and lowest few excited electronic states was resolved for a small polybenzoid. Notably, electronic excitations that are optically forbidden can be strongly allowed for particular positions of the perturbing point charge. Application of the methods detailed here can lead to an improved understanding of the electronic response of materials under irradiation by beams of charged particles. | David Lingerfelt; Panchapakesan Ganesh; Jacek Jakowski; Bobby Sumpter | Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics; Quasiparticles and Excitations; Radiation | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9ba19551c4fdef3c4c2e6/original/understanding-beam-induced-electronic-excitations-in-materials.pdf |
60c7456d337d6c6037e26f94 | 10.26434/chemrxiv.8135777.v3 | Sequence specificity despite intrinsic disorder: how a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein | <p>The role of electrostatic interactions and mutations that change charge states in intrinsically disordered proteins (IDPs) is well-established, but many disease-associated mutations in IDPs are charge-neutral. The Val66Met single nucleotide polymorphism (SNP) in precursor brain-derived neurotrophic factor (BDNF) is one of the earliest SNPs to be associated with neuropsychiatric disorders, and the underlying molecular mechanism is unknown. Here we report on over 250 μs of fully-atomistic, explicit solvent, temperature replica exchange molecular dynamics (MD) simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence. The simulations were able to correctly reproduce the location of both local and non-local secondary changes due to the Val66Met mutation when compared with NMR spectroscopy. We find that the change in local structure is mediated via entropic and sequence specific effects. We developed a hierarchical sequence-based framework for analysis and conceptualization, which first identifies “blobs” of 5-15 residues representing local globular regions or linkers. We use this framework within a novel test for enrichment of higher-order (tertiary) structure in disordered proteins; the size and shape of each blob is extracted from MD simulation of the real protein (RP), and used to parameterize a self-avoiding heterogenous polymer (SAHP). The SAHP version of the BDNF prodomain suggested a protein segmented into three regions, with a central long, highly disordered polyampholyte linker separating two globular regions. This effective segmentation was also observed in full simulations of the RP, but the Val66Met substitution significantly increased interactions across the linker, as well as the number of participating residues. The Val66Met substitution replaces β-bridging between Val66 and Val94 (on either side of the linker) with specific side-chain interactions between Met66 and Met95.The protein backbone in the vicinity of Met95 is then free to form β-bridges with residues 31-41 near the N-terminus, which condenses the protein. A significant role for Met/Met interactions is consistent with previously-observed non-local effects of the Val66Met SNP, as well as established interactions between the Met66 sequence and a Met-rich receptor that initiates neuronal growth cone retraction.</p> | Ruchi Lohia; Reza Salari; Grace Brannigan | Biopolymers; Bioinformatics and Computational Biology; Biophysics; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7456d337d6c6037e26f94/original/sequence-specificity-despite-intrinsic-disorder-how-a-disease-associated-val-met-polymorphism-rearranges-tertiary-interactions-in-a-long-disordered-protein.pdf |
60c7410ff96a0014f128639c | 10.26434/chemrxiv.7895891.v1 | Flow Chemistry Controls Both Self-Assembly and the Entrapped Oscillatory Cargo in Belousov-Zhabotinsky Driven Polymerization-Induced Self-Assembly | <p></p><p>Belousov-Zhabotinsky (B-Z) reaction driven
polymerization-induced self-assembly (PISA), or B-Z PISA, is a novel method for
the autonomous one-pot synthesis of polymer vesicles from a macroCTA (macro
chain transfer agent) and monomer solution (“soup”) containing the above and
the BZ reaction components. In it, the polymerization is driven (and
controlled) by periodically generated radicals generated in the oscillations of
the B-Z reaction. These are inhibitor/activator radicals for the
polymerization. Until now B-Z PISA has only been carried out in batch reactors.
In this manuscript we present the results of running the system using a
continuously stirred tank reactor (CSTR) configuration which offers some
interesting advantages.Indeed, by controlling the CSTR parameters we achieve
reproducible and simultaneous control of the PISA process and of the properties
of the oscillatory cargo encapsulated in the resulting vesicles. Furthermore,
the use of flow chemistry enables a more precise morphology control and chemical
cargo tuning. Finally, in the context of biomimetic applications a CSTR
operation mimics more closely the open non-equilibrium conditions of living
systems and their surrounding environments.</p><p></p> | Liman Hou; Marta Dueñas-Diez; Rohit Srivastava; Juan Perez-Mercader | Inorganic Polymers; Polymerization (Polymers); Polymerization kinetics; Polymer morphology; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7410ff96a0014f128639c/original/flow-chemistry-controls-both-self-assembly-and-the-entrapped-oscillatory-cargo-in-belousov-zhabotinsky-driven-polymerization-induced-self-assembly.pdf |
65f84c5d9138d23161b72dda | 10.26434/chemrxiv-2024-bcf3x | Solid-State Oxidation of Alcohols in Gold-Coated Milling Vessels via Direct Mechanocatalysis | Alcohols are selectively oxidized to their corresponding aldehydes catalytically via mechanochemistry using a gold-coated milling vessel. Superior catalytic efficiency and selectivity was achieved through the meticulous modulation of milling frequency, duration, and media, complemented by controlled heating. Achieving a turnover number (TON) near 8200 and a turnover frequency (TOF) of 0.77 s-1, the system notably surpasses existing alternatives. Utilizing atmospheric oxygen as the primary oxidant facilitated significant yields, with the highest reaching up to 99% for selected substrates. The catalytic reaction indeed occurring on the surface of the vibrating milling ball was confirmed via X-ray photoelectron spectroscopy (XPS). This study highlights the pivotal role of operational parameter optimization in enhancing catalysis, emphasizing the method's sustainability and broad applicability across various alcohol substrates. The findings contribute significantly to green chemistry, offering an efficient, sustainable approach to alcohol oxidation. | Maximilian Wohlgemuth; Sarah Schmidt; Maike Mayer; Wilm Pickhardt; Sven Graetz; Lars Borchardt | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Process Chemistry; Heterogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f84c5d9138d23161b72dda/original/solid-state-oxidation-of-alcohols-in-gold-coated-milling-vessels-via-direct-mechanocatalysis.pdf |
67502da77be152b1d0e824f1 | 10.26434/chemrxiv-2024-cd4tz | Discovery of de novo Macrocycle Inhibitors of Histone Deacetylase 11 | Histone deacetylase (HDAC) enzymes are epigenetic regulators that affect diverse protein function by removing acyl groups from lysine side chains throughout the proteome. The most recently discovered human isozyme, HDAC11, differs from other HDACs in substrate preference and tissue expression profile. Elucidation of the biological function of this enzyme has been scarce and only a few chemical probes to help advance this insight have been developed thus far. Here we discovered macrocyclic inhibitors that exhibit selectivity for HDAC11 and penetrate the cytoplasmic membrane in cultured cells as determined by the chloroalkane penetration assay. Our work establishes the combination of de novo macrocycle synthesis with incorporation of N-alkylated hydroxamic acid moieties as a viable strategy for targeting HDAC11. Further, this study demonstrates the potential of applying macrocyclic peptide-based library synthesis to directly furnish high-affinity, cell-permeating ligands. The discovered inhibitors comprise tool compounds for the investigation of the biological function of HDAC11. | Daniela Danková; Alexander Nielsen; Anna Zarda; Tobias Hansen; Marie Hesse; Michaela Benová; Athanasios Tsiris; Christian R. O. Bartling; Edward J. Will; Kristian Strømgaard; Carlos Moreno-Yruela; Christian Heinis; Christian Adam Olsen | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67502da77be152b1d0e824f1/original/discovery-of-de-novo-macrocycle-inhibitors-of-histone-deacetylase-11.pdf |
655947b12c3c11ed71ae4d55 | 10.26434/chemrxiv-2023-85m7b | Imaging mass spectrometry of isotopically-resolved intact proteins on a trapped ion-mobility quadrupole time-of-flight mass spectrometer | In this work, we demonstrate rapid, high spatial, and high spectral resolution imaging of intact proteins by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) on a hybrid quadrupole-reflectron time-of-flight (qTOF) mass spectrometer equipped with trapped ion mobility spectrometry (TIMS). Historically, untargeted MALDI IMS of proteins has been performed on TOF mass spectrometers. While advances in TOF instrumentation have enabled rapid, high spatial resolution IMS of intact proteins, TOF mass spectrometers generate relatively low-resolution mass spectra with limited mass accuracy. Conversely, the implementation of MALDI sources on high-resolving power Fourier transform (FT) mass spectrometers has allowed IMS experiments to be conducted with high spectral resolution with the caveat of increasingly long data acquisition times. As illustrated here, qTOF mass spectrometers enable protein imaging with the combined advantages of TOF and FT mass spectrometers. Protein isotope distributions were resolved for both a protein standard mixture and proteins detected from a whole-body mouse pup tissue section. Rapid (~10 pixels/s) 10 μm lateral spatial resolution IMS was performed on a rat brain tissue section while maintaining isotopic spectral resolution. Lastly, proof-of-concept MALDI-TIMS data was acquired from a protein mixture to demonstrate the ability to differentiate charge states by ion mobility. These experiments highlight the advantages of qTOF and timsTOF platforms for resolving and interpreting complex protein spectra generated from tissue by IMS. | Dustin Klein; Emilio Rivera; Richard Caprioli; Jeffrey Spraggins | Biological and Medicinal Chemistry; Analytical Chemistry; Imaging; Mass Spectrometry; Cell and Molecular Biology | CC BY NC 4.0 | CHEMRXIV | 2023-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655947b12c3c11ed71ae4d55/original/imaging-mass-spectrometry-of-isotopically-resolved-intact-proteins-on-a-trapped-ion-mobility-quadrupole-time-of-flight-mass-spectrometer.pdf |
6353baddecdad5530ae7ff30 | 10.26434/chemrxiv-2022-dnc48 | AQME: Automated Quantum Mechanical Environments for Researchers and Educators | AQME, Automated Quantum Mechanical Environments, is a free and open-source Python package for the rapid deployment of automated workflows using cheminformatics and quantum chemistry. AQME workflows integrate tasks performed across multiple computational chemistry packages and data formats, preserving all computational protocols, data, and metadata for machine and human users to access and reuse. AQME has a modular structure of independent modules that can be implemented in any sequence, allowing the users to use only the desired parts of the program. The code is intended for researchers with basic familiarity with the Python programming language. The CSEARCH module interfaces to molecular mechanics and semi-empirical QM (SQM) conformer generation tools (e.g., RDKit and Conformer–Rotamer Ensemble Sampling Tool, CREST) starting from various initial structure formats. The CMIN module enables geometry refinement with SQM and neural network potentials, such ANI-1. The QPREP module interfaces with multiple QM programs, such as Gaussian, ORCA, and PySCF. The QCORR module processes QM results, storing structural, energetic, and property data while also enabling automated error handling (i.e., convergence errors, wrong number of imaginary frequencies, isomerization, etc.) and job resubmission. The QDESCP module provides easy access to QM ensemble-averaged molecular descriptors and computed properties, such as NMR spectra. Overall, AQME provides automated, transparent, and reproducible workflows to produce, analyze and archive computational chemistry results. SMILES inputs can be used, and many aspects of tedious human manipulation can be avoided. Installation and execution on Windows, macOS, and Linux platforms has been tested, and the code has been developed to support access through Jupyter Notebooks, the command line, and job submission (e.g., Slurm) scripts. Examples of pre-configured workflows are available in various formats, and hands-on video tutorials illustrate their use. | Juan V. Alegre-Requena; Shree Sowndarya; Turki Alturaifi; Raúl Pérez-Soto; Robert Paton | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6353baddecdad5530ae7ff30/original/aqme-automated-quantum-mechanical-environments-for-researchers-and-educators.pdf |
60c7520f337d6c401fe28670 | 10.26434/chemrxiv.13249559.v1 | Retrained Generic Antibodies Can Recognize SARS-CoV-2 | <div>The dramatic impact which novel viruses can have on the human society could be mitigated without the need of vaccination if antibodies present within the population are retrained to recognize these viruses. With this idea in mind, a double-faced peptide-based boosters are computationally designed to allow recognition of SARS-CoV-2 by Hepatitis B antibodies. One booster face is made of ACE2-mimic peptides that can bind to the receptor binding domain (RBD) of SARS-CoV-2. The other booster face is composed of a Hepatitis B core-antigen, targeting the Hepatitis B antibody fragment. Molecular dynamics simulations revealed that the designed boosters have a highly specific and stable binding</div><div>both to RBD and the antibody fragment (AF). This approach can provide a cheap and efficient neutralization of emerging pathogens.</div> | Yanxiao Han; Katherine McReynolds; Petr Kral | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7520f337d6c401fe28670/original/retrained-generic-antibodies-can-recognize-sars-co-v-2.pdf |
60c74d444c8919d836ad37ac | 10.26434/chemrxiv.11877492.v2 | Computational study of the strong binding mechanism of SARS-CoV-2 spike and ACE2 | <p></p><p>The spike protein of SARS-CoV-2 (SARS-CoV-2-S) helps
the virus attach to and infect human cells. W<a>ith various
computational methods applied in this work, the accessibility of its RBD to
ACE2, its key residues for stronger binding to ACE2 than the SARS-CoV spike
(SARS-CoV-S), the origin of the stronger binding, and its potential sites for
drug and antibody design</a> were explored. It was found that the SARS-CoV-2-S
could bind ACE2 with an RBD-angle ranging from 52.2º to 84.8º, which demonstrated
that the RBD does not need to fully open to bind ACE2. Free energy calculation
by an MM/GBSA approach not only revealed much stronger binding of SARS-CoV-2-S
to ACE2 (Δ<i>G</i>=-21.7~-29.9 kcal/mol)
than SARS-CoV-S (Δ<i>G</i>=-10.2~-16.4
kcal/mol) at different RBD-angles but also demonstrated that the binding becomes
increasingly stronger as the RBD-angle increases. In comparison with the experimental
results, the free energy decomposition disclosed more key residues interacting strongly
with ACE2 than with the SARS-CoV-S, among which the Q493 might be the decisive
residue variation (-5.84 kcal/mol) to the strong binding. With the mutation of
all 18 different residues of SARS-CoV-S on the spike-ACE2 interface to the
corresponding residues of SARS-CoV-2-S, it was found that the mutated
SARS-CoV-S has almost the same binding affinity as SARS-CoV-2-S to ACE2,
demonstrating that the remaining mutations outside the spike-ACE2 interface have
little effect on its binding affinity to ACE2. Simulation of the conformational change pathway
from “down” to “up” states disclosed <a>5 potential
ligand-binding pockets correlated to the conformational change.</a> Taking
together the key residues, accessible RBD-angle and pocket correlation, potential sites for
drug and antibody design were proposed, which should be helpful for
interpreting the high infectiousness of SARS-CoV-2 and for developing a cure.<br /></p><p></p> | Cheng Peng; Zhengdan Zhu; Yulong Shi; Xiaoyu Wang; Kaijie Mu; Yanqing Yang; Xinben Zhang; Zhijian Xu; weiliang zhu | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d444c8919d836ad37ac/original/computational-study-of-the-strong-binding-mechanism-of-sars-co-v-2-spike-and-ace2.pdf |
6647292591aefa6ce13d49cb | 10.26434/chemrxiv-2024-cprs3-v3 | Molybdenum Disulfide MoS2 and the q-BWF line shapes (Raman Spectroscopy) | RRUFF database is proposing the Raman spectra of two molybdenum disulfide MoS_2 samples. Here we show the q-BWF fitted functions to the E_2g and A_1g Raman bands of these samples. The q-BWF functions are generalizing the Breit-Wigner-Fano line shape in the framework of the q-exponential function proposed by Constantino Tsallis and his statistics. The fitted q-BWF functions to pyramid and monolayer Raman spectra by Fabbri et al., 2022, are also proposed. Some review of Raman spectroscopy of MoS_2 is proposed too, especially about Fano-Raman and Davydov splitting effect. | Amelia Carolina Sparavigna | Materials Science | CC BY 4.0 | CHEMRXIV | 2024-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6647292591aefa6ce13d49cb/original/molybdenum-disulfide-mo-s2-and-the-q-bwf-line-shapes-raman-spectroscopy.pdf |
6752dbd5f9980725cf3c5c4d | 10.26434/chemrxiv-2024-qqbpj-v2 | Surfactant-free colloidal gold nanoparticles: room temperature synthesis, size control and opportunities for catalysis | Nanomaterials are at the forefront to develop and improve several technologies spanning from catalysis to medicine and sensing. Simple(r) preparation methods of nanomaterials can greatly benefit to fundamental studies and facilitate the development of nanomaterials towards real-life applications. Here, an easily implementable surfactant-free colloidal synthesis, simply achieved in alkaline mixtures of water and mono-alcohol (e.g. ethanol), performed at room temperature in the case of gold nanoparticles, and compatible with the principles of Green Chemistry, is exploited and further developed to easily perform size-effects studies at the nanoscale. Gold nanoparticles in the size range of 5 to 22 nm are easily prepared from a solution of 0.5 mM HAuCl4, 2 mM NaOH and 20 v.% ethanol or methanol, by initiating the synthesis in different simple ways: sonochemistry, stirring, manual shaking, using different grades of precursors, using different solvents. The nanomaterials are shown to be suitable model systems to study size effects at the nanoscale, with the example of alcohol electrocatalytic oxidations performed in alkaline media. | Dionysis Panagopoulos; Armin Asghari Alamdari; Jonathan Quinson | Inorganic Chemistry; Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Electrocatalysis; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6752dbd5f9980725cf3c5c4d/original/surfactant-free-colloidal-gold-nanoparticles-room-temperature-synthesis-size-control-and-opportunities-for-catalysis.pdf |
60c74997bdbb891a6aa391d4 | 10.26434/chemrxiv.12084768.v1 | Kinetic Study of Disulfonimide Catalyzed Cyanosilylation of Aldehyde Using a Method of Progress Rates | Kinetic study of organic reactions, especially
multistep catalytic reactions, is crucial to in-depth understanding of reaction
mechanisms. Here we report our kinetic study of the chiral disulfonimide
catalyzed cyanosilylation of aldehyde, which reveals that two molecules of
TMSCN are involved in the rate-determining C-C bond forming step. In addition,
the apparent activation energy, enthalpy of activation and entropy of
activation were deduced through the study of temperature dependence of the
reaction rates. More importantly, a novel and efficient method which makes use
of the progress rates was developed to treat the kinetic data obtained from continuous monitoring of the reaction progress with <i>in situ</i> FT-IR. | Zhipeng Zhang; Martin Klussmann; Benjamin List | Organic Synthesis and Reactions; Homogeneous Catalysis; Organocatalysis; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74997bdbb891a6aa391d4/original/kinetic-study-of-disulfonimide-catalyzed-cyanosilylation-of-aldehyde-using-a-method-of-progress-rates.pdf |
60c7574e567dfe6c2cec6663 | 10.26434/chemrxiv.14387885.v1 | Novel Antibiotics from a ‘White Box’ 2D Structural Fingerprint Decision Tree | <p>The paper is concerned with
repurposing drugs based on chemical similarity to existing drugs, with an
application to antibiotics. A simple ‘white box’ 2D chemical fingerprint-based
decision tree approach is shown to largely recapitulate a neural network study
in the literature. In particular, the repurposing of halicin is shown to be
based on an explicit fingerprint pattern, unlike the neural network ‘black box’
methodology.</p> | Gareth Williams | Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7574e567dfe6c2cec6663/original/novel-antibiotics-from-a-white-box-2d-structural-fingerprint-decision-tree.pdf |
60c755d54c89194feead4765 | 10.26434/chemrxiv.14170439.v1 | Identification of a Zika NS2B Epitope for Which Absence of IgG Response Is Associated with Severe Neurological Symptoms and the Design of a Biomarker Capable of Discriminatory Diagnostics Between Severe and Non4 Severe Clinical Phenotypes | <div>
<div>
<div><p><a></a>In this manuscript we describe the engineering of a biomarker for the diagnosis and prognosis of Zika-associated neurological disease. Although the causal association between congenital Zika virus (ZIKV) infection and neurological manifestations has been well documented in the recent years, biomarkers for proper diagnostic and disease outcome still remain to be defined. Combining high-density peptide array and multivariate analysis, we have identified an ZIKV epitope that is associated to a lack of IgG antibody response in patients with severe neurological symptoms. An engineered chimera was developed to discriminate between mild and severe clinical forms of the disease.</p></div>
</div>
</div> | Felix Loeffler; Isabelle F. T. Viana; Nico Fischer; Danilo F. Coêlho; Carolina Santos; Antonio Purificacao Jr; Catarina Araujo; Bruno Leite; Ricardo Durães-Carvalho; Thereza Magalhaes; Clarice Morais; Marli Tenório Cordeiro; Roberto Lins; Ernesto T.A. Marques; Thomas Jaenisch | Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755d54c89194feead4765/original/identification-of-a-zika-ns2b-epitope-for-which-absence-of-ig-g-response-is-associated-with-severe-neurological-symptoms-and-the-design-of-a-biomarker-capable-of-discriminatory-diagnostics-between-severe-and-non4-severe-clinical-phenotypes.pdf |
60c74ae4842e65573edb2fff | 10.26434/chemrxiv.12269480.v1 | Learning Machine Reasoning for Bioactivity Prediction of Chemicals | <p>We describe a method for learning higher-level vector representations of interactions between molecular features and biology. We named the representations as the <i>reason vectors</i>. In contrast to the high-dimensional chemical fingerprints, reason vectors are much simpler with only about 5 dimensions. They allow abstract reasoning for bioactivity of chemicals or absence thereof, uncover causal factors in interactions between chemical features and generalize beyond specific chemical classes or bioactivity. These qualities enable us to perform powerful similarity searches that are vague and conceptual in nature. The methodology can handle novel combinations of features in query molecules and can evaluate chemical classes that are entirely absent in training data. The method consists of similarity-based near neighbor search on a reference database of biologically tested chemicals by a series of substructures obtained from stepwise reconstruction of the test molecule. A data-driven continuous representation of molecular fragments was used for molecular similarity computations. The technique was inspired by the ability of humans to learn and generalize complex concepts by interacting with the physical world. We also show that activity prediction of chemicals using the abstract reason vectors is very easy and straightforward, as compared to modeling in the raw chemistry space, and can be applied to both binary and continuous activity outcomes. Except for utilizing an unsupervised training to construct continuous molecular fingerprints, the methodology is devoid of gradient optimization or statistical fitting.</p> | Suman Chakravarti | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ae4842e65573edb2fff/original/learning-machine-reasoning-for-bioactivity-prediction-of-chemicals.pdf |
660be98b9138d23161f1e032 | 10.26434/chemrxiv-2024-wtv9l | Light Induced Cobalt(III) Carbene Radical Formation from Dime-thyl Malonate as Carbene Precursor | Radical-type carbene transfer catalysis is an efficient method for the direct functionalization of C–H and C=C bonds. However, carbene radical complexes are currently formed via high-energy carbene precursors, such as diazo compounds or iodonium ylides. Many of these carbene precursors require additional synthetic steps, have an explosive nature or generate halogenated waste. Con-sequently, the utilization of carbene radical catalysis is limited by specific carbene precursors to access the carbene radical inter-mediate. In this study, we generate a cobalt(III) carbene radical complex from dimethyl malonate, which is commercially available and bench-stable. EPR and NMR spectroscopy were used to identify the intermediates and showed that the cobalt(III) carbene radical complex is formed upon light irradiation. In presence of styrene, carbene transfer occurred, forming cyclopropane as the product. With this photochemical method, we demonstrate that dimethyl malonate can be used as an alternative carbene precursor in the formation of a cobalt(III) carbene radical complex. | Demi D. Snabilié ; Bas de Bruin; Rens Ham; Joost N. H. Reek | Organometallic Chemistry; Bond Activation; Reaction (Organomet.); Spectroscopy (Organomet.) | CC BY 4.0 | CHEMRXIV | 2024-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660be98b9138d23161f1e032/original/light-induced-cobalt-iii-carbene-radical-formation-from-dime-thyl-malonate-as-carbene-precursor.pdf |
67ad7cb4fa469535b9204d13 | 10.26434/chemrxiv-2025-g0jdg | The Unique Factor Governing Atomistic Rh-Catalyzed Dehydrogenation of CH₄ | We uncovered that the valence density-of-states (DOS) gain, denoted as polarity (), of the catalyst Rh- uniquely governs the efficiency of CH4 dehydrogenation based on quantum computations of CH4-Rh(111;100) surfaces with and without Rh1 adatoms and Rh0 vacancies. Atomic undercoordination shortens the ligand-catalyst distance, transforming the undercoordinated Rh into a dipole Rh- species that forms the Rh-:H+-C- coupling bonds, where “:” denotes the electron-rich pole. The Rh-:H+ attraction and Rh-:C- repulsion shorten the RhP:H distance and elongate the H-C bond. The extents of Rh-:H-C segmental relaxation, catalyst valence band upward shift, and adsorption energy all vary exponentially with . The adsorption energy follows the order: Rh30(111) > Rh1/Rh(111) > Rh10(100) > Rh1/Rh(100) > Rh10(111) > Rh(100) > Rh(111) order, highlighting the significance of the dipolar coordination configuration. These findings should apply to undercoordinated catalytic reactions where the electric field of the dipolar catalyst plays a key role. | Changqing Sun | Catalysis; Homogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ad7cb4fa469535b9204d13/original/the-unique-factor-governing-atomistic-rh-catalyzed-dehydrogenation-of-ch4.pdf |
634c53afa2c7903edc4988ba | 10.26434/chemrxiv-2022-p7gnq | Polystyrene Laboratory Analysis: A Hands-On Experience to Determine the Molecular Weight of Polystyrene Through Spin Casting in A University Laboratory Setting | Hands-on learning is a staple in high school science education, as it provides students with a fast-learning curve and a great degree of field competency. However, due to the safety risks associated with high school students in university chemistry laboratory settings, high school students rarely engage in authentic hands-on chemical learning. To bridge the gap between the benefits and drawbacks, this study investigates a method to educate high school students (with no previous experience) about standard chemical laboratory practices. 98 high school students experimented throughout two days to determine the molecular weights and characteristics of various polystyrene samples, essential knowledge for polymer recycling. Students were split into 5 groups so that laboratory usage be organized and staggered. After laboratory safety training was administered, students created different types and concentrations of toluene-based samples and spin casted these samples onto silicon wafers, determining thickness through ellipsometry. With the data, each group calculated molecular weight, propagated error, and wrote laboratory reports. In order to evaluate the extent of learning through this process, students were given pre-training and post-experimentation assessments with the same questions pertaining to laboratory safety, equipment usage, and materials science related topics. On average, students displayed scores 63% higher on the post-experiment assessment compared to those of the pre-training assessment. The results suggest the experience not only taught students about the various materials science concepts, but also improved their laboratory logic. Therefore, our method is recommended to be implemented at the university level for motivated high school and first-year undergraduate students. | Sahil Sood; Sean Fang; Alexander Wang; Thomas Luong; Justin Kim; Arkajyoti Sinha; John Jerome; Miriam Rafailovich | Chemical Education; Chemical Education - General | CC BY 4.0 | CHEMRXIV | 2022-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634c53afa2c7903edc4988ba/original/polystyrene-laboratory-analysis-a-hands-on-experience-to-determine-the-molecular-weight-of-polystyrene-through-spin-casting-in-a-university-laboratory-setting.pdf |
6630e06c91aefa6ce1ce789a | 10.26434/chemrxiv-2024-nmm8w | Exploring the stereochemistry-specific tendency for interdigitation in synthetic monomycoloyl glycerol analogs through molecular dynamics simulations | Synthetic monomycoloyl glycerol (MMG) analogs possess robust immunostimulatory activity and are investigated as adjuvants for subunit vaccines in preclinical and clinical studies. These synthetic lipids consist of a glycerol moiety attached to a corynomycolic acid. Previous experimental studies have shown that the stereochemistry of the lipid acid moiety affects whether the MMG analogs self-assemble into interdigitated or non-interdigitated structures below the main phase transition temperature (Tm). In this study, we elucidated possible thermodynamic mechanisms governing the phase behavior of MMG analogs by exploring their conformations, interactions, and dynamics using molecular dynamics (MD) simulations. We compared two analogs, MMG-1 and MMG-6, which differ only by the stereochemistry of the lipid acid moiety; the former has a configuration different from the natural MMG, and the latter displays a native-like stereochemistry. Three different membrane states were simulated: 1) a non-interdigitated single bilayer, 2) a non-interdigitated double bilayer, and 3) a fully interdigitated double bilayer. Our results indicate that the propensity for interdigitation of the MMG analogs is linked to the degree to which their hydrocarbon chains are ordered and oriented, and the extent of the intermolecular interactions in their hydrophilic region. This study demonstrates how MD simulations can enhance the molecular understanding of vaccine adjuvants. | Suvi Heinonen; Artturi Koivuniemi; Matthew Davies; Mikko Karttunen; Camilla Foged; Alex Bunker | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6630e06c91aefa6ce1ce789a/original/exploring-the-stereochemistry-specific-tendency-for-interdigitation-in-synthetic-monomycoloyl-glycerol-analogs-through-molecular-dynamics-simulations.pdf |
62c5208925302155498ad512 | 10.26434/chemrxiv-2022-46vsh-v2 | Acetoxymethyl-BODIPY Dyes: A Universal Platform for the Fluorescence Labeling of Nucleophiles | Current methods for the preparation of functional small-molecule fluorophores generally require labor-intensive, multi-step synthetic routes for all the major chromophore groups. In spite of recent significant contributions from numerous laboratories, the paucity of rapid, straightforward and wide-scope synthetic strategies in this field is limiting the development of advanced probes for bioimaging, sensing and therapeutic applications. We describe herein a general and robust methodology for the one-step fluorescent labeling of a wide variety of molecules having C-, N-, P-, O-, S-, or halide-nucleophilic centers, using stable and readily available acetoxymethyl-BODIPYs as reagents in the presence of an acid catalyst. This modular methodology allows a very facile preparation of mono- and di-functional probes incorporating a broad assortment of biomolecules, enzyme cofactors, natural products, and other chromophores, as well as chemical functionalities for a wide range of applications including bioorthogonal conjugation, polymerization, and supramolecular chemistry, among others. The photophysical properties and preliminary applications of the new probes in live-cell imaging were also studied. The described strategy could enable the high-throughput engineering of novel BODIPY dyes with diverse functionalities for basic and applied research with potential for innovative technological applications. | Alberto Blazquez-Moraleja; Larissa Maierhofer; Enrique Mann; Ruth Prieto-Montero; Ainhoa Oliden-Sanchez; Lucia Celada; Virginia Martinez-Martinez; Maria-Dolores Chiara; Jose Luis Chiara | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c5208925302155498ad512/original/acetoxymethyl-bodipy-dyes-a-universal-platform-for-the-fluorescence-labeling-of-nucleophiles.pdf |
6646b1c8418a5379b07e4a02 | 10.26434/chemrxiv-2024-drdpr | Size-Dependent Spin Crossover and Bond Flexibility in Metal-Organic Framework Nanoparticles | Size reduction offers a synthetic route to tunable phase change behavior. Preparing materials as nanoparticles causes drastic modulations to critical temperatures (Tc), hysteresis widths, and the “sharpness” of first-order versus second-order phase transitions. A microscopic picture of the chemistry underlying this size dependence in phenomena ranging from melting to superconductivity remains debated. As a case study with broad implica-tions, we report that size-dependent spin crossover (SCO) in nanocrystals of the metal-organic framework (MOF) Fe(1,2,3-triazolate)2 arises from metal-linker bonds becoming more labile in smaller particles. In comparison to the bulk material, differential scanning calorimetry indicates a ~30-40% reduction in Tc and H in the smallest particles. Variable-temperature vibrational spectroscopy reveals a diminished long-range structural cooperativi-ty, while X-ray diffraction evidences an over three-fold increase in the thermal expansion coefficients. This “phonon softening” provides a molecular mechanism for designing size-dependent behavior in framework ma-terials and for understanding phase changes in general. | Audrey Davenport; Checkers Marshall; Taichi Nishiguchi; Kentaro Kadota; Anastasia Andreeva; Satoshi Horike; Carl Brozek | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Magnetism; Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6646b1c8418a5379b07e4a02/original/size-dependent-spin-crossover-and-bond-flexibility-in-metal-organic-framework-nanoparticles.pdf |
64f4e51c79853bbd78062846 | 10.26434/chemrxiv-2023-tqv4p-v4 | Predicting the Solubility of Gases, Vapors, and Supercritical Fluids in Amorphous Polymers from Electron Density using Convolutional Neural Networks | A twin convolutional neural network is proposed to predict the pressure and temperature-dependent sorption of gases, vapors, and supercritical fluids in amorphous polymers based solely on spatial electron density distribution. Quantum chemical data as 3D tensors (3D images) is derived from DFT calculations. A dataset of almost 15000 experimentally measured uptakes (0.01-50 wt%) of 79 gases in 102 different polymers under pressures from 1E-3 – 7E+2 bar range and temperatures from 233-508 K range is collected from over 250 literature sources. The dataset includes measurements on almost 500 solvent-polymer systems spanning from typical low-pressure sorption in membrane glassy polymers to high-pressure solubility of supercritical fluids in molten polymers. Irreducible mean absolute percentage error (MAPE) is approximately estimated to be ~20%. The sources of inherent data variability are briefly discussed. In 150 epochs, the model achieved 31% MAPE on a test set of 1600 experimental measurements concerning 22 polymers previously unseen by the model. | Oleg Gromov | Theoretical and Computational Chemistry; Physical Chemistry; Polymer Science; Computational Chemistry and Modeling; Machine Learning; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f4e51c79853bbd78062846/original/predicting-the-solubility-of-gases-vapors-and-supercritical-fluids-in-amorphous-polymers-from-electron-density-using-convolutional-neural-networks.pdf |
671fa36883f22e421472fe4f | 10.26434/chemrxiv-2024-3m084 | Resonant Auger Decay in Benzene | We present ab initio calculations of the resonant Auger spectrum of benzene. In the
resonant process, Auger decay ensues following the excitation of a core-level electron to
a virtual orbital. Hence, resonant Auger decay manifests itself in the Auger spectrum by
features with higher Auger electron energy compared to non-resonant decay. We apply
equation-of-motion coupled-cluster (EOM-CC) methods to compute the spectrum in order
to explain the main features in the experimental spectrum and to assess the capability
and limitations of the available theoretical approaches. The results indicate that participator
decay can be well described with the Feshbach–Fano approach based on EOM-CC
wavefunctions in the singles and doubles (SD) approximation, but spectator decay is more
difficult to describe. This is because the target states of spectator decay are doubly excited,
resulting in the need to include triple excitations in the EOM-CC wave function.
Resonant Auger decay in benzene is thus a challenging test case for EOM-CC theory. We
examine the performance of different noniterative triple corrections to EOM-IP-CCSD and
our numerical results highlight the need to include triple excitations iteratively. | Nayanthara Karippara Jayadev; Thomas-C Jagau; Anna I. Krylov | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671fa36883f22e421472fe4f/original/resonant-auger-decay-in-benzene.pdf |
60c7457a567dfe1e6cec447e | 10.26434/chemrxiv.10028603.v1 | Anionic and Cationic Redox Processes in β-Li2IrO3 and Their Structural Implications on Electrochemical Cycling in Li-Ion Cell | The recent discovery of anionic redox as a means to increase the energy density of transition metal oxide positive electrodes is now a well established approach in the Li-ion battery field. However, the science behind this new phenomenon pertaining to various Li-rich materials is still debated. Thus, it is of paramount importance to develop a robust set of analytical techniques to address this issue. Herein, we use a suite of synchrotron-based X-ray spectroscopies as well as diffraction techniques to thoroughly characterize the different redox processes taking place in a model Li-rich compound, the tridimentional hyperhoneycomb β-Li2IrO3. We clearly establish that the reversible removal of Li+ from this compound is associated to a previously described reductive coupling mechanism and the formation of the M-(O-O) and M-(O-O)* states. We further show that the respective contributions to these states determine the spectroscopic response for both Ir L3-edge X-ray absorption spectroscopy (XAS) and X-ray photoemissions spectroscopy (XPS). Although the high covalency and the robust tridimentional structure of this compound enable a high degree of reversibile delithiation, we found that pushing the limits of this charge compensation mechanism has significant effects on the local as well as average structure, leading to electrochemical instability over cycling and voltage decay. Overall, this work highlights the practical limits to which anionic redox can be exploited and sheds some light on the nature of the oxidized species formed in certain lithium-rich compounds.<br /> | Paul Pearce; Gaurav Assat; Antonella Iadecola; François Fauth; Rémi Dedryvère; Artem Abakumov; Gwenaëlle Rousse; Jean-Marie Tarascon | Electrochemistry; Solid State Chemistry; Spectroscopy (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7457a567dfe1e6cec447e/original/anionic-and-cationic-redox-processes-in-li2ir-o3-and-their-structural-implications-on-electrochemical-cycling-in-li-ion-cell.pdf |
621e3c33011b58c289b953ed | 10.26434/chemrxiv-2022-dz4zc | Beyond Atoms and Bonds: Contextual Explainability via Molecular Graphical Depictions | The field of explainable AI applied to molecular property prediction models has often been reduced to deriving atomic contributions. This has impaired the interpretability of such models, as chemists rather think in terms of larger, chemically meaningful structures, which often do not simply reduce to the sum of their atomic constituents. We develop an explanatory framework yielding both local as well as more complex structural attributions. We derive such contextual explanations in pixel space, exploiting the property that a molecule is not merely encoded through a collection of atoms and bonds, as is the case for string- or graph-based approaches. We provide evidence that the proposed explanation method satisfies desirable properties, namely sparsity and invariance with respect to the molecule’s symmetries. | Marco Bertolini; Linlin Zhao; Djork-Arné Clevert; Floriane Montanari | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2022-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621e3c33011b58c289b953ed/original/beyond-atoms-and-bonds-contextual-explainability-via-molecular-graphical-depictions.pdf |
63455f1d69f4403dcd787966 | 10.26434/chemrxiv-2022-s1s9x-v2 | Beyond single-crystal surfaces: The GAL21 water/metal force field | Solvent effects are notoriously difficult to describe for metallic nano-particles (NPs). Here, we introduce GAL21 the first pair wise additive force field that is specifically designed to modulate the near chemisorption energy of water as a function of the coordination numbers of the metallic atoms. We find a quadratic dependence to be most suitable for capturing the dependence of the adsorption energy of water on the generalized coordination number (GCN) of the metal atoms. GAL21 has been fitted against DFT adsorption energies for Cu, Ag, Au, Ni, Pd, Pt, and Co on 500 configurations and validated on about 3000 configurations for each metal, constructed on five surfaces with GCNs varying from 2.5 to 11.25. Depending on the metals, the RMSD is found between 0.7 kcal·mol−1 (Au) to 1.6 kcal·mol−1 (Ni). Using GAL21, as implemented in the open-source code CP2K, we then evaluate the solvation energy of Au55 and Pt55 NPs in water using thermodynamic integration. The solvation free energy is found to be larger for Pt and Au, and systematically larger than 200 kcal·mol−1, demonstrating the large impact of solvent on the surface energetics of NPs. Still, given that the amorphous NPs are both, the most stable and the most solvated ones, we do not predict a change in preferred morphology between the gas-phase and in water. | Paul Clabaut; Matthieu Beisert; Carine Michel; Stephan Steinmann | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2022-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63455f1d69f4403dcd787966/original/beyond-single-crystal-surfaces-the-gal21-water-metal-force-field.pdf |
60c73fdf4c891965adad201b | 10.26434/chemrxiv.7533407.v1 | Inorganic Co-Crystal Formation and Thermal Disproportionation in a Dicyanometallate 'Superperovskite' | <div>
<div>
<div>
<p>We report the synthesis, crystal structure, and thermally-
driven phase transformation of the dicyanometallate super-
perovskite co-crystal [NBu4]Mn[Au(CN)2]3·[NBu4]ClO4. This
phase is understandable in terms of the conventional ABX3
perovskite structure type, but with the NBu+4 A-site cation
displaced onto the perovskite cage face and 1-dimensional
AX′ chains included within framework pores opened up by
these displacements. On heating to 380K, the co-crystal
disproportionates into its two inorganic components: a
bcs-structured ABX3 phase and [NBu4 ]ClO4 . This system
illustrates a new type of structural and phase complexity
accessible to dicyanometallate perovskites.
</p>
</div>
</div>
</div> | Joshua A. Hill; Claire
A. Murray; Chiu C. Tang; Peter M. M. Thygesen; Amber L. Thompson; Andrew Goodwin | Hybrid Organic-Inorganic Materials; Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fdf4c891965adad201b/original/inorganic-co-crystal-formation-and-thermal-disproportionation-in-a-dicyanometallate-superperovskite.pdf |
649aa71aba3e99daef1d1756 | 10.26434/chemrxiv-2023-962ht | Could Acinetobacter baumannii Lol-abaucin docking be improved? | To explore alternative abaucin antibiotics predicting nanomolar affinities against Acinetobacter baumannii, thousands of virtual abaucin-derived molecules were randomly generated and selected. For this, alphafold-modeled A.baumannii lipoprotein outer membrane localization (Lol) complex proteins were targeted by DataWarrior "build evolutionary libraries". Abaucin-children libraries were generated from the abaucin-parent iteratively selecting those predicting higher affinities to the most probable A.baumannii LolCE docking-cavity. To improve accuracies, ~4000 abaucin-children docking-scores were consensed with those from AutoDockVina. The resulting laydown table provided with filter sliders would allow user-criteria to be applied. One example explored candidates predicting both higher nanomolar affinities to A.baumannii LolCE (to favor putative antibiotics) and lower affinities to E.coli LolCE (to favor narrow-bacterial spectrum hits). Despite being highly hypothetical, some of these abaucin-derived chemotypes may constitute another step towards exploring possible improvements for anti-A.baumannii antibiotics. | julio coll | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2023-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649aa71aba3e99daef1d1756/original/could-acinetobacter-baumannii-lol-abaucin-docking-be-improved.pdf |
60c73f1a567dfe548bec3912 | 10.26434/chemrxiv.7123193.v2 | SDFEater: A Parser for Chemoinformatics Formats | The use of computers to store and process different types of data is growing every day. The same applies to chemical data. SDF and Open Babel are recognized solutions in this field. However, each solution has its drawbacks, which are revealed in specific applications. It is important to be able to easily convert the collected data from one format to another. For this reason, we present SDFEater – a parser that allows to move data written in SDF to other formats including OpenCypher. This query language allows to import data on chemical compounds and store them in a graph database using our named property graphs model.<br /> | Łukasz Szeremeta | Chemoinformatics | CC BY 4.0 | CHEMRXIV | 2018-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1a567dfe548bec3912/original/sdf-eater-a-parser-for-chemoinformatics-formats.pdf |
66d84cd051558a15ef046443 | 10.26434/chemrxiv-2024-xpfm1 | SYNERGY OF ADVANCED MACHINE LEARNING AND DEEP NEURAL NETWORKS WITH CONSENSUS MOLECULAR DOCKING FOR ENHANCED POTENCY PREDICTION OF ALK INHIBITORS | This study addresses the urgent need for novel Anaplastic lymphoma kinase (ALK) inhibitors in Non-Small Cell Lung Cancer (NSCLC) treatment, focusing on the ALK-positive mutation variant (5% of the cases). As only five Food and Drug Administration (FDA)-approved ALK inhibitors are on the market, the demand for effective drugs persists. Leveraging the power of Artificial Intelligence (AI) including machine learning (ML), and deep learning, our research aimed to expedite the screening of novel ALK inhibitors. Notably, the machine learning-based XGBoost algorithm exhibited compelling results with an external validation (EV)-f1 score of 0.921, and an EV-Average Precision (AP) of 0.961, alongside a cross-validation (CV)-f1 score of 0.888±0.039 and a CV-AP of 0.939±0.032. Besides, the deep learning-based Artificial Neural Network (ANN) model demonstrated excellent performance with an EV-f1 score of 0.930 and an EV-AP of 0.955, complemented by a CV-f1 score of 0.891±0.037 and a CV-AP of 0.934±0.040. The present study undertook a comparative analysis between the traditional ML models, the ANN model, and the Graph Neural Network (GNN) model, which is a product of our recent research endeavors. The findings reveal that, despite the advancements in neural network models, traditional machine learning models exhibited superior performance over the GNN model. During this research, these models were employed in conjunction with a consensus molecular docking model to screen a total of 120,571 compounds virtually, leading to the identification of three promising ALK inhibitors: CHEMBL1689515, CHEMBL2380351, and CHEMBL102714. The study recommends further molecular dynamic simulations, in vitro tests, target-specific experimental data acquisition for active learning, and application of advanced AI models like geometric interaction GNN and generative AI for molecular optimization. | The-Chuong Trinh; Tieu-Long Phan; Van-Thinh To; Thanh-An Pham; Gia-Bao Truong; Hoang-Son Le; Xuan-Truc Tran; Tuyen Ngoc Truong | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d84cd051558a15ef046443/original/synergy-of-advanced-machine-learning-and-deep-neural-networks-with-consensus-molecular-docking-for-enhanced-potency-prediction-of-alk-inhibitors.pdf |
62b08fb5b7bbed6e0188aa0c | 10.26434/chemrxiv-2022-zd012 | A Cobalt Adduct of an N-hydroxy-piperidinium Cation | Cooperativity between organic ligands and transition metals in H-atom (proton/electron) transfer catalysis has been an important recent area of investigation. Tetramethylpiperidine-N-oxyl (TEMPO) radicals feature prominently in this area, prompting us to examine cooperativity between its hydrogenated congener, TEMPOH, and Co centers ligated by dihydrazonopyrrole ligands which have previously been shown to also store H-atom equivalents. Addition of TEMPOH to (tBu,TolDHP)CoOTf results in the formation of an unusual Co-adduct of 1-hydroxy-2,2,6,6-tetramethylpiperidin-1-ium (TEMPOH2+) which has been characterized with IR spectroscopy and single crystal X-ray diffraction. This adduct is thermally unstable, and decomposes, putatively via N–O homolysis, to generate 2,2,6,6-tetramethylpiperidine and the Co-hydroxide complex [(tBu,TolDHP)CoOH][OTf]. Computational investigations suggest a proton-coupled electron transfer step to generate the TEMPOH2+ adduct where the Co center serves as an electron acceptor. Despite the prevalence of aminoxyl reagents in catalysis, particularly in aerobic transformations, metal complexes of differently hydrogenated congeners of TEMPO are rare. The isolation of a TEMPOH2+ adduct and investigations into its formation shed light on related transformations that may occur during metal-aminoxyl cooperative catalysis. | Sophie Anferov; John Anderson | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Ligands (Inorg.); Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b08fb5b7bbed6e0188aa0c/original/a-cobalt-adduct-of-an-n-hydroxy-piperidinium-cation.pdf |
65665f4acf8b3c3cd7590658 | 10.26434/chemrxiv-2023-zbzgm | Organocatalytic Enantioselective [1,2]-Stevens Rearrangement of Azetidinium Salts | An organocatalyzed enantioselective [1,2]-Stevens rearrangement of ammonium ylides is reported. Using an isothiourea Lewis base organocatalyst, azetidinium salts underwent ring expansion to generate 4-alkylideneproline derivatives in high yield and good er. Products are readily recrystallizable to provide er’s of up to >99.5:0.5. Product configuration was established through X-ray crystallography and was opposite that predicted based on existing stereochemical models for this catalyst class. DFT calculations revealed that the facial selectivity of new bond formation is dictated by the pyramidalization of the enolate alpha-carbon in the ring-opening transition state. Notably, it is the catalyst benzylic hydrogen, and not the stereodirecting catalyst Ph, that influences this facial selectivity by stabilizing the developing pyramidalization of the enolate alpha-carbon in the transition state leading to the major enantiomer of product. Finally, under these reaction conditions, a tetrahydroisoquinolinium salt also underwent ring expansion to generate a benzazepine product as a single diastereomer in modest er. This result illustrates that this catalytic strategy for enantioselective [1,2]-Stevens rearrangement can be adapted for use with other synthetically- and medicinally-useful heterocyclic amine scaffolds. | Ana De Oliveira Silva; Shruti Masand; Abdikani Omar Farah; Jacqueline Laddusaw; Kelvin Urbina; Melanie Rodriguez-Alvarado; Roger Lalancette; Paul Ha-Yeon Cheong; Stacey Brenner-Moyer | Organic Chemistry; Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65665f4acf8b3c3cd7590658/original/organocatalytic-enantioselective-1-2-stevens-rearrangement-of-azetidinium-salts.pdf |
65676b5f5bc9fcb5c9a9b8f1 | 10.26434/chemrxiv-2023-7bt78 | Exploiting Response Surface Methodology to Advance Alginate-based Hydrogels for Precision Medicine | Tissue composition and cell organization rely on the extracellular matrix (ECM) which generates and transmits mechanical signals, triggering different cellular responses. Alginates are used in precision medicine, but as substrate for cells growth they lack adhesive domains and do not degrade. To overcome these key challenges, we developed a library of alginate-based hydrogels prepared following a two-step crosslinking. The compressive moduli and stability of hydrogels in vitro were modelled using a response surface method, enabling to decouple biochemical and biophysical properties. As biological systems use mechanical forces to regulate several processes, from tissue regeneration to cancer development, we selected alginate-based hydrogels with compressive moduli of breast tissues (1-20 kPa) model different stages of breast cancer development in vitro, and as new drug screening technologies. Human breast cancer cells (MDA-MB-231) were cultured on several hydrogels and as different in vitro models (i.e., 3D models and 2.5D models). All hydrogels are cytocompatible, allowing cells growth up to 1 week. We selected 2.5D in vitro models to investigate the correlation between drug efficacy and microenvironment/ECM stiffness, as more similar to standard 2D in vitro models (i.e., 2D/TCP). We selected doxorubicin as models drug, as first-line treatment for breast cancer. Interestingly, doxorubicin was less effective in cells cultured in softer hydrogels (EC50 0.495 ± 0.248 μM, 6.9 ± 0.6 kPa) than in stiffer ones (EC50 0.189 ± 0.032 μM, 21.0 ± 3.8 kPa), with the latter being similar to 2D/TCP controls (EC50 0.129 ± 0.028 μM, > 106 kPa). Obtained results demonstrate that the proposed hydrogel library with decoupled biophysical and biochemical properties enables to better study how microenvironmental cues impact on cell behaviour in vitro. Moreover, results suggest the need to use new approaches in precision medicine to study drug efficacy and resistance in the context of cancer, using in vitro models able to mimic different tumour progression microenvironments as in vivo. | Alessio Bucciarelli; Chen Zhao; Xue Bai; Ayse Latif; Kaye Williams; Annalisa Tirella | Materials Science; Polymer Science; Biocompatible Materials; Biopolymers; Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65676b5f5bc9fcb5c9a9b8f1/original/exploiting-response-surface-methodology-to-advance-alginate-based-hydrogels-for-precision-medicine.pdf |
65d642dc66c13817292f5eed | 10.26434/chemrxiv-2024-jcn9d | For Catching-by-Polymerization Oligo Purification: Scalable Synthesis of the Precursors to the Polymerizable Tagging Phosphoramidites | The catching-by-polymerization (CBP) oligodeoxynucleotide (oligo or ODN) purification method has been demonstrated suitable for large-scale, parallel, and long oligo purification. The authenticity of the oligos has been verified via DNA sequencing. Gene construction and expression have been demonstrated. A remaining obstacle to the practical utility of the CBP method is affordable polymerizable tagging phosphoramidites (PTPs) that are needed for the method. In this article, we report scalable synthesis of the four nucleoside (dA, dC, dG and dT) precursors to the PTPs using a route having six steps from inexpensive starting materials. The overall yields ranged from 21% to 35%. The scales of the synthesis presented here are up to 2.1 grams of the precursors. Because the syntheses are chromatography-free, they are predicted to be readily scalable. With the precursors, the PTPs can be synthesized in one step using standard methods involving a chromatography purification. | Yipeng Yin; Komal Chillar; Alexander Apostle; Bhaskar Halami; Adikari M. D. N. Eriyagama; Marina Tanasova; Shiyue Fang | Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Process Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d642dc66c13817292f5eed/original/for-catching-by-polymerization-oligo-purification-scalable-synthesis-of-the-precursors-to-the-polymerizable-tagging-phosphoramidites.pdf |
65e9108c9138d23161dcf37a | 10.26434/chemrxiv-2023-98n6q-v2 | Reproducible mass spectrometry data processing and compound annotation in MZmine 3 | Untargeted MS experiments produce complex, multi-dimensional data that are practically impossible to investigate manually. For this reason, computational pipelines are needed to extract relevant information from raw spectral data and convert it into a more comprehensible format. Based on the sample type and/or goal of the study, a variety of MS platforms can be used for such analysis. MZmine is open-source software for the processing of raw spectral data generated by different MS platforms: liquid chromatography–MS (LC–MS), gas chromatography–MS (GC–MS), and MS–imaging. Moreover, the third version of the software, described herein, supports the processing of ion mobility spectrometry (IMS) data. The present protocol provides three distinct procedures to perform feature detection and annotation of untargeted MS data produced by different instrumental setups: LC–(IMS–)MS, GC–MS, and (IMS–)MS imaging. For training purposes, example datasets are provided together with configuration batch files (i.e. list of processing steps and parameters) to allow new users to easily replicate the described workflows. Depending on the number of data files and available computing resources, we anticipate this to take between 2 and 24 hours for new MZmine users and non-experts. Within each procedure, we provide a detailed description for all processing parameters together with instructions/recommendations for their optimization. The main generated outputs are represented by aligned feature tables and fragmentation spectra lists that can be used by other third-party tools for further downstream analysis. | Tito Damiani; Steffen Heuckeroth; Aleksandr Smirnov; Olena Mokshyna; Corinna Brungs; Ansgar Korf; Joshua Smith; Paolo Stincone; Nicola Dreolin; Louis-Félix Nothias; Tuulia Hyötyläinen; Matej Orešič; Uwe Karst; Pieter Dorrestein; Daniel Petras; Xiuxia Du; Justin van der Hooft; Robin Schmid; Tomáš Pluskal | Analytical Chemistry; Chemoinformatics; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e9108c9138d23161dcf37a/original/reproducible-mass-spectrometry-data-processing-and-compound-annotation-in-m-zmine-3.pdf |
651656bda69febde9ee4c1c2 | 10.26434/chemrxiv-2023-lpj11 | Models for the Structure and Function of the Ethylene Receptor | A chemical model for the ethylene receptor in higher plants has been supported through the synthesis, spectroscopy, and structural characterization of several copper complexes with model ligands representing those in the native receptor protein, combined with alkene ligands. Some corresponding silver complexes have been investigated owing to the well-known effects of silver ion as an inhibitor of ethylene physiological action. | Yunfan Zou; Michael Pirrung | Biological and Medicinal Chemistry; Organometallic Chemistry; Chemical Biology; Bioorganometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651656bda69febde9ee4c1c2/original/models-for-the-structure-and-function-of-the-ethylene-receptor.pdf |
60c756febb8c1a11503dc6ee | 10.26434/chemrxiv.14355422.v1 | Bifunctional Iminophosphorane Catalyzed Enantioselective Sulfa-Michael Addition to Unactivated α,β-Unsaturated Amides | <div>The first metal-free catalytic intermolecular enantioselective sulfa-Michael addition to unactivated <i>α</i>,<i>β</i>- unsaturated amides is described. Consistently high enantiomeric excesses, and yields were obtained over a wide range of alkyl thiol pronucleophiles and electrophiles under mild reaction conditions, enabled by a novel squaramide-based bifunctional iminophosphorane (BIMP) catalyst. Low catalyst loadings (2 mol%) were achieved on a decagram scale, demonstrating the scalability of the reaction. Computational analysis revealed the origin of the high enantiofacial selectivity, corresponding transition states, and provided substantial evidence for specific non-covalent activation of the carbonyl group of the <i>α</i>,<i>β</i>-unsaturated amide by the catalyst.</div> | Daniel Rozsar; Michele Formica; Ken Yamazaki; Trevor Hamlin; Darren J. Dixon | Base Catalysis; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756febb8c1a11503dc6ee/original/bifunctional-iminophosphorane-catalyzed-enantioselective-sulfa-michael-addition-to-unactivated-unsaturated-amides.pdf |
6516e4c200659409121f2c64 | 10.26434/chemrxiv-2023-9gkk4-v2 | Rediscovering the particle in a box: Machine learning regression analysis for hypothesis generation in physical chemistry lab | Given the growing prevalence of computational methods in chemistry, it is essential that undergraduate curricula introduce students to these approaches. One such area is the application of machine learning (ML) techniques to chemistry. Here we describe a new activity that applies ML regression analysis to the common physical chemistry laboratory experiment on the electronic absorption spectra of cyanine dyes. In the classic version of this experiment, students collect experimental spectra and interpret them using the Kuhn free electron model, based on the quantum mechanical particle-in-a-box (PIB). Our new computational activity has students train regression models of increasing complexity to predict the wavelength of maximum absorption for different cyanine dyes using a set of 13 molecular features. In addition, the activity introduces methods for evaluating and interpreting regression models. Ultimately, students are prompted to use their regression analysis results to generate hypotheses for what molecular properties underlie cyanine dye absorption, leading them naturally to the PIB model. In this report, we provide a dataset, reference code implementations in Mathematica and Python notebooks, and an example lab protocol with an introduction to cyanine dyes and the ML techniques. This activity can be completed in a single 3-hour lab period by upper-level undergraduate students with relatively little prior programming experience. Although intended to complement the experimental measurement of cyanine dye spectra, this activity can also be performed on its own; alternatively, it can form the basis of more involved projects in a computational chemistry or machine learning course. | Elizabeth Thrall; Fernando Martinez Lopez; Thomas Egg; Seung Eun Lee; Joshua Schrier; Yijun Zhao | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Education; Chemical Education - General; Machine Learning; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6516e4c200659409121f2c64/original/rediscovering-the-particle-in-a-box-machine-learning-regression-analysis-for-hypothesis-generation-in-physical-chemistry-lab.pdf |
66265b07418a5379b061d849 | 10.26434/chemrxiv-2024-w1c2r | Leveraging Magnetic Resonance Imaging to Study Biocompatible Scaffolds Diffusion and Perfusion for Lab-on-a-Chip Systems | To foster the efficient development of 3D cell culture models, we developed a strategy to assess the liquid flow perfusion through biocompatible scaffolds. Biocompatible scaffolds play a crucial role in creating 3D in vitro models for precision medicine. Therefore, it is imperative to thoroughly characterise the physical properties of these scaffolds. In this study, we leverage nuclear magnetic resonance imaging (MRI) to examine the diffusivity and perfusion properties of commonly used cryogels and hydrogels. We used deuterium oxide (i.e. heavy water) as a contrast agent to monitor the reduction in proton concentration from water within the scaffolds due to molecular motion. By analysing pixel intensity in MRI images, we extract information on the diffusion speed and perfusion efficacy of these materials. This approach allowed us to investigate passive water diffusion in a carboxymethyl cellulose cryogel and polyethylene glycol diacrylate hydrogel. The diffusion rates differed by 50% between the two scaffolds. Furthermore, we measured their perfusion properties in a PDMS microfluidic chip. | Marc Azagra; David Gomez-Cabeza; Alejandro Portela; Gergo Matajsz; Nuria Torras; Elena Martinez; Irene Marco-Rius | Biological and Medicinal Chemistry; Materials Science; Biocompatible Materials; Biological Materials; Imaging Agents | CC BY 4.0 | CHEMRXIV | 2024-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66265b07418a5379b061d849/original/leveraging-magnetic-resonance-imaging-to-study-biocompatible-scaffolds-diffusion-and-perfusion-for-lab-on-a-chip-systems.pdf |
65c9c3f59138d23161ea5d32 | 10.26434/chemrxiv-2023-02n4r-v2 | From Humorous Post to Detailed Quantum-Chemical Study: Isocyanate Synthesis Revisited | Isocyanates play an essential role in modern manufacturing processes, especially in polyurethane production. There are numerous synthesis strategies for isocyanates both in industrial and laboratory conditions, which do not prevent searching for alternative highly efficient synthetic protocols. Here, we report a detailed theoretical investigation of the mechanism of sulfur dioxide-catalyzed rearrangement of the phenylnitrile oxide into phenyl isocyanate, which was first reported in 1977. The DLPNO-CCSD(T) method and up-to-date DFT protocols were used to perform a highly accurate quantum-chemical study of the rearrangement mechanism. An overview of various organic and inorganic catalysts has revealed other potential catalysts, such as sulfur trioxide and selenium dioxide. Furthermore, the present study elucidated how substituents in phenylnitrile oxide influence reaction kinetics. This study was performed by a self-organized collaboration of scientists initiated by a humorous post on the VK social network. | Oleg B. Beletsan; Igor Gordiy; Sergey S. Lunkov; Mikhail A. Kalinin; Larisa E. Alkhimova; Egor A. Nosach; Egor A. Ilin; Alexandr V. Bespalov; Olgert L. Dallakyan; Aleksandr A. Chamkin; Ilya V. Prolomov; Radion A. Zaripov; Andrey A. Pershin; Bogdan O. Protsenko; Yury V. Rusalev; Ruslan A. Oganov; Diana K. Kovaleva; Vladimir A. Mironov; Victor V. Dotsenko; Alexandr M. Genaev; Dmitry I. Sharapa; Denis Tikhonov | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Computational Chemistry and Modeling; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c9c3f59138d23161ea5d32/original/from-humorous-post-to-detailed-quantum-chemical-study-isocyanate-synthesis-revisited.pdf |
67af28ea81d2151a0269d411 | 10.26434/chemrxiv-2025-c498w | New Osmocene and Ruthenocene Phases Reveal the Common Conformational Behavior Regulated by Anagostic Bonds in Prototypical Metallocenes | Ruthenocene and osmocene, at normal conditions isostructural to low-temperature ferrocene phase III, are regarded as prototypic metallocenes exclusively present in the energetically-favored eclipsed conformation. This strong preference contrasts with ferrocene, exhibiting the staggered, rotated, eclipsed, disordered and modulated conformations in its five polymorphic forms. Here we show that ruthenocene at 394.0 K and osmocene at 421.5 K transform to new higher-symmetry phases, disordered between the staggered and eclipsed conformers. For the prototypic metallocenes, a common pattern of transformations leading to disordered conformations has been connected with intramolecular anagostic bonds CH‧‧‧M (M = Fe, Ni, Ru, Os). Their strength correlates with the critical temperatures of phase transitions, when the anagostic bonds are broken. | Ida Moszczyńska; Marek Szafrański; Andrzej Katrusiak | Physical Chemistry; Organometallic Chemistry; Small Molecule Activation (Organomet.); Physical and Chemical Properties; Thermodynamics (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67af28ea81d2151a0269d411/original/new-osmocene-and-ruthenocene-phases-reveal-the-common-conformational-behavior-regulated-by-anagostic-bonds-in-prototypical-metallocenes.pdf |
655534bc6e0ec7777f05100f | 10.26434/chemrxiv-2023-xzt9f | Ruthenium-Based Electrode Modified by Gold Particles as Voltammetric Sensor for Non-Enzymatic Epinephrine Detection | A simple and efficient technique for voltammetric enzymeless detection of epinephrine (EP) is proposed. The technique applies hierarchical Ru-based electrodes modified by Au nano- to micro-sized particles, which were produced with laser-assisted synthesis. The cyclic voltammetry (CV) and differential pulse voltammetry (DPV) were employed to characterize electrochemical properties of the electrodes. For EP detection, we obtained two DPV calibration curves that are linear in the range of 0.01-5 μM and 5-500 μM. The highest sensitivity (46.9 μA μM−1 cm−2) and the lowest detection limit (6.1 nM) are observed for the first linear range, whereas the estimated sensitivity and limit of detection for the second linear range are 2.1 μA μM−1 cm−2 and 17.8 nM, respectively. We also demonstrated that the proposed technique can be used for selective EP determination in the presence of such common interfering analytes as ascorbic acid and dopamine. The results of this study can be employed for development of low-cost voltammetric sensor platforms for non-enzymatic epinephrine detection in a physiological environment. | Maxim S. Panov; Dmitrii M. Nikolaev; Andrey A. Shtyrov; Sergey Yu. Vyazmin; Andrey S. Mereshchenko; Andrey V. Vasin; Mikhail N. Ryazantsev | Biological and Medicinal Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655534bc6e0ec7777f05100f/original/ruthenium-based-electrode-modified-by-gold-particles-as-voltammetric-sensor-for-non-enzymatic-epinephrine-detection.pdf |
65780d4dbec7913d276a05fa | 10.26434/chemrxiv-2023-7606k | Stereoretentive Decarboxylative C-3 Func-tionalization of Chromone-3-carboxylic Acids via Visible Light Irradiation | ABSTRACT: Herein, we report a stereoretentive and decar-boxylative C-3 functionalization of chromone-3-carboxylic acids with optically active aziridines via visible light irradia-tion. This metal-free and operationally simple protocol utilizes a simple combination of stable and inexpensive tetrabu-tylammonium iodide and visible light irradiation. It enables a facile and direct access to chiral 3-substituted chromenones with maintaining the optical purity of starting aziri-dines.Cross-coupling reactions allowing for efficient carbon–carbon as well as carbon–heteroatom bond formations are of crucial importance in the modern organic chemistry.1 Among them transition-metal-catalyzed decarboxylative cross-couplings utilizing carboxylic acids as substrates occupy a prominent position.2 They offer several distinctive advantages related to availability and price of carboxylic acid derivatives, their stability and handling as well as generation of less-toxic carbon dioxide as the by-product that reduces the waste treatment costs. While these methods have proven particularly useful for C(sp2)-C(sp2) bond formations and were applied for the synthesis of numerous relevant products ranging from pharmaceuticals to organic materials, their application in the C(sp2)-C(sp3) remains limited. Consequently, there is a need for the development of alternative, transition-metal-free cross-coupling reactions allowing for C(sp2)-C(sp3) bond formations. | Mohsen Monirialamdari; Ewelina Kowalska; Lesław Sieroń; Łukasz Albrecht; Anna Albrecht | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65780d4dbec7913d276a05fa/original/stereoretentive-decarboxylative-c-3-func-tionalization-of-chromone-3-carboxylic-acids-via-visible-light-irradiation.pdf |
62a176e5769c5e664049856b | 10.26434/chemrxiv-2022-dnstl | Actinide Arene-Metalates: 2. A Neutral Uranium Bis(Anthracenide) Sandwich Complex and Elucidation of its Electronic Structure | An unprecedented sandwich complex of the actinides is synthesized from the treatment of [UI2(HMPA)4]I (HMPA = OP(NMe2)3) (2) with 3 equiv. of K[C14H10] to give the neutral, bis(arenide) species U(η6-C14H10)(η4-C14H10)(HMPA)2 (1). Solid-state X-ray, SQUID magnetometry, and XANES analyses are consistent with tetravalent uranium supported by [C14H10]2- ligands. In one case, treatment of 1 with an equiv. of AgOTf led to the isolation of U(η6-C14H10)2(HMPA)(THF) (3), formed from ring migration and haptotropic rearrangement. Complete active space (CASSCF) calculations indicate the U-C bonding to solely consist of π-interactions, presenting a unique electronic structure distinct from classic actinide sandwich compounds. | Jesse Murillo; Rina Bhowmick; Katie Harriman; Alejandra Gomez-Torres; Joshua Wright; Pere Miro; Alejandro Metta-Magana; Muralee Murugesu; Bess Vlaisavljevich; Skye Fortier | Organometallic Chemistry; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a176e5769c5e664049856b/original/actinide-arene-metalates-2-a-neutral-uranium-bis-anthracenide-sandwich-complex-and-elucidation-of-its-electronic-structure.pdf |
6419e228dab08ad68f7b5702 | 10.26434/chemrxiv-2023-486mp | Arylidene Meldrum's Acid: A Versatile Structural Motif for the Design of Enzyme-Responsive "Covalent-Assembly" Fluorescent Probes with Tailor-Made Properties | Latent cyclic carbon-centered nucleophiles (latent C-nucleophiles) are recently proving their value in the field of reaction-based fluorescent probes, far beyond their primary utility in organic synthesis. They are typically used to introduce a Michael acceptor moiety acting as a recognition/reaction site for analyte to be detected or as a kinetic promoter of fluorogenic cascade reactions triggered by a reactive species. C-nucleophiles bearing a further reactive handle offer an additional opportunity for tuning the physicochemical/targeting properties or providing drug-releasing capabilities to these probes, through the covalent attachment of ad hoc chemical moiety. In order to implement such strategy to fluorogenic/chromogenic enzyme substrates based on the "covalent-assembly" principle, we have explored the potential of some functionalized derivatives of barbituric acid, piperidine-2,4-dione and Meldrum's acid. Our investigations based on the rational design and analytical validations of enzyme-responsive caged precursors of fluorescent pyronin dyes and 7-(diethylamino)coumarin-3-carboxylic acid, led to identify a versatile candidate suitable for this late-stage structural optimization approach with a minor impact on stability and activation kinetics of probe. This Meldrum's acid derivative, synthesized from levulinic acid, enables to either enhance water solubility or achieve the reversible conjugation of a targeting ligand, while promoting in situ formation of fluorophore upon enzymatic activation. This study opens the way to novel multifunctional fluorescence imaging probes and optically modulated small conjugate-based theranostics drawing on the promising "covalent-assembly" strategy. | Kévin RENAULT; Yoan CAPELLO; Shun YAO; Sami HALILA; Anthony ROMIEU | Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6419e228dab08ad68f7b5702/original/arylidene-meldrum-s-acid-a-versatile-structural-motif-for-the-design-of-enzyme-responsive-covalent-assembly-fluorescent-probes-with-tailor-made-properties.pdf |
62345e7d13d478def692d7cb | 10.26434/chemrxiv-2022-6kpmj | Efficient and accurate description of Diels-Alder
reactions using density functional theory | Modeling chemical reactions using Quantum Chemistry is a widely used predictive
strategy capable to complement experiments in order to understand the intrinsic mech-
anisms guiding the chemicals towards the most favorable reaction products. However,
to do so, it is mandatory to use reliable and computationally tractable theoretical meth-
ods. In this work, we focus on six Diels-Alder reactions of increasing complexity and
perform an extensive benchmark of middle- to low-cost computational approaches to
predict the characteristic reactions energy barriers. We found that Density Functional
Theory, using the ωB97XD, LC-ωPBE, CAM-B3LYP, M11 and MN12SX functionals,
with empirical dispersion corrections coupled to an affordable 6-31G basis set, provides
quality results for this class of reactions, at a small computational effort.
Such efficient and reliable simulation protocol opens perspectives for hybrid QM/MM
molecular dynamics simulations of Diels-Alder reactions including explicit solvation. | Daniele Loco; Isabelle Chataigner; Jean-Philip Piquemal; Riccardo Spezia | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62345e7d13d478def692d7cb/original/efficient-and-accurate-description-of-diels-alder-reactions-using-density-functional-theory.pdf |
6473ba994f8b1884b76d46c4 | 10.26434/chemrxiv-2023-mfngl | The poisonous truth about the mercury drop test: the effect of elemental mercury on Pd(0) and Pd(II)ArX intermediates | The mercury drop test is a widely used method for distinguishing between homogeneous and heterogeneous catalysis in organometallic systems. However, recent research has highlighted the limitations of this test due to the intrinsic reactivity of some organometallic compounds towards elemental mercury. In this study, we used real-time mass spectrometry with charge-tagged substrates to investigate the effect of elemental mercury on LnPd0 and PdIIArX intermediates common in palladium-catalysed cross-coupling reactions. Our findings demonstrate that mercury can interact with both species through redox-transmetallation and amalgamation processes, leading to a decrease in catalytic activity. This result further calls into question the fundamental assumption of mercury selectivity towards heterogeneous catalytic species. These results highlight the importance of careful consideration of the results the mercury drop test provides and encourages further research to gain a more comprehensive understanding of catalyst poisoning mechanisms. | Ian Chagunda; Tiago Fisher; Makenna Schierling; Scott McIndoe | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Heterogeneous Catalysis; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6473ba994f8b1884b76d46c4/original/the-poisonous-truth-about-the-mercury-drop-test-the-effect-of-elemental-mercury-on-pd-0-and-pd-ii-ar-x-intermediates.pdf |
60fab7d38f6bf6494c707259 | 10.26434/chemrxiv-2021-5q4mb | Evaluation of an Internal Standard for Qualitative DART-MS Analysis of Seized Drugs | Rapid and accurate screening tools for seized drug analysis continue to be needed due to the complexities associated with the emerging drug landscape. Direct analysis in real-time mass spectrometry (DART-MS) is one technique that has been used for this purpose and is seeing increased implementation due to its ability to provide high-fidelity information rapidly. As with any analytical technique, ensuring data integrity with DART-MS results is critical. To further enhance data integrity and eliminate some of the challenges associated with qualitative analysis of seized drugs using DART-MS, the incorporation of an internal standard was investigated. After evaluating a number of candidate compounds, tetracaine was chosen because of its desirable characteristics. An appropriate concentration of tetracaine was established that provided similar sensitivity to GC-MS for a panel of drugs. The presence of tetracaine in a drug extract was found to cause a reduction in signal for some common drugs due to competitive ionization but did not cause complete suppression of signal at relevant concentrations. Evaluation of a set of 60 representative case samples with and without internal standard found that the presence of internal standard did not negatively impact the results and that its presence eliminated the false identification of noise peaks in negative samples. The use of an internal standard also provided within-sample mass calibration and analyte concentration checks. It also allowed for automated mass drift compensation, removing a time-consuming process for high resolution DART-MS data processing. | Edward Sisco; Amber Burns; Elizabeth Schneider; Ikenna Ikpeama | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60fab7d38f6bf6494c707259/original/evaluation-of-an-internal-standard-for-qualitative-dart-ms-analysis-of-seized-drugs.pdf |
6739d2237be152b1d05dfeda | 10.26434/chemrxiv-2024-d35f7 | Novel tetrapeptides, tengupeptins A and B, produced by
Lecanicillium aphanocladii FKI-9593 fungal strain
| The discovery of novel natural products through the exploration of distinct microorganisms is crucial for advancing drug discovery research. In this study, we focus on a unique environmental resource, microbial masses known as "Tengu-no-Mugimeshi." From the culture broth of Lecanicillium aphanocladii FKI-9593, isolated from Tengu-no-Mugimeshi collected at Mount Kurohime, Nagano Prefecture, Japan, we report the isolation of two novel tetrapeptides, tengupeptins A (1) and B (2), as well as the known compound oosporein. Structural analysis revealed that tengupeptins are composed of four amino acids: L-pyroglutamic acid for 1 (or L-glutamic acid for 2), (Z)-α,β-didehydro tryptophan (ΔZTrp), (Z)-α,β-didehydro-phenylalanine (ΔZPhe), and L-aspartic acid. Notably, dehydroamino acids containing an aromatic moiety conjugated with a double bond connected via two or more consecutive linkages are rare in natural products, and the ΔZTrp-ΔZPhe fragment represents the first example. The isolation of secondary metabolites from filamentous fungi inhabiting unique environments, such as Tengu-no-Mugimeshi, is anticipated to offer significant potential for future research. | Akihiro Sugawara; Hiroki Kojima; Yoshihiro Watanabe; Mayuka Higo; Taiga Kasuya; Kenichi Nonaka; Masato Iwatsuki | Organic Chemistry; Natural Products; Organic Compounds and Functional Groups | CC BY NC 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6739d2237be152b1d05dfeda/original/novel-tetrapeptides-tengupeptins-a-and-b-produced-by-lecanicillium-aphanocladii-fki-9593-fungal-strain.pdf |
67c3d6c081d2151a02abf886 | 10.26434/chemrxiv-2025-fnhdd | Spontaneous Trisulfide Metathesis in Polar Aprotic Solvents | Sulfur-sulfur bonds are ubiquitous across broad classes of natural products, peptides and proteins, drug molecules, and synthetic polymers and materials. The ability to make and break these bonds in a controlled manner is critical for their many scientific and technological applications. In this study, we report the discovery of a new and unusual S-S metathesis reaction of linear organic trisulfides. When exposed to certain polar aprotic solvents, trisulfides were found to undergo spontaneous metathesis, with equilibrium established in seconds in some cases. No exogenous reagents, heat, light, or other stimuli were required to provoke this reaction. Understanding the scope and mechanism of this reaction enabled diverse applications of this chemistry in dynamic combinatorial library synthesis, covalent modification of complex natural products, and S-S metathesis polymerization and depolymerization as a platform for chemically recyclable plastics. | Harshal Patel; Alfrets Tikoalu; James Smith; Zhipeng Pei; Ryan Shapter; Samuel Tonkin; Peiyao Yan; Witold Bloch; Martin Johnston; Jeffrey Harmer; Christopher Gibson; Michael Perkins; Tom Hasell; Michelle Coote; Zhongfan Jia; Justin Chalker | Theoretical and Computational Chemistry; Organic Chemistry; Polymer Science; Combinatorial Chemistry; Organic Compounds and Functional Groups; Polymerization (Polymers) | CC BY 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c3d6c081d2151a02abf886/original/spontaneous-trisulfide-metathesis-in-polar-aprotic-solvents.pdf |
67c78a706dde43c9088481f3 | 10.26434/chemrxiv-2025-7j16n | Design of Light Driven Hole Bifurcating Proteins | Electron bifurcation reactions divide electrons from two-electron donors into high- and low-energy pools by transporting charge on spatially separated low- and high-potential electron hopping pathways. Bifurcation delivers electrons at potentials that drive downstream reactions in photosynthesis, respiration, and biocatalysis. Recent theoretical studies have described the requirements for effective ground-state electron bifurcation. The aim of this study is to design synthetic bifurcation constructs that can be driven by light. We describe a strategy to bifurcate holes (oxidizing equivalents) efficiently with light, and we present an illustrative energy landscape that could support this design. The design focuses on the electrochemical potentials and distances between cofactors. The analysis finds that hole bifurcation may be driven efficiently with light, guiding the further development of bioinspired networks that bifurcate charge and deliver the charges with prescribed electrochemical potentials. | Xiao Huang; Jonathon Yuly; Peng Zhang; William DeGrado; Michael Therien; David Beratan | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c78a706dde43c9088481f3/original/design-of-light-driven-hole-bifurcating-proteins.pdf |
630a75f890802de0d16c74ef | 10.26434/chemrxiv-2022-l2mlb | Steric, Electronic and Conformational Synergistic Effects in the Au(I)-catalyzed alpha-C-H Bond Functionalization of Tertiary Amines | Direct C-H bond functionalization is a useful strategy for the straightforward formation of C-C and C-Heteroatom bonds. In the present work, a unique approach for the challenging electrophilic Au-catalyzed alpha-C-H bond functionalization of tertiary amines is presented. Electronic, steric and conformational synergistic effects exerted by the use of a malonate unit in the substrate were key to the success of this transformation. This new reactivity was applied to the synthesis of tetrahydro-g-carboline products which, under oxidative conditions, could be converted into valuable structural motifs found in bioactive alkaloid natural products | David F. León Rayo; Ali Mansour; Wenbin Wu; Benjamin N. Bhawal; Fabien Gagosz | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630a75f890802de0d16c74ef/original/steric-electronic-and-conformational-synergistic-effects-in-the-au-i-catalyzed-alpha-c-h-bond-functionalization-of-tertiary-amines.pdf |
662c15a891aefa6ce1889468 | 10.26434/chemrxiv-2024-nqgk1 | Control of iron(II)-tris(2,2'-bipyridine) light-induced excited-state trapping via external electromagnetic fields | Photoinduced spin crossover reactions in iron pyridinic complexes allow the iron's lowto-high spin transition in a sub-picosecond timescale. Employing a recently developed model for [Fe(2,2'-bipyridine)3]2+ photochemical spin-crossover reaction in conjunction with quantum wavepacket dynamics, we explore the possibility of controlling the reaction through external electromagnetic fields, aiming at stabilizing the initial metal-to-ligand charge transfer states. We show that simple Gaussian-shaped electromagnetic fields have a minor effect on the population kinetics. However, introducing vibrationally excited initial wavepacket representations allow to maintain trapped the population into the metal-to-ligand charge transfer states. Using optimal control theory, we propose an electromagnetic field shape that increases the lifetime of metal-to-ligand charge transfer states. These results open the route for controlling the iron photochemistry through the action of external electric fields. | Marc Alías-Rodríguez; Miquel Huix-Rotllant | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662c15a891aefa6ce1889468/original/control-of-iron-ii-tris-2-2-bipyridine-light-induced-excited-state-trapping-via-external-electromagnetic-fields.pdf |
64c967be658ec5f7e5932996 | 10.26434/chemrxiv-2023-8z9gp | High throughput mass spectrometry assay for early chick gender determination: less than 3s total analysis time per sample. | Chicken eggs are one of the most consumed foods around the world. However, male chickens from egg-producing species are considered unprofitable as they produce too little meat and no eggs. For this reason, day-old male chicks are discarded, lead-ing to animal welfare concerns. As an alternative for chick culling, we have recently reported 3-[(2-aminoethyl)sulfanyl]butanoic acid (ASBA) as a biomarker for early in ovo gender determination. In the present work, we describe the optimization of acoustic droplet ejection-mass spectrometry (ADE-MS) conditions and automated sample prepa-ration compatibility for the high throughput quantification of ASBA from allantoic fluid. Special attention is given to the optimization of ADE-MS compatible liquid handling and the development of the data processing to ensure a reliable gender prediction. We have been able to accurately determine the gender of day-9 eggs with a prediction accuracy of 96%, with a throughput of 1800 samples per hour. | Nicolas Drouin; Chang Liu; David M. Cox; J. Bryce Young; Serge Desmoulins; Kelly Hoogkamer; Leonard van Bommel; Farzana Azam; James Wighton; Thomas R. Covey; Wouter Bruins; Wil Stutterheim; Amy C. Harms; Thomas Hankemeier | Analytical Chemistry; Agriculture and Food Chemistry; Biochemical Analysis; Mass Spectrometry; High-throughput Screening | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c967be658ec5f7e5932996/original/high-throughput-mass-spectrometry-assay-for-early-chick-gender-determination-less-than-3s-total-analysis-time-per-sample.pdf |
6121aa74fa49ac720857e3b8 | 10.26434/chemrxiv-2021-jl06r | High-contrast Background-free Magnetic Resonance Molecular Imaging | One of the holy grails in cancer detection and therapy is to simultaneously image and deliver drugs to the tumor site using a safe nanoparticle. Liposomes are a well-known safe and stable nanoparticles that can be loaded with a drug and suitable contrast agent for magnetic resonance imaging (MRI). However, the loading of a contrast agent such as gadolinium in liposomes generally results in poor contrast and various artifacts in in vivo experiments, compared to free gadolinium chelate experiments. Current work demonstrates the effective filtering of artifacts and contrast enhancement to obtain high quality images of the tumor sites in mouse models using paramagnetic liposome nanoparticles as contrast agent, a novel pulse sequence in active-feedback MRI, and nonlinear fitting. Our results show a significant improvement in eliminating artifacts and increasing contrast compared to the standard MRI techniques, and a close correlation with histopathology and inductively coupled mass spectrometry results. This newly developed protocol could be used for any paramagnetic nanoparticle to improve detection sensitivity. We expect this methodology to produce similar improvements in human imaging, having the potential to significantly improve early tumor detection in clinical practice and opening up the possibility of its theranostic use. | Sayoni Ray; Chao-Hsiung Hsu; Zhao Li; Fang-Chu Lin; Yung-Ya Lin | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Biophysical Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6121aa74fa49ac720857e3b8/original/high-contrast-background-free-magnetic-resonance-molecular-imaging.pdf |
60c74bf79abda2b1bff8d1ae | 10.26434/chemrxiv.12408581.v1 | Identification of Phosphatidylcholine Isomers in Imaging Mass Spectrometry Using Gas-Phase Charge Inversion Ion/Ion Reactions | <p>Gas-phase
ion/ion reactions have been enabled on a commercial dual source, hybrid QhFT-ICR
mass spectrometer for use during imaging mass spectrometry experiments. These
reactions allow for the transformation of the ion type most readily generated
from the tissue surface to an ion type that gives improved chemical structural
information upon tandem mass spectrometry (MS/MS) without manipulating the
tissue sample. This process is demonstrated via the charge inversion reaction of
phosphatidylcholine (PC) lipid cations generated from rat brain tissue via
matrix-assisted laser desorption/ionization (MALDI) with 1,4-phenylenedipropionic
acid (PDPA) reagent dianions generated via electrospray ionization (ESI).
Collision induced dissociation (CID) of the resulting demethylated PC product anions
allows for the determination of the lipid fatty acyl tail identities and
positions, which is not possible via CID of the precursor lipid cations. The
abundance of lipid isomers revealed by this workflow is found to vary significantly
in different regions of the brain. As each isoform may have a unique cellular
function, these results underscore the importance of accurately separating and
identifying the many isobaric and isomeric lipids and metabolites that can
complicate image interpretation and spectral analysis.</p> | Jonathan T. Specker; Steve L. Van Orden; Mark. E. Ridgeway; Boone Prentice | Analytical Chemistry - General; Biochemical Analysis; Imaging; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bf79abda2b1bff8d1ae/original/identification-of-phosphatidylcholine-isomers-in-imaging-mass-spectrometry-using-gas-phase-charge-inversion-ion-ion-reactions.pdf |
616f8a2df718df400ee49195 | 10.26434/chemrxiv-2021-3nm6w | Design, Synthesis and Biological Evaluation of P2-modified Proline Analogues Targeting the HtrA Serine Protease in Chlamydia | High temperature requirement A (HtrA) serine proteases have emerged as a novel class of antibacterial target, which are crucial in protein quality control and are involved in the pathogenesis of a wide array of bacterial infections. Previously, we demonstrated that HtrA in Chlamydia is essential for bacterial survival, replication and virulence. Here, we report a new series of proline (P2)-modified inhibitors of Chlamydia trachomatis HtrA (CtHtrA) developed by proline ring expansion and Cγ-substitutions. The structure-based drug optimization process was guided by molecular modelling and in vitro pharmacological evaluation of inhibitory potency, selectivity and cytotoxicity. Compound 25 from the first-generation 4-substituted proline analogues increased antiCtHtrA potency and selectivity over human neutrophil elastase (HNE) by approximately 6- and 12-fold, respectively, relative to the peptidic lead compound 1. Based on this compound, second-generation substituted proline residues containing 1,2,3-triazole moieties were synthesized by regioselective azide-alkyne click chemistry. Compound 49 demonstrated significantly improved antichlamydial activity in whole cell assays, diminishing the bacterial infectious progeny below the detection limit at the lowest dose tested. Compound 49 resulted in approximately 9- and 22-fold improvement in the inhibitory potency and selectivity relative to 1, respectively. To date, compound 49 is the most potent HtrA inhibitor developed against Chlamydia spp. | Jimin Hwang; Natalie Strange; Rami Mazraanib; Matthew Philips; Allan Gamble; Wilhelmina Huston; Joel Tyndall | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616f8a2df718df400ee49195/original/design-synthesis-and-biological-evaluation-of-p2-modified-proline-analogues-targeting-the-htr-a-serine-protease-in-chlamydia.pdf |
60c74c680f50db4576396e44 | 10.26434/chemrxiv.12469316.v1 | A Connectivity Map-Based Drug Repurposing Study and Integrative Analysis of Transcriptomic Profiling of SARS-CoV-2 Infection | <div>Aims: The recent outbreak of COVID-19 has become a global health concern. There are currently no effective treatment strategies and vaccines for the treatment or prevention of this fatal disease. The current study aims to determine promising treatment options for the COVID-19 through a computational drug repurposing approach.</div><div>Materials and methods: In this study, we focus on differentially expressed genes (DEGs), detected in SARS-CoV-2 infected cell lines including “the primary human lung epithelial cell line NHBE” and “the transformed lung alveolar cell line A549”. Next, the identified DEGs are used in the connectivity map (CMap) analysis to identify similarly acting therapeutic candidates. Furthermore, to interpret lists of DEGs, pathway enrichment and protein network analysis are performed. Genes are categorized into easily interpretable pathways based on their biological functions, and overrepresentations of each pathway are tested in comparison to what is expected randomly.</div><div>Key findings: The results suggest the effectiveness of Saquinavir, lansoprazole, folic acid, ebselen, aminocaproic acid, simvastatin, surfactant stimulant drugs, heat shock protein 90 (HSP90) inhibitors, histone deacetylase (HDAC) inhibitors, metronidazole, inhaled corticosteroids (ICS) and many other clinically approved drugs and investigational compounds as potent drugs against COVID-19 outbreak.</div><div>Significance: Making new drugs remain a lengthy process, so the drug repurposing approach provides an insight into the therapeutics that might be helpful in this pandemic. In this study, pathway enrichment and protein network analysis are also performed, and the effectiveness of some drugs obtained from the CMap analysis has been investigated according to previous research.</div> | seyedeh zahra mousavi; mojdeh rahmanian; ashkan sami | Biochemistry; Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c680f50db4576396e44/original/a-connectivity-map-based-drug-repurposing-study-and-integrative-analysis-of-transcriptomic-profiling-of-sars-co-v-2-infection.pdf |
614839dfaeaa6e1dd4f258b1 | 10.26434/chemrxiv-2021-x1s5k | Single-Macromolecular Level Imaging of a Hydrogel Structure | Hydrogels are promising materials for several applications, including cell scaffolds and artificial load-bearing substitutes (cartilages, ligaments, tendons, etc.). Direct observation of the nanoscale polymer network of hydrogels is essential in understanding its properties. However, imaging of individual network strands at the molecular level is not achieved yet due to the lack of suitable methods. Herein, for the first time, we developed a novel mineral-staining method and network fixation method for transmission electron microscopy observation to visualize the hydrogel network in its unperturbed conformation with nanometer resolution. Surface network observation indicates that the length of surface dangling chains, which play a major role in friction and wetting, can be estimated from the gel mesh size. Moreover, bulk observations reveals a hierarchical formation mechanism of gel heterogeneity. These observations have the great potential to advance gel science by providing comprehensive perspective that link bulk gel properties with nanoscale. | Ryuji Kiyama; Takayuki Nonoyama; Sedlacik Tomas; Hiroshi Jinnai; Jian Ping Gong | Materials Science; Polymer Science; Nanoscience; Hybrid Organic-Inorganic Materials; Hydrogels; Polymer morphology | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614839dfaeaa6e1dd4f258b1/original/single-macromolecular-level-imaging-of-a-hydrogel-structure.pdf |
62994b85468a087b7449c3ff | 10.26434/chemrxiv-2022-jcwcw | Copper-Catalyzed Three-Component Photo-ATRA-Type Reaction for Asymmetric Intermolecular C-O Coupling | Atom transfer radical addition (ATRA) reaction of alkenes has had a tremendous impact on the field of radical difunctionalizations of alkenes. Particularly in the three-component photo-ATRA-type processes, a rich chemical space and structural diversity could be achieved by smart combination of redox-active radical precursors and the third coupling components (e.g., halides, C-, N-, and O-nucleophiles) under mild con-ditions. However, the inherent complicated mechanisms involving radical chain or outer-sphere SET of the incipient radical intermediates render dearth of general catalytic methods for highly enantioselective variants, especially these regarding asymmetric intermolecular C-O bond formation. Here, we report a visible-light-induced copper-catalyzed asymmetric three-component photo-ATRA-type reaction of alkenes with oxime esters and carboxylic acids. In this process, a highly enantioselective intermolecular C-O cross-coupling between incipient sp3-hybridized carbon radicals and carboxylic acids was enabled by aryl π-bond-engaged [σ + π]-copper complex. This three-component photo-ATRA-type reaction exhibits broad substrate scope and high functional group tolerance with respect to each component, giving the desired cross-coupled products with generally good yields and excellent enantioselectivity (>70 examples; up to 97% ee). Combined experimental and computational studies are also performed to gain insight into the mechanism. This finding provides a new platform for the development of other enantioselective benzylic-type radical-based cross-coupling reactions. | Peng-Zi Wang; Yu-Jie Liang; Xue Wu; Wei Guan; Wen-Jing Xiao; Jia-Rong Chen | Organic Chemistry; Catalysis; Photochemistry (Org.); Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62994b85468a087b7449c3ff/original/copper-catalyzed-three-component-photo-atra-type-reaction-for-asymmetric-intermolecular-c-o-coupling.pdf |
60c74019bdbb89674da380e2 | 10.26434/chemrxiv.6995018.v3 | Machine Learning for Organic Cage Property Prediction | <p>We use machine learning to predict shape persistence and cavity size in porous organic cages. The majority of hypothetical organic cages suffer from a lack of shape persistence and as a result lack intrinsic porosity, rendering them unsuitable for many applications. We have created the largest computational database of these molecules to date, numbering 63,472 cages, formed through a range of reaction chemistries and in</p>
<p>multiple topologies. We study our database and identify features which lead to the formation of shape persistent cages. We find that the imine condensation of trialdehydes and diamines in a [4+6] reaction is the most likely to result in shape persistent cages, whereas thiol reactions are most likely to give collapsed cages. Using this database, we develop machine learning models capable of predicting shape persistence with an accuracy of up to 93%, reducing the time taken to predict this property to milliseconds, and removing the need for specialist software. In addition, we develop machine learning models for two other key properties of these molecules, cavity size and symmetry. We provide open-source implementations of our models, together with the accompanying</p>
<p>data sets, and an online tool giving users access to our models to easily obtain predictions for a hypothetical cage prior to a synthesis attempt.</p> | Lukas Turcani; Rebecca L. Greenaway; Kim Jelfs | Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74019bdbb89674da380e2/original/machine-learning-for-organic-cage-property-prediction.pdf |
633568d6f764e656390764cb | 10.26434/chemrxiv-2022-wcskr | Non-destructive all-optical readout through photoswitching of intramolecular excimer emission | We report the first intramolecular excimer photoswitching induced by molecular motion within a dithienylethene (DTE) molecule, without destructive readout. The photochromic compounds DTE 1 bears two pyrene chromophores, judiciously positioned to face each other in the DTE’s open form. The close proximity of the pyrenes in the open form is confirmed by NMR experiments and geometry optimization. Intense pyrene excimer luminescence is recorded, both upon one- and two-photon excitation (OPE and TPE). The photocyclization reaction of the DTE core induces a molecular motion of one pyrene moiety which thus prevents the possibility of formation of an excimer. Our DTE-based pyrene 1 is stable upon TPE irradiation and shows a high photo-cyclization quantum yield. Such properties specifications, allow us to report the original non-destructive readout fluorescence by alternative exposure to OPE and TPE. | Marie Barale; Muriel Escadeillas; Grégory Taupier; Yann Molard; Clément Orione; Elsa Caytan; Rémi Métivier; Julien Boixel | Organic Chemistry; Photochemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2022-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633568d6f764e656390764cb/original/non-destructive-all-optical-readout-through-photoswitching-of-intramolecular-excimer-emission.pdf |
60c74065bdbb892feda3817f | 10.26434/chemrxiv.7732685.v1 | Nitrile Reduction Reverses the Micropollutant Uptake Selectivity of a Tetrafluoroterephthalonitrile-β-Cyclodextrin Polymer | A post-polymerization reduction of nitrile groups to primary amines reverses the selectivity of a crosslinked cyclodextrin polymer network. The as-polymerized material had previously been shown to have a high affinity for cationic organic micropollutants. The reduced polymer has a high affinity for anionic pollutants, including a broad range of per- and polyfluorinated alkyl substances (PFASs). | Max Justin Klemes; Yuhan Ling; Casey Ching; congyue wu; Leilei Xiao; Damian E Helbling; William Dichtel | Organic Polymers; Polymerization (Polymers); Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74065bdbb892feda3817f/original/nitrile-reduction-reverses-the-micropollutant-uptake-selectivity-of-a-tetrafluoroterephthalonitrile-cyclodextrin-polymer.pdf |
60c756cc469df47df6f45388 | 10.26434/chemrxiv.14331056.v1 | A Practical, Component-Based Synthetic Route to Methylthiolincosamine Permitting Facile Northern-Half Diversification of Lincosamide Antibiotics | The development of a flexible, component-based synthetic
route to the aminosugar fragment of the lincosamide antibiotics is described.
This synthetic route hinges on the application and extension of nitroaldol
chemistry to forge strategic bonds within complex aminosugar targets, and employs
a glycal epoxide as a versatile glycosyl donor for the installation of various anomeric
groups. Through building-block exchange and late-stage functionalization, this
route affords access to a host of rationally designed lincosamides otherwise
inaccessible by semisynthesis, and underpins a platform for the discovery of
new lincosamide antibiotics. | Matthew Mitcheltree; Jack W. Stevenson; Amarnath Pisipati; Andrew G. Myers | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756cc469df47df6f45388/original/a-practical-component-based-synthetic-route-to-methylthiolincosamine-permitting-facile-northern-half-diversification-of-lincosamide-antibiotics.pdf |
66c8d79c20ac769e5f9b3165 | 10.26434/chemrxiv-2024-rmg0p-v2 | Injectable and photocurable precursors with their improved adhesive elastomeric films by nature-inspired marine mussels chemistry | Photocurable materials, capable of being delivered as liquids and rapidly cured in situ within seconds using UV light, are garnering increased interest in advanced minimally invasive procedures. Examining living organisms to extract novel principles and technologies, and subsequently applying them into synthetic materials to enhance their performances holds a central position in biomimetics (bioinspiration). In this exploration, we delve into the multifaceted world of marine mussel adhesion, emphasizing the pivotal role of 3,4-dihydroxy-L-phenylalanine (L-DOPA) in adhesive proteins. Simultaneously, we navigated the promising realm of elastomers derived from fatty acid dimers. 90° peeling test and fluorescence microscope indicate that the adhesiveness of the catechol-containing samples (5% and 10%) versus control samples were ~4 and 8 times higher, respectively, as compared to within the tested group. Overall, our results suggest that the incorporation of methacrylated L-DOPA in the synthesis of photocured elastomeric networks leads to improved water contact angle and adhesiveness, creating new avenues for potential biomedical applications. | Gokhan Demirci; Malwina Niedzwiedz; Nina Stefaniak; Peter Sobolewski; Miroslawa El Fray | Materials Science; Polymer Science; Organic Polymers; Polymerization (Polymers) | CC BY 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c8d79c20ac769e5f9b3165/original/injectable-and-photocurable-precursors-with-their-improved-adhesive-elastomeric-films-by-nature-inspired-marine-mussels-chemistry.pdf |
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